From d57f6ab8609134ff114140645f0c423b9ad638eb Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 10 Jun 2021 16:44:32 +0000 Subject: [PATCH 01/98] Replace recursive by iterative implementation of heapify --- .../Tpetra_TestBlockCrsMeshDatabase.hpp | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/packages/tpetra/core/example/BlockCrs/Tpetra_TestBlockCrsMeshDatabase.hpp b/packages/tpetra/core/example/BlockCrs/Tpetra_TestBlockCrsMeshDatabase.hpp index 777a0eabe7c9..b722be73a433 100644 --- a/packages/tpetra/core/example/BlockCrs/Tpetra_TestBlockCrsMeshDatabase.hpp +++ b/packages/tpetra/core/example/BlockCrs/Tpetra_TestBlockCrsMeshDatabase.hpp @@ -117,16 +117,18 @@ namespace BlockCrsTest { template KOKKOS_INLINE_FUNCTION static void heapify(T1 *v, T2 n, T2 i) { - T2 largest = i; - T2 l = 2*i + 1; - T2 r = 2*i + 2; - - if (l < n && v[l] > v[largest]) largest = l; - if (r < n && v[r] > v[largest]) largest = r; - if (largest != i) { + while (true) { + T2 largest = i; + T2 l = 2*i + 1; + T2 r = 2*i + 2; + + if (l < n && v[l] > v[largest]) largest = l; + if (r < n && v[r] > v[largest]) largest = r; + if (largest == i) + break; // swap T1 tmp = v[i]; v[i] = v[largest]; v[largest] = tmp; - heapify(v, n, largest); + i = largest; } } From e2359aea1986b54f0878ffdc9543f46f88bb61f1 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 10 Jun 2021 13:19:54 +0000 Subject: [PATCH 02/98] Tpetra: Enable more SYCL tests --- .../core/ext/TpetraExt_MatrixMatrix_SYCL.hpp | 826 ++++++++++++++++++ .../core/ext/TpetraExt_MatrixMatrix_def.hpp | 1 + .../TpetraExt_TripleMatrixMultiply_def.hpp | 1 + .../ImportExport2/ImportExport2_UnitTests.cpp | 15 +- .../MatrixMatrix/MatrixMatrix_UnitTests.cpp | 13 +- 5 files changed, 851 insertions(+), 5 deletions(-) create mode 100644 packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp diff --git a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp new file mode 100644 index 000000000000..d29c8292ea62 --- /dev/null +++ b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp @@ -0,0 +1,826 @@ +// @HEADER +// *********************************************************************** +// +// Tpetra: Templated Linear Algebra Services Package +// Copyright (2008) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +// @HEADER + +#ifndef TPETRA_MATRIXMATRIX_SYCL_DEF_HPP +#define TPETRA_MATRIXMATRIX_SYCL_DEF_HPP + +#ifdef HAVE_TPETRA_INST_SYCL +namespace Tpetra { +namespace MMdetails { + +/*********************************************************************************************************/ +// MMM KernelWrappers for Partial Specialization to SYCL +template +struct KernelWrappers { + static inline void mult_A_B_newmatrix_kernel_wrapper(CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label = std::string(), + const Teuchos::RCP& params = Teuchos::null); + + + + static inline void mult_A_B_reuse_kernel_wrapper(CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label = std::string(), + const Teuchos::RCP& params = Teuchos::null); + +}; + +// Jacobi KernelWrappers for Partial Specialization to SYCL +template +struct KernelWrappers2 { + static inline void jacobi_A_B_newmatrix_kernel_wrapper(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label = std::string(), + const Teuchos::RCP& params = Teuchos::null); + + static inline void jacobi_A_B_reuse_kernel_wrapper(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label = std::string(), + const Teuchos::RCP& params = Teuchos::null); + + static inline void jacobi_A_B_newmatrix_KokkosKernels(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label = std::string(), + const Teuchos::RCP& params = Teuchos::null); +}; + + +/*********************************************************************************************************/ +// AB NewMatrix Kernel wrappers (KokkosKernels/SYCL Version) +template +void KernelWrappers::mult_A_B_newmatrix_kernel_wrapper(CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label, + const Teuchos::RCP& params) { + + +#ifdef HAVE_TPETRA_MMM_TIMINGS + std::string prefix_mmm = std::string("TpetraExt ") + label + std::string(": "); + using Teuchos::TimeMonitor; + Teuchos::RCP MM = rcp(new TimeMonitor(*(TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Newmatrix SYCLWrapper"))))); +#endif + // Node-specific code + typedef Kokkos::Compat::KokkosSYCLWrapperNode Node; + std::string nodename("SYCL"); + + // Lots and lots of typedefs + using Teuchos::RCP; + typedef typename Tpetra::CrsMatrix::local_matrix_device_type KCRS; + typedef typename KCRS::device_type device_t; + typedef typename KCRS::StaticCrsGraphType graph_t; + typedef typename graph_t::row_map_type::non_const_type lno_view_t; + typedef typename graph_t::row_map_type::const_type c_lno_view_t; + typedef typename graph_t::entries_type::non_const_type lno_nnz_view_t; + typedef typename KCRS::values_type::non_const_type scalar_view_t; + //typedef typename graph_t::row_map_type::const_type lno_view_t_const; + + // Options + int team_work_size = 16; // Defaults to 16 as per Deveci 12/7/16 - csiefer + std::string myalg("SPGEMM_KK_MEMORY"); + if(!params.is_null()) { + if(params->isParameter("sycl: algorithm")) + myalg = params->get("sycl: algorithm",myalg); + if(params->isParameter("sycl: team work size")) + team_work_size = params->get("sycl: team work size",team_work_size); + } + + // KokkosKernelsHandle + typedef KokkosKernels::Experimental::KokkosKernelsHandle< + typename lno_view_t::const_value_type,typename lno_nnz_view_t::const_value_type, typename scalar_view_t::const_value_type, + typename device_t::execution_space, typename device_t::memory_space,typename device_t::memory_space > KernelHandle; + + // Grab the Kokkos::SparseCrsMatrices + const KCRS & Amat = Aview.origMatrix->getLocalMatrixDevice(); + const KCRS & Bmat = Bview.origMatrix->getLocalMatrixDevice(); + + c_lno_view_t Arowptr = Amat.graph.row_map, + Browptr = Bmat.graph.row_map; + const lno_nnz_view_t Acolind = Amat.graph.entries, + Bcolind = Bmat.graph.entries; + const scalar_view_t Avals = Amat.values, + Bvals = Bmat.values; + + c_lno_view_t Irowptr; + lno_nnz_view_t Icolind; + scalar_view_t Ivals; + if(!Bview.importMatrix.is_null()) { + auto lclB = Bview.importMatrix->getLocalMatrixDevice(); + Irowptr = lclB.graph.row_map; + Icolind = lclB.graph.entries; + Ivals = lclB.values; + } + + + // Get the algorithm mode + std::string alg = nodename+std::string(" algorithm"); + // printf("DEBUG: Using kernel: %s\n",myalg.c_str()); + if(!params.is_null() && params->isParameter(alg)) myalg = params->get(alg,myalg); + KokkosSparse::SPGEMMAlgorithm alg_enum = KokkosSparse::StringToSPGEMMAlgorithm(myalg); + + // Merge the B and Bimport matrices + const KCRS Bmerged = Tpetra::MMdetails::merge_matrices(Aview,Bview,Acol2Brow,Acol2Irow,Bcol2Ccol,Icol2Ccol,C.getColMap()->getNodeNumElements()); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Newmatrix SYCLCore")))); +#endif + + // Do the multiply on whatever we've got + typename KernelHandle::nnz_lno_t AnumRows = Amat.numRows(); + typename KernelHandle::nnz_lno_t BnumRows = Bmerged.numRows(); + typename KernelHandle::nnz_lno_t BnumCols = Bmerged.numCols(); + + lno_view_t row_mapC (Kokkos::ViewAllocateWithoutInitializing("non_const_lnow_row"), AnumRows + 1); + lno_nnz_view_t entriesC; + scalar_view_t valuesC; + KernelHandle kh; + kh.create_spgemm_handle(alg_enum); + kh.set_team_work_size(team_work_size); + + KokkosSparse::Experimental::spgemm_symbolic(&kh,AnumRows,BnumRows,BnumCols,Amat.graph.row_map,Amat.graph.entries,false,Bmerged.graph.row_map,Bmerged.graph.entries,false,row_mapC); + + size_t c_nnz_size = kh.get_spgemm_handle()->get_c_nnz(); + if (c_nnz_size){ + entriesC = lno_nnz_view_t (Kokkos::ViewAllocateWithoutInitializing("entriesC"), c_nnz_size); + valuesC = scalar_view_t (Kokkos::ViewAllocateWithoutInitializing("valuesC"), c_nnz_size); + } + KokkosSparse::Experimental::spgemm_numeric(&kh,AnumRows,BnumRows,BnumCols,Amat.graph.row_map,Amat.graph.entries,Amat.values,false,Bmerged.graph.row_map,Bmerged.graph.entries,Bmerged.values,false,row_mapC,entriesC,valuesC); + kh.destroy_spgemm_handle(); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Newmatrix SYCLSort")))); +#endif + + // Sort & set values + if (params.is_null() || params->get("sort entries",true)) + Import_Util::sortCrsEntries(row_mapC, entriesC, valuesC); + C.setAllValues(row_mapC,entriesC,valuesC); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Newmatrix SYCLESFC")))); +#endif + + // Final Fillcomplete + RCP labelList = rcp(new Teuchos::ParameterList); + labelList->set("Timer Label",label); + if(!params.is_null()) labelList->set("compute global constants",params->get("compute global constants",true)); + RCP > dummyExport; + C.expertStaticFillComplete(Bview.origMatrix->getDomainMap(), Aview.origMatrix->getRangeMap(), Cimport,dummyExport,labelList); +} + + +/*********************************************************************************************************/ +template +void KernelWrappers::mult_A_B_reuse_kernel_wrapper( + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & targetMapToOrigRow_dev, + const LocalOrdinalViewType & targetMapToImportRow_dev, + const LocalOrdinalViewType & Bcol2Ccol_dev, + const LocalOrdinalViewType & Icol2Ccol_dev, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label, + const Teuchos::RCP& params) { + + // FIXME: Right now, this is a cut-and-paste of the serial kernel + typedef Kokkos::Compat::KokkosSYCLWrapperNode Node; + +#ifdef HAVE_TPETRA_MMM_TIMINGS + std::string prefix_mmm = std::string("TpetraExt ") + label + std::string(": "); + using Teuchos::TimeMonitor; + Teuchos::RCP MM = rcp(new TimeMonitor(*TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Reuse SerialCore")))); + Teuchos::RCP MM2; +#endif + using Teuchos::RCP; + using Teuchos::rcp; + + + // Lots and lots of typedefs + typedef typename Tpetra::CrsMatrix::local_matrix_host_type KCRS; + typedef typename KCRS::StaticCrsGraphType graph_t; + typedef typename graph_t::row_map_type::const_type c_lno_view_t; + typedef typename graph_t::entries_type::non_const_type lno_nnz_view_t; + typedef typename KCRS::values_type::non_const_type scalar_view_t; + + typedef Scalar SC; + typedef LocalOrdinal LO; + typedef GlobalOrdinal GO; + typedef Node NO; + typedef Map map_type; + const size_t ST_INVALID = Teuchos::OrdinalTraits::invalid(); + const LO LO_INVALID = Teuchos::OrdinalTraits::invalid(); + const SC SC_ZERO = Teuchos::ScalarTraits::zero(); + + // Since this is being run on SYCL, we need to fence because the below code will use UVM + // typename graph_t::execution_space().fence(); + + // KDDKDD UVM Without UVM, need to copy targetMap arrays to host. + // KDDKDD UVM Ideally, this function would run on device and use + // KDDKDD UVM KokkosKernels instead of this host implementation. + auto targetMapToOrigRow = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + targetMapToOrigRow_dev); + auto targetMapToImportRow = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + targetMapToImportRow_dev); + auto Bcol2Ccol = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + Bcol2Ccol_dev); + auto Icol2Ccol = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + Icol2Ccol_dev); + + // Sizes + RCP Ccolmap = C.getColMap(); + size_t m = Aview.origMatrix->getNodeNumRows(); + size_t n = Ccolmap->getNodeNumElements(); + + // Grab the Kokkos::SparseCrsMatrices & inner stuff + const KCRS & Amat = Aview.origMatrix->getLocalMatrixHost(); + const KCRS & Bmat = Bview.origMatrix->getLocalMatrixHost(); + const KCRS & Cmat = C.getLocalMatrixHost(); + + c_lno_view_t Arowptr = Amat.graph.row_map, + Browptr = Bmat.graph.row_map, + Crowptr = Cmat.graph.row_map; + const lno_nnz_view_t Acolind = Amat.graph.entries, + Bcolind = Bmat.graph.entries, + Ccolind = Cmat.graph.entries; + const scalar_view_t Avals = Amat.values, Bvals = Bmat.values; + scalar_view_t Cvals = Cmat.values; + + c_lno_view_t Irowptr; + lno_nnz_view_t Icolind; + scalar_view_t Ivals; + if(!Bview.importMatrix.is_null()) { + auto lclB = Bview.importMatrix->getLocalMatrixHost(); + Irowptr = lclB.graph.row_map; + Icolind = lclB.graph.entries; + Ivals = lclB.values; + } + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM2 = Teuchos::null; MM2 = rcp(new TimeMonitor(*TimeMonitor::getNewTimer(prefix_mmm + std::string("MMM Newmatrix SerialCore - Compare")))); +#endif + + // Classic csr assembly (low memory edition) + // mfh 27 Sep 2016: The c_status array is an implementation detail + // of the local sparse matrix-matrix multiply routine. + + // The status array will contain the index into colind where this entry was last deposited. + // c_status[i] < CSR_ip - not in the row yet + // c_status[i] >= CSR_ip - this is the entry where you can find the data + // We start with this filled with INVALID's indicating that there are no entries yet. + // Sadly, this complicates the code due to the fact that size_t's are unsigned. + std::vector c_status(n, ST_INVALID); + + // For each row of A/C + size_t CSR_ip = 0, OLD_ip = 0; + for (size_t i = 0; i < m; i++) { + // First fill the c_status array w/ locations where we're allowed to + // generate nonzeros for this row + OLD_ip = Crowptr[i]; + CSR_ip = Crowptr[i+1]; + for (size_t k = OLD_ip; k < CSR_ip; k++) { + c_status[Ccolind[k]] = k; + + // Reset values in the row of C + Cvals[k] = SC_ZERO; + } + + for (size_t k = Arowptr[i]; k < Arowptr[i+1]; k++) { + LO Aik = Acolind[k]; + const SC Aval = Avals[k]; + if (Aval == SC_ZERO) + continue; + + if (targetMapToOrigRow[Aik] != LO_INVALID) { + // Local matrix + size_t Bk = Teuchos::as(targetMapToOrigRow[Aik]); + + for (size_t j = Browptr[Bk]; j < Browptr[Bk+1]; ++j) { + LO Bkj = Bcolind[j]; + LO Cij = Bcol2Ccol[Bkj]; + + TEUCHOS_TEST_FOR_EXCEPTION(c_status[Cij] < OLD_ip || c_status[Cij] >= CSR_ip, + std::runtime_error, "Trying to insert a new entry (" << i << "," << Cij << ") into a static graph " << + "(c_status = " << c_status[Cij] << " of [" << OLD_ip << "," << CSR_ip << "))"); + + Cvals[c_status[Cij]] += Aval * Bvals[j]; + } + + } else { + // Remote matrix + size_t Ik = Teuchos::as(targetMapToImportRow[Aik]); + for (size_t j = Irowptr[Ik]; j < Irowptr[Ik+1]; ++j) { + LO Ikj = Icolind[j]; + LO Cij = Icol2Ccol[Ikj]; + + TEUCHOS_TEST_FOR_EXCEPTION(c_status[Cij] < OLD_ip || c_status[Cij] >= CSR_ip, + std::runtime_error, "Trying to insert a new entry (" << i << "," << Cij << ") into a static graph " << + "(c_status = " << c_status[Cij] << " of [" << OLD_ip << "," << CSR_ip << "))"); + + Cvals[c_status[Cij]] += Aval * Ivals[j]; + } + } + } + } + + C.fillComplete(C.getDomainMap(), C.getRangeMap()); +} + +/*********************************************************************************************************/ +template +void KernelWrappers2::jacobi_A_B_newmatrix_kernel_wrapper(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label, + const Teuchos::RCP& params) { + +#ifdef HAVE_TPETRA_MMM_TIMINGS + std::string prefix_mmm = std::string("TpetraExt ") + label + std::string(": "); + using Teuchos::TimeMonitor; + Teuchos::RCP MM; +#endif + + // Node-specific code + using Teuchos::RCP; + + // Options + //int team_work_size = 16; // Defaults to 16 as per Deveci 12/7/16 - csiefer // unreferenced + std::string myalg("KK"); + if(!params.is_null()) { + if(params->isParameter("sycl: jacobi algorithm")) + myalg = params->get("sycl: jacobi algorithm",myalg); + } + + if(myalg == "MSAK") { + ::Tpetra::MatrixMatrix::ExtraKernels::jacobi_A_B_newmatrix_MultiplyScaleAddKernel(omega,Dinv,Aview,Bview,Acol2Brow,Acol2Irow,Bcol2Ccol,Icol2Ccol,C,Cimport,label,params); + } + else if(myalg == "KK") { + jacobi_A_B_newmatrix_KokkosKernels(omega,Dinv,Aview,Bview,Acol2Brow,Acol2Irow,Bcol2Ccol,Icol2Ccol,C,Cimport,label,params); + } + else { + throw std::runtime_error("Tpetra::MatrixMatrix::Jacobi newmatrix unknown kernel"); + } + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Newmatrix SYCLESFC")))); +#endif + + // Final Fillcomplete + RCP labelList = rcp(new Teuchos::ParameterList); + labelList->set("Timer Label",label); + if(!params.is_null()) labelList->set("compute global constants",params->get("compute global constants",true)); + + // NOTE: MSAK already fillCompletes, so we have to check here + if(!C.isFillComplete()) { + RCP > dummyExport; + C.expertStaticFillComplete(Bview.origMatrix->getDomainMap(), Aview.origMatrix->getRangeMap(), Cimport,dummyExport,labelList); + } + +} + + + +/*********************************************************************************************************/ +template +void KernelWrappers2::jacobi_A_B_reuse_kernel_wrapper(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & targetMapToOrigRow_dev, + const LocalOrdinalViewType & targetMapToImportRow_dev, + const LocalOrdinalViewType & Bcol2Ccol_dev, + const LocalOrdinalViewType & Icol2Ccol_dev, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label, + const Teuchos::RCP& params) { + + // FIXME: Right now, this is a cut-and-paste of the serial kernel + typedef Kokkos::Compat::KokkosSYCLWrapperNode Node; + +#ifdef HAVE_TPETRA_MMM_TIMINGS + std::string prefix_mmm = std::string("TpetraExt ") + label + std::string(": "); + using Teuchos::TimeMonitor; + Teuchos::RCP MM = rcp(new TimeMonitor(*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Reuse SYCLCore")))); + Teuchos::RCP MM2; +#endif + using Teuchos::RCP; + using Teuchos::rcp; + + // Lots and lots of typedefs + typedef typename Tpetra::CrsMatrix::local_matrix_host_type KCRS; + typedef typename KCRS::StaticCrsGraphType graph_t; + typedef typename graph_t::row_map_type::const_type c_lno_view_t; + typedef typename graph_t::entries_type::non_const_type lno_nnz_view_t; + typedef typename KCRS::values_type::non_const_type scalar_view_t; + typedef typename scalar_view_t::memory_space scalar_memory_space; + + typedef Scalar SC; + typedef LocalOrdinal LO; + typedef GlobalOrdinal GO; + typedef Node NO; + typedef Map map_type; + const size_t ST_INVALID = Teuchos::OrdinalTraits::invalid(); + const LO LO_INVALID = Teuchos::OrdinalTraits::invalid(); + const SC SC_ZERO = Teuchos::ScalarTraits::zero(); + + // Since this is being run on SYCL, we need to fence because the below host code will use UVM + // KDDKDD typename graph_t::execution_space().fence(); + + // KDDKDD UVM Without UVM, need to copy targetMap arrays to host. + // KDDKDD UVM Ideally, this function would run on device and use + // KDDKDD UVM KokkosKernels instead of this host implementation. + auto targetMapToOrigRow = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + targetMapToOrigRow_dev); + auto targetMapToImportRow = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + targetMapToImportRow_dev); + auto Bcol2Ccol = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + Bcol2Ccol_dev); + auto Icol2Ccol = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), + Icol2Ccol_dev); + + + // Sizes + RCP Ccolmap = C.getColMap(); + size_t m = Aview.origMatrix->getNodeNumRows(); + size_t n = Ccolmap->getNodeNumElements(); + + // Grab the Kokkos::SparseCrsMatrices & inner stuff + const KCRS & Amat = Aview.origMatrix->getLocalMatrixHost(); + const KCRS & Bmat = Bview.origMatrix->getLocalMatrixHost(); + const KCRS & Cmat = C.getLocalMatrixHost(); + + c_lno_view_t Arowptr = Amat.graph.row_map, Browptr = Bmat.graph.row_map, Crowptr = Cmat.graph.row_map; + const lno_nnz_view_t Acolind = Amat.graph.entries, Bcolind = Bmat.graph.entries, Ccolind = Cmat.graph.entries; + const scalar_view_t Avals = Amat.values, Bvals = Bmat.values; + scalar_view_t Cvals = Cmat.values; + + c_lno_view_t Irowptr; + lno_nnz_view_t Icolind; + scalar_view_t Ivals; + if(!Bview.importMatrix.is_null()) { + auto lclB = Bview.importMatrix->getLocalMatrixHost(); + Irowptr = lclB.graph.row_map; + Icolind = lclB.graph.entries; + Ivals = lclB.values; + } + + // Jacobi-specific inner stuff + auto Dvals = + Dinv.template getLocalView(Access::ReadOnly); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM2 = Teuchos::null; MM2 = rcp(new TimeMonitor(*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Reuse SYCLCore - Compare")))); +#endif + + // The status array will contain the index into colind where this entry was last deposited. + // c_status[i] < CSR_ip - not in the row yet + // c_status[i] >= CSR_ip - this is the entry where you can find the data + // We start with this filled with INVALID's indicating that there are no entries yet. + // Sadly, this complicates the code due to the fact that size_t's are unsigned. + std::vector c_status(n, ST_INVALID); + + // For each row of A/C + size_t CSR_ip = 0, OLD_ip = 0; + for (size_t i = 0; i < m; i++) { + + // First fill the c_status array w/ locations where we're allowed to + // generate nonzeros for this row + OLD_ip = Crowptr[i]; + CSR_ip = Crowptr[i+1]; + for (size_t k = OLD_ip; k < CSR_ip; k++) { + c_status[Ccolind[k]] = k; + + // Reset values in the row of C + Cvals[k] = SC_ZERO; + } + + SC minusOmegaDval = -omega*Dvals(i,0); + + // Entries of B + for (size_t j = Browptr[i]; j < Browptr[i+1]; j++) { + Scalar Bval = Bvals[j]; + if (Bval == SC_ZERO) + continue; + LO Bij = Bcolind[j]; + LO Cij = Bcol2Ccol[Bij]; + + TEUCHOS_TEST_FOR_EXCEPTION(c_status[Cij] < OLD_ip || c_status[Cij] >= CSR_ip, + std::runtime_error, "Trying to insert a new entry into a static graph"); + + Cvals[c_status[Cij]] = Bvals[j]; + } + + // Entries of -omega * Dinv * A * B + for (size_t k = Arowptr[i]; k < Arowptr[i+1]; k++) { + LO Aik = Acolind[k]; + const SC Aval = Avals[k]; + if (Aval == SC_ZERO) + continue; + + if (targetMapToOrigRow[Aik] != LO_INVALID) { + // Local matrix + size_t Bk = Teuchos::as(targetMapToOrigRow[Aik]); + + for (size_t j = Browptr[Bk]; j < Browptr[Bk+1]; ++j) { + LO Bkj = Bcolind[j]; + LO Cij = Bcol2Ccol[Bkj]; + + TEUCHOS_TEST_FOR_EXCEPTION(c_status[Cij] < OLD_ip || c_status[Cij] >= CSR_ip, + std::runtime_error, "Trying to insert a new entry into a static graph"); + + Cvals[c_status[Cij]] += minusOmegaDval * Aval * Bvals[j]; + } + + } else { + // Remote matrix + size_t Ik = Teuchos::as(targetMapToImportRow[Aik]); + for (size_t j = Irowptr[Ik]; j < Irowptr[Ik+1]; ++j) { + LO Ikj = Icolind[j]; + LO Cij = Icol2Ccol[Ikj]; + + TEUCHOS_TEST_FOR_EXCEPTION(c_status[Cij] < OLD_ip || c_status[Cij] >= CSR_ip, + std::runtime_error, "Trying to insert a new entry into a static graph"); + + Cvals[c_status[Cij]] += minusOmegaDval * Aval * Ivals[j]; + } + } + } + } + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM2= Teuchos::null; + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Reuse ESFC")))); +#endif + + C.fillComplete(C.getDomainMap(), C.getRangeMap()); + +} + +/*********************************************************************************************************/ +template +void KernelWrappers2::jacobi_A_B_newmatrix_KokkosKernels(Scalar omega, + const Vector & Dinv, + CrsMatrixStruct& Aview, + CrsMatrixStruct& Bview, + const LocalOrdinalViewType & Acol2Brow, + const LocalOrdinalViewType & Acol2Irow, + const LocalOrdinalViewType & Bcol2Ccol, + const LocalOrdinalViewType & Icol2Ccol, + CrsMatrix& C, + Teuchos::RCP > Cimport, + const std::string& label, + const Teuchos::RCP& params) { + +#ifdef HAVE_TPETRA_MMM_TIMINGS + std::string prefix_mmm = std::string("TpetraExt ") + label + std::string(": "); + using Teuchos::TimeMonitor; + Teuchos::RCP MM; +#endif + + // Check if the diagonal entries exist in debug mode + const bool debug = Tpetra::Details::Behavior::debug(); + if(debug) { + + auto rowMap = Aview.origMatrix->getRowMap(); + Tpetra::Vector diags(rowMap); + Aview.origMatrix->getLocalDiagCopy(diags); + size_t diagLength = rowMap->getNodeNumElements(); + Teuchos::Array diagonal(diagLength); + diags.get1dCopy(diagonal()); + + for(size_t i = 0; i < diagLength; ++i) { + TEUCHOS_TEST_FOR_EXCEPTION(diagonal[i] == Teuchos::ScalarTraits::zero(), + std::runtime_error, + "Matrix A has a zero/missing diagonal: " << diagonal[i] << std::endl << + "KokkosKernels Jacobi-fused SpGEMM requires nonzero diagonal entries in A" << std::endl); + } + } + + // Usings + using device_t = typename Kokkos::Compat::KokkosSYCLWrapperNode::device_type; + using matrix_t = typename Tpetra::CrsMatrix::local_matrix_device_type; + using graph_t = typename matrix_t::StaticCrsGraphType; + using lno_view_t = typename graph_t::row_map_type::non_const_type; + using c_lno_view_t = typename graph_t::row_map_type::const_type; + using lno_nnz_view_t = typename graph_t::entries_type::non_const_type; + using scalar_view_t = typename matrix_t::values_type::non_const_type; + + // KokkosKernels handle + using handle_t = typename KokkosKernels::Experimental::KokkosKernelsHandle< + typename lno_view_t::const_value_type,typename lno_nnz_view_t::const_value_type, typename scalar_view_t::const_value_type, + typename device_t::execution_space, typename device_t::memory_space,typename device_t::memory_space >; + + // Get the rowPtr, colInd and vals of importMatrix + c_lno_view_t Irowptr; + lno_nnz_view_t Icolind; + scalar_view_t Ivals; + if(!Bview.importMatrix.is_null()) { + auto lclB = Bview.importMatrix->getLocalMatrixDevice(); + Irowptr = lclB.graph.row_map; + Icolind = lclB.graph.entries; + Ivals = lclB.values; + } + + // Merge the B and Bimport matrices + const matrix_t Bmerged = Tpetra::MMdetails::merge_matrices(Aview,Bview,Acol2Brow,Acol2Irow,Bcol2Ccol,Icol2Ccol,C.getColMap()->getNodeNumElements()); + + // Get the properties and arrays of input matrices + const matrix_t & Amat = Aview.origMatrix->getLocalMatrixDevice(); + const matrix_t & Bmat = Bview.origMatrix->getLocalMatrixDevice(); + + typename handle_t::nnz_lno_t AnumRows = Amat.numRows(); + typename handle_t::nnz_lno_t BnumRows = Bmerged.numRows(); + typename handle_t::nnz_lno_t BnumCols = Bmerged.numCols(); + + c_lno_view_t Arowptr = Amat.graph.row_map, Browptr = Bmerged.graph.row_map; + const lno_nnz_view_t Acolind = Amat.graph.entries, Bcolind = Bmerged.graph.entries; + const scalar_view_t Avals = Amat.values, Bvals = Bmerged.values; + + // Arrays of the output matrix + lno_view_t row_mapC (Kokkos::ViewAllocateWithoutInitializing("non_const_lnow_row"), AnumRows + 1); + lno_nnz_view_t entriesC; + scalar_view_t valuesC; + + // Options + int team_work_size = 16; + std::string myalg("SPGEMM_KK_MEMORY"); + if(!params.is_null()) { + if(params->isParameter("sycl: algorithm")) + myalg = params->get("sycl: algorithm",myalg); + if(params->isParameter("sycl: team work size")) + team_work_size = params->get("sycl: team work size",team_work_size); + } + + // Get the algorithm mode + std::string nodename("SYCL"); + std::string alg = nodename + std::string(" algorithm"); + if(!params.is_null() && params->isParameter(alg)) myalg = params->get(alg,myalg); + KokkosSparse::SPGEMMAlgorithm alg_enum = KokkosSparse::StringToSPGEMMAlgorithm(myalg); + + + // KokkosKernels call + handle_t kh; + kh.create_spgemm_handle(alg_enum); + kh.set_team_work_size(team_work_size); + + KokkosSparse::Experimental::spgemm_symbolic(&kh, AnumRows, BnumRows, BnumCols, + Arowptr, Acolind, false, + Browptr, Bcolind, false, + row_mapC); + + size_t c_nnz_size = kh.get_spgemm_handle()->get_c_nnz(); + if (c_nnz_size){ + entriesC = lno_nnz_view_t (Kokkos::ViewAllocateWithoutInitializing("entriesC"), c_nnz_size); + valuesC = scalar_view_t (Kokkos::ViewAllocateWithoutInitializing("valuesC"), c_nnz_size); + } + + KokkosSparse::Experimental::spgemm_jacobi(&kh, AnumRows, BnumRows, BnumCols, + Arowptr, Acolind, Avals, false, + Browptr, Bcolind, Bvals, false, + row_mapC, entriesC, valuesC, + omega, Dinv.getLocalViewDevice(Access::ReadOnly)); + kh.destroy_spgemm_handle(); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Newmatrix SYCLSort")))); +#endif + + // Sort & set values + if (params.is_null() || params->get("sort entries",true)) + Import_Util::sortCrsEntries(row_mapC, entriesC, valuesC); + C.setAllValues(row_mapC,entriesC,valuesC); + +#ifdef HAVE_TPETRA_MMM_TIMINGS + MM = Teuchos::null; MM = rcp(new TimeMonitor (*TimeMonitor::getNewTimer(prefix_mmm + std::string("Jacobi Newmatrix SYCLESFC")))); +#endif + + // Final Fillcomplete + Teuchos::RCP labelList = rcp(new Teuchos::ParameterList); + labelList->set("Timer Label",label); + if(!params.is_null()) labelList->set("compute global constants",params->get("compute global constants",true)); + Teuchos::RCP > dummyExport; + C.expertStaticFillComplete(Bview.origMatrix->getDomainMap(), Aview.origMatrix->getRangeMap(), Cimport,dummyExport,labelList); +} + + }//MMdetails +}//Tpetra + +#endif//SYCL + +#endif diff --git a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp index 37101e7a8a29..63048b9b5a2a 100644 --- a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp +++ b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp @@ -82,6 +82,7 @@ #include "TpetraExt_MatrixMatrix_OpenMP.hpp" #include "TpetraExt_MatrixMatrix_Cuda.hpp" #include "TpetraExt_MatrixMatrix_HIP.hpp" +#include "TpetraExt_MatrixMatrix_SYCL.hpp" namespace Tpetra { diff --git a/packages/tpetra/core/ext/TpetraExt_TripleMatrixMultiply_def.hpp b/packages/tpetra/core/ext/TpetraExt_TripleMatrixMultiply_def.hpp index 2a2c082d739f..5df1da47daed 100644 --- a/packages/tpetra/core/ext/TpetraExt_TripleMatrixMultiply_def.hpp +++ b/packages/tpetra/core/ext/TpetraExt_TripleMatrixMultiply_def.hpp @@ -74,6 +74,7 @@ #include "TpetraExt_MatrixMatrix_OpenMP.hpp" #include "TpetraExt_MatrixMatrix_Cuda.hpp" #include "TpetraExt_MatrixMatrix_HIP.hpp" +#include "TpetraExt_MatrixMatrix_SYCL.hpp" namespace Tpetra { diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 0451932d45d0..0c5e007a220d 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -2845,11 +2845,20 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO TEUCHOS_UNIT_TEST_TEMPLATE_2_INSTANT( Import_Util, GetPids, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_2_INSTANT( Import_Util, GetTwoTransferOwnershipVector, LO, GO ) -#define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ +#define UNIT_TEST_GROUP_SC_LO_GO_COMMON( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, MueLuStyle, LO, GO, SC ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) + +// FIXME_SYCL requires quering free device memory +#ifdef HAVE_TPETRA_SYCL + #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ + UNIT_TEST_GROUP_SC_LO_GO_COMMON( SC, LO, GO ) +#else + #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ + UNIT_TEST_GROUP_SC_LO_GO_COMMON( SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, MueLuStyle, LO, GO, SC ) +#endif // Note: This test fails. Should fix later. // TEUCHOS_UNIT_TEST_TEMPLATE_2_INSTANT( ReverseImportExport, doImport, ORDINAL, SCALAR ) diff --git a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp index 0256eafe3f78..f28e19289b4c 100644 --- a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp @@ -2209,8 +2209,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMatAdd, locally_unsorted, SC, LO, GO }*/ -#define UNIT_TEST_GROUP_SC_LO_GO_NO( SC, LO, GO, NT ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, operations_test,SC, LO, GO, NT) \ +#define UNIT_TEST_GROUP_SC_LO_GO_NO_COMMON( SC, LO, GO, NT ) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, range_row_test, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, ATI_range_row_test, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, threaded_add_sorted, SC, LO, GO, NT) \ @@ -2222,6 +2221,16 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMatAdd, locally_unsorted, SC, LO, GO TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_col_maps, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_index_base, SC, LO, GO, NT) +// FIXME_SYCL requires quering free device memory +#ifdef HAVE_TPETRA_SYCL + #define UNIT_TEST_GROUP_SC_LO_GO_NO( SC, LO, GO, NT ) \ + UNIT_TEST_GROUP_SC_LO_GO_NO_COMMON( SC, LO, GO, NT ) +#else + #define UNIT_TEST_GROUP_SC_LO_GO_NO( SC, LO, GO, NT ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, operations_test,SC, LO, GO, NT) \ + UNIT_TEST_GROUP_SC_LO_GO_NO_COMMON( SC, LO, GO, NT ) +#endif + TPETRA_ETI_MANGLING_TYPEDEFS() TPETRA_INSTANTIATE_SLGN_NO_ORDINAL_SCALAR( UNIT_TEST_GROUP_SC_LO_GO_NO ) From 76e1cd9ed50a94541b5c58074d49d35c7deefec6 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Wed, 9 Jun 2021 19:42:43 -0600 Subject: [PATCH 03/98] tpetra: move sort_crs_matrix out of Impl namespace Compatibility change for kokkos-kernels, see kokkos/kokkos-kernels#932 --- packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp b/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp index d3c87118e9f9..abf00b35c7ef 100644 --- a/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp +++ b/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp @@ -49,6 +49,7 @@ #include "Teuchos_ParameterList.hpp" #include "Teuchos_TimeMonitor.hpp" #include "KokkosKernels_SparseUtils.hpp" +#include "KokkosKernels_Sorting.hpp" namespace Tpetra { @@ -177,7 +178,7 @@ createTransposeLocal (const Teuchos::RCP& params) local_matrix_device_type lclMatrix = crsMatrix->getLocalMatrixDevice (); local_matrix_device_type lclTransposeMatrix = KokkosKernels::Impl::transpose_matrix(lclMatrix); if (sort) - KokkosKernels::Impl::sort_crs_matrix(lclTransposeMatrix); + KokkosKernels::sort_crs_matrix(lclTransposeMatrix); // Prebuild the importers and exporters the no-communication way, // flipping the importers and exporters around. From da10abee897c0b59d0c67c482e4f1c446cfbd7e9 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 8 Jul 2021 10:20:14 -0600 Subject: [PATCH 04/98] amesos2: move sort_crs_matrix out of Impl namespace Compatibility change for kokkos-kernels, see kokkos/kokkos-kernels#932 --- packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp b/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp index 84fe54e163bb..4cb885a92c98 100644 --- a/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp +++ b/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp @@ -52,6 +52,7 @@ #define TESTING_AMESOS2_WITH_TPETRA_REMOVE_UVM #if defined(TESTING_AMESOS2_WITH_TPETRA_REMOVE_UVM) #include "KokkosKernels_SparseUtils.hpp" +#include "KokkosKernels_Sorting.hpp" #endif namespace Amesos2 { @@ -608,7 +609,7 @@ namespace Amesos2 { // sort if( ordering == SORTED_INDICES ) { using execution_space = typename KV_GS::execution_space; - KokkosKernels::Impl::sort_crs_matrix + KokkosKernels::sort_crs_matrix (rowptr, colind, nzval); } #endif From f8c911dc674536830c229830c8eff4cd6dc20a14 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Mon, 12 Jul 2021 14:52:37 -0600 Subject: [PATCH 05/98] zoltan2: modify "Vector" alias in Test_Sphynx MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Address errors of form: ../../packages/zoltan2/test/sphynx/Test_Sphynx.cpp:86:18: error: reference to ‘Vector’ is ambiguous typedef Vector::node_type Node; ^~~~~~ --- packages/zoltan2/test/sphynx/Test_Sphynx.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/packages/zoltan2/test/sphynx/Test_Sphynx.cpp b/packages/zoltan2/test/sphynx/Test_Sphynx.cpp index 3b48e83096cc..81290f7abe59 100644 --- a/packages/zoltan2/test/sphynx/Test_Sphynx.cpp +++ b/packages/zoltan2/test/sphynx/Test_Sphynx.cpp @@ -82,12 +82,12 @@ typedef zscalar_t z2TestScalar; typedef Tpetra::CrsMatrix SparseMatrix; typedef Tpetra::CrsGraph SparseGraph; -typedef Tpetra::Vector Vector; -typedef Vector::node_type Node; +typedef Tpetra::Vector VectorT; +typedef VectorT::node_type Node; typedef Zoltan2::XpetraCrsMatrixAdapter SparseMatrixAdapter; typedef Zoltan2::XpetraCrsGraphAdapter SparseGraphAdapter; -typedef Zoltan2::XpetraMultiVectorAdapter MultiVectorAdapter; +typedef Zoltan2::XpetraMultiVectorAdapter MultiVectorAdapter; // Integer vector @@ -209,7 +209,7 @@ int main(int narg, char** arg) << "NumLocalRows (rank 0) = " << origMatrix->getNodeNumRows() << std::endl; ////// Create a vector to use with the matrix. - RCP origVector, origProd; + RCP origVector, origProd; origProd = Tpetra::createVector( origMatrix->getRangeMap()); origVector = Tpetra::createVector( @@ -393,12 +393,12 @@ int main(int narg, char** arg) } if (me == 0) std::cout << "Redistributing vectors..." << std::endl; - Vector *redistribVector; + VectorT *redistribVector; MultiVectorAdapter adapterVector(origVector); //, weights, weightStrides); adapterVector.applyPartitioningSolution(*origVector, redistribVector, problem.getSolution()); - RCP redistribProd; + RCP redistribProd; redistribProd = Tpetra::createVector( redistribMatrix->getRangeMap()); From f310e1236c1b3e846a0bcd62a5d3ae90ef52c26f Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 22 Jul 2021 16:08:35 -0400 Subject: [PATCH 06/98] Improve comments --- packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp | 3 +++ .../core/test/ImportExport2/ImportExport2_UnitTests.cpp | 4 +++- .../tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp | 4 +++- 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp index d29c8292ea62..8a76ac813b08 100644 --- a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp +++ b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_SYCL.hpp @@ -39,6 +39,9 @@ // ************************************************************************ // @HEADER + +// This is a verbatim copy of the other TpetraExt_MatrixMatrix_*.hpp files +// replacing the execution/memory space by the ones corresponding to SYCL. #ifndef TPETRA_MATRIXMATRIX_SYCL_DEF_HPP #define TPETRA_MATRIXMATRIX_SYCL_DEF_HPP diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 0c5e007a220d..decb2583f0ac 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -2845,12 +2845,14 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO TEUCHOS_UNIT_TEST_TEMPLATE_2_INSTANT( Import_Util, GetPids, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_2_INSTANT( Import_Util, GetTwoTransferOwnershipVector, LO, GO ) +// These are the tests associated to UNIT_TEST_GROUP_SC_LO_GO that work for all backends. #define UNIT_TEST_GROUP_SC_LO_GO_COMMON( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) -// FIXME_SYCL requires quering free device memory +// FIXME_SYCL requires querying free device memory in KokkosKernels. +// The SYCL specifications don't allow asking for that. #ifdef HAVE_TPETRA_SYCL #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ UNIT_TEST_GROUP_SC_LO_GO_COMMON( SC, LO, GO ) diff --git a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp index f28e19289b4c..e0b5770eb83a 100644 --- a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp @@ -2209,6 +2209,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMatAdd, locally_unsorted, SC, LO, GO }*/ +// These are the tests associated to UNIT_TEST_GROUP_SC_LO_GO_NO that work for all backends. #define UNIT_TEST_GROUP_SC_LO_GO_NO_COMMON( SC, LO, GO, NT ) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, range_row_test, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMat, ATI_range_row_test, SC, LO, GO, NT) \ @@ -2221,7 +2222,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMatAdd, locally_unsorted, SC, LO, GO TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_col_maps, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_index_base, SC, LO, GO, NT) -// FIXME_SYCL requires quering free device memory +// FIXME_SYCL requires querying free device memory in KokkosKernels. +// The SYCL specifications don't allow asking for that. #ifdef HAVE_TPETRA_SYCL #define UNIT_TEST_GROUP_SC_LO_GO_NO( SC, LO, GO, NT ) \ UNIT_TEST_GROUP_SC_LO_GO_NO_COMMON( SC, LO, GO, NT ) From 544eedaef44840b0079897a0ddafcbf4c854050b Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 22 Jul 2021 14:48:05 -0600 Subject: [PATCH 07/98] sacado, stokhos: replace KOKKOS_IMPL_CUDA_* macros with Cuda functions Change made for compatibiltility with kokkos/kokkos#4138 --- .../src/new_design/Sacado_Fad_Exp_Atomic.hpp | 28 ++++--------------- .../kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp | 6 ++-- 2 files changed, 9 insertions(+), 25 deletions(-) diff --git a/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp b/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp index e1e0dc090887..25843e04f45c 100644 --- a/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp +++ b/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp @@ -122,12 +122,8 @@ namespace Sacado { return_type return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask() ; + unsigned int active = __ballot_sync(mask, 1); unsigned int done_active = 0; while (active != done_active) { if (!done) { @@ -140,11 +136,7 @@ namespace Sacado { done = 1; } } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, done); -#else - done_active = KOKKOS_IMPL_CUDA_BALLOT(done); -#endif + done_active = __ballot_sync(mask, done); } return return_val; } @@ -218,12 +210,8 @@ namespace Sacado { return_type return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask() ; + unsigned int active = __ballot_sync(mask, 1); unsigned int done_active = 0; while (active != done_active) { if (!done) { @@ -236,11 +224,7 @@ namespace Sacado { done = 1; } } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, done); -#else - done_active = KOKKOS_IMPL_CUDA_BALLOT(done); -#endif + done_active = __ballot_sync(mask, done); } return return_val; } diff --git a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp index 8dcb0e5c1d9c..e01a3d15320e 100644 --- a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp +++ b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp @@ -72,19 +72,19 @@ template KOKKOS_INLINE_FUNCTION Scalar shfl_down(const Scalar &val, const int& delta, const int& width, const int& mask){ - return KOKKOS_IMPL_CUDA_SHFL_DOWN_MASK(mask, val, delta, width); + return __shfl_down_sync(mask, val, delta, width); } template KOKKOS_INLINE_FUNCTION Scalar shfl_up(const Scalar &val, const int& delta, const int& width, const int& mask){ - return KOKKOS_IMPL_CUDA_SHFL_UP_MASK(mask, val, delta, width); + return __shfl_up_sync(mask, val, delta, width); } KOKKOS_INLINE_FUNCTION void sync_warp(const int& mask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(mask); + __syncwarp(mask); } } // namespace Stokhos From 3b4f1164fa086cfefd2fdd61aa0f2edde8820b93 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 22 Jul 2021 17:42:59 -0400 Subject: [PATCH 08/98] Mention KokkosKernel issue --- .../tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp | 3 ++- .../tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index decb2583f0ac..5a5b787b4b95 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -2851,7 +2851,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) -// FIXME_SYCL requires querying free device memory in KokkosKernels. +// FIXME_SYCL requires querying free device memory in KokkosKernels, see +// https://github.com/kokkos/kokkos-kernels/issues/1062. // The SYCL specifications don't allow asking for that. #ifdef HAVE_TPETRA_SYCL #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ diff --git a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp index e0b5770eb83a..63b13fd6a208 100644 --- a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp @@ -2222,7 +2222,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMatAdd, locally_unsorted, SC, LO, GO TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_col_maps, SC, LO, GO, NT) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(Tpetra_MatMatAdd, different_index_base, SC, LO, GO, NT) -// FIXME_SYCL requires querying free device memory in KokkosKernels. +// FIXME_SYCL requires querying free device memory in KokkosKernels, see +// https://github.com/kokkos/kokkos-kernels/issues/1062. // The SYCL specifications don't allow asking for that. #ifdef HAVE_TPETRA_SYCL #define UNIT_TEST_GROUP_SC_LO_GO_NO( SC, LO, GO, NT ) \ From 60e27ce1bc1e27717a8d156f86ec86ad391c4a2d Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Wed, 9 Jun 2021 19:42:43 -0600 Subject: [PATCH 09/98] tpetra: move sort_crs_matrix out of Impl namespace Compatibility change for kokkos-kernels, see kokkos/kokkos-kernels#932 --- packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp b/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp index d3c87118e9f9..abf00b35c7ef 100644 --- a/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp +++ b/packages/tpetra/core/src/Tpetra_RowMatrixTransposer_def.hpp @@ -49,6 +49,7 @@ #include "Teuchos_ParameterList.hpp" #include "Teuchos_TimeMonitor.hpp" #include "KokkosKernels_SparseUtils.hpp" +#include "KokkosKernels_Sorting.hpp" namespace Tpetra { @@ -177,7 +178,7 @@ createTransposeLocal (const Teuchos::RCP& params) local_matrix_device_type lclMatrix = crsMatrix->getLocalMatrixDevice (); local_matrix_device_type lclTransposeMatrix = KokkosKernels::Impl::transpose_matrix(lclMatrix); if (sort) - KokkosKernels::Impl::sort_crs_matrix(lclTransposeMatrix); + KokkosKernels::sort_crs_matrix(lclTransposeMatrix); // Prebuild the importers and exporters the no-communication way, // flipping the importers and exporters around. From c0e1471ba1c44b23ffe49cf5f66139659b1af363 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 8 Jul 2021 10:20:14 -0600 Subject: [PATCH 10/98] amesos2: move sort_crs_matrix out of Impl namespace Compatibility change for kokkos-kernels, see kokkos/kokkos-kernels#932 --- packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp b/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp index 84fe54e163bb..4cb885a92c98 100644 --- a/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp +++ b/packages/amesos2/src/Amesos2_MatrixAdapter_def.hpp @@ -52,6 +52,7 @@ #define TESTING_AMESOS2_WITH_TPETRA_REMOVE_UVM #if defined(TESTING_AMESOS2_WITH_TPETRA_REMOVE_UVM) #include "KokkosKernels_SparseUtils.hpp" +#include "KokkosKernels_Sorting.hpp" #endif namespace Amesos2 { @@ -608,7 +609,7 @@ namespace Amesos2 { // sort if( ordering == SORTED_INDICES ) { using execution_space = typename KV_GS::execution_space; - KokkosKernels::Impl::sort_crs_matrix + KokkosKernels::sort_crs_matrix (rowptr, colind, nzval); } #endif From a891ab2828f486273fd27584de8c2d048f928778 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Mon, 12 Jul 2021 14:52:37 -0600 Subject: [PATCH 11/98] zoltan2: modify "Vector" alias in Test_Sphynx MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Address errors of form: ../../packages/zoltan2/test/sphynx/Test_Sphynx.cpp:86:18: error: reference to ‘Vector’ is ambiguous typedef Vector::node_type Node; ^~~~~~ --- packages/zoltan2/test/sphynx/Test_Sphynx.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/packages/zoltan2/test/sphynx/Test_Sphynx.cpp b/packages/zoltan2/test/sphynx/Test_Sphynx.cpp index 3b48e83096cc..81290f7abe59 100644 --- a/packages/zoltan2/test/sphynx/Test_Sphynx.cpp +++ b/packages/zoltan2/test/sphynx/Test_Sphynx.cpp @@ -82,12 +82,12 @@ typedef zscalar_t z2TestScalar; typedef Tpetra::CrsMatrix SparseMatrix; typedef Tpetra::CrsGraph SparseGraph; -typedef Tpetra::Vector Vector; -typedef Vector::node_type Node; +typedef Tpetra::Vector VectorT; +typedef VectorT::node_type Node; typedef Zoltan2::XpetraCrsMatrixAdapter SparseMatrixAdapter; typedef Zoltan2::XpetraCrsGraphAdapter SparseGraphAdapter; -typedef Zoltan2::XpetraMultiVectorAdapter MultiVectorAdapter; +typedef Zoltan2::XpetraMultiVectorAdapter MultiVectorAdapter; // Integer vector @@ -209,7 +209,7 @@ int main(int narg, char** arg) << "NumLocalRows (rank 0) = " << origMatrix->getNodeNumRows() << std::endl; ////// Create a vector to use with the matrix. - RCP origVector, origProd; + RCP origVector, origProd; origProd = Tpetra::createVector( origMatrix->getRangeMap()); origVector = Tpetra::createVector( @@ -393,12 +393,12 @@ int main(int narg, char** arg) } if (me == 0) std::cout << "Redistributing vectors..." << std::endl; - Vector *redistribVector; + VectorT *redistribVector; MultiVectorAdapter adapterVector(origVector); //, weights, weightStrides); adapterVector.applyPartitioningSolution(*origVector, redistribVector, problem.getSolution()); - RCP redistribProd; + RCP redistribProd; redistribProd = Tpetra::createVector( redistribMatrix->getRangeMap()); From f86c91a8bf1257941f9793deb6454dc4cff1a27c Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 22 Jul 2021 14:48:05 -0600 Subject: [PATCH 12/98] sacado, stokhos: replace KOKKOS_IMPL_CUDA_* macros with Cuda functions Change made for compatibiltility with kokkos/kokkos#4138 --- .../src/new_design/Sacado_Fad_Exp_Atomic.hpp | 28 ++++--------------- .../kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp | 6 ++-- 2 files changed, 9 insertions(+), 25 deletions(-) diff --git a/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp b/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp index e1e0dc090887..25843e04f45c 100644 --- a/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp +++ b/packages/sacado/src/new_design/Sacado_Fad_Exp_Atomic.hpp @@ -122,12 +122,8 @@ namespace Sacado { return_type return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask() ; + unsigned int active = __ballot_sync(mask, 1); unsigned int done_active = 0; while (active != done_active) { if (!done) { @@ -140,11 +136,7 @@ namespace Sacado { done = 1; } } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, done); -#else - done_active = KOKKOS_IMPL_CUDA_BALLOT(done); -#endif + done_active = __ballot_sync(mask, done); } return return_val; } @@ -218,12 +210,8 @@ namespace Sacado { return_type return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask() ; + unsigned int active = __ballot_sync(mask, 1); unsigned int done_active = 0; while (active != done_active) { if (!done) { @@ -236,11 +224,7 @@ namespace Sacado { done = 1; } } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, done); -#else - done_active = KOKKOS_IMPL_CUDA_BALLOT(done); -#endif + done_active = __ballot_sync(mask, done); } return return_val; } diff --git a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp index 8dcb0e5c1d9c..e01a3d15320e 100644 --- a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp +++ b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp @@ -72,19 +72,19 @@ template KOKKOS_INLINE_FUNCTION Scalar shfl_down(const Scalar &val, const int& delta, const int& width, const int& mask){ - return KOKKOS_IMPL_CUDA_SHFL_DOWN_MASK(mask, val, delta, width); + return __shfl_down_sync(mask, val, delta, width); } template KOKKOS_INLINE_FUNCTION Scalar shfl_up(const Scalar &val, const int& delta, const int& width, const int& mask){ - return KOKKOS_IMPL_CUDA_SHFL_UP_MASK(mask, val, delta, width); + return __shfl_up_sync(mask, val, delta, width); } KOKKOS_INLINE_FUNCTION void sync_warp(const int& mask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(mask); + __syncwarp(mask); } } // namespace Stokhos From d72eb85100a6d8fc9eeed43607d2eb39a7d78489 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 30 Sep 2021 20:51:58 -0600 Subject: [PATCH 13/98] atdm/contributed/weaver: update modules --- cmake/std/atdm/contributed/weaver/environment.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/std/atdm/contributed/weaver/environment.sh b/cmake/std/atdm/contributed/weaver/environment.sh index 897711ef1e62..388abfb4c58f 100755 --- a/cmake/std/atdm/contributed/weaver/environment.sh +++ b/cmake/std/atdm/contributed/weaver/environment.sh @@ -177,7 +177,7 @@ elif [[ "$ATDM_CONFIG_COMPILER" == "CUDA"* ]] ; then fi # Ninja -module load ninja/1.7.2 +#module load ninja/1.7.2 # CMake #module swap cmake/3.6.2 cmake/3.12.3 From e6aee98a85cb88637a16e07d1e9698eb9e9ef0a0 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 30 Sep 2021 21:05:28 -0600 Subject: [PATCH 14/98] intrepid2: workaround intel internal compiler error in Intrepid2_Data --- packages/intrepid2/src/Shared/Intrepid2_Data.hpp | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/packages/intrepid2/src/Shared/Intrepid2_Data.hpp b/packages/intrepid2/src/Shared/Intrepid2_Data.hpp index a33cf77e6f0a..f2e04b3dd66a 100644 --- a/packages/intrepid2/src/Shared/Intrepid2_Data.hpp +++ b/packages/intrepid2/src/Shared/Intrepid2_Data.hpp @@ -1655,6 +1655,21 @@ class ZeroView { //! Copies 0.0 to the underlying View. void clear() const { +#ifdef KOKKOS_COMPILER_INTEL +// Workaround intel internal compiler errors + DataScalar zero = DataScalar(0); + switch (dataRank_) + { + case 1: {Kokkos::parallel_for(Kokkos::RangePolicy(0, data1_.extent(0)), KOKKOS_LAMBDA(int i) {data1_(i) = zero;}); break; } + case 2: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0},{data2_.extent(0),data2_.extent(1)}), KOKKOS_LAMBDA(int i0, int i1) {data2_(i0, i1) = zero;}); break; } + case 3: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0,0},{data3_.extent(0),data3_.extent(1),data3_.extent(2)}), KOKKOS_LAMBDA(int i0, int i1, int i2) {data3_(i0, i1, i2) = zero;}); break; } + case 4: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0,0,0},{data4_.extent(0),data4_.extent(1),data4_.extent(2),data4_.extent(3)}), KOKKOS_LAMBDA(int i0, int i1, int i2, int i3) {data4_(i0, i1, i2, i3) = zero;}); break; } + case 5: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0,0,0,0},{data5_.extent(0),data5_.extent(1),data5_.extent(2),data5_.extent(3),data5_.extent(4)}), KOKKOS_LAMBDA(int i0, int i1, int i2, int i3, int i4) {data5_(i0, i1, i2, i3, i4) = zero;}); break; } + case 6: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0,0,0,0,0},{data6_.extent(0),data6_.extent(1),data6_.extent(2),data6_.extent(3),data6_.extent(4),data6_.extent(5)}), KOKKOS_LAMBDA(int i0, int i1, int i2, int i3, int i4, int i5) {data6_(i0, i1, i2, i3, i4, i5) = zero;}); break; } + case 7: {Kokkos::parallel_for(Kokkos::MDRangePolicy, execution_space>({0,0,0,0,0,0},{data7_.extent(0),data7_.extent(1),data7_.extent(2),data7_.extent(3),data7_.extent(4),data7_.extent(5)}), KOKKOS_LAMBDA(int i0, int i1, int i2, int i3, int i4, int i5 ) {for (int i6 = 0; i6 < data7_.extent(6); ++i6) data7_(i0, i1, i2, i3, i4, i5, i6) = zero;}); break; } + default: INTREPID2_TEST_FOR_EXCEPTION(true, std::invalid_argument, "Invalid data rank"); + } +#else switch (dataRank_) { case 1: Kokkos::deep_copy(data1_, 0.0); break; @@ -1666,6 +1681,7 @@ class ZeroView { case 7: Kokkos::deep_copy(data7_, 0.0); break; default: INTREPID2_TEST_FOR_EXCEPTION(true, std::invalid_argument, "Invalid data rank"); } +#endif } //! Copies from the provided DynRankView into the underlying Kokkos::View container storing the unique data. From b539d1a3200034d8eaa1dcdb83436d7fa92fd340 Mon Sep 17 00:00:00 2001 From: Roger Pawlowski Date: Wed, 6 Oct 2021 12:40:18 -0600 Subject: [PATCH 15/98] Panzer: fix 1D line mesh issue on cuda --- packages/panzer/disc-fe/src/Panzer_IntegrationValues2.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/packages/panzer/disc-fe/src/Panzer_IntegrationValues2.cpp b/packages/panzer/disc-fe/src/Panzer_IntegrationValues2.cpp index cbe5c45a2d3d..77e14cb368bd 100644 --- a/packages/panzer/disc-fe/src/Panzer_IntegrationValues2.cpp +++ b/packages/panzer/disc-fe/src/Panzer_IntegrationValues2.cpp @@ -1717,6 +1717,7 @@ getCubaturePointsRef(const bool cache, Kokkos::parallel_for("copy values",policy,KOKKOS_LAMBDA (const int cell,const int point, const int dim) { aux(cell,point_offset + point,dim) = side_cub_points(point,dim); }); + PHX::Device::execution_space().fence(); } } else { From 54a5a70f77e091a0a93e28230725d17b94942d61 Mon Sep 17 00:00:00 2001 From: Julia Plews Date: Tue, 12 Oct 2021 15:38:56 -0600 Subject: [PATCH 16/98] MiniTensor: fix or at least work around some __host__ __device__ marking problems on CUDA build. Use std:: instead of boost:: in some places? --- .../minitensor/src/MiniTensor_LinearAlgebra.h | 135 +++------ .../src/MiniTensor_LinearAlgebra.i.h | 109 ++++--- .../src/MiniTensor_LinearAlgebra.t.h | 267 +++++++----------- .../minitensor/src/MiniTensor_Mechanics.t.h | 2 +- .../minitensor/src/MiniTensor_Solvers.t.h | 4 +- packages/minitensor/src/MiniTensor_Storage.h | 114 +++----- packages/minitensor/src/MiniTensor_Tensor.i.h | 16 +- .../minitensor/src/MiniTensor_TensorBase.i.h | 7 +- .../minitensor/src/MiniTensor_Utilities.h | 15 +- .../minitensor/src/MiniTensor_Utilities.i.h | 18 +- packages/minitensor/src/MiniTensor_Vector.h | 1 - packages/minitensor/src/MiniTensor_Vector.i.h | 16 +- packages/minitensor/test/test_01.cc | 22 +- 13 files changed, 278 insertions(+), 448 deletions(-) diff --git a/packages/minitensor/src/MiniTensor_LinearAlgebra.h b/packages/minitensor/src/MiniTensor_LinearAlgebra.h index cf373bfd617c..c702a66486df 100644 --- a/packages/minitensor/src/MiniTensor_LinearAlgebra.h +++ b/packages/minitensor/src/MiniTensor_LinearAlgebra.h @@ -183,10 +183,7 @@ I3(Tensor const & A); /// Exponential map. /// \return \f$ \exp A \f$ /// -template -KOKKOS_INLINE_FUNCTION -Tensor -exp(Tensor const & A); +template Tensor exp(Tensor const &A); /// /// Exponential map by Taylor series, radius of convergence is infinity @@ -202,10 +199,7 @@ exp_taylor(Tensor const & A); /// See algorithm 10.20 in Functions of Matrices, N.J. Higham, SIAM, 2008. /// \return \f$ \exp A \f$ /// -template -KOKKOS_INLINE_FUNCTION -Tensor -exp_pade(Tensor const & A); +template Tensor exp_pade(Tensor const &A); /// /// Logarithmic map. @@ -338,20 +332,16 @@ norm_off_diagonal(Tensor const & A); /// that rely on Jacobi-type procedures. /// \return \f$ (p,q) = arg max_{i,j} |a_{ij}| \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair -arg_max_abs(Tensor const & A); +template +std::pair arg_max_abs(Tensor const &A); /// /// Arg max off-diagonal. Useful for SVD and other algorithms /// that rely on Jacobi-type procedures. /// \return \f$ (p,q) = arg max_{i \neq j} |a_{ij}| \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair -arg_max_off_diagonal(Tensor const & A); +template +std::pair arg_max_off_diagonal(Tensor const &A); /// /// Sort and index. Useful for ordering singular values @@ -360,18 +350,15 @@ arg_max_off_diagonal(Tensor const & A); /// \param u vector to sort /// \return v P sorted vector, permutation matrix such that v = P^T u /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -sort_permutation(Vector const & u); +template +std::pair, Tensor> sort_permutation(Vector const &u); /// /// Singular value decomposition (SVD) /// \return \f$ A = USV^T\f$ /// -template -boost::tuple, Tensor, Tensor> -svd(Tensor const & A); +template +std::tuple, Tensor, Tensor> svd(Tensor const &A); /// /// Project to O(N) (Orthogonal Group) using a Newton-type algorithm. @@ -392,62 +379,54 @@ polar_rotation(Tensor const & A); /// \param A tensor (often a deformation-gradient-like tensor) /// \return \f$ VR = A \f$ with \f$ R \in SO(N) \f$ and \f$ V \in SPD(N) \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_left(Tensor const & A); +template +std::pair, Tensor> polar_left(Tensor const &A); /// /// Right polar decomposition /// \param A tensor (often a deformation-gradient-like tensor) /// \return \f$ RU = A \f$ with \f$ R \in SO(N) \f$ and \f$ U \in SPD(N) \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_right(Tensor const & A); +template +std::pair, Tensor> polar_right(Tensor const &A); /// /// Left polar decomposition computed with eigenvalue decomposition /// \param A tensor (often a deformation-gradient-like tensor) /// \return \f$ VR = A \f$ with \f$ R \in SO(N) \f$ and \f$ V \in SPD(N) \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_left_eig(Tensor const & A); +template +std::pair, Tensor> polar_left_eig(Tensor const &A); /// /// R^3 right polar decomposition /// \param A tensor (often a deformation-gradient-like tensor) /// \return \f$ RU = F \f$ with \f$ R \in SO(N) \f$ and \f$ U \in SPD(N) \f$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_right_eig(Tensor const & A); +template +std::pair, Tensor> polar_right_eig(Tensor const &A); /// /// Left polar decomposition with matrix logarithm for V /// \param F tensor (often a deformation-gradient-like tensor) /// \return \f$ VR = F \f$ with \f$ R \in SO(N) \f$ and V SPD, and log V /// -template -boost::tuple, Tensor, Tensor> -polar_left_logV(Tensor const & F); +template +std::tuple, Tensor, Tensor> +polar_left_logV(Tensor const &F); -template -boost::tuple, Tensor, Tensor> -polar_left_logV_eig(Tensor const & F); +template +std::tuple, Tensor, Tensor> +polar_left_logV_eig(Tensor const &F); /// /// Left polar decomposition with matrix logarithm for V using eig_spd_cos /// \param F tensor (often a deformation-gradient-like tensor) /// \return \f$ VR = F \f$ with \f$ R \in SO(N) \f$ and V SPD, and log V /// -template -boost::tuple, Tensor, Tensor> -polar_left_logV_lame(Tensor const & F); +template +std::tuple, Tensor, Tensor> +polar_left_logV_lame(Tensor const &F); /// /// Logarithmic map using BCH expansion (4 terms) @@ -465,37 +444,28 @@ bch(Tensor const & v, Tensor const & r); /// \param \f$ A = [f, g; g, h] \in S(2) \f$ /// \return \f$ c, s \rightarrow [c, -s; s, c]\f$ diagonalizes A$ /// -template -KOKKOS_INLINE_FUNCTION -std::pair -schur_sym(const T f, const T g, const T h); +template +std::pair schur_sym(const T f, const T g, const T h); /// /// Givens rotation. [c, -s; s, c] [a; b] = [r; 0] /// \return c and s /// -template -KOKKOS_INLINE_FUNCTION -std::pair -givens(T const & a, T const & b); +template std::pair givens(T const &a, T const &b); /// /// Eigenvalue decomposition for symmetric 2nd-order tensor /// \return V eigenvectors, D eigenvalues in diagonal Matlab-style /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_sym(Tensor const & A); +template +std::pair, Tensor> eig_sym(Tensor const &A); /// /// Eigenvalue decomposition for SPD 2nd-order tensor /// \return V eigenvectors, D eigenvalues in diagonal Matlab-style /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_spd(Tensor const & A); +template +std::pair, Tensor> eig_spd(Tensor const &A); /// /// Eigenvalue decomposition for SPD 2nd-order tensor @@ -503,10 +473,8 @@ eig_spd(Tensor const & A); /// This algorithm comes from the journal article /// Scherzinger and Dohrmann, CMAME 197 (2008) 4007-4015 /// -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_spd_cos(Tensor const & A); +template +std::pair, Tensor> eig_spd_cos(Tensor const &A); /// /// Cholesky decomposition, rank-1 update algorithm @@ -515,10 +483,8 @@ eig_spd_cos(Tensor const & A); /// \return G Cholesky factor A = GG^T and completed (bool) /// algorithm ran to completion /// -template -KOKKOS_INLINE_FUNCTION -std::pair, bool > -cholesky(Tensor const & A); +template +std::pair, bool> cholesky(Tensor const &A); /// /// Preconditioner types @@ -535,10 +501,9 @@ enum class PreconditionerType /// Compute a preconditioner for improving the conditioning of a /// linear system. /// -template -KOKKOS_INLINE_FUNCTION -std::pair, RHS> -precon(PreconditionerType const pt, Tensor const & A, RHS const & B); +template +std::pair, RHS> precon(PreconditionerType const pt, + Tensor const &A, RHS const &B); /// /// Solve linear system of equations. @@ -551,11 +516,9 @@ precon(PreconditionerType const pt, Tensor const & A, RHS const & B); /// \param b rhs of the system Ax=b /// \return x solution(s) to the system Ax=b /// -template -KOKKOS_INLINE_FUNCTION -RHS -solve(Tensor const & A, RHS const & b, - PreconditionerType const pt = PreconditionerType::IDENTITY); +template +RHS solve(Tensor const &A, RHS const &b, + PreconditionerType const pt = PreconditionerType::IDENTITY); template KOKKOS_INLINE_FUNCTION @@ -565,18 +528,12 @@ solve_full_pivot(Tensor const & A, RHS const & b); /// /// Condition number: ratio of largest to smalest singular values. /// -template -KOKKOS_INLINE_FUNCTION -T -cond(Tensor const & A); +template T cond(Tensor const &A); /// /// Reciprocal condition number: ratio of smallest to largest singular values. /// -template -KOKKOS_INLINE_FUNCTION -T -inv_cond(Tensor const & A); +template T inv_cond(Tensor const &A); } // namespace minitensor diff --git a/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h b/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h index 91e6123822dd..92e4aa540653 100644 --- a/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h +++ b/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h @@ -96,6 +96,8 @@ KOKKOS_INLINE_FUNCTION T norm_1(Tensor const & A) { + using KAT = Kokkos::ArithTraits; + Index const dimension = A.get_dimension(); @@ -107,40 +109,39 @@ norm_1(Tensor const & A) switch (dimension) { - default: + default: - for (Index i = 0; i < dimension; ++i) { - T t = 0.0; - for (Index j = 0; j < dimension; ++j) { - t += std::abs(A(j, i)); - } - v(i) = t; + for (Index i = 0; i < dimension; ++i) { + T t = 0.0; + for (Index j = 0; j < dimension; ++j) { + t += KAT::abs(A(j, i)); } + v(i) = t; + } - for (Index i = 0; i < dimension; ++i) { - s = std::max(s, v(i)); - } - break; - - case 3: - v(0) = std::abs(A(0,0)) + std::abs(A(1,0)) + std::abs(A(2,0)); - v(1) = std::abs(A(0,1)) + std::abs(A(1,1)) + std::abs(A(2,1)); - v(2) = std::abs(A(0,2)) + std::abs(A(1,2)) + std::abs(A(2,2)); + for (Index i = 0; i < dimension; ++i) { + s = max(s, v(i)); + } + break; - s = std::max(std::max(v(0),v(1)),v(2)); - break; + case 3: + v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(1, 0)) + KAT::abs(A(2, 0)); + v(1) = KAT::abs(A(0, 1)) + KAT::abs(A(1, 1)) + KAT::abs(A(2, 1)); + v(2) = KAT::abs(A(0, 2)) + KAT::abs(A(1, 2)) + KAT::abs(A(2, 2)); - case 2: - v(0) = std::abs(A(0,0)) + std::abs(A(1,0)); - v(1) = std::abs(A(0,1)) + std::abs(A(1,1)); + s = max(max(v(0), v(1)), v(2)); + break; - s = std::max(v(0),v(1)); - break; + case 2: + v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(1, 0)); + v(1) = KAT::abs(A(0, 1)) + KAT::abs(A(1, 1)); - case 1: - s = std::abs(A(0,0)); - break; + s = max(v(0), v(1)); + break; + case 1: + s = KAT::abs(A(0, 0)); + break; } return s; @@ -155,6 +156,8 @@ KOKKOS_INLINE_FUNCTION T norm_infinity(Tensor const & A) { + using KAT = Kokkos::ArithTraits; + Index const dimension = A.get_dimension(); @@ -169,33 +172,33 @@ norm_infinity(Tensor const & A) for (Index i = 0; i < dimension; ++i) { T t = 0.0; for (Index j = 0; j < dimension; ++j) { - t += std::abs(A(i, j)); + t += KAT::abs(A(i, j)); } v(i) = t; } for (Index i = 0; i < dimension; ++i) { - s = std::max(s, v(i)); + s = max(s, v(i)); } break; case 3: - v(0) = std::abs(A(0,0)) + std::abs(A(0,1)) + std::abs(A(0,2)); - v(1) = std::abs(A(1,0)) + std::abs(A(1,1)) + std::abs(A(1,2)); - v(2) = std::abs(A(2,0)) + std::abs(A(2,1)) + std::abs(A(2,2)); + v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(0, 1)) + KAT::abs(A(0, 2)); + v(1) = KAT::abs(A(1, 0)) + KAT::abs(A(1, 1)) + KAT::abs(A(1, 2)); + v(2) = KAT::abs(A(2, 0)) + KAT::abs(A(2, 1)) + KAT::abs(A(2, 2)); - s = std::max(std::max(v(0),v(1)),v(2)); + s = max(max(v(0), v(1)), v(2)); break; case 2: - v(0) = std::abs(A(0,0)) + std::abs(A(0,1)); - v(1) = std::abs(A(1,0)) + std::abs(A(1,1)); + v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(0, 1)); + v(1) = KAT::abs(A(1, 0)) + KAT::abs(A(1, 1)); - s = std::max(v(0),v(1)); + s = max(v(0), v(1)); break; case 1: - s = std::abs(A(0,0)); + s = KAT::abs(A(0, 0)); break; } @@ -375,10 +378,11 @@ I2(Tensor const & A) default: #ifdef KOKKOS_ENABLE_CUDA Kokkos::abort("I2 for N > 3 not implemented."); + return T(); #else std::cerr << "I2 for N > 3 not implemented." << std::endl; -#endif exit(1); +#endif break; case 3: @@ -420,10 +424,11 @@ I3(Tensor const & A) default: #ifdef KOKKOS_ENABLE_CUDA Kokkos::abort("I3 for N > 3 not implemented."); -#else + return T(); +#else std::cerr << "I3 for N > 3 not implemented." << std::endl; -#endif exit(1); +#endif break; case 3: @@ -446,16 +451,11 @@ I3(Tensor const & A) // // Condition number. // -template -KOKKOS_INLINE_FUNCTION -T -cond(Tensor const & A) -{ +template T cond(Tensor const &A) { Index const dimension = A.get_dimension(); - Tensor const - S = boost::get<1>(svd(A)); + Tensor const S = std::get<1>(svd(A)); T const k = S(0, 0) / S(dimension - 1, dimension - 1); @@ -466,16 +466,11 @@ cond(Tensor const & A) // // Reciprocal condition number. // -template -KOKKOS_INLINE_FUNCTION -T -inv_cond(Tensor const & A) -{ +template T inv_cond(Tensor const &A) { Index const dimension = A.get_dimension(); - Tensor const - S = boost::get<1>(svd(A)); + Tensor const S = std::get<1>(svd(A)); T const k = S(dimension - 1, dimension - 1) / S(0, 0); @@ -487,11 +482,8 @@ inv_cond(Tensor const & A) // Sort and index in descending order. Useful for ordering singular values // and eigenvalues and corresponding vectors in the respective decompositions. // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -sort_permutation(Vector const & u) -{ +template +std::pair, Tensor> sort_permutation(Vector const &u) { Index const dimension = u.get_dimension(); @@ -517,7 +509,6 @@ sort_permutation(Vector const & u) } return std::make_pair(v, P); - } } // namespace minitensor diff --git a/packages/minitensor/src/MiniTensor_LinearAlgebra.t.h b/packages/minitensor/src/MiniTensor_LinearAlgebra.t.h index 85d14a5e164d..bb6674069e1f 100644 --- a/packages/minitensor/src/MiniTensor_LinearAlgebra.t.h +++ b/packages/minitensor/src/MiniTensor_LinearAlgebra.t.h @@ -39,6 +39,7 @@ // ************************************************************************ // @HEADER +#include "Kokkos_ArithTraits.hpp" #if !defined(MiniTensor_LinearAlgebra_t_h) #define MiniTensor_LinearAlgebra_t_h @@ -289,11 +290,7 @@ subtensor(Tensor const & A, Index const i, Index const j) // // Exponential map // -template -KOKKOS_INLINE_FUNCTION -Tensor -exp(Tensor const & A) -{ +template Tensor exp(Tensor const &A) { return exp_pade(A); } @@ -438,11 +435,9 @@ polynomial_coefficient(Index const order, Index const index) // // Padé approximant polynomial odd and even terms. // -template -KOKKOS_INLINE_FUNCTION +template std::pair, Tensor> -pade_polynomial_terms(Tensor const & A, Index const order) -{ +pade_polynomial_terms(Tensor const &A, Index const order) { Index const dimension = A.get_dimension(); @@ -549,11 +544,7 @@ binary_powering(Tensor const & A, Index const exponent) // \param A tensor // \return \f$ \exp A \f$ // -template -KOKKOS_INLINE_FUNCTION -Tensor -exp_pade(Tensor const & A) -{ +template Tensor exp_pade(Tensor const &A) { Index const dimension = A.get_dimension(); @@ -588,7 +579,7 @@ exp_pade(Tensor const & A) Tensor V; - boost::tie(U, V) = pade_polynomial_terms(A, order); + std::tie(U, V) = pade_polynomial_terms(A, order); B = inverse(V - U) * (U + V); @@ -810,7 +801,7 @@ log_eig_sym(Tensor const & A) Tensor D(dimension); - boost::tie(V, D) = eig_sym(A); + std::tie(V, D) = eig_sym(A); for (Index i = 0; i < dimension; ++i) { D(i, i) = std::log(D(i, i)); @@ -1159,11 +1150,8 @@ norm_off_diagonal(Tensor const & A) // \param A // \return \f$ (p,q) = arg max_{i,j} |a_{ij}| \f$ // -template -//KOKKOS_INLINE_FUNCTION -std::pair -arg_max_abs(Tensor const & A) -{ +template +std::pair arg_max_abs(Tensor const &A) { Index p = 0; Index q = 0; @@ -1193,11 +1181,8 @@ arg_max_abs(Tensor const & A) // \param A // \return \f$ (p,q) = arg max_{i \neq j} |a_{ij}| \f$ // -template -KOKKOS_INLINE_FUNCTION -std::pair -arg_max_off_diagonal(Tensor const & A) -{ +template +std::pair arg_max_off_diagonal(Tensor const &A) { Index p = 0; Index q = 1; @@ -1229,10 +1214,9 @@ namespace { // \param f, g, h where A = [f, g; 0, h] // \return \f$ A = USV^T\f$ // -template -boost::tuple, Tensor, Tensor> -svd_bidiagonal(T f, T g, T h) -{ +template +std::tuple, Tensor, Tensor> svd_bidiagonal(T f, T g, + T h) { T fa = std::abs(f); T ga = std::abs(g); T ha = std::abs(h); @@ -1312,7 +1296,7 @@ svd_bidiagonal(T f, T g, T h) Tensor S(s0, 0.0, 0.0, s1); Tensor V(cv, -sv, sv, cv); - return boost::make_tuple(U, S, V); + return std::make_tuple(U, S, V); } // @@ -1320,16 +1304,15 @@ svd_bidiagonal(T f, T g, T h) // \param A tensor // \return \f$ A = USV^T\f$ // -template -boost::tuple, Tensor, Tensor> -svd_2x2(Tensor const & A) -{ +template +std::tuple, Tensor, Tensor> +svd_2x2(Tensor const &A) { assert(A.get_dimension() == 2); // First compute a givens rotation to eliminate 1,0 entry in tensor T c = 1.0; T s = 0.0; - boost::tie(c, s) = givens(A(0,0), A(1,0)); + std::tie(c, s) = givens(A(0, 0), A(1, 0)); Tensor R(c, -s, s, c); @@ -1341,13 +1324,13 @@ svd_2x2(Tensor const & A) Tensor X(2), S(2), V(2); - boost::tie(X, S, V) = svd_bidiagonal(B(0,0), B(0,1), B(1,1)); + std::tie(X, S, V) = svd_bidiagonal(B(0, 0), B(0, 1), B(1, 1)); // Complete general 2x2 SVD with givens rotation calculated above Tensor U = transpose(R) * X; - return boost::make_tuple(U, S, V); + return std::make_tuple(U, S, V); } // @@ -1355,10 +1338,9 @@ svd_2x2(Tensor const & A) // \param A tensor // \return \f$ A = USV^T\f$ // -template -boost::tuple, Tensor, Tensor> -svd_NxN(Tensor const & A) -{ +template +std::tuple, Tensor, Tensor> +svd_NxN(Tensor const &A) { // Scale first T const norm_a = norm(A); @@ -1399,7 +1381,7 @@ svd_NxN(Tensor const & A) Index q = 0; - boost::tie(p,q) = arg_max_off_diagonal(S); + std::tie(p, q) = arg_max_off_diagonal(S); if (p > q) { std::swap(p, q); @@ -1412,7 +1394,7 @@ svd_NxN(Tensor const & A) Tensor L(2), D(2), R(2); - boost::tie(L, D, R) = svd_2x2(Spq); + std::tie(L, D, R) = svd_2x2(Spq); T const & cl = L(0,0); @@ -1456,12 +1438,12 @@ svd_NxN(Tensor const & A) Vector s(dimension); Tensor P(dimension); - boost::tie(s, P) = sort_permutation(diag(S)); + std::tie(s, P) = sort_permutation(diag(S)); S = scale * diag(s); U = U * P; V = V * P; - return boost::make_tuple(U, diag(diag(S)), transpose(V)); + return std::make_tuple(U, diag(diag(S)), transpose(V)); } } // anonymous namespace @@ -1471,10 +1453,9 @@ svd_NxN(Tensor const & A) // \param A tensor // \return \f$ A = USV^T\f$ // -template -boost::tuple, Tensor, Tensor> -svd(Tensor const & A) -{ +template +std::tuple, Tensor, Tensor> +svd(Tensor const &A) { Index const dimension = A.get_dimension(); @@ -1484,16 +1465,16 @@ svd(Tensor const & A) switch (dimension) { default: - boost::tie(U, S, V) = svd_NxN(A); + std::tie(U, S, V) = svd_NxN(A); break; case 2: - boost::tie(U, S, V) = svd_2x2(A); + std::tie(U, S, V) = svd_2x2(A); break; } - return boost::make_tuple(U, S, V); + return std::make_tuple(U, S, V); } // @@ -1519,8 +1500,8 @@ polar_rotation(Tensor const & A) T const tol_scale = 0.01; - T const - tol_conv = std::sqrt(dimension) * machine_epsilon(); + T const tol_conv = + Kokkos::ArithTraits::sqrt(dimension) * machine_epsilon(); Tensor X = A; @@ -1588,11 +1569,8 @@ polar_rotation(Tensor const & A) // \param A tensor (often a deformation-gradient-like tensor) // \return \f$ VR = A \f$ with \f$ R \in SO(N) \f$ and \f$ V \in SPD(N) \f$ // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_left(Tensor const & A) -{ +template +std::pair, Tensor> polar_left(Tensor const &A) { Tensor R = polar_rotation(A); @@ -1607,11 +1585,8 @@ polar_left(Tensor const & A) // \param A tensor (often a deformation-gradient-like tensor) // \return \f$ RU = A \f$ with \f$ R \in SO(N) \f$ and \f$ U \in SPD(N) \f$ // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_right(Tensor const & A) -{ +template +std::pair, Tensor> polar_right(Tensor const &A) { Tensor R = polar_rotation(A); @@ -1626,11 +1601,8 @@ polar_right(Tensor const & A) // \param F tensor (often a deformation-gradient-like tensor) // \return \f$ VR = F \f$ with \f$ R \in SO(3) \f$ and V SPD(3) // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_left_eig(Tensor const & F) -{ +template +std::pair, Tensor> polar_left_eig(Tensor const &F) { assert(F.get_dimension() == 3); // set up return tensors @@ -1654,7 +1626,7 @@ polar_left_eig(Tensor const & F) Tensor eVec(3); - boost::tie(eVec, eVal) = eig_spd(b); + std::tie(eVec, eVal) = eig_spd(b); // compute sqrt() and inv(sqrt()) of eigenvalues Tensor @@ -1683,11 +1655,8 @@ polar_left_eig(Tensor const & F) // \param F tensor (often a deformation-gradient-like tensor) // \return \f$ RU = F \f$ with \f$ R \in SO(3) \f$ and U SPD(3) // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -polar_right_eig(Tensor const & F) -{ +template +std::pair, Tensor> polar_right_eig(Tensor const &F) { Index const dimension = F.get_dimension(); @@ -1714,7 +1683,7 @@ polar_right_eig(Tensor const & F) Tensor eVec(dimension); - boost::tie(eVec, eVal) = eig_spd(C); + std::tie(eVec, eVal) = eig_spd(C); // compute sqrt() and inv(sqrt()) of eigenvalues Tensor @@ -1744,17 +1713,16 @@ polar_right_eig(Tensor const & F) // \param F tensor (often a deformation-gradient-like tensor) // \return \f$ VR = F \f$ with \f$ R \in SO(N) \f$ and V SPD(N), and log V // -template -boost::tuple, Tensor, Tensor> -polar_left_logV(Tensor const & F) -{ +template +std::tuple, Tensor, Tensor> +polar_left_logV(Tensor const &F) { Index const dimension = F.get_dimension(); Tensor X(dimension), S(dimension), Y(dimension); - boost::tie(X, S, Y) = svd(F); + std::tie(X, S, Y) = svd(F); Tensor R = X * transpose(Y); @@ -1772,13 +1740,12 @@ polar_left_logV(Tensor const & F) Tensor v = X * s * transpose(X); - return boost::make_tuple(V, R, v); + return std::make_tuple(V, R, v); } -template -boost::tuple, Tensor, Tensor> -polar_left_logV_eig(Tensor const & F) -{ +template +std::tuple, Tensor, Tensor> +polar_left_logV_eig(Tensor const &F) { Index const dimension = F.get_dimension(); @@ -1788,7 +1755,7 @@ polar_left_logV_eig(Tensor const & F) Tensor V(dimension), D(dimension); - boost::tie(V, D) = eig_sym(b); + std::tie(V, D) = eig_sym(b); Tensor DQ(dimension, Filler::ZEROS), DI(dimension, Filler::ZEROS), DL(dimension, Filler::ZEROS); @@ -1808,7 +1775,7 @@ polar_left_logV_eig(Tensor const & F) Tensor const x = V * dot_t(DL, V); - return boost::make_tuple(X, R, x); + return std::make_tuple(X, R, x); } // @@ -1816,10 +1783,9 @@ polar_left_logV_eig(Tensor const & F) // \param F tensor (often a deformation-gradient-like tensor) // \return \f$ VR = F \f$ with \f$ R \in SO(N) \f$ and V SPD(N), and log V // -template -boost::tuple, Tensor, Tensor> -polar_left_logV_lame(Tensor const & F) -{ +template +std::tuple, Tensor, Tensor> +polar_left_logV_lame(Tensor const &F) { Index const dimension = F.get_dimension(); @@ -1832,7 +1798,7 @@ polar_left_logV_lame(Tensor const & F) // get eigenvalues/eigenvectors Tensor eVal(dimension); Tensor eVec(dimension); - boost::tie(eVec,eVal) = eig_spd_cos(b); + std::tie(eVec, eVal) = eig_spd_cos(b); // compute sqrt() and inv(sqrt()) of eigenvalues Tensor x = zero(3); @@ -1853,7 +1819,7 @@ polar_left_logV_lame(Tensor const & F) v = eVec*lnx*transpose(eVec); R = Vinv*F; - return boost::make_tuple(V,R,v); + return std::make_tuple(V, R, v); } // @@ -1888,11 +1854,8 @@ bch(Tensor const & x, Tensor const & y) // \param \f$ A = [f, g; g, h] \in S(2) \f$ // \return \f$ c, s \rightarrow [c, -s; s, c]\f diagonalizes A$ // -template -KOKKOS_INLINE_FUNCTION -std::pair -schur_sym(T const f, T const g, T const h) -{ +template +std::pair schur_sym(T const f, T const g, T const h) { T c = 1.0; T s = 0.0; @@ -1916,11 +1879,7 @@ schur_sym(T const f, T const g, T const h) // \param a, b // \return c, s // -template -KOKKOS_INLINE_FUNCTION -std::pair -givens(T const & a, T const & b) -{ +template std::pair givens(T const &a, T const &b) { T c = 1.0; T s = 0.0; @@ -1947,11 +1906,8 @@ namespace { // \return V eigenvectors, D eigenvalues in diagonal Matlab-style // See algorithm 8.4.2 in Matrix Computations, Golub & Van Loan 1996 // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_sym_NxN(Tensor const & A) -{ +template +std::pair, Tensor> eig_sym_NxN(Tensor const &A) { Tensor D = sym(A); @@ -1984,7 +1940,7 @@ eig_sym_NxN(Tensor const & A) Index q = 0; - boost::tie(p,q) = arg_max_off_diagonal(D); + std::tie(p, q) = arg_max_off_diagonal(D); if (p > q) { std::swap(p,q); } @@ -2002,7 +1958,7 @@ eig_sym_NxN(Tensor const & A) T c, s; - boost::tie(c, s) = schur_sym(f, g, h); + std::tie(c, s) = schur_sym(f, g, h); // Apply Givens rotation to matrices // that are converging to eigenvalues and eigenvectors @@ -2018,7 +1974,7 @@ eig_sym_NxN(Tensor const & A) Vector d(dimension); Tensor P(dimension); - boost::tie(d, P) = sort_permutation(diag(D)); + std::tie(d, P) = sort_permutation(diag(D)); D = diag(d); V = V * P; @@ -2030,11 +1986,8 @@ eig_sym_NxN(Tensor const & A) // \param A tensor // \return V eigenvectors, D eigenvalues in diagonal Matlab-style // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_sym_2x2(Tensor const & A) -{ +template +std::pair, Tensor> eig_sym_2x2(Tensor const &A) { assert(A.get_dimension() == 2); T const f = A(0,0); @@ -2093,15 +2046,15 @@ eig_sym_2x2(Tensor const & A) T c, s; - boost::tie(c, s) = schur_sym(f, g, h); + std::tie(c, s) = schur_sym(f, g, h); Tensor V(c, -s, s, c); if (swap_diag == true) { // swap eigenvectors if eigenvalues were swapped - std::swap(V(0,0), V(0,1)); - std::swap(V(1,0), V(1,1)); + std::swap(V(0, 0), V(0, 1)); + std::swap(V(1, 0), V(1, 1)); } return std::make_pair(V, D); @@ -2114,11 +2067,8 @@ eig_sym_2x2(Tensor const & A) // \param A tensor // \return V eigenvectors, D eigenvalues in diagonal Matlab-style // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_sym(Tensor const & A) -{ +template +std::pair, Tensor> eig_sym(Tensor const &A) { Index const dimension = A.get_dimension(); @@ -2128,11 +2078,11 @@ eig_sym(Tensor const & A) switch (dimension) { default: - boost::tie(V, D) = eig_sym_NxN(A); + std::tie(V, D) = eig_sym_NxN(A); break; case 2: - boost::tie(V, D) = eig_sym_2x2(A); + std::tie(V, D) = eig_sym_2x2(A); break; } @@ -2145,11 +2095,8 @@ eig_sym(Tensor const & A) // \param A tensor // \return V eigenvectors, D eigenvalues in diagonal Matlab-style // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_spd(Tensor const & A) -{ +template +std::pair, Tensor> eig_spd(Tensor const &A) { return eig_sym(A); } @@ -2158,11 +2105,8 @@ eig_spd(Tensor const & A) // \param A tensor // \return V eigenvectors, D eigenvalues in diagonal Matlab-style // -template -KOKKOS_INLINE_FUNCTION -std::pair, Tensor> -eig_spd_cos(Tensor const & A) -{ +template +std::pair, Tensor> eig_spd_cos(Tensor const &A) { Index const dimension = A.get_dimension(); @@ -2415,11 +2359,8 @@ eig_spd_cos(Tensor const & A) // \return G Cholesky factor A = GG^T // \return completed (bool) algorithm ran to completion // -template -KOKKOS_INLINE_FUNCTION -std::pair, bool > -cholesky(Tensor const & A) -{ +template +std::pair, bool> cholesky(Tensor const &A) { Tensor G = sym(A); @@ -2465,22 +2406,18 @@ namespace { // // // -template -KOKKOS_INLINE_FUNCTION -std::pair, RHS> -identity_precon(Tensor const & A, RHS const & B) -{ +template +std::pair, RHS> identity_precon(Tensor const &A, + RHS const &B) { return std::make_pair(A, B); } // // // -template -KOKKOS_INLINE_FUNCTION -std::pair, RHS> -diagonal_precon(Tensor const & A, RHS const & B) -{ +template +std::pair, RHS> diagonal_precon(Tensor const &A, + RHS const &B) { Vector const d = diag(A); @@ -2496,11 +2433,8 @@ diagonal_precon(Tensor const & A, RHS const & B) // // // -template -KOKKOS_INLINE_FUNCTION -std::pair, RHS> -maxabsrow_precon(Tensor const & A, RHS & B) -{ +template +std::pair, RHS> maxabsrow_precon(Tensor const &A, RHS &B) { Index const dimension = A.get_dimension(); @@ -2519,11 +2453,9 @@ maxabsrow_precon(Tensor const & A, RHS & B) // // // -template -KOKKOS_INLINE_FUNCTION -std::pair, RHS> -precon(PreconditionerType const pt, Tensor const & A, RHS const & B) -{ +template +std::pair, RHS> precon(PreconditionerType const pt, + Tensor const &A, RHS const &B) { switch (pt) { default: MT_ERROR_EXIT("Unknown preconditioner type."); @@ -2550,18 +2482,15 @@ precon(PreconditionerType const pt, Tensor const & A, RHS const & B) // as it just Gauss-Jordan elimination. It is intended to be used in // conjunction with Kokkos to take advantage of thread parallelism. // -template -KOKKOS_INLINE_FUNCTION -RHS -solve(Tensor const & A, RHS const & b, PreconditionerType const pt) -{ +template +RHS solve(Tensor const &A, RHS const &b, PreconditionerType const pt) { Tensor PA; RHS Pb; - boost::tie(PA, Pb) = precon(pt, A, b); + std::tie(PA, Pb) = precon(pt, A, b); return solve_full_pivot(PA, Pb); } diff --git a/packages/minitensor/src/MiniTensor_Mechanics.t.h b/packages/minitensor/src/MiniTensor_Mechanics.t.h index d9d4ec23d23c..61df4c1950bc 100644 --- a/packages/minitensor/src/MiniTensor_Mechanics.t.h +++ b/packages/minitensor/src/MiniTensor_Mechanics.t.h @@ -663,7 +663,7 @@ check_strong_ellipticity(Tensor4 const & A) Tensor D; - boost::tie(V, D) = eig_sym(Q); + std::tie(V, D) = eig_sym(Q); curr_eigenvalue = D(dimension - 1, dimension - 1); diff --git a/packages/minitensor/src/MiniTensor_Solvers.t.h b/packages/minitensor/src/MiniTensor_Solvers.t.h index 2cf4dd758d2a..ec6a37b34b2b 100644 --- a/packages/minitensor/src/MiniTensor_Solvers.t.h +++ b/packages/minitensor/src/MiniTensor_Solvers.t.h @@ -564,7 +564,7 @@ step(Tensor const & Hessian, Vector const & gradient) bool is_posdef{false}; - boost::tie(L, is_posdef) = cholesky(K); + std::tie(L, is_posdef) = cholesky(K); if (is_posdef == false) { MT_ERROR_EXIT("Trust region subproblem encountered singular Hessian."); @@ -635,7 +635,7 @@ step(Tensor const & Hessian, Vector const & gradient) bool is_posdef{false}; - boost::tie(L, is_posdef) = cholesky(K); + std::tie(L, is_posdef) = cholesky(K); if (is_posdef == false) { MT_ERROR_EXIT("Trust region subproblem encountered singular Hessian."); diff --git a/packages/minitensor/src/MiniTensor_Storage.h b/packages/minitensor/src/MiniTensor_Storage.h index 56b00c903253..5fa993169ec5 100644 --- a/packages/minitensor/src/MiniTensor_Storage.h +++ b/packages/minitensor/src/MiniTensor_Storage.h @@ -39,6 +39,7 @@ // ************************************************************************ // @HEADER +#include "Kokkos_Macros.hpp" #if !defined(MiniTensor_Storage_h) #define MiniTensor_Storage_h @@ -49,12 +50,12 @@ namespace minitensor { /// Set to constant value if not dynamic template struct dimension_const { - static Index const value = C; + static constexpr Index value = C; }; template struct dimension_const { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; /// Validate dimension @@ -64,13 +65,13 @@ struct check_static { #if defined(KOKKOS_ENABLE_CUDA) // Empty #else - static Index const - maximum_dimension = static_cast(std::numeric_limits::digits); + static constexpr Index maximum_dimension = + static_cast(std::numeric_limits::digits); static_assert(D > maximum_dimension, "Dimension is too large"); #endif - static Index const value = D; + static constexpr Index value = D; }; template @@ -91,132 +92,105 @@ check_dynamic(Index const dimension) /// Integer power template restricted to orders defined below template struct dimension_power { - static Index const value = 0; + static constexpr Index value = 0; }; template struct dimension_power { - static Index const value = D; + static constexpr Index value = D; }; template struct dimension_power { - static Index const value = D * D; + static constexpr Index value = D * D; }; template struct dimension_power { - static Index const value = D * D * D; + static constexpr Index value = D * D * D; }; template struct dimension_power { - static Index const value = D * D * D * D; + static constexpr Index value = D * D * D * D; }; /// Integer square for manipulations between 2nd and 4rd-order tensors. template struct dimension_square { - static Index const value = 0; + static constexpr Index value = 0; }; template<> struct dimension_square { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; -template<> -struct dimension_square<1> { - static Index const value = 1; -}; +template <> struct dimension_square<1> { static constexpr Index value = 1; }; -template<> -struct dimension_square<2> { - static Index const value = 4; -}; +template <> struct dimension_square<2> { static constexpr Index value = 4; }; -template<> -struct dimension_square<3> { - static Index const value = 9; -}; +template <> struct dimension_square<3> { static constexpr Index value = 9; }; -template<> -struct dimension_square<4> { - static Index const value = 16; -}; +template <> struct dimension_square<4> { static constexpr Index value = 16; }; /// Integer square root template restricted to dimensions defined below. /// Useful for constructing a 2nd-order tensor from a 4th-order /// tensor with static storage. -template -struct dimension_sqrt { - static Index const value = 0; -}; +template struct dimension_sqrt { static constexpr Index value = 0; }; template<> struct dimension_sqrt { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; -template<> -struct dimension_sqrt<1> { - static Index const value = 1; -}; +template <> struct dimension_sqrt<1> { static constexpr Index value = 1; }; -template<> -struct dimension_sqrt<4> { - static Index const value = 2; -}; +template <> struct dimension_sqrt<4> { static constexpr Index value = 2; }; -template<> -struct dimension_sqrt<9> { - static Index const value = 3; -}; +template <> struct dimension_sqrt<9> { static constexpr Index value = 3; }; -template<> -struct dimension_sqrt<16> { - static Index const value = 4; -}; +template <> struct dimension_sqrt<16> { static constexpr Index value = 4; }; /// Manipulation of static and dynamic dimensions. template struct dimension_add { - static Index const value = N + P; + static constexpr Index value = N + P; }; template struct dimension_add { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; template struct dimension_subtract { - static Index const value = N - P; + static constexpr Index value = N - P; }; template struct dimension_subtract { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; template struct dimension_product { - static Index const value = N * P; + static constexpr Index value = N * P; }; template struct dimension_product { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; template struct dimension_product { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; template<> struct dimension_product { - static Index const value = DYNAMIC; + static constexpr Index value = DYNAMIC; }; /// @@ -240,13 +214,12 @@ class Storage bool IS_DYNAMIC = false; + KOKKOS_INLINE_FUNCTION Storage() { } - explicit - Storage(Index const number_entries) - { + explicit KOKKOS_INLINE_FUNCTION Storage(Index const number_entries) { resize(number_entries); } @@ -255,6 +228,7 @@ class Storage Storage & operator=(Storage const & s) = delete; + KOKKOS_INLINE_FUNCTION ~Storage() { } @@ -316,12 +290,7 @@ class Storage return &storage_[0]; } - static constexpr - Index - static_size() - { - return N; - } + static KOKKOS_INLINE_FUNCTION constexpr Index static_size() { return N; } private: @@ -353,13 +322,12 @@ class Storage bool IS_STATIC = false; + KOKKOS_INLINE_FUNCTION Storage() { } - explicit - Storage(Index const number_entries) - { + explicit KOKKOS_INLINE_FUNCTION Storage(Index const number_entries) { resize(number_entries); } @@ -368,6 +336,7 @@ class Storage Storage & operator=(Storage const & s) = delete; + KOKKOS_INLINE_FUNCTION ~Storage() { clear(); @@ -432,12 +401,7 @@ class Storage return storage_; } - static constexpr - Index - static_size() - { - return 0; - } + static KOKKOS_INLINE_FUNCTION constexpr Index static_size() { return 0; } private: diff --git a/packages/minitensor/src/MiniTensor_Tensor.i.h b/packages/minitensor/src/MiniTensor_Tensor.i.h index e92855003ed8..97e07d3aa085 100644 --- a/packages/minitensor/src/MiniTensor_Tensor.i.h +++ b/packages/minitensor/src/MiniTensor_Tensor.i.h @@ -1646,25 +1646,31 @@ transpose(Tensor const & A) Tensor B = A; + auto my_swap = [&](T &a, T &b) { + T c = a; + a = b; + b = c; + }; + switch (dimension) { default: for (Index i = 0; i < dimension; ++i) { for (Index j = i + 1; j < dimension; ++j) { - std::swap(B(i, j), B(j, i)); + my_swap(B(i, j), B(j, i)); } } break; case 3: - std::swap(B(0, 1), B(1, 0)); - std::swap(B(0, 2), B(2, 0)); + my_swap(B(0, 1), B(1, 0)); + my_swap(B(0, 2), B(2, 0)); - std::swap(B(1, 2), B(2, 1)); + my_swap(B(1, 2), B(2, 1)); break; case 2: - std::swap(B(0, 1), B(1, 0)); + my_swap(B(0, 1), B(1, 0)); break; } diff --git a/packages/minitensor/src/MiniTensor_TensorBase.i.h b/packages/minitensor/src/MiniTensor_TensorBase.i.h index cc2b782cd7d9..572ffd60b702 100644 --- a/packages/minitensor/src/MiniTensor_TensorBase.i.h +++ b/packages/minitensor/src/MiniTensor_TensorBase.i.h @@ -399,6 +399,8 @@ TensorBase::fill(Filler const value) } break; +#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST + case Filler::RANDOM: for (Index i = 0; i < number_components; ++i) { auto & entry = (*this)[i]; @@ -423,6 +425,8 @@ TensorBase::fill(Filler const value) } break; +#endif + case Filler::NANS: for (Index i = 0; i < number_components; ++i) { auto & entry = (*this)[i]; @@ -432,7 +436,8 @@ TensorBase::fill(Filler const value) break; default: - MT_ERROR_EXIT("Unknown specification of value for filling components."); + MT_ERROR_EXIT("Unknown or undefined (in execution space) specification of " + "value for filling components."); break; } diff --git a/packages/minitensor/src/MiniTensor_Utilities.h b/packages/minitensor/src/MiniTensor_Utilities.h index 565536f1ccaa..7e149ba65a5f 100644 --- a/packages/minitensor/src/MiniTensor_Utilities.h +++ b/packages/minitensor/src/MiniTensor_Utilities.h @@ -141,26 +141,17 @@ tau(); /// Random number generation. Uniform distribution U(-1,1) /// which is the Teuchos default (!). /// -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random(); +template typename Sacado::ScalarType::type random(); /// /// Random number generation. Uniform distribution U(0,1). /// -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random_uniform(); +template typename Sacado::ScalarType::type random_uniform(); /// /// Random number generation. Normal distribution N(0,1). /// -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random_normal(); +template typename Sacado::ScalarType::type random_normal(); /// /// Fill all levels of AD to specified constant. diff --git a/packages/minitensor/src/MiniTensor_Utilities.i.h b/packages/minitensor/src/MiniTensor_Utilities.i.h index 60b7a7b52d1a..dbdbedfe86b3 100644 --- a/packages/minitensor/src/MiniTensor_Utilities.i.h +++ b/packages/minitensor/src/MiniTensor_Utilities.i.h @@ -187,11 +187,7 @@ tau() // // Random number generation. Teuchos [-1,1] // -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random() -{ +template typename Sacado::ScalarType::type random() { using S = typename Sacado::ScalarType::type; return Teuchos::ScalarTraits().random(); } @@ -199,11 +195,7 @@ random() // // Uniform [0,1] random number generation. // -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random_uniform() -{ +template typename Sacado::ScalarType::type random_uniform() { using S = typename Sacado::ScalarType::type; return static_cast(0.5 * random() + 0.5); } @@ -211,11 +203,7 @@ random_uniform() // // Normal N(0,1) random number generation. // -template -KOKKOS_INLINE_FUNCTION -typename Sacado::ScalarType::type -random_normal() -{ +template typename Sacado::ScalarType::type random_normal() { using S = typename Sacado::ScalarType::type; S const diff --git a/packages/minitensor/src/MiniTensor_Vector.h b/packages/minitensor/src/MiniTensor_Vector.h index 7b2c57ed9aec..9455dc4d46b5 100644 --- a/packages/minitensor/src/MiniTensor_Vector.h +++ b/packages/minitensor/src/MiniTensor_Vector.h @@ -506,7 +506,6 @@ unit(Vector const & u); /// \return v, beta /// template -KOKKOS_INLINE_FUNCTION std::pair, T> house(Vector const & x); diff --git a/packages/minitensor/src/MiniTensor_Vector.i.h b/packages/minitensor/src/MiniTensor_Vector.i.h index 0f90b39c3e5a..ebe5e5545272 100644 --- a/packages/minitensor/src/MiniTensor_Vector.i.h +++ b/packages/minitensor/src/MiniTensor_Vector.i.h @@ -39,6 +39,7 @@ // ************************************************************************ // @HEADER +#include "Kokkos_ArithTraits.hpp" #if !defined(MiniTensor_Vector_i_h) #define MiniTensor_Vector_i_h @@ -802,6 +803,8 @@ KOKKOS_INLINE_FUNCTION T norm_infinity(Vector const & u) { + using KAT = Kokkos::ArithTraits; + Index const dimension = u.get_dimension(); @@ -812,16 +815,16 @@ norm_infinity(Vector const & u) default: for (Index i = 0; i < dimension; ++i) { - s = std::max(s, std::abs(u(i))); + s = max(KAT::abs(u(i)), s); } break; case 3: - s = std::max(std::max(std::abs(u(0)), std::abs(u(1))), std::abs(u(2))); + s = max(max(KAT::abs(u(0)), KAT::abs(u(1))), KAT::abs(u(2))); break; case 2: - s = std::max(std::abs(u(0)), std::abs(u(1))); + s = max(KAT::abs(u(0)), KAT::abs(u(1))); break; } @@ -842,11 +845,8 @@ unit(Vector const & u) // // Compute Householder vector // -template -KOKKOS_INLINE_FUNCTION -std::pair, T> -house(Vector const & x) -{ +template +std::pair, T> house(Vector const &x) { Vector v = x; diff --git a/packages/minitensor/test/test_01.cc b/packages/minitensor/test/test_01.cc index 975d36871f3c..fa0ba3f9701d 100644 --- a/packages/minitensor/test/test_01.cc +++ b/packages/minitensor/test/test_01.cc @@ -901,7 +901,7 @@ TEST(MiniTensor, SymmetricEigen) Tensor V(3); Tensor D(3); - boost::tie(V, D) = eig_sym(A); + std::tie(V, D) = eig_sym(A); ASSERT_LE(std::abs(D(0, 0) - 1.1), machine_epsilon()); ASSERT_LE(std::abs(D(1, 1) - 1.0), machine_epsilon()); @@ -921,7 +921,7 @@ TEST(MiniTensor, LeftPolarDecomposition) Tensor V(3); Tensor R(3); - boost::tie(V, R) = polar_left(F); + std::tie(V, R) = polar_left(F); Real const error_x = norm(V - X) / norm(X); @@ -1031,7 +1031,7 @@ TEST(MiniTensor, PolarLeftLog) Tensor V(3), R(3), v(3); - boost::tie(V, R, v) = polar_left_logV(F); + std::tie(V, R, v) = polar_left_logV(F); Real const error = norm(v - x) / norm(x); @@ -1084,7 +1084,7 @@ TEST(MiniTensor, SVD2x2) Tensor U(2), S(2), V(2); - boost::tie(U, S, V) = svd(A); + std::tie(U, S, V) = svd(A); Tensor B = U * S * transpose(V); @@ -1099,7 +1099,7 @@ TEST(MiniTensor, SVD3x3) Tensor U(3), S(3), V(3); - boost::tie(U, S, V) = svd(A); + std::tie(U, S, V) = svd(A); Tensor const B = U * S * transpose(V); @@ -1115,7 +1115,7 @@ TEST(MiniTensor, SVD3x3Fad) Tensor> U(3), S(3), V(3); - boost::tie(U, S, V) = svd(A); + std::tie(U, S, V) = svd(A); Tensor> const B = U * S * transpose(V); @@ -1183,7 +1183,7 @@ TEST(MiniTensor, SymmetricEigen2x2) Tensor V(2), D(2); - boost::tie(V, D) = eig_sym(A); + std::tie(V, D) = eig_sym(A); Tensor const B = V * D * transpose(V); @@ -1198,7 +1198,7 @@ TEST(MiniTensor, SymmetricEigen3x3) Tensor V(3), D(3); - boost::tie(V, D) = eig_sym(A); + std::tie(V, D) = eig_sym(A); Tensor const B = V * D * transpose(V); @@ -1213,11 +1213,11 @@ TEST(MiniTensor, Polar3x3) Tensor R(3), U(3); - boost::tie(R, U) = polar_right(A); + std::tie(R, U) = polar_right(A); Tensor X(3), D(3), Y(3); - boost::tie(X, D, Y) = svd(A); + std::tie(X, D, Y) = svd(A); Tensor const B = R - X * transpose(Y) + U - Y * D * transpose(Y); @@ -1234,7 +1234,7 @@ TEST(MiniTensor, Cholesky) bool is_spd; - boost::tie(G, is_spd) = cholesky(A); + std::tie(G, is_spd) = cholesky(A); Tensor const B(1.0, 0.0, 0.0, 1.0, 2.0, 0.0, 1.0, 1.0, 1.0); From 536a3841d2c0f5e4d3df992c76620810cf495665 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Wed, 13 Oct 2021 20:41:51 -0600 Subject: [PATCH 17/98] tpetra: move sort_crs_* out of Impl namespace More compatibility changes for kokkos-kernels, see kokkos/kokkos-kernels#932 --- packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp | 2 +- packages/tpetra/core/src/Tpetra_CrsGraphTransposer_def.hpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp index a11686002906..a9d5994f122f 100644 --- a/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp +++ b/packages/tpetra/core/ext/TpetraExt_MatrixMatrix_def.hpp @@ -813,7 +813,7 @@ add (const Scalar& alpha, col_inds_array, global_col_inds_array, typename map_type::local_map_type> (localColinds, globalColinds, CcolMap->getLocalMap())); - KokkosKernels::Impl::sort_crs_matrix(rowptrs, localColinds, vals); + KokkosKernels::sort_crs_matrix(rowptrs, localColinds, vals); C.setAllValues(rowptrs, localColinds, vals); C.fillComplete(CDomainMap, CRangeMap, params); if(!doFillComplete) diff --git a/packages/tpetra/core/src/Tpetra_CrsGraphTransposer_def.hpp b/packages/tpetra/core/src/Tpetra_CrsGraphTransposer_def.hpp index 28e63f3fcd78..dc4310f47aa7 100644 --- a/packages/tpetra/core/src/Tpetra_CrsGraphTransposer_def.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsGraphTransposer_def.hpp @@ -362,7 +362,7 @@ namespace Tpetra { bool sort = true; if (sort) - KokkosKernels::Impl::sort_crs_graph(rowptrsSym, colindsSym); + KokkosKernels::sort_crs_graph(rowptrsSym, colindsSym); local_graph_device_type lclGraphSym = local_graph_device_type(colindsSym, rowptrsSym); @@ -475,7 +475,7 @@ namespace Tpetra { lclGraphT_rowmap, lclGraphT_entries); if (sort) - KokkosKernels::Impl::sort_crs_graph< + KokkosKernels::sort_crs_graph< typename local_graph_device_type::execution_space, rowmap_t, entries_t>( lclGraphT_rowmap, From 2cf5e8134f79f08cfa7fd4e0ea52725a9843bcac Mon Sep 17 00:00:00 2001 From: Tim Fuller Date: Wed, 6 Oct 2021 16:05:12 -0600 Subject: [PATCH 18/98] adding "start owned" parameter to FECrsMatrix to start the matrix in FE_ACTIVE_OWNED mode closes 9638 --- packages/tpetra/core/src/Tpetra_FECrsMatrix_def.hpp | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/packages/tpetra/core/src/Tpetra_FECrsMatrix_def.hpp b/packages/tpetra/core/src/Tpetra_FECrsMatrix_def.hpp index 81d8ffc754e5..0132d6aceab5 100644 --- a/packages/tpetra/core/src/Tpetra_FECrsMatrix_def.hpp +++ b/packages/tpetra/core/src/Tpetra_FECrsMatrix_def.hpp @@ -71,7 +71,17 @@ FECrsMatrix(const Teuchos::RCP& graph, ( *graph->activeCrsGraph_!= fe_crs_graph_type::FE_ACTIVE_OWNED,std::runtime_error, "Input graph must be in FE_ACTIVE_OWNED mode when this constructor is called."); - activeCrsMatrix_ = Teuchos::rcp(new FEWhichActive(FE_ACTIVE_OWNED_PLUS_SHARED)); + bool start_owned = false; + if (! params.is_null ()) { + if (params->isParameter ("start owned")) { + start_owned = params->get("start owned", start_owned); + } + } + if(start_owned) { + activeCrsMatrix_ = Teuchos::rcp(new FEWhichActive(FE_ACTIVE_OWNED)); + } else { + activeCrsMatrix_ = Teuchos::rcp(new FEWhichActive(FE_ACTIVE_OWNED_PLUS_SHARED)); + } // Make an "inactive" matrix, if we need to if(!graph->inactiveCrsGraph_.is_null() ) { From 96820bd35316017da45c79e83e7ced4101899b45 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Thu, 14 Oct 2021 12:19:28 -0600 Subject: [PATCH 19/98] STK: Snapshot 10-14-21 12:18 --- .../stk_doc_tests/cmake/Dependencies.cmake | 2 +- .../stk_emend/independent_set/CMakeLists.txt | 10 + .../independent_set/IndependentSetDummy.cpp | 3 + .../stk_expreval/stk_expreval/Evaluator.cpp | 1 + .../stk_expreval/stk_expreval/Evaluator.hpp | 9 +- .../generate_tpl_paths_from_sierra_proj | 84 -- .../cmake_install_test/load_gcc_modules | 1 - .../cmake_install_test/run_cmake_stk | 2 +- packages/stk/stk_io/cmake/Dependencies.cmake | 2 +- packages/stk/stk_io/stk_io/Heartbeat.cpp | 66 - packages/stk/stk_io/stk_io/Heartbeat.hpp | 28 - packages/stk/stk_io/stk_io/OutputFile.cpp | 31 - packages/stk/stk_io/stk_io/OutputFile.hpp | 10 - packages/stk/stk_io/stk_io/StkIoUtils.hpp | 4 - .../stk/stk_io/stk_io/StkMeshIoBroker.cpp | 38 - .../stk/stk_io/stk_io/StkMeshIoBroker.hpp | 103 +- .../stk/stk_mesh/stk_mesh/base/Bucket.cpp | 532 ++------ .../stk/stk_mesh/stk_mesh/base/Bucket.hpp | 317 +---- .../stk_mesh/base/BucketConnectivity.hpp | 1170 ----------------- .../stk/stk_mesh/stk_mesh/base/BulkData.cpp | 64 +- .../stk/stk_mesh/stk_mesh/base/BulkData.hpp | 219 ++- .../stk_mesh/base/ConnectedSparseNodes.hpp | 115 ++ .../stk_mesh/base/ConnectedTopologyNodes.hpp | 101 ++ .../stk_mesh/stk_mesh/base/Connectivity.cpp | 250 ++++ .../stk_mesh/stk_mesh/base/Connectivity.hpp | 249 ++++ .../stk_mesh/stk_mesh/base/DeviceField.hpp | 68 +- .../stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp | 84 +- .../stk/stk_mesh/stk_mesh/base/DeviceMesh.hpp | 16 +- .../stk/stk_mesh/stk_mesh/base/EntityKey.hpp | 5 +- .../stk/stk_mesh/stk_mesh/base/FieldBLAS.hpp | 28 + .../stk/stk_mesh/stk_mesh/base/FieldBase.cpp | 62 +- .../stk/stk_mesh/stk_mesh/base/FieldBase.hpp | 8 +- .../stk_mesh/base/FieldDataManager.cpp | 22 +- .../stk_mesh/base/FieldDataManager.hpp | 1 - .../stk_mesh/base/FindRestriction.cpp | 6 +- .../stk_mesh/stk_mesh/base/GetNgpField.hpp | 1 + .../stk/stk_mesh/stk_mesh/base/HostField.hpp | 55 +- .../stk/stk_mesh/stk_mesh/base/MetaData.cpp | 9 +- .../stk_mesh/stk_mesh/base/NgpFieldBase.hpp | 5 + .../stk/stk_mesh/stk_mesh/base/NgpTypes.hpp | 2 +- .../stk_mesh/base/SparseConnectivity.cpp | 193 +++ .../stk_mesh/base/SparseConnectivity.hpp | 151 +++ packages/stk/stk_mesh/stk_mesh/base/Types.hpp | 3 + .../stk_mesh/baseImpl/BucketRepository.cpp | 47 - .../stk_mesh/baseImpl/BucketRepository.hpp | 3 - .../stk_mesh/baseImpl/MeshImplUtils.cpp | 53 +- .../stk_mesh/baseImpl/MeshImplUtils.hpp | 33 +- .../stk_mesh/baseImpl/MeshModification.cpp | 1 + .../stk_mesh/baseImpl/MeshPrintUtils.cpp | 16 +- .../stk_mesh/baseImpl/MeshPrintUtils.hpp | 3 + .../stk_search/stk_search/CoarseSearch.hpp | 21 +- .../stk_tools/mesh_tools/DetectHingesImpl.cpp | 2 +- .../stk_topology/topology_decl.hpp | 7 +- .../stk_unit_test_utils/BucketTester.hpp | 2 +- .../Search_UnitTestUtils.hpp | 5 +- .../stk_unit_test_utils/TextMesh.cpp | 329 +++-- .../stk_unit_tests/cmake/Dependencies.cmake | 2 +- .../stk_mesh/FieldBlas/UnitTestFieldBLAS.cpp | 37 + .../stk_mesh/UnitTestBucket.cpp | 91 +- .../stk_mesh/UnitTestBucketConnectivity.cpp | 345 ----- .../stk_mesh/UnitTestBulkData.cpp | 2 +- .../stk_mesh/UnitTestConnectivity.cpp | 386 ++++++ .../stk_mesh/UnitTestFEMMetaData.cpp | 13 +- .../stk_mesh/UnitTestSparseConnectivity.cpp | 256 ++++ .../stk_mesh/UnitTestTextMesh.cpp | 38 +- ...okkosBulkDataBucketCentroidCalculation.cpp | 8 +- .../stk_mesh/ngp/NgpParallelCommTest.cpp | 16 +- .../stk_unit_tests/stk_mesh/ngp/howToNgp.cpp | 82 +- .../stk_mesh/ngp/ngpFieldTest.cpp | 240 ++-- .../stk_mesh/ngp/ngpMultiStateFieldTests.cpp | 64 + .../stk_search/UnitTestCoarseSearch.cpp | 354 +++-- .../stk_simd_old/UnitTestStkSimdView2d.cpp | 2 + .../mesh_clone/UnitTestBulkDataClone.cpp | 4 +- .../stk_unit_tests/stk_util/CMakeLists.txt | 1 + .../environment/UnitTestOutputLog.cpp | 311 +++-- .../ngp/UnitTestNgpVirtualFunction.cpp | 85 ++ packages/stk/stk_util/Jamfile | 2 + .../stk_util/parallel/ParallelIndex.hpp | 4 +- .../stk_util/registry/ProductRegistry.cpp | 2 +- .../stk_util/stk_util/util/ParameterList.hpp | 7 +- 80 files changed, 3467 insertions(+), 3537 deletions(-) create mode 100644 packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp delete mode 100755 packages/stk/stk_integration_tests/cmake_install_test/generate_tpl_paths_from_sierra_proj delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/ConnectedTopologyNodes.hpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/Connectivity.hpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp create mode 100644 packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp delete mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp create mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp create mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp create mode 100644 packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp diff --git a/packages/stk/stk_doc_tests/cmake/Dependencies.cmake b/packages/stk/stk_doc_tests/cmake/Dependencies.cmake index 5d2024b68528..e37ee08c0e37 100644 --- a/packages/stk/stk_doc_tests/cmake/Dependencies.cmake +++ b/packages/stk/stk_doc_tests/cmake/Dependencies.cmake @@ -5,4 +5,4 @@ SET(TEST_REQUIRED_DEP_PACKAGES Gtest STKUtil STKNGP_TEST STKUnit_test_utils) SET(LIB_REQUIRED_DEP_TPLS) SET(LIB_OPTIONAL_DEP_TPLS) SET(TEST_REQUIRED_DEP_TPLS) -SET(TEST_OPTIONAL_DEP_TPLS Boost MPI) +SET(TEST_OPTIONAL_DEP_TPLS MPI) diff --git a/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt b/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt index 65456ef38091..961a9218c3b9 100644 --- a/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt +++ b/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt @@ -46,8 +46,18 @@ # SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + stk_emend + HEADERS ${HEADERS} + SOURCES ${SOURCES} + ) INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_emend/independent_set) diff --git a/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp b/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp new file mode 100644 index 000000000000..b2ef6c6c65a0 --- /dev/null +++ b/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp @@ -0,0 +1,3 @@ +namespace independent_set { +void IndependentSetDummy() {} +} diff --git a/packages/stk/stk_expreval/stk_expreval/Evaluator.cpp b/packages/stk/stk_expreval/stk_expreval/Evaluator.cpp index a8f0a09d698f..3f26dc2f03ba 100644 --- a/packages/stk/stk_expreval/stk_expreval/Evaluator.cpp +++ b/packages/stk/stk_expreval/stk_expreval/Evaluator.cpp @@ -149,6 +149,7 @@ class Node Eval* m_owner; }; +KOKKOS_FUNCTION NgpNode::NgpNode() : m_opcode(OPCODE_UNDEFINED), m_data{{0.0}}, diff --git a/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp b/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp index 46c06efd7abe..420e0cef16c9 100644 --- a/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp +++ b/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp @@ -315,7 +315,6 @@ class NgpNode KOKKOS_FUNCTION NgpNode(); - KOKKOS_FUNCTION explicit NgpNode(const Node& node); KOKKOS_DEFAULTED_FUNCTION @@ -505,7 +504,11 @@ class ParsedEval double evaluate(DeviceVariableMap& deviceVariableMap) const { + #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST return m_deviceNodes[m_headNodeIndex].eval(deviceVariableMap); + #else + return m_hostNodes[m_headNodeIndex].eval(deviceVariableMap); + #endif } private: @@ -535,7 +538,11 @@ class DeviceVariableMap { NGP_ThrowRequireMsg(parsedEval.get_num_variables() <= NUMVARS, "Size of DeviceVariableMap is too small"); +#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST const ParsedEval::NodeView& deviceNodes = parsedEval.m_deviceNodes; +#else + const auto & deviceNodes = parsedEval.m_hostNodes; +#endif for (unsigned nodeIndex = 0u; nodeIndex < deviceNodes.extent(0); ++nodeIndex) { if (deviceNodes(nodeIndex).m_opcode == OPCODE_ASSIGN) { diff --git a/packages/stk/stk_integration_tests/cmake_install_test/generate_tpl_paths_from_sierra_proj b/packages/stk/stk_integration_tests/cmake_install_test/generate_tpl_paths_from_sierra_proj deleted file mode 100755 index a6f96138e1cd..000000000000 --- a/packages/stk/stk_integration_tests/cmake_install_test/generate_tpl_paths_from_sierra_proj +++ /dev/null @@ -1,84 +0,0 @@ -#!/bin/bash - -findlibdir() { - local libname=$1 - local fullpath=`eval "find ${output_dir}/trilinos_tpls -name ${libname}"` - local libdir=$2 - local dir=`eval "dirname ${fullpath}"` - eval $libdir="'$dir'" -} - -findincdir() { - local header=$1 - local incdir=$2 - local fullpath=`eval "find ${output_dir}/trilinos_tpls/TPLs_src -name ${header}"` - local dir=`eval "dirname ${fullpath}"` - eval $incdir="'$dir'" -} - -sierra_dir=$1 -output_dir=$2 -tpl_paths_file=$3 - -printf "sierra_proj = ${sierra_dir}\n"; -printf "output_dir = ${output_dir}\n"; -printf "output tpl_paths_file= ${tpl_paths_file}\n"; - -rm -f ${tpl_paths_file} - -cd ${sierra_dir} -echo "using bake to generate TPLs..." -bake -j8 --no-trilinos --no-seacas --builddir=${output_dir}/BAKE --installdir=${output_dir}/trilinos_tpls /tpl/trilinos//install-trilinos-tpls >& ${output_dir}/bake-tpls.out - -if [ $? -ne 0 ] ; then - echo "!! error using bake to generate tpls. check output in ${output_dir}/bake-tpls.out"; - exit 1; -fi - -echo "------------------------" - -boost_inc_dir=$sierra_dir/TPLs_src/boost - -blas_lib=/usr/lib64/libblas.so -lapack_lib=/usr/lib64/liblapack.so - -netcdf_root_dir=$sierra_dir/TPLs_src/netcdf/netcdf-c-4.7.4 -findincdir netcdf.h netcdf_inc_dir -findlibdir libnetcdf.a netcdf_lib_dir -echo "netcdf_lib_dir: $netcdf_lib_dir" - -findincdir hdf5.h hdf_inc_dir -findlibdir libhdf5.a hdf_lib_dir -echo "hdf_lib_dir: $hdf_lib_dir" - -findincdir pnetcdf.h pnetcdf_inc_dir -findlibdir libpnetcdf.a pnetcdf_lib_dir -echo "pnetcdf_lib_dir: $pnetcdf_lib_dir" - -parmetis_inc_dir=$sierra_dir/TPLs_src/parmetis/include -metis_inc_dir=$sierra_dir/TPLs_src/parmetis/metis/include - -findlibdir libparmetis.a parmetis_lib_dir -echo "parmetis_lib_dir: ${parmetis_lib_dir}" - -findlibdir libmetis.a metis_lib_dir -echo "metis_lib_dir: ${metis_lib_dir}" - -echo "------------------------" - -cat << EOF > ${tpl_paths_file} -BLAS_LIBRARIES=${blas_lib} -LAPACK_LIBRARIES=${lapack_lib} -BOOST_INC_DIR=${boost_inc_dir} -NETCDF_INC_DIR=${netcdf_inc_dir} -NETCDF_LIB_DIR=${netcdf_lib_dir} -PNETCDF_INC_DIR=${pnetcdf_inc_dir} -PNETCDF_LIB_DIR=${pnetcdf_lib_dir} -HDF_INC_DIR=${hdf_inc_dir} -HDF_LIB_DIR=${hdf_lib_dir} -METIS_INC_DIR=${metis_inc_dir} -METIS_LIB_DIR=${metis_lib_dir} -PARMETIS_INC_DIR=${parmetis_inc_dir} -PARMETIS_LIB_DIR=${parmetis_lib_dir} -EOF - diff --git a/packages/stk/stk_integration_tests/cmake_install_test/load_gcc_modules b/packages/stk/stk_integration_tests/cmake_install_test/load_gcc_modules index 7b57261e312e..e7e9a1d0b8a9 100644 --- a/packages/stk/stk_integration_tests/cmake_install_test/load_gcc_modules +++ b/packages/stk/stk_integration_tests/cmake_install_test/load_gcc_modules @@ -4,7 +4,6 @@ module load cde/v2/cmake/3.19.2 module load cde/v2/compiler/gcc/7.2.0 module load cde/v2/gcc/7.2.0/openmpi/4.0.5 module load cde/v2/gcc/7.2.0/netlib-lapack/3.8.0 -module load cde/v2/gcc/7.2.0/boost/1.73.0 module load cde/v2/gcc/7.2.0/hdf5/1.10.6 module load cde/v2/gcc/7.2.0/netcdf-c/4.7.3 module load cde/v2/gcc/7.2.0/parallel-netcdf/1.12.1 diff --git a/packages/stk/stk_integration_tests/cmake_install_test/run_cmake_stk b/packages/stk/stk_integration_tests/cmake_install_test/run_cmake_stk index c5da6dd7afb9..c19fadf7dcff 100755 --- a/packages/stk/stk_integration_tests/cmake_install_test/run_cmake_stk +++ b/packages/stk/stk_integration_tests/cmake_install_test/run_cmake_stk @@ -78,7 +78,7 @@ cmake \ -DTpetra_ENABLE_CUDA:BOOL=${cuda_on_or_off} \ -DTrilinos_ENABLE_KokkosKernels:BOOL=ON \ -DTrilinos_ENABLE_Zoltan:BOOL=ON \ --DTrilinos_ENABLE_Fortran:BOOL=OFF \ +-DTrilinos_ENABLE_Fortran:BOOL=ON \ -DCMAKE_CXX_FLAGS:STRING="-DNOT_HAVE_STK_SEACASAPREPRO_LIB -D${fortran_macro} ${cmake_cxx_flags} -Werror=dangling-else" \ -DSTK_ENABLE_TESTS:BOOL=ON \ -DTrilinos_ENABLE_STK:BOOL=ON \ diff --git a/packages/stk/stk_io/cmake/Dependencies.cmake b/packages/stk/stk_io/cmake/Dependencies.cmake index 2d7cc69d9feb..3dae5591447b 100644 --- a/packages/stk/stk_io/cmake/Dependencies.cmake +++ b/packages/stk/stk_io/cmake/Dependencies.cmake @@ -3,6 +3,6 @@ SET(LIB_OPTIONAL_DEP_PACKAGES) SET(TEST_REQUIRED_DEP_PACKAGES Gtest) SET(TEST_OPTIONAL_DEP_PACKAGES) SET(LIB_REQUIRED_DEP_TPLS) -SET(LIB_OPTIONAL_DEP_TPLS Boost) +SET(LIB_OPTIONAL_DEP_TPLS) SET(TEST_REQUIRED_DEP_TPLS) SET(TEST_OPTIONAL_DEP_TPLS) diff --git a/packages/stk/stk_io/stk_io/Heartbeat.cpp b/packages/stk/stk_io/stk_io/Heartbeat.cpp index 45c4499d98d1..830dc79ea39d 100644 --- a/packages/stk/stk_io/stk_io/Heartbeat.cpp +++ b/packages/stk/stk_io/stk_io/Heartbeat.cpp @@ -238,37 +238,6 @@ void impl::Heartbeat::add_global_ref(const std::string &name, } } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void impl::Heartbeat::define_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies, - Ioss::Field::RoleType role) -{ - internal_define_global_ref(name, value, type, copies, role); -} - -STK_DEPRECATED void impl::Heartbeat::add_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies, - Ioss::Field::RoleType role) -{ - if (m_processor == 0) { - ThrowErrorMsgIf (m_currentStep != 0, - "At least one output step has been written to the history/heartbeat file. " - "Variables cannot be added anymore."); - - Ioss::State currentState = m_region->get_state(); - if(currentState != Ioss::STATE_DEFINE_TRANSIENT) { - m_region->begin_mode(Ioss::STATE_DEFINE_TRANSIENT); - } - - internal_define_global_ref(name, value, type, copies, role); - } -} -#endif - void impl::Heartbeat::internal_define_global_ref(const std::string &name, const STK_ANY_NAMESPACE::any *value, const std::string &storage, @@ -291,18 +260,6 @@ void impl::Heartbeat::internal_define_global_ref(const std::string &name, } } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void impl::Heartbeat::define_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies, - Ioss::Field::RoleType role) -{ - internal_define_global_ref(name, value, storage, dataType, copies, role); -} -#endif - void impl::Heartbeat::define_global_ref(const std::string &name, const stk::util::Parameter ¶m, const std::string &storage, @@ -334,29 +291,6 @@ void impl::Heartbeat::add_global_ref(const std::string &name, } } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void impl::Heartbeat::add_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies, - Ioss::Field::RoleType role) -{ - if (m_processor == 0) { - ThrowErrorMsgIf (m_currentStep != 0, - "At least one output step has been written to the history/heartbeat file. " - "Variables cannot be added anymore."); - - Ioss::State currentState = m_region->get_state(); - if(currentState != Ioss::STATE_DEFINE_TRANSIENT) { - m_region->begin_mode(Ioss::STATE_DEFINE_TRANSIENT); - } - - internal_define_global_ref(name, value, storage, dataType, copies, role); - } -} -#endif - void impl::Heartbeat::process_output_pre_write(int step, double time) { if (m_processor == 0) { diff --git a/packages/stk/stk_io/stk_io/Heartbeat.hpp b/packages/stk/stk_io/stk_io/Heartbeat.hpp index 83a6f61865fb..daae8903993f 100644 --- a/packages/stk/stk_io/stk_io/Heartbeat.hpp +++ b/packages/stk/stk_io/stk_io/Heartbeat.hpp @@ -112,34 +112,6 @@ class Heartbeat { int copies = 1, Ioss::Field::RoleType role = Ioss::Field::TRANSIENT); -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void define_global_ref(const std::string &variableName, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::TRANSIENT); - - STK_DEPRECATED void define_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::TRANSIENT); - - STK_DEPRECATED void add_global_ref(const std::string &variableName, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::TRANSIENT); - - STK_DEPRECATED void add_global_ref(const std::string &name, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::TRANSIENT); -#endif - void process_output(int step, double time); void process_output_pre_write(int step, double time); void process_output_write(int step, double time); diff --git a/packages/stk/stk_io/stk_io/OutputFile.cpp b/packages/stk/stk_io/stk_io/OutputFile.cpp index b56c87708b4e..ca323a5ec51a 100644 --- a/packages/stk/stk_io/stk_io/OutputFile.cpp +++ b/packages/stk/stk_io/stk_io/OutputFile.cpp @@ -394,17 +394,6 @@ void OutputFile::add_global_ref(const std::string &name, const stk::util::Parame internal_add_global(m_region, name, parameter_type.first, parameter_type.second); m_globalAnyFields.emplace_back(name, ¶m.value, param.type); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void OutputFile::add_global_ref(const std::string &name, const STK_ANY_NAMESPACE::any *value, stk::util::ParameterType::Type type) -{ - ThrowErrorMsgIf (m_fieldsDefined, - "On region named " << m_region->name() << - " Attempting to add global variable after data has already been written to the database."); - std::pair parameter_type = get_io_parameter_size_and_type(type, *value); - internal_add_global(m_region, name, parameter_type.first, parameter_type.second); - m_globalAnyFields.emplace_back(name, value, type); -} -#endif bool OutputFile::has_global(const std::string &globalVarName) const { @@ -421,18 +410,6 @@ void OutputFile::add_global(const std::string &name, const stk::util::Parameter internal_add_global(m_region, name, parameter_type.first, parameter_type.second); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void OutputFile::add_global(const std::string &name, const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type) -{ - ThrowErrorMsgIf (m_fieldsDefined, - "On region named " << m_region->name() << - " Attempting to add global variable after data has already been written to the database."); - std::pair parameter_type = get_io_parameter_size_and_type(type, value); - m_anyGlobalVariablesDefined = true; // This output file has at least 1 global variable. - internal_add_global(m_region, name, parameter_type.first, parameter_type.second); -} -#endif - void OutputFile::add_global(const std::string &globalVarName, Ioss::Field::BasicType dataType) { ThrowErrorMsgIf (m_fieldsDefined, @@ -460,14 +437,6 @@ void OutputFile::add_global(const std::string &globalVarName, const std::string internal_add_global(m_region, globalVarName, storage, dataType); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void OutputFile::write_global(const std::string &globalVarName, - const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type) -{ - internal_write_parameter(m_region, globalVarName, value, type); -} -#endif - void OutputFile::write_global(const std::string &globalVarName, const stk::util::Parameter ¶m) { diff --git a/packages/stk/stk_io/stk_io/OutputFile.hpp b/packages/stk/stk_io/stk_io/OutputFile.hpp index 47e98528de26..8228f934d727 100644 --- a/packages/stk/stk_io/stk_io/OutputFile.hpp +++ b/packages/stk/stk_io/stk_io/OutputFile.hpp @@ -161,23 +161,13 @@ class OutputFile internal_add_global(m_region, variableName, parameter_type.first, parameter_type.second); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void add_global(const std::string &variableName, const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type); -#endif void add_global_ref(const std::string &variableName, const stk::util::Parameter &value); -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void add_global_ref(const std::string &variableName, const STK_ANY_NAMESPACE::any *value, stk::util::ParameterType::Type type); -#endif void add_global(const std::string &variableName, Ioss::Field::BasicType dataType); void add_global(const std::string &variableName, const std::string &type, Ioss::Field::BasicType dataType); void add_global(const std::string &variableName, int component_count, Ioss::Field::BasicType dataType); void write_global(const std::string &variableName, const stk::util::Parameter ¶m); -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void write_global(const std::string &variableName, - const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type); -#endif void write_global(const std::string &variableName, double globalVarData); void write_global(const std::string &variableName, int globalVarData); void write_global(const std::string &variableName, std::vector& globalVarData); diff --git a/packages/stk/stk_io/stk_io/StkIoUtils.hpp b/packages/stk/stk_io/stk_io/StkIoUtils.hpp index 8588fc5cb334..a1530d2364c5 100644 --- a/packages/stk/stk_io/stk_io/StkIoUtils.hpp +++ b/packages/stk/stk_io/stk_io/StkIoUtils.hpp @@ -47,10 +47,6 @@ #include "stk_util/util/ParameterList.hpp" #include "Ioss_Field.h" -#ifdef STK_HAVE_BOOST -#include -#endif - namespace stk { namespace io { class StkMeshIoBroker; } } namespace stk { namespace mesh { class BulkData; } } namespace stk { namespace mesh { class MetaData; } } diff --git a/packages/stk/stk_io/stk_io/StkMeshIoBroker.cpp b/packages/stk/stk_io/stk_io/StkMeshIoBroker.cpp index 51bd6a29fd3f..e2b5340f0ad7 100644 --- a/packages/stk/stk_io/stk_io/StkMeshIoBroker.cpp +++ b/packages/stk/stk_io/stk_io/StkMeshIoBroker.cpp @@ -921,17 +921,6 @@ bool StkMeshIoBroker::get_global(const std::string &globalVarName, return internal_read_parameter(region, globalVarName, param.value, param.type, abort_if_not_found); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED bool StkMeshIoBroker::get_global(const std::string &globalVarName, - STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type, - bool abort_if_not_found) const -{ - validate_input_file_index(m_activeMeshIndex); - auto region = m_inputFiles[m_activeMeshIndex]->get_input_io_region(); - return internal_read_parameter(region, globalVarName, value, type, abort_if_not_found); -} -#endif - size_t StkMeshIoBroker::get_global_variable_length(const std::string& globalVarName) const { validate_input_file_index(m_activeMeshIndex); @@ -994,15 +983,6 @@ void StkMeshIoBroker::add_global(size_t output_file_index, const std::string &na m_outputFiles[output_file_index]->add_global(name, param); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void StkMeshIoBroker::add_global(size_t output_file_index, const std::string &name, - const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type) -{ - validate_output_file_index(output_file_index); - m_outputFiles[output_file_index]->add_global(name, value, type); -} -#endif - void StkMeshIoBroker::add_global_ref(size_t output_file_index, const std::string &name, const stk::util::Parameter ¶m) { @@ -1010,15 +990,6 @@ void StkMeshIoBroker::add_global_ref(size_t output_file_index, const std::string m_outputFiles[output_file_index]->add_global_ref(name, param); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void StkMeshIoBroker::add_global_ref(size_t output_file_index, const std::string &name, - const STK_ANY_NAMESPACE::any *value, stk::util::ParameterType::Type type) -{ - validate_output_file_index(output_file_index); - m_outputFiles[output_file_index]->add_global_ref(name, value, type); -} -#endif - void StkMeshIoBroker::add_global(size_t output_file_index, const std::string &globalVarName, Ioss::Field::BasicType dataType) { validate_output_file_index(output_file_index); @@ -1045,15 +1016,6 @@ void StkMeshIoBroker::write_global(size_t output_file_index, m_outputFiles[output_file_index]->write_global(variableName, param); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 -STK_DEPRECATED void StkMeshIoBroker::write_global(size_t output_file_index, const std::string &globalVarName, - const STK_ANY_NAMESPACE::any &value, stk::util::ParameterType::Type type) const -{ - validate_output_file_index(output_file_index); - m_outputFiles[output_file_index]->write_global(globalVarName, value, type); -} -#endif - void StkMeshIoBroker::write_global(size_t output_file_index, const std::string &globalVarName, double globalVarData) const { validate_output_file_index(output_file_index); diff --git a/packages/stk/stk_io/stk_io/StkMeshIoBroker.hpp b/packages/stk/stk_io/stk_io/StkMeshIoBroker.hpp index be6f7f7ac573..c94501ce0b3a 100644 --- a/packages/stk/stk_io/stk_io/StkMeshIoBroker.hpp +++ b/packages/stk/stk_io/stk_io/StkMeshIoBroker.hpp @@ -389,12 +389,6 @@ namespace stk { bool get_global(const std::string &variableName, stk::util::Parameter ¶m, bool abort_if_not_found=true) const; -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED bool get_global(const std::string &variableName, - STK_ANY_NAMESPACE::any &value, - stk::util::ParameterType::Type type, - bool abort_if_not_found=true) const; -#endif bool get_global(const std::string &variableName, int &globalVar, bool abort_if_not_found=true) const; @@ -489,16 +483,7 @@ namespace stk { validate_output_file_index(output_file_index); m_outputFiles[output_file_index]->add_global(variableName, value, type); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void add_global_ref(size_t output_file_index, - const std::string &variableName, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type); - STK_DEPRECATED void add_global(size_t output_file_index, - const std::string &variableName, - const STK_ANY_NAMESPACE::any &value, - stk::util::ParameterType::Type type); -#endif + void add_global(size_t output_file_index, const std::string &variableName, Ioss::Field::BasicType dataType); @@ -557,12 +542,6 @@ namespace stk { const std::string& variableName, const stk::util::Parameter& param) const; -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void write_global(size_t output_file_index, - const std::string &variableName, - const STK_ANY_NAMESPACE::any &value, - stk::util::ParameterType::Type type) const; -#endif void write_global(size_t output_file_index, const std::string &variableName, double data) const; @@ -610,38 +589,6 @@ namespace stk { int copies = 1, Ioss::Field::RoleType role = Ioss::Field::REDUCTION); -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED void define_heartbeat_global(size_t index, - const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::REDUCTION); - - STK_DEPRECATED void define_heartbeat_global(size_t index, - const std::string &globalVarName, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::REDUCTION); - - STK_DEPRECATED void add_heartbeat_global(size_t index, - const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::REDUCTION); - - STK_DEPRECATED void add_heartbeat_global(size_t index, - const std::string &globalVarName, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies = 1, - Ioss::Field::RoleType role = Ioss::Field::REDUCTION); -#endif - bool has_heartbeat_global(size_t output_file_index, const std::string &globalVarName) const; size_t get_heartbeat_global_component_count(size_t output_file_index, @@ -962,54 +909,6 @@ namespace stk { m_heartbeat[index]->add_global_ref(globalVarName, param, storage, dataType, copies, role); } -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 - STK_DEPRECATED inline void StkMeshIoBroker::define_heartbeat_global(size_t index, - const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies, - Ioss::Field::RoleType role) - { - STKIORequire(index < m_heartbeat.size()); - m_heartbeat[index]->define_global_ref(name, value, type, copies, role); - } - - inline void StkMeshIoBroker::define_heartbeat_global(size_t index, - const std::string &globalVarName, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies, - Ioss::Field::RoleType role) - { - STKIORequire(index < m_heartbeat.size()); - m_heartbeat[index]->define_global_ref(globalVarName, value, storage, dataType, copies, role); - } - - STK_DEPRECATED inline void StkMeshIoBroker::add_heartbeat_global(size_t index, - const std::string &name, - const STK_ANY_NAMESPACE::any *value, - stk::util::ParameterType::Type type, - int copies, - Ioss::Field::RoleType role) - { - STKIORequire(index < m_heartbeat.size()); - m_heartbeat[index]->add_global_ref(name, value, type, copies, role); - } - - STK_DEPRECATED inline void StkMeshIoBroker::add_heartbeat_global(size_t index, - const std::string &globalVarName, - const STK_ANY_NAMESPACE::any *value, - const std::string &storage, - Ioss::Field::BasicType dataType, - int copies, - Ioss::Field::RoleType role) - { - STKIORequire(index < m_heartbeat.size()); - m_heartbeat[index]->add_global_ref(globalVarName, value, storage, dataType, copies, role); - } -#endif - inline void StkMeshIoBroker::process_heartbeat_output(size_t index, int step, double time) { STKIORequire(index < m_heartbeat.size()); diff --git a/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp b/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp index e18d12a7653f..18696c21f07f 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp @@ -38,8 +38,9 @@ #include // for operator<<, basic_ostream, etc #include // for BulkData, field_data, etc #include // for Entity +#include +#include #include // for MetaData, get_cell_topology, etc -#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity #include "stk_mesh/base/FieldBase.hpp" // for FieldBase #include #include "stk_mesh/base/Part.hpp" // for Part @@ -50,127 +51,20 @@ namespace stk { namespace mesh { namespace impl { template class BucketConnectivity; } } } - //---------------------------------------------------------------------- namespace stk { namespace mesh { namespace { -#ifndef NDEBUG -struct CheckSizeFunctor -{ - template - void operator()(const Bucket& bucket, const Connectivity& connectivity, const Bucket*) const - { ThrowAssert(bucket.size() == static_cast(connectivity.size())); } - - bool is_modifying() const { return false; } -}; -#endif - -struct AddEntityFunctor -{ - template - void operator()(Bucket&, Connectivity& connectivity, Bucket*) - { connectivity.add_entity(); } - - bool is_modifying() const { return true; } -}; - -struct RemoveEntityFunctor -{ - template - void operator()(Bucket&, Connectivity& connectivity, Bucket*) - { connectivity.remove_entity(); } - - bool is_modifying() const { return true; } -}; - -struct DeclareRelationFunctor -{ - DeclareRelationFunctor(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, - Permutation permutation) - : m_bucket_ordinal(bucket_ordinal), - m_to(to), - m_ordinal(ordinal), - m_permutation(permutation), - m_modified(false) - {} - - template - void operator()(Bucket& bucket, Connectivity& connectivity) - { - ThrowAssert( (Connectivity::target_rank == static_cast(stk::topology::INVALID_RANK) && - bucket.mesh().entity_rank(m_to) > static_cast(stk::topology::ELEMENT_RANK)) || - bucket.mesh().entity_rank(m_to) == Connectivity::target_rank ); - ThrowAssert(!m_modified); - m_modified = connectivity.add_connectivity(m_bucket_ordinal, m_to, m_ordinal, m_permutation); - } - - unsigned m_bucket_ordinal; - Entity m_to; - ConnectivityOrdinal m_ordinal; - Permutation m_permutation; - bool m_modified; -}; - -struct DestroyRelationFunctor -{ - DestroyRelationFunctor(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) - : m_bucket_ordinal(bucket_ordinal), - m_to(to), - m_ordinal(ordinal), - m_modified(false) - {} - - template - void operator()(Bucket& bucket, Connectivity& connectivity) - { - ThrowAssert( (Connectivity::target_rank == static_cast(stk::topology::INVALID_RANK) && - bucket.mesh().entity_rank(m_to) > static_cast(stk::topology::ELEMENT_RANK)) || - bucket.mesh().entity_rank(m_to) == Connectivity::target_rank); - ThrowAssert(!m_modified); - m_modified = connectivity.remove_connectivity(m_bucket_ordinal, m_to, m_ordinal); - } - - unsigned m_bucket_ordinal; - Entity m_to; - ConnectivityOrdinal m_ordinal; - bool m_modified; -}; - -struct DebugPrintFunctor -{ - DebugPrintFunctor(std::ostream& out, unsigned ordinal = -1u) : m_out(out), m_ordinal(ordinal) {} - - template - void operator()(const Bucket&, const Connectivity& connectivity, const Bucket*) const - { - if (m_ordinal == -1u) { - connectivity.debug_dump(m_out); - } - else { - connectivity.debug_dump(m_out, m_ordinal); - } - } - - bool is_modifying() const { return false; } - - std::ostream& m_out; - unsigned m_ordinal; -}; - -template void setup_connectivity(stk::topology bucket_topology, EntityRank from_rank, EntityRank to_rank, - ConnectivityType& conn_type, - FixedConnectivity& fixed_conn) + ConnectivityType& conn_type) { if (bucket_topology != stk::topology::END_TOPOLOGY && bucket_topology.num_sub_topology(to_rank) > 0 && to_rank == stk::topology::NODE_RANK) { - fixed_conn.set_num_connectivity(bucket_topology.num_sub_topology(to_rank)); conn_type = FIXED_CONNECTIVITY; } else if (from_rank > stk::topology::ELEMENT_RANK || @@ -182,31 +76,6 @@ void setup_connectivity(stk::topology bucket_topology, } //namespace anonymous -namespace impl { - -struct OverwriteEntityFunctor -{ - OverwriteEntityFunctor(unsigned old_ordinal, unsigned new_ordinal) : m_old_ordinal(old_ordinal), m_new_ordinal(new_ordinal) {} - - template - void operator()(Bucket& bucket, Connectivity& connectivity, Bucket* otherBucket) - { - impl::BucketConnectivity & otherConnectivity = get_other_connectivity(otherBucket); - otherConnectivity.copy_entity(m_old_ordinal, connectivity, m_new_ordinal); - } - - bool is_modifying() const { return true; } - - template - static - impl::BucketConnectivity& get_other_connectivity(Bucket* other_bucket); - - unsigned m_old_ordinal; - unsigned m_new_ordinal; -}; - -} - //---------------------------------------------------------------------- bool raw_part_equal( const unsigned * lhs , const unsigned * rhs ) @@ -239,18 +108,17 @@ bool BucketLess::operator()( const unsigned * lhs , const Bucket * rhs_bucket ) const { return bucket_key_less( lhs , rhs_bucket->key() ); } -//---------------------------------------------------------------------- - Bucket::Bucket(BulkData & arg_mesh, EntityRank arg_entity_rank, const std::vector & arg_key, size_t arg_capacity, unsigned bucket_id) : m_mesh(arg_mesh), + m_sparse_connectivity(arg_mesh.get_sparse_connectivity()), m_entity_rank(arg_entity_rank), - m_topology(), m_key(arg_key), m_partOrdsBeginEnd(m_key.data()+1,m_key.data()+m_key[0]), + m_topology(get_topology(m_mesh.mesh_meta_data(), arg_entity_rank, superset_part_ordinals())), m_capacity(arg_capacity), m_size(0), m_bucket_id(bucket_id), @@ -261,28 +129,16 @@ Bucket::Bucket(BulkData & arg_mesh, m_node_kind(INVALID_CONNECTIVITY_TYPE), m_edge_kind(INVALID_CONNECTIVITY_TYPE), m_face_kind(INVALID_CONNECTIVITY_TYPE), - m_element_kind(INVALID_CONNECTIVITY_TYPE), - m_fixed_node_connectivity(), - m_fixed_edge_connectivity(), - m_fixed_face_connectivity(), - m_fixed_element_connectivity(), - m_dynamic_node_connectivity(arg_entity_rank, &m_mesh), - m_dynamic_edge_connectivity(arg_entity_rank, &m_mesh), - m_dynamic_face_connectivity(arg_entity_rank, &m_mesh), - m_dynamic_element_connectivity(arg_entity_rank, &m_mesh), - m_dynamic_other_connectivity(arg_entity_rank, &m_mesh), + m_topoNodes(m_topology, m_entities), + m_sparseNodes(m_sparse_connectivity, m_entity_rank, m_entities), m_owned(has_superset(*this, m_mesh.mesh_meta_data().locally_owned_part())), m_shared(has_superset(*this, m_mesh.mesh_meta_data().globally_shared_part())), m_aura(has_superset(*this, m_mesh.mesh_meta_data().aura_part())) { ThrowAssertMsg(arg_capacity != 0, "Buckets should never have zero capacity"); - - m_topology = get_topology(m_mesh.mesh_meta_data(), arg_entity_rank, superset_part_ordinals()); - - setup_connectivity(m_topology, arg_entity_rank, stk::topology::NODE_RANK, m_node_kind, m_fixed_node_connectivity); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::EDGE_RANK, m_edge_kind, m_fixed_edge_connectivity); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::FACE_RANK, m_face_kind, m_fixed_face_connectivity); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::ELEMENT_RANK, m_element_kind, m_fixed_element_connectivity); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::NODE_RANK, m_node_kind); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::EDGE_RANK, m_edge_kind); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::FACE_RANK, m_face_kind); m_parts.reserve(m_key.size()); supersets(m_parts); @@ -296,93 +152,36 @@ Bucket::~Bucket() m_mesh.destroy_bucket_callback(m_entity_rank, *this, m_capacity); } -size_t Bucket::memory_size_in_bytes() const -{ - size_t bytes = sizeof(Bucket); - bytes += impl::capacity_in_bytes(m_entities); - bytes += m_fixed_node_connectivity.heap_memory_in_bytes(); - bytes += m_fixed_edge_connectivity.heap_memory_in_bytes(); - bytes += m_fixed_face_connectivity.heap_memory_in_bytes(); - bytes += m_fixed_element_connectivity.heap_memory_in_bytes(); - bytes += m_dynamic_node_connectivity.heap_memory_in_bytes(); - bytes += m_dynamic_edge_connectivity.heap_memory_in_bytes(); - bytes += m_dynamic_face_connectivity.heap_memory_in_bytes(); - bytes += m_dynamic_element_connectivity.heap_memory_in_bytes(); - bytes += m_dynamic_other_connectivity.heap_memory_in_bytes(); - return bytes; -} - -void Bucket::change_existing_connectivity(unsigned bucket_ordinal, stk::mesh::Entity* new_nodes) +void Bucket::change_connected_nodes(unsigned bucket_ordinal, stk::mesh::Entity* new_nodes) { - unsigned num_nodes = this->num_nodes(bucket_ordinal); - Entity *nodes=0; - if (m_node_kind == FIXED_CONNECTIVITY) - { - nodes = m_fixed_node_connectivity.begin(bucket_ordinal); - } - else - { - nodes = m_dynamic_node_connectivity.begin(bucket_ordinal); - } - - for (unsigned i=0;i stk::topology::NODE_RANK && + entity_rank() <= stk::topology::ELEM_RANK) { + const unsigned numNodes = m_topology.num_nodes(); + ThrowRequireMsg(m_node_kind == FIXED_CONNECTIVITY, "Bucket topo="< 0 && fromNumNodes == numNodes) { + const Entity* entityNodes = from_bucket.begin_nodes(from_ordinal); + if (m_topology == stk::topology::INVALID_TOPOLOGY || from_bucket.topology() == stk::topology::INVALID_TOPOLOGY) { + const ConnectivityOrdinal* ords = from_bucket.begin_node_ordinals(from_ordinal); + for(unsigned i=0; imesh().add_entity_callback(entity_rank(), bucket_id(), m_size); ++m_size; - - AddEntityFunctor functor; - process_all_connectivity(functor); } bool Bucket::destroy_relation(Entity e_from, Entity e_to, const RelationIdentifier local_id ) { - const unsigned from_bucket_ordinal = mesh().bucket_ordinal(e_from); - DestroyRelationFunctor functor(from_bucket_ordinal, e_to, static_cast(local_id)); - modify_connectivity(functor, m_mesh.entity_rank(e_to)); + EntityRank toRank = mesh().entity_rank(e_to); + if (toRank != stk::topology::NODE_RANK) { + EntityRank fromRank = mesh().entity_rank(e_from); + return m_sparse_connectivity.remove_connectivity(fromRank, e_from, toRank, e_to, local_id); + } + + Bucket& fromBucket = mesh().bucket(e_from); + if (fromBucket.bucket_id() != bucket_id()) { + return fromBucket.destroy_relation(e_from, e_to, local_id); + } - return functor.m_modified; + const unsigned from_bucket_ordinal = mesh().bucket_ordinal(e_from); + + CONN_TYPE(m_node_kind, m_topoNodes.set_connected_node(from_bucket_ordinal, Entity(), local_id), m_sparseNodes.set_connected_node(from_bucket_ordinal, Entity(), local_id)); + return true; } bool Bucket::declare_relation(unsigned bucket_ordinal, Entity e_to, const ConnectivityOrdinal ordinal, Permutation permutation ) { - DeclareRelationFunctor functor(bucket_ordinal, e_to, ordinal, permutation); - modify_connectivity(functor, m_mesh.entity_rank(e_to)); + EntityRank toRank = mesh().entity_rank(e_to); + if (toRank == stk::topology::NODE_RANK) { + return (m_node_kind==FIXED_CONNECTIVITY ? m_topoNodes.set_connected_node(bucket_ordinal, e_to, ordinal) : m_sparseNodes.reset_connected_node(bucket_ordinal, e_to, ordinal)); + } - return functor.m_modified; + return m_sparse_connectivity.add_connectivity(entity_rank(), m_entities[bucket_ordinal], + toRank, e_to, ordinal, permutation); } void Bucket::remove_entity() @@ -722,9 +522,6 @@ void Bucket::remove_entity() --m_size; initialize_slot(m_size, Entity()); - - RemoveEntityFunctor functor; - process_all_connectivity(functor); } void Bucket::copy_entity(Entity entity) @@ -737,73 +534,11 @@ void Bucket::copy_entity(Entity entity) ThrowAssert(mesh().entity_rank(entity) == m_entity_rank); mark_for_modification(); - Bucket* old_bucket = mesh().bucket_ptr(entity); - const unsigned old_ordinal = mesh().bucket_ordinal(entity); this->mesh().add_entity_callback(this->entity_rank(), this->bucket_id(), m_size); reset_entity_location(entity, m_size); ++m_size; - - // Unfortunately, we had to copy/paste modify_connectivity to allow dynamic->fixed moves. The - // modify_connectivity framework couldn't elegantly handle this case. - switch(m_node_kind) { - case FIXED_CONNECTIVITY: - if (old_bucket->m_node_kind == FIXED_CONNECTIVITY) { - old_bucket->m_fixed_node_connectivity.copy_entity(old_ordinal, m_fixed_node_connectivity); - } - else { - ThrowAssert(old_bucket->m_node_kind != INVALID_CONNECTIVITY_TYPE); - old_bucket->m_dynamic_node_connectivity.copy_to_fixed(old_ordinal, m_fixed_node_connectivity); - } - break; - case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_node_connectivity.copy_entity(old_ordinal, m_dynamic_node_connectivity); break; - default: break; - } - - switch(m_edge_kind) { - case FIXED_CONNECTIVITY: - if (old_bucket->m_edge_kind == FIXED_CONNECTIVITY) { - old_bucket->m_fixed_edge_connectivity.copy_entity(old_ordinal, m_fixed_edge_connectivity); - } - else { - ThrowAssert(old_bucket->m_edge_kind != INVALID_CONNECTIVITY_TYPE); - old_bucket->m_dynamic_edge_connectivity.copy_to_fixed(old_ordinal, m_fixed_edge_connectivity); - } - break; - case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_edge_connectivity.copy_entity(old_ordinal, m_dynamic_edge_connectivity); break; - default: break; - } - - switch(m_face_kind) { - case FIXED_CONNECTIVITY: - if (old_bucket->m_face_kind == FIXED_CONNECTIVITY) { - old_bucket->m_fixed_face_connectivity.copy_entity(old_ordinal, m_fixed_face_connectivity); - } - else { - ThrowAssert(old_bucket->m_face_kind != INVALID_CONNECTIVITY_TYPE); - old_bucket->m_dynamic_face_connectivity.copy_to_fixed(old_ordinal, m_fixed_face_connectivity); - } - break; - case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_face_connectivity.copy_entity(old_ordinal, m_dynamic_face_connectivity); break; - default: break; - } - - switch(m_element_kind) { - case FIXED_CONNECTIVITY: - if (old_bucket->m_element_kind == FIXED_CONNECTIVITY) { - old_bucket->m_fixed_element_connectivity.copy_entity(old_ordinal, m_fixed_element_connectivity); - } - else { - ThrowAssert(old_bucket->m_element_kind != INVALID_CONNECTIVITY_TYPE); - old_bucket->m_dynamic_element_connectivity.copy_to_fixed(old_ordinal, m_fixed_element_connectivity); - } - break; - case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_element_connectivity.copy_entity(old_ordinal, m_dynamic_element_connectivity); break; - default: break; - } - - old_bucket->m_dynamic_other_connectivity.copy_entity(old_ordinal, m_dynamic_other_connectivity); } void Bucket::overwrite_entity(unsigned to_ordinal, Entity entity, const FieldVector* fields) @@ -813,11 +548,7 @@ void Bucket::overwrite_entity(unsigned to_ordinal, Entity entity, const FieldVec ThrowAssert(mesh().bucket_ptr(entity) != nullptr); ThrowAssert(mesh().entity_rank(entity) == m_entity_rank); - const MeshIndex from_index = m_mesh.mesh_index(entity); reset_entity_location(entity, to_ordinal, fields); - - impl::OverwriteEntityFunctor functor(from_index.bucket_ordinal, to_ordinal); - process_all_connectivity(functor, from_index.bucket); } @@ -838,96 +569,5 @@ void Bucket::parent_topology( EntityRank parent_rank, std::vector stk::util::sort_and_unique(parent_topologies); } -void Bucket::check_size_invariant() const -{ -#ifndef NDEBUG -// for (size_t i = 0; i < m_entities.size(); ++i) { -// if (i < m_size) { -// ThrowAssert(mesh().is_valid(m_entities[i])); -// } -// else { -// ThrowAssert(!mesh().is_valid(m_entities[i])); -// } -// } - - CheckSizeFunctor functor; - const_cast(this)->process_all_connectivity(functor); -#endif -} - -void Bucket::debug_dump(std::ostream& out, unsigned ordinal) const -{ - DebugPrintFunctor functor(out, ordinal); - const_cast(this)->process_all_connectivity(functor); -} - -void Bucket::debug_check_for_invalid_connectivity_request(ConnectivityType const* type) const -{ -#ifndef NDEBUG - EntityRank rank = stk::topology::END_RANK; - if (type == &m_node_kind) { - rank = stk::topology::NODE_RANK; - } - else if (type == &m_edge_kind) { - rank = stk::topology::EDGE_RANK; - } - else if (type == &m_face_kind) { - rank = stk::topology::FACE_RANK; - } - else if (type == &m_element_kind) { - rank = stk::topology::ELEMENT_RANK; - } - else { - ThrowAssert(false); - } - // Asking for connectivity between entities of equal rank is always invalid and ok to ask for - // Asking for connectivity between for FACE_RANK in 2d is always invalid and ok to ask for - bool isThisEntityAskingForConnectivityToItsOwnRank = entity_rank() == rank; - bool isThisEntityAskingForFaceConnectivityOnTwoDimensionalMesh = rank == stk::topology::FACE_RANK && mesh().mesh_meta_data().spatial_dimension() == 2; - ThrowAssert( isThisEntityAskingForConnectivityToItsOwnRank || isThisEntityAskingForFaceConnectivityOnTwoDimensionalMesh); -#endif -} - -namespace impl { - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_fixed_node_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_fixed_edge_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_fixed_face_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_fixed_element_connectivity; } - - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_dynamic_node_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_dynamic_edge_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_dynamic_face_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_dynamic_element_connectivity; } - -template <> -impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) -{ return other_bucket->m_dynamic_other_connectivity; } - -} - } // namespace mesh } // namespace stk diff --git a/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp b/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp index c22360e04b29..5a4b3966bd6f 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp @@ -38,10 +38,12 @@ #include // for size_t, NULL #include // for lower_bound #include // for ostream -#include // for BucketConnectivity #include // for Entity #include // for contains_ordinal, Part #include +#include +#include +#include #include // for topology, etc #include // for ThrowAssert, etc #include @@ -54,7 +56,6 @@ namespace stk { namespace mesh { class FieldBase; } } namespace stk { namespace mesh { class DeviceMesh; } } namespace stk { namespace mesh { namespace impl { class BucketRepository; } } } namespace stk { namespace mesh { namespace impl { class Partition; } } } -namespace stk { namespace mesh { namespace impl { struct OverwriteEntityFunctor; } } } namespace stk { namespace mesh { @@ -75,36 +76,28 @@ print( std::ostream & , const std::string & indent , const Bucket & ); // The part count and parts are equal bool raw_part_equal( const unsigned * lhs , const unsigned * rhs ); -#define CONNECTIVITY_TYPE_SWITCH(entity_kind, fixed_func_sig, dynamic_func_sig, check_invalid) \ - switch(entity_kind) { \ - case FIXED_CONNECTIVITY: \ - return fixed_func_sig; \ - case DYNAMIC_CONNECTIVITY: \ - return dynamic_func_sig; \ - default: \ - if (check_invalid) { \ - check_for_invalid_connectivity_request(&entity_kind); \ - } \ - return 0; \ - } +#define CONN_TYPE(conn_type, fixed_conn, sparse_conn) \ + ((conn_type == FIXED_CONNECTIVITY) ? fixed_conn : sparse_conn) -#define RANK_SWITCH(rank, begin_or_end, postfix, bucket_ordinal) \ +#define RANK_SWITCH(rank, begin_or_end, item_type, bucket_ordinal) \ \ - switch(rank) { \ - case stk::topology::NODE_RANK: return begin_or_end##_node##postfix(bucket_ordinal); \ - case stk::topology::EDGE_RANK: return begin_or_end##_edge##postfix(bucket_ordinal); \ - case stk::topology::FACE_RANK: return begin_or_end##_face##postfix(bucket_ordinal); \ - case stk::topology::ELEMENT_RANK: return begin_or_end##_element##postfix(bucket_ordinal); \ - default: \ - return begin_other##postfix(bucket_ordinal) + get_others_##begin_or_end##_index(bucket_ordinal, rank); \ + switch(rank) { \ + case stk::topology::NODE_RANK: \ + switch(m_node_kind) { \ + case FIXED_CONNECTIVITY: return m_topoNodes.begin_or_end##item_type(bucket_ordinal); \ + case DYNAMIC_CONNECTIVITY: return m_sparseNodes.begin_or_end##item_type(bucket_ordinal); \ + default: return nullptr; \ + } \ + default: \ + return m_sparse_connectivity.begin_or_end##item_type(m_entities[bucket_ordinal], rank); \ } //---------------------------------------------------------------------- -/** \brief A container for the connectivity for a homogeneous collection of +/** \brief A container for a homogeneous collection of * \ref stk::mesh::Entity "entities". * - * The entities are homogeneous in that they are of the same entity type - * and are members of the same of parts. + * The entities are homogeneous in that they are of the same rank and topology + * and are members of the same parts. */ class Bucket { @@ -134,8 +127,6 @@ class Bucket /** \brief Number of entities associated with this bucket */ size_type size() const { return m_size ; } - size_t memory_size_in_bytes() const; - /** \brief Capacity of this bucket */ size_t capacity() const { return m_capacity ; } @@ -212,87 +203,83 @@ class Bucket int parallel_owner_rank(unsigned ordinal) const; - void check_size_invariant() const; - //generic rank connectivity calls Entity const* begin(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, begin, s, bucket_ordinal) } + { RANK_SWITCH(rank, begin, _connectivity, bucket_ordinal) } ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal, EntityRank rank) const { RANK_SWITCH(rank, begin, _ordinals, bucket_ordinal) } Permutation const* begin_permutations(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, begin, _permutations, bucket_ordinal) } + { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], rank); } Entity const* end(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, end, s, bucket_ordinal) } + { RANK_SWITCH(rank, end, _connectivity, bucket_ordinal) } ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal, EntityRank rank) const { RANK_SWITCH(rank, end, _ordinals, bucket_ordinal) } Permutation const* end_permutations(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, end, _permutations, bucket_ordinal) } + { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], rank); } unsigned num_connectivity(unsigned bucket_ordinal, EntityRank rank) const; Entity const* begin_nodes(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin(bucket_ordinal), m_dynamic_node_connectivity.begin(bucket_ordinal), true) } + { return CONN_TYPE(m_node_kind, m_topoNodes.begin_connectivity(bucket_ordinal), m_sparseNodes.begin_connectivity(bucket_ordinal)); } Entity const* begin_edges(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin(bucket_ordinal), m_dynamic_edge_connectivity.begin(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } Entity const* begin_faces(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin(bucket_ordinal), m_dynamic_face_connectivity.begin(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } Entity const* begin_elements(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin(bucket_ordinal), m_dynamic_element_connectivity.begin(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } ConnectivityOrdinal const* begin_node_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_node_connectivity.begin_ordinals(bucket_ordinal), true) } + { return CONN_TYPE(m_node_kind, m_topoNodes.begin_ordinals(bucket_ordinal), m_sparseNodes.begin_ordinals(bucket_ordinal)); } ConnectivityOrdinal const* begin_edge_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_edge_connectivity.begin_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } ConnectivityOrdinal const* begin_face_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_face_connectivity.begin_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } ConnectivityOrdinal const* begin_element_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_element_connectivity.begin_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } - Permutation const* begin_node_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin_permutations(bucket_ordinal), m_dynamic_node_connectivity.begin_permutations(bucket_ordinal), true) } + Permutation const* begin_node_permutations(unsigned bucket_ordinal) const { return nullptr; } Permutation const* begin_edge_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin_permutations(bucket_ordinal), m_dynamic_edge_connectivity.begin_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } Permutation const* begin_face_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin_permutations(bucket_ordinal), m_dynamic_face_connectivity.begin_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } Permutation const* begin_element_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin_permutations(bucket_ordinal), m_dynamic_element_connectivity.begin_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } unsigned num_nodes(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.num_connectivity(bucket_ordinal), m_dynamic_node_connectivity.num_connectivity(bucket_ordinal), false) } + { return CONN_TYPE(m_node_kind, m_topoNodes.num_nodes_per_entity(bucket_ordinal), m_sparseNodes.num_nodes_per_entity(bucket_ordinal)); } unsigned num_edges(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.num_connectivity(bucket_ordinal), m_dynamic_edge_connectivity.num_connectivity(bucket_ordinal), false) } + { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } unsigned num_faces(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.num_connectivity(bucket_ordinal), m_dynamic_face_connectivity.num_connectivity(bucket_ordinal), false) } + { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } unsigned num_elements(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.num_connectivity(bucket_ordinal), m_dynamic_element_connectivity.num_connectivity(bucket_ordinal), false) } + { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } Entity const* end_nodes(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end(bucket_ordinal), m_dynamic_node_connectivity.end(bucket_ordinal), true) } + { return CONN_TYPE(m_node_kind, m_topoNodes.end_connectivity(bucket_ordinal), m_sparseNodes.end_connectivity(bucket_ordinal)); } Entity const* end_edges(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end(bucket_ordinal), m_dynamic_edge_connectivity.end(bucket_ordinal), true) } + { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } Entity const* end_faces(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end(bucket_ordinal), m_dynamic_face_connectivity.end(bucket_ordinal), true) } + { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } Entity const* end_elements(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end(bucket_ordinal), m_dynamic_element_connectivity.end(bucket_ordinal), true) } + { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } ConnectivityOrdinal const* end_node_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end_ordinals(bucket_ordinal), m_dynamic_node_connectivity.end_ordinals(bucket_ordinal), true) } + { return CONN_TYPE(m_node_kind, m_topoNodes.end_ordinals(bucket_ordinal), m_sparseNodes.end_ordinals(bucket_ordinal)); } ConnectivityOrdinal const* end_edge_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end_ordinals(bucket_ordinal), m_dynamic_edge_connectivity.end_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } ConnectivityOrdinal const* end_face_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end_ordinals(bucket_ordinal), m_dynamic_face_connectivity.end_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } ConnectivityOrdinal const* end_element_ordinals(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end_ordinals(bucket_ordinal), m_dynamic_element_connectivity.end_ordinals(bucket_ordinal), true) } + { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } - Permutation const* end_node_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end_permutations(bucket_ordinal), m_dynamic_node_connectivity.end_permutations(bucket_ordinal), true) } + Permutation const* end_node_permutations(unsigned bucket_ordinal) const { return nullptr; } Permutation const* end_edge_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end_permutations(bucket_ordinal), m_dynamic_edge_connectivity.end_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } Permutation const* end_face_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end_permutations(bucket_ordinal), m_dynamic_face_connectivity.end_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } Permutation const* end_element_permutations(unsigned bucket_ordinal) const - { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end_permutations(bucket_ordinal), m_dynamic_element_connectivity.end_permutations(bucket_ordinal), true) } + { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } bool has_permutation(EntityRank rank) const; @@ -304,7 +291,9 @@ class Bucket using ConnectedOrdinals = util::StridedArray; using Permutations = util::StridedArray; - unsigned get_num_nodes_per_entity() const { return topology().num_nodes(); } +#ifndef STK_HIDE_DEPRECATED_CODE // Delete after November 2021 + STK_DEPRECATED unsigned get_num_nodes_per_entity() const { return topology().num_nodes(); } +#endif ConnectedEntities get_connected_entities(unsigned offsetIntoBucket, stk::mesh::EntityRank connectedRank) const { return ConnectedEntities(begin(offsetIntoBucket, connectedRank), @@ -347,44 +336,17 @@ class Bucket void reset_bucket_parts(const OrdinalVector& newPartOrdinals); protected: - void change_existing_connectivity(unsigned bucket_ordinal, stk::mesh::Entity* new_nodes); - void change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, unsigned elem_connectivity_ordinal, stk::mesh::Permutation permut); - void change_existing_permutation_for_connected_edge(unsigned bucket_ordinal_of_higher_ranked_entity, unsigned edge_connectivity_ordinal, stk::mesh::Permutation permut); - void change_existing_permutation_for_connected_face(unsigned bucket_ordinal_of_higher_ranked_entity, unsigned face_connectivity_ordinal, stk::mesh::Permutation permut); + void change_connected_nodes(unsigned bucket_ordinal, Entity* new_nodes); + void change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, ConnectivityOrdinal elem_connectivity_ordinal, Permutation permut); + void change_existing_permutation_for_connected_edge(unsigned bucket_ordinal_of_higher_ranked_entity, ConnectivityOrdinal edge_connectivity_ordinal, Permutation permut); + void change_existing_permutation_for_connected_face(unsigned bucket_ordinal_of_higher_ranked_entity, ConnectivityOrdinal face_connectivity_ordinal, Permutation permut); virtual ~Bucket(); -private: - +protected: bool destroy_relation(Entity e_from, Entity e_to, const RelationIdentifier local_id ); bool declare_relation(unsigned bucket_ordinal, Entity e_to, const ConnectivityOrdinal ordinal, Permutation permutation); - // The following *_other* functions should not be made available externally, in - // order to avoid external confusion with "constraint" and "other" connectivities. - // They are currently used within this class to provide connectivities - // externally through another interface. - Entity const* begin_others(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.begin(bucket_ordinal); - } - ConnectivityOrdinal const* begin_other_ordinals(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.begin_ordinals(bucket_ordinal); - } - Permutation const* begin_other_permutations(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.begin_permutations(bucket_ordinal); - } - unsigned num_other(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.num_connectivity(bucket_ordinal); - } - Entity const* end_others(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.end(bucket_ordinal); - } - ConnectivityOrdinal const* end_other_ordinals(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.end_ordinals(bucket_ordinal); - } - Permutation const* end_other_permutations(unsigned bucket_ordinal) const { - return m_dynamic_other_connectivity.end_permutations(bucket_ordinal); - } - void supersets( PartVector & ) const ; /** \brief The \ref stk::mesh::BulkData "bulk data manager" @@ -441,65 +403,34 @@ class Bucket // Optional fields argument, only copy listed fields void reset_entity_location(Entity entity, unsigned to_ordinal, const std::vector* fields = nullptr); - unsigned get_others_begin_index(unsigned bucket_ordinal, EntityRank rank) const; - unsigned get_others_end_index(unsigned bucket_ordinal, EntityRank rank) const; - unsigned get_others_index_count(unsigned bucket_ordinal, EntityRank rank) const; - - template - void modify_connectivity(T& callable, EntityRank rank); - - template - void process_all_connectivity(T& callable, Bucket* other_bucket = nullptr); - - void check_for_invalid_connectivity_request(ConnectivityType const* type) const - { -#ifndef NDEBUG - debug_check_for_invalid_connectivity_request(type); -#endif - } - - void debug_check_for_invalid_connectivity_request(ConnectivityType const* type) const; - - friend class impl::BucketRepository; + friend class BulkData; friend class impl::Partition; - friend struct impl::OverwriteEntityFunctor; - friend class BulkData; // Replacement friend. - friend struct Entity; + friend class impl::BucketRepository; friend class DeviceMesh; BulkData & m_mesh ; // Where this bucket resides + SparseConnectivity & m_sparse_connectivity; const EntityRank m_entity_rank ; // Type of entities for this bucket - stk::topology m_topology ; // The topology of this bucket std::vector m_key ; // REFACTOR std::pair m_partOrdsBeginEnd; + stk::topology m_topology ; // The topology of this bucket const size_t m_capacity ; // Capacity for entities size_type m_size ; // Number of entities - unsigned m_bucket_id; // Index into its BucketRepository's m_bucket[entity_rank()], these are NOT unique + unsigned m_bucket_id; unsigned m_ngp_bucket_id; bool m_is_modified; PartVector m_parts; // Entity data - std::vector m_entities; // Array of entity handles; will be removed soon + std::vector m_entities; impl::Partition *m_partition; ConnectivityType m_node_kind; ConnectivityType m_edge_kind; ConnectivityType m_face_kind; - ConnectivityType m_element_kind; - - impl::BucketConnectivity m_fixed_node_connectivity; // fixed connectivity to nodes - impl::BucketConnectivity m_fixed_edge_connectivity; // fixed connectivity to edges - impl::BucketConnectivity m_fixed_face_connectivity; // fixed connectivity to faces - impl::BucketConnectivity m_fixed_element_connectivity; // fixed connectivity to elements - - impl::BucketConnectivity m_dynamic_node_connectivity; // dynamic connectivity to nodes - impl::BucketConnectivity m_dynamic_edge_connectivity; // dynamic connectivity to edges - impl::BucketConnectivity m_dynamic_face_connectivity; // dynamic connectivity to faces - impl::BucketConnectivity m_dynamic_element_connectivity; // dynamic connectivity to elements - - impl::BucketConnectivity m_dynamic_other_connectivity; // dynamic connectivity to everything else + ConnectedTopologyNodes m_topoNodes; + ConnectedSparseNodes m_sparseNodes; bool m_owned; bool m_shared; @@ -508,8 +439,6 @@ class Bucket std::vector m_ngp_field_bucket_id; std::vector m_ngp_field_is_modified; }; -#undef CONNECTIVITY_TYPE_SWITCH -#undef RANK_SWITCH /** \brief Is this bucket a subset of the given * \ref stk::mesh::Part "part" by partID @@ -590,31 +519,16 @@ inline unsigned Bucket::num_connectivity(unsigned bucket_ordinal, EntityRank rank) const { switch(rank) { - case stk::topology::NODE_RANK: return num_nodes(bucket_ordinal); - case stk::topology::EDGE_RANK: return num_edges(bucket_ordinal); - case stk::topology::FACE_RANK: return num_faces(bucket_ordinal); - case stk::topology::ELEMENT_RANK: return num_elements(bucket_ordinal); + case stk::topology::NODE_RANK: return num_nodes(bucket_ordinal); default: - return get_others_index_count(bucket_ordinal, rank); + return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], rank); } } inline bool Bucket::has_permutation(EntityRank rank) const { - switch(rank) { - case stk::topology::NODE_RANK: - return m_node_kind == FIXED_CONNECTIVITY ? m_fixed_node_connectivity.has_permutation() : m_dynamic_node_connectivity.has_permutation(); - case stk::topology::EDGE_RANK: - return m_edge_kind == FIXED_CONNECTIVITY ? m_fixed_edge_connectivity.has_permutation() : m_dynamic_edge_connectivity.has_permutation(); - case stk::topology::FACE_RANK: - return m_face_kind == FIXED_CONNECTIVITY ? m_fixed_face_connectivity.has_permutation() : m_dynamic_face_connectivity.has_permutation(); - case stk::topology::ELEMENT_RANK: - return m_element_kind == FIXED_CONNECTIVITY ? m_fixed_element_connectivity.has_permutation() : m_dynamic_element_connectivity.has_permutation(); - case stk::topology::CONSTRAINT_RANK: - default: - return false; - } + return SparseConnectivity::has_permutation(entity_rank(), rank); } inline @@ -627,106 +541,15 @@ ConnectivityType Bucket::connectivity_type(EntityRank rank) const return m_edge_kind; case stk::topology::FACE_RANK: return m_face_kind; - case stk::topology::ELEMENT_RANK: - return m_element_kind; default: return DYNAMIC_CONNECTIVITY; } } -template -inline -void Bucket::process_all_connectivity(T& callable, Bucket* other_bucket) -{ - if (callable.is_modifying()) { - mark_for_modification(); - } - - switch(m_node_kind) { - case FIXED_CONNECTIVITY: - callable.template operator()(*this, m_fixed_node_connectivity, other_bucket); break; - case DYNAMIC_CONNECTIVITY: - callable.template operator()(*this, m_dynamic_node_connectivity, other_bucket); break; - default: break; - } - - switch(m_edge_kind) { - case FIXED_CONNECTIVITY: - callable.template operator()(*this, m_fixed_edge_connectivity, other_bucket); break; - case DYNAMIC_CONNECTIVITY: - callable.template operator()(*this, m_dynamic_edge_connectivity, other_bucket); break; - default: break; - } - - switch(m_face_kind) { - case FIXED_CONNECTIVITY: - callable.template operator()(*this, m_fixed_face_connectivity, other_bucket); break; - case DYNAMIC_CONNECTIVITY: - callable.template operator()(*this, m_dynamic_face_connectivity, other_bucket); break; - default: break; - } - - switch(m_element_kind) { - case FIXED_CONNECTIVITY: - callable.template operator()(*this, m_fixed_element_connectivity, other_bucket); break; - case DYNAMIC_CONNECTIVITY: - callable.template operator()(*this, m_dynamic_element_connectivity, other_bucket); break; - default: break; - } - - callable.template operator()(*this, m_dynamic_other_connectivity, other_bucket); -} - -template -inline -void Bucket::modify_connectivity(T& callable, EntityRank rank) -{ - switch(rank) { - case stk::topology::NODE_RANK: - ThrowAssert(m_node_kind != INVALID_CONNECTIVITY_TYPE); - mark_for_modification(); - - switch(m_node_kind) { - case FIXED_CONNECTIVITY: callable(*this, m_fixed_node_connectivity); break; - case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_node_connectivity); break; - default: break; - } - break; - case stk::topology::EDGE_RANK: - ThrowAssert(m_edge_kind != INVALID_CONNECTIVITY_TYPE); - switch(m_edge_kind) { - case FIXED_CONNECTIVITY: callable(*this, m_fixed_edge_connectivity); break; - case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_edge_connectivity); break; - default: break; - } - break; - case stk::topology::FACE_RANK: - ThrowAssert(m_face_kind != INVALID_CONNECTIVITY_TYPE); - switch(m_face_kind) { - case FIXED_CONNECTIVITY: callable(*this, m_fixed_face_connectivity); break; - case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_face_connectivity); break; - default: break; - } - break; - case stk::topology::ELEMENT_RANK: - ThrowAssert(m_element_kind != INVALID_CONNECTIVITY_TYPE); - switch(m_element_kind) { - case FIXED_CONNECTIVITY: callable(*this, m_fixed_element_connectivity); break; - case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_element_connectivity); break; - default: break; - } - break; - default: - callable(*this, m_dynamic_other_connectivity); - break; - } -} - typedef Bucket::iterator BucketIterator; } // namespace mesh } // namespace stk - - #endif + diff --git a/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp b/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp deleted file mode 100644 index c5d6391af751..000000000000 --- a/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp +++ /dev/null @@ -1,1170 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#ifndef STK_MESH_BUCKET_CONNECTIVITY_HPP -#define STK_MESH_BUCKET_CONNECTIVITY_HPP - -#include "stk_mesh/base/Types.hpp" // for ConnectivityOrdinal, etc -#include // for Entity -#include "stk_util/util/ReportHandler.hpp" - -namespace stk { -namespace mesh { - -class BulkData; - -namespace impl { - -struct LowerConnectivityCompare -{ - bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const - { - // only compare ordinals - return first_ordinal < second_ordinal; - } -}; - -template -struct LowerConnectivitityRankSensitiveCompare -{ - LowerConnectivitityRankSensitiveCompare(const BULKDATA &bulk_data) : m_mesh(bulk_data) { } - - const BULKDATA &m_mesh; - - bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, - Entity second_entity, ConnectivityOrdinal second_ordinal) const; -}; - -struct HigherConnectivityCompare -{ - bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const - { - // Needs to match LessRelation in BulkData.hpp - return std::make_pair(first_ordinal, first_entity.is_local_offset_valid() ? first_entity.local_offset() : Entity::MaxEntity) < - std::make_pair(second_ordinal, second_entity.is_local_offset_valid() ? second_entity.local_offset() : Entity::MaxEntity); - } -}; - -template -struct HigherConnectivityRankSensitiveCompare -{ - HigherConnectivityRankSensitiveCompare(const BULKDATA &bulk_data) : m_mesh(bulk_data) { } - - const BULKDATA &m_mesh; - - bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, - ConnectivityOrdinal second_ordinal) const; -}; - -template -inline void check_bucket_ordinal(unsigned bucket_ordinal, Connectivity const* connectivity) -{ - ThrowAssertMsg(bucket_ordinal < connectivity->size(), - "bucket_ordinal " << bucket_ordinal << " is out of range, bucket size is " << connectivity->size()); -} - -template -class BucketConnectivity; - -template -size_t capacity_in_bytes(const VecType& v) -{ - return sizeof(typename VecType::value_type)*v.capacity(); -} - -template -class BucketConnectivity -{ - public: - typedef BucketConnectivity SelfType; - typedef BucketConnectivity OtherType; - - static const EntityRank target_rank = TargetRank; - static const ConnectivityType connectivity_type = FIXED_CONNECTIVITY; - - typedef std::vector EntityVector; - typedef std::vector ConnectivityOrdinalVector; - typedef std::vector PermutationVector; - - BucketConnectivity() //default constructed BucketConnectivity implies connectivity is not used - : m_num_connectivity(0u) - , m_targets() - , m_ordinals() - , m_permutations() - {} - - BucketConnectivity(unsigned arg_num_connectivity) - : m_num_connectivity(0) - , m_targets() - , m_ordinals() - , m_permutations() - { - set_num_connectivity(arg_num_connectivity); - } - - void set_num_connectivity(unsigned arg_num_connectivity) - { - ThrowAssertMsg(m_num_connectivity == 0, "Cannot reset num_connectivity"); - ThrowAssertMsg(arg_num_connectivity != 0, "Cannot set num connectivity to 0 for fixed connectivity"); - - m_num_connectivity = arg_num_connectivity; - - // Ordinal is the same for all fixed, just counts up - m_ordinals.resize(m_num_connectivity); - for (ConnectivityOrdinal ord=static_cast(0); ord < static_cast(m_num_connectivity); ++ord) { - m_ordinals[ord] = ord; - } - } - - // Entity iterator - - Entity const* begin(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[bucket_ordinal * m_num_connectivity]; } - - Entity * begin(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[bucket_ordinal * m_num_connectivity]; } - - Entity const* end(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[(bucket_ordinal + 1) * m_num_connectivity]; } - - Entity * end(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[(bucket_ordinal + 1) * m_num_connectivity]; } - - // Ordinal iterator - - ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return m_ordinals.data(); } - - ConnectivityOrdinal * begin_ordinals(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return m_ordinals.data(); } - - ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return m_ordinals.data() + m_num_connectivity; } - - ConnectivityOrdinal * end_ordinals(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return m_ordinals.data() + m_num_connectivity; } - - // Permutation iterator - - Permutation const* begin_permutations(unsigned bucket_ordinal) const - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[bucket_ordinal * m_num_connectivity]; - } - - Permutation * begin_permutations(unsigned bucket_ordinal) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[bucket_ordinal * m_num_connectivity]; - } - - Permutation const* end_permutations(unsigned bucket_ordinal) const - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[(bucket_ordinal + 1) * m_num_connectivity]; - } - - Permutation * end_permutations(unsigned bucket_ordinal) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[(bucket_ordinal + 1) * m_num_connectivity]; - } - - // Queries - - unsigned num_connectivity(unsigned /*bucket_ordinal*/) const - { return m_num_connectivity; } - - // return number of entities - unsigned size() const - { return m_targets.size() / m_num_connectivity; } - - // Modification API - - bool add_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation = INVALID_PERMUTATION) - { - ThrowAssertMsg(ordinal < m_num_connectivity, - "Ordinal " << (uint32_t)ordinal << " exceeds topological limit: " << m_num_connectivity); - impl::check_bucket_ordinal(bucket_ordinal, this); -#ifndef NDEBUG - // TODO - Add topology invariant; target entity should match a sub topology -#endif - - unsigned index = m_num_connectivity*bucket_ordinal + ordinal; - - if (m_targets[index] == to) { - ThrowAssert(!has_permutation() || m_permutations[index] == permutation); - // Already exists - return false; - } - - m_targets[index] = to; - - if (has_permutation()) { - m_permutations[index] = permutation; - } - - return true; - } - - bool remove_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) - { - ThrowAssertMsg(ordinal < m_num_connectivity, - "Ordinal " << (uint32_t)ordinal << " exceeds topological limit: " << m_num_connectivity); - impl::check_bucket_ordinal(bucket_ordinal, this); - - unsigned index = m_num_connectivity*bucket_ordinal + ordinal; - if (m_targets[index] != to) { - return false; - } - - // Clear - m_targets[index] = Entity(); - if (has_permutation()) { - m_permutations[index] = INVALID_PERMUTATION; - } - - return true; - } - - void begin_modification() - {} - - template // hack to get around dependency - void end_modification(BULKDATA* mesh = NULL); - - void add_entity() - { - const unsigned new_conn_size = m_targets.size() + m_num_connectivity; - Entity invalid; - m_targets.resize(new_conn_size, invalid); // Not a perf issue: vectors are smart when resizing - if (has_permutation()) { - m_permutations.resize(new_conn_size, INVALID_PERMUTATION); - } - } - - // Always removes last entity - void remove_entity() - { - ThrowAssertMsg(size() > 0, "Cannot remove, connectivity is already empty"); - - const unsigned new_conn_size = m_targets.size() - m_num_connectivity; - m_targets.resize(new_conn_size); - if (has_permutation()) { - m_permutations.resize(new_conn_size); - } - } - - void copy_entity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal=-1u) - { - ThrowAssertMsg(size() > 0, "Cannot move, connectivity is empty"); - - if (to_ordinal == -1u) { // check if we should just append - to_ordinal = to.size(); - to.add_entity(); // make room for new entity - } - - // Copy connectivity to other BucketConnectivity - copy_connectivity(from_ordinal, to, to_ordinal); - } - - void copy_to_fixed(unsigned from_ordinal, SelfType& to) - { ThrowAssert(false); } - - void copy_to_fixed(unsigned from_ordinal, OtherType& to) - { ThrowAssert(false); } - - bool has_permutation() const - { - const static bool rv = TargetRank != stk::topology::NODE_RANK; - return rv; - } - - size_t heap_memory_in_bytes() const - { - return capacity_in_bytes(m_targets) - + capacity_in_bytes(m_ordinals) - + capacity_in_bytes(m_permutations); - } - - void debug_dump(std::ostream& out) const - { - out << "For fixed connectivity to rank: " << TargetRank << "\n"; - out << " size is: " << size() << "\n"; - for (int i = 0, ie = size(); i < ie; ++i) { - out << " At ordinal " << i << "\n"; - debug_dump(out, i); - } - out << std::endl; - } - - void debug_dump(std::ostream& out, unsigned ordinal) const - { - for (int j = m_num_connectivity * ordinal, je = m_num_connectivity*(ordinal+1); j < je; ++j) { - out << " target:" << m_targets[j].local_offset() << "\n"; - } - } - -private: - - void copy_connectivity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal) - { - unsigned to_offset = to_ordinal * m_num_connectivity; - unsigned from_offset = from_ordinal * m_num_connectivity; - - std::copy(m_targets.begin() + from_offset, - m_targets.begin() + from_offset + m_num_connectivity, - to.m_targets.begin() + to_offset); - - if (has_permutation()) { - std::copy(m_permutations.begin() + from_offset, - m_permutations.begin() + from_offset + m_num_connectivity, - to.m_permutations.begin() + to_offset); - } - } - - // Illegal - BucketConnectivity(const SelfType&); - SelfType& operator=(const SelfType&); - - // MEMBERS - - unsigned m_num_connectivity; - - // connectivity data - EntityVector m_targets; - ConnectivityOrdinalVector m_ordinals; // shared for all entities - PermutationVector m_permutations; - - // friend OtherType; // 1337! Will have to wait for c++11 - friend class BucketConnectivity; -}; - -// Want a way for all dynamic connectivity instantiations to share the same id space -struct Counter -{ - static int counter; -}; - -// Profiling data for an individual dynamic connectivity object -struct DynConnData -{ - // from-rank for the associated dynamic connectivity - EntityRank m_from_rank; - - // to-rank for the associated dynamic connectivity - EntityRank m_to_rank; - - // the maximum capacity ever achieved by connectivity vectors - size_t m_max_capacity; - - // at the point at which maximum capacity (member above) was achieved, how much memory - // was lost due to "abandoned space". - // "abandoned space" - When an entity overflows its current chunks, it gets additional - // chunks but must be copied to the end. The space left behind is abandoned and will - // not be reused until the next compress (resize_and_order_by_index). - size_t m_abandoned_space; - - // at the point at which maximum capacity (member above) was achieved, how much memory - // was lost due to unused chunk capacity. If chunk size is > 1, it's possible that an - // entity is not using all the space available in it's chunk. For example, if chunk size - // is 8 and an entity has 5 connectivities, then unused chunk capacity is 3 for that - // entity. This member stores the sum over all entities. - size_t m_unused_chunk_capacity; - - // The number of times this dynamic connectivity had to be grown - size_t m_num_growths; - - // The number of times any entity overflowed it's chunk allocation and had to be - // copied to the end - size_t m_num_entity_relocations; - - // at the point at which maximum capacity (member above) was achieved, what is the - // total amount of wasted memory - size_t m_total_unused_memory; - - // at the point at which maximum capacity (member above) was achieved, what is the - // amount of memory that is wasted due to vector capacity growth over-provisioning. - size_t m_unused_capacity; - - // at the point at which maximum capacity (member above) was achieved, what is the - // number of connectivity being stored. - size_t m_total_num_conn; - - DynConnData(EntityRank from_rank, EntityRank to_rank) : - m_from_rank(from_rank), - m_to_rank(to_rank), - m_max_capacity(0), - m_abandoned_space(0), - m_unused_chunk_capacity(0), - m_num_growths(0), - m_num_entity_relocations(0), - m_total_unused_memory(0), - m_unused_capacity(0), - m_total_num_conn(0) - {} -}; - -template -class BucketConnectivity -{ - enum connectivity_direction { Lower=0,Higher=1,Adjacent=2 }; - -public: - typedef BucketConnectivity SelfType; - typedef BucketConnectivity OtherType; - - static const EntityRank target_rank = TargetRank; - static const ConnectivityType connectivity_type = DYNAMIC_CONNECTIVITY; - - typedef std::vector EntityVector; - typedef std::vector ConnectivityOrdinalVector; - typedef std::vector PermutationVector; - typedef std::vector UInt32Vector; - typedef std::vector UInt16Vector; - - static const unsigned chunk_size = 1u; - - BucketConnectivity(EntityRank from_rank, BulkData *bulk_data) - : m_from_rank(from_rank) - , m_direction( (m_from_rank > TargetRank) ? Lower : ((m_from_rank == TargetRank) ? Adjacent : Higher)) - , m_active(false) - , m_needs_shrink_to_fit(false) - , m_num_inactive(0) - , m_indices() - , m_num_connectivities() - , m_total_connectivities(0) - , m_targets() - , m_ordinals() - , m_permutations() - , m_bulk_data(bulk_data) - , m_id(Counter::counter++) - , m_rank_sensitive_higher_connectivity_cmp(*m_bulk_data) - , m_rank_sensitive_lower_connectivity_cmp(*m_bulk_data) - , m_last_capacity(0) - { - } - - // Entity iterator - - Entity const* begin(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[m_active ? m_indices[bucket_ordinal] : 0]; } - - Entity * begin(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_targets[m_active ? m_indices[bucket_ordinal] : 0]; } - - Entity const* end(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return begin(bucket_ordinal) + num_connectivity(bucket_ordinal); } - - Entity * end(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return begin(bucket_ordinal) + num_connectivity(bucket_ordinal); } - - // Ordinal iterator - - ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_ordinals[m_active ? m_indices[bucket_ordinal] : 0]; } - - ConnectivityOrdinal * begin_ordinals(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return &m_ordinals[m_active ? m_indices[bucket_ordinal] : 0]; } - - ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return begin_ordinals(bucket_ordinal) + num_connectivity(bucket_ordinal); } - - ConnectivityOrdinal * end_ordinals(unsigned bucket_ordinal) - { impl::check_bucket_ordinal(bucket_ordinal, this); - return begin_ordinals(bucket_ordinal) + num_connectivity(bucket_ordinal); } - - // Permutation iterator - - Permutation const* begin_permutations(unsigned bucket_ordinal) const - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[m_active ? m_indices[bucket_ordinal] : 0]; - } - - Permutation * begin_permutations(unsigned bucket_ordinal) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return &m_permutations[m_active ? m_indices[bucket_ordinal] : 0]; - } - - Permutation const* end_permutations(unsigned bucket_ordinal) const - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return begin_permutations(bucket_ordinal) + num_connectivity(bucket_ordinal); - } - - Permutation * end_permutations(unsigned bucket_ordinal) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - if (!has_permutation()) return NULL; - return begin_permutations(bucket_ordinal) + num_connectivity(bucket_ordinal); - } - - // Queries - - unsigned num_connectivity(unsigned bucket_ordinal) const - { impl::check_bucket_ordinal(bucket_ordinal, this); - return m_active ? m_num_connectivities[bucket_ordinal] : 0; } - - // return number of entities - unsigned size() const - { return m_active ? m_indices.size() : m_num_inactive; } - - // Modification API - - bool add_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation = INVALID_PERMUTATION) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - - m_needs_shrink_to_fit = true; - - if (!m_active) { - activate(); - } - - if (target_rank <= stk::topology::ELEMENT_RANK) { - switch(m_direction) - { - case Lower: return add_helper(bucket_ordinal, to, ordinal, permutation, LowerConnectivityCompare()); - case Higher: return add_helper(bucket_ordinal, to, ordinal, permutation, HigherConnectivityCompare()); - case Adjacent: return add_helper(bucket_ordinal, to, ordinal, permutation, LowerConnectivityCompare()); // same comparing as lower - default: - ThrowAssertMsg(false, "What type of connectivity are you trying to add? " << m_direction); - return false; - } - } - else { - switch(m_direction) - { - case Lower: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_lower_connectivity_cmp); - case Higher: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_higher_connectivity_cmp); - case Adjacent: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_lower_connectivity_cmp); - default: - ThrowAssertMsg(false, "What type of connectivity are you trying to add? " << m_direction); - return false; - } - } - } - - bool remove_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) - { - impl::check_bucket_ordinal(bucket_ordinal, this); - - if (!m_active) return false; - - uint32_t found_idx = ~0u; - const uint32_t end_i = m_indices[bucket_ordinal]+m_num_connectivities[bucket_ordinal]; - for (uint32_t i = m_indices[bucket_ordinal]; i < end_i; ++i) - { - //remove connectivity - if ( m_targets[i] == to && m_ordinals[i] == ordinal ) { - found_idx = i; - --m_num_connectivities[bucket_ordinal]; - --m_total_connectivities; - break; - } - } - - //slide memory down - if (found_idx != ~0u) { - m_needs_shrink_to_fit = true; - for (uint32_t i = found_idx; i < end_i - 1; ++i) { - m_targets[i] = m_targets[i+1]; - m_ordinals[i] = m_ordinals[i+1]; - if (has_permutation()) { - m_permutations[i] = m_permutations[i+1]; - } - } - } - - return found_idx != ~0u; - } - - void begin_modification() - {} - - template - void end_modification(BULKDATA* mesh = NULL); - - void add_entity() - { - if (m_active) { - m_indices.push_back(m_targets.size()); - m_num_connectivities.push_back(0); - m_needs_shrink_to_fit = true; - } - else { - ++m_num_inactive; - } - } - - void remove_entity() - { - ThrowAssertMsg(size() > 0, "Cannot remove, connectivity is already empty"); - - if (m_active) { - m_indices.pop_back(); - m_total_connectivities -= m_num_connectivities.back(); - m_num_connectivities.pop_back(); - m_needs_shrink_to_fit = true; - } - else { - --m_num_inactive; - } - } - - void copy_entity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal=-1u) - { - ThrowAssert(m_from_rank == to.m_from_rank); - impl::check_bucket_ordinal(from_ordinal, this); - - if (to_ordinal == -1u) { - to_ordinal = to.size(); - to.add_entity(); - } - impl::check_bucket_ordinal(to_ordinal, &to); - - // Manage activation state - if (!m_active) { - if (to.m_active) { - to.m_total_connectivities -= to.m_num_connectivities[to_ordinal]; - to.m_num_connectivities[to_ordinal] = 0; - to.m_needs_shrink_to_fit = true; - } - return; - } - if (m_active && !to.m_active) { - to.activate(); - } - - // Copy data - if (&to == this) { - // easy - // note this implements swap semantics instead of copy, but this is necessary - // to avoid aliasing in certain situations when sorting Partitions - std::swap(m_indices[to_ordinal], m_indices[from_ordinal]); - std::swap(m_num_connectivities[to_ordinal], m_num_connectivities[from_ordinal]); - - m_needs_shrink_to_fit = true; - to.m_needs_shrink_to_fit = true; - } - else { - // much harder - const unsigned from_num = m_num_connectivities[from_ordinal]; - const unsigned to_num = to.m_num_connectivities[to_ordinal]; - const int delta_num = from_num - to_num; - if (delta_num > 0) { - // If adding additional connectivity, need to reserve space - to.add_connectivity_helper(to_ordinal, delta_num); - } - else { - to.m_num_connectivities[to_ordinal] = from_num; - to.m_total_connectivities += delta_num; - } - if (delta_num != 0) { - to.m_needs_shrink_to_fit = true; - } - copy_connectivity(from_ordinal, to, to_ordinal); - } - } - - void copy_to_fixed(unsigned from_ordinal, OtherType& to) - { - const unsigned num_conn_to_move = m_active ? m_num_connectivities[from_ordinal] : 0; - - ThrowAssert(OtherType::connectivity_type == FIXED_CONNECTIVITY); - ThrowAssertMsg(size() > 0, "Cannot move, connectivity is empty"); - ThrowAssertMsg(num_conn_to_move <= to.num_connectivity(666 /*any unsigned, doesn't matter*/), "Incompatible"); - - const unsigned to_offset = to.m_targets.size(); - to.add_entity(); // make room for new entity - - const unsigned from_offset = m_active ? m_indices[from_ordinal] : 0; - -#ifndef NDEBUG - // Check the ordinals are compatible with fixed connectivity - ConnectivityOrdinal const* ordinals = m_ordinals.data() + from_offset; - for (unsigned i = 0; i < num_conn_to_move; ++i) { - ThrowAssert(ordinals[i] == i); - } -#endif - - std::copy(m_targets.begin() + from_offset, - m_targets.begin() + from_offset + num_conn_to_move, - to.m_targets.begin() + to_offset); - - if (has_permutation()) { - std::copy(m_permutations.begin() + from_offset, - m_permutations.begin() + from_offset + num_conn_to_move, - to.m_permutations.begin() + to_offset); - } - } - - void copy_to_fixed(unsigned from_ordinal, SelfType& to) - { ThrowAssert(false); } - - bool has_permutation() const - { return does_rank_have_valid_permutations(TargetRank) && does_rank_have_valid_permutations(m_from_rank); } - - size_t heap_memory_in_bytes() const - { - return capacity_in_bytes(m_targets) - + capacity_in_bytes(m_ordinals) - + capacity_in_bytes(m_permutations); - } - - void debug_dump(std::ostream& out) const - { - out << "For dynamic connectivity to rank: " << TargetRank << ", with id: " << m_id << "\n"; - if (m_active) { - out << " size is: " << m_indices.size() << "\n"; - for (int i = 0, ie = m_indices.size(); i < ie; ++i) { - out << " At ordinal " << i << "\n"; - debug_dump(out, i, false); - } - out << std::endl; - } - else { - out << " size is: " << m_num_inactive << ", but inactive" << std::endl; - } - } - - void debug_dump(std::ostream& out, unsigned ordinal, bool add_context=true) const - { - if (m_active) { - int idx = m_indices[ordinal]; - int num = m_num_connectivities[ordinal]; - if (add_context) { - out << "For dynamic connectivity to rank: " << TargetRank << ", with id: " << m_id << "\n"; - } - out << " Index is: " << idx << ", Num is: " << num << "\n"; - for (int j = idx, je = idx + num; j < je; ++j) { - out << " (target:" << m_targets[j].local_offset() << ", ordinal:" << (uint32_t)m_ordinals[j] << ")\n"; - } - } - else { - out << " Index is: 0, Num is: 0\n"; - } - } - -private: - - bool does_rank_have_valid_permutations(stk::mesh::EntityRank rank) const - { - return rank > stk::topology::NODE_RANK && rank < stk::topology::CONSTRAINT_RANK; - } - - void copy_connectivity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal) - { - unsigned num_conn = m_num_connectivities[from_ordinal]; - unsigned to_offset = to.m_indices[to_ordinal]; - unsigned from_offset = m_indices[from_ordinal]; - ThrowAssert(to.m_num_connectivities[to_ordinal] == num_conn); - - std::copy(m_targets.begin() + from_offset, - m_targets.begin() + from_offset + num_conn, - to.m_targets.begin() + to_offset); - - std::copy(m_ordinals.begin() + from_offset, - m_ordinals.begin() + from_offset + num_conn, - to.m_ordinals.begin() + to_offset); - - if (has_permutation()) { - std::copy(m_permutations.begin() + from_offset, - m_permutations.begin() + from_offset + num_conn, - to.m_permutations.begin() + to_offset); - } - } - - static unsigned num_chunks(unsigned num) - { return (num + chunk_size -1)/chunk_size; } - - void activate() - { - ThrowAssert(!m_active); - - m_indices.resize(m_num_inactive, 0); - m_num_connectivities.resize(m_num_inactive, 0); - - m_active = true; - m_num_inactive = 0; - } - - template - void resize_and_order_by_index_helper(Vector & data, unsigned capacity, bool update_index = false) - { - Vector temp; - temp.reserve(capacity); - - uint32_t current_index=0; - for(size_t i=0, e=m_indices.size(); i 0 ? 2 * old_capacity : 8*chunk_size; - while (new_capacity < minimum_size) { - new_capacity *= 2; - } - return new_capacity; - } - - // The old capacity is at or above the threshold for being careful about growing - // the connectivity representation(and memory footprint). Only grow the capacity - // if compressing the representation will not yield sufficient unused capacity. - if (capacity_ratio * m_total_connectivities > old_capacity) - { - return 2 * old_capacity; - } - else - { - return old_capacity; - } - } - - void add_connectivity_helper(unsigned bucket_ordinal, unsigned num_to_add=1) - { - const unsigned chunks_needed_by_entity = num_chunks(m_num_connectivities[bucket_ordinal]+num_to_add); - const unsigned chunks_used_by_entity = num_chunks(m_num_connectivities[bucket_ordinal]); - - if (chunks_needed_by_entity == chunks_used_by_entity) - { - m_total_connectivities += num_to_add; - m_num_connectivities[bucket_ordinal] += num_to_add; - return; - } - - const unsigned chunks_available = num_chunks(m_targets.capacity() - m_targets.size()); - - if (chunks_available < chunks_needed_by_entity) - { - const unsigned new_capacity = compute_new_connectivity_capacity(m_targets.size() + chunks_needed_by_entity * chunk_size); - resize_and_order_by_index(new_capacity); - } - - const bool last_entity_by_index = (chunks_used_by_entity > 0) && - (m_indices[bucket_ordinal] + chunks_used_by_entity*chunk_size == m_targets.size()); - Entity invalid; - - //copy to end - if (!last_entity_by_index) - { - uint32_t new_index = static_cast(m_targets.size()); - - m_targets.insert(m_targets.end(), chunks_needed_by_entity*chunk_size, invalid); - std::copy(begin(bucket_ordinal), end(bucket_ordinal), m_targets.begin() + new_index); - - m_ordinals.insert(m_ordinals.end(), chunks_needed_by_entity*chunk_size, INVALID_CONNECTIVITY_ORDINAL); - std::copy(begin_ordinals(bucket_ordinal), end_ordinals(bucket_ordinal), m_ordinals.begin() + new_index); - - if (has_permutation()) { - m_permutations.insert(m_permutations.end(), chunks_needed_by_entity*chunk_size, INVALID_PERMUTATION); - std::copy(begin_permutations(bucket_ordinal), end_permutations(bucket_ordinal), m_permutations.begin() + new_index); - } - - m_indices[bucket_ordinal] = new_index; - } - //add new chunk to end - else { - const unsigned extra_chunks_needed = chunks_needed_by_entity - chunks_used_by_entity; - m_targets.insert(m_targets.end(), extra_chunks_needed*chunk_size, invalid); - m_ordinals.insert(m_ordinals.end(), extra_chunks_needed*chunk_size, INVALID_CONNECTIVITY_ORDINAL); - if (has_permutation()) { - m_permutations.insert(m_permutations.end(), extra_chunks_needed*chunk_size, INVALID_PERMUTATION); - } - } - - m_total_connectivities += num_to_add; - m_num_connectivities[bucket_ordinal] += num_to_add; - } - - template - bool add_helper(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation, - const ConnectivityComparator &compare) - { -#ifndef NDEBUG - // TODO - If downward conn, check to's rank and topology -#endif - bool rv = true; - - add_connectivity_helper(bucket_ordinal); - - const uint32_t begin_index = m_indices[bucket_ordinal] + m_num_connectivities[bucket_ordinal] - 1; - - if (m_num_connectivities[bucket_ordinal] == 1) { - m_targets[begin_index] = to; - m_ordinals[begin_index] = ordinal; - if (has_permutation()) { - m_permutations[begin_index] = permutation; - } - return true; - } - - for (uint32_t i = begin_index, e = m_indices[bucket_ordinal]; i > e; --i) - { - //slide up - if ( compare(to, ordinal, m_targets[i-1], m_ordinals[i-1u]) ) { - m_targets[i] = m_targets[i-1u]; - m_ordinals[i] = m_ordinals[i-1u]; - if (has_permutation()) { - m_permutations[i] = m_permutations[i-1u]; - } - //insert if on last iteration - if ((i-1)==e) { - m_targets[i-1u] = to; - m_ordinals[i-1u] = ordinal; - if (has_permutation()) { - m_permutations[i-1u] = permutation; - } - } - } - //insert - else if ( compare(m_targets[i-1], m_ordinals[i-1u], to, ordinal) ) { - m_targets[i] = to; - m_ordinals[i] = ordinal; - if (has_permutation()) { - m_permutations[i] = permutation; - } - break; - } - //duplicate -- insert new and remove the original - else - { - m_targets[i] = to; - m_ordinals[i] = ordinal; - if (has_permutation()) { - m_permutations[i] = permutation; - } - remove_connectivity(bucket_ordinal, to, ordinal); - rv = false; - break; - } - } - - return rv; - } - - // Illegal - BucketConnectivity(const SelfType&); - SelfType& operator=(const SelfType&); - - // MEMBERS - - EntityRank m_from_rank; - connectivity_direction m_direction; - - bool m_active; // In many cases, uses will not make use of dynamic connectivity, so don't even waste the memory unless it looks like they want it - bool m_needs_shrink_to_fit; // True if this object potentially has partially full vectors or out-of-order entities - unsigned m_num_inactive; - - // meta data - UInt32Vector m_indices; // Common index into vectors below that stores where connectivity starts for a partition_offset (entity). - UInt32Vector m_num_connectivities; - unsigned m_total_connectivities; - - // connectivity data - EntityVector m_targets; - ConnectivityOrdinalVector m_ordinals; - PermutationVector m_permutations; - - BulkData * m_bulk_data; - int m_id; - - impl::HigherConnectivityRankSensitiveCompare m_rank_sensitive_higher_connectivity_cmp; - impl::LowerConnectivitityRankSensitiveCompare m_rank_sensitive_lower_connectivity_cmp; - - size_t m_last_capacity; - - size_t m_data_idx; -}; - -} - -// -// BucketConnectivity -// - -template -template // hack to get around dependency -inline -void impl::BucketConnectivity::end_modification(BULKDATA* mesh) -{ - //TODO: If bucket is blocked, no longer need to shrink to fit! - - if (m_targets.size() < m_targets.capacity()) { - - { - EntityVector temp(m_targets.begin(), m_targets.end()); - m_targets.swap(temp); - } - - { - PermutationVector temp(m_permutations.begin(), m_permutations.end()); - m_permutations.swap(temp); - } - } - -} - -template -template -inline -void impl::BucketConnectivity::end_modification(BULKDATA* mesh) -{ - if (m_active && m_needs_shrink_to_fit) { - resize_and_order_by_index(); - - { - UInt32Vector temp(m_indices.begin(), m_indices.end()); - m_indices.swap(temp); - } - - { - UInt32Vector temp(m_num_connectivities.begin(), m_num_connectivities.end()); - m_num_connectivities.swap(temp); - } - - m_needs_shrink_to_fit = false; - } -} - -template -inline -bool impl::LowerConnectivitityRankSensitiveCompare::operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, - Entity second_entity, ConnectivityOrdinal second_ordinal) const -{ - const EntityRank first_rank = m_mesh.entity_rank(first_entity); - const EntityRank second_rank = m_mesh.entity_rank(second_entity); - - return (first_rank < second_rank) - || ((first_rank == second_rank) && (first_ordinal < second_ordinal)); -} - -template -inline -bool impl::HigherConnectivityRankSensitiveCompare::operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const -{ - const EntityRank first_rank = m_mesh.entity_rank(first_entity); - const EntityRank second_rank = m_mesh.entity_rank(second_entity); - - if (first_rank < second_rank) { - return true; - } - if (first_rank > second_rank) { - return false; - } - // Needs to match LessRelation in BulkData.hpp - return std::make_pair(first_ordinal, first_entity.is_local_offset_valid() ? first_entity.local_offset() : Entity::MaxEntity) < - std::make_pair(second_ordinal, second_entity.is_local_offset_valid() ? second_entity.local_offset() : Entity::MaxEntity); -} - - - - - -}} //namespace stk::mesh::impl - -#endif diff --git a/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp b/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp index 614bd2e82048..94a407d97780 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp @@ -100,10 +100,6 @@ namespace stk { namespace mesh { -namespace impl { -int Counter::counter = 0; -} - // Static constant on BulkData: const uint16_t BulkData::orphaned_node_marking = 25000; @@ -376,6 +372,7 @@ BulkData::BulkData(MetaData & mesh_meta_data, *this, mesh_meta_data.entity_rank_count(), bucket_capacity), + m_sparse_connectivity(mesh_meta_data.entity_rank_count()), m_use_identifiers_for_resolving_sharing(false), m_modSummary(*this), m_meshDiagnosticObserver(std::make_shared(*this)), @@ -528,7 +525,7 @@ void BulkData::require_entity_owner( const Entity entity , void BulkData::require_good_rank_and_id(EntityRank ent_rank, EntityId ent_id) const { - const EntityRank rank_count = static_cast(m_mesh_meta_data.entity_rank_count()); + const EntityRank rank_count = m_mesh_meta_data.entity_rank_count(); const bool ok_id = EntityKey::is_valid_id(ent_id); const bool ok_rank = ent_rank < rank_count && !(ent_rank == stk::topology::FACE_RANK && mesh_meta_data().spatial_dimension() == 2); @@ -552,13 +549,11 @@ void BulkData::mark_entity_and_upward_related_entities_as_modified(Entity entity size_t BulkData::count_relations(Entity entity) const { - const MeshIndex &mesh_idx = mesh_index(entity); - const EntityRank end_rank = static_cast(m_mesh_meta_data.entity_rank_count()); size_t count = 0; for (EntityRank irank = stk::topology::BEGIN_RANK; irank < end_rank; ++irank) { - count += mesh_idx.bucket->num_connectivity(mesh_idx.bucket_ordinal, irank); + count += num_connectivity(entity, irank); } return count; } @@ -611,6 +606,7 @@ Entity BulkData::generate_new_entity(unsigned preferred_offset) } else if (!m_deleted_entities.empty()) { new_local_offset = m_deleted_entities.front(); + m_sparse_connectivity.get_connectivity(Entity(new_local_offset)).clear(); m_deleted_entities.pop_front(); } @@ -626,6 +622,7 @@ Entity BulkData::generate_new_entity(unsigned preferred_offset) m_mark_entity.push_back(NOT_MARKED); m_closure_count.push_back(static_cast(0)); m_local_ids.push_back(stk::mesh::GetInvalidLocalId()); + m_sparse_connectivity.update_size_of_entity_index_space(m_mesh_indexes.size()); #ifdef SIERRA_MIGRATION if (m_add_fmwk_data) { @@ -799,6 +796,7 @@ PARTVECTOR add_root_topology_part(const PARTVECTOR &parts, stk::mesh::Part &root PARTVECTOR initialParts(parts.size() + 1); initialParts = parts; initialParts.push_back(&rootTopoPart); + stk::util::sort_and_unique(initialParts, PartLess()); return initialParts; } @@ -1634,10 +1632,12 @@ void BulkData::comm_procs( EntityKey key, std::vector & procs ) const void BulkData::comm_procs(Entity entity, std::vector & procs ) const { + procs.clear(); ThrowAssertMsg(is_valid(entity), "BulkData::comm_procs ERROR, input entity "<comm_map), procs); + } } void BulkData::comm_shared_procs(EntityKey key, std::vector & procs ) const @@ -2299,7 +2299,7 @@ void BulkData::internal_declare_relation( Entity entity , { require_ok_to_modify(); - stk::mesh::EntityRank erank = entity_rank(entity); + stk::mesh::EntityRank entityRank = entity_rank(entity); OrdinalVector scratch2, scratch3; @@ -2308,14 +2308,15 @@ void BulkData::internal_declare_relation( Entity entity , Entity e = i->entity(); const unsigned n = i->relation_ordinal(); const Permutation permut = i->getPermutation(); - if ( entity_rank(e) < erank ) { + const EntityRank eRank = entity_rank(e); + if ( eRank < entityRank ) { internal_declare_relation( entity , e , n, permut, ordinal_scratch, scratch2, scratch3); } - else if ( erank < entity_rank(e) ) { + else if ( entityRank < eRank ) { internal_declare_relation( e , entity , n, permut, ordinal_scratch, scratch2, scratch3); } else { - ThrowErrorMsg("declare_relation given entities of the same entity rank ("< " < ghostStatus(get_size_of_entity_index_space(), false); + m_entity_repo->clear_all_cache(); + stk::mesh::impl::comm_sync_aura_send_recv(*this, add_send, entityProcMapping, ghostStatus ); @@ -3664,25 +3667,22 @@ void BulkData::fill_list_of_entities_to_send_for_aura_ghosting(EntityProcMapping // Iterate over all shared entities, ensure that upwardly related // entities to each shared entity will be ghosted to the sharing proc. Selector shared = mesh_meta_data().globally_shared_part(); + const SparseConnectivity& sparseConnectivity = m_sparse_connectivity; std::vector sharingProcs; impl::for_each_selected_entity_run_no_threads(*this, stk::topology::NODE_RANK, shared, - [&sendAuraEntityProcs, &entitySharing, &sharingProcs, &end_rank] + [&sendAuraEntityProcs, &sparseConnectivity, &entitySharing, &sharingProcs, &end_rank] (const BulkData& bulk, const MeshIndex& meshIndex) { const Bucket& bucket = *meshIndex.bucket; const unsigned bucketOrd = meshIndex.bucket_ordinal; - const EntityRank nextHigherRank = stk::topology::EDGE_RANK; + const Connectivity& connObject = sparseConnectivity.get_connectivity(bucket[bucketOrd]); bulk.comm_shared_procs(bucket[bucketOrd], sharingProcs); - for (const int sharingProc : sharingProcs) { - - for (EntityRank higherRank = nextHigherRank; higherRank < end_rank; ++higherRank) { - const unsigned num_rels = bucket.num_connectivity(bucketOrd, higherRank); - const Entity* rels = bucket.begin(bucketOrd, higherRank); - - for (unsigned r = 0; r < num_rels; ++r) { - stk::mesh::impl::insert_upward_relations(bulk, entitySharing, rels[r], stk::topology::NODE_RANK, sharingProc, sendAuraEntityProcs); - } + PairIterEntity conn = connObject.get_connectivity(stk::topology::EDGE_RANK, end_rank); + for (Entity relEntity : conn) { + const Connectivity& relConnectivity = sparseConnectivity.get_connectivity(relEntity); + for (const int sharingProc : sharingProcs) { + stk::mesh::impl::insert_upward_relations(bulk, relConnectivity, entitySharing, relEntity, sharingProc, sendAuraEntityProcs); } } } @@ -3881,7 +3881,7 @@ void BulkData::change_connectivity_for_edge_or_face(stk::mesh::Entity side, cons if(bucket(elements[i]).owned()) { stk::mesh::Bucket& bucket_edge = bucket(side); - bucket_edge.change_existing_connectivity(bucket_ordinal(side), nodes.data()); + bucket_edge.change_connected_nodes(bucket_ordinal(side), nodes.data()); stk::mesh::Permutation new_permutation = get_permutation(*this, elements[i], nodes); ThrowRequireWithSierraHelpMsg(new_permutation!=stk::mesh::INVALID_PERMUTATION); @@ -4685,7 +4685,7 @@ void BulkData::internal_finish_modification_end(ModEndOptimizationFlag opt) m_bucket_repository.internal_default_sort_bucket_entities(should_sort_faces_by_node_ids()); } - m_bucket_repository.internal_modification_end(); + m_bucket_repository.sync_from_partitions(); m_meshModification.set_sync_state_synchronized(); m_add_node_sharing_called = false; @@ -5083,12 +5083,8 @@ void BulkData::internal_update_all_sharing_procs() const EntityCommListInfoVector& all_comm = m_entity_comm_list; for (const EntityCommListInfo& info : all_comm) { - const Entity entity = info.entity; - const Bucket& bkt = bucket(entity); - - if (bkt.shared() && info.entity_comm != nullptr) { - const EntityRank rank = bkt.entity_rank(); - + if (info.entity_comm != nullptr && info.entity_comm->isShared) { + const EntityRank rank = info.key.rank(); const EntityCommInfoVector& commInfo = info.entity_comm->comm_map; const unsigned len = commInfo.size(); unsigned i = 0; @@ -6359,7 +6355,7 @@ void BulkData::sort_entities(const stk::mesh::EntitySorterBase& sorter) ThrowRequireMsg(in_synchronized_state(), "Error, sort_entities cannot be called from inside a modification cycle."); m_bucket_repository.internal_custom_sort_bucket_entities(sorter); - m_bucket_repository.internal_modification_end(); + m_bucket_repository.sync_from_partitions(); if(parallel_size() > 1) check_mesh_consistency(); diff --git a/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp b/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp index 4976764cea06..bd73f2e42267 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp @@ -62,6 +62,7 @@ #include "stk_mesh/base/Bucket.hpp" // for Bucket #include "stk_mesh/base/EntityKey.hpp" // for EntityKey, hash_value #include "stk_mesh/base/FieldDataManager.hpp" +#include "stk_mesh/base/SparseConnectivity.hpp" #include "stk_mesh/base/Relation.hpp" // for Relation, etc #include "stk_topology/topology.hpp" // for topology, etc #include "stk_util/util/ReportHandler.hpp" // for ThrowAssert, etc @@ -869,6 +870,9 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu void set_large_ids_flag(bool largeIds) { m_supportsLargeIds = largeIds; } protected: //functions + SparseConnectivity& get_sparse_connectivity() { return m_sparse_connectivity; } + const SparseConnectivity& get_sparse_connectivity() const { return m_sparse_connectivity; } + Entity declare_entity( EntityRank ent_rank , EntityId ent_id);// Mod Mark @@ -1581,6 +1585,7 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu FieldDataManager *m_field_data_manager; mutable std::vector m_selector_to_buckets_maps; impl::BucketRepository m_bucket_repository; // needs to be destructed first! + SparseConnectivity m_sparse_connectivity; bool m_use_identifiers_for_resolving_sharing; std::string m_lastModificationDescription; stk::EmptyModificationSummary m_modSummary; @@ -1604,9 +1609,11 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu inline unsigned BulkData::num_connectivity(Entity entity, EntityRank rank) const { - ThrowAssert(bucket_ptr(entity)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->num_connectivity(mesh_idx.bucket_ordinal, rank); + if (rank == stk::topology::NODE_RANK) { + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket==nullptr ? 0 : mesh_idx.bucket->num_nodes(mesh_idx.bucket_ordinal); + } + return m_sparse_connectivity.num_connectivity(entity, rank); } inline unsigned @@ -1631,8 +1638,11 @@ inline Entity const* BulkData::begin(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin(mesh_idx.bucket_ordinal, rank); + if (rank == stk::topology::NODE_RANK) { + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_nodes(mesh_idx.bucket_ordinal); + } + return m_sparse_connectivity.begin_connectivity(entity, rank); } inline Entity const* @@ -1643,28 +1653,25 @@ BulkData::begin_nodes(Entity entity) const return mesh_idx.bucket->begin_nodes(mesh_idx.bucket_ordinal); } -inline Entity const* -BulkData::begin_edges(Entity entity) const +inline +Entity const* BulkData::begin_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_edges(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_connectivity(entity, stk::topology::EDGE_RANK); } -inline Entity const* -BulkData::begin_faces(Entity entity) const +inline +Entity const* BulkData::begin_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_faces(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_connectivity(entity, stk::topology::FACE_RANK); } -inline Entity const* -BulkData::begin_elements(Entity entity) const +inline +Entity const* BulkData::begin_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_elements(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_connectivity(entity, stk::topology::ELEM_RANK); } inline ConnectivityOrdinal const* @@ -1683,68 +1690,60 @@ BulkData::begin_node_ordinals(Entity entity) const return mesh_idx.bucket->begin_node_ordinals(mesh_idx.bucket_ordinal); } -inline ConnectivityOrdinal const* -BulkData::begin_edge_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::begin_edge_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_edge_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_ordinals(entity, stk::topology::EDGE_RANK); } -inline ConnectivityOrdinal const* -BulkData::begin_face_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::begin_face_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_face_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_ordinals(entity, stk::topology::FACE_RANK); } -inline ConnectivityOrdinal const* -BulkData::begin_element_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::begin_element_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_element_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_ordinals(entity, stk::topology::ELEM_RANK); } inline Permutation const* BulkData::begin_permutations(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_permutations(mesh_idx.bucket_ordinal, rank); + return m_sparse_connectivity.begin_permutations(entity, rank); } -inline Permutation const* -BulkData::begin_node_permutations(Entity entity) const +inline +Permutation const* BulkData::begin_node_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::NODE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_node_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_permutations(entity, stk::topology::NODE_RANK); } -inline Permutation const* -BulkData::begin_edge_permutations(Entity entity) const +inline +Permutation const* BulkData::begin_edge_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_edge_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_permutations(entity, stk::topology::EDGE_RANK); } -inline Permutation const* -BulkData::begin_face_permutations(Entity entity) const +inline +Permutation const* BulkData::begin_face_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_face_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_permutations(entity, stk::topology::FACE_RANK); } -inline Permutation const* -BulkData::begin_element_permutations(Entity entity) const +inline +Permutation const* BulkData::begin_element_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_element_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.begin_permutations(entity, stk::topology::ELEM_RANK); } inline unsigned @@ -1755,36 +1754,36 @@ BulkData::num_nodes(Entity entity) const return mesh_idx.bucket->num_nodes(mesh_idx.bucket_ordinal); } -inline unsigned -BulkData::num_edges(Entity entity) const +inline +unsigned BulkData::num_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->num_edges(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.num_connectivity(entity, stk::topology::EDGE_RANK); } -inline unsigned -BulkData::num_faces(Entity entity) const +inline +unsigned BulkData::num_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->num_faces(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.num_connectivity(entity, stk::topology::FACE_RANK); } -inline unsigned -BulkData::num_elements(Entity entity) const +inline +unsigned BulkData::num_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->num_elements(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.num_connectivity(entity, stk::topology::ELEM_RANK); } inline Entity const* BulkData::end(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end(mesh_idx.bucket_ordinal, rank); + if (rank == stk::topology::NODE_RANK) { + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_nodes(mesh_idx.bucket_ordinal); + } + return m_sparse_connectivity.end_connectivity(entity, rank); } inline Entity const* @@ -1795,28 +1794,25 @@ BulkData::end_nodes(Entity entity) const return mesh_idx.bucket->end_nodes(mesh_idx.bucket_ordinal); } -inline Entity const* -BulkData::end_edges(Entity entity) const +inline +Entity const* BulkData::end_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_edges(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_connectivity(entity, stk::topology::EDGE_RANK); } -inline Entity const* -BulkData::end_faces(Entity entity) const +inline +Entity const* BulkData::end_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_faces(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_connectivity(entity, stk::topology::FACE_RANK); } -inline Entity const* -BulkData::end_elements(Entity entity) const +inline +Entity const* BulkData::end_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_elements(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_connectivity(entity, stk::topology::ELEMENT_RANK); } inline ConnectivityOrdinal const* @@ -1835,75 +1831,67 @@ BulkData::end_node_ordinals(Entity entity) const return mesh_idx.bucket->end_node_ordinals(mesh_idx.bucket_ordinal); } -inline ConnectivityOrdinal const* -BulkData::end_edge_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::end_edge_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_edge_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_ordinals(entity, stk::topology::EDGE_RANK); } -inline ConnectivityOrdinal const* -BulkData::end_face_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::end_face_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_face_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_ordinals(entity, stk::topology::FACE_RANK); } -inline ConnectivityOrdinal const* -BulkData::end_element_ordinals(Entity entity) const +inline +ConnectivityOrdinal const* BulkData::end_element_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_element_ordinals(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_ordinals(entity, stk::topology::ELEM_RANK); } -inline Permutation const* -BulkData::end_permutations(Entity entity, EntityRank rank) const +inline +Permutation const* BulkData::end_permutations(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_permutations(mesh_idx.bucket_ordinal, rank); + return m_sparse_connectivity.end_permutations(entity, rank); } -inline Permutation const* -BulkData::end_node_permutations(Entity entity) const +inline +Permutation const* BulkData::end_node_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::NODE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_node_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_permutations(entity, stk::topology::NODE_RANK); } -inline Permutation const* -BulkData::end_edge_permutations(Entity entity) const +inline +Permutation const* BulkData::end_edge_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_edge_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_permutations(entity, stk::topology::EDGE_RANK); } -inline Permutation const* -BulkData::end_face_permutations(Entity entity) const +inline +Permutation const* BulkData::end_face_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_face_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_permutations(entity, stk::topology::FACE_RANK); } -inline Permutation const* -BulkData::end_element_permutations(Entity entity) const +inline +Permutation const* BulkData::end_element_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_element_permutations(mesh_idx.bucket_ordinal); + return m_sparse_connectivity.end_permutations(entity, stk::topology::ELEM_RANK); } -inline bool -BulkData::has_permutation(Entity entity, EntityRank rank) const +inline +bool BulkData::has_permutation(Entity entity, EntityRank rank) const { ThrowAssert(bucket_ptr(entity)); - return bucket(entity).has_permutation(rank); + return m_sparse_connectivity.has_permutation(entity_rank(entity), rank); } inline bool @@ -1930,13 +1918,16 @@ BulkData::in_receive_ghost( EntityKey key ) const inline bool BulkData::in_receive_ghost( Entity entity ) const { - const std::vector & ghosts= ghostings(); - for (size_t i=ghosts.size()-1;i>=AURA;--i) - { - if ( in_receive_ghost(*ghosts[i], entity) ) - return true; + if (m_entitycomm[entity.local_offset()] == nullptr) { + return false; } - return false; + + const int owner_rank = parallel_owner_rank(entity); + if (owner_rank == parallel_rank()) { + return false; + } + + return m_entitycomm[entity.local_offset()]->isGhost; } inline bool diff --git a/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp b/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp new file mode 100644 index 000000000000..2f7fb3dd4c58 --- /dev/null +++ b/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp @@ -0,0 +1,115 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#ifndef STK_MESH_CONNECTED_SPARSE_NODES_HPP +#define STK_MESH_CONNECTED_SPARSE_NODES_HPP + +#include +#include +#include +#include +#include + +namespace stk { +namespace mesh { + +class ConnectedSparseNodes { +public: + ConnectedSparseNodes(SparseConnectivity& sparseConnectivity, + EntityRank fromRank, + const EntityVector& fromEntities) + : m_sparseConnectivity(sparseConnectivity), + m_fromEntities(fromEntities), + m_fromRank(fromRank) + {} + + ~ConnectedSparseNodes(){} + + unsigned num_nodes_per_entity(unsigned fromEntity) const + { return m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } + + const Entity* begin_connectivity(unsigned fromEntity) const + { return m_sparseConnectivity.begin_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } + + const Entity* end_connectivity(unsigned fromEntity) const + { return m_sparseConnectivity.end_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } + + const ConnectivityOrdinal* begin_ordinals(unsigned fromEntity) const + { return m_sparseConnectivity.begin_ordinals(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } + + const ConnectivityOrdinal* end_ordinals(unsigned fromEntity) const + { return m_sparseConnectivity.end_ordinals(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } + + bool set_connected_node(unsigned fromEntity, Entity connectedNode, ConnectivityOrdinal ordinal) + { + if (connectedNode.local_offset() > 0) { + return m_sparseConnectivity.add_connectivity(m_fromRank, m_fromEntities[fromEntity], + stk::topology::NODE_RANK, connectedNode, ordinal, + INVALID_PERMUTATION); + } + else { + const unsigned numBefore = m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); + bool returnVal = m_sparseConnectivity.remove_connectivity(m_fromRank, m_fromEntities[fromEntity], + stk::topology::NODE_RANK, connectedNode, ordinal); + const unsigned numAfter = m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); + ThrowRequireMsg((numBefore==0 && numAfter==0) || (numBefore>0 && numAfter==numBefore-1),"remove didn't work"); + return returnVal; + } + } + + bool reset_connected_node(unsigned fromEntity, Entity connectedNode, ConnectivityOrdinal ordinal) + { + return m_sparseConnectivity.replace_or_add_connectivity(m_fromRank, m_fromEntities[fromEntity], + stk::topology::NODE_RANK, connectedNode, ordinal); + } + + void reset_connected_nodes(unsigned fromEntity, unsigned numNodes, const Entity* connectedNodes) + { + for(unsigned i=0; i +#include // for EntityRank, ConnectivityOrdinal, EntityVector +#include +#include + +namespace stk { +namespace mesh { + +class ConnectedTopologyNodes { +public: + ConnectedTopologyNodes(stk::topology fromTopology, const EntityVector& fromEntities) + : m_connectedNodes(fromTopology.num_nodes()*fromEntities.size(), Entity()), + m_ordinals(fromTopology.num_nodes()), + m_numNodesPerEntity(fromTopology.num_nodes()) + { + for (unsigned n=0; n m_ordinals; + unsigned m_numNodesPerEntity; +}; + +} // namespace mesh +} // namespace stk + +#endif //STK_MESH_CONNECTED_TOPOLOGY_NODES_HPP + diff --git a/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp b/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp new file mode 100644 index 000000000000..790ebf1bcb12 --- /dev/null +++ b/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp @@ -0,0 +1,250 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include +#include +#include + +namespace stk { +namespace mesh { + +Connectivity::Connectivity() + : m_connectivity(nullptr), + m_offsetsAndOrdinals(nullptr) +{ + m_offsetsAndOrdinals = new ConnectivityOrdinal[m_capacityIndex + 1]; + for(unsigned i=0; i +#include // for EntityRank +#include +#include +#include + +namespace stk { +namespace mesh { + +class Connectivity { +public: + Connectivity(); + + static constexpr uint16_t MAX_NUM_RANKS = stk::topology::NUM_RANKS+1; + + Connectivity(const Connectivity& rhs) + : m_connectivity(nullptr), + m_offsetsAndOrdinals(nullptr) + { + *this = rhs; + } + + Connectivity(Connectivity && rhs) noexcept + : m_connectivity(nullptr), + m_offsetsAndOrdinals(nullptr) + { + *this = std::move(rhs); + } + + Connectivity& operator=(const Connectivity& rhs) + { + delete [] m_connectivity; + delete [] m_offsetsAndOrdinals; + + unsigned capacity = rhs.get_capacity(); + if (capacity > 0) { + m_connectivity = new Entity[capacity]; + } + + m_offsetsAndOrdinals = new ConnectivityOrdinal[m_firstOrdinalIndex + capacity]; + for(unsigned i=0; i("needSyncToDevice"); - const int maxStates = static_cast(MaximumFieldStates); for (int s=0; sclear_sync_state(); + } + + void clear_host_sync_state() override + { + hostField->clear_host_sync_state(); + } + + void clear_device_sync_state() override + { + hostField->clear_device_sync_state(); } void sync_to_host() override @@ -390,21 +395,20 @@ class DeviceField : public NgpFieldBase void swap(DeviceField &other) { swap_views(deviceData, other.deviceData); - swap_views(needSyncToHost, other.needSyncToHost); - swap_views(needSyncToDevice, other.needSyncToDevice); } -protected: - bool need_sync_to_host() const + bool need_sync_to_host() const override { - return needSyncToHost(); + return hostField->need_sync_to_host(); } - bool need_sync_to_device() const + bool need_sync_to_device() const override { - return needSyncToDevice(); + return hostField->need_sync_to_device(); } +protected: + void debug_modification_begin() override { fieldSyncDebugger.detect_device_field_modification(this); @@ -427,24 +431,17 @@ class DeviceField : public NgpFieldBase void set_modify_on_host() { -#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK - ThrowRequireMsg(needSyncToHost() == false, "field " << hostField->name()); -#endif - needSyncToDevice() = true; + hostField->modify_on_host(); } void set_modify_on_device() { -#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK - ThrowRequireMsg(needSyncToDevice() == false, "field " << hostField->name()); -#endif - needSyncToHost() = true; + hostField->modify_on_device(); } void clear_sync_state_flags() { - needSyncToHost() = false; - needSyncToDevice() = false; + hostField->clear_sync_state(); } void construct_view(const BucketVector& buckets, const std::string& name, unsigned numPerEntity) @@ -661,7 +658,7 @@ class DeviceField : public NgpFieldBase { if (hostField) { impl::transpose_to_pinned_and_mapped_memory(asyncCopyState.execSpace, *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); - clear_sync_state_flags(); + clear_device_sync_state(); hostField->increment_num_syncs_to_host(); } } @@ -679,16 +676,14 @@ class DeviceField : public NgpFieldBase { if (hostField) { impl::transpose_from_pinned_and_mapped_memory(asyncCopyState.execSpace, *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); - clear_sync_state_flags(); + clear_host_sync_state(); hostField->increment_num_syncs_to_device(); } } void internal_sync_to_device() { - bool needToSyncToDevice = need_sync_to_device(); - - if (needToSyncToDevice) { + if (need_sync_to_device()) { ProfilingBlock prof("copy_to_device for " + hostField->name()); if(hostBulk->synchronized_count() != synchronizedCount) { update_field(); @@ -721,9 +716,6 @@ class DeviceField : public NgpFieldBase FieldDataPointerHostViewType hostBucketPtrData; FieldDataPointerDeviceViewType deviceBucketPtrData; - Kokkos::View needSyncToHost; - Kokkos::View needSyncToDevice; - typename UnsignedViewType::HostMirror hostSelectedBucketOffset; UnsignedViewType deviceSelectedBucketOffset; typename UnsignedViewType::HostMirror newHostSelectedBucketOffset; diff --git a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp index d876b846dfeb..6481f55e257c 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp @@ -47,18 +47,30 @@ void DeviceBucket::initialize_bucket_attributes(const stk::mesh::Bucket &bucket) void DeviceBucket::allocate(const stk::mesh::Bucket &bucket) { - unsigned numNodesPerEntity = bucket.topology().num_nodes(); + nodeOffsets = OrdinalViewType(Kokkos::view_alloc(Kokkos::WithoutInitializing, "NodeOffsets"), bucket.size()+1); + hostNodeOffsets = Kokkos::create_mirror_view(Kokkos::HostSpace(), nodeOffsets, Kokkos::WithoutInitializing); + + unsigned maxNodesPerEntity = bucketTopology.num_nodes(); + unsigned totalNumNodes = bucketTopology.num_nodes()*bucketCapacity; + if (bucket.topology() == stk::topology::INVALID_TOPOLOGY) { + maxNodesPerEntity = 0; + totalNumNodes = 0; + for(unsigned i=0; i(numNodesPerEntity)); + static_cast(maxNodesPerEntity)); hostNodeOrdinals = Kokkos::create_mirror_view(Kokkos::HostSpace(), nodeOrdinals, Kokkos::WithoutInitializing); partOrdinals = PartOrdinalViewType(Kokkos::view_alloc(Kokkos::WithoutInitializing, "PartOrdinals"), parts.size()); @@ -67,8 +79,15 @@ void DeviceBucket::allocate(const stk::mesh::Bucket &bucket) void DeviceBucket::initialize_from_host(const stk::mesh::Bucket &bucket) { - unsigned numNodesPerEntity = bucket.topology().num_nodes(); - for (unsigned i = 0; i < numNodesPerEntity; ++i) { + unsigned maxNodesPerEntity = bucket.topology().num_nodes(); + if (bucket.topology() == stk::topology::INVALID_TOPOLOGY) { + maxNodesPerEntity = 0; + for(unsigned i=0; i(i); } Kokkos::deep_copy(nodeOrdinals, hostNodeOrdinals); @@ -85,17 +104,55 @@ void DeviceBucket::initialize_from_host(const stk::mesh::Bucket &bucket) void DeviceBucket::update_from_host(const stk::mesh::Bucket &bucket) { bucketSize = bucket.size(); - unsigned nodesPerElem = bucket.topology().num_nodes(); + + if (bucketSize+1 != hostNodeOffsets.size()) { + nodeOffsets = OrdinalViewType(Kokkos::view_alloc(Kokkos::WithoutInitializing, "NodeOffsets"), bucketSize+1); + hostNodeOffsets = Kokkos::create_mirror_view(Kokkos::HostSpace(), nodeOffsets, Kokkos::WithoutInitializing); + } + + unsigned totalNumNodes = bucket.topology().num_nodes()*bucketCapacity; + unsigned maxNodesPerEntity = bucket.topology().num_nodes(); + if (bucket.topology() == stk::topology::INVALID_TOPOLOGY) { + totalNumNodes = 0; + maxNodesPerEntity = 0; + for(unsigned i=0; i(maxNodesPerEntity)); + hostNodeOrdinals = Kokkos::create_mirror_view(Kokkos::HostSpace(), nodeOrdinals, Kokkos::WithoutInitializing); + for (unsigned i = 0; i < maxNodesPerEntity; ++i) { + hostNodeOrdinals(i) = static_cast(i); + } + Kokkos::deep_copy(nodeOrdinals, hostNodeOrdinals); + } + + unsigned nodeOffset = 0; for (unsigned iEntity = 0; iEntity < bucket.size(); ++iEntity) { stk::mesh::Entity entity = bucket[iEntity]; hostEntities(iEntity) = entity; + const unsigned nodesPerEntity = bucket.num_nodes(iEntity); const stk::mesh::Entity * elemNodes = bucket.begin_nodes(iEntity); - for (unsigned iNode = 0; iNode < nodesPerElem; ++iNode) { - hostNodeConnectivity(iEntity, iNode) = elemNodes[iNode]; + for (unsigned iNode = 0; iNode < nodesPerEntity; ++iNode) { + hostNodeConnectivity(nodeOffset + iNode) = elemNodes[iNode]; } + hostNodeOffsets(iEntity) = nodeOffset; + nodeOffset += nodesPerEntity; } + hostNodeOffsets(bucket.size()) = nodeOffset; + Kokkos::deep_copy(entities, hostEntities); Kokkos::deep_copy(nodeConnectivity, hostNodeConnectivity); + Kokkos::deep_copy(nodeOffsets, hostNodeOffsets); } void DeviceMesh::update_mesh() @@ -273,13 +330,13 @@ void DeviceMesh::fill_sparse_connectivities(const stk::mesh::BulkData& bulk_in) for(stk::mesh::EntityRank connectedRank=stk::topology::EDGE_RANK; connectedRank( static_cast(arg_rank) << RANK_SHIFT | arg_id) ) { - NGP_ThrowAssertMsg( arg_rank <= static_cast(255), "Error: given an out of range entity rank"); - NGP_ThrowAssertMsg( arg_id <= MAX_ID, "Error: given an out of range entity id"); + NGP_ThrowAssertMsg((arg_rank >= stk::topology::BEGIN_RANK) && (arg_rank < stk::topology::INVALID_RANK), + "Error: given an out of range entity rank"); + NGP_ThrowAssertMsg(arg_id <= MAX_ID, "Error: given an out of range entity id"); } KOKKOS_FUNCTION diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldBLAS.hpp b/packages/stk/stk_mesh/stk_mesh/base/FieldBLAS.hpp index 0134cf525ccf..a678e8ffb33b 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldBLAS.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldBLAS.hpp @@ -939,6 +939,26 @@ void field_fill(const Scalar alpha, const FieldBase& xField, const Selector& sel unfix_omp_threads(orig_thread_count); } +template +inline +void field_fill(const Scalar alpha, const std::vector& xFields, const Selector& selector) +{ + ThrowAssert(xFields.size() >= 1 ); + + stk::mesh::EntityRank fieldEntityRank = xFields[0]->entity_rank(); + BucketVector const& buckets = xFields[0]->get_mesh().get_buckets(fieldEntityRank,selector); + + for (auto&& bucket : buckets){ + for (unsigned int i=0; i(xField) ); + ThrowAssert(fieldEntityRank == xField.entity_rank()); + BucketSpan x(xField, *bucket); + FortranBLAS::fill(x.size(),alpha,x.data()); + } + } +} + template inline void field_fill(const Scalar alpha, const FieldBase& xField) @@ -947,6 +967,14 @@ void field_fill(const Scalar alpha, const FieldBase& xField) field_fill(alpha,xField,selector); } +template +inline +void field_fill(const Scalar alpha, const std::vector& xFields) +{ + const Selector selector = selectField(*xFields[0]); + field_fill(alpha,xFields,selector); +} + template inline void INTERNAL_field_swap(const FieldBase& xField, const FieldBase& yField, const Selector& selector) diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldBase.cpp b/packages/stk/stk_mesh/stk_mesh/base/FieldBase.cpp index 72c551db680e..e452658267a8 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldBase.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldBase.cpp @@ -342,7 +342,7 @@ unsigned FieldBase::max_size( EntityRank ent_rank) const { unsigned max = 0 ; - if(static_cast(entity_rank()) == ent_rank) + if (entity_rank() == ent_rank) { const FieldRestrictionVector & rMap = restrictions(); const FieldRestrictionVector::const_iterator ie = rMap.end() ; @@ -367,6 +367,12 @@ void FieldBase::rotate_multistate_data() for (unsigned s = 1; s < numStates; ++s) { FieldBase* sField = field_state(static_cast(s)); m_field_meta_data.swap(sField->m_field_meta_data); + + std::swap(m_numSyncsToDevice, sField->m_numSyncsToDevice); + std::swap(m_numSyncsToHost, sField->m_numSyncsToHost); + + std::swap(m_modifiedOnHost, sField->m_modifiedOnHost); + std::swap(m_modifiedOnDevice, sField->m_modifiedOnDevice); } } } @@ -374,33 +380,43 @@ void FieldBase::rotate_multistate_data() void FieldBase::modify_on_host() const { - if (m_ngpField != nullptr) { - m_ngpField->modify_on_host(); - } + ThrowRequireMsg(m_modifiedOnDevice == false, + "Modify on host called for Field: " << name() << " but it has an uncleared modified_on_device"); + + m_modifiedOnHost = true; } void FieldBase::modify_on_device() const { - if (m_ngpField != nullptr) { - m_ngpField->modify_on_device(); - } + ThrowRequireMsg(m_modifiedOnHost == false, + "Modify on device called for Field: " << name() << " but it has an uncleared modified_on_host"); + + m_modifiedOnDevice = true; } void FieldBase::modify_on_host(const Selector& s) const { - if (m_ngpField != nullptr) { - m_ngpField->modify_on_host(s); - } + modify_on_host(); } void FieldBase::modify_on_device(const Selector& s) const { - if (m_ngpField != nullptr) { - m_ngpField->modify_on_device(s); - } + modify_on_device(); +} + +bool +FieldBase::need_sync_to_device() const +{ + return m_modifiedOnHost; +} + +bool +FieldBase::need_sync_to_host() const +{ + return m_modifiedOnDevice; } void @@ -408,6 +424,8 @@ FieldBase::sync_to_host() const { if (m_ngpField != nullptr) { m_ngpField->sync_to_host(); + } else { + clear_device_sync_state(); } } @@ -416,31 +434,37 @@ FieldBase::sync_to_device() const { if (m_ngpField != nullptr) { m_ngpField->sync_to_device(); + } else { + clear_host_sync_state(); } } void FieldBase::clear_sync_state() const { - if (m_ngpField != nullptr) { - m_ngpField->clear_sync_state(); + if(m_ngpField != nullptr) { + m_ngpField->notify_sync_debugger_clear_sync_state(); } + m_modifiedOnHost = false; + m_modifiedOnDevice = false; } void FieldBase::clear_host_sync_state() const { - if (m_ngpField != nullptr) { - m_ngpField->clear_host_sync_state(); + if(m_ngpField != nullptr) { + m_ngpField->notify_sync_debugger_clear_host_sync_state(); } + m_modifiedOnHost = false; } void FieldBase::clear_device_sync_state() const { - if (m_ngpField != nullptr) { - m_ngpField->clear_device_sync_state(); + if(m_ngpField != nullptr) { + m_ngpField->notify_sync_debugger_clear_device_sync_state(); } + m_modifiedOnDevice = false; } void diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldBase.hpp b/packages/stk/stk_mesh/stk_mesh/base/FieldBase.hpp index 7af36a9dad56..aff73d7445d7 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldBase.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldBase.hpp @@ -231,6 +231,8 @@ class FieldBase void modify_on_device() const; void modify_on_host(const Selector& s) const; void modify_on_device(const Selector& s) const; + bool need_sync_to_host() const; + bool need_sync_to_device() const; void sync_to_host() const; void sync_to_device() const; void clear_sync_state() const; @@ -344,7 +346,9 @@ class FieldBase m_this_state(arg_this_state), m_ngpField(nullptr), m_numSyncsToHost(0), - m_numSyncsToDevice(0) + m_numSyncsToDevice(0), + m_modifiedOnHost(false), + m_modifiedOnDevice(false) { FieldBase * const pzero = nullptr ; const shards::ArrayDimTag * const dzero = nullptr ; @@ -377,6 +381,8 @@ class FieldBase mutable NgpFieldBase * m_ngpField; mutable size_t m_numSyncsToHost; mutable size_t m_numSyncsToDevice; + mutable bool m_modifiedOnHost; + mutable bool m_modifiedOnDevice; mutable Teuchos::any m_stkFieldSyncDebugger; }; diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.cpp b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.cpp index 993520c27c58..abae4a408231 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.cpp @@ -134,7 +134,7 @@ void DefaultFieldDataManager::allocate_bucket_field_data(const EntityRank rank, FieldMetaData field_meta_data = {nullptr, 0}; const FieldBase & field = *fields[i]; - if(static_cast(field.entity_rank()) == rank) + if (field.entity_rank() == rank) { size_t num_bytes_per_entity = getNumBytesForField(field, rank, superset_parts); if(num_bytes_per_entity > 0) @@ -159,7 +159,7 @@ void DefaultFieldDataManager::allocate_bucket_field_data(const EntityRank rank, for(size_t i = 0; i < fields.size(); ++i) { const FieldBase & field = *fields[i]; - if(static_cast(field.entity_rank()) == rank) + if (field.entity_rank() == rank) { const unsigned char* init_val = reinterpret_cast(field.get_initial_value()); FieldMetaData& field_meta_data = const_cast(field.get_meta_data_for_field().back()); @@ -177,7 +177,7 @@ void DefaultFieldDataManager::allocate_bucket_field_data(const EntityRank rank, void DefaultFieldDataManager::allocate_new_field_meta_data(const EntityRank rank, const unsigned bucketId, const std::vector& allFields) { for (FieldBase* field : allFields) { - if (static_cast(field->entity_rank()) == rank) { + if (field->entity_rank() == rank) { if (bucketId >= field->get_meta_data_for_field().size()) { FieldMetaData fieldMetaData = {nullptr, 0}; field->get_meta_data_for_field().push_back(fieldMetaData); @@ -195,7 +195,7 @@ std::vector DefaultFieldDataManager::get_old_bucket_field_offsets(const size_t currentFieldOldOffset = 0; for (unsigned int i = 0; i < allFields.size(); ++i) { const bool isFieldValid = (allFields[i] != nullptr); - const bool isTargetRank = (static_cast(allFields[i]->entity_rank()) == rank); + const bool isTargetRank = (allFields[i]->entity_rank() == rank); if (isFieldValid && isTargetRank) { const bool isBucketInRange = (bucketId < allFields[i]->get_meta_data_for_field().size()); @@ -220,7 +220,7 @@ std::vector DefaultFieldDataManager::get_new_bucket_field_offsets(const size_t currentFieldNewOffset = 0; for (size_t i = 0; i < allFields.size(); ++i) { const FieldBase& field = *allFields[i]; - if (static_cast(field.entity_rank()) == rank) { + if (field.entity_rank() == rank) { size_t numBytesPerEntity = getNumBytesForField(field, rank, supersetParts); size_t fieldDataSizeThisBucket = stk::adjust_up_to_alignment_boundary(numBytesPerEntity * capacity, alignment_increment_bytes); @@ -246,7 +246,7 @@ void DefaultFieldDataManager::copy_field_data_from_old_to_new_bucket(const Entit { size_t fieldIndex = 0; for (const FieldBase* field : allFields) { - if (static_cast(field->entity_rank()) == rank) { + if (field->entity_rank() == rank) { size_t oldFieldAllocationSize = oldOffsetForField[fieldIndex + 1] - oldOffsetForField[fieldIndex]; std::memcpy(newAllocationAllFields + newOffsetForField[fieldIndex], oldAllocationAllFields + oldOffsetForField[fieldIndex], oldFieldAllocationSize); @@ -264,7 +264,7 @@ void DefaultFieldDataManager::update_field_pointers_to_new_bucket(const EntityRa size_t currentFieldOffset = 0; for (size_t i = 0; i < allFields.size(); ++i) { const FieldBase& field = *allFields[i]; - if (static_cast(field.entity_rank()) == rank) { + if (field.entity_rank() == rank) { FieldMetaData& fieldMetaData = const_cast(field.get_meta_data_for_field()[bucketId]); updateFieldPointer(fieldMetaData, capacity, currentFieldOffset, newAllocationAllFields, alignment_increment_bytes); } @@ -273,7 +273,7 @@ void DefaultFieldDataManager::update_field_pointers_to_new_bucket(const EntityRa void DefaultFieldDataManager::initialize_new_field_values(FieldBase& currentField, const EntityRank rank, const unsigned bucketId, const size_t capacity) { - if (static_cast(currentField.entity_rank()) == rank) { + if (currentField.entity_rank() == rank) { const unsigned char* initVal = reinterpret_cast(currentField.get_initial_value()); FieldMetaData& fieldMetaData = const_cast(currentField.get_meta_data_for_field()[bucketId]); initializeField(fieldMetaData, initVal, capacity); @@ -317,7 +317,7 @@ void DefaultFieldDataManager::deallocate_bucket_field_data(const EntityRank rank for(unsigned int i = 0; i < fields.size(); ++i) { if(fields[i] == nullptr || - static_cast(fields[i]->entity_rank()) != rank || + fields[i]->entity_rank() != rank || fields[i]->get_meta_data_for_field().size() <= bucket_id) continue; FieldMetaData& field_data = fields[i]->get_meta_data_for_field()[bucket_id]; @@ -346,7 +346,7 @@ void DefaultFieldDataManager::reorder_bucket_field_data(EntityRank rank, const s for(size_t i = 0; i < fields.size(); ++i) { - if(static_cast(fields[i]->entity_rank()) == rank) + if (fields[i]->entity_rank() == rank) { FieldMetaDataVector new_field_meta_data_vector(reorderedBucketIds.size()); for(unsigned m = 0, e = reorderedBucketIds.size(); m < e; ++m) @@ -388,7 +388,7 @@ void DefaultFieldDataManager::initialize_entity_field_data(EntityRank rank, unsi for(size_t i = 0; i < fields.size(); ++i) { const FieldBase & field = *fields[i]; - if(static_cast(field.entity_rank()) == rank) + if (field.entity_rank() == rank) { const FieldMetaData& field_meta_data = fields[i]->get_meta_data_for_field()[bucket_id]; const int num_bytes_per_entity = field_meta_data.m_bytes_per_entity; diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp index c117cd39be7c..0a02b25b0c84 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp @@ -70,7 +70,6 @@ class AllocatorAdaptor : public AllocatorAdaptorInterface { } }; - class FieldDataManager { public: diff --git a/packages/stk/stk_mesh/stk_mesh/base/FindRestriction.cpp b/packages/stk/stk_mesh/stk_mesh/base/FindRestriction.cpp index 329957478b71..a139a0449c7f 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FindRestriction.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FindRestriction.cpp @@ -87,7 +87,7 @@ const FieldBase::Restriction& find_restriction(const FieldBase& field, EntityRank erank, const PartVector& parts) { - if(static_cast(field.entity_rank()) == erank) + if (field.entity_rank() == erank) { const std::vector & restrictions = field.restrictions(); for(std::vector::const_iterator it=restrictions.begin(), it_end=restrictions.end(); it != it_end; ++it) { @@ -104,7 +104,7 @@ const FieldBase::Restriction& find_restriction(const FieldBase& field, EntityRank erank, const Part & part) { - if(static_cast(field.entity_rank()) == erank) + if (field.entity_rank() == erank) { const std::vector & restrictions = field.restrictions(); for(std::vector::const_iterator it=restrictions.begin(), it_end=restrictions.end(); it != it_end; ++it) { @@ -125,7 +125,7 @@ const FieldBase::Restriction& find_and_check_restriction(const FieldBase& field, const FieldBase::Restriction & empty = empty_field_restriction(); const FieldBase::Restriction * restriction = & empty; - if(static_cast(field.entity_rank()) == erank) + if (field.entity_rank() == erank) { const std::vector & restrictions = field.restrictions(); for(std::vector::const_iterator it=restrictions.begin(), it_end=restrictions.end(); it != it_end; ++it) { diff --git a/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp b/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp index fc3b4f6cfabb..358d24d4b571 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp @@ -49,6 +49,7 @@ NgpField & get_updated_ngp_field_async(const FieldBase & stkFiel if (ngpField == nullptr) { ngpField = new NgpField(stkField.get_mesh(), stkField, execSpace, true); impl::set_ngp_field(stkField, ngpField); + ngpField->clear_host_sync_state(); } else { if (stkField.get_mesh().synchronized_count() != ngpField->synchronized_count()) { diff --git a/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp b/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp index ef6f378c5583..5cfc1794dcc7 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp @@ -68,8 +68,6 @@ class HostField : public NgpFieldBase synchronizedCount(0), asyncCopyState(impl::AsyncCopyState()) { - needSyncToHost = std::make_shared(false); - needSyncToDevice = std::make_shared(false); } HostField(const stk::mesh::BulkData& b, const stk::mesh::FieldBase& f, bool isFromGetUpdatedNgpField = false) @@ -80,8 +78,6 @@ class HostField : public NgpFieldBase asyncCopyState(impl::AsyncCopyState()) { field->template make_field_sync_debugger(); - needSyncToHost = std::make_shared(false); - needSyncToDevice = std::make_shared(false); update_field(); } @@ -99,9 +95,7 @@ class HostField : public NgpFieldBase void update_field() override { - if (hostBulk->synchronized_count() != synchronizedCount) { - copy_host_to_device(); - } + field->increment_num_syncs_to_device(); synchronizedCount = hostBulk->synchronized_count(); } @@ -183,28 +177,27 @@ class HostField : public NgpFieldBase }); } - void modify_on_host() override { set_modify_on_host(); } + void modify_on_host() override { field->modify_on_host(); } - void modify_on_device() override { set_modify_on_device(); } + void modify_on_device() override { field->modify_on_device(); } void clear_sync_state() override { - *needSyncToHost = false; - *needSyncToDevice = false; + field->clear_sync_state(); } - void modify_on_host(const Selector& selector) override { set_modify_on_host(); } + void modify_on_host(const Selector& selector) override { field->modify_on_host(selector); } - void modify_on_device(const Selector& selector) override { set_modify_on_device(); } + void modify_on_device(const Selector& selector) override { field->modify_on_device(selector); } void clear_host_sync_state() override { - *needSyncToDevice = false; + field->clear_host_sync_state(); } void clear_device_sync_state() override { - *needSyncToHost = false; + field->clear_device_sync_state(); } void sync_to_host() override @@ -217,6 +210,7 @@ class HostField : public NgpFieldBase { if (need_sync_to_host()) { copy_device_to_host(); + clear_device_sync_state(); } } @@ -233,6 +227,7 @@ class HostField : public NgpFieldBase update_field(); } copy_host_to_device(); + clear_host_sync_state(); } } @@ -244,10 +239,7 @@ class HostField : public NgpFieldBase void update_bucket_pointer_view() override { } - void swap(HostField &other) { - needSyncToHost.swap(other.needSyncToHost); - needSyncToDevice.swap(other.needSyncToDevice); - } + void swap(HostField &other) { } stk::mesh::EntityRank get_rank() const { return field ? field->entity_rank() : stk::topology::INVALID_RANK; } @@ -257,44 +249,33 @@ class HostField : public NgpFieldBase void debug_modification_end(size_t) override {} void debug_detect_device_field_modification() override {} -protected: - bool need_sync_to_host() const { return *needSyncToHost; } + bool need_sync_to_host() const override { return field->need_sync_to_host(); } + + bool need_sync_to_device() const override { return field->need_sync_to_device(); } - bool need_sync_to_device() const { return *needSyncToDevice; } + void notify_sync_debugger_clear_sync_state() override {} + void notify_sync_debugger_clear_host_sync_state() override {} + void notify_sync_debugger_clear_device_sync_state() override {} private: - void set_modify_on_host() { -#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK - ThrowRequireMsg(*needSyncToHost == false, "field " << field->name()); -#endif - *needSyncToDevice = true; - } void set_modify_on_device() { -#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK - ThrowRequireMsg(*needSyncToDevice == false, "field " << field->name()); -#endif - *needSyncToHost = true; + field->modify_on_device(); } void copy_host_to_device() { field->increment_num_syncs_to_device(); - clear_sync_state(); } void copy_device_to_host() { field->increment_num_syncs_to_host(); - clear_sync_state(); } const BulkData* hostBulk; const stk::mesh::FieldBase * field; - std::shared_ptr needSyncToHost; - std::shared_ptr needSyncToDevice; - size_t synchronizedCount; impl::AsyncCopyState asyncCopyState; }; diff --git a/packages/stk/stk_mesh/stk_mesh/base/MetaData.cpp b/packages/stk/stk_mesh/stk_mesh/base/MetaData.cpp index c6f178a13d96..2666ef879c78 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/MetaData.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/MetaData.cpp @@ -1095,12 +1095,9 @@ get_topology(const MetaData& meta_data, EntityRank entity_rank, const std::pair< first_found_part = ∂ } else { - if ( top != stk::topology::INVALID_TOPOLOGY && top != topology) { - std::ostringstream os; - os << "topology defined as both " << topology.name() << " and as " << top.name() - << "; a given mesh entity must have only one topology."; - throw std::runtime_error(os.str()); - } + ThrowRequireMsg(top == stk::topology::INVALID_TOPOLOGY || top == topology, + "topology defined as both " << topology.name() << " and as " << top.name() + << "; a given mesh entity must have only one topology."); } } } diff --git a/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp b/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp index 0fedde4861c3..3cdbcc52481a 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp @@ -26,6 +26,8 @@ class NgpFieldBase virtual void modify_on_host(const Selector& selector) = 0; virtual void modify_on_device() = 0; virtual void modify_on_device(const Selector& selector) = 0; + virtual bool need_sync_to_host() const = 0; + virtual bool need_sync_to_device() const = 0; virtual void clear_sync_state() = 0; virtual void clear_host_sync_state() = 0; virtual void clear_device_sync_state() = 0; @@ -43,6 +45,9 @@ class NgpFieldBase virtual void debug_modification_end(size_t synchronizationCount) = 0; virtual void debug_detect_device_field_modification() = 0; virtual unsigned debug_get_bucket_offset(unsigned bucketOrdinal) const = 0; + virtual void notify_sync_debugger_clear_sync_state() = 0; + virtual void notify_sync_debugger_clear_host_sync_state() = 0; + virtual void notify_sync_debugger_clear_device_sync_state() = 0; }; } diff --git a/packages/stk/stk_mesh/stk_mesh/base/NgpTypes.hpp b/packages/stk/stk_mesh/stk_mesh/base/NgpTypes.hpp index 8a2c990faa94..a01887716a7e 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/NgpTypes.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/NgpTypes.hpp @@ -45,7 +45,7 @@ namespace mesh { using DeviceCommMapIndices = Kokkos::View; using EntityKeyViewType = Kokkos::View; using EntityViewType = Kokkos::View; -using BucketConnectivityType = Kokkos::View; +using BucketConnectivityType = Kokkos::View; using UnsignedViewType = Kokkos::View; using BoolViewType = Kokkos::View; using OrdinalViewType = Kokkos::View; diff --git a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp new file mode 100644 index 000000000000..b0b351e3d407 --- /dev/null +++ b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp @@ -0,0 +1,193 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include +#include +#include + +namespace stk { +namespace mesh { + +SparseConnectivity::SparseConnectivity(unsigned numRanks) + : m_numRanks(numRanks) +{ + update_num_ranks(numRanks); +} + +void SparseConnectivity::update_num_ranks(unsigned numRanks) +{ + const unsigned minNumRanks = stk::topology::NUM_RANKS; + m_numRanks = std::max(numRanks, minNumRanks); + + m_entityPermutationOffset.resize(m_numRanks); + m_permutations.resize(m_numRanks); + for(unsigned rank=0; rank()); + } +} + +void SparseConnectivity::update_size_of_entity_index_space(unsigned numEntities) +{ + m_meshConnectivity.resize(numEntities); +} + +bool SparseConnectivity::has_permutation(EntityRank fromRank, EntityRank toRank) +{ + return (fromRank > stk::topology::NODE_RANK && fromRank < stk::topology::CONSTRAINT_RANK) + && (toRank > stk::topology::NODE_RANK && toRank < stk::topology::CONSTRAINT_RANK); +} + +const Permutation* SparseConnectivity::begin_permutations(Entity fromEntity, + EntityRank connectedRank) const +{ + if (static_cast(connectedRank) < m_entityPermutationOffset.size() && + fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { + const int entityOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; + return m_permutations[connectedRank][entityOffset].data(); + } + return nullptr; +} + +const Permutation* SparseConnectivity::end_permutations(Entity fromEntity, + EntityRank connectedRank) const +{ + if (static_cast(connectedRank) < m_entityPermutationOffset.size() && + fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { + const int entityOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; + const std::vector& perms = m_permutations[connectedRank][entityOffset]; + return (perms.data()+perms.size()); + } + return nullptr; +} + +bool SparseConnectivity::add_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal, + Permutation permutation) +{ + Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; + int insertLocation = conn.add_connectivity(connectedRank, + connectedEntity, ordinal, (connectedRank > fromRank)); + + if (insertLocation >= 0 && has_permutation(fromRank, connectedRank)) { + if (fromEntity.local_offset() >= m_entityPermutationOffset[connectedRank].size()) { + m_entityPermutationOffset[connectedRank].resize(fromEntity.local_offset()+1); + m_entityPermutationOffset[connectedRank][fromEntity.local_offset()] = 0; + } + unsigned& permOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; + if (permOffset == 0) { + permOffset = m_permutations[connectedRank].size(); + m_permutations[connectedRank].push_back(std::vector(1, permutation)); + return true; + } + std::vector& permutations = m_permutations[connectedRank][permOffset]; + permutations.insert(permutations.begin()+insertLocation, permutation); + } + + return insertLocation >= 0; +} + +bool SparseConnectivity::replace_or_add_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal) +{ + Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; + int insertLocation = conn.replace_or_add_connectivity(connectedRank, + connectedEntity, ordinal); + + return insertLocation >= 0; +} + +bool SparseConnectivity::remove_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal) +{ + Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; + int location = conn.remove_connectivity(connectedRank, connectedEntity, ordinal); + + if (location >= 0) { + if (has_permutation(fromRank, connectedRank)) { + const unsigned permOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; + std::vector& permutations = m_permutations[connectedRank][permOffset]; + permutations.erase(permutations.begin()+location); + } + return true; + } + return false; +} + +bool SparseConnectivity::replace_permutation(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + ConnectivityOrdinal ordinal, + Permutation newPermutation) +{ + if (fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { + const ConnectivityOrdinal* ordsBegin = begin_ordinals(fromEntity, connectedRank); + const ConnectivityOrdinal* ordsEnd = end_ordinals(fromEntity, connectedRank); + + bool foundIt = false; + const bool downward = fromRank > connectedRank; + unsigned idx = ordsEnd - ordsBegin; + if (downward) { + const ConnectivityOrdinal* iter = std::lower_bound(ordsBegin, ordsEnd, ordinal); + idx = iter - ordsBegin; + foundIt = (iter != ordsEnd && *iter == ordinal); + } + else { + const ConnectivityOrdinal* iter = std::find(ordsBegin, ordsEnd, ordinal); + idx = iter - ordsBegin; + foundIt = (iter != ordsEnd); + } + if (foundIt) { + const int entityPermOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; + std::vector& perms = m_permutations[connectedRank][entityPermOffset]; + perms[idx] = newPermutation; + return true; + } + } + return false; +} + +} // namespace mesh +} // namespace stk + diff --git a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp new file mode 100644 index 000000000000..a05f87d84a73 --- /dev/null +++ b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp @@ -0,0 +1,151 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#ifndef STK_MESH_SPARSECONNECTIVITY_HPP +#define STK_MESH_SPARSECONNECTIVITY_HPP + +#include +#include // for EntityRank +#include +#include +#include + +namespace stk { +namespace mesh { + +class SparseConnectivity { +public: + SparseConnectivity(unsigned numRanks = stk::topology::NUM_RANKS); + virtual ~SparseConnectivity(){} + + void update_num_ranks(unsigned numRanks); + void update_size_of_entity_index_space(unsigned numEntities); + + static bool has_permutation(EntityRank fromRank, EntityRank toRank); + + unsigned num_connectivity(Entity fromEntity, EntityRank connectedRank) const; + + const Entity* begin_connectivity(Entity fromEntity, EntityRank connectedRank) const; + const Entity* end_connectivity(Entity fromEntity, EntityRank connectedRank) const; + + const ConnectivityOrdinal* begin_ordinals(Entity fromEntity, EntityRank connectedRank) const; + const ConnectivityOrdinal* end_ordinals(Entity fromEntity, EntityRank connectedRank) const; + + const Permutation* begin_permutations(Entity fromEntity, EntityRank connectedRank) const; + const Permutation* end_permutations(Entity fromEntity, EntityRank connectedRank) const; + + bool add_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal, + Permutation permutation); + + bool replace_or_add_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal); + + bool remove_connectivity(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + Entity connectedEntity, + ConnectivityOrdinal ordinal); + + bool replace_permutation(EntityRank fromRank, + Entity fromEntity, + EntityRank connectedRank, + ConnectivityOrdinal ordinal, + Permutation newPermutation); + + PairIterEntity get_connectivity(Entity fromEntity, EntityRank connectedRank) const; + + const Connectivity& get_connectivity(Entity entity) const { return m_meshConnectivity[entity.local_offset()]; } + Connectivity& get_connectivity(Entity entity) { return m_meshConnectivity[entity.local_offset()]; } + +private: + + std::vector m_meshConnectivity; + std::vector> m_entityPermutationOffset; + std::vector>> m_permutations; + unsigned m_numRanks; +}; + +inline +unsigned SparseConnectivity::num_connectivity(Entity fromEntity, + EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].num_connectivity(connectedRank); +} + +inline +const Entity* SparseConnectivity::begin_connectivity(Entity fromEntity, + EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].begin_connectivity(connectedRank); +} + +inline +const Entity* SparseConnectivity::end_connectivity(Entity fromEntity, + EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].end_connectivity(connectedRank); +} + +inline +PairIterEntity SparseConnectivity::get_connectivity(Entity fromEntity, EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].get_connectivity(connectedRank); +} + +inline +const ConnectivityOrdinal* SparseConnectivity::begin_ordinals(Entity fromEntity, + EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].begin_ordinals(connectedRank); +} + +inline +const ConnectivityOrdinal* SparseConnectivity::end_ordinals(Entity fromEntity, + EntityRank connectedRank) const +{ + return m_meshConnectivity[fromEntity.local_offset()].end_ordinals(connectedRank); +} + +} // namespace mesh +} // namespace stk + +#endif //STK_MESH_SPARSECONNECTIVITY_HPP + diff --git a/packages/stk/stk_mesh/stk_mesh/base/Types.hpp b/packages/stk/stk_mesh/stk_mesh/base/Types.hpp index 083a6e1018ba..13729f625b3c 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Types.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Types.hpp @@ -236,6 +236,9 @@ typedef std::vector EntityCommInfoVector; typedef PairIter< EntityCommInfoVector::const_iterator > PairIterEntityComm ; #endif + +using PairIterEntity = PairIter; + /** \} */ //---------------------------------------------------------------------- diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp index 2143cdaf75f2..575e12b98169 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp @@ -42,7 +42,6 @@ #include // for Partition, lower_bound #include #include -#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity #include "stk_mesh/base/FieldBase.hpp" // for FieldBase #include "stk_mesh/base/MetaData.hpp" // for MetaData #include "stk_mesh/base/Types.hpp" // for BucketVector, EntityRank, etc @@ -278,52 +277,6 @@ Partition* BucketRepository::create_partition( return partition; } -void BucketRepository::internal_modification_end() -{ - sync_from_partitions(); - - for(EntityRank from_rank = stk::topology::NODE_RANK; from_rank < stk::topology::NUM_RANKS; ++from_rank) - { - const BucketVector &buckets = this->buckets(from_rank); - unsigned num_buckets = buckets.size(); - for(unsigned j = 0; j < num_buckets; ++j) - { - ThrowAssert(buckets[j] != NULL); - Bucket &bucket = *buckets[j]; - - // Update the hop-saving connectivity data on this bucket. - // - for(EntityRank to_rank = stk::topology::NODE_RANK; to_rank < stk::topology::NUM_RANKS; ++to_rank) - { - if (from_rank == to_rank) { - continue; - } - - switch(to_rank) - { - case stk::topology::NODE_RANK: - bucket.m_fixed_node_connectivity.end_modification(&bucket.m_mesh); - break; - case stk::topology::EDGE_RANK: - bucket.m_dynamic_edge_connectivity.end_modification(&bucket.m_mesh); - break; - case stk::topology::FACE_RANK: - bucket.m_dynamic_face_connectivity.end_modification(&bucket.m_mesh); - break; - case stk::topology::ELEMENT_RANK: - bucket.m_dynamic_element_connectivity.end_modification(&bucket.m_mesh); - break; - case stk::topology::INVALID_RANK: - break; - default: - bucket.m_dynamic_other_connectivity.end_modification(&bucket.m_mesh); - break; - } - } - } - } -} - void BucketRepository::sync_from_partitions() { for (EntityRank rank = stk::topology::NODE_RANK; rank < static_cast(m_partitions.size()); ++rank) diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp index 11398d136ee8..db99005a0d88 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp @@ -132,9 +132,6 @@ class BucketRepository PartOrdinal* keyPtr, PartOrdinal* keyEnd); - // For use by BulkData::internal_modification_end(). - void internal_modification_end(); - // Update m_buckets from the partitions. void sync_from_partitions(); void sync_from_partitions(EntityRank rank); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp index 3b5dc54a2c99..7d66af99bfbd 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp @@ -1264,52 +1264,10 @@ void comm_sync_aura_send_recv( } } -void insert_upward_relations(const BulkData& bulk_data, Entity rel_entity, - const EntityRank rank_of_orig_entity, - const int share_proc, - std::vector& send) -{ - EntityRank rel_entity_rank = bulk_data.entity_rank(rel_entity); - ThrowAssert(rel_entity_rank > rank_of_orig_entity); - - // If related entity is higher rank, I own it, and it is not - // already shared by proc, ghost it to the sharing processor. - if ( bulk_data.bucket(rel_entity).owned() && ! bulk_data.in_shared(rel_entity, share_proc) ) { - - send.emplace_back(rel_entity,share_proc); - - // There may be even higher-ranking entities that need to be ghosted, so we must recurse - const EntityRank end_rank = static_cast(bulk_data.mesh_meta_data().entity_rank_count()); - for (EntityRank irank = static_cast(rel_entity_rank + 1); irank < end_rank; ++irank) - { - const int num_rels = bulk_data.num_connectivity(rel_entity, irank); - Entity const* rels = bulk_data.begin(rel_entity, irank); - - for (int r = 0; r < num_rels; ++r) - { - Entity const rel_of_rel_entity = rels[r]; - if (bulk_data.is_valid(rel_of_rel_entity)) { - insert_upward_relations(bulk_data, rel_of_rel_entity, rel_entity_rank, share_proc, send); - } - } - } - } -} - -EntityRank get_highest_upward_connected_rank(const BulkData& mesh, Entity entity) -{ - const EntityRank entityRank = mesh.entity_rank(entity); - EntityRank highestRank = static_cast(mesh.mesh_meta_data().entity_rank_count()-1); - while(highestRank > entityRank && mesh.num_connectivity(entity, highestRank) == 0) { - highestRank = static_cast(highestRank-1); - } - return highestRank; -} - void insert_upward_relations(const BulkData& bulk_data, + const Connectivity& entityConnectivity, const EntityProcMapping& entitySharing, Entity rel_entity, - const EntityRank rank_of_orig_entity, const int share_proc, EntityProcMapping& send) { @@ -1321,13 +1279,8 @@ void insert_upward_relations(const BulkData& bulk_data, send.addEntityProc(rel_entity,share_proc); - const unsigned bucketOrd = idx.bucket_ordinal; - const EntityRank upwardRank = get_highest_upward_connected_rank(bulk_data, rel_entity); - const int numRels = bucket.num_connectivity(bucketOrd, upwardRank); - Entity const* rels = bucket.begin(bucketOrd, upwardRank); - - for (int r = 0; r < numRels; ++r) { - Entity const upwardEntity = rels[r]; + PairIterEntity conn = entityConnectivity.get_highest_rank_connectivity(bulk_data.entity_rank(rel_entity)); + for( Entity upwardEntity : conn) { if (bulk_data.is_valid(upwardEntity) && bulk_data.bucket(upwardEntity).owned()) { if (!entitySharing.find(upwardEntity, share_proc)) { send.addEntityProc(upwardEntity, share_proc); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp index e3f049063a23..8403ea4f2a17 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp @@ -59,8 +59,34 @@ struct EntityGhostData; //stk-mesh capabilities. //---------------------------------------------------------------------- +void remove_entities_not_connected_to_other_nodes(const BulkData& mesh, EntityRank rank, + unsigned numNodes, const Entity* nodes, + std::vector& elementsInCommon); + void find_entities_these_nodes_have_in_common(const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); +template +void find_entities_these_nodes_have_in_common_and(const BulkData& mesh, EntityRank rank, + unsigned numNodes, const Entity* nodes, + std::vector& elementsInCommon, + const Pred& pred) +{ + elementsInCommon.clear(); + if(numNodes > 0) + { + const Entity* begin = mesh.begin(nodes[0], rank); + const Entity* end = mesh.end(nodes[0], rank); + elementsInCommon.reserve(std::distance(begin,end)); + for(const Entity* ent = begin; ent != end; ++ent) { + if (pred(*ent)) { + elementsInCommon.push_back(*ent); + } + } + + remove_entities_not_connected_to_other_nodes(mesh, rank, numNodes, nodes, elementsInCommon); + } +} + void find_entities_with_larger_ids_these_nodes_have_in_common_and_locally_owned(stk::mesh::EntityId id, const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); bool do_these_nodes_have_any_shell_elements_in_common(BulkData& mesh, unsigned numNodes, const Entity* nodes); @@ -218,15 +244,10 @@ void comm_sync_aura_send_recv( EntityProcMapping& entityProcMapping, std::vector& ghostStatus ); -void insert_upward_relations(const BulkData& bulk_data, Entity rel_entity, - const EntityRank rank_of_orig_entity, - const int share_proc, - std::vector& send); - void insert_upward_relations(const BulkData& bulk_data, + const Connectivity& entityConnectivity, const EntityProcMapping& entitySharing, Entity rel_entity, - const EntityRank rank_of_orig_entity, const int share_proc, EntityProcMapping& send); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp index b7bb82c7bb7a..c301ada91b24 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp @@ -21,6 +21,7 @@ bool MeshModification::modification_begin(const std::string description) if (numRanks > m_bulkData.m_selector_to_buckets_maps.size()) { m_bulkData.m_selector_to_buckets_maps.resize(numRanks); } + m_bulkData.m_sparse_connectivity.update_num_ranks(m_bulkData.mesh_meta_data().entity_rank_count()); } if ( this->in_modifiable_state() ) return false ; diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp index 100a2c2e1f68..8945a5620fe3 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp @@ -95,7 +95,7 @@ void print_field_data_for_entity(const BulkData& mesh, const MeshIndex& meshInde size_t b_ord = meshIndex.bucket_ordinal; const FieldVector& all_fields = mesh.mesh_meta_data().get_fields(); for(FieldBase* field : all_fields) { - if(static_cast(field->entity_rank()) != bucket->entity_rank()) continue; + if(field->entity_rank() != bucket->entity_rank()) continue; FieldMetaData field_meta_data = field->get_meta_data_for_field()[bucket->bucket_id()]; unsigned data_size = field_meta_data.m_bytes_per_entity; if (data_size > 0) { // entity has this field? @@ -187,6 +187,20 @@ void print_connectivity_of_rank(const BulkData& M, Entity entity, } } +void print_upward_connectivity(const BulkData& bulk, Entity entity, std::ostream& out) +{ + EntityRank nextRank = static_cast(bulk.entity_rank(entity)+1); + EntityRank endRank = static_cast(bulk.mesh_meta_data().entity_rank_count()); + + for(EntityRank rank = nextRank; rank < endRank; ++rank) { + const unsigned num = bulk.num_connectivity(entity, rank); + const Entity* conn = bulk.begin(entity, rank); + for(unsigned i=0; i -void coarse_search( std::vector > const& domain, - std::vector > const& range, - SearchMethod method, - stk::ParallelMachine comm, - std::vector< std::pair< DomainIdent, RangeIdent> > & intersections, - bool communicateRangeBoxInfo=true - ) +void coarse_search(std::vector> const& domain, + std::vector> const& range, + SearchMethod method, + stk::ParallelMachine comm, + std::vector>& intersections, + bool communicateRangeBoxInfo = true, + bool determineDomainAndRange = true) { switch( method ) { case KDTREE: - coarse_search_kdtree_driver(domain,range,comm,intersections,communicateRangeBoxInfo); + if (determineDomainAndRange) { + coarse_search_kdtree_driver(domain,range,comm,intersections,communicateRangeBoxInfo); + } + else { + coarse_search_kdtree(domain,range,comm,intersections,communicateRangeBoxInfo); + } break; default: std::cerr << "coarse_search(..) interface used does not support SearchMethod " << method << std::endl; diff --git a/packages/stk/stk_tools/stk_tools/mesh_tools/DetectHingesImpl.cpp b/packages/stk/stk_tools/stk_tools/mesh_tools/DetectHingesImpl.cpp index 9c0ef6a62420..56557ebaf3f0 100644 --- a/packages/stk/stk_tools/stk_tools/mesh_tools/DetectHingesImpl.cpp +++ b/packages/stk/stk_tools/stk_tools/mesh_tools/DetectHingesImpl.cpp @@ -106,7 +106,7 @@ class SideFinder std::sort(m_scratchSpace, m_scratchSpace+subTopo.num_nodes()); if(are_equal(m_scratchSpace, nodes)) { - elementTopo.sub_topology_nodes(elemNodes, subRank, i, nodes.begin()); + elementTopo.sub_topology_nodes(elemNodes, subRank, i, nodes.data()); return true; } } diff --git a/packages/stk/stk_topology/stk_topology/topology_decl.hpp b/packages/stk/stk_topology/stk_topology/topology_decl.hpp index 414e412a2707..7079e82884e2 100644 --- a/packages/stk/stk_topology/stk_topology/topology_decl.hpp +++ b/packages/stk/stk_topology/stk_topology/topology_decl.hpp @@ -4,6 +4,8 @@ // IWYU pragma: private, include "stk_topology/topology.hpp" #include "stk_util/stk_config.h" #include +#include +#include namespace stk { @@ -25,7 +27,7 @@ struct EquivalentPermutation struct topology { - enum rank_t + enum rank_t : int8_t { BEGIN_RANK , NODE_RANK = BEGIN_RANK @@ -35,8 +37,7 @@ struct topology , CONSTRAINT_RANK , END_RANK , NUM_RANKS = END_RANK - , INVALID_RANK = 256 - , FORCE_RANK_TO_UNSIGNED = 256 + , INVALID_RANK = std::numeric_limits::max() }; //To add new topologies consult the toolkit team diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp index 3a7d0423dd7a..58d544df65f0 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp @@ -49,7 +49,7 @@ class BucketTester : public stk::mesh::Bucket void my_change_connected_nodes(unsigned bucket_ordinal, Entity* new_nodes) { - this->change_existing_connectivity(bucket_ordinal, new_nodes); + this->change_connected_nodes(bucket_ordinal, new_nodes); } void my_change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/Search_UnitTestUtils.hpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/Search_UnitTestUtils.hpp index 127325993050..60fc4fecc6ba 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/Search_UnitTestUtils.hpp +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/Search_UnitTestUtils.hpp @@ -59,9 +59,8 @@ typedef std::vector< StkBoxWithId > StkBoxVector; typedef stk::search::Box FloatBox; typedef std::vector > SearchResults; -typedef std::pair BoxWithId; -typedef std::vector< BoxWithId > FloatBoxVector; - +typedef std::pair FloatBoxWithId; +typedef std::vector FloatBoxVector; template VolumeType generateBoundingVolume(double x, double y, double z, double radius); diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp index 4394de07b491..94884859a0d0 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp @@ -35,7 +35,7 @@ namespace stk namespace unit_test_util { -typedef std::set EntityIdSet; +using EntityIdSet = std::set; class TopologyMapping { @@ -97,16 +97,6 @@ class TopologyMapping }; }; -struct ElementData -{ - int proc; - stk::topology topology; - stk::mesh::EntityId identifier; - stk::mesh::EntityIdVector nodeIds; - std::string partName = ""; - unsigned partId; -}; - class PartIdMapping { public: @@ -206,6 +196,16 @@ class PartIdMapping bool m_idsAssigned; }; +struct ElementData +{ + int proc; + stk::mesh::EntityId identifier; + stk::topology topology; + stk::mesh::EntityIdVector nodeIds; + std::string partName = ""; + unsigned partId; +}; + struct TextMeshData { unsigned spatialDim; @@ -244,173 +244,267 @@ struct TextMeshData std::unordered_map m_nodesOnProc; }; -class TextMeshParser +class Lexer { public: - TextMeshParser(unsigned dim) - : m_spatialDim(dim) + Lexer() + : m_token(""), + m_isNumber(false) + { } + + void set_input_string(const std::string& input) { - validate_spatial_dim(); + m_input = input; + m_currentIndex = 0; + read_next_token(); } - TextMeshData parse(const std::string& meshDescription) + int get_int() { - TextMeshData data; - data.spatialDim = m_spatialDim; - - const std::vector lines = split(meshDescription, '\n'); - - m_lineNumber = 1; - for (const std::string& line : lines) { - ElementData elem = parse_element(line); - data.add_element(elem); - m_lineNumber++; - } - - for (ElementData& elem : data.elementDataVec) { - set_part_id(elem); - } - - return data; + read_next_token(); + return std::stoi(m_oldToken); } -private: - void validate_spatial_dim() + unsigned get_unsigned() { - ThrowRequireMsg(m_spatialDim == 2 || m_spatialDim == 3, "Error! Spatial dimension not defined to be 2 or 3!"); + read_next_token(); + return std::stoul(m_oldToken); } - std::vector split(const std::string &s, char delim) + std::string get_string() { - std::vector tokens; - std::stringstream ss(s); - std::string item; - while (std::getline(ss, item, delim)) { - tokens.push_back(item); - } - return tokens; + read_next_token(); + return make_upper_case(m_oldToken); } - ElementData parse_element(const std::string& rawLine) + void get_newline() { - std::string line = make_upper_case(remove_spaces(rawLine)); + read_next_token(); + } - const std::vector tokens = split(line, ','); - validate_min_token_count(tokens.size()); + bool has_token() const { return m_token != ""; } + bool has_newline() const { return m_token == "\n"; } + bool has_number() const { return has_token() && m_isNumber; } + bool has_string() const { return has_token() && !has_number() && !has_newline(); } - ElementData elementData; - elementData.proc = parse_proc(tokens[0]); - elementData.identifier = parse_identifier(tokens[1]); - elementData.topology = parse_topology(tokens[2]); +private: + void read_next_token() + { + m_oldToken = m_token; - unsigned numNodes = elementData.topology.num_nodes(); + if (char_is_newline()) { + m_isNumber = false; + m_token = "\n"; + m_currentIndex++; + return; + } - validate_token_count(tokens.size(), numNodes, elementData.topology.name()); + m_token = ""; + m_isNumber = true; - for (unsigned i=0; i= numNodes+4) { - elementData.partName = tokens[3+numNodes]; - } - else { - elementData.partName = "block_" + elementData.topology.name(); - } - validate_part_name(elementData.partName); + if (char_is_comma()) { + m_currentIndex++; + break; + } - if (tokens.size() >= numNodes+5) { - m_partIds.register_part_name_with_id(elementData.partName, parse_part_id(tokens[4+numNodes])); - } - else { - m_partIds.register_part_name(elementData.partName); + if (char_is_newline()) { + break; + } + + m_isNumber &= char_is_digit(); + m_token += current_char(); + m_currentIndex++; } + } - return elementData; + bool has_more_input() + { + return m_currentIndex < m_input.size(); } + bool char_is_whitespace() { return current_char() == ' '; } + bool char_is_comma() { return current_char() == ','; } + bool char_is_newline() { return current_char() == '\n'; } + bool char_is_digit() { return std::isdigit(static_cast(current_char())); } + + char current_char() { return m_input[m_currentIndex]; } + std::string make_upper_case(std::string str) { std::transform(str.begin(), str.end(), str.begin(), ::toupper); return str; } - std::string remove_spaces(std::string str) + std::string m_input; + unsigned m_currentIndex; + + std::string m_oldToken; + std::string m_token; + + bool m_isNumber; +}; + +class TextMeshParser +{ +public: + TextMeshParser(unsigned dim) { - std::string::iterator end_pos = std::remove(str.begin(), str.end(), ' '); - str.erase(end_pos, str.end()); - return str; + m_data.spatialDim = dim; } - void validate_min_token_count(size_t numTokens) + TextMeshData parse(const std::string& meshDescription) { - ThrowRequireMsg(numTokens >= 4, - "Error! Each line must contain the following fields (with at least one node): " - "Processor, GlobalId, Element Topology, NodeIds. Error on line " << m_lineNumber << "."); + initialize_parse(meshDescription); + parse_description(); + set_part_ids(); + return m_data; + } + +private: + void initialize_parse(const std::string& meshDescription) + { + m_lexer.set_input_string(meshDescription); + m_lineNumber = 1; + validate_required_field(m_lexer.has_token()); + } + + void parse_description() + { + while (m_lexer.has_token()) { + ElementData elemData = parse_element(); + m_data.add_element(elemData); + + validate_no_extra_fields(); + parse_newline(); + } + } + + ElementData parse_element() + { + ElementData elem; + elem.proc = parse_proc_id(); + elem.identifier = parse_elem_id(); + elem.topology = parse_topology(); + elem.nodeIds = parse_node_ids(elem.topology); + elem.partName = parse_part(elem.topology); + return elem; } - int parse_proc(const std::string& token) + int parse_proc_id() { - return std::stoi(token); + validate_required_field(m_lexer.has_number()); + return parse_int(); } - stk::mesh::EntityId parse_identifier(const std::string& token) + stk::mesh::EntityId parse_elem_id() { - return static_cast(std::stoul(token)); + validate_required_field(m_lexer.has_number()); + return parse_unsigned(); } - stk::topology parse_topology(const std::string& token) + stk::topology parse_topology() { - stk::topology topology = m_topologyMapping.topology(token); - validate_topology(topology, token); + validate_required_field(m_lexer.has_string()); + std::string topologyName = parse_string(); + + stk::topology topology = m_topologyMapping.topology(topologyName); + validate_topology(topology, topologyName); + return topology; } - unsigned parse_part_id(const std::string& token) + stk::mesh::EntityIdVector parse_node_ids(const stk::topology& topology) { - return std::stoul(token); + stk::mesh::EntityIdVector nodeIds; + while (m_lexer.has_number()) { + nodeIds.push_back(parse_unsigned()); + } + validate_node_count(topology, nodeIds.size()); + return nodeIds; } - void validate_topology(const stk::topology& topology, const std::string& token) + std::string parse_part(const stk::topology& topology) { - ThrowRequireMsg(topology != stk::topology::INVALID_TOPOLOGY, - "Error! Topology = >>" << token << "<< is invalid from line " << m_lineNumber << "."); - ThrowRequireMsg(topology.defined_on_spatial_dimension(m_spatialDim), - "Error on input line " << m_lineNumber << ". Topology = " << topology - << " is not defined on spatial dimension = " << m_spatialDim - << " set in MetaData."); + std::string partName; + + if (m_lexer.has_string()) { + partName = parse_string(); + } + else { + partName = "block_" + topology.name(); + } + + if (m_lexer.has_number()) { + unsigned partId = parse_unsigned(); + m_partIds.register_part_name_with_id(partName, partId); + } + else { + m_partIds.register_part_name(partName); + } + + return partName; + } + + int parse_int() { return m_lexer.get_int(); } + unsigned parse_unsigned() { return m_lexer.get_unsigned(); } + std::string parse_string() { return m_lexer.get_string(); } + + void parse_newline() + { + m_lexer.get_newline(); + m_lineNumber++; + } + + void validate_required_field(bool hasNextRequiredField) + { + ThrowRequireMsg(hasNextRequiredField, + "Error! Each line must contain the following fields (with at least one node): " + "Processor, GlobalId, Element Topology, NodeIds. Error on line " << m_lineNumber << "."); } - void validate_token_count(size_t numTokens, unsigned numNodes, const std::string& topologyName) + void validate_no_extra_fields() { - ThrowRequireMsg(numTokens >= numNodes+3 && numTokens <= numNodes+5, - "Error! The input line appears to contain " << numTokens-3 << " nodes, but the topology " - << topologyName << " needs " << numNodes << " nodes on line " << m_lineNumber << "."); + ThrowRequireMsg(!m_lexer.has_token() || m_lexer.has_newline(), + "Error! Each line should not contain more than the following fields (with at least one node): " + "Processor, GlobalId, Element Topology, NodeIds, Part Name, PartId. " + "Error on line " << m_lineNumber << "."); } - void validate_part_name(const std::string& name) + void validate_topology(const stk::topology& topology, const std::string& providedName) { - ThrowRequireMsg(!is_number(name), - "The input line " << m_lineNumber << " specifies the numeric part name " << name); + ThrowRequireMsg(topology != stk::topology::INVALID_TOPOLOGY, + "Error! Topology = >>" << providedName << "<< is invalid from line " << m_lineNumber << "."); + ThrowRequireMsg(topology.defined_on_spatial_dimension(m_data.spatialDim), + "Error on input line " << m_lineNumber << ". Topology = " << topology + << " is not defined on spatial dimension = " << m_data.spatialDim + << " set in MetaData."); } - bool is_number(const std::string& name) + void validate_node_count(const stk::topology& topology, size_t numNodes) { - unsigned num; - std::istringstream nameStream(name); - nameStream >> num; - return !nameStream.fail(); + size_t numTopologyNodes = topology.num_nodes(); + ThrowRequireMsg(numNodes == numTopologyNodes, + "Error! The input line appears to contain " << numNodes << " nodes, but the topology " + << topology << " needs " << numTopologyNodes << " nodes on line " << m_lineNumber << "."); } - void set_part_id(ElementData& elem) + void set_part_ids() { - elem.partId = m_partIds.get(elem.partName); + for (ElementData& elem : m_data.elementDataVec) { + elem.partId = m_partIds.get(elem.partName); + } } - unsigned m_spatialDim; + unsigned m_lineNumber; + TextMeshData m_data; + Lexer m_lexer; TopologyMapping m_topologyMapping; - size_t m_lineNumber; PartIdMapping m_partIds; }; @@ -612,9 +706,11 @@ class TextMesh TextMesh(stk::mesh::BulkData& b, const std::string& meshDesc) : m_bulk(b), m_meta(m_bulk.mesh_meta_data()), - m_parser(m_meta.spatial_dimension()), - m_data(m_parser.parse(meshDesc)) - { } + m_parser(m_meta.spatial_dimension()) + { + validate_spatial_dim(m_meta.spatial_dimension()); + m_data = m_parser.parse(meshDesc); + } void setup_mesh() { @@ -632,6 +728,11 @@ class TextMesh } private: + void validate_spatial_dim(unsigned spatialDim) + { + ThrowRequireMsg(spatialDim == 2 || spatialDim == 3, "Error! Spatial dimension not defined to be 2 or 3!"); + } + stk::mesh::BulkData& m_bulk; stk::mesh::MetaData& m_meta; diff --git a/packages/stk/stk_unit_tests/cmake/Dependencies.cmake b/packages/stk/stk_unit_tests/cmake/Dependencies.cmake index 9ddd99b2705d..04cfd890cb24 100644 --- a/packages/stk/stk_unit_tests/cmake/Dependencies.cmake +++ b/packages/stk/stk_unit_tests/cmake/Dependencies.cmake @@ -5,4 +5,4 @@ SET(TEST_OPTIONAL_DEP_PACKAGES Shards STKCoupling STKTopology STKMath STKSimd ST SET(LIB_REQUIRED_DEP_TPLS) SET(LIB_OPTIONAL_DEP_TPLS) SET(TEST_REQUIRED_DEP_TPLS) -SET(TEST_OPTIONAL_DEP_TPLS Boost MPI) +SET(TEST_OPTIONAL_DEP_TPLS MPI) diff --git a/packages/stk/stk_unit_tests/stk_mesh/FieldBlas/UnitTestFieldBLAS.cpp b/packages/stk/stk_unit_tests/stk_mesh/FieldBlas/UnitTestFieldBLAS.cpp index 13d0d782e504..5fadeca39b18 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/FieldBlas/UnitTestFieldBLAS.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/FieldBlas/UnitTestFieldBLAS.cpp @@ -804,6 +804,15 @@ void test_fill(const Scalar alpha,const Scalar initial1) testFieldValidation(Fixture,alpha,alpha,Scalar()); } +template +void test_fill_many(const Scalar alpha,const Scalar initial1) +{ + BLASFixture Fixture (initial1,initial1,initial1); + + stk::mesh::field_fill(alpha,{Fixture.fieldBase1, Fixture.fieldBase2, Fixture.fieldBase3}); + testFieldValidation(Fixture,alpha,alpha,alpha); +} + TEST(FieldBLAS,fill_double) { const double alpha = 4.27; @@ -811,6 +820,13 @@ TEST(FieldBLAS,fill_double) test_fill(alpha,initial1); } +TEST(FieldBLAS,fill_many_double) +{ + const double alpha = 4.27; + const double initial1 = -3.73; + test_fill_many(alpha,initial1); +} + TEST(FieldBLAS,fill_float) { const float alpha = 4.2; @@ -818,6 +834,13 @@ TEST(FieldBLAS,fill_float) test_fill(alpha,initial1); } +TEST(FieldBLAS,fill_float_many) +{ + const float alpha = 4.2; + const float initial1 = -3.7; + test_fill_many(alpha,initial1); +} + TEST(FieldBLAS,fill_complex) { const std::complex alpha = std::complex(4.11,-7.63); @@ -825,6 +848,13 @@ TEST(FieldBLAS,fill_complex) test_fill(alpha,initial1); } +TEST(FieldBLAS,fill_complex_many) +{ + const std::complex alpha = std::complex(4.11,-7.63); + const std::complex initial1 = std::complex(-7.21,-1.23); + test_fill_many(alpha,initial1); +} + TEST(FieldBLAS,fill_int) { const int alpha = 4; @@ -832,6 +862,13 @@ TEST(FieldBLAS,fill_int) test_fill(alpha,initial1); } +TEST(FieldBLAS,fill_int_many) +{ + const int alpha = 4; + const int initial1 = -3; + test_fill_many(alpha,initial1); +} + template void test_fill_selector(Scalar alpha,Scalar initial1,Scalar initial2) { diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp index 59838cf9313d..232600e5ed98 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp @@ -194,7 +194,7 @@ TEST(UnitTestingOfBucket, bucketSortChangeEntityId) void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity elem, stk::mesh::Entity side, stk::mesh::EntityVector& nodes) { - stk::mesh::EntityRank rank = bulk.entity_rank(side); + stk::mesh::EntityRank sideRank = bulk.entity_rank(side); Entity const *rels_itr = bulk.begin_nodes(side); unsigned num_nodes = bulk.num_nodes(side); @@ -205,7 +205,7 @@ void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity ele stk::mesh::Permutation const *perms = bulk.begin_permutations(side, stk::topology::ELEM_RANK); std::pair ordinalAndPermutation = - stk::mesh::get_ordinal_and_permutation(bulk, elem, rank, nodes); + stk::mesh::get_ordinal_and_permutation(bulk, elem, sideRank, nodes); stk::mesh::Permutation gold_permutation = ordinalAndPermutation.second; ASSERT_TRUE(gold_permutation!=stk::mesh::INVALID_PERMUTATION); @@ -226,8 +226,8 @@ void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity ele stk::mesh::ConnectivityOrdinal elements_side_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; - unsigned num_sides = bulk.num_connectivity(elem, rank); - const stk::mesh::Entity *sides = bulk.begin(elem, rank); + unsigned num_sides = bulk.num_connectivity(elem, sideRank); + const stk::mesh::Entity *sides = bulk.begin(elem, sideRank); for (unsigned i=0;i 1) { GTEST_SKIP(); } + + setup_mesh(1, 1, 1); + + stk::mesh::Entity elem1 = get_bulk().get_entity(stk::topology::ELEM_RANK, 1); + stk::mesh::Bucket& bucket = get_bulk().bucket(elem1); + unsigned bucket_ordinal = get_bulk().bucket_ordinal(elem1); + EXPECT_EQ(0u, bucket_ordinal); + + const stk::mesh::Entity* nodes = bucket.begin_nodes(bucket_ordinal); + stk::mesh::ConnectivityOrdinal ord = 0; + stk::mesh::Permutation perm = stk::mesh::INVALID_PERMUTATION; + + BucketTester& bktTester = static_cast(bucket); + EXPECT_FALSE(bktTester.my_declare_relation(bucket_ordinal, nodes[0], ord, perm)); +} + TEST_F(BucketHex, changing_conn_on_bucket_for_face_to_element) { if (stk::parallel_machine_size(MPI_COMM_WORLD) == 1) @@ -356,41 +386,31 @@ TEST_F(BucketHex, changing_conn_on_bucket_for_face_to_element) std::pair ordinalAndPermutation = stk::mesh::get_ordinal_and_permutation(bulk, elem, stk::topology::FACE_RANK, new_nodes); + stk::mesh::ConnectivityOrdinal faceElemOrdinal = ordinalAndPermutation.first; stk::mesh::Permutation new_permutation = ordinalAndPermutation.second; - unsigned faces_element_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; - unsigned num_elems = bulk.num_elements(side); - const stk::mesh::Entity *elements = bulk.begin_elements(side); - for (unsigned i=0;i(i); - break; - } - } - - unsigned elements_face_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + stk::mesh::ConnectivityOrdinal elemFaceOrdinal = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; unsigned num_faces = bulk.num_faces(elem); const stk::mesh::Entity *faces = bulk.begin_faces(elem); + const stk::mesh::ConnectivityOrdinal *faceOrds = bulk.begin_ordinals(elem, stk::topology::FACE_RANK); for (unsigned i=0;i(i); + elemFaceOrdinal = faceOrds[i]; break; } } - ASSERT_TRUE(elements_face_offset!=stk::mesh::INVALID_CONNECTIVITY_ORDINAL); + ASSERT_TRUE(elemFaceOrdinal!=stk::mesh::INVALID_CONNECTIVITY_ORDINAL); stk::mesh::unit_test::BucketTester& bucket_side = static_cast(bulk.bucket(side)); bucket_side.my_change_connected_nodes(bulk.bucket_ordinal(side), &new_nodes[0]); - bucket_side.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(side), faces_element_offset, new_permutation); + bucket_side.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(side), faceElemOrdinal, new_permutation); stk::mesh::unit_test::BucketTester& bucket_elem = static_cast(bulk.bucket(elem)); - bucket_elem.my_change_existing_permutation_for_connected_face(bulk.bucket_ordinal(elem), elements_face_offset, new_permutation); + bucket_elem.my_change_existing_permutation_for_connected_face(bulk.bucket_ordinal(elem), elemFaceOrdinal, new_permutation); test_nodes_and_permutation(bulk, elem, side, new_nodes); } @@ -424,42 +444,33 @@ TEST_F(BucketHex, changing_conn_on_bucket_for_edge_to_element) std::pair ordinalAndPermutation = stk::mesh::get_ordinal_and_permutation(bulk, elem, stk::topology::EDGE_RANK, new_nodes); + stk::mesh::ConnectivityOrdinal edgeElemOrdinal = ordinalAndPermutation.first; stk::mesh::Permutation new_permutation = ordinalAndPermutation.second; - unsigned edges_element_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; - unsigned num_elems = bulk.num_elements(edge); - const stk::mesh::Entity *elements = bulk.begin_elements(edge); - for (unsigned i=0;i(i); - break; - } - } - - unsigned elements_edge_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + stk::mesh::ConnectivityOrdinal elemEdgeOrdinal = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; unsigned num_edges = bulk.num_edges(elem); const stk::mesh::Entity *edges = bulk.begin_edges(elem); + const stk::mesh::ConnectivityOrdinal *edgeOrds = bulk.begin_ordinals(elem, stk::topology::EDGE_RANK); for (unsigned i=0;i(i); + elemEdgeOrdinal = edgeOrds[i]; break; } } - ASSERT_TRUE(elements_edge_offset != stk::mesh::INVALID_CONNECTIVITY_ORDINAL); + ASSERT_TRUE(elemEdgeOrdinal != stk::mesh::INVALID_CONNECTIVITY_ORDINAL); stk::mesh::unit_test::BucketTester& bucket_edge = static_cast(bulk.bucket(edge)); bucket_edge.my_change_connected_nodes(bulk.bucket_ordinal(edge), &new_nodes[0]); - bucket_edge.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(edge), edges_element_offset, new_permutation); + + bucket_edge.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(edge), edgeElemOrdinal, new_permutation); stk::mesh::unit_test::BucketTester& bucket_elem = static_cast(bulk.bucket(elem)); - bucket_elem.my_change_existing_permutation_for_connected_edge(bulk.bucket_ordinal(elem), elements_edge_offset, new_permutation); + bucket_elem.my_change_existing_permutation_for_connected_edge(bulk.bucket_ordinal(elem), elemEdgeOrdinal, new_permutation); test_nodes_and_permutation(bulk, elem, edge, new_nodes); } @@ -471,8 +482,6 @@ void do_nonmodifying_debug_check(const stk::mesh::BulkData & bulk, const stk::me const stk::mesh::BucketVector & buckets = bulk.buckets(stk::topology::NODE_RANK); ASSERT_EQ(buckets.size(), 1u); - buckets[0]->check_size_invariant(); - EXPECT_FALSE(buckets[0]->get_ngp_field_bucket_is_modified(coordsField.mesh_meta_data_ordinal())); } diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp deleted file mode 100644 index 81e4d791a248..000000000000 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp +++ /dev/null @@ -1,345 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include // for NULL -#include // for uint64_t -#include // for copy -#include -#include // for vector -#include "gtest/gtest.h" // for AssertHelper, TEST - -// CRW: this should be in BucketConnectivity.hpp, but circular dependency for now -#include "stk_mesh/base/BulkData.hpp" - -#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity -#include "stk_mesh/base/Entity.hpp" // for Entity, operator<< -#include "stk_mesh/base/Types.hpp" // for ConnectivityOrdinal, etc -#include "stk_topology/topology.hpp" // for topology, etc -namespace stk { namespace mesh { class BulkData; } } - -using namespace stk::mesh; - -namespace { - -typedef impl::BucketConnectivity fixed_conn; -typedef impl::BucketConnectivity dynamic_conn; - -void check_uninit_conn_size(fixed_conn& conn, unsigned num_conn, unsigned ordinal) -{ - EXPECT_EQ(conn.num_connectivity(ordinal), num_conn); -} - -void check_uninit_conn_size(dynamic_conn& conn, unsigned num_conn, unsigned ordinal) -{ - EXPECT_EQ(conn.num_connectivity(ordinal), 0u); -} - -void check_even_conn_removed(fixed_conn& conn, unsigned num_conn, unsigned ordinal) -{ - EXPECT_EQ(conn.num_connectivity(ordinal), num_conn); - - Entity const* targets = conn.begin(ordinal); - for (unsigned i = 0; i < num_conn; ++i) { - Entity e_to(ordinal * num_conn + i + 1); - if ( (i % 2) == 0 ) { - EXPECT_EQ(targets[i], Entity()); - } - else { - EXPECT_EQ(targets[i], e_to); - } - } -} - -void check_even_conn_removed(dynamic_conn& conn, unsigned num_conn, unsigned ordinal) -{ - EXPECT_EQ(conn.num_connectivity(ordinal), num_conn / 2); - - Entity const* targets = conn.begin(ordinal); - ConnectivityOrdinal const* ordinals = conn.begin_ordinals(ordinal); - for (unsigned i = 0; i < num_conn / 2; ++i) { - Entity e_to(ordinal * num_conn + ((2*i) + 1) + 1); - EXPECT_EQ(targets[i], e_to); - EXPECT_EQ(ordinals[i], static_cast((2*i) + 1)); - } -} - -template -void test_simple_add(Connectivity& connectivity, unsigned num_entities_to_add, unsigned num_to_add) -{ - // Populate connectivity all at once for each entity - - EXPECT_EQ(connectivity.size(), 0u); - - for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { - connectivity.add_entity(); - - EXPECT_EQ(connectivity.size(), ord + 1); - check_uninit_conn_size(connectivity, num_to_add, ord); - - for (uint64_t i = 0; i < num_to_add; ++i) { - Entity e_to(ord * num_to_add + i + 1); - connectivity.add_connectivity(ord, e_to, static_cast(i)); - } - - EXPECT_EQ(connectivity.num_connectivity(ord), num_to_add); - - Entity const* begin = connectivity.begin(ord); - Entity const* end = connectivity.end(ord); - ConnectivityOrdinal const* begin_ord = connectivity.begin_ordinals(ord); - ConnectivityOrdinal const* end_ord = connectivity.end_ordinals(ord); - - EXPECT_EQ(end - begin, num_to_add); - EXPECT_EQ(end_ord - begin_ord, num_to_add); - - for (uint64_t i = 0; i < num_to_add; ++i) { - Entity expected_to(ord * num_to_add + i + 1); - EXPECT_EQ(expected_to, begin[i]); - EXPECT_EQ(static_cast(i), begin_ord[i]); - } - } -} - -template -void test_complex_add(Connectivity& connectivity, unsigned num_entities_to_add, unsigned num_to_add) -{ - // Populate connectivity one at a time for each entity - - EXPECT_EQ(connectivity.size(), 0u); - - for (uint64_t i = 0; i < num_to_add; ++i) { - for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { - if (i == 0) { - connectivity.add_entity(); - } - - if (i == 0) { - EXPECT_EQ(connectivity.size(), ord + 1); - } - else { - EXPECT_EQ(connectivity.size(), num_entities_to_add); - } - - Entity e_to(ord * num_to_add + i + 1); - connectivity.add_connectivity(ord, e_to, static_cast(i)); - } - } - - for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { - EXPECT_EQ(connectivity.num_connectivity(ord), num_to_add); - - Entity const* begin = connectivity.begin(ord); - Entity const* end = connectivity.end(ord); - ConnectivityOrdinal const* begin_ord = connectivity.begin_ordinals(ord); - ConnectivityOrdinal const* end_ord = connectivity.end_ordinals(ord); - - EXPECT_EQ(end - begin, num_to_add); - EXPECT_EQ(end_ord - begin_ord, num_to_add); - - for (uint64_t i = 0; i < num_to_add; ++i) { - Entity expected_to(ord * num_to_add + i + 1); - EXPECT_EQ(expected_to, begin[i]); - EXPECT_EQ(static_cast(i), begin_ord[i]); - } - } -} - -template -void test_remove(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) -{ - test_simple_add(connectivity, num_entities, num_to_add); - - unsigned ord_to_remove_from = num_entities / 2; - - for (uint64_t i = 0; i < num_to_add; ++i) { - Entity e_to(ord_to_remove_from * num_to_add + i + 1); - if ( (i % 2) == 0 ) { - bool rv = connectivity.remove_connectivity(ord_to_remove_from, e_to, static_cast(i)); - EXPECT_TRUE(rv); - } - } - - check_even_conn_removed(connectivity, num_to_add, ord_to_remove_from); -} - -template -void test_inter_conn_copy(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) -{ - // TODO -} - -template -void test_intra_conn_copy(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) -{ - // TODO -} - -template -void test_mod_end(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) -{ - // TODO -} - -} - -TEST(BucketConnectivity, fixed_simple_add) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_simple_add(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_simple_add) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_simple_add(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, fixed_complex_add) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_complex_add(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_complex_add) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_complex_add(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, fixed_remove) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_remove(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_remove) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_remove(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, fixed_intra_conn_copy) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_intra_conn_copy(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_intra_conn_copy) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_intra_conn_copy(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, fixed_inter_conn_copy) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_inter_conn_copy(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_inter_conn_copy) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_inter_conn_copy(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, fixed_mod_end) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - fixed_conn conn(num_to_add); - - test_mod_end(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} - -TEST(BucketConnectivity, dynamic_mod_end) -{ - const unsigned num_to_add = 8; - const unsigned num_entities = 100; - BulkData * bulk = NULL; - dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); - - test_mod_end(conn, num_entities, num_to_add); - conn.end_modification(bulk); -} diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBulkData.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBulkData.cpp index 472e9bebe15d..49fbc9e8560e 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBulkData.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBulkData.cpp @@ -5967,7 +5967,7 @@ TEST(BulkData, makeElementWithConflictingTopologies) mesh.modification_begin(); - EXPECT_THROW(stk::mesh::declare_element(mesh, parts, element_ids[0], elem_node_ids[0]), std::runtime_error); + EXPECT_THROW(stk::mesh::declare_element(mesh, parts, element_ids[0], elem_node_ids[0]), std::logic_error); mesh.modification_end(); } diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp new file mode 100644 index 000000000000..2939e67a3119 --- /dev/null +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp @@ -0,0 +1,386 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include +#include +#include +#include + +namespace { + +const stk::mesh::EntityRank nodeRank = stk::topology::NODE_RANK; +const stk::mesh::EntityRank edgeRank = stk::topology::EDGE_RANK; +const stk::mesh::EntityRank faceRank = stk::topology::FACE_RANK; +const stk::mesh::EntityRank elemRank = stk::topology::ELEM_RANK; +const stk::mesh::EntityRank constraintRank = stk::topology::CONSTRAINT_RANK; + +class ConnectivityTester : public stk::mesh::Connectivity { +public: + void expect_null_ptrs() + { + EXPECT_EQ(nullptr, m_connectivity); + EXPECT_EQ(nullptr, m_offsetsAndOrdinals); + } + + void expect_zeros_and_empty() + { + const unsigned numOffsets = stk::mesh::Connectivity::MAX_NUM_RANKS+1; + for(unsigned r=0; r& numPerRank) + { + EXPECT_TRUE(stk::mesh::Connectivity::MAX_NUM_RANKS == numPerRank.size()); + for(unsigned r=0; r(r))); + } + } + + void expect_connectivity(const std::vector& conn) + { + EXPECT_EQ(conn.size(), m_offsetsAndOrdinals[stk::mesh::Connectivity::MAX_NUM_RANKS]); + for(unsigned i=0; i& ords) + { + EXPECT_EQ(ords.size(), m_offsetsAndOrdinals[stk::mesh::Connectivity::MAX_NUM_RANKS]); + for(unsigned i=0; i& numPerRank) + { + ConnectivityTester& connTester = static_cast(connObject); + connTester.expect_num_per_rank(numPerRank); + } + + void expect_num_per_rank(const std::vector& numPerRank) + { + expect_num_per_rank(connectivity, numPerRank); + } + + void expect_connectivity(stk::mesh::Connectivity& connObject, const std::vector& conn) + { + ConnectivityTester& connTester = static_cast(connObject); + connTester.expect_connectivity(conn); + } + + void expect_connectivity(const std::vector& conn) + { + expect_connectivity(connectivity, conn); + } + + void expect_ordinals(const std::vector& ords) + { + ConnectivityTester& connTester = static_cast(connectivity); + connTester.expect_ordinals(ords); + } + + void add_2nodes_2elems() + { + const bool allowDuplicateOrdinals = true; + + EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + } + +protected: + stk::mesh::Connectivity connectivity; + stk::mesh::Entity node1, node2, node3; + stk::mesh::Entity face1, face2, face3; + stk::mesh::Entity elem1, elem2, elem3; + stk::mesh::Entity constraint1; + stk::mesh::Entity highest1; + stk::mesh::ConnectivityOrdinal ordinal1, ordinal2, ordinal3; +}; + +TEST_F(TestConnectivity, defaultConstruct_zerosAndEmpty) +{ + ConnectivityTester& connTester = static_cast(connectivity); + connTester.expect_zeros_and_empty(); +} + +TEST_F(TestConnectivity, addConnectivity) +{ + add_2nodes_2elems(); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + expect_connectivity({node1, node2, elem1, elem2}); + expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); +} + +TEST_F(TestConnectivity, addConnectivity_then_clear) +{ + add_2nodes_2elems(); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + connectivity.clear(); + expect_num_per_rank({0, 0, 0, 0, 0, 0}); +} + +TEST_F(TestConnectivity, assignment) +{ + add_2nodes_2elems(); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + + stk::mesh::Connectivity connCopy = connectivity; + expect_num_per_rank(connCopy, {2, 0, 0, 2, 0, 0}); + expect_num_per_rank(connectivity, {2, 0, 0, 2, 0, 0}); + + connCopy = std::move(connectivity); + expect_num_per_rank(connCopy, {2, 0, 0, 2, 0, 0}); + ConnectivityTester& connTester = static_cast(connectivity); + connTester.expect_null_ptrs(); +} + +TEST_F(TestConnectivity, replaceOrAddConnectivity_not_pre_existing) +{ + EXPECT_EQ(0, connectivity.replace_or_add_connectivity(nodeRank, node1, ordinal1)); + EXPECT_EQ(1, connectivity.replace_or_add_connectivity(nodeRank, node2, ordinal2)); + EXPECT_EQ(0, connectivity.replace_or_add_connectivity(elemRank, elem1, ordinal1)); + EXPECT_EQ(1, connectivity.replace_or_add_connectivity(elemRank, elem2, ordinal2)); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + expect_connectivity({node1, node2, elem1, elem2}); + expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); +} + +TEST_F(TestConnectivity, replaceOrAddConnectivity_pre_existing) +{ + const bool allowDuplicateOrdinals = true; + EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(nodeRank, node1, ordinal1)); + EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(nodeRank, node2, ordinal2)); + EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(elemRank, elem1, ordinal1)); + EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(elemRank, elem2, ordinal2)); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + expect_connectivity({node1, node2, elem1, elem2}); + expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); +} + +TEST_F(TestConnectivity, addAndRemoveConnectivity) +{ + const bool allowDuplicateOrdinals = true; + + EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + expect_num_per_rank({2, 0, 0, 2, 0, 0}); + expect_connectivity({node1, node2, elem1, elem2}); + expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); + + EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); + expect_num_per_rank({2, 0, 0, 1, 0, 0}); + expect_connectivity({node1, node2, elem2}); + expect_ordinals({ordinal1, ordinal2, ordinal2}); + + stk::mesh::PairIterEntity conn = connectivity.get_connectivity(elemRank); + const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); + const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); + EXPECT_EQ(elem2, elems[0]); + EXPECT_EQ(1u, conn.size()); + EXPECT_EQ(conn.begin(), elems); + EXPECT_EQ(conn.end(), elems+1); + EXPECT_EQ(ordinal2, ords[0]); + + EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); + expect_num_per_rank({2, 0, 0, 0, 0, 0}); + expect_connectivity({node1, node2}); + expect_ordinals({ordinal1, ordinal2}); + conn = connectivity.get_connectivity(elemRank); + EXPECT_EQ(connectivity.begin_connectivity(elemRank), connectivity.end_connectivity(elemRank)); + EXPECT_TRUE(conn.empty()); + EXPECT_EQ(conn.begin(), conn.end()); + EXPECT_EQ(connectivity.begin_ordinals(elemRank), connectivity.end_ordinals(elemRank)); +} + +TEST_F(TestConnectivity, addAndRemoveMultipleRanks) +{ + const bool allowDuplicateOrdinals = true; + + EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(faceRank, face1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(0, connectivity.add_connectivity(constraintRank, constraint1, ordinal1, allowDuplicateOrdinals)); + expect_num_per_rank({1, 0, 1, 2, 1, 0}); + + EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); + expect_num_per_rank({1, 0, 1, 1, 1, 0}); + + const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); + const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); + EXPECT_EQ(elem2, elems[0]); + EXPECT_EQ(ordinal2, ords[0]); + + EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); + expect_num_per_rank({1, 0, 1, 0, 1, 0}); + + EXPECT_EQ(connectivity.begin_connectivity(elemRank), connectivity.end_connectivity(elemRank)); + EXPECT_EQ(connectivity.begin_ordinals(elemRank), connectivity.end_ordinals(elemRank)); + EXPECT_NE(connectivity.begin_connectivity(faceRank), connectivity.end_connectivity(faceRank)); + EXPECT_NE(connectivity.begin_ordinals(faceRank), connectivity.end_ordinals(faceRank)); +} + +TEST_F(TestConnectivity, addRemoveAddAddRemoveAdd) +{ + const bool allowDuplicateOrdinals = true; + + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + expect_num_per_rank({0, 0, 0, 1, 0, 0}); + + EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); + expect_num_per_rank({0, 0, 0, 0, 0, 0}); + + EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); + expect_num_per_rank({0, 0, 0, 1, 0, 0}); + + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + expect_num_per_rank({0, 0, 0, 2, 0, 0}); + + EXPECT_EQ(1, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); + expect_num_per_rank({0, 0, 0, 1, 0, 0}); + + EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); + expect_num_per_rank({0, 0, 0, 2, 0, 0}); + + const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); + const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); + EXPECT_EQ(elem1, elems[0]); + EXPECT_EQ(elem2, elems[1]); + EXPECT_EQ(ordinal1, ords[0]); + EXPECT_EQ(ordinal2, ords[1]); +} + +TEST_F(TestConnectivity, addAndRemoveMultipleConnectivity) +{ + const bool allowDuplicateOrdinals = true; + + EXPECT_EQ(0, connectivity.add_connectivity(faceRank, face1, ordinal1, allowDuplicateOrdinals)); + EXPECT_EQ(1, connectivity.add_connectivity(faceRank, face2, ordinal2, allowDuplicateOrdinals)); + EXPECT_EQ(2, connectivity.add_connectivity(faceRank, face3, ordinal3, allowDuplicateOrdinals)); + expect_num_per_rank({0, 0, 3, 0, 0, 0}); + + { + const stk::mesh::Entity* faces = connectivity.begin_connectivity(faceRank); + const stk::mesh::ConnectivityOrdinal* ordinals = connectivity.begin_ordinals(faceRank); + + EXPECT_EQ(face1, faces[0]); + EXPECT_EQ(face2, faces[1]); + EXPECT_EQ(face3, faces[2]); + EXPECT_EQ(ordinal1, ordinals[0]); + EXPECT_EQ(ordinal2, ordinals[1]); + EXPECT_EQ(ordinal3, ordinals[2]); + } + + EXPECT_EQ(1, connectivity.remove_connectivity(faceRank, face2, ordinal2)); + expect_num_per_rank({0, 0, 2, 0, 0, 0}); + + int indexOfRemovedEntity = connectivity.remove_connectivity(faceRank, face2, ordinal2); + bool duplicateRemoveCausedNoChange = (indexOfRemovedEntity == -1); + EXPECT_TRUE(duplicateRemoveCausedNoChange); + + expect_num_per_rank({0, 0, 2, 0, 0, 0}); + expect_connectivity({face1, face3}); + expect_ordinals({ordinal1, ordinal3}); + + EXPECT_EQ(1, connectivity.remove_connectivity(faceRank, face3, ordinal3)); + expect_num_per_rank({0, 0, 1, 0, 0, 0}); + expect_connectivity({face1}); + expect_ordinals({ordinal1}); + + EXPECT_EQ(0, connectivity.remove_connectivity(faceRank, face1, ordinal1)); + expect_num_per_rank({0, 0, 0, 0, 0, 0}); + + EXPECT_EQ(connectivity.begin_connectivity(faceRank), connectivity.end_connectivity(faceRank)); + EXPECT_EQ(connectivity.begin_ordinals(faceRank), connectivity.end_ordinals(faceRank)); +} + +TEST_F(TestConnectivity, moveInVector) +{ + const bool allowDuplicateOrdinals = true; + std::vector connectivities(1); + connectivities[0].add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals); + { + ConnectivityTester& connTester = static_cast(connectivities[0]); + connTester.expect_num_per_rank({1, 0, 0, 0, 0, 0}); + connTester.expect_connectivity({node1}); + connTester.expect_ordinals({ordinal1}); + } + + connectivities.resize(2); + { + ConnectivityTester& connTester = static_cast(connectivities[0]); + connTester.expect_num_per_rank({1, 0, 0, 0, 0, 0}); + connTester.expect_connectivity({node1}); + connTester.expect_ordinals({ordinal1}); + } +} + +class MyClass { +public: + stk::mesh::Entity* entityPtr; + stk::mesh::ConnectivityOrdinal* ordPtr; +}; + +TEST_F(TestConnectivity, simpleStructSize) +{ + EXPECT_EQ(16u, sizeof(MyClass)); + EXPECT_EQ(sizeof(MyClass), sizeof(stk::mesh::Connectivity)); +} + +} + diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestFEMMetaData.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestFEMMetaData.cpp index ecd207774314..f3b82cea459f 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestFEMMetaData.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestFEMMetaData.cpp @@ -54,7 +54,7 @@ TEST ( UnitTestMetaData, create ) EXPECT_TRUE ( true ); EXPECT_FALSE( fem_meta.is_initialized() ); EXPECT_EQ( fem_meta.spatial_dimension(), 0u ); - EXPECT_EQ( fem_meta.side_rank(), static_cast(stk::topology::INVALID_RANK) ); + EXPECT_EQ( fem_meta.side_rank(), stk::topology::INVALID_RANK ); // Verify throws/etc for FEM calls prior to initialization: stk::mesh::Part & universal_part = fem_meta.universal_part(); @@ -84,7 +84,7 @@ TEST( UnitTestMetaData, entity_ranks_1 ) stk::mesh::MetaData fem_meta; const size_t spatial_dimension = 1; fem_meta.initialize(spatial_dimension); - EXPECT_EQ( fem_meta.side_rank(), static_cast(stk::topology::NODE_RANK) ); + EXPECT_EQ( fem_meta.side_rank(), stk::topology::NODE_RANK ); } TEST( UnitTestMetaData, entity_ranks_2 ) @@ -92,7 +92,7 @@ TEST( UnitTestMetaData, entity_ranks_2 ) stk::mesh::MetaData fem_meta; const size_t spatial_dimension = 2; fem_meta.initialize(spatial_dimension); - EXPECT_EQ( fem_meta.side_rank(), static_cast(stk::topology::EDGE_RANK) ); + EXPECT_EQ( fem_meta.side_rank(), stk::topology::EDGE_RANK ); } TEST( UnitTestMetaData, entity_ranks_3 ) @@ -100,7 +100,7 @@ TEST( UnitTestMetaData, entity_ranks_3 ) stk::mesh::MetaData fem_meta; const size_t spatial_dimension = 3; fem_meta.initialize(spatial_dimension); - EXPECT_EQ( fem_meta.side_rank(), static_cast(stk::topology::FACE_RANK) ); + EXPECT_EQ( fem_meta.side_rank(), stk::topology::FACE_RANK ); } TEST( UnitTestMetaData, get_topology_trivial ) @@ -111,7 +111,7 @@ TEST( UnitTestMetaData, get_topology_trivial ) stk::mesh::Part & hex_part = fem_meta.get_topology_root_part(stk::topology::HEX_8); EXPECT_TRUE( stk::mesh::is_auto_declared_part(hex_part) ); - EXPECT_EQ( hex_part.primary_entity_rank(), spatial_dimension ); + EXPECT_EQ( hex_part.primary_entity_rank(), stk::topology::ELEM_RANK ); stk::topology hex_topology = fem_meta.get_topology(hex_part); EXPECT_EQ( (hex_topology == stk::topology::HEX_8), true ); @@ -126,9 +126,8 @@ TEST( UnitTestMetaData, cell_topology_subsetting ) { stk::mesh::MetaData fem_meta; const size_t spatial_dimension = 3; - const stk::mesh::EntityRank element_rank = static_cast(spatial_dimension); fem_meta.initialize(spatial_dimension); - stk::mesh::Part & element_part = fem_meta.declare_part("element part", element_rank ); + stk::mesh::Part & element_part = fem_meta.declare_part("element part", stk::topology::ELEM_RANK ); stk::mesh::set_topology( element_part, stk::topology::HEX_8 ); stk::mesh::Part & hex_part = fem_meta.get_topology_root_part(stk::topology::HEX_8); diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp new file mode 100644 index 000000000000..6692f677c238 --- /dev/null +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp @@ -0,0 +1,256 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include +#include +#include +#include + +namespace { + +const stk::mesh::EntityRank nodeRank = stk::topology::NODE_RANK; +const stk::mesh::EntityRank edgeRank = stk::topology::EDGE_RANK; +const stk::mesh::EntityRank faceRank = stk::topology::FACE_RANK; +const stk::mesh::EntityRank elemRank = stk::topology::ELEM_RANK; +const stk::mesh::EntityRank constraintRank = stk::topology::CONSTRAINT_RANK; + +TEST(SparseConnectivity, hasPermutation) +{ + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, elemRank)); + EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(edgeRank, elemRank)); + EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(faceRank, elemRank)); + EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(edgeRank, faceRank)); + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, edgeRank)); + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, faceRank)); + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, constraintRank)); + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(faceRank, constraintRank)); + EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(elemRank, constraintRank)); +} + +TEST(SparseConnectivity, addAndRemoveConnectivity) +{ + stk::mesh::SparseConnectivity sparseConnectivity; + + unsigned nodeEntityOffset = 1; + unsigned elemEntityOffset = 9; + sparseConnectivity.update_size_of_entity_index_space(10); + + stk::mesh::Entity node(nodeEntityOffset); + stk::mesh::Entity elem(elemEntityOffset); + stk::mesh::ConnectivityOrdinal ordinal = 0; + stk::mesh::Permutation perm = stk::mesh::Permutation::INVALID_PERMUTATION; + + EXPECT_TRUE(sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm)); + bool addAlreadyExistingShouldBeFalse = sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm); + EXPECT_FALSE(addAlreadyExistingShouldBeFalse); + + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); + + stk::mesh::Entity elem2(elemEntityOffset+1); + sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1, perm); + + EXPECT_EQ(2u, sparseConnectivity.num_connectivity(node, elemRank)); + + sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, ordinal); + + stk::mesh::PairIterEntity conn = sparseConnectivity.get_connectivity(node, elemRank); + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); + EXPECT_EQ(1u, conn.size()); + + const stk::mesh::Entity* elems = sparseConnectivity.begin_connectivity(node, elemRank); + EXPECT_EQ(elem2, elems[0]); + EXPECT_EQ(elems, conn.begin()); + + sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); + + EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); + conn = sparseConnectivity.get_connectivity(node, elemRank); + EXPECT_TRUE(conn.empty()); +} + +TEST(SparseConnectivity, replaceOrAddAndRemoveConnectivity) +{ + stk::mesh::SparseConnectivity sparseConnectivity; + + unsigned nodeEntityOffset = 1; + unsigned elemEntityOffset = 9; + sparseConnectivity.update_size_of_entity_index_space(10); + + stk::mesh::Entity node(nodeEntityOffset); + stk::mesh::Entity elem(elemEntityOffset); + stk::mesh::Entity elem2(elemEntityOffset+1); + stk::mesh::ConnectivityOrdinal ordinal = 0; + + EXPECT_TRUE(sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal)); + bool replaceAlreadyExistingShouldBeFalse = sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal); + EXPECT_FALSE(replaceAlreadyExistingShouldBeFalse); + + bool replaceWithDifferentElemShouldBeTrue = sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem, ordinal); + EXPECT_TRUE(replaceWithDifferentElemShouldBeTrue); + + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); + + sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); + + EXPECT_EQ(2u, sparseConnectivity.num_connectivity(node, elemRank)); + + sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, ordinal); + + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); + + const stk::mesh::Entity* elems = sparseConnectivity.begin_connectivity(node, elemRank); + EXPECT_EQ(elem2, elems[0]); + + sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); + + EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); +} + +TEST(SparseConnectivity, beginEnd) +{ + stk::mesh::SparseConnectivity sparseConnectivity; + + unsigned nodeEntityOffset = 1; + unsigned elemEntityOffset = 9; + sparseConnectivity.update_size_of_entity_index_space(10); + stk::mesh::Entity node(nodeEntityOffset); + stk::mesh::Entity elem(elemEntityOffset); + stk::mesh::ConnectivityOrdinal ordinal = 0; + stk::mesh::Permutation perm = stk::mesh::Permutation::INVALID_PERMUTATION; + + sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm); + + stk::mesh::Entity elem2(elemEntityOffset+1); + sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1, perm); + + const stk::mesh::Entity* beginElems = sparseConnectivity.begin_connectivity(node, elemRank); + const stk::mesh::Entity* endElems = sparseConnectivity.end_connectivity(node, elemRank); + + EXPECT_EQ(2u, std::distance(beginElems, endElems)); + + EXPECT_EQ(elem, beginElems[0]); + EXPECT_EQ(elem2, beginElems[1]); + + const stk::mesh::ConnectivityOrdinal* beginElemOrds = sparseConnectivity.begin_ordinals(node, elemRank); + const stk::mesh::ConnectivityOrdinal* endElemOrds = sparseConnectivity.end_ordinals(node, elemRank); + + EXPECT_EQ(2u, std::distance(beginElemOrds, endElemOrds)); + + EXPECT_EQ(ordinal, beginElemOrds[0]); + EXPECT_EQ(ordinal+1, beginElemOrds[1]); + + EXPECT_EQ(nullptr, sparseConnectivity.begin_permutations(node, elemRank)); + EXPECT_EQ(nullptr, sparseConnectivity.end_permutations(node, elemRank)); +} + +TEST(SparseConnectivity, permutations) +{ + stk::mesh::SparseConnectivity sparseConnectivity; + + unsigned faceEntityOffset = 1; + unsigned elemEntityOffset = 9; + sparseConnectivity.update_size_of_entity_index_space(10); + stk::mesh::Entity face(faceEntityOffset); + stk::mesh::Entity elem(elemEntityOffset); + stk::mesh::ConnectivityOrdinal ordinal = 0; + stk::mesh::Permutation perm = static_cast(1); + stk::mesh::Permutation perm2 = static_cast(-1); + + sparseConnectivity.add_connectivity(faceRank, face, elemRank, elem, ordinal, perm); + + stk::mesh::Entity elem2(elemEntityOffset+1); + sparseConnectivity.add_connectivity(faceRank, face, elemRank, elem2, ordinal+1, perm2); + + const stk::mesh::Permutation* beginElemPerms = sparseConnectivity.begin_permutations(face, elemRank); + const stk::mesh::Permutation* endElemPerms = sparseConnectivity.end_permutations(face, elemRank); + + EXPECT_EQ(2u, std::distance(beginElemPerms, endElemPerms)); + + EXPECT_EQ(perm, beginElemPerms[0]); + EXPECT_EQ(perm2, beginElemPerms[1]); +} + +TEST(SparseConnectivity, addConnMultiple) +{ + stk::mesh::SparseConnectivity sparseConnectivity; + + unsigned nodeEntityOffset = 1; + unsigned node2EntityOffset = 2; + unsigned elemEntityOffset = 3; + unsigned faceEntityOffset = 10; + sparseConnectivity.update_size_of_entity_index_space(4); + + stk::mesh::Entity node(nodeEntityOffset); + stk::mesh::Entity node2(node2EntityOffset); + stk::mesh::Entity face(faceEntityOffset); + stk::mesh::Entity elem(elemEntityOffset); + stk::mesh::ConnectivityOrdinal nodeElemOrd = 5; + stk::mesh::ConnectivityOrdinal node2ElemOrd = 6; + stk::mesh::ConnectivityOrdinal nodeFaceOrd = 2; + stk::mesh::ConnectivityOrdinal elemFaceOrd = 3; + stk::mesh::Permutation invalidPerm = stk::mesh::Permutation::INVALID_PERMUTATION; + stk::mesh::Permutation perm = static_cast(0); + + sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, nodeElemOrd, invalidPerm); + const stk::mesh::Connectivity& nodeConn = sparseConnectivity.get_connectivity(node); + (void)nodeConn; + + sparseConnectivity.add_connectivity(nodeRank, node, faceRank, face, nodeFaceOrd, invalidPerm); + sparseConnectivity.add_connectivity(elemRank, elem, faceRank, face, elemFaceOrd, perm); + + sparseConnectivity.update_size_of_entity_index_space(11); + + sparseConnectivity.add_connectivity(nodeRank, node2, elemRank, elem, node2ElemOrd, invalidPerm); + + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, faceRank)); + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(elem, faceRank)); + EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node2, elemRank)); + + const stk::mesh::Permutation* perms = sparseConnectivity.begin_permutations(elem, faceRank); + const stk::mesh::Permutation* endPerms = sparseConnectivity.end_permutations(elem, faceRank); + EXPECT_TRUE(perms != nullptr); + EXPECT_TRUE(endPerms != nullptr); + EXPECT_EQ(1u, std::distance(perms, endPerms)); + EXPECT_EQ(perm, perms[0]); + + EXPECT_TRUE(sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, nodeElemOrd)); + EXPECT_TRUE(sparseConnectivity.remove_connectivity(nodeRank, node2, elemRank, elem, node2ElemOrd)); + + EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); + EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node2, elemRank)); +} + +} + diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp index ed63d5772fa5..87bb2ea7f49a 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp @@ -773,12 +773,36 @@ TEST_F(TestTextMesh, tooManyCoordinates) EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc, coordinates), std::logic_error); } -TEST_F(TestTextMesh, tooLittleData) +TEST_F(TestTextMesh, tooLittleData_empty) +{ + std::string meshDesc = ""; + EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); +} + +TEST_F(TestTextMesh, tooLittleData_startsWithString) +{ + std::string meshDesc = "hi"; + EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); +} + +TEST_F(TestTextMesh, tooLittleData_noGlobalId) +{ + std::string meshDesc = "0 "; + EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); +} + +TEST_F(TestTextMesh, tooLittleData_noTopology) { std::string meshDesc = "0,1,"; EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); } +TEST_F(TestTextMesh, tooLittleData_noNodes) +{ + std::string meshDesc = "0,1,HEX_8"; + EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); +} + TEST_F(TestTextMesh, tooLittleDataWithCoordinates) { std::string meshDesc = "0,1,"; @@ -827,6 +851,18 @@ TEST_F(TestTextMesh, spatialDimInconsistentWithMetaDataWithCoordinates) EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc, coordinates), std::logic_error); } +TEST_F(TestTextMesh, endingWithNewlineIsOk) +{ + std::string meshDesc = "0,1,HEX_8,1,2,3,4,5,6,7,8\n"; + EXPECT_NO_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc)); +} + +TEST_F(TestTextMesh, stringAfterPartNameIsError) +{ + std::string meshDesc = "0,1,HEX_8,1,2,3,4,5,6,7,8,block_1,bogus\n"; + EXPECT_THROW(stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc), std::logic_error); +} + TEST_F(TestTextMesh, particleHex) { if (get_parallel_size() != 1) return; diff --git a/packages/stk/stk_unit_tests/stk_mesh/ngp/KokkosBulkDataBucketCentroidCalculation.cpp b/packages/stk/stk_unit_tests/stk_mesh/ngp/KokkosBulkDataBucketCentroidCalculation.cpp index 553f031af6d1..5e8ac559153e 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/ngp/KokkosBulkDataBucketCentroidCalculation.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/ngp/KokkosBulkDataBucketCentroidCalculation.cpp @@ -75,7 +75,7 @@ struct GpuGatherBucketScratchData { const stk::mesh::NgpMesh::BucketType& bucket = ngpMesh.get_bucket(stk::topology::ELEM_RANK, elementBucketIndex); const unsigned numElements = bucket.size(); - const unsigned nodesPerElem = bucket.get_num_nodes_per_entity(); + const unsigned nodesPerElem = bucket.topology().num_nodes(); const unsigned dim = elementCentroids.extent(1); double temp[3] = {0.0, 0.0, 0.0}; for(unsigned elementIndex=0; elementIndex; class ParallelDataExchangeSymPackUnpackHandler { public: - ParallelDataExchangeSymPackUnpackHandler(std::vector> & neighbors, - ValueViewType & deviceValues) + ParallelDataExchangeSymPackUnpackHandler(std::vector>& neighbors, + ValueViewType& deviceValues) : m_neighbors(neighbors), m_deviceNeighbors(Kokkos::create_staticcrsgraph("DeviceNeighborsCrs", neighbors)), m_deviceValues(deviceValues) { } - ParallelDataExchangeSymPackUnpackHandler(const ParallelDataExchangeSymPackUnpackHandler & rhs) = default; + ParallelDataExchangeSymPackUnpackHandler(const ParallelDataExchangeSymPackUnpackHandler& rhs) = default; - void hostSizeMessages(int proc, size_t & numValues) const + void hostSizeMessages(int proc, size_t& numValues) const { numValues = 0; for (size_t i = 0; i < m_neighbors.size(); ++i) { @@ -45,7 +45,7 @@ class ParallelDataExchangeSymPackUnpackHandler } STK_FUNCTION - void devicePackMessage(int myProc, int proc, ValueViewType & sendData) const + void devicePackMessage(int myProc, int proc, ValueViewType& sendData) const { size_t bufIdx = 0; for (size_t i = 0; i < m_deviceNeighbors.numRows(); ++i) { @@ -60,7 +60,7 @@ class ParallelDataExchangeSymPackUnpackHandler } STK_FUNCTION - void deviceUnpackMessage(int myProc, int proc, ValueViewType & recvData) const + void deviceUnpackMessage(int myProc, int proc, ValueViewType& recvData) const { size_t valueLocation[3]; size_t valueLocationIdx = 0; @@ -97,7 +97,7 @@ class ParallelDataExchangeSymPackUnpackHandler } private: - std::vector> m_neighbors; + std::vector>& m_neighbors; NeighborCrsViewType m_deviceNeighbors; ValueViewType m_deviceValues; }; @@ -197,7 +197,7 @@ std::vector> get_neighbors(int pSize, int pRank) return neighbors; } -NGP_TEST_F(NgpParallelComm, DISABLED_symmetricPackUnpack) +NGP_TEST_F(NgpParallelComm, symmetricPackUnpack) { const int pSize = stk::parallel_machine_size(MPI_COMM_WORLD); const int pRank = stk::parallel_machine_rank(MPI_COMM_WORLD); diff --git a/packages/stk/stk_unit_tests/stk_mesh/ngp/howToNgp.cpp b/packages/stk/stk_unit_tests/stk_mesh/ngp/howToNgp.cpp index 3fd46cd14b09..077efdc5ab25 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/ngp/howToNgp.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/ngp/howToNgp.cpp @@ -380,7 +380,7 @@ void run_connected_face_test(const stk::mesh::BulkData& bulk) TEST_F(NgpHowTo, loopOverElemFaces) { if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { - return; + GTEST_SKIP(); } auto &field = get_meta().declare_field>(stk::topology::NODE_RANK, "myField"); double init = 0.0; @@ -390,6 +390,79 @@ TEST_F(NgpHowTo, loopOverElemFaces) run_connected_face_test(get_bulk()); } +void add_constraint_on_nodes_1_thru_4(stk::mesh::BulkData& bulk, + stk::mesh::EntityId constraintId) +{ + bulk.modification_begin(); + stk::mesh::Entity constraintEntity = bulk.declare_constraint(constraintId); + for(stk::mesh::EntityId nodeId = 1; nodeId <= 4; ++nodeId) { + stk::mesh::Entity node = bulk.get_entity(stk::topology::NODE_RANK, nodeId); + stk::mesh::ConnectivityOrdinal ord = static_cast(nodeId-1); + bulk.declare_relation(constraintEntity, node, ord); + } + bulk.modification_end(); +} + +void run_constraint_node_test(const stk::mesh::BulkData& bulk, + stk::mesh::EntityId constraintId) +{ + stk::mesh::Entity constraint = bulk.get_entity(stk::topology::CONSTRAINT_RANK, constraintId); + ASSERT_TRUE(bulk.is_valid(constraint)); + stk::mesh::Entity node0 = bulk.begin_nodes(constraint)[0]; + stk::mesh::Entity node1 = bulk.begin_nodes(constraint)[1]; + stk::mesh::Entity node2 = bulk.begin_nodes(constraint)[2]; + stk::mesh::Entity node3 = bulk.begin_nodes(constraint)[3]; + ASSERT_TRUE(bulk.is_valid(node0)); + ASSERT_TRUE(bulk.is_valid(node1)); + ASSERT_TRUE(bulk.is_valid(node2)); + ASSERT_TRUE(bulk.is_valid(node3)); + + const unsigned expectedNumNodes = bulk.num_nodes(constraint); + + const stk::mesh::NgpMesh & ngpMesh = stk::mesh::get_updated_ngp_mesh(bulk); + Kokkos::parallel_for(1, + KOKKOS_LAMBDA(const unsigned& i) { + stk::mesh::FastMeshIndex constraintMeshIndex = ngpMesh.fast_mesh_index(constraint); + + stk::mesh::NgpMesh::ConnectedEntities ngpNodes = ngpMesh.get_connected_entities(stk::topology::CONSTRAINT_RANK, constraintMeshIndex, stk::topology::NODE_RANK); + NGP_EXPECT_EQ(expectedNumNodes, ngpNodes.size()); + NGP_EXPECT_EQ(node0, ngpNodes[0]); + NGP_EXPECT_EQ(node1, ngpNodes[1]); + NGP_EXPECT_EQ(node2, ngpNodes[2]); + NGP_EXPECT_EQ(node3, ngpNodes[3]); + + stk::mesh::NgpMesh::ConnectedOrdinals ngpOrdinals = ngpMesh.get_connected_ordinals(stk::topology::CONSTRAINT_RANK, constraintMeshIndex, stk::topology::NODE_RANK); + NGP_EXPECT_EQ(4u, ngpOrdinals.size()); + NGP_EXPECT_EQ(0, ngpOrdinals[0]); + NGP_EXPECT_EQ(1, ngpOrdinals[1]); + NGP_EXPECT_EQ(2, ngpOrdinals[2]); + NGP_EXPECT_EQ(3, ngpOrdinals[3]); + } + ); +} + +class NgpHowToConstraint : public stk::unit_test_util::MeshFixture +{ +public: + NgpHowToConstraint() : MeshFixture(3, {"node", "edge", "face", "elem", "constraint"}) + {} +}; + +TEST_F(NgpHowToConstraint, checkNodalConnectivity) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { + GTEST_SKIP(); + } + auto &field = get_meta().declare_field>(stk::topology::NODE_RANK, "myField"); + double init = 0.0; + stk::mesh::put_field_on_mesh(field, get_meta().universal_part(), &init); + setup_mesh("generated:1x1x1", stk::mesh::BulkData::NO_AUTO_AURA); + stk::mesh::EntityId constraintId = 1; + add_constraint_on_nodes_1_thru_4(get_bulk(), constraintId); + + run_constraint_node_test(get_bulk(), constraintId); +} + void run_connected_face_ordinal_test(const stk::mesh::BulkData& bulk) { stk::topology elemTopo = stk::topology::HEX_8; @@ -794,6 +867,7 @@ TEST_F(NgpHowTo, setAllScalarFieldValues) double initialValue = 0.0; stk::mesh::Field &stkField = create_field_with_num_states_and_init(get_meta(), "myField", numStates, initialValue); setup_mesh("generated:1x1x4", stk::mesh::BulkData::AUTO_AURA); + stkField.sync_to_device(); stk::mesh::NgpField& ngpField = stk::mesh::get_updated_ngp_field(stkField); stk::mesh::NgpMesh & ngpMesh = stk::mesh::get_updated_ngp_mesh(get_bulk()); @@ -818,6 +892,7 @@ TEST_F(NgpHowTo, setAllVectorFieldValues) fieldDimension, initialValue); setup_mesh("generated:1x1x4", stk::mesh::BulkData::AUTO_AURA); + stkField.sync_to_device(); stk::mesh::NgpField& ngpField = stk::mesh::get_updated_ngp_field(stkField); const stk::mesh::NgpMesh& ngpMesh = stk::mesh::get_updated_ngp_mesh(get_bulk()); @@ -1078,6 +1153,10 @@ NGP_TEST_F(NgpHowTo, ReuseNgpField) stk::mesh::Field &doubleStkField = create_field_with_num_states_and_init(get_meta(), "field10", numStates, (double)0); setup_mesh("generated:1x1x4", stk::mesh::BulkData::AUTO_AURA); + auto fields = get_meta().get_fields(); + for(auto field : fields) { + field->sync_to_device(); + } { fill_field_on_device(get_bulk(), shortStkField, (short)42); @@ -1208,6 +1287,7 @@ TEST(NgpMesh, meshIndices) stk::mesh::put_field_on_mesh(field, meta.universal_part(), &init); stk::io::fill_mesh("generated:1x1x1", bulk); + field.sync_to_device(); stk::mesh::NgpMesh& ngpMesh = stk::mesh::get_updated_ngp_mesh(bulk); stk::mesh::NgpField & ngpField = stk::mesh::get_updated_ngp_field(field); int fieldVal = 5; diff --git a/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpFieldTest.cpp b/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpFieldTest.cpp index c5e2cac892c8..83740cb44f11 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpFieldTest.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpFieldTest.cpp @@ -80,6 +80,22 @@ class NgpFieldFixture : public stk::unit_test_util::MeshFixture return field; } + void setup_one_field_one_element_mesh() + { + const unsigned bucketCapacity = 1; + setup_empty_mesh(stk::mesh::BulkData::NO_AUTO_AURA, bucketCapacity); + + stk::mesh::Field& stkField = get_meta().declare_field>( + stk::topology::ELEM_RANK, "field1"); + stk::mesh::Part& block = get_meta().declare_part_with_topology("block_1", stk::topology::SHELL_QUAD_4); + + const int init1 = 1; + stk::mesh::put_field_on_mesh(stkField, block, 1, &init1); + + const std::string meshDesc = "0,1,SHELL_QUAD_4,1,2,5,6,block_1\n"; + stk::unit_test_util::setup_text_mesh(get_bulk(), meshDesc); + } + void setup_two_field_two_element_mesh() { const unsigned bucketCapacity = 1; @@ -806,13 +822,12 @@ void move_data_between_fields_on_host(const stk::mesh::BulkData & bulk, ngpDest.modify_on_host(); } -void test_field_values_on_device(stk::mesh::BulkData& bulk, - const stk::mesh::Field& stkField, - const stk::mesh::Part& part, - const int expectedFieldValue) +void test_field_values_on_device_without_initial_sync(stk::mesh::BulkData& bulk, + const stk::mesh::Field& stkField, + const stk::mesh::Part& part, + const int expectedFieldValue) { stk::mesh::NgpField & ngpField = stk::mesh::get_updated_ngp_field(stkField); - ngpField.sync_to_device(); stk::mesh::Selector selection = bulk.mesh_meta_data().locally_owned_part() & part; const stk::mesh::BucketVector& buckets = bulk.get_buckets(stkField.entity_rank(), selection); @@ -826,6 +841,17 @@ void test_field_values_on_device(stk::mesh::BulkData& bulk, }); } +void test_field_values_on_device(stk::mesh::BulkData& bulk, + const stk::mesh::Field& stkField, + const stk::mesh::Part& part, + const int expectedFieldValue) +{ + stk::mesh::NgpField & ngpField = stk::mesh::get_updated_ngp_field(stkField); + ngpField.sync_to_device(); + + test_field_values_on_device_without_initial_sync(bulk, stkField, part, expectedFieldValue); +} + void test_field_values_on_device(stk::mesh::BulkData &bulk, const stk::mesh::Field & stkField, const int expectedFieldValue) @@ -833,13 +859,11 @@ void test_field_values_on_device(stk::mesh::BulkData &bulk, test_field_values_on_device(bulk, stkField, bulk.mesh_meta_data().locally_owned_part(), expectedFieldValue); } -void test_field_values_on_host(const stk::mesh::BulkData& bulk, - const stk::mesh::Field& stkField, - const stk::mesh::Part& part, - const int expectedFieldValue) +void test_field_values_on_host_without_initial_sync(const stk::mesh::BulkData& bulk, + const stk::mesh::Field& stkField, + const stk::mesh::Part& part, + const int expectedFieldValue) { - stkField.sync_to_host(); - stk::mesh::Selector selection = bulk.mesh_meta_data().locally_owned_part() & part; const stk::mesh::BucketVector& buckets = bulk.get_buckets(stkField.entity_rank(), selection); for (size_t iBucket=0; iBucket& stkField, + const stk::mesh::Part& part, + const int expectedFieldValue) +{ + stkField.sync_to_host(); + + test_field_values_on_host_without_initial_sync(bulk, stkField, part, expectedFieldValue); +} + void test_field_values_on_host(const stk::mesh::BulkData& bulk, const stk::mesh::Field& stkField, const int expectedFieldValue) @@ -869,7 +903,7 @@ void initialize_ngp_field(stk::mesh::Field & stkField) } template -void modify_field_on_host(stk::mesh::BulkData & bulk, stk::mesh::Field & field, int multiplier) +void multiply_field_data_on_host(stk::mesh::BulkData & bulk, stk::mesh::Field & field, int multiplier) { const stk::mesh::BucketVector& buckets = bulk.buckets(field.entity_rank()); for (stk::mesh::Bucket * bucket : buckets) { @@ -878,6 +912,12 @@ void modify_field_on_host(stk::mesh::BulkData & bulk, stk::mesh::Field & fiel fieldData[iEntity] *= multiplier; } } +} + +template +void modify_field_on_host(stk::mesh::BulkData & bulk, stk::mesh::Field & field, int multiplier) +{ + multiply_field_data_on_host(bulk, field, multiplier); field.modify_on_host(); } @@ -900,12 +940,11 @@ void sync_field_to_device(stk::mesh::Field & field) } template -void modify_field_on_device(stk::mesh::BulkData & bulk, stk::mesh::Field & stkField, int multiplier) +void multiply_field_data_on_device(stk::mesh::BulkData & bulk, stk::mesh::Field & stkField, int multiplier) { stk::mesh::NgpMesh & ngpMesh = stk::mesh::get_updated_ngp_mesh(bulk); const stk::mesh::MetaData & meta = bulk.mesh_meta_data(); stk::mesh::NgpField & ngpField = stk::mesh::get_updated_ngp_field(stkField); - ngpField.sync_to_device(); stk::mesh::for_each_entity_run(ngpMesh, stk::topology::ELEM_RANK, meta.locally_owned_part(), KOKKOS_LAMBDA(const stk::mesh::FastMeshIndex& entity) { @@ -914,6 +953,16 @@ void modify_field_on_device(stk::mesh::BulkData & bulk, stk::mesh::Field & st ngpField(entity, component) *= multiplier; } }); +} + +template +void modify_field_on_device(stk::mesh::BulkData & bulk, stk::mesh::Field & stkField, int multiplier) +{ + stk::mesh::NgpField & ngpField = stk::mesh::get_updated_ngp_field(stkField); + ngpField.sync_to_device(); + + multiply_field_data_on_device(bulk, stkField, multiplier); + stkField.modify_on_device(); } @@ -972,6 +1021,58 @@ TEST_F(NgpFieldFixture, noFieldDataTest) EXPECT_NO_THROW(stk::mesh::get_updated_ngp_field(field)); } +TEST_F(NgpFieldFixture, ModifyOnHostFlagClearedOnInitialNgpFieldConstruction) +{ + if (get_parallel_size() != 1) return; + + setup_one_field_one_element_mesh(); + + stk::mesh::Field& field1 = dynamic_cast&>( + *get_meta().get_field(stk::topology::ELEM_RANK, "field1")); + EXPECT_FALSE(field1.need_sync_to_device()); + field1.modify_on_host(); + + auto ngpfield = stk::mesh::get_updated_ngp_field(field1); + EXPECT_FALSE(field1.need_sync_to_device()); +} + +TEST_F(NgpFieldFixture, InvalidModifyFlagCondition) +{ + if (get_parallel_size() != 1) return; + + setup_one_field_one_element_mesh(); + + stk::mesh::Field& field1 = dynamic_cast&>( + *get_meta().get_field(stk::topology::ELEM_RANK, "field1")); + EXPECT_FALSE(field1.need_sync_to_device()); + + auto ngpfield = stk::mesh::get_updated_ngp_field(field1); + EXPECT_FALSE(field1.need_sync_to_device()); + + field1.modify_on_host(); + EXPECT_THROW(ngpfield.modify_on_device(), std::logic_error); +} + +TEST_F(NgpFieldFixture, PersistentModifyOnDeviceFlag) +{ + if (get_parallel_size() != 1) return; + + setup_one_field_one_element_mesh(); + + stk::mesh::Field& field1 = dynamic_cast&>( + *get_meta().get_field(stk::topology::ELEM_RANK, "field1")); + EXPECT_FALSE(field1.need_sync_to_host()); + field1.modify_on_device(); + + auto ngpfield = stk::mesh::get_updated_ngp_field(field1); + EXPECT_TRUE(field1.need_sync_to_host()); + + multiply_field_data_on_device(get_bulk(), field1, 2); + ngpfield.sync_to_host(); + + test_field_values_on_host_without_initial_sync(get_bulk(), field1, get_meta().universal_part(), 2); +} + TEST_F(NgpFieldFixture, noOverwriteInVariableLengthFields) { if (get_parallel_size() != 1) return; @@ -1442,117 +1543,6 @@ TEST_F(NgpFieldFixture, updateBucketPtrView) ngpField.update_bucket_pointer_view(); } -class NgpFieldSwapFixture : public NgpFieldFixture { -public: - void setup_fields_for_swap() { - stk::mesh::Field& stkIntField1 = create_field(stk::topology::ELEM_RANK, "intField1"); - stk::mesh::Field& stkIntField2 = create_field(stk::topology::ELEM_RANK, "intField2"); - setup_mesh("generated:1x1x1", stk::mesh::BulkData::NO_AUTO_AURA); - - stk::mesh::NgpField& ngpField1 = stk::mesh::get_updated_ngp_field(stkIntField1); - stk::mesh::NgpField& ngpField2 = stk::mesh::get_updated_ngp_field(stkIntField2); - testNgpField1 = static_cast&>(ngpField1); - testNgpField2 = static_cast&>(ngpField2); - } - -protected: - NgpFieldTester testNgpField1; - NgpFieldTester testNgpField2; - -}; - -TEST_F(NgpFieldSwapFixture, SwapSyncState_ModFlagsUnset) -{ - if(stk::parallel_machine_size(MPI_COMM_WORLD) != 1) { return; } - - setup_fields_for_swap(); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); - - testNgpField1.swap(testNgpField2); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); -} - -TEST_F(NgpFieldSwapFixture, SwapSyncState_ModFlagsSetModDevice) -{ - if(stk::parallel_machine_size(MPI_COMM_WORLD) != 1) { return; } - - setup_fields_for_swap(); - - testNgpField1.modify_on_device(); - - EXPECT_TRUE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); - - testNgpField1.swap(testNgpField2); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_TRUE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); -} - -TEST_F(NgpFieldSwapFixture, SwapSyncState_ModFlagsSetModHost) -{ - if(stk::parallel_machine_size(MPI_COMM_WORLD) != 1) { return; } - - setup_fields_for_swap(); - - testNgpField2.modify_on_host(); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_TRUE(testNgpField2.test_need_sync_to_device()); - - testNgpField1.swap(testNgpField2); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_TRUE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); -} - -TEST_F(NgpFieldSwapFixture, SwapSyncState_ModFlagsSetModHostDevice) -{ - if(stk::parallel_machine_size(MPI_COMM_WORLD) != 1) { return; } - - setup_fields_for_swap(); - - testNgpField1.modify_on_host(); - testNgpField2.modify_on_device(); - - EXPECT_FALSE(testNgpField1.test_need_sync_to_host()); - EXPECT_TRUE(testNgpField2.test_need_sync_to_host()); - EXPECT_TRUE(testNgpField1.test_need_sync_to_device()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_device()); - - testNgpField1.swap(testNgpField2); - - EXPECT_TRUE(testNgpField1.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField2.test_need_sync_to_host()); - EXPECT_FALSE(testNgpField1.test_need_sync_to_device()); - EXPECT_TRUE(testNgpField2.test_need_sync_to_device()); -} - -TEST_F(OptimizedNgpFieldFixture, ChangeBucketContentsByUserWithSingleComponent) -{ - if (get_parallel_size() != 1) return; - - unsigned numComponents = 1; - - run_change_bucket_content_by_user(numComponents); -} - // ------------------------- ------------------------- // | | | | | | | | // | 1 | 2 | 3 | ===> | 1 | 2 | 3 | diff --git a/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpMultiStateFieldTests.cpp b/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpMultiStateFieldTests.cpp index 89cc02fed60b..1733400126b9 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpMultiStateFieldTests.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/ngp/ngpMultiStateFieldTests.cpp @@ -229,3 +229,67 @@ NGP_TEST_F(NgpMultiStateFieldTest, persistentDeviceField_hasCorrectDataAfterStat delete_class_on_device(persistentDeviceClass); } + +NGP_TEST_F(NgpMultiStateFieldTest, persistentSyncToDeviceCountAfterStateRotation) +{ + if (get_parallel_size() != 1) GTEST_SKIP(); + setup_multistate_field(); + setup_mesh(2, 2, 2); + + stk::mesh::NgpField& ngpFieldNew = stk::mesh::get_updated_ngp_field(get_field_new()); + stk::mesh::NgpField& ngpFieldOld = stk::mesh::get_updated_ngp_field(get_field_old()); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_device(), ngpFieldOld.num_syncs_to_device()); + + ngpFieldNew.modify_on_host(); + ngpFieldNew.sync_to_device(); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_device(), ngpFieldOld.num_syncs_to_device()+1); + + perform_field_state_rotation(); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_device()+1, ngpFieldOld.num_syncs_to_device()); +} + +NGP_TEST_F(NgpMultiStateFieldTest, persistentSyncToHostCountAfterStateRotation) +{ + if (get_parallel_size() != 1) GTEST_SKIP(); + setup_multistate_field(); + setup_mesh(2, 2, 2); + + stk::mesh::NgpField& ngpFieldNew = stk::mesh::get_updated_ngp_field(get_field_new()); + stk::mesh::NgpField& ngpFieldOld = stk::mesh::get_updated_ngp_field(get_field_old()); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_device(), ngpFieldOld.num_syncs_to_device()); + + ngpFieldOld.modify_on_device(); + ngpFieldOld.sync_to_host(); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_host()+1, ngpFieldOld.num_syncs_to_host()); + + perform_field_state_rotation(); + + EXPECT_EQ(ngpFieldNew.num_syncs_to_host(), ngpFieldOld.num_syncs_to_host()+1); +} + +NGP_TEST_F(NgpMultiStateFieldTest, persistentModifyOnHostAfterStateRotation) +{ + if (get_parallel_size() != 1) GTEST_SKIP(); + setup_multistate_field(); + setup_mesh(2, 2, 2); + + stk::mesh::NgpField& ngpFieldNew = stk::mesh::get_updated_ngp_field(get_field_new()); + stk::mesh::NgpField& ngpFieldOld = stk::mesh::get_updated_ngp_field(get_field_old()); + ngpFieldNew.clear_sync_state(); + ngpFieldOld.clear_sync_state(); + + ngpFieldNew.modify_on_host(); + + EXPECT_TRUE(ngpFieldNew.need_sync_to_device()); + EXPECT_FALSE(ngpFieldOld.need_sync_to_device()); + + get_bulk().update_field_data_states(); + + EXPECT_FALSE(ngpFieldNew.need_sync_to_device()); + EXPECT_TRUE(ngpFieldOld.need_sync_to_device()); +} \ No newline at end of file diff --git a/packages/stk/stk_unit_tests/stk_search/UnitTestCoarseSearch.cpp b/packages/stk/stk_unit_tests/stk_search/UnitTestCoarseSearch.cpp index 64595f794cdf..403f4ffe173d 100644 --- a/packages/stk/stk_unit_tests/stk_search/UnitTestCoarseSearch.cpp +++ b/packages/stk/stk_unit_tests/stk_search/UnitTestCoarseSearch.cpp @@ -6,15 +6,15 @@ // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: -// +// // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. -// +// // * Redistributions in binary form must reproduce the above // copyright notice, this list of conditions and the following // disclaimer in the documentation and/or other materials provided // with the distribution. -// +// // * Neither the name of NTESS nor the names of its contributors // may be used to endorse or promote products derived from this // software without specific prior written permission. @@ -30,19 +30,23 @@ // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include -#include +// #include #include -#include -#include #include -#include #include +#include +#include +#include +#include +#include +#include + +typedef stk::search::Point Point; +typedef stk::search::Box StkBox; +typedef std::vector< std::pair > BoxVector; namespace std { template @@ -52,52 +56,44 @@ std::ostream & operator<<(std::ostream & out, std::pair Point; - typedef stk::search::Box StkBox; - typedef std::vector< std::pair > BoxVector; - int num_procs = stk::parallel_machine_size(comm); int proc_id = stk::parallel_machine_rank(comm); @@ -130,7 +126,153 @@ void testCoarseSearchForAlgorithm(stk::search::SearchMethod algorithm, MPI_Comm expect_search_results(num_procs, proc_id, searchResults); } -void testCoarseSearchForAlgorithmUsingFloatAABoxes(stk::search::SearchMethod algorithm, MPI_Comm comm) +std::pair build_range_boxes_and_nested_domain_boxes(int num_procs, int proc_id, int sizeParam=1) +{ + BoxVector local_domain, local_range; + + int startID = 0; + if (proc_id == 0) { + for (int i = 0; i < sizeParam; ++i) { + for (int j = 0; j < sizeParam; ++j, ++startID) { + StkBox box( Point(num_procs*i, num_procs*j, 0.0), Point(num_procs*(i+1), num_procs*(j+1), 1.0)); + Ident id(startID, proc_id); + local_range.push_back(std::make_pair(box,id)); + } + } + } + + for (int procShift = 0; procShift < num_procs; ++procShift) { + for (int i = 0; i < sizeParam; ++i) { + for (int j = 0; j < sizeParam; ++j, ++startID) { + StkBox box( Point(procShift*sizeParam+i, sizeParam*proc_id+j, 0.0), Point(procShift*sizeParam+i+1.0, sizeParam*proc_id+j+1, 1.0)); + Ident id(startID, proc_id); + local_domain.push_back(std::make_pair(box,id)); + } + } + } + + return std::make_pair(local_domain, local_range); + +} + +void expect_coarse_search_range_box_communication(int num_procs, + int proc_id, + const SearchResults& searchResultsCommunicateOn, + const SearchResults& searchResultsCommunicateOff) +{ + if (num_procs == 1) { + ASSERT_EQ(searchResultsCommunicateOn.size(), 1u); + ASSERT_EQ(searchResultsCommunicateOff.size(), 1u); + EXPECT_EQ(searchResultsCommunicateOn[0], std::make_pair(Ident(1, 0), Ident(0, 0))); + EXPECT_EQ(searchResultsCommunicateOff[0], std::make_pair(Ident(1, 0), Ident(0, 0))); + } + + else { + bool onRangeBoxProc = (proc_id == 0); + if (onRangeBoxProc) { + ASSERT_GT(searchResultsCommunicateOn.size(), searchResultsCommunicateOff.size()); + ASSERT_EQ(searchResultsCommunicateOn.size(), static_cast(num_procs * num_procs)); + } else { + ASSERT_EQ(searchResultsCommunicateOn.size(), static_cast(num_procs)); + } + ASSERT_EQ(searchResultsCommunicateOff.size(), static_cast(num_procs)); + + for (auto searchResult : searchResultsCommunicateOff) { + EXPECT_EQ(searchResult.first.proc(), proc_id); + } + } +} + +void test_coarse_search_range_box_communication(stk::search::SearchMethod algorithm, MPI_Comm comm) +{ + + BoxVector local_domain, local_range; + int num_procs = stk::parallel_machine_size(comm); + int proc_id = stk::parallel_machine_rank(comm); + + std::tie(local_domain, local_range) = build_range_boxes_and_nested_domain_boxes(num_procs, proc_id); + + SearchResults searchResultsCommunicateOn; + SearchResults searchResultsCommunicateOff; + + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsCommunicateOn, true, false); + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsCommunicateOff, false, false); + + expect_coarse_search_range_box_communication(num_procs, proc_id, searchResultsCommunicateOn, searchResultsCommunicateOff); +} + +TEST(stk_search, coarse_search_range_box_communication) +{ + test_coarse_search_range_box_communication(stk::search::KDTREE, MPI_COMM_WORLD); +} + +void test_coarse_search_determine_domain_and_range_communicate_on(stk::search::SearchMethod algorithm, MPI_Comm comm) +{ + + BoxVector local_domain, local_range; + int num_procs = stk::parallel_machine_size(comm); + int proc_id = stk::parallel_machine_rank(comm); + + std::tie(local_domain, local_range) = build_range_boxes_and_nested_domain_boxes(num_procs, proc_id); + + SearchResults searchResultsDetermineOn; + SearchResults searchResultsDetermineOff; + + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsDetermineOn, true, true); + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsDetermineOff, true, false); + + std::sort(searchResultsDetermineOn.begin(), searchResultsDetermineOn.end()); + std::sort(searchResultsDetermineOff.begin(), searchResultsDetermineOff.end()); + + EXPECT_EQ(searchResultsDetermineOn, searchResultsDetermineOff); +} + +TEST(stk_search, coarse_search_determine_domain_and_range_communicate_on) +{ + test_coarse_search_determine_domain_and_range_communicate_on(stk::search::KDTREE, MPI_COMM_WORLD); +} + +void test_coarse_search_two_pass(stk::search::SearchMethod algorithm, MPI_Comm comm, int sizeParam) +{ + BoxVector local_domain, local_range, additional_domain; + int num_procs = stk::parallel_machine_size(comm); + int proc_id = stk::parallel_machine_rank(comm); + + std::tie(local_domain, local_range) = build_range_boxes_and_nested_domain_boxes(num_procs, proc_id, sizeParam); + if (proc_id == num_procs - 1) { + StkBox box( Point(0.0, 0.0, 0.0), Point(1.0, 1.0, 1.0)); + Ident id(local_domain.size(), proc_id); + additional_domain.push_back(std::make_pair(box,id)); + } + + SearchResults searchResultsPassOne; + SearchResults searchResultsPassTwo; + SearchResults searchResultsAllBoxes; + + bool communicate = false; + bool determine = false; + + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsPassOne, communicate, determine); + stk::search::coarse_search(additional_domain, local_range, algorithm, comm, searchResultsPassTwo, communicate, determine); + + local_domain.insert(local_domain.end(), additional_domain.begin(), additional_domain.end()); + + stk::search::coarse_search(local_domain, local_range, algorithm, comm, searchResultsAllBoxes, communicate, determine); + + searchResultsPassOne.insert(searchResultsPassOne.end(), searchResultsPassTwo.begin(), searchResultsPassTwo.end()); + + std::sort(searchResultsPassOne.begin(), searchResultsPassOne.end()); + std::sort(searchResultsAllBoxes.begin(), searchResultsAllBoxes.end()); + + EXPECT_EQ(searchResultsPassOne, searchResultsAllBoxes); +} + +TEST(stk_search, coarse_search_two_pass) +{ + test_coarse_search_two_pass(stk::search::KDTREE, MPI_COMM_WORLD, 2); +} + +void test_coarse_search_for_algorithm_using_float_boxes(stk::search::SearchMethod algorithm, MPI_Comm comm) { int num_procs = stk::parallel_machine_size(comm); int proc_id = stk::parallel_machine_rank(comm); @@ -166,83 +308,70 @@ void testCoarseSearchForAlgorithmUsingFloatAABoxes(stk::search::SearchMethod alg TEST(stk_search, coarse_search_kdtree) { - testCoarseSearchForAlgorithm(stk::search::KDTREE, MPI_COMM_WORLD); + test_coarse_search_for_algorithm(stk::search::KDTREE, MPI_COMM_WORLD); } TEST(stk_search, coarse_search_kdtree_using_float_aa_boxes) { - testCoarseSearchForAlgorithmUsingFloatAABoxes(stk::search::KDTREE, MPI_COMM_WORLD); + test_coarse_search_for_algorithm_using_float_boxes(stk::search::KDTREE, MPI_COMM_WORLD); } -void testIdentProcWithSearch(stk::search::SearchMethod searchMethod) +void test_ident_proc_with_search(stk::search::SearchMethod searchMethod) { - MPI_Comm comm = MPI_COMM_WORLD; - int procId=-1; - MPI_Comm_rank(comm, &procId); - int numProcs = -1; - MPI_Comm_size(comm, &numProcs); - - if ( numProcs != 1 ) - { - FloatBox box1(0,0,0,1,1,1); - FloatBox box2(0.5, 0.5, 0.5, 1.5, 1.5, 1.5); - Ident id1(1, 0); - Ident id2(1, 1); - - FloatBoxVector boxes; - if ( procId == 0 ) - { - boxes.push_back(std::make_pair(box1, id1)); - } - else if ( procId == 1 ) - { - boxes.push_back(std::make_pair(box2, id2)); - } + MPI_Comm comm = MPI_COMM_WORLD; + int procId = -1; + MPI_Comm_rank(comm, &procId); + int numProcs = -1; + MPI_Comm_size(comm, &numProcs); + + if (numProcs != 1) { + FloatBox box1(0, 0, 0, 1, 1, 1); + FloatBox box2(0.5, 0.5, 0.5, 1.5, 1.5, 1.5); + Ident id1(1, 0); + Ident id2(1, 1); + + FloatBoxVector boxes; + if (procId == 0) { + boxes.push_back(std::make_pair(box1, id1)); + } else if (procId == 1) { + boxes.push_back(std::make_pair(box2, id2)); + } - SearchResults searchResults; + SearchResults searchResults; - coarse_search(boxes, boxes, searchMethod, comm, searchResults); + coarse_search(boxes, boxes, searchMethod, comm, searchResults); - SearchResults goldResults; + SearchResults goldResults; - Ident goldId1(1, 0); - Ident goldId2(1, 1); + Ident goldId1(1, 0); + Ident goldId2(1, 1); - if (procId == 0 ) - { - goldResults.push_back(std::make_pair(goldId1, goldId1)); - goldResults.push_back(std::make_pair(goldId1, goldId2)); - goldResults.push_back(std::make_pair(goldId2, goldId1)); - ASSERT_EQ(goldResults.size(), searchResults.size()); - } - else if ( procId == 1 ) - { - goldResults.push_back(std::make_pair(goldId1, goldId2)); - goldResults.push_back(std::make_pair(goldId2, goldId1)); - goldResults.push_back(std::make_pair(goldId2, goldId2)); - ASSERT_EQ(3u, searchResults.size()); - } + if (procId == 0) { + goldResults.push_back(std::make_pair(goldId1, goldId1)); + goldResults.push_back(std::make_pair(goldId1, goldId2)); + goldResults.push_back(std::make_pair(goldId2, goldId1)); + ASSERT_EQ(goldResults.size(), searchResults.size()); + } else if (procId == 1) { + goldResults.push_back(std::make_pair(goldId1, goldId2)); + goldResults.push_back(std::make_pair(goldId2, goldId1)); + goldResults.push_back(std::make_pair(goldId2, goldId2)); + ASSERT_EQ(3u, searchResults.size()); + } - for (size_t i=0;i Ident; - typedef stk::search::Point Point; - typedef stk::search::Box StkBox; - typedef std::vector > BoxVector; - typedef std::vector > SearchResults; - stk::ParallelMachine comm = MPI_COMM_WORLD; //int num_procs = stk::parallel_machine_size(comm); int proc_id = stk::parallel_machine_rank(comm); @@ -289,10 +418,10 @@ void testCoarseSearchOnePoint(stk::search::SearchMethod searchMethod) TEST(stk_search, coarse_search_one_point_KDTREE) { - testCoarseSearchOnePoint(stk::search::KDTREE); + test_coarse_search_one_point(stk::search::KDTREE); } -void testCoarseSearchForDeterminingSharingAllAllCase(stk::search::SearchMethod searchMethod) +void test_coarse_search_for_determining_sharing_all_all_case(stk::search::SearchMethod searchMethod) { const stk::ParallelMachine comm = MPI_COMM_WORLD; const int p_rank = stk::parallel_machine_rank(comm); @@ -343,12 +472,11 @@ void testCoarseSearchForDeterminingSharingAllAllCase(stk::search::SearchMethod s TEST(CoarseSearch, forDeterminingSharingAllAllCase_KDTREE) { - testCoarseSearchForDeterminingSharingAllAllCase(stk::search::KDTREE); + test_coarse_search_for_determining_sharing_all_all_case(stk::search::KDTREE); } - -void testCoarseSearchForDeterminingSharingLinearAdjacentCase(stk::search::SearchMethod searchMethod, - int numLoops = 1) +void test_coarse_search_for_determining_sharing_linear_adjacent_case( + stk::search::SearchMethod searchMethod, int numLoops = 1) { const stk::ParallelMachine comm = MPI_COMM_WORLD; const int p_rank = stk::parallel_machine_rank(comm); @@ -446,12 +574,12 @@ void testCoarseSearchForDeterminingSharingLinearAdjacentCase(stk::search::Search TEST(CoarseSearch, forDeterminingSharingLinearAdjacentCase_KDTREE) { - testCoarseSearchForDeterminingSharingLinearAdjacentCase(stk::search::KDTREE); + test_coarse_search_for_determining_sharing_linear_adjacent_case(stk::search::KDTREE); } TEST(CoarseSearchScaling, forDeterminingSharingLinearAdjacentCase_KDTREE) { - testCoarseSearchForDeterminingSharingLinearAdjacentCase(stk::search::KDTREE, 1000); + test_coarse_search_for_determining_sharing_linear_adjacent_case(stk::search::KDTREE, 1000); } } //namespace diff --git a/packages/stk/stk_unit_tests/stk_simd_old/UnitTestStkSimdView2d.cpp b/packages/stk/stk_unit_tests/stk_simd_old/UnitTestStkSimdView2d.cpp index 011d46d984ad..48700d20f9ea 100644 --- a/packages/stk/stk_unit_tests/stk_simd_old/UnitTestStkSimdView2d.cpp +++ b/packages/stk/stk_unit_tests/stk_simd_old/UnitTestStkSimdView2d.cpp @@ -84,10 +84,12 @@ class StkSimdView2dTester { set_b_to_2a_plus_b_functor_with_tag(a, b); test_view_equal_to_index_multiple(stk::simd::copy_from_device(b), 5); +#ifndef KOKKOS_ENABLE_CUDA auto aHost = stk::simd::copy_from_device(a); auto bHost = stk::simd::copy_from_device(b); set_b_to_3a_plus_b_for_each_lambda(aHost, bHost); test_view_equal_to_index_multiple(bHost, 8); +#endif } void parallel_reduce_test(int loopSize, int j) const { diff --git a/packages/stk/stk_unit_tests/stk_tools/mesh_clone/UnitTestBulkDataClone.cpp b/packages/stk/stk_unit_tests/stk_tools/mesh_clone/UnitTestBulkDataClone.cpp index 8fd3c1be43b9..c7b94b2dbe4a 100644 --- a/packages/stk/stk_unit_tests/stk_tools/mesh_clone/UnitTestBulkDataClone.cpp +++ b/packages/stk/stk_unit_tests/stk_tools/mesh_clone/UnitTestBulkDataClone.cpp @@ -321,7 +321,7 @@ class CloningMesh : public stk::unit_test_util::MeshFixture expect_equal_entity_counts(oldBulk, universalPart, newBulk); const stk::mesh::MetaData &oldMeta = oldBulk.mesh_meta_data(); - ASSERT_EQ(5u, oldMeta.entity_rank_count()); + ASSERT_EQ(5u, static_cast(oldMeta.entity_rank_count())); stk::mesh::Selector localOrSharedSelector = oldMeta.locally_owned_part() | oldMeta.globally_shared_part(); stk::mesh::EntityRank endRank = static_cast(oldMeta.entity_rank_count()); stk::mesh::EntityVector oldEntities; @@ -364,7 +364,7 @@ class CloningMesh : public stk::unit_test_util::MeshFixture expect_equal_entity_counts(oldBulk, copySelector, newBulk); const stk::mesh::MetaData &oldMeta = oldBulk.mesh_meta_data(); - ASSERT_EQ(5u, oldMeta.entity_rank_count()); + ASSERT_EQ(5u, static_cast(oldMeta.entity_rank_count())); stk::mesh::Selector localOrSharedSelector = copySelector & (oldMeta.locally_owned_part() | oldMeta.globally_shared_part()); stk::mesh::EntityRank endRank = static_cast(oldMeta.entity_rank_count()); stk::mesh::EntityVector oldEntities; diff --git a/packages/stk/stk_unit_tests/stk_util/CMakeLists.txt b/packages/stk/stk_unit_tests/stk_util/CMakeLists.txt index 2866fae9e89e..a6198872f16e 100644 --- a/packages/stk/stk_unit_tests/stk_util/CMakeLists.txt +++ b/packages/stk/stk_unit_tests/stk_util/CMakeLists.txt @@ -38,6 +38,7 @@ FILE(GLOB SOURCES *.cpp command_line/*.cpp diag/*.cpp environment/*.cpp + ngp/*.cpp parallel/*.cpp registry/*.cpp util/*.cpp) diff --git a/packages/stk/stk_unit_tests/stk_util/environment/UnitTestOutputLog.cpp b/packages/stk/stk_unit_tests/stk_util/environment/UnitTestOutputLog.cpp index 74d5a9470cd4..e4fd3bac33f6 100644 --- a/packages/stk/stk_unit_tests/stk_util/environment/UnitTestOutputLog.cpp +++ b/packages/stk/stk_unit_tests/stk_util/environment/UnitTestOutputLog.cpp @@ -35,169 +35,226 @@ #include "gtest/gtest.h" #include "stk_util/parallel/Parallel.hpp" #include "stk_util/environment/OutputLog.hpp" +#include "stk_util/environment/EnvData.hpp" +#include "stk_util/environment/Env.hpp" #include #include #include -TEST(UnitTestOutputLog, UnitTest) +class TestOutputStreams : public ::testing::Test { - if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } - - // UseCase-Environment registers a bunch of things automatically, some of - // which conflict with this test. We unregister the conflicting streams - // here. - if (stk::get_log_ostream("cout") != NULL) { - stk::unregister_log_ostream(*stk::get_log_ostream("cout")); - } - if (stk::get_log_ostream("cerr") != NULL) { - stk::unregister_log_ostream(*stk::get_log_ostream("cerr")); - } - if (stk::get_ostream_ostream("out") != NULL) { - stk::unregister_ostream(*stk::get_ostream_ostream("out")); - } - if (stk::get_ostream_ostream("pout") != NULL) { - stk::unregister_ostream(*stk::get_ostream_ostream("pout")); +protected: + virtual void SetUp() override + { + // We unregister any conflicting streams here. + if (stk::get_log_ostream("cout") != NULL) { + stk::unregister_log_ostream(*stk::get_log_ostream("cout")); + } + if (stk::get_log_ostream("cerr") != NULL) { + stk::unregister_log_ostream(*stk::get_log_ostream("cerr")); + } + if (stk::get_ostream_ostream("out") != NULL) { + stk::unregister_ostream(*stk::get_ostream_ostream("out")); + } + if (stk::get_ostream_ostream("pout") != NULL) { + stk::unregister_ostream(*stk::get_ostream_ostream("pout")); + } } +}; + +TEST_F(TestOutputStreams, RegisterBindUnregister) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } // Make cout and cerr available as log stream targets. stk::register_log_ostream(std::cout, "cout"); stk::register_log_ostream(std::cerr, "cerr"); - // Test registration, binding, rebinding and unregistration - { - std::ostringstream log1; - std::ostringstream log2; - - std::ostream out(std::cout.rdbuf()); - - stk::register_ostream(out, "out"); - - ASSERT_TRUE(stk::is_registered_ostream("out")); - - stk::register_log_ostream(log1, "log1"); - stk::register_log_ostream(log2, "log2"); - - stk::bind_output_streams("out>log1"); - - out << "stk::bind_output_streams(\"out>log1\");" << std::endl; - - stk::bind_output_streams("out>+log2"); - out << "stk::bind_output_streams(\"out>+log2\");" << std::endl; - - stk::bind_output_streams("out>-log1"); - out << "stk::bind_output_streams(\"out>-log1\");" << std::endl; - - stk::bind_output_streams("out>-log2"); - out << "stk::bind_output_streams(\"out>-log2\");" << std::endl; - - std::ostringstream log1_result; - log1_result << "stk::bind_output_streams(\"out>log1\");" << std::endl - << "stk::bind_output_streams(\"out>+log2\");" << std::endl; - - std::ostringstream log2_result; - log2_result << "stk::bind_output_streams(\"out>+log2\");" << std::endl - << "stk::bind_output_streams(\"out>-log1\");" << std::endl; - - ASSERT_EQ((log1_result.str() == log1.str()), true); - ASSERT_EQ((log2_result.str() == log2.str()), true); - - stk::unregister_log_ostream(log1); - stk::unregister_log_ostream(log2); - stk::unregister_ostream(out); - - ASSERT_EQ(out.rdbuf(), std::cout.rdbuf()); - } + std::ostringstream log1; + std::ostringstream log2; + + std::ostream out(std::cout.rdbuf()); - // Test logging to a file - { - std::ostream out(std::cout.rdbuf()); + stk::register_ostream(out, "out"); - stk::register_ostream(out, "out"); + ASSERT_TRUE(stk::is_registered_ostream("out")); + + stk::register_log_ostream(log1, "log1"); + stk::register_log_ostream(log2, "log2"); - stk::bind_output_streams("log=\"logfile\" out>log"); + stk::bind_output_streams("out>log1"); - ASSERT_EQ((std::string("logfile") == stk::get_log_path("log")), true); - - out << "This is a test" << std::endl; + out << "stk::bind_output_streams(\"out>log1\");" << std::endl; - stk::bind_output_streams("log=\"\""); - - stk::unregister_ostream(out); + stk::bind_output_streams("out>+log2"); + out << "stk::bind_output_streams(\"out>+log2\");" << std::endl; + + stk::bind_output_streams("out>-log1"); + out << "stk::bind_output_streams(\"out>-log1\");" << std::endl; - std::ostringstream log_result; - log_result << "This is a test"; - - std::ifstream log_stream("logfile"); - std::string log_string; - getline(log_stream, log_string); - ASSERT_EQ((log_result.str() == log_string), true); + stk::bind_output_streams("out>-log2"); + out << "stk::bind_output_streams(\"out>-log2\");" << std::endl; + + std::ostringstream log1_result; + log1_result << "stk::bind_output_streams(\"out>log1\");" << std::endl + << "stk::bind_output_streams(\"out>+log2\");" << std::endl; + + std::ostringstream log2_result; + log2_result << "stk::bind_output_streams(\"out>+log2\");" << std::endl + << "stk::bind_output_streams(\"out>-log1\");" << std::endl; + + ASSERT_EQ((log1_result.str() == log1.str()), true); + ASSERT_EQ((log2_result.str() == log2.str()), true); + + stk::unregister_log_ostream(log1); + stk::unregister_log_ostream(log2); + stk::unregister_ostream(out); + + ASSERT_EQ(out.rdbuf(), std::cout.rdbuf()); +} + +TEST_F(TestOutputStreams, LogToFile) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } + + std::ostream out(std::cout.rdbuf()); + + stk::register_ostream(out, "out"); + + stk::bind_output_streams("log=\"logfile\" out>log"); + + ASSERT_EQ((std::string("logfile") == stk::get_log_path("log")), true); + + out << "This is a test" << std::endl; + + stk::bind_output_streams("log=\"\""); + + stk::unregister_ostream(out); + + std::ostringstream log_result; + log_result << "This is a test"; + + std::ifstream log_stream("logfile"); + std::string log_string; + getline(log_stream, log_string); + ASSERT_EQ((log_result.str() == log_string), true); +} + +TEST_F(TestOutputStreams, LogViaOutputP0) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } + + stk::bind_output_streams("log=\"myfile.log\""); + stk::EnvData::instance().m_outputP0 = stk::get_log_ostream("log"); + + ASSERT_EQ((std::string("myfile.log") == stk::get_log_path("log")), true); + + sierra::Env::outputP0() << "This is a test" << std::endl; + + stk::bind_output_streams("log=\"\""); + + std::ostringstream log_result; + log_result << "This is a test"; + + std::ifstream log_stream("myfile.log"); + std::string log_string; + getline(log_stream, log_string); + ASSERT_EQ((log_result.str() == log_string), true); +} + +TEST_F(TestOutputStreams, LogViaSierraOut) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } + + if (stk::get_ostream_ostream("out") == NULL) { + stk::register_ostream(sierra::out(), "out"); } - // Test results of unregistration of an output stream bound as a log stream - { - std::ostringstream default_log; - std::ostream out(default_log.rdbuf()); - std::ostream pout(std::cout.rdbuf()); + stk::bind_output_streams("log=\"myfile.log\" out>log"); + + ASSERT_EQ((std::string("myfile.log") == stk::get_log_path("log")), true); + + sierra::out() << "This is a test" << std::endl; - stk::register_ostream(out, "out"); - stk::register_ostream(pout, "pout"); + stk::bind_output_streams("log=\"\""); - // Constructing the log streams after the registered output stream is not exception safe. - std::ostringstream log; - stk::register_log_ostream(log, "log"); + std::ostringstream log_result; + log_result << "This is a test"; + + std::ifstream log_stream("myfile.log"); + std::string log_string; + getline(log_stream, log_string); + ASSERT_EQ((log_result.str() == log_string), true); +} - // As a result, this try catch block must be represent to ensure the that unregistration - // happens correctly. - try { - stk::bind_output_streams("out>pout pout>log"); +TEST_F(TestOutputStreams, UnregisterOutputBoundAsLog) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } - out << "This is to out" << std::endl; - pout << "This is to pout" << std::endl; + std::ostringstream default_log; + std::ostream out(default_log.rdbuf()); + std::ostream pout(std::cout.rdbuf()); - std::ostringstream log_result; - log_result << "This is to out" << std::endl - << "This is to pout" << std::endl; - - ASSERT_EQ((log_result.str() == log.str()), true); + stk::register_ostream(out, "out"); + stk::register_ostream(pout, "pout"); - throw std::exception(); - } - catch (...) { - } + // Constructing the log streams after the registered output stream is not exception safe. + std::ostringstream log; + stk::register_log_ostream(log, "log"); - stk::unregister_log_ostream(log); - stk::unregister_ostream(pout); - stk::unregister_ostream(out); + // As a result, this try catch block must be represent to ensure the that unregistration + // happens correctly. + try { + stk::bind_output_streams("out>pout pout>log"); out << "This is to out" << std::endl; + pout << "This is to pout" << std::endl; std::ostringstream log_result; - log_result << "This is to out" << std::endl; - ASSERT_EQ((log_result.str() == default_log.str()), true); + log_result << "This is to out" << std::endl + << "This is to pout" << std::endl; + + ASSERT_EQ((log_result.str() == log.str()), true); + + throw std::exception(); + } + catch (...) { } - // Test exception of registration with existing name - { - std::ostringstream log1; - std::ostringstream log2; - - std::ostream out(std::cout.rdbuf()); - std::ostream pout(std::cout.rdbuf()); + stk::unregister_log_ostream(log); + stk::unregister_ostream(pout); + stk::unregister_ostream(out); - stk::register_ostream(out, "out"); - ASSERT_THROW(stk::register_ostream(pout, "out"), std::runtime_error); + out << "This is to out" << std::endl; - ASSERT_EQ(&out, stk::get_ostream_ostream("out")); + std::ostringstream log_result; + log_result << "This is to out" << std::endl; + ASSERT_EQ((log_result.str() == default_log.str()), true); +} - stk::register_log_ostream(log1, "log"); - - ASSERT_THROW(stk::bind_output_streams("badout>log"), std::runtime_error); - - ASSERT_THROW(stk::bind_output_streams("out>badlog"), std::runtime_error); +TEST_F(TestOutputStreams, RegisterExistingName) +{ + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) { GTEST_SKIP(); } - stk::unregister_log_ostream(log1); - stk::unregister_ostream(out); - } + std::ostringstream log1; + std::ostringstream log2; + + std::ostream out(std::cout.rdbuf()); + std::ostream pout(std::cout.rdbuf()); + + stk::register_ostream(out, "out"); + ASSERT_THROW(stk::register_ostream(pout, "out"), std::runtime_error); + + ASSERT_EQ(&out, stk::get_ostream_ostream("out")); + + stk::register_log_ostream(log1, "log"); + + ASSERT_THROW(stk::bind_output_streams("badout>log"), std::runtime_error); + + ASSERT_THROW(stk::bind_output_streams("out>badlog"), std::runtime_error); + + stk::unregister_log_ostream(log1); + stk::unregister_ostream(out); } diff --git a/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp b/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp new file mode 100644 index 000000000000..62e284586ce3 --- /dev/null +++ b/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp @@ -0,0 +1,85 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include "gtest/gtest.h" +#include +#include + +namespace ngp { + +class NgpBase { +public: + KOKKOS_DEFAULTED_FUNCTION NgpBase() = default; + KOKKOS_FUNCTION virtual ~NgpBase() {} + + virtual void host_function() = 0; +}; + +template +class NgpDerived : public NgpBase +{ +public: + KOKKOS_FUNCTION + NgpDerived() + : NgpBase() + {} + + KOKKOS_FUNCTION + ~NgpDerived() {} + + virtual void host_function() { } +}; + +} + +namespace { + +void test_device_class() +{ + int constructionFinished = 0; + Kokkos::parallel_reduce(1, KOKKOS_LAMBDA(const unsigned& i, int& localFinished) { + ngp::NgpDerived derivedClass; + localFinished = 1; + }, constructionFinished); + + EXPECT_EQ(1, constructionFinished); +} + +TEST(NgpDevice, virtualFunction) +{ + test_device_class(); +} + +} + diff --git a/packages/stk/stk_util/Jamfile b/packages/stk/stk_util/Jamfile index 06e57e3c1ed6..f6d32d725c09 100644 --- a/packages/stk/stk_util/Jamfile +++ b/packages/stk/stk_util/Jamfile @@ -173,6 +173,7 @@ exe stk_util_utest [ glob $(stk_util-root)/../stk_unit_tests/stk_util/environment/*.cpp ] [ glob $(stk_util-root)/../stk_unit_tests/stk_util/command_line/*.cpp ] [ glob $(stk_util-root)/../stk_unit_tests/stk_util/diag/*.cpp ] + [ glob $(stk_util-root)/../stk_unit_tests/stk_util/ngp/*.cpp ] [ glob $(stk_util-root)/../stk_unit_tests/stk_util/parallel/*.cpp ] /sierra/stk_unit_test_utils//stk_unit_main /sierra/stk_unit_test_utils//stk_unit_test_utils @@ -311,6 +312,7 @@ lib stk_util_util [ glob $(stk_util-root)/stk_util/util/*.cpp ] ] /mpi//mpi + /tpl/trilinos//teuchoscore /tpl/trilinos//kokkoscore /tpl/boost//boost_header_only_libs : diff --git a/packages/stk/stk_util/stk_util/parallel/ParallelIndex.hpp b/packages/stk/stk_util/stk_util/parallel/ParallelIndex.hpp index 9836831a3a78..71ad80b76783 100644 --- a/packages/stk/stk_util/stk_util/parallel/ParallelIndex.hpp +++ b/packages/stk/stk_util/stk_util/parallel/ParallelIndex.hpp @@ -96,8 +96,9 @@ class ParallelIndex { #endif /* DOXYGEN_COMPILE */ +#ifndef STK_HIDE_DEPRECATED_CODE Delete this whole header after June 2021 /** \brief Construct with locally-submitted keys */ - ParallelIndex( ParallelMachine comm, +STK_DEPRECATED ParallelIndex( ParallelMachine comm, const std::vector & local ) : m_comm( comm ), m_key_proc(), @@ -117,6 +118,7 @@ class ParallelIndex { sort_unique( m_key_proc ); } +#endif // STK_HIDE_DEPRECATED_CODE ~ParallelIndex() {} diff --git a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp index 2eb71e574bd9..6f3012616b9b 100644 --- a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp +++ b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp @@ -42,7 +42,7 @@ //In Sierra, STK_VERSION_STRING is provided on the compile line by bake. //For Trilinos stk snapshots, the following macro definition gets populated with //the real version string by the trilinos_snapshot.sh script. -#define STK_VERSION_STRING "5.1.9-59-g9d464b74" +#define STK_VERSION_STRING "5.3.1-48-ga8ff7841" #endif namespace stk { diff --git a/packages/stk/stk_util/stk_util/util/ParameterList.hpp b/packages/stk/stk_util/stk_util/util/ParameterList.hpp index 102bdbd482c8..8fa7563e2ae8 100644 --- a/packages/stk/stk_util/stk_util/util/ParameterList.hpp +++ b/packages/stk/stk_util/stk_util/util/ParameterList.hpp @@ -35,15 +35,10 @@ #ifndef PARAMETERLIST_HPP #define PARAMETERLIST_HPP -#include "stk_util/stk_config.h" // for STK_HAVE_BOOST +#include "stk_util/stk_config.h" -#ifdef STK_HAVE_BOOST -#include "boost/any.hpp" // for any, any_cast -#define STK_ANY_NAMESPACE boost -#else #include "Teuchos_any.hpp" #define STK_ANY_NAMESPACE Teuchos -#endif #include // for int64_t #include // for operator<<, basic_ostream, ostream, cerr From fa115c10f82348066bf89cf7aff9fa129acff585 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 14 Oct 2021 16:31:35 -0600 Subject: [PATCH 20/98] ifpack2,sacado: rename CUDA_SAFE_CALL -> KOKKOS_IMPL_CUDA_SAFE_CALL Rename CUDA_SAFE_CALL for compatibility with kokkos/kokkos#4249 See issue #9587 --- .../ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp | 8 ++++---- packages/sacado/src/Sacado_DynamicArrayTraits.hpp | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/packages/ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp b/packages/ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp index 73790de2bf78..dd5db17ab029 100644 --- a/packages/ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp +++ b/packages/ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp @@ -315,10 +315,10 @@ namespace Ifpack2 { #if defined(KOKKOS_ENABLE_CUDA) && defined(IFPACK2_BLOCKTRIDICONTAINER_ENABLE_PROFILE) #define IFPACK2_BLOCKTRIDICONTAINER_PROFILER_REGION_BEGIN \ - CUDA_SAFE_CALL(cudaProfilerStart()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaProfilerStart()); #define IFPACK2_BLOCKTRIDICONTAINER_PROFILER_REGION_END \ - { CUDA_SAFE_CALL( cudaProfilerStop() ); } + { KOKKOS_IMPL_CUDA_SAFE_CALL( cudaProfilerStop() ); } #else /// later put vtune profiler region #define IFPACK2_BLOCKTRIDICONTAINER_PROFILER_REGION_BEGIN @@ -676,7 +676,7 @@ namespace Ifpack2 { exec_instances.clear(); exec_instances.resize(num_streams); for (local_ordinal_type i=0;i::createInstance(stream[i], exec_instances[i]); } } @@ -688,7 +688,7 @@ namespace Ifpack2 { { const local_ordinal_type num_streams = stream.size(); for (local_ordinal_type i=0;i(0,1),f); @@ -136,7 +136,7 @@ namespace Sacado { inline void destroyGlobalMemoryPool(const Kokkos::Cuda& space) { - CUDA_SAFE_CALL( cudaFree( (void*) Impl::global_sacado_cuda_memory_pool_device ) ); + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaFree( (void*) Impl::global_sacado_cuda_memory_pool_device ) ); delete Impl::global_sacado_cuda_memory_pool_host; } @@ -193,7 +193,7 @@ namespace Sacado { #if defined( CUDA_VERSION ) && ( 6000 <= CUDA_VERSION ) && defined(KOKKOS_ENABLE_CUDA_UVM) && !defined( __CUDA_ARCH__ ) T* m = 0; if (sz > 0) - CUDA_SAFE_CALL( cudaMallocManaged( (void**) &m, sz*sizeof(T), cudaMemAttachGlobal ) ); + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaMallocManaged( (void**) &m, sz*sizeof(T), cudaMemAttachGlobal ) ); #elif defined(HAVE_SACADO_KOKKOSCORE) && defined(SACADO_KOKKOS_USE_MEMORY_POOL) && !defined(SACADO_DISABLE_CUDA_IN_KOKKOS) && defined(__CUDA_ARCH__) // This code assumes all threads enter ds_alloc, even those with sz == 0 T* m = 0; @@ -235,7 +235,7 @@ namespace Sacado { static void ds_free(T* m, int sz) { #if defined( CUDA_VERSION ) && ( 6000 <= CUDA_VERSION ) && defined(KOKKOS_ENABLE_CUDA_UVM) && !defined( __CUDA_ARCH__ ) if (sz > 0) - CUDA_SAFE_CALL( cudaFree(m) ); + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaFree(m) ); #elif defined(HAVE_SACADO_KOKKOSCORE) && defined(SACADO_KOKKOS_USE_MEMORY_POOL) && !defined(SACADO_DISABLE_CUDA_IN_KOKKOS) && defined(__CUDA_ARCH__) const int total_sz = warpReduce(sz); const int lane = warpLane(); From 189fe360cfb17acd95eed6013f1cdb895fbcd4fd Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Fri, 15 Oct 2021 10:57:58 -0600 Subject: [PATCH 21/98] TrilinosCouplings: Adding 2D anisotropic diffusion --- .../examples/scaling/CMakeLists.txt | 1 + ...ouplings_IntrepidPoissonExampleHelpers.cpp | 16 +++++++ ...ouplings_IntrepidPoissonExampleHelpers.hpp | 5 +++ .../scaling/example_Poisson2D_pn_tpetra.cpp | 44 ++++++++++++++++--- 4 files changed, 61 insertions(+), 5 deletions(-) diff --git a/packages/trilinoscouplings/examples/scaling/CMakeLists.txt b/packages/trilinoscouplings/examples/scaling/CMakeLists.txt index 0145d4f9df78..d579fca201ad 100644 --- a/packages/trilinoscouplings/examples/scaling/CMakeLists.txt +++ b/packages/trilinoscouplings/examples/scaling/CMakeLists.txt @@ -172,6 +172,7 @@ IF(${PACKAGE_NAME}_ENABLE_Epetra AND ${PACKAGE_NAME}_ENABLE_EpetraExt AND Example_Poisson2D_pn_tpetra SOURCES example_Poisson2D_pn_tpetra.cpp TrilinosCouplings_Pamgen_Utils.cpp + TrilinosCouplings_IntrepidPoissonExampleHelpers.cpp COMM mpi ) diff --git a/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.cpp b/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.cpp index 7cec51bec895..dcab796e5b84 100644 --- a/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.cpp +++ b/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.cpp @@ -113,6 +113,8 @@ double materialTensorOffDiagonalValue_; Matrix3 rotation_, strength_,diff_total_; +std::vector matrix2D_; + bool useDiffusionMatrix() { return use_diffusion_; } @@ -136,6 +138,20 @@ const std::vector& getDiffusionMatrix() { +const std::vector& getDiffusionMatrix2D() { + // Gets the x/y sub-matrix + if(!use_diffusion_) + throw std::runtime_error("setDiffusionRotationStrength has not been called"); + matrix2D_.resize(4); + matrix2D_[0] = diff_total_(0,0); + matrix2D_[1] = diff_total_(0,1); + matrix2D_[2] = diff_total_(1,0); + matrix2D_[3] = diff_total_(1,1); + + return matrix2D_; +} + + void setDiffusionRotationAndStrength(const std::vector& theta, const std::vector& diagonal) { rotation_ = Z_Rotation(theta[2]*M_PI/180.0) * Y_Rotation(theta[1]*M_PI/180.0) * X_Rotation(theta[0]*M_PI/180.0); diff --git a/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.hpp b/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.hpp index 35f7e680cab8..5daf4cda0bd5 100644 --- a/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.hpp +++ b/packages/trilinoscouplings/examples/scaling/TrilinosCouplings_IntrepidPoissonExampleHelpers.hpp @@ -110,6 +110,11 @@ void setDiffusionRotationAndStrength(const std::vector& diff_rotation_an /// \brief Gets the diffusion Tensor const std::vector & getDiffusionMatrix(); + +/// \brief Gets the 2D diffusion Tensor (for 2D problems) +const std::vector & getDiffusionMatrix2D(); + + /// \brief Use the diffusion tensor rather than the off-diagonal values bool useDiffusionMatrix(); diff --git a/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp b/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp index 3eefdc36f7ca..f25806937d62 100644 --- a/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp +++ b/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp @@ -87,6 +87,8 @@ // TrilinosCouplings includes #include "TrilinosCouplings_config.h" #include "TrilinosCouplings_Pamgen_Utils.hpp" +#include "TrilinosCouplings_IntrepidPoissonExampleHelpers.hpp" + // Intrepid includes #include "Intrepid_FunctionSpaceTools.hpp" @@ -469,6 +471,25 @@ int main(int argc, char *argv[]) { clp.setOption ("seed", &randomSeed, "Random Seed."); + // Material diffusion strength and rotation (in 3D) + // We'll get the 2D version of this later + std::vector diff_rotation_angle {0.0, 0.0, 0.0}; + std::vector diff_strength {1.0, 1.0, 1.0}; + for(int i=0; i<3; i++) { + char letter[4] = "xyz"; + char str1[80], str2[80]; + // Rotation + sprintf(str1,"rot_%c_angle",letter[i]); + sprintf(str2,"Rotation around %c axis, in degrees",letter[i]); + clp.setOption(str1,&diff_rotation_angle[i],str2); + + // Strength + sprintf(str1,"strength_%c",letter[i]); + sprintf(str2,"Strength of pre-rotation %c-diffusion",letter[i]); + clp.setOption(str1,&diff_strength[i],str2); + } + + switch (clp.parse(argc, argv)) { case Teuchos::CommandLineProcessor::PARSE_HELP_PRINTED: return EXIT_SUCCESS; case Teuchos::CommandLineProcessor::PARSE_ERROR: @@ -499,6 +520,15 @@ int main(int argc, char *argv[]) { } + // Diffusion Tensor + ::TrilinosCouplings::IntrepidPoissonExample::setDiffusionRotationAndStrength(diff_rotation_angle, diff_strength); + if(MyPID == 0) { + const std::vector & A = ::TrilinosCouplings::IntrepidPoissonExample::getDiffusionMatrix2D(); + std::cout<<"[ "< diffusion_tensor; + template void materialTensor(Scalar material[][2], const Scalar& x, const Scalar& y) { - - material[0][0] = 1.; - material[0][1] = 0.; + if(diffusion_tensor.size() == 0) + diffusion_tensor = ::TrilinosCouplings::IntrepidPoissonExample::getDiffusionMatrix2D(); + material[0][0] = (Scalar)diffusion_tensor[0]; + material[0][1] = (Scalar)diffusion_tensor[1]; // - material[1][0] = 0.; - material[1][1] = 1.; + material[1][0] = (Scalar)diffusion_tensor[2]; + material[1][1] = (Scalar)diffusion_tensor[3]; } /**********************************************************************************/ From 7b63df4de5b60b9b5461521eb92637242a97b394 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Fri, 15 Oct 2021 12:17:55 -0600 Subject: [PATCH 22/98] Update packages to move Kokkos::Timer out of impl namespace Silences deprecation warnings, compatibility with kokkos/kokkos#4201 Affected packaged: ifpack2, intrepid2, mortel, muelu, shylu_node{basker, fastilu, tacho}, sacado, stokhos, trilinoscouplings Commands used: grep -Rl --exclude-dir=kokkos --exclude-dir=kokkos-kernels "Impl::Timer" * | xargs sed -i 's/Impl::Timer/Timer/g' grep -Rl --exclude-dir=kokkos --exclude-dir=kokkos-kernels "Kokkos_Timer" * | xargs sed -i 's:Kokkos_Timer:Kokkos_Timer:g' --- .../src/Ifpack2_Details_FastILU_Base_def.hpp | 6 +-- .../ifpack2/src/Ifpack2_Details_Fic_def.hpp | 2 +- .../ifpack2/src/Ifpack2_Details_Fildl_def.hpp | 2 +- .../ifpack2/src/Ifpack2_Details_Filu_def.hpp | 2 +- .../ComputeBasis/Cuda/test_hgrad.cpp | 2 +- .../ComputeBasis/OpenMP/test_hgrad.cpp | 2 +- .../ComputeBasis/Serial/test_hgrad.cpp | 2 +- .../perf-test/ComputeBasis/test_hgrad.hpp | 2 +- .../ComputeBasis/test_hgrad_vector.hpp | 2 +- .../perf-test/DynRankView/Cuda/test_01.cpp | 2 +- .../perf-test/DynRankView/OpenMP/test_01.cpp | 2 +- .../perf-test/DynRankView/Serial/test_01.cpp | 2 +- .../perf-test/DynRankView/Serial/test_02.cpp | 2 +- .../perf-test/DynRankView/test_01.hpp | 2 +- .../perf-test/DynRankView/test_02.hpp | 2 +- packages/intrepid2/perf-test/test_util.hpp | 2 +- .../src/mrk_default_kokkos_device_type.hpp | 2 +- .../test/perf_tests_kokkos/KokkosKernels.cpp | 4 +- .../test/performance/advection/advection.cpp | 12 +++--- .../advection/advection_hierarchical.cpp | 6 +-- .../advection/advection_hierarchical_dfad.cpp | 6 +-- .../advection_const_basis/advection.cpp | 12 +++--- .../advection_hierarchical.cpp | 6 +-- .../advection_hierarchical_dfad.cpp | 6 +-- .../fenl_assembly/TestAssembly.hpp | 2 +- .../fenl_assembly/fenl_functors.hpp | 4 +- .../fenl_assembly_view/TestAssembly.hpp | 2 +- .../fenl_assembly_view/fenl_functors.hpp | 4 +- .../test/performance/mat_vec/common.hpp | 2 +- .../mat_vec/fad_kokkos_mat_vec_perf.cpp | 8 ++-- .../test/performance/mat_vec/mat_vec.cpp | 14 +++---- .../mat_vec/mat_vec_hierarchical.cpp | 4 +- .../mat_vec/mat_vec_hierarchical_dfad.cpp | 6 +-- .../shylu_node/basker/src/shylubasker_def.hpp | 2 +- .../basker/src/shylubasker_error_manager.hpp | 2 +- .../basker/src/shylubasker_matrix_def.hpp | 2 +- .../basker/src/shylubasker_nfactor.hpp | 10 ++--- .../basker/src/shylubasker_nfactor_blk.hpp | 4 +- .../src/shylubasker_nfactor_blk_inc.hpp | 4 +- .../basker/src/shylubasker_nfactor_col.hpp | 4 +- .../basker/src/shylubasker_nfactor_col2.hpp | 10 ++--- .../src/shylubasker_nfactor_col_inc.hpp | 2 +- .../basker/src/shylubasker_nfactor_diag.hpp | 2 +- .../basker/src/shylubasker_nfactor_inc.hpp | 8 ++-- .../basker/src/shylubasker_nfactor_kokkos.hpp | 38 +++++++++---------- .../basker/src/shylubasker_order.hpp | 4 +- .../basker/src/shylubasker_order_amd.hpp | 2 +- .../basker/src/shylubasker_order_scotch.hpp | 4 +- .../basker/src/shylubasker_sfactor.hpp | 2 +- .../basker/src/shylubasker_solve_rhs.hpp | 2 +- .../src/shylubasker_solve_rhs_kokkos.hpp | 2 +- .../basker/src/shylubasker_util.hpp | 4 +- .../basker/test/basker_test_inc.cpp | 4 +- .../shylu_node/fastilu/src/shylu_fastic.hpp | 8 ++-- .../shylu_node/fastilu/src/shylu_fastildl.hpp | 8 ++-- .../shylu_node/fastilu/src/shylu_fastilu.hpp | 8 ++-- .../example/Tacho_ExampleCholCuSolver.cpp | 4 +- .../example/Tacho_ExampleCholLevelSet.cpp | 4 +- .../example/Tacho_ExampleCholPardiso.cpp | 4 +- .../example/Tacho_ExampleCholSupernodes.cpp | 4 +- .../example/Tacho_ExampleCholTriSolve.cpp | 4 +- ...ampleCombineDataFileToMatrixMarketFile.cpp | 2 +- .../example/Tacho_ExampleCuSparseTriSolve.cpp | 4 +- .../example/Tacho_ExampleDenseByBlocks.cpp | 4 +- .../Tacho_ExampleDeviceDenseCholesky.hpp | 2 +- .../example/Tacho_ExampleDeviceDenseLDL.hpp | 2 +- .../Tacho_ExampleDeviceDenseSolver.hpp | 2 +- .../Tacho_ExampleExternalInterface.cpp | 2 +- .../Tacho_ExampleExternalInterface.hpp | 4 +- .../tacho/example/Tacho_ExamplePerfTest.cpp | 6 +-- packages/shylu/shylu_node/tacho/src/Tacho.hpp | 2 +- .../shylu_node/tacho/src/Tacho_CuSolver.hpp | 6 +-- .../tacho/src/Tacho_CuSparseTriSolve.hpp | 4 +- .../shylu_node/tacho/src/Tacho_Driver.hpp | 2 +- .../tacho/src/Tacho_MatrixMarket.hpp | 2 +- .../shylu_node/tacho/src/Tacho_Solver.hpp.org | 2 +- .../tacho/src/impl/Tacho_Driver_Impl.hpp | 4 +- .../tacho/src/impl/Tacho_GraphTools_CAMD.hpp | 2 +- .../tacho/src/impl/Tacho_GraphTools_Metis.cpp | 2 +- .../src/impl/Tacho_GraphTools_MetisMT.hpp | 2 +- .../src/impl/Tacho_GraphTools_Scotch.hpp | 2 +- .../tacho/src/impl/Tacho_Internal.hpp | 2 +- .../tacho/src/impl/Tacho_LevelSetTools.hpp | 6 +-- .../tacho/src/impl/Tacho_NumericTools.hpp | 20 +++++----- .../src/impl/Tacho_NumericTools_LevelSet.hpp | 10 ++--- .../src/impl/Tacho_NumericTools_Serial.hpp | 10 ++--- .../tacho/src/impl/Tacho_Solver_Impl.hpp | 8 ++-- .../tacho/src/impl/Tacho_SymbolicTools.cpp | 4 +- .../tacho/src/impl/Tacho_TriSolveTools.hpp | 6 +-- .../shylu_node/tacho/src/impl/Tacho_Util.hpp | 2 +- .../unit-test/Tacho_TestCrsMatrixBase.hpp | 2 +- .../unit-test/Tacho_TestCuda_dcomplex.cpp | 2 +- .../tacho/unit-test/Tacho_TestCuda_double.cpp | 2 +- .../unit-test/Tacho_TestDenseByBlocks.hpp | 2 +- .../Tacho_TestDenseLinearAlgebra.hpp | 2 +- .../unit-test/Tacho_TestDenseMatrixView.hpp | 2 +- .../tacho/unit-test/Tacho_TestGraph.hpp | 2 +- .../tacho/unit-test/Tacho_TestNumeric.hpp | 2 +- .../unit-test/Tacho_TestOpenMP_dcomplex.cpp | 2 +- .../unit-test/Tacho_TestOpenMP_double.cpp | 2 +- .../unit-test/Tacho_TestSerial_dcomplex.cpp | 2 +- .../unit-test/Tacho_TestSerial_double.cpp | 2 +- .../tacho/unit-test/Tacho_TestSymbolic.hpp | 2 +- .../tacho/unit-test/Tacho_TestTaskFunctor.hpp | 2 +- .../FadMPAssembly/TestAssembly.hpp | 4 +- .../FadMPAssembly/fenl_functors.hpp | 4 +- .../KokkosArraySPMVKernels/TestEpetra.cpp | 4 +- .../KokkosArraySPMVKernels/TestStochastic.hpp | 24 ++++++------ .../test/Performance/KokkosSpMM/TestSpMM.hpp | 8 ++-- .../Performance/MPAssembly/TestAssembly.hpp | 4 +- .../Performance/MPAssembly/fenl_functors.hpp | 4 +- .../Performance/MPVectorKernels/TestSpMv.hpp | 6 +-- .../PCEMeanMultiply/TestMeanMultiply.hpp | 12 +++--- .../examples/fenl/CGSolve.hpp | 6 +-- .../examples/fenl/fenl_functors.hpp | 4 +- .../examples/fenl/fenl_impl.hpp | 8 ++-- 116 files changed, 267 insertions(+), 267 deletions(-) diff --git a/packages/ifpack2/src/Ifpack2_Details_FastILU_Base_def.hpp b/packages/ifpack2/src/Ifpack2_Details_FastILU_Base_def.hpp index 802991269cdd..7a12468a8dbd 100644 --- a/packages/ifpack2/src/Ifpack2_Details_FastILU_Base_def.hpp +++ b/packages/ifpack2/src/Ifpack2_Details_FastILU_Base_def.hpp @@ -46,7 +46,7 @@ #define __IFPACK2_FASTILU_BASE_DEF_HPP__ #include -#include +#include #include #include "Teuchos_TimeMonitor.hpp" @@ -164,7 +164,7 @@ initialize() { throw std::runtime_error(std::string("Called ") + getName() + "::initialize() but matrix was null (call setMatrix() with a non-null matrix first)"); } - Kokkos::Impl::Timer copyTimer; + Kokkos::Timer copyTimer; CrsArrayReader::getStructure(mat_.get(), localRowPtrsHost_, localRowPtrs_, localColInds_); crsCopyTime_ = copyTimer.seconds(); initLocalPrec(); //note: initLocalPrec updates initTime @@ -196,7 +196,7 @@ compute() //get copy of values array from matrix - Kokkos::Impl::Timer copyTimer; + Kokkos::Timer copyTimer; CrsArrayReader::getValues(mat_.get(), localValues_, localRowPtrsHost_); crsCopyTime_ += copyTimer.seconds(); //add to the time spent getting rowptrs/colinds computeLocalPrec(); //this updates computeTime_ diff --git a/packages/ifpack2/src/Ifpack2_Details_Fic_def.hpp b/packages/ifpack2/src/Ifpack2_Details_Fic_def.hpp index 578f188b8b52..ea43f0438462 100644 --- a/packages/ifpack2/src/Ifpack2_Details_Fic_def.hpp +++ b/packages/ifpack2/src/Ifpack2_Details_Fic_def.hpp @@ -47,7 +47,7 @@ #include "Ifpack2_Details_Fic_decl.hpp" #include "Ifpack2_Details_CrsArrays.hpp" -#include +#include #include namespace Ifpack2 diff --git a/packages/ifpack2/src/Ifpack2_Details_Fildl_def.hpp b/packages/ifpack2/src/Ifpack2_Details_Fildl_def.hpp index 89428adf81d2..f34c588a3417 100644 --- a/packages/ifpack2/src/Ifpack2_Details_Fildl_def.hpp +++ b/packages/ifpack2/src/Ifpack2_Details_Fildl_def.hpp @@ -47,7 +47,7 @@ #include "Ifpack2_Details_Fildl_decl.hpp" #include "Ifpack2_Details_CrsArrays.hpp" -#include +#include #include namespace Ifpack2 diff --git a/packages/ifpack2/src/Ifpack2_Details_Filu_def.hpp b/packages/ifpack2/src/Ifpack2_Details_Filu_def.hpp index 2576b32a91bd..1c6cb3b4fb2b 100644 --- a/packages/ifpack2/src/Ifpack2_Details_Filu_def.hpp +++ b/packages/ifpack2/src/Ifpack2_Details_Filu_def.hpp @@ -47,7 +47,7 @@ #include "Ifpack2_Details_Filu_decl.hpp" #include "Ifpack2_Details_CrsArrays.hpp" -#include +#include #include namespace Ifpack2 diff --git a/packages/intrepid2/perf-test/ComputeBasis/Cuda/test_hgrad.cpp b/packages/intrepid2/perf-test/ComputeBasis/Cuda/test_hgrad.cpp index d546ecd70650..b95bee32b7ba 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/Cuda/test_hgrad.cpp +++ b/packages/intrepid2/perf-test/ComputeBasis/Cuda/test_hgrad.cpp @@ -48,7 +48,7 @@ #include #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/ComputeBasis/OpenMP/test_hgrad.cpp b/packages/intrepid2/perf-test/ComputeBasis/OpenMP/test_hgrad.cpp index a20f5cbe6290..5c519082b500 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/OpenMP/test_hgrad.cpp +++ b/packages/intrepid2/perf-test/ComputeBasis/OpenMP/test_hgrad.cpp @@ -48,7 +48,7 @@ #include #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/ComputeBasis/Serial/test_hgrad.cpp b/packages/intrepid2/perf-test/ComputeBasis/Serial/test_hgrad.cpp index f8c74d46b5e7..267698c9acd5 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/Serial/test_hgrad.cpp +++ b/packages/intrepid2/perf-test/ComputeBasis/Serial/test_hgrad.cpp @@ -48,7 +48,7 @@ #include #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp index a124196a9234..fbc85c747cef 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp +++ b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp @@ -100,7 +100,7 @@ namespace Intrepid2 { constexpr size_t LLC_CAPACITY = 32*1024*1024; Intrepid2::Test::Flush flush; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_horizontal = 0, t_vertical = 0; int errorFlag = 0; diff --git a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp index 7a657389a828..b2166912709a 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp +++ b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp @@ -105,7 +105,7 @@ namespace Intrepid2 { constexpr size_t LLC_CAPACITY = 32*1024*1024; Intrepid2::Test::Flush flush; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_vectorize = 0; int errorFlag = 0; diff --git a/packages/intrepid2/perf-test/DynRankView/Cuda/test_01.cpp b/packages/intrepid2/perf-test/DynRankView/Cuda/test_01.cpp index 3153701d4989..34906730acc4 100644 --- a/packages/intrepid2/perf-test/DynRankView/Cuda/test_01.cpp +++ b/packages/intrepid2/perf-test/DynRankView/Cuda/test_01.cpp @@ -46,7 +46,7 @@ */ #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/DynRankView/OpenMP/test_01.cpp b/packages/intrepid2/perf-test/DynRankView/OpenMP/test_01.cpp index 6d495563ca66..815eb62d1277 100644 --- a/packages/intrepid2/perf-test/DynRankView/OpenMP/test_01.cpp +++ b/packages/intrepid2/perf-test/DynRankView/OpenMP/test_01.cpp @@ -46,7 +46,7 @@ */ #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/DynRankView/Serial/test_01.cpp b/packages/intrepid2/perf-test/DynRankView/Serial/test_01.cpp index 94d154596a4a..c35c074d04fc 100644 --- a/packages/intrepid2/perf-test/DynRankView/Serial/test_01.cpp +++ b/packages/intrepid2/perf-test/DynRankView/Serial/test_01.cpp @@ -46,7 +46,7 @@ */ #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/DynRankView/Serial/test_02.cpp b/packages/intrepid2/perf-test/DynRankView/Serial/test_02.cpp index 12b887f10810..0e41ada32299 100644 --- a/packages/intrepid2/perf-test/DynRankView/Serial/test_02.cpp +++ b/packages/intrepid2/perf-test/DynRankView/Serial/test_02.cpp @@ -46,7 +46,7 @@ */ #include "Kokkos_Core.hpp" -#include +#include #include "Teuchos_CommandLineProcessor.hpp" diff --git a/packages/intrepid2/perf-test/DynRankView/test_01.hpp b/packages/intrepid2/perf-test/DynRankView/test_01.hpp index b73baf402f99..08f0676c4510 100644 --- a/packages/intrepid2/perf-test/DynRankView/test_01.hpp +++ b/packages/intrepid2/perf-test/DynRankView/test_01.hpp @@ -162,7 +162,7 @@ namespace Intrepid2 { << " Test Array Structure (C,P,D) = " << C << ", " << P << ", " << D << "\n" << "===============================================================================\n"; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_dynrankview[20] = {}, t_view[20] = {}; int errorFlag = 0, itest = 0; diff --git a/packages/intrepid2/perf-test/DynRankView/test_02.hpp b/packages/intrepid2/perf-test/DynRankView/test_02.hpp index ea573bfc109b..d71b6965fbdb 100644 --- a/packages/intrepid2/perf-test/DynRankView/test_02.hpp +++ b/packages/intrepid2/perf-test/DynRankView/test_02.hpp @@ -159,7 +159,7 @@ namespace Intrepid2 { << " Test Array Structure (C,P,D) = " << C << ", " << P << ", " << D << "\n" << "===============================================================================\n"; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_without_subview[20] = {}, t_with_subview[20] = {}; int errorFlag = 0, itest = 0; diff --git a/packages/intrepid2/perf-test/test_util.hpp b/packages/intrepid2/perf-test/test_util.hpp index cbe840de3b58..46b5fa4d1597 100644 --- a/packages/intrepid2/perf-test/test_util.hpp +++ b/packages/intrepid2/perf-test/test_util.hpp @@ -45,7 +45,7 @@ \author Created by Kyungjoo Kim. */ #include "Kokkos_Core.hpp" -#include +#include namespace Intrepid2 { diff --git a/packages/moertel/morkon/src/mrk_default_kokkos_device_type.hpp b/packages/moertel/morkon/src/mrk_default_kokkos_device_type.hpp index 72930d5376fd..3d81918fa556 100644 --- a/packages/moertel/morkon/src/mrk_default_kokkos_device_type.hpp +++ b/packages/moertel/morkon/src/mrk_default_kokkos_device_type.hpp @@ -104,6 +104,6 @@ struct morkon_base_impl { #include #include -#include +#include #endif diff --git a/packages/muelu/test/perf_tests_kokkos/KokkosKernels.cpp b/packages/muelu/test/perf_tests_kokkos/KokkosKernels.cpp index 05b3ec8fc35f..d5adf4e38b7e 100644 --- a/packages/muelu/test/perf_tests_kokkos/KokkosKernels.cpp +++ b/packages/muelu/test/perf_tests_kokkos/KokkosKernels.cpp @@ -2,7 +2,7 @@ #include #include #include -#include +#include template class LWGraph_kokkos { @@ -285,7 +285,7 @@ int main_(int argc, char **argv) { local_matrix_type A = kernel_construct(n); execution_space().fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; #ifdef KOKKOS_ENABLE_SERIAL if (typeid(device_type) == typeid(Kokkos::Serial)) { diff --git a/packages/sacado/test/performance/advection/advection.cpp b/packages/sacado/test/performance/advection/advection.cpp index 7d9b7c9492d6..28e514a4a1a8 100644 --- a/packages/sacado/test/performance/advection/advection.cpp +++ b/packages/sacado/test/performance/advection/advection.cpp @@ -31,7 +31,7 @@ #include "advection.hpp" #include "common.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template @@ -242,7 +242,7 @@ double time_fad_flat(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux, wgb, src, wbs, residual); Kokkos::fence(); @@ -344,7 +344,7 @@ double time_analytic_const(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux_const, wgb, src, wbs, residual); Kokkos::fence(); @@ -380,7 +380,7 @@ double time_analytic_team(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux_const, wgb, src, wbs, residual); Kokkos::fence(); diff --git a/packages/sacado/test/performance/advection/advection_hierarchical.cpp b/packages/sacado/test/performance/advection/advection_hierarchical.cpp index 680287ebc11f..1ba13d8e1a32 100644 --- a/packages/sacado/test/performance/advection/advection_hierarchical.cpp +++ b/packages/sacado/test/performance/advection/advection_hierarchical.cpp @@ -34,7 +34,7 @@ #include "advection_hierarchical.hpp" #include "common.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template @@ -144,7 +144,7 @@ double time_fad_hierarchical_flat(int ncells, int num_basis, int num_points, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i @@ -160,7 +160,7 @@ double time_dfad_hierarchical_team(int ncells, int num_basis, int num_points, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i @@ -241,7 +241,7 @@ double time_fad_flat(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux, wgb, src, wbs, residual); Kokkos::fence(); @@ -346,7 +346,7 @@ double time_analytic_const(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux_const, wgb, src, wbs, residual); Kokkos::fence(); @@ -383,7 +383,7 @@ double time_analytic_team(int ncells, int num_basis, int num_points, int ndim, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i(flux_const, wgb, src, wbs, residual); Kokkos::fence(); diff --git a/packages/sacado/test/performance/advection_const_basis/advection_hierarchical.cpp b/packages/sacado/test/performance/advection_const_basis/advection_hierarchical.cpp index c22cb121bc6f..b374642e5801 100644 --- a/packages/sacado/test/performance/advection_const_basis/advection_hierarchical.cpp +++ b/packages/sacado/test/performance/advection_const_basis/advection_hierarchical.cpp @@ -34,7 +34,7 @@ #include "advection_hierarchical.hpp" #include "common.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template @@ -145,7 +145,7 @@ double time_fad_hierarchical_flat(int ncells, int num_basis, int num_points, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i @@ -161,7 +161,7 @@ double time_dfad_hierarchical_team(int ncells, int num_basis, int num_points, // Time execution Kokkos::fence(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int i=0; i #include -#include +#include #include #include @@ -161,7 +161,7 @@ class NodeNodeGraph { //-------------------------------- // Guess at capacity required for the map: - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; wall_clock.reset(); phase = FILL_NODE_SET ; diff --git a/packages/sacado/test/performance/fenl_assembly_view/TestAssembly.hpp b/packages/sacado/test/performance/fenl_assembly_view/TestAssembly.hpp index 5f8925c74f6a..06b4bee9ddc6 100644 --- a/packages/sacado/test/performance/fenl_assembly_view/TestAssembly.hpp +++ b/packages/sacado/test/performance/fenl_assembly_view/TestAssembly.hpp @@ -109,7 +109,7 @@ Perf fenl_assembly( //------------------------------------ - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; Perf perf_stats = Perf() ; diff --git a/packages/sacado/test/performance/fenl_assembly_view/fenl_functors.hpp b/packages/sacado/test/performance/fenl_assembly_view/fenl_functors.hpp index c8ab92ec893c..749e22d518bb 100644 --- a/packages/sacado/test/performance/fenl_assembly_view/fenl_functors.hpp +++ b/packages/sacado/test/performance/fenl_assembly_view/fenl_functors.hpp @@ -58,7 +58,7 @@ #include #include -#include +#include #include #include @@ -161,7 +161,7 @@ class NodeNodeGraph { //-------------------------------- // Guess at capacity required for the map: - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; wall_clock.reset(); phase = FILL_NODE_SET ; diff --git a/packages/sacado/test/performance/mat_vec/common.hpp b/packages/sacado/test/performance/mat_vec/common.hpp index 4e157717f8d5..100448f5b473 100644 --- a/packages/sacado/test/performance/mat_vec/common.hpp +++ b/packages/sacado/test/performance/mat_vec/common.hpp @@ -31,7 +31,7 @@ //#define SACADO_DISABLE_FAD_VIEW_SPEC -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" struct Perf { double time; diff --git a/packages/sacado/test/performance/mat_vec/fad_kokkos_mat_vec_perf.cpp b/packages/sacado/test/performance/mat_vec/fad_kokkos_mat_vec_perf.cpp index e5c49429bb37..fd45718a56d4 100644 --- a/packages/sacado/test/performance/mat_vec/fad_kokkos_mat_vec_perf.cpp +++ b/packages/sacado/test/performance/mat_vec/fad_kokkos_mat_vec_perf.cpp @@ -39,7 +39,7 @@ #include "Teuchos_StandardCatchMacros.hpp" #include "Teuchos_Time.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" // For vtune #include @@ -244,7 +244,7 @@ do_time_fad(const size_t m, const size_t n, const size_t p, const size_t nloop, Kokkos::deep_copy(A, a); Kokkos::deep_copy(b, a); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -327,7 +327,7 @@ do_time_fad_hierarchical(const size_t m, const size_t n, const size_t p, Kokkos::deep_copy(A, a); Kokkos::deep_copy(b, a); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; #if defined(SACADO_KOKKOS_USE_MEMORY_POOL) @@ -388,7 +388,7 @@ do_time_val(const size_t m, const size_t n, const size_t nloop, Kokkos::deep_copy(A, 1.0); Kokkos::deep_copy(b, 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up diff --git a/packages/sacado/test/performance/mat_vec/mat_vec.cpp b/packages/sacado/test/performance/mat_vec/mat_vec.cpp index f17740c46ef3..fbeff8d07ec6 100644 --- a/packages/sacado/test/performance/mat_vec/mat_vec.cpp +++ b/packages/sacado/test/performance/mat_vec/mat_vec.cpp @@ -33,7 +33,7 @@ #include "mat_vec.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template void run_mat_vec(const ViewTypeA& A, const ViewTypeB& b, const ViewTypeC& c) { @@ -250,7 +250,7 @@ do_time_val(const size_t m, const size_t n, const size_t nloop, Kokkos::deep_copy(A, 1.0); Kokkos::deep_copy(b, 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -310,7 +310,7 @@ do_time_fad(const size_t m, const size_t n, const size_t p, const size_t nloop, Kokkos::deep_copy(typename ViewTypeA::array_type(A), 1.0); Kokkos::deep_copy(typename ViewTypeB::array_type(b), 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -365,7 +365,7 @@ do_time_scratch(const size_t m, const size_t n, const size_t p, const size_t nlo Kokkos::deep_copy(typename ViewTypeA::array_type(A), 1.0); Kokkos::deep_copy(typename ViewTypeB::array_type(b), 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -411,7 +411,7 @@ do_time_analytic(const size_t m, const size_t n, const size_t p, Kokkos::deep_copy(A, 1.0); Kokkos::deep_copy(b, 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -450,7 +450,7 @@ do_time_analytic_sl(const size_t m, const size_t n, const size_t p, Kokkos::deep_copy(A, 1.0); Kokkos::deep_copy(b, 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up @@ -489,7 +489,7 @@ do_time_analytic_s(const size_t m, const size_t n, Kokkos::deep_copy(A, 1.0); Kokkos::deep_copy(b, 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up diff --git a/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical.cpp b/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical.cpp index 9a6f0783096f..e1c2f6c36922 100644 --- a/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical.cpp +++ b/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical.cpp @@ -34,7 +34,7 @@ #include "mat_vec_hierarchical.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template void run_mat_vec_hierarchical(const ViewTypeA& A, const ViewTypeB& b, @@ -137,7 +137,7 @@ do_time_fad_hierarchical(const size_t m, const size_t n, const size_t p, Kokkos::deep_copy(typename ConViewTypeA::array_type(A), 1.0); Kokkos::deep_copy(typename ConViewTypeB::array_type(b), 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up diff --git a/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical_dfad.cpp b/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical_dfad.cpp index a47fd693f614..9759b5c962ec 100644 --- a/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical_dfad.cpp +++ b/packages/sacado/test/performance/mat_vec/mat_vec_hierarchical_dfad.cpp @@ -34,7 +34,7 @@ #include "mat_vec_hierarchical_dfad.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template void run_mat_vec_hierarchical_dfad(const ViewTypeA& A, const ViewTypeB& b, @@ -159,7 +159,7 @@ do_time_fad_hierarchical_dfad(const size_t m, const size_t n, const size_t p, Kokkos::deep_copy(typename ConViewTypeA::array_type(A), 1.0); Kokkos::deep_copy(typename ConViewTypeB::array_type(b), 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; #if defined (KOKKOS_ENABLE_CUDA) @@ -231,7 +231,7 @@ do_time_fad_hierarchical_dfad_scratch( Kokkos::deep_copy(typename ConViewTypeA::array_type(A), 1.0); Kokkos::deep_copy(typename ConViewTypeB::array_type(b), 1.0); - Kokkos::Impl::Timer wall_clock; + Kokkos::Timer wall_clock; Perf perf; // Execute the kernel once to warm up diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp index b5f973fb1248..3040c44c0873 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp @@ -20,7 +20,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_error_manager.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_error_manager.hpp index 1fd4c26d5f1e..e3ffd0690d04 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_error_manager.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_error_manager.hpp @@ -12,7 +12,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_matrix_def.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_matrix_def.hpp index 145adc9a7162..742c235f5bae 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_matrix_def.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_matrix_def.hpp @@ -7,7 +7,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor.hpp index db0f590da4fd..986eaabb0533 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor.hpp @@ -18,7 +18,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif @@ -74,7 +74,7 @@ namespace BaskerNS gm = A.nrow; BASKER_MATRIX ATEMP; - //Kokkos::Impl::Timer tza; + //Kokkos::Timer tza; int info = BASKER_SUCCESS; if(Options.btf == BASKER_TRUE) { @@ -87,7 +87,7 @@ namespace BaskerNS //printf("Switch time: %f \n", tza.seconds()); #ifdef BASKER_KOKKOS - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; typedef Kokkos::TeamPolicy TeamPolicy; // --------------------------------------------------------------- // @@ -185,7 +185,7 @@ namespace BaskerNS for(Int l=1; l <= tree.nlvls; l++) { #ifdef BASKER_TIMER - Kokkos::Impl::Timer timer_inner_sep; + Kokkos::Timer timer_inner_sep; #endif //#ifdef BASKER_OLD_BARRIER //Int lthreads = pow(2,l); @@ -350,7 +350,7 @@ namespace BaskerNS } }//end btf call - Kokkos::Impl::Timer tzback; + Kokkos::Timer tzback; if(Options.btf == BASKER_TRUE) { A = ATEMP; diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk.hpp index 25e28a292310..3c2dafbf0359 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk.hpp @@ -11,7 +11,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif #include "Teuchos_ScalarTraits.hpp" @@ -164,7 +164,7 @@ namespace BaskerNS #endif #ifdef BASKER_TIME - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; #endif Int i, j; diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk_inc.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk_inc.hpp index 6aa2370f4b69..fc843c070aaa 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk_inc.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_blk_inc.hpp @@ -9,7 +9,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif namespace BaskerNS @@ -203,7 +203,7 @@ namespace BaskerNS //for(i = M.col_ptr(k); i < M.col_ptr(k+1); ++i) //Debug of dim - //Kokkos::Impl::Timer timer; + //Kokkos::Timer timer; if(Options.same_pattern == BASKER_FALSE) { for(Int i = M.col_ptr(k+1)-1; i >= M.col_ptr(k); --i) diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col.hpp index 961fc57160ad..ea759af07375 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col.hpp @@ -15,7 +15,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif #ifdef BASKER_DEBUG @@ -155,7 +155,7 @@ namespace BaskerNS BASKER_BOOL sep_lvl_flg = BASKER_FALSE; #ifdef BASKER_DEBUG_TIME - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; #endif //-----------Upper Col Factor------------// diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col2.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col2.hpp index 5fa26deb81fb..a39633346ffa 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col2.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col2.hpp @@ -14,7 +14,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif #ifdef BASKER_DEBUG @@ -137,7 +137,7 @@ namespace BaskerNS } #ifdef BASKER_TIMER - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; #endif #ifdef BASKER_DEBUG_NFACTOR_COL2 @@ -261,9 +261,9 @@ namespace BaskerNS double time_extend = 0.0; double time_faccol = 0.0; double time_facoff = 0.0; - Kokkos::Impl::Timer timer_extend; - Kokkos::Impl::Timer timer_faccol; - Kokkos::Impl::Timer timer_facoff; + Kokkos::Timer timer_extend; + Kokkos::Timer timer_faccol; + Kokkos::Timer timer_facoff; #endif for(Int k = 0; k < ncol && info == BASKER_SUCCESS; ++k) { diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col_inc.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col_inc.hpp index 7f04f00f19b2..1c500bed8d3b 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col_inc.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_col_inc.hpp @@ -10,7 +10,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif namespace BaskerNS diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_diag.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_diag.hpp index fdaf60ce5b11..6aa17db19023 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_diag.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_diag.hpp @@ -10,7 +10,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif //#define BASKER_TIMER diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_inc.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_inc.hpp index f5761ab6316d..851b217098f5 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_inc.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_inc.hpp @@ -18,7 +18,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif @@ -55,7 +55,7 @@ namespace BaskerNS //====TIMER== #ifdef BASKER_TIME - //Kokkos::Impl::Timer timer; + //Kokkos::Timer timer; #endif //===TIMER=== @@ -158,7 +158,7 @@ namespace BaskerNS } #ifdef BASKER_KOKKOS - //Kokkos::Impl::Timer timer_inner_sep; + //Kokkos::Timer timer_inner_sep; #ifdef BASKER_NO_LAMBDA kokkos_nfactor_sep2_inc_lvl @@ -240,7 +240,7 @@ namespace BaskerNS { //=====Timer #ifdef BASKER_TIME - //Kokkos::Impl::Timer timer_btf; + //Kokkos::Timer timer_btf; #endif //====Timer diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_kokkos.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_kokkos.hpp index 67c054808e13..a0e7bc32530c 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_kokkos.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_nfactor_kokkos.hpp @@ -10,7 +10,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif //#include @@ -425,7 +425,7 @@ namespace Basker #endif #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_reach; + Kokkos::Timer timer_reach; #endif //Search reach if not yet considered @@ -456,7 +456,7 @@ namespace Basker #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_solve; + Kokkos::Timer timer_solve; #endif back_solve @@ -691,7 +691,7 @@ namespace Basker void operator()(const team_member &thread) const { #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; #endif //Need to wrap around Exe_Space @@ -875,7 +875,7 @@ namespace Basker { #ifdef BASKER_TIME_NFACTOR - Kokkos::Impl::Timer timer_total; + Kokkos::Timer timer_total; #endif Int bcol = U.scol; @@ -944,7 +944,7 @@ namespace Basker #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_reach; + Kokkos::Timer timer_reach; double t_i_reach = 0; #endif @@ -967,7 +967,7 @@ namespace Basker #ifdef BASKER_TIME_NFACTOR - Kokkos::Impl::Timer timer_l_r; + Kokkos::Timer timer_l_r; #endif //if not colored find local reach @@ -1021,7 +1021,7 @@ namespace Basker //printf("kid: %d xnnz: %d \n", kid, xnnz); #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_solve; + Kokkos::Timer timer_solve; #endif //call an atomic backsolve @@ -1037,7 +1037,7 @@ namespace Basker #endif #ifdef BASKER_TIME_NFACTOR - Kokkos::Impl::Timer timer_book; + Kokkos::Timer timer_book; #endif //count nnz will be need in this column @@ -1777,7 +1777,7 @@ namespace Basker #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_reach; + Kokkos::Timer timer_reach; #endif for(i = A.col_ptr(k); i < A.col_ptr(k+1); i++) @@ -1823,7 +1823,7 @@ namespace Basker #endif #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_solve; + Kokkos::Timer timer_solve; #endif /* @@ -2114,7 +2114,7 @@ namespace Basker void operator()(const team_member &thread) const { #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_sep; + Kokkos::Timer timer_sep; #endif //#ifdef BASKER_TIME @@ -2190,7 +2190,7 @@ namespace Basker //--------------------TRI SOLVE-----------------------// //check module for all level p #ifdef BASKER_TIME_EXTEND - Kokkos::Impl::Timer timer_tri_solve; + Kokkos::Timer timer_tri_solve; #endif //if((kid%(l+1)) == 0) @@ -2203,7 +2203,7 @@ namespace Basker #endif #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_tri_solve_start; + Kokkos::Timer timer_tri_solve_start; #endif @@ -2263,7 +2263,7 @@ namespace Basker #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_tri_solve_fill; + Kokkos::Timer timer_tri_solve_fill; #endif @@ -2290,7 +2290,7 @@ namespace Basker #endif #ifdef BASKER_TIME_DETAIL - Kokkos::Impl::Timer timer_tri_solve_col; + Kokkos::Timer timer_tri_solve_col; #endif column_tri_solve @@ -2344,7 +2344,7 @@ namespace Basker #endif #ifdef BASKER_TIME_EXTEND - Kokkos::Impl::Timer timer_reduce; + Kokkos::Timer timer_reduce; #endif //-----------------REDUCE---------------------/// @@ -2452,7 +2452,7 @@ namespace Basker #endif #ifdef BASKER_TIME_EXTEND - Kokkos::Impl::Timer timer_factor; + Kokkos::Timer timer_factor; #endif ///-------------Col Factor--------------------// @@ -2582,7 +2582,7 @@ namespace Basker #ifdef BASKER_TIME_EXTEND - Kokkos::Impl::Timer timer_rollback; + Kokkos::Timer timer_rollback; #endif if(roll_back) diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_order.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_order.hpp index 94b8f2326589..76351a4b7b67 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_order.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_order.hpp @@ -1,7 +1,7 @@ #ifndef SHYLUBASKER_ORDER_HPP #define SHYLUBASKER_ORDER_HPP -#include +#include //Basker Includes #include "shylubasker_types.hpp" @@ -452,7 +452,7 @@ static int basker_sort_matrix_col(const void *arg1, const void *arg2) void Basker::order_incomplete() { - Kokkos::Impl::Timer timer_one; + Kokkos::Timer timer_one; if(Options.matching == BASKER_TRUE) { diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_order_amd.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_order_amd.hpp index 09b8b35b2c4b..5398ca86ff13 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_order_amd.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_order_amd.hpp @@ -607,7 +607,7 @@ namespace BaskerNS BBT.col_ptr(i+1) = nnz2; } - Kokkos::Impl::Timer timer_metis; + Kokkos::Timer timer_metis; #if 1 // allocate inv-permutation vectors INT_1DARRAY metis_iperm; diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_order_scotch.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_order_scotch.hpp index 06fad98289ba..5df4622cc404 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_order_scotch.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_order_scotch.hpp @@ -143,7 +143,7 @@ namespace BaskerNS #else using scotch_integral_type = int32_t; //NDE: make this depend on the scotch type #endif - Kokkos::Impl::Timer timer_scotch; + Kokkos::Timer timer_scotch; Int num_levels = num_domains; Int num_doms = pow(2.0, (double)(num_levels+1)) - 1; @@ -173,7 +173,7 @@ namespace BaskerNS #if !defined(HAVE_SHYLU_NODEBASKER_METIS) BASKER_ASSERT(false, ">> BASKER ASSERT: METIS is not enabled <<"); #else - Kokkos::Impl::Timer timer_metis; + Kokkos::Timer timer_metis; double time_metis = 0.0; //idx_t metis_offset = btf_tabs(btf_tabs_offset-1); diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_sfactor.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_sfactor.hpp index be82342aac9a..3e77c9f9cefd 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_sfactor.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_sfactor.hpp @@ -24,7 +24,7 @@ using namespace std; #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs.hpp index ecb7b909ce3f..88ff1c1cefff 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs.hpp @@ -11,7 +11,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs_kokkos.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs_kokkos.hpp index be4d06b98f0c..7eaba33e8757 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs_kokkos.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_solve_rhs_kokkos.hpp @@ -13,7 +13,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #endif #include diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_util.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_util.hpp index 09aaa7a41056..8968a514b868 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_util.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_util.hpp @@ -10,7 +10,7 @@ /*Kokkos Includes*/ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif @@ -1677,7 +1677,7 @@ namespace BaskerNS { printf( "\n get_L \n\n" ); //Add Check - //Kokkos::Impl::Timer timer; + //Kokkos::Timer timer; n = gn; nnz = get_Lnnz(); (*col_ptr) = new Int[gn+1](); diff --git a/packages/shylu/shylu_node/basker/test/basker_test_inc.cpp b/packages/shylu/shylu_node/basker/test/basker_test_inc.cpp index 40dd2d4e804a..af09566dd00a 100644 --- a/packages/shylu/shylu_node/basker/test/basker_test_inc.cpp +++ b/packages/shylu/shylu_node/basker/test/basker_test_inc.cpp @@ -8,7 +8,7 @@ #ifdef BASKER_KOKKOS #include -#include +#include #else #include #endif @@ -209,7 +209,7 @@ int main(int argc, char* argv[]) cout << "--------------Done Setting Threads----------" << endl; mybasker.Symbolic(m,n,nnz,col_ptr,row_idx,vals); cout << "--------------Done SFactor------------------" << endl; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; mybasker.Factor_Inc(0); cout << "--------------Done NFactor-----------------" << endl; cout << "First Factor Time: " << timer.seconds() << endl; diff --git a/packages/shylu/shylu_node/fastilu/src/shylu_fastic.hpp b/packages/shylu/shylu_node/fastilu/src/shylu_fastic.hpp index 6bb2dae53178..fe2b6bc20c85 100644 --- a/packages/shylu/shylu_node/fastilu/src/shylu_fastic.hpp +++ b/packages/shylu/shylu_node/fastilu/src/shylu_fastic.hpp @@ -56,7 +56,7 @@ #include #include -#include +#include #include "shylu_fastilu.hpp" @@ -167,7 +167,7 @@ class FastICPrec void initialize() { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; //Here we have to allocate memory for L, U. if((level > 0) && (guessFlag != 0)) { @@ -755,7 +755,7 @@ class FastICPrec void compute() { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; if((level > 0) && (guessFlag != 0)) { initGuessPrec->compute(); @@ -784,7 +784,7 @@ class FastICPrec void apply(ScalarArray &x, ScalarArray &y) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; ParCopyFunctor parCopyFunctor(nRows, xTemp, x); ExecSpace().fence(); Kokkos::parallel_for(nRows, parCopyFunctor); diff --git a/packages/shylu/shylu_node/fastilu/src/shylu_fastildl.hpp b/packages/shylu/shylu_node/fastilu/src/shylu_fastildl.hpp index c3a6f2ea72c9..844d6efa9191 100644 --- a/packages/shylu/shylu_node/fastilu/src/shylu_fastildl.hpp +++ b/packages/shylu/shylu_node/fastilu/src/shylu_fastildl.hpp @@ -55,7 +55,7 @@ #include #include -#include +#include #include "shylu_fastilu.hpp" @@ -169,7 +169,7 @@ class FastILDLPrec void initialize() { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; //Here we have to allocate memory for L, U. if((level > 0) && (guessFlag != 0)) { @@ -737,7 +737,7 @@ class FastILDLPrec { initGuessPrec->compute(); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; numericILU(); FastILDLFunctor icFunctor(nRows, aRowMap, aColIdx, aRowIdx, aVal, lRowMap, lColIdx, lVal, diagElems, omega); @@ -762,7 +762,7 @@ class FastILDLPrec void apply(ScalarArray &x, ScalarArray &y) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; ParCopyFunctor parCopyFunctor(nRows, xTemp, x); ExecSpace().fence(); Kokkos::parallel_for(nRows, parCopyFunctor); diff --git a/packages/shylu/shylu_node/fastilu/src/shylu_fastilu.hpp b/packages/shylu/shylu_node/fastilu/src/shylu_fastilu.hpp index f76e339ea508..7572efd7c2a7 100644 --- a/packages/shylu/shylu_node/fastilu/src/shylu_fastilu.hpp +++ b/packages/shylu/shylu_node/fastilu/src/shylu_fastilu.hpp @@ -56,7 +56,7 @@ #include #include -#include +#include //whether to print extra debug output at runtime to stdout //comment out next line to disable @@ -846,7 +846,7 @@ class FastILUPrec //Symbolic Factorization Phase void initialize() { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; if ((level > 0) && (guessFlag !=0)) { initGuessPrec->initialize(); @@ -902,7 +902,7 @@ class FastILUPrec // void compute() { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; if ((level > 0) && (guessFlag !=0)) { initGuessPrec->compute(); @@ -937,7 +937,7 @@ class FastILUPrec //*not* support multiple right hand sizes. void apply(ScalarArray &x, ScalarArray &y) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; //required to prevent contamination of the input. ParCopyFunctor parCopyFunctor(nRows, xTemp, x); diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholCuSolver.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholCuSolver.cpp index 965ec219fe03..1cdb45c17357 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholCuSolver.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholCuSolver.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -38,7 +38,7 @@ int main (int argc, char *argv[]) { Tacho::printExecSpaceConfiguration("DeviceSpace", detail); Tacho::printExecSpaceConfiguration("HostSpace", detail); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; int r_val = 0; #if defined(KOKKOS_ENABLE_CUDA) { diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholLevelSet.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholLevelSet.cpp index fca902a5d623..33db60f960c7 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholLevelSet.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholLevelSet.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -90,7 +90,7 @@ int main (int argc, char *argv[]) { typedef Tacho::CrsMatrixBase CrsMatrixBaseTypeHost; typedef Kokkos::View DenseMatrixBaseType; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t = 0.0; if (is_root()) std::cout << "CholLevelSet:: import input file = " << file << std::endl; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholPardiso.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholPardiso.cpp index 63d77df00e90..4b6804d3ed01 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholPardiso.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholPardiso.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -47,7 +47,7 @@ int main (int argc, char *argv[]) { mkl_set_dynamic(0); mkl_set_num_threads(nthreads); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t = 0.0; Pardiso pardiso; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholSupernodes.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholSupernodes.cpp index 21254ad47fdb..935db7538cb0 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholSupernodes.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholSupernodes.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -68,7 +68,7 @@ int main (int argc, char *argv[]) { typedef CrsMatrixBase CrsMatrixBaseTypeHost; typedef Kokkos::View DenseMatrixBaseType; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t = 0.0; std::cout << "CholSupernodes:: import input file = " << file << std::endl; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholTriSolve.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholTriSolve.cpp index 82db50333f61..304b25f36f40 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholTriSolve.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholTriSolve.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -79,7 +79,7 @@ int main (int argc, char *argv[]) { typedef Tacho::CrsMatrixBase CrsMatrixBaseTypeHost; typedef Kokkos::View DenseMatrixBaseType; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t = 0.0; std::cout << "CholTriSolve:: import input file = " << file << std::endl; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp index 45b8d79a9734..05b20ff19186 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCuSparseTriSolve.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCuSparseTriSolve.cpp index ab228c5f44cb..801b5f6f093c 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCuSparseTriSolve.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleCuSparseTriSolve.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_Solver.hpp" @@ -57,7 +57,7 @@ int main (int argc, char *argv[]) { typedef Kokkos::TaskSchedulerMultiple scheduler_type; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; int r_val = 0; #if defined(KOKKOS_ENABLE_CUDA) { diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDenseByBlocks.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDenseByBlocks.cpp index 2e3ecf60824e..462f28755536 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDenseByBlocks.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDenseByBlocks.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include "Tacho_Internal.hpp" #include "Tacho_CommandLineParser.hpp" @@ -66,7 +66,7 @@ int main (int argc, char *argv[]) { typedef DenseMatrixView DenseMatrixViewHostType; typedef DenseMatrixView DenseMatrixOfBlocksHostType; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; scheduler_type sched; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseCholesky.hpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseCholesky.hpp index c575f0aeedfd..4bb3d92e22ba 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseCholesky.hpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseCholesky.hpp @@ -20,7 +20,7 @@ template int driver_chol (const int m, const bool verbose) { int max_iter = 1; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; const bool detail = false; typedef typename Tacho::UseThisDevice::type device_type; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseLDL.hpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseLDL.hpp index e73f1b3cecdf..0b384c6c8784 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseLDL.hpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseLDL.hpp @@ -28,7 +28,7 @@ template int driver_ldl (const int m, const bool verbose) { int max_iter = 1; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; const bool detail = false; typedef typename Tacho::UseThisDevice::type device_type; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseSolver.hpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseSolver.hpp index 4a13a5097e1b..ba0c12beec73 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseSolver.hpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleDeviceDenseSolver.hpp @@ -25,7 +25,7 @@ int driver (int argc, char *argv[]) { if (r_parse) return 0; // print help return Kokkos::initialize(argc, argv); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; const bool detail = false; typedef typename Tacho::UseThisDevice::type device_type; diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.cpp index 2f4af505f861..6fcb2b9969a5 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.cpp @@ -36,7 +36,7 @@ void testTachoSolver(int nSolvers, const int posDef = 1, const int numRuns = 1) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; const double tol = 1e-10;// tol *= 10; // original tolerance may be too tight /// diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.hpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.hpp index 3a4b5169f9b1..dfceb6269d71 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.hpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.hpp @@ -124,7 +124,7 @@ namespace tacho { value_type_array ax(values, numTerms); #endif - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); if (numGraphRows > 0) { @@ -208,7 +208,7 @@ namespace tacho { value_type_array ax(values, numSolvers*numTerms); #endif - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); /// m_Solver holds symbolic factorization to be shared with array solver diff --git a/packages/shylu/shylu_node/tacho/example/Tacho_ExamplePerfTest.cpp b/packages/shylu/shylu_node/tacho/example/Tacho_ExamplePerfTest.cpp index 266e7b05bde3..0de486a71d6b 100644 --- a/packages/shylu/shylu_node/tacho/example/Tacho_ExamplePerfTest.cpp +++ b/packages/shylu/shylu_node/tacho/example/Tacho_ExamplePerfTest.cpp @@ -146,7 +146,7 @@ int main (int argc, char *argv[]) { #if defined( __INTEL_MKL__ ) flush.run(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_solve = 0, t_solve_niter = 0; typedef Tacho::Pardiso Pardiso; @@ -270,7 +270,7 @@ int main (int argc, char *argv[]) { #if defined( TACHO_HAVE_SUITESPARSE ) flush.run(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_analyze = 0, t_factor = 0, t_solve = 0, t_solve_niter = 0; cholmod_sparse *AA ; @@ -419,7 +419,7 @@ int main (int argc, char *argv[]) { if (test_tacho) { flush.run(); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_solve = 0, t_solve_niter = 0; /// diff --git a/packages/shylu/shylu_node/tacho/src/Tacho.hpp b/packages/shylu/shylu_node/tacho/src/Tacho.hpp index 2b5d3182e051..4dd86d161b5f 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho.hpp +++ b/packages/shylu/shylu_node/tacho/src/Tacho.hpp @@ -4,7 +4,7 @@ #include "Tacho_config.h" #include "Kokkos_Core.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" #include #include diff --git a/packages/shylu/shylu_node/tacho/src/Tacho_CuSolver.hpp b/packages/shylu/shylu_node/tacho/src/Tacho_CuSolver.hpp index 233e031e0bc4..06296e3f21dd 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho_CuSolver.hpp +++ b/packages/shylu/shylu_node/tacho/src/Tacho_CuSolver.hpp @@ -82,7 +82,7 @@ namespace Tacho { printf("cuSolver: Analyze\n"); printf("=================\n"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _m = m; @@ -140,7 +140,7 @@ namespace Tacho { printf("cuSolver: Factorize\n"); printf("===================\n"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); size_t internalDataInBytes, workspaceInBytes; @@ -186,7 +186,7 @@ namespace Tacho { printf("cuSolver: Solve\n"); printf("===============\n"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); /// solve A x = t diff --git a/packages/shylu/shylu_node/tacho/src/Tacho_CuSparseTriSolve.hpp b/packages/shylu/shylu_node/tacho/src/Tacho_CuSparseTriSolve.hpp index bcab0246722c..f5270295c7d3 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho_CuSparseTriSolve.hpp +++ b/packages/shylu/shylu_node/tacho/src/Tacho_CuSparseTriSolve.hpp @@ -112,7 +112,7 @@ namespace Tacho { printf("cuSparse: Analyze\n"); printf("=================\n"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _m = m; @@ -239,7 +239,7 @@ namespace Tacho { printf("cuSolver: Solve\n"); printf("===============\n"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); diff --git a/packages/shylu/shylu_node/tacho/src/Tacho_Driver.hpp b/packages/shylu/shylu_node/tacho/src/Tacho_Driver.hpp index e20a4ba82446..c26f9e188846 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho_Driver.hpp +++ b/packages/shylu/shylu_node/tacho/src/Tacho_Driver.hpp @@ -8,7 +8,7 @@ #include "Tacho.hpp" #include -#include +#include namespace Tacho { diff --git a/packages/shylu/shylu_node/tacho/src/Tacho_MatrixMarket.hpp b/packages/shylu/shylu_node/tacho/src/Tacho_MatrixMarket.hpp index af7122c9e567..ccaf7f329268 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho_MatrixMarket.hpp +++ b/packages/shylu/shylu_node/tacho/src/Tacho_MatrixMarket.hpp @@ -137,7 +137,7 @@ namespace Tacho { typename DeviceType::memory_space >::assignable, "DeviceType is not assignable from HostSpace" ); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); diff --git a/packages/shylu/shylu_node/tacho/src/Tacho_Solver.hpp.org b/packages/shylu/shylu_node/tacho/src/Tacho_Solver.hpp.org index 21db17b797c5..326d70aa7e4f 100644 --- a/packages/shylu/shylu_node/tacho/src/Tacho_Solver.hpp.org +++ b/packages/shylu/shylu_node/tacho/src/Tacho_Solver.hpp.org @@ -8,7 +8,7 @@ #include "Tacho.hpp" #include -#include +#include namespace Tacho { diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Driver_Impl.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Driver_Impl.hpp index 18c1d65a90cb..80a5ed91812c 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Driver_Impl.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Driver_Impl.hpp @@ -511,7 +511,7 @@ namespace Tacho { ::factorize_small_host(const value_type_array &ax) { double t_copy(0), t_factor(0); { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); _A = value_type_matrix_host("A", _m, _m); @@ -605,7 +605,7 @@ namespace Tacho { ::solve_small_host(const value_type_matrix &x, const value_type_matrix &b, const value_type_matrix &t) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_copy(0), t_solve(0); { timer.reset(); diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_CAMD.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_CAMD.hpp index 6c6fa3c0bbe3..d0c6359a6e90 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_CAMD.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_CAMD.hpp @@ -118,7 +118,7 @@ namespace Tacho { } void reorder(const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_camd = 0; TACHO_SUITESPARSE(camd_defaults)(_control); diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Metis.cpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Metis.cpp index 9f9d80bec4fe..8fb318281fe6 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Metis.cpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Metis.cpp @@ -53,7 +53,7 @@ namespace Tacho { /// void GraphTools_Metis::reorder(const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_metis = 0; int ierr = 0; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_MetisMT.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_MetisMT.hpp index e16685d8d19c..464995db6011 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_MetisMT.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_MetisMT.hpp @@ -111,7 +111,7 @@ namespace Tacho { /// void reorder(const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_metis = 0; int ierr = 0; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Scotch.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Scotch.hpp index cec56d74cca4..0e1cbe2f2290 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Scotch.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_GraphTools_Scotch.hpp @@ -118,7 +118,7 @@ namespace Tacho { /// void reorder(const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_scotch = 0; _verbose = verbose; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Internal.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Internal.hpp index e2b0474cd379..d426aebdce21 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Internal.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Internal.hpp @@ -10,7 +10,7 @@ #include #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_Partition.hpp" diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_LevelSetTools.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_LevelSetTools.hpp index 752affc7780a..702e4d5ebf39 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_LevelSetTools.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_LevelSetTools.hpp @@ -335,7 +335,7 @@ namespace Tacho { stat.n_device_factorize = 0; stat.n_device_solve = 0; stat.n_team_factorize= 0; stat.n_team_solve = 0; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -841,7 +841,7 @@ namespace Tacho { factorizeCholesky(const value_type_array &ax, const ordinal_type verbose = 0) { constexpr bool is_host = std::is_same::value; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); value_type_array work; @@ -1303,7 +1303,7 @@ namespace Tacho { // solve U^{H} (U x) = b const ordinal_type nrhs = x.extent(1); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; stat.n_kernel_launching = 0; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools.hpp index d7a58331fa7a..c13c84c231a5 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools.hpp @@ -455,7 +455,7 @@ namespace Tacho { return; } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -506,7 +506,7 @@ namespace Tacho { return; } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -571,7 +571,7 @@ namespace Tacho { t.data() == b.data(), std::logic_error, "x, b and t have the same data pointer"); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _info.x = t; @@ -621,7 +621,7 @@ namespace Tacho { return; } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -687,7 +687,7 @@ namespace Tacho { t.data() == b.data(), std::logic_error, "x, b and t have the same data pointer"); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _info.x = t; @@ -738,7 +738,7 @@ namespace Tacho { void factorizeCholesky_Parallel(const value_type_array &ax, const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -857,7 +857,7 @@ namespace Tacho { factorizeCholesky_ParallelPanel(const value_type_array &ax, const ordinal_type panelsize, const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -992,7 +992,7 @@ namespace Tacho { t.data() == b.data(), std::logic_error, "x, b and t have the same data pointer"); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _info.x = t; @@ -1102,7 +1102,7 @@ namespace Tacho { factorizeCholesky_ParallelByBlocks(const value_type_array &ax, const ordinal_type blksize, const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -1230,7 +1230,7 @@ namespace Tacho { const ordinal_type blksize, const ordinal_type panelsize, const ordinal_type verbose = 0) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_LevelSet.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_LevelSet.hpp index 9730acaf0525..975e0edd9b4a 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_LevelSet.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_LevelSet.hpp @@ -310,7 +310,7 @@ namespace Tacho { stat_level.n_device_factorize = 0; stat_level.n_device_solve = 0; stat_level.n_team_factorize= 0; stat_level.n_team_solve = 0; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -931,7 +931,7 @@ namespace Tacho { factorizeCholesky(const value_type_array &ax, const ordinal_type verbose) { constexpr bool is_host = std::is_same::value; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); value_type_array work; @@ -1505,7 +1505,7 @@ namespace Tacho { // solve U^{H} (U x) = b const ordinal_type nrhs = x.extent(1); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; stat_level.n_kernel_launching = 0; @@ -1690,7 +1690,7 @@ namespace Tacho { factorizeLDL(const value_type_array &ax, const ordinal_type verbose) { constexpr bool is_host = std::is_same::value; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); value_type_array work; @@ -1840,7 +1840,7 @@ namespace Tacho { // solve L D L^{H} x = b const ordinal_type nrhs = x.extent(1); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; stat_level.n_kernel_launching = 0; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_Serial.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_Serial.hpp index 7c5cd3c6cd4c..1cc43da13be9 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_Serial.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_NumericTools_Serial.hpp @@ -110,7 +110,7 @@ namespace Tacho { void factorizeCholesky(const value_type_array &ax, const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -155,7 +155,7 @@ namespace Tacho { factorizeCholesky(const value_type_array &ax, const ordinal_type panelsize, const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -204,7 +204,7 @@ namespace Tacho { const value_type_matrix &b, // right hand side const value_type_matrix &t, // temporary workspace (store permuted vectors) const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _info.x = t; @@ -256,7 +256,7 @@ namespace Tacho { "Serial interface works on host device only"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; { timer.reset(); { @@ -322,7 +322,7 @@ namespace Tacho { "x, b and t have the same data pointer"); } - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; _info.x = t; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Solver_Impl.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Solver_Impl.hpp index 88ad61d03262..d6f308b3db4a 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Solver_Impl.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Solver_Impl.hpp @@ -459,7 +459,7 @@ namespace Tacho { printf("======================\n"); } if (_m < _small_problem_thres) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); _A = value_type_matrix_host("A", _m, _m); @@ -565,7 +565,7 @@ namespace Tacho { printf("======================\n"); } if (_m < _small_problem_thres) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); _A = value_type_matrix_host("A", _m, _m); @@ -650,7 +650,7 @@ namespace Tacho { } if (_m < _small_problem_thres) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); Kokkos::deep_copy(x, b); @@ -713,7 +713,7 @@ namespace Tacho { } if (_m < _small_problem_thres) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); Kokkos::deep_copy(x, b); diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_SymbolicTools.cpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_SymbolicTools.cpp index 2d1ef3b819f4..f275e75ce2e5 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_SymbolicTools.cpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_SymbolicTools.cpp @@ -664,7 +664,7 @@ namespace Tacho { void SymbolicTools:: symbolicFactorize(const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_symfact = 0, t_supernode = 0, t_extra = 0, m_used =0, m_peak = 0; auto track_alloc = [&](const double in) { @@ -839,7 +839,7 @@ namespace Tacho { void SymbolicTools:: evaporateSymbolicFactors(const ordinal_type_array &aw, const ordinal_type verbose) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; double t_evaporate = 0, m_used =0, m_peak = 0; auto track_alloc = [&](const double in) { diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_TriSolveTools.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_TriSolveTools.hpp index 2cc5e0bd7a81..5b3157d00b38 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_TriSolveTools.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_TriSolveTools.hpp @@ -255,7 +255,7 @@ namespace Tacho { stat.n_device_problems = 0; stat.n_team_problems = 0; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); @@ -760,7 +760,7 @@ namespace Tacho { stat.n_device_problems = 0; stat.n_team_problems = 0; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; timer.reset(); #if defined(KOKKOS_ENABLE_CUDA) @@ -866,7 +866,7 @@ namespace Tacho { TACHO_TEST_FOR_EXCEPTION(nrhs > _max_nrhs, std::logic_error, "nrhs is bigger than max nrhs"); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; stat.n_kernel_launching = 0; diff --git a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Util.hpp b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Util.hpp index 500329075934..29fed790df77 100644 --- a/packages/shylu/shylu_node/tacho/src/impl/Tacho_Util.hpp +++ b/packages/shylu/shylu_node/tacho/src/impl/Tacho_Util.hpp @@ -24,7 +24,7 @@ #include #include "Kokkos_Core.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" #if defined (__INTEL_MKL__) #include "mkl.h" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCrsMatrixBase.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCrsMatrixBase.hpp index bc3a7d3b511a..6aebc10573af 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCrsMatrixBase.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCrsMatrixBase.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_CrsMatrixBase.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_dcomplex.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_dcomplex.cpp index 31386aa794ce..44c6688b9593 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_dcomplex.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_dcomplex.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_dcomplex"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_double.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_double.cpp index 80b6b029800b..75659731f2de 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_double.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestCuda_double.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_double"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseByBlocks.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseByBlocks.hpp index c1c6b9c7ebc4..8c5fe063de9f 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseByBlocks.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseByBlocks.hpp @@ -6,7 +6,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_DenseMatrixView.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseLinearAlgebra.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseLinearAlgebra.hpp index 19eac4d2aca2..73b8670cd621 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseLinearAlgebra.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseLinearAlgebra.hpp @@ -7,7 +7,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_Blas_Team.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseMatrixView.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseMatrixView.hpp index 65af77e30c87..28f1567473b1 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseMatrixView.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestDenseMatrixView.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_DenseMatrixView.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestGraph.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestGraph.hpp index 6cb3600a6dd7..9e05e32bccce 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestGraph.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestGraph.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_CrsMatrixBase.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestNumeric.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestNumeric.hpp index cc3f19750318..0db1fec23ed9 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestNumeric.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestNumeric.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_CrsMatrixBase.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_dcomplex.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_dcomplex.cpp index b4545c107457..fac278da1e33 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_dcomplex.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_dcomplex.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_dcomplex"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_double.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_double.cpp index ddc344eb41c3..2762908c5fef 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_double.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestOpenMP_double.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_double"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_dcomplex.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_dcomplex.cpp index fda170ce198a..a4802f1661e0 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_dcomplex.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_dcomplex.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_dcomplex"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_double.cpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_double.cpp index 07025658a14e..9735bfd956c7 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_double.cpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSerial_double.cpp @@ -1,7 +1,7 @@ #include #include -#include +#include static const std::string MM_TEST_FILE="test_double"; diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSymbolic.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSymbolic.hpp index f9758134353b..2f6952193674 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSymbolic.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestSymbolic.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_CrsMatrixBase.hpp" diff --git a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestTaskFunctor.hpp b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestTaskFunctor.hpp index f1f2d00f90f9..3e751039571a 100644 --- a/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestTaskFunctor.hpp +++ b/packages/shylu/shylu_node/tacho/unit-test/Tacho_TestTaskFunctor.hpp @@ -4,7 +4,7 @@ #include #include -#include +#include #include "Tacho_Util.hpp" #include "Tacho_TaskFunctor_MemoryPool.hpp" diff --git a/packages/stokhos/test/Performance/FadMPAssembly/TestAssembly.hpp b/packages/stokhos/test/Performance/FadMPAssembly/TestAssembly.hpp index 0c8963c858b4..ec907687147d 100644 --- a/packages/stokhos/test/Performance/FadMPAssembly/TestAssembly.hpp +++ b/packages/stokhos/test/Performance/FadMPAssembly/TestAssembly.hpp @@ -52,7 +52,7 @@ // Kokkos libraries' headers: #include #include -#include +#include // Utilities #include @@ -188,7 +188,7 @@ Perf fenl_assembly( //------------------------------------ - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; Perf perf_stats = Perf() ; diff --git a/packages/stokhos/test/Performance/FadMPAssembly/fenl_functors.hpp b/packages/stokhos/test/Performance/FadMPAssembly/fenl_functors.hpp index baf9f80d799f..9f6d6c232877 100644 --- a/packages/stokhos/test/Performance/FadMPAssembly/fenl_functors.hpp +++ b/packages/stokhos/test/Performance/FadMPAssembly/fenl_functors.hpp @@ -56,7 +56,7 @@ #include #include -#include +#include #include #include @@ -253,7 +253,7 @@ class NodeNodeGraph { //-------------------------------- // Guess at capacity required for the map: - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; wall_clock.reset(); phase = FILL_NODE_SET ; diff --git a/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestEpetra.cpp b/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestEpetra.cpp index e5f3e934d627..2fa9e2aaab17 100644 --- a/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestEpetra.cpp +++ b/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestEpetra.cpp @@ -49,7 +49,7 @@ #include "Stokhos_Sparse3TensorUtilities.hpp" #include "EpetraExt_BlockUtility.h" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" #ifdef HAVE_MPI #include "Epetra_MpiComm.h" @@ -173,7 +173,7 @@ run_test(const int p, const int d, const int nGrid, const int nIter, sg_y->init(0.0); // Apply operator - Kokkos::Impl::Timer clock; + Kokkos::Timer clock; for (int iter=0; iterApply( *(sg_x->getBlockVector()), *(sg_y->getBlockVector()) ); diff --git a/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestStochastic.hpp b/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestStochastic.hpp index f37cb5e948ba..b9cd8824ed91 100644 --- a/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestStochastic.hpp +++ b/packages/stokhos/test/Performance/KokkosArraySPMVKernels/TestStochastic.hpp @@ -43,7 +43,7 @@ #include #include "Kokkos_Core.hpp" -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" #include "Stokhos_Update.hpp" #include "Stokhos_CrsMatrix.hpp" @@ -221,7 +221,7 @@ test_product_tensor_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Kokkos::deep_copy( x, x0 ); // akin to import Stokhos::multiply( matrix , x , y ); @@ -322,7 +322,7 @@ test_product_tensor_diagonal_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -481,7 +481,7 @@ test_product_flat_commuted_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -636,7 +636,7 @@ test_product_flat_original_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -739,7 +739,7 @@ test_tiled_product_tensor_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -849,7 +849,7 @@ test_simple_tiled_product_tensor_matrix( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -954,7 +954,7 @@ test_lexo_block_tensor( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -1062,7 +1062,7 @@ test_linear_tensor( //------------------------------ Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for ( int iter = 0 ; iter < iterCount ; ++iter ) { Stokhos::multiply( matrix , x , y ); } @@ -1163,7 +1163,7 @@ test_original_matrix_free_vec( Device().fence(); SparseMatOps smo; - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; int n_apply = 0; int n_add = 0; for ( int iter = 0 ; iter < iterCount ; ++iter ) { @@ -1301,7 +1301,7 @@ test_original_matrix_free_view( Device().fence(); SparseMatOps smo; - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; int n_apply = 0; int n_add = 0; for ( int iter = 0 ; iter < iterCount ; ++iter ) { @@ -1451,7 +1451,7 @@ test_original_matrix_free_kokkos( } Device().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; int n_apply = 0; int n_add = 0; for ( int iter = 0 ; iter < iterCount ; ++iter ) { diff --git a/packages/stokhos/test/Performance/KokkosSpMM/TestSpMM.hpp b/packages/stokhos/test/Performance/KokkosSpMM/TestSpMM.hpp index 113969fa490c..764b2299de29 100644 --- a/packages/stokhos/test/Performance/KokkosSpMM/TestSpMM.hpp +++ b/packages/stokhos/test/Performance/KokkosSpMM/TestSpMM.hpp @@ -46,7 +46,7 @@ // Utilities -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template< typename IntType > inline @@ -161,7 +161,7 @@ test_spmm(const OrdinalType ensemble_length, } execution_space().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for (ordinal_type iter = 0; iter < iterCount; ++iter) { for (ordinal_type e=0; e #include -#include +#include // Utilities #include @@ -204,7 +204,7 @@ Perf fenl_assembly( //------------------------------------ - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; Perf perf_stats = Perf() ; diff --git a/packages/stokhos/test/Performance/MPAssembly/fenl_functors.hpp b/packages/stokhos/test/Performance/MPAssembly/fenl_functors.hpp index 250f4a52f344..8771314d2e0f 100644 --- a/packages/stokhos/test/Performance/MPAssembly/fenl_functors.hpp +++ b/packages/stokhos/test/Performance/MPAssembly/fenl_functors.hpp @@ -56,7 +56,7 @@ #include #include -#include +#include #include #include @@ -249,7 +249,7 @@ class NodeNodeGraph { //-------------------------------- // Guess at capacity required for the map: - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; wall_clock.reset(); phase = FILL_NODE_SET ; diff --git a/packages/stokhos/test/Performance/MPVectorKernels/TestSpMv.hpp b/packages/stokhos/test/Performance/MPVectorKernels/TestSpMv.hpp index d1a72cb47132..868975b6395d 100644 --- a/packages/stokhos/test/Performance/MPVectorKernels/TestSpMv.hpp +++ b/packages/stokhos/test/Performance/MPVectorKernels/TestSpMv.hpp @@ -52,7 +52,7 @@ #include "Sacado_mpl_integral_c.hpp" // Utilities -#include "impl/Kokkos_Timer.hpp" +#include "Kokkos_Timer.hpp" template< typename IntType > inline @@ -164,7 +164,7 @@ test_mpvector_spmv(const int ensemble_length, Stokhos::multiply( matrix, x, y, tag ); execution_space().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for (int iter = 0; iter < iterCount; ++iter) { Stokhos::multiply( matrix, x, y, tag ); } @@ -242,7 +242,7 @@ test_scalar_spmv(const int ensemble_length, } execution_space().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for (int iter = 0; iter < iterCount; ++iter) { for (int e=0; e inline @@ -238,7 +238,7 @@ test_mean_multiply(const OrdinalType order, } execution_space().fence(); - Kokkos::Impl::Timer clock ; + Kokkos::Timer clock ; for (ordinal_type iter = 0; iter < iterCount; ++iter) { for (ordinal_type col=0; col #include #include -#include +#include #include #include @@ -119,7 +119,7 @@ result_struct cg_solve( Kokkos::Details::ArithTraits::epsilon(), int print = 0) { - Kokkos::Impl::Timer total_timer; + Kokkos::Timer total_timer; typedef typename CrsMatrix::scalar_type ScalarType; typedef Kokkos::Details::ArithTraits KAT; @@ -147,7 +147,7 @@ result_struct cg_solve( double addtime = 0; double matvectime = 0; - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; p->update(1.0,*x,0.0,*x,0.0); addtime += timer.seconds(); timer.reset(); diff --git a/packages/trilinoscouplings/examples/fenl/fenl_functors.hpp b/packages/trilinoscouplings/examples/fenl/fenl_functors.hpp index 4fa3fa16e1bd..d96293e2faa0 100644 --- a/packages/trilinoscouplings/examples/fenl/fenl_functors.hpp +++ b/packages/trilinoscouplings/examples/fenl/fenl_functors.hpp @@ -56,7 +56,7 @@ #include #include -#include +#include #include #include @@ -134,7 +134,7 @@ class NodeNodeGraph { //-------------------------------- // Guess at capacity required for the map: - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; wall_clock.reset(); diff --git a/packages/trilinoscouplings/examples/fenl/fenl_impl.hpp b/packages/trilinoscouplings/examples/fenl/fenl_impl.hpp index 6a694513f67e..07de6070b1cb 100644 --- a/packages/trilinoscouplings/examples/fenl/fenl_impl.hpp +++ b/packages/trilinoscouplings/examples/fenl/fenl_impl.hpp @@ -51,7 +51,7 @@ #include #include #include -#include +#include #include #include @@ -356,8 +356,8 @@ class Problem { typedef DirichletComputation< FixtureType , LocalMatrixType > DirichletComputationType ; typedef ResponseComputation< FixtureType , LocalVectorType > ResponseComputationType ; - Kokkos::Impl::Timer wall_clock ; - Kokkos::Impl::Timer newton_clock ; + Kokkos::Timer wall_clock ; + Kokkos::Timer newton_clock ; newton_clock.reset(); LocalMatrixType jacobian = g_jacobian.getLocalMatrixDevice(); @@ -753,7 +753,7 @@ Perf fenl( //------------------------------------ - Kokkos::Impl::Timer wall_clock ; + Kokkos::Timer wall_clock ; Perf perf_stats = Perf() ; From 0d9ab221cb0bcc6dc14ca8526f86d9dadcc78fda Mon Sep 17 00:00:00 2001 From: "K. Devine" Date: Fri, 15 Oct 2021 14:38:31 -0600 Subject: [PATCH 23/98] tpetra: fixed shadow warnings, including one true bug where loop index was re-used as a loop index in a nested loop --- .../test/ImportExport2/ImportExport2_UnitTests.cpp | 1 - .../tpetra/core/test/RowMatrixTransposer/sorted.cpp | 12 ++++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 95ec17d71174..46d026504efa 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -497,7 +497,6 @@ namespace { // constructor. The returned matrix should also be diagonal and // should equal tgt_mat. Teuchos::ParameterList dummy; - typedef CrsMatrix crs_type; RCP A_tgt2 = Tpetra::importAndFillCompleteCrsMatrix (src_mat, importer, Teuchos::null, diff --git a/packages/tpetra/core/test/RowMatrixTransposer/sorted.cpp b/packages/tpetra/core/test/RowMatrixTransposer/sorted.cpp index 2ad0a00b2555..38f380131bc8 100644 --- a/packages/tpetra/core/test/RowMatrixTransposer/sorted.cpp +++ b/packages/tpetra/core/test/RowMatrixTransposer/sorted.cpp @@ -247,12 +247,12 @@ testTranspose (bool& success, valsBuf.begin ()); bool good = true; - for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { - if (lclColIndsBuf[lclRow] != lclRow) { + for (LO lclInd = 0; lclInd < lclNumRows; ++lclInd) { + if (lclColIndsBuf[lclInd] != lclInd) { good = false; break; } - else if (valsBuf[lclRow] != 1.0) { + else if (valsBuf[lclInd] != 1.0) { good = false; break; } @@ -308,12 +308,12 @@ testTranspose (bool& success, if (success) { bool good = true; - for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { - if (lclColInds[lclRow] != lclRow) { + for (LO lclInd = 0; lclInd < lclNumRows; ++lclInd) { + if (lclColInds[lclInd] != lclInd) { good = false; break; } - else if (vals[lclRow] != 1.0) { + else if (vals[lclInd] != 1.0) { good = false; break; } From d7b6eacc33d51d0c5a19f8a9927509a7632ebb2b Mon Sep 17 00:00:00 2001 From: Vinh Dang Date: Fri, 15 Oct 2021 23:12:29 -0700 Subject: [PATCH 24/98] Set Cuda host pinned memory as default --- packages/adelus/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/adelus/CMakeLists.txt b/packages/adelus/CMakeLists.txt index 1c1de927e4eb..5b48737ea4df 100644 --- a/packages/adelus/CMakeLists.txt +++ b/packages/adelus/CMakeLists.txt @@ -55,7 +55,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_TIMING TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_CUDAHOSTPINNED CUDA_HOST_PINNED_MPI "Use Cuda Host Pinned memory for MPI." - OFF ) + ON ) TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_USEDEEPCOPY USE_DEEPCOPY From b9a2b4de588e727e8dcbc2bc149a6d7ff0171b10 Mon Sep 17 00:00:00 2001 From: Vinh Dang Date: Sun, 17 Oct 2021 15:28:29 -0700 Subject: [PATCH 25/98] Enable using Cuda host pinned mem --- packages/adelus/src/Adelus_perm1.hpp | 34 +++++++++++++-- packages/adelus/src/Adelus_solve.hpp | 62 ++++++++++++++-------------- 2 files changed, 62 insertions(+), 34 deletions(-) diff --git a/packages/adelus/src/Adelus_perm1.hpp b/packages/adelus/src/Adelus_perm1.hpp index 53e8eda5b868..bf51426c688a 100644 --- a/packages/adelus/src/Adelus_perm1.hpp +++ b/packages/adelus/src/Adelus_perm1.hpp @@ -300,6 +300,9 @@ namespace Adelus { int ptr1_idx, myfirstrow; #ifdef GET_TIMING + #if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + double t1, copyhostpinnedtime; + #endif double t2; double totalpermtime; #endif @@ -316,10 +319,18 @@ namespace Adelus { #endif typedef typename ZDView::device_type::memory_space memory_space; typedef Kokkos::View ViewMatrixType; - + + #if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + typedef Kokkos::View View2DHostPinnType;//CudaHostPinnedSpace + #endif + if (my_rhs_ > 0) { - ViewMatrixType rhs_temp ( "rhs_temp", nrows_matrix, my_rhs_ );//allocate full-size RHS vectors + ViewMatrixType rhs_temp ( "rhs_temp", nrows_matrix, my_rhs_ );//allocate full-size RHS vectors + #if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + View2DHostPinnType h_rhs_temp( "h_rhs_temp", nrows_matrix, my_rhs_ ); + #endif + Kokkos::deep_copy(rhs_temp, 0);//initialize with 0s ncols_proc1 = ncols_matrix/nprocs_row; @@ -357,18 +368,35 @@ namespace Adelus { ptr1_idx++; } + #if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + #ifdef GET_TIMING + t1 = MPI_Wtime(); + #endif + Kokkos::deep_copy(h_rhs_temp,rhs_temp); + #ifdef GET_TIMING + copyhostpinnedtime = (MPI_Wtime()-t1); + #endif + MPI_Allreduce( MPI_IN_PLACE, h_rhs_temp.data(), nrows_matrix*my_rhs_, ADELUS_MPI_DATA_TYPE, MPI_SUM, col_comm); + + Kokkos::deep_copy( subview(ZV, Kokkos::ALL(), Kokkos::make_pair(0, my_rhs_)), + subview(h_rhs_temp, Kokkos::make_pair(myfirstrow-1, myfirstrow-1+my_rows), Kokkos::ALL()) ); + #else //CUDA-aware MPI MPI_Allreduce( MPI_IN_PLACE, rhs_temp.data(), nrows_matrix*my_rhs_, ADELUS_MPI_DATA_TYPE, MPI_SUM, col_comm); Kokkos::deep_copy( subview(ZV, Kokkos::ALL(), Kokkos::make_pair(0, my_rhs_)), subview(rhs_temp, Kokkos::make_pair(myfirstrow-1, myfirstrow-1+my_rows), Kokkos::ALL()) ); - + #endif } #ifdef GET_TIMING totalpermtime = MPI_Wtime() - t2; #endif + #ifdef GET_TIMING + #if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + showtime("Time to copy dev mem --> host pinned mem",©hostpinnedtime); + #endif showtime("Total time in perm",&totalpermtime); #endif } diff --git a/packages/adelus/src/Adelus_solve.hpp b/packages/adelus/src/Adelus_solve.hpp index d04c3a2c72f7..4e7620da206d 100644 --- a/packages/adelus/src/Adelus_solve.hpp +++ b/packages/adelus/src/Adelus_solve.hpp @@ -149,9 +149,9 @@ void back_solve6(ZDView& ZV) double t1,t2; double allocviewtime,eliminaterhstime,bcastrowtime,updrhstime,xchgrhstime; double totalsolvetime; -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -// double copyhostpinnedtime; -//#endif +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + double copyhostpinnedtime; +#endif #endif MPI_Request msgrequest; @@ -181,9 +181,9 @@ void back_solve6(ZDView& ZV) #ifdef GET_TIMING allocviewtime=eliminaterhstime=bcastrowtime=updrhstime=xchgrhstime=0.0; -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -// copyhostpinnedtime=0.0; -//#endif +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + copyhostpinnedtime=0.0; +#endif t1 = MPI_Wtime(); #endif @@ -251,15 +251,15 @@ void back_solve6(ZDView& ZV) #endif } -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -//#ifdef GET_TIMING -// t1 = MPI_Wtime(); -//#endif -// Kokkos::deep_copy(h_row1,row1); -//#ifdef GET_TIMING -// copyhostpinnedtime += (MPI_Wtime()-t1); -//#endif -//#endif +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) +#ifdef GET_TIMING + t1 = MPI_Wtime(); +#endif + Kokkos::deep_copy(h_row1,row1); +#ifdef GET_TIMING + copyhostpinnedtime += (MPI_Wtime()-t1); +#endif +#endif #ifdef GET_TIMING t1 = MPI_Wtime(); @@ -268,11 +268,11 @@ void back_solve6(ZDView& ZV) type[0] = SOCOLTYPE+j; //MPI_Bcast((char *) row1, bytes[0], MPI_CHAR, mesh_row(root), col_comm); -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -// MPI_Bcast(reinterpret_cast(h_row1.data()), bytes[0], MPI_CHAR, mesh_row(root), col_comm); -//#else //CUDA-aware MPI -- Note: Looks like MPI_Bcast is still working well with device (cuda) pointers (and faster than using cuda host pinned memory) +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + MPI_Bcast(reinterpret_cast(h_row1.data()), bytes[0], MPI_CHAR, mesh_row(root), col_comm); +#else //CUDA-aware MPI MPI_Bcast(reinterpret_cast(row1.data()), bytes[0], MPI_CHAR, mesh_row(root), col_comm); -//#endif +#endif // added this barrier for CPLANT operation MPI_Barrier(col_comm); @@ -280,15 +280,15 @@ void back_solve6(ZDView& ZV) bcastrowtime += (MPI_Wtime()-t1); #endif -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -//#ifdef GET_TIMING -// t1 = MPI_Wtime(); -//#endif -// Kokkos::deep_copy(row1,h_row1); -//#ifdef GET_TIMING -// copyhostpinnedtime += (MPI_Wtime()-t1); -//#endif -//#endif +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) +#ifdef GET_TIMING + t1 = MPI_Wtime(); +#endif + Kokkos::deep_copy(row1,h_row1); +#ifdef GET_TIMING + copyhostpinnedtime += (MPI_Wtime()-t1); +#endif +#endif #ifdef GET_TIMING t1 = MPI_Wtime(); @@ -376,9 +376,9 @@ void back_solve6(ZDView& ZV) showtime("Time to eliminate rhs",&eliminaterhstime); showtime("Time to bcast temp row",&bcastrowtime); showtime("Time to update rhs",&updrhstime); -//#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) -// showtime("Time to copy host pinned mem <--> dev mem",©hostpinnedtime); -//#endif +#if defined(CUDA_HOST_PINNED_MPI) && defined(KOKKOS_ENABLE_CUDA) + showtime("Time to copy host pinned mem <--> dev mem",©hostpinnedtime); +#endif showtime("Time to xchg rhs",&xchgrhstime); showtime("Total time in solve",&totalsolvetime); #endif From 67fe3bf5430602b2d2d1807932ba3f3566210be7 Mon Sep 17 00:00:00 2001 From: Vinh Dang Date: Sun, 17 Oct 2021 21:27:35 -0700 Subject: [PATCH 26/98] Check requested number of GPUs against available number of GPUs --- packages/adelus/test/vector_random/cxx_main.cpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/packages/adelus/test/vector_random/cxx_main.cpp b/packages/adelus/test/vector_random/cxx_main.cpp index b51a0c326b66..5c7772a64465 100644 --- a/packages/adelus/test/vector_random/cxx_main.cpp +++ b/packages/adelus/test/vector_random/cxx_main.cpp @@ -210,6 +210,16 @@ int main(int argc, char *argv[]) #ifdef KOKKOS_ENABLE_CUDA int gpu_count; cudaGetDeviceCount ( &gpu_count ); + if (nptile > gpu_count) { + if( rank == 0 ) { + std::cout << "Request more GPUs than the number of GPUs available " + << "to MPI processes (requested: " << nptile + << " vs. available: " << gpu_count + << "). Exit without test." << std::endl; + } + return 0; + } + Kokkos::InitArguments args; args.num_threads = 0; args.num_numa = 0; From fd27eb3418b60fc65ab91dabb1317cd600971a8a Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Mon, 18 Oct 2021 20:57:19 -0600 Subject: [PATCH 27/98] MueLu: Adding signed SA style dropping option --- .../MueLu_CoalesceDropFactory_def.hpp | 58 ++++++++++++++----- 1 file changed, 45 insertions(+), 13 deletions(-) diff --git a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp index c4b903035125..9af45faff43f 100644 --- a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp +++ b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp @@ -132,7 +132,8 @@ namespace MueLu { { typedef Teuchos::StringToIntegralParameterEntryValidator validatorType; - validParamList->getEntry("aggregation: drop scheme").setValidator(rcp(new validatorType(Teuchos::tuple("classical", "distance laplacian","signed classical","block diagonal","block diagonal classical","block diagonal distance laplacian","block diagonal signed classical","block diagonal colored signed classical"), "aggregation: drop scheme"))); + // "signed classical" is the Ruge-Stuben style (relative to max off-diagonal), "sign classical sa" is the signed version of the sa criterion (relative to the diagonal values) + validParamList->getEntry("aggregation: drop scheme").setValidator(rcp(new validatorType(Teuchos::tuple("signed classical sa","classical", "distance laplacian","signed classical","block diagonal","block diagonal classical","block diagonal distance laplacian","block diagonal signed classical","block diagonal colored signed classical"), "aggregation: drop scheme"))); } SET_VALID_ENTRY("aggregation: distance laplacian algo"); @@ -174,7 +175,7 @@ namespace MueLu { void CoalesceDropFactory::Build(Level ¤tLevel) const { FactoryMonitor m(*this, "Build", currentLevel); - + typedef Teuchos::ScalarTraits STS; typedef typename STS::magnitudeType real_type; typedef Xpetra::MultiVector RealValuedMultiVector; @@ -196,7 +197,8 @@ namespace MueLu { bool use_block_algorithm=false; LO interleaved_blocksize = as(pL.get("aggregation: block diagonal: interleaved blocksize")); - bool useSignedClassical = false; + bool useSignedClassicalRS = false; + bool useSignedClassicalSA = false; bool generateColoringGraph = false; // NOTE: If we're doing blockDiagonal, we'll not want to do rowSum twice (we'll do it @@ -210,8 +212,13 @@ namespace MueLu { Coords = Get< RCP >(currentLevel, "Coordinates"); A = realA; } + else if(algo == "signed classical sa") { + useSignedClassicalSA = true; + algo = "classical"; + A = realA; + } else if(algo == "signed classical" || algo == "block diagonal colored signed classical" || algo == "block diagonal signed classical") { - useSignedClassical = true; + useSignedClassicalRS = true; // if(realA->GetFixedBlockSize() > 1) { RCP BlockNumber = Get >(currentLevel, "BlockNumber"); // Ghost the column block numbers if we need to @@ -378,12 +385,14 @@ namespace MueLu { const typename STS::magnitudeType dirichletThreshold = STS::magnitude(as(pL.get("aggregation: Dirichlet threshold"))); - // NOTE: We don't support signed classical with cut drop at present - TEUCHOS_TEST_FOR_EXCEPTION(useSignedClassical && classicalAlgo != defaultAlgo, Exceptions::RuntimeError, "\"aggregation: classical algo\" != default is not supported for scalled classical aggregation"); - + // NOTE: We don't support signed classical RS or SA with cut drop at present + TEUCHOS_TEST_FOR_EXCEPTION(useSignedClassicalRS && classicalAlgo != defaultAlgo, Exceptions::RuntimeError, "\"aggregation: classical algo\" != default is not supported for scalled classical aggregation"); + TEUCHOS_TEST_FOR_EXCEPTION(useSignedClassicalSA && classicalAlgo != defaultAlgo, Exceptions::RuntimeError, "\"aggregation: classical algo\" != default is not supported for scalled classical sa aggregation"); GO numDropped = 0, numTotal = 0; std::string graphType = "unamalgamated"; //for description purposes only + + /************************** RS or SA-style Classical Dropping (and variants) **************************/ if (algo == "classical") { if (predrop_ == null) { // ap: this is a hack: had to declare predrop_ as mutable @@ -404,7 +413,7 @@ namespace MueLu { // At this points we either have // (predrop_ != null) // Therefore, it is sufficient to check only threshold - if (A->GetFixedBlockSize() == 1 && threshold == STS::zero() && !useSignedClassical && A->hasCrsGraph()) { + if (A->GetFixedBlockSize() == 1 && threshold == STS::zero() && !useSignedClassicalRS && !useSignedClassicalSA && A->hasCrsGraph()) { // Case 1: scalar problem, no dropping => just use matrix graph RCP graph = rcp(new Graph(A->getCrsGraph(), "graph of A")); // Detect and record rows that correspond to Dirichlet boundary conditions @@ -431,7 +440,8 @@ namespace MueLu { } else if ( (A->GetFixedBlockSize() == 1 && threshold != STS::zero()) || (A->GetFixedBlockSize() == 1 && threshold == STS::zero() && !A->hasCrsGraph()) || - (A->GetFixedBlockSize() == 1 && useSignedClassical) ) { + (A->GetFixedBlockSize() == 1 && useSignedClassicalRS) || + (A->GetFixedBlockSize() == 1 && useSignedClassicalSA) ) { // Case 2: scalar problem with dropping => record the column indices of undropped entries, but still use original // graph's map information, e.g., whether index is local // OR a matrix without a CrsGraph @@ -444,7 +454,8 @@ namespace MueLu { RCP ghostedDiag; ArrayRCP ghostedDiagVals; ArrayRCP negMaxOffDiagonal; - if(useSignedClassical) { + // RS style needs the max negative off-diagonal, SA style needs the diagonal + if(useSignedClassicalRS) { if(ghostedBlockNumber.is_null()) { negMaxOffDiagonal = MueLu::Utilities::GetMatrixMaxMinusOffDiagonal(*A); if (GetVerbLevel() & Statistics1) @@ -489,12 +500,12 @@ namespace MueLu { //FIXME For now, hardwiring the dropping in here LO rownnz = 0; - if(useSignedClassical) { - // Signed classical + if(useSignedClassicalRS) { + // Signed classical RS style for (LO colID = 0; colID < Teuchos::as(nnz); colID++) { LO col = indices[colID]; MT max_neg_aik = realThreshold * STS::real(negMaxOffDiagonal[row]); - MT neg_aij = - STS::real(vals[colID]); + MT neg_aij = - STS::real(vals[colID]); /* if(row==1326) printf("A(%d,%d) = %6.4e, block = (%d,%d) neg_aij = %6.4e max_neg_aik = %6.4e\n",row,col,vals[colID], g_block_id.is_null() ? -1 : g_block_id[row], g_block_id.is_null() ? -1 : g_block_id[col], @@ -507,6 +518,27 @@ namespace MueLu { } rows[row+1] = realnnz; } + else if(useSignedClassicalSA) { + // Signed classical SA style + for (LO colID = 0; colID < Teuchos::as(nnz); colID++) { + LO col = indices[colID]; + + bool is_nonpositive = STS::real(vals[colID]) <= 0; + MT aiiajj = STS::magnitude(threshold*threshold * ghostedDiagVals[col]*ghostedDiagVals[row]); // eps^2*|a_ii|*|a_jj| + MT aij = is_nonpositive ? STS::magnitude(vals[colID]*vals[colID]) : (-STS::magnitude(vals[colID]*vals[colID])); // + |a_ij|^2, if a_ij < 0, - |a_ij|^2 if a_ij >=0 + + if(row==1326) printf("A(%d,%d) = %6.4e, raw_aij = %6.4e aij = %6.4e aiiajj = %6.4e\n",row,col,vals[colID], + vals[colID],aij, aiiajj); + + + if ((!rowIsDirichlet && aij > aiiajj) || row == col) { + columns[realnnz++] = col; + rownnz++; + } else + numDropped++; + } + rows[row+1] = realnnz; + } else { // Standard abs classical for (LO colID = 0; colID < Teuchos::as(nnz); colID++) { From 13007a8aa2bc4e7795b82c31f6f29076e5e75bb9 Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Mon, 18 Oct 2021 21:09:25 -0600 Subject: [PATCH 28/98] MueLu: Adding signed SA style dropping option --- .../MueLu_CoalesceDropFactory_def.hpp | 4 +- .../test/unit_tests/CoalesceDropFactory.cpp | 44 ++++++++++++++++++- 2 files changed, 46 insertions(+), 2 deletions(-) diff --git a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp index 9af45faff43f..ded2947f9a3a 100644 --- a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp +++ b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp @@ -164,7 +164,9 @@ namespace MueLu { if (algo == "distance laplacian" || algo == "block diagonal distance laplacian") { Input(currentLevel, "Coordinates"); } - if (algo.find("block diagonal") != std::string::npos || algo.find("signed classical") != std::string::npos) { + if(algo == "signed classical sa") + ; + else if (algo.find("block diagonal") != std::string::npos || algo.find("signed classical") != std::string::npos) { Input(currentLevel, "BlockNumber"); } } diff --git a/packages/muelu/test/unit_tests/CoalesceDropFactory.cpp b/packages/muelu/test/unit_tests/CoalesceDropFactory.cpp index c730e165e812..63883e9521c8 100644 --- a/packages/muelu/test/unit_tests/CoalesceDropFactory.cpp +++ b/packages/muelu/test/unit_tests/CoalesceDropFactory.cpp @@ -1620,6 +1620,47 @@ namespace MueLuTests { + TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(CoalesceDropFactory, SignedClassicalSA, Scalar, LocalOrdinal, GlobalOrdinal, Node) { +# include + typedef Teuchos::ScalarTraits STS; + typedef typename STS::magnitudeType real_type; + + MUELU_TESTING_SET_OSTREAM; + MUELU_TESTING_LIMIT_SCOPE(Scalar,GlobalOrdinal,Node); + out << "version: " << MueLu::Version() << std::endl; + + RCP > comm = Parameters::getDefaultComm(); + Xpetra::UnderlyingLib lib = TestHelpers::Parameters::getLib(); + + GO nx = 10*comm->getSize(); + Teuchos::ParameterList matrixList; + matrixList.set("nx",nx); + matrixList.set("ny",(GO)10); + matrixList.set("nz",(GO)10); + matrixList.set("matrixType","Laplace3D"); + RCP A =TestHelpers::TestFactory::BuildMatrix(matrixList,lib); + + Level fineLevel; + fineLevel.Set("A", A); + + + RCP amalgFact = rcp(new AmalgamationFactory()); + CoalesceDropFactory coalesceDropFact; + coalesceDropFact.SetFactory("UnAmalgamationInfo",amalgFact); + coalesceDropFact.SetParameter("aggregation: drop tol",Teuchos::ParameterEntry(0.0)); + coalesceDropFact.SetParameter("aggregation: drop scheme",Teuchos::ParameterEntry(std::string("signed classical sa"))); + fineLevel.Request("Graph",&coalesceDropFact); + fineLevel.Request("DofsPerNode", &coalesceDropFact); + + coalesceDropFact.Build(fineLevel); + + RCP graph = fineLevel.Get >("Graph", &coalesceDropFact); + LO myDofsPerNode = fineLevel.Get("DofsPerNode", &coalesceDropFact); + TEST_EQUALITY(Teuchos::as(myDofsPerNode) == 1, true); + } + + + #define MUELU_ETI_GROUP(SC,LO,GO,Node) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,Constructor,SC,LO,GO,Node) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,Build,SC,LO,GO,Node) \ @@ -1642,7 +1683,8 @@ namespace MueLuTests { TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,BlockDiagonalDistanceLaplacian,SC,LO,GO,Node) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,BlockDiagonalDistanceLaplacianWeighted,SC,LO,GO,Node) \ TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,DistanceLaplacianWeighted,SC,LO,GO,Node) \ - TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,AggresiveDroppingIsMarkedAsBoundary,SC,LO,GO,Node) + TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,AggresiveDroppingIsMarkedAsBoundary,SC,LO,GO,Node) \ + TEUCHOS_UNIT_TEST_TEMPLATE_4_INSTANT(CoalesceDropFactory,SignedClassicalSA,SC,LO,GO,Node) \ #include From 2d80622c1cb6d8021145f5421cd1f406290d2b96 Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Mon, 18 Oct 2021 21:14:38 -0600 Subject: [PATCH 29/98] TrilinosCouplings: Output mods --- .../examples/scaling/example_Poisson2D_pn_tpetra.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp b/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp index f25806937d62..caea27002639 100644 --- a/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp +++ b/packages/trilinoscouplings/examples/scaling/example_Poisson2D_pn_tpetra.cpp @@ -2106,9 +2106,10 @@ int TestMultiLevelPreconditionerLaplace(char ProblemType[], ParameterList belosList; belosList.set("Maximum Iterations", maxIts); // Maximum number of iterations allowed belosList.set("Convergence Tolerance", tol); // Relative convergence tolerance requested - belosList.set("Verbosity", Belos::Errors + Belos::Warnings + Belos::StatusTestDetails); + // belosList.set("Verbosity", Belos::Errors + Belos::Warnings + Belos::StatusTestDetails); belosList.set("Output Frequency", 1); - belosList.set("Output Style", Belos::Brief); + belosList.set("Output Style", 1); + belosList.set ("Verbosity", 33); bool scaleResidualHist = true; if (!scaleResidualHist) belosList.set("Implicit Residual Scaling", "None"); From f7b64daabfa49abaa8b2f82171937cf0890a78e1 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 4 Oct 2021 18:26:23 -0600 Subject: [PATCH 30/98] Tpetra: Added outline of a test for async MultiVector transfers --- .../ImportExport2/ImportExport2_UnitTests.cpp | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 95ec17d71174..de65b768a563 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -871,6 +871,111 @@ namespace { } + template + class MultiVectorTransferFixture { + private: + using map_type = Map; + using mv_type = MultiVector; + + public: + MultiVectorTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~MultiVectorTransferFixture() { } + + bool shouldSkipTest() { + return isSerial(); + } + + void setupMultiVectors(int collectRank) { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = 3; + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMV = rcp(new mv_type(sourceMap, 1)); + sourceMV->randomize(); + + const size_t totalElements = numProcs*sourceNumLocalElements; + const size_t targetNumLocalElements = (myRank == collectRank) ? totalElements : 0; + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMV = rcp(new mv_type(targetMap, 1)); + targetMV->putScalar(Teuchos::ScalarTraits::zero()); + } + + void performTransfer() { + Import importer(sourceMap, targetMap, getImportParameterList()); + targetMV->doImport(*sourceMV, importer, INSERT); + } + + void checkResults() { + RCP referenceMV = generateReferenceWithClassicalCodePath(); + compareMultiVectors(targetMV, referenceMV); + } + + private: + void compareMultiVectors(RCP resultMV, RCP referenceMV) { + auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); + auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); + + for (GO globalRow = targetMap->getMinGlobalIndex(); globalRow <= targetMap->getMaxGlobalIndex(); ++globalRow) { + const LO localRow = targetMap->getLocalElement(globalRow); + TEST_EQUALITY(data(localRow, 0), referenceData(localRow, 0)); + } + } + + RCP generateReferenceWithClassicalCodePath() { + Import importer(sourceMap, targetMap, getImportParameterList()); + expertSetRemoteLIDsContiguous(importer, false); + TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); + + RCP referenceMV = rcp(new mv_type(targetMap, 1)); + referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->doImport(*sourceMV, importer, INSERT); + TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); + + return referenceMV; + } + + bool isSerial() { + if (numProcs < 2) { + out << "This test is only meaningful if running with multiple MPI " + "processes, but you ran it with only 1 process." << endl; + return true; + } + else return false; + } + + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMV; + RCP targetMV; + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) return; + + fixture.setupMultiVectors(0); + fixture.performTransfer(); + fixture.checkResults(); + } + + template bool graphs_are_same(const RCP& G1, const RCP& G2) { @@ -3038,6 +3143,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorImport, doImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, MueLuStyle, LO, GO, SC ) From bfbeb3da7e6914f8b650307a89f52595c0fa62fc Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Fri, 8 Oct 2021 12:02:03 -0600 Subject: [PATCH 31/98] Tpetra: update async MultiVector transfer test to be independent of transfer method --- .../ImportExport2/ImportExport2_UnitTests.cpp | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index de65b768a563..f154be9dfb8b 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -908,18 +908,18 @@ namespace { targetMV->putScalar(Teuchos::ScalarTraits::zero()); } - void performTransfer() { - Import importer(sourceMap, targetMap, getImportParameterList()); - targetMV->doImport(*sourceMV, importer, INSERT); + template + void performTransfer(const TransferMethod& transferMethod) { + transferMethod(sourceMV, targetMV); } void checkResults() { - RCP referenceMV = generateReferenceWithClassicalCodePath(); + RCP referenceMV = generateReferenceWithClassicalCodePath(); compareMultiVectors(targetMV, referenceMV); } private: - void compareMultiVectors(RCP resultMV, RCP referenceMV) { + void compareMultiVectors(RCP resultMV, RCP referenceMV) { auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); @@ -965,13 +965,25 @@ namespace { RCP targetMV; }; + template + class ForwardImport { + private: + using mv_type = MultiVector; + + public: + void operator()(RCP sourceMV, RCP targetMV) const { + Import importer(sourceMV->getMap(), targetMV->getMap(), getImportParameterList()); + targetMV->doImport(*sourceMV, importer, INSERT); + } + }; + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) return; fixture.setupMultiVectors(0); - fixture.performTransfer(); + fixture.performTransfer(ForwardImport()); fixture.checkResults(); } From 31d9c298600b135526ca1df86dc5227a32e211e7 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Fri, 8 Oct 2021 12:18:26 -0600 Subject: [PATCH 32/98] Tpetra: update async MultiVector transfer test to be independent of reference solution --- .../ImportExport2/ImportExport2_UnitTests.cpp | 46 +++++++++++-------- 1 file changed, 28 insertions(+), 18 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index f154be9dfb8b..c44e2bdc0248 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -909,12 +909,13 @@ namespace { } template - void performTransfer(const TransferMethod& transferMethod) { - transferMethod(sourceMV, targetMV); + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMV, targetMV); } - void checkResults() { - RCP referenceMV = generateReferenceWithClassicalCodePath(); + template + void checkResults(const ReferenceSolution& referenceSolution) { + RCP referenceMV = referenceSolution.generateWithClassicalCodePath(sourceMV, targetMap); compareMultiVectors(targetMV, referenceMV); } @@ -929,19 +930,6 @@ namespace { } } - RCP generateReferenceWithClassicalCodePath() { - Import importer(sourceMap, targetMap, getImportParameterList()); - expertSetRemoteLIDsContiguous(importer, false); - TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); - - RCP referenceMV = rcp(new mv_type(targetMap, 1)); - referenceMV->putScalar(Teuchos::ScalarTraits::zero()); - referenceMV->doImport(*sourceMV, importer, INSERT); - TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); - - return referenceMV; - } - bool isSerial() { if (numProcs < 2) { out << "This test is only meaningful if running with multiple MPI " @@ -965,6 +953,28 @@ namespace { RCP targetMV; }; + template + class ReferenceImport { + private: + using map_type = Map; + using mv_type = MultiVector; + + public: + RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { + RCP sourceMap = sourceMV->getMap(); + Import importer(sourceMap, targetMap, getImportParameterList()); + expertSetRemoteLIDsContiguous(importer, false); + TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); + + RCP referenceMV = rcp(new mv_type(targetMap, 1)); + referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->doImport(*sourceMV, importer, INSERT); + TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); + + return referenceMV; + } + }; + template class ForwardImport { private: @@ -984,7 +994,7 @@ namespace { fixture.setupMultiVectors(0); fixture.performTransfer(ForwardImport()); - fixture.checkResults(); + fixture.checkResults(ReferenceImport()); } From 7258c08dda1daad410cb9a4e30ae8091eb988de6 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 11 Oct 2021 16:41:36 -0600 Subject: [PATCH 33/98] Tpetra: Added outline of tests for async CrsMatrix transfers --- .../ImportExport2/ImportExport2_UnitTests.cpp | 306 ++++++++++++++++++ 1 file changed, 306 insertions(+) diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index c44e2bdc0248..3cdd1a121b21 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -998,6 +998,310 @@ namespace { } + template + class CrsMatrixDiagonalTransferFixture { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + CrsMatrixDiagonalTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~CrsMatrixDiagonalTransferFixture() { } + + bool shouldSkipTest() { + return isSerial(); + } + + void setupMatrices(int collectRank) { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t targetNumLocalElements = 3; + const size_t totalElements = numProcs*targetNumLocalElements; + const size_t sourceNumLocalElements = (myRank == collectRank) ? totalElements : 0; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); + + if (sourceNumLocalElements != 0) { + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); + } + } + sourceMat->fillComplete(); + + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); + } + + template + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMat, targetMat); + } + + template + void checkResults(const ReferenceSolution& referenceSolution) { + RCP referenceMat = referenceSolution.generateUsingAllInOneImport(sourceMat, targetMap); + checkMatrixIsDiagonal(targetMat); + checkMatrixIsDiagonal(referenceMat); + compareMatrices(targetMat, referenceMat); + } + + private: + void checkMatrixIsDiagonal(RCP matrix) { + for (GO gblRow = targetMap->getMinGlobalIndex (); + gblRow <= targetMap->getMaxGlobalIndex (); + ++gblRow) { + const LO lclRow = targetMap->getLocalElement (gblRow); + + typename crs_type::local_inds_host_view_type lclInds; + typename crs_type::values_host_view_type lclVals; + matrix->getLocalRowView (lclRow, lclInds, lclVals); + TEST_EQUALITY_CONST(lclInds.size(), 1); + TEST_EQUALITY_CONST(lclVals.size(), 1); + + if (lclInds.size () != 0) { // don't segfault in error case + TEST_EQUALITY(matrix->getColMap ()->getGlobalElement (lclInds[0]), gblRow); + } + if (lclVals.size () != 0) { // don't segfault in error case + TEST_EQUALITY(lclVals[0], as (gblRow)); + } + } + } + + void compareMatrices(RCP resultMat, RCP referenceMat) { + using size_type = typename Array::size_type; + using magnitude_type = typename ScalarTraits::magnitudeType; + + using lids_type = typename crs_type::nonconst_local_inds_host_view_type; + using vals_type = typename crs_type::nonconst_values_host_view_type; + + const magnitude_type tol = as(10)*ScalarTraits::eps(); + + lids_type resultRowIndices; + vals_type resultRowValues; + lids_type referenceRowIndices; + vals_type referenceRowValues; + for (LO localRow = targetMap->getMinLocalIndex(); localRow <= targetMap->getMaxLocalIndex(); ++localRow) + { + size_t resultNumEntries = resultMat->getNumEntriesInLocalRow(localRow); + size_t referenceNumEntries = referenceMat->getNumEntriesInLocalRow(localRow); + TEST_EQUALITY(resultNumEntries, referenceNumEntries); + + if (resultNumEntries > as(resultRowIndices.size())) { + Kokkos::resize(resultRowIndices, resultNumEntries); + Kokkos::resize(resultRowValues, resultNumEntries); + } + if (referenceNumEntries > as(referenceRowIndices.size())) { + Kokkos::resize(referenceRowIndices, referenceNumEntries); + Kokkos::resize(referenceRowValues, referenceNumEntries); + } + + resultMat->getLocalRowCopy(localRow, resultRowIndices, resultRowValues, resultNumEntries); + referenceMat->getLocalRowCopy(localRow, referenceRowIndices, referenceRowValues, referenceNumEntries); + + Tpetra::sort2(resultRowIndices, resultRowIndices.extent(0), resultRowValues); + Tpetra::sort2(referenceRowIndices, referenceRowIndices.extent(0), referenceRowValues); + + for (size_type k = 0; k < static_cast(resultNumEntries); ++k) { + TEST_EQUALITY(resultRowIndices[k], referenceRowIndices[k]); + TEST_FLOATING_EQUALITY(resultRowValues[k], referenceRowValues[k], tol); + } + } + } + + bool isSerial() { + if (numProcs < 2) { + out << "This test is only meaningful if running with multiple MPI " + "processes, but you ran it with only 1 process." << endl; + return true; + } + else return false; + } + + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMat; + RCP targetMat; + }; + + template + class ReferenceImportMatrix { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + RCP generateUsingAllInOneImport(RCP sourceMat, RCP targetMap) const { + RCP sourceMap = sourceMat->getMap(); + Import importer(sourceMap, targetMap, getImportParameterList()); + + Teuchos::ParameterList dummy; + RCP referenceMat = Tpetra::importAndFillCompleteCrsMatrix( + sourceMat, importer, Teuchos::null, Teuchos::null, rcp(&dummy,false)); + return referenceMat; + } + }; + + template + class ForwardImportMatrix { + private: + using crs_type = CrsMatrix; + + public: + void operator()(RCP sourceMat, RCP targetMat) const { + Import importer(sourceMat->getMap(), targetMat->getMap(), getImportParameterList()); + targetMat->doImport(*sourceMat, importer, INSERT); + targetMat->fillComplete(); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, Scalar ) + { + CrsMatrixDiagonalTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) return; + + fixture.setupMatrices(0); + fixture.performTransfer(ForwardImportMatrix()); + fixture.checkResults(ReferenceImportMatrix()); + } + + + template + class CrsMatrixLowerTriangularTransferFixture { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + CrsMatrixLowerTriangularTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~CrsMatrixLowerTriangularTransferFixture() { } + + bool shouldSkipTest() { + return hasOddNumProcs(); + } + + void setupMatrices() { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; + const size_t targetNumLocalElements = 4; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); + + Array cols(1); + Array vals(1); + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + if (row > 0) { + cols.resize(row); + vals.resize(row); + for (GO col=0; col(col); + vals[col] = as(col); + } + sourceMat->insertGlobalValues(row, cols, vals); + } + } + sourceMat->fillComplete(); + + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); + } + + template + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMat, targetMat); + } + + void checkResults() { + using lids_type = typename crs_type::local_inds_host_view_type; + using vals_type = typename crs_type::values_host_view_type; + + const RCP colMap = targetMat->getColMap(); + + for (GO globalRow=targetMap->getMinGlobalIndex(); globalRow<=targetMap->getMaxGlobalIndex(); ++globalRow) { + LO localRow = targetMap->getLocalElement(globalRow); + lids_type rowIndices; + vals_type rowValues; + + targetMat->getLocalRowView(localRow, rowIndices, rowValues); + TEST_EQUALITY(rowIndices.extent(0), (size_t) globalRow); + TEST_EQUALITY(rowValues.extent(0), (size_t) globalRow); + + Array indices(rowIndices.size()); + Array values(rowValues.size()); + + for (decltype (rowIndices.size()) j=0; jgetGlobalElement(rowIndices[j]); + values[j] = rowValues[j]; + } + Tpetra::sort2(indices.begin(), indices.end(), values.begin()); + + for (decltype (rowIndices.size()) j=0; j(j)); + TEST_EQUALITY(values[j], as(j)); + } + } + } + + private: + bool hasOddNumProcs() { + if (numProcs%2 != 0) { + out << "This test is only meaningful if running with an even number of MPI processes." << endl; + return true; + } + else return false; + } + + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMat; + RCP targetMat; + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, Scalar ) + { + CrsMatrixLowerTriangularTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) return; + + fixture.setupMatrices(); + fixture.performTransfer(ForwardImportMatrix()); + fixture.checkResults(); + } + + template bool graphs_are_same(const RCP& G1, const RCP& G2) { @@ -3166,6 +3470,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorImport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, MueLuStyle, LO, GO, SC ) From f6c4d6928d90241394e50030b4d76dc22e455496 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 09:26:30 -0600 Subject: [PATCH 34/98] Tpetra: separate file for async transfer tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 653 ++++++++++++++++++ .../core/test/ImportExport2/CMakeLists.txt | 10 + .../ImportExport2/ImportExport2_UnitTests.cpp | 434 ------------ 3 files changed, 663 insertions(+), 434 deletions(-) create mode 100644 packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp new file mode 100644 index 000000000000..7f51425495a2 --- /dev/null +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -0,0 +1,653 @@ +// @HEADER +// *********************************************************************** +// +// Tpetra: Templated Linear Algebra Services Package +// Copyright (2008) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +// @HEADER + +#include +#include + +#include +#include +#include +#include +#include +#include "Tpetra_CrsGraph.hpp" +#include "Tpetra_CrsMatrix.hpp" +#include "Tpetra_MultiVector.hpp" +#include "Tpetra_Core.hpp" +#include "Tpetra_Distributor.hpp" +#include "Tpetra_Map.hpp" +#include "Tpetra_Util.hpp" +#include "Tpetra_Import.hpp" +#include "Tpetra_Import_Util.hpp" +#include "Tpetra_Import_Util2.hpp" +#include "Tpetra_Details_packCrsMatrix.hpp" +#include "Tpetra_Details_unpackCrsMatrixAndCombine.hpp" +#include "Tpetra_Export.hpp" +#include "Tpetra_RowMatrixTransposer.hpp" +#include "TpetraExt_MatrixMatrix.hpp" +#include "Tpetra_Details_Behavior.hpp" +#include "Tpetra_Details_gathervPrint.hpp" +#include +#include + +namespace { + + using Teuchos::as; + using Teuchos::Array; + using Teuchos::ArrayRCP; + using Teuchos::ArrayView; + using Teuchos::arrayViewFromVector; + using Teuchos::Comm; + using Teuchos::FancyOStream; + using Teuchos::getFancyOStream; + using Teuchos::includesVerbLevel; + using Teuchos::OrdinalTraits; + using Teuchos::OSTab; + using Teuchos::outArg; + using Teuchos::ParameterList; + using Teuchos::parameterList; + using Teuchos::RCP; + using Teuchos::rcp; + using Teuchos::rcpFromRef; + using Teuchos::REDUCE_MAX; + using Teuchos::reduceAll; + using Teuchos::ScalarTraits; + using Teuchos::tuple; + + using Tpetra::ADD; + using Tpetra::createContigMap; + using Tpetra::CrsGraph; + using Tpetra::CrsMatrix; + using Tpetra::MultiVector; + using Tpetra::Export; + using Tpetra::Import; + using Tpetra::INSERT; + using Tpetra::Map; + using Tpetra::REPLACE; + using Tpetra::StaticProfile; + + using std::cerr; + using std::cout; + using std::ostream_iterator; + using std::endl; + + using Node = Tpetra::Map<>::node_type; + + // Command-line argument values (initially set to defaults). + bool testMpi = true; + double errorTolSlack = 1e+1; + std::string distributorSendType ("Send"); + bool barrierBetween = true; + bool verbose = false; + + TEUCHOS_STATIC_SETUP() + { + Teuchos::CommandLineProcessor &clp = Teuchos::UnitTestRepository::getCLP(); + clp.addOutputSetupOptions(true); + clp.setOption( + "test-mpi", "test-serial", &testMpi, + "Test MPI (if available) or force test of serial. In a serial build," + " this option is ignored and a serial comm is always used." ); + clp.setOption( + "error-tol-slack", &errorTolSlack, + "Slack off of machine epsilon used to check test results" ); + // FIXME (mfh 02 Apr 2012) It would be better to ask Distributor + // for the list of valid send types, but setOption() needs a const + // char[], not an std::string. + clp.setOption ("distributor-send-type", &distributorSendType, + "In MPI tests, the type of send operation that the Tpetra::" + "Distributor will use. Valid values include \"Isend\", " + "\"Rsend\", \"Send\", and \"Ssend\"."); + clp.setOption ("barrier-between", "no-barrier-between", &barrierBetween, + "In MPI tests, whether Tpetra::Distributor will execute a " + "barrier between posting receives and posting sends."); + clp.setOption ("verbose", "quiet", &verbose, "Whether to print verbose " + "output."); + } + + RCP > + getDefaultComm() + { + if (testMpi) { + return Tpetra::getDefaultComm (); + } + else { + return rcp (new Teuchos::SerialComm ()); + } + } + + RCP + getDistributorParameterList () + { + static RCP plist; // NOT THREAD SAFE, but that's OK here. + if (plist.is_null ()) { + plist = parameterList ("Tpetra::Distributor"); + plist->set ("Send type", distributorSendType); + plist->set ("Barrier between receives and sends", barrierBetween); + + if (verbose && getDefaultComm()->getRank() == 0) { + cout << "ParameterList for Distributor: " << *plist << endl; + } + + if (verbose) { + // Tell Distributor to print verbose output. + Teuchos::VerboseObject::setDefaultVerbLevel (Teuchos::VERB_EXTREME); + } + } + return plist; + } + + RCP getImportParameterList () { + return getDistributorParameterList (); // For now. + } + + RCP getExportParameterList () { + return parameterList (* (getDistributorParameterList ())); // For now. + } + + RCP getCrsGraphParameterList () { + static RCP plist; // NOT THREAD SAFE, but that's OK here. + if (plist.is_null ()) { + plist = parameterList ("Tpetra::CrsGraph"); + plist->set ("Import", * (getImportParameterList ())); + plist->set ("Export", * (getExportParameterList ())); + + if (verbose && getDefaultComm()->getRank() == 0) { + cout << "ParameterList for CrsGraph: " << *plist << endl; + } + } + return plist; + } + + RCP getCrsMatrixParameterList () { + return parameterList (* (getCrsGraphParameterList ())); // For now. + } + + + + // + // UNIT TESTS + // + + + template + class MultiVectorTransferFixture { + private: + using map_type = Map; + using mv_type = MultiVector; + + public: + MultiVectorTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~MultiVectorTransferFixture() { } + + bool shouldSkipTest() { + return numProcs < 2; + } + + void printSkippedTestMessage() { + out << "This test is only meaningful if running with multiple MPI " + "processes, but you ran it with only 1 process." << endl; + } + + void setupMultiVectors(int collectRank) { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = 3; + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMV = rcp(new mv_type(sourceMap, 1)); + sourceMV->randomize(); + + const size_t totalElements = numProcs*sourceNumLocalElements; + const size_t targetNumLocalElements = (myRank == collectRank) ? totalElements : 0; + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMV = rcp(new mv_type(targetMap, 1)); + targetMV->putScalar(Teuchos::ScalarTraits::zero()); + } + + template + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMV, targetMV); + } + + template + void checkResults(const ReferenceSolution& referenceSolution) { + RCP referenceMV = referenceSolution.generateWithClassicalCodePath(sourceMV, targetMap); + compareMultiVectors(targetMV, referenceMV); + } + + private: + void compareMultiVectors(RCP resultMV, RCP referenceMV) { + auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); + auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); + + for (GO globalRow = targetMap->getMinGlobalIndex(); globalRow <= targetMap->getMaxGlobalIndex(); ++globalRow) { + const LO localRow = targetMap->getLocalElement(globalRow); + TEST_EQUALITY(data(localRow, 0), referenceData(localRow, 0)); + } + } + + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMV; + RCP targetMV; + }; + + template + class ReferenceImport { + private: + using map_type = Map; + using mv_type = MultiVector; + + public: + RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { + RCP sourceMap = sourceMV->getMap(); + Import importer(sourceMap, targetMap, getImportParameterList()); + expertSetRemoteLIDsContiguous(importer, false); + TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); + + RCP referenceMV = rcp(new mv_type(targetMap, 1)); + referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->doImport(*sourceMV, importer, INSERT); + TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); + + return referenceMV; + } + }; + + template + class ForwardImport { + private: + using mv_type = MultiVector; + + public: + void operator()(RCP sourceMV, RCP targetMV) const { + Import importer(sourceMV->getMap(), targetMV->getMap(), getImportParameterList()); + targetMV->doImport(*sourceMV, importer, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setupMultiVectors(0); + fixture.performTransfer(ForwardImport()); + fixture.checkResults(ReferenceImport()); + } + + + template + class CrsMatrixDiagonalTransferFixture { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + CrsMatrixDiagonalTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~CrsMatrixDiagonalTransferFixture() { } + + bool shouldSkipTest() { + return numProcs < 2; + } + + void printSkippedTestMessage() { + out << "This test is only meaningful if running with multiple MPI " + "processes, but you ran it with only 1 process." << endl; + } + + + void setupMatrices(int collectRank) { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t targetNumLocalElements = 3; + const size_t totalElements = numProcs*targetNumLocalElements; + const size_t sourceNumLocalElements = (myRank == collectRank) ? totalElements : 0; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); + + if (sourceNumLocalElements != 0) { + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); + } + } + sourceMat->fillComplete(); + + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); + } + + template + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMat, targetMat); + } + + template + void checkResults(const ReferenceSolution& referenceSolution) { + RCP referenceMat = referenceSolution.generateUsingAllInOneImport(sourceMat, targetMap); + checkMatrixIsDiagonal(targetMat); + checkMatrixIsDiagonal(referenceMat); + compareMatrices(targetMat, referenceMat); + } + + private: + void checkMatrixIsDiagonal(RCP matrix) { + for (GO gblRow = targetMap->getMinGlobalIndex (); + gblRow <= targetMap->getMaxGlobalIndex (); + ++gblRow) { + const LO lclRow = targetMap->getLocalElement (gblRow); + + typename crs_type::local_inds_host_view_type lclInds; + typename crs_type::values_host_view_type lclVals; + matrix->getLocalRowView (lclRow, lclInds, lclVals); + TEST_EQUALITY_CONST(lclInds.size(), 1); + TEST_EQUALITY_CONST(lclVals.size(), 1); + + if (lclInds.size () != 0) { // don't segfault in error case + TEST_EQUALITY(matrix->getColMap ()->getGlobalElement (lclInds[0]), gblRow); + } + if (lclVals.size () != 0) { // don't segfault in error case + TEST_EQUALITY(lclVals[0], as (gblRow)); + } + } + } + + void compareMatrices(RCP resultMat, RCP referenceMat) { + using size_type = typename Array::size_type; + using magnitude_type = typename ScalarTraits::magnitudeType; + + using lids_type = typename crs_type::nonconst_local_inds_host_view_type; + using vals_type = typename crs_type::nonconst_values_host_view_type; + + const magnitude_type tol = as(10)*ScalarTraits::eps(); + + lids_type resultRowIndices; + vals_type resultRowValues; + lids_type referenceRowIndices; + vals_type referenceRowValues; + for (LO localRow = targetMap->getMinLocalIndex(); localRow <= targetMap->getMaxLocalIndex(); ++localRow) + { + size_t resultNumEntries = resultMat->getNumEntriesInLocalRow(localRow); + size_t referenceNumEntries = referenceMat->getNumEntriesInLocalRow(localRow); + TEST_EQUALITY(resultNumEntries, referenceNumEntries); + + if (resultNumEntries > as(resultRowIndices.size())) { + Kokkos::resize(resultRowIndices, resultNumEntries); + Kokkos::resize(resultRowValues, resultNumEntries); + } + if (referenceNumEntries > as(referenceRowIndices.size())) { + Kokkos::resize(referenceRowIndices, referenceNumEntries); + Kokkos::resize(referenceRowValues, referenceNumEntries); + } + + resultMat->getLocalRowCopy(localRow, resultRowIndices, resultRowValues, resultNumEntries); + referenceMat->getLocalRowCopy(localRow, referenceRowIndices, referenceRowValues, referenceNumEntries); + + Tpetra::sort2(resultRowIndices, resultRowIndices.extent(0), resultRowValues); + Tpetra::sort2(referenceRowIndices, referenceRowIndices.extent(0), referenceRowValues); + + for (size_type k = 0; k < static_cast(resultNumEntries); ++k) { + TEST_EQUALITY(resultRowIndices[k], referenceRowIndices[k]); + TEST_FLOATING_EQUALITY(resultRowValues[k], referenceRowValues[k], tol); + } + } + } + + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMat; + RCP targetMat; + }; + + template + class ReferenceImportMatrix { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + RCP generateUsingAllInOneImport(RCP sourceMat, RCP targetMap) const { + RCP sourceMap = sourceMat->getMap(); + Import importer(sourceMap, targetMap, getImportParameterList()); + + Teuchos::ParameterList dummy; + RCP referenceMat = Tpetra::importAndFillCompleteCrsMatrix( + sourceMat, importer, Teuchos::null, Teuchos::null, rcp(&dummy,false)); + return referenceMat; + } + }; + + template + class ForwardImportMatrix { + private: + using crs_type = CrsMatrix; + + public: + void operator()(RCP sourceMat, RCP targetMat) const { + Import importer(sourceMat->getMap(), targetMat->getMap(), getImportParameterList()); + targetMat->doImport(*sourceMat, importer, INSERT); + targetMat->fillComplete(); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, Scalar ) + { + CrsMatrixDiagonalTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setupMatrices(0); + fixture.performTransfer(ForwardImportMatrix()); + fixture.checkResults(ReferenceImportMatrix()); + } + + + template + class CrsMatrixLowerTriangularTransferFixture { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + CrsMatrixLowerTriangularTransferFixture(Teuchos::FancyOStream& o, bool& s) + : out(o), + success(s), + comm(getDefaultComm()), + numProcs(comm->getSize()), + myRank(comm->getRank()) + { } + + ~CrsMatrixLowerTriangularTransferFixture() { } + + bool shouldSkipTest() { + return numProcs%2 != 0; + } + + void printSkippedTestMessage() { + out << "This test is only meaningful if running with an even number of MPI processes." << endl; + } + + void setupMatrices() { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; + const size_t targetNumLocalElements = 4; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); + + Array cols(1); + Array vals(1); + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + if (row > 0) { + cols.resize(row); + vals.resize(row); + for (GO col=0; col(col); + vals[col] = as(col); + } + sourceMat->insertGlobalValues(row, cols, vals); + } + } + sourceMat->fillComplete(); + + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); + } + + template + void performTransfer(const TransferMethod& transfer) { + transfer(sourceMat, targetMat); + } + + void checkResults() { + using lids_type = typename crs_type::local_inds_host_view_type; + using vals_type = typename crs_type::values_host_view_type; + + const RCP colMap = targetMat->getColMap(); + + for (GO globalRow=targetMap->getMinGlobalIndex(); globalRow<=targetMap->getMaxGlobalIndex(); ++globalRow) { + LO localRow = targetMap->getLocalElement(globalRow); + lids_type rowIndices; + vals_type rowValues; + + targetMat->getLocalRowView(localRow, rowIndices, rowValues); + TEST_EQUALITY(rowIndices.extent(0), (size_t) globalRow); + TEST_EQUALITY(rowValues.extent(0), (size_t) globalRow); + + Array indices(rowIndices.size()); + Array values(rowValues.size()); + + for (decltype (rowIndices.size()) j=0; jgetGlobalElement(rowIndices[j]); + values[j] = rowValues[j]; + } + Tpetra::sort2(indices.begin(), indices.end(), values.begin()); + + for (decltype (rowIndices.size()) j=0; j(j)); + TEST_EQUALITY(values[j], as(j)); + } + } + } + + private: + Teuchos::FancyOStream& out; + bool& success; + + RCP> comm; + const int numProcs; + const int myRank; + + RCP sourceMap; + RCP targetMap; + + RCP sourceMat; + RCP targetMat; + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, Scalar ) + { + CrsMatrixLowerTriangularTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setupMatrices(); + fixture.performTransfer(ForwardImportMatrix()); + fixture.checkResults(); + } + + + // + // INSTANTIATIONS + // + +#define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, SC ) \ + + TPETRA_ETI_MANGLING_TYPEDEFS() + + // Test for all Scalar, LO, GO template parameter + // combinations, and the default Node type. + TPETRA_INSTANTIATE_SLG_NO_ORDINAL_SCALAR( UNIT_TEST_GROUP_SC_LO_GO ) +} diff --git a/packages/tpetra/core/test/ImportExport2/CMakeLists.txt b/packages/tpetra/core/test/ImportExport2/CMakeLists.txt index eb8ea85f2569..c1a2f26f55de 100644 --- a/packages/tpetra/core/test/ImportExport2/CMakeLists.txt +++ b/packages/tpetra/core/test/ImportExport2/CMakeLists.txt @@ -8,6 +8,16 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST( STANDARD_PASS_OUTPUT ) +TRIBITS_ADD_EXECUTABLE_AND_TEST( + AsyncTransfer_UnitTests + SOURCES + AsyncTransfer_UnitTests.cpp + ${TEUCHOS_STD_UNIT_TEST_MAIN} + COMM serial mpi + ARGS "--globally-reduce-test-result --output-show-proc-rank --output-to-root-rank-only=-1" + STANDARD_PASS_OUTPUT + ) + TRIBITS_ADD_EXECUTABLE_AND_TEST( ImportExport2_CrsSortingUtils SOURCES diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 3cdd1a121b21..95ec17d71174 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -871,437 +871,6 @@ namespace { } - template - class MultiVectorTransferFixture { - private: - using map_type = Map; - using mv_type = MultiVector; - - public: - MultiVectorTransferFixture(Teuchos::FancyOStream& o, bool& s) - : out(o), - success(s), - comm(getDefaultComm()), - numProcs(comm->getSize()), - myRank(comm->getRank()) - { } - - ~MultiVectorTransferFixture() { } - - bool shouldSkipTest() { - return isSerial(); - } - - void setupMultiVectors(int collectRank) { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t sourceNumLocalElements = 3; - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMV = rcp(new mv_type(sourceMap, 1)); - sourceMV->randomize(); - - const size_t totalElements = numProcs*sourceNumLocalElements; - const size_t targetNumLocalElements = (myRank == collectRank) ? totalElements : 0; - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMV = rcp(new mv_type(targetMap, 1)); - targetMV->putScalar(Teuchos::ScalarTraits::zero()); - } - - template - void performTransfer(const TransferMethod& transfer) { - transfer(sourceMV, targetMV); - } - - template - void checkResults(const ReferenceSolution& referenceSolution) { - RCP referenceMV = referenceSolution.generateWithClassicalCodePath(sourceMV, targetMap); - compareMultiVectors(targetMV, referenceMV); - } - - private: - void compareMultiVectors(RCP resultMV, RCP referenceMV) { - auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); - auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); - - for (GO globalRow = targetMap->getMinGlobalIndex(); globalRow <= targetMap->getMaxGlobalIndex(); ++globalRow) { - const LO localRow = targetMap->getLocalElement(globalRow); - TEST_EQUALITY(data(localRow, 0), referenceData(localRow, 0)); - } - } - - bool isSerial() { - if (numProcs < 2) { - out << "This test is only meaningful if running with multiple MPI " - "processes, but you ran it with only 1 process." << endl; - return true; - } - else return false; - } - - Teuchos::FancyOStream& out; - bool& success; - - RCP> comm; - const int numProcs; - const int myRank; - - RCP sourceMap; - RCP targetMap; - - RCP sourceMV; - RCP targetMV; - }; - - template - class ReferenceImport { - private: - using map_type = Map; - using mv_type = MultiVector; - - public: - RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { - RCP sourceMap = sourceMV->getMap(); - Import importer(sourceMap, targetMap, getImportParameterList()); - expertSetRemoteLIDsContiguous(importer, false); - TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); - - RCP referenceMV = rcp(new mv_type(targetMap, 1)); - referenceMV->putScalar(Teuchos::ScalarTraits::zero()); - referenceMV->doImport(*sourceMV, importer, INSERT); - TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); - - return referenceMV; - } - }; - - template - class ForwardImport { - private: - using mv_type = MultiVector; - - public: - void operator()(RCP sourceMV, RCP targetMV) const { - Import importer(sourceMV->getMap(), targetMV->getMap(), getImportParameterList()); - targetMV->doImport(*sourceMV, importer, INSERT); - } - }; - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) - { - MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) return; - - fixture.setupMultiVectors(0); - fixture.performTransfer(ForwardImport()); - fixture.checkResults(ReferenceImport()); - } - - - template - class CrsMatrixDiagonalTransferFixture { - private: - using map_type = Map; - using crs_type = CrsMatrix; - - public: - CrsMatrixDiagonalTransferFixture(Teuchos::FancyOStream& o, bool& s) - : out(o), - success(s), - comm(getDefaultComm()), - numProcs(comm->getSize()), - myRank(comm->getRank()) - { } - - ~CrsMatrixDiagonalTransferFixture() { } - - bool shouldSkipTest() { - return isSerial(); - } - - void setupMatrices(int collectRank) { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t targetNumLocalElements = 3; - const size_t totalElements = numProcs*targetNumLocalElements; - const size_t sourceNumLocalElements = (myRank == collectRank) ? totalElements : 0; - - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); - - if (sourceNumLocalElements != 0) { - for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { - sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); - } - } - sourceMat->fillComplete(); - - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); - } - - template - void performTransfer(const TransferMethod& transfer) { - transfer(sourceMat, targetMat); - } - - template - void checkResults(const ReferenceSolution& referenceSolution) { - RCP referenceMat = referenceSolution.generateUsingAllInOneImport(sourceMat, targetMap); - checkMatrixIsDiagonal(targetMat); - checkMatrixIsDiagonal(referenceMat); - compareMatrices(targetMat, referenceMat); - } - - private: - void checkMatrixIsDiagonal(RCP matrix) { - for (GO gblRow = targetMap->getMinGlobalIndex (); - gblRow <= targetMap->getMaxGlobalIndex (); - ++gblRow) { - const LO lclRow = targetMap->getLocalElement (gblRow); - - typename crs_type::local_inds_host_view_type lclInds; - typename crs_type::values_host_view_type lclVals; - matrix->getLocalRowView (lclRow, lclInds, lclVals); - TEST_EQUALITY_CONST(lclInds.size(), 1); - TEST_EQUALITY_CONST(lclVals.size(), 1); - - if (lclInds.size () != 0) { // don't segfault in error case - TEST_EQUALITY(matrix->getColMap ()->getGlobalElement (lclInds[0]), gblRow); - } - if (lclVals.size () != 0) { // don't segfault in error case - TEST_EQUALITY(lclVals[0], as (gblRow)); - } - } - } - - void compareMatrices(RCP resultMat, RCP referenceMat) { - using size_type = typename Array::size_type; - using magnitude_type = typename ScalarTraits::magnitudeType; - - using lids_type = typename crs_type::nonconst_local_inds_host_view_type; - using vals_type = typename crs_type::nonconst_values_host_view_type; - - const magnitude_type tol = as(10)*ScalarTraits::eps(); - - lids_type resultRowIndices; - vals_type resultRowValues; - lids_type referenceRowIndices; - vals_type referenceRowValues; - for (LO localRow = targetMap->getMinLocalIndex(); localRow <= targetMap->getMaxLocalIndex(); ++localRow) - { - size_t resultNumEntries = resultMat->getNumEntriesInLocalRow(localRow); - size_t referenceNumEntries = referenceMat->getNumEntriesInLocalRow(localRow); - TEST_EQUALITY(resultNumEntries, referenceNumEntries); - - if (resultNumEntries > as(resultRowIndices.size())) { - Kokkos::resize(resultRowIndices, resultNumEntries); - Kokkos::resize(resultRowValues, resultNumEntries); - } - if (referenceNumEntries > as(referenceRowIndices.size())) { - Kokkos::resize(referenceRowIndices, referenceNumEntries); - Kokkos::resize(referenceRowValues, referenceNumEntries); - } - - resultMat->getLocalRowCopy(localRow, resultRowIndices, resultRowValues, resultNumEntries); - referenceMat->getLocalRowCopy(localRow, referenceRowIndices, referenceRowValues, referenceNumEntries); - - Tpetra::sort2(resultRowIndices, resultRowIndices.extent(0), resultRowValues); - Tpetra::sort2(referenceRowIndices, referenceRowIndices.extent(0), referenceRowValues); - - for (size_type k = 0; k < static_cast(resultNumEntries); ++k) { - TEST_EQUALITY(resultRowIndices[k], referenceRowIndices[k]); - TEST_FLOATING_EQUALITY(resultRowValues[k], referenceRowValues[k], tol); - } - } - } - - bool isSerial() { - if (numProcs < 2) { - out << "This test is only meaningful if running with multiple MPI " - "processes, but you ran it with only 1 process." << endl; - return true; - } - else return false; - } - - Teuchos::FancyOStream& out; - bool& success; - - RCP> comm; - const int numProcs; - const int myRank; - - RCP sourceMap; - RCP targetMap; - - RCP sourceMat; - RCP targetMat; - }; - - template - class ReferenceImportMatrix { - private: - using map_type = Map; - using crs_type = CrsMatrix; - - public: - RCP generateUsingAllInOneImport(RCP sourceMat, RCP targetMap) const { - RCP sourceMap = sourceMat->getMap(); - Import importer(sourceMap, targetMap, getImportParameterList()); - - Teuchos::ParameterList dummy; - RCP referenceMat = Tpetra::importAndFillCompleteCrsMatrix( - sourceMat, importer, Teuchos::null, Teuchos::null, rcp(&dummy,false)); - return referenceMat; - } - }; - - template - class ForwardImportMatrix { - private: - using crs_type = CrsMatrix; - - public: - void operator()(RCP sourceMat, RCP targetMat) const { - Import importer(sourceMat->getMap(), targetMat->getMap(), getImportParameterList()); - targetMat->doImport(*sourceMat, importer, INSERT); - targetMat->fillComplete(); - } - }; - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, Scalar ) - { - CrsMatrixDiagonalTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) return; - - fixture.setupMatrices(0); - fixture.performTransfer(ForwardImportMatrix()); - fixture.checkResults(ReferenceImportMatrix()); - } - - - template - class CrsMatrixLowerTriangularTransferFixture { - private: - using map_type = Map; - using crs_type = CrsMatrix; - - public: - CrsMatrixLowerTriangularTransferFixture(Teuchos::FancyOStream& o, bool& s) - : out(o), - success(s), - comm(getDefaultComm()), - numProcs(comm->getSize()), - myRank(comm->getRank()) - { } - - ~CrsMatrixLowerTriangularTransferFixture() { } - - bool shouldSkipTest() { - return hasOddNumProcs(); - } - - void setupMatrices() { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; - const size_t targetNumLocalElements = 4; - - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); - - Array cols(1); - Array vals(1); - for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { - if (row > 0) { - cols.resize(row); - vals.resize(row); - for (GO col=0; col(col); - vals[col] = as(col); - } - sourceMat->insertGlobalValues(row, cols, vals); - } - } - sourceMat->fillComplete(); - - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); - } - - template - void performTransfer(const TransferMethod& transfer) { - transfer(sourceMat, targetMat); - } - - void checkResults() { - using lids_type = typename crs_type::local_inds_host_view_type; - using vals_type = typename crs_type::values_host_view_type; - - const RCP colMap = targetMat->getColMap(); - - for (GO globalRow=targetMap->getMinGlobalIndex(); globalRow<=targetMap->getMaxGlobalIndex(); ++globalRow) { - LO localRow = targetMap->getLocalElement(globalRow); - lids_type rowIndices; - vals_type rowValues; - - targetMat->getLocalRowView(localRow, rowIndices, rowValues); - TEST_EQUALITY(rowIndices.extent(0), (size_t) globalRow); - TEST_EQUALITY(rowValues.extent(0), (size_t) globalRow); - - Array indices(rowIndices.size()); - Array values(rowValues.size()); - - for (decltype (rowIndices.size()) j=0; jgetGlobalElement(rowIndices[j]); - values[j] = rowValues[j]; - } - Tpetra::sort2(indices.begin(), indices.end(), values.begin()); - - for (decltype (rowIndices.size()) j=0; j(j)); - TEST_EQUALITY(values[j], as(j)); - } - } - } - - private: - bool hasOddNumProcs() { - if (numProcs%2 != 0) { - out << "This test is only meaningful if running with an even number of MPI processes." << endl; - return true; - } - else return false; - } - - Teuchos::FancyOStream& out; - bool& success; - - RCP> comm; - const int numProcs; - const int myRank; - - RCP sourceMap; - RCP targetMap; - - RCP sourceMat; - RCP targetMat; - }; - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, Scalar ) - { - CrsMatrixLowerTriangularTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) return; - - fixture.setupMatrices(); - fixture.performTransfer(ForwardImportMatrix()); - fixture.checkResults(); - } - - template bool graphs_are_same(const RCP& G1, const RCP& G2) { @@ -3469,9 +3038,6 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Import_Util,GetTwoTransferOwnershipVector, LO #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorImport, doImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, doImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Import_Util, UnpackAndCombineWithOwningPIDs, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( FusedImportExport, MueLuStyle, LO, GO, SC ) From 4d0359e8d59d1768db86e9cf3755e85b3764ee25 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:05:05 -0600 Subject: [PATCH 35/98] Tpetra: decouple import method from tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 30 +++++++------------ 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 7f51425495a2..ccfe84c50de7 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -92,6 +92,7 @@ namespace { using Teuchos::tuple; using Tpetra::ADD; + using Tpetra::DistObject; using Tpetra::createContigMap; using Tpetra::CrsGraph; using Tpetra::CrsMatrix; @@ -307,15 +308,15 @@ namespace { } }; - template + template class ForwardImport { private: - using mv_type = MultiVector; + using DistObjectRCP = RCP>; public: - void operator()(RCP sourceMV, RCP targetMV) const { - Import importer(sourceMV->getMap(), targetMV->getMap(), getImportParameterList()); - targetMV->doImport(*sourceMV, importer, INSERT); + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Import importer(source->getMap(), target->getMap(), getImportParameterList()); + target->doImport(*source, importer, INSERT); } }; @@ -385,6 +386,7 @@ namespace { template void performTransfer(const TransferMethod& transfer) { transfer(sourceMat, targetMat); + targetMat->fillComplete(); } template @@ -490,19 +492,6 @@ namespace { } }; - template - class ForwardImportMatrix { - private: - using crs_type = CrsMatrix; - - public: - void operator()(RCP sourceMat, RCP targetMat) const { - Import importer(sourceMat->getMap(), targetMat->getMap(), getImportParameterList()); - targetMat->doImport(*sourceMat, importer, INSERT); - targetMat->fillComplete(); - } - }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, Scalar ) { CrsMatrixDiagonalTransferFixture fixture(out, success); @@ -512,7 +501,7 @@ namespace { } fixture.setupMatrices(0); - fixture.performTransfer(ForwardImportMatrix()); + fixture.performTransfer(ForwardImport()); fixture.checkResults(ReferenceImportMatrix()); } @@ -574,6 +563,7 @@ namespace { template void performTransfer(const TransferMethod& transfer) { transfer(sourceMat, targetMat); + targetMat->fillComplete(); } void checkResults() { @@ -631,7 +621,7 @@ namespace { } fixture.setupMatrices(); - fixture.performTransfer(ForwardImportMatrix()); + fixture.performTransfer(ForwardImport()); fixture.checkResults(); } From 1fd4addbc09757fc8519e4123fa7fa02eb1a5145 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:10:47 -0600 Subject: [PATCH 36/98] Tpetra: cleanup MultiVectorTransferFixture --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 52 ++++++++++++------- 1 file changed, 33 insertions(+), 19 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index ccfe84c50de7..b97bb68a3624 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -202,9 +202,8 @@ namespace { } - // - // UNIT TESTS + // UNIT TEST FIXTURES // @@ -234,20 +233,9 @@ namespace { "processes, but you ran it with only 1 process." << endl; } - void setupMultiVectors(int collectRank) { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t sourceNumLocalElements = 3; - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMV = rcp(new mv_type(sourceMap, 1)); - sourceMV->randomize(); - - const size_t totalElements = numProcs*sourceNumLocalElements; - const size_t targetNumLocalElements = (myRank == collectRank) ? totalElements : 0; - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMV = rcp(new mv_type(targetMap, 1)); - targetMV->putScalar(Teuchos::ScalarTraits::zero()); + void setup(int collectRank) { + setupMaps(collectRank); + setupMultiVectors(); } template @@ -262,6 +250,26 @@ namespace { } private: + void setupMaps(int collectRank) { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = 3; + const size_t totalElements = numProcs*sourceNumLocalElements; + const size_t targetNumLocalElements = (myRank == collectRank) ? totalElements : 0; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + } + + void setupMultiVectors() { + sourceMV = rcp(new mv_type(sourceMap, 1)); + sourceMV->randomize(); + + targetMV = rcp(new mv_type(targetMap, 1)); + targetMV->putScalar(Teuchos::ScalarTraits::zero()); + } + void compareMultiVectors(RCP resultMV, RCP referenceMV) { auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); @@ -287,7 +295,7 @@ namespace { }; template - class ReferenceImport { + class ReferenceImportMultiVector { private: using map_type = Map; using mv_type = MultiVector; @@ -308,6 +316,12 @@ namespace { } }; + + // + // UNIT TESTS + // + + template class ForwardImport { private: @@ -328,9 +342,9 @@ namespace { return; } - fixture.setupMultiVectors(0); + fixture.setup(0); fixture.performTransfer(ForwardImport()); - fixture.checkResults(ReferenceImport()); + fixture.checkResults(ReferenceImportMultiVector()); } From b84b02a822aaf346a595d1fc6182c83a6832555f Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:28:21 -0600 Subject: [PATCH 37/98] Tpetra: cleanup DiagonalCrsMatrixTransferFixture --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 155 +++++++++--------- 1 file changed, 79 insertions(+), 76 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index b97bb68a3624..da76ebfef571 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -317,45 +317,14 @@ namespace { }; - // - // UNIT TESTS - // - - - template - class ForwardImport { - private: - using DistObjectRCP = RCP>; - - public: - void operator()(DistObjectRCP source, DistObjectRCP target) const { - Import importer(source->getMap(), target->getMap(), getImportParameterList()); - target->doImport(*source, importer, INSERT); - } - }; - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) - { - MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } - - fixture.setup(0); - fixture.performTransfer(ForwardImport()); - fixture.checkResults(ReferenceImportMultiVector()); - } - - template - class CrsMatrixDiagonalTransferFixture { + class DiagonalCrsMatrixTransferFixture { private: using map_type = Map; using crs_type = CrsMatrix; public: - CrsMatrixDiagonalTransferFixture(Teuchos::FancyOStream& o, bool& s) + DiagonalCrsMatrixTransferFixture(Teuchos::FancyOStream& o, bool& s) : out(o), success(s), comm(getDefaultComm()), @@ -363,7 +332,7 @@ namespace { myRank(comm->getRank()) { } - ~CrsMatrixDiagonalTransferFixture() { } + ~DiagonalCrsMatrixTransferFixture() { } bool shouldSkipTest() { return numProcs < 2; @@ -374,27 +343,9 @@ namespace { "processes, but you ran it with only 1 process." << endl; } - - void setupMatrices(int collectRank) { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t targetNumLocalElements = 3; - const size_t totalElements = numProcs*targetNumLocalElements; - const size_t sourceNumLocalElements = (myRank == collectRank) ? totalElements : 0; - - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); - - if (sourceNumLocalElements != 0) { - for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { - sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); - } - } - sourceMat->fillComplete(); - - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); + void setup() { + setupMaps(); + setupMatrices(); } template @@ -412,23 +363,44 @@ namespace { } private: + void setupMaps() { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t targetNumLocalElements = 3; + const size_t totalElements = numProcs*targetNumLocalElements; + const size_t sourceNumLocalElements = (myRank == 0) ? totalElements : 0; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + } + + void setupMatrices() { + sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); + targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); + + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); + } + sourceMat->fillComplete(); + } + void checkMatrixIsDiagonal(RCP matrix) { - for (GO gblRow = targetMap->getMinGlobalIndex (); - gblRow <= targetMap->getMaxGlobalIndex (); - ++gblRow) { - const LO lclRow = targetMap->getLocalElement (gblRow); - - typename crs_type::local_inds_host_view_type lclInds; - typename crs_type::values_host_view_type lclVals; - matrix->getLocalRowView (lclRow, lclInds, lclVals); - TEST_EQUALITY_CONST(lclInds.size(), 1); - TEST_EQUALITY_CONST(lclVals.size(), 1); - - if (lclInds.size () != 0) { // don't segfault in error case - TEST_EQUALITY(matrix->getColMap ()->getGlobalElement (lclInds[0]), gblRow); + for (GO globalRow = targetMap->getMinGlobalIndex(); globalRow <= targetMap->getMaxGlobalIndex(); ++globalRow) { + const LO localRow = targetMap->getLocalElement(globalRow); + + typename crs_type::local_inds_host_view_type localInds; + typename crs_type::values_host_view_type localVals; + matrix->getLocalRowView(localRow, localInds, localVals); + + TEST_EQUALITY_CONST(localInds.size(), 1); + if (localInds.size() == 1) { + TEST_EQUALITY(matrix->getColMap()->getGlobalElement(localInds[0]), globalRow); } - if (lclVals.size () != 0) { // don't segfault in error case - TEST_EQUALITY(lclVals[0], as (gblRow)); + + TEST_EQUALITY_CONST(localVals.size(), 1); + if (localVals.size() == 1) { + TEST_EQUALITY(localVals[0], as(globalRow)); } } } @@ -446,8 +418,8 @@ namespace { vals_type resultRowValues; lids_type referenceRowIndices; vals_type referenceRowValues; - for (LO localRow = targetMap->getMinLocalIndex(); localRow <= targetMap->getMaxLocalIndex(); ++localRow) - { + + for (LO localRow = targetMap->getMinLocalIndex(); localRow <= targetMap->getMaxLocalIndex(); ++localRow) { size_t resultNumEntries = resultMat->getNumEntriesInLocalRow(localRow); size_t referenceNumEntries = referenceMat->getNumEntriesInLocalRow(localRow); TEST_EQUALITY(resultNumEntries, referenceNumEntries); @@ -506,15 +478,46 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, Scalar ) + + // + // UNIT TESTS + // + + + template + class ForwardImport { + private: + using DistObjectRCP = RCP>; + + public: + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Import importer(source->getMap(), target->getMap(), getImportParameterList()); + target->doImport(*source, importer, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(0); + fixture.performTransfer(ForwardImport()); + fixture.checkResults(ReferenceImportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) { - CrsMatrixDiagonalTransferFixture fixture(out, success); + DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { fixture.printSkippedTestMessage(); return; } - fixture.setupMatrices(0); + fixture.setup(); fixture.performTransfer(ForwardImport()); fixture.checkResults(ReferenceImportMatrix()); } @@ -646,7 +649,7 @@ namespace { #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_diagonal, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 262bb8107ee224351c630a24927cdd24ea7410e5 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:35:06 -0600 Subject: [PATCH 38/98] Tpetra: cleanup LowerTriangularCrsMatrixTransferFixture --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 167 +++++++++--------- 1 file changed, 87 insertions(+), 80 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index da76ebfef571..1b31f8d7dda2 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -479,58 +479,14 @@ namespace { }; - // - // UNIT TESTS - // - - - template - class ForwardImport { - private: - using DistObjectRCP = RCP>; - - public: - void operator()(DistObjectRCP source, DistObjectRCP target) const { - Import importer(source->getMap(), target->getMap(), getImportParameterList()); - target->doImport(*source, importer, INSERT); - } - }; - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) - { - MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } - - fixture.setup(0); - fixture.performTransfer(ForwardImport()); - fixture.checkResults(ReferenceImportMultiVector()); - } - - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) - { - DiagonalCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } - - fixture.setup(); - fixture.performTransfer(ForwardImport()); - fixture.checkResults(ReferenceImportMatrix()); - } - - template - class CrsMatrixLowerTriangularTransferFixture { + class LowerTriangularCrsMatrixTransferFixture { private: using map_type = Map; using crs_type = CrsMatrix; public: - CrsMatrixLowerTriangularTransferFixture(Teuchos::FancyOStream& o, bool& s) + LowerTriangularCrsMatrixTransferFixture(Teuchos::FancyOStream& o, bool& s) : out(o), success(s), comm(getDefaultComm()), @@ -538,7 +494,7 @@ namespace { myRank(comm->getRank()) { } - ~CrsMatrixLowerTriangularTransferFixture() { } + ~LowerTriangularCrsMatrixTransferFixture() { } bool shouldSkipTest() { return numProcs%2 != 0; @@ -548,33 +504,9 @@ namespace { out << "This test is only meaningful if running with an even number of MPI processes." << endl; } - void setupMatrices() { - const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); - - const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; - const size_t targetNumLocalElements = 4; - - sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); - sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); - - Array cols(1); - Array vals(1); - for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { - if (row > 0) { - cols.resize(row); - vals.resize(row); - for (GO col=0; col(col); - vals[col] = as(col); - } - sourceMat->insertGlobalValues(row, cols, vals); - } - } - sourceMat->fillComplete(); - - targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); - targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); + void setup() { + setupMaps(); + setupMatrices(); } template @@ -601,13 +533,13 @@ namespace { Array indices(rowIndices.size()); Array values(rowValues.size()); - for (decltype (rowIndices.size()) j=0; jgetGlobalElement(rowIndices[j]); values[j] = rowValues[j]; } Tpetra::sort2(indices.begin(), indices.end(), values.begin()); - for (decltype (rowIndices.size()) j=0; j(j)); TEST_EQUALITY(values[j], as(j)); } @@ -615,6 +547,37 @@ namespace { } private: + void setupMaps() { + const GO indexBase = 0; + const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + + const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; + const size_t targetNumLocalElements = 4; + + sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); + targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); + } + + void setupMatrices() { + sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); + targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); + + Array cols(1); + Array vals(1); + for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { + if (row > 0) { + cols.resize(row); + vals.resize(row); + for (GO col=0; col(col); + vals[col] = as(col); + } + sourceMat->insertGlobalValues(row, cols, vals); + } + } + sourceMat->fillComplete(); + } + Teuchos::FancyOStream& out; bool& success; @@ -629,15 +592,59 @@ namespace { RCP targetMat; }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, Scalar ) + + // + // UNIT TESTS + // + + + template + class ForwardImport { + private: + using DistObjectRCP = RCP>; + + public: + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Import importer(source->getMap(), target->getMap(), getImportParameterList()); + target->doImport(*source, importer, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) { - CrsMatrixLowerTriangularTransferFixture fixture(out, success); + MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { fixture.printSkippedTestMessage(); return; } - fixture.setupMatrices(); + fixture.setup(0); + fixture.performTransfer(ForwardImport()); + fixture.checkResults(ReferenceImportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) + { + DiagonalCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ForwardImport()); + fixture.checkResults(ReferenceImportMatrix()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( LowerTriangularCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) + { + LowerTriangularCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); fixture.performTransfer(ForwardImport()); fixture.checkResults(); } @@ -650,7 +657,7 @@ namespace { #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( CrsMatrixTransfer, asyncImport_lowerTriangular, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( LowerTriangularCrsMatrixTransfer, asyncImport, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 37f0f36eb5acafeb29c4fc271c5139840a66b197 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:38:00 -0600 Subject: [PATCH 39/98] Tpetra: change ForwardImport implementation to be truly asynchronous --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 1b31f8d7dda2..b08583171cf9 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -606,11 +606,12 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { Import importer(source->getMap(), target->getMap(), getImportParameterList()); - target->doImport(*source, importer, INSERT); + target->beginImport(*source, importer, INSERT); + target->endImport(*source, importer, INSERT); } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncForwardImport, LO, GO, Scalar ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -623,7 +624,7 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncForwardImport, LO, GO, Scalar ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -636,7 +637,7 @@ namespace { fixture.checkResults(ReferenceImportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( LowerTriangularCrsMatrixTransfer, asyncImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( LowerTriangularCrsMatrixTransfer, asyncForwardImport, LO, GO, Scalar ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -655,9 +656,9 @@ namespace { // #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( DiagonalCrsMatrixTransfer, asyncImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( LowerTriangularCrsMatrixTransfer, asyncImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncForwardImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( DiagonalCrsMatrixTransfer, asyncForwardImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( LowerTriangularCrsMatrixTransfer, asyncForwardImport, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 8df998165523c03ff627242ed1870e7fea29607f Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:41:54 -0600 Subject: [PATCH 40/98] Tpetra: rearrange test names --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 26 ++++++++++++++----- 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index b08583171cf9..7016a64d9e6f 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -611,7 +611,7 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( MultiVectorTransfer, asyncForwardImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank0, LO, GO, Scalar ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -624,7 +624,20 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( DiagonalCrsMatrixTransfer, asyncForwardImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank1, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(1); + fixture.performTransfer(ForwardImport()); + fixture.checkResults(ReferenceImportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, DiagonalCrsMatrix, LO, GO, Scalar ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -637,7 +650,7 @@ namespace { fixture.checkResults(ReferenceImportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( LowerTriangularCrsMatrixTransfer, asyncForwardImport, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, LowerTriangularCrsMatrix, LO, GO, Scalar ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -656,9 +669,10 @@ namespace { // #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( MultiVectorTransfer, asyncForwardImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( DiagonalCrsMatrixTransfer, asyncForwardImport, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( LowerTriangularCrsMatrixTransfer, asyncForwardImport, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank0, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank1, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, DiagonalCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 132c004a8296ec56a3a65c7bbc8d4ecc33ed8170 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 21:44:52 -0600 Subject: [PATCH 41/98] Tpetra: add ReverseImport tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 7016a64d9e6f..d127a6379876 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -664,6 +664,72 @@ namespace { } + template + class ReverseImport { + private: + using DistObjectRCP = RCP>; + + public: + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Export exporter(target->getMap(), source->getMap(), getImportParameterList()); + target->beginImport(*source, exporter, INSERT); + target->endImport(*source, exporter, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank0, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(0); + fixture.performTransfer(ReverseImport()); + fixture.checkResults(ReferenceImportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank1, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(1); + fixture.performTransfer(ReverseImport()); + fixture.checkResults(ReferenceImportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, DiagonalCrsMatrix, LO, GO, Scalar ) + { + DiagonalCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ReverseImport()); + fixture.checkResults(ReferenceImportMatrix()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + { + LowerTriangularCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ReverseImport()); + fixture.checkResults(); + } + + // // INSTANTIATIONS // @@ -673,6 +739,10 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank1, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, DiagonalCrsMatrix, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank0, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank1, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, DiagonalCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 0985c3a336ed72b267ec5483cb8f9a622414bff2 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 22:01:42 -0600 Subject: [PATCH 42/98] Tpetra: add ForwardExport tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 116 +++++++++++++++++- 1 file changed, 113 insertions(+), 3 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index d127a6379876..27a357f209c1 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -316,6 +316,28 @@ namespace { } }; + template + class ReferenceExportMultiVector { + private: + using map_type = Map; + using mv_type = MultiVector; + + public: + RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { + RCP sourceMap = sourceMV->getMap(); + Export exporter(sourceMap, targetMap, getExportParameterList()); + expertSetRemoteLIDsContiguous(exporter, false); + TEUCHOS_ASSERT(!exporter.areRemoteLIDsContiguous()); + + RCP referenceMV = rcp(new mv_type(targetMap, 1)); + referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->doExport(*sourceMV, exporter, INSERT); + TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); + + return referenceMV; + } + }; + template class DiagonalCrsMatrixTransferFixture { @@ -356,7 +378,7 @@ namespace { template void checkResults(const ReferenceSolution& referenceSolution) { - RCP referenceMat = referenceSolution.generateUsingAllInOneImport(sourceMat, targetMap); + RCP referenceMat = referenceSolution.generateUsingAllInOne(sourceMat, targetMap); checkMatrixIsDiagonal(targetMat); checkMatrixIsDiagonal(referenceMat); compareMatrices(targetMat, referenceMat); @@ -467,7 +489,7 @@ namespace { using crs_type = CrsMatrix; public: - RCP generateUsingAllInOneImport(RCP sourceMat, RCP targetMap) const { + RCP generateUsingAllInOne(RCP sourceMat, RCP targetMap) const { RCP sourceMap = sourceMat->getMap(); Import importer(sourceMap, targetMap, getImportParameterList()); @@ -478,6 +500,24 @@ namespace { } }; + template + class ReferenceExportMatrix { + private: + using map_type = Map; + using crs_type = CrsMatrix; + + public: + RCP generateUsingAllInOne(RCP sourceMat, RCP targetMap) const { + RCP sourceMap = sourceMat->getMap(); + Export exporter(sourceMap, targetMap, getExportParameterList()); + + Teuchos::ParameterList dummy; + RCP referenceMat = Tpetra::exportAndFillCompleteCrsMatrix( + sourceMat, exporter, Teuchos::null, Teuchos::null, rcp(&dummy,false)); + return referenceMat; + } + }; + template class LowerTriangularCrsMatrixTransferFixture { @@ -671,7 +711,7 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { - Export exporter(target->getMap(), source->getMap(), getImportParameterList()); + Export exporter(target->getMap(), source->getMap(), getExportParameterList()); target->beginImport(*source, exporter, INSERT); target->endImport(*source, exporter, INSERT); } @@ -730,6 +770,72 @@ namespace { } + template + class ForwardExport { + private: + using DistObjectRCP = RCP>; + + public: + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Export exporter(source->getMap(), target->getMap(), getExportParameterList()); + target->beginExport(*source, exporter, INSERT); + target->endExport(*source, exporter, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank0, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(0); + fixture.performTransfer(ForwardExport()); + fixture.checkResults(ReferenceExportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank1, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(1); + fixture.performTransfer(ForwardExport()); + fixture.checkResults(ReferenceExportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, DiagonalCrsMatrix, LO, GO, Scalar ) + { + DiagonalCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ForwardExport()); + fixture.checkResults(ReferenceExportMatrix()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + { + LowerTriangularCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ForwardExport()); + fixture.checkResults(); + } + + // // INSTANTIATIONS // @@ -743,6 +849,10 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank1, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, DiagonalCrsMatrix, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank0, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank1, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, DiagonalCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, LowerTriangularCrsMatrix, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From d5b43ee358e87366c5b7bd1e271b45705f22880e Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 18 Oct 2021 22:03:57 -0600 Subject: [PATCH 43/98] Tpetra: add ReverseExport tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 27a357f209c1..e80c4f8ddd6b 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -836,6 +836,72 @@ namespace { } + template + class ReverseExport { + private: + using DistObjectRCP = RCP>; + + public: + void operator()(DistObjectRCP source, DistObjectRCP target) const { + Import importer(target->getMap(), source->getMap(), getImportParameterList()); + target->beginExport(*source, importer, INSERT); + target->endExport(*source, importer, INSERT); + } + }; + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank0, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(0); + fixture.performTransfer(ReverseExport()); + fixture.checkResults(ReferenceExportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank1, LO, GO, Scalar ) + { + MultiVectorTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(1); + fixture.performTransfer(ReverseExport()); + fixture.checkResults(ReferenceExportMultiVector()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, DiagonalCrsMatrix, LO, GO, Scalar ) + { + DiagonalCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ReverseExport()); + fixture.checkResults(ReferenceExportMatrix()); + } + + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + { + LowerTriangularCrsMatrixTransferFixture fixture(out, success); + if (fixture.shouldSkipTest()) { + fixture.printSkippedTestMessage(); + return; + } + + fixture.setup(); + fixture.performTransfer(ReverseExport()); + fixture.checkResults(); + } + + // // INSTANTIATIONS // @@ -853,6 +919,10 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank1, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, DiagonalCrsMatrix, LO, GO, SC ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, LowerTriangularCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank0, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank1, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, DiagonalCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, LowerTriangularCrsMatrix, LO, GO, SC ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From 01ddff6d5a260976f09c884d2348c197fe8de45d Mon Sep 17 00:00:00 2001 From: Vinh Dang Date: Mon, 18 Oct 2021 23:14:55 -0700 Subject: [PATCH 44/98] Add MPI_Finalize before return --- packages/adelus/test/vector_random/cxx_main.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/packages/adelus/test/vector_random/cxx_main.cpp b/packages/adelus/test/vector_random/cxx_main.cpp index 5c7772a64465..1e1408e7dac4 100644 --- a/packages/adelus/test/vector_random/cxx_main.cpp +++ b/packages/adelus/test/vector_random/cxx_main.cpp @@ -217,6 +217,7 @@ int main(int argc, char *argv[]) << " vs. available: " << gpu_count << "). Exit without test." << std::endl; } + MPI_Finalize() ; return 0; } From 03f4904c34de80b947b4ef0c82be958da7711a7c Mon Sep 17 00:00:00 2001 From: iyamazaki Date: Tue, 19 Oct 2021 01:03:01 -0600 Subject: [PATCH 45/98] Amesos2::SuperLU_dist: add option to apply Equil --- .../src/Amesos2_Superludist_FunctionMap.hpp | 4 +- .../amesos2/src/Amesos2_Superludist_def.hpp | 97 +++++++++++-------- 2 files changed, 60 insertions(+), 41 deletions(-) diff --git a/packages/amesos2/src/Amesos2_Superludist_FunctionMap.hpp b/packages/amesos2/src/Amesos2_Superludist_FunctionMap.hpp index 7eb5862b1b6d..cd92961a72b1 100644 --- a/packages/amesos2/src/Amesos2_Superludist_FunctionMap.hpp +++ b/packages/amesos2/src/Amesos2_Superludist_FunctionMap.hpp @@ -532,14 +532,14 @@ namespace Amesos2 { } static void gsequ_loc(SLUD::SuperMatrix* A, double* r, double* c, - double* rowcnd, double* colcnd, double* amax, int* info, + double* rowcnd, double* colcnd, double* amax, SLUD::int_t* info, SLUD::gridinfo_t* grid) { SLUD::Z::pzgsequ(A, r, c, rowcnd, colcnd, amax, info, grid); } static void gsequ(SLUD::SuperMatrix* A, double* r, double* c, - double* rowcnd, double* colcnd, double* amax, int* info) + double* rowcnd, double* colcnd, double* amax, SLUD::int_t* info) { SLUD::Z::zgsequ_dist(A, r, c, rowcnd, colcnd, amax, info); } diff --git a/packages/amesos2/src/Amesos2_Superludist_def.hpp b/packages/amesos2/src/Amesos2_Superludist_def.hpp index f312b2b48e44..4cd1fea25c5d 100644 --- a/packages/amesos2/src/Amesos2_Superludist_def.hpp +++ b/packages/amesos2/src/Amesos2_Superludist_def.hpp @@ -355,17 +355,17 @@ namespace Amesos2 { free( data_.fstVtxSep ); #endif } + float info = 0.0; + { #ifdef HAVE_AMESOS2_TIMERS - Teuchos::TimeMonitor preOrderTime( this->timers_.preOrderTime_ ); + Teuchos::TimeMonitor preOrderTime( this->timers_.preOrderTime_ ); #endif - - float info = 0.0; - info = SLUD::get_perm_c_parmetis( &(data_.A), - data_.perm_r.getRawPtr(), data_.perm_c.getRawPtr(), - data_.grid.nprow * data_.grid.npcol, data_.domains, - &(data_.sizes), &(data_.fstVtxSep), - &(data_.grid), &(data_.symb_comm) ); - + info = SLUD::get_perm_c_parmetis( &(data_.A), + data_.perm_r.getRawPtr(), data_.perm_c.getRawPtr(), + data_.grid.nprow * data_.grid.npcol, data_.domains, + &(data_.sizes), &(data_.fstVtxSep), + &(data_.grid), &(data_.symb_comm) ); + } TEUCHOS_TEST_FOR_EXCEPTION( info > 0.0, std::runtime_error, "SuperLU_DIST pre-ordering ran out of memory after allocating " @@ -389,18 +389,18 @@ namespace Amesos2 { if( in_grid_ ){ + float info = 0.0; + { #ifdef HAVE_AMESOS2_TIMERS - Teuchos::TimeMonitor symFactTime( this->timers_.symFactTime_ ); + Teuchos::TimeMonitor symFactTime( this->timers_.symFactTime_ ); #endif - - float info = 0.0; - info = SLUD::symbfact_dist((data_.grid.nprow) * (data_.grid.npcol), - data_.domains, &(data_.A), data_.perm_c.getRawPtr(), - data_.perm_r.getRawPtr(), data_.sizes, - data_.fstVtxSep, &(data_.pslu_freeable), - &(data_.grid.comm), &(data_.symb_comm), - &(data_.mem_usage)); - + info = SLUD::symbfact_dist((data_.grid.nprow) * (data_.grid.npcol), + data_.domains, &(data_.A), data_.perm_c.getRawPtr(), + data_.perm_r.getRawPtr(), data_.sizes, + data_.fstVtxSep, &(data_.pslu_freeable), + &(data_.grid.comm), &(data_.symb_comm), + &(data_.mem_usage)); + } TEUCHOS_TEST_FOR_EXCEPTION( info > 0.0, std::runtime_error, "SuperLU_DIST symbolic factorization ran out of memory after" @@ -420,17 +420,25 @@ namespace Amesos2 { // loadA_impl(); // Refresh the matrix values - // if( data_.options.Equil == SLUD::YES ){ - // // Apply the scalings computed in preOrdering - // function_map::laqgs(&(data_.A), data_.R.getRawPtr(), - // data_.C.getRawPtr(), data_.rowcnd, data_.colcnd, - // data_.amax, &(data_.equed)); + if( in_grid_ ) { + if( data_.options.Equil == SLUD::YES ) { + SLUD::int_t info = 0; - // data_.rowequ = (data_.equed == SLUD::ROW) || (data_.equed == SLUD::BOTH); - // data_.colequ = (data_.equed == SLUD::COL) || (data_.equed == SLUD::BOTH); - // } + // Compute scaling + data_.R.resize(this->globalNumRows_); + data_.C.resize(this->globalNumCols_); + function_map::gsequ_loc(&(data_.A), data_.R.getRawPtr(), data_.C.getRawPtr(), + &(data_.rowcnd), &(data_.colcnd), &(data_.amax), &info, &(data_.grid)); + + // Apply the scalings + function_map::laqgs_loc(&(data_.A), data_.R.getRawPtr(), data_.C.getRawPtr(), + data_.rowcnd, data_.colcnd, data_.amax, + &(data_.equed)); + + data_.rowequ = (data_.equed == SLUD::ROW) || (data_.equed == SLUD::BOTH); + data_.colequ = (data_.equed == SLUD::COL) || (data_.equed == SLUD::BOTH); + } - if( in_grid_ ){ // Apply the column ordering, so that AC is the column-permuted A, and compute etree size_t nnz_loc = ((SLUD::NRformat_loc*)data_.A.Store)->nnz_loc; for( size_t i = 0; i < nnz_loc; ++i ) colind_[i] = data_.perm_c[colind_[i]]; @@ -462,7 +470,6 @@ namespace Amesos2 { #ifdef HAVE_AMESOS2_TIMERS Teuchos::TimeMonitor numFactTimer(this->timers_.numFactTime_); #endif - function_map::gstrf(&(data_.options), this->globalNumRows_, this->globalNumCols_, anorm, &(data_.lu), &(data_.grid), &(data_.stat), &info); @@ -511,7 +518,6 @@ namespace Amesos2 { #ifdef HAVE_AMESOS2_TIMERS Teuchos::TimeMonitor convTimer(this->timers_.vecConvTime_); #endif - { // The input dense matrix for B should be distributed in the // same manner as the superlu_dist matrix. That is, if a @@ -522,7 +528,6 @@ namespace Amesos2 { #ifdef HAVE_AMESOS2_TIMERS Teuchos::TimeMonitor redistTimer(this->timers_.vecRedistTime_); #endif - // get grid-distributed mv data. The multivector data will be // distributed across the processes in the SuperLU_DIST grid. typedef Util::get_1d_copy_helper,slu_type> copy_helper; @@ -563,12 +568,20 @@ namespace Amesos2 { same_solve_struct_ = true; } + // Apply row-scaling if requested + if (data_.options.Equil == SLUD::YES && data_.rowequ) { + SLUD::int_t ld = as(local_len_rhs); + for(global_size_type j = 0; j < nrhs; ++j) { + for(size_t i = 0; i < local_len_rhs; ++i) bvals_[i + j*ld] *= data_.R[i]; + } + } + + // Solve int ierr = 0; // returned error code { #ifdef HAVE_AMESOS2_TIMERS Teuchos::TimeMonitor solveTimer(this->timers_.solveTime_); #endif - function_map::gstrs(as(this->globalNumRows_), &(data_.lu), &(data_.scale_perm), &(data_.grid), bvals_.getRawPtr(), as(local_len_rhs), as(first_global_row_b), @@ -606,6 +619,14 @@ namespace Amesos2 { as(nrhs), &(data_.grid)); } + + // Apply col-scaling if requested + if (data_.options.Equil == SLUD::YES && data_.colequ) { + SLUD::int_t ld = as(local_len_rhs); + for(global_size_type j = 0; j < nrhs; ++j) { + for(size_t i = 0; i < local_len_rhs; ++i) xvals_[i + j*ld] *= data_.C[i]; + } + } } /* Update X's global values */ @@ -613,7 +634,6 @@ namespace Amesos2 { #ifdef HAVE_AMESOS2_TIMERS Teuchos::TimeMonitor redistTimer(this->timers_.vecRedistTime_); #endif - typedef Util::put_1d_data_helper,slu_type> put_helper; put_helper::do_put(X, xvals_(), @@ -672,10 +692,9 @@ namespace Amesos2 { data_.options.Trans = SLUD::NOTRANS; // should always be set this way; - // TODO: Uncomment when supported - // bool equil = parameterList->get("Equil", true); - // data_.options.Equil = equil ? SLUD::YES : SLUD::NO; - data_.options.Equil = SLUD::NO; + // Equilbration option + bool equil = parameterList->get("Equil", false); + data_.options.Equil = equil ? SLUD::YES : SLUD::NO; if( parameterList->isParameter("ColPerm") ){ RCP colperm_validator = valid_params->getEntry("ColPerm").validator(); @@ -743,8 +762,8 @@ namespace Amesos2 { tuple(SLUD::NOTRANS), pl.getRawPtr()); - // TODO: uncomment when supported - // pl->set("Equil", false, "Whether to equilibrate the system before solve"); + // Equillbration + pl->set("Equil", false, "Whether to equilibrate the system before solve"); // TODO: uncomment when supported // setStringToIntegralParameter("IterRefine", "NOREFINE", From a72563ad7881c971e8edeef6bc76927409785bc5 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Tue, 19 Oct 2021 09:36:52 -0400 Subject: [PATCH 46/98] update config/config.* to build on summit downloaded latest versions from git://git.savannah.gnu.org/config.git 191bcb948f7191c36eefe634336f5fc5c0c4c2be --- packages/zoltan/config/config.guess | 1702 +++++++++-------- packages/zoltan/config/config.sub | 2630 ++++++++++++++------------- 2 files changed, 2338 insertions(+), 1994 deletions(-) diff --git a/packages/zoltan/config/config.guess b/packages/zoltan/config/config.guess index 49ba16f15c66..e81d3ae7c210 100755 --- a/packages/zoltan/config/config.guess +++ b/packages/zoltan/config/config.guess @@ -1,14 +1,14 @@ #! /bin/sh # Attempt to guess a canonical system name. -# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, -# 2011, 2012 Free Software Foundation, Inc. +# Copyright 1992-2021 Free Software Foundation, Inc. -timestamp='2012-01-01' +# shellcheck disable=SC2006,SC2268 # see below for rationale + +timestamp='2021-06-03' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or +# the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but @@ -17,26 +17,30 @@ timestamp='2012-01-01' # General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program; if not, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. - - -# Originally written by Per Bothner. Please send patches (context -# diff format) to and include a ChangeLog -# entry. +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). # -# This script attempts to guess a canonical system name similar to -# config.sub. If it succeeds, it prints the system name on stdout, and -# exits with 0. Otherwise, it exits with 1. +# Originally written by Per Bothner; maintained since 2000 by Ben Elliston. # # You can get the latest version of this script from: -# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD +# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess +# +# Please send patches to . + + +# The "shellcheck disable" line above the timestamp inhibits complaints +# about features and limitations of the classic Bourne shell that were +# superseded or lifted in POSIX. However, this script identifies a wide +# variety of pre-POSIX systems that do not have POSIX shells at all, and +# even some reasonably current systems (Solaris 10 as case-in-point) still +# have a pre-POSIX /bin/sh. + me=`echo "$0" | sed -e 's,.*/,,'` @@ -45,7 +49,7 @@ Usage: $0 [OPTION] Output the configuration name of the system \`$me' is run on. -Operation modes: +Options: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit @@ -56,9 +60,7 @@ version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, -2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 -Free Software Foundation, Inc. +Copyright 1992-2021 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -92,7 +94,8 @@ if test $# != 0; then exit 1 fi -trap 'exit 1' 1 2 15 +# Just in case it came from the environment. +GUESS= # CC_FOR_BUILD -- compiler used by this script. Note that the use of a # compiler to aid in system detection is discouraged as it requires @@ -104,45 +107,90 @@ trap 'exit 1' 1 2 15 # Portable tmp directory creation inspired by the Autoconf team. -set_cc_for_build=' -trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; -trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; -: ${TMPDIR=/tmp} ; - { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || - { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || - { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || - { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; -dummy=$tmp/dummy ; -tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; -case $CC_FOR_BUILD,$HOST_CC,$CC in - ,,) echo "int x;" > $dummy.c ; - for c in cc gcc c89 c99 ; do - if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then - CC_FOR_BUILD="$c"; break ; - fi ; - done ; - if test x"$CC_FOR_BUILD" = x ; then - CC_FOR_BUILD=no_compiler_found ; - fi - ;; - ,,*) CC_FOR_BUILD=$CC ;; - ,*,*) CC_FOR_BUILD=$HOST_CC ;; -esac ; set_cc_for_build= ;' +tmp= +# shellcheck disable=SC2172 +trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15 + +set_cc_for_build() { + # prevent multiple calls if $tmp is already set + test "$tmp" && return 0 + : "${TMPDIR=/tmp}" + # shellcheck disable=SC2039,SC3028 + { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } + dummy=$tmp/dummy + case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in + ,,) echo "int x;" > "$dummy.c" + for driver in cc gcc c89 c99 ; do + if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then + CC_FOR_BUILD=$driver + break + fi + done + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; + esac +} # This is needed to find uname on a Pyramid OSx when run in the BSD universe. # (ghazi@noc.rutgers.edu 1994-08-24) -if (test -f /.attbin/uname) >/dev/null 2>&1 ; then +if test -f /.attbin/uname ; then PATH=$PATH:/.attbin ; export PATH fi UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown -UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown +UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown +case $UNAME_SYSTEM in +Linux|GNU|GNU/*) + LIBC=unknown + + set_cc_for_build + cat <<-EOF > "$dummy.c" + #include + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #elif defined(__GLIBC__) + LIBC=gnu + #else + #include + /* First heuristic to detect musl libc. */ + #ifdef __DEFINED_va_list + LIBC=musl + #endif + #endif + EOF + cc_set_libc=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'` + eval "$cc_set_libc" + + # Second heuristic to detect musl libc. + if [ "$LIBC" = unknown ] && + command -v ldd >/dev/null && + ldd --version 2>&1 | grep -q ^musl; then + LIBC=musl + fi + + # If the system lacks a compiler, then just pick glibc. + # We could probably try harder. + if [ "$LIBC" = unknown ]; then + LIBC=gnu + fi + ;; +esac + # Note: order is significant - the case branches are not exclusive. -case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in +case $UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION in *:NetBSD:*:*) # NetBSD (nbsd) targets should (where applicable) match one or # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*, @@ -154,22 +202,32 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # # Note: NetBSD doesn't particularly care about the vendor # portion of the name. We always set it to "unknown". - sysctl="sysctl -n hw.machine_arch" - UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ - /usr/sbin/$sysctl 2>/dev/null || echo unknown)` - case "${UNAME_MACHINE_ARCH}" in + UNAME_MACHINE_ARCH=`(uname -p 2>/dev/null || \ + /sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + /usr/sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + echo unknown)` + case $UNAME_MACHINE_ARCH in + aarch64eb) machine=aarch64_be-unknown ;; armeb) machine=armeb-unknown ;; arm*) machine=arm-unknown ;; sh3el) machine=shl-unknown ;; sh3eb) machine=sh-unknown ;; sh5el) machine=sh5le-unknown ;; - *) machine=${UNAME_MACHINE_ARCH}-unknown ;; + earmv*) + arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'` + endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'` + machine=${arch}${endian}-unknown + ;; + *) machine=$UNAME_MACHINE_ARCH-unknown ;; esac # The Operating System including object format, if it has switched - # to ELF recently, or will in the future. - case "${UNAME_MACHINE_ARCH}" in + # to ELF recently (or will in the future) and ABI. + case $UNAME_MACHINE_ARCH in + earm*) + os=netbsdelf + ;; arm*|i386|m68k|ns32k|sh3*|sparc|vax) - eval $set_cc_for_build + set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ELF__ then @@ -184,41 +242,80 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in os=netbsd ;; esac + # Determine ABI tags. + case $UNAME_MACHINE_ARCH in + earm*) + expr='s/^earmv[0-9]/-eabi/;s/eb$//' + abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"` + ;; + esac # The OS release # Debian GNU/NetBSD machines have a different userland, and # thus, need a distinct triplet. However, they do not need # kernel version information, so it can be replaced with a # suitable tag, in the style of linux-gnu. - case "${UNAME_VERSION}" in + case $UNAME_VERSION in Debian*) release='-gnu' ;; *) - release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` + release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2` ;; esac # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: # contains redundant information, the shorter form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. - echo "${machine}-${os}${release}" - exit ;; + GUESS=$machine-${os}${release}${abi-} + ;; + *:Bitrig:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'` + GUESS=$UNAME_MACHINE_ARCH-unknown-bitrig$UNAME_RELEASE + ;; *:OpenBSD:*:*) UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` - echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE_ARCH-unknown-openbsd$UNAME_RELEASE + ;; + *:SecBSD:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/SecBSD.//'` + GUESS=$UNAME_MACHINE_ARCH-unknown-secbsd$UNAME_RELEASE + ;; + *:LibertyBSD:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'` + GUESS=$UNAME_MACHINE_ARCH-unknown-libertybsd$UNAME_RELEASE + ;; + *:MidnightBSD:*:*) + GUESS=$UNAME_MACHINE-unknown-midnightbsd$UNAME_RELEASE + ;; *:ekkoBSD:*:*) - echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-unknown-ekkobsd$UNAME_RELEASE + ;; *:SolidBSD:*:*) - echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-unknown-solidbsd$UNAME_RELEASE + ;; + *:OS108:*:*) + GUESS=$UNAME_MACHINE-unknown-os108_$UNAME_RELEASE + ;; macppc:MirBSD:*:*) - echo powerpc-unknown-mirbsd${UNAME_RELEASE} - exit ;; + GUESS=powerpc-unknown-mirbsd$UNAME_RELEASE + ;; *:MirBSD:*:*) - echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-unknown-mirbsd$UNAME_RELEASE + ;; + *:Sortix:*:*) + GUESS=$UNAME_MACHINE-unknown-sortix + ;; + *:Twizzler:*:*) + GUESS=$UNAME_MACHINE-unknown-twizzler + ;; + *:Redox:*:*) + GUESS=$UNAME_MACHINE-unknown-redox + ;; + mips:OSF1:*.*) + GUESS=mips-dec-osf1 + ;; alpha:OSF1:*:*) + # Reset EXIT trap before exiting to avoid spurious non-zero exit code. + trap '' 0 case $UNAME_RELEASE in *4.0) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` @@ -232,163 +329,158 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # covers most systems running today. This code pipes the CPU # types through head -n 1, so we only detect the type of CPU 0. ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` - case "$ALPHA_CPU_TYPE" in + case $ALPHA_CPU_TYPE in "EV4 (21064)") - UNAME_MACHINE="alpha" ;; + UNAME_MACHINE=alpha ;; "EV4.5 (21064)") - UNAME_MACHINE="alpha" ;; + UNAME_MACHINE=alpha ;; "LCA4 (21066/21068)") - UNAME_MACHINE="alpha" ;; + UNAME_MACHINE=alpha ;; "EV5 (21164)") - UNAME_MACHINE="alphaev5" ;; + UNAME_MACHINE=alphaev5 ;; "EV5.6 (21164A)") - UNAME_MACHINE="alphaev56" ;; + UNAME_MACHINE=alphaev56 ;; "EV5.6 (21164PC)") - UNAME_MACHINE="alphapca56" ;; + UNAME_MACHINE=alphapca56 ;; "EV5.7 (21164PC)") - UNAME_MACHINE="alphapca57" ;; + UNAME_MACHINE=alphapca57 ;; "EV6 (21264)") - UNAME_MACHINE="alphaev6" ;; + UNAME_MACHINE=alphaev6 ;; "EV6.7 (21264A)") - UNAME_MACHINE="alphaev67" ;; + UNAME_MACHINE=alphaev67 ;; "EV6.8CB (21264C)") - UNAME_MACHINE="alphaev68" ;; + UNAME_MACHINE=alphaev68 ;; "EV6.8AL (21264B)") - UNAME_MACHINE="alphaev68" ;; + UNAME_MACHINE=alphaev68 ;; "EV6.8CX (21264D)") - UNAME_MACHINE="alphaev68" ;; + UNAME_MACHINE=alphaev68 ;; "EV6.9A (21264/EV69A)") - UNAME_MACHINE="alphaev69" ;; + UNAME_MACHINE=alphaev69 ;; "EV7 (21364)") - UNAME_MACHINE="alphaev7" ;; + UNAME_MACHINE=alphaev7 ;; "EV7.9 (21364A)") - UNAME_MACHINE="alphaev79" ;; + UNAME_MACHINE=alphaev79 ;; esac # A Pn.n version is a patched version. # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. - echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` - # Reset EXIT trap before exiting to avoid spurious non-zero exit code. - exitcode=$? - trap '' 0 - exit $exitcode ;; - Alpha\ *:Windows_NT*:*) - # How do we know it's Interix rather than the generic POSIX subsystem? - # Should we change UNAME_MACHINE based on the output of uname instead - # of the specific Alpha model? - echo alpha-pc-interix - exit ;; - 21064:Windows_NT:50:3) - echo alpha-dec-winnt3.5 - exit ;; + OSF_REL=`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz` + GUESS=$UNAME_MACHINE-dec-osf$OSF_REL + ;; Amiga*:UNIX_System_V:4.0:*) - echo m68k-unknown-sysv4 - exit ;; + GUESS=m68k-unknown-sysv4 + ;; *:[Aa]miga[Oo][Ss]:*:*) - echo ${UNAME_MACHINE}-unknown-amigaos - exit ;; + GUESS=$UNAME_MACHINE-unknown-amigaos + ;; *:[Mm]orph[Oo][Ss]:*:*) - echo ${UNAME_MACHINE}-unknown-morphos - exit ;; + GUESS=$UNAME_MACHINE-unknown-morphos + ;; *:OS/390:*:*) - echo i370-ibm-openedition - exit ;; + GUESS=i370-ibm-openedition + ;; *:z/VM:*:*) - echo s390-ibm-zvmoe - exit ;; + GUESS=s390-ibm-zvmoe + ;; *:OS400:*:*) - echo powerpc-ibm-os400 - exit ;; + GUESS=powerpc-ibm-os400 + ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) - echo arm-acorn-riscix${UNAME_RELEASE} - exit ;; - arm:riscos:*:*|arm:RISCOS:*:*) - echo arm-unknown-riscos - exit ;; + GUESS=arm-acorn-riscix$UNAME_RELEASE + ;; + arm*:riscos:*:*|arm*:RISCOS:*:*) + GUESS=arm-unknown-riscos + ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) - echo hppa1.1-hitachi-hiuxmpp - exit ;; + GUESS=hppa1.1-hitachi-hiuxmpp + ;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. - if test "`(/bin/universe) 2>/dev/null`" = att ; then - echo pyramid-pyramid-sysv3 - else - echo pyramid-pyramid-bsd - fi - exit ;; + case `(/bin/universe) 2>/dev/null` in + att) GUESS=pyramid-pyramid-sysv3 ;; + *) GUESS=pyramid-pyramid-bsd ;; + esac + ;; NILE*:*:*:dcosx) - echo pyramid-pyramid-svr4 - exit ;; + GUESS=pyramid-pyramid-svr4 + ;; DRS?6000:unix:4.0:6*) - echo sparc-icl-nx6 - exit ;; + GUESS=sparc-icl-nx6 + ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in - sparc) echo sparc-icl-nx7; exit ;; - esac ;; + sparc) GUESS=sparc-icl-nx7 ;; + esac + ;; s390x:SunOS:*:*) - echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=$UNAME_MACHINE-ibm-solaris2$SUN_REL + ;; sun4H:SunOS:5.*:*) - echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=sparc-hal-solaris2$SUN_REL + ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) - echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=sparc-sun-solaris2$SUN_REL + ;; i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) - echo i386-pc-auroraux${UNAME_RELEASE} - exit ;; + GUESS=i386-pc-auroraux$UNAME_RELEASE + ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) - eval $set_cc_for_build - SUN_ARCH="i386" + set_cc_for_build + SUN_ARCH=i386 # If there is a compiler, see if it is configured for 64-bit objects. # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. # This test works for both compilers. - if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if test "$CC_FOR_BUILD" != no_compiler_found; then if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ - (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then - SUN_ARCH="x86_64" + SUN_ARCH=x86_64 fi fi - echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=$SUN_ARCH-pc-solaris2$SUN_REL + ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. - echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=sparc-sun-solaris3$SUN_REL + ;; sun4*:SunOS:*:*) - case "`/usr/bin/arch -k`" in + case `/usr/bin/arch -k` in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. - echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/-/_/'` + GUESS=sparc-sun-sunos$SUN_REL + ;; sun3*:SunOS:*:*) - echo m68k-sun-sunos${UNAME_RELEASE} - exit ;; + GUESS=m68k-sun-sunos$UNAME_RELEASE + ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` - test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 - case "`/bin/arch`" in + test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3 + case `/bin/arch` in sun3) - echo m68k-sun-sunos${UNAME_RELEASE} + GUESS=m68k-sun-sunos$UNAME_RELEASE ;; sun4) - echo sparc-sun-sunos${UNAME_RELEASE} + GUESS=sparc-sun-sunos$UNAME_RELEASE ;; esac - exit ;; + ;; aushp:SunOS:*:*) - echo sparc-auspex-sunos${UNAME_RELEASE} - exit ;; + GUESS=sparc-auspex-sunos$UNAME_RELEASE + ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor @@ -398,44 +490,44 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) - echo m68k-atari-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-atari-mint$UNAME_RELEASE + ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) - echo m68k-atari-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-atari-mint$UNAME_RELEASE + ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) - echo m68k-atari-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-atari-mint$UNAME_RELEASE + ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) - echo m68k-milan-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-milan-mint$UNAME_RELEASE + ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) - echo m68k-hades-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-hades-mint$UNAME_RELEASE + ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) - echo m68k-unknown-mint${UNAME_RELEASE} - exit ;; + GUESS=m68k-unknown-mint$UNAME_RELEASE + ;; m68k:machten:*:*) - echo m68k-apple-machten${UNAME_RELEASE} - exit ;; + GUESS=m68k-apple-machten$UNAME_RELEASE + ;; powerpc:machten:*:*) - echo powerpc-apple-machten${UNAME_RELEASE} - exit ;; + GUESS=powerpc-apple-machten$UNAME_RELEASE + ;; RISC*:Mach:*:*) - echo mips-dec-mach_bsd4.3 - exit ;; + GUESS=mips-dec-mach_bsd4.3 + ;; RISC*:ULTRIX:*:*) - echo mips-dec-ultrix${UNAME_RELEASE} - exit ;; + GUESS=mips-dec-ultrix$UNAME_RELEASE + ;; VAX*:ULTRIX*:*:*) - echo vax-dec-ultrix${UNAME_RELEASE} - exit ;; + GUESS=vax-dec-ultrix$UNAME_RELEASE + ;; 2020:CLIX:*:* | 2430:CLIX:*:*) - echo clipper-intergraph-clix${UNAME_RELEASE} - exit ;; + GUESS=clipper-intergraph-clix$UNAME_RELEASE + ;; mips:*:*:UMIPS | mips:*:*:RISCos) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { @@ -444,95 +536,96 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) - printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); + printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) - printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); + printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) - printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); + printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF - $CC_FOR_BUILD -o $dummy $dummy.c && - dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && - SYSTEM_NAME=`$dummy $dummyarg` && + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && + dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` && + SYSTEM_NAME=`"$dummy" "$dummyarg"` && { echo "$SYSTEM_NAME"; exit; } - echo mips-mips-riscos${UNAME_RELEASE} - exit ;; + GUESS=mips-mips-riscos$UNAME_RELEASE + ;; Motorola:PowerMAX_OS:*:*) - echo powerpc-motorola-powermax - exit ;; + GUESS=powerpc-motorola-powermax + ;; Motorola:*:4.3:PL8-*) - echo powerpc-harris-powermax - exit ;; + GUESS=powerpc-harris-powermax + ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) - echo powerpc-harris-powermax - exit ;; + GUESS=powerpc-harris-powermax + ;; Night_Hawk:Power_UNIX:*:*) - echo powerpc-harris-powerunix - exit ;; + GUESS=powerpc-harris-powerunix + ;; m88k:CX/UX:7*:*) - echo m88k-harris-cxux7 - exit ;; + GUESS=m88k-harris-cxux7 + ;; m88k:*:4*:R4*) - echo m88k-motorola-sysv4 - exit ;; + GUESS=m88k-motorola-sysv4 + ;; m88k:*:3*:R3*) - echo m88k-motorola-sysv3 - exit ;; + GUESS=m88k-motorola-sysv3 + ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` - if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] + if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110 then - if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ - [ ${TARGET_BINARY_INTERFACE}x = x ] + if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \ + test "$TARGET_BINARY_INTERFACE"x = x then - echo m88k-dg-dgux${UNAME_RELEASE} + GUESS=m88k-dg-dgux$UNAME_RELEASE else - echo m88k-dg-dguxbcs${UNAME_RELEASE} + GUESS=m88k-dg-dguxbcs$UNAME_RELEASE fi else - echo i586-dg-dgux${UNAME_RELEASE} + GUESS=i586-dg-dgux$UNAME_RELEASE fi - exit ;; + ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) - echo m88k-dolphin-sysv3 - exit ;; + GUESS=m88k-dolphin-sysv3 + ;; M88*:*:R3*:*) # Delta 88k system running SVR3 - echo m88k-motorola-sysv3 - exit ;; + GUESS=m88k-motorola-sysv3 + ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) - echo m88k-tektronix-sysv3 - exit ;; + GUESS=m88k-tektronix-sysv3 + ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) - echo m68k-tektronix-bsd - exit ;; + GUESS=m68k-tektronix-bsd + ;; *:IRIX*:*:*) - echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` - exit ;; + IRIX_REL=`echo "$UNAME_RELEASE" | sed -e 's/-/_/g'` + GUESS=mips-sgi-irix$IRIX_REL + ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. - echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id - exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' + GUESS=romp-ibm-aix # uname -m gives an 8 hex-code CPU id + ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) - echo i386-ibm-aix - exit ;; + GUESS=i386-ibm-aix + ;; ia64:AIX:*:*) - if [ -x /usr/bin/oslevel ] ; then + if test -x /usr/bin/oslevel ; then IBM_REV=`/usr/bin/oslevel` else - IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + IBM_REV=$UNAME_VERSION.$UNAME_RELEASE fi - echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} - exit ;; + GUESS=$UNAME_MACHINE-ibm-aix$IBM_REV + ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" #include main() @@ -543,76 +636,77 @@ EOF exit(0); } EOF - if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` + if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` then - echo "$SYSTEM_NAME" + GUESS=$SYSTEM_NAME else - echo rs6000-ibm-aix3.2.5 + GUESS=rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then - echo rs6000-ibm-aix3.2.4 + GUESS=rs6000-ibm-aix3.2.4 else - echo rs6000-ibm-aix3.2 + GUESS=rs6000-ibm-aix3.2 fi - exit ;; + ;; *:AIX:*:[4567]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` - if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then + if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi - if [ -x /usr/bin/oslevel ] ; then - IBM_REV=`/usr/bin/oslevel` + if test -x /usr/bin/lslpp ; then + IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc | \ + awk -F: '{ print $3 }' | sed s/[0-9]*$/0/` else - IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + IBM_REV=$UNAME_VERSION.$UNAME_RELEASE fi - echo ${IBM_ARCH}-ibm-aix${IBM_REV} - exit ;; + GUESS=$IBM_ARCH-ibm-aix$IBM_REV + ;; *:AIX:*:*) - echo rs6000-ibm-aix - exit ;; - ibmrt:4.4BSD:*|romp-ibm:BSD:*) - echo romp-ibm-bsd4.4 - exit ;; + GUESS=rs6000-ibm-aix + ;; + ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*) + GUESS=romp-ibm-bsd4.4 + ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and - echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to - exit ;; # report: romp-ibm BSD 4.3 + GUESS=romp-ibm-bsd$UNAME_RELEASE # 4.3 with uname added to + ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) - echo rs6000-bull-bosx - exit ;; + GUESS=rs6000-bull-bosx + ;; DPX/2?00:B.O.S.:*:*) - echo m68k-bull-sysv3 - exit ;; + GUESS=m68k-bull-sysv3 + ;; 9000/[34]??:4.3bsd:1.*:*) - echo m68k-hp-bsd - exit ;; + GUESS=m68k-hp-bsd + ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) - echo m68k-hp-bsd4.4 - exit ;; + GUESS=m68k-hp-bsd4.4 + ;; 9000/[34678]??:HP-UX:*:*) - HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` - case "${UNAME_MACHINE}" in - 9000/31? ) HP_ARCH=m68000 ;; - 9000/[34]?? ) HP_ARCH=m68k ;; + HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'` + case $UNAME_MACHINE in + 9000/31?) HP_ARCH=m68000 ;; + 9000/[34]??) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) - if [ -x /usr/bin/getconf ]; then + if test -x /usr/bin/getconf; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` - case "${sc_cpu_version}" in - 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 - 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + case $sc_cpu_version in + 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 + 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 - case "${sc_kernel_bits}" in - 32) HP_ARCH="hppa2.0n" ;; - 64) HP_ARCH="hppa2.0w" ;; - '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 + case $sc_kernel_bits in + 32) HP_ARCH=hppa2.0n ;; + 64) HP_ARCH=hppa2.0w ;; + '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 esac ;; esac fi - if [ "${HP_ARCH}" = "" ]; then - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + if test "$HP_ARCH" = ""; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" #define _HPUX_SOURCE #include @@ -645,13 +739,13 @@ EOF exit (0); } EOF - (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` + (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac - if [ ${HP_ARCH} = "hppa2.0w" ] + if test "$HP_ARCH" = hppa2.0w then - eval $set_cc_for_build + set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler @@ -662,23 +756,23 @@ EOF # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 - if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | + if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then - HP_ARCH="hppa2.0w" + HP_ARCH=hppa2.0w else - HP_ARCH="hppa64" + HP_ARCH=hppa64 fi fi - echo ${HP_ARCH}-hp-hpux${HPUX_REV} - exit ;; + GUESS=$HP_ARCH-hp-hpux$HPUX_REV + ;; ia64:HP-UX:*:*) - HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` - echo ia64-hp-hpux${HPUX_REV} - exit ;; + HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'` + GUESS=ia64-hp-hpux$HPUX_REV + ;; 3050*:HI-UX:*:*) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" #include int main () @@ -703,38 +797,38 @@ EOF exit (0); } EOF - $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` && { echo "$SYSTEM_NAME"; exit; } - echo unknown-hitachi-hiuxwe2 - exit ;; - 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) - echo hppa1.1-hp-bsd - exit ;; + GUESS=unknown-hitachi-hiuxwe2 + ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) + GUESS=hppa1.1-hp-bsd + ;; 9000/8??:4.3bsd:*:*) - echo hppa1.0-hp-bsd - exit ;; + GUESS=hppa1.0-hp-bsd + ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) - echo hppa1.0-hp-mpeix - exit ;; - hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) - echo hppa1.1-hp-osf - exit ;; + GUESS=hppa1.0-hp-mpeix + ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) + GUESS=hppa1.1-hp-osf + ;; hp8??:OSF1:*:*) - echo hppa1.0-hp-osf - exit ;; + GUESS=hppa1.0-hp-osf + ;; i*86:OSF1:*:*) - if [ -x /usr/sbin/sysversion ] ; then - echo ${UNAME_MACHINE}-unknown-osf1mk + if test -x /usr/sbin/sysversion ; then + GUESS=$UNAME_MACHINE-unknown-osf1mk else - echo ${UNAME_MACHINE}-unknown-osf1 + GUESS=$UNAME_MACHINE-unknown-osf1 fi - exit ;; + ;; parisc*:Lites*:*:*) - echo hppa1.1-hp-lites - exit ;; + GUESS=hppa1.1-hp-lites + ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) - echo c1-convex-bsd - exit ;; + GUESS=c1-convex-bsd + ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd @@ -742,129 +836,145 @@ EOF fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) - echo c34-convex-bsd - exit ;; + GUESS=c34-convex-bsd + ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) - echo c38-convex-bsd - exit ;; + GUESS=c38-convex-bsd + ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) - echo c4-convex-bsd - exit ;; + GUESS=c4-convex-bsd + ;; CRAY*Y-MP:*:*:*) - echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' - exit ;; + CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` + GUESS=ymp-cray-unicos$CRAY_REL + ;; CRAY*[A-Z]90:*:*:*) - echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ + echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) - echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' - exit ;; + CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` + GUESS=t90-cray-unicos$CRAY_REL + ;; CRAY*T3E:*:*:*) - echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' - exit ;; + CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` + GUESS=alphaev5-cray-unicosmk$CRAY_REL + ;; CRAY*SV1:*:*:*) - echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' - exit ;; + CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` + GUESS=sv1-cray-unicos$CRAY_REL + ;; *:UNICOS/mp:*:*) - echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' - exit ;; + CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` + GUESS=craynv-cray-unicosmp$CRAY_REL + ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) - FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` - FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` - FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` - echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" - exit ;; + FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz` + FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` + FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'` + GUESS=${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} + ;; 5000:UNIX_System_V:4.*:*) - FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` - FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` - echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" - exit ;; + FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` + FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'` + GUESS=sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} + ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) - echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-pc-bsdi$UNAME_RELEASE + ;; sparc*:BSD/OS:*:*) - echo sparc-unknown-bsdi${UNAME_RELEASE} - exit ;; + GUESS=sparc-unknown-bsdi$UNAME_RELEASE + ;; *:BSD/OS:*:*) - echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-unknown-bsdi$UNAME_RELEASE + ;; + arm:FreeBSD:*:*) + UNAME_PROCESSOR=`uname -p` + set_cc_for_build + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` + GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabi + else + FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` + GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabihf + fi + ;; *:FreeBSD:*:*) UNAME_PROCESSOR=`/usr/bin/uname -p` - case ${UNAME_PROCESSOR} in + case $UNAME_PROCESSOR in amd64) - echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; - *) - echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + UNAME_PROCESSOR=x86_64 ;; + i386) + UNAME_PROCESSOR=i586 ;; esac - exit ;; + FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` + GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL + ;; i*:CYGWIN*:*) - echo ${UNAME_MACHINE}-pc-cygwin - exit ;; + GUESS=$UNAME_MACHINE-pc-cygwin + ;; + *:MINGW64*:*) + GUESS=$UNAME_MACHINE-pc-mingw64 + ;; *:MINGW*:*) - echo ${UNAME_MACHINE}-pc-mingw32 - exit ;; - i*:MSYS*:*) - echo ${UNAME_MACHINE}-pc-msys - exit ;; - i*:windows32*:*) - # uname -m includes "-pc" on this system. - echo ${UNAME_MACHINE}-mingw32 - exit ;; + GUESS=$UNAME_MACHINE-pc-mingw32 + ;; + *:MSYS*:*) + GUESS=$UNAME_MACHINE-pc-msys + ;; i*:PW*:*) - echo ${UNAME_MACHINE}-pc-pw32 - exit ;; + GUESS=$UNAME_MACHINE-pc-pw32 + ;; *:Interix*:*) - case ${UNAME_MACHINE} in + case $UNAME_MACHINE in x86) - echo i586-pc-interix${UNAME_RELEASE} - exit ;; + GUESS=i586-pc-interix$UNAME_RELEASE + ;; authenticamd | genuineintel | EM64T) - echo x86_64-unknown-interix${UNAME_RELEASE} - exit ;; + GUESS=x86_64-unknown-interix$UNAME_RELEASE + ;; IA64) - echo ia64-unknown-interix${UNAME_RELEASE} - exit ;; + GUESS=ia64-unknown-interix$UNAME_RELEASE + ;; esac ;; - [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) - echo i${UNAME_MACHINE}-pc-mks - exit ;; - 8664:Windows_NT:*) - echo x86_64-pc-mks - exit ;; - i*:Windows_NT*:* | Pentium*:Windows_NT*:*) - # How do we know it's Interix rather than the generic POSIX subsystem? - # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we - # UNAME_MACHINE based on the output of uname instead of i386? - echo i586-pc-interix - exit ;; i*:UWIN*:*) - echo ${UNAME_MACHINE}-pc-uwin - exit ;; + GUESS=$UNAME_MACHINE-pc-uwin + ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) - echo x86_64-unknown-cygwin - exit ;; - p*:CYGWIN*:*) - echo powerpcle-unknown-cygwin - exit ;; + GUESS=x86_64-pc-cygwin + ;; prep*:SunOS:5.*:*) - echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` - exit ;; + SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` + GUESS=powerpcle-unknown-solaris2$SUN_REL + ;; *:GNU:*:*) # the GNU system - echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` - exit ;; + GNU_ARCH=`echo "$UNAME_MACHINE" | sed -e 's,[-/].*$,,'` + GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's,/.*$,,'` + GUESS=$GNU_ARCH-unknown-$LIBC$GNU_REL + ;; *:GNU/*:*:*) # other systems with GNU libc and userland - echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu - exit ;; - i*86:Minix:*:*) - echo ${UNAME_MACHINE}-pc-minix - exit ;; + GNU_SYS=`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"` + GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` + GUESS=$UNAME_MACHINE-unknown-$GNU_SYS$GNU_REL-$LIBC + ;; + *:Minix:*:*) + GUESS=$UNAME_MACHINE-unknown-minix + ;; + aarch64:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; + aarch64_be:Linux:*:*) + UNAME_MACHINE=aarch64_be + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; alpha:Linux:*:*) - case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; @@ -874,168 +984,226 @@ EOF EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 - if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi - echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} - exit ;; + if test "$?" = 0 ; then LIBC=gnulibc1 ; fi + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; + arc:Linux:*:* | arceb:Linux:*:* | arc32:Linux:*:* | arc64:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; arm*:Linux:*:*) - eval $set_cc_for_build + set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then - echo ${UNAME_MACHINE}-unknown-linux-gnu + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC else if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_PCS_VFP then - echo ${UNAME_MACHINE}-unknown-linux-gnueabi + GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabi else - echo ${UNAME_MACHINE}-unknown-linux-gnueabihf + GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabihf fi fi - exit ;; + ;; avr32*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; cris:Linux:*:*) - echo ${UNAME_MACHINE}-axis-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-axis-linux-$LIBC + ;; crisv32:Linux:*:*) - echo ${UNAME_MACHINE}-axis-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-axis-linux-$LIBC + ;; + e2k:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; frv:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; hexagon:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; i*86:Linux:*:*) - LIBC=gnu - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #ifdef __dietlibc__ - LIBC=dietlibc - #endif -EOF - eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` - echo "${UNAME_MACHINE}-pc-linux-${LIBC}" - exit ;; + GUESS=$UNAME_MACHINE-pc-linux-$LIBC + ;; ia64:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; + k1om:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; + loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; m32r*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; m68*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; mips:Linux:*:* | mips64:Linux:*:*) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + set_cc_for_build + IS_GLIBC=0 + test x"${LIBC}" = xgnu && IS_GLIBC=1 + sed 's/^ //' << EOF > "$dummy.c" #undef CPU - #undef ${UNAME_MACHINE} - #undef ${UNAME_MACHINE}el + #undef mips + #undef mipsel + #undef mips64 + #undef mips64el + #if ${IS_GLIBC} && defined(_ABI64) + LIBCABI=gnuabi64 + #else + #if ${IS_GLIBC} && defined(_ABIN32) + LIBCABI=gnuabin32 + #else + LIBCABI=${LIBC} + #endif + #endif + + #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa64r6 + #else + #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa32r6 + #else + #if defined(__mips64) + CPU=mips64 + #else + CPU=mips + #endif + #endif + #endif + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=${UNAME_MACHINE}el + MIPS_ENDIAN=el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=${UNAME_MACHINE} + MIPS_ENDIAN= #else - CPU= + MIPS_ENDIAN= #endif #endif EOF - eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` - test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + cc_set_vars=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI'` + eval "$cc_set_vars" + test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } + ;; + mips64el:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; + openrisc*:Linux:*:*) + GUESS=or1k-unknown-linux-$LIBC + ;; + or32:Linux:*:* | or1k*:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; - or32:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; padre:Linux:*:*) - echo sparc-unknown-linux-gnu - exit ;; + GUESS=sparc-unknown-linux-$LIBC + ;; parisc64:Linux:*:* | hppa64:Linux:*:*) - echo hppa64-unknown-linux-gnu - exit ;; + GUESS=hppa64-unknown-linux-$LIBC + ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in - PA7*) echo hppa1.1-unknown-linux-gnu ;; - PA8*) echo hppa2.0-unknown-linux-gnu ;; - *) echo hppa-unknown-linux-gnu ;; + PA7*) GUESS=hppa1.1-unknown-linux-$LIBC ;; + PA8*) GUESS=hppa2.0-unknown-linux-$LIBC ;; + *) GUESS=hppa-unknown-linux-$LIBC ;; esac - exit ;; + ;; ppc64:Linux:*:*) - echo powerpc64-unknown-linux-gnu - exit ;; + GUESS=powerpc64-unknown-linux-$LIBC + ;; ppc:Linux:*:*) - echo powerpc-unknown-linux-gnu - exit ;; + GUESS=powerpc-unknown-linux-$LIBC + ;; + ppc64le:Linux:*:*) + GUESS=powerpc64le-unknown-linux-$LIBC + ;; + ppcle:Linux:*:*) + GUESS=powerpcle-unknown-linux-$LIBC + ;; + riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; s390:Linux:*:* | s390x:Linux:*:*) - echo ${UNAME_MACHINE}-ibm-linux - exit ;; + GUESS=$UNAME_MACHINE-ibm-linux-$LIBC + ;; sh64*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; sh*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; sparc:Linux:*:* | sparc64:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; tile*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; vax:Linux:*:*) - echo ${UNAME_MACHINE}-dec-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-dec-linux-$LIBC + ;; x86_64:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + set_cc_for_build + LIBCABI=$LIBC + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_X32 >/dev/null + then + LIBCABI=${LIBC}x32 + fi + fi + GUESS=$UNAME_MACHINE-pc-linux-$LIBCABI + ;; xtensa*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu - exit ;; + GUESS=$UNAME_MACHINE-unknown-linux-$LIBC + ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. - echo i386-sequent-sysv4 - exit ;; + GUESS=i386-sequent-sysv4 + ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. - echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} - exit ;; + GUESS=$UNAME_MACHINE-pc-sysv4.2uw$UNAME_VERSION + ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. - echo ${UNAME_MACHINE}-pc-os2-emx - exit ;; + GUESS=$UNAME_MACHINE-pc-os2-emx + ;; i*86:XTS-300:*:STOP) - echo ${UNAME_MACHINE}-unknown-stop - exit ;; + GUESS=$UNAME_MACHINE-unknown-stop + ;; i*86:atheos:*:*) - echo ${UNAME_MACHINE}-unknown-atheos - exit ;; + GUESS=$UNAME_MACHINE-unknown-atheos + ;; i*86:syllable:*:*) - echo ${UNAME_MACHINE}-pc-syllable - exit ;; + GUESS=$UNAME_MACHINE-pc-syllable + ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) - echo i386-unknown-lynxos${UNAME_RELEASE} - exit ;; + GUESS=i386-unknown-lynxos$UNAME_RELEASE + ;; i*86:*DOS:*:*) - echo ${UNAME_MACHINE}-pc-msdosdjgpp - exit ;; - i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) - UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` + GUESS=$UNAME_MACHINE-pc-msdosdjgpp + ;; + i*86:*:4.*:*) + UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then - echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} + GUESS=$UNAME_MACHINE-univel-sysv$UNAME_REL else - echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} + GUESS=$UNAME_MACHINE-pc-sysv$UNAME_REL fi - exit ;; + ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in @@ -1043,12 +1211,12 @@ EOF *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac - echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} - exit ;; + GUESS=$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} + ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 @@ -1058,43 +1226,43 @@ EOF && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 - echo ${UNAME_MACHINE}-pc-sco$UNAME_REL + GUESS=$UNAME_MACHINE-pc-sco$UNAME_REL else - echo ${UNAME_MACHINE}-pc-sysv32 + GUESS=$UNAME_MACHINE-pc-sysv32 fi - exit ;; + ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub - # prints for the "djgpp" host, or else GDB configury will decide that + # prints for the "djgpp" host, or else GDB configure will decide that # this is a cross-build. - echo i586-pc-msdosdjgpp - exit ;; + GUESS=i586-pc-msdosdjgpp + ;; Intel:Mach:3*:*) - echo i386-pc-mach3 - exit ;; + GUESS=i386-pc-mach3 + ;; paragon:*:*:*) - echo i860-intel-osf1 - exit ;; + GUESS=i860-intel-osf1 + ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then - echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 + GUESS=i860-stardent-sysv$UNAME_RELEASE # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. - echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 + GUESS=i860-unknown-sysv$UNAME_RELEASE # Unknown i860-SVR4 fi - exit ;; + ;; mini*:CTIX:SYS*5:*) # "miniframe" - echo m68010-convergent-sysv - exit ;; + GUESS=m68010-convergent-sysv + ;; mc68k:UNIX:SYSTEM5:3.51m) - echo m68k-convergent-sysv - exit ;; + GUESS=m68k-convergent-sysv + ;; M680?0:D-NIX:5.3:*) - echo m68k-diab-dnix - exit ;; + GUESS=m68k-diab-dnix + ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) @@ -1102,9 +1270,9 @@ EOF test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ - && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; @@ -1113,223 +1281,281 @@ EOF test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ - && { echo i586-ncr-sysv4.3${OS_REL}; exit; } + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ - && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) - echo m68k-unknown-lynxos${UNAME_RELEASE} - exit ;; + GUESS=m68k-unknown-lynxos$UNAME_RELEASE + ;; mc68030:UNIX_System_V:4.*:*) - echo m68k-atari-sysv4 - exit ;; + GUESS=m68k-atari-sysv4 + ;; TSUNAMI:LynxOS:2.*:*) - echo sparc-unknown-lynxos${UNAME_RELEASE} - exit ;; + GUESS=sparc-unknown-lynxos$UNAME_RELEASE + ;; rs6000:LynxOS:2.*:*) - echo rs6000-unknown-lynxos${UNAME_RELEASE} - exit ;; + GUESS=rs6000-unknown-lynxos$UNAME_RELEASE + ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) - echo powerpc-unknown-lynxos${UNAME_RELEASE} - exit ;; + GUESS=powerpc-unknown-lynxos$UNAME_RELEASE + ;; SM[BE]S:UNIX_SV:*:*) - echo mips-dde-sysv${UNAME_RELEASE} - exit ;; + GUESS=mips-dde-sysv$UNAME_RELEASE + ;; RM*:ReliantUNIX-*:*:*) - echo mips-sni-sysv4 - exit ;; + GUESS=mips-sni-sysv4 + ;; RM*:SINIX-*:*:*) - echo mips-sni-sysv4 - exit ;; + GUESS=mips-sni-sysv4 + ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` - echo ${UNAME_MACHINE}-sni-sysv4 + GUESS=$UNAME_MACHINE-sni-sysv4 else - echo ns32k-sni-sysv + GUESS=ns32k-sni-sysv fi - exit ;; + ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says - echo i586-unisys-sysv4 - exit ;; + GUESS=i586-unisys-sysv4 + ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm - echo hppa1.1-stratus-sysv4 - exit ;; + GUESS=hppa1.1-stratus-sysv4 + ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. - echo i860-stratus-sysv4 - exit ;; + GUESS=i860-stratus-sysv4 + ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. - echo ${UNAME_MACHINE}-stratus-vos - exit ;; + GUESS=$UNAME_MACHINE-stratus-vos + ;; *:VOS:*:*) # From Paul.Green@stratus.com. - echo hppa1.1-stratus-vos - exit ;; + GUESS=hppa1.1-stratus-vos + ;; mc68*:A/UX:*:*) - echo m68k-apple-aux${UNAME_RELEASE} - exit ;; + GUESS=m68k-apple-aux$UNAME_RELEASE + ;; news*:NEWS-OS:6*:*) - echo mips-sony-newsos6 - exit ;; + GUESS=mips-sony-newsos6 + ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) - if [ -d /usr/nec ]; then - echo mips-nec-sysv${UNAME_RELEASE} + if test -d /usr/nec; then + GUESS=mips-nec-sysv$UNAME_RELEASE else - echo mips-unknown-sysv${UNAME_RELEASE} + GUESS=mips-unknown-sysv$UNAME_RELEASE fi - exit ;; + ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. - echo powerpc-be-beos - exit ;; + GUESS=powerpc-be-beos + ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. - echo powerpc-apple-beos - exit ;; + GUESS=powerpc-apple-beos + ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. - echo i586-pc-beos - exit ;; + GUESS=i586-pc-beos + ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. - echo i586-pc-haiku - exit ;; + GUESS=i586-pc-haiku + ;; + x86_64:Haiku:*:*) + GUESS=x86_64-unknown-haiku + ;; SX-4:SUPER-UX:*:*) - echo sx4-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx4-nec-superux$UNAME_RELEASE + ;; SX-5:SUPER-UX:*:*) - echo sx5-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx5-nec-superux$UNAME_RELEASE + ;; SX-6:SUPER-UX:*:*) - echo sx6-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx6-nec-superux$UNAME_RELEASE + ;; SX-7:SUPER-UX:*:*) - echo sx7-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx7-nec-superux$UNAME_RELEASE + ;; SX-8:SUPER-UX:*:*) - echo sx8-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx8-nec-superux$UNAME_RELEASE + ;; SX-8R:SUPER-UX:*:*) - echo sx8r-nec-superux${UNAME_RELEASE} - exit ;; + GUESS=sx8r-nec-superux$UNAME_RELEASE + ;; + SX-ACE:SUPER-UX:*:*) + GUESS=sxace-nec-superux$UNAME_RELEASE + ;; Power*:Rhapsody:*:*) - echo powerpc-apple-rhapsody${UNAME_RELEASE} - exit ;; + GUESS=powerpc-apple-rhapsody$UNAME_RELEASE + ;; *:Rhapsody:*:*) - echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-apple-rhapsody$UNAME_RELEASE + ;; + arm64:Darwin:*:*) + GUESS=aarch64-apple-darwin$UNAME_RELEASE + ;; *:Darwin:*:*) - UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown + UNAME_PROCESSOR=`uname -p` case $UNAME_PROCESSOR in - i386) - eval $set_cc_for_build - if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then - if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ - (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ - grep IS_64BIT_ARCH >/dev/null - then - UNAME_PROCESSOR="x86_64" - fi - fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac - echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} - exit ;; + if command -v xcode-select > /dev/null 2> /dev/null && \ + ! xcode-select --print-path > /dev/null 2> /dev/null ; then + # Avoid executing cc if there is no toolchain installed as + # cc will be a stub that puts up a graphical alert + # prompting the user to install developer tools. + CC_FOR_BUILD=no_compiler_found + else + set_cc_for_build + fi + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + case $UNAME_PROCESSOR in + i386) UNAME_PROCESSOR=x86_64 ;; + powerpc) UNAME_PROCESSOR=powerpc64 ;; + esac + fi + # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc + if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_PPC >/dev/null + then + UNAME_PROCESSOR=powerpc + fi + elif test "$UNAME_PROCESSOR" = i386 ; then + # uname -m returns i386 or x86_64 + UNAME_PROCESSOR=$UNAME_MACHINE + fi + GUESS=$UNAME_PROCESSOR-apple-darwin$UNAME_RELEASE + ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` - if test "$UNAME_PROCESSOR" = "x86"; then + if test "$UNAME_PROCESSOR" = x86; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi - echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_PROCESSOR-$UNAME_MACHINE-nto-qnx$UNAME_RELEASE + ;; *:QNX:*:4*) - echo i386-pc-qnx - exit ;; - NEO-?:NONSTOP_KERNEL:*:*) - echo neo-tandem-nsk${UNAME_RELEASE} - exit ;; - NSE-?:NONSTOP_KERNEL:*:*) - echo nse-tandem-nsk${UNAME_RELEASE} - exit ;; - NSR-?:NONSTOP_KERNEL:*:*) - echo nsr-tandem-nsk${UNAME_RELEASE} - exit ;; + GUESS=i386-pc-qnx + ;; + NEO-*:NONSTOP_KERNEL:*:*) + GUESS=neo-tandem-nsk$UNAME_RELEASE + ;; + NSE-*:NONSTOP_KERNEL:*:*) + GUESS=nse-tandem-nsk$UNAME_RELEASE + ;; + NSR-*:NONSTOP_KERNEL:*:*) + GUESS=nsr-tandem-nsk$UNAME_RELEASE + ;; + NSV-*:NONSTOP_KERNEL:*:*) + GUESS=nsv-tandem-nsk$UNAME_RELEASE + ;; + NSX-*:NONSTOP_KERNEL:*:*) + GUESS=nsx-tandem-nsk$UNAME_RELEASE + ;; *:NonStop-UX:*:*) - echo mips-compaq-nonstopux - exit ;; + GUESS=mips-compaq-nonstopux + ;; BS2000:POSIX*:*:*) - echo bs2000-siemens-sysv - exit ;; + GUESS=bs2000-siemens-sysv + ;; DS/*:UNIX_System_V:*:*) - echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} - exit ;; + GUESS=$UNAME_MACHINE-$UNAME_SYSTEM-$UNAME_RELEASE + ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. - if test "$cputype" = "386"; then + if test "${cputype-}" = 386; then UNAME_MACHINE=i386 - else - UNAME_MACHINE="$cputype" + elif test "x${cputype-}" != x; then + UNAME_MACHINE=$cputype fi - echo ${UNAME_MACHINE}-unknown-plan9 - exit ;; + GUESS=$UNAME_MACHINE-unknown-plan9 + ;; *:TOPS-10:*:*) - echo pdp10-unknown-tops10 - exit ;; + GUESS=pdp10-unknown-tops10 + ;; *:TENEX:*:*) - echo pdp10-unknown-tenex - exit ;; + GUESS=pdp10-unknown-tenex + ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) - echo pdp10-dec-tops20 - exit ;; + GUESS=pdp10-dec-tops20 + ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) - echo pdp10-xkl-tops20 - exit ;; + GUESS=pdp10-xkl-tops20 + ;; *:TOPS-20:*:*) - echo pdp10-unknown-tops20 - exit ;; + GUESS=pdp10-unknown-tops20 + ;; *:ITS:*:*) - echo pdp10-unknown-its - exit ;; + GUESS=pdp10-unknown-its + ;; SEI:*:*:SEIUX) - echo mips-sei-seiux${UNAME_RELEASE} - exit ;; + GUESS=mips-sei-seiux$UNAME_RELEASE + ;; *:DragonFly:*:*) - echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` - exit ;; + DRAGONFLY_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` + GUESS=$UNAME_MACHINE-unknown-dragonfly$DRAGONFLY_REL + ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` - case "${UNAME_MACHINE}" in - A*) echo alpha-dec-vms ; exit ;; - I*) echo ia64-dec-vms ; exit ;; - V*) echo vax-dec-vms ; exit ;; + case $UNAME_MACHINE in + A*) GUESS=alpha-dec-vms ;; + I*) GUESS=ia64-dec-vms ;; + V*) GUESS=vax-dec-vms ;; esac ;; *:XENIX:*:SysV) - echo i386-pc-xenix - exit ;; + GUESS=i386-pc-xenix + ;; i*86:skyos:*:*) - echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' - exit ;; + SKYOS_REL=`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'` + GUESS=$UNAME_MACHINE-pc-skyos$SKYOS_REL + ;; i*86:rdos:*:*) - echo ${UNAME_MACHINE}-pc-rdos - exit ;; - i*86:AROS:*:*) - echo ${UNAME_MACHINE}-pc-aros - exit ;; + GUESS=$UNAME_MACHINE-pc-rdos + ;; + *:AROS:*:*) + GUESS=$UNAME_MACHINE-unknown-aros + ;; + x86_64:VMkernel:*:*) + GUESS=$UNAME_MACHINE-unknown-esx + ;; + amd64:Isilon\ OneFS:*:*) + GUESS=x86_64-unknown-onefs + ;; + *:Unleashed:*:*) + GUESS=$UNAME_MACHINE-unknown-unleashed$UNAME_RELEASE + ;; esac -#echo '(No uname command or uname output not recognized.)' 1>&2 -#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 +# Do we have a guess based on uname results? +if test "x$GUESS" != x; then + echo "$GUESS" + exit +fi -eval $set_cc_for_build -cat >$dummy.c < "$dummy.c" < -# include +#include +#include +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#include +#if defined(_SIZE_T_) || defined(SIGLOST) +#include +#endif +#endif #endif main () { @@ -1342,20 +1568,12 @@ main () #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 - "4" + "4" #else - "" -#endif - ); exit (0); -#endif + "" #endif - -#if defined (__arm) && defined (__acorn) && defined (__unix) - printf ("arm-acorn-riscix\n"); exit (0); + ); exit (0); #endif - -#if defined (hp300) && !defined (hpux) - printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) @@ -1397,39 +1615,54 @@ main () #endif #if defined (_SEQUENT_) - struct utsname un; - - uname(&un); - - if (strncmp(un.version, "V2", 2) == 0) { - printf ("i386-sequent-ptx2\n"); exit (0); - } - if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ - printf ("i386-sequent-ptx1\n"); exit (0); - } - printf ("i386-sequent-ptx\n"); exit (0); + struct utsname un; + uname(&un); + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) -# if !defined (ultrix) -# include -# if defined (BSD) -# if BSD == 43 - printf ("vax-dec-bsd4.3\n"); exit (0); -# else -# if BSD == 199006 - printf ("vax-dec-bsd4.3reno\n"); exit (0); -# else - printf ("vax-dec-bsd\n"); exit (0); -# endif -# endif -# else - printf ("vax-dec-bsd\n"); exit (0); -# endif -# else - printf ("vax-dec-ultrix\n"); exit (0); -# endif +#if !defined (ultrix) +#include +#if defined (BSD) +#if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +#else +#if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#endif +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#else +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname un; + uname (&un); + printf ("vax-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("vax-dec-ultrix\n"); exit (0); +#endif +#endif +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname *un; + uname (&un); + printf ("mips-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("mips-dec-ultrix\n"); exit (0); +#endif +#endif #endif #if defined (alliant) && defined (i860) @@ -1440,54 +1673,46 @@ main () } EOF -$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && +$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=`"$dummy"` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. +test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } -test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } +echo "$0: unable to guess system type" >&2 -# Convex versions that predate uname can use getsysinfo(1) +case $UNAME_MACHINE:$UNAME_SYSTEM in + mips:Linux | mips64:Linux) + # If we got here on MIPS GNU/Linux, output extra information. + cat >&2 <&2 < in order to provide the needed -information to handle your system. +our_year=`echo $timestamp | sed 's,-.*,,'` +thisyear=`date +%Y` +# shellcheck disable=SC2003 +script_age=`expr "$thisyear" - "$our_year"` +if test "$script_age" -lt 3 ; then + cat >&2 </dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` -UNAME_MACHINE = ${UNAME_MACHINE} -UNAME_RELEASE = ${UNAME_RELEASE} -UNAME_SYSTEM = ${UNAME_SYSTEM} -UNAME_VERSION = ${UNAME_VERSION} +UNAME_MACHINE = "$UNAME_MACHINE" +UNAME_RELEASE = "$UNAME_RELEASE" +UNAME_SYSTEM = "$UNAME_SYSTEM" +UNAME_VERSION = "$UNAME_VERSION" EOF +fi exit 1 # Local variables: -# eval: (add-hook 'write-file-hooks 'time-stamp) +# eval: (add-hook 'before-save-hook 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" diff --git a/packages/zoltan/config/config.sub b/packages/zoltan/config/config.sub index d6b6b3c768ff..d74fb6deac94 100755 --- a/packages/zoltan/config/config.sub +++ b/packages/zoltan/config/config.sub @@ -1,38 +1,33 @@ #! /bin/sh # Configuration validation subroutine script. -# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, -# 2011, 2012 Free Software Foundation, Inc. +# Copyright 1992-2021 Free Software Foundation, Inc. -timestamp='2012-01-01' +# shellcheck disable=SC2006,SC2268 # see below for rationale -# This file is (in principle) common to ALL GNU software. -# The presence of a machine in this file suggests that SOME GNU software -# can handle that machine. It does not imply ALL GNU software can. -# -# This file is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or +timestamp='2021-08-14' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program; if not, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). -# Please send patches to . Submit a context -# diff and a properly formatted GNU ChangeLog entry. +# Please send patches to . # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. @@ -40,7 +35,7 @@ timestamp='2012-01-01' # Otherwise, we print the canonical config type on stdout and succeed. # You can get the latest version of this script from: -# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD +# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases @@ -57,15 +52,21 @@ timestamp='2012-01-01' # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. +# The "shellcheck disable" line above the timestamp inhibits complaints +# about features and limitations of the classic Bourne shell that were +# superseded or lifted in POSIX. However, this script identifies a wide +# variety of pre-POSIX systems that do not have POSIX shells at all, and +# even some reasonably current systems (Solaris 10 as case-in-point) still +# have a pre-POSIX /bin/sh. + me=`echo "$0" | sed -e 's,.*/,,'` usage="\ -Usage: $0 [OPTION] CPU-MFR-OPSYS - $0 [OPTION] ALIAS +Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS Canonicalize a configuration name. -Operation modes: +Options: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit @@ -75,9 +76,7 @@ Report bugs and patches to ." version="\ GNU config.sub ($timestamp) -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, -2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 -Free Software Foundation, Inc. +Copyright 1992-2021 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -99,12 +98,12 @@ while test $# -gt 0 ; do - ) # Use stdin as input. break ;; -* ) - echo "$me: invalid option $1$help" + echo "$me: invalid option $1$help" >&2 exit 1 ;; *local*) # First pass through any local machine types. - echo $1 + echo "$1" exit ;; * ) @@ -120,1181 +119,1181 @@ case $# in exit 1;; esac -# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). -# Here we must recognize all the valid KERNEL-OS combinations. -maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` -case $maybe_os in - nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \ - linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \ - knetbsd*-gnu* | netbsd*-gnu* | \ - kopensolaris*-gnu* | \ - storm-chaos* | os2-emx* | rtmk-nova*) - os=-$maybe_os - basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` - ;; - *) - basic_machine=`echo $1 | sed 's/-[^-]*$//'` - if [ $basic_machine != $1 ] - then os=`echo $1 | sed 's/.*-/-/'` - else os=; fi - ;; -esac +# Split fields of configuration type +# shellcheck disable=SC2162 +saved_IFS=$IFS +IFS="-" read field1 field2 field3 field4 <&2 + exit 1 ;; - -ptx*) - basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` + *-*-*-*) + basic_machine=$field1-$field2 + basic_os=$field3-$field4 ;; - -windowsnt*) - os=`echo $os | sed -e 's/windowsnt/winnt/'` + *-*-*) + # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two + # parts + maybe_os=$field2-$field3 + case $maybe_os in + nto-qnx* | linux-* | uclinux-uclibc* \ + | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \ + | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \ + | storm-chaos* | os2-emx* | rtmk-nova*) + basic_machine=$field1 + basic_os=$maybe_os + ;; + android-linux) + basic_machine=$field1-unknown + basic_os=linux-android + ;; + *) + basic_machine=$field1-$field2 + basic_os=$field3 + ;; + esac ;; - -psos*) - os=-psos + *-*) + # A lone config we happen to match not fitting any pattern + case $field1-$field2 in + decstation-3100) + basic_machine=mips-dec + basic_os= + ;; + *-*) + # Second component is usually, but not always the OS + case $field2 in + # Prevent following clause from handling this valid os + sun*os*) + basic_machine=$field1 + basic_os=$field2 + ;; + zephyr*) + basic_machine=$field1-unknown + basic_os=$field2 + ;; + # Manufacturers + dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \ + | att* | 7300* | 3300* | delta* | motorola* | sun[234]* \ + | unicom* | ibm* | next | hp | isi* | apollo | altos* \ + | convergent* | ncr* | news | 32* | 3600* | 3100* \ + | hitachi* | c[123]* | convex* | sun | crds | omron* | dg \ + | ultra | tti* | harris | dolphin | highlevel | gould \ + | cbm | ns | masscomp | apple | axis | knuth | cray \ + | microblaze* | sim | cisco \ + | oki | wec | wrs | winbond) + basic_machine=$field1-$field2 + basic_os= + ;; + *) + basic_machine=$field1 + basic_os=$field2 + ;; + esac + ;; + esac ;; - -mint | -mint[0-9]*) - basic_machine=m68k-atari - os=-mint + *) + # Convert single-component short-hands not valid as part of + # multi-component configurations. + case $field1 in + 386bsd) + basic_machine=i386-pc + basic_os=bsd + ;; + a29khif) + basic_machine=a29k-amd + basic_os=udi + ;; + adobe68k) + basic_machine=m68010-adobe + basic_os=scout + ;; + alliant) + basic_machine=fx80-alliant + basic_os= + ;; + altos | altos3068) + basic_machine=m68k-altos + basic_os= + ;; + am29k) + basic_machine=a29k-none + basic_os=bsd + ;; + amdahl) + basic_machine=580-amdahl + basic_os=sysv + ;; + amiga) + basic_machine=m68k-unknown + basic_os= + ;; + amigaos | amigados) + basic_machine=m68k-unknown + basic_os=amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + basic_os=sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + basic_os=sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + basic_os=bsd + ;; + aros) + basic_machine=i386-pc + basic_os=aros + ;; + aux) + basic_machine=m68k-apple + basic_os=aux + ;; + balance) + basic_machine=ns32k-sequent + basic_os=dynix + ;; + blackfin) + basic_machine=bfin-unknown + basic_os=linux + ;; + cegcc) + basic_machine=arm-unknown + basic_os=cegcc + ;; + convex-c1) + basic_machine=c1-convex + basic_os=bsd + ;; + convex-c2) + basic_machine=c2-convex + basic_os=bsd + ;; + convex-c32) + basic_machine=c32-convex + basic_os=bsd + ;; + convex-c34) + basic_machine=c34-convex + basic_os=bsd + ;; + convex-c38) + basic_machine=c38-convex + basic_os=bsd + ;; + cray) + basic_machine=j90-cray + basic_os=unicos + ;; + crds | unos) + basic_machine=m68k-crds + basic_os= + ;; + da30) + basic_machine=m68k-da30 + basic_os= + ;; + decstation | pmax | pmin | dec3100 | decstatn) + basic_machine=mips-dec + basic_os= + ;; + delta88) + basic_machine=m88k-motorola + basic_os=sysv3 + ;; + dicos) + basic_machine=i686-pc + basic_os=dicos + ;; + djgpp) + basic_machine=i586-pc + basic_os=msdosdjgpp + ;; + ebmon29k) + basic_machine=a29k-amd + basic_os=ebmon + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + basic_os=ose + ;; + gmicro) + basic_machine=tron-gmicro + basic_os=sysv + ;; + go32) + basic_machine=i386-pc + basic_os=go32 + ;; + h8300hms) + basic_machine=h8300-hitachi + basic_os=hms + ;; + h8300xray) + basic_machine=h8300-hitachi + basic_os=xray + ;; + h8500hms) + basic_machine=h8500-hitachi + basic_os=hms + ;; + harris) + basic_machine=m88k-harris + basic_os=sysv3 + ;; + hp300 | hp300hpux) + basic_machine=m68k-hp + basic_os=hpux + ;; + hp300bsd) + basic_machine=m68k-hp + basic_os=bsd + ;; + hppaosf) + basic_machine=hppa1.1-hp + basic_os=osf + ;; + hppro) + basic_machine=hppa1.1-hp + basic_os=proelf + ;; + i386mach) + basic_machine=i386-mach + basic_os=mach + ;; + isi68 | isi) + basic_machine=m68k-isi + basic_os=sysv + ;; + m68knommu) + basic_machine=m68k-unknown + basic_os=linux + ;; + magnum | m3230) + basic_machine=mips-mips + basic_os=sysv + ;; + merlin) + basic_machine=ns32k-utek + basic_os=sysv + ;; + mingw64) + basic_machine=x86_64-pc + basic_os=mingw64 + ;; + mingw32) + basic_machine=i686-pc + basic_os=mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + basic_os=mingw32ce + ;; + monitor) + basic_machine=m68k-rom68k + basic_os=coff + ;; + morphos) + basic_machine=powerpc-unknown + basic_os=morphos + ;; + moxiebox) + basic_machine=moxie-unknown + basic_os=moxiebox + ;; + msdos) + basic_machine=i386-pc + basic_os=msdos + ;; + msys) + basic_machine=i686-pc + basic_os=msys + ;; + mvs) + basic_machine=i370-ibm + basic_os=mvs + ;; + nacl) + basic_machine=le32-unknown + basic_os=nacl + ;; + ncr3000) + basic_machine=i486-ncr + basic_os=sysv4 + ;; + netbsd386) + basic_machine=i386-pc + basic_os=netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + basic_os=linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + basic_os=newsos + ;; + news1000) + basic_machine=m68030-sony + basic_os=newsos + ;; + necv70) + basic_machine=v70-nec + basic_os=sysv + ;; + nh3000) + basic_machine=m68k-harris + basic_os=cxux + ;; + nh[45]000) + basic_machine=m88k-harris + basic_os=cxux + ;; + nindy960) + basic_machine=i960-intel + basic_os=nindy + ;; + mon960) + basic_machine=i960-intel + basic_os=mon960 + ;; + nonstopux) + basic_machine=mips-compaq + basic_os=nonstopux + ;; + os400) + basic_machine=powerpc-ibm + basic_os=os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + basic_os=ose + ;; + os68k) + basic_machine=m68k-none + basic_os=os68k + ;; + paragon) + basic_machine=i860-intel + basic_os=osf + ;; + parisc) + basic_machine=hppa-unknown + basic_os=linux + ;; + psp) + basic_machine=mipsallegrexel-sony + basic_os=psp + ;; + pw32) + basic_machine=i586-unknown + basic_os=pw32 + ;; + rdos | rdos64) + basic_machine=x86_64-pc + basic_os=rdos + ;; + rdos32) + basic_machine=i386-pc + basic_os=rdos + ;; + rom68k) + basic_machine=m68k-rom68k + basic_os=coff + ;; + sa29200) + basic_machine=a29k-amd + basic_os=udi + ;; + sei) + basic_machine=mips-sei + basic_os=seiux + ;; + sequent) + basic_machine=i386-sequent + basic_os= + ;; + sps7) + basic_machine=m68k-bull + basic_os=sysv2 + ;; + st2000) + basic_machine=m68k-tandem + basic_os= + ;; + stratus) + basic_machine=i860-stratus + basic_os=sysv4 + ;; + sun2) + basic_machine=m68000-sun + basic_os= + ;; + sun2os3) + basic_machine=m68000-sun + basic_os=sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + basic_os=sunos4 + ;; + sun3) + basic_machine=m68k-sun + basic_os= + ;; + sun3os3) + basic_machine=m68k-sun + basic_os=sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + basic_os=sunos4 + ;; + sun4) + basic_machine=sparc-sun + basic_os= + ;; + sun4os3) + basic_machine=sparc-sun + basic_os=sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + basic_os=sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + basic_os=solaris2 + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + basic_os= + ;; + sv1) + basic_machine=sv1-cray + basic_os=unicos + ;; + symmetry) + basic_machine=i386-sequent + basic_os=dynix + ;; + t3e) + basic_machine=alphaev5-cray + basic_os=unicos + ;; + t90) + basic_machine=t90-cray + basic_os=unicos + ;; + toad1) + basic_machine=pdp10-xkl + basic_os=tops20 + ;; + tpf) + basic_machine=s390x-ibm + basic_os=tpf + ;; + udi29k) + basic_machine=a29k-amd + basic_os=udi + ;; + ultra3) + basic_machine=a29k-nyu + basic_os=sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + basic_os=none + ;; + vaxv) + basic_machine=vax-dec + basic_os=sysv + ;; + vms) + basic_machine=vax-dec + basic_os=vms + ;; + vsta) + basic_machine=i386-pc + basic_os=vsta + ;; + vxworks960) + basic_machine=i960-wrs + basic_os=vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + basic_os=vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + basic_os=vxworks + ;; + xbox) + basic_machine=i686-pc + basic_os=mingw32 + ;; + ymp) + basic_machine=ymp-cray + basic_os=unicos + ;; + *) + basic_machine=$1 + basic_os= + ;; + esac ;; esac -# Decode aliases for certain CPU-COMPANY combinations. +# Decode 1-component or ad-hoc basic machines case $basic_machine in - # Recognize the basic CPU types without company name. - # Some are omitted here because they have special meanings below. - 1750a | 580 \ - | a29k \ - | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ - | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ - | am33_2.0 \ - | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ - | be32 | be64 \ - | bfin \ - | c4x | clipper \ - | d10v | d30v | dlx | dsp16xx \ - | epiphany \ - | fido | fr30 | frv \ - | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ - | hexagon \ - | i370 | i860 | i960 | ia64 \ - | ip2k | iq2000 \ - | le32 | le64 \ - | lm32 \ - | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep | metag \ - | mips | mipsbe | mipseb | mipsel | mipsle \ - | mips16 \ - | mips64 | mips64el \ - | mips64octeon | mips64octeonel \ - | mips64orion | mips64orionel \ - | mips64r5900 | mips64r5900el \ - | mips64vr | mips64vrel \ - | mips64vr4100 | mips64vr4100el \ - | mips64vr4300 | mips64vr4300el \ - | mips64vr5000 | mips64vr5000el \ - | mips64vr5900 | mips64vr5900el \ - | mipsisa32 | mipsisa32el \ - | mipsisa32r2 | mipsisa32r2el \ - | mipsisa64 | mipsisa64el \ - | mipsisa64r2 | mipsisa64r2el \ - | mipsisa64sb1 | mipsisa64sb1el \ - | mipsisa64sr71k | mipsisa64sr71kel \ - | mipstx39 | mipstx39el \ - | mn10200 | mn10300 \ - | moxie \ - | mt \ - | msp430 \ - | nds32 | nds32le | nds32be \ - | nios | nios2 \ - | ns16k | ns32k \ - | open8 \ - | or32 \ - | pdp10 | pdp11 | pj | pjl \ - | powerpc | powerpc64 | powerpc64le | powerpcle \ - | pyramid \ - | rl78 | rx \ - | score \ - | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ - | sh64 | sh64le \ - | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ - | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ - | spu \ - | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \ - | ubicom32 \ - | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \ - | we32k \ - | x86 | xc16x | xstormy16 | xtensa \ - | z8k | z80) - basic_machine=$basic_machine-unknown - ;; - c54x) - basic_machine=tic54x-unknown - ;; - c55x) - basic_machine=tic55x-unknown - ;; - c6x) - basic_machine=tic6x-unknown - ;; - m6811 | m68hc11 | m6812 | m68hc12 | picochip) - basic_machine=$basic_machine-unknown - os=-none - ;; - m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) - ;; - ms1) - basic_machine=mt-unknown + # Here we handle the default manufacturer of certain CPU types. It is in + # some cases the only manufacturer, in others, it is the most popular. + w89k) + cpu=hppa1.1 + vendor=winbond ;; - - strongarm | thumb | xscale) - basic_machine=arm-unknown + op50n) + cpu=hppa1.1 + vendor=oki ;; - - xscaleeb) - basic_machine=armeb-unknown + op60c) + cpu=hppa1.1 + vendor=oki ;; - - xscaleel) - basic_machine=armel-unknown + ibm*) + cpu=i370 + vendor=ibm ;; - - # We use `pc' rather than `unknown' - # because (1) that's what they normally are, and - # (2) the word "unknown" tends to confuse beginning users. - i*86 | x86_64) - basic_machine=$basic_machine-pc - ;; - # Object if more than one company name word. - *-*-*) - echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 - exit 1 + orion105) + cpu=clipper + vendor=highlevel ;; - # Recognize the basic CPU types with company name. - 580-* \ - | a29k-* \ - | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ - | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ - | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ - | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ - | avr-* | avr32-* \ - | be32-* | be64-* \ - | bfin-* | bs2000-* \ - | c[123]* | c30-* | [cjt]90-* | c4x-* \ - | clipper-* | craynv-* | cydra-* \ - | d10v-* | d30v-* | dlx-* \ - | elxsi-* \ - | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ - | h8300-* | h8500-* \ - | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ - | hexagon-* \ - | i*86-* | i860-* | i960-* | ia64-* \ - | ip2k-* | iq2000-* \ - | le32-* | le64-* \ - | lm32-* \ - | m32c-* | m32r-* | m32rle-* \ - | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ - | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ - | mips16-* \ - | mips64-* | mips64el-* \ - | mips64octeon-* | mips64octeonel-* \ - | mips64orion-* | mips64orionel-* \ - | mips64r5900-* | mips64r5900el-* \ - | mips64vr-* | mips64vrel-* \ - | mips64vr4100-* | mips64vr4100el-* \ - | mips64vr4300-* | mips64vr4300el-* \ - | mips64vr5000-* | mips64vr5000el-* \ - | mips64vr5900-* | mips64vr5900el-* \ - | mipsisa32-* | mipsisa32el-* \ - | mipsisa32r2-* | mipsisa32r2el-* \ - | mipsisa64-* | mipsisa64el-* \ - | mipsisa64r2-* | mipsisa64r2el-* \ - | mipsisa64sb1-* | mipsisa64sb1el-* \ - | mipsisa64sr71k-* | mipsisa64sr71kel-* \ - | mipstx39-* | mipstx39el-* \ - | mmix-* \ - | mt-* \ - | msp430-* \ - | nds32-* | nds32le-* | nds32be-* \ - | nios-* | nios2-* \ - | none-* | np1-* | ns16k-* | ns32k-* \ - | open8-* \ - | orion-* \ - | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ - | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \ - | pyramid-* \ - | rl78-* | romp-* | rs6000-* | rx-* \ - | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ - | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ - | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ - | sparclite-* \ - | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \ - | tahoe-* \ - | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ - | tile*-* \ - | tron-* \ - | ubicom32-* \ - | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \ - | vax-* \ - | we32k-* \ - | x86-* | x86_64-* | xc16x-* | xps100-* \ - | xstormy16-* | xtensa*-* \ - | ymp-* \ - | z8k-* | z80-*) - ;; - # Recognize the basic CPU types without company name, with glob match. - xtensa*) - basic_machine=$basic_machine-unknown + mac | mpw | mac-mpw) + cpu=m68k + vendor=apple + ;; + pmac | pmac-mpw) + cpu=powerpc + vendor=apple ;; + # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. - 386bsd) - basic_machine=i386-unknown - os=-bsd - ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) - basic_machine=m68000-att + cpu=m68000 + vendor=att ;; 3b*) - basic_machine=we32k-att - ;; - a29khif) - basic_machine=a29k-amd - os=-udi - ;; - abacus) - basic_machine=abacus-unknown - ;; - adobe68k) - basic_machine=m68010-adobe - os=-scout - ;; - alliant | fx80) - basic_machine=fx80-alliant - ;; - altos | altos3068) - basic_machine=m68k-altos - ;; - am29k) - basic_machine=a29k-none - os=-bsd - ;; - amd64) - basic_machine=x86_64-pc - ;; - amd64-*) - basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - amdahl) - basic_machine=580-amdahl - os=-sysv - ;; - amiga | amiga-*) - basic_machine=m68k-unknown - ;; - amigaos | amigados) - basic_machine=m68k-unknown - os=-amigaos - ;; - amigaunix | amix) - basic_machine=m68k-unknown - os=-sysv4 - ;; - apollo68) - basic_machine=m68k-apollo - os=-sysv - ;; - apollo68bsd) - basic_machine=m68k-apollo - os=-bsd - ;; - aros) - basic_machine=i386-pc - os=-aros - ;; - aux) - basic_machine=m68k-apple - os=-aux - ;; - balance) - basic_machine=ns32k-sequent - os=-dynix - ;; - blackfin) - basic_machine=bfin-unknown - os=-linux - ;; - blackfin-*) - basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` - os=-linux + cpu=we32k + vendor=att ;; bluegene*) - basic_machine=powerpc-ibm - os=-cnk - ;; - c54x-*) - basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - c55x-*) - basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - c6x-*) - basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - c90) - basic_machine=c90-cray - os=-unicos - ;; - cegcc) - basic_machine=arm-unknown - os=-cegcc - ;; - convex-c1) - basic_machine=c1-convex - os=-bsd - ;; - convex-c2) - basic_machine=c2-convex - os=-bsd - ;; - convex-c32) - basic_machine=c32-convex - os=-bsd - ;; - convex-c34) - basic_machine=c34-convex - os=-bsd - ;; - convex-c38) - basic_machine=c38-convex - os=-bsd - ;; - cray | j90) - basic_machine=j90-cray - os=-unicos - ;; - craynv) - basic_machine=craynv-cray - os=-unicosmp - ;; - cr16 | cr16-*) - basic_machine=cr16-unknown - os=-elf - ;; - crds | unos) - basic_machine=m68k-crds - ;; - crisv32 | crisv32-* | etraxfs*) - basic_machine=crisv32-axis - ;; - cris | cris-* | etrax*) - basic_machine=cris-axis - ;; - crx) - basic_machine=crx-unknown - os=-elf - ;; - da30 | da30-*) - basic_machine=m68k-da30 - ;; - decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) - basic_machine=mips-dec + cpu=powerpc + vendor=ibm + basic_os=cnk ;; decsystem10* | dec10*) - basic_machine=pdp10-dec - os=-tops10 + cpu=pdp10 + vendor=dec + basic_os=tops10 ;; decsystem20* | dec20*) - basic_machine=pdp10-dec - os=-tops20 + cpu=pdp10 + vendor=dec + basic_os=tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) - basic_machine=m68k-motorola - ;; - delta88) - basic_machine=m88k-motorola - os=-sysv3 - ;; - dicos) - basic_machine=i686-pc - os=-dicos - ;; - djgpp) - basic_machine=i586-pc - os=-msdosdjgpp - ;; - dpx20 | dpx20-*) - basic_machine=rs6000-bull - os=-bosx - ;; - dpx2* | dpx2*-bull) - basic_machine=m68k-bull - os=-sysv3 - ;; - ebmon29k) - basic_machine=a29k-amd - os=-ebmon + cpu=m68k + vendor=motorola ;; - elxsi) - basic_machine=elxsi-elxsi - os=-bsd + dpx2*) + cpu=m68k + vendor=bull + basic_os=sysv3 ;; encore | umax | mmax) - basic_machine=ns32k-encore + cpu=ns32k + vendor=encore ;; - es1800 | OSE68k | ose68k | ose | OSE) - basic_machine=m68k-ericsson - os=-ose + elxsi) + cpu=elxsi + vendor=elxsi + basic_os=${basic_os:-bsd} ;; fx2800) - basic_machine=i860-alliant + cpu=i860 + vendor=alliant ;; genix) - basic_machine=ns32k-ns - ;; - gmicro) - basic_machine=tron-gmicro - os=-sysv - ;; - go32) - basic_machine=i386-pc - os=-go32 + cpu=ns32k + vendor=ns ;; h3050r* | hiux*) - basic_machine=hppa1.1-hitachi - os=-hiuxwe2 - ;; - h8300hms) - basic_machine=h8300-hitachi - os=-hms - ;; - h8300xray) - basic_machine=h8300-hitachi - os=-xray - ;; - h8500hms) - basic_machine=h8500-hitachi - os=-hms - ;; - harris) - basic_machine=m88k-harris - os=-sysv3 - ;; - hp300-*) - basic_machine=m68k-hp - ;; - hp300bsd) - basic_machine=m68k-hp - os=-bsd - ;; - hp300hpux) - basic_machine=m68k-hp - os=-hpux + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) - basic_machine=hppa1.0-hp + cpu=hppa1.0 + vendor=hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) - basic_machine=m68000-hp + cpu=m68000 + vendor=hp ;; hp9k3[2-9][0-9]) - basic_machine=m68k-hp + cpu=m68k + vendor=hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) - basic_machine=hppa1.0-hp + cpu=hppa1.0 + vendor=hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) - basic_machine=hppa1.1-hp + cpu=hppa1.1 + vendor=hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp - basic_machine=hppa1.1-hp + cpu=hppa1.1 + vendor=hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp - basic_machine=hppa1.1-hp + cpu=hppa1.1 + vendor=hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) - basic_machine=hppa1.1-hp + cpu=hppa1.1 + vendor=hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) - basic_machine=hppa1.0-hp - ;; - hppa-next) - os=-nextstep3 - ;; - hppaosf) - basic_machine=hppa1.1-hp - os=-osf - ;; - hppro) - basic_machine=hppa1.1-hp - os=-proelf - ;; - i370-ibm* | ibm*) - basic_machine=i370-ibm + cpu=hppa1.0 + vendor=hp ;; i*86v32) - basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` - os=-sysv32 + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv32 ;; i*86v4*) - basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` - os=-sysv4 + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv4 ;; i*86v) - basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` - os=-sysv + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv ;; i*86sol2) - basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` - os=-solaris2 - ;; - i386mach) - basic_machine=i386-mach - os=-mach + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=solaris2 ;; - i386-vsta | vsta) - basic_machine=i386-unknown - os=-vsta + j90 | j90-cray) + cpu=j90 + vendor=cray + basic_os=${basic_os:-unicos} ;; iris | iris4d) - basic_machine=mips-sgi - case $os in - -irix*) + cpu=mips + vendor=sgi + case $basic_os in + irix*) ;; *) - os=-irix4 + basic_os=irix4 ;; esac ;; - isi68 | isi) - basic_machine=m68k-isi - os=-sysv - ;; - m68knommu) - basic_machine=m68k-unknown - os=-linux - ;; - m68knommu-*) - basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` - os=-linux - ;; - m88k-omron*) - basic_machine=m88k-omron - ;; - magnum | m3230) - basic_machine=mips-mips - os=-sysv - ;; - merlin) - basic_machine=ns32k-utek - os=-sysv - ;; - microblaze) - basic_machine=microblaze-xilinx - ;; - mingw32) - basic_machine=i386-pc - os=-mingw32 - ;; - mingw32ce) - basic_machine=arm-unknown - os=-mingw32ce - ;; miniframe) - basic_machine=m68000-convergent + cpu=m68000 + vendor=convergent ;; - *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) - basic_machine=m68k-atari - os=-mint - ;; - mips3*-*) - basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` - ;; - mips3*) - basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown - ;; - monitor) - basic_machine=m68k-rom68k - os=-coff - ;; - morphos) - basic_machine=powerpc-unknown - os=-morphos - ;; - msdos) - basic_machine=i386-pc - os=-msdos - ;; - ms1-*) - basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` - ;; - msys) - basic_machine=i386-pc - os=-msys - ;; - mvs) - basic_machine=i370-ibm - os=-mvs - ;; - nacl) - basic_machine=le32-unknown - os=-nacl - ;; - ncr3000) - basic_machine=i486-ncr - os=-sysv4 - ;; - netbsd386) - basic_machine=i386-unknown - os=-netbsd - ;; - netwinder) - basic_machine=armv4l-rebel - os=-linux - ;; - news | news700 | news800 | news900) - basic_machine=m68k-sony - os=-newsos - ;; - news1000) - basic_machine=m68030-sony - os=-newsos + *mint | mint[0-9]* | *MiNT | *MiNT[0-9]*) + cpu=m68k + vendor=atari + basic_os=mint ;; news-3600 | risc-news) - basic_machine=mips-sony - os=-newsos - ;; - necv70) - basic_machine=v70-nec - os=-sysv - ;; - next | m*-next ) - basic_machine=m68k-next - case $os in - -nextstep* ) + cpu=mips + vendor=sony + basic_os=newsos + ;; + next | m*-next) + cpu=m68k + vendor=next + case $basic_os in + openstep*) + ;; + nextstep*) ;; - -ns2*) - os=-nextstep2 + ns2*) + basic_os=nextstep2 ;; *) - os=-nextstep3 + basic_os=nextstep3 ;; esac ;; - nh3000) - basic_machine=m68k-harris - os=-cxux - ;; - nh[45]000) - basic_machine=m88k-harris - os=-cxux - ;; - nindy960) - basic_machine=i960-intel - os=-nindy - ;; - mon960) - basic_machine=i960-intel - os=-mon960 - ;; - nonstopux) - basic_machine=mips-compaq - os=-nonstopux - ;; np1) - basic_machine=np1-gould - ;; - neo-tandem) - basic_machine=neo-tandem - ;; - nse-tandem) - basic_machine=nse-tandem - ;; - nsr-tandem) - basic_machine=nsr-tandem + cpu=np1 + vendor=gould ;; op50n-* | op60c-*) - basic_machine=hppa1.1-oki - os=-proelf - ;; - openrisc | openrisc-*) - basic_machine=or32-unknown - ;; - os400) - basic_machine=powerpc-ibm - os=-os400 - ;; - OSE68000 | ose68000) - basic_machine=m68000-ericsson - os=-ose - ;; - os68k) - basic_machine=m68k-none - os=-os68k + cpu=hppa1.1 + vendor=oki + basic_os=proelf ;; pa-hitachi) - basic_machine=hppa1.1-hitachi - os=-hiuxwe2 - ;; - paragon) - basic_machine=i860-intel - os=-osf - ;; - parisc) - basic_machine=hppa-unknown - os=-linux - ;; - parisc-*) - basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` - os=-linux + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 ;; pbd) - basic_machine=sparc-tti + cpu=sparc + vendor=tti ;; pbb) - basic_machine=m68k-tti - ;; - pc532 | pc532-*) - basic_machine=ns32k-pc532 - ;; - pc98) - basic_machine=i386-pc - ;; - pc98-*) - basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` + cpu=m68k + vendor=tti ;; - pentium | p5 | k5 | k6 | nexgen | viac3) - basic_machine=i586-pc - ;; - pentiumpro | p6 | 6x86 | athlon | athlon_*) - basic_machine=i686-pc - ;; - pentiumii | pentium2 | pentiumiii | pentium3) - basic_machine=i686-pc - ;; - pentium4) - basic_machine=i786-pc - ;; - pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) - basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - pentiumpro-* | p6-* | 6x86-* | athlon-*) - basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) - basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - pentium4-*) - basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` + pc532) + cpu=ns32k + vendor=pc532 ;; pn) - basic_machine=pn-gould - ;; - power) basic_machine=power-ibm - ;; - ppc | ppcbe) basic_machine=powerpc-unknown - ;; - ppc-* | ppcbe-*) - basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` + cpu=pn + vendor=gould ;; - ppcle | powerpclittle | ppc-le | powerpc-little) - basic_machine=powerpcle-unknown - ;; - ppcle-* | powerpclittle-*) - basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - ppc64) basic_machine=powerpc64-unknown - ;; - ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` - ;; - ppc64le | powerpc64little | ppc64-le | powerpc64-little) - basic_machine=powerpc64le-unknown - ;; - ppc64le-* | powerpc64little-*) - basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` + power) + cpu=power + vendor=ibm ;; ps2) - basic_machine=i386-ibm - ;; - pw32) - basic_machine=i586-unknown - os=-pw32 - ;; - rdos) - basic_machine=i386-pc - os=-rdos - ;; - rom68k) - basic_machine=m68k-rom68k - os=-coff + cpu=i386 + vendor=ibm ;; rm[46]00) - basic_machine=mips-siemens + cpu=mips + vendor=siemens ;; rtpc | rtpc-*) - basic_machine=romp-ibm - ;; - s390 | s390-*) - basic_machine=s390-ibm + cpu=romp + vendor=ibm ;; - s390x | s390x-*) - basic_machine=s390x-ibm - ;; - sa29200) - basic_machine=a29k-amd - os=-udi - ;; - sb1) - basic_machine=mipsisa64sb1-unknown + sde) + cpu=mipsisa32 + vendor=sde + basic_os=${basic_os:-elf} ;; - sb1el) - basic_machine=mipsisa64sb1el-unknown + simso-wrs) + cpu=sparclite + vendor=wrs + basic_os=vxworks ;; - sde) - basic_machine=mipsisa32-sde - os=-elf + tower | tower-32) + cpu=m68k + vendor=ncr ;; - sei) - basic_machine=mips-sei - os=-seiux + vpp*|vx|vx-*) + cpu=f301 + vendor=fujitsu ;; - sequent) - basic_machine=i386-sequent + w65) + cpu=w65 + vendor=wdc ;; - sh) - basic_machine=sh-hitachi - os=-hms + w89k-*) + cpu=hppa1.1 + vendor=winbond + basic_os=proelf ;; - sh5el) - basic_machine=sh5le-unknown + none) + cpu=none + vendor=none ;; - sh64) - basic_machine=sh64-unknown + leon|leon[3-9]) + cpu=sparc + vendor=$basic_machine ;; - sparclite-wrs | simso-wrs) - basic_machine=sparclite-wrs - os=-vxworks + leon-*|leon[3-9]-*) + cpu=sparc + vendor=`echo "$basic_machine" | sed 's/-.*//'` ;; - sps7) - basic_machine=m68k-bull - os=-sysv2 + + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read cpu vendor <&2 - exit 1 + # Recognize the canonical CPU types that are allowed with any + # company name. + case $cpu in + 1750a | 580 \ + | a29k \ + | aarch64 | aarch64_be \ + | abacus \ + | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] \ + | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] \ + | alphapca5[67] | alpha64pca5[67] \ + | am33_2.0 \ + | amdgcn \ + | arc | arceb | arc32 | arc64 \ + | arm | arm[lb]e | arme[lb] | armv* \ + | avr | avr32 \ + | asmjs \ + | ba \ + | be32 | be64 \ + | bfin | bpf | bs2000 \ + | c[123]* | c30 | [cjt]90 | c4x \ + | c8051 | clipper | craynv | csky | cydra \ + | d10v | d30v | dlx | dsp16xx \ + | e2k | elxsi | epiphany \ + | f30[01] | f700 | fido | fr30 | frv | ft32 | fx80 \ + | h8300 | h8500 \ + | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ + | hexagon \ + | i370 | i*86 | i860 | i960 | ia16 | ia64 \ + | ip2k | iq2000 \ + | k1om \ + | le32 | le64 \ + | lm32 \ + | loongarch32 | loongarch64 | loongarchx32 \ + | m32c | m32r | m32rle \ + | m5200 | m68000 | m680[012346]0 | m68360 | m683?2 | m68k \ + | m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x \ + | m88110 | m88k | maxq | mb | mcore | mep | metag \ + | microblaze | microblazeel \ + | mips | mipsbe | mipseb | mipsel | mipsle \ + | mips16 \ + | mips64 | mips64eb | mips64el \ + | mips64octeon | mips64octeonel \ + | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ + | mips64vr4100 | mips64vr4100el \ + | mips64vr4300 | mips64vr4300el \ + | mips64vr5000 | mips64vr5000el \ + | mips64vr5900 | mips64vr5900el \ + | mipsisa32 | mipsisa32el \ + | mipsisa32r2 | mipsisa32r2el \ + | mipsisa32r3 | mipsisa32r3el \ + | mipsisa32r5 | mipsisa32r5el \ + | mipsisa32r6 | mipsisa32r6el \ + | mipsisa64 | mipsisa64el \ + | mipsisa64r2 | mipsisa64r2el \ + | mipsisa64r3 | mipsisa64r3el \ + | mipsisa64r5 | mipsisa64r5el \ + | mipsisa64r6 | mipsisa64r6el \ + | mipsisa64sb1 | mipsisa64sb1el \ + | mipsisa64sr71k | mipsisa64sr71kel \ + | mipsr5900 | mipsr5900el \ + | mipstx39 | mipstx39el \ + | mmix \ + | mn10200 | mn10300 \ + | moxie \ + | mt \ + | msp430 \ + | nds32 | nds32le | nds32be \ + | nfp \ + | nios | nios2 | nios2eb | nios2el \ + | none | np1 | ns16k | ns32k | nvptx \ + | open8 \ + | or1k* \ + | or32 \ + | orion \ + | picochip \ + | pdp10 | pdp11 | pj | pjl | pn | power \ + | powerpc | powerpc64 | powerpc64le | powerpcle | powerpcspe \ + | pru \ + | pyramid \ + | riscv | riscv32 | riscv32be | riscv64 | riscv64be \ + | rl78 | romp | rs6000 | rx \ + | s390 | s390x \ + | score \ + | sh | shl \ + | sh[1234] | sh[24]a | sh[24]ae[lb] | sh[23]e | she[lb] | sh[lb]e \ + | sh[1234]e[lb] | sh[12345][lb]e | sh[23]ele | sh64 | sh64le \ + | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet \ + | sparclite \ + | sparcv8 | sparcv9 | sparcv9b | sparcv9v | sv1 | sx* \ + | spu \ + | tahoe \ + | thumbv7* \ + | tic30 | tic4x | tic54x | tic55x | tic6x | tic80 \ + | tron \ + | ubicom32 \ + | v70 | v850 | v850e | v850e1 | v850es | v850e2 | v850e2v3 \ + | vax \ + | visium \ + | w65 \ + | wasm32 | wasm64 \ + | we32k \ + | x86 | x86_64 | xc16x | xgate | xps100 \ + | xstormy16 | xtensa* \ + | ymp \ + | z8k | z80) + ;; + + *) + echo Invalid configuration \`"$1"\': machine \`"$cpu-$vendor"\' not recognized 1>&2 + exit 1 + ;; + esac ;; esac # Here we canonicalize certain aliases for manufacturers. -case $basic_machine in - *-digital*) - basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` +case $vendor in + digital*) + vendor=dec ;; - *-commodore*) - basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` + commodore*) + vendor=cbm ;; *) ;; @@ -1302,203 +1301,215 @@ esac # Decode manufacturer-specific aliases for certain operating systems. -if [ x"$os" != x"" ] +if test x$basic_os != x then -case $os in - # First match some system type aliases - # that might get confused with valid system types. - # -solaris* is a basic system type, with this one exception. - -auroraux) - os=-auroraux + +# First recognize some ad-hoc caes, or perhaps split kernel-os, or else just +# set os. +case $basic_os in + gnu/linux*) + kernel=linux + os=`echo "$basic_os" | sed -e 's|gnu/linux|gnu|'` + ;; + os2-emx) + kernel=os2 + os=`echo "$basic_os" | sed -e 's|os2-emx|emx|'` + ;; + nto-qnx*) + kernel=nto + os=`echo "$basic_os" | sed -e 's|nto-qnx|qnx|'` + ;; + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read kernel os <&2 - exit 1 + # No normalization, but not necessarily accepted, that comes below. ;; esac + else # Here we handle the default operating systems that come with various machines. @@ -1511,255 +1522,362 @@ else # will signal an error saying that MANUFACTURER isn't an operating # system, and we'll never get to this point. -case $basic_machine in +kernel= +case $cpu-$vendor in score-*) - os=-elf + os=elf ;; spu-*) - os=-elf + os=elf ;; *-acorn) - os=-riscix1.2 + os=riscix1.2 ;; arm*-rebel) - os=-linux + kernel=linux + os=gnu ;; arm*-semi) - os=-aout + os=aout ;; c4x-* | tic4x-*) - os=-coff + os=coff + ;; + c8051-*) + os=elf + ;; + clipper-intergraph) + os=clix + ;; + hexagon-*) + os=elf ;; tic54x-*) - os=-coff + os=coff ;; tic55x-*) - os=-coff + os=coff ;; tic6x-*) - os=-coff + os=coff ;; # This must come before the *-dec entry. pdp10-*) - os=-tops20 + os=tops20 ;; pdp11-*) - os=-none + os=none ;; *-dec | vax-*) - os=-ultrix4.2 + os=ultrix4.2 ;; m68*-apollo) - os=-domain + os=domain ;; i386-sun) - os=-sunos4.0.2 + os=sunos4.0.2 ;; m68000-sun) - os=-sunos3 + os=sunos3 ;; m68*-cisco) - os=-aout + os=aout ;; mep-*) - os=-elf + os=elf ;; mips*-cisco) - os=-elf + os=elf ;; mips*-*) - os=-elf + os=elf ;; or32-*) - os=-coff + os=coff ;; *-tti) # must be before sparc entry or we get the wrong os. - os=-sysv3 + os=sysv3 ;; sparc-* | *-sun) - os=-sunos4.1.1 + os=sunos4.1.1 ;; - *-be) - os=-beos + pru-*) + os=elf ;; - *-haiku) - os=-haiku + *-be) + os=beos ;; *-ibm) - os=-aix + os=aix ;; *-knuth) - os=-mmixware + os=mmixware ;; *-wec) - os=-proelf + os=proelf ;; *-winbond) - os=-proelf + os=proelf ;; *-oki) - os=-proelf + os=proelf ;; *-hp) - os=-hpux + os=hpux ;; *-hitachi) - os=-hiux + os=hiux ;; i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent) - os=-sysv + os=sysv ;; *-cbm) - os=-amigaos + os=amigaos ;; *-dg) - os=-dgux + os=dgux ;; *-dolphin) - os=-sysv3 + os=sysv3 ;; m68k-ccur) - os=-rtu + os=rtu ;; m88k-omron*) - os=-luna + os=luna ;; - *-next ) - os=-nextstep + *-next) + os=nextstep ;; *-sequent) - os=-ptx + os=ptx ;; *-crds) - os=-unos + os=unos ;; *-ns) - os=-genix + os=genix ;; i370-*) - os=-mvs - ;; - *-next) - os=-nextstep3 + os=mvs ;; *-gould) - os=-sysv + os=sysv ;; *-highlevel) - os=-bsd + os=bsd ;; *-encore) - os=-bsd + os=bsd ;; *-sgi) - os=-irix + os=irix ;; *-siemens) - os=-sysv4 + os=sysv4 ;; *-masscomp) - os=-rtu + os=rtu ;; f30[01]-fujitsu | f700-fujitsu) - os=-uxpv + os=uxpv ;; *-rom68k) - os=-coff + os=coff ;; *-*bug) - os=-coff + os=coff ;; *-apple) - os=-macos + os=macos ;; *-atari*) - os=-mint + os=mint + ;; + *-wrs) + os=vxworks ;; *) - os=-none + os=none ;; esac + fi +# Now, validate our (potentially fixed-up) OS. +case $os in + # Sometimes we do "kernel-libc", so those need to count as OSes. + musl* | newlib* | relibc* | uclibc*) + ;; + # Likewise for "kernel-abi" + eabi* | gnueabi*) + ;; + # VxWorks passes extra cpu info in the 4th filed. + simlinux | simwindows | spe) + ;; + # Now accept the basic system types. + # The portable systems comes first. + # Each alternative MUST end in a * to match a version number. + gnu* | android* | bsd* | mach* | minix* | genix* | ultrix* | irix* \ + | *vms* | esix* | aix* | cnk* | sunos | sunos[34]* \ + | hpux* | unos* | osf* | luna* | dgux* | auroraux* | solaris* \ + | sym* | plan9* | psp* | sim* | xray* | os68k* | v88r* \ + | hiux* | abug | nacl* | netware* | windows* \ + | os9* | macos* | osx* | ios* \ + | mpw* | magic* | mmixware* | mon960* | lnews* \ + | amigaos* | amigados* | msdos* | newsos* | unicos* | aof* \ + | aos* | aros* | cloudabi* | sortix* | twizzler* \ + | nindy* | vxsim* | vxworks* | ebmon* | hms* | mvs* \ + | clix* | riscos* | uniplus* | iris* | isc* | rtu* | xenix* \ + | mirbsd* | netbsd* | dicos* | openedition* | ose* \ + | bitrig* | openbsd* | secbsd* | solidbsd* | libertybsd* | os108* \ + | ekkobsd* | freebsd* | riscix* | lynxos* | os400* \ + | bosx* | nextstep* | cxux* | aout* | elf* | oabi* \ + | ptx* | coff* | ecoff* | winnt* | domain* | vsta* \ + | udi* | lites* | ieee* | go32* | aux* | hcos* \ + | chorusrdb* | cegcc* | glidix* | serenity* \ + | cygwin* | msys* | pe* | moss* | proelf* | rtems* \ + | midipix* | mingw32* | mingw64* | mint* \ + | uxpv* | beos* | mpeix* | udk* | moxiebox* \ + | interix* | uwin* | mks* | rhapsody* | darwin* \ + | openstep* | oskit* | conix* | pw32* | nonstopux* \ + | storm-chaos* | tops10* | tenex* | tops20* | its* \ + | os2* | vos* | palmos* | uclinux* | nucleus* | morphos* \ + | scout* | superux* | sysv* | rtmk* | tpf* | windiss* \ + | powermax* | dnix* | nx6 | nx7 | sei* | dragonfly* \ + | skyos* | haiku* | rdos* | toppers* | drops* | es* \ + | onefs* | tirtos* | phoenix* | fuchsia* | redox* | bme* \ + | midnightbsd* | amdhsa* | unleashed* | emscripten* | wasi* \ + | nsk* | powerunix* | genode* | zvmoe* | qnx* | emx* | zephyr*) + ;; + # This one is extra strict with allowed versions + sco3.2v2 | sco3.2v[4-9]* | sco5v6*) + # Don't forget version if it is 3.2v4 or newer. + ;; + none) + ;; + *) + echo Invalid configuration \`"$1"\': OS \`"$os"\' not recognized 1>&2 + exit 1 + ;; +esac + +# As a final step for OS-related things, validate the OS-kernel combination +# (given a valid OS), if there is a kernel. +case $kernel-$os in + linux-gnu* | linux-dietlibc* | linux-android* | linux-newlib* \ + | linux-musl* | linux-relibc* | linux-uclibc* ) + ;; + uclinux-uclibc* ) + ;; + -dietlibc* | -newlib* | -musl* | -relibc* | -uclibc* ) + # These are just libc implementations, not actual OSes, and thus + # require a kernel. + echo "Invalid configuration \`$1': libc \`$os' needs explicit kernel." 1>&2 + exit 1 + ;; + kfreebsd*-gnu* | kopensolaris*-gnu*) + ;; + vxworks-simlinux | vxworks-simwindows | vxworks-spe) + ;; + nto-qnx*) + ;; + os2-emx) + ;; + *-eabi* | *-gnueabi*) + ;; + -*) + # Blank kernel with real OS is always fine. + ;; + *-*) + echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2 + exit 1 + ;; +esac + # Here we handle the case where we know the os, and the CPU type, but not the # manufacturer. We pick the logical manufacturer. -vendor=unknown -case $basic_machine in - *-unknown) - case $os in - -riscix*) +case $vendor in + unknown) + case $cpu-$os in + *-riscix*) vendor=acorn ;; - -sunos*) + *-sunos*) vendor=sun ;; - -cnk*|-aix*) + *-cnk* | *-aix*) vendor=ibm ;; - -beos*) + *-beos*) vendor=be ;; - -hpux*) + *-hpux*) vendor=hp ;; - -mpeix*) + *-mpeix*) vendor=hp ;; - -hiux*) + *-hiux*) vendor=hitachi ;; - -unos*) + *-unos*) vendor=crds ;; - -dgux*) + *-dgux*) vendor=dg ;; - -luna*) + *-luna*) vendor=omron ;; - -genix*) + *-genix*) vendor=ns ;; - -mvs* | -opened*) + *-clix*) + vendor=intergraph + ;; + *-mvs* | *-opened*) + vendor=ibm + ;; + *-os400*) vendor=ibm ;; - -os400*) + s390-* | s390x-*) vendor=ibm ;; - -ptx*) + *-ptx*) vendor=sequent ;; - -tpf*) + *-tpf*) vendor=ibm ;; - -vxsim* | -vxworks* | -windiss*) + *-vxsim* | *-vxworks* | *-windiss*) vendor=wrs ;; - -aux*) + *-aux*) vendor=apple ;; - -hms*) + *-hms*) vendor=hitachi ;; - -mpw* | -macos*) + *-mpw* | *-macos*) vendor=apple ;; - -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*) vendor=atari ;; - -vos*) + *-vos*) vendor=stratus ;; esac - basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` ;; esac -echo $basic_machine$os +echo "$cpu-$vendor-${kernel:+$kernel-}$os" exit # Local variables: -# eval: (add-hook 'write-file-hooks 'time-stamp) +# eval: (add-hook 'before-save-hook 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" From 49eda37d4872d091642d42863e04ef3a6cae016e Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Tue, 19 Oct 2021 08:34:11 -0600 Subject: [PATCH 47/98] MueLu: Removing printf --- .../MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp index ded2947f9a3a..60b76d6dc427 100644 --- a/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp +++ b/packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp @@ -528,10 +528,10 @@ namespace MueLu { bool is_nonpositive = STS::real(vals[colID]) <= 0; MT aiiajj = STS::magnitude(threshold*threshold * ghostedDiagVals[col]*ghostedDiagVals[row]); // eps^2*|a_ii|*|a_jj| MT aij = is_nonpositive ? STS::magnitude(vals[colID]*vals[colID]) : (-STS::magnitude(vals[colID]*vals[colID])); // + |a_ij|^2, if a_ij < 0, - |a_ij|^2 if a_ij >=0 - + /* if(row==1326) printf("A(%d,%d) = %6.4e, raw_aij = %6.4e aij = %6.4e aiiajj = %6.4e\n",row,col,vals[colID], vals[colID],aij, aiiajj); - + */ if ((!rowIsDirichlet && aij > aiiajj) || row == col) { columns[realnnz++] = col; From d91d3fcf845d8f550253dc34fa936bdec38a2253 Mon Sep 17 00:00:00 2001 From: rstumin Date: Tue, 19 Oct 2021 13:38:56 -0600 Subject: [PATCH 48/98] new version of prolongator constraint satisfication capability --- .../MueLu_SaPFactory_decl.hpp | 4 + .../MueLu_SaPFactory_def.hpp | 324 +++++++++++++++++- 2 files changed, 327 insertions(+), 1 deletion(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_decl.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_decl.hpp index 43c926dda95f..eb6dabbad4d9 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_decl.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_decl.hpp @@ -146,6 +146,10 @@ template A, RCP& P) const; + void newSatisfyPConstraints(RCP& P) const; + + bool constrainRow(Scalar *orig, LocalOrdinal nEntries, Scalar leftBound, Scalar rghtBound,Scalar rsumTarget, Scalar *fixedUnsorted, Scalar *scalarData) const; + //@} diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp index b1480a2f065c..9a6bc42eb819 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp @@ -226,7 +226,10 @@ namespace MueLu { // finalP = Ptent + (I - \omega D^{-1}A) Ptent finalP = Xpetra::IteratorOps::Jacobi(omega, *invDiag, *A, *Ptent, finalP, GetOStream(Statistics2), std::string("MueLu::SaP-")+levelIDs, APparams); - if (enforceConstraints) SatisfyPConstraints( A, finalP); + if (enforceConstraints) { + if (A->GetFixedBlockSize() == 1) newSatisfyPConstraints( finalP); + else SatisfyPConstraints( A, finalP); + } } } else { @@ -377,6 +380,325 @@ namespace MueLu { } // for (size_t i = 0; i < as(P->getRowMap()->getNumNodeElements()); i++) ... } //SatsifyPConstraints() + template + void SaPFactory::newSatisfyPConstraints(RCP& P) const { + + const Scalar zero = Teuchos::ScalarTraits::zero(); + const Scalar one = Teuchos::ScalarTraits::one(); + + LocalOrdinal maxEntriesPerRow = 100; // increased later if needed + Teuchos::ArrayRCP scalarData(3*maxEntriesPerRow); + bool hasFeasible; + + for (size_t i = 0; i < as(P->getRowMap()->getNodeNumElements()); i++) { + + Teuchos::ArrayView indices; + Teuchos::ArrayView vals1; + Teuchos::ArrayView< Scalar> vals; + P->getLocalRowView((LocalOrdinal) i, indices, vals1); + size_t nnz = indices.size(); + if (nnz != 0) { + + vals = ArrayView(const_cast(vals1.getRawPtr()), nnz); + Scalar rsumTarget = Teuchos::ScalarTraits::zero(); + for (size_t j = 0; j < nnz; j++) rsumTarget += vals[j]; + + if (nnz > as(maxEntriesPerRow)) { + maxEntriesPerRow = nnz*3; + scalarData.resize(3*maxEntriesPerRow); + } + hasFeasible = constrainRow(vals.getRawPtr(), as(nnz), zero , one, rsumTarget, vals.getRawPtr(), scalarData.getRawPtr()); + + if (!hasFeasible) { // just set all entries to the same value giving a row sum of 1 + for (size_t j = 0; j < nnz; j++) vals[j] = one/as(nnz); + } + } + + } // for (size_t i = 0; i < as(P->getRowMap()->getNumNodeElements()); i++) ... + } //SatsifyPConstraints() + + template + bool SaPFactory::constrainRow(Scalar *orig, LocalOrdinal nEntries, Scalar leftBound, Scalar rghtBound,Scalar rsumTarget, Scalar *fixedUnsorted, Scalar *scalarData) const { +/* + Input + orig data that should be adjusted to satisfy bound constraints and + row sum constraint. orig is not modified by this function. + + nEntries length or 'orig' + + leftBound, define bound constraints for the results. + rghtBound + + rsumTarget defines an equality constraint for the row sum + + fixedUnsorted on output, if a feasible solutuion exists then + || orig - fixedUnsorted || = min when also + leftBound <= fixedUnsorted[i] <= rghtBound for all i + and sum(fixedUnsorted) = rsumTarget. + + Note: it is possible to use the same pointer for + fixedUnsorted and orig. In this case, orig gets + overwritten with the new constraint satisfying values. + + scalarData a work array that should be 3x nEntries. + + On return constrain() indicates whether or not a feasible solution exists. +*/ + +/* + Given a sequence of numbers o1 ... on, fix these so that they are as + close as possible to the original but satisfy bound constraints and also + have the same row sum as the oi's. If we know who is going to lie on a + bound, then the "best" answer (i.e., || o - f ||_2 = min) perturbs + each element that doesn't lie on a bound by the same amount. + + We can represent the oi's by considering scattered points on a number line + + | | + | | + o o o | o o o o o o |o o + | | + + \____/ \____/ + <---- <---- + delta delta + + Bounds are shown by vertical lines. The fi's must lie within the bounds, so + the 3 leftmost points must be shifted to the right and the 2 rightmost must + be shifted to the left. If these fi points are all shifted to the bounds + while the others remain in the same location, the row sum constraint is + likely not satisfied and so more shifting is necessary. In the figure, the f + rowsum is too large and so there must be more shifting to the left. + + To minimize || o - f ||_2, we basically shift all "interiors" by the same + amount, denoted delta. The only trick is that some points near bounds are + still affected by the bounds and so these points might be shifted more or less + than delta. In the example,t he 3 rightmost points are shifted in the opposite + direction as delta to the bound. The 4th point is shifted by something less + than delta so it does not violate the lower bound. The rightmost point is + shifted to the bound by some amount larger than delta. However, the 2nd point + is shifted by delta (i.e., it lies inside the two bounds). + + If we know delta, we can figure out everything. If we know which points + are special (not shifted by delta), we can also figure out everything. + The problem is these two things (delta and the special points) are + inter-connected. An algorithm for computing follows. + + 1) move exterior points to the bounds and compute how much the row sum is off + (rowSumDeviation). We assume now that the new row sum is high, so interior + points must be shifted left. + + 2) Mark closest point just left of the leftmost bound, closestToLeftBound, + and compute its distance to the leftmost bound. Mark closest point to the + left of the rightmost bound, closestToRghtBound, and compute its distance to + right bound. There are two cases to consider. + + 3) Case 1: closestToLeftBound is closer than closestToRghtBound. + Assume that shifting by delta does not move closestToLeftBound past the + left bound. This means that it will be shifted by delta. However, + closestToRghtBound will be shifted by more than delta. So the total + number of points shifted by delta (|interiorToBounds|) includes + closestToLeftBound up to and including the point just to the left of + closestToRghtBound. So + + delta = rowSumDeviation/ |interiorToBounds| . + + Recall that rowSumDeviation already accounts for the non-delta shift of + of closestToRightBound. Now check whether our assumption is valid. + + If delta <= closestToLeftBoundDist, assumption is true so delta can be + applied to interiorToBounds ... and we are done. + Else assumption is false. Shift closestToLeftBound to the left bound. + Update rowSumDeviation, interiorToBounds, and identify new + closestToLeftBound. Repeat step 3). + + Case 2: closestToRghtBound is closer than closestToLeftBound. + Assume that shifting by delta does not move closestToRghtBound past right + bound. This means that it must be shifted by more than delta to right + bound. So the total number of points shifted by delta again includes + closestToLeftBound up to and including the point just to the left of + closestToRghtBound. So again compute + + delta = rowSumDeviation/ |interiorToBounds| . + + If delta <= closestToRghtBoundDist, assumption is true so delta is + can be applied to interiorToBounds ... and we are done + Else assumption is false. Put closestToRghtBound in the + interiorToBounds set. Remove it's contribution to rowSumDeviation, + identify new closestToRghtBound. Repeat step 3) + + + To implement, sort the oi's so things like closestToLeftBound is just index + into sorted array. Updaing closestToLeftBound or closestToRghtBound requires + increment by 1. |interiorToBounds|= closestToRghtBound - closestToLeftBound + To handle the case when the rowsum is low (requiring right interior shifts), + just flip the signs on data and use the left-shift code (and then flip back + before exiting function. +*/ + bool hasFeasibleSol; + Scalar notFlippedLeftBound, notFlippedRghtBound, aBigNumber, *origSorted; + Scalar rowSumDeviation, temp, *fixedSorted, delta; + Scalar closestToLeftBoundDist, closestToRghtBoundDist; + LocalOrdinal closestToLeftBound, closestToRghtBound; + LocalOrdinal *inds; + bool flipped; + + notFlippedLeftBound = leftBound; + notFlippedRghtBound = rghtBound; + + if ((Teuchos::ScalarTraits::real(rsumTarget) >= Teuchos::ScalarTraits::real(leftBound*nEntries)) && + (Teuchos::ScalarTraits::real(rsumTarget) <= Teuchos::ScalarTraits::real(rghtBound*nEntries))) + hasFeasibleSol = true; + else { + hasFeasibleSol=false; + return hasFeasibleSol; + } + flipped = false; + // compute aBigNumber to handle some corner cases where we need + // something large so that an if statement will be false + aBigNumber = Teuchos::ScalarTraits::zero(); + for (LocalOrdinal i = 0; i < nEntries; i++) { + if ( Teuchos::ScalarTraits::magnitude(orig[i]) > aBigNumber) + aBigNumber = Teuchos::ScalarTraits::magnitude(orig[i]); + } + aBigNumber = aBigNumber+ (Teuchos::ScalarTraits::magnitude(leftBound) + Teuchos::ScalarTraits::magnitude(rghtBound))*as(100.0); + + origSorted = &scalarData[0]; + fixedSorted = &(scalarData[nEntries]); + inds = (LocalOrdinal *) &(scalarData[2*nEntries]); + + for (LocalOrdinal i = 0; i < nEntries; i++) inds[i] = i; + for (LocalOrdinal i = 0; i < nEntries; i++) origSorted[i] = orig[i]; /* orig no longer used */ + + // sort so that orig[inds] is sorted. + std::sort(inds, inds+nEntries, + [origSorted](LocalOrdinal leftIndex, LocalOrdinal rightIndex) + { return Teuchos::ScalarTraits::real(origSorted[leftIndex]) < Teuchos::ScalarTraits::real(origSorted[rightIndex]);}); + + for (LocalOrdinal i = 0; i < nEntries; i++) origSorted[i] = orig[inds[i]]; + // find entry in origSorted just to the right of the leftBound + closestToLeftBound = 0; + while ((closestToLeftBound < nEntries) && (Teuchos::ScalarTraits::real(origSorted[closestToLeftBound]) <= Teuchos::ScalarTraits::real(leftBound))) closestToLeftBound++; + + // find entry in origSorted just to the right of the rghtBound + closestToRghtBound = closestToLeftBound; + while ((closestToRghtBound < nEntries) && (Teuchos::ScalarTraits::real(origSorted[closestToRghtBound]) <= Teuchos::ScalarTraits::real(rghtBound))) closestToRghtBound++; + + // compute distance between closestToLeftBound and the left bound and the + // distance between closestToRghtBound and the right bound. + + closestToLeftBoundDist = origSorted[closestToLeftBound] - leftBound; + if (closestToRghtBound==nEntries) closestToRghtBoundDist= aBigNumber; + else closestToRghtBoundDist= origSorted[closestToRghtBound] - rghtBound; + + // compute how far the rowSum is off from the target row sum taking into account + // numbers that have been shifted to satisfy bound constraint + + rowSumDeviation = leftBound*closestToLeftBound + (nEntries-closestToRghtBound)*rghtBound - rsumTarget; + for (LocalOrdinal i=closestToLeftBound; i < closestToRghtBound; i++) rowSumDeviation += origSorted[i]; + + // the code that follow after this if statement assumes that rowSumDeviation is positive. If this + // is not the case, flip the signs of everything so that rowSumDeviation is now positive. + // Later we will flip the data back to its original form. + if (rowSumDeviation < Teuchos::ScalarTraits::zero()) { + flipped = true; + temp = leftBound; leftBound = -rghtBound; rghtBound = temp; + + /* flip sign of origSorted and reverse ordering so that the negative version is sorted */ + + if ((nEntries%2) == 1) origSorted[(nEntries/2) ] = -origSorted[(nEntries/2) ]; + for (LocalOrdinal i=0; i < nEntries/2; i++) { + temp=origSorted[i]; + origSorted[i] = -origSorted[nEntries-1-i]; + origSorted[nEntries-i-1] = -temp; + } + + /* reverse bounds */ + + temp = closestToLeftBound; + closestToLeftBound = nEntries-closestToRghtBound; + closestToRghtBound = nEntries-temp; + closestToLeftBoundDist = origSorted[closestToLeftBound] - leftBound; + if (closestToRghtBound==nEntries) closestToRghtBoundDist= aBigNumber; + else closestToRghtBoundDist= origSorted[closestToRghtBound] - rghtBound; + + rowSumDeviation = -rowSumDeviation; + } + + // initial fixedSorted so bounds are satisfied and interiors correspond to origSorted + + for (LocalOrdinal i = 0; i < closestToLeftBound; i++) fixedSorted[i] = leftBound; + for (LocalOrdinal i = closestToLeftBound; i < closestToRghtBound; i++) fixedSorted[i] = origSorted[i]; + for (LocalOrdinal i = closestToRghtBound; i < nEntries; i++) fixedSorted[i] = rghtBound; + + while ((Teuchos::ScalarTraits::magnitude(rowSumDeviation) > Teuchos::ScalarTraits::magnitude(as(1.e-10)*rsumTarget))){ // && ( (closestToLeftBound < nEntries ) || (closestToRghtBound < nEntries))) { + if (closestToRghtBound != closestToLeftBound) + delta = rowSumDeviation/ (closestToRghtBound - closestToLeftBound); + else delta = aBigNumber; + + if (Teuchos::ScalarTraits::magnitude(closestToLeftBoundDist) <= Teuchos::ScalarTraits::magnitude(closestToRghtBoundDist)) { + if (Teuchos::ScalarTraits::magnitude(delta) <= Teuchos::ScalarTraits::magnitude(closestToLeftBoundDist)) { + rowSumDeviation = Teuchos::ScalarTraits::zero(); + for (LocalOrdinal i = closestToLeftBound; i < closestToRghtBound ; i++) fixedSorted[i] = origSorted[i] - delta; + } + else { + rowSumDeviation = rowSumDeviation - closestToLeftBoundDist; + fixedSorted[closestToLeftBound] = leftBound; + closestToLeftBound++; + if (closestToLeftBound < nEntries) closestToLeftBoundDist = origSorted[closestToLeftBound] - leftBound; + else closestToLeftBoundDist = aBigNumber; + } + } + else { + if (Teuchos::ScalarTraits::magnitude(delta) <= Teuchos::ScalarTraits::magnitude(closestToRghtBoundDist)) { + rowSumDeviation = 0; + for (LocalOrdinal i = closestToLeftBound; i < closestToRghtBound ; i++) fixedSorted[i] = origSorted[i] - delta; + } + else { + rowSumDeviation = rowSumDeviation + closestToRghtBoundDist; +// if (closestToRghtBound < nEntries) { + fixedSorted[closestToRghtBound] = origSorted[closestToRghtBound]; + closestToRghtBound++; + // } + if (closestToRghtBound >= nEntries) closestToRghtBoundDist = aBigNumber; + else closestToRghtBoundDist = origSorted[closestToRghtBound] - rghtBound; + } + } + } + + if (flipped) { + /* flip sign of fixedSorted and reverse ordering so that the positve version is sorted */ + + if ((nEntries%2) == 1) fixedSorted[(nEntries/2) ] = -fixedSorted[(nEntries/2) ]; + for (LocalOrdinal i=0; i < nEntries/2; i++) { + temp=fixedSorted[i]; + fixedSorted[i] = -fixedSorted[nEntries-1-i]; + fixedSorted[nEntries-i-1] = -temp; + } + } + for (LocalOrdinal i = 0; i < nEntries; i++) fixedUnsorted[inds[i]] = fixedSorted[i]; + + /* check that no constraints are violated */ + + bool lowerViolation = false; + bool upperViolation = false; + bool sumViolation = false; + temp = Teuchos::ScalarTraits::zero(); + for (LocalOrdinal i = 0; i < nEntries; i++) { + if (Teuchos::ScalarTraits::real(fixedUnsorted[i]) < Teuchos::ScalarTraits::real(notFlippedLeftBound)) lowerViolation = true; + if (Teuchos::ScalarTraits::real(fixedUnsorted[i]) > Teuchos::ScalarTraits::real(notFlippedRghtBound)) upperViolation = true; + temp += fixedUnsorted[i]; + } + if (Teuchos::ScalarTraits::magnitude(temp - rsumTarget) > Teuchos::ScalarTraits::magnitude(as(1.0e-8)*rsumTarget)) sumViolation = true; + + TEUCHOS_TEST_FOR_EXCEPTION(lowerViolation, Exceptions::RuntimeError, "MueLu::SaPFactory::constrainRow: feasible solution but computation resulted in a lower bound violation??? "); + TEUCHOS_TEST_FOR_EXCEPTION(upperViolation, Exceptions::RuntimeError, "MueLu::SaPFactory::constrainRow: feasible solution but computation resulted in an upper bound violation??? "); + TEUCHOS_TEST_FOR_EXCEPTION(sumViolation, Exceptions::RuntimeError, "MueLu::SaPFactory::constrainRow: feasible solution but computation resulted in a row sum violation??? "); + + return hasFeasibleSol; +} + + } //namespace MueLu #endif // MUELU_SAPFACTORY_DEF_HPP From 31ff38eb0d52a12e4ba3f300633d2443ec94b0be Mon Sep 17 00:00:00 2001 From: Alan Williams Date: Tue, 19 Oct 2021 14:33:54 -0600 Subject: [PATCH 49/98] Percept changes needed for stk entity-rank changes. --- .../percept/src/adapt/CompareCoordinates.hpp | 42 +++++++++++++++++++ packages/percept/src/adapt/NodeRegistry.cpp | 32 +++++++++++--- .../src/adapt/RefinementInfoByType.cpp | 9 ++-- packages/percept/src/adapt/Refiner.cpp | 6 +-- .../src/adapt/RefinerPattern_Pyr5_Het_N.hpp | 4 +- .../src/adapt/RefinerPattern_Tet4_Tet4_N.hpp | 13 +++--- packages/percept/src/adapt/RefinerUtil.cpp | 2 +- .../src/adapt/SerializeNodeRegistry.hpp | 6 +-- packages/percept/src/adapt/TriangulateTri.hpp | 23 +++++++--- ...ormRefinerPattern_Line2_Line2_2_sierra.hpp | 4 +- ...iformRefinerPattern_Tet4_Tet4_8_sierra.hpp | 13 +++--- packages/percept/src/percept/PerceptMesh.cpp | 6 +-- packages/percept/src/percept/PerceptUtils.cpp | 4 +- .../geometry/kernel/GeometryKernelPGEOM.cpp | 4 +- .../geometry/kernel/GeometryKernelPGEOM.hpp | 6 +-- .../stk_geom/3D/FitGregoryPatchesPBGL.cpp | 11 ----- packages/percept/src/percept/norm/H1Norm.hpp | 2 + 17 files changed, 128 insertions(+), 59 deletions(-) create mode 100644 packages/percept/src/adapt/CompareCoordinates.hpp diff --git a/packages/percept/src/adapt/CompareCoordinates.hpp b/packages/percept/src/adapt/CompareCoordinates.hpp new file mode 100644 index 000000000000..7c44ac413743 --- /dev/null +++ b/packages/percept/src/adapt/CompareCoordinates.hpp @@ -0,0 +1,42 @@ +#ifndef adapt_CompareCoordinates_hpp +#define adapt_CompareCoordinates_hpp + +#include +#include + +inline bool float_less(double a, double b) +{ + return static_cast(a) < static_cast(b); +} + +inline bool is_less_than_in_x_then_y_then_z(const double * A, const double * B) +{ + if (float_less(A[0], B[0])) return true; + if (float_less(B[0], A[0])) return false; + if (float_less(A[1], B[1])) return true; + if (float_less(B[1], A[1])) return false; + if (float_less(A[2], B[2])) return true; + if (float_less(B[2], A[2])) return false; + + // How do you want to handle a tie? + return false; +} + +template +std::array get_rank_of_nodes_based_on_coordinates(std::array & node_coords) +{ + // initialize original index locations + std::array index; + std::iota(index.begin(), index.end(), 0); + + std::stable_sort(index.begin(), index.end(), + [&node_coords](size_t i1, size_t i2) {return is_less_than_in_x_then_y_then_z(node_coords[i1], node_coords[i2]);}); + + // invert indices to get node rank by coordinates + std::array rank; + for (size_t i=0; i < SIZE; ++i) + rank[index[i]] = i; + return rank; +} + +#endif diff --git a/packages/percept/src/adapt/NodeRegistry.cpp b/packages/percept/src/adapt/NodeRegistry.cpp index 60cea730238d..27987f7b13c2 100644 --- a/packages/percept/src/adapt/NodeRegistry.cpp +++ b/packages/percept/src/adapt/NodeRegistry.cpp @@ -531,7 +531,7 @@ { if (field_data[ipts]) { - for (int isp = 0; isp < fieldDim; isp++) + for (int isp = 0; isp < std::min(fieldDim,3); isp++) { c_p[isp] += field_data[ipts][isp]*spc[ipts][isp]; } @@ -1488,7 +1488,7 @@ stk::mesh::EntityRank db_rank = std::get(nodeId_elementOwnerId).rank(); stk::mesh::EntityId element_id = m_eMesh.identifier(element); - stk::mesh::EntityId element_rank = m_eMesh.entity_rank(element); + stk::mesh::EntityRank element_rank = m_eMesh.entity_rank(element); bool should_put_in_id = (element_id < db_id); bool should_put_in_rank_gt = (element_rank > db_rank); bool should_put_in_rank_gte = (element_rank >= db_rank); @@ -1560,7 +1560,7 @@ // if empty or if my id is the smallest, make this element the owner stk::mesh::EntityId db_id = std::get(nodeId_elementOwnerId).id(); - stk::mesh::EntityId db_rank = std::get(nodeId_elementOwnerId).rank(); + stk::mesh::EntityRank db_rank = std::get(nodeId_elementOwnerId).rank(); bool should_put_in_id = (m_eMesh.identifier(element) < db_id); bool should_put_in_rank_gt = (m_eMesh.entity_rank(element) > db_rank); @@ -1603,7 +1603,7 @@ stk::mesh::EntityRank db_rank = std::get(nodeId_elementOwnerId).rank(); stk::mesh::EntityId element_id = m_eMesh.identifier(element); - stk::mesh::EntityId element_rank = m_eMesh.entity_rank(element); + stk::mesh::EntityRank element_rank = m_eMesh.entity_rank(element); bool should_put_in_id = (element_id < db_id); bool should_put_in_rank_gt = (element_rank > db_rank); bool should_put_in_rank_gte = (element_rank >= db_rank); @@ -2656,9 +2656,29 @@ // set map values to new node id's unsigned inode=0; - for (SubDimCellToDataMap::iterator cell_iter = m_cell_2_data_map.begin(); cell_iter != m_cell_2_data_map.end(); ++cell_iter) + struct MySubDimCellCompare + { + bool + operator()(const SubDimCell_SDCEntityType& x, + const SubDimCell_SDCEntityType& y) const + { + MyEntityLess el = MyEntityLess(x.m_eMesh); + return std::lexicographical_compare(x.begin(), x.end(), + y.begin(), y.end(), el); + } + } mySubDimCellCompare; + + typedef std::vector SubDimCellVector; + SubDimCellVector keys; + keys.reserve(m_cell_2_data_map.size()); + for (SubDimCellToDataMap::iterator cell_iter = m_cell_2_data_map.begin(); cell_iter != m_cell_2_data_map.end(); ++cell_iter) { + keys.push_back((*cell_iter).first); + } + std::sort(keys.begin(), keys.end(), mySubDimCellCompare); + + for (SubDimCellVector::const_iterator cell_iter = keys.begin(); cell_iter != keys.end(); ++cell_iter) { - SubDimCellData& data = (*cell_iter).second; + SubDimCellData& data = m_cell_2_data_map[*cell_iter]; NodeIdsOnSubDimEntityType& nodeIds_onSE = std::get(data); if (!nodeIds_onSE.size()) continue; diff --git a/packages/percept/src/adapt/RefinementInfoByType.cpp b/packages/percept/src/adapt/RefinementInfoByType.cpp index 2beb57180679..641e9f05e39a 100644 --- a/packages/percept/src/adapt/RefinementInfoByType.cpp +++ b/packages/percept/src/adapt/RefinementInfoByType.cpp @@ -283,16 +283,15 @@ //const percept::MyPairIterRelation elem_nodes (m_eMesh, element, stk::topology::NODE_RANK); if (num_elem_marked) { - for (unsigned irank=1; irank <= ((unsigned)rank); ++irank) + for (stk::mesh::EntityRank irank=stk::topology::EDGE_RANK; irank <= rank; ++irank) { unsigned numSubDimNeededEntities = 0; - stk::mesh::EntityRank crank = (stk::mesh::EntityRank)irank; - if (irank == (unsigned)eMesh.edge_rank()) + if (irank == eMesh.edge_rank()) { numSubDimNeededEntities = cell_topo_data->edge_count; } - else if (irank == (unsigned)eMesh.side_rank()) + else if (irank == eMesh.side_rank()) { numSubDimNeededEntities = cell_topo_data->side_count; } @@ -303,7 +302,7 @@ for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++) { - NodeIdsOnSubDimEntityType* nodeIds_onSE_ptr = nodeRegistry.getNewNodesOnSubDimEntity(element, crank, iSubDimOrd); + NodeIdsOnSubDimEntityType* nodeIds_onSE_ptr = nodeRegistry.getNewNodesOnSubDimEntity(element, irank, iSubDimOrd); if (nodeIds_onSE_ptr == 0) { continue; diff --git a/packages/percept/src/adapt/Refiner.cpp b/packages/percept/src/adapt/Refiner.cpp index 837166d67dea..aa3c0abacf3b 100644 --- a/packages/percept/src/adapt/Refiner.cpp +++ b/packages/percept/src/adapt/Refiner.cpp @@ -1552,7 +1552,7 @@ bool stk_auto= stk::mesh::is_auto_declared_part(*parts[ip]); if (stk_auto) continue; - unsigned per = parts[ip]->primary_entity_rank(); + stk::mesh::EntityRank per = parts[ip]->primary_entity_rank(); if (per == m_eMesh.side_rank()) { @@ -1934,7 +1934,7 @@ numSubDimNeededEntities = 1; } - if (needed_entity_ranks[ineed_ent].first >= new_sub_entity_nodes.size()) + if (static_cast(needed_entity_ranks[ineed_ent].first) >= new_sub_entity_nodes.size()) { throw std::logic_error("Refiner::createNewNeededNodeIds logic err #1"); } @@ -2129,7 +2129,7 @@ if (side_auto_part) continue; - unsigned per = side_parts[isp]->primary_entity_rank(); + stk::mesh::EntityRank per = side_parts[isp]->primary_entity_rank(); if (per != side_rank_iter) continue; diff --git a/packages/percept/src/adapt/RefinerPattern_Pyr5_Het_N.hpp b/packages/percept/src/adapt/RefinerPattern_Pyr5_Het_N.hpp index 30d29b100caf..89ba192d8dd9 100644 --- a/packages/percept/src/adapt/RefinerPattern_Pyr5_Het_N.hpp +++ b/packages/percept/src/adapt/RefinerPattern_Pyr5_Het_N.hpp @@ -231,7 +231,7 @@ namespace percept { std::vector new_nodes; bool useAltNode = false; - if (new_sub_entity_nodes.size() > m_primaryEntityRank && new_sub_entity_nodes[m_primaryEntityRank].size() && !new_sub_entity_nodes[m_primaryEntityRank][0].size()) + if (new_sub_entity_nodes.size() > static_cast(m_primaryEntityRank) && new_sub_entity_nodes[m_primaryEntityRank].size() && !new_sub_entity_nodes[m_primaryEntityRank][0].size()) { //throw std::runtime_error("no centroid node available"); // std::cout << " bad element: " << std::endl; @@ -527,7 +527,7 @@ namespace percept { std::vector new_nodes; bool useAltNode = false; - if (new_sub_entity_nodes.size() > m_primaryEntityRank && new_sub_entity_nodes[m_primaryEntityRank].size() && !new_sub_entity_nodes[m_primaryEntityRank][0].size()) + if (new_sub_entity_nodes.size() > static_cast(m_primaryEntityRank) && new_sub_entity_nodes[m_primaryEntityRank].size() && !new_sub_entity_nodes[m_primaryEntityRank][0].size()) { //throw std::runtime_error("no centroid node availabled"); // std::cout << " bad element: " << std::endl; diff --git a/packages/percept/src/adapt/RefinerPattern_Tet4_Tet4_N.hpp b/packages/percept/src/adapt/RefinerPattern_Tet4_Tet4_N.hpp index 2f6c461e4fd4..86b8102d4365 100644 --- a/packages/percept/src/adapt/RefinerPattern_Tet4_Tet4_N.hpp +++ b/packages/percept/src/adapt/RefinerPattern_Tet4_Tet4_N.hpp @@ -13,7 +13,7 @@ //#include "UniformRefinerPattern.hpp" #include #include - +#include #include #include @@ -226,7 +226,7 @@ // general case (now includes uniform refinement (all edges marked)) else { - double * node_coords[4]; + std::array node_coords; for (int inode=0; inode < 4; inode++) { node_coords[inode] = stk::mesh::field_data( *eMesh.get_coordinates_field() , tet_elem_nodes[inode] ); @@ -236,14 +236,15 @@ << node_coords[inode][2] << std::endl; } + const std::array node_rank = get_rank_of_nodes_based_on_coordinates(node_coords); std::vector new_tets; bool choose_best_tets = true; moab::SimplexTemplateRefiner str(choose_best_tets); str.refine_3_simplex(new_tets, edge_marks, 1, - node_coords[0], 0, eMesh.identifier(tet_elem_nodes[0]), - node_coords[1], 0, eMesh.identifier(tet_elem_nodes[1]), - node_coords[2], 0, eMesh.identifier(tet_elem_nodes[2]), - node_coords[3], 0, eMesh.identifier(tet_elem_nodes[3]) ); + node_coords[0], 0, node_rank[0], + node_coords[1], 0, node_rank[1], + node_coords[2], 0, node_rank[2], + node_coords[3], 0, node_rank[3] ); if (0) { diff --git a/packages/percept/src/adapt/RefinerUtil.cpp b/packages/percept/src/adapt/RefinerUtil.cpp index a7bb98c87c9b..7234b9e19550 100644 --- a/packages/percept/src/adapt/RefinerUtil.cpp +++ b/packages/percept/src/adapt/RefinerUtil.cpp @@ -364,7 +364,7 @@ namespace percept { } // change so all -block get removed and replaced with + only - for (unsigned irank=eMesh.side_rank(); irank <= eMesh.element_rank(); irank++) + for (stk::mesh::EntityRank irank=eMesh.side_rank(); irank <= eMesh.element_rank(); irank++) { bool found_minus = false, found_plus = false; for (unsigned ib=0; ib < blocks[irank].size(); ++ib) diff --git a/packages/percept/src/adapt/SerializeNodeRegistry.hpp b/packages/percept/src/adapt/SerializeNodeRegistry.hpp index 02e7b260030d..c0d830183702 100644 --- a/packages/percept/src/adapt/SerializeNodeRegistry.hpp +++ b/packages/percept/src/adapt/SerializeNodeRegistry.hpp @@ -1520,14 +1520,14 @@ SubDimCellToDataMap& map = nodeRegistry.getMap(); //std::cout << msg << " tmp serialize_write map size: " << map.size() << std::endl; - if (0) emitter << YAML::Anchor("NodeRegistry::map"); YAML_ERRCHECK; + //if (0) emitter << YAML::Anchor("NodeRegistry::map"); YAML_ERRCHECK; //emitter << YAML::Flow; YAML_ERRCHECK; emitter << YAML::BeginMap; YAML_ERRCHECK; // key.serialized = { nodeid_0,... : set } // value.serialized = { {new_nid0, new_nid1,...}:vector, {elem_own[rank, ele_id]:EntityKey} } - int jj=0; + //int jj=0; for (iter = map.begin(); iter != map.end(); ++iter) { const SubDimCell_SDCEntityType& subDimEntity = (*iter).first; @@ -1560,7 +1560,7 @@ emitter << YAML::Key; YAML_ERRCHECK; emitter << YAML::Flow; YAML_ERRCHECK; emitter << YAML::BeginSeq; YAML_ERRCHECK; - if (0) emitter << YAML::Anchor(std::string("seq")+std::to_string(jj++)); YAML_ERRCHECK; + //if (0) emitter << YAML::Anchor(std::string("seq")+std::to_string(jj++)); YAML_ERRCHECK; for (unsigned k=0; k < subDimEntity.size(); k++) { //std::cout << " " << subDimEntity[k]->identifier() << " "; diff --git a/packages/percept/src/adapt/TriangulateTri.hpp b/packages/percept/src/adapt/TriangulateTri.hpp index 801ac1ca4d24..a0162faf1b4e 100644 --- a/packages/percept/src/adapt/TriangulateTri.hpp +++ b/packages/percept/src/adapt/TriangulateTri.hpp @@ -11,6 +11,7 @@ #include #include +#include namespace percept { @@ -60,6 +61,13 @@ namespace percept { //const percept::MyPairIterRelation elem_nodes (m_eMesh, element,stk::topology::NODE_RANK); /NLM CoordinatesFieldType* coordField = eMesh.get_coordinates_field(); + std::array node_coords; + for (int i=0; i<3; ++i) + { + node_coords[i] = stk::mesh::field_data( *coordField , elem_nodes[i] ); + } + const std::array node_rank = get_rank_of_nodes_based_on_coordinates( node_coords ); + unsigned num_edges_marked=0; for (int iedge = 0; iedge < 3; iedge++) { @@ -137,15 +145,20 @@ namespace percept { { stk::mesh::Entity node_0 = elem_nodes[cell_topo_data->edge[iedge].node[0]]; stk::mesh::Entity node_1 = elem_nodes[cell_topo_data->edge[iedge].node[1]]; + int rank_node_0 = node_rank[cell_topo_data->edge[iedge].node[0]]; + int rank_node_1 = node_rank[cell_topo_data->edge[iedge].node[1]]; //bool reverse = false; // ensure edge_len is computed identically, independent of edge orientation - if (eMesh.identifier(node_0) > eMesh.identifier(node_1)) + if (node_rank[cell_topo_data->edge[iedge].node[0]] > node_rank[cell_topo_data->edge[iedge].node[1]]) { //reverse = true; stk::mesh::Entity node_temp = node_0; node_0 = node_1; node_1 = node_temp; + const int rank_temp = rank_node_0; + rank_node_0 = rank_node_1; + rank_node_1 = rank_temp; } double * const coord_0 = stk::mesh::field_data( *coordField , node_0 ); @@ -160,16 +173,16 @@ namespace percept { if (edge_len_squared > max_edge_length) { - id_diff_0 = eMesh.identifier(node_0); - id_diff_1 = eMesh.identifier(node_1); + id_diff_0 = rank_node_0; + id_diff_1 = rank_node_1; max_edge_length = edge_len_squared; jedge_max_edge = iedge; } // intentional floating-point comparison (tie-break) else if (edge_len_squared == max_edge_length) { - unsigned loc_id_diff_0 = eMesh.identifier(node_0); - unsigned loc_id_diff_1 = eMesh.identifier(node_1); + unsigned loc_id_diff_0 = rank_node_0; + unsigned loc_id_diff_1 = rank_node_1; bool lexical_less = false; if (loc_id_diff_0 < id_diff_0) { diff --git a/packages/percept/src/adapt/UniformRefinerPattern_Line2_Line2_2_sierra.hpp b/packages/percept/src/adapt/UniformRefinerPattern_Line2_Line2_2_sierra.hpp index 9796bb948fdb..20f656f52982 100644 --- a/packages/percept/src/adapt/UniformRefinerPattern_Line2_Line2_2_sierra.hpp +++ b/packages/percept/src/adapt/UniformRefinerPattern_Line2_Line2_2_sierra.hpp @@ -144,14 +144,14 @@ create_side_element(eMesh, use_declare_element_side, nodes, 2, newElement); stk::mesh::FieldBase * proc_rank_field_edge = m_eMesh.get_field(stk::topology::EDGE_RANK, "proc_rank_edge"); - if (proc_rank_field_edge && proc_rank_field_edge->field_array_rank() != m_eMesh.edge_rank()) + if (proc_rank_field_edge && proc_rank_field_edge->field_array_rank() != static_cast(m_eMesh.edge_rank())) { if (0) std::cout << "P[" << m_eMesh.get_rank() << "] tmp newElement.entity_rank = " << m_eMesh.entity_rank(newElement) << " proc_rank_field_edge->rank() = " << proc_rank_field_edge->field_array_rank() << " m_eMesh.edge_rank() = " << m_eMesh.edge_rank() << std::endl; } - else if (proc_rank_field_edge && proc_rank_field_edge->field_array_rank() == m_eMesh.edge_rank()) + else if (proc_rank_field_edge && proc_rank_field_edge->field_array_rank() == static_cast(m_eMesh.edge_rank())) { double *fdata =stk::mesh::field_data( *static_cast(proc_rank_field_edge) , newElement ); fdata[0] = double(eMesh.owner_rank(newElement)); diff --git a/packages/percept/src/adapt/UniformRefinerPattern_Tet4_Tet4_8_sierra.hpp b/packages/percept/src/adapt/UniformRefinerPattern_Tet4_Tet4_8_sierra.hpp index b1ed08796fb2..669a63c5ba01 100644 --- a/packages/percept/src/adapt/UniformRefinerPattern_Tet4_Tet4_8_sierra.hpp +++ b/packages/percept/src/adapt/UniformRefinerPattern_Tet4_Tet4_8_sierra.hpp @@ -13,7 +13,7 @@ //#include "UniformRefinerPattern.hpp" #include #include - +#include #include #define USE_FACE_BREAKER_T4_T4_8 1 @@ -114,7 +114,7 @@ // uniform refinement tets.resize(8); - double * node_coords[4]; + std::array node_coords; for (int inode=0; inode < 4; inode++) { node_coords[inode] = stk::mesh::field_data( *eMesh.get_coordinates_field() , tet_elem_nodes[inode] ); @@ -124,14 +124,15 @@ << node_coords[inode][2] << std::endl; } + const std::array node_rank = get_rank_of_nodes_based_on_coordinates(node_coords); std::vector new_tets; bool choose_best_tets = true; moab::SimplexTemplateRefiner str(choose_best_tets); str.refine_3_simplex(new_tets, edge_marks, 1, - node_coords[0], 0, eMesh.identifier(tet_elem_nodes[0]), - node_coords[1], 0, eMesh.identifier(tet_elem_nodes[1]), - node_coords[2], 0, eMesh.identifier(tet_elem_nodes[2]), - node_coords[3], 0, eMesh.identifier(tet_elem_nodes[3]) ); + node_coords[0], 0, node_rank[0], + node_coords[1], 0, node_rank[1], + node_coords[2], 0, node_rank[2], + node_coords[3], 0, node_rank[3] ); if (0) { diff --git a/packages/percept/src/percept/PerceptMesh.cpp b/packages/percept/src/percept/PerceptMesh.cpp index b1af440fd263..8ca87124d473 100644 --- a/packages/percept/src/percept/PerceptMesh.cpp +++ b/packages/percept/src/percept/PerceptMesh.cpp @@ -5490,11 +5490,11 @@ { bool stk_auto= stk::mesh::is_auto_declared_part(*parts[ip]); if (stk_auto) continue; - unsigned per = parts[ip]->primary_entity_rank(); + stk::mesh::EntityRank per = parts[ip]->primary_entity_rank(); if (per == element_rank()) { const CellTopologyData *const topology = this->get_cell_topology(*parts[ip]); - if (!topology || topology->dimension != per) + if (!topology || topology->dimension != static_cast(per)) { std::cout << "Warning: PerceptMesh::get_skin_part: skipping part with dimension < element_rank, part name= " << parts[ip]->name() << std::endl; continue; @@ -6158,7 +6158,7 @@ if (!data_traits.is_floating_point) continue; - unsigned field_rank = field->entity_rank(); + stk::mesh::EntityRank field_rank = field->entity_rank(); if (field_rank == stk::topology::NODE_RANK) { continue; diff --git a/packages/percept/src/percept/PerceptUtils.cpp b/packages/percept/src/percept/PerceptUtils.cpp index 253838155f59..20dab1ffee85 100644 --- a/packages/percept/src/percept/PerceptUtils.cpp +++ b/packages/percept/src/percept/PerceptUtils.cpp @@ -189,7 +189,9 @@ void convert_stk_topology_to_ioss_name( const stk::topology stk_topo, std::string& ioss_topo) { - if (stk_topo == stk::topology::LINE_2) + if (stk_topo == stk::topology::NODE) + ioss_topo = "sphere"; + else if (stk_topo == stk::topology::LINE_2) ioss_topo = "edge2"; else if (stk_topo == stk::topology::LINE_3) ioss_topo = "edge3"; diff --git a/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.cpp b/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.cpp index 3f926f90fc9a..47f218988c76 100644 --- a/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.cpp +++ b/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.cpp @@ -78,7 +78,7 @@ namespace percept { } bool get_beam_from_ids(const stk::mesh::BulkData *mesh, - std::vector edge_node_ids, stk::mesh::Entity &beam) + const std::vector& edge_node_ids, stk::mesh::Entity &beam) { std::vector edgeNodes(edge_node_ids.size()); @@ -116,7 +116,7 @@ namespace percept { } bool get_shell_from_ids(const stk::mesh::BulkData *mesh, - std::vector face_node_ids, stk::mesh::Entity &shell) + const std::vector& face_node_ids, stk::mesh::Entity &shell) { std::vector faceNodes(face_node_ids.size()); diff --git a/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.hpp b/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.hpp index 122753458e71..edef8442c18c 100644 --- a/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.hpp +++ b/packages/percept/src/percept/mesh/geometry/kernel/GeometryKernelPGEOM.hpp @@ -27,14 +27,14 @@ bool get_node_from_id(const stk::mesh::BulkData *mesh, int node_id, stk::mesh::Entity &node); bool get_beam_from_ids(const stk::mesh::BulkData *mesh, - std::vector edge_node_ids, stk::mesh::Entity &edge); + const std::vector& edge_node_ids, stk::mesh::Entity &edge); bool get_shell_from_ids(const stk::mesh::BulkData *mesh, - std::vector face_node_ids, stk::mesh::Entity &quad); + const std::vector& face_node_ids, stk::mesh::Entity &quad); // UNUSED FUNCTION WILL PROBABLY DISCARD bool get_shell_from_ids_LIBERAL(const stk::mesh::BulkData *mesh, - std::vector face_node_ids, stk::mesh::Entity &shell); + const std::vector& face_node_ids, stk::mesh::Entity &shell); bool get_hex_from_id(const stk::mesh::BulkData *mesh, int hex_id, stk::mesh::Entity &hex); diff --git a/packages/percept/src/percept/mesh/geometry/stk_geom/3D/FitGregoryPatchesPBGL.cpp b/packages/percept/src/percept/mesh/geometry/stk_geom/3D/FitGregoryPatchesPBGL.cpp index 0f1259e9252a..68b78564a12f 100644 --- a/packages/percept/src/percept/mesh/geometry/stk_geom/3D/FitGregoryPatchesPBGL.cpp +++ b/packages/percept/src/percept/mesh/geometry/stk_geom/3D/FitGregoryPatchesPBGL.cpp @@ -39,23 +39,12 @@ #endif // __INTEL_COMPILER #include -#include -#include #include #include #include -#include #include #include -#include -#include #include -#include - -#include -#include - -#include #include #if (BOOST_VERSION / 100 % 1000) > 55 diff --git a/packages/percept/src/percept/norm/H1Norm.hpp b/packages/percept/src/percept/norm/H1Norm.hpp index 19a2d58291bb..fd7656722bf2 100644 --- a/packages/percept/src/percept/norm/H1Norm.hpp +++ b/packages/percept/src/percept/norm/H1Norm.hpp @@ -151,7 +151,9 @@ //std::cout << "type= " << typeid(integrand).name() << " " << typeid(FieldFunction).name() << std::endl; if (typeid(integrand) == typeid(FieldFunction)) + { VERIFY_OP_ON(m_turboOpt, !=, TURBO_NONE, "Can't use TURBO_NONE with Norm of FieldFunction"); + } { // FIXME - make all percept code const-correct From 48770fec0596930b137559801c55f897a6b47997 Mon Sep 17 00:00:00 2001 From: Alejandro Mota Date: Tue, 19 Oct 2021 19:30:29 -0700 Subject: [PATCH 50/98] Changes to fix errors in LCM --- .../src/MiniTensor_LinearAlgebra.i.h | 32 ++++++++----------- packages/minitensor/src/MiniTensor_Tensor.i.h | 19 +++-------- .../minitensor/src/MiniTensor_Utilities.h | 12 +++++-- .../minitensor/src/MiniTensor_Utilities.i.h | 24 +++++++++----- packages/minitensor/src/MiniTensor_Vector.i.h | 8 ++--- 5 files changed, 48 insertions(+), 47 deletions(-) diff --git a/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h b/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h index 92e4aa540653..9b57ef699f94 100644 --- a/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h +++ b/packages/minitensor/src/MiniTensor_LinearAlgebra.i.h @@ -96,8 +96,6 @@ KOKKOS_INLINE_FUNCTION T norm_1(Tensor const & A) { - using KAT = Kokkos::ArithTraits; - Index const dimension = A.get_dimension(); @@ -114,7 +112,7 @@ norm_1(Tensor const & A) for (Index i = 0; i < dimension; ++i) { T t = 0.0; for (Index j = 0; j < dimension; ++j) { - t += KAT::abs(A(j, i)); + t += minitensor::abs(A(j, i)); } v(i) = t; } @@ -125,22 +123,22 @@ norm_1(Tensor const & A) break; case 3: - v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(1, 0)) + KAT::abs(A(2, 0)); - v(1) = KAT::abs(A(0, 1)) + KAT::abs(A(1, 1)) + KAT::abs(A(2, 1)); - v(2) = KAT::abs(A(0, 2)) + KAT::abs(A(1, 2)) + KAT::abs(A(2, 2)); + v(0) = minitensor::abs(A(0, 0)) + minitensor::abs(A(1, 0)) + minitensor::abs(A(2, 0)); + v(1) = minitensor::abs(A(0, 1)) + minitensor::abs(A(1, 1)) + minitensor::abs(A(2, 1)); + v(2) = minitensor::abs(A(0, 2)) + minitensor::abs(A(1, 2)) + minitensor::abs(A(2, 2)); s = max(max(v(0), v(1)), v(2)); break; case 2: - v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(1, 0)); - v(1) = KAT::abs(A(0, 1)) + KAT::abs(A(1, 1)); + v(0) = minitensor::abs(A(0, 0)) + minitensor::abs(A(1, 0)); + v(1) = minitensor::abs(A(0, 1)) + minitensor::abs(A(1, 1)); s = max(v(0), v(1)); break; case 1: - s = KAT::abs(A(0, 0)); + s = minitensor::abs(A(0, 0)); break; } @@ -156,8 +154,6 @@ KOKKOS_INLINE_FUNCTION T norm_infinity(Tensor const & A) { - using KAT = Kokkos::ArithTraits; - Index const dimension = A.get_dimension(); @@ -172,7 +168,7 @@ norm_infinity(Tensor const & A) for (Index i = 0; i < dimension; ++i) { T t = 0.0; for (Index j = 0; j < dimension; ++j) { - t += KAT::abs(A(i, j)); + t += minitensor::abs(A(i, j)); } v(i) = t; } @@ -183,22 +179,22 @@ norm_infinity(Tensor const & A) break; case 3: - v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(0, 1)) + KAT::abs(A(0, 2)); - v(1) = KAT::abs(A(1, 0)) + KAT::abs(A(1, 1)) + KAT::abs(A(1, 2)); - v(2) = KAT::abs(A(2, 0)) + KAT::abs(A(2, 1)) + KAT::abs(A(2, 2)); + v(0) = minitensor::abs(A(0, 0)) + minitensor::abs(A(0, 1)) + minitensor::abs(A(0, 2)); + v(1) = minitensor::abs(A(1, 0)) + minitensor::abs(A(1, 1)) + minitensor::abs(A(1, 2)); + v(2) = minitensor::abs(A(2, 0)) + minitensor::abs(A(2, 1)) + minitensor::abs(A(2, 2)); s = max(max(v(0), v(1)), v(2)); break; case 2: - v(0) = KAT::abs(A(0, 0)) + KAT::abs(A(0, 1)); - v(1) = KAT::abs(A(1, 0)) + KAT::abs(A(1, 1)); + v(0) = minitensor::abs(A(0, 0)) + minitensor::abs(A(0, 1)); + v(1) = minitensor::abs(A(1, 0)) + minitensor::abs(A(1, 1)); s = max(v(0), v(1)); break; case 1: - s = KAT::abs(A(0, 0)); + s = minitensor::abs(A(0, 0)); break; } diff --git a/packages/minitensor/src/MiniTensor_Tensor.i.h b/packages/minitensor/src/MiniTensor_Tensor.i.h index 97e07d3aa085..7bde2f3b1302 100644 --- a/packages/minitensor/src/MiniTensor_Tensor.i.h +++ b/packages/minitensor/src/MiniTensor_Tensor.i.h @@ -1646,32 +1646,23 @@ transpose(Tensor const & A) Tensor B = A; - auto my_swap = [&](T &a, T &b) { - T c = a; - a = b; - b = c; - }; - switch (dimension) { default: for (Index i = 0; i < dimension; ++i) { for (Index j = i + 1; j < dimension; ++j) { - my_swap(B(i, j), B(j, i)); + minitensor::swap(B(i, j), B(j, i)); } } break; case 3: - my_swap(B(0, 1), B(1, 0)); - my_swap(B(0, 2), B(2, 0)); - - my_swap(B(1, 2), B(2, 1)); - + minitensor::swap(B(0, 1), B(1, 0)); + minitensor::swap(B(0, 2), B(2, 0)); + minitensor::swap(B(1, 2), B(2, 1)); break; case 2: - my_swap(B(0, 1), B(1, 0)); - + minitensor::swap(B(0, 1), B(1, 0)); break; } diff --git a/packages/minitensor/src/MiniTensor_Utilities.h b/packages/minitensor/src/MiniTensor_Utilities.h index 7e149ba65a5f..2e6091fee574 100644 --- a/packages/minitensor/src/MiniTensor_Utilities.h +++ b/packages/minitensor/src/MiniTensor_Utilities.h @@ -49,6 +49,14 @@ namespace minitensor { +// +// abs function +// +template +KOKKOS_INLINE_FUNCTION +T +abs(T const & a); + // //swap function // @@ -63,7 +71,7 @@ swap(T & a, T & b); template KOKKOS_INLINE_FUNCTION T -max(const T & a,const T & b); +max(T const & a, T const & b); // // max function @@ -71,7 +79,7 @@ max(const T & a,const T & b); template KOKKOS_INLINE_FUNCTION T -min(const T & a,const T & b); +min(T const & a,T const & b); /// /// Sign function diff --git a/packages/minitensor/src/MiniTensor_Utilities.i.h b/packages/minitensor/src/MiniTensor_Utilities.i.h index dbdbedfe86b3..9e19785e7a5c 100644 --- a/packages/minitensor/src/MiniTensor_Utilities.i.h +++ b/packages/minitensor/src/MiniTensor_Utilities.i.h @@ -50,6 +50,17 @@ namespace minitensor { +// +// +// +template +KOKKOS_INLINE_FUNCTION +T +abs(T const & a) +{ + return a < T(0) ? -a : a; +} + // // // @@ -61,12 +72,9 @@ swap(T & a, T & b) // Guard against the same memory location. if (&a == &b) return; - // XOR algorithm - a ^= b; - b ^= a; - a ^= b; - - return; + auto const c = a; + a = b; + b = c; } // @@ -75,7 +83,7 @@ swap(T & a, T & b) template KOKKOS_INLINE_FUNCTION T -max(const T & a, const T & b) +max(T const & a, T const & b) { return a > b ? a : b; } @@ -86,7 +94,7 @@ max(const T & a, const T & b) template KOKKOS_INLINE_FUNCTION T -min(const T & a, const T & b) +min(T const & a, T const & b) { return a < b ? a : b; } diff --git a/packages/minitensor/src/MiniTensor_Vector.i.h b/packages/minitensor/src/MiniTensor_Vector.i.h index ebe5e5545272..6c0ebfac6536 100644 --- a/packages/minitensor/src/MiniTensor_Vector.i.h +++ b/packages/minitensor/src/MiniTensor_Vector.i.h @@ -803,8 +803,6 @@ KOKKOS_INLINE_FUNCTION T norm_infinity(Vector const & u) { - using KAT = Kokkos::ArithTraits; - Index const dimension = u.get_dimension(); @@ -815,16 +813,16 @@ norm_infinity(Vector const & u) default: for (Index i = 0; i < dimension; ++i) { - s = max(KAT::abs(u(i)), s); + s = max(minitensor::abs(u(i)), s); } break; case 3: - s = max(max(KAT::abs(u(0)), KAT::abs(u(1))), KAT::abs(u(2))); + s = max(max(minitensor::abs(u(0)), minitensor::abs(u(1))), minitensor::abs(u(2))); break; case 2: - s = max(KAT::abs(u(0)), KAT::abs(u(1))); + s = max(minitensor::abs(u(0)), minitensor::abs(u(1))); break; } From 186a40ba6549ff196909ef8d069342ffb13a8f65 Mon Sep 17 00:00:00 2001 From: drnobleabq <44879870+drnobleabq@users.noreply.github.com> Date: Wed, 20 Oct 2021 13:22:30 -0600 Subject: [PATCH 51/98] First krino commit (#9825) * First krino commit * Floating point comparison fix and clang cleanup --- PackagesList.cmake | 1 + packages/krino/CMakeLists.txt | 13 + packages/krino/LICENSE | 30 + packages/krino/cmake/Dependencies.cmake | 8 + .../build_sierra_krino_as_Trilinos_package.sh | 108 + .../krino/cmake_install_test/load_gcc_modules | 13 + .../krino/cmake_install_test/run_cmake_krino | 52 + .../Akri_DeleteSmallElementsMain.cpp | 187 + .../delete_small_elements/CMakeLists.txt | 12 + packages/krino/krino/Apps_krino.cpp | 47 + packages/krino/krino/CMakeLists.txt | 17 + .../Akri_AdaptivityInterface.cpp | 679 +++ .../Akri_AdaptivityInterface.hpp | 36 + .../krino/adaptivity_interface/CMakeLists.txt | 19 + .../Akri_InterfaceGeometry.hpp | 79 + .../Akri_InterfaceGeometry_dummy.cpp | 3 + .../CMakeLists.txt | 18 + .../krino_lib/Akri_AdaptivityHelpers.cpp | 138 + .../krino_lib/Akri_AdaptivityHelpers.hpp | 41 + .../krino/krino_lib/Akri_AnalyticSurf.cpp | 323 ++ .../krino/krino_lib/Akri_AnalyticSurf.hpp | 186 + .../Akri_AnalyticSurfaceInterfaceGeometry.cpp | 203 + .../Akri_AnalyticSurfaceInterfaceGeometry.hpp | 111 + .../krino/krino_lib/Akri_AuxMetaData.cpp | 396 ++ .../krino/krino_lib/Akri_AuxMetaData.hpp | 180 + .../krino/krino_lib/Akri_BoundingBox.cpp | 214 + .../krino/krino_lib/Akri_BoundingBox.hpp | 212 + .../krino/krino_lib/Akri_BoundingBoxMesh.cpp | 697 ++++ .../krino/krino_lib/Akri_BoundingBoxMesh.hpp | 157 + .../krino_lib/Akri_CDFEM_Parent_Edge.cpp | 636 +++ .../krino_lib/Akri_CDFEM_Parent_Edge.hpp | 137 + .../krino_lib/Akri_CDFEM_Parent_Edges.cpp | 492 +++ .../krino_lib/Akri_CDFEM_Parent_Edges.hpp | 86 + .../krino/krino_lib/Akri_CDFEM_Snapper.hpp | 31 + .../krino/krino_lib/Akri_CDFEM_Support.cpp | 364 ++ .../krino/krino_lib/Akri_CDFEM_Support.hpp | 259 ++ .../krino/krino/krino_lib/Akri_CDMesh.cpp | 3689 +++++++++++++++++ .../krino/krino/krino_lib/Akri_CDMesh.hpp | 333 ++ .../krino/krino_lib/Akri_CDMesh_Debug.cpp | 229 + .../krino/krino_lib/Akri_CDMesh_Debug.hpp | 20 + .../krino_lib/Akri_CDMesh_Refinement.cpp | 367 ++ .../krino_lib/Akri_CDMesh_Refinement.hpp | 31 + .../krino/krino_lib/Akri_CDMesh_Utils.cpp | 143 + .../krino/krino_lib/Akri_CDMesh_Utils.hpp | 34 + .../krino_lib/Akri_Composite_Surface.cpp | 108 + .../krino_lib/Akri_Composite_Surface.hpp | 64 + .../Akri_Compute_Surface_Distance.cpp | 122 + .../Akri_Compute_Surface_Distance.hpp | 42 + .../krino/krino_lib/Akri_ContourElement.cpp | 556 +++ .../krino/krino_lib/Akri_ContourElement.hpp | 130 + .../krino_lib/Akri_ContourSubElement.cpp | 2565 ++++++++++++ .../krino_lib/Akri_ContourSubElement.hpp | 311 ++ .../krino/krino_lib/Akri_Cutting_Surface.cpp | 170 + .../krino/krino_lib/Akri_Cutting_Surface.hpp | 81 + .../Akri_DecompositionHasChanged.cpp | 302 ++ .../Akri_DecompositionHasChanged.hpp | 25 + .../krino/krino/krino_lib/Akri_DiagWriter.cpp | 54 + .../krino/krino/krino_lib/Akri_DiagWriter.hpp | 63 + .../krino/krino_lib/Akri_DiagWriter_fwd.hpp | 37 + .../krino/krino_lib/Akri_DistanceSweeper.cpp | 177 + .../krino/krino_lib/Akri_DistanceSweeper.hpp | 22 + .../krino/krino/krino_lib/Akri_Element.cpp | 1077 +++++ .../krino/krino/krino_lib/Akri_Element.hpp | 207 + .../krino_lib/Akri_ElementCutterUtils.cpp | 184 + .../krino_lib/Akri_ElementCutterUtils.hpp | 37 + .../krino/krino_lib/Akri_Element_Cutter.cpp | 1064 +++++ .../krino/krino_lib/Akri_Element_Cutter.hpp | 132 + .../krino_lib/Akri_Element_Intersections.cpp | 28 + .../krino_lib/Akri_Element_Intersections.hpp | 34 + .../krino/krino_lib/Akri_EntityIdPool.cpp | 92 + .../krino/krino_lib/Akri_EntityIdPool.hpp | 39 + packages/krino/krino/krino_lib/Akri_Facet.cpp | 197 + packages/krino/krino/krino_lib/Akri_Facet.hpp | 158 + .../krino/krino_lib/Akri_Faceted_Surface.cpp | 494 +++ .../krino/krino_lib/Akri_Faceted_Surface.hpp | 69 + .../krino/krino_lib/Akri_Fast_Marching.cpp | 726 ++++ .../krino/krino_lib/Akri_Fast_Marching.hpp | 104 + .../krino/krino/krino_lib/Akri_FieldRef.cpp | 54 + .../krino/krino/krino_lib/Akri_FieldRef.hpp | 168 + .../krino/krino/krino_lib/Akri_IC_Alg.cpp | 225 + .../krino/krino/krino_lib/Akri_IC_Alg.hpp | 55 + .../krino/krino_lib/Akri_IC_Calculator.cpp | 100 + .../krino/krino_lib/Akri_IC_Calculator.hpp | 53 + .../krino/krino/krino_lib/Akri_IO_Helpers.cpp | 101 + .../krino/krino/krino_lib/Akri_IO_Helpers.hpp | 66 + .../krino/krino_lib/Akri_InterfaceID.hpp | 98 + .../Akri_Interface_Name_Generator.hpp | 71 + .../krino_lib/Akri_Intersection_Points.cpp | 267 ++ .../krino_lib/Akri_Intersection_Points.hpp | 75 + .../krino/krino/krino_lib/Akri_LevelSet.cpp | 1822 ++++++++ .../krino/krino/krino_lib/Akri_LevelSet.hpp | 339 ++ .../Akri_LevelSetInterfaceGeometry.cpp | 931 +++++ .../Akri_LevelSetInterfaceGeometry.hpp | 122 + .../krino_lib/Akri_LevelSet_Identifier.hpp | 37 + .../krino/krino_lib/Akri_LowerEnvelope.cpp | 317 ++ .../krino/krino_lib/Akri_LowerEnvelope.hpp | 120 + .../Akri_MasterElementDeterminer.cpp | 105 + .../Akri_MasterElementDeterminer.hpp | 30 + .../krino/krino/krino_lib/Akri_MathUtil.cpp | 233 ++ .../krino/krino/krino_lib/Akri_MathUtil.hpp | 35 + .../krino/krino/krino_lib/Akri_MeshClone.cpp | 629 +++ .../krino/krino/krino_lib/Akri_MeshClone.hpp | 67 + .../krino/krino_lib/Akri_MeshDiagnostics.cpp | 70 + .../krino/krino_lib/Akri_MeshDiagnostics.hpp | 23 + .../krino/krino_lib/Akri_MeshHelpers.cpp | 2560 ++++++++++++ .../krino/krino_lib/Akri_MeshHelpers.hpp | 182 + .../krino/krino_lib/Akri_MeshInputOptions.cpp | 52 + .../krino/krino_lib/Akri_MeshInputOptions.hpp | 112 + .../krino/krino_lib/Akri_MeshSurface.cpp | 1019 +++++ .../krino/krino_lib/Akri_MeshSurface.hpp | 177 + .../krino/krino_lib/Akri_MortonIndex.hpp | 58 + .../krino_lib/Akri_NodeToCapturedDomains.cpp | 121 + .../krino_lib/Akri_NodeToCapturedDomains.hpp | 31 + .../krino/krino_lib/Akri_OrderedIdPair.hpp | 50 + .../krino_lib/Akri_ParallelCommHelpers.hpp | 77 + .../krino_lib/Akri_ParallelErrorMessage.cpp | 30 + .../krino_lib/Akri_ParallelErrorMessage.hpp | 43 + .../krino_lib/Akri_ParentsToChildMapper.cpp | 188 + .../krino_lib/Akri_ParentsToChildMapper.hpp | 78 + .../krino/krino/krino_lib/Akri_PhaseTag.cpp | 112 + .../krino/krino/krino_lib/Akri_PhaseTag.hpp | 171 + .../krino/krino_lib/Akri_Phase_Support.cpp | 961 +++++ .../krino/krino_lib/Akri_Phase_Support.hpp | 212 + packages/krino/krino/krino_lib/Akri_Plane.hpp | 20 + .../krino_lib/Akri_Plane_Intersections.cpp | 144 + .../krino_lib/Akri_Plane_Intersections.hpp | 31 + .../krino/krino_lib/Akri_ProlongationData.cpp | 659 +++ .../krino/krino_lib/Akri_ProlongationData.hpp | 139 + .../krino/krino_lib/Akri_QualityMetric.cpp | 127 + .../krino/krino_lib/Akri_QualityMetric.hpp | 76 + .../krino/krino_lib/Akri_RegionInterface.cpp | 15 + .../krino/krino_lib/Akri_RegionInterface.hpp | 65 + .../krino/krino_lib/Akri_ReportHandler.hpp | 21 + .../krino/krino/krino_lib/Akri_SearchTree.cpp | 257 ++ .../krino/krino/krino_lib/Akri_SearchTree.hpp | 119 + .../krino/krino/krino_lib/Akri_Segment.hpp | 83 + packages/krino/krino/krino_lib/Akri_Snap.cpp | 633 +++ packages/krino/krino/krino_lib/Akri_Snap.hpp | 35 + .../Akri_SnapIndependentSetFinder.hpp | 34 + .../krino/krino/krino_lib/Akri_SnapInfo.cpp | 71 + .../krino/krino/krino_lib/Akri_SnapInfo.hpp | 87 + .../krino/krino/krino_lib/Akri_SnapToNode.cpp | 59 + .../krino/krino/krino_lib/Akri_SnapToNode.hpp | 26 + .../krino/krino/krino_lib/Akri_SubElement.cpp | 2833 +++++++++++++ .../krino/krino/krino_lib/Akri_SubElement.hpp | 431 ++ .../Akri_SubElementChildNodeAncestry.cpp | 246 ++ .../Akri_SubElementChildNodeAncestry.hpp | 49 + .../krino_lib/Akri_SubElementNodeAncestry.cpp | 32 + .../krino_lib/Akri_SubElementNodeAncestry.hpp | 65 + .../krino/krino/krino_lib/Akri_Surface.cpp | 28 + .../krino/krino/krino_lib/Akri_Surface.hpp | 98 + .../krino/krino_lib/Akri_Transformation.cpp | 112 + .../krino/krino_lib/Akri_Transformation.hpp | 65 + .../krino/krino/krino_lib/Akri_Triangle.hpp | 169 + .../krino/krino/krino_lib/Akri_TypeDefs.hpp | 27 + .../krino/krino/krino_lib/Akri_Utility.hpp | 66 + packages/krino/krino/krino_lib/Akri_Vec.cpp | 38 + packages/krino/krino/krino_lib/Akri_Vec.hpp | 26 + packages/krino/krino/krino_lib/CMakeLists.txt | 19 + .../master_element/Akri_MasterElement.hpp | 21 + .../Akri_MasterElementBasis.hpp | 701 ++++ .../master_element/Akri_MasterElementCalc.cpp | 456 ++ .../master_element/Akri_MasterElementCalc.hpp | 122 + .../Akri_MasterElementHybrid.cpp | 181 + .../Akri_MasterElementHybrid.hpp | 137 + .../Akri_MasterElementIntrepid.cpp | 287 ++ .../Akri_MasterElementIntrepid.hpp | 135 + .../krino/krino/master_element/CMakeLists.txt | 19 + .../parser/Akri_CDFEM_Options_Parser.cpp | 139 + .../parser/Akri_CDFEM_Options_Parser.hpp | 21 + .../krino/krino/parser/Akri_IC_Parser.cpp | 457 ++ .../krino/krino/parser/Akri_IC_Parser.hpp | 21 + .../krino/parser/Akri_LevelSet_Parser.cpp | 167 + .../krino/parser/Akri_LevelSet_Parser.hpp | 21 + .../krino/parser/Akri_MeshInput_Parser.cpp | 181 + .../krino/parser/Akri_MeshInput_Parser.hpp | 22 + .../krino/krino/parser/Akri_Phase_Parser.cpp | 101 + .../krino/krino/parser/Akri_Phase_Parser.hpp | 22 + .../krino/krino/parser/Akri_Region_Parser.cpp | 84 + .../krino/krino/parser/Akri_Region_Parser.hpp | 21 + .../parser/Akri_ResultsOutput_Parser.cpp | 72 + .../parser/Akri_ResultsOutput_Parser.hpp | 21 + .../krino/parser/Akri_Simulation_Parser.cpp | 54 + .../krino/parser/Akri_Simulation_Parser.hpp | 20 + packages/krino/krino/parser/Akri_YAML.hpp | 48 + .../krino/krino/parser/Akri_YAML_Parser.cpp | 235 ++ .../krino/krino/parser/Akri_YAML_Parser.hpp | 60 + packages/krino/krino/parser/CMakeLists.txt | 19 + .../rebalance_utils/Akri_RebalanceUtils.cpp | 230 + .../rebalance_utils/Akri_RebalanceUtils.hpp | 46 + .../Akri_RebalanceUtils_Impl.cpp | 348 ++ .../Akri_RebalanceUtils_Impl.hpp | 44 + .../krino/rebalance_utils/CMakeLists.txt | 19 + packages/krino/krino/region/Akri_Region.cpp | 664 +++ packages/krino/krino/region/Akri_Region.hpp | 81 + 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.../unit_tests/Akri_Unit_LogRedirecter.cpp | 27 + .../unit_tests/Akri_Unit_LogRedirecter.hpp | 32 + .../unit_tests/Akri_Unit_LowerEnvelope.cpp | 260 ++ .../unit_tests/Akri_Unit_MeshHelpers.cpp | 278 ++ .../unit_tests/Akri_Unit_MeshHelpers.hpp | 24 + .../unit_tests/Akri_Unit_MortonIndex.cpp | 52 + .../Akri_Unit_ParallelErrorMessage.cpp | 42 + .../Akri_Unit_Part_Decomposition_Fixture.cpp | 197 + .../Akri_Unit_Part_Decomposition_Fixture.hpp | 75 + .../unit_tests/Akri_Unit_Phase_Support.cpp | 231 ++ .../unit_tests/Akri_Unit_RebalanceUtils.cpp | 446 ++ .../Akri_Unit_Single_Element_Fixtures.cpp | 136 + .../Akri_Unit_Single_Element_Fixtures.hpp | 79 + .../krino/krino/unit_tests/Akri_Unit_main.cpp | 32 + .../krino/krino/unit_tests/CMakeLists.txt | 14 + .../stk_emend/independent_set/CMakeLists.txt | 10 + .../independent_set/IndependentSetDummy.cpp | 3 + 231 files changed, 54507 insertions(+) create mode 100644 packages/krino/CMakeLists.txt create mode 100644 packages/krino/LICENSE create mode 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packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.cpp create mode 100644 packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.hpp create mode 100644 packages/krino/krino/unit_tests/Akri_Unit_main.cpp create mode 100644 packages/krino/krino/unit_tests/CMakeLists.txt create mode 100644 packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp diff --git a/PackagesList.cmake b/PackagesList.cmake index 4a44aafd4eb9..08dc43e67ae0 100644 --- a/PackagesList.cmake +++ b/PackagesList.cmake @@ -112,6 +112,7 @@ TRIBITS_REPOSITORY_DEFINE_PACKAGES( Compadre packages/compadre ST STK packages/stk PT # Depends on boost Percept packages/percept PT # Depends on boost + Krino packages/krino PT # Depends on boost SCORECapf_zoltan SCOREC/zoltan ST SCORECapf_stk SCOREC/stk ST SCORECma SCOREC/ma ST diff --git a/packages/krino/CMakeLists.txt b/packages/krino/CMakeLists.txt new file mode 100644 index 000000000000..2f2c2ab9c734 --- /dev/null +++ b/packages/krino/CMakeLists.txt @@ -0,0 +1,13 @@ + +message("Building Krino as a Trilinos package") +TRIBITS_PACKAGE(Krino) + +TRIBITS_ADD_DEBUG_OPTION() +TRIBITS_ADD_SHOW_DEPRECATED_WARNINGS_OPTION() + +if (${Trilinos_ENABLE_Krino}) + add_subdirectory(krino) + add_subdirectory(delete_small_elements) +endif() + +TRIBITS_PACKAGE_POSTPROCESS() diff --git a/packages/krino/LICENSE b/packages/krino/LICENSE new file mode 100644 index 000000000000..33d63e2fe002 --- /dev/null +++ b/packages/krino/LICENSE @@ -0,0 +1,30 @@ +Copyright 2002 - 2008, 2010, 2011 National Technology & Engineering +Solutions of Sandia, LLC (NTESS). + +Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government +retains certain rights in this software. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software without + specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/krino/cmake/Dependencies.cmake b/packages/krino/cmake/Dependencies.cmake new file mode 100644 index 000000000000..76d77c60821f --- /dev/null +++ b/packages/krino/cmake/Dependencies.cmake @@ -0,0 +1,8 @@ +SET(LIB_REQUIRED_DEP_PACKAGES SEACASIoss SEACASExodus STKBalance STKMath STKIO STKSearch STKTopology STKUtil STKTools STKEmend Percept Intrepid) +SET(LIB_OPTIONAL_DEP_PACKAGES) +SET(TEST_REQUIRED_DEP_PACKAGES Gtest STKUnit_test_utils) +SET(TEST_OPTIONAL_DEP_PACKAGES) +SET(LIB_REQUIRED_DEP_TPLS Boost) +SET(LIB_OPTIONAL_DEP_TPLS MPI yaml-cpp) +SET(TEST_REQUIRED_DEP_TPLS) +SET(TEST_OPTIONAL_DEP_TPLS) diff --git a/packages/krino/cmake_install_test/build_sierra_krino_as_Trilinos_package.sh b/packages/krino/cmake_install_test/build_sierra_krino_as_Trilinos_package.sh new file mode 100755 index 000000000000..650cc502eca4 --- /dev/null +++ b/packages/krino/cmake_install_test/build_sierra_krino_as_Trilinos_package.sh @@ -0,0 +1,108 @@ +#!/bin/sh + +function execute() { + stdbuf -o0 -e0 echo "% $@" ; + eval "$@" ; + if [ $? -ne 0 ] ; then + echo "'$@' failed."; + exit 1; + fi +} + +function cd_to_new_dir() +{ + execute rm -rf $1 + execute mkdir $1 + execute cd $1 +} + +function exit_with_message() +{ + echo $1 + exit 1 +} + +function make_and_install() +{ + make -j 16 || exit_with_message "Failed building $1" + make install || exit_with_message "Failed installing $1" +} + +function build_yaml() +{ + productName=yaml + + cd_to_new_dir ${output_dir}/${productName} + execute tar -xzf ${sierra_proj}/TPLs_src/spack/spack_tpls/yaml-cpp/*.tar.gz + cd_to_new_dir ${productName}_build + + export CC=gcc + export CXX=g++ + execute cmake -DCMAKE_BUILD_TYPE=${build_type^^} -DYAML_CPP_BUILD_TESTS=false -DCMAKE_INSTALL_PREFIX=../${productName}_install ../yaml-cpp + make_and_install $productName + unset CC + unset CXX +} + +function build_trilinos_with_krino() +{ + productName=trilinos + + trilinos_dir=${output_dir}/${productName} + if [ ! -d ${trilinos_dir} ] ; then + execute mkdir ${trilinos_dir} + fi + execute cd ${trilinos_dir} + + if [ ! -d Trilinos ] ; then + execute git clone -b develop https://github.com/trilinos/Trilinos.git Trilinos + #else + #execute cd Trilinos + #execute git checkout develop + #execute git reset --hard origin/develop + #execute git pull + #execute cd .. + fi + + if [ -d Trilinos/packages/krino ] ; then + execute rm -rf Trilinos/packages/krino; + fi + if [ ! -L Trilinos/packages/krino ] ; then + execute ln -s ${sierra_proj}/krino Trilinos/packages + fi + + rm -rf ${productName}_install + cd_to_new_dir ${productName}_build + + export TRILINOS_INSTALL_DIR=../${productName}_install + $sierra_proj/krino/cmake_install_test/run_cmake_krino + make_and_install $productName +} + +function runTests() +{ + cd $1 + ctest -j 16 || exit_with_message "$2 tests failed" + cd ../.. +} + +sierra_proj=${SIERRA_PROJ:-${PWD}} +output_dir=${OUTPUT_DIR:-${PWD}/../krino-cmake-testing} + +cuda_on_or_off=${CUDA:-OFF} +build_type=${CMAKE_BUILD_TYPE:-release} +date_suffix=`date +%F_%H-%M-%S` + +source $sierra_proj/krino/cmake_install_test/load_gcc_modules + +if [ ! -d ${output_dir} ] ; then + execute mkdir ${output_dir} +fi + +build_yaml +build_trilinos_with_krino + +#runTests morph/morph_build "Morph" +#runTests morph_and_sgm/morph_and_sgm_build "Morph and SGM" +#runTests morphWithExe/morphWithExe_build "MorphWithExe" + diff --git a/packages/krino/cmake_install_test/load_gcc_modules b/packages/krino/cmake_install_test/load_gcc_modules new file mode 100644 index 000000000000..7b57261e312e --- /dev/null +++ b/packages/krino/cmake_install_test/load_gcc_modules @@ -0,0 +1,13 @@ +#!/bin/bash + +module load cde/v2/cmake/3.19.2 +module load cde/v2/compiler/gcc/7.2.0 +module load cde/v2/gcc/7.2.0/openmpi/4.0.5 +module load cde/v2/gcc/7.2.0/netlib-lapack/3.8.0 +module load cde/v2/gcc/7.2.0/boost/1.73.0 +module load cde/v2/gcc/7.2.0/hdf5/1.10.6 +module load cde/v2/gcc/7.2.0/netcdf-c/4.7.3 +module load cde/v2/gcc/7.2.0/parallel-netcdf/1.12.1 +module load cde/v2/gcc/7.2.0/metis/5.1.0 +module load cde/v2/gcc/7.2.0/parmetis/4.0.3 + diff --git a/packages/krino/cmake_install_test/run_cmake_krino b/packages/krino/cmake_install_test/run_cmake_krino new file mode 100755 index 000000000000..9f052313e1f0 --- /dev/null +++ b/packages/krino/cmake_install_test/run_cmake_krino @@ -0,0 +1,52 @@ +#!/bin/bash + +trilinos_src_dir=${TRILINOS_DIR:-${PWD}/../Trilinos} +build_dir=${BUILD_DIR:-${PWD}} +build_type=${CMAKE_BUILD_TYPE:-release} +trilinos_install_dir=${TRILINOS_INSTALL_DIR:-${PWD}/../trilinos_install_dir} + +yaml_install_dir=${YAML_INSTALL_DIR:-${build_dir}/../../yaml/yaml_install} + +printf "\nTRILINOS_DIR=${trilinos_src_dir}\n"; +printf "BUILD_DIR=${build_dir}\n"; +printf "CMAKE_BUILD_TYPE=${build_type}\n"; +printf "TRILINOS_INSTALL_DIR=${trilinos_install_dir}\n"; +printf "YAML_INSTALL_DIR=${yaml_install_dir}\n"; +printf "\nTo change these vars, set as env vars or pass to this script like 'VAR=value run_cmake_stk'\n\n"; + +if [ ! -d ${trilinos_src_dir}/packages/seacas ] && [ ! -L ${trilinos_src_dir}/packages/seacas ] ; then + echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/seacas directory. If using a Sierra project, make a soft-link to Sierra's seacas directory."; + exit 1; +fi +if [ ! -d ${trilinos_src_dir}/packages/stk ] && [ ! -L ${trilinos_src_dir}/packages/stk ]; then + echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/stk directory. If using a Sierra project, make a soft-link to Sierra's stk directory."; + exit 1; +fi +if [ ! -d ${trilinos_src_dir}/packages/krino ] && [ ! -L ${trilinos_src_dir}/packages/krino ]; then + echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/krino directory. If using a Sierra project, make a soft-link to Sierra's krino directory."; + exit 1; +fi + +mkdir -p $trilinos_install_dir +mkdir -p $build_dir + +cd ${build_dir} + +# Cleanup old cache before we configure +rm -rf CMakeFiles CMakeCache.txt + +cmake \ +-DCMAKE_INSTALL_PREFIX=$trilinos_install_dir \ +-DCMAKE_BUILD_TYPE=${build_type^^} \ +-DKrino_ENABLE_TESTS:BOOL=ON \ +-DTrilinos_ENABLE_Krino:BOOL=ON \ +-DTrilinos_ENABLE_Fortran:BOOL=ON \ +-DTPL_ENABLE_yaml-cpp=ON \ +-Dyaml-cpp_INCLUDE_DIRS=${yaml_install_dir}/include \ +-Dyaml-cpp_LIBRARY_DIRS=${yaml_install_dir}/lib \ +-DTPL_ENABLE_Boost:BOOL=ON \ +-DTPL_ENABLE_MPI=ON \ +-DTPL_ENABLE_Pnetcdf:BOOL=ON \ +-DTPL_ENABLE_HDF5:BOOL=ON \ +${trilinos_src_dir}/ + diff --git a/packages/krino/delete_small_elements/Akri_DeleteSmallElementsMain.cpp b/packages/krino/delete_small_elements/Akri_DeleteSmallElementsMain.cpp new file mode 100644 index 000000000000..1a5fd03eaabc --- /dev/null +++ b/packages/krino/delete_small_elements/Akri_DeleteSmallElementsMain.cpp @@ -0,0 +1,187 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +struct DeleteSmallElementsInputData +{ + static constexpr const char * mDefaultString{"None"}; + std::string meshIn{mDefaultString}; + std::string meshOut{mDefaultString}; + bool blockNameSpecified{false}; + std::string blockName{mDefaultString}; + double minNodalVolume{0.0}; + bool minNodalVolumeSpecified{false}; + double minRelativeNodalVolume{-1.0}; + bool minRelativeNodalVolumeSpecified{false}; +}; + +bool read_command_line( int argc, char *argv[], DeleteSmallElementsInputData & inputData, stk::ParallelMachine comm) +{ + DeleteSmallElementsInputData defaultValues; + + const stk::CommandLineOption inmeshOption{"inmesh", "i", "Filename of input genesis mesh."}; + const stk::CommandLineOption outmeshOption{"outmesh", "o", "Filename of output genesis mesh to write."}; + + const stk::CommandLineOption minNodalVolumeOption{"min_nodal_volume", "m", "Remove all nodes and attached entities smaller than this size. Either --min_nodal_volume or --min_relative_nodal_volume can be specified, but not both."}; + const stk::CommandLineOption minRelativeNodalVolumeOption{"min_relative_nodal_volume", "r", "Remove all all nodes and attached entities smaller than this factor times the maximum element volume in the input mesh. Either --min_nodal_volume or --min_relative_nodal_volume can be specified, but not both"}; + const stk::CommandLineOption blockNameOption{"block", "b", "Confine consideration to the specified block."}; + + stk::CommandLineParserParallel commandLine(comm); + commandLine.disallow_unrecognized(); + + commandLine.add_required(inmeshOption); + commandLine.add_required(outmeshOption); + commandLine.add_optional(blockNameOption, inputData.blockName); + commandLine.add_optional(minNodalVolumeOption, inputData.minNodalVolume); + commandLine.add_optional(minRelativeNodalVolumeOption, inputData.minRelativeNodalVolume); + + + stk::CommandLineParser::ParseState state = commandLine.parse(argc, const_cast(argv)); + if(state == stk::CommandLineParser::ParseComplete) + { + inputData.meshIn = commandLine.get_option_value(inmeshOption.name); + inputData.meshOut = commandLine.get_option_value(outmeshOption.name); + + inputData.blockNameSpecified = commandLine.is_option_parsed(blockNameOption.name); + inputData.minNodalVolumeSpecified = commandLine.is_option_parsed(minNodalVolumeOption.name); + inputData.minRelativeNodalVolumeSpecified = commandLine.is_option_parsed(minRelativeNodalVolumeOption.name); + + if(inputData.blockNameSpecified) + { + inputData.blockName = commandLine.get_option_value(blockNameOption.name); + } + + if(inputData.minNodalVolumeSpecified && inputData.minRelativeNodalVolumeSpecified) + { + sierra::Env::outputP0() << "ERROR: You cannot specify both --"+minNodalVolumeOption.name+" and --"+minRelativeNodalVolumeOption.name+"." << std::endl; + state = stk::CommandLineParser::ParseError; + } + + if(inputData.minNodalVolumeSpecified) + { + inputData.minNodalVolume = commandLine.get_option_value(minNodalVolumeOption.name); + if (inputData.minNodalVolume < 0.0) + { + sierra::Env::outputP0() << "ERROR: size specified via --"+minNodalVolumeOption.name+" must be >= 0." << std::endl; + state = stk::CommandLineParser::ParseError; + } + } + + if(inputData.minRelativeNodalVolumeSpecified) + { + inputData.minRelativeNodalVolume = commandLine.get_option_value(minRelativeNodalVolumeOption.name); + if (inputData.minRelativeNodalVolume < 0.0) + { + sierra::Env::outputP0() << "ERROR: edge length ratio specified via --"+minRelativeNodalVolumeOption.name+" must be >= 0." << std::endl; + state = stk::CommandLineParser::ParseError; + } + } + } + + if(state != stk::CommandLineParser::ParseComplete) + sierra::Env::outputP0() << commandLine.get_usage() << std::endl; + + return state == stk::CommandLineParser::ParseComplete; +} + +static bool delete_small_elements(const DeleteSmallElementsInputData& inputData, + const stk::ParallelMachine comm) +{ + stk::mesh::MetaData meta; + stk::mesh::BulkData bulk(meta, comm); + + stk::io::fill_mesh_with_auto_decomp(inputData.meshIn, bulk); + + // delete infinitesimal elements + double minEdgeLength, maxEdgeLength, minElementVolume, maxElementVolume; + compute_element_quality(bulk, minEdgeLength, maxEdgeLength, minElementVolume, maxElementVolume); + sierra::Env::outputP0() << "Overall mesh size results: minEdgeLength=" << minEdgeLength << ", maxEdgeLength=" << maxEdgeLength << ", minElementVolume=" << minElementVolume << ", maxElementVolume=" << maxElementVolume << std::endl; + + stk::mesh::Selector blockSelector = meta.universal_part(); + if (inputData.blockNameSpecified) + { + stk::mesh::Part * block = meta.get_part(inputData.blockName); + if (!block) + { + sierra::Env::outputP0() << "Did not find part with name " << inputData.blockName << "." << std::endl; + return false; + } + blockSelector = *block; + } + + const double minRetainedElementVolume = inputData.minNodalVolumeSpecified ? inputData.minNodalVolume : (inputData.minRelativeNodalVolume*maxElementVolume); + if (minElementVolume < minRetainedElementVolume) + delete_all_entities_using_nodes_with_nodal_volume_below_threshold(bulk, blockSelector, minRetainedElementVolume); + else + sierra::Env::outputP0() << "All nodes already have nodal volume larger than " << minRetainedElementVolume << "." << std::endl; + + stk::io::StkMeshIoBroker io_broker; + io_broker.set_bulk_data(bulk); + size_t resultFileIndex = io_broker.create_output_mesh(inputData.meshOut, stk::io::WRITE_RESULTS); + io_broker.write_output_mesh(resultFileIndex); + + return true; +} + +static bool run_delete_small_elements(int argc, char **argv, stk::ParallelMachine comm) +{ + int proc = stk::parallel_machine_rank(comm); + if(proc != 0) + stk::EnvData::instance().m_outputP0 = &stk::EnvData::instance().m_outputNull; + + DeleteSmallElementsInputData inputData; + bool didParseOk = read_command_line(argc, argv, inputData, comm); + + bool successfullyRun{false}; + + if (didParseOk) + { + successfullyRun = delete_small_elements(inputData, comm); + + stk::parallel_machine_barrier(comm); + } + + return successfullyRun; +} + +} + +int main(int argc, char **argv) +{ + stk::ParallelMachine comm{stk::parallel_machine_init(&argc, &argv)}; + + bool successfullyRun{false}; + + try + { + successfullyRun = krino::run_delete_small_elements(argc, argv, comm); + } + catch(std::exception &e) + { + std::cerr << "Proc " << stk::parallel_machine_rank(comm) << ": " << e.what() << std::endl; + const int errorCode{-1}; + MPI_Abort(comm, errorCode); + } + + stk::parallel_machine_finalize(); + + return successfullyRun ? 0 : 1; +} diff --git a/packages/krino/delete_small_elements/CMakeLists.txt b/packages/krino/delete_small_elements/CMakeLists.txt new file mode 100644 index 000000000000..864b989c454e --- /dev/null +++ b/packages/krino/delete_small_elements/CMakeLists.txt @@ -0,0 +1,12 @@ +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +SET(SOURCES_MAIN Akri_DeleteSmallElementsMain.cpp) + +set(EXE_NAME delete_small_elements) +TRIBITS_ADD_EXECUTABLE( + ${EXE_NAME} + SOURCES ${SOURCES_MAIN} + NOEXEPREFIX INSTALLABLE + ) diff --git a/packages/krino/krino/Apps_krino.cpp b/packages/krino/krino/Apps_krino.cpp new file mode 100644 index 000000000000..dd24cd296feb --- /dev/null +++ b/packages/krino/krino/Apps_krino.cpp @@ -0,0 +1,47 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +int main( int argc, char ** argv ) +{ + krino::Startup startup(argc, argv); + + if (startup.exit_early()) { + return 0; + } + + bool is_parsing = true; + + try { + krino::YAML_Parser::parse(); + + is_parsing = false; + krino::Simulation & simulation = krino::Simulation::get(); + simulation.commit(); + simulation.initialize(); + simulation.execute(); + } + catch (std::exception &x) { + stk::diag::Trace::Preserve preserve__; + startup.handle_exception(x.what(),is_parsing); + } + catch (...) { + stk::diag::Trace::Preserve preserve__; + startup.handle_exception("Unknown",is_parsing); + } + + // call Simulation::reset() manually to make sure the associated static objects are destroyed before MPI_FINALIZE is called by ~Startup + krino::Simulation::reset(); + + // all done + return 0; +} diff --git a/packages/krino/krino/CMakeLists.txt b/packages/krino/krino/CMakeLists.txt new file mode 100644 index 000000000000..4e8c7ece3d53 --- /dev/null +++ b/packages/krino/krino/CMakeLists.txt @@ -0,0 +1,17 @@ +add_subdirectory(interface_geometry_interface) +add_subdirectory(master_element) +add_subdirectory(krino_lib) +add_subdirectory(adaptivity_interface) +add_subdirectory(region) +add_subdirectory(rebalance_utils) +add_subdirectory(parser) +add_subdirectory(unit_tests) + +SET(SOURCES_MAIN Apps_krino.cpp) + +set(EXE_NAME krino) +TRIBITS_ADD_EXECUTABLE( + ${EXE_NAME} + SOURCES ${SOURCES_MAIN} + NOEXEPREFIX NOEXESUFFIX INSTALLABLE + ) diff --git a/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.cpp b/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.cpp new file mode 100644 index 000000000000..47ea5ae3d3ed --- /dev/null +++ b/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.cpp @@ -0,0 +1,679 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +#ifdef __INTEL_COMPILER +#include // for ElementRefinePredicate +#include +#include +#include // for UniformRefiner +#include +#include +#include +#include +#include +#else +// this disables the checking of shadowed variables on GCC only +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#include // for ElementRefinePredicate +#include +#include +#include // for UniformRefiner +#include +#include +#include +#include +#include +#pragma GCC diagnostic pop +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino +{ + +namespace +{ + +class HAdaptImpl +{ +public: + HAdaptImpl(stk::mesh::MetaData & meta) + : my_meta(meta), + my_active_part(nullptr), + my_root_timer(nullptr) + { + } + void setup(stk::mesh::Part & active_part, stk::diag::Timer & root_timer); + void do_adaptive_refinement(const std::string & marker_field_name); + void do_initial_uniform_refinement(const int num_levels); + +private: + void get_counts(const stk::mesh::FieldBase & marker_field, + unsigned & refinement_count, + unsigned & unrefinement_count) const; + void check_supported_element_types() const; + + stk::mesh::MetaData & my_meta; + std::unique_ptr my_pMesh; + std::unique_ptr my_adaptive_refinement_pattern; + std::unique_ptr my_element_refine_predicate; + std::unique_ptr> my_breaker; + stk::mesh::Selector my_selector; + stk::mesh::Part * my_active_part; + stk::diag::Timer * my_root_timer; +}; + +HAdaptImpl & get(stk::mesh::MetaData & meta) +{ + HAdaptImpl * hadapt = const_cast(meta.get_attribute()); + if (nullptr == hadapt) + { + hadapt = new HAdaptImpl(meta); + meta.declare_attribute_with_delete(hadapt); + } + return *hadapt; +} + +void HAdaptImpl::check_supported_element_types() const +{ + const stk::mesh::PartVector & all_parts = my_meta.get_parts(); + for (size_t i = 0; i < all_parts.size(); ++i) + { + const stk::mesh::Part & part = *all_parts[i]; + if (stk::io::is_part_io_part(part) && part.primary_entity_rank() == stk::topology::ELEMENT_RANK) + { + if ((2 == my_meta.spatial_dimension() && + part.topology() == stk::topology::TRIANGLE_3_2D) || + (3 == my_meta.spatial_dimension() && + part.topology() == stk::topology::TETRAHEDRON_4) || + part.topology() == stk::topology::PARTICLE) + { + continue; + } + ThrowErrorMsg("Elements in block " + << part.name() << " have topology " << part.topology().name() + << " which is currently not supported for adaptive refinement."); + } + } +} + +void HAdaptImpl::get_counts(const stk::mesh::FieldBase & marker_field, + unsigned & refinement_count, + unsigned & unrefinement_count) const +{ + stk::mesh::BulkData & mesh = marker_field.get_mesh(); + stk::mesh::Part & active_part = *my_active_part; + stk::mesh::Selector field_selector = stk::mesh::selectField(marker_field) & active_part & mesh.mesh_meta_data().locally_owned_part(); + + unsigned local_refinement_count = 0; + unsigned local_unrefinement_count = 0; + + const stk::mesh::BucketVector & buckets = + mesh.get_buckets(stk::topology::ELEMENT_RANK, field_selector); + + for (stk::mesh::BucketVector::const_iterator ib = buckets.begin(); ib != buckets.end(); ++ib) + { + const stk::mesh::Bucket & b = **ib; + const int length = b.size(); + + for (int i = 0; i < length; ++i) + { + stk::mesh::Entity elem = b[i]; + + const int & marker = *((int *)stk::mesh::field_data(marker_field, elem)); + if (marker < 0) + { + ++local_unrefinement_count; + } + else if (marker > 0) + { + ++local_refinement_count; + } + } + } + refinement_count = 0; + unrefinement_count = 0; + stk::all_reduce_sum( + mesh.parallel(), (int *)&local_refinement_count, (int *)&refinement_count, 1); + stk::all_reduce_sum(mesh.parallel(), + (int *)&local_unrefinement_count, + (int *)&unrefinement_count, + 1); +} + +void HAdaptImpl::setup(stk::mesh::Part & active_part, stk::diag::Timer & root_timer) +{ + /* %TRACE[ON]% */ Trace trace__( + "void HAdapt::setup(stk::mesh::Part & active_part)"); /* %TRACE% */ + + my_active_part = &active_part; + my_root_timer = &root_timer; + + static stk::diag::Timer timerAdapt_("Adapt", *my_root_timer); + static stk::diag::Timer timerSetup_("Setup", timerAdapt_); + stk::diag::TimeBlock tbTimerSetup_(timerSetup_); + + const unsigned nDim = my_meta.spatial_dimension(); + + my_pMesh = std::make_unique(&my_meta, nullptr, false); + + typedef stk::mesh::Field PerceptVector; + const stk::mesh::FieldBase & coordinates_base = *my_meta.coordinate_field(); + PerceptVector & typed_coordinates = + reinterpret_cast(const_cast(coordinates_base)); + my_pMesh->setCoordinatesField(&typed_coordinates); + + my_pMesh->register_and_set_refine_fields(); + my_pMesh->add_field_int("refine_field", stk::topology::NODE_RANK, 0); + + if (2 == nDim) + { + my_adaptive_refinement_pattern = std::make_unique(*my_pMesh); + } + else + { + my_adaptive_refinement_pattern = std::make_unique(*my_pMesh); + } + + my_pMesh->output_active_children_only(true); + my_pMesh->setProperty("Refiner_skip_side_part_fixes", "true"); +} + +namespace +{ +void limit_coarsening_to_child_elements_with_all_siblings_marked_for_coarsening_and_no_children( + percept::PerceptMesh & eMesh, + const stk::mesh::FieldBase & marker_field) +{ + const stk::mesh::BulkData & mesh = *eMesh.get_bulk_data(); + const auto & local_buckets = + mesh.get_buckets(stk::topology::ELEMENT_RANK, mesh.mesh_meta_data().locally_owned_part()); + + std::vector children; + std::vector childrenOfChild; + + // Only mark element for COARSEN if all children are marked COARSEN + for (auto && b_ptr : local_buckets) + { + for (auto && elem : *b_ptr) + { + eMesh.getChildren(elem, children, false, false); + if (!children.empty()) + { + bool all_children_marked_COARSEN = true; + for (auto && child : children) + { + int & marker = (*((int *)stk::mesh::field_data( marker_field, child ))); + + if (marker == -1) + eMesh.getChildren(child, childrenOfChild, false, false); + if (marker != -1 || !childrenOfChild.empty()) + { + all_children_marked_COARSEN = false; + break; + } + } + if (!all_children_marked_COARSEN) + { + for (auto && child : children) + { + int & marker = (*((int *)stk::mesh::field_data( marker_field, child ))); + if (marker == -1) + { + marker = 0; + } + } + } + } + } + } +} + + +void fill_percept_refine_field(percept::PerceptMesh & eMesh, + const stk::mesh::FieldBase & marker_field) +{ + limit_coarsening_to_child_elements_with_all_siblings_marked_for_coarsening_and_no_children(eMesh, marker_field); + + stk::mesh::BulkData & mesh = *eMesh.get_bulk_data(); + stk::mesh::communicate_field_data(mesh, {&marker_field}); + + stk::mesh::Part &parent_part = *mesh.mesh_meta_data().get_part("refine_inactive_elements_part_3"); + stk::mesh::FieldBase & refine_field = *eMesh.m_refine_field; + + for (auto && b_ptr : mesh.get_buckets(stk::topology::ELEMENT_RANK, stk::mesh::selectField(marker_field))) + { + const stk::mesh::Bucket & b = *b_ptr; + const bool is_parent = b.member(parent_part); + const int length = b.size(); + const unsigned marker_field_length = stk::mesh::field_scalars_per_entity(marker_field, b); + ThrowRequire(1 == stk::mesh::field_scalars_per_entity(refine_field, b)); + + int * marker = (int *)stk::mesh::field_data(marker_field, b); + int * refine = (int *)stk::mesh::field_data(refine_field, b); + if (is_parent) + { + for (int i = 0; i < length; ++i) + { + marker[i*marker_field_length] = 0; + } + } + + for (int i = 0; i < length; ++i) + { + refine[i] = marker[i*marker_field_length]; + } + } +} + +void delete_partless_faces_and_edges(stk::mesh::BulkData & mesh) +{ + std::vector entities; + std::vector relatives; + std::vector relative_ordinals; + + mesh.modification_begin(); + + for (stk::mesh::EntityRank entity_rank : {stk::topology::FACE_RANK, stk::topology::EDGE_RANK}) + { + stk::mesh::get_entities(mesh, entity_rank, entities); + + for (auto && entity : entities) + { + stk::mesh::Bucket & bucket = mesh.bucket(entity); + + const stk::mesh::PartVector & bucket_parts = bucket.supersets(); + bool bucket_has_same_rank_part = + std::find_if(bucket_parts.begin(), + bucket_parts.end(), + [&](const stk::mesh::Part * bucket_part) + { + return (bucket_part->primary_entity_rank() == bucket.entity_rank() && + !stk::mesh::is_auto_declared_part(*bucket_part)); + }) != bucket_parts.end(); + + if (!bucket_has_same_rank_part && + mesh.num_connectivity(entity, stk::topology::CONSTRAINT_RANK) == 0) + { + for (stk::mesh::EntityRank irank = stk::topology::ELEMENT_RANK; irank != entity_rank; + --irank) + { + // Previously this attempted to delete forward or backward and still the list got + // corrupted, + // so just copy into vector and delete from there. + relatives.assign(mesh.begin(entity, irank), mesh.end(entity, irank)); + relative_ordinals.assign( + mesh.begin_ordinals(entity, irank), mesh.end_ordinals(entity, irank)); + + for (size_t irel = 0; irel < relatives.size(); ++irel) + { + ThrowRequireMsg(mesh.destroy_relation(relatives[irel], entity, relative_ordinals[irel]), + "Could not destroy relation between " << mesh.entity_key(relatives[irel]) << " and " + << mesh.entity_key(entity)); + } + } + ThrowRequireMsg( + mesh.destroy_entity(entity), "Could not destroy entity " << mesh.entity_key(entity)); + } + } + } + + mesh.modification_end(); +} + +void update_active_inactive_entities(stk::mesh::BulkData & mesh, + stk::mesh::Part & active_part) +{ + const auto & meta = mesh.mesh_meta_data(); + stk::mesh::PartVector active_part_vec(1, &active_part); + stk::mesh::PartVector inactive_part_vec; + stk::mesh::Selector select_locally_owned(meta.locally_owned_part()); + stk::mesh::Selector percept_active_selector = get_refinement_active_part(meta, stk::topology::ELEMENT_RANK); + + mesh.modification_begin(); + std::vector entities; + for (stk::mesh::EntityRank entity_rank = stk::topology::NODE_RANK; + entity_rank <= stk::topology::ELEMENT_RANK; + ++entity_rank) + { + stk::mesh::get_selected_entities(select_locally_owned, mesh.buckets(entity_rank), entities); + for (auto && entity : entities) + { + if (percept_active_selector(mesh.bucket(entity))) + mesh.change_entity_parts(entity, active_part_vec, inactive_part_vec); + else + mesh.change_entity_parts(entity, inactive_part_vec, active_part_vec); + } + } + mesh.modification_end(); +} + +void +fixup_side_permutation(stk::mesh::BulkData & mesh) +{ + mesh.modification_begin(); + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + + const stk::mesh::BucketVector & buckets = mesh.buckets(stk::topology::ELEMENT_RANK); + + for (auto&& bucket_ptr : buckets) + { + for (auto&& elem : *bucket_ptr) + { + const stk::mesh::Entity* elem_sides = mesh.begin(elem, meta.side_rank()); + const unsigned num_elem_sides = mesh.num_connectivity(elem, meta.side_rank()); + + for (size_t it_side = 0; it_side < num_elem_sides; ++it_side) + { + auto relationship = determine_ordinal_and_permutation(mesh, elem, elem_sides[it_side]); + set_relation_permutation(mesh, elem, elem_sides[it_side], relationship.first, relationship.second); + } + } + } + mesh.modification_end(); +} + +} + +void HAdaptImpl::do_adaptive_refinement(const std::string & marker_field_name) +{ + /* %TRACE[ON]% */ Trace trace__( + "void HAdapt::do_adaptive_refinement(const std::string &marker_field)"); /* %TRACE% */ + + ThrowAssertMsg(my_root_timer != nullptr, "HAdapt::setup() not called."); + static stk::diag::Timer timerAdapt_("Adapt", *my_root_timer); + static stk::diag::Timer timerSetup_("Setup", timerAdapt_); + static stk::diag::Timer timerFmwkUpdating_("Update Active Part", timerAdapt_); + static stk::diag::Timer timerRefine_("Refine", timerAdapt_); + static stk::diag::Timer timerUnrefine_("Unrefine", timerAdapt_); + + stk::diag::TimeBlock tbTimerAdapt_(timerAdapt_); + + constexpr bool debug = false; + + check_supported_element_types(); + + stk::mesh::BulkData & bulk = my_meta.mesh_bulk_data(); + if (!my_pMesh->get_bulk_data()) + { + my_pMesh->set_bulk_data(&bulk); + } + + const stk::mesh::FieldBase * element_marker_field = + my_meta.get_field(stk::topology::ELEMENT_RANK, marker_field_name); + ThrowRequire(element_marker_field); + my_selector = stk::mesh::selectField(*element_marker_field); + + if (!my_breaker) + { + const double tolerance = 0.0; // not used + stk::mesh::FieldBase * refine_field = my_pMesh->m_refine_field; + my_element_refine_predicate = std::make_unique( + *my_pMesh, &my_selector, refine_field, tolerance); // Note that this stores pointer to selector so temporary is not ok + my_breaker = std::make_unique>( + *my_element_refine_predicate, *my_pMesh, *my_adaptive_refinement_pattern, nullptr, debug); + my_breaker->setRemoveOldElements(false); + my_breaker->setAlwaysInitializeNodeRegistry(false); + } + + my_breaker->initializeRefine(); + + unsigned refinement_count = 0; + unsigned unrefinement_count = 0; + + fill_percept_refine_field(*my_pMesh, *element_marker_field); + + get_counts(*element_marker_field, refinement_count, unrefinement_count); + krinolog << "Number of elements marked for refinement = " << refinement_count << "\n"; + krinolog << "Number of elements marked for unrefinement = " << unrefinement_count << stk::diag::dendl; + + const unsigned total_marked_count = refinement_count + unrefinement_count; + if (0 == total_marked_count) + { + krinolog << "Adapt: No elements marked for refinement or unrefinement. " + "Skipping adaptivity" << stk::diag::dendl; + return; + } + + delete_partless_faces_and_edges(bulk); + + { + stk::diag::TimeBlock tbTimerRefine_(timerRefine_); + my_breaker->setAlternateRootTimer(&timerRefine_); + my_breaker->setModBegEndRootTimer(&timerAdapt_); + + std::vector counts; + stk::mesh::comm_mesh_counts(bulk, counts); + + krinolog << "Adapt: before refine, mesh has " << counts[0] << " nodes, " << counts[1] + << " edges, " << counts[2] << " faces, " << counts[3] << " elements" << stk::diag::dendl; + + my_breaker->refine(); + + stk::mesh::comm_mesh_counts(bulk, counts); + + krinolog << "Adapt: after refine, mesh has " << counts[0] << " nodes, " << counts[1] + << " edges, " << counts[2] << " faces, " << counts[3] << " elements" << stk::diag::dendl; + + my_breaker->setAlternateRootTimer(0); + my_breaker->setModBegEndRootTimer(0); + } + + // update refine field to include newly created children + fill_percept_refine_field(*my_pMesh, *element_marker_field); + + { + stk::diag::TimeBlock tbTimerUnrefine_(timerUnrefine_); + my_breaker->setAlternateRootTimer(&timerUnrefine_); + my_breaker->setModBegEndRootTimer(&timerAdapt_); + my_breaker->unrefine(); + my_breaker->setAlternateRootTimer(0); + my_breaker->setModBegEndRootTimer(0); + } + + { + stk::diag::TimeBlock tbTimerRebuilding_(timerFmwkUpdating_); + // The Encore-Percept interface also called induce_nodal_unranked_superset_parts + // and topology nodeset inducer but I don't believe those are needed here. + ThrowRequireMsg(my_active_part != nullptr, "Active part not set for krino::HAdapt"); + update_active_inactive_entities(bulk, *my_active_part); + fixup_side_permutation(bulk); + } +} + +void HAdaptImpl::do_initial_uniform_refinement(const int num_levels) +{ + /* %TRACE[ON]% */ Trace trace__( + "void HAdapt::do_uniform_refinement()"); /* %TRACE% */ + + ThrowAssertMsg(my_root_timer != nullptr, "HAdapt::setup() not called."); + static stk::diag::Timer timerAdapt_("Adapt", *my_root_timer); + static stk::diag::Timer timerSetup_("Setup", timerAdapt_); + static stk::diag::Timer timerFmwkUpdating_("Update Active Part", timerAdapt_); + static stk::diag::Timer timerRefine_("Refine", timerAdapt_); + + stk::diag::TimeBlock tbTimerAdapt_(timerAdapt_); + + check_supported_element_types(); + + stk::mesh::BulkData & bulk = my_meta.mesh_bulk_data(); + if (!my_pMesh->get_bulk_data()) + { + my_pMesh->set_bulk_data(&bulk); + } + + percept::UniformRefiner urefine(*my_pMesh, *my_adaptive_refinement_pattern, nullptr); + urefine.setAlternateRootTimer(&timerAdapt_); + + { + stk::diag::TimeBlock tbTimerRefine_(timerRefine_); + + std::vector counts; + stk::mesh::comm_mesh_counts(bulk, counts); + + krinolog << "Adapt: before refine, mesh has " << counts[0] << " nodes, " << counts[1] + << " edges, " << counts[2] << " faces, " << counts[3] << " elements" << stk::diag::dendl; + + for (int level=0; level counts; + stk::mesh::comm_mesh_counts(bulk, counts); + num_initial_elements = counts[3]; + } + + const auto & meta = bulk.mesh_meta_data(); + percept::MarkerInfo markerInfo; + markerInfo.errorIndicator_ = meta.get_field(stk::topology::ELEMENT_RANK, indicator_field_name); + markerInfo.refineField_ = meta.get_field(stk::topology::ELEMENT_RANK, marker_field_name); + markerInfo.refineFieldOrig_ = meta.get_field(stk::topology::ELEMENT_RANK, "refine_field_orig"); + markerInfo.refineLevelField_ = meta.get_field(stk::topology::ELEMENT_RANK, "refine_level"); + /* + markerInfo.useMarker_ = true; + + markerInfo.numInitialElements_ = num_initial_elements; + markerInfo.maxRefinementLevel_ = max_refinement_level; + markerInfo.maxRefinementNumberOfElementsFraction_ = max_element_growth_factor; + markerInfo.debug_ = false; + + markerInfo.refineFraction_ = refine_fraction; + markerInfo.unrefineFraction_ = unrefine_fraction; + + percept::MarkerUsingErrIndFraction marker(const_cast(bulk), markerInfo); + marker.mark();*/ + + const auto & percept_parent_part = get_refinement_inactive_part(meta, stk::topology::ELEMENT_RANK); + const auto & active_buckets = + bulk.get_buckets(stk::topology::ELEMENT_RANK, + stk::mesh::selectField(*markerInfo.errorIndicator_) & + !percept_parent_part & + meta.locally_owned_part()); + const int buckets_to_sample = std::min(1000ul, active_buckets.size()); + std::vector sample_values; + sample_values.reserve(512*buckets_to_sample); + int j=0; + for(int i=0; i < buckets_to_sample; ++i) + { + const double * ind_data = field_data(*markerInfo.errorIndicator_, *active_buckets[i]); + const int size = active_buckets[i]->size(); + j += size; + sample_values.insert(sample_values.end(), ind_data, ind_data + size); + } + + // This is not scalable + std::vector global_vals; + stk::parallel_vector_concat(bulk.parallel(), sample_values, global_vals); + std::sort(global_vals.begin(), global_vals.end()); + + const auto current_active_elements = global_vals.size(); + + const double remaining_levels = max_refinement_level - current_refinement_level; + const double fraction_to_refine = + current_active_elements >= target_elem_count ? 0: + 1./12. * ( + std::pow( + static_cast(target_elem_count) / static_cast(current_active_elements), + 1./remaining_levels) + - 1.); + + const int global_fraction_index = (1.-fraction_to_refine) * current_active_elements; + const double threshold_val = global_vals[global_fraction_index]; + + for(auto && b_ptr : active_buckets) + { + const auto & bucket = *b_ptr; + const double * ind_data = field_data(*markerInfo.errorIndicator_, bucket); + int * marker_data = field_data(*markerInfo.refineField_, bucket); + const int size = bucket.size(); + for(int i=0; i < size; ++i) + { + marker_data[i] = ind_data[i] > threshold_val ? 1 : 0; + } + } +} + +} +} // namespace krino diff --git a/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.hpp b/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.hpp new file mode 100644 index 000000000000..84c5b21c340d --- /dev/null +++ b/packages/krino/krino/adaptivity_interface/Akri_AdaptivityInterface.hpp @@ -0,0 +1,36 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_ADAPTIVITYINTERFACE_H_ +#define KRINO_INCLUDE_AKRI_ADAPTIVITYINTERFACE_H_ + +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace mesh { class Part; } } +namespace stk { namespace diag { class Timer; } } + +namespace krino { + +namespace HAdapt +{ + void setup(stk::mesh::MetaData & meta, stk::mesh::Part & active_part, stk::diag::Timer & root_timer); + void do_adaptive_refinement(stk::mesh::MetaData & meta, const std::string & marker_field_name); + void do_uniform_refinement(stk::mesh::MetaData & meta, const int num_levels); + void mark_based_on_indicator_field(const stk::mesh::BulkData & bulk, + const std::string & marker_field_name, + const std::string & indicator_field_name, + const int max_refinement_level, + const int current_refinement_level, + const uint64_t target_elem_count); +} + +} // namespace krino + +#endif /* KRINO_INCLUDE_AKRI_ADAPTIVITYINTERFACE_H_ */ diff --git a/packages/krino/krino/adaptivity_interface/CMakeLists.txt b/packages/krino/krino/adaptivity_interface/CMakeLists.txt new file mode 100644 index 000000000000..6c8d3a739a32 --- /dev/null +++ b/packages/krino/krino/adaptivity_interface/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_adaptivity_interface_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + DEPLIBS krino_lib) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_adaptivity_interface_lib) + diff --git a/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry.hpp b/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry.hpp new file mode 100644 index 000000000000..2f2a3a32d69d --- /dev/null +++ b/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry.hpp @@ -0,0 +1,79 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_INTERFACEGEOMETRY_H_ +#define AKRI_INTERFACEGEOMETRY_H_ +#include +#include +#include +#include +#include +#include + +namespace krino { + +class SnapInfo; + +class ElementCutter +{ +public: + virtual ~ElementCutter() {} + virtual std::vector get_sorted_cutting_interfaces() const = 0; + virtual std::vector get_interface_signs_based_on_crossings(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains) const = 0; + virtual void fill_tetrahedron_face_interior_intersections(const std::array & faceNodes, + const InterfaceID & interface1, + const InterfaceID & interface2, + const ElementIntersectionPointFilter & intersectionPointFilter, + std::vector & intersections) const = 0; + virtual bool might_have_interior_or_face_intersections() const = 0; + virtual void fill_interior_intersections(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const = 0; + virtual std::string visualize(const stk::mesh::BulkData & mesh) const = 0; + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const = 0; + virtual double interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const = 0; + virtual int sign_at_position(const InterfaceID interface, const Vector3d & paramCoords) const = 0; + virtual int get_starting_phase_for_cutting_surfaces() const = 0; +}; + +class InterfaceGeometry { +public: + InterfaceGeometry() {} + + virtual ~InterfaceGeometry() {} + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, const NodeToCapturedDomainsMap & nodesToCapturedDomains) const = 0; + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const std::vector & elementsToIntersect, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const = 0; + + virtual std::vector get_edge_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const = 0; + + virtual void append_element_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const std::vector & elementsToIntersect, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) const = 0; + + // FIXME: Temporary methods + virtual void store_phase_for_uncut_elements(const stk::mesh::BulkData & mesh) const = 0; + virtual void store_phase_for_elements_that_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + const std::vector & independentSnapInfos, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const = 0; + + virtual const ElementToDomainMap & get_phase_for_uncut_elements() const = 0; + + virtual std::unique_ptr build_element_cutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::function &)> & intersectingPlanesDiagonalPicker) const = 0; + + virtual PhaseTag get_starting_phase(const ElementCutter * cutter) const = 0; +}; +} + +#endif // AKRI_INTERFACEGEOMETRY_H_ diff --git a/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry_dummy.cpp b/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry_dummy.cpp new file mode 100644 index 000000000000..5879b01607a9 --- /dev/null +++ b/packages/krino/krino/interface_geometry_interface/Akri_InterfaceGeometry_dummy.cpp @@ -0,0 +1,3 @@ +namespace krino { +void InterfaceGeometryDummy() {} +} diff --git a/packages/krino/krino/interface_geometry_interface/CMakeLists.txt b/packages/krino/krino/interface_geometry_interface/CMakeLists.txt new file mode 100644 index 000000000000..917ba031808d --- /dev/null +++ b/packages/krino/krino/interface_geometry_interface/CMakeLists.txt @@ -0,0 +1,18 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + interface_geometry_interface_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES}) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/interface_geometry_interface_lib) + diff --git a/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.cpp b/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.cpp new file mode 100644 index 000000000000..cd9709bd0f33 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.cpp @@ -0,0 +1,138 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino +{ + +stk::mesh::Part & get_refinement_active_part(const stk::mesh::MetaData & meta, stk::mesh::EntityRank rank) +{ + const std::string active_part_name = "refine_active_elements_part_"+std::to_string((int)rank); + stk::mesh::Part* active_part = meta.get_part(active_part_name); + ThrowRequireMsg(nullptr != active_part, "Active part not found: " << active_part_name); + return *active_part; +} +stk::mesh::Part & get_refinement_inactive_part(const stk::mesh::MetaData & meta, stk::mesh::EntityRank rank) +{ + const std::string inactive_part_name = "refine_inactive_elements_part_"+std::to_string((int)rank); + stk::mesh::Part* inactive_part = meta.get_part(inactive_part_name); + ThrowRequireMsg(nullptr != inactive_part, "Inactive part not found: " << inactive_part_name); + return *inactive_part; +} + +void filter_refinement_marker(const stk::mesh::BulkData & mesh, FieldRef elem_marker, const stk::mesh::Selector & do_not_refine_or_unrefine_selector) +{ + const auto & perceptParentPart = get_refinement_inactive_part(mesh.mesh_meta_data(), stk::topology::ELEMENT_RANK); + + for (auto && bucketPtr : mesh.get_buckets(stk::topology::ELEMENT_RANK, mesh.mesh_meta_data().locally_owned_part())) + { + int * markers = field_data(elem_marker, *bucketPtr); + const int size = bucketPtr->size(); + if (do_not_refine_or_unrefine_selector(*bucketPtr)) + { + for (int i = 0; i < size; ++i) + if (markers[i] == Refinement_Marker::REFINE || markers[i] == Refinement_Marker::COARSEN) + markers[i] = Refinement_Marker::NOTHING; + } + else if (bucketPtr->member(perceptParentPart)) + { + for (int i = 0; i < size; ++i) + if (markers[i] == Refinement_Marker::REFINE) + markers[i] = Refinement_Marker::NOTHING; + } + } +} + +stk::mesh::Selector cdfem_do_not_refine_or_unrefine_selector(const CDFEM_Support & cdfem_support) +{ + const stk::mesh::Selector parent_or_child_selector = + cdfem_support.get_child_part() | cdfem_support.get_parent_part(); + const stk::mesh::Selector decomposed_blocks_selector = + krino::Phase_Support::get(cdfem_support.get_mesh_meta()).get_all_decomposed_blocks_selector(); + const stk::mesh::Selector do_not_refine_selector = (!decomposed_blocks_selector) | parent_or_child_selector; + return do_not_refine_selector; +} + + +void perform_multilevel_adaptivity(stk::mesh::BulkData & mesh, + const std::string & marker_field_name, + const std::function & marker_function, + const std::function & adapt_function, + const stk::mesh::Selector & do_not_refine_selector) +{ + Tracespec trace__("perform_multilevel_adaptivity()"); + + const auto & aux_meta = AuxMetaData::get(mesh.mesh_meta_data()); + + const FieldRef elem_marker = aux_meta.get_field( + stk::topology::ELEMENT_RANK, marker_field_name, stk::mesh::StateNew); + + const stk::mesh::Selector active_selector = aux_meta.active_part(); + const stk::mesh::Selector locally_owned_selector = mesh.mesh_meta_data().locally_owned_part(); + + std::vector children; + + bool done = false; + int num_refinements = 0; + while (!done) + { + marker_function(marker_field_name, num_refinements); + filter_refinement_marker(mesh, elem_marker, do_not_refine_selector); + + const auto & local_buckets = mesh.get_buckets(stk::topology::ELEMENT_RANK, locally_owned_selector); + unsigned num_marked_refine = 0; + for (auto && b_ptr : local_buckets) + { + int * markers = field_data(elem_marker, *b_ptr); + for (size_t i = 0; i < b_ptr->size(); ++i) + { + if (markers[i] == Refinement_Marker::REFINE) ++num_marked_refine; + } + } + + // Only worth cost of adaptive refinement if any elements are marked for refinement + unsigned global_num_marked_refine = 0; + stk::all_reduce_sum(mesh.parallel(), &num_marked_refine, &global_num_marked_refine, 1); + if (global_num_marked_refine > 0) + { + const int debug_level = 0; + adapt_function(marker_field_name, debug_level); + + ++num_refinements; + } + else + { + done = true; + } + } + + // This probably should not be needed. + CDMesh::fixup_adapted_element_parts(mesh); + + // This probably should not be needed. + attach_sides_to_elements(mesh); +} +} diff --git a/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.hpp b/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.hpp new file mode 100644 index 000000000000..17a29e7ccafb --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AdaptivityHelpers.hpp @@ -0,0 +1,41 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_ADAPTIVITYHELPERS_H_ +#define KRINO_INCLUDE_AKRI_ADAPTIVITYHELPERS_H_ + +#include +#include +#include +#include + +namespace krino { + +class CDFEM_Support; + +stk::mesh::Part & get_refinement_active_part(const stk::mesh::MetaData & meta, stk::mesh::EntityRank rank); +stk::mesh::Part & get_refinement_inactive_part(const stk::mesh::MetaData & meta, stk::mesh::EntityRank rank); +stk::mesh::Selector cdfem_do_not_refine_or_unrefine_selector(const CDFEM_Support & cdfem_support); + +enum Refinement_Marker + { + COARSEN = -1, + NOTHING = 0, + REFINE = 1 + }; + +void +perform_multilevel_adaptivity(stk::mesh::BulkData & mesh, + const std::string & marker_field_name, + const std::function & marker_function, + const std::function & adapt_function, + const stk::mesh::Selector & do_not_refine_selector = stk::mesh::Selector()); + +} + +#endif /* KRINO_INCLUDE_AKRI_ADAPTIVITYHELPERS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_AnalyticSurf.cpp b/packages/krino/krino/krino_lib/Akri_AnalyticSurf.cpp new file mode 100644 index 000000000000..374396fb7bbf --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AnalyticSurf.cpp @@ -0,0 +1,323 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +#include + +namespace krino{ + +Cylinder::Cylinder(const std::string & n, // surface name + const double e1[3], // first endpoint of axis + const double e2[3], // second endpoint of axis + const double r, // radius of cylinder + const int sign) + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + dist_sign(sign) +{ + // initialize internal description of cylinder + radius = r; + + p1 = Vector3d(e1); + p2 = Vector3d(e2); + + xi = p2 - p1; + + length = xi.length(); + + xi.unitize(); +} + +void +Cylinder::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) +{ + if (NULL == my_transformation) + { + return; + } + + my_transformation->update(time); + my_transformation->apply(p1); + my_transformation->apply(p2); + + xi = p2 - p1; + + length = xi.length(); + + xi.unitize(); +} + +BoundingBox +Cylinder::get_bounding_box() +{ + BoundingBox bbox; + bbox.accommodate(p1); + bbox.accommodate(p2); + bbox.pad(radius); + return bbox; +} + +double +Cylinder::point_signed_distance(const Vector3d &x) const +{ + double D = std::numeric_limits::max(); + + // convert x to cylindrical coordinates + + // v is the vector from p1 to x. + Vector3d v = x - p1; + + // Xix is the projection of v along the axis of the cylinder + const double Xix = Dot(v,xi); + + // u is the associated vector + Vector3d u = Xix*xi; + + // Rx is the distance from the axis of the cylinder to x + + const double Rx = (v - u).length(); + + if ( Xix <= 0 ) + { + // x is behind the cylinder. + // The closest point on the cylinder lies on the rear circular face. + + if ( Rx <= radius ) + { + D = -Xix; + } + else + { + D = std::sqrt(Xix*Xix + (Rx-radius)*(Rx-radius)); + } + } + else if( Xix > 0 && Xix < length) + { + // x is not in front of or behind the cylinder: it is alongside the cylinder. + // the signed distance is given by Rx - radius unless this point is closer + // to one of the circular faces + + if ( Rx >= radius ) + { + D = Rx - radius; + } + else + { + D = std::max( std::max(Rx - radius, -Xix), Xix-length ); + } + } + else + { + // x is in front of the cylinder. + // The closest point on the cylinder lies on the front circular face. + + if ( Rx <= radius ) + { + D = Xix-length; + } + else + { + D = std::sqrt((Xix-length)*(Xix-length) + (Rx-radius)*(Rx-radius)); + } + } + + return dist_sign*D; +} + +Point::Point(const std::string & n, // surface name + const Vector3d & coords) + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + my_coords(coords) +{ +} + +double +Point::point_signed_distance(const Vector3d &x) const +{ + return (x-my_coords).length_squared(); +} + +BoundingBox +Point::get_bounding_box() +{ + BoundingBox bbox; + bbox.accommodate(my_coords); + return bbox; +} + +Sphere::Sphere(const std::string & n, // surface name + const Vector3d & center, + const double radius, + const int sign) + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + myDistSign(sign), + myCenter(center), + myRadius(radius) +{ +} + +void +Sphere::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) +{ + if (nullptr != my_transformation) + { + my_transformation->update(time); + my_transformation->apply(myCenter); + } +} + +BoundingBox +Sphere::get_bounding_box() +{ + return BoundingBox( + Vector3d(myCenter[0]-myRadius, myCenter[1]-myRadius, myCenter[2]-myRadius), + Vector3d(myCenter[0]+myRadius, myCenter[1]+myRadius, myCenter[2]+myRadius) + ); +} + +double +Sphere::point_signed_distance(const Vector3d &x) const +{ + return (myDistSign*((x-myCenter).length() - myRadius)); +} + +Ellipsoid::Ellipsoid( + const std::string & name, // surface name + const std::vector & center, + const std::vector & semiAxes, + const std::vector & rotationVec, + const int sign) +: SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + mySign(sign) +{ + ThrowAssert(center.size() == 3 && semiAxes.size() == 3); + mySemiAxesNorm = 0.0; + for(unsigned i = 0; i < 3; ++i) { + myCenter[i] = center[i]; + mySemiAxes[i] = semiAxes[i]; + mySemiAxesNorm += mySemiAxes[i]*mySemiAxes[i]; + } + mySemiAxesNorm = std::sqrt(mySemiAxesNorm); + + if (!rotationVec.empty()) + { + ThrowAssert(rotationVec.size() == 3); + Vector3d pointRotation(-rotationVec[0], -rotationVec[1], -rotationVec[2]); // myRotation is the rotation used for the query point locations, which is the opposite of the rotation of the ellipsoid + myRotation = std::make_unique(); + myRotation->set_from_rotation_vector(pointRotation); + } +} + +BoundingBox +Ellipsoid::get_bounding_box() +{ + if (!myRotation) + return BoundingBox(myCenter-mySemiAxes, myCenter+mySemiAxes); + + const Vector3d min = myCenter-mySemiAxes; + const Vector3d max = myCenter+mySemiAxes; + BoundingBox rotatedBbox; + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(min[0],min[1],min[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(min[0],min[1],max[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(min[0],max[1],min[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(min[0],max[1],max[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(max[0],min[1],min[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(max[0],min[1],max[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(max[0],max[1],min[2]))); + rotatedBbox.accommodate(myRotation->reverse_rotate_3d_vector(Vector3d(max[0],max[1],max[2]))); + + return rotatedBbox; +} + +double +Ellipsoid::point_signed_distance(const Vector3d &x) const +{ + Vector3d delta = x-myCenter; + if (myRotation) + delta = myRotation->rotate_3d_vector(delta); + // Not an exact distance except in the case of a sphere + const double dx = delta[0]/mySemiAxes[0]; + const double dy = delta[1]/mySemiAxes[1]; + const double dz = delta[2]/mySemiAxes[2]; + return mySign*(mySemiAxesNorm*std::sqrt(dx*dx+dy*dy+dz*dz)-mySemiAxesNorm); +} + +Plane::Plane(const std::string & n, // surface name + const double normal[3], + const double offset, + const double multiplier) + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + myMultiplier(multiplier), + myNormal(normal), + myOffset(offset) +{ + myNormal.unitize(); +} + +double +Plane::point_signed_distance(const Vector3d &x) const +{ + return myMultiplier*(Dot(myNormal, x) + myOffset); +} + +BoundingBox +Plane::get_bounding_box() +{ + //bounding box is entire domain + return BoundingBox(Vector3d(-std::numeric_limits::max(), -std::numeric_limits::max(), -std::numeric_limits::max()), + Vector3d(std::numeric_limits::max(), std::numeric_limits::max(), std::numeric_limits::max())); +} + +Random::Random(const unsigned long seed) + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign(), + my_amplitude(1.0) +{ + my_srand(seed); +} + +double +Random::point_signed_distance(const Vector3d &x) const +{ + // generate random number between -my_amplitude and my_amplitude + return my_amplitude * (-1.0 + 2.0 * my_rand()); +} + +BoundingBox +Random::get_bounding_box() +{ + //bounding box is entire domain + return BoundingBox(Vector3d(-std::numeric_limits::max(), -std::numeric_limits::max(), -std::numeric_limits::max()), + Vector3d(std::numeric_limits::max(), std::numeric_limits::max(), std::numeric_limits::max())); +} + +Analytic_Isosurface::Analytic_Isosurface() + : SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign() +{ +} + +BoundingBox +Analytic_Isosurface::get_bounding_box() +{ + return BoundingBox( + Vector3d(-1.,-1.,-1.), + Vector3d(1.,1.,1.) + ); +} + +double +Analytic_Isosurface::point_signed_distance(const Vector3d &coord) const +{ + const double x = coord[0]; + const double y = coord[1]; + const double z = coord[2]; + return 2.*y*(y*y-3.*x*x)*(1.-z*z) + std::pow(x*x+y*y,2) - (9.*z*z-1.)*(1.-z*z); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_AnalyticSurf.hpp b/packages/krino/krino/krino_lib/Akri_AnalyticSurf.hpp new file mode 100644 index 000000000000..18f70a5bb0e1 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AnalyticSurf.hpp @@ -0,0 +1,186 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_AnalyticSurf_h +#define Akri_AnalyticSurf_h + +#include +#include +#include + +#include +#include + +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class Entity; } } +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace mesh { class Selector; } } + +namespace krino { + +class Cylinder: public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Cylinder(const std::string & n, // surface name + const double e1[3], // first endpoint of axis + const double e2[3], // second endpoint of axis + const double r, // radius of cylinder + const int sign); + + virtual ~Cylinder() {} + + virtual Surface_Type type() const override { return CYLINDER; } + virtual size_t storage_size() const override { return sizeof(Cylinder); } + + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) override; + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + int dist_sign; + double radius; + double length; + + // two end points + Vector3d p1, p2; + + // unit vector in direction of axis. + Vector3d xi; +}; + +class Sphere: public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Sphere(const std::string & n, // surface name + const Vector3d & center, + const double radius, + const int sign = 1); + + virtual ~Sphere() {} + + virtual Surface_Type type() const override { return SPHERE; } + virtual size_t storage_size() const override { return sizeof(Sphere); } + + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) override; + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + int myDistSign; + Vector3d myCenter; + double myRadius; +}; + +class Ellipsoid : public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Ellipsoid( + const std::string & name, // surface name + const std::vector & center, + const std::vector & semiAxes, + const std::vector & rotationVec, + const int sign); + + virtual ~Ellipsoid() {} + + virtual Surface_Type type() const override { return ELLIPSOID; } + virtual size_t storage_size() const override { return sizeof(Ellipsoid); } + + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + int mySign; + + //center of ellipsoid + Vector3d myCenter; + + Vector3d mySemiAxes; + double mySemiAxesNorm; + std::unique_ptr myRotation; +}; + +class Plane: public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Plane(const std::string & n, // surface name + const double normal[3], + const double offset, + const double multiplier); + + virtual ~Plane() {} + + virtual Surface_Type type() const override { return PLANE; } + virtual size_t storage_size() const override { return sizeof(Plane); } + + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + double myMultiplier; + + Vector3d myNormal; //unit normal to plane + double myOffset; //eq of plane is 0 = offset + normal \dot x +}; + +class Point: public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Point(const std::string & n, // surface name + const Vector3d & coords); + + virtual ~Point() {} + + virtual Surface_Type type() const override { return POINT; } + virtual size_t storage_size() const override { return sizeof(Point); } + + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + Vector3d my_coords; +}; + +class Random : public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Random(const unsigned long seed); + + virtual ~Random() {} + + virtual Surface_Type type() const override { return RANDOM; } + virtual size_t storage_size() const override { return sizeof(Random); } + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) override + { + if (truncation_length > 0.0) my_amplitude = truncation_length; + } + + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; + +private: + mutable unsigned long iseed; + double my_amplitude; + + double my_rand() const { iseed = (1664525L*iseed + 1013904223L) & 0xffffffff; + return( ((double) iseed) / ((double) 0xffffffff) ); } + void my_srand(unsigned int seed) const {iseed = seed;} +}; + +class Analytic_Isosurface: public SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign { +public: + Analytic_Isosurface(); + + virtual ~Analytic_Isosurface() {} + + virtual Surface_Type type() const override { return SPHERE; } + virtual size_t storage_size() const override { return sizeof(Analytic_Isosurface); } + + virtual double point_signed_distance(const Vector3d &x) const override; + virtual BoundingBox get_bounding_box() override; +}; + +} // namespace krino + +#endif // Akri_AnalyticSurf_h diff --git a/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.cpp b/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.cpp new file mode 100644 index 000000000000..5062a28d0c4b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.cpp @@ -0,0 +1,203 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +static int surface_sign_at_position(const Surface & surface, const Vector3d & pt) +{ + const double phi = surface.point_signed_distance(pt); + return ( (phi < 0.) ? -1 : 1 ); // GOMA sign convention +} + +static std::function build_edge_distance_function(const Surface & surface, const Segment3d & edge) +{ + std::function distanceFunction = + [&surface, &edge](const double x) + { + return surface.point_signed_distance((1.-x)*edge.GetNode(0) + x*edge.GetNode(1)); + }; + return distanceFunction; +} + +static double find_crossing_position(const Surface & surface, const Segment3d & edge) +{ + const double phi0 = surface.point_signed_distance(edge.GetNode(0)); + const double phi1 = surface.point_signed_distance(edge.GetNode(1)); + const auto result = find_root(build_edge_distance_function(surface, edge), 0., 1., phi0, phi1); + ThrowRequire(result.first); + return result.second; +} + +SurfaceElementCutter::SurfaceElementCutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const Surface & surface) +: myMasterElem(MasterElementDeterminer::getMasterElement(mesh.bucket(element).topology())), + mySurface(surface) +{ + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + fill_element_node_coordinates(mesh, element, coordsField, myElementNodeCoords); +} + +bool SurfaceElementCutter::have_crossing(const InterfaceID interface, const Segment3d & edge) const +{ + return surface_sign_at_position(mySurface, parametric_to_global_coordinates(edge.GetNode(0))) != + surface_sign_at_position(mySurface, parametric_to_global_coordinates(edge.GetNode(1))); +} + +double SurfaceElementCutter::interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const +{ + const Segment3d globalEdge(parametric_to_global_coordinates(edge.GetNode(0)), parametric_to_global_coordinates(edge.GetNode(1))); + return find_crossing_position(mySurface, globalEdge); +} + +int SurfaceElementCutter::sign_at_position(const InterfaceID interface, const Vector3d & paramCoords) const +{ + return surface_sign_at_position(mySurface, parametric_to_global_coordinates(paramCoords)); +} + +Vector3d SurfaceElementCutter::parametric_to_global_coordinates(const Vector3d & pCoords) const +{ + std::vector nodalShapeFunctions(myMasterElem.num_nodes()); + myMasterElem.shape_fcn(1, pCoords.data(), nodalShapeFunctions.data()); + Vector3d pt(Vector3d::ZERO); + for (unsigned n=0; n & elementsToIntersect, + const Surface & surface, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) +{ + const bool intersectionPointIsOwned = true; + std::vector intersectionPointSortedDomains; + const int dim = mesh.mesh_meta_data().spatial_dimension(); + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + std::set> edgesAlreadyChecked; + for (auto && elem : elementsToIntersect) + { + const stk::topology topology = mesh.bucket(elem).topology(); + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(elem); + const unsigned numEdges = topology.num_edges(); + + for (unsigned iedge = 0; iedge < numEdges; ++iedge) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topology, iedge); + const stk::mesh::Entity node0 = elem_nodes[edge_node_ordinals[0]]; + const stk::mesh::Entity node1 = elem_nodes[edge_node_ordinals[1]]; + const stk::mesh::EntityId node0Id = mesh.identifier(node0); + const stk::mesh::EntityId node1Id = mesh.identifier(node1); + const std::array edgeNodeIds = (node0Id < node1Id) ? std::array{node0Id, node1Id} : std::array{node1Id, node0Id}; + auto iter = edgesAlreadyChecked.lower_bound(edgeNodeIds); + if (iter == edgesAlreadyChecked.end() || edgeNodeIds != *iter) + { + edgesAlreadyChecked.insert(iter, edgeNodeIds); + const Vector3d node0Coords(field_data(coordsField, node0), dim); + const Vector3d node1Coords(field_data(coordsField, node1), dim); + const double phi0 = surface.point_signed_distance(node0Coords); + const double phi1 = surface.point_signed_distance(node1Coords); + const bool haveCrossing = (phi0 < 0.) ? (phi1 >= 0.) : (phi1 < 0.); + if (haveCrossing) + { + const InterfaceID interface(0,0); + const double location = find_crossing_position(surface, Segment3d(node0Coords, node1Coords)); + interface.fill_sorted_domains(intersectionPointSortedDomains); + const std::vector intersectionPointNodes{node0,node1}; + if (intersectionPointFilter(intersectionPointNodes, intersectionPointSortedDomains)) + intersectionPoints.emplace_back(intersectionPointIsOwned, intersectionPointNodes, std::vector{1.-location, location}, intersectionPointSortedDomains); + } + } + } + } +} + +static BoundingBox compute_nodal_bounding_box(const stk::mesh::BulkData & mesh) +{ + const int nDim = mesh.mesh_meta_data().spatial_dimension(); + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + + BoundingBox nodeBbox; + for ( auto && bucket : mesh.buckets(stk::topology::NODE_RANK) ) + { + double *coord = field_data(coordsField, *bucket); + for (size_t n = 0; n < bucket->size(); ++n) + nodeBbox.accommodate( Vector3d(coord+n*nDim, nDim) ); + } + + return nodeBbox; +} + +static void prepare_to_compute_with_surface(const stk::mesh::BulkData & mesh, const Surface & surface) +{ + const BoundingBox nodeBbox = compute_nodal_bounding_box(mesh); + Surface & nonConstSurface = const_cast(surface); + nonConstSurface.prepare_to_compute(0.0, nodeBbox, 0.); // Setup including communication of facets that are within this processors narrow band +} + +void AnalyticSurfaceInterfaceGeometry::prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + myElementsToIntersect = get_owned_parent_elements(mesh, myActivePart, myCdfemSupport, myPhaseSupport); + prepare_to_compute_with_surface(mesh, mySurface); +} + +void AnalyticSurfaceInterfaceGeometry::prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const std::vector & elementsToIntersect, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + myElementsToIntersect = elementsToIntersect; + prepare_to_compute_with_surface(mesh, mySurface); +} + +std::vector AnalyticSurfaceInterfaceGeometry::get_edge_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + const IntersectionPointFilter intersectionPointFilter = keep_all_intersection_points_filter(); + std::vector intersectionPoints; + append_surface_edge_intersection_points(mesh, myElementsToIntersect, mySurface, intersectionPointFilter, intersectionPoints); + return intersectionPoints; +} + +void AnalyticSurfaceInterfaceGeometry::append_element_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const std::vector & elementsToIntersect, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) const +{ + prepare_to_process_elements(mesh, elementsToIntersect, nodesToCapturedDomains); + append_surface_edge_intersection_points(mesh, myElementsToIntersect, mySurface, intersectionPointFilter, intersectionPoints); +} + +std::unique_ptr AnalyticSurfaceInterfaceGeometry::build_element_cutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::function &)> & intersectingPlanesDiagonalPicker) const +{ + std::unique_ptr cutter; + cutter.reset( new SurfaceElementCutter(mesh, element, mySurface) ); + return cutter; +} + +PhaseTag AnalyticSurfaceInterfaceGeometry::get_starting_phase(const ElementCutter * cutter) const +{ + PhaseTag phase; + ThrowRequire(1 == myCdfemSupport.num_ls_fields()); + phase.add(myCdfemSupport.ls_field(0).identifier, 0); + return phase; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.hpp b/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.hpp new file mode 100644 index 000000000000..f72ce103d4d1 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AnalyticSurfaceInterfaceGeometry.hpp @@ -0,0 +1,111 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_AnalyticSurfaceInterfaceGeometry_h +#define Akri_AnalyticSurfaceInterfaceGeometry_h + +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +class CDFEM_Support; +class Phase_Support; + +class SurfaceElementCutter : public ElementCutter +{ +public: + SurfaceElementCutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const Surface & surface); + virtual ~SurfaceElementCutter() {} + + virtual bool might_have_interior_or_face_intersections() const override { return false; } + virtual void fill_interior_intersections(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const override {} + virtual std::vector get_sorted_cutting_interfaces() const override + { std::vector interfaces; interfaces.push_back(InterfaceID(0,0)); return interfaces; } + virtual std::vector get_interface_signs_based_on_crossings(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains) const override + { std::vector interfaceSigns(1,0); return interfaceSigns; } + virtual void fill_tetrahedron_face_interior_intersections(const std::array & faceNodes, + const InterfaceID & interface1, + const InterfaceID & interface2, + const ElementIntersectionPointFilter & intersectionPointFilter, + std::vector & intersections) const override {} + virtual std::string visualize(const stk::mesh::BulkData & mesh) const override { std::string empty; return empty; } + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const override; + virtual double interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const override; + virtual int sign_at_position(const InterfaceID interface, const Vector3d & paramCoords) const override; + virtual int get_starting_phase_for_cutting_surfaces() const override { return 0; } + +private: + Vector3d parametric_to_global_coordinates(const Vector3d & pCoords) const; + + const MasterElement & myMasterElem; + std::vector myElementNodeCoords; + const Surface & mySurface; +}; + +class AnalyticSurfaceInterfaceGeometry : public InterfaceGeometry { + +public: + AnalyticSurfaceInterfaceGeometry(const Surface & surface, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +: mySurface(surface), + myActivePart(activePart), + myCdfemSupport(cdfemSupport), + myPhaseSupport(phaseSupport) {} + + virtual ~AnalyticSurfaceInterfaceGeometry() {} + + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToSnappedDomains) const override; + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const std::vector & elementsToIntersect, + const NodeToCapturedDomainsMap & nodesToSnappedDomains) const override; + + virtual std::vector get_edge_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToSnappedDomains) const override; + virtual void append_element_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToSnappedDomains, + const std::vector & elementsToIntersect, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) const override; + + virtual void store_phase_for_uncut_elements(const stk::mesh::BulkData & mesh) const override {} + virtual void store_phase_for_elements_that_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + const std::vector & independentSnapInfos, + const NodeToCapturedDomainsMap & nodesToSnappedDomains) const override {} + virtual const ElementToDomainMap & get_phase_for_uncut_elements() const override { return myUncutElementPhases; } + + virtual std::unique_ptr build_element_cutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::function &)> & intersectingPlanesDiagonalPicker) const override; + + virtual PhaseTag get_starting_phase(const ElementCutter * cutter) const override; + +private: + const Surface & mySurface; + const stk::mesh::Part & myActivePart; + const CDFEM_Support & myCdfemSupport; + const Phase_Support & myPhaseSupport; + ElementToDomainMap myUncutElementPhases; + mutable std::vector myElementsToIntersect; +}; + +} // namespace krino + +#endif diff --git a/packages/krino/krino/krino_lib/Akri_AuxMetaData.cpp b/packages/krino/krino/krino_lib/Akri_AuxMetaData.cpp new file mode 100644 index 000000000000..99584a22279a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AuxMetaData.cpp @@ -0,0 +1,396 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include "Akri_FieldRef.hpp" // for FieldRef + +#include +#include "stk_mesh/base/FieldBase.hpp" // for FieldState +#include "stk_mesh/base/MetaData.hpp" +#include "stk_mesh/base/Part.hpp" // for Part +#include "stk_topology/topology.hpp" // for topology, etc +#include +#include "stk_util/util/ReportHandler.hpp" // for ThrowAssert, etc + +namespace krino +{ +const FieldType FieldType::UNSIGNED_INTEGER_64("UNSIGNED INTEGER 64", typeid(uint64_t), 1); +const FieldType FieldType::UNSIGNED_INTEGER("UNSIGNED INTEGER", typeid(unsigned), 1); +const FieldType FieldType::INTEGER("INTEGER", typeid(int), 1); +const FieldType FieldType::REAL("REAL", typeid(double), 1); + +const FieldType FieldType::VECTOR_2D("VECTOR_2D", typeid(double), 2); +const FieldType FieldType::VECTOR_3D("VECTOR_3D", typeid(double), 3); +const FieldType FieldType::MATRIX_22("MATRIX_22", typeid(double), 4); +const FieldType FieldType::MATRIX_33("MATRIX_33", typeid(double), 9); + +AuxMetaData & +AuxMetaData::get(const stk::mesh::MetaData & stk_meta) +{ + AuxMetaData * aux_meta = const_cast(stk_meta.get_attribute()); + ThrowRequireMsg(nullptr != aux_meta, "AuxMetaData not found on MetaData."); + return *aux_meta; +} + +AuxMetaData & +AuxMetaData::create(stk::mesh::MetaData & stk_meta) +{ + AuxMetaData * aux_meta = const_cast(stk_meta.get_attribute()); + ThrowRequireMsg(nullptr == aux_meta, "AuxMetaData::create should be caled only once per MetaData."); + if (nullptr == aux_meta) + { + aux_meta = new AuxMetaData(stk_meta); + stk_meta.declare_attribute_with_delete(aux_meta); + } + return *aux_meta; +} + +AuxMetaData::AuxMetaData(stk::mesh::MetaData & stk_meta) + : my_meta(stk_meta), + is_fmwk(false), + my_assert_32bit_flag(false), + my_force_64bit_flag(true), // just to guarantee testing 64 bit as much as possible + my_active_part(nullptr), + my_exposed_boundary_part(nullptr), + my_block_boundary_part(nullptr) +{ + stk::mesh::Part * existing_active_part = my_meta.get_part("ACTIVE_CONTEXT_BIT"); + if (nullptr != existing_active_part) + { + my_active_part = existing_active_part; + my_exposed_boundary_part = my_meta.get_part("EXPOSED_BOUNDARY_CONTEXT_BIT"); + my_block_boundary_part = my_meta.get_part("BLOCK_BOUNDARY_CONTEXT_BIT"); + } + else + { + ThrowRequireMsg(my_meta.spatial_dimension() > 0, "For non-Fmwk usage, AuxMetaData cannot be created until after the spatial_dimension is set on the stk::mesh::MetaData."); + ThrowRequireMsg(!my_meta.is_commit(), "For non-Fmwk usage, AuxMetaData must be created before the stk::mesh::MetaData is committed."); + my_active_part = &my_meta.declare_part("ACTIVE_CONTEXT_BIT"); + my_exposed_boundary_part = &my_meta.declare_part("EXPOSED_BOUNDARY_CONTEXT_BIT", my_meta.side_rank()); + my_block_boundary_part = &my_meta.declare_part("BLOCK_BOUNDARY_CONTEXT_BIT", my_meta.side_rank()); + } + + my_active_globally_shared_selector = stk::mesh::Selector(*my_active_part & my_meta.globally_shared_part()); + my_active_not_ghost_selector = stk::mesh::Selector(*my_active_part & (my_meta.locally_owned_part() | my_meta.globally_shared_part())); + my_active_locally_owned_selector = stk::mesh::Selector(*my_active_part & my_meta.locally_owned_part()); +} + +void +AuxMetaData::set_fmwk_functions( + const std::function & in_fmwk_get_iopart, + const std::function & in_fmwk_iopart, + const std::function & in_fmwk_define_iopart_alias, + const std::function & in_fmwk_register_field, + stk::mesh::Part * in_exposed_boundary_part, + stk::mesh::Part * in_block_boundary_part) +{ + is_fmwk = true; + clear_force_64bit_flag(); + fmwk_get_iopart = in_fmwk_get_iopart; + fmwk_iopart = in_fmwk_iopart; + fmwk_define_iopart_alias = in_fmwk_define_iopart_alias; + fmwk_register_field = in_fmwk_register_field; + my_exposed_boundary_part = in_exposed_boundary_part; + my_block_boundary_part = in_block_boundary_part; +} + +void +AuxMetaData::set_inducer_functions( + const std::function & in_inducer_induce_topology_nodesets, + const std::function & in_inducer_get_nodal_field_topology, + const std::function & in_inducer_selectField) +{ + fn_induce_topology_nodesets = in_inducer_induce_topology_nodesets; + fn_get_nodal_field_topology = in_inducer_get_nodal_field_topology; + fn_selectField = in_inducer_selectField; +} + +stk::mesh::Part & AuxMetaData::block_boundary_part() const +{ + ThrowAssert(nullptr != my_block_boundary_part); return *my_block_boundary_part; +} + +stk::mesh::Part & AuxMetaData::exposed_boundary_part() const +{ + ThrowAssert(nullptr != my_exposed_boundary_part); return *my_exposed_boundary_part; +} + +bool +AuxMetaData::has_field( const stk::mesh::EntityRank obj_type, const std::string& name ) const +{ + return NULL != my_meta.get_field(obj_type, name); +} + +bool +AuxMetaData::has_field( const stk::mesh::EntityRank obj_type, const std::string& name, stk::mesh::FieldState state ) const +{ + stk::mesh::FieldBase* field_ptr = my_meta.get_field(obj_type, name); + if (NULL == field_ptr) return false; + return NULL != field_ptr->field_state(state); +} + +FieldRef +AuxMetaData::get_field( const stk::mesh::EntityRank obj_type, const std::string& name ) const +{ + stk::mesh::FieldBase* field_ptr = my_meta.get_field(obj_type, name); + ThrowRequireMsg(NULL != field_ptr, "Field \"" << name << "\" not found."); + return FieldRef(field_ptr); +} + + +FieldRef +AuxMetaData::get_field( const stk::mesh::EntityRank obj_type, const std::string& name, stk::mesh::FieldState state ) const +{ + stk::mesh::FieldBase* field_ptr = my_meta.get_field(obj_type, name); + if(field_ptr == nullptr) + { + std::ostringstream err_msg; + err_msg << "Field \"" << name << "\" not found.\n"; + err_msg << "Registered fields are:\n"; + for(auto && field : my_meta.get_fields(obj_type)) + { + err_msg << field->name() << "\n"; + } + throw std::runtime_error(err_msg.str()); + } + return FieldRef(field_ptr, state); +} + +bool +AuxMetaData::has_part( const std::string& name ) const +{ + stk::mesh::Part * part = my_meta.get_part(name); + // If the part is not found see if the name is actually a Fmwk alias + if (!part && is_fmwk) part = fmwk_get_iopart(name); + return NULL != part; +} + +stk::mesh::Part& +AuxMetaData::get_part( const std::string& name ) const +{ + stk::mesh::Part * part = my_meta.get_part(name); + // If the part is not found see if the name is actually a Fmwk alias + if (!part && is_fmwk) part = fmwk_get_iopart(name); + ThrowRequireMsg(part, "Could not find part " << name;); + return *part; +} + +void +AuxMetaData::define_part_alias( stk::mesh::Part & part , const std::string & alias ) +{ + if (is_fmwk) + { + fmwk_define_iopart_alias(part, alias); + return; + } + // Silent no-op +} + +void +AuxMetaData::assign_part_id(stk::mesh::Part& part) +{ + static int64_t max_existing_part_id = stk::mesh::Part::INVALID_ID; + if (max_existing_part_id == stk::mesh::Part::INVALID_ID) + { + max_existing_part_id = 0; + for (auto && existing_part : my_meta.get_parts()) + { + max_existing_part_id = std::max(max_existing_part_id, existing_part->id()); + } + } + if (part.id() == stk::mesh::Part::INVALID_ID) + { + const int64_t part_id = ++max_existing_part_id; + my_meta.set_part_id(part, part_id); + } +} + +stk::mesh::Part& +AuxMetaData::declare_io_part( const std::string& name, const stk::mesh::EntityRank obj_type, const bool restartOnlyIOPart ) +{ + if (is_fmwk) + { + stk::mesh::Part & part = fmwk_iopart(name, obj_type); + if (restartOnlyIOPart) + { + myRestartOnlyIOParts.push_back(&part); + } + assign_part_id(part); + return part; + } + + stk::mesh::Part & part = my_meta.declare_part(name, obj_type); + + if (restartOnlyIOPart) + { + myRestartOnlyIOParts.push_back(&part); + } + else + { + if (!stk::io::is_part_io_part(part)) + { + stk::io::put_io_part_attribute(part); + } + } + + assign_part_id(part); + + return part; +} + +stk::mesh::Part& +AuxMetaData::declare_io_part_with_topology( const std::string& name, const stk::topology topology, const bool restartOnlyIOPart ) +{ + if (is_fmwk) + { + stk::mesh::Part & root_part = my_meta.get_topology_root_part(topology); + stk::mesh::Part & part = fmwk_iopart(name, root_part.primary_entity_rank()); + my_meta.declare_part_subset(root_part, part); + if (restartOnlyIOPart) + { + myRestartOnlyIOParts.push_back(&part); + } + assign_part_id(part); + return part; + } + + stk::mesh::Part & part = my_meta.declare_part_with_topology(name, topology); + + if (restartOnlyIOPart) + { + myRestartOnlyIOParts.push_back(&part); + } + else + { + if (!stk::io::is_part_io_part(part)) + { + stk::io::put_io_part_attribute(part); + } + } + + assign_part_id(part); + + return part; +} + +FieldRef +AuxMetaData::declare_field( + const std::string & fld_name, + const FieldType & field_type, + const stk::mesh::EntityRank entity_rank, + const unsigned num_states) +{ + stk::mesh::FieldBase * field = NULL; + const std::type_info & value_type = field_type.type_info(); + if (value_type == typeid(int)) + field = &my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + else if (value_type == typeid(double)) + field = &my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + else if (value_type == typeid(unsigned)) + field = &my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + else if (value_type == typeid(int64_t)) + field = &my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + else if (value_type == typeid(uint64_t)) + field = &my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + else { + ThrowRequireMsg(false, "Unhandled primitive type " << value_type.name()); + } + + return FieldRef(field); +} + +FieldRef +AuxMetaData::register_field( + const std::string & fld_name, + const FieldType & field_type, + const stk::mesh::EntityRank entity_rank, + const unsigned num_states, + const unsigned dimension, + const stk::mesh::Part & part, + const void * value_type_init) +{ + // don't rely on induction of non-ranked superset parts + // Note that we are only checking nodal fields here, but this could also be a problem if we are counting on a non-ranked superset part to be induced on faces or edges (unlikely?). + //ThrowRequire(entity_rank != stk::topology::NODE_RANK || !is_unranked_superset_part(part)); + + if (is_fmwk) + { + return FieldRef(fmwk_register_field(fld_name, field_type.name(), field_type.type_info(), field_type.dimension(), entity_rank, num_states, dimension, part, value_type_init)); + } + + const unsigned field_length = field_type.dimension()*dimension; + if (field_type.name() == FieldType::VECTOR_2D.name()) + { + auto & field = my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + stk::mesh::put_field_on_mesh(field, part, field_length, nullptr); + return FieldRef(field); + } + else if (field_type.name() == FieldType::VECTOR_3D.name()) + { + auto & field = my_meta.declare_field< stk::mesh::Field >(entity_rank, fld_name, num_states); + stk::mesh::put_field_on_mesh(field, part, field_length, nullptr); + return FieldRef(field); + } + + FieldRef field = declare_field(fld_name, field_type, entity_rank, num_states); + stk::mesh::put_field_on_mesh(field.field(), part, field_length, value_type_init); + return field; +} + +void +AuxMetaData::induce_topology_nodesets(stk::mesh::Selector selector) const +{ + if (fn_induce_topology_nodesets) + { + fn_induce_topology_nodesets(selector); + } + // no-op if inducer is not set + return; +} + +stk::topology +AuxMetaData::get_nodal_field_topology( const stk::mesh::FieldBase & field, stk::mesh::Entity entity ) const +{ + return get_nodal_field_topology(field, my_meta.mesh_bulk_data().bucket(entity)); +} + +stk::topology AuxMetaData::get_nodal_field_topology( const stk::mesh::FieldBase & field, const stk::mesh::Bucket & bucket ) const +{ + if (fn_get_nodal_field_topology) + { + return fn_get_nodal_field_topology(field, bucket); + } + // return bucket topology if inducer is not set and field is defined on bucket + const stk::mesh::Selector field_selector = stk::mesh::selectField(field); + stk::topology field_topology = stk::topology::INVALID_TOPOLOGY; + if (field_selector(bucket)) field_topology = bucket.topology(); + return field_topology; +} + +stk::mesh::Selector AuxMetaData::selectField( const stk::mesh::FieldBase & field, const stk::mesh::EntityRank target_rank ) const +{ + if (fn_selectField && field.entity_rank() == stk::topology::NODE_RANK) + { + return fn_selectField( field, target_rank ); + } + // return stk::mesh::selectField if inducer is not set + return stk::mesh::selectField(field); +} + +//---------------------------------------------------------------------- + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_AuxMetaData.hpp b/packages/krino/krino/krino_lib/Akri_AuxMetaData.hpp new file mode 100644 index 000000000000..e7590663a4be --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_AuxMetaData.hpp @@ -0,0 +1,180 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_AuxMetaData_h +#define Akri_AuxMetaData_h + +#include +#include // for operator<<, basic_string, etc +#include "stk_mesh/base/FieldState.hpp" // for FieldState +#include "stk_mesh/base/Selector.hpp" // for Selector +#include "stk_mesh/base/Entity.hpp" // for Entity + +namespace krino { class FieldRef; } + +#if ((__GNUC__ == 4) && (__GNUC_MINOR__ == 9)) || (__GNUC__ == 5) +// Looks like there is an issue with these compilers +// related to instatiating std::function with an incomplete +// type leading to undefine behavior +#include "stk_mesh/base/Part.hpp" // for Part +#include "stk_mesh/base/MetaData.hpp" +#include "stk_mesh/base/FieldBase.hpp" // for FieldState +#else +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace mesh { class Part; } } +namespace stk { namespace mesh { class FieldBase; } } +#endif + +namespace krino +{ + +class FieldType { +public: + static const FieldType UNSIGNED_INTEGER_64; + static const FieldType UNSIGNED_INTEGER; + static const FieldType INTEGER; + static const FieldType REAL; + + static const FieldType VECTOR_2D; + static const FieldType VECTOR_3D; + static const FieldType MATRIX_22; + static const FieldType MATRIX_33; + + const std::string & name() const { return my_name; } + const std::type_info & type_info() const { return my_type_info; } + unsigned dimension() const { return my_dimension; } + + FieldType(const std::string & nme, const std::type_info & type, const unsigned dim) : my_name(nme), my_type_info(type), my_dimension(dim) {} + +private: + const std::string my_name; + const std::type_info & my_type_info; + const unsigned my_dimension; +}; + +class AuxMetaData final +{ +public: + static AuxMetaData & get(const stk::mesh::MetaData & stk_meta); + + static AuxMetaData & create(stk::mesh::MetaData & stk_meta); // must be called before calling get + + AuxMetaData ( const AuxMetaData & ) = delete; + AuxMetaData & operator= ( const AuxMetaData & ) = delete; + + bool using_fmwk() const { return is_fmwk; } + + stk::mesh::Part & active_part() const { return *my_active_part; } + stk::mesh::Part & block_boundary_part() const; + stk::mesh::Part & exposed_boundary_part() const; + + const stk::mesh::Selector & active_not_ghost_selector() const { return my_active_not_ghost_selector; } + const stk::mesh::Selector & active_locally_owned_selector() const { return my_active_locally_owned_selector; } + const stk::mesh::Selector & active_globally_shared_selector() const { return my_active_globally_shared_selector; } + + bool get_force_64bit_flag() const { return my_force_64bit_flag; } + void clear_force_64bit_flag() { my_force_64bit_flag = false; } + bool get_assert_32bit_flag() { return my_assert_32bit_flag; } + void set_assert_32bit_flag() { my_force_64bit_flag = false; my_assert_32bit_flag = true; } + + FieldRef declare_field( + const std::string & fld_name, + const FieldType & field_type, + const stk::mesh::EntityRank entity_rank, + const unsigned num_states); + + FieldRef register_field( + const std::string & fld_name, + const FieldType & field_type, + const stk::mesh::EntityRank entity_rank, + const unsigned num_states, + const unsigned dimension, + const stk::mesh::Part & part, + const void * value_type_init = nullptr); + + void assign_part_id(stk::mesh::Part& part); + stk::mesh::Part & declare_io_part(const std::string & name, stk::mesh::EntityRank entityRank, const bool restartOnlyIOPart=false); + stk::mesh::Part & declare_io_part_with_topology(const std::string & name, const stk::topology topology, const bool restartOnlyIOPart=false); + + const std::vector & get_restart_only_io_parts() const { return myRestartOnlyIOParts; } + + bool has_part( const std::string& name ) const; + stk::mesh::Part& get_part( const std::string& name ) const; + + void define_part_alias( stk::mesh::Part & part, const std::string & alias ); + + bool has_field( const stk::mesh::EntityRank obj_type, const std::string& name ) const; + bool has_field( const stk::mesh::EntityRank obj_type, const std::string& name, stk::mesh::FieldState state ) const; + + FieldRef get_field( const stk::mesh::EntityRank obj_type, const std::string& name ) const; + FieldRef get_field( const stk::mesh::EntityRank obj_type, const std::string& name, stk::mesh::FieldState state ) const; + + void induce_topology_nodesets(stk::mesh::Selector selector = stk::mesh::Selector()) const; + stk::topology get_nodal_field_topology( const stk::mesh::FieldBase & field, stk::mesh::Entity entity ) const; + stk::topology get_nodal_field_topology( const stk::mesh::FieldBase & field, const stk::mesh::Bucket & bucket ) const; + stk::mesh::Selector selectField( const stk::mesh::FieldBase & field, const stk::mesh::EntityRank target_rank ) const; + bool is_cell_edge(stk::mesh::Entity node0, stk::mesh::Entity node1) const { return fn_is_cell_edge(node0, node1); } + + void set_fmwk_functions( + const std::function & in_fmwk_get_iopart, + const std::function & in_fmwk_iopart, + const std::function & in_fmwk_define_iopart_alias, + const std::function & in_fmwk_register_field, + stk::mesh::Part * in_exposed_boundary_part, + stk::mesh::Part * in_block_boundary_part); + void set_inducer_functions( + const std::function & in_inducer_induce_topology_nodesets, + const std::function & in_inducer_get_nodal_field_topology, + const std::function & in_inducer_selectField); + void set_is_cell_edge_function(const std::function & in_is_cell_edge) { fn_is_cell_edge = in_is_cell_edge; } + +private: + explicit AuxMetaData(stk::mesh::MetaData & stk_meta); +private: + stk::mesh::MetaData & my_meta; + bool is_fmwk; + bool my_assert_32bit_flag; + bool my_force_64bit_flag; + stk::mesh::Part * my_active_part; + stk::mesh::Part * my_exposed_boundary_part; + stk::mesh::Part * my_block_boundary_part; + stk::mesh::Selector my_active_not_ghost_selector; + stk::mesh::Selector my_active_locally_owned_selector; + stk::mesh::Selector my_active_globally_shared_selector; + std::function fmwk_get_iopart; + std::function fmwk_iopart; + std::function fmwk_define_iopart_alias; + std::function fmwk_register_field; + std::function fn_induce_topology_nodesets; + std::function fn_get_nodal_field_topology; + std::function fn_selectField; + std::function fn_is_cell_edge; + std::vector myRestartOnlyIOParts; +}; + +} // namespace krino + +#endif // Akri_AuxMetaData_h diff --git a/packages/krino/krino/krino_lib/Akri_BoundingBox.cpp b/packages/krino/krino/krino_lib/Akri_BoundingBox.cpp new file mode 100644 index 000000000000..f456350ca065 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_BoundingBox.cpp @@ -0,0 +1,214 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +#include +#include +#include + +#include + +namespace krino{ + +template +void +BoundingBox_T::pad_epsilon() +{ + if (!valid()) return; + + const double eps = std::numeric_limits::epsilon(); + + for (int i = 0; i < DIM; i++ ) + { + min[i] -= std::abs(min[i])*eps; + max[i] += std::abs(max[i])*eps; + } +} + +template +void +BoundingBox_T::gather_bboxes( const BoundingBox_T & local_bbox, + std::vector < BoundingBox_T > & all_bboxes ) +{ /* %TRACE% */ /* %TRACE% */ + + // + // globally communicate the bounding box sizes for all procs + // + + all_bboxes.clear(); + all_bboxes.reserve( stk::EnvData::parallel_size() ); + + // put bbox data in Real vector for communication + + std::vector bbox_data( 2*DIM ); + for (int i = 0, j = 0; i < DIM; i++ ) + { + bbox_data[j++] = local_bbox.min[i]; + bbox_data[j++] = local_bbox.max[i]; + } + + std::vector bboxes_data( 2*DIM * stk::EnvData::parallel_size() ); + stk::parallel_vector_concat(stk::EnvData::parallel_comm(), bbox_data, bboxes_data); + + VecType remote_min, remote_max; + for ( int i = 0; i < stk::EnvData::parallel_size(); i++ ) + { + int index = 2*DIM * i; + for (int j = 0; j < DIM; j++ ) + { + remote_min[j] = bboxes_data[index++]; + remote_max[j] = bboxes_data[index++]; + } + all_bboxes.emplace_back( remote_min, remote_max ); + } +} + +template +void +BoundingBox_T::global_reduce() +{ + const VecType local_min = min; + const VecType local_max = max; + + stk::all_reduce_min(stk::EnvData::parallel_comm(), local_min.data(), min.data(), 3); + stk::all_reduce_max(stk::EnvData::parallel_comm(), local_max.data(), max.data(), 3); +} + +template +REAL +BoundingBox_T::SqrDistLowerBnd( const VecType & pt ) const +{ + // make sure bbox is valid + ThrowAssert( valid() ); + + Real delta, SqrDist = 0.; + + for ( int i = 0; i < DIM; i++ ) + { + if ( pt[i] < min[i] ) + { + delta = min[i] - pt[i]; + SqrDist += delta * delta; + } + else if ( pt[i] > max[i] ) + { + delta = pt[i] - max[i]; + SqrDist += delta * delta; + } + } + return ( SqrDist ); +} + +template +REAL +BoundingBox_T::SqrDistUpperBnd( const VecType & pt ) const +{ /* %TRACE% */ /* %TRACE% */ +// make sure bbox is valid + ThrowAssert( valid() ); + + // We are guaranteed that there is a point on the surface on each face of the + // bounding box. So we know that the upper bound for the distance to a face is + // the distance to the farthest point on that face. So the upper bound for this + // bounding box is the minimum of the upper bounds for each face. In other words, + // the upper bound is the minimum distance to the farthest point on each face. + + VecType close_pt; + VecType far_pt; + + for ( int i = 0; i < DIM; i++ ) + { + if ( pt[i] < min[i] ) + { + close_pt[i] = min[i]; + far_pt[i] = max[i]; + } + else if ( pt[i] > max[i] ) + { + close_pt[i] = max[i]; + far_pt[i] = min[i]; + } + else + { + if (pt[i]-min[i] < max[i]-pt[i]) + { + close_pt[i] = min[i]; + far_pt[i] = max[i]; + } + else + { + close_pt[i] = max[i]; + far_pt[i] = min[i]; + } + } + } + + Real SqrDistMin; + if (3 == DIM) + { + SqrDistMin = (pt-VecType(close_pt[0],far_pt[1],far_pt[2])).length_squared(); + SqrDistMin = std::min(SqrDistMin,(pt-VecType(far_pt[0],close_pt[1],far_pt[2])).length_squared()); + SqrDistMin = std::min(SqrDistMin,(pt-VecType(far_pt[0],far_pt[1],close_pt[2])).length_squared()); + } + else + { + ThrowAssert(2 == DIM); + const Real zero = 0.0; + SqrDistMin = (pt-VecType(close_pt[0],far_pt[1],zero)).length_squared(); + SqrDistMin = std::min(SqrDistMin,(pt-VecType(far_pt[0],close_pt[1],zero)).length_squared()); + } + return ( SqrDistMin ); +} + +template +REAL +BoundingBox_T::SqrDistUpperBnd( const BoundingBox_T & pt_box ) const +{ /* %TRACE% */ /* %TRACE% */ + // This is somewhat conservative. More aggressive methods might be able to reduce this estimate + // while still always being an upper bound. + // Here we just estimate the upper bound of this distance from any point in pt_bbox to the + // surface contained in *this by the following: + // Loop the faces of *this. + // Find the maximum distance from any point in pt_bbox to any point of the face. + // Take the minimum of these maximum face distances. + + if( !pt_box.valid() ) + return std::numeric_limits::max(); + + // make sure bbox is valid + ThrowAssert( valid() ); + + Real SqrDistMin = 0.0; + for ( int j = 0; j < DIM; j++ ) + { + for ( int side = 0; side < 2; ++side) + { + Real SqrDistSideMin = 0.0; + for ( int i = 0; i < DIM; i++ ) + { + const Real delta = (i!=j) ? std::max(pt_box.max[i]-min[i],max[i]-pt_box.min[i]) : + ((side==0) ? std::max(min[i]-pt_box.min[i], pt_box.max[i]-min[i]) : std::max(max[i]-pt_box.min[i], pt_box.max[i]-max[i])); + ThrowAssert(delta >= 0.0); + SqrDistSideMin += delta*delta; + } + if (SqrDistMin==0.0 || SqrDistSideMin; +template class BoundingBox_T; + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_BoundingBox.hpp b/packages/krino/krino/krino_lib/Akri_BoundingBox.hpp new file mode 100644 index 000000000000..e64ce337df88 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_BoundingBox.hpp @@ -0,0 +1,212 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_BoundingBox_h +#define Akri_BoundingBox_h + +#include + +#include + +#include +#include + +namespace krino { + +template +class BoundingBox_T { + +public: + typedef REAL Real; + typedef Vec VecType; + +private: + VecType min; + VecType max; + +public: + static void gather_bboxes( const BoundingBox_T & local_bbox, + std::vector< BoundingBox_T > & all_bboxes ); + + void global_reduce(); + + template + void accommodate( const VECTYPE & pt ); + + template + void accommodate( const BoundingBox_T & bbox ); + + const VecType & get_min() const { return min; } + const VecType & get_max() const { return max; } + + template + bool contains( const VECTYPE & pt ) const; + + // Lower bound on the square of the distance from the point pt to surfaces contained in *this + Real SqrDistLowerBnd( const VecType & pt ) const; + + // Upper bound on the square of the distance from the point pt to surfaces contained in *this + Real SqrDistUpperBnd( const VecType & pt ) const; + + // Upper bound on the square of the distance from any point in pt_bbox to surfaces contained in *this + Real SqrDistUpperBnd( const BoundingBox_T & pt_box ) const; + + void pad( const Real & dist ); + void pad_epsilon(); + + void scale( const Real & fraction ); + + Real SqrSize() const; + + bool valid() const + { + bool is_not_valid = (min[0]>max[0]); + return !is_not_valid; + } + + bool intersects( const BoundingBox_T & bbox ) const; + bool contains( const BoundingBox_T & bbox ) const; + + int max_span_direction() const; + + VecType center() const { return Real(0.5)*(min+max); } + + void clear() { + min = VecType(std::numeric_limits::max(),std::numeric_limits::max(),std::numeric_limits::max()); + max = VecType(-std::numeric_limits::max(),-std::numeric_limits::max(),-std::numeric_limits::max()); + } + + template + BoundingBox_T( const VECTYPE & pt_min, + const VECTYPE & pt_max ) + : min(pt_min[0], pt_min[1], pt_min[2]), + max(pt_max[0], pt_max[1], pt_max[2]) {} + + BoundingBox_T() + : min(std::numeric_limits::max(),std::numeric_limits::max(),std::numeric_limits::max()), + max(-std::numeric_limits::max(),-std::numeric_limits::max(),-std::numeric_limits::max()) {} +}; + +template +template +inline void +BoundingBox_T::accommodate( const VECTYPE & pt ) +{ + for ( int i = 0; i < DIM; ++i ) + { + if ( pt[i] < min[i] ) min[i] = pt[i]; + if ( pt[i] > max[i] ) max[i] = pt[i]; + } +} + +template +template +inline void +BoundingBox_T::accommodate( const BoundingBox_T & bbox ) +{ + for ( int i = 0; i < DIM; ++i ) + { + if ( bbox.get_min()[i] < min[i] ) min[i] = bbox.get_min()[i]; + if ( bbox.get_max()[i] > max[i] ) max[i] = bbox.get_max()[i]; + } +} + +template +template +inline bool +BoundingBox_T::contains( const VECTYPE & pt ) const +{ + for ( int i = 0; i < DIM; ++i ) + { + if ( pt[i] < min[i] || pt[i] > max[i] ) return false; + } + return true; +} + +template +inline bool +BoundingBox_T::intersects( const BoundingBox_T & bbox ) const +{ + for ( int i = 0; i < DIM; ++i ) + { + if ( bbox.max[i] < min[i] || bbox.min[i] > max[i] ) return false; + } + return true; +} + +template +inline bool +BoundingBox_T::contains( const BoundingBox_T & bbox ) const +{ + for ( int i = 0; i < DIM; ++i ) + { + if ( bbox.min[i] < min[i] || bbox.max[i] > max[i] ) return false; + } + return true; +} + +template +inline int +BoundingBox_T::max_span_direction() const +{ + int max_dir = 0; + for ( int i = 1; i < DIM; ++i ) + { + if ( max[i] - min[i] > max[max_dir] - min[max_dir] ) max_dir = i; + } + return max_dir; +} + +template +inline REAL +BoundingBox_T::SqrSize() const +{ + Real sqrSize = 0.0; + if (valid()) + { + for ( int i = 0; i < DIM; ++i ) + { + sqrSize += (max[i]-min[i])*(max[i]-min[i]); + } + } + return sqrSize; +} + +template +inline void +BoundingBox_T::pad( const Real & dist ) +{ + if (!valid()) return; + + VecType extension; + for (int i = 0; i < DIM; i++ ) + extension[i] = dist; + + min -= extension; + max += extension; +} + +template +inline void +BoundingBox_T::scale( const Real & scale_factor ) +{ + if (!valid()) return; + + Real fraction = 0.5 * ( scale_factor - 1. ); + VecType extension; + for (int i = 0; i < DIM; i++ ) + extension[i] = fraction * ( max[i] - min[i] ); + min -= extension; + max += extension; +} + +typedef BoundingBox_T BoundingBox; + +} // namespace krino + +#endif // Akri_BoundingBox_h diff --git a/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.cpp b/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.cpp new file mode 100644 index 000000000000..32bd6e2b02b6 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.cpp @@ -0,0 +1,697 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +namespace krino{ + +BoundingBoxMesh::BoundingBoxMesh(stk::topology element_topology, const std::vector & entity_rank_names) +: m_element_topology(element_topology), m_nx(0), m_ny(0), m_nz(0) +{ + ThrowRequire(element_topology == stk::topology::TRIANGLE_3_2D || + element_topology == stk::topology::QUADRILATERAL_4_2D || + element_topology == stk::topology::TETRAHEDRON_4 || + element_topology == stk::topology::HEXAHEDRON_8); + + m_meta = std::make_unique(element_topology.dimension(), entity_rank_names); + AuxMetaData & aux_meta = AuxMetaData::create(*m_meta); + stk::mesh::Part & block_part = m_meta->declare_part_with_topology( "block_1", element_topology ); + stk::io::put_io_part_attribute(block_part); + m_elem_parts.push_back(&block_part); + m_elem_parts.push_back(&aux_meta.active_part()); + m_node_parts.push_back(&aux_meta.active_part()); + + declare_domain_side_parts(block_part); +} + +void +BoundingBoxMesh::set_domain(const BoundingBoxType & mesh_bbox, const double mesh_size, const int pad_size) +{ + m_mesh_bbox = mesh_bbox; + const Vector3d padding(0.5*mesh_size*pad_size, 0.5*mesh_size*pad_size, 0.5*mesh_size*pad_size); + m_mesh_bbox = BoundingBoxType(mesh_bbox.get_min() - padding, mesh_bbox.get_max() + padding); + + const typename BoundingBoxType::VecType min = m_mesh_bbox.get_min(); + const typename BoundingBoxType::VecType max = m_mesh_bbox.get_max(); + const typename BoundingBoxType::VecType span = max-min; + m_nx = (size_t) (0.5 + span[0] / mesh_size); + const bool isTriangularLattice = (TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType || FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType); + const double dy = isTriangularLattice ? (0.5*mesh_size*std::sqrt(3.0)) : mesh_size; + m_ny = (size_t) (0.5 + span[1] / dy); + m_nz = (m_element_topology.dimension() == 2) ? 1 : ((size_t) (0.5 + span[2] / mesh_size)); + + if (m_element_topology.dimension() == 2) + { + krinolog << "Generated mesh with for domain " + << "(min,max) = ((" << min[0] << "," << min[1] << "),("<< max[0] << "," << max[1] << ")" + << ", (nx,ny) = (" << m_nx << "," << m_ny << ")" << stk::diag::dendl; + } + else + { + krinolog << "Generated mesh with for domain " + << "(min,max) = ((" << min[0] << "," << min[1] << "," << min[2] << "),("<< max[0] << "," << max[1] << "," << max[2] << ")" + << ", (nx,ny,nz) = (" << m_nx << "," << m_ny << "," << m_nz << ")" << stk::diag::dendl; + } + +} + +void BoundingBoxMesh::set_is_cell_edge_function_for_cell_based_mesh() const +{ + const std::array N = {m_nx, m_ny, m_nz}; + const int dim = m_meta->spatial_dimension(); + ThrowRequireMsg(m_mesh, "Cannot call set_is_cell_edge_function() before BulkData is created."); + const stk::mesh::BulkData & mesh = *m_mesh; + + auto is_cell_edge = [N,dim,&mesh](stk::mesh::Entity node0, stk::mesh::Entity node1) + { + const auto node0Indices = get_node_x_y_z(mesh.identifier(node0), N); + const auto node1Indices = get_node_x_y_z(mesh.identifier(node1), N); + if (dim == 2) + { + return node0Indices[0] == node1Indices[0] || node0Indices[1] == node1Indices[1]; + } + const bool matchX = node0Indices[0] == node1Indices[0]; + const bool matchY = node0Indices[1] == node1Indices[1]; + const bool matchZ = node0Indices[2] == node1Indices[2]; + return (matchX && matchY) || (matchX && matchZ) || (matchY && matchZ); + }; + + AuxMetaData & aux_meta = AuxMetaData::get(*m_meta); + aux_meta.set_is_cell_edge_function(is_cell_edge); +} + +void BoundingBoxMesh::set_is_cell_edge_function_for_BCC_mesh() const +{ + auto is_cell_edge = [](stk::mesh::Entity node0, stk::mesh::Entity node1) + { + return true; + }; + + AuxMetaData & aux_meta = AuxMetaData::get(*m_meta); + aux_meta.set_is_cell_edge_function(is_cell_edge); +} + +void +BoundingBoxMesh::populate_mesh(stk::ParallelMachine pm, const stk::mesh::BulkData::AutomaticAuraOption auto_aura_option) +{ /* %TRACE[ON]% */ Trace trace__("krino::BoundingBoxMesh::populate_mesh()"); /* %TRACE% */ + ThrowRequireMsg(m_mesh_bbox.valid(), "Must call set_domain() before populate_mesh()"); + m_mesh = std::make_unique(*m_meta, pm, auto_aura_option); + if (CUBIC_BOUNDING_BOX_MESH == myMeshStructureType) + populate_cell_based_mesh(); + else if (TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType || FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType) + populate_2D_triangular_lattice_based_mesh(); + else if (BCC_BOUNDING_BOX_MESH == myMeshStructureType || FLAT_WALLED_BCC_BOUNDING_BOX_MESH == myMeshStructureType) + populate_BCC_mesh(); + else + ThrowRequireMsg(false, "Unsupported or unrecognized mesh structure type " << myMeshStructureType); +} + +enum BCCNode { BCC_NODE=8, BCC_NODE_XMINUS=9, BCC_NODE_XPLUS=10, BCC_NODE_YMINUS=11, BCC_NODE_YPLUS=12, BCC_NODE_ZMINUS=13, BCC_NODE_ZPLUS=14 }; + +void +BoundingBoxMesh::build_face_tets( size_t cell_id, size_t ix , size_t iy , size_t iz, int iface, const std::vector & cell_node_ids ) +{ + std::vector>> faceTets = { + {{BCC_NODE, BCC_NODE_XMINUS, 0, 4}, + {BCC_NODE, BCC_NODE_XMINUS, 4, 7}, + {BCC_NODE, BCC_NODE_XMINUS, 7, 3}, + {BCC_NODE, BCC_NODE_XMINUS, 3, 0}}, + {{BCC_NODE, BCC_NODE_XPLUS, 1, 2}, + {BCC_NODE, BCC_NODE_XPLUS, 2, 6}, + {BCC_NODE, BCC_NODE_XPLUS, 6, 5}, + {BCC_NODE, BCC_NODE_XPLUS, 5, 1}}, + {{BCC_NODE, BCC_NODE_YMINUS, 0, 1}, + {BCC_NODE, BCC_NODE_YMINUS, 1, 5}, + {BCC_NODE, BCC_NODE_YMINUS, 5, 4}, + {BCC_NODE, BCC_NODE_YMINUS, 4, 0}}, + {{BCC_NODE, BCC_NODE_YPLUS, 2, 3}, + {BCC_NODE, BCC_NODE_YPLUS, 3, 7}, + {BCC_NODE, BCC_NODE_YPLUS, 7, 6}, + {BCC_NODE, BCC_NODE_YPLUS, 6, 2}}, + {{BCC_NODE, BCC_NODE_ZMINUS, 0, 3}, + {BCC_NODE, BCC_NODE_ZMINUS, 3, 2}, + {BCC_NODE, BCC_NODE_ZMINUS, 2, 1}, + {BCC_NODE, BCC_NODE_ZMINUS, 1, 0}}, + {{BCC_NODE, BCC_NODE_ZPLUS, 4, 5}, + {BCC_NODE, BCC_NODE_ZPLUS, 5, 6}, + {BCC_NODE, BCC_NODE_ZPLUS, 6, 7}, + {BCC_NODE, BCC_NODE_ZPLUS, 7, 4}} + }; + + const stk::mesh::EntityId elem_id_start = 1; + const int num_elem_per_face = 4; + const int num_faces_per_cell = 6; + const int num_nodes_per_elem = 4; + std::vector elemNodes(num_nodes_per_elem); + + const auto & faceTet = faceTets[iface]; + for (int ielem = 0; ielem < num_elem_per_face; ++ielem) + { + stk::mesh::EntityId elem_id = num_elem_per_face*num_faces_per_cell*cell_id + num_elem_per_face*iface + ielem + elem_id_start; // Uses twice as many IDs as necessary + for (int elem_node_index = 0; elem_node_indexcoordinate_field(); + stk::mesh::EntityId nodeId = get_node_id(ix, iy, iz); + stk::mesh::Entity const node = m_mesh->get_entity( stk::topology::NODE_RANK, nodeId ); + if (m_mesh->is_valid(node)) + { + m_mesh->change_entity_parts(node, m_node_parts); + + double * coord_data = static_cast(stk::mesh::field_data( *coord_field, node )); + my_coord_mapping->get_node_coordinates(coord_data, m_meta->spatial_dimension(), {ix, iy, iz}); + } +} + +void +BoundingBoxMesh::setup_BCC_node( size_t ix , size_t iy , size_t iz, int dx, int dy, int dz ) +{ + stk::mesh::FieldBase const* coord_field = m_meta->coordinate_field(); + stk::mesh::EntityId nodeId = get_BCC_node_id(ix, iy, iz, dx, dy, dz); + stk::mesh::Entity const node = m_mesh->get_entity( stk::topology::NODE_RANK, nodeId ); + if (m_mesh->is_valid(node)) + { + m_mesh->change_entity_parts(node, m_node_parts); + + const bool flattenBoundaries = FLAT_WALLED_BCC_BOUNDING_BOX_MESH == myMeshStructureType; + double * coord_data = static_cast(stk::mesh::field_data( *coord_field, node )); + my_coord_mapping->get_BCC_node_coordinates(coord_data, m_meta->spatial_dimension(), flattenBoundaries, {ix, iy, iz}, {dx, dy, dz}); + } +} + +size_t get_triangle_lattice_node_id(size_t ix, size_t iy, size_t nx, size_t ny) +{ + return 1 + iy*(nx+1) + ix + ((iy%2 == 0) ? (iy/2) : ((iy-1)/2)); +} + +void fill_triangle_lattice_node_indices(const size_t ix, const size_t iy, std::array,3> & triNodeIndices) +{ + if (iy%2 == 0) + { + if (ix%2 == 0) + triNodeIndices = {{ {{ix/2,iy}}, {{ix/2+1,iy+1}}, {{ix/2,iy+1}} }}; + else + triNodeIndices = {{ {{(ix-1)/2,iy}}, {{(ix-1)/2+1,iy}}, {{(ix-1)/2+1,iy+1}} }}; + } + else + { + if (ix%2 == 0) + triNodeIndices = {{ {{ix/2,iy}}, {{ix/2+1,iy}}, {{ix/2,iy+1}} }}; + else + triNodeIndices = {{ {{(ix-1)/2+1,iy}}, {{(ix-1)/2+1,iy+1}}, {{(ix-1)/2,iy+1}} }}; + } +} + +void +BoundingBoxMesh::populate_2D_triangular_lattice_based_mesh() +{ /* %TRACE[ON]% */ Trace trace__("krino::BoundingBoxMesh::populate_2D_triangular_lattice_based_mesh()"); /* %TRACE% */ + ThrowRequire(m_mesh); + + const int p_size = m_mesh->parallel_size(); + const int p_rank = m_mesh->parallel_rank(); + stk::mesh::FieldBase const* coord_field = m_meta->coordinate_field(); + my_coord_mapping = std::make_unique(m_nx, m_ny, m_nz, m_mesh_bbox); + + ThrowRequire(m_element_topology == stk::topology::TRIANGLE_3_2D); + const bool flattenBoundaries = FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType; + + const size_t NelemPerSlabInY = (2*m_nx+1); + const size_t Nelem = m_ny*NelemPerSlabInY; + const size_t beg_elem = ( Nelem * p_rank ) / p_size ; + const size_t end_elem = ( Nelem * ( p_rank + 1 ) ) / p_size ; + + const size_t num_local_cells = end_elem-beg_elem; + krinolog << "BoundingBoxMesh creating " << num_local_cells << " local cells." << stk::diag::dendl; + + std::vector triNodes(3); + std::array,3> triNodeIndices; + + m_mesh->modification_begin(); + + { + for (size_t elemIndex=beg_elem; elemIndex!=end_elem; ++elemIndex) + { + const size_t iy = elemIndex / NelemPerSlabInY; + const size_t ix = elemIndex - iy*NelemPerSlabInY; + + fill_triangle_lattice_node_indices(ix, iy, triNodeIndices); + + triNodes = {get_triangle_lattice_node_id(triNodeIndices[0][0], triNodeIndices[0][1], m_nx, m_ny), + get_triangle_lattice_node_id(triNodeIndices[1][0], triNodeIndices[1][1], m_nx, m_ny), + get_triangle_lattice_node_id(triNodeIndices[2][0], triNodeIndices[2][1], m_nx, m_ny)}; + + stk::mesh::declare_element( *m_mesh, m_elem_parts, elemIndex+1, triNodes ); + + for (int n=0; n<3; ++n) + { + stk::mesh::Entity const node = m_mesh->get_entity( stk::topology::NODE_RANK , triNodes[n] ); + m_mesh->change_entity_parts(node, m_node_parts); + + double * coord_data = static_cast(stk::mesh::field_data( *coord_field, node )); + + my_coord_mapping->get_triangle_lattice_node_coordinates(coord_data, flattenBoundaries, {{triNodeIndices[n][0], triNodeIndices[n][1]}}); + } + } + stk::tools::fix_node_sharing_via_search(*m_mesh); + } + m_mesh->modification_end(); + + std::vector counts; + stk::mesh::count_entities( m_meta->locally_owned_part(), *m_mesh, counts ); + krinolog << "Generated mesh with " << counts[stk::topology::ELEM_RANK] << " local elements and " << counts[stk::topology::NODE_RANK] << " local nodes." << stk::diag::dendl; +} + +void +BoundingBoxMesh::populate_BCC_mesh() +{ /* %TRACE[ON]% */ Trace trace__("krino::BoundingBoxMesh::populate_BCC_mesh()"); /* %TRACE% */ + ThrowRequire(m_mesh); + set_is_cell_edge_function_for_BCC_mesh(); + + const int p_size = m_mesh->parallel_size(); + const int p_rank = m_mesh->parallel_rank(); + + std::vector> hex_cell_node_locations = { {0,0,0}, {1,0,0}, {1,1,0}, {0,1,0}, {0,0,1}, {1,0,1}, {1,1,1}, {0,1,1} }; + std::vector>> BCC_cell_neighbors = { {BCC_NODE,{0,0,0}}, + {BCC_NODE_XMINUS,{-1,0,0}}, {BCC_NODE_XPLUS,{+1,0,0}}, + {BCC_NODE_YMINUS,{0,-1,0}}, {BCC_NODE_YPLUS,{0,+1,0}}, + {BCC_NODE_ZMINUS,{0,0,-1}}, {BCC_NODE_ZPLUS,{0,0,+1}}}; + + my_coord_mapping = std::make_unique(m_nx, m_ny, m_nz, m_mesh_bbox); + + std::pair proc_cell_range = determine_processor_cells(p_size, p_rank); + const size_t num_local_cells = proc_cell_range.second-proc_cell_range.first; + krinolog << "BoundingBoxMesh creating " << num_local_cells << " local cells." << stk::diag::dendl; + + const int num_nodes_per_cell = 8; + const int num_nodes_per_cell_plus_BCC_nodes = 15; + std::vector cell_node_ids(num_nodes_per_cell_plus_BCC_nodes); + + m_mesh->modification_begin(); + + { + size_t count = 0; + for (size_t cell_id=proc_cell_range.first; cell_id!=proc_cell_range.second; ++cell_id) + { + size_t ix = 0, iy = 0, iz = 0; + get_cell_x_y_z(cell_id, ix, iy, iz); + + if ( count != 0 && count % 1000000 == 0) + { + krinolog << "Creating local cell " << count << " ." << stk::diag::dendl; + } + ++count; + + for (int cell_node_index=0; cell_node_indexmodification_end(); + + std::vector counts; + stk::mesh::count_entities( m_meta->locally_owned_part(), *m_mesh, counts ); + krinolog << "Generated mesh with " << counts[stk::topology::ELEM_RANK] << " local elements and " << counts[stk::topology::NODE_RANK] << " local nodes." << stk::diag::dendl; +} + +void +BoundingBoxMesh::populate_cell_based_mesh() +{ /* %TRACE[ON]% */ Trace trace__("krino::BoundingBoxMesh::populate_cell_based_mesh()"); /* %TRACE% */ + ThrowRequire(m_mesh); + set_is_cell_edge_function_for_cell_based_mesh(); + + const int p_size = m_mesh->parallel_size(); + const int p_rank = m_mesh->parallel_rank(); + const int dim = m_element_topology.dimension(); + stk::mesh::FieldBase const* coord_field = m_meta->coordinate_field(); + + std::vector> hex_cell_node_locations = { {0,0,0}, {1,0,0}, {1,1,0}, {0,1,0}, {0,0,1}, {1,0,1}, {1,1,1}, {0,1,1} }; + std::vector> hex_cell_elem_nodes = {{0, 1, 2, 3, 4, 6, 7}}; + + std::vector> tet_even_cell_elem_nodes = {{0, 1, 2, 5}, + {0, 2, 7, 5}, + {0, 2, 3, 7}, + {0, 5, 7, 4}, + {2, 7, 5, 6}}; + std::vector> tet_odd_cell_elem_nodes = {{0, 1, 3, 4}, + {1, 2, 3, 6}, + {1, 3, 4, 6}, + {3, 4, 6, 7}, + {1, 6, 4, 5}}; + + std::vector> quad_cell_node_locations = { {0,0,0}, {1,0,0}, {1,1,0}, {0,1,0} }; + std::vector> quad_cell_elem_nodes = {{0, 1, 2, 3}}; + + std::vector> tri_even_cell_elem_nodes = {{0, 1, 2}, {0, 2, 3}}; + std::vector> tri_odd_cell_elem_nodes = {{0, 1, 3}, {1, 2, 3}}; + + const std::vector> & cell_node_locations = (dim == 2) ? quad_cell_node_locations : hex_cell_node_locations; + const std::vector> & even_cell_elem_nodes = + (m_element_topology == stk::topology::TRIANGLE_3_2D) ? tri_even_cell_elem_nodes : + ((m_element_topology == stk::topology::QUADRILATERAL_4) ? quad_cell_elem_nodes : + ((m_element_topology == stk::topology::TETRAHEDRON_4) ? tet_even_cell_elem_nodes : + hex_cell_elem_nodes)); + const std::vector> & odd_cell_elem_nodes = + (m_element_topology == stk::topology::TRIANGLE_3_2D) ? tri_odd_cell_elem_nodes : + ((m_element_topology == stk::topology::QUADRILATERAL_4) ? quad_cell_elem_nodes : + ((m_element_topology == stk::topology::TETRAHEDRON_4) ? tet_odd_cell_elem_nodes : + hex_cell_elem_nodes)); + + std::unordered_map> nodes_to_procs; + generate_node_to_processor_map(p_size, p_rank, cell_node_locations, nodes_to_procs); + const int num_elem_per_cell = even_cell_elem_nodes.size(); + const int num_nodes_per_cell = cell_node_locations.size(); + const int num_nodes_per_elem = even_cell_elem_nodes[0].size(); + const stk::mesh::EntityId elem_id_start = 1; + std::vector cell_node_ids(num_nodes_per_cell); + std::vector elem_nodes(num_nodes_per_elem); + + my_coord_mapping = std::make_unique(m_nx, m_ny, m_nz, m_mesh_bbox); + + std::pair proc_cell_range = determine_processor_cells(p_size, p_rank); + const size_t num_local_cells = proc_cell_range.second-proc_cell_range.first; + krinolog << "BoundingBoxMesh creating " << num_local_cells << " local cells." << stk::diag::dendl; + + m_mesh->modification_begin(); + + { + size_t count = 0; + for (size_t cell_id=proc_cell_range.first; cell_id!=proc_cell_range.second; ++cell_id) + { + size_t ix = 0, iy = 0, iz = 0; + get_cell_x_y_z(cell_id, ix, iy, iz); + + const std::vector> & cell_elem_nodes = ((ix+iy+iz)%2 == 0) ? even_cell_elem_nodes : odd_cell_elem_nodes; + + if ( count % 1000000 == 0) + { + krinolog << "Creating local cell " << count << " ." << stk::diag::dendl; + } + ++count; + + for (int cell_node_index=0; cell_node_indexget_entity( stk::topology::NODE_RANK , node_id ); + m_mesh->change_entity_parts(node, m_node_parts); + + auto map_it = nodes_to_procs.find(node_id); + if (map_it != nodes_to_procs.end()) + { + for (auto other_proc : map_it->second) + { + m_mesh->add_node_sharing(node, other_proc); + } + } + + // Compute and assign coordinates to the node + get_node_x_y_z(node_id, ix, iy, iz); + + double * coord_data = static_cast(stk::mesh::field_data( *coord_field, node )); + my_coord_mapping->get_node_coordinates(coord_data, dim, {ix, iy, iz}); + } + } + } + } + m_mesh->modification_end(); + + std::vector counts; + stk::mesh::count_entities( m_meta->locally_owned_part(), *m_mesh, counts ); + krinolog << "Generated mesh with " << counts[stk::topology::ELEM_RANK] << " local elements and " << counts[stk::topology::NODE_RANK] << " local nodes." << stk::diag::dendl; +} + +void +BoundingBoxMesh::declare_domain_side_parts(const stk::mesh::Part & blockPart) +{ + AuxMetaData & aux_meta = AuxMetaData::get(*m_meta); + + stk::topology side_topology = m_element_topology.side_topology(); + + mySideParts.clear(); + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Xminus", side_topology)); + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Xplus", side_topology)); + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Yminus", side_topology)); + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Yplus", side_topology)); + if (m_meta->spatial_dimension() == 3) + { + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Zminus", side_topology)); + mySideParts.push_back(&aux_meta.declare_io_part_with_topology("Zplus", side_topology)); + } + + for (auto && sidePart : mySideParts) + m_meta->set_surface_to_block_mapping(sidePart, {&blockPart}); +} + +void BoundingBoxMesh::require_has_flat_boundaries() const +{ + ThrowRequireMsg(has_flat_boundaries(), "Domain sides can only be added for CUBIC or FLAT_WALLED_BC generated meshes."); +} + +static bool equal_within_tol(const double x1, const double x2, const double tol) +{ + return std::abs(x1-x2) < tol; +} + +void +BoundingBoxMesh::create_domain_sides() +{ + if (mySideParts.empty()) + return; + + require_has_flat_boundaries(); + + AuxMetaData & aux_meta = AuxMetaData::get(*m_meta); + stk::mesh::create_exposed_block_boundary_sides(*m_mesh, m_meta->universal_part(), {&aux_meta.exposed_boundary_part()}); + + stk::topology side_topology = m_element_topology.side_topology(); + ThrowRequire(mySideParts.size() >= m_meta->spatial_dimension()*2); + + std::vector sides; + stk::mesh::get_selected_entities( aux_meta.exposed_boundary_part() & m_meta->locally_owned_part(), m_mesh->buckets( m_meta->side_rank() ), sides ); + std::vector add_parts(sides.size()); + std::vector remove_parts(sides.size()); + stk::mesh::FieldBase const* coord_field = m_meta->coordinate_field(); + + const auto & min = m_mesh_bbox.get_min(); + const auto & max = m_mesh_bbox.get_max(); + const double relativeTol = 0.01; // should not be at all sensitive to this tolerance + const std::array tol {(max[0]-min[0])/m_nx*relativeTol, (max[1]-min[1])/m_ny*relativeTol, ((m_meta->spatial_dimension() == 3) ? ((max[2]-min[2])/m_nz*relativeTol) : 0.)}; + + const unsigned num_side_nodes = side_topology.num_nodes(); + for (size_t iside=0; isidebegin_nodes(sides[iside]); + std::array domainSide {-2,-2,-2}; + for (unsigned n=0; n(stk::mesh::field_data( *coord_field, side_nodes[n] )); + for (unsigned i=0; ispatial_dimension(); ++i ) + { + if (equal_within_tol(coords[i],min[i],tol[i])) + { + ThrowRequire(domainSide[i] != 1); + if (domainSide[i] == -2) domainSide[i] = -1; + } + else if (equal_within_tol(coords[i],max[i],tol[i])) + { + ThrowRequire(domainSide[i] != -1); + if (domainSide[i] == -2) domainSide[i] = 1; + } + else + { + domainSide[i] = 0; + } + } + } + + const int num_sides_set = ((domainSide[0]==-1||domainSide[0]==1) ? 1 : 0) + ((domainSide[1]==-1||domainSide[1]==1) ? 1 : 0) + ((domainSide[2]==-1||domainSide[2]==1) ? 1 : 0); + ThrowRequire(num_sides_set == 1); + stk::mesh::Part * side_part = nullptr; + if (domainSide[0] == -1) side_part = mySideParts[0]; + else if (domainSide[0] == 1) side_part = mySideParts[1]; + else if (domainSide[1] == -1) side_part = mySideParts[2]; + else if (domainSide[1] == 1) side_part = mySideParts[3]; + else if (domainSide[2] == -1) side_part = mySideParts[4]; + else if (domainSide[2] == 1) side_part = mySideParts[5]; + + add_parts[iside].push_back(side_part); + } + + m_mesh->batch_change_entity_parts(sides, add_parts, remove_parts); +} + +void +BoundingBoxMesh::get_cell_x_y_z( stk::mesh::EntityId cell_id, size_t &ix , size_t &iy , size_t &iz ) const +{ + ix = cell_id % m_nx; + cell_id /= m_nx; + + iy = cell_id % m_ny; + cell_id /= m_ny; + + iz = cell_id; +} + +std::array +BoundingBoxMesh::get_node_x_y_z( stk::mesh::EntityId entity_id, const std::array & N ) +{ + const size_t node_id_start = 1; + entity_id -= node_id_start; + + std::array indices; + indices[0] = entity_id % (N[0]+1); + entity_id /= (N[0]+1); + + indices[1] = entity_id % (N[1]+1); + entity_id /= (N[2]+1); + + indices[2] = entity_id; + return indices; +} + +void +BoundingBoxMesh::get_node_x_y_z( stk::mesh::EntityId entity_id, size_t &ix , size_t &iy , size_t &iz ) const +{ + auto indices = get_node_x_y_z(entity_id, {{m_nx,m_ny,m_nz}}); + ix = indices[0]; + iy = indices[1]; + iz = indices[2]; +} + +std::pair +BoundingBoxMesh::determine_processor_cells(const int p_size, const int p_rank) const +{ + const size_t Ntot = m_nx*m_ny*m_nz; + const size_t beg_elem = ( Ntot * p_rank ) / p_size ; + const size_t end_elem = ( Ntot * ( p_rank + 1 ) ) / p_size ; + return std::make_pair(beg_elem, end_elem); +} + +void +BoundingBoxMesh::generate_node_to_processor_map(const int p_size, + const int p_rank, + const std::vector> & cell_node_locations, + std::unordered_map> & nodes_to_procs) const +{ + std::unordered_set locally_used_nodes; + + std::pair proc_cell_range = determine_processor_cells(p_size, p_rank); + + // First create set of all nodes used by local elements + for (size_t cell_id=proc_cell_range.first; cell_id!=proc_cell_range.second; ++cell_id) + { + size_t ix = 0, iy = 0, iz = 0; + get_cell_x_y_z(cell_id, ix, iy, iz); + + for (size_t cell_node_index=0; cell_node_index other_proc_cell_range = determine_processor_cells(p_size, other_p_rank); + + for (size_t cell_id=other_proc_cell_range.first; cell_id!=other_proc_cell_range.second; ++cell_id) + { + size_t ix = 0, iy = 0, iz = 0; + get_cell_x_y_z(cell_id, ix, iy, iz); + + for (size_t cell_node_index=0; cell_node_index & node_procs = nodes_to_procs[nodeId]; + if (std::find(node_procs.begin(), node_procs.end(), other_p_rank) == node_procs.end()) + { + node_procs.push_back(other_p_rank); + } + } + } + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.hpp b/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.hpp new file mode 100644 index 000000000000..45572ed5ea79 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_BoundingBoxMesh.hpp @@ -0,0 +1,157 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_BoundingBoxMesh_h +#define Akri_BoundingBoxMesh_h + +#include +#include +#include +#include +#include + +namespace krino { + +class CartesianCoordinateMapping +{ +public: + CartesianCoordinateMapping(const size_t nx, const size_t ny, const size_t nz, + const BoundingBox_T & bbox) + : m_N{nx, ny, nz}, + m_bbox(bbox) + {} + void get_node_coordinates(double * node_coords, const int spatial_dim, const std::array & ijk) const + { + const Vector3d & min = m_bbox.get_min(); + const Vector3d & max = m_bbox.get_max(); + for (int i=0; i < spatial_dim; ++i) + node_coords[i] = min[i] + (max[i]-min[i])*ijk[i]/m_N[i]; + } + void get_triangle_lattice_node_coordinates(double * node_coords, const bool flattenBoundaries, const std::array & ij) const + { + const Vector3d & min = m_bbox.get_min(); + const Vector3d & max = m_bbox.get_max(); + const double offset = ij[1]%2==0 ? 0.0 : -0.5; + node_coords[0] = min[0] + (max[0]-min[0])/m_N[0] * (ij[0]+offset); + if (flattenBoundaries) + node_coords[0] = std::min(max[0], std::max(min[0], node_coords[0])); + node_coords[1] = min[1] + (max[1]-min[1])/m_N[1] * ij[1]; + } + void get_BCC_node_coordinates(double * node_coords, const int spatial_dim, const bool flattenBoundaries, const std::array & ijk, const std::array & dijk) const + { + const Vector3d & min = m_bbox.get_min(); + const Vector3d & max = m_bbox.get_max(); + for (int i=0; i < spatial_dim; ++i) + { + node_coords[i] = min[i] + (max[i]-min[i])*(0.5+ijk[i]+dijk[i])/m_N[i]; + if (flattenBoundaries) + node_coords[i] = std::min(max[i], std::max(min[i], node_coords[i])); + } + } +private: + const std::array m_N; + const BoundingBox_T m_bbox; +}; + +enum BoundingBoxMeshStructureType +{ + CUBIC_BOUNDING_BOX_MESH = 0, + BCC_BOUNDING_BOX_MESH = 1, + FLAT_WALLED_BCC_BOUNDING_BOX_MESH = 2, + TRIANGULAR_LATTICE_BOUNDING_BOX_MESH = 3, + FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH = 4 +}; + +class BoundingBoxMesh { +public: + typedef BoundingBox_T BoundingBoxType; + static std::array get_node_x_y_z( stk::mesh::EntityId entity_id, const std::array & N ); + +public: + BoundingBoxMesh(stk::topology element_topology, const std::vector& rank_names = std::vector()); + void set_domain(const BoundingBoxType & mesh_bbox, const double mesh_size, const int pad_cells = 0); + void populate_mesh(stk::ParallelMachine pm = MPI_COMM_WORLD, const stk::mesh::BulkData::AutomaticAuraOption auto_aura_option = stk::mesh::BulkData::AUTO_AURA); + stk::mesh::MetaData & meta_data() { ThrowAssert( nullptr != m_meta.get() ) ; return *m_meta; } + stk::mesh::BulkData & bulk_data() { ThrowAssert( nullptr != m_mesh.get() ) ; return *m_mesh; } + const stk::mesh::MetaData & meta_data() const { ThrowAssert( nullptr != m_meta.get() ) ; return *m_meta; } + const stk::mesh::BulkData & bulk_data() const { ThrowAssert( nullptr != m_mesh.get() ) ; return *m_mesh; } + + void create_domain_sides(); + const CartesianCoordinateMapping & get_coord_mapping() const { return *my_coord_mapping; } + void get_node_x_y_z( stk::mesh::EntityId entity_id, size_t &ix , size_t &iy , size_t &iz ) const; + void set_mesh_structure_type(BoundingBoxMeshStructureType type) { myMeshStructureType = type; } + bool has_flat_boundaries() const { return CUBIC_BOUNDING_BOX_MESH == myMeshStructureType || FLAT_WALLED_BCC_BOUNDING_BOX_MESH == myMeshStructureType || FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == myMeshStructureType; } +private: + void declare_domain_side_parts(const stk::mesh::Part & blockPart); + void require_has_flat_boundaries() const; + void populate_2D_triangular_lattice_based_mesh(); + void populate_BCC_mesh(); + void populate_cell_based_mesh(); + void setup_cell_node( size_t ix , size_t iy , size_t iz ); + void setup_BCC_node( size_t ix , size_t iy , size_t iz, int dx, int dy, int dz ); + void build_face_tets( size_t cell_id, size_t ix , size_t iy , size_t iz, int iface, const std::vector & cell_node_ids ); + stk::mesh::EntityId get_node_id(const size_t ix, const size_t iy, const size_t iz ) const + { + const size_t node_id_start = 1; + return node_id_start + ix + ( m_nx + 1 ) * ( iy + ( m_ny + 1 ) * iz ); + } + stk::mesh::EntityId get_BCC_node_id(const size_t ix, const size_t iy, const size_t iz, const int dx, const int dy, const int dz ) const + { + const size_t node_id_start = 1; + const size_t num_nodes = ( m_nx + 1 ) * ( m_ny + 1 ) * ( m_nz + 1 ); + return node_id_start + num_nodes + (ix+1+dx) + ( m_nx + 2 ) * ( (iy+1+dy) + ( m_ny + 2 ) * (iz+1+dz) ); + } + void get_cell_x_y_z( stk::mesh::EntityId cell_id, size_t &ix , size_t &iy , size_t &iz ) const; + std::pair determine_processor_cells(const int p_size, const int p_rank) const; + void generate_node_to_processor_map(const int p_size, + const int p_rank, + const std::vector> & cell_node_locations, + std::unordered_map> & nodes_to_procs) const; + void set_is_cell_edge_function_for_BCC_mesh() const; + void set_is_cell_edge_function_for_cell_based_mesh() const; +private: + std::unique_ptr m_meta; + std::unique_ptr m_mesh; + std::unique_ptr my_coord_mapping; + stk::mesh::PartVector m_elem_parts; + stk::mesh::PartVector m_node_parts; + const stk::topology m_element_topology; + BoundingBoxMeshStructureType myMeshStructureType{CUBIC_BOUNDING_BOX_MESH}; + size_t m_nx, m_ny, m_nz; + BoundingBoxType m_mesh_bbox; + std::vector mySideParts; +}; + +class BoundingBoxMeshTri3 : public BoundingBoxMesh +{ +public: + BoundingBoxMeshTri3() : BoundingBoxMesh(stk::topology::TRIANGLE_3_2D) {} +}; + +class BoundingBoxMeshQuad4 : public BoundingBoxMesh +{ +public: + BoundingBoxMeshQuad4() : BoundingBoxMesh(stk::topology::QUADRILATERAL_4_2D) {} +}; + +class BoundingBoxMeshTet4 : public BoundingBoxMesh +{ +public: + BoundingBoxMeshTet4() : BoundingBoxMesh(stk::topology::TETRAHEDRON_4) {} +}; + +class BoundingBoxMeshHex8 : public BoundingBoxMesh +{ +public: + BoundingBoxMeshHex8() : BoundingBoxMesh(stk::topology::HEXAHEDRON_8) {} +}; + +} // namespace krino + +#endif // Akri_BoundingBoxMesh_h diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.cpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.cpp new file mode 100644 index 000000000000..b856b61eed17 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.cpp @@ -0,0 +1,636 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include + +namespace krino{ + +CDFEM_Parent_Edge::CDFEM_Parent_Edge(const std::vector & edgeNodes, + const std::vector & edgeNodePositions) +: my_edge_nodes(edgeNodes), + my_edge_node_positions(edgeNodePositions) +{ +} + +double CDFEM_Parent_Edge::MinSize() +{ + return SegmentLowerEnvelope::MinSize(); +} + +double CDFEM_Parent_Edge::get_edge_node_position(stk::mesh::Entity edgeNode) const +{ + for (size_t i=0; isecond << " "; + } + krinolog << "}" << "\n"; +} + +void +CDFEM_Parent_Edge::find_crossings(const std::vector > & nodes_isovar) +{ + my_crossings.clear(); + my_crossing_signs.clear(); + + const int num_nodes = get_num_nodes(); + ThrowAssert(static_cast(nodes_isovar.size()) == num_nodes); + const int num_ls = nodes_isovar[0].size(); + if (num_ls > 1 && Phase_Support::has_one_levelset_per_phase()) + { + find_crossings_multiple_levelset(nodes_isovar); + find_crossings_including_fake_ones(nodes_isovar); + return; + } + + // TODO: respect minimum_internal_edge_size + + for ( int ls_index = 0; ls_index < num_ls; ++ls_index ) + { + InterfaceID iface(ls_index, ls_index); + my_crossing_signs[iface] = LevelSet::sign(nodes_isovar[num_nodes-1][ls_index]); + if( !LevelSet::sign_change(nodes_isovar[0][ls_index], nodes_isovar[num_nodes-1][ls_index]) ) continue; + for ( int s = 0; s < num_nodes-1; ++s ) + { + const double ls0 = nodes_isovar[s][ls_index]; + const double ls1 = nodes_isovar[s+1][ls_index]; + if ( LevelSet::sign_change(ls0, ls1) ) + { + const double interval_position = ls0 / ( ls0 - ls1 ); + const double abs_position = (1.-interval_position)*my_edge_node_positions[s] + interval_position*my_edge_node_positions[s+1]; + my_crossings[iface] = abs_position; + my_crossing_signs[iface] = LevelSet::sign(ls1); + } + } + } + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + debug_print_crossings(); + } +} + +std::vector*> get_sorted_internal_crossings(CrossingMap & crossings) +{ + std::vector*> sortedCrossings; + sortedCrossings.reserve(crossings.size()); + for (auto && crossing : crossings) + if (crossing.second > 0. && crossing.second < 1.) + sortedCrossings.push_back(&crossing); + + std::sort(sortedCrossings.begin(), sortedCrossings.end(), + [](const std::pair* crossing0, const std::pair* crossing1) + { return crossing0->second < crossing1->second || (crossing0->second == crossing1->second && crossing0->first < crossing1->first); }); + return sortedCrossings; +} + +void collapse_small_internal_segments_while_perserving_topology(CrossingMap &crossings, const double snapTol) +{ + const std::vector*> sortedCrossings = get_sorted_internal_crossings(crossings); + + bool done = false; + while (!done) + { + size_t minSegment = 0; + double minSegmentSize = snapTol; + for (size_t i=1; isecond - sortedCrossings[i-1]->second); + if (segmentSize > 0 && segmentSize <= minSegmentSize) + { + minSegment = i; + minSegmentSize = segmentSize; + } + } + done = minSegment == 0; + if (!done) + { + double & loc0 = sortedCrossings[minSegment-1]->second; + double & loc1 = sortedCrossings[minSegment]->second; + const double newLoc = 0.5*(loc0+loc1); + loc0 = newLoc; + loc1 = newLoc; + } + } +} + +void CDFEM_Parent_Edge::collapse_small_segments_while_preserving_topology(const double snapTol) +{ + for (auto && crossing : my_crossings) + { + if (crossing.second <= snapTol) + crossing.second = 0.0; + else if (crossing.second >= 1.-snapTol ) + crossing.second = 1.0; + } + collapse_small_internal_segments_while_perserving_topology(my_crossings, snapTol); +} + +std::vector get_effective_sorted_parent_node_domains(const int parentNodeIndex, const CrossingMap & crossings, const std::vector & sortedParentNodeDomains) +{ + std::vector effectiveSortedParentNodeDomains = sortedParentNodeDomains; + double endPoint = (parentNodeIndex == 0) ? 0. : 1.; + for (auto && crossing : crossings) + { + if (std::binary_search(sortedParentNodeDomains.begin(), sortedParentNodeDomains.end(), crossing.first.first_ls()) || + std::binary_search(sortedParentNodeDomains.begin(), sortedParentNodeDomains.end(), crossing.first.second_ls())) + { + endPoint = (parentNodeIndex == 0) ? std::max(endPoint, crossing.second) : std::min(endPoint, crossing.second); + } + } + for (auto && crossing : crossings) + { + const bool inRange = (parentNodeIndex == 0) ? (crossing.second < endPoint) : (crossing.second > endPoint); + if (inRange) + { + effectiveSortedParentNodeDomains.push_back(crossing.first.first_ls()); + effectiveSortedParentNodeDomains.push_back(crossing.first.second_ls()); + } + } + + stk::util::sort_and_unique(effectiveSortedParentNodeDomains); + return effectiveSortedParentNodeDomains; +} + +void adjust_crossing_locations_based_on_node_captured_domains_for_level_set_per_interface(const std::vector & sortedParentNode0Domains, const std::vector & sortedParentNode1Domains, CrossingMap & crossings) +{ + if (sortedParentNode0Domains.empty() && sortedParentNode1Domains.empty()) + return; + + for (auto && crossing : crossings) + { + const InterfaceID & iface = crossing.first; + ThrowAssert(iface.first_ls() == iface.second_ls()); + const bool in0 = std::binary_search(sortedParentNode0Domains.begin(), sortedParentNode0Domains.end(), iface.first_ls()); + const bool in1 = std::binary_search(sortedParentNode1Domains.begin(), sortedParentNode1Domains.end(), iface.first_ls()); + + double & loc = crossing.second; + if (in0 && (!in1 || loc<0.5)) + loc = 0.; + else if (in1 && (!in0 || loc>=0.5)) + loc = 1.; + } +} + +void adjust_crossing_locations_based_on_node_captured_domains_for_level_set_per_phase(const int parentNodeIndex, const std::vector & sortedParentNodeDomains, CrossingMap & allCrossings) +{ + if (sortedParentNodeDomains.empty()) + return; + + ThrowAssert(parentNodeIndex == 0 || parentNodeIndex == 1); + const double nodePos = (parentNodeIndex == 0) ? 0. : 1.; + + double furthestLocationToAdjust = (parentNodeIndex == 0) ? 0. : 1.; + for (auto && crossing : allCrossings) + { + const InterfaceID & iface = crossing.first; + if (std::binary_search(sortedParentNodeDomains.begin(), sortedParentNodeDomains.end(), iface.first_ls()) && + std::binary_search(sortedParentNodeDomains.begin(), sortedParentNodeDomains.end(), iface.second_ls())) + { + furthestLocationToAdjust = (parentNodeIndex == 0) ? std::max(furthestLocationToAdjust, crossing.second) : std::min(furthestLocationToAdjust, crossing.second); + crossing.second = nodePos; + } + } + + for (auto && crossing : allCrossings) + { + if ((parentNodeIndex == 0 && crossing.second < furthestLocationToAdjust) || + (parentNodeIndex == 1 && crossing.second > furthestLocationToAdjust)) + { + crossing.second = nodePos; + } + } +} + +void adjust_crossing_locations_based_on_node_captured_domains_for_level_set_per_phase(const std::vector & sortedParentNode0Domains, const std::vector & sortedParentNode1Domains, CrossingMap & allCrossings) +{ + if (sortedParentNode0Domains.empty() && sortedParentNode1Domains.empty()) + return; + + double highestLocToSendTo0 = 0.; + double lowestLocToSendTo1 = 1.; + for (auto && crossing : allCrossings) + { + const InterfaceID & iface = crossing.first; + const bool in0 = + std::binary_search(sortedParentNode0Domains.begin(), sortedParentNode0Domains.end(), iface.first_ls()) && + std::binary_search(sortedParentNode0Domains.begin(), sortedParentNode0Domains.end(), iface.second_ls()); + const bool in1 = + std::binary_search(sortedParentNode1Domains.begin(), sortedParentNode1Domains.end(), iface.first_ls()) && + std::binary_search(sortedParentNode1Domains.begin(), sortedParentNode1Domains.end(), iface.second_ls()); + + double & loc = crossing.second; + if (in0 && (!in1 || loc<0.5)) + { + highestLocToSendTo0 = std::max(loc, highestLocToSendTo0); + loc = 0.; + } + if (in1 && (!in0 || loc>=0.5)) + { + highestLocToSendTo0 = std::min(loc, lowestLocToSendTo1); + loc = 1.; + } + } + + for (auto && crossing : allCrossings) + { + double & loc = crossing.second; + if (loc < highestLocToSendTo0) + loc = 0.; + if (loc > lowestLocToSendTo1) + loc = 1.; + } +} + +void copy_real_crossing_locations_to_fake_crossing_locations(const CrossingMap & realCrossings, CrossingMap & allCrossings) +{ + for (auto && crossing : allCrossings) + { + auto iter = realCrossings.find(crossing.first); + if (iter != realCrossings.end()) + crossing.second = iter->second; + } +} + +std::pair get_begin_and_end_phases(const CrossingMap & realCrossings, const CrossingSignMap & realCrossingSign) +{ + double begLoc = 1.; + double endLoc = 0.; + int begPhase = -1; + int endPhase = -1; + for (auto && crossing : realCrossings) + { + const InterfaceID iface = crossing.first; + const double loc = crossing.second; + const int sign = realCrossingSign.at(iface); + const int fromPhase = (sign == 1) ? iface.first_ls() : iface.second_ls(); + if (loc < begLoc || (loc == begLoc && fromPhase > begPhase)) + { + begPhase = fromPhase; + begLoc = loc; + } + const int toPhase = (sign == -1) ? iface.first_ls() : iface.second_ls(); + if (loc > endLoc || (loc == endLoc && toPhase > endPhase)) + { + endPhase = toPhase; + endLoc = loc; + } + } + return {begPhase,endPhase}; +} + +static double find_next_crossing_location(const CrossingMap & crossings, + const CrossingSignMap & crossingSigns, + const double currentLocation, + const int currentPhase) +{ + double nextLocation = 1.; + for (auto && crossing : crossings) + { + if (crossing.second >= currentLocation) + { + const InterfaceID iface = crossing.first; + const int fromPhase = (crossingSigns.at(iface) == 1) ? iface.first_ls() : iface.second_ls(); + if (fromPhase == currentPhase) + nextLocation = std::min(nextLocation, crossing.second); + } + } + return nextLocation; +} + +static std::vector find_next_phase_candidates_at_location(const CrossingMap & crossings, + const CrossingSignMap & crossingSigns, + const double nextLocation, + const int currentPhase) +{ + std::vector nextPhaseCandidates; + for (auto && crossing : crossings) + { + if (crossing.second == nextLocation) + { + const InterfaceID iface = crossing.first; + const int sign = crossingSigns.at(iface); + const int fromPhase = (sign == 1) ? iface.first_ls() : iface.second_ls(); + if (fromPhase == currentPhase) + { + const int toPhase = (sign == -1) ? iface.first_ls() : iface.second_ls(); + nextPhaseCandidates.push_back(toPhase); + } + } + } + return nextPhaseCandidates; +} + +std::vector find_next_phase_candidates(const CrossingMap & crossings, + const CrossingSignMap & crossingSigns, + const double currentLocation, + const int currentPhase) +{ + const double nextLocation = find_next_crossing_location(crossings, crossingSigns, currentLocation, currentPhase); + return find_next_phase_candidates_at_location(crossings, crossingSigns, nextLocation, currentPhase); +} + +std::vector> shortest_path_to_end(const std::vector> & pathSoFar, + const CrossingMap & crossings, + const CrossingSignMap & crossingSigns, + const double currentLocation, + const int currentPhase, + const int endPhase) +{ + const std::vector nextPhaseCandidates = find_next_phase_candidates(crossings, crossingSigns, currentLocation, currentPhase); + if (nextPhaseCandidates.empty()) + { + if (currentPhase == endPhase) + return pathSoFar; + else + return {}; + } + + std::vector> shortestPath; + size_t shortestPathSize = std::numeric_limits::max(); + for (int nextPhase : nextPhaseCandidates) + { + std::vector> path = pathSoFar; + const InterfaceID iface(currentPhase, nextPhase); + const double nextLocation = crossings.at(iface); + path.emplace_back(iface, nextLocation); + const auto fullPath = shortest_path_to_end(path, crossings, crossingSigns, nextLocation, nextPhase, endPhase); + if (!fullPath.empty() && fullPath.size() < shortestPathSize) + { + shortestPath = fullPath; + shortestPathSize = fullPath.size(); + } + } + return shortestPath; +} + +std::vector> shortest_path_from_begin_to_end(const CrossingMap & crossings, + const CrossingSignMap & crossingSigns, + const int beginPhase, + const int endPhase) +{ + std::vector> emptyPath; + double beginLocation = -1.; + return shortest_path_to_end(emptyPath, crossings, crossingSigns, beginLocation, beginPhase, endPhase); +} + +bool determine_real_crossings_from_locations(CrossingMap & realCrossings, CrossingSignMap & realCrossingSigns, std::set & edgePhases, const CrossingMap & allCrossings, const CrossingSignMap & allCrossingSigns) +{ + const auto begEndPhases = get_begin_and_end_phases(realCrossings, realCrossingSigns); + + if (begEndPhases.first == begEndPhases.second) + { + return true; + } + + realCrossings.clear(); + realCrossingSigns.clear(); + edgePhases.clear(); + + const auto shortestPath = shortest_path_from_begin_to_end(allCrossings, allCrossingSigns, begEndPhases.first, begEndPhases.second); + if (shortestPath.empty()) + return false; + + for (auto && crossing : shortestPath) + { + realCrossings[crossing.first] = crossing.second; + realCrossingSigns[crossing.first] = allCrossingSigns.at(crossing.first); + edgePhases.insert(crossing.first.first_ls()); + edgePhases.insert(crossing.first.second_ls()); + } + return true; +} + +void CDFEM_Parent_Edge::adjust_crossing_locations_based_on_node_captured_domains(const std::vector & sortedParentNode0Domains, const std::vector & sortedParentNode1Domains) +{ + if (sortedParentNode0Domains.empty() && sortedParentNode1Domains.empty()) + return; + if (Phase_Support::has_one_levelset_per_phase()) + { + if (my_crossings_including_fake.empty()) + return; + + adjust_crossing_locations_based_on_node_captured_domains_for_level_set_per_phase(sortedParentNode0Domains, sortedParentNode1Domains, my_crossings_including_fake); + + const bool success = determine_real_crossings_from_locations(my_crossings, my_crossing_signs, edge_phases, my_crossings_including_fake, my_crossing_signs_including_fake); + if (!success) + krinolog << "Failed to adjust crossings " << *this << stk::diag::dendl; + } + else + { + if (my_crossings.empty()) + return; + adjust_crossing_locations_based_on_node_captured_domains_for_level_set_per_interface(sortedParentNode0Domains, sortedParentNode1Domains, my_crossings); + } +} + +void +CDFEM_Parent_Edge::find_crossings_multiple_levelset(const std::vector > & nodes_isovar) +{ + const Segment_Vector lower_envelope = SegmentLowerEnvelope::find_lower_envelope(my_edge_node_positions, nodes_isovar); + + edge_phases.clear(); + for(auto && it : lower_envelope) + { + edge_phases.insert(it.ls_index()); + } + + // Create crossings between the segments of the lower_envelope + for(Segment_Vector::const_iterator it = lower_envelope.begin(); it != lower_envelope.end()-1; ++it) + { + const LS_Segment & cur = *it; + const LS_Segment & next = *(it+1); + if (cur.ls_index() == next.ls_index()) continue; + + const double cur_right = cur.right_endpoint(); + const double next_left = next.left_endpoint(); + ThrowRequire(cur_right == next_left); + ThrowRequire(cur.ls_index() != next.ls_index()); + InterfaceID iface(cur.ls_index(), next.ls_index()); + ThrowRequireMsg(my_crossings.find(iface) == my_crossings.end(), "Multiple interface crossing error after pruning."); + my_crossings[iface] = cur_right; + my_crossing_signs[iface] = (cur.ls_index() < next.ls_index()) ? 1 : -1; + } + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + debug_print_crossings(); + } +} + +bool +CDFEM_Parent_Edge::have_any_crossings() const +{ + return !my_crossings.empty(); +} + +std::tuple +CDFEM_Parent_Edge::get_crossing_position_and_sign(const InterfaceID key) const +{ + ThrowRequire(Phase_Support::has_one_levelset_per_phase()); + + if(have_crossing(key)) + { + return std::make_tuple(get_crossing_position(key), get_crossing_sign(key), false); + } + + return std::make_tuple(get_fake_crossing_position(key), get_fake_crossing_sign(key), true); +} + +typedef std::array*,2> CrossingInterval; + +static CrossingInterval get_crossing_interval(const CDFEM_Parent_Edge & edge, const std::pair & fakeCrossing) +{ + const double fakeLoc = fakeCrossing.second; + const std::pair * before = nullptr; + const std::pair * after = nullptr; + for (auto && crossing : edge.get_crossings()) + { + const double loc = crossing.second; + if (loc == fakeLoc) + { + return {&crossing, &crossing}; + } + else if (loc < fakeLoc) + { + if (before == nullptr || loc > before->second) + before = &crossing; + } + else + { + if (after == nullptr || loc < after->second) + after = &crossing; + } + } + return {before, after}; +} + +static int get_phase_on_interval(const CDFEM_Parent_Edge & edge, const CrossingInterval & crossingInterval) +{ + const std::pair * before = crossingInterval[0]; + const std::pair * after = crossingInterval[1]; + ThrowRequire(before != nullptr || after != nullptr); + if (before != nullptr) + { + return (edge.get_crossing_sign(before->first) == -1) ? before->first.first_ls() : before->first.second_ls(); + } + return (edge.get_crossing_sign(after->first) == -1) ? after->first.second_ls() : after->first.first_ls(); +} + +static bool fake_crossing_is_actually_real(const CDFEM_Parent_Edge & edge, const CrossingInterval & crossingInterval, const std::pair & fakeCrossing) +{ + if (crossingInterval[0] != crossingInterval[1]) + { + const int phaseOnInterval = get_phase_on_interval(edge, crossingInterval); + const InterfaceID fakeInterface = fakeCrossing.first; + const bool crossingIsActuallyReal = (fakeInterface.first_ls() == phaseOnInterval || fakeInterface.second_ls() == phaseOnInterval); + return crossingIsActuallyReal; + } + return false; +} + +static void fixup_fake_crossing_location_for_consistency(CDFEM_Parent_Edge & edge, std::pair & fakeCrossing) +{ + const CrossingInterval & crossingInterval = get_crossing_interval(edge, fakeCrossing); + if (fake_crossing_is_actually_real(edge, crossingInterval, fakeCrossing)) + { + const std::pair * before = crossingInterval[0]; + const std::pair * after = crossingInterval[1]; + double & loc = fakeCrossing.second; + const bool useBefore = before ? (after ? (loc-before->second < after->second-loc) : true) : false; + loc = useBefore ? before->second : after->second; + } +} + +static bool fake_crossing_is_actually_real(const CDFEM_Parent_Edge & edge, const std::pair & fakeCrossing) +{ + const CrossingInterval & crossingInterval = get_crossing_interval(edge, fakeCrossing); + return fake_crossing_is_actually_real(edge, crossingInterval, fakeCrossing); +} + +bool CDFEM_Parent_Edge::all_fake_crossings_are_really_fake() const +{ + for (auto && crossing : my_crossings_including_fake) + if (!have_crossing(crossing.first) && fake_crossing_is_actually_real(*this, crossing)) + return false; + return true; +} + +void CDFEM_Parent_Edge::fixup_fake_crossing_locations_for_consistency() +{ + for (auto && crossing : my_crossings_including_fake) + if (!have_crossing(crossing.first)) + fixup_fake_crossing_location_for_consistency(*this, crossing); +} + +void +CDFEM_Parent_Edge::find_crossings_including_fake_ones(const std::vector > & nodes_isovar) +{ + my_crossings_including_fake.clear(); + my_crossing_signs_including_fake.clear(); + + ThrowRequire(Phase_Support::has_one_levelset_per_phase()); + const int numLS = nodes_isovar[0].size(); + std::vector lsMins(numLS,std::numeric_limits::max()); + std::vector lsMaxs(numLS,std::numeric_limits::lowest()); + for (auto && nodeIsovar : nodes_isovar) + { + for (int i=0; i result = have_crossing(iface) ? + std::make_pair(get_crossing_position(iface), get_crossing_sign(iface)) : + find_crossing_position_and_sign(iface, nodes_isovar); + if (result.first >= 0.) + { + my_crossings_including_fake[iface] = result.first; + my_crossing_signs_including_fake[iface] = result.second; + } + } + } + } + + fixup_fake_crossing_locations_for_consistency(); +} + +std::pair +CDFEM_Parent_Edge::find_crossing_position_and_sign(const InterfaceID key, const std::vector > & nodes_isovar) const +{ + ThrowRequire(Phase_Support::has_one_levelset_per_phase()); + return krino::find_crossing_position_and_sign(key, my_edge_node_positions, nodes_isovar); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.hpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.hpp new file mode 100644 index 000000000000..cceb31cf10e1 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edge.hpp @@ -0,0 +1,137 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_CDFEM_Parent_Edge_h +#define Akri_CDFEM_Parent_Edge_h + +#include +#include +#include + +#include +#include +#include + +namespace stk { namespace mesh { class BulkData; } } + +namespace krino { + +class CDFEM_Parent_Edge { +public: + CDFEM_Parent_Edge(const std::vector & edgeNodes, + const std::vector & edgeNodePositions, + const std::vector > & nodes_isovar) + : my_edge_nodes(edgeNodes), + my_edge_node_positions(edgeNodePositions) + { + ThrowAssert(edgeNodePositions.size() == nodes_isovar.size()); + find_crossings(nodes_isovar); + } + + CDFEM_Parent_Edge(const std::vector & edgeNodePositions, + const std::vector > & nodes_isovar) + : CDFEM_Parent_Edge({}, edgeNodePositions, nodes_isovar) {} + + CDFEM_Parent_Edge(const std::vector & edgeNodes, + const std::vector > & nodes_isovar) + : CDFEM_Parent_Edge(edgeNodes, {0.,1.}, nodes_isovar) {} + + CDFEM_Parent_Edge(const std::vector > & nodes_isovar) + : CDFEM_Parent_Edge({0.,1.}, nodes_isovar) {} + + CDFEM_Parent_Edge(const std::vector & edgeNodes, + const std::vector & edgeNodePositions); + CDFEM_Parent_Edge() {} + + // Must be larger than machine epsilon, but puts limit on smallest effective snap tolerance + static double MinSize(); + + bool valid() const { return !my_edge_node_positions.empty(); } + + void find_crossings(const std::vector > & nodes_isovar); + void collapse_small_segments_while_preserving_topology(const double snapTol); + + void adjust_crossing_locations_based_on_node_captured_domains(const std::vector & sortedParentNode0Domains, const std::vector & sortedParentNode1Domains); + + bool have_crossing(const InterfaceID key) const { return my_crossings.find(key) != my_crossings.end(); } + const CrossingMap & get_crossings() const { return my_crossings; } + const CrossingMap & get_crossings_including_fake() const { return my_crossings_including_fake; } + bool all_fake_crossings_are_really_fake() const; + + double get_crossing_position(const InterfaceID key) const { + CrossingMap::const_iterator it = my_crossings.find(key); + return it != my_crossings.end() ? it->second : -1.0; + } + // Crossing sign is defined as whether the interface is + or - for x > crossing point + // For multiple LS problems we'll say that -1 corresponds to InterfaceID.first being lower for x > x_crossing_point + // For uncrossed edges it will be the sign of both parent nodes + int get_crossing_sign(const InterfaceID key) const { + CrossingSignMap::const_iterator it = my_crossing_signs.find(key); + return it->second; + } + std::tuple get_crossing_position_and_sign(const InterfaceID key) const; + unsigned get_num_nodes() const { return my_edge_node_positions.size(); } + const std::vector & get_nodes() const { return my_edge_nodes; } + bool have_any_crossings() const; + std::pair get_parent_nodes() const { return std::pair(my_edge_nodes.front(), my_edge_nodes.back()); } + int get_uncrossed_phase() const { return (edge_phases.size() == 1) ? (*edge_phases.begin()) : -1; } + const std::set & get_edge_phases() const { return edge_phases; } + double get_edge_node_position(stk::mesh::Entity edgeNode) const; + + friend std::ostream & operator << (std::ostream &os, const CDFEM_Parent_Edge & edge); + void debug_print_crossings() const; + +private: + void find_crossings_multiple_levelset(const std::vector > & nodes_isovar); + std::pair find_crossing_position_and_sign(const InterfaceID key, const std::vector > & nodes_isovar) const; + void find_crossings_including_fake_ones(const std::vector > & nodes_isovar); + double get_fake_crossing_position(const InterfaceID key) const { + CrossingMap::const_iterator it = my_crossings_including_fake.find(key); + return it != my_crossings_including_fake.end() ? it->second : -1.0; + } + int get_fake_crossing_sign(const InterfaceID key) const { + CrossingSignMap::const_iterator it = my_crossing_signs_including_fake.find(key); + return it->second; + } + void fixup_fake_crossing_locations_for_consistency(); + + std::vector my_edge_nodes; + std::vector my_edge_node_positions; + CrossingMap my_crossings; + CrossingSignMap my_crossing_signs; + CrossingMap my_crossings_including_fake; + CrossingSignMap my_crossing_signs_including_fake; + std::set edge_phases; +}; + +inline std::ostream & operator << (std::ostream &os, const CDFEM_Parent_Edge & edge) +{ + const unsigned num_nodes = edge.get_num_nodes(); + os << "CDFEM parent edge has " << num_nodes << " nodes and phases { "; + for (int phase : edge.get_edge_phases()) + os << phase << " "; + os << "}\n crossings: { "; + const auto oldPrecision = os.precision(); + os.precision(16); + for ( auto && crossing : edge.get_crossings() ) + { + os << crossing.first << "@" << crossing.second << ", sign=" << edge.get_crossing_sign(crossing.first) << " "; + } + os << "}" << "\n crossings including fake: { "; + for ( auto && crossing : edge.get_crossings_including_fake() ) + { + os << crossing.first << "@" << crossing.second << ", sign=" << edge.get_fake_crossing_sign(crossing.first) << " "; + } + os << "}" << "\n"; + os.precision(oldPrecision); + return os; +} + +} // namespace krino + +#endif // Akri_CDFEM_Parent_Edge_h diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.cpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.cpp new file mode 100644 index 000000000000..d3eab40fb058 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.cpp @@ -0,0 +1,492 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino +{ + +std::set get_phases_present_on_edges(const std::vector & parentEdges) +{ + std::set phasesPresent; + for(auto && parentEdge : parentEdges) + if(parentEdge) + for (int phase : parentEdge->get_edge_phases()) + phasesPresent.insert(phase); + return phasesPresent; +} + +static void add_interface_phases(const InterfaceID & interface, std::set & phases) +{ + phases.insert(interface.first_ls()); + phases.insert(interface.second_ls()); +} + +static std::set get_all_interfaces_including_fake(const std::vector & parentEdges) +{ + std::set allInterfacesIncludingFake; + for(auto && parentEdge : parentEdges) + if(parentEdge) + for (auto && crossing : parentEdge->get_crossings_including_fake()) + allInterfacesIncludingFake.insert(crossing.first); + return allInterfacesIncludingFake; +} + +bool phase_has_interfaces_to_all_other_phases(const int phase, const std::set & phasesPresent, const std::set & interfaces) +{ + for (int otherPhase : phasesPresent) + if (interfaces.find(InterfaceID(phase,otherPhase)) == interfaces.end()) + return false; + return true; +} + +void add_phases_possibly_present_on_interior(const std::vector & parentEdges, std::set & phasesPresent) +{ + const std::set allInterfacesIncludingFake = get_all_interfaces_including_fake(parentEdges); + + std::set phasesPossiblyPresent; + for (auto && interface : allInterfacesIncludingFake) + add_interface_phases(interface, phasesPossiblyPresent); + + // This should be unit tested. What about order dependency? + for (int phase : phasesPossiblyPresent) + if (phasesPresent.find(phase) == phasesPresent.end()) + if (phase_has_interfaces_to_all_other_phases(phase, phasesPresent, allInterfacesIncludingFake)) + phasesPresent.insert(phase); +} + +std::set get_phases_present_on_edges_and_interior(const std::vector & elementParentEdges) +{ + std::set phasesPresent = get_phases_present_on_edges(elementParentEdges); + add_phases_possibly_present_on_interior(elementParentEdges, phasesPresent); + return phasesPresent; +} + +static +std::set get_interfaces_with_any_real_edge_crossings(const std::vector & elementParentEdges) +{ + std::set interfacesPresent; + for(auto && parentEdge : elementParentEdges) + if(parentEdge) + for(const auto & crossing : parentEdge->get_crossings()) + interfacesPresent.insert(crossing.first); + return interfacesPresent; +} + +std::set get_interfaces_present(const std::vector & elementParentEdges) +{ + return get_interfaces_with_any_real_edge_crossings(elementParentEdges); +} + +void fill_element_parent_edges(const stk::mesh::BulkData & mesh, + const stk::mesh::Entity elem, + const ParentEdgeMap & parentEdges, + std::vector & elementParentEdges, + std::vector & areParentEdgesAreOrientedSameAsElementEdges) +{ + const stk::topology stk_topology = mesh.bucket(elem).topology(); + const unsigned numEdges = stk_topology.num_edges(); + const stk::mesh::Entity * const nodes = mesh.begin_nodes(elem); + elementParentEdges.assign(numEdges, nullptr); + areParentEdgesAreOrientedSameAsElementEdges.assign(numEdges, true); + for(unsigned i=0; i < numEdges; ++i) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(stk_topology, i); + const CDFEM_Parent_Edge * parent_edge = + find_parent_edge(mesh, parentEdges, nodes[edge_node_ordinals[0]], nodes[edge_node_ordinals[1]]); + elementParentEdges[i] = parent_edge; + if(parent_edge && parent_edge->get_parent_nodes().first != nodes[edge_node_ordinals[0]]) + areParentEdgesAreOrientedSameAsElementEdges[i] = false; + } +} + +void fill_face_nodes_and_parent_edges(const stk::topology & elementTopology, + const int iFace, + const std::vector & elementNodes, + const std::vector & elementParentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + std::vector & faceNodes, + std::vector & faceParentEdges, + std::vector & areParentEdgesOrientedSameAsFaceEdges) +{ + ThrowAssert(elementTopology == stk::topology::TETRAHEDRON_4); + constexpr std::array,4> faceEdges = {{ {{0,4,3}}, {{1,5,4}}, {{3,5,2}}, {{2,1,0}} }}; + constexpr std::array,4> isFaceEdgeOrientedSameAsElementEdge = {{ {{true,true,false}}, {{true,true,false}}, {{true,false,true}}, {{false,false,false}} }}; + + faceNodes.resize(3); + elementTopology.face_nodes(elementNodes, iFace, faceNodes.data()); + + constexpr int numFaceEdges = 3; + faceParentEdges.resize(numFaceEdges); + areParentEdgesOrientedSameAsFaceEdges.resize(3); + for (int i=0; iprimary_entity_rank() != stk::topology::ELEMENT_RANK) continue; + + const stk::mesh::Part * nonconformal_node_iopart = phaseSupport.find_nonconformal_part(*part_ptr); + + if (phaseSupport.level_set_is_used_by_nonconformal_part(cdfemSupport.ls_field(ls_index).ptr, nonconformal_node_iopart)) + { + return true; + } + } + + return false; +} + +static bool +has_io_part_containing_phase(const Phase_Support & phase_support, const stk::mesh::PartVector & parts, const PhaseTag & phase) +{ + for(stk::mesh::PartVector::const_iterator part_iter = parts.begin(); part_iter != parts.end(); ++part_iter) + { + const stk::mesh::Part * const part = *part_iter; + if (part->primary_entity_rank() != stk::topology::ELEMENT_RANK || // limit ourselves to volume parts + !(stk::io::is_part_io_part(*part) || + phase_support.is_nonconformal(part))) + continue; + + const PhaseTag & iopart_phase = phase_support.get_iopart_phase(*part); + if (iopart_phase.contain(phase)) + { + return true; + } + } + + return false; +} + +static bool node_touches_alive_block(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity node, + const int ls_index ) +{ + const CDFEM_Inequality_Spec * death_spec = cdfemSupport.get_death_spec(ls_index); + if (nullptr == death_spec) return false; + + const PhaseTag & alive_phase = death_spec->get_active_phase(); + const stk::mesh::PartVector & node_parts = mesh.bucket(node).supersets(); + return has_io_part_containing_phase(phaseSupport, node_parts, alive_phase); +} + +static bool node_touches_dead_block(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity node, + const int ls_index ) +{ + const CDFEM_Inequality_Spec * death_spec = cdfemSupport.get_death_spec(ls_index); + if (nullptr == death_spec) return false; + + const PhaseTag & dead_phase = death_spec->get_deactivated_phase(); + const stk::mesh::PartVector & node_parts = mesh.bucket(node).supersets(); + return has_io_part_containing_phase(phaseSupport, node_parts, dead_phase); +} + +static bool node_has_real_ls_value(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity node, + const int ls_index ) +{ + if( node_touches_dead_block(mesh, cdfemSupport, phaseSupport, node, ls_index) && + !node_touches_alive_block(mesh, cdfemSupport, phaseSupport, node, ls_index) ) + return false; + + return in_block_decomposed_by_ls(mesh, cdfemSupport, phaseSupport, node, ls_index); +} + +static void debug_print_edge_info(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const std::vector & edge_nodes, + const std::vector > & nodes_isovar) +{ + const int num_nodes = nodes_isovar.size(); + if(krinolog.shouldPrint(LOG_DEBUG)) + { + const auto old_precision = krinolog.getStream().precision(); + krinolog.getStream().precision(16); + const int num_ls = cdfemSupport.num_ls_fields(); + krinolog << stk::diag::dendl << "CDFEM_Parent_Edge::find_crossings():" << "\n"; + for ( int n = 0; n < num_nodes; ++n ) + { + krinolog << " Node: " << mesh.identifier(edge_nodes[n]) << ", in_block_decomposed_by_ls = { "; + for ( int ls_index = 0; ls_index < num_ls; ++ls_index ) krinolog << in_block_decomposed_by_ls(mesh, cdfemSupport, phaseSupport, edge_nodes[n], ls_index) << " "; + krinolog << "}, has_real_ls_value = { "; + for ( int ls_index = 0; ls_index < num_ls; ++ls_index ) krinolog << node_has_real_ls_value(mesh, cdfemSupport, phaseSupport, edge_nodes[n], ls_index) << " "; + krinolog << "}, ls = { "; + for ( int ls_index = 0; ls_index < num_ls; ++ls_index ) krinolog << nodes_isovar[n][ls_index] << " "; + krinolog << "}"; + krinolog << stk::diag::dendl; + } + krinolog.getStream().precision(old_precision); + } +} + +static void edge_ls_node_values(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const std::vector & edge_nodes, + std::vector >& nodes_isovar) +{ + const unsigned num_nodes = edge_nodes.size(); + const int num_ls = cdfemSupport.num_ls_fields(); + + nodes_isovar.assign(num_nodes, std::vector(num_ls, -1.0)); + for (unsigned n = 0; n < num_nodes; ++n) + { + for (int ls_index = 0; ls_index < num_ls; ++ls_index) + { + const CDFEM_Inequality_Spec * death_spec = cdfemSupport.get_death_spec(ls_index); + FieldRef isovar = cdfemSupport.ls_field(ls_index).isovar; + + const bool node_has_ls = node_has_real_ls_value(mesh, cdfemSupport, phaseSupport, edge_nodes[n], ls_index); + nodes_isovar[n][ls_index] = 0.0; + if (node_has_ls) + { + if (nullptr != death_spec && isovar.entity_rank() == stk::topology::ELEMENT_RANK) + { + // currently requires aura to work correctly in parallel + ThrowAssertMsg(mesh.is_automatic_aura_on(), "Capability requires aura."); + bool have_pos_elem = false; + bool have_neg_elem = false; + const unsigned num_node_elems = mesh.num_elements(edge_nodes[n]); + const stk::mesh::Entity* node_elems = mesh.begin_elements(edge_nodes[n]); + for (unsigned node_elem_index=0; node_elem_index(isovar, node_elem); + if (nullptr != isoptr) + { + if (*isoptr - cdfemSupport.ls_field(ls_index).isoval < 0.) + have_neg_elem = true; + else + have_pos_elem = true; + } + } + nodes_isovar[n][ls_index] = (have_pos_elem) ? (have_neg_elem ? 0.0 : 1.0) : -1.0; + } + else + { + const double * isoptr = field_data(isovar, edge_nodes[n]); + ThrowRequireMsg(nullptr != isoptr, "Isovar " << isovar.name() << " missing on node " << debug_entity(mesh, edge_nodes[n])); + nodes_isovar[n][ls_index] = *isoptr - cdfemSupport.ls_field(ls_index).isoval; + } + } + else if (nullptr != death_spec && node_touches_dead_block(mesh, cdfemSupport, phaseSupport, edge_nodes[n], ls_index)) + { + const bool dead_is_positive = death_spec->get_deactivated_phase().contain(cdfemSupport.ls_field(ls_index).identifier,+1); + if (dead_is_positive) nodes_isovar[n][ls_index] = 1.0; + } + + if (nullptr != death_spec && node_touches_dead_block(mesh, cdfemSupport, phaseSupport, edge_nodes[n], ls_index)) + { + const bool dead_is_positive = death_spec->get_deactivated_phase().contain(cdfemSupport.ls_field(ls_index).identifier, +1); + if (dead_is_positive && nodes_isovar[n][ls_index] < 0.0) + { + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Setting node " << mesh.identifier(edge_nodes[n]) << " to zero to enforce irreversibility, ls = " << nodes_isovar[n][ls_index] << "\n"; + nodes_isovar[n][ls_index] = 0.0; + } + else if (!dead_is_positive && nodes_isovar[n][ls_index] >= 0.0) + { + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Setting node " << mesh.identifier(edge_nodes[n]) << " to -REAL_MIN to enforce irreversibility, ls = " << nodes_isovar[n][ls_index] << "\n"; + nodes_isovar[n][ls_index] = -std::numeric_limits::min(); + } + } + } + } +} + +static CDFEM_Parent_Edge & +build_parent_edge(const stk::mesh::BulkData & mesh, ParentEdgeMap & parentEdges, const ParentsToChildMapper & parentsToChildMapper, const bool linearizeEdge, stk::mesh::Entity node0, stk::mesh::Entity node1) +{ + const stk::mesh::EntityId id0 = mesh.identifier(node0); + const stk::mesh::EntityId id1 = mesh.identifier(node1); + const ParentEdgeKey edge_key(id0, id1); + CDFEM_Parent_Edge & edge = parentEdges[edge_key]; + + std::vector edgeNodes; + std::vector edgeNodePositions; + + if(!edge.valid()) + { + const std::array nodes = (id0 < id1) ? std::array{node0, node1} : std::array{node1, node0}; + if (linearizeEdge) + fill_linear_edge_nodes_and_positions(nodes[0], nodes[1], edgeNodes, edgeNodePositions); + else + fill_edge_nodes_and_positions(mesh, nodes[0], nodes[1], parentsToChildMapper, edgeNodes, edgeNodePositions); + edge = CDFEM_Parent_Edge(edgeNodes, edgeNodePositions); + } + return edge; +} + +static void find_parent_edge_crossings(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + ParentEdgeMap & parentEdges) +{ + std::vector> nodes_isovar; + + for (auto && map_entry : parentEdges) + { + CDFEM_Parent_Edge & edge = map_entry.second; + const std::vector edge_nodes = edge.get_nodes(); + edge_ls_node_values(mesh, cdfemSupport, phaseSupport, edge_nodes, nodes_isovar); + debug_print_edge_info(mesh, cdfemSupport, phaseSupport, edge_nodes, nodes_isovar); + edge.find_crossings(nodes_isovar); + } + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << stk::diag::dendl; +} + +stk::mesh::Selector get_parent_element_selector(const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + stk::mesh::Selector parentElementSelector = + (cdfemSupport.get_parent_part() | (activePart & !cdfemSupport.get_child_part())) & + phaseSupport.get_all_decomposed_blocks_selector(); + + return parentElementSelector; +} + +stk::mesh::Selector get_owned_parent_element_selector(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + stk::mesh::Selector parentElementSelector = + (cdfemSupport.get_parent_part() | (activePart & !cdfemSupport.get_child_part())) & + phaseSupport.get_all_decomposed_blocks_selector() & + mesh.mesh_meta_data().locally_owned_part(); + + return parentElementSelector; +} + +std::vector get_owned_parent_elements(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + const stk::mesh::Selector parentElementSelector = get_owned_parent_element_selector(mesh, activePart, cdfemSupport, phaseSupport); + std::vector parentElements; + stk::mesh::get_selected_entities( parentElementSelector, mesh.get_buckets(stk::topology::ELEMENT_RANK, parentElementSelector), parentElements, false ); + return parentElements; +} + +ParentEdgeMap +build_parent_edges(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper & parentsToChildMapper, + const std::function & should_build_linear_edge, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + std::vector elements; + stk::mesh::get_entities( mesh, stk::topology::ELEMENT_RANK, mesh.mesh_meta_data().locally_owned_part(), elements, false); + + return build_parent_edges_using_elements(mesh, parentsToChildMapper, should_build_linear_edge, elements, activePart, cdfemSupport, phaseSupport); +} + +std::function build_no_linearized_edges_function() +{ + return [](stk::mesh::Entity node0, stk::mesh::Entity node1) + { return false; }; +} + +std::function build_all_linearized_edges_function() +{ + return [](stk::mesh::Entity node0, stk::mesh::Entity node1) + { return true; }; +} + +ParentEdgeMap +build_parent_edges_using_elements(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper & parentsToChildMapper, + const std::function & should_build_linear_edge, + const std::vector & elements, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + const stk::mesh::Selector parentElementSelector = get_owned_parent_element_selector(mesh, activePart, cdfemSupport, phaseSupport); + + ParentEdgeMap parentEdges; + + for (auto && elem : elements) + { + if (parentElementSelector(mesh.bucket(elem))) + { + const stk::topology topology = mesh.bucket(elem).topology(); + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(elem); + const unsigned numEdges = topology.num_edges(); + + for (unsigned iedge = 0; iedge < numEdges; ++iedge) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topology, iedge); + stk::mesh::Entity node0 = elem_nodes[edge_node_ordinals[0]]; + stk::mesh::Entity node1 = elem_nodes[edge_node_ordinals[1]]; + + const bool linearizeEdge = should_build_linear_edge(node0, node1); + build_parent_edge(mesh, parentEdges, parentsToChildMapper, linearizeEdge, node0, node1); + } + } + } + + find_parent_edge_crossings(mesh, cdfemSupport, phaseSupport, parentEdges); + + return parentEdges; +} + +const CDFEM_Parent_Edge * +find_parent_edge(const stk::mesh::BulkData & mesh, const ParentEdgeMap & parentEdges, stk::mesh::Entity node0, stk::mesh::Entity node1) +{ + const stk::mesh::EntityId id0 = mesh.identifier(node0); + const stk::mesh::EntityId id1 = mesh.identifier(node1); + const ParentEdgeKey edge_key(id0, id1); + + ParentEdgeMap::const_iterator it = parentEdges.find(edge_key); + + if (it != parentEdges.end()) + return &(it->second); + + return nullptr; +} + +} // namespace diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.hpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.hpp new file mode 100644 index 000000000000..50003bf3a910 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Parent_Edges.hpp @@ -0,0 +1,86 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_CDFEM_PARENT_EDGES_H_ +#define KRINO_INCLUDE_AKRI_CDFEM_PARENT_EDGES_H_ +#include +#include +#include + +namespace krino +{ +class CDFEM_Support; +class Phase_Support; +class InterfaceID; +class ParentsToChildMapper; + +typedef OrderedIdPair ParentEdgeKey; +typedef std::map ParentEdgeMap; + +std::set get_phases_present_on_edges(const std::vector & parentEdges); +std::set get_phases_present_on_edges_and_interior(const std::vector & elementParentEdges); +std::set get_interfaces_present(const std::vector & elementParentEdges); + +const CDFEM_Parent_Edge * find_parent_edge(const stk::mesh::BulkData & mesh, const ParentEdgeMap & parentEdges, stk::mesh::Entity node0, stk::mesh::Entity node1); + +std::function build_no_linearized_edges_function(); + +std::function build_all_linearized_edges_function(); + +ParentEdgeMap +build_parent_edges_using_elements(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper & parentsToChildMapper, + const std::function & should_build_linear_edge, + const std::vector & elements, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +ParentEdgeMap +build_parent_edges(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper & parentsToChildMapper, + const std::function & should_build_linear_edge, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +void fill_element_parent_edges(const stk::mesh::BulkData & mesh, + const stk::mesh::Entity elem, + const ParentEdgeMap & parentEdges, + std::vector & elementParentEdges, + std::vector & areParentEdgesAreOrientedSameAsElementEdges); + +void fill_face_nodes_and_parent_edges(const stk::topology & elementTopology, + const int iFace, + const std::vector & elementNodes, + const std::vector & elementParentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + std::vector & faceNodes, + std::vector & faceParentEdges, + std::vector & areParentEdgesOrientedSameAsFaceEdges); + +stk::mesh::Selector get_parent_element_selector(const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +stk::mesh::Selector get_owned_parent_element_selector(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +std::vector get_owned_parent_elements(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +} + + + + +#endif /* KRINO_INCLUDE_AKRI_CDFEM_PARENT_EDGES_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Snapper.hpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Snapper.hpp new file mode 100644 index 000000000000..d63c5af7b6b9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Snapper.hpp @@ -0,0 +1,31 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_CDFEM_SNAPPER_H_ +#define KRINO_INCLUDE_AKRI_CDFEM_SNAPPER_H_ +#include + +namespace krino { + +class CDFEM_Snapper { +public: + CDFEM_Snapper() : my_cdfem_edge_tol(default_edge_tol) {} + + void set_edge_tolerance(double edge_tol) { my_cdfem_edge_tol = edge_tol; } + double get_edge_tolerance() const { ThrowRequireMsg(my_cdfem_edge_tol < 0.5, "Should not be requesting tolerance when always snapping."); return my_cdfem_edge_tol; } + bool always_snap() const { return my_cdfem_edge_tol > 0.5; } + bool snap_lo(double crossingVal) const { return always_snap() ? (crossingVal <= 0.5) : (crossingVal < get_edge_tolerance()); } + bool snap_hi(double crossingVal) const { return always_snap() ? (crossingVal > 0.5) : (crossingVal > 1.0-get_edge_tolerance()); } +private: + static constexpr double default_edge_tol = 1.e-3; + double my_cdfem_edge_tol; +}; + +} + +#endif /* KRINO_INCLUDE_AKRI_CDFEM_SNAPPER_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Support.cpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Support.cpp new file mode 100644 index 000000000000..55ed155e5b0e --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Support.cpp @@ -0,0 +1,364 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +namespace krino{ + +Edge_Interpolation_Model CDFEM_Support::the_edge_interpolation_model = PIECEWISE_LINEAR; + +CDFEM_Support & +CDFEM_Support::get(stk::mesh::MetaData & meta) +{ + CDFEM_Support * support = const_cast(meta.get_attribute()); + if (NULL == support) + { + support = new CDFEM_Support(meta); + meta.declare_attribute_with_delete(support); + } + return *support; +} + +CDFEM_Support & +CDFEM_Support::get(const stk::mesh::MetaData & meta) +{ + CDFEM_Support * support = const_cast(meta.get_attribute()); + ThrowRequireMsg(nullptr != support, "Could not find CDFEM_Support attribute on MetaData."); + return *support; +} + +CDFEM_Support::CDFEM_Support(stk::mesh::MetaData & meta) + : my_meta(meta), + my_aux_meta(AuxMetaData::get(meta)), + my_simplex_generation_method(CUT_QUADS_BY_LARGEST_ANGLE), + my_fully_coupled_cdfem(false), + my_num_initial_decomposition_cycles(1), + myGlobalIDsAreParallelConsistent(true), + my_interface_minimum_refinement_level(0), + my_interface_maximum_refinement_level(0), + my_post_adapt_uniform_refinement_levels(0), + my_post_cdfem_refinement_levels(0), + my_nonconformal_adapt_target_element_count(0), + my_cdfem_edge_degeneracy_handling(SNAP_TO_NODE), + my_cdfem_snapper(), + my_cdfem_dof_edge_tol(0.0), + my_internal_face_stabilization_multiplier(0.0), + my_flag_use_hierarchical_dofs(false), + my_flag_constrain_CDFEM_to_XFEM_space(false), + my_flag_use_nonconformal_element_size(true), + my_timer_cdfem("CDFEM", sierra::Diag::sierraTimer()), + my_timer_adapt("Nonconformal Adapt", my_timer_cdfem) +{ + my_prolongation_model = ALE_NEAREST_POINT; + + if (3 == my_meta.spatial_dimension()) + my_simplex_generation_method = CUT_QUADS_BY_NEAREST_EDGE_CUT; + + create_parts(); +} + +void CDFEM_Support::create_parts() +{ + my_parent_part = &my_meta.declare_part("CDFEM_PARENT_CONTEXT_BIT"); + my_child_part = &my_meta.declare_part("CDFEM_CHILD_CONTEXT_BIT"); + my_internal_side_part = &my_meta.declare_part("CDFEM_INTERNAL_SIDE"); + + if (my_aux_meta.using_fmwk()) + { + const bool restartOnlyIOPart = true; + my_child_edge_node_part = &my_aux_meta.declare_io_part_with_topology("CDFEM_EDGE_NODE_2_PARENTS", stk::topology::NODE, restartOnlyIOPart); + } + else + { + // Currently no need to output nodeset for krino usage + my_child_edge_node_part = &my_meta.declare_part_with_topology("CDFEM_EDGE_NODE_2_PARENTS", stk::topology::NODE); + } +} + +void CDFEM_Support::register_cdfem_mesh_displacements_field() +{ + ThrowRequireMsg(my_meta.spatial_dimension() > 1, "Spatial dimension must be set and equal to 2 or 3."); + + const FieldType & vec_type = (my_meta.spatial_dimension() == 3) ? FieldType::VECTOR_3D : FieldType::VECTOR_2D; + FieldRef cdfem_disp_field = my_aux_meta.register_field(cdfem_mesh_displacements_field_name(), vec_type, stk::topology::NODE_RANK, 2, 1, get_universal_part()); + set_cdfem_displacement_field(cdfem_disp_field); +} + +void CDFEM_Support::register_parent_node_ids_field() +{ + FieldType id_field_type = (my_aux_meta.get_assert_32bit_flag()) ? FieldType::UNSIGNED_INTEGER : FieldType::UNSIGNED_INTEGER_64; + my_parent_node_ids_field = my_aux_meta.register_field("CDFEM_2_PARENT_NODE_IDS", + id_field_type, stk::topology::NODE_RANK, 1, + 2, *my_child_edge_node_part); +} + +stk::mesh::Selector +CDFEM_Support::get_post_cdfem_refinement_selector() const +{ + stk::mesh::Selector selector = my_aux_meta.active_part(); + if (!my_post_cdfem_refinement_blocks.empty()) + { + stk::mesh::PartVector blocks; + for (auto && block_name : my_post_cdfem_refinement_blocks) + { + if (my_aux_meta.has_part(block_name)) + { + stk::mesh::Part & block = my_aux_meta.get_part(block_name); + blocks.push_back(&block); + } + else + { + stk::RuntimeDoomedAdHoc() << "post_cdfem_refinement_block " << block_name << " not found.\n"; + } + } + selector &= stk::mesh::selectUnion(blocks); + } + return selector; +} + +void +CDFEM_Support::setup_fields() +{ + my_coords_field = LevelSet::get_current_coordinates(my_meta); + + Phase_Support::get(my_meta).check_phase_parts(); + + my_ls_fields.clear(); + const LevelSetManager & region_ls = LevelSetManager::get(my_meta); + for (auto&& ls : region_ls) + { + LS_Field calc_ls_field(ls->name(),ls->get_identifier(),ls->get_isovar_field(),ls->get_isoval(),ls.get()); + my_ls_fields.push_back(calc_ls_field); + } + + const unsigned num_ls = region_ls.numberLevelSets(); + my_death_specs.resize(num_ls, nullptr); + for (unsigned i=0; i(is); + my_ale_prolongation_fields.insert(field.field_state(state)); + } +} + +void +CDFEM_Support::add_interpolation_field(const FieldRef field) +{ + ThrowAssert(field.valid()); + ThrowRequireMsg(!is_ale_prolongation_field(field), "Cannot add " << field.name() << " as interpolation field because it is already an ALE prolongation field."); + for ( unsigned is = 0; is < field.number_of_states(); ++is ) + { + const stk::mesh::FieldState state = static_cast(is); + my_interpolation_fields.insert(field.field_state(state)); + } +} + +void +CDFEM_Support::finalize_fields() +{ + krinolog << "Finalizing field prolongation strategies for CDFEM." << stk::diag::push << stk::diag::dendl; + for ( auto && field_ptr : my_meta.get_fields() ) + { + const FieldRef field(field_ptr); + if( !field.type_is() || field.field_state(stk::mesh::StateNew) == my_cdfem_displacements_field ) continue; + + if( field.entity_rank()==stk::topology::ELEMENT_RANK && + !stk::equal_case(field.name(), "transition_element") && + !stk::equal_case(field.name(), "transition_element_3") && + !stk::equal_case(field.name(), "parent_element") ) + { + my_element_fields.insert(field); + } + + if( field.entity_rank()!=stk::topology::NODE_RANK ) continue; + + const auto& initial_prolong_field_name_entry = my_initial_prolongation_field_name_map.find(field.name()); + if (initial_prolong_field_name_entry != my_initial_prolongation_field_name_map.end()) + { + const std::string & src_field_name = initial_prolong_field_name_entry->second; + ThrowErrorMsgIf(!my_aux_meta.has_field(stk::topology::NODE_RANK, src_field_name), + "Error: Could not find initial prolongation field with name " << src_field_name); + + // If the src field does not have the desired state, use StateNone (which is the same as StateNew). + FieldRef src_field = my_aux_meta.get_field(stk::topology::NODE_RANK, src_field_name); + stk::mesh::FieldState src_state = (field.state() < src_field.number_of_states()) ? field.state() : stk::mesh::StateNone; + src_field = src_field.field_state(src_state); + + my_initial_prolongation_field_map[field] = src_field; + krinolog << "Added " + << src_field.name() << " (" << state_string(src_state) << ") as initial prolongation field for " + << field.name() << " (" << state_string(field.state()) << ")" << stk::diag::dendl; + } + + if (std::find(my_force_ale_prolongation_fields.begin(), + my_force_ale_prolongation_fields.end(), + field.name()) != my_force_ale_prolongation_fields.end()) + { + add_ale_prolongation_field(field); + } + + if(is_interpolation_field(field)) + { + krinolog << field.name() << " will use interpolation." << stk::diag::dendl; + continue; + } + else if(is_ale_prolongation_field(field)) + { + krinolog << field.name() << " will use ALE prolongation." << stk::diag::dendl; + continue; + } + else if (field.name() == "node_registry") + { + krinolog << field.name() << " will not be modified." << stk::diag::dendl; + continue; + } + + krinolog << field.name() << " will be zeroed." << stk::diag::dendl; + my_zeroed_fields.insert(field); + } + krinolog << stk::diag::pop << stk::diag::dendl; +} + +void CDFEM_Support::force_ale_prolongation_for_field(const std::string & field_name) +{ + my_force_ale_prolongation_fields.push_back(field_name); +} + +bool +CDFEM_Support::add_initial_prolongation_field(const std::string & dest_field_name, const std::string & src_field_name) +{ + if (my_initial_prolongation_field_name_map.find(dest_field_name) != my_initial_prolongation_field_name_map.end()) + { + return false; + } + my_initial_prolongation_field_name_map[dest_field_name] = src_field_name; + return true; +} + +FieldRef +CDFEM_Support::get_initial_prolongation_field(const FieldRef field) const +{ + auto iter = my_initial_prolongation_field_map.find(field); + if (iter == my_initial_prolongation_field_map.end()) + return FieldRef(); + return iter->second; +} + +void +CDFEM_Support::set_simplex_generation_method(const Simplex_Generation_Method & method) +{ + ThrowAssert(method < MAX_SIMPLEX_GENERATION_METHOD); + ThrowRequireMsg(3 == my_meta.spatial_dimension() || method != CUT_QUADS_BY_NEAREST_EDGE_CUT, "Simplex generation method CUT_QUADS_BY_NEAREST_EDGE_CUT only supported in 3d."); + my_simplex_generation_method = method; +} + +void +CDFEM_Support::activate_interface_refinement(int minimumLevel, int maximumLevel) +{ + /* %TRACE% */ Traceback trace__("krino::CDFEM_Support::activate_interface_refinement(int minimum_level, int maximum_level)"); /* %TRACE% */ + + ThrowRequireMsg(my_interface_minimum_refinement_level == 0 && my_interface_maximum_refinement_level == 0, + "Interface refinement levels should only be specified once."); + ThrowRequireMsg(maximumLevel >= minimumLevel || maximumLevel == 0, + "Maximum interface refinement level must be greater than or equal to the minimum interface refinement level or left unspecified."); + if (maximumLevel == 0) maximumLevel = minimumLevel; + + my_interface_minimum_refinement_level = minimumLevel; + my_interface_maximum_refinement_level = maximumLevel; + + setup_refinement_marker(); + + if (maximumLevel > 0) + set_global_ids_are_NOT_parallel_consistent(); +} + +void +CDFEM_Support::activate_nonconformal_adaptivity(const int numLevels) +{ + /* %TRACE% */ Traceback trace__("krino::CDFEM_Support::activate_nonconformal_adaptivity(const int num_levels)"); /* %TRACE% */ + + if (numLevels < my_interface_maximum_refinement_level) + { + krinolog << "Ignoring request to activate " << numLevels << " of CDFEM nonconformal adaptivity because a maximum of " << my_interface_maximum_refinement_level << " have already been activated." << stk::diag::dendl; + return; + } + + my_interface_minimum_refinement_level = numLevels; + my_interface_maximum_refinement_level = numLevels; + + setup_refinement_marker(); + + if (numLevels > 0) + set_global_ids_are_NOT_parallel_consistent(); +} + +void +CDFEM_Support::setup_refinement_marker() +{ + /* %TRACE% */ Traceback trace__("krino::CDFEM_Support::activate_nonconformal_adaptivity(const int num_levels)"); /* %TRACE% */ + + my_nonconformal_adapt_marker_name = "CDFEM_NONCONFORMAL_MARKER"; + + my_aux_meta.register_field(my_nonconformal_adapt_marker_name, FieldType::INTEGER, stk::topology::ELEMENT_RANK, 1, 1, get_universal_part()); + my_aux_meta.register_field(my_nonconformal_adapt_marker_name, FieldType::INTEGER, stk::topology::NODE_RANK, 1, 1, get_universal_part()); +} + +int +CDFEM_Support::get_ls_index(const LevelSet * ls) const +{ + for ( unsigned ls_index = 0; ls_index < my_ls_fields.size(); ++ls_index ) + { + if (ls == ls_field(ls_index).ptr) return ls_index; + } + ThrowRuntimeError("Invalid level set field index"); +} + +void +CDFEM_Support::activate_nonconformal_adapt_target_count(const uint64_t target_count) +{ + /* %TRACE% */ Traceback trace__("CDFEM_Support::activate_nonconformal_adapt_target_count(const uint64_t target_count)"); /* %TRACE% */ + + my_nonconformal_adapt_target_element_count = target_count; + my_nonconformal_adapt_indicator_name = "CDFEM_ADAPTIVITY_ERROR_INDICATOR"; + + my_aux_meta.register_field(my_nonconformal_adapt_indicator_name, + FieldType::REAL, + stk::topology::ELEMENT_RANK, + 1, + 1, + get_universal_part()); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_CDFEM_Support.hpp b/packages/krino/krino/krino_lib/Akri_CDFEM_Support.hpp new file mode 100644 index 000000000000..3d07bd11f63a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDFEM_Support.hpp @@ -0,0 +1,259 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_CDFEM_Support_h +#define Akri_CDFEM_Support_h +// +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +namespace krino { + +class LevelSet; +class CDFEM_Inequality_Spec; + +struct LS_Field +{ + LS_Field(const std::string & name_, const LevelSet_Identifier & identifier_, const FieldRef isovar_, const double isoval_, const LevelSet * const ptr_) + : name(name_), identifier(identifier_), isovar(isovar_), isoval(isoval_), ptr(ptr_) { + ThrowRequireMsg(isovar_.valid(), "Invalid field " + isovar_.name() + " used in CDFEM initialization"); + } + + // Constructor just for unit tests + LS_Field(const std::string & name_, const LevelSet_Identifier & identifier_) + : name(name_), identifier(identifier_), isoval(0), ptr(NULL) { + } + + std::string name; + LevelSet_Identifier identifier; + FieldRef isovar; + double isoval; + const LevelSet * ptr; +}; + +enum Prolongation_Model +{ + ALE_NEAREST_NODE=0, + ALE_NEAREST_POINT, + INTERPOLATION, + MAX_PROLONGATION_MODEL +}; + +enum Edge_Interpolation_Model +{ + PIECEWISE_LINEAR=0, + CONSTRAINED_LINEAR, + MAX_EDGE_INTERPOLATION_MODEL +}; + +enum Edge_Degeneracy_Handling +{ + SNAP_TO_NODE=0, + SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE, + MAX_EDGE_DEGENERACY_HANDLING_TYPE +}; + +enum Simplex_Generation_Method +{ + CUT_QUADS_BY_GLOBAL_IDENTIFIER=0, + CUT_QUADS_BY_LARGEST_ANGLE, + CUT_QUADS_BY_NEAREST_EDGE_CUT, + MAX_SIMPLEX_GENERATION_METHOD +}; + +class CDFEM_Support { +public: + + CDFEM_Support(stk::mesh::MetaData & meta); + ~CDFEM_Support() {} + CDFEM_Support(CDFEM_Support const&) = delete; + CDFEM_Support& operator=(CDFEM_Support const&) = delete; + + static CDFEM_Support & get(stk::mesh::MetaData & meta); + static CDFEM_Support & get(const stk::mesh::MetaData & meta); + static void use_constrained_edge_interpolation() { the_edge_interpolation_model = CONSTRAINED_LINEAR; } + static Edge_Interpolation_Model get_edge_interpolation_model() { return the_edge_interpolation_model; } + static bool use_nonconformal_adaptivity(stk::mesh::MetaData & meta) { CDFEM_Support & cdfem_support = get(meta); return cdfem_support.get_interface_maximum_refinement_level() > 0; } + static std::string cdfem_mesh_displacements_field_name() { return "CDFEM_MESH_DISPLACEMENTS"; } + + static bool is_active(const stk::mesh::MetaData & meta) + { + return Phase_Support::exists_and_has_phases_defined(meta); + } + + stk::mesh::MetaData & get_mesh_meta() { return my_meta; } + const stk::mesh::MetaData & get_mesh_meta() const { return my_meta; } + int num_ls_fields() const { return my_ls_fields.size(); } + const LS_Field & ls_field(int i) const { return my_ls_fields[i]; } + LS_Field & ls_field(int i) { return my_ls_fields[i]; } + const std::vector & ls_fields() const { return my_ls_fields; } + Prolongation_Model get_prolongation_model() const { return my_prolongation_model; } + void set_prolongation_model(const Prolongation_Model & model) { my_prolongation_model = model; } + Simplex_Generation_Method get_simplex_generation_method() const { return my_simplex_generation_method; } + void set_simplex_generation_method(const Simplex_Generation_Method & method); + bool get_global_ids_are_parallel_consistent() const { return myGlobalIDsAreParallelConsistent; } + void set_global_ids_are_NOT_parallel_consistent() { myGlobalIDsAreParallelConsistent = false; } + const CDFEM_Inequality_Spec * get_death_spec(int ls_index) const { return my_death_specs[ls_index]; } + void activate_interface_refinement(int minimum_level, int maximum_level); + void activate_nonconformal_adaptivity(const int num_levels); + int get_ls_index(const LevelSet * ls) const; + + void create_parts(); + + void register_cdfem_mesh_displacements_field(); + void register_parent_node_ids_field(); + + void setup_fields(); + void finalize_fields(); + void set_cdfem_displacement_field(const FieldRef field) { my_cdfem_displacements_field = field; } + void set_cdfem_snap_displacement_field(const FieldRef field) { myCDFEMSnapDisplacementsField = field; } + void add_ale_prolongation_field(const FieldRef field); + void add_interpolation_field(const FieldRef field); + // Just for unit test setup purposes + void add_ls_field(const LS_Field & to_add, const CDFEM_Inequality_Spec * death_spec = nullptr) { my_ls_fields.push_back(to_add); my_death_specs.push_back(death_spec); } + + void set_coords_field(const FieldRef coords_field) { my_coords_field = coords_field; } + const FieldRef get_coords_field() const { return my_coords_field; } + const FieldRef get_cdfem_displacements_field() { return my_cdfem_displacements_field; } + const FieldRef get_cdfem_snap_displacements_field() const { return myCDFEMSnapDisplacementsField; } + const FieldSet & get_ale_prolongation_fields() const { return my_ale_prolongation_fields; } + const FieldSet & get_interpolation_fields() const { return my_interpolation_fields; } + const FieldSet & get_zeroed_fields() const { return my_zeroed_fields; } + const FieldSet & get_element_fields() const { return my_element_fields; } + + bool add_initial_prolongation_field(const std::string & dest_field_name, const std::string & src_field_name); + FieldRef get_initial_prolongation_field(const FieldRef field) const; + + stk::mesh::Part & get_parent_part() const { return *my_parent_part; } + stk::mesh::Part & get_child_part() const { return *my_child_part; } + stk::mesh::Part & get_internal_side_part() const { return *my_internal_side_part; } + stk::mesh::Part & get_active_part() const { return my_aux_meta.active_part(); } + stk::mesh::Part & get_universal_part() const { return my_meta.universal_part(); } + stk::mesh::Part & get_locally_owned_part() const { return my_meta.locally_owned_part(); } + stk::mesh::Part & get_globally_shared_part() const { return my_meta.globally_shared_part(); } + + stk::mesh::Selector get_post_cdfem_refinement_selector() const; + + stk::mesh::Part & get_child_edge_node_part() const { return *my_child_edge_node_part; } + FieldRef get_parent_node_ids_field() const { return my_parent_node_ids_field; } + + void activate_fully_coupled_cdfem() { my_fully_coupled_cdfem = true; } + bool fully_coupled_cdfem() const { return my_fully_coupled_cdfem; } + + void activate_nonconformal_adapt_target_count(uint64_t val); + uint64_t get_nonconformal_adapt_target_count() const { return my_nonconformal_adapt_target_element_count; } + int get_interface_minimum_refinement_level() const { return my_interface_minimum_refinement_level; } + int get_interface_maximum_refinement_level() const { return my_interface_maximum_refinement_level; } + void set_post_adapt_refinement_levels(int levels) { my_post_adapt_uniform_refinement_levels = levels; } + int get_post_adapt_refinement_levels() const { return my_post_adapt_uniform_refinement_levels; } + void set_post_cdfem_refinement_levels(int levels) { my_post_cdfem_refinement_levels = levels; } + int get_post_cdfem_refinement_levels() const { return my_post_cdfem_refinement_levels; } + void set_post_cdfem_refinement_blocks(const std::vector & post_cdfem_refinement_blocks) { my_post_cdfem_refinement_blocks = post_cdfem_refinement_blocks; } + void set_num_initial_decomposition_cycles(int num_initial_decomposition_cycles) { my_num_initial_decomposition_cycles = num_initial_decomposition_cycles; } + // In case of both nonconformal adaptivity, perform at least 2 rounds of level set initialization and decomposition. + // This is to capture features that might be missed on the unrefined mesh. + int get_num_initial_decomposition_cycles() const { return (my_num_initial_decomposition_cycles > 1) ? my_num_initial_decomposition_cycles : ((my_interface_maximum_refinement_level > 0) ? 2 : 1); } + const std::string & get_nonconformal_adapt_marker_name() const { return my_nonconformal_adapt_marker_name; } + const std::string & get_nonconformal_adapt_indicator_name() const { return my_nonconformal_adapt_indicator_name; } + void set_nonconformal_hadapt(const std::function & hadapt) { my_nonconformal_hadapt = hadapt; } + const std::function & get_nonconformal_hadapt() const { return my_nonconformal_hadapt; } + + bool is_ale_prolongation_field(const FieldRef field) const + { + return (my_ale_prolongation_fields.find(field) != my_ale_prolongation_fields.end()); + } + bool is_interpolation_field(const FieldRef field) const + { + return (my_interpolation_fields.find(field) != my_interpolation_fields.end()); + } + + void use_nonconformal_element_size(bool flag) { my_flag_use_nonconformal_element_size = flag; } + bool use_nonconformal_element_size() const { return my_flag_use_nonconformal_element_size; } + + Edge_Degeneracy_Handling get_cdfem_edge_degeneracy_handling() const { return my_cdfem_edge_degeneracy_handling; } + void set_cdfem_edge_degeneracy_handling( const Edge_Degeneracy_Handling type ) { my_cdfem_edge_degeneracy_handling = type; } + + stk::diag::Timer & get_timer_cdfem() const { return my_timer_cdfem; } + stk::diag::Timer & get_timer_adapt() const { return my_timer_adapt; } + + void set_cdfem_edge_tol( const double tol ) { my_cdfem_snapper.set_edge_tolerance(tol); } + const CDFEM_Snapper & get_snapper() const { return my_cdfem_snapper; } + const double & get_cdfem_dof_edge_tol() const { return my_cdfem_dof_edge_tol; } + void set_cdfem_dof_edge_tol( const double tol ) { my_cdfem_dof_edge_tol = tol; } + bool use_internal_face_stabilization() const { return my_internal_face_stabilization_multiplier > 0.0; } + double get_internal_face_stabilization_multiplier() const { return my_internal_face_stabilization_multiplier; } + void set_internal_face_stabilization_multiplier( const double mult ) { my_internal_face_stabilization_multiplier = mult; } + bool get_use_hierarchical_dofs() const { return my_flag_use_hierarchical_dofs; } + void set_use_hierarchical_dofs(bool flag) { my_flag_use_hierarchical_dofs = flag; } + bool get_constrain_CDFEM_to_XFEM_space() const { return my_flag_constrain_CDFEM_to_XFEM_space; } + void set_constrain_CDFEM_to_XFEM_space(bool flag) { my_flag_constrain_CDFEM_to_XFEM_space = flag; } + + void force_ale_prolongation_for_field(const std::string & field_name); + +private: + void setup_refinement_marker(); + +private: + stk::mesh::MetaData & my_meta; + AuxMetaData & my_aux_meta; + + FieldRef my_coords_field; + std::vector my_ls_fields; + std::vector my_death_specs; + FieldRef my_cdfem_displacements_field; + FieldRef myCDFEMSnapDisplacementsField; + Prolongation_Model my_prolongation_model; + Simplex_Generation_Method my_simplex_generation_method; + std::vector my_force_ale_prolongation_fields; + FieldSet my_ale_prolongation_fields; + FieldSet my_interpolation_fields; + FieldSet my_zeroed_fields; + FieldSet my_element_fields; + std::map my_initial_prolongation_field_name_map; + std::map my_initial_prolongation_field_map; + static Edge_Interpolation_Model the_edge_interpolation_model; + stk::mesh::Part * my_parent_part; + stk::mesh::Part * my_child_part; + stk::mesh::Part * my_internal_side_part; + stk::mesh::Part * my_child_edge_node_part; + FieldRef my_parent_node_ids_field; + bool my_fully_coupled_cdfem; + int my_num_initial_decomposition_cycles; + bool myGlobalIDsAreParallelConsistent; + int my_interface_minimum_refinement_level; + int my_interface_maximum_refinement_level; + int my_post_adapt_uniform_refinement_levels; + int my_post_cdfem_refinement_levels; + std::vector my_post_cdfem_refinement_blocks; + uint64_t my_nonconformal_adapt_target_element_count; + std::string my_nonconformal_adapt_marker_name; + std::string my_nonconformal_adapt_indicator_name; + std::function my_nonconformal_hadapt; + Edge_Degeneracy_Handling my_cdfem_edge_degeneracy_handling; + CDFEM_Snapper my_cdfem_snapper; + double my_cdfem_dof_edge_tol; + double my_internal_face_stabilization_multiplier; + bool my_flag_use_hierarchical_dofs; + bool my_flag_constrain_CDFEM_to_XFEM_space; + bool my_flag_use_nonconformal_element_size; + mutable stk::diag::Timer my_timer_cdfem; + mutable stk::diag::Timer my_timer_adapt; +}; + +} // namespace krino + +#endif // Akri_CDFEM_Support_h diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh.cpp b/packages/krino/krino/krino_lib/Akri_CDMesh.cpp new file mode 100644 index 000000000000..71b66be817d4 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh.cpp @@ -0,0 +1,3689 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include // Needed for all_reduce_max +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace krino{ + +std::shared_ptr CDMesh::the_new_mesh; + +//-------------------------------------------------------------------------------- + +CDMesh::CDMesh( stk::mesh::BulkData & mesh, const std::shared_ptr & old_mesh ) + : my_meta(mesh.mesh_meta_data()), + my_aux_meta(AuxMetaData::get(my_meta)), + my_entity_id_pool(my_meta), + my_spatial_dim( my_meta.spatial_dimension() ), + my_cdfem_support(CDFEM_Support::get(my_meta)), + my_phase_support(Phase_Support::get(my_meta)), + my_old_mesh(old_mesh), + my_stash_step_count(-1), + my_missing_remote_prolong_facets(false), + my_timer_decompose("Decompose", my_cdfem_support.get_timer_cdfem()), + my_timer_decomposition_has_changed("Need CDFEM", my_cdfem_support.get_timer_cdfem()), + my_timer_snap("Snapping", my_timer_decompose), + my_timer_stash_field_data("Stash Field Data", my_timer_decompose), + my_timer_modify_mesh("Modify Mesh", my_cdfem_support.get_timer_cdfem()), + my_timer_prolongation("Prolongation", my_cdfem_support.get_timer_cdfem()), + my_timer_compute_CFL("Compute CFL", my_cdfem_support.get_timer_cdfem()) +{ /* %TRACE[ON]% */ Trace trace__("CDMesh::CDMesh( stk::mesh::BulkData & mesh )"); /* %TRACE% */ + + stk::mesh::insert(my_attribute_parts, my_aux_meta.active_part()); + stk::mesh::insert(my_attribute_parts, my_aux_meta.exposed_boundary_part()); + stk::mesh::insert(my_attribute_parts, my_aux_meta.block_boundary_part()); + + if(my_old_mesh) + { + my_old_mesh->my_old_mesh.reset(); + } +} + +CDMesh::~CDMesh() +{ + clear(); +} + +SubElementNode * CDMesh::add_managed_node(std::unique_ptr node) +{ + nodes.emplace_back(std::move(node)); + return nodes.back().get(); +} + +//-------------------------------------------------------------------------------- + + +stk::mesh::Part & CDMesh::get_locally_owned_part() const { return my_meta.locally_owned_part(); } +stk::mesh::Part & CDMesh::get_globally_shared_part() const { return my_meta.globally_shared_part(); } +stk::mesh::Part & CDMesh::get_active_part() const { return my_aux_meta.active_part(); } +stk::mesh::Part & CDMesh::get_block_boundary_part() const { return my_aux_meta.block_boundary_part(); } + +//-------------------------------------------------------------------------------- + +void CDMesh::add_periodic_node_pair(stk::mesh::Entity node1, stk::mesh::Entity node2) +{ + my_periodic_node_id_map[stk_bulk().identifier(node1)].push_back(stk_bulk().identifier(node2)); + my_periodic_node_id_map[stk_bulk().identifier(node2)].push_back(stk_bulk().identifier(node1)); +} + +const std::vector & CDMesh::all_interface_ids() const +{ + if(crossing_keys.empty()) + { + const int num_ls = num_ls_fields(); + if(num_ls < 2 || !Phase_Support::has_one_levelset_per_phase()) + { + crossing_keys.resize(num_ls_fields()); + for(int i=0; i < num_ls_fields(); ++i) + { + crossing_keys[i] = InterfaceID(i,i); + } + } + else + { + for(int i=0; i < num_ls_fields(); ++i) + { + for(int j=i+1; j < num_ls_fields(); ++j) + { + crossing_keys.push_back(InterfaceID(i,j)); + } + } + } + } + return crossing_keys; +} + +std::vector CDMesh::active_interface_ids() const +{ + const std::vector all_interfaces = all_interface_ids(); + if (all_interfaces.size() == 1) return all_interfaces; + + std::vector id_is_active_locally(all_interfaces.size(), false); + for (const auto & elem : elements) + { + for (auto && elemInterface : elem->get_sorted_cutting_interfaces()) + { + const auto lower = std::lower_bound(all_interfaces.begin(), all_interfaces.end(), elemInterface); + ThrowAssert(*lower == elemInterface); + id_is_active_locally[std::distance(all_interfaces.begin(), lower)] = true; + } + } + + std::vector id_is_active_globally(all_interfaces.size()); + stk::all_reduce_sum(stk_bulk().parallel(), id_is_active_locally.data(), id_is_active_globally.data(), id_is_active_locally.size()); + + std::vector active_ids; + for (size_t id=0; id & oldMesh = the_new_mesh->my_old_mesh; + const bool noSuccessfulDecompositionSinceLastFailedStep = nullptr == oldMesh; + const bool lastStepFailed = nullptr != oldMesh && oldMesh->my_stash_step_count == step_count; + const bool restoreMesh = lastStepFailed || + noSuccessfulDecompositionSinceLastFailedStep; // Even though mesh has already been restored, another process might have modified it (ie rayTracer) + if (restoreMesh) + { + the_new_mesh = std::make_shared(mesh, std::shared_ptr()); + the_new_mesh->generate_nonconformal_elements(); + the_new_mesh->restore_subelement_edge_nodes(); + the_new_mesh->restore_subelements(); + } + } +} + +void CDMesh::build_and_stash_old_mesh(const int stepCount) +{ + std::shared_ptr & old_mesh = my_old_mesh; + if (!old_mesh) + { + old_mesh = std::make_shared(stk_bulk(), std::shared_ptr()); + old_mesh->generate_nonconformal_elements(); + old_mesh->stash_field_data(-1, *this); + } + else + { + if (my_cdfem_support.get_interface_maximum_refinement_level() > 0) + { + old_mesh = std::make_shared(stk_bulk(), std::shared_ptr()); + old_mesh->rebuild_child_part(); + old_mesh->rebuild_parent_and_active_parts_using_nonconformal_and_child_parts(); + old_mesh->generate_nonconformal_elements(); + old_mesh->restore_subelement_edge_nodes(); + old_mesh->restore_subelements(); + } + + old_mesh->stash_field_data(stepCount, *this); + } +} + +static FieldSet get_snap_fields(const CDFEM_Support & cdfemSupport) +{ + FieldSet snapFields = cdfemSupport.get_interpolation_fields(); + + FieldRef cdfemSnapField = cdfemSupport.get_cdfem_snap_displacements_field(); + if (cdfemSnapField.valid()) + { + for ( unsigned is = 0; is < cdfemSnapField.number_of_states(); ++is ) + { + const stk::mesh::FieldState state = static_cast(is); + snapFields.erase(cdfemSnapField.field_state(state)); + } + + for (auto && field : cdfemSupport.ls_fields()) + { + const FieldRef lsField = field.isovar.field(); + for ( unsigned is = 0; is < lsField.number_of_states(); ++is ) + { + const stk::mesh::FieldState state = static_cast(is); + if (state != stk::mesh::StateNew) + snapFields.erase(lsField.field_state(state)); + } + } + } + return snapFields; +} + +static void interpolate_nodal_field(const FieldRef field, + stk::mesh::Entity node, + const std::vector & interpNodes, + const std::vector & interpWeights) +{ + const unsigned fieldLength = field.length(); + + double * val = field_data(field, node); + if (nullptr == val) return; + + for (unsigned i=0; i(field, interpNodes[iNode]); + ThrowRequire(nullptr != nodeVal); + + for (unsigned i=0; i & parentNodes, + std::vector & parentWeights) +{ + std::map nodeStencil; + node.build_stencil(nodeStencil); + + parentNodes.clear(); + parentWeights.clear(); + for (auto && entry : nodeStencil) + { + parentNodes.push_back(entry.first->entity()); + parentWeights.push_back(entry.second); + } +} + +static bool any_node_was_snapped(const std::vector & nodes, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + for (auto && node : nodes) + { + const auto iter = nodesToCapturedDomains.find(node); + if (iter != nodesToCapturedDomains.end() && !iter->second.empty()) + return true; + } + return false; +} + +static void apply_snapping_to_children_of_snapped_nodes(const CDFEM_Support & cdfemSupport, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const krino::SubElementNode & node, + std::vector & parentNodes, + std::vector & parentWeights) +{ + fill_parent_nodes_and_weights(node, parentNodes, parentWeights); + if (any_node_was_snapped(parentNodes, nodesToCapturedDomains)) + { + for (auto && field : cdfemSupport.get_interpolation_fields()) + interpolate_nodal_field(field, node.entity(), parentNodes, parentWeights); + } +} + +void CDMesh::snap_and_update_fields_and_captured_domains(const InterfaceGeometry & interfaceGeometry, + NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + const FieldSet snapFields = get_snap_fields(my_cdfem_support); + + FieldRef cdfemSnapField = my_cdfem_support.get_cdfem_snap_displacements_field(); + if (cdfemSnapField.valid()) + stk::mesh::field_copy(my_cdfem_support.get_coords_field(), cdfemSnapField); + + const stk::mesh::Selector parentElementSelector = get_parent_element_selector(get_active_part(), my_cdfem_support, my_phase_support); + nodesToCapturedDomains = snap_as_much_as_possible_while_maintaining_quality(stk_bulk(), parentElementSelector, snapFields, interfaceGeometry, my_cdfem_support.get_global_ids_are_parallel_consistent()); + + if (cdfemSnapField.valid()) + stk::mesh::field_axpby(+1.0, my_cdfem_support.get_coords_field(), -1.0, cdfemSnapField); + + std::vector parentNodes; + std::vector parentWeights; + + if (cdfemSnapField.valid() && my_old_mesh) + for (auto && node : my_old_mesh->nodes) + if (!node->is_mesh_node()) + apply_snapping_to_children_of_snapped_nodes(my_cdfem_support, nodesToCapturedDomains, *node, parentNodes, parentWeights); +} + +int +CDMesh::decompose_mesh(stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const int step_count, + const std::vector> & periodic_node_pairs) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::decompose_mesh()"); /* %TRACE% */ + stk::diag::TimeBlock root_timer__(CDFEM_Support::get(mesh.mesh_meta_data()).get_timer_cdfem()); + + CDFEM_Support & cdfemSupport = CDFEM_Support::get(mesh.mesh_meta_data()); + + if (!the_new_mesh) + { + // FIXME: This can cause problems for shells. + attach_sides_to_elements(mesh); + } + + + krinolog << "Decomposing mesh for region into phase conformal elements." << stk::diag::dendl; + NodeToCapturedDomainsMap nodesToCapturedDomains; + + { + the_new_mesh = std::make_shared(mesh, the_new_mesh); + + for(auto && pair : periodic_node_pairs) + { + the_new_mesh->add_periodic_node_pair(pair.first, pair.second); + } + + // Not sure if this is krino's responsibility or the driving application. If we have + // elemental death fields, these need to be parallel consistent on aura elements. + the_new_mesh->parallel_communicate_elemental_death_fields(); + + stk::diag::TimeBlock timer__(the_new_mesh->my_timer_decompose); + + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + the_new_mesh->snap_and_update_fields_and_captured_domains(interfaceGeometry, nodesToCapturedDomains); + + interfaceGeometry.prepare_to_process_elements(the_new_mesh->stk_bulk(), nodesToCapturedDomains); + } + + { + stk::diag::TimeBlock timer__(the_new_mesh->my_timer_decompose); + + the_new_mesh->generate_nonconformal_elements(); + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + the_new_mesh->snap_nearby_intersections_to_nodes(interfaceGeometry, nodesToCapturedDomains); + the_new_mesh->set_phase_of_uncut_elements(interfaceGeometry); + the_new_mesh->triangulate(interfaceGeometry); + the_new_mesh->decompose(); + } + + the_new_mesh->build_and_stash_old_mesh(step_count); + + const bool mesh_modified = the_new_mesh->modify_mesh(); + + the_new_mesh->prolongation(); + + // debugging + if ( krinolog.shouldPrint(LOG_DEBUG) ) + { + the_new_mesh->debug_output(); + } + + { + const ScaledJacobianQualityMetric qualityMetric; + krinolog << "After cutting quality is " << determine_quality(mesh, the_new_mesh->get_active_part(), qualityMetric) << stk::diag::dendl; + } + + + if (!the_new_mesh->aux_meta().using_fmwk()) + { + the_new_mesh->print_conformal_volumes_and_surface_areas(); + } + + const int status = mesh_modified ? (COORDINATES_MAY_BE_MODIFIED | MESH_MODIFIED) : COORDINATES_MAY_BE_MODIFIED; + return status; +} + +bool +CDMesh::modify_mesh() +{/* %TRACE[ON]% */ Trace trace__("krino::Mesh::modify_mesh()"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer_modify_mesh); + + ParallelThrowAssert(stk_bulk().parallel(), check_face_and_edge_ownership(stk_bulk())); + ParallelThrowAssert(stk_bulk().parallel(), check_face_and_edge_relations(stk_bulk())); + + set_entities_for_identical_nodes(); + const bool all_elems_are_set_and_correct = set_entities_for_existing_child_elements(); + + std::vector< stk::mesh::Entity> unused_old_child_elems; + get_unused_old_child_elements(unused_old_child_elems); + + const bool modificationIsNeeded = (my_cdfem_support.get_interface_maximum_refinement_level() > 0) || stk::is_true_on_any_proc(stk_bulk().parallel(), !all_elems_are_set_and_correct || !unused_old_child_elems.empty()); + + if (modificationIsNeeded) + { + stk::mesh::toggle_sideset_updaters(stk_bulk(), false); + + stk_bulk().modification_begin(); + create_node_entities(); + std::vector side_requests; + create_element_and_side_entities(side_requests); + destroy_custom_ghostings(stk_bulk()); + delete_mesh_entities(stk_bulk(), unused_old_child_elems); + stk_bulk().modification_end(); + ParallelThrowAssert(stk_bulk().parallel(), check_shared_entity_nodes(stk_bulk())); + + add_possible_interface_sides(side_requests); + batch_create_sides(stk_bulk(), side_requests); + + stk::mesh::toggle_sideset_updaters(stk_bulk(), true); + stk_bulk().modification_begin(); + update_node_activation(stk_bulk(), aux_meta().active_part()); // we should be able to skip this step if there are no higher order elements + update_element_side_parts(); + stk_bulk().modification_end(); + + ParallelThrowAssert(stk_bulk().parallel(), check_element_side_connectivity(stk_bulk(), aux_meta().exposed_boundary_part(), aux_meta().active_part())); + ParallelThrowAssert(stk_bulk().parallel(), check_element_side_parts()); + + aux_meta().induce_topology_nodesets(aux_meta().active_locally_owned_selector()); + + ParallelThrowAssert(stk_bulk().parallel(), check_induced_parts(stk_bulk())); + } + + return modificationIsNeeded; +} + +void +CDMesh::set_entities_for_identical_nodes() +{ + CDMesh* old_mesh = get_old_mesh(); + if (nullptr == old_mesh) return; + + for (auto && node : nodes) + { + if (!node->entity_is_valid(stk_bulk())) + { + const SubElementNode * old_node = node->find_node_with_common_ancestry(*old_mesh); + if (nullptr != old_node) + { + stk::mesh::Entity old_node_entity = old_node->entity(); + if (stk_bulk().is_valid(old_node_entity)) + { + node->set_entity(stk_bulk(), old_node_entity); + } + } + } + } +} + +void +CDMesh::parallel_communicate_elemental_death_fields() const +{ + std::vector< const stk::mesh::FieldBase *> element_fields; + for (auto && field : ls_fields()) + { + if (field.isovar.entity_rank() == stk::topology::ELEMENT_RANK) + { + element_fields.push_back(&field.isovar.field()); + } + } + stk::mesh::communicate_field_data(stk_bulk(), element_fields); +} + +bool +CDMesh::set_entities_for_existing_child_elements() +{ + CDMesh* old_mesh = get_old_mesh(); + if (nullptr == old_mesh) return false; + + std::vector subelem_node_entities; + std::vector existing_elems; + + bool all_element_entities_are_set_and_correct = true; + for (const auto & elem : elements) + { + if (elem->have_subelements()) + { + std::vector conformal_subelems; + elem->get_subelements(conformal_subelems); + + for (auto && subelem : conformal_subelems) + { + // If all nodes are set, look for existing element using the nodes. + subelem_node_entities.clear(); + for (auto&& subelem_node : subelem->get_nodes()) + { + stk::mesh::Entity node = subelem_node->entity(); + if (stk_bulk().is_valid(node)) subelem_node_entities.push_back(node); + } + existing_elems.clear(); + if (subelem_node_entities.size() == subelem->get_nodes().size()) + { + stk::mesh::get_entities_through_relations(stk_bulk(), subelem_node_entities, stk::topology::ELEMENT_RANK, existing_elems); + ThrowAssert(existing_elems.size() <= 1); + } + + if (existing_elems.empty()) + { + all_element_entities_are_set_and_correct = false; + } + else + { + subelem->set_entity(stk_bulk(), existing_elems[0]); + ThrowAssert(subelem->check_entity_nodes(stk_bulk())); + if (all_element_entities_are_set_and_correct && elem_io_part_changed(*subelem)) all_element_entities_are_set_and_correct = false; + } + } + } + else + { + if (all_element_entities_are_set_and_correct && elem_io_part_changed(*elem)) all_element_entities_are_set_and_correct = false; + } + } + return all_element_entities_are_set_and_correct; +} + +void +CDMesh::get_unused_old_child_elements(std::vector & unused_old_child_elems) +{ + stk::mesh::Selector selector = get_child_part(); + std::vector old_child_elems; + stk::mesh::get_selected_entities( selector, stk_bulk().buckets( stk::topology::ELEMENT_RANK ), old_child_elems ); + + unused_old_child_elems.clear(); + unused_old_child_elems.reserve(old_child_elems.size()); + + for (auto&& old_child_elem : old_child_elems) + { + const SubElement * subelem = find_child_element(old_child_elem); + if (subelem == nullptr) + { + unused_old_child_elems.push_back(old_child_elem); + } + } + child_elements.clear(); // reset child element vector +} + +bool +CDMesh::decomposition_needs_update(const InterfaceGeometry & interfaceGeometry, + const std::vector> & periodic_node_pairs) +{ + return !the_new_mesh || the_new_mesh->decomposition_has_changed(interfaceGeometry); +} + +void +CDMesh::mark_interface_elements_for_adaptivity(stk::mesh::BulkData & mesh, const InterfaceGeometry & interfaceGeometry, const std::string & marker_field_name, const int num_refinements) +{/* %TRACE[SPEC]% */ Tracespec trace__("CDMesh::mark_interface_elements_for_adaptivity(stk::mesh::BulkData & mesh, const std::string & marker_field_name, const int num_refinements)"); /* %TRACE% */ + + CDMesh cdmesh(mesh, std::shared_ptr()); + krino::mark_interface_elements_for_adaptivity(cdmesh.stk_bulk(), interfaceGeometry, cdmesh.active_interface_ids(), cdmesh.get_snapper(), cdmesh.aux_meta(), cdmesh.get_cdfem_support(), cdmesh.get_coords_field(), marker_field_name, num_refinements); +} + +void +CDMesh::nonconformal_adaptivity(stk::mesh::BulkData & mesh, const InterfaceGeometry & interfaceGeometry) +{/* %TRACE[SPEC]% */ Tracespec trace__("CDMesh::nonconformal_adaptivity(stk::mesh::BulkData & mesh)"); /* %TRACE% */ + + const auto & cdfem_support = CDFEM_Support::get(mesh.mesh_meta_data()); + stk::diag::TimeBlock timer__(cdfem_support.get_timer_adapt()); + + const std::string & marker_name = cdfem_support.get_nonconformal_adapt_marker_name(); + auto & h_adapt = cdfem_support.get_nonconformal_hadapt(); + + std::function marker_function = + [&mesh, &interfaceGeometry](const std::string & marker_field_name, int num_refinements) + { + mark_interface_elements_for_adaptivity(mesh, interfaceGeometry, marker_field_name, num_refinements); + }; + + perform_multilevel_adaptivity(mesh, marker_name, marker_function, h_adapt, cdfem_do_not_refine_or_unrefine_selector(cdfem_support)); +} + +void +CDMesh::rebuild_after_rebalance() +{ + clear(); + generate_nonconformal_elements(); + restore_subelement_edge_nodes(); + restore_subelements(); +} + +static bool side_is_adaptivity_or_cdfem_parent(stk::mesh::BulkData & mesh, stk::mesh::Entity side, const stk::mesh::Part & cdfemParentPart) +{ + if (mesh.num_connectivity(side, stk::topology::CONSTRAINT_RANK) > 0) + return true; + for (auto element : StkMeshEntities{mesh.begin_elements(side), mesh.end_elements(side)}) + if (mesh.bucket(element).member(cdfemParentPart)) + return true; + return false; +} + +void delete_extraneous_inactive_sides(stk::mesh::BulkData & mesh, const stk::mesh::Part & cdfemParentPart, const stk::mesh::Part & activePart) +{ + stk::mesh::Selector notActive = !activePart; + + std::vector sides; + stk::mesh::get_selected_entities(notActive, mesh.buckets(mesh.mesh_meta_data().side_rank()), sides, false); + + mesh.modification_begin(); + + for (auto && side : sides) + if (!side_is_adaptivity_or_cdfem_parent(mesh, side, cdfemParentPart)) + ThrowRequireMsg(disconnect_and_destroy_entity(mesh, side), "Could not destroy entity " << mesh.entity_key(side)); + + mesh.modification_end(); +} + +void +CDMesh::rebuild_from_restart_mesh(stk::mesh::BulkData & mesh) +{ + ParallelThrowRequire(mesh.parallel(), !the_new_mesh); + + the_new_mesh = std::make_shared(mesh, the_new_mesh); + the_new_mesh->rebuild_child_part(); + the_new_mesh->rebuild_parent_and_active_parts_using_nonconformal_and_child_parts(); + the_new_mesh->generate_nonconformal_elements(); + the_new_mesh->restore_subelement_edge_nodes(); + the_new_mesh->restore_subelements(); + + // rebuild conformal side parts + the_new_mesh->stk_bulk().modification_begin(); + the_new_mesh->update_element_side_parts(); + the_new_mesh->stk_bulk().modification_end(); + + delete_extraneous_inactive_sides(mesh, the_new_mesh->get_parent_part(), the_new_mesh->get_active_part()); +} + +void +CDMesh::rebuild_child_part() +{ + auto & child_part = get_child_part(); + auto & mesh = stk_bulk(); + + // Need to iterate all locally owned elements to find child elements, + // which are identified by detecting that they use child edge nodes + stk::mesh::EntityVector local_elements; + stk::mesh::Selector sel = get_active_part() & get_locally_owned_part(); + stk::mesh::get_selected_entities(sel, mesh.buckets(stk::topology::ELEMENT_RANK), + local_elements); + + auto conformal_selector = stk::mesh::selectUnion(my_phase_support.get_conformal_parts()); + const auto & child_edge_node_part = get_child_edge_node_part(); + mesh.modification_begin(); + for(auto && elem : local_elements) + { + auto elem_nodes = mesh.begin_nodes(elem); + auto num_nodes = mesh.num_nodes(elem); + bool is_child_elem = false; + for(unsigned i=0; i < num_nodes; ++i) + { + if(mesh.bucket(elem_nodes[i]).member(child_edge_node_part)) + { + is_child_elem = true; + break; + } + } + + if(is_child_elem) + { + mesh.change_entity_parts(elem, stk::mesh::ConstPartVector{&child_part}, stk::mesh::ConstPartVector{}); + } + } + mesh.modification_end(); +} + +void +CDMesh::rebuild_parent_and_active_parts_using_nonconformal_and_child_parts() +{ + auto & parent_part = get_parent_part(); + auto & mesh = stk_bulk(); + + stk::mesh::EntityVector entities; + stk::mesh::Selector sel = get_active_part() & get_locally_owned_part() & + stk::mesh::selectUnion(my_phase_support.get_nonconformal_parts()); + stk::mesh::get_selected_entities(sel, mesh.buckets(stk::topology::ELEMENT_RANK), + entities); + + mesh.modification_begin(); + for(auto && elem : entities) + { + mesh.change_entity_parts(elem, stk::mesh::ConstPartVector{&parent_part}, stk::mesh::ConstPartVector{&get_active_part()}); + } + + // Also remove active part from nonconformal sides + entities.clear(); + auto side_rank = mesh.mesh_meta_data().side_rank(); + stk::mesh::get_selected_entities(sel, mesh.buckets(side_rank), entities); + for(auto && side : entities) + { + mesh.change_entity_parts(side, stk::mesh::ConstPartVector{}, stk::mesh::ConstPartVector{&get_active_part()}); + } + + // Also need to mark parents in undecomposed blocks that have children due to hanging + // nodes + entities.clear(); + stk::mesh::Selector undecomposed_child_sel = get_active_part() & get_locally_owned_part() & + !my_phase_support.get_all_decomposed_blocks_selector() & + get_child_part(); + stk::mesh::get_selected_entities(undecomposed_child_sel, mesh.buckets(stk::topology::ELEMENT_RANK), + entities); + for(auto && elem : entities) + { + auto parent_elem = get_parent_element(elem); + ThrowRequire(mesh.is_valid(parent_elem)); + mesh.change_entity_parts(parent_elem, stk::mesh::ConstPartVector{&parent_part}, stk::mesh::ConstPartVector{&get_active_part()}); + } + mesh.modification_end(); +} + +const SubElementNode * +CDMesh::build_subelement_edge_node(const stk::mesh::Entity node_entity) +{ + const auto & mesh = stk_bulk(); + + // This is super inefficient but lets just get it working for now. + ThrowRequire(mesh.is_valid(node_entity)); + auto id = mesh.identifier(node_entity); + auto find_existing = std::find_if(nodes.begin(), nodes.end(), + [id](const std::unique_ptr & compare) + { return compare->entityId() == id; }); + if(find_existing != nodes.end()) + return find_existing->get(); + + auto parent_ids = get_edge_node_parent_ids(mesh, get_parent_node_ids_field(), node_entity); + + auto search0 = std::find_if(nodes.begin(), nodes.end(), + [parent_ids](const std::unique_ptr & compare) + { return compare->entityId() == parent_ids[0]; }); + const SubElementNode * immediate_parent0 = (search0 == nodes.end()) ? + build_subelement_edge_node(mesh.get_entity(stk::topology::NODE_RANK, parent_ids[0])) : + search0->get(); + + auto search1 = std::find_if(nodes.begin(), nodes.end(), + [parent_ids](const std::unique_ptr & compare) + { return compare->entityId() == parent_ids[1]; }); + const SubElementNode * immediate_parent1 = (search1 == nodes.end()) ? + build_subelement_edge_node(mesh.get_entity(stk::topology::NODE_RANK, parent_ids[1])) : + search1->get(); + + // For LS per phase the immediate parents are not necessarily actual parent element nodes, + // we need to go all the way up the parentage tree to find the original parent nodes so we can + // get the parent Mesh_Element. + std::set parent_elem_nodes_set; + get_parent_nodes_from_child( + mesh, node_entity, get_parent_node_ids_field(), parent_elem_nodes_set); + std::vector parent_elem_nodes( + parent_elem_nodes_set.begin(), parent_elem_nodes_set.end()); + std::vector parent_elems; + stk::mesh::get_entities_through_relations(stk_bulk(), parent_elem_nodes, stk::topology::ELEMENT_RANK, parent_elems); + + stk::mesh::Entity owner_entity; + const stk::mesh::Selector locally_owned_parent_selector = get_locally_owned_part() & get_parent_part(); + for(auto && e : parent_elems) + { + if(locally_owned_parent_selector(mesh.bucket(e))) + { + owner_entity = e; + break; + } + } + if(!mesh.is_valid(owner_entity)) + { + std::ostringstream err_msg; + err_msg << "Failed to find locally owned element connected to nodes" + << immediate_parent0->entityId() << " and " << immediate_parent1->entityId() + << " when restoring CDFEM data structures after restart.\n"; + err_msg << "Possible parent elems:\n"; + for(auto && e : parent_elems) + { + err_msg << " " << debug_entity(mesh, e) << "\n"; + } + throw std::runtime_error(err_msg.str()); + } + + auto owner_id = mesh.identifier(owner_entity); + const Mesh_Element * owner = find_mesh_element(owner_id); + ThrowRequireMsg(owner, "Could not find Mesh_Element for owner element " << owner_id << " " << debug_entity(mesh, owner_entity)); + const double position = compute_child_position( + mesh, node_entity, immediate_parent0->entity(), immediate_parent1->entity()); + std::unique_ptr newNode = std::make_unique(owner, position, immediate_parent0, immediate_parent1); + SubElementNode * edgeNode = add_managed_node(std::move(newNode)); + edgeNode->set_entity(stk_bulk(), node_entity); + return edgeNode; +} + +void +CDMesh::restore_subelement_edge_nodes() +{ + stk::mesh::Selector selector = get_child_edge_node_part() & + (get_locally_owned_part() | get_globally_shared_part()); + const auto & mesh = stk_bulk(); + const auto & buckets = mesh.get_buckets(stk::topology::NODE_RANK, selector); + const auto parent_id_field = get_parent_node_ids_field(); + + std::vector< const stk::mesh::FieldBase *> fields(1, &parent_id_field.field()); + stk::mesh::communicate_field_data(mesh, fields); + + for(const auto & b_ptr : buckets) + { + for(unsigned i=0; i < b_ptr->size(); ++i) + { + build_subelement_edge_node((*b_ptr)[i]); + } + } +} + +void +CDMesh::restore_subelements() +{ + stk::mesh::Selector selector = get_locally_owned_part() & get_child_part(); + const auto & mesh = stk_bulk(); + const auto & buckets = mesh.get_buckets(stk::topology::ELEMENT_RANK, selector); + NodeVec subelem_nodes; + for(const auto & b_ptr : buckets) + { + const stk::topology & topo = b_ptr->topology(); + const unsigned num_nodes = topo.num_nodes(); + subelem_nodes.reserve(num_nodes); + for(const auto & elem : *b_ptr) + { + const stk::mesh::Entity parent = get_parent_element(elem); + ThrowRequire(mesh.is_valid(parent) && parent != elem); + + auto parent_mesh_elem = find_mesh_element(mesh.identifier(parent)); + ThrowRequire(parent_mesh_elem); + + subelem_nodes.clear(); + // TODO: May need to create subelement edge nodes somehow + const auto * elem_nodes = mesh.begin_nodes(elem); + ThrowAssert(mesh.num_nodes(elem) == num_nodes); + for(unsigned i=0; i < num_nodes; ++i) + { + auto node_id = mesh.identifier(elem_nodes[i]); + auto find_node = std::find_if(nodes.begin(), nodes.end(), + [node_id](const std::unique_ptr & compare) + { return compare->entityId() == node_id; }); + ThrowRequire(find_node != nodes.end()); + subelem_nodes.push_back(find_node->get()); + } + + std::unique_ptr subelem; + switch(topo) + { + case stk::topology::TRIANGLE_3_2D: + subelem = std::make_unique(subelem_nodes, std::vector{-1, -1, -1}, parent_mesh_elem); + break; + case stk::topology::TETRAHEDRON_4: + subelem = std::make_unique(subelem_nodes, std::vector{-1, -1, -1, -1}, parent_mesh_elem); + break; + default: + ThrowRuntimeError("At present only Tri3 and Tet4 topologies are supported for restart of CDFEM problems."); + } + ThrowAssert(subelem); + subelem->set_entity(stk_bulk(), elem); + const_cast(parent_mesh_elem)->add_subelement(std::move(subelem)); + } + } +} + +void +CDMesh::delete_cdfem_parent_elements() +{/* %TRACE[SPEC]% */ Tracespec trace__("Mesh::delete_cdfem_parent_elements(stk::mesh::BulkData & mesh)"); /* %TRACE% */ + // Percept messes up the cdfem child/parent parts, the active part, and the percept refined part for post-cdfem refinement. + // This is kind of an extreme work-around, but here we delete all of the cdfem parents prior to the post-cdfem refiment so that + // there is nothing to mess up. + + std::vector< stk::mesh::Entity> cdfem_parent_elements; + + stk::mesh::Selector selector = get_parent_part(); + stk::mesh::get_selected_entities( selector, stk_bulk().buckets( stk::topology::ELEMENT_RANK ), cdfem_parent_elements ); + + stk_bulk().modification_begin(); + delete_mesh_entities(stk_bulk(), cdfem_parent_elements); + stk_bulk().modification_end(); +} + +void +CDMesh::fixup_adapted_element_parts(stk::mesh::BulkData & mesh) +{/* %TRACE[SPEC]% */ Tracespec trace__("Mesh::fixup_adapted_element_parts(CDFEM_Support & cdfem_support)"); /* %TRACE% */ + // Fixup volume parts that currently can be messed up by adaptivity. + // There are two types of fixes: + // 1. CDFEM parent elements that are activated by Encore adaptivity (this is expected, but needs to be fixed). + // 2. Conformal elements that have somehow picked up the non-conformal part (this probably shouldn't happen). + + Phase_Support & phase_support = Phase_Support::get(mesh.mesh_meta_data()); + CDFEM_Support & cdfem_support = CDFEM_Support::get(mesh.mesh_meta_data()); + AuxMetaData & aux_meta = AuxMetaData::get(mesh.mesh_meta_data()); + stk::mesh::Selector cdfem_parent_selector = cdfem_support.get_parent_part(); + + stk::mesh::Selector locally_owned_selector(mesh.mesh_meta_data().locally_owned_part()); + std::vector entities; + + std::vector remove_parts; + stk::mesh::PartVector bucket_remove_parts; + const stk::mesh::BucketVector & buckets = mesh.get_buckets(stk::topology::ELEMENT_RANK, locally_owned_selector); + for (auto&& bucket_ptr : buckets) + { + unsigned num_volume_parts = 0; + stk::mesh::Part * extraneous_nonconformal_part = nullptr; + const stk::mesh::PartVector & bucket_parts = bucket_ptr->supersets(); + bucket_remove_parts.clear(); + for(auto&& part : bucket_parts) + { + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK && part->subsets().empty() && part->topology() != stk::topology::INVALID_TOPOLOGY) + { + ++num_volume_parts; + if (phase_support.is_nonconformal(part)) + { + extraneous_nonconformal_part = part; + } + } + } + if (num_volume_parts > 1) + { + bucket_remove_parts.push_back(extraneous_nonconformal_part); + } + if (cdfem_parent_selector(*bucket_ptr)) + { + bucket_remove_parts.push_back(&aux_meta.active_part()); + } + if (!bucket_remove_parts.empty()) + { + entities.insert(entities.end(), bucket_ptr->begin(), bucket_ptr->end()); + remove_parts.insert(remove_parts.end(), bucket_ptr->size(), bucket_remove_parts); + } + } + stk::mesh::PartVector empty; + std::vector add_parts(entities.size(), empty); + + // This seems like a bug. For some reason batch_change_entity_parts does not work the same as calling change_entity_parts within a full modification cycle. + //mesh.bulk().batch_change_entity_parts(entities, add_parts, remove_parts); + mesh.modification_begin(); + for(size_t i=0; iget_edge_interpolation_model()) + { + return; + } + + for (auto && node : mesh->nodes) + { + const krino::SubElementEdgeNode* edge_node = dynamic_cast(node.get()); + if (nullptr == edge_node) continue; + + NodeVec parents = edge_node->get_parents(); + const double ratio = edge_node->get_position(); + + stk::mesh::Entity node_obj = edge_node->entity(); + stk::mesh::Entity parent0_obj = parents[0]->entity(); + stk::mesh::Entity parent1_obj = parents[1]->entity(); + + const int num_ls_fields = mesh->num_ls_fields(); + for (int ls_index=0; ls_indexls_field(ls_index); + double & node_val = *field_data( ls_field.isovar , node_obj); + const double & parent0_val = *field_data( ls_field.isovar , parent0_obj); + const double & parent1_val = *field_data( ls_field.isovar , parent1_obj); + + const double interp_val = (1.-ratio) * parent0_val + ratio * parent1_val; + node_val = interp_val; + } + } +} + +void +CDMesh::stash_field_data(const int step_count, const CDMesh & new_mesh) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::stash_field_data(const int step_count)"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer_stash_field_data); + my_stash_step_count = step_count; + clear_prolongation_data(); + + stash_nodal_field_data(new_mesh); + stash_elemental_field_data(); +} + +//-------------------------------------------------------------------------------- + +static void fill_nodes_of_elements_with_subelements_or_changed_phase(const stk::mesh::BulkData & mesh, + const std::vector> & newMeshElements, + const std::vector> & oldMeshElements, + std::set & nodesOfElements) +{ + nodesOfElements.clear(); + + for (auto && element : newMeshElements) + { + bool haveSubelementsOrChangedPhase = false; + if (element->have_subelements()) + { + haveSubelementsOrChangedPhase = true; + } + else + { + const Mesh_Element * oldElement = CDMesh::find_mesh_element(element->entityId(), oldMeshElements); + if (nullptr == oldElement || element->get_phase() != oldElement->get_phase()) + haveSubelementsOrChangedPhase = true; + } + + if (haveSubelementsOrChangedPhase) + for (auto && node : element->get_nodes()) + nodesOfElements.insert(node->entity()); + } +} + +static +void pack_shared_nodes_for_sharing_procs(const stk::mesh::BulkData & mesh, + const std::set & nodes, + stk::CommSparse &commSparse) +{ + std::vector nodeSharedProcs; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto node : nodes) + { + if (mesh.bucket(node).shared()) + { + mesh.comm_shared_procs(node, nodeSharedProcs); + for (int procId : nodeSharedProcs) + commSparse.send_buffer(procId).pack(mesh.identifier(node)); + } + } + }); +} + +static +void unpack_shared_nodes(const stk::mesh::BulkData & mesh, + std::set & nodes, + stk::CommSparse &commSparse) +{ + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + stk::mesh::EntityId nodeId; + commSparse.recv_buffer(procId).unpack(nodeId); + stk::mesh::Entity node = mesh.get_entity(stk::topology::NODE_RANK, nodeId); + ThrowRequire(mesh.is_valid(node)); + nodes.insert(node); + } + }); +} + +static std::set get_nodes_of_elements_with_subelements_or_have_changed_phase(const stk::mesh::BulkData & mesh, const std::vector> & newMeshElements, + const std::vector> & oldMeshElements) +{ + std::set nodesOfElements; + fill_nodes_of_elements_with_subelements_or_changed_phase(mesh, newMeshElements, oldMeshElements, nodesOfElements); + + stk::CommSparse commSparse(mesh.parallel()); + pack_shared_nodes_for_sharing_procs(mesh, nodesOfElements, commSparse); + unpack_shared_nodes(mesh, nodesOfElements, commSparse); + + return nodesOfElements; +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::stash_nodal_field_data(const CDMesh & new_mesh) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::stash_nodal_field_data()"); /* %TRACE% */ + + // stash child nodes + { + stk::mesh::Selector selector = get_locally_owned_part() & get_child_part(); + + stk::mesh::BucketVector const& buckets = stk_bulk().get_buckets( stk::topology::ELEMENT_RANK, selector ); + for ( auto&& bucket_ptr : buckets ) + { + const stk::mesh::Bucket & b = *bucket_ptr; + const size_t length = b.size(); + for (size_t ielem = 0; ielem < length; ++ielem) + { + stk::mesh::Entity elem = b[ielem]; + const unsigned num_elem_nodes = stk_bulk().num_nodes(elem); + const stk::mesh::Entity* elem_nodes = stk_bulk().begin_nodes(elem); + + for (unsigned inode = 0; inode < num_elem_nodes; ++inode) + { + stk::mesh::Entity node = elem_nodes[inode]; + ThrowAssert((stk_bulk().bucket(node).member(get_active_part()))); + ProlongationNodeData *& node_data = my_prolong_node_map[stk_bulk().identifier(node)]; + if (nullptr == node_data) + { + const bool communicate_me_to_all_sharers = stk_bulk().bucket(node).member(get_globally_shared_part()); + node_data = new ProlongationNodeData(*this, node, communicate_me_to_all_sharers); + } + } + } + } + } + + // Stash all nodes of elements that have child elements or have changed phase. + // Due to hanging nodes, etc, this is more than just the cut elements. + for (auto&& node : get_nodes_of_elements_with_subelements_or_have_changed_phase(stk_bulk(), new_mesh.elements, elements)) + { + if (stk_bulk().bucket(node).member(get_active_part())) // Don't stash inactive midside nodes + { + ThrowAssert(stk_bulk().is_valid(node)); + ProlongationNodeData *& node_data = my_prolong_node_map[stk_bulk().identifier(node)]; + if (nullptr == node_data) + { + const bool communicate_me_to_all_sharers = stk_bulk().bucket(node).member(get_globally_shared_part()); + node_data = new ProlongationNodeData(*this, node, communicate_me_to_all_sharers); + } + } + } + + // stash all inter-block nodes + if (need_nodes_for_prolongation()) + { + stk::mesh::Selector active_not_ghost_selector(get_active_part() & (get_locally_owned_part() | get_globally_shared_part())); + const stk::mesh::BucketVector & buckets = stk_bulk().get_buckets(stk::topology::NODE_RANK, active_not_ghost_selector); + for (auto&& bucket_ptr : buckets) + { + unsigned num_conformal_parts = 0; + const stk::mesh::PartVector & node_parts = bucket_ptr->supersets(); + for(auto&& node_part_ptr : node_parts) + { + // This is designed to catch side with block_2 + block_1_air, block_1_air + block_1_solid, etc. + if (node_part_ptr->primary_entity_rank() == stk::topology::ELEMENT_RANK && + !my_phase_support.is_nonconformal(node_part_ptr) && + stk::io::is_part_io_part(*node_part_ptr)) + { + ++num_conformal_parts; + } + } + + if (num_conformal_parts > 1) + { + for (auto&& node : *bucket_ptr) + { + ProlongationNodeData *& node_data = my_prolong_node_map[stk_bulk().identifier(node)]; + if (nullptr == node_data) + { + node_data = new ProlongationNodeData(*this, node, false); + } + } + } + } + } + + // build facets if needed + if (need_facets_for_prolongation()) + { + stk::mesh::Selector active_locally_owned_selector(get_active_part() & get_locally_owned_part()); + + const stk::mesh::BucketVector & buckets = stk_bulk().get_buckets(stk_bulk().mesh_meta_data().side_rank(), active_locally_owned_selector); + for (auto&& bucket_ptr : buckets) + { + unsigned num_conformal_parts = 0; + const stk::mesh::PartVector & side_parts = bucket_ptr->supersets(); + for(auto&& side_part_ptr : side_parts) + { + // This is designed to catch side with block_2 + block_1_air, block_1_air + block_1_solid, etc. + if (side_part_ptr->primary_entity_rank() == stk::topology::ELEMENT_RANK && + !my_phase_support.is_nonconformal(side_part_ptr) && + stk::io::is_part_io_part(*side_part_ptr)) + { + ++num_conformal_parts; + } + } + + if (num_conformal_parts > 1) + { + for (auto&& side : *bucket_ptr) + { + ThrowAssert( stk_bulk().num_elements(side) > 0 ); + + ProlongationFacet * prolong_facet = new ProlongationFacet(*this, side); + my_prolong_facets.push_back(prolong_facet); + } + } + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::stash_elemental_field_data() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::stash_elemental_field_data()"); /* %TRACE% */ + const FieldSet & element_fields = get_element_fields(); + if (element_fields.empty()) return; + + for (const auto & mesh_elem : elements) + { + const stk::mesh::EntityId elem_id = mesh_elem->entityId(); + stk::mesh::Entity elem = mesh_elem->entity(); + ThrowAssert(stk_bulk().is_valid(elem)); + + if(mesh_elem->have_subelements()) + { + std::vector conformal_subelems; + mesh_elem->get_subelements(conformal_subelems); + + const unsigned num_child = conformal_subelems.size(); + std::vector child_data(num_child); + std::vector< std::vector > child_intg_wts(num_child); + + for (unsigned j=0; jentityId(); + stk::mesh::Entity subelem_entity = stk_bulk().get_entity(stk::topology::ELEMENT_RANK, subelem_id); //EXPENSIVE! + ProlongationElementData * subelem_data = new ProlongationElementData(stk_bulk(), subelem_entity); + ThrowAssertMsg(0 == my_prolong_element_map.count(subelem_id), "Duplicate subelement entityId " << subelem_id); + my_prolong_element_map[subelem_id] = subelem_data; + subelem->set_prolongation_data(subelem_data); + child_data[j] = subelem_data; + + subelem->integration_weights(child_intg_wts[j]); + } + + const bool single_coincident_subelement = (num_child == 1); + if (!single_coincident_subelement) + { + ProlongationElementData * elem_data = new ProlongationElementData(stk_bulk(), child_data, child_intg_wts); + ThrowAssert(0 == my_prolong_element_map.count(elem_id)); + my_prolong_element_map[elem_id] = elem_data; + mesh_elem->set_prolongation_data(elem_data); + } + } + else + { + ProlongationElementData * elem_data = new ProlongationElementData(stk_bulk(), elem); + ThrowAssert(0 == my_prolong_element_map.count(elem_id)); + my_prolong_element_map[elem_id] = elem_data; + mesh_elem->set_prolongation_data(elem_data); + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::clear_prolongation_trees() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::clear_prolongation_trees() const"); /* %TRACE% */ + my_phase_prolong_tree_map.clear(); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::build_prolongation_trees() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::build_prolongation_trees() const"); /* %TRACE% */ + + clear_prolongation_trees(); + + if (need_facets_for_prolongation()) + { + std::map,std::vector> phase_prolong_facet_map; + + for ( unsigned n=0; nget_common_fields()].push_back(prolong_facet); + } + + for (auto && entry : phase_prolong_facet_map) + { + const std::vector & fields = entry.first; + std::vector & facets = entry.second; + + my_phase_prolong_tree_map[fields] = std::make_unique>(facets, ProlongationFacet::get_bounding_box); + ThrowAssert(!my_phase_prolong_tree_map[fields]->empty()); + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::communicate_prolongation_facet_fields() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::communicate_prolongation_facet_fields() const"); /* %TRACE% */ + + if (!need_facets_for_prolongation()) + return; + + const int num_procs = stk_bulk().parallel_size(); + if ( num_procs == 1 ) return; // Don't talk to yourself, it's embarrassing + const int me = stk_bulk().parallel_rank(); + + // formulate messages + stk::CommSparse comm_sparse(stk_bulk().parallel()); + + const size_t map_size = my_phase_prolong_tree_map.size(); + + for (int pass=0; pass<2; ++pass) + { + for ( int p=0; p & facet_fields = entry.first; + b.pack(facet_fields.size()); + for (unsigned field : facet_fields) + b.pack(field); + } + + ThrowAssert( pass == 0 || 0 == b.remaining() ); + } + + if (pass == 0) + { + comm_sparse.allocate_buffers(); + } + else + { + // send/receive + comm_sparse.communicate(); + } + } + + for ( int p=0; p facet_fields(num_fields); + for (size_t ifield = 0; ifield fieldOrdinals) +{ + const stk::mesh::FieldVector & all_fields = meta.get_fields(); + std::ostringstream os; + os << "Fields { "; + for (unsigned fieldOrdinal : fieldOrdinals) + os << all_fields[fieldOrdinal]->name() << " "; + os << "}"; + return os.str(); +} + +//-------------------------------------------------------------------------------- + +const ProlongationPointData * +CDMesh::find_prolongation_node(const SubElementNode & dst_node) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::find_prolongation_node(const SubElementNode & dst_node) const"); /* %TRACE% */ + + const Vector3d & dst_node_coords = dst_node.coordinates(); + const ProlongationPointData * src_data = nullptr; + + const std::vector required_fields = dst_node.prolongation_node_fields(*this); + + ThrowRequire(need_facets_for_prolongation()); + + const ProlongationFacet * nearest_prolong_facet = nullptr; + bool matching_empty_tree = false; + FacetDistanceQuery nearest_facet_query; + for (auto && entry : my_phase_prolong_tree_map) + { + const std::vector & tree_fields = entry.first; + SearchTree * facet_tree = entry.second.get(); + + if (std::includes(tree_fields.begin(), tree_fields.end(), required_fields.begin(), required_fields.end())) + { + if (nullptr == facet_tree) + { + matching_empty_tree = true; + continue; + } + std::vector nearest_prolong_facets; + facet_tree->find_closest_entities( dst_node_coords, nearest_prolong_facets ); + ThrowAssert(!nearest_prolong_facets.empty()); + + for (auto && prolong_facet : nearest_prolong_facets) + { + FacetDistanceQuery facet_query(*prolong_facet->get_facet(), dst_node_coords); + if (nearest_facet_query.empty() || facet_query.distance_squared() < nearest_facet_query.distance_squared()) + { + nearest_prolong_facet = prolong_facet; + nearest_facet_query = facet_query; + } + } + } + } + + if(nullptr != nearest_prolong_facet) + { + src_data = nearest_prolong_facet->get_prolongation_point_data(nearest_facet_query); + if (krinolog.shouldPrint(LOG_DEBUG)) + { + const std::vector & facet_nodes = nearest_prolong_facet->get_prolongation_nodes(); + krinolog << "Prolongation facet for " << dst_node.entityId() << " has nodes "; + for (auto&& node : facet_nodes) + { + krinolog << node->entityId() << " "; + } + krinolog << stk::diag::dendl; + } + } + + if( nullptr == src_data ) + { + if (matching_empty_tree) + { + my_missing_remote_prolong_facets = true; + if (krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Found missing remote prolong facet for node for " << dst_node.entityId() << stk::diag::dendl; + return nullptr; + } + // Search for facet failed. Now try nodes. This will handle triple points. Something better that handles an actual edge search might be better in 3d. + const ProlongationNodeData * closest_node = nullptr; + double closest_dist2 = std::numeric_limits::max(); + for (auto && entry : my_prolong_node_map) + { + const ProlongationNodeData * node = entry.second; + const std::vector & tree_fields = node->get_fields(); + if (std::includes(tree_fields.begin(), tree_fields.end(), required_fields.begin(), required_fields.end())) + { + const double dist2 = (node->get_coordinates()-dst_node_coords).length_squared(); + if (dist2 < closest_dist2) + { + closest_node = node; + closest_dist2 = dist2; + } + } + } + if (nullptr != closest_node) + { + src_data = closest_node; + if (krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Prolongation node for " << dst_node.entityId() << " is " << closest_node->entityId() << stk::diag::dendl; + } + } + + if (nullptr == src_data) + { + krinolog << "Failed to find prolongation node for node#" << dst_node.entityId() << stk::diag::dendl; + if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << " with required part fields=" << print_fields(stk_meta(), required_fields) << stk::diag::dendl; + krinolog << " with parts="; + const stk::mesh::PartVector & parts = stk_bulk().bucket(dst_node.entity()).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = parts.begin(); part_iter != parts.end(); ++part_iter) + { + const stk::mesh::Part * const part = *part_iter; + krinolog << "\"" << part->name() << "\"" << " "; + } + krinolog << stk::diag::dendl; + const unsigned num_dst_node_elements = stk_bulk().num_elements(dst_node.entity()); + const stk::mesh::Entity* dst_node_elements = stk_bulk().begin_elements(dst_node.entity()); + for (unsigned dst_node_elem_index=0; dst_node_elem_indexname() << "\"" << " "; + } + krinolog << stk::diag::dendl; + } + + krinolog << "Candidate prolongation facets:" << stk::diag::dendl; + for (auto && entry : my_phase_prolong_tree_map) + { + const std::vector & tree_fields = entry.first; + krinolog << " matching fields=" << std::includes(tree_fields.begin(), tree_fields.end(), required_fields.begin(), required_fields.end()) + << ", tree fields=" << print_fields(stk_meta(), tree_fields) + << stk::diag::dendl; + } + } + } + else if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Prolongation data for node#" << stk_bulk().identifier(dst_node.entity()) << " (" << dst_node.coordinates() << ")" + << " will be point at location (" << src_data->get_coordinates() << ")" << stk::diag::dendl; + + } + + return src_data; +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::find_node_with_common_ancestry(const SubElementNode * new_node) const +{ + return new_node->find_node_with_common_ancestry(*this); +} + +static bool entity_has_any_node_in_selector(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const stk::mesh::Selector & selector) +{ + const unsigned numNodes = mesh.num_nodes(entity); + stk::mesh::Entity const* entityNodes = mesh.begin_nodes(entity); + for (unsigned n=0; n +CDMesh::get_nonconformal_elements() const +{ + std::vector elems; + const auto & all_decomposed_blocks_selector = my_phase_support.get_all_decomposed_blocks_selector(); + stk::mesh::Selector selector = get_locally_owned_part() & (get_parent_part() | (get_active_part() & !get_child_part())); + stk::mesh::BucketVector const& buckets = stk_bulk().get_buckets(stk::topology::ELEMENT_RANK, selector); + + for (auto&& bucket : buckets) + { + const stk::topology topology = bucket->topology(); + if (Mesh_Element::is_supported_topology(topology)) + for (auto&& elem : *bucket) + if (entity_has_any_node_in_selector(stk_bulk(), elem, all_decomposed_blocks_selector)) + elems.push_back(elem); + } + + std::sort(elems.begin(), elems.end(), stk::mesh::EntityLess(stk_bulk())); + + return elems; +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::generate_nonconformal_elements() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::generate_nonconformal_elements()"); /* %TRACE% */ + ParallelThrowRequire(stk_bulk().parallel(), nodes.empty()); + ParallelThrowRequire(stk_bulk().parallel(), elements.empty()); + + const std::vector nonconformalElems = get_nonconformal_elements(); + elements.reserve(nonconformalElems.size()); + for(auto && elem : nonconformalElems) + { + auto mesh_elem = std::make_unique(*this, elem); + elements.emplace_back(std::move(mesh_elem)); + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::clear() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::clear()"); /* %TRACE% */ + + nodes.clear(); + elements.clear(); + + clear_prolongation_data(); + + mesh_node_map.clear(); + child_elements.clear(); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::clear_prolongation_data() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::clear()"); /* %TRACE% */ + for (auto && map_entry : my_prolong_node_map) + { + delete map_entry.second; + } + my_prolong_node_map.clear(); + for (auto && map_entry : my_prolong_element_map) + { + delete map_entry.second; + } + my_prolong_element_map.clear(); + + for (auto && prolong_facet : my_prolong_facets) + { + delete prolong_facet; + } + my_prolong_facets.clear(); + + clear_prolongation_trees(); +} + +bool +CDMesh::is_interface(const PhaseTag & phase, const InterfaceID interface) const +{ + return phase_matches_interface(my_cdfem_support, phase, interface); +} + +//-------------------------------------------------------------------------------- + +PhaseTag +CDMesh::determine_entity_phase(stk::mesh::Entity entity) const +{ + return determine_phase_for_entity(stk_bulk(), entity, my_phase_support); +} + +//-------------------------------------------------------------------------------- + +bool +CDMesh::elem_io_part_changed(const ElementObj & elem) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::verify_elem_part(const Mesh_Element * elem) const"); /* %TRACE% */ + const stk::mesh::Part & current_elem_io_part = find_element_part(stk_bulk(),elem.entity()); + const stk::mesh::Part * const conformal_elem_io_part = my_phase_support.find_conformal_io_part(current_elem_io_part, elem.get_phase()); + return (¤t_elem_io_part != conformal_elem_io_part || !stk_bulk().bucket(elem.entity()).member(get_active_part())); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::determine_nonconformal_parts( + stk::mesh::Entity entity, + stk::mesh::PartVector & add_parts, + stk::mesh::PartVector & remove_parts) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::determine_nonconformal_parts(stk::mesh::Entity entity, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const"); /* %TRACE% */ + + add_parts.clear(); + remove_parts.clear(); + + const auto & all_decomposed_blocks_selector = my_phase_support.get_all_decomposed_blocks_selector(); + stk::mesh::EntityRank entity_rank = stk_bulk().entity_rank(entity); + const stk::mesh::PartVector & current_parts = stk_bulk().bucket(entity).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = current_parts.begin(); part_iter != current_parts.end(); ++part_iter) + { + stk::mesh::Part & part = **part_iter; + if( part.primary_entity_rank() == entity_rank && all_decomposed_blocks_selector(part) ) + { + stk::mesh::Part * nonconformal_io_part = const_cast(my_phase_support.find_nonconformal_part(part)); + if (nullptr != nonconformal_io_part && nonconformal_io_part != &part) + { + add_parts.push_back(nonconformal_io_part); + remove_parts.push_back(&part); + + for(stk::mesh::PartVector::const_iterator sup_it = part.supersets().begin(); sup_it != part.supersets().end(); ++sup_it) + { + stk::mesh::Part & superset = **sup_it; + if (!stk::mesh::is_auto_declared_part(superset)) + { + remove_parts.push_back(&superset); + } + } + } + } + } + + // Set to inactive + remove_parts.push_back(&aux_meta().active_part()); + + if (entity_rank == stk::topology::ELEMENT_RANK) + { + add_parts.push_back(&get_parent_part()); + remove_parts.push_back(&get_child_part()); + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::determine_conformal_parts( + const stk::mesh::PartVector & current_parts, + const stk::mesh::EntityRank entity_rank, + const PhaseTag & phase, + stk::mesh::PartVector & add_parts, + stk::mesh::PartVector & remove_parts) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::determine_conformal_parts(stk::mesh::Entity entity, const PhaseTag & phase, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const"); /* %TRACE% */ + + const auto & all_decomposed_blocks_selector = my_phase_support.get_all_decomposed_blocks_selector(); + for(stk::mesh::PartVector::const_iterator part_iter = current_parts.begin(); part_iter != current_parts.end(); ++part_iter) + { + stk::mesh::Part & part = **part_iter; + if( part.primary_entity_rank() == entity_rank && + (stk::io::is_part_io_part(part) || all_decomposed_blocks_selector(&part)) ) + { + stk::mesh::Part * conformal_elem_io_part = const_cast(my_phase_support.find_conformal_io_part(part, phase)); + if (nullptr != conformal_elem_io_part && conformal_elem_io_part != &part) + { + add_parts.push_back(conformal_elem_io_part); + remove_parts.push_back(&part); + + for(stk::mesh::PartVector::const_iterator sup_it = part.supersets().begin(); sup_it != part.supersets().end(); ++sup_it) + { + stk::mesh::Part & superset = **sup_it; + if (!stk::mesh::is_auto_declared_part(superset)) + { + remove_parts.push_back(&superset); + } + } + } + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::determine_conformal_parts( + stk::mesh::Entity entity, + const PhaseTag & phase, + stk::mesh::PartVector & add_parts, + stk::mesh::PartVector & remove_parts) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::determine_conformal_parts(stk::mesh::Entity entity, const PhaseTag & phase, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const"); /* %TRACE% */ + + add_parts.clear(); + remove_parts.clear(); + + ThrowAssert(stk_bulk().is_valid(entity)); + + stk::mesh::EntityRank entity_rank = stk_bulk().entity_rank(entity); + const stk::mesh::PartVector & current_parts = stk_bulk().bucket(entity).supersets(); + determine_conformal_parts(current_parts, entity_rank, phase, add_parts, remove_parts); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::determine_child_conformal_parts( + stk::topology topology, + const stk::mesh::PartVector & parent_parts, + const PhaseTag & phase, + stk::mesh::PartVector & child_parts) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::determine_child_conformal_parts(stk::mesh::Entity entity, const PhaseTag & phase, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const"); /* %TRACE% */ + + child_parts.clear(); + + const auto & all_decomposed_blocks_selector = my_phase_support.get_all_decomposed_blocks_selector(); + stk::mesh::EntityRank entity_rank = topology.rank(); + for(stk::mesh::PartVector::const_iterator part_iter = parent_parts.begin(); part_iter != parent_parts.end(); ++part_iter) + { + stk::mesh::Part & part = **part_iter; + if( part.primary_entity_rank() == entity_rank && + (stk::io::is_part_io_part(part) || all_decomposed_blocks_selector(&part)) ) + { + stk::mesh::Part * conformal_elem_io_part = const_cast(my_phase_support.find_conformal_io_part(part, phase)); + if (nullptr != conformal_elem_io_part && !my_phase_support.is_interface(&part)) + { + child_parts.push_back(conformal_elem_io_part); + } + } + else if (stk::mesh::contain(my_attribute_parts, part)) + { + child_parts.push_back(&part); + } + } + + child_parts.push_back(&stk_meta().get_topology_root_part(topology)); + + if (entity_rank == stk::topology::ELEMENT_RANK) + { + child_parts.push_back(&get_child_part()); + } + + // Set to active + child_parts.push_back(&aux_meta().active_part()); +} + +//-------------------------------------------------------------------------------- + +bool +CDMesh::triangulate(const InterfaceGeometry & interfaceGeometry) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::triangulate(InterfaceGeometry & interfaceGeometry)"); /* %TRACE% */ + bool made_changes = false; + for (auto && elem : elements) + { + made_changes |= elem->triangulate(*this, interfaceGeometry); + } + return made_changes; +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::cut_sharp_features() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::cut_sharp_features(void)"); /* %TRACE% */ + for (auto && elem : elements) + { + elem->cut_interior_intersection_points(*this); + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::set_phase_of_uncut_elements(const InterfaceGeometry & interfaceGeometry) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::snap_nearby_intersections_to_nodes(void)"); /* %TRACE% */ + + const bool oneLSPerPhase = Phase_Support::has_one_levelset_per_phase(); + for (auto && entry : interfaceGeometry.get_phase_for_uncut_elements()) + { + Mesh_Element * elem = find_mesh_element(stk_bulk().identifier(entry.first)); + if (elem) + { + PhaseTag elemPhase; + if (oneLSPerPhase) + { + elemPhase.add(ls_field(entry.second).identifier, -1); + elem->set_phase(elemPhase); + } + else + { + ThrowRequire(1 == num_ls_fields()); + elemPhase.add(ls_field(0).identifier, entry.second); + elem->set_phase(elemPhase); + } + if (false) + krinolog << "Set phase for elem " << stk_bulk().identifier(entry.first) << ".\n" << elem->visualize(*this) << stk::diag::dendl; + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::snap_nearby_intersections_to_nodes(const InterfaceGeometry & interfaceGeometry, NodeToCapturedDomainsMap & domainsAtNodes) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::snap_nearby_intersections_to_nodes(void)"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer_snap); + + snap_to_node(stk_bulk(), interfaceGeometry, get_snapper(), domainsAtNodes); + for (auto && entry : domainsAtNodes) + { + const SubElementNode * node = get_mesh_node(stk_bulk().identifier(entry.first)); + if (node) + node->set_node_domains(entry.second); + } + + domainsAtNodes.clear(); // done using this +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::decompose() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::decompose(void)"); /* %TRACE% */ + + if (my_cdfem_support.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + cut_sharp_features(); + + // TODO: N^2 in number of phases + for (auto && interface : active_interface_ids()) + { + determine_node_signs(interface); + decompose_edges(interface); + determine_node_scores(interface); + handle_hanging_children(interface); + } + for (auto && elem : elements) + { + elem->build_quadratic_subelements(*this); + } + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << stk::diag::dendl; + + for (auto && elem : elements ) + { + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Determining subelement phases for Mesh_Element local_id=" << " identifier=" << elem->entityId(); + krinolog << "\n"; + } + elem->determine_decomposed_elem_phase(*this); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "\n"; + } + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << stk::diag::dendl; +} + +void +CDMesh::build_parallel_hanging_edge_nodes() +{ /* %TRACE[ON]% */ Trace trace__("krino::CDMesh::build_parallel_hanging_edge_nodes(void)"); /* %TRACE% */ + stk::mesh::BulkData & mesh = stk_bulk(); + + if (mesh.parallel_size() < 2) return; + + // Get all cut edges in the mesh that are parallel shared. Processing by edge nodes should be cheaper than processing + // by elements since we don't have to deal with duplicates. + std::vector shared_edge_nodes; + for (auto&& node : nodes) + { + const SubElementEdgeNode * edge_node = dynamic_cast( node.get() ); + if (nullptr != edge_node) + { + if (SubElementChildNodeAncestry::is_shared(mesh, edge_node)) + { + shared_edge_nodes.emplace_back(edge_node); + } + } + } + + std::vector sharing_procs; + std::vector edge_node_keys; + + stk::CommSparse comm_spec(mesh.parallel()); + + for (int phase=0;phase<2;++phase) + { + for (auto&& shared_edge_node : shared_edge_nodes) + { + shared_edge_node.get_parent_node_keys(edge_node_keys); + stk_bulk().shared_procs_intersection(edge_node_keys, sharing_procs); + + for (auto&& other_proc : sharing_procs) + { + if (other_proc != mesh.parallel_rank()) + { + shared_edge_node.pack_into_buffer(comm_spec.send_buffer(other_proc)); + } + } + } + + if ( phase == 0 ) + { + comm_spec.allocate_buffers(); + } + else + { + comm_spec.communicate(); + } + } + + for(int i = 0; i < mesh.parallel_size(); ++i) + { + if(i != mesh.parallel_rank()) + { + while(comm_spec.recv_buffer(i).remaining()) + { + SubElementChildNodeAncestry shared_child_node(comm_spec.recv_buffer(i)); + shared_child_node.build_missing_child_nodes(*this); + } + } + } +} + +void +CDMesh::determine_node_signs(const InterfaceID & interface) +{ + for (auto && node : nodes) + { + node->clear_node_sign(); + } + for (auto && elem : elements) + { + elem->determine_node_signs(*this, interface); + } + sync_node_signs_on_constrained_nodes(); + parallel_sync_node_signs_on_shared_nodes(); +} + +void +CDMesh::decompose_edges(const InterfaceID & interface) +{ + for (auto && elem : elements) + { + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Decomposing Mesh_Element local_id=" << " identifier=" << elem->entityId(); + krinolog << "\n"; + } + elem->decompose(*this, interface); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "\n"; + } +} + +void +CDMesh::determine_node_scores(const InterfaceID & interface) +{ + for (auto && node : nodes) + { + node->clear_node_score(); + } + for (auto && elem : elements) + { + elem->determine_node_scores(*this, interface); + } + sync_node_scores_on_constrained_nodes(); + parallel_sync_node_scores_on_shared_nodes(); +} + +template +std::vector> determine_owning_procs_of_nodes_in_ancestries(const stk::mesh::BulkData & mesh, const std::vector> & constrainedNodesAndData) +{ + std::vector edgeNodeKeys; + + std::vector> owningProcsOfNodesInAncestries; + owningProcsOfNodesInAncestries.reserve(constrainedNodesAndData.size()); + for (auto&& constrainedNodeAndData : constrainedNodesAndData) + { + owningProcsOfNodesInAncestries.emplace_back(); + std::vector & owningProcs = owningProcsOfNodesInAncestries.back(); + + const auto & nodeAncestry = constrainedNodeAndData.first; + nodeAncestry.get_parent_node_keys(edgeNodeKeys); + for (auto && edgeNodeKey : edgeNodeKeys) + owningProcs.push_back(mesh.parallel_owner_rank(mesh.get_entity(edgeNodeKey))); //Expensive? + + stk::util::sort_and_unique(owningProcs); + } + + return owningProcsOfNodesInAncestries; +} + +template +std::vector> determine_sharing_procs_of_nodes_in_ancestries(const stk::mesh::BulkData & mesh, const std::vector> & sharedNodesAndData) +{ + std::vector edgeNodeKeys; + + std::vector> sharingProcsOfNodesInAncestries; + sharingProcsOfNodesInAncestries.reserve(sharedNodesAndData.size()); + for (auto&& sharedNodeAndData : sharedNodesAndData) + { + sharingProcsOfNodesInAncestries.emplace_back(); + std::vector & sharingProcs = sharingProcsOfNodesInAncestries.back(); + + const auto & nodeAncestry = sharedNodeAndData.first; + nodeAncestry.get_parent_node_keys(edgeNodeKeys); + mesh.shared_procs_intersection(edgeNodeKeys, sharingProcs); + } + + return sharingProcsOfNodesInAncestries; +} + +template +void pack_node_data_for_node_ancestries(const stk::mesh::BulkData & mesh, const std::vector> & nodeAncestriesAndData, const std::vector> & destinationProcs, stk::CommSparse &commSparse) +{ + stk::pack_and_communicate(commSparse,[&]() + { + ThrowAssert(nodeAncestriesAndData.size() == destinationProcs.size()); + std::vector edgeNodeKeys; + + for (size_t i=0; i +void set_node_sign_or_score(const SubElementNode * node, const T & signOrScore) { ThrowRequireMsg(false, "Unsupported type in set_node_sign_or_score."); } + +template <> +void set_node_sign_or_score(const SubElementNode * node, const int & sign) { node->set_node_sign(sign); } + +template <> +void set_node_sign_or_score(const SubElementNode * node, const double & score) { node->set_node_score(score); } + +template +T get_node_sign_or_score(const SubElementNode * node) { ThrowRequireMsg(false, "Unsupported type in get_node_sign_or_score."); } + +template <> +int get_node_sign_or_score(const SubElementNode * node) { return node->get_node_sign(); } + +template <> +double get_node_sign_or_score(const SubElementNode * node) { return node->get_node_score(); } + +template +bool node_sign_or_score_is_set(const SubElementNode * node) { ThrowRequireMsg(false, "Unsupported type in node_sign_or_score_is_set."); return false; } + +template <> +bool node_sign_or_score_is_set(const SubElementNode * node) { return node->node_sign_is_set(); } + +template <> +bool node_sign_or_score_is_set(const SubElementNode * node) { return node->node_score_is_set(); } + +template +std::vector> gather_constrained_node_ancestries_and_sign_or_score(const std::vector> & nodes, + const std::unordered_map > & periodicNodeIDMap) +{ + std::vector> ancestriesAndNodeOrScore; + for (auto && node : nodes) + { + if (node_sign_or_score_is_set(node.get())) + { + SubElementChildNodeAncestry nodeAncestry(node.get()); + const auto & constrainedNodeAncestries = nodeAncestry.get_constrained_node_ancestries(periodicNodeIDMap); + for (auto && constrainedNodeAncestry : constrainedNodeAncestries) + ancestriesAndNodeOrScore.emplace_back(constrainedNodeAncestry,get_node_sign_or_score(node.get())); + } + } + return ancestriesAndNodeOrScore; +} + +template +std::vector> gather_shared_node_ancestries_and_sign_or_score(const stk::mesh::BulkData & mesh, + const std::vector> & nodes) +{ + // Get all cut edges in the mesh that are parallel shared. Processing by edge nodes should be cheaper than processing + // by elements since we don't have to deal with duplicates. + + std::vector> sharedNodeAncestriesAndSignOrScore; + for (auto && node : nodes) + if (node_sign_or_score_is_set(node.get()) && SubElementChildNodeAncestry::is_shared(mesh, node.get())) + sharedNodeAncestriesAndSignOrScore.emplace_back(node.get(),get_node_sign_or_score(node.get())); + + return sharedNodeAncestriesAndSignOrScore; +} + +template +void receive_node_sign_or_score(CDMesh & cdmesh, stk::CommSparse &commSparse) +{ + stk::unpack_communications(commSparse, [&commSparse, &cdmesh](int procId) + { + auto & buffer = commSparse.recv_buffer(procId); + SubElementChildNodeAncestry shared_edge_node(buffer); + T signOrScore = 0; + buffer.unpack(signOrScore); + + const SubElementNode * node = shared_edge_node.find_subelement_node(cdmesh); + if (node) + set_node_sign_or_score(node, signOrScore); + }); +} + +template +void sync_node_sign_or_score_on_local_constrained_nodes(CDMesh & cdmesh, const std::vector> & constrainedNodesAndSignOrScore, const std::vector> & owningProcsOfNodesInAncestries) +{ + ThrowAssert(constrainedNodesAndSignOrScore.size() == owningProcsOfNodesInAncestries.size()); + + for (size_t i=0; i +void sync_node_sign_or_score_on_constrained_nodes(CDMesh & cdmesh, + const stk::mesh::BulkData & mesh, + const std::vector> & nodes, + const std::unordered_map > & periodicNodeIDMap) +{ + if (stk::is_true_on_all_procs(cdmesh.stk_bulk().parallel(), periodicNodeIDMap.empty())) + return; + + const std::vector> constrainedNodeAncestriesAndSignOrScore = gather_constrained_node_ancestries_and_sign_or_score(nodes, periodicNodeIDMap); + const std::vector> owningProcsOfNodesInAncestries = determine_owning_procs_of_nodes_in_ancestries(mesh, constrainedNodeAncestriesAndSignOrScore); + + sync_node_sign_or_score_on_local_constrained_nodes(cdmesh, constrainedNodeAncestriesAndSignOrScore, owningProcsOfNodesInAncestries); + + if (mesh.parallel_size() < 2) return; + + stk::CommSparse commSparse(mesh.parallel()); + pack_node_data_for_node_ancestries(mesh, constrainedNodeAncestriesAndSignOrScore, owningProcsOfNodesInAncestries, commSparse); + receive_node_sign_or_score(cdmesh, commSparse); +} + +template +void sync_node_sign_or_score_on_shared_nodes(CDMesh & cdmesh, + const stk::mesh::BulkData & mesh, + const std::vector> & nodes) +{ + if (mesh.parallel_size() < 2) return; + + const std::vector> sharedNodeAncestriesAndSignOrScore = gather_shared_node_ancestries_and_sign_or_score(mesh, nodes); + const std::vector> sharingProcsOfNodesInAncestries = determine_sharing_procs_of_nodes_in_ancestries(mesh, sharedNodeAncestriesAndSignOrScore); + + stk::CommSparse commSparse(mesh.parallel()); + pack_node_data_for_node_ancestries(mesh, sharedNodeAncestriesAndSignOrScore, sharingProcsOfNodesInAncestries, commSparse); + receive_node_sign_or_score(cdmesh, commSparse); +} + +void +CDMesh::sync_node_signs_on_constrained_nodes() +{ + sync_node_sign_or_score_on_constrained_nodes(*this, stk_bulk(), nodes, my_periodic_node_id_map); +} + +void +CDMesh::sync_node_scores_on_constrained_nodes() +{ + sync_node_sign_or_score_on_constrained_nodes(*this, stk_bulk(), nodes, my_periodic_node_id_map); +} + +void +CDMesh::parallel_sync_node_signs_on_shared_nodes() +{ + sync_node_sign_or_score_on_shared_nodes(*this, stk_bulk(), nodes); +} + +void +CDMesh::parallel_sync_node_scores_on_shared_nodes() +{ + sync_node_sign_or_score_on_shared_nodes(*this, stk_bulk(), nodes); +} + +void +CDMesh::handle_hanging_children(const InterfaceID & interface) +{ /* %TRACE[ON]% */ Trace trace__("krino::CDMesh::handle_hanging_children(const InterfaceID & interface)"); /* %TRACE% */ + + build_parallel_hanging_edge_nodes(); + + for (auto && elem : elements) + { + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Handling hanging children Mesh_Element identifier=" << elem->entityId(); + krinolog << "\n"; + } + elem->handle_hanging_children(*this, interface); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "\n"; + } +} + +//-------------------------------------------------------------------------------- + +const SubElementMeshNode * +CDMesh::get_mesh_node( stk::mesh::EntityId node_id ) const +{ + NodeMap::const_iterator it = mesh_node_map.find( node_id ); + return ( it != mesh_node_map.end() ) ? it->second : nullptr; +} + +const SubElementMeshNode * +CDMesh::get_mesh_node(const SubElementNode * new_node) const +{ + const SubElementMeshNode * mesh_node = dynamic_cast( new_node ); + if (nullptr != mesh_node) + { + return get_mesh_node(new_node->entityId()); + } + return nullptr; +} + +SubElementMeshNode * +CDMesh::add_managed_mesh_node( std::unique_ptr node ) +{ + SubElementMeshNode * ptr = node.get(); + mesh_node_map.insert( NodeMap::value_type( node->entityId(), ptr ) ); + add_managed_node(std::move(node)); + return ptr; +} + +//-------------------------------------------------------------------------------- +void +CDMesh::check_isovariable_field_existence_on_decomposed_blocks(stk::mesh::BulkData & mesh, + const bool conformal_parts_require_field) +{ + CDMesh cdmesh(mesh, std::shared_ptr()); + cdmesh.check_isovariable_field_existence_on_decomposed_blocks(conformal_parts_require_field); +} + +namespace { +bool field_exists_on_part(const FieldRef field, const stk::mesh::Part & part) +{ + stk::mesh::Selector field_selector = AuxMetaData::get(part.mesh_meta_data()).selectField(field, stk::topology::ELEMENT_RANK); + return field_selector(part); +} +std::ostream & dump_fields_on_part(std::ostream & os, const stk::mesh::Part & part) +{ + const auto & meta = part.mesh_meta_data(); + for(auto && field : meta.get_fields(stk::topology::NODE_RANK)) + { + if(field_exists_on_part(*field, part)) + os << " * " << field->name() << "\n"; + } + return os; +} +} +void +CDMesh::check_isovariable_field_existence_on_decomposed_blocks(const bool conformal_parts_require_field) const +{ + const int num_ls = num_ls_fields(); + for(auto && part : stk_meta().get_mesh_parts()) + { + if(part->primary_entity_rank() != stk::topology::ELEMENT_RANK) continue; + + const auto nonconformal_part = my_phase_support.find_nonconformal_part(*part); + if(!nonconformal_part) continue; + + /* 4 cases we care about here: + * 1) Nonconformal part - Skip + * 2) Initial IO part (i.e. block_1) - Must have field + * 3) Active conformal part (either LS or active part for irreversible) - Must have field + * 4) Deactivated conformal part (irreversible only) - Skip + */ + if(my_phase_support.is_nonconformal(part)) continue; + + // If part is the initial IO part the phase will be empty + const auto & phase = my_phase_support.get_iopart_phase(*part); + + // Steady state problems that only do a single decomposition can + // get away with only defining the isovariable on the initial IO part + // so skip checking for the field in that case. + if(!conformal_parts_require_field && !phase.empty()) continue; + + for(int ls=0; ls < num_ls; ++ls) + { + const auto * LS = ls_field(ls).ptr; + const auto * death_spec = get_death_spec(ls); + const bool is_dead_block = death_spec && phase.contain(death_spec->get_deactivated_phase()); + const bool LS_uses_part = + my_phase_support.level_set_is_used_by_nonconformal_part(LS, nonconformal_part); + if(LS_uses_part && !is_dead_block) + { + const auto field = ls_field(ls).isovar; + if(!field_exists_on_part(field, *part)) + { + std::ostringstream err_msg; + err_msg << "CDFEM isovariable field " << field.name() << " is not defined on " + << part->name() << " that is supposed to be decomposed.\n" + << "Available fields on " << part->name() << " are:\n"; + dump_fields_on_part(err_msg, *part); + throw std::runtime_error(err_msg.str()); + } + } + } + } +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::create_mesh_node( + const Mesh_Element * owner, + const int lnn, + stk::mesh::Entity nodeEntity ) +{ + const stk::mesh::EntityId nodeId = stk_bulk().identifier(nodeEntity); + const SubElementMeshNode * subnode = get_mesh_node(nodeId); + + if ( nullptr == subnode ) + { + const Vector3d owner_coords = owner->get_node_parametric_coords( lnn ); + const double * global_coords_ptr = field_data(get_coords_field(), nodeEntity); + + Vector3d global_coords(global_coords_ptr, my_spatial_dim); + + std::unique_ptr meshNode = std::make_unique( owner, nodeEntity, nodeId, owner_coords, global_coords ); + subnode = add_managed_mesh_node(std::move(meshNode)); + } + + return subnode; +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::create_edge_node( const Mesh_Element * owner, + const SubElementNode * parent1, + const SubElementNode * parent2, + const double position) +{ + const SubElementNode * subnode = SubElementNode::common_child({parent1, parent2}); + + if (subnode == nullptr) + { + std::unique_ptr newNode = std::make_unique(owner, position, parent1, parent2); + subnode = add_managed_node(std::move(newNode)); + + parent1->add_child(subnode); + parent2->add_child(subnode); + } + + return subnode; +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::create_midside_node( const Mesh_Element * owner, + const SubElementNode * parent1, + const SubElementNode * parent2, + stk::mesh::Entity entity) +{ + std::pair parents = + parent1second; + } + else + { + std::unique_ptr newNode = (stk_bulk().is_valid(entity)) ? + std::make_unique(owner, parent1, parent2, entity, stk_bulk().identifier(entity)) : + std::make_unique(owner, parent1, parent2); + subnode = add_managed_node(std::move(newNode)); + my_midside_node_map[parents] = subnode; + } + + return subnode; +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::create_steiner_node( const Mesh_Element * owner, + const NodeVec & parents, + const std::vector & weights ) +{ + std::unique_ptr newNode = std::make_unique( owner, parents, weights ); + return add_managed_node(std::move(newNode)); +} + +//-------------------------------------------------------------------------------- + +const SubElementNode * +CDMesh::create_child_internal_or_face_node( const Mesh_Element * owner, + const NodeVec & parents, + const std::vector & weights ) +{ + const SubElementNode * subnode = SubElementNode::common_child(parents); + + if (subnode == nullptr) + { + std::unique_ptr newNode = std::make_unique( owner, parents, weights ); + subnode = add_managed_node(std::move(newNode)); + + for (auto && parent : parents) + parent->add_child(subnode); + } + + return subnode; +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::create_subelement_mesh_entities( + const Mesh_Element & elem, + const std::vector conformal_subelems) +{ + stk::mesh::Entity parent_elem = elem.entity(); + for (auto && subelem : conformal_subelems) + { + const stk::mesh::PartVector & parent_parts = stk_bulk().bucket(parent_elem).supersets(); + const stk::topology parent_topology = stk_bulk().bucket(parent_elem).topology(); + stk::mesh::PartVector subelem_parts; + determine_child_conformal_parts(parent_topology, parent_parts, subelem->get_phase(), subelem_parts); + + if (0 == subelem->entityId()) + { + const stk::mesh::EntityId new_id = my_entity_id_pool.get_EntityId(stk::topology::ELEMENT_RANK); + ThrowAssert(!stk_bulk().is_valid(stk_bulk().get_entity(stk::topology::ELEMENT_RANK, new_id))); + stk::mesh::Entity subelem_entity = stk_bulk().declare_element(new_id, subelem_parts); + subelem->set_entity( stk_bulk(), subelem_entity ); + ThrowAssert(stk_bulk().bucket(subelem_entity).topology() != stk::topology::INVALID_TOPOLOGY); + + const NodeVec & elem_nodes = subelem->get_nodes(); + for (unsigned n=0; nentity(); + stk_bulk().declare_relation( subelem_entity, node , n ); + } + } + else + { + stk::mesh::Entity subelem_entity = subelem->entity(); + stk_bulk().change_entity_parts(subelem_entity, subelem_parts, get_removable_parts(stk_bulk(), subelem_entity)); + } + } +} + +void +CDMesh::attach_existing_and_identify_missing_subelement_sides( + const Mesh_Element & elem, + const std::vector conformal_subelems, + std::vector & side_requests) +{ + stk::mesh::BulkData & stk_mesh = stk_bulk(); + const bool build_internal_sides = my_cdfem_support.use_internal_face_stabilization(); + + for (auto && subelem : conformal_subelems) + { + const stk::topology topology = subelem->topology(); + const stk::mesh::Entity * elem_nodes = stk_bulk().begin_nodes(subelem->entity()); + + for (unsigned s=0; s side_nodes(side_topology.num_nodes()); + topology.side_nodes(elem_nodes, s, side_nodes.data()); + + std::vector sides; + stk::mesh::get_entities_through_relations(stk_mesh, side_nodes, stk_meta().side_rank(), sides); + + if (sides.empty()) + { + stk::mesh::Entity parent_side = find_entity_by_ordinal(stk_bulk(), elem.entity(), stk_meta().side_rank(), subelem->parent_side_id(s)); + const bool have_parent_side = stk_bulk().is_valid(parent_side); + const bool is_internal_side = subelem->parent_side_id(s) == -1; + + if (have_parent_side || (is_internal_side && build_internal_sides)) + { + static stk::mesh::PartVector empty_parts; + const stk::mesh::PartVector & parent_parts = have_parent_side ? stk_bulk().bucket(parent_side).supersets() : empty_parts; + + // We have to make sure that pre-existing sideset parts are added to the side so that we + // can figure out the correct conformal side parts during the second modification pass. + stk::mesh::PartVector side_parts; + determine_child_conformal_parts(side_topology, parent_parts, subelem->get_phase(), side_parts); + if (is_internal_side) + { + side_parts.push_back(&get_internal_side_part()); + } + + side_requests.emplace_back(subelem->entity(), s, side_parts); + } + } + else + { + ThrowRequire(sides.size() == 1); + stk::mesh::Entity elem_side_entity = sides[0]; + attach_entity_to_elements(stk_bulk(), elem_side_entity); + } + } + } +} + +bool +CDMesh::check_element_side_parts() const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::check_element_side_parts()"); /* %TRACE% */ + // This method requires aura to work correctly. + if (!stk_bulk().is_automatic_aura_on()) + { + // Skip check if we don't have aura + return true; + } + + bool success = true; + stk::mesh::Selector active_locally_owned = aux_meta().active_locally_owned_selector(); + stk::mesh::BucketVector const& buckets = stk_bulk().get_buckets(stk::topology::ELEMENT_RANK, active_locally_owned); + + std::vector side_nodes; + + for (auto&& bucket : buckets) + { + const stk::topology topology = bucket->topology(); + const unsigned num_sides = topology.num_sides(); + for (auto&& elem : *bucket) + { + auto elem_nodes = stk_bulk().begin(elem, stk::topology::NODE_RANK); + for (unsigned s=0; s elems; + stk::mesh::get_entities_through_relations(stk_bulk(), side_nodes, stk::topology::ELEMENT_RANK, elems); + for(auto && touching_elem : elems) krinolog << debug_entity(stk_bulk(), touching_elem) << stk::diag::dendl; + + success = false; + } + } + } + } + + return success; +} + +std::vector get_conformal_volume_part_ordinals(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, stk::mesh::Entity entity) +{ + std::vector conformalVolumeParts; + + for(auto && part : mesh.bucket(entity).supersets()) + { + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK) + { + if (phaseSupport.is_conformal(part)) + { + conformalVolumeParts.push_back(part->mesh_meta_data_ordinal()); + } + } + } + + return conformalVolumeParts; +} + +bool have_multiple_conformal_volume_parts_in_common(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, const std::vector & sideNodes) +{ + const int numSideNodes = sideNodes.size(); + ThrowRequire(numSideNodes > 0); + + std::vector commonConformalVolumeParts = get_conformal_volume_part_ordinals(mesh, phaseSupport, sideNodes[0]); + + for (int n=1; n nodeConformalVolumeParts = get_conformal_volume_part_ordinals(mesh, phaseSupport, sideNodes[n]); + + std::vector workingSet; + workingSet.swap(commonConformalVolumeParts); + std::set_intersection(workingSet.begin(),workingSet.end(),nodeConformalVolumeParts.begin(),nodeConformalVolumeParts.end(),std::back_inserter(commonConformalVolumeParts)); + + if (commonConformalVolumeParts.empty()) + return false; + } + return true; +} + +void +CDMesh::add_possible_interface_sides(std::vector & sideRequests) const +{ + // This will add sides that *might be* interface sides. + // Because this probes the nodes, it will add "keyhole" sides that aren't actually on an interface + // This should be harmless, however, and avoids extra communication or requiring aura. + + stk::mesh::Selector active_locally_owned = aux_meta().active_locally_owned_selector(); + stk::mesh::BucketVector const& buckets = stk_bulk().get_buckets(stk::topology::ELEMENT_RANK, active_locally_owned); + + std::vector sideNodes; + + for (auto&& bucket : buckets) + { + const stk::topology topology = bucket->topology(); + const unsigned num_sides = topology.num_sides(); + for (auto&& elem : *bucket) + { + auto elem_nodes = stk_bulk().begin(elem, stk::topology::NODE_RANK); + for (unsigned s=0; s & side_nodes) const +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::check_element_side_parts(const std::vector & side_nodes)"); /* %TRACE% */ + + // This method requires aura. + ThrowRequire(stk_bulk().is_automatic_aura_on()); + + std::vector elems; + stk::mesh::get_entities_through_relations(stk_bulk(), side_nodes, stk::topology::ELEMENT_RANK, elems); + + std::vector conformal_volume_parts; + for (auto&& elem : elems) + { + if (!stk_bulk().bucket(elem).member(get_active_part())) + { + continue; + } + auto& elem_parts = stk_bulk().bucket(elem).supersets(); + for(auto&& part : elem_parts) + { + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK && my_phase_support.is_conformal(part)) + { + if (std::find(conformal_volume_parts.begin(), conformal_volume_parts.end(), part) == conformal_volume_parts.end()) + { + conformal_volume_parts.push_back(part); + } + } + } + } + + if (conformal_volume_parts.empty()) + { + return true; + } + + if (conformal_volume_parts.size() > 2) + { + krinolog << "Expected to find 1 or 2 conformal side parts when examining side nodes: "; + for (auto&& side_node : side_nodes) krinolog << stk_bulk().identifier(side_node) << " "; + krinolog << " but instead found the parts: "; + for (auto&& part : conformal_volume_parts) krinolog << part->name() << " "; + krinolog << stk::diag::dendl; + return false; + } + + std::vector side_phases(conformal_volume_parts.size()); + for (unsigned iphase = 0; iphase sides; + stk::mesh::get_entities_through_relations(stk_bulk(), side_nodes, stk_meta().side_rank(), sides); + + if (conformal_volume_parts.size() == 2 && side_phases[0] != side_phases[1]) + { + stk::mesh::PartVector conformal_side_parts; + const stk::mesh::Part * conformal_side_part = my_phase_support.find_interface_part(*conformal_volume_parts[0], *conformal_volume_parts[1]); + if (nullptr != conformal_side_part) conformal_side_parts.push_back(const_cast(conformal_side_part)); + conformal_side_part = my_phase_support.find_interface_part(*conformal_volume_parts[1], *conformal_volume_parts[0]); + if (nullptr != conformal_side_part) conformal_side_parts.push_back(const_cast(conformal_side_part)); + + if (!conformal_side_parts.empty()) + { + // Check that side exists and has conformal side parts + if (sides.size() != 1) + { + krinolog << "Expected to find 1 conformal side, but instead found " << sides.size() << " when examining side nodes: "; + for (auto&& side_node : side_nodes) krinolog << stk_bulk().identifier(side_node) << " "; + krinolog << " with conformal volume parts: "; + for (auto&& part : conformal_volume_parts) krinolog << part->name() << " "; + krinolog << stk::diag::dendl; + return false; + } + else + { + auto& side_bucket = stk_bulk().bucket(sides[0]); + if (!side_bucket.member_all(conformal_side_parts)) + { + krinolog << "Side " << stk_bulk().identifier(sides[0]) << " is missing at least one of the conformal side parts: "; + for (auto&& part : conformal_side_parts) krinolog << part->name() << " "; + krinolog << ", actual parts: "; + auto& side_parts = side_bucket.supersets(); + for (auto&& part : side_parts) krinolog << part->name() << " "; + krinolog << stk::diag::dendl; + return false; + } + } + } + } + else + { + // Check that if the side exists, then it does not have any interface sides + if (sides.size() > 1) + { + krinolog << "Expected to find 0 or 1 side, but instead found " << sides.size() << " when examining side nodes: "; + for (auto&& side_node : side_nodes) krinolog << stk_bulk().identifier(side_node) << " "; + krinolog << " with conformal volume parts: "; + for (auto&& part : conformal_volume_parts) krinolog << part->name() << " "; + krinolog << stk::diag::dendl; + return false; + } + + const stk::mesh::PartVector & existing_side_parts = stk_bulk().bucket(sides[0]).supersets(); + for(auto && sidePart : existing_side_parts) + { + if(sidePart->primary_entity_rank() == stk_meta().side_rank() && my_phase_support.is_interface(sidePart)) + { + krinolog << "Side " << stk_bulk().identifier(sides[0]) << " has an erroneous interface part " << sidePart->name() << "." << stk::diag::dendl; + return false; + } + } + } + + return true; +} + +void +CDMesh::update_element_side_parts() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::update_element_side_parts()"); /* %TRACE% */ + + // This method makes sure the correct conformal side parts are on the element sides + stk::mesh::Selector locally_owned = get_locally_owned_part(); + + std::vector< stk::mesh::Entity> sides; + stk::mesh::get_selected_entities( locally_owned, stk_bulk().buckets( stk_bulk().mesh_meta_data().side_rank() ), sides ); + + stk::mesh::PartVector add_parts; + stk::mesh::PartVector remove_parts; + + for (auto && side : sides) + { + determine_element_side_parts(side, add_parts, remove_parts); + stk_bulk().change_entity_parts(side, add_parts, remove_parts); + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "After changes: " << debug_entity(stk_bulk(), side); + } + } +} + +void +CDMesh::determine_element_side_parts(const stk::mesh::Entity side, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const +{ + if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Analyzing side " << stk_bulk().identifier(side) << " with nodes "; + const unsigned num_side_nodes = stk_bulk().num_nodes(side); + stk::mesh::Entity const* side_nodes = stk_bulk().begin_nodes(side); + for (unsigned n=0; n volume_parts; + std::vector conformal_volume_parts; + std::vector nonconformal_volume_parts; + const stk::mesh::PartVector & existing_side_parts = stk_bulk().bucket(side).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = existing_side_parts.begin(); part_iter != existing_side_parts.end(); ++part_iter) + { + const stk::mesh::Part * const side_part = *part_iter; + if (side_part->primary_entity_rank() == stk::topology::ELEMENT_RANK) + { + if (my_phase_support.is_conformal(side_part)) + { + conformal_volume_parts.push_back(side_part); + } + if (my_phase_support.is_nonconformal(side_part)) + { + nonconformal_volume_parts.push_back(side_part); + } + else if (stk::io::is_part_io_part(*side_part)) + { + volume_parts.push_back(side_part); + } + } + } + + ThrowRequire(volume_parts.size() <= 2); // Can be zero for inactive elements supporting a face + + if (conformal_volume_parts.empty()) + { + /* There are two possible cases where no conformal volume parts are found: + * 1) This side is part of a surface that does not touch any blocks that are being decomposed. + * Only the active parts for these sides should be updated. + * 2) This side is a parent side that should be deactivated and moved to the nonconformal part. + * These sides will have at least 1 nonconformal volume part from the parent volume element. + */ + if(nonconformal_volume_parts.empty()) + { + if(element_side_should_be_active(side)) + { + add_parts.push_back(&aux_meta().active_part()); + } + else + { + remove_parts.push_back(&aux_meta().active_part()); + } + } + else + { + determine_nonconformal_parts(side, add_parts, remove_parts); + } + } + + if (volume_parts.size() == 2) + { + add_parts.push_back(&get_block_boundary_part()); + } + else + { + remove_parts.push_back(&get_block_boundary_part()); + } + + if (conformal_volume_parts.empty()) + { + return; + } + + ThrowRequire(conformal_volume_parts.size() == 1 || conformal_volume_parts.size() == 2); + + std::vector side_phases(conformal_volume_parts.size()); + for (unsigned iphase = 0; iphase(my_phase_support.find_interface_part(*conformal_volume_parts[0], *conformal_volume_parts[1])); + if (nullptr != conformal_side0) add_parts.push_back(conformal_side0); + stk::mesh::Part * conformal_side1 = const_cast(my_phase_support.find_interface_part(*conformal_volume_parts[1], *conformal_volume_parts[0])); + if (nullptr != conformal_side1) add_parts.push_back(conformal_side1); + } + + for (auto && side_phase : side_phases) + { + determine_conformal_parts(existing_side_parts, stk_meta().side_rank(), side_phase, add_parts, remove_parts); + } + + if(element_side_should_be_active(side)) + { + add_parts.push_back(&aux_meta().active_part()); + } + else + { + remove_parts.push_back(&aux_meta().active_part()); + } +} + +bool +CDMesh::element_side_should_be_active(const stk::mesh::Entity side) const +{ + auto num_elems = stk_bulk().num_connectivity(side, stk::topology::ELEMENT_RANK); + const auto * touching_elems = stk_bulk().begin(side, stk::topology::ELEMENT_RANK); + auto & active_part = aux_meta().active_part(); + bool active = false; + for(unsigned i=0; i < num_elems; ++i) + { + if(stk_bulk().bucket(touching_elems[i]).member(active_part)) + { + active = true; + break; + } + } + return active; +} +void +CDMesh::handle_single_coincident_subelement(const Mesh_Element & elem, const SubElement * subelem, std::vector & side_requests) +{ + stk::mesh::Entity elem_entity = elem.entity(); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "single coincident subelement for elem #" << stk_bulk().identifier(elem_entity) << " with phase " << subelem->get_phase() << stk::diag::dendl; + subelem->set_entity( stk_bulk(), elem_entity ); + stk::mesh::PartVector add_parts; + stk::mesh::PartVector remove_parts; + determine_conformal_parts(elem_entity, subelem->get_phase(), add_parts, remove_parts); + + add_parts.push_back(&get_active_part()); + remove_parts.push_back(&get_parent_part()); + + stk_bulk().change_entity_parts(elem_entity, add_parts, remove_parts); + + std::vector subelem_vec(1, subelem); + attach_existing_and_identify_missing_subelement_sides(elem, subelem_vec, side_requests); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::generate_sorted_child_elements() +{ + child_elements.clear(); + + for (const auto & elem : elements) + { + if (elem->have_subelements()) + { + std::vector conformal_subelems; + elem->get_subelements(conformal_subelems); + + for (auto && subelem : conformal_subelems) + { + child_elements.push_back(subelem); + } + } + } + + std::sort(child_elements.begin(),child_elements.end(), ElementObj::is_less); +} + +//-------------------------------------------------------------------------------- + +const SubElement * +CDMesh::find_child_element(stk::mesh::Entity elem_mesh_obj) const +{ + // Ugh + CDMesh *const mesh = const_cast(this); + + if (child_elements.empty()) + { + mesh->generate_sorted_child_elements(); + } + + const stk::mesh::EntityId elem_id = stk_bulk().identifier(elem_mesh_obj); + auto lb_cmp = [](const ElementObj * elem, stk::mesh::EntityId target_id) { return elem->entityId() < target_id; }; + auto first = std::lower_bound(child_elements.begin(),child_elements.end(), elem_id, lb_cmp); + + if (first != child_elements.end() && (*first)->entityId() == elem_id) + { + return dynamic_cast(*first); + } + return nullptr; +} + +//-------------------------------------------------------------------------------- + +stk::mesh::Entity +CDMesh::get_parent_element(stk::mesh::Entity elem_entity) const +{ + std::set parent_elem_node_set; + + const stk::mesh::Entity * elem_nodes = stk_bulk().begin_nodes(elem_entity); + const unsigned num_base_elem_nodes = stk_bulk().bucket(elem_entity).topology().base().num_nodes(); + + for (unsigned inode=0; inode parent_elem_nodes(parent_elem_node_set.begin(), parent_elem_node_set.end()); + std::vector parent_elems; + stk::mesh::get_entities_through_relations(stk_bulk(), parent_elem_nodes, stk::topology::ELEMENT_RANK, parent_elems); + + ThrowAssert(parent_elems.size() <= 1); + + if (parent_elems.empty()) + { + krinolog << "Did not find parent element for element \n" << debug_entity(stk_bulk(), elem_entity) << stk::diag::dendl; + return stk::mesh::Entity(); + } + else + { + return parent_elems.front(); + } +} + +//-------------------------------------------------------------------------------- + +bool +CDMesh::get_parent_child_coord_transformation(stk::mesh::Entity elem_mesh_obj, double * dParentdChild) const +{ + ThrowAssert(my_cdfem_support.use_nonconformal_element_size()); + + const SubElement * subelem = find_child_element(elem_mesh_obj); + + if (nullptr == subelem) + { + krinolog << "did not find element " << stk_bulk().identifier(elem_mesh_obj) << stk::diag::dendl; + return false; + } + + subelem->get_owner_coord_transform(dParentdChild); + return true; +} + +void +CDMesh::get_parent_nodes_and_weights(stk::mesh::Entity child, stk::mesh::Entity & parent0, stk::mesh::Entity & parent1, double & position) const +{ + // Really slow! + auto id = stk_bulk().identifier(child); + auto find_existing = std::find_if(nodes.begin(), nodes.end(), + [id](const std::unique_ptr & compare) + { return compare->entityId() == id; }); + ThrowAssert(find_existing != nodes.end()); + ThrowAssert(dynamic_cast(find_existing->get()) != nullptr); + const krino::SubElementEdgeNode& edge_node = dynamic_cast(*find_existing->get()); + krino::NodeVec edge_node_parents = edge_node.get_parents(); + position = edge_node.get_position(); + parent0 = edge_node_parents[0]->entity(); + parent1 = edge_node_parents[1]->entity(); +} + +//-------------------------------------------------------------------------------- + +std::function build_get_element_volume_function(const CDMesh & cdmesh) +{ + auto get_element_size = + [&cdmesh](stk::mesh::Entity elem) + { + stk::mesh::Entity volumeElement = cdmesh.get_cdfem_support().use_nonconformal_element_size() ? cdmesh.get_parent_element(elem) : elem; + ThrowRequire(cdmesh.stk_bulk().is_valid(volumeElement)); + const double elemVolume = ElementObj::volume( cdmesh.stk_bulk(), volumeElement, cdmesh.get_coords_field() ); + return elemVolume; + }; + return get_element_size; +} + +Vector3d get_side_average_cdfem_displacement(const stk::mesh::BulkData& mesh, + const FieldRef cdfemDisplacementsField, + stk::mesh::Entity side) +{ + const int spatialDim = mesh.mesh_meta_data().spatial_dimension(); + + Vector3d avg{Vector3d::ZERO}; + int numNodes = 0; + for (auto node : StkMeshEntities{mesh.begin_nodes(side), mesh.end_nodes(side)}) + { + double * cdfemDispPtr = field_data(cdfemDisplacementsField, node); + if(nullptr != cdfemDispPtr) + { + const Vector3d cdfemDisp(cdfemDispPtr, spatialDim); + avg += cdfemDisp; + ++numNodes; + } + } + if (numNodes > 0) + avg /= numNodes; + + return avg; +} + +Vector3d get_side_normal(const stk::mesh::BulkData& mesh, + const FieldRef coordsField, + stk::mesh::Entity side) +{ + const auto * sideNodes = mesh.begin_nodes(side); + const stk::topology sideTopology = mesh.bucket(side).topology(); + if (sideTopology == stk::topology::TRIANGLE_3 || sideTopology == stk::topology::TRIANGLE_6) + { + const Vector3d v0(field_data(coordsField, sideNodes[0])); + const Vector3d v1(field_data(coordsField, sideNodes[1])); + const Vector3d v2(field_data(coordsField, sideNodes[2])); + return Cross(v1-v0,v2-v0).unit_vector(); + } + else if (sideTopology == stk::topology::LINE_2 || sideTopology == stk::topology::LINE_3) + { + const Vector3d v0(field_data(coordsField, sideNodes[0]), 2); + const Vector3d v1(field_data(coordsField, sideNodes[1]), 2); + return crossZ(v1-v0).unit_vector(); + } + ThrowRequireMsg(false, "Unsupported topology " << sideTopology); + + return Vector3d::ZERO; +} + +double get_side_cdfem_cfl(const stk::mesh::BulkData& mesh, + const FieldRef cdfemDisplacementsField, + const FieldRef coordsField, + const stk::mesh::Selector & elementSelector, + const std::function & get_element_volume, + stk::mesh::Entity side) +{ + const Vector3d sideCDFEMDisplacement = get_side_average_cdfem_displacement(mesh, cdfemDisplacementsField, side); + const Vector3d sideNormal = get_side_normal(mesh, coordsField, side); + const double sideNormalDisplacement = Dot(sideCDFEMDisplacement, sideNormal); + + double minElemVolume = 0.; + for (auto elem : StkMeshEntities{mesh.begin_elements(side), mesh.end_elements(side)}) + { + if (elementSelector(mesh.bucket(elem))) + { + const double elemVol = get_element_volume(elem); + if (minElemVolume == 0. || elemVol < minElemVolume) + minElemVolume = elemVol; + } + } + double sideCFL = 0.; + if (minElemVolume > 0.) + { + const double invDim = 1.0 / mesh.mesh_meta_data().spatial_dimension(); + const double lengthScale = std::pow(minElemVolume, invDim); + sideCFL = sideNormalDisplacement / lengthScale; + } + return sideCFL; +} + +double CDMesh::compute_cdfem_cfl() const +{ + stk::diag::TimeBlock timer__(my_timer_compute_CFL); + + const stk::mesh::Selector interfaceSideSelector = my_phase_support.get_all_conformal_surfaces_selector(); + const stk::mesh::Selector elementSelector = selectUnion(my_phase_support.get_conformal_parts()) & get_active_part() & get_locally_owned_part(); + + auto get_element_volume = build_get_element_volume_function(*this); + + double cfl = 0.; + for( auto&& bucket : stk_bulk().get_buckets(stk_bulk().mesh_meta_data().side_rank(), interfaceSideSelector) ) + { + for (auto && side : *bucket) + { + const double sideCFL = get_side_cdfem_cfl(stk_bulk(), get_cdfem_displacements_field(), get_coords_field(), elementSelector, get_element_volume, side); + if (sideCFL > 0.) + cfl = std::max(cfl, sideCFL); + } + } + + const double localCFL = cfl; + stk::all_reduce_max(stk_bulk().parallel(), &localCFL, &cfl, 1); + + return cfl; +} + + +void +CDMesh::update_adaptivity_parent_entities() +{ + if (my_cdfem_support.get_interface_maximum_refinement_level() <= 0) + { + return; + } + + stk::mesh::BulkData& stk_mesh = stk_bulk(); + + stk::mesh::Part & refine_inactive_part = get_refinement_inactive_part(stk_meta(), stk::topology::ELEMENT_RANK); + stk::mesh::Selector adaptive_parent_locally_owned_selector = get_locally_owned_part() & refine_inactive_part; + + stk::mesh::PartVector add_parts; + stk::mesh::PartVector remove_parts; + + std::vector parents; + stk::mesh::get_selected_entities( adaptive_parent_locally_owned_selector, stk_mesh.buckets( stk::topology::ELEMENT_RANK ), parents ); + + for( auto&& parent : parents ) + { + std::vector leaf_children; + get_refinement_leaf_children(stk_mesh, parent, leaf_children); + std::set child_element_parts; + for (auto&& child : leaf_children) + { + const stk::mesh::Part & child_element_part = find_element_part(stk_mesh, child); + child_element_parts.insert(&child_element_part); + } + ThrowRequire(!child_element_parts.empty()); + + if (child_element_parts.size() > 1 || my_phase_support.is_nonconformal(*child_element_parts.begin())) + { + determine_nonconformal_parts(parent, add_parts, remove_parts); + const auto& add_it = std::find(add_parts.begin(), add_parts.end(), &get_parent_part()); + if (add_it != add_parts.end()) + { + add_parts.erase(add_it); + } + } + else if (child_element_parts.size() == 1 && !my_phase_support.is_nonconformal(*child_element_parts.begin())) + { + const PhaseTag & parent_phase = my_phase_support.get_iopart_phase(**child_element_parts.begin()); + determine_conformal_parts(parent, parent_phase, add_parts, remove_parts); + remove_parts.push_back(&get_parent_part()); + remove_parts.push_back(&get_child_part()); + } + stk_mesh.change_entity_parts(parent, add_parts, remove_parts); + } +} + +void +CDMesh::update_uncut_element(const Mesh_Element & elem) +{ + const stk::mesh::Entity elem_entity = elem.entity(); + stk::mesh::BulkData & stk_mesh = stk_bulk(); + if (stk_mesh.bucket(elem_entity).member(get_parent_part()) || elem_io_part_changed(elem)) + { + stk::mesh::PartVector add_parts; + stk::mesh::PartVector remove_parts; + determine_conformal_parts(elem_entity, elem.get_phase(), add_parts, remove_parts); + add_parts.push_back(&get_active_part()); + remove_parts.push_back(&get_parent_part()); + remove_parts.push_back(&get_child_part()); + + stk_mesh.change_entity_parts(elem_entity, add_parts, remove_parts); + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::create_node_entities() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::create_node_entities(void)"); /* %TRACE% */ + stk::mesh::BulkData& stk_mesh = stk_bulk(); + + std::vector node_parents; + std::vector node_requests; + std::vector higher_order_node_requests; + for (auto && node : nodes) + { + stk::mesh::Entity & node_entity = node->entity(); + if (!stk_bulk().is_valid(node_entity)) + { + node->get_parent_entities(node_parents); + if (nullptr == dynamic_cast(node.get())) + node_requests.push_back(ChildNodeRequest(node_parents, &node_entity)); + else + higher_order_node_requests.push_back(ChildNodeRequest(node_parents, &node_entity)); + } + } + + stk::mesh::PartVector node_parts = {&aux_meta().active_part(), + &get_child_edge_node_part(), + &stk_meta().get_topology_root_part(stk::topology::NODE) + }; + batch_create_child_nodes(stk_mesh, node_requests, node_parts, my_aux_meta.get_assert_32bit_flag(), my_aux_meta.get_force_64bit_flag()); + + stk::mesh::PartVector higher_order_node_parts = {&aux_meta().active_part(), + &stk_meta().get_topology_root_part(stk::topology::NODE) + }; + batch_create_child_nodes(stk_mesh, higher_order_node_requests, higher_order_node_parts, my_aux_meta.get_assert_32bit_flag(), my_aux_meta.get_force_64bit_flag()); + + for (auto && node_request : node_requests) + { + stk::mesh::Entity new_node = *node_request.child; + if (stk_mesh.bucket(new_node).member(stk_meta().locally_owned_part())) + { + if (get_parent_node_ids_field().valid()) + { + if (node_request.parents.size() != 2) + krinolog << "Created Steiner node that cannot be restored on restart: " << stk_mesh.identifier(new_node) << " " << node_request.parents.size() << stk::diag::dendl; + store_edge_node_parent_ids(stk_bulk(), get_parent_node_ids_field(), new_node, stk_bulk().identifier(*node_request.parents.front()), stk_bulk().identifier(*node_request.parents.back())); + } + } + } + + // Since batch_create_child_nodes took pointers to the entities, the entityIds were not updated, Ugh. + for (auto&& node : nodes) + { + node->set_entityId_from_entity(stk_mesh); + if(krinolog.shouldPrint(LOG_DEBUG)) + { + if (!node->is_mesh_node()) + krinolog << "NODE ID : " << node->entityId() << ": ancestry: [" << node->get_ancestry() << "]" << stk::diag::dendl; + } + } +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::create_element_and_side_entities(std::vector & side_requests) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::create_element_and_side_entities(void)"); /* %TRACE% */ + + // Count how many we need to set pool size + unsigned num_local_subelems = 0; + for (auto && elem : elements) + { + if (elem->have_subelements()) + { + std::vector conformal_subelems; + elem->get_subelements(conformal_subelems); + num_local_subelems += conformal_subelems.size(); + } + } + + my_entity_id_pool.reserve(stk::topology::ELEMENT_RANK, num_local_subelems, my_aux_meta.get_assert_32bit_flag(), my_aux_meta.get_force_64bit_flag()); + + stk::mesh::PartVector add_parts; + stk::mesh::PartVector remove_parts; + + for (const auto & elem : elements) + { + if (elem->have_subelements()) + { + std::vector conformal_subelems; + elem->get_subelements(conformal_subelems); + + // check for corner case of a single subelement that is coincident with parent + if (elem->is_single_coincident()) + { + handle_single_coincident_subelement(*elem, conformal_subelems[0], side_requests); + } + else + { + create_subelement_mesh_entities(*elem, conformal_subelems); + attach_existing_and_identify_missing_subelement_sides(*elem, conformal_subelems, side_requests); + + determine_nonconformal_parts(elem->entity(), add_parts, remove_parts); + stk_bulk().change_entity_parts(elem->entity(), add_parts, remove_parts); + } + } + else + { + update_uncut_element(*elem); + } + } + + update_adaptivity_parent_entities(); +} + +//-------------------------------------------------------------------------------- + +void +CDMesh::prolongation() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::prolongation(void)"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer_prolongation); + + BoundingBox proc_target_bbox; + for (auto && node : nodes) + { + proc_target_bbox.accommodate(node->coordinates()); + } + if(nodes.empty()) + { + proc_target_bbox.accommodate(Vector3d::ZERO); + } + + const bool guess_and_check_proc_padding = + my_old_mesh->stash_step_count() >= 0 && + stk_bulk().parallel_size() > 1; + double proc_padding = 0.0; + if (guess_and_check_proc_padding) + { + const double max_elem_size = compute_maximum_element_size(stk_bulk()); + proc_padding = 3.0*max_elem_size; + proc_target_bbox.pad(proc_padding); + } + else + { + proc_target_bbox.pad_epsilon(); + } + + bool done = false; + while (!done) + { + done = true; + + std::vector proc_target_bboxes; + BoundingBox::gather_bboxes( proc_target_bbox, proc_target_bboxes ); + + const size_t facet_precomm_size = my_old_mesh->my_prolong_facets.size(); + ProlongationFacet::communicate(*my_old_mesh, my_old_mesh->my_prolong_facets, my_old_mesh->my_prolong_node_map, proc_target_bboxes); + + my_old_mesh->build_prolongation_trees(); + + my_old_mesh->communicate_prolongation_facet_fields(); + + const stk::mesh::Part & active_part = get_active_part(); + + // update nodal fields + my_missing_remote_prolong_facets = false; + for (auto && node : nodes) + { + if(!(node->is_prolonged()) && stk_bulk().bucket(node->entity()).member(active_part)) + { + node->prolongate_fields(*this); + } + } + + const double max_cdfem_displacement = get_maximum_cdfem_displacement(); + if (guess_and_check_proc_padding && (my_missing_remote_prolong_facets || max_cdfem_displacement > proc_padding)) + { + const double growth_multiplier = 1.5; + krinolog << "Must redo ghosting for prolongation. New size = " << growth_multiplier*max_cdfem_displacement <<"\n"; + proc_target_bbox.pad(growth_multiplier*max_cdfem_displacement-proc_padding); + proc_padding = growth_multiplier*max_cdfem_displacement; + done = false; + + for (size_t i = facet_precomm_size; i < my_old_mesh->my_prolong_facets.size(); i++ ) + delete my_old_mesh->my_prolong_facets[i]; + my_old_mesh->my_prolong_facets.resize(facet_precomm_size); + + for (auto && node : nodes) + { + node->set_prolonged_flag(false); + } + } + } + + rebase_cdfem_displacements(); + + // prolongate element fields + for (const auto & elem : elements) + { + if (elem->have_subelements()) + { + std::vector conformal_subelems; + elem->get_subelements(conformal_subelems); + + for (auto && subelem : conformal_subelems) + { + subelem->prolongate_fields(*this); + } + } + else + { + elem->prolongate_fields(*this); + } + } + + // We might want to check what causes any parallel discrepencies, but sync everything here + const stk::mesh::FieldVector & all_fields = stk_bulk().mesh_meta_data().get_fields(); + const std::vector const_fields(all_fields.begin(), all_fields.end()); + for (auto && f : all_fields) + { + f->sync_to_host(); + f->modify_on_host(); + } + stk::mesh::communicate_field_data(stk_bulk(), const_fields); +} + +void +CDMesh::rebase_cdfem_displacements() +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::rebase_cdfem_displacements(void)"); /* %TRACE% */ + // rebase cdfem mesh displacements such that STATE_OLD is zero + const FieldRef cdfem_displacements_field = get_cdfem_displacements_field(); + if (cdfem_displacements_field.valid()) + { + const unsigned field_length = cdfem_displacements_field.length(); + std::vector stk_fields(cdfem_displacements_field.number_of_states()); + for ( unsigned is = 0 ; is < cdfem_displacements_field.number_of_states(); ++is ) + { + const stk::mesh::FieldState state = static_cast(is); + stk_fields[is] = cdfem_displacements_field.field_state(state); + } + + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities( stk::mesh::selectField(cdfem_displacements_field), stk_bulk().buckets( stk::topology::NODE_RANK ), objs ); + + std::vector old_displacement(field_length); + + const unsigned len = objs.size(); + for ( unsigned iObj(0); iObj < len; ++iObj ) + { + stk::mesh::Entity node = objs[iObj]; + + const double * old_data = field_data( stk_fields[stk::mesh::StateOld], node); + ThrowRequire(nullptr != old_data); + for (unsigned d=0; d( stk_fields[is], node); + ThrowRequire(nullptr != displacement); + for (unsigned d=0; d(cdfem_displacements_field, *b); + ThrowAssert(nullptr != cdfem_displacements); + + const unsigned field_length = cdfem_displacements_field.length(*b); + + const int num_nodes = b->size(); + for(int n=0; nprimary_entity_rank() == stk::topology::ELEMENT_RANK) + { + volume_conformal_parts.push_back(conformal_part); + } + else if (my_phase_support.is_interface(conformal_part)) + { + interfacial_conformal_parts.push_back(conformal_part); + } + } + + print_volume_or_surface_area(stk_bulk(), stk::topology::ELEMENT_RANK, get_active_part(), volume_conformal_parts); + print_volume_or_surface_area(stk_bulk(), stk_meta().side_rank(), get_active_part(), interfacial_conformal_parts); +} + +void +CDMesh::debug_output() const +{ + for (const auto & elem : elements) + debug_elem_parts_and_relations(stk_bulk(), *elem); + krinolog << stk::diag::dendl; + + for (auto && node : nodes) + debug_nodal_parts_and_fields(stk_bulk(), node.get()); + krinolog << stk::diag::dendl; + + debug_sides(stk_bulk(), get_active_part()); +} + +const Mesh_Element * CDMesh::find_mesh_element(stk::mesh::EntityId elemId, const std::vector> & searchElements) +{ + auto lb_cmp = [](const std::unique_ptr & elem, stk::mesh::EntityId target_id) { return elem->entityId() < target_id; }; + auto first = std::lower_bound(searchElements.begin(),searchElements.end(), elemId, lb_cmp); + + if (first != searchElements.end() && (*first)->entityId() == elemId) + { + return (*first).get(); + } + + return nullptr; +} + +} // namespace krino + + diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh.hpp b/packages/krino/krino/krino_lib/Akri_CDMesh.hpp new file mode 100644 index 000000000000..39155fa144c0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh.hpp @@ -0,0 +1,333 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_CDMesh_h +#define Akri_CDMesh_h + +#include + +#include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +template +class CompleteDecompositionFixture; +class SubElement; +class ElementObj; +class Mesh_Element; +class SubElementNode; +class SubElementMeshNode; +class ProlongationNodeData; +class ProlongationPointData; +class ProlongationElementData; +class ProlongationFacet; +class InterpolationEdge; +class LevelSet; +class Phase_Support; +class AuxMetaData; +struct SideRequest; +class InterfaceGeometry; + +typedef std::vector< const SubElementNode * > NodeVec; +typedef std::set< const SubElementNode * > NodeSet; +typedef std::vector< const ProlongationFacet * > ProlongFacetVec; +typedef std::unordered_map EntityProlongationNodeMap; +typedef std::unordered_map EntityProlongationElementMap; + +enum CDMeshStatus +{ + MESH_MODIFIED = 1, + COORDINATES_MAY_BE_MODIFIED = 2 +}; + +class CDMesh { +public: + + CDMesh( stk::mesh::BulkData & mesh, const std::shared_ptr & old_mesh); + + virtual ~CDMesh(); + + static void check_isovariable_field_existence_on_decomposed_blocks(stk::mesh::BulkData & mesh, + const bool conformal_parts_require_field); + static bool decomposition_needs_update(const InterfaceGeometry & interfaceGeometry, + const std::vector> & periodic_node_pairs); + static void handle_possible_failed_time_step( stk::mesh::BulkData & mesh, const int step_count ); + static int decompose_mesh( stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const int step_count, + const std::vector> & periodic_node_pairs ); + static void nonconformal_adaptivity(stk::mesh::BulkData & mesh, const InterfaceGeometry & interfaceGeometry); + static void mark_interface_elements_for_adaptivity(stk::mesh::BulkData & mesh, const InterfaceGeometry & interfaceGeometry, const std::string & marker_field_name, const int num_refinements); + void delete_cdfem_parent_elements(); + static void fixup_adapted_element_parts(stk::mesh::BulkData & mesh); + static void rebuild_from_restart_mesh(stk::mesh::BulkData & mesh); + void rebuild_after_rebalance(); + + CDMesh* get_old_mesh() { return my_old_mesh.get(); } + const CDMesh* get_old_mesh() const { return my_old_mesh.get(); } + static CDMesh* get_new_mesh() { return the_new_mesh.get(); } + + static void update_cdfem_constrained_nodes(); + void snap_and_update_fields_and_captured_domains(const InterfaceGeometry & interfaceGeometry, + NodeToCapturedDomainsMap & nodesToCapturedDomains) const; + + void communicate_prolongation_facet_fields() const; + const ProlongationPointData * find_prolongation_node(const SubElementNode & node) const; + const SubElementNode * find_node_with_common_ancestry(const SubElementNode * new_node) const; + + bool is_interface(const PhaseTag & phase, const InterfaceID interface) const; + PhaseTag determine_entity_phase(stk::mesh::Entity obj) const; + + void check_isovariable_field_existence_on_decomposed_blocks(const bool conformal_parts_require_field) const; + + std::vector get_nonconformal_elements() const; + void generate_nonconformal_elements(); + + bool triangulate(const InterfaceGeometry & interfaceGeometry); //return value indicates if any changes were made + void decompose(); + void cut_sharp_features(); + void snap_nearby_intersections_to_nodes(const InterfaceGeometry & interfaceGeometry, NodeToCapturedDomainsMap & domainsAtNodes); + void set_phase_of_uncut_elements(const InterfaceGeometry & interfaceGeometry); + + int spatial_dim() const { return my_spatial_dim; } + + const Phase_Support & get_phase_support() const { return my_phase_support; } + const CDFEM_Support & get_cdfem_support() const { return my_cdfem_support; } + CDFEM_Support & get_cdfem_support() { return my_cdfem_support; } + bool need_nodes_for_prolongation() const { return INTERPOLATION != get_prolongation_model() && my_stash_step_count >= 0; } + bool need_facets_for_prolongation() const { return ALE_NEAREST_POINT == get_prolongation_model() && my_stash_step_count >= 0; } + Prolongation_Model get_prolongation_model() const { return my_cdfem_support.get_prolongation_model(); } + Edge_Interpolation_Model get_edge_interpolation_model() const { return my_cdfem_support.get_edge_interpolation_model(); } + int num_ls_fields() const { return my_cdfem_support.num_ls_fields(); } + int get_ls_index(const LevelSet * ls) const { return my_cdfem_support.get_ls_index(ls); } + const LS_Field & ls_field(int i) const { return my_cdfem_support.ls_field(i); } + const std::vector & ls_fields() const { return my_cdfem_support.ls_fields(); } + const std::vector & all_interface_ids() const; + std::vector active_interface_ids() const; + // This should really only be used for unit test purposes. + void add_interface_id(const InterfaceID id) { crossing_keys.push_back(id); } + + const FieldRef get_coords_field() const { return my_cdfem_support.get_coords_field(); } + const FieldRef get_cdfem_displacements_field() const { return my_cdfem_support.get_cdfem_displacements_field(); } + const FieldSet & get_ale_prolongation_fields() const { return my_cdfem_support.get_ale_prolongation_fields(); } + const FieldSet & get_interpolation_fields() const { return my_cdfem_support.get_interpolation_fields(); } + const FieldSet & get_zeroed_fields() const { return my_cdfem_support.get_zeroed_fields(); } + const FieldSet & get_element_fields() const { return my_cdfem_support.get_element_fields(); } + const CDFEM_Snapper & get_snapper() const { return my_cdfem_support.get_snapper(); } + + const CDFEM_Inequality_Spec * get_death_spec(int ls_index) const { return my_cdfem_support.get_death_spec(ls_index); } + + stk::mesh::Part & get_parent_part() const { return my_cdfem_support.get_parent_part(); } + stk::mesh::Part & get_child_part() const { return my_cdfem_support.get_child_part(); } + stk::mesh::Part & get_internal_side_part() const { return my_cdfem_support.get_internal_side_part(); } + stk::mesh::Part & get_active_part() const; + stk::mesh::Part & get_locally_owned_part() const; + stk::mesh::Part & get_globally_shared_part() const; + stk::mesh::Part & get_block_boundary_part() const; + + // methods for finding or creating subelement nodes + const SubElementNode * create_mesh_node( const Mesh_Element * owner, + const int lnn, + stk::mesh::Entity nodeEntity ); + const SubElementNode * create_steiner_node( const Mesh_Element * owner, + const NodeVec & parents, + const std::vector & weights ); + const SubElementNode * create_child_internal_or_face_node( const Mesh_Element * owner, + const NodeVec & parents, + const std::vector & weights ); + const SubElementNode * create_edge_node( const Mesh_Element * owner, + const SubElementNode * parent1, const SubElementNode * parent2, + const double position); + const SubElementNode * create_midside_node( const Mesh_Element * owner, + const SubElementNode * parent1, const SubElementNode * parent2, stk::mesh::Entity entity = stk::mesh::Entity()); + void create_node_obj( const SubElementNode * node, NodeVec & parents ); + + void determine_node_signs(const InterfaceID & interface); + void decompose_edges(const InterfaceID & interface); + void determine_node_scores(const InterfaceID & interface); + + const AuxMetaData& aux_meta() const { return my_aux_meta; } + AuxMetaData& aux_meta() { return my_aux_meta; } + const stk::mesh::MetaData& stk_meta() const { return my_meta; } + stk::mesh::MetaData& stk_meta() { return my_meta; } + const stk::mesh::BulkData& stk_bulk() const { return my_meta.mesh_bulk_data(); } + stk::mesh::BulkData& stk_bulk() { return my_meta.mesh_bulk_data(); } + + void add_periodic_node_pair(stk::mesh::Entity node1, stk::mesh::Entity node2); + + // just search for existing mesh node and return NULL if not found + const SubElementMeshNode * get_mesh_node( stk::mesh::EntityId node_id ) const; + // just search for existing mesh node and return NULL if not found, starting with subelement node (possibly from another mesh) + const SubElementMeshNode * get_mesh_node(const SubElementNode * new_node) const; + + bool check_element_side_parts() const; + + const SubElement * find_child_element(stk::mesh::Entity elem_mesh_obj) const; + static const Mesh_Element * find_mesh_element(stk::mesh::EntityId elemId, const std::vector > & searchElements); + const Mesh_Element * find_mesh_element(stk::mesh::EntityId elemId) const { return find_mesh_element(elemId, elements); } + Mesh_Element * find_mesh_element(stk::mesh::EntityId elemId) { return const_cast(find_mesh_element(elemId, elements)); } // Scott Meyers says this is the right way + bool get_parent_child_coord_transformation(stk::mesh::Entity elem_mesh_obj, double * dParentdChild) const; + void get_parent_nodes_and_weights(stk::mesh::Entity child, stk::mesh::Entity & parent0, stk::mesh::Entity & parent1, double & position) const; + stk::mesh::Entity get_parent_element(stk::mesh::Entity elem_mesh_obj) const; + + double compute_cdfem_cfl() const; + + int stash_step_count() const { return my_stash_step_count; } + const ProlongationNodeData * fetch_prolong_node(stk::mesh::EntityId node_id) const { EntityProlongationNodeMap::const_iterator it = my_prolong_node_map.find(node_id); return ( (it == my_prolong_node_map.end()) ? NULL : (it->second) ); } + const ProlongationElementData * fetch_prolong_element(stk::mesh::EntityId elem_id) const { EntityProlongationElementMap::const_iterator it = my_prolong_element_map.find(elem_id); return ( (it == my_prolong_element_map.end()) ? NULL : (it->second) ); } + + void debug_output() const; + void print_conformal_volumes_and_surface_areas() const; + std::vector> & get_elements() { return elements; } + const std::vector> & get_elements() const { return elements; } + + // FIXME: Make these private. + SubElementNode * add_managed_node(std::unique_ptr node); + // expose vector of nodes + std::vector > nodes; + // expose vector of elements + std::vector > elements; + // expose vector of sorted child elements + std::vector child_elements; + +private: + //: Default constructor not allowed + CDMesh(); + + template + friend class CompleteDecompositionFixture; + + template + friend class AnalyticDecompositionFixture; + + void build_parallel_hanging_edge_nodes(); + void handle_hanging_children(const InterfaceID & interface); + void parallel_sync_nodes_on_interface(); + + void sync_node_signs_on_constrained_nodes(); + void parallel_sync_node_signs_on_shared_nodes(); + void sync_node_scores_on_constrained_nodes(); + void parallel_sync_node_scores_on_shared_nodes(); + + bool decomposition_has_changed(const InterfaceGeometry & interfaceGeometry); + bool elem_io_part_changed(const ElementObj & elem) const; + void determine_nonconformal_parts(stk::mesh::Entity entity, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const; + void determine_conformal_parts(stk::mesh::Entity entity, const PhaseTag & phase, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const; + void determine_conformal_parts(const stk::mesh::PartVector & current_parts, const stk::mesh::EntityRank entity_rank, const PhaseTag & phase, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const; + void determine_child_conformal_parts(stk::topology topology, const stk::mesh::PartVector & parent_parts, const PhaseTag & phase, stk::mesh::PartVector & child_parts) const; + void determine_element_side_parts(const stk::mesh::Entity side, stk::mesh::PartVector & add_parts, stk::mesh::PartVector & remove_parts) const; + bool element_side_should_be_active(const stk::mesh::Entity side) const; + void build_and_stash_old_mesh(const int stepCount); + void stash_field_data(const int step_count, const CDMesh & new_mesh) const; + void stash_nodal_field_data(const CDMesh & new_mesh) const; + void stash_elemental_field_data() const; + + void clear_prolongation_trees() const; + void build_prolongation_trees() const; + + void clear(); + void clear_prolongation_data() const; + + Mesh_Element * create_mesh_element(stk::mesh::Entity mesh_obj); + SubElementMeshNode * add_managed_mesh_node( std::unique_ptr node ); + + bool modify_mesh(); + void update_adaptivity_parent_entities(); + void handle_single_coincident_subelement(const Mesh_Element & elem, const SubElement * subelem, std::vector & side_requests); + void create_subelement_mesh_entities(const Mesh_Element & elem, + const std::vector conformal_subelems); + void attach_existing_and_identify_missing_subelement_sides(const Mesh_Element & elem, + const std::vector conformal_subelems, + std::vector & side_requests); + void update_uncut_element(const Mesh_Element & elem); + + void get_unused_old_child_elements(std::vector & unused_old_child_elems); + void set_entities_for_identical_nodes(); + bool set_entities_for_existing_child_elements(); + void create_new_mesh_entities(); + void create_node_entities(); + void create_element_and_side_entities(std::vector & side_requests); + + void prolongation(); + void rebase_cdfem_displacements(); + double get_maximum_cdfem_displacement() const; + + void add_possible_interface_sides(std::vector & sideRequests) const; + bool check_element_side_parts(const std::vector & side_nodes) const; + void update_element_side_parts(); + + void parallel_communicate_elemental_death_fields() const; + + void generate_sorted_child_elements(); + void cache_node_ids(); + + stk::mesh::Part & get_child_edge_node_part() const { return my_cdfem_support.get_child_edge_node_part(); } + FieldRef get_parent_node_ids_field() const { return my_cdfem_support.get_parent_node_ids_field(); } + + void rebuild_child_part(); + void rebuild_parent_and_active_parts_using_nonconformal_and_child_parts(); + void restore_subelement_edge_nodes(); + void restore_subelements(); + const SubElementNode * build_subelement_edge_node(const stk::mesh::Entity node_entity); + + stk::mesh::MetaData& my_meta; + AuxMetaData& my_aux_meta; + EntityIdPool my_entity_id_pool; + + const int my_spatial_dim; + CDFEM_Support & my_cdfem_support; + Phase_Support & my_phase_support; + typedef std::unordered_map NodeMap; + NodeMap mesh_node_map; + + std::shared_ptr my_old_mesh; + static std::shared_ptr the_new_mesh; + + std::unordered_map > my_periodic_node_id_map; + + mutable int my_stash_step_count; + mutable std::map,std::unique_ptr>> my_phase_prolong_tree_map; + + mutable bool my_missing_remote_prolong_facets; + mutable EntityProlongationNodeMap my_prolong_node_map; + mutable EntityProlongationElementMap my_prolong_element_map; + mutable ProlongFacetVec my_prolong_facets; + + mutable std::vector crossing_keys; + + mutable stk::diag::Timer my_timer_decompose; + mutable stk::diag::Timer my_timer_decomposition_has_changed; + mutable stk::diag::Timer my_timer_snap; + mutable stk::diag::Timer my_timer_stash_field_data; + mutable stk::diag::Timer my_timer_modify_mesh; + mutable stk::diag::Timer my_timer_prolongation; + mutable stk::diag::Timer my_timer_compute_CFL; + stk::mesh::PartVector my_attribute_parts; + + mutable std::map,const SubElementNode*> my_midside_node_map; +}; + +} // namespace krino + +#endif // Akri_CDMesh_h diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh_Debug.cpp b/packages/krino/krino/krino_lib/Akri_CDMesh_Debug.cpp new file mode 100644 index 000000000000..eccd3249c341 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh_Debug.cpp @@ -0,0 +1,229 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +namespace krino { + +void +debug_elem_parts_and_relations(const stk::mesh::BulkData & mesh, const Mesh_Element & elem) +{ + const stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::mesh::Entity elem_obj = elem.entity(); + + krinolog << "Elem: id=" << mesh.identifier(elem_obj) << "\n"; + krinolog << " Mesh parts="; + for(auto && elem_part : mesh.bucket(elem_obj).supersets()) + { + krinolog << "\"" << elem_part->name() << "\"" << " "; + } + krinolog << "\n"; + + krinolog << " Nodes: "; + for (auto && elem_node : elem.get_nodes()) + { + krinolog << elem_node->entityId() << " "; + } + krinolog << "\n"; + + const stk::topology topology = elem.coord_topology(); + std::vector side_nodes; + for (unsigned s = 0; s < topology.num_sides(); ++s) + { + stk::mesh::Entity side_obj = find_entity_by_ordinal(mesh, elem_obj, meta.side_rank(), s); + if (!mesh.is_valid(side_obj)) continue; + krinolog << " Elem side: side=" << s << ", id=" << mesh.identifier(side_obj); + krinolog << ", side node ids: "; + const stk::topology side_topology = topology.side_topology(s); + const stk::mesh::Entity * elem_nodes_ptr = mesh.begin_nodes(elem_obj); + side_nodes.resize(side_topology.num_nodes()); + topology.side_nodes(elem_nodes_ptr, s, side_nodes.begin()); + for (unsigned n=0; nname() << "\"" << " "; + } + krinolog << "\n"; + } + + if (elem.have_subelements()) + { + std::vector conformal_subelems; + elem.get_subelements(conformal_subelems); + + for (auto && subelem : conformal_subelems) + { + stk::mesh::Entity subelem_obj = subelem->entity(); + if (!mesh.is_valid(subelem_obj)) + { + // single conformal subelement + if (1 == conformal_subelems.size()) + { + subelem_obj = elem.entity(); + } + if (!mesh.is_valid(subelem_obj)) + { + // For debugging intermediate stage before subelement mesh objects are determined. + krinolog << " Subelem: id=-1" << "\n"; + continue; + } + } + + krinolog << " Subelem: id=" << mesh.identifier(subelem_obj) << "\n"; + krinolog << " Mesh parts="; + for(auto && subelem_part : mesh.bucket(subelem_obj).supersets()) + { + krinolog << "\"" << subelem_part->name() << "\"" << " "; + } + krinolog << "\n"; + + krinolog << " SubElemNodes: "; + for (auto && sub_node : subelem->get_nodes()) + { + krinolog << sub_node->entityId() << " "; + } + krinolog << "\n"; + + for (unsigned s = 0; s < topology.num_sides(); ++s) + { + stk::mesh::Entity side_obj = find_entity_by_ordinal(mesh, subelem_obj, meta.side_rank(), s); + if (!mesh.is_valid(side_obj)) continue; + krinolog << " Subelem side: side=" << s << ", id=" << mesh.identifier(side_obj); + krinolog << ", side node ids: "; + const stk::topology side_topology = topology.side_topology(s); + const stk::mesh::Entity * elem_nodes_ptr = mesh.begin_nodes(subelem_obj); + side_nodes.resize(side_topology.num_nodes()); + topology.side_nodes(elem_nodes_ptr, s, side_nodes.begin()); + for (unsigned n=0; nname() << "\"" << " "; + } + krinolog << "\n"; + } + } + } +} + +void +debug_nodal_parts_and_fields(const stk::mesh::BulkData & mesh, const SubElementNode * node) +{ + stk::mesh::Entity node_obj = node->entity(); + if (!mesh.is_valid(node_obj)) + { + krinolog << "Node: identifier=nullptr\n"; + return; + } + + std::string type = "UNKNOWN"; + if (nullptr != dynamic_cast(node)) type = "internal"; + if (nullptr != dynamic_cast(node)) type = "edge"; + if (nullptr != dynamic_cast(node)) type = "mesh"; + + krinolog << "Node: identifier=" << mesh.identifier(node_obj) << ", type=" << type << "\n"; + if (mesh.mesh_meta_data().spatial_dimension() == 2) + { + krinolog << " coords =" << "(" << node->coordinates()[0] << ", " << node->coordinates()[1] << ")" << "\n"; + } + else if (mesh.mesh_meta_data().spatial_dimension() == 3) + { + krinolog << " coords =" << "(" << node->coordinates()[0] << ", " << node->coordinates()[1] << ", " << node->coordinates()[2] << ")" << "\n"; + } + krinolog << " Mesh parts="; + for(auto && node_part : mesh.bucket(node_obj).supersets()) + { + krinolog << "\"" << node_part->name() << "\"" << " "; + } + krinolog << "\n"; + + for ( auto && stk_field : mesh.mesh_meta_data().get_fields() ) + { + const FieldRef field(stk_field); + + if( field.entity_rank()!=stk::topology::NODE_RANK || !field.type_is() ) continue; + + const unsigned field_length = field.length(); + + double * data = field_data(field, node_obj); + if (nullptr == data) + { + krinolog << " Field: field_name=" << field.name() << ", field_state=" << field.state() << " -> NOT DEFINED." << "\n"; + } + else + { + if (1 == field_length) + { + krinolog << " Field: field_name=" << field.name() << ", field_state=" << field.state() << ", value=" << *data << "\n"; + } + else + { + for (unsigned i=0; i objs; + stk::mesh::get_entities( mesh, mesh.mesh_meta_data().side_rank(), objs ); + + const unsigned len = objs.size(); + for ( unsigned iObj(0); iObj < len; ++iObj ) { + + stk::mesh::Entity side = objs[iObj]; + + krinolog << "side, id=" << mesh.identifier(side) << ", active = " << mesh.bucket(side).member(active_part) << ", num elem = " << mesh.num_elements(side) << ", ioparts="; + const stk::mesh::PartVector & side_parts = mesh.bucket(side).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = side_parts.begin(); part_iter != side_parts.end(); ++part_iter) + { + const stk::mesh::Part * const part = *part_iter; + if (stk::io::is_part_io_part(*part)) krinolog << part->name() << " "; + } + krinolog << "\n"; + const unsigned num_side_elems = mesh.num_elements(side); + const stk::mesh::Entity* side_elems = mesh.begin_elements(side); + for (unsigned side_elem_index=0; side_elem_index +#include + +namespace krino { + void debug_elem_parts_and_relations(const stk::mesh::BulkData & mesh, const Mesh_Element & elem); + void debug_nodal_parts_and_fields(const stk::mesh::BulkData & mesh, const SubElementNode * node); + void debug_sides(const stk::mesh::BulkData & mesh, stk::mesh::Part & active_part); +} + +#endif /* KRINO_INCLUDE_AKRI_CDMESH_DEBUG_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.cpp b/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.cpp new file mode 100644 index 000000000000..840750152089 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.cpp @@ -0,0 +1,367 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" +namespace krino { + +namespace { + void set_refine_if_not_reached_max_refine(stk::mesh::Entity elem, + const int interface_max_refine_level, + FieldRef elem_marker, + FieldRef refine_level_field, + FieldRef transition_element_field) + { + int & marker = *field_data(elem_marker, elem); + const int refine_level = *field_data(refine_level_field, elem); + const int transition_element = *field_data(transition_element_field, elem); + + if (refine_level >= transition_element+interface_max_refine_level ) + { + marker = Refinement_Marker::NOTHING; + } + else + { + marker = Refinement_Marker::REFINE; + } + } +} + +static bool node_is_snapped_to_interface(stk::mesh::Entity node, + const InterfaceID & interface, + const std::unordered_map> & nodesSnappedInterfaces) +{ + auto nodeSnappedInterfaces = nodesSnappedInterfaces.find(node); + const bool nodeIsSnapped = nodeSnappedInterfaces != nodesSnappedInterfaces.end() && + nodeSnappedInterfaces->second.find(interface) != nodeSnappedInterfaces->second.end(); + return nodeIsSnapped; +} + +void +refine_edges_with_multiple_unsnapped_crossings(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + const int interface_max_refine_level, + FieldRef elem_marker_field, + FieldRef refine_level_field, + FieldRef transition_element_field, + const std::unordered_map> & nodesSnappedInterfaces) +{ + // Refine any edge with multiple crossings that are not snapped to the nodes + std::set> edgesWithUnsnappedCrossings; + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + + const InterfaceID & interface = edge.interface; + const bool node1IsSnapped = node_is_snapped_to_interface(edge.nodes[0], interface, nodesSnappedInterfaces); + const bool node2IsSnapped = node_is_snapped_to_interface(edge.nodes[1], interface, nodesSnappedInterfaces); + if (!node1IsSnapped && !node2IsSnapped) + { + const auto insertion = edgesWithUnsnappedCrossings.insert(edge.nodes); + const bool alreadyInSet = !insertion.second; + if (alreadyInSet) + { + std::vector edge_elems; + stk::mesh::get_entities_through_relations(mesh, {edge.nodes[0], edge.nodes[1]}, + stk::topology::ELEMENT_RANK, edge_elems); + for (auto && elem : edge_elems) + { + set_refine_if_not_reached_max_refine(elem, interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field); + } + } + } + } +} + +void +refine_edges_with_nodes_with_multiple_snapped_interfaces(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + const int interface_max_refine_level, + FieldRef elem_marker_field, + FieldRef refine_level_field, + FieldRef transition_element_field, + const std::unordered_map> & node_snapped_interfaces) +{ + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + + auto node1_snapped_interfaces = node_snapped_interfaces.find(edge.nodes[0]); + auto node2_snapped_interfaces = node_snapped_interfaces.find(edge.nodes[1]); + const unsigned num_node1_interfaces = (node1_snapped_interfaces != node_snapped_interfaces.end()) ? + node1_snapped_interfaces->second.size() : 0; + const unsigned num_node2_interfaces = (node2_snapped_interfaces != node_snapped_interfaces.end()) ? + node2_snapped_interfaces->second.size() : 0; + if (num_node1_interfaces > 1 || num_node2_interfaces > 1) + { + std::vector edge_elems; + stk::mesh::get_entities_through_relations(mesh, {edge.nodes[0], edge.nodes[1]}, + stk::topology::ELEMENT_RANK, edge_elems); + for (auto && elem : edge_elems) + { + set_refine_if_not_reached_max_refine(elem, interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field); + } + } + } +} + +void +determine_which_interfaces_snap_to_each_node_and_unsnappable_nodes(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + const std::vector & active_interface_ids, + const CDFEM_Snapper & snapper, + FieldRef node_marker_field, + std::unordered_map> & node_snapped_interfaces, + std::set & unsnappable_nodes) +{ + for (auto && interface : active_interface_ids) + { + stk::mesh::field_fill(0, node_marker_field); + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + + int & node1_marker = *field_data(node_marker_field, edge.nodes[0]); + int & node2_marker = *field_data(node_marker_field, edge.nodes[1]); + if (snapper.snap_lo(edge.crossingLocation)) + { + if (parts_are_compatible_for_snapping(mesh, edge.nodes[0], edge.nodes[1])) + node1_marker = 2; + else + node1_marker = std::max(node1_marker, 1); + } + if (snapper.snap_hi(edge.crossingLocation)) + { + if (parts_are_compatible_for_snapping(mesh, edge.nodes[1], edge.nodes[0])) + node2_marker = 2; + else + node2_marker = std::max(node2_marker, 1); + } + } + stk::mesh::parallel_max(mesh, {&node_marker_field.field()}); + + for(const auto & b_ptr : mesh.buckets( stk::topology::NODE_RANK )) + { + stk::mesh::Bucket & b = *b_ptr; + int * node_marker = field_data(node_marker_field, b); + for(unsigned i=0; i < b.size(); ++i) + { + if (node_marker[i] == 1) + { + unsnappable_nodes.insert(b[i]); + } + else if (node_marker[i] == 2) + { + node_snapped_interfaces[b[i]].insert(interface); + } + } + } + } +} + +void +resolve_fine_features(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + const std::vector & active_interface_ids, + const CDFEM_Snapper & snapper, + const int interface_max_refine_level, + FieldRef elem_marker_field, + FieldRef node_marker_field, + FieldRef refine_level_field, + FieldRef transition_element_field) +{ + std::unordered_map> node_snapped_interfaces; + std::set unsnappable_nodes; + + determine_which_interfaces_snap_to_each_node_and_unsnappable_nodes(mesh, edgeIntersections, active_interface_ids, snapper, node_marker_field, node_snapped_interfaces, unsnappable_nodes); + + // Attempt at minimally aggressive. Works pretty well and has has lower element counts. + refine_edges_with_multiple_unsnapped_crossings(mesh, edgeIntersections, interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field, node_snapped_interfaces); + //refine_edges_with_unsnappable_nodes(interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field, unsnappable_nodes); + refine_edges_with_nodes_with_multiple_snapped_interfaces(mesh, edgeIntersections, interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field, node_snapped_interfaces); +} + +void +mark_nearest_node_on_cut_edges(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + FieldRef node_marker_field) +{ + const double overlap = 0.25; + + stk::mesh::field_fill(0, node_marker_field); + + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + + if (edge.crossingLocation < 0.5+overlap) + *field_data(node_marker_field, edge.nodes[0]) = 1; + if (edge.crossingLocation > 0.5-overlap) + *field_data(node_marker_field, edge.nodes[1]) = 1; + } + stk::mesh::parallel_max(mesh, {&node_marker_field.field()}); +} + +void +mark_interface_elements_for_adaptivity(const stk::mesh::BulkData& mesh, + const InterfaceGeometry & interfaceGeometry, + const std::vector & active_interface_ids, + const CDFEM_Snapper & snapper, + const AuxMetaData& aux_meta, + const CDFEM_Support & cdfem_support, + const FieldRef coords_field, + const std::string & marker_field_name, + const int num_refinements) +{ +/* %TRACE[SPEC]% */ Tracespec trace__("CDMesh::mark_interface_elements_for_adaptivity(const std::string & marker_field_name, const int num_refinements)"); /* %TRACE% */ + + // This refinement strategy cuts elements by the user-specified number of adapt levels + // before the conformal decomposition. + + const FieldRef elem_marker = aux_meta.get_field(stk::topology::ELEMENT_RANK, marker_field_name, stk::mesh::StateNew); + const FieldRef refine_level_field = aux_meta.get_field(stk::topology::ELEMENT_RANK, "refine_level"); + const std::string transition_field_name = (mesh.mesh_meta_data().spatial_dimension() == 2) ? + "transition_element" : "transition_element_3"; + const FieldRef transition_element_field = aux_meta.get_field(stk::topology::ELEMENT_RANK, transition_field_name); + + const stk::mesh::Selector active_selector(cdfem_support.get_active_part()); + const stk::mesh::Selector locally_owned_selector(cdfem_support.get_locally_owned_part()); + const stk::mesh::Selector parent_or_child_selector = cdfem_support.get_child_part() | cdfem_support.get_parent_part(); + const int interface_min_refine_level = cdfem_support.get_interface_minimum_refinement_level(); + std::vector entities; + std::vector children; + + const NodeToCapturedDomainsMap nodesToCapturedDomains; + const std::vector edgeIntersections = interfaceGeometry.get_edge_intersection_points(mesh, nodesToCapturedDomains); + + FieldRef node_marker_field = aux_meta.get_field(stk::topology::NODE_RANK, marker_field_name, stk::mesh::StateNew); + mark_nearest_node_on_cut_edges(mesh, edgeIntersections, node_marker_field); + + std::vector min_edge_lengths(cdfem_support.get_interface_maximum_refinement_level()+1, std::numeric_limits::max()); + std::vector max_edge_lengths(cdfem_support.get_interface_maximum_refinement_level()+1, 0.0); + + const std::vector debugElementIds{}; + + stk::mesh::get_selected_entities( locally_owned_selector, mesh.buckets( stk::topology::ELEMENT_RANK ), entities ); + for( auto&& elem : entities ) + { + int & marker = *field_data(elem_marker, elem); + + bool has_crossing = false; + const stk::topology stk_topology = mesh.bucket(elem).topology(); + const unsigned num_nodes = stk_topology.num_nodes(); + const stk::mesh::Entity * const elem_nodes = mesh.begin(elem, stk::topology::NODE_RANK); + for(unsigned i=0; i < num_nodes; ++i) + { + const int node_marker = *field_data(node_marker_field, elem_nodes[i]); + if(node_marker) + { + has_crossing = true; + break; + } + } + + const int target_refine_level = has_crossing ? interface_min_refine_level : 0; + const int refine_level = *field_data(refine_level_field, elem); + const int transition_element = *field_data(transition_element_field, elem); + + if (!transition_element) + { + std::vector edge_nodes; + for (unsigned i = 0; i < stk_topology.num_edges(); ++i) + { + edge_nodes.resize(stk_topology.edge_topology(i).num_nodes()); + stk_topology.edge_nodes(elem_nodes, i, edge_nodes.data()); + + const Vector3d edge_node1_coords(field_data(coords_field, edge_nodes[0]), mesh.mesh_meta_data().spatial_dimension()); + const Vector3d edge_node2_coords(field_data(coords_field, edge_nodes[1]), mesh.mesh_meta_data().spatial_dimension()); + const double length = (edge_node2_coords-edge_node1_coords).length(); + + min_edge_lengths[refine_level] = std::min(min_edge_lengths[refine_level], length); + max_edge_lengths[refine_level] = std::max(max_edge_lengths[refine_level], length); + } + } + + if (!debugElementIds.empty() && std::find(debugElementIds.begin(), debugElementIds.end(), mesh.identifier(elem)) != debugElementIds.end()) + krinolog << "Considering refinement of element " << mesh.identifier(elem) << " " << has_crossing << " " << target_refine_level << " " << refine_level << " " << transition_element << stk::diag::dendl; + + if (refine_level < target_refine_level+transition_element) + { + marker = Refinement_Marker::REFINE; + } + else if (num_refinements < interface_min_refine_level && + refine_level > target_refine_level+transition_element) + { + // Stop coarsening after num_levels of refinement to avoid infinite looping + // from the interface position moving between elements because of snapping changes + // with refinement + marker = Refinement_Marker::COARSEN; + } + else + { + marker = Refinement_Marker::NOTHING; + } + } + + { + for (int i=0; i interface_min_refine_level) + { + resolve_fine_features(mesh, edgeIntersections, active_interface_ids, snapper, interface_max_refine_level, elem_marker, node_marker_field, refine_level_field, transition_element_field); + } +} + +void +refine_edges_with_unsnappable_nodes(const stk::mesh::BulkData& mesh, + const std::vector & edgeIntersections, + const CDFEM_Snapper & snapper, + const int interface_max_refine_level, + FieldRef elem_marker_field, + FieldRef refine_level_field, + FieldRef transition_element_field, + std::set unsnappable_nodes) +{ + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + + if ((snapper.snap_lo(edge.crossingLocation) && unsnappable_nodes.find(edge.nodes[0]) != unsnappable_nodes.end()) || + (snapper.snap_hi(edge.crossingLocation) && unsnappable_nodes.find(edge.nodes[1]) != unsnappable_nodes.end())) + { + krinolog << "Refining unsnappable edge " << mesh.identifier(edge.nodes[0]) << " " << mesh.identifier(edge.nodes[1]) << " " << debug_output(mesh, edgeIntersection) << stk::diag::dendl; + std::vector edge_elems; + stk::mesh::get_entities_through_relations(mesh, {edge.nodes[0], edge.nodes[1]}, + stk::topology::ELEMENT_RANK, edge_elems); + for (auto && elem : edge_elems) + { + set_refine_if_not_reached_max_refine(elem, interface_max_refine_level, elem_marker_field, refine_level_field, transition_element_field); + } + } + } +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.hpp b/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.hpp new file mode 100644 index 000000000000..0f7725594ad9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh_Refinement.hpp @@ -0,0 +1,31 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_CDMESH_REFINEMENT_H_ +#define KRINO_INCLUDE_AKRI_CDMESH_REFINEMENT_H_ +#include +#include +#include +#include + +namespace krino { + +void +mark_interface_elements_for_adaptivity(const stk::mesh::BulkData& mesh, + const InterfaceGeometry & interfaceGeometry, + const std::vector & active_interface_ids, + const CDFEM_Snapper & snapper, + const AuxMetaData& aux_meta, + const CDFEM_Support & cdfem_support, + const FieldRef coords_field, + const std::string & marker_field_name, + const int num_refinements); + +} + +#endif /* KRINO_INCLUDE_AKRI_CDMESH_REFINEMENT_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.cpp b/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.cpp new file mode 100644 index 000000000000..717cf7a0f255 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.cpp @@ -0,0 +1,143 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +namespace krino { + +bool +parts_are_compatible_for_snapping(const stk::mesh::BulkData & mesh, stk::mesh::Entity possible_snap_node, stk::mesh::Entity fixed_node) +{ + const stk::mesh::PartVector & possible_snap_node_parts = mesh.bucket(possible_snap_node).supersets(); + const stk::mesh::PartVector & fixed_node_parts = mesh.bucket(fixed_node).supersets(); + for (auto && possible_snap_node_part : possible_snap_node_parts) + { + if ((possible_snap_node_part->primary_entity_rank() == stk::topology::ELEMENT_RANK || + possible_snap_node_part->primary_entity_rank() == mesh.mesh_meta_data().side_rank()) && + !stk::mesh::is_auto_declared_part(*possible_snap_node_part) && + possible_snap_node_part->name().compare(0,7,"refine_") != 0 && + !stk::mesh::contain(fixed_node_parts, *possible_snap_node_part)) + { + return false; + } + } + return true; +} + +static stk::mesh::Part * get_nonconformal_part(const Phase_Support & phaseSupport, stk::mesh::Part * part) +{ + return const_cast(phaseSupport.find_nonconformal_part(*part)); +} + +static bool is_part_to_check(const Phase_Support & phaseSupport, const AuxMetaData & auxMeta, const stk::mesh::Part & part) +{ + const stk::mesh::Part & exposedBoundaryPart = auxMeta.exposed_boundary_part(); + return part.primary_entity_rank() != stk::topology::INVALID_RANK && + (&part == &exposedBoundaryPart || stk::io::is_part_io_part(part)) && + part.name().compare(0,7,"refine_") != 0 && + !phaseSupport.is_interface(&part); +} + +static stk::mesh::PartVector get_nonconformal_parts_to_check(const AuxMetaData & auxMeta, const Phase_Support & phaseSupport, const stk::mesh::PartVector & inputParts) +{ + stk::mesh::PartVector partsToCheck; + partsToCheck.reserve(inputParts.size()); + for (auto && part : inputParts) + if (is_part_to_check(phaseSupport, auxMeta, *part)) + partsToCheck.push_back(get_nonconformal_part(phaseSupport, part)); + stk::util::sort_and_unique(partsToCheck, stk::mesh::PartLess()); + return partsToCheck; +} + +bool +parts_are_compatible_for_snapping_when_ignoring_phase(const stk::mesh::BulkData & mesh, const AuxMetaData & auxMeta, const Phase_Support & phaseSupport, stk::mesh::Entity possibleSnapNode, stk::mesh::Entity fixedNode) +{ + const stk::mesh::PartVector & possibleSnapNodeParts = mesh.bucket(possibleSnapNode).supersets(); + const stk::mesh::PartVector nonconformalPartsToCheck = get_nonconformal_parts_to_check(auxMeta, phaseSupport, mesh.bucket(fixedNode).supersets()); + for (auto && possibleSnapNodePart : possibleSnapNodeParts) + { + if (is_part_to_check(phaseSupport, auxMeta, *possibleSnapNodePart)) + { + stk::mesh::Part * nonconformalPart = get_nonconformal_part(phaseSupport, possibleSnapNodePart); + if (!stk::mesh::contain(nonconformalPartsToCheck, *nonconformalPart)) + return false; + } + } + return true; +} + +bool phase_matches_interface(const CDFEM_Support & cdfemSupport, const PhaseTag & phase, const InterfaceID interface) +{ + if(cdfemSupport.num_ls_fields() > 1 && Phase_Support::has_one_levelset_per_phase()) + { + return (phase.contain(cdfemSupport.ls_field(interface.first_ls()).identifier, -1) && + phase.contain(cdfemSupport.ls_field(interface.second_ls()).identifier, -1)); + } + return (phase.contain(cdfemSupport.ls_field(interface.first_ls()).identifier, -1) && + phase.contain(cdfemSupport.ls_field(interface.first_ls()).identifier, +1)); +} + +bool determine_phase_from_parts(PhaseTag & phase, const stk::mesh::PartVector & parts, const Phase_Support & phaseSupport) +{ + ThrowAssert(phase.empty()); + bool has_conformal_ioparts = false; + + for (auto && part : parts) + { + if (part->primary_entity_rank() != stk::topology::ELEMENT_RANK || // limit ourselves to phase-specific volumes + !(stk::io::is_part_io_part(*part) || + phaseSupport.is_nonconformal(part))) + continue; + + const PhaseTag & iopart_phase = phaseSupport.get_iopart_phase(*part); + + if (!iopart_phase.empty()) + has_conformal_ioparts = true; + + phase.add(iopart_phase); + } + + return (has_conformal_ioparts); +} + +PhaseTag determine_phase_for_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const Phase_Support & phaseSupport) +{ + PhaseTag phase; + const stk::mesh::PartVector & parts = mesh.bucket(entity).supersets(); + determine_phase_from_parts(phase, parts, phaseSupport); + return phase; +} + +bool node_is_on_interface(const stk::mesh::BulkData & mesh, const CDFEM_Support & cdfemSupport, const Phase_Support & phaseSupport, stk::mesh::Entity node, const InterfaceID & interface) +{ + const PhaseTag nodePhase = determine_phase_for_entity(mesh, node, phaseSupport); + return phase_matches_interface(cdfemSupport, nodePhase, interface); +} + +bool nodes_are_on_any_interface(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, const stk::mesh::Bucket & nodeBucket) +{ + auto side_rank = mesh.mesh_meta_data().side_rank(); + for(auto && part : nodeBucket.supersets()) + if(part->primary_entity_rank() == side_rank && stk::io::is_part_io_part(*part) && phaseSupport.is_interface(part)) + return true; + return false; +} + +bool node_is_on_any_interface(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, const stk::mesh::Entity node) +{ + return nodes_are_on_any_interface(mesh, phaseSupport, mesh.bucket(node)); +} + +} + + diff --git a/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.hpp b/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.hpp new file mode 100644 index 000000000000..a3007222587b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_CDMesh_Utils.hpp @@ -0,0 +1,34 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_CDMESH_UTILS_H_ +#define KRINO_INCLUDE_AKRI_CDMESH_UTILS_H_ +#include + +namespace krino { + +class CDFEM_Support; +class PhaseTag; +class InterfaceID; +class AuxMetaData; +class Phase_Support; + +bool parts_are_compatible_for_snapping(const stk::mesh::BulkData & mesh, stk::mesh::Entity possible_snap_node, stk::mesh::Entity fixed_node); +bool parts_are_compatible_for_snapping_when_ignoring_phase(const stk::mesh::BulkData & mesh, const AuxMetaData & auxMeta, const Phase_Support & phaseSupport, stk::mesh::Entity possible_snap_node, stk::mesh::Entity fixed_node); +bool phase_matches_interface(const CDFEM_Support & cdfemSupport, const PhaseTag & phase, const InterfaceID interface); +bool determine_phase_from_parts(PhaseTag & phase, const stk::mesh::PartVector & parts, const Phase_Support & phaseSupport); +PhaseTag determine_phase_for_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const Phase_Support & phaseSupport); +bool nodes_are_on_any_interface(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, const stk::mesh::Bucket & nodeBucket); +bool node_is_on_any_interface(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, const stk::mesh::Entity node); +bool node_is_on_interface(const stk::mesh::BulkData & mesh, const CDFEM_Support & cdfemSupport, const Phase_Support & phaseSupport, stk::mesh::Entity node, const InterfaceID & interface); + +} + + + +#endif /* KRINO_INCLUDE_AKRI_CDMESH_UTILS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_Composite_Surface.cpp b/packages/krino/krino/krino_lib/Akri_Composite_Surface.cpp new file mode 100644 index 000000000000..941580cc6e98 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Composite_Surface.cpp @@ -0,0 +1,108 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +namespace krino{ + +Composite_Surface::Composite_Surface(const std::string & sn) + : SurfaceThatTakesAdvantageOfNarrowBandAndThereforeMightHaveWrongSign(), + my_name(sn), + my_composition_method(MINIMUM_SIGNED_DISTANCE) {} + +Composite_Surface::~Composite_Surface() {} + +void +Composite_Surface::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) +{ /* %TRACE[ON]% */ Trace trace__("krino::Composite_Surface::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length)"); /* %TRACE% */ + + for ( auto&& surface : my_subsurfaces ) + { + surface->prepare_to_compute(time, point_bbox, truncation_length); + } + + if (truncation_length > 0.) + { + BoundingBox padded_point_bbox = point_bbox; + padded_point_bbox.pad(truncation_length); + + SurfaceAutoVec nearby_surfaces; + for ( auto&& surface : my_subsurfaces ) + { + // keep nearby or moving surfaces + if (FACETED_SURFACE == surface->type() || + nullptr != surface->get_transformation() || + point_bbox.intersects(surface->get_bounding_box())) + { + nearby_surfaces.emplace_back(std::move(surface)); + } + } + nearby_surfaces.swap(my_subsurfaces); + } + + int subsurfaces_might_produce_wrong_sign = false; + for ( auto&& surface : my_subsurfaces ) + { + if (surface->truncated_distance_may_have_wrong_sign()) + { + subsurfaces_might_produce_wrong_sign = true; + break; + } + } + int local_subsurfaces_might_produce_wrong_sign = subsurfaces_might_produce_wrong_sign; + stk::all_reduce_max(stk::EnvData::parallel_comm(), &local_subsurfaces_might_produce_wrong_sign, &subsurfaces_might_produce_wrong_sign, 1); + my_subsurfaces_might_produce_wrong_sign = subsurfaces_might_produce_wrong_sign; +} + +double +Composite_Surface::truncated_point_signed_distance(const Vector3d &x, const double narrow_band, const double far_field_value) const +{ /* %TRACE% */ /* %TRACE% */ + + if (my_composition_method == MINIMUM_SIGNED_DISTANCE) + { + ThrowRequireMsg(far_field_value >= narrow_band, "Composite surfaces have a specific requirement for far_field_value due to min/max operations."); + double dist = (narrow_band == 0.) ? std::numeric_limits::max() : far_field_value; + for ( auto&& surface : my_subsurfaces ) + { + dist = std::min(dist, surface->truncated_point_signed_distance(x, narrow_band, far_field_value)); + } + return dist; + } + else + { + ThrowRequire(my_composition_method == MAXIMUM_SIGNED_DISTANCE); + ThrowRequireMsg(far_field_value <= -narrow_band, "Composite surfaces have a specific requirement for far_field_value due to min/max operations."); + double dist = (narrow_band == 0.) ? -std::numeric_limits::max() : far_field_value; + for ( auto&& surface : my_subsurfaces ) + { + dist = std::max(dist, surface->truncated_point_signed_distance(x, narrow_band, far_field_value)); + } + return dist; + } +} + +BoundingBox +Composite_Surface::get_bounding_box() +{ + BoundingBox bbox; + for (auto && subsurf : my_subsurfaces) + { + bbox.accommodate(subsurf->get_bounding_box()); + } + return bbox; +} + + +} // namespace krino + + + diff --git a/packages/krino/krino/krino_lib/Akri_Composite_Surface.hpp b/packages/krino/krino/krino_lib/Akri_Composite_Surface.hpp new file mode 100644 index 000000000000..92dfe0ba31c0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Composite_Surface.hpp @@ -0,0 +1,64 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Composite_Surface_h +#define Akri_Composite_Surface_h + +#include + +namespace krino { + +class SurfaceTree; +class Transformation; + +class Composite_Surface : public SurfaceThatTakesAdvantageOfNarrowBandAndThereforeMightHaveWrongSign { + +public: + Composite_Surface(const std::string & sn); + virtual ~Composite_Surface(); + + enum CompositionMethod{ MINIMUM_SIGNED_DISTANCE, MAXIMUM_SIGNED_DISTANCE }; + + virtual Surface_Type type() const override { return COMPOSITE_SURFACE; } + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) override; + virtual size_t storage_size() const override { size_t tot_size = 0; for (auto && surf : my_subsurfaces) tot_size += surf->storage_size(); return tot_size; } + + // query/modify subsurfaces + void add( Surface * surf ) { my_subsurfaces.emplace_back(surf); } + void reserve(unsigned size_) { my_subsurfaces.reserve(size_); } + unsigned size() const { return my_subsurfaces.size(); } + Surface * operator()( const unsigned index ) const { return my_subsurfaces[index].get(); } + void clear() { my_subsurfaces.clear(); } + void swap(Composite_Surface & other) { my_subsurfaces.swap(other.my_subsurfaces); } + SurfaceAutoVec & get_surfaces() { return my_subsurfaces; } + const SurfaceAutoVec & get_surfaces() const { return my_subsurfaces; } + + virtual void set_transformation(Transformation * trans) override { Surface::set_transformation(trans); for (auto && subsurf : my_subsurfaces) subsurf->set_transformation(trans);} + void set_composition_method(const CompositionMethod composition_method) { my_composition_method = composition_method; } + virtual BoundingBox get_bounding_box() override; + virtual double truncated_point_signed_distance(const Vector3d &x, const double truncation_length, const double far_field_value) const override; + double point_signed_distance_with_narrow_band(const Vector3d &x, const double narrow_band) const + { + // Special to this class, this version of point_signed_distance automatically determines the far_field_value from the composition_method + return truncated_point_signed_distance(x, narrow_band, get_signed_narrow_band_size(narrow_band)); + } + + virtual bool truncated_distance_may_have_wrong_sign() const override { return my_subsurfaces_might_produce_wrong_sign; } + double get_signed_narrow_band_size(const double pos_narrow_band) const { return (my_composition_method == MINIMUM_SIGNED_DISTANCE) ? pos_narrow_band : -pos_narrow_band; } + +protected: + std::string my_name; + CompositionMethod my_composition_method; + SurfaceAutoVec my_subsurfaces; + bool my_subsurfaces_might_produce_wrong_sign = true; +}; + +} // namespace krino + + +#endif // Akri_Composite_Surface_h diff --git a/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.cpp b/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.cpp new file mode 100644 index 000000000000..0c5b01db83b9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.cpp @@ -0,0 +1,122 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino{ + +void +Compute_Surface_Distance::calculate( + const stk::mesh::BulkData & mesh, + const stk::diag::Timer &parent_timer, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & surface_selector, + const double narrowBandSize, + const double farFieldValue) +{ + calculate(mesh, parent_timer, coordinates, distance, mesh.mesh_meta_data().universal_part(), surface_selector, narrowBandSize, farFieldValue); +} + +static BoundingBox compute_nodal_bounding_box(const stk::mesh::BulkData & mesh, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & volume_selector) +{ + const int spatial_dimension = mesh.mesh_meta_data().spatial_dimension(); + + // The bounding box for that contains all the nodes on that proc + BoundingBox nodeBbox; + for ( auto && bucket : mesh.get_buckets(stk::topology::NODE_RANK, volume_selector & stk::mesh::selectField(distance)) ) + { + const size_t length = bucket->size(); + double *coord = stk::mesh::field_data(coordinates, *bucket); + + for (size_t n = 0; n < length; ++n) + nodeBbox.accommodate( Vector3d(coord+n*spatial_dimension, spatial_dimension) ); + } + + return nodeBbox; +} + +static void compute_distance_to_facets(const stk::mesh::BulkData & mesh, + const MeshSurface & facet_list, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & volume_selector, + const double narrowBandSize, + const double userFarFieldValue) +{ + const int spatial_dimension = mesh.mesh_meta_data().spatial_dimension(); + const double farFieldValue = (userFarFieldValue > 0.0) ? userFarFieldValue : narrowBandSize; // Use farFieldValue, if specified, otherwise, use narrowBandSize + for ( auto && bucket : mesh.get_buckets(stk::topology::NODE_RANK, volume_selector & stk::mesh::selectField(distance)) ) + { + const size_t length = bucket->size(); + double *dist = stk::mesh::field_data(distance, *bucket); + double * coord = stk::mesh::field_data(coordinates, *bucket); + + for (size_t n = 0; n < length; ++n) + { + ThrowAssert(&(dist[n]) != NULL); + + const Vector3d xvec(coord+n*spatial_dimension, spatial_dimension); + dist[n] = facet_list.point_unsigned_distance(xvec, narrowBandSize, farFieldValue); + } + } +} + +void print_facet_info(const MeshSurface & facet_list, stk::ParallelMachine parallel) +{ + constexpr int vec_size = 3; + std::array local_sizes, global_min, global_max; + local_sizes[0] = facet_list.storage_size(); + local_sizes[1] = facet_list.size(); + local_sizes[2] = facet_list.size()+facet_list.nonlocal_size(); + + stk::all_reduce_min( parallel, local_sizes.data(), global_min.data(), vec_size ); + stk::all_reduce_max( parallel, local_sizes.data(), global_max.data(), vec_size ); + + krinolog << "Compute Surface Distance: "<< stk::diag::dendl; + krinolog << " Local facet count: min=" << global_min[1] << ", max=" << global_max[1] << stk::diag::dendl; + krinolog << " Total facet count: min=" << global_min[2] << ", max=" << global_max[2] << stk::diag::dendl; + krinolog << " Memory usage (mb): min=" << global_min[0]/(1024.0*1024.0) << ", max=" << global_max[0]/(1024.0*1024.0) << stk::diag::dendl; +} + + +void +Compute_Surface_Distance::calculate( + const stk::mesh::BulkData & mesh, + const stk::diag::Timer &parent_timer, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & volume_selector, + const stk::mesh::Selector & surface_selector, + const double narrowBandSize, + const double farFieldValue) +{ /* %TRACE[ON]% */ Trace trace__("krino::Compute_Surface_Distance::compute_surface_distance(void)"); /* %TRACE% */ + + stk::diag::Timer timer( "Compute Surface Distance", parent_timer ); + stk::diag::TimeBlock timer_(timer); + + MeshSurface facet_list(mesh.mesh_meta_data(), coordinates, surface_selector, +1); + const BoundingBox nodeBbox = compute_nodal_bounding_box(mesh, coordinates, distance, volume_selector); + facet_list.prepare_to_compute(0.0, nodeBbox, narrowBandSize); // Setup including communication of facets that are within this processors narrow band + + print_facet_info(facet_list, mesh.parallel()); + + compute_distance_to_facets(mesh, facet_list, coordinates, distance, volume_selector, narrowBandSize, farFieldValue); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.hpp b/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.hpp new file mode 100644 index 000000000000..6795cd4002f5 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Compute_Surface_Distance.hpp @@ -0,0 +1,42 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Compute_Surface_Distance_h +#define Akri_Compute_Surface_Distance_h + +#include +#include +#include + +namespace krino { + +class Compute_Surface_Distance { +public: + static void calculate( + const stk::mesh::BulkData & mesh, + const stk::diag::Timer &parent_timer, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & surface_selector, + const double narrowBandSize = 0.0, + const double farFieldValue = 0.0); + + static void calculate( + const stk::mesh::BulkData & mesh, + const stk::diag::Timer &parent_timer, + const stk::mesh::Field& coordinates, + const stk::mesh::Field& distance, + const stk::mesh::Selector & volume_selector, + const stk::mesh::Selector & surface_selector, + const double narrowBandSize = 0.0, + const double farFieldValue = 0.0); + }; + +} // namespace krino + +#endif // Akri_Compute_Surface_Distance_h diff --git a/packages/krino/krino/krino_lib/Akri_ContourElement.cpp b/packages/krino/krino/krino_lib/Akri_ContourElement.cpp new file mode 100644 index 000000000000..9ec313d5897e --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ContourElement.cpp @@ -0,0 +1,556 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino{ + +ContourElement::ContourElement( const stk::mesh::BulkData & mesh, + stk::mesh::Entity in_mesh_obj, + const FieldRef coords_field, + const FieldRef dist_field, + const double iso_dist ) + : my_mesh( mesh ), + my_entity( in_mesh_obj ), + my_spatial_dim( mesh.mesh_meta_data().spatial_dimension() ), + my_coords_master_elem(MasterElementDeterminer::getMasterElement(mesh.bucket(in_mesh_obj), coords_field)), + my_dist_master_elem(MasterElementDeterminer::getMasterElement(mesh.bucket(in_mesh_obj), dist_field)), + my_coords_field( coords_field ), + my_dist_field( dist_field ), + my_length_scale(-1.0), + my_edge_linear_tolerance(-1.0), + my_edge_nonlinear_tolerance(-1.0) +{ /* %TRACE% */ /* %TRACE% */ + + // + // Gather obj's coordinates, distance, and velocity into ArrayContainer's. + // + + const int dim = my_spatial_dim; + + const int npe_coords = my_coords_master_elem.get_topology().num_nodes(); + const int npe_dist = my_dist_master_elem.get_topology().num_nodes(); + + my_coords.resize( dim, npe_coords ); + my_dist.resize( npe_dist ); + + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(my_entity); + + for ( int i = 0; i < npe_coords; ++i ) + { + double * var = field_data( my_coords_field, elem_nodes[i]); + for ( int d = 0; d < dim; d++ ) + { + my_coords(d,i) = var[d]; + } + } + + for ( int i = 0; i < npe_dist; ++i ) + { + double * var = field_data( my_dist_field, elem_nodes[i]); + my_dist(i) = *var - iso_dist; + } + + // the interpolate master element methods require the transpose?!? + my_coords_transpose.resize( npe_coords, dim ); + for (int i = 0; i < npe_coords; i++) + { + for (int d = 0; d < dim; d++) + { + my_coords_transpose(i,d) = my_coords(d,i); + } + } +} + +ContourElement::~ContourElement() {} + +std::ostream & +ContourElement::put( std::ostream& os ) const +{ /* %TRACE% */ /* %TRACE% */ + const int dim = my_spatial_dim; + + os << "Element description:" << std::endl + << " Coordinates topolology is " << coord_topology().name() + << ", Distance topology is " << dist_topology().name() << std::endl; + + int lnn = 0; + int coord_counter = 0; + int dist_counter = 0; + const unsigned num_nodes = my_mesh.num_nodes(my_entity); + const stk::mesh::Entity* nodes = my_mesh.begin_nodes(my_entity); + for (unsigned node_index=0; node_index(my_coords_field, node); + if ( NULL != var ) + { + Vector3d coords(Vector3d::ZERO); + for ( int d = 0; d < dim; d++ ) + coords[d] = my_coords(d,coord_counter); + os << ", coords = (" << coords[0] << "," + << coords[1] << "," + << coords[2] << ")"; + coord_counter++; + } + + var = field_data(my_dist_field, node); + if ( NULL != var ) + { + os << ", dist = " << my_dist(dist_counter++); + } + os << std::endl; + } + return os ; +} + +bool +ContourElement::have_interface_sides() const +{ + ThrowAssert(my_base_subelement); + return my_base_subelement->have_interface_sides(); +} + +double +ContourElement::distance( const Vector3d & p_coords ) const + { /* %TRACE% */ /* %TRACE% */ + double dist; + my_dist_master_elem.interpolate_point(my_spatial_dim, p_coords.data(), 1, my_dist.ptr(), &dist); + return dist; + } + +Vector3d +ContourElement::coordinates( const Vector3d & p_coords ) const + { /* %TRACE% */ /* %TRACE% */ + Vector3d coords(Vector3d::ZERO); + my_coords_master_elem.interpolate_point(my_spatial_dim, p_coords.data(), my_spatial_dim, my_coords.ptr(), coords.data()); + return coords; + } + +double +ContourElement::determinant( const Vector3d & p_coords ) const + { /* %TRACE% */ /* %TRACE% */ + double detJ, detJ_error; + + const int num_coord_dofs = coord_topology().num_nodes(); + + // temporary data + static sierra::ArrayContainer d_shapef_coords; + + // reserve enough space for results + d_shapef_coords.resize(my_spatial_dim, num_coord_dofs, 1); + + my_coords_master_elem.shape_fcn_deriv(1, p_coords.data(), d_shapef_coords.ptr()); + my_coords_master_elem.determinant( + my_spatial_dim, // Number of coordinate dimensions + 1, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.ptr(),// Mesh shape function derivatives + 1, // Number of elements + my_coords.ptr(), // Mesh coordinate values + &detJ, // Determinant of the transformation Jacobian for each element (output) + &detJ_error ); // Determinant error (output) + return detJ; + } + +Vector3d +ContourElement::continuous_distance_gradient( const Vector3d & p_coords ) const + { /* %TRACE% */ /* %TRACE% */ + // gather continuous distance gradient + sierra::ArrayContainer grad_distance; + const int npe = dist_topology().num_nodes(); + grad_distance.resize( my_spatial_dim, npe ); + stk::mesh::FieldBase* field_ptr = my_mesh.mesh_meta_data().get_field(stk::topology::NODE_RANK, "CONT_GRAD"); + ThrowRequireMsg(nullptr != field_ptr, "Field CONT_GRAD not found."); + const FieldRef contGradField(field_ptr); + const stk::mesh::Entity* elem_nodes = my_mesh.begin_nodes(my_entity); + for ( int i = 0; i < npe; ++i ) + { + double * var = field_data(contGradField, elem_nodes[i]); + for(int d = 0; d < my_spatial_dim; ++d) + grad_distance(d,i) = var[d]; + } + + Vector3d grad_dist(Vector3d::ZERO); + my_vel_master_elem->interpolate_point(my_spatial_dim, p_coords.data(), my_spatial_dim, grad_distance.ptr(), grad_dist.data()); + return grad_dist; + } + +Vector3d +ContourElement::distance_gradient( const Vector3d & p_coords ) const + { /* %TRACE% */ /* %TRACE% */ + const int dim = my_spatial_dim; + const int num_coord_dofs = my_coords.dimension(); + const int num_dist_dofs = my_dist.dimension(); + + // temporary data + static sierra::ArrayContainer d_shapef_coords; + static sierra::ArrayContainer d_shapef_dist; + static sierra::ArrayContainer grad_op; + + // reserve enough space for results + d_shapef_coords.resize(dim, num_coord_dofs); + d_shapef_dist.resize(dim, num_dist_dofs); + grad_op.resize(dim, num_dist_dofs); + Vector3d grad_dist( Vector3d::ZERO ); + double det_J; + + // pointers to array data + const double * intg_pt_loc_ptr = p_coords.data(); + double * grad_dist_ptr = grad_dist.data(); + + double gradop_error; + + my_coords_master_elem.shape_fcn_deriv(1, intg_pt_loc_ptr, d_shapef_coords.ptr()); + my_dist_master_elem.shape_fcn_deriv(1, intg_pt_loc_ptr, d_shapef_dist.ptr()); + + my_dist_master_elem.gradient_operator( + dim, // Number of coordinate dimensions + 1, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.ptr(),// Mesh shape function derivatives + num_dist_dofs, // Number of dof shape functions + d_shapef_dist.ptr(), // Dof shape function derivatives + 1, // Number of elements + my_coords.ptr(), // Mesh coordinate values + grad_op.ptr(), // Gradient operator values (output) + &det_J, // Determinant of the transformation Jacobian for each element (output) + &gradop_error ); // Gradop error (output) + + my_dist_master_elem.scalar_gradient( + 1, // Number of target points + 1, // Number of elements + grad_op.ptr(), // Gradient operator values + &det_J, // Determinant of the transformation Jacobian for each element + my_dist.ptr(), // nodal distance + grad_dist_ptr ); // Gradient of distance at integration pts (output) + return( grad_dist ); + } + +void +ContourElement::compute_distance_gradient( const sierra::Array & intg_pt_locations, + sierra::ArrayContainer & grad_dist ) const + { /* %TRACE% */ /* %TRACE% */ + const int dim = intg_pt_locations.dimension(); + const int num_intg_pts = intg_pt_locations.dimension(); + + const int num_coord_dofs = my_coords.dimension(); + const int num_dist_dofs = my_dist.dimension(); + + // temporary data + static sierra::ArrayContainer d_shapef_coords; + static sierra::ArrayContainer d_shapef_dist; + static sierra::ArrayContainer det_J; + static sierra::ArrayContainer grad_op; + + // reserve enough space for results + d_shapef_coords.resize(dim, num_coord_dofs, num_intg_pts); + d_shapef_dist.resize(dim, num_dist_dofs, num_intg_pts); + det_J.resize(num_intg_pts); + grad_op.resize(dim, num_dist_dofs, num_intg_pts); + grad_dist.resize(dim, num_intg_pts); + + double gradop_error; + + my_coords_master_elem.shape_fcn_deriv(num_intg_pts, intg_pt_locations.ptr(), d_shapef_coords.ptr()); + my_dist_master_elem.shape_fcn_deriv(num_intg_pts, intg_pt_locations.ptr(), d_shapef_dist.ptr()); + + my_dist_master_elem.gradient_operator( + dim, // Number of coordinate dimensions + num_intg_pts, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.ptr(), // Mesh shape function derivatives + num_dist_dofs, // Number of dof shape functions + d_shapef_dist.ptr(), // Dof shape function derivatives + 1, // Number of elements + my_coords.ptr(), // Mesh coordinate values + grad_op.ptr(), // Gradient operator values (output) + det_J.ptr(), // Determinant of the transformation Jacobian for each element (output) + &gradop_error ); // Gradop error (output) + + my_dist_master_elem.scalar_gradient( + num_intg_pts, // Number of target points + 1, // Number of elements + grad_op.ptr(), // Gradient operator values + det_J.ptr(), // Determinant of the transformation Jacobian for each element + my_dist.ptr(), // nodal distance + grad_dist.ptr() ); // Gradient of distance at integration pts (output) + } + +void +ContourElement::compute_subelement_decomposition(const double in_length_scale, const double in_edge_linear_tolerance, const double in_edge_nonlinear_tolerance) const + { /* %TRACE% */ /* %TRACE% */ + my_length_scale = in_length_scale; + my_edge_linear_tolerance = in_edge_linear_tolerance; + my_edge_nonlinear_tolerance = in_edge_nonlinear_tolerance; + + stk::topology topology = dist_topology(); + const int num_sides = topology.num_sides(); + std::vector side_ids(num_sides); + for (int i=0; i( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::HEXAHEDRON_27 == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::TETRAHEDRON_4 == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::TETRAHEDRON_10 == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::WEDGE_6 == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::QUADRILATERAL_4_2D == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::QUADRILATERAL_9_2D == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::TRIANGLE_3_2D == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + else if (stk::topology::TRIANGLE_6_2D == topology) + { + my_base_subelement = std::make_unique( my_dist_p_coords, side_ids, this ); + } + ThrowErrorMsgIf(!my_base_subelement, "Element with topology " << topology.name() << " not supported."); + + if ( krinolog.shouldPrint(LOG_SUBELEMENT) ) + { + if ( krinolog.shouldPrint(LOG_DEBUG) ) + { + dump_subelement_details(); + } + else + { + dump_subelement_structure(); + } + } + } + +double +ContourElement::volume() const + { /* %TRACE% */ /* %TRACE% */ + + sierra::Array intg_pt_locations; + sierra::Array intg_weights; + sierra::ArrayContainer determinants; + + std_intg_pts( intg_pt_locations, intg_weights, determinants ); + + double vol = 0.0; + + const int num_intg_pts = intg_pt_locations.dimension(); + + for ( int ip = 0; ip < num_intg_pts; ++ip ) + { + vol += intg_weights(ip) * determinants(ip); + } + return vol; + } + +double +ContourElement::average_edge_length() const +{ /* %TRACE% */ /* %TRACE% */ + const stk::topology Top = coord_topology(); + int num_edges = Top.num_edges(); + + double sum_edge_lengths = 0.0; + + for ( int edge = 0; edge < num_edges; edge++ ) + { + const unsigned * const lnn = get_edge_node_ordinals(Top, edge); + + double sqr_length = 0.0; + for ( int d = 0; d < my_spatial_dim; d++ ) sqr_length += (my_coords(d,lnn[0]) - my_coords(d,lnn[1])) * + (my_coords(d,lnn[0]) - my_coords(d,lnn[1])); + sum_edge_lengths += std::sqrt(sqr_length); + } + + return sum_edge_lengths/num_edges; +} + +double +ContourElement::elem_size() const + { /* %TRACE% */ /* %TRACE% */ + const double vol = volume(); + const double vol_root = 1.0 / my_spatial_dim; + const double h = pow( vol, vol_root ); + return h; + } + +void +ContourElement::dump_subelement_structure() const + { /* %TRACE% */ /* %TRACE% */ + ThrowErrorMsgIf(!my_base_subelement, "\ncompute_subelement_decomposition(...) must be called prior to calling dump_subelement_structure()."); + + krinolog << "***********************************************" << stk::diag::dendl; + krinolog << *this; + krinolog << "Subelement structure:" << stk::diag::dendl; + my_base_subelement->dump_structure(); + krinolog << "***********************************************" << stk::diag::dendl; + } + +void +ContourElement::dump_subelement_details() const + { /* %TRACE% */ /* %TRACE% */ + ThrowErrorMsgIf(!my_base_subelement, "\ncompute_subelement_decomposition(...) must be called prior to calling dump_subelement_details()."); + + krinolog << "***********************************************" << stk::diag::dendl; + krinolog << *this; + krinolog << "Subelement details:" << stk::diag::dendl; + my_base_subelement->dump_details(); + krinolog << "***********************************************" << stk::diag::dendl; + } + +int +ContourElement::build_subelement_facets( Faceted_Surface & facets ) +{ + ThrowErrorMsgIf(!my_base_subelement, "\ncompute_subelement_decomposition(...) must be called prior to calling build_subelement_facets(...)."); + return my_base_subelement->build_facets( facets ); +} + +int +ContourElement::gather_intg_pts( const int intg_pt_sign, + sierra::ArrayContainer & intg_pt_locations, + sierra::ArrayContainer & intg_weights, + sierra::ArrayContainer & determinants, + const bool map_to_real_coords ) +{ + ThrowErrorMsgIf(0 == intg_pt_sign && !map_to_real_coords, + "\nSubelement decomposition can currently only provide the surface integration with the overall determinant."); + ThrowErrorMsgIf(!my_base_subelement, + "\ncompute_subelement_decomposition(...) must be called prior to calling gather_intg_pts(...)."); + + const int num_intg_pts = my_base_subelement->num_intg_pts(intg_pt_sign); + + intg_pt_locations.resize(my_spatial_dim,num_intg_pts); + intg_weights.resize(num_intg_pts); + determinants.resize(num_intg_pts); + + my_base_subelement->gather_intg_pts( intg_pt_sign, + intg_pt_locations, + intg_weights, + determinants ); + + if ( 0 != intg_pt_sign && map_to_real_coords ) + { + // + // Include the determinant from element to real space + // + const int num_coord_dofs = coord_topology().num_nodes(); + + // temporary data + static sierra::ArrayContainer d_shapef_coords; + static sierra::ArrayContainer det_J; + + // reserve enough space for results + d_shapef_coords.resize(my_spatial_dim, num_coord_dofs, num_intg_pts); + det_J.resize(num_intg_pts); + + double det_J_error; + + my_coords_master_elem.shape_fcn_deriv(num_intg_pts, intg_pt_locations.ptr(), d_shapef_coords.ptr()); + my_coords_master_elem.determinant( + my_spatial_dim, // Number of coordinate dimensions + num_intg_pts, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.ptr(),// Mesh shape function derivatives + 1, // Number of elements + my_coords.ptr(), // Mesh coordinate values + det_J.ptr(), // Determinant of the transformation Jacobian for each element (output) + &det_J_error ); // Determinant error (output) + for ( int i=0; i & intg_pt_locations, + sierra::Array & intg_weights, + sierra::ArrayContainer & det_J, + const MasterElement & me ) const + { + const int num_intg_pts = me.num_intg_pts(); + const double * intg_pt_loc_ptr = me.intg_pt_locations(); + const double * intg_wt_ptr = me.intg_weights(); + + intg_pt_locations.set(intg_pt_loc_ptr,my_spatial_dim,num_intg_pts); + intg_weights.set(intg_wt_ptr,num_intg_pts); + det_J.resize( num_intg_pts ); + + double det_J_error; + + if ( me.get_topology() == my_coords_master_elem.get_topology() ) + { + my_coords_master_elem.determinant( my_spatial_dim, 1, my_coords.ptr(), det_J.ptr(), &det_J_error ); + } + else + { + const int num_coord_dofs = coord_topology().num_nodes(); + sierra::ArrayContainer d_shapef_coords(my_spatial_dim, num_coord_dofs, num_intg_pts); + my_coords_master_elem.shape_fcn_deriv(num_intg_pts, intg_pt_locations.ptr(), d_shapef_coords.ptr()); + my_coords_master_elem.determinant( + my_spatial_dim, // Number of coordinate dimensions + num_intg_pts, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.ptr(),// Mesh shape function derivatives + 1, // Number of elements + my_coords.ptr(), // Mesh coordinate values + det_J.ptr(), // Determinant of the transformation Jacobian for each element (output) + &det_J_error ); // Determinant error (output) + } + + return( num_intg_pts ); + } + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_ContourElement.hpp b/packages/krino/krino/krino_lib/Akri_ContourElement.hpp new file mode 100644 index 000000000000..f7ee798316ca --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ContourElement.hpp @@ -0,0 +1,130 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_ContourElement_h +#define Akri_ContourElement_h + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +namespace krino { + +class ContourSubElement; + +class ContourElement { +public: + + ContourElement( const stk::mesh::BulkData & mesh, + stk::mesh::Entity mesh_obj, + const FieldRef coords_field, + const FieldRef dist_field, + const double iso_dist = 0.0 ); + ~ContourElement(); // Definition must in implementation file because SubElement is incomplete + + std::ostream & put( std::ostream& os ) const; + friend std::ostream & operator << ( std::ostream &os , const ContourElement &s ) { + return s.put(os); + } + + const MasterElement & coord_master_elem() const { return my_coords_master_elem; } + const MasterElement & dist_master_elem() const { return my_dist_master_elem; } + const MasterElement & vel_master_elem() const { return *my_vel_master_elem; } + + const stk::topology coord_topology() const { return my_coords_master_elem.get_topology(); } + const stk::topology dist_topology() const { return my_dist_master_elem.get_topology(); } + const stk::topology vel_topology() const { return my_vel_master_elem->get_topology(); } + + bool dist_is_linear() const { return dist_topology() == stk::topology::TRIANGLE_3_2D || dist_topology() == stk::topology::TETRAHEDRON_4; } + + stk::mesh::Entity entity() const { return my_entity; } + stk::mesh::EntityId elem_id() const { return my_mesh.identifier(my_entity); } + bool have_interface_sides() const; + + Vector3d coordinates( const Vector3d & p_coords ) const; + double distance( const Vector3d & p_coords ) const; + const PointVec & nodal_parametric_coordinates() const { return my_dist_p_coords; } + double determinant( const Vector3d & p_coords ) const; + + Vector3d continuous_distance_gradient( const Vector3d & p_coords ) const; + Vector3d distance_gradient( const Vector3d & p_coords ) const; + void compute_distance_gradient( const sierra::Array & intg_pt_locations, + sierra::ArrayContainer & grad_dist ) const; + + void dump_subelement_structure( void ) const; + void dump_subelement_details( void ) const; + const ContourSubElement * get_base_subelement() const { return my_base_subelement.get(); } + + int build_subelement_facets( Faceted_Surface & facets ); + + int gather_intg_pts( const int intg_pt_sign, + sierra::ArrayContainer & intg_pt_locations, + sierra::ArrayContainer & intg_weights, + sierra::ArrayContainer & determinants, + const bool map_to_real_coords ); + + int std_intg_pts( sierra::Array & intg_pt_locations, + sierra::Array & intg_weights, + sierra::ArrayContainer & determinants, + const MasterElement & me ) const; + int std_intg_pts( sierra::Array & intg_pt_locations, + sierra::Array & intg_weights, + sierra::ArrayContainer & determinants ) const { return std_intg_pts(intg_pt_locations, intg_weights, determinants, my_coords_master_elem); } + + int spatial_dim() const { return my_spatial_dim; } + double length_scale() const { return my_length_scale; } + double edge_linear_tolerance() const { return my_edge_linear_tolerance; } + double edge_nonlinear_tolerance() const { return my_edge_nonlinear_tolerance; } + + double volume() const; + double elem_size() const; + double average_edge_length() const; + + void compute_subelement_decomposition(const double length_scale, const double edge_linear_tolerance = 1.e-4, const double edge_nonlinear_tolerance = 1.0e-2) const; + +private: + const stk::mesh::BulkData & my_mesh; + stk::mesh::Entity my_entity; + const int my_spatial_dim; + + const MasterElement & my_coords_master_elem; + const MasterElement & my_dist_master_elem; + const MasterElement * my_vel_master_elem; + + const FieldRef my_coords_field; + const FieldRef my_dist_field; + const FieldRef my_vel_field; + + sierra::ArrayContainer my_coords; + sierra::ArrayContainer my_coords_transpose; + sierra::ArrayContainer my_dist; + sierra::ArrayContainer my_vel; + sierra::ArrayContainer my_vel_transpose; + + mutable PointVec my_dist_p_coords; + mutable double my_length_scale; + mutable double my_edge_linear_tolerance; + mutable double my_edge_nonlinear_tolerance; + mutable std::unique_ptr my_base_subelement; + + //: Default constructor not allowed + ContourElement(); + +}; + +} // namespace krino + +#endif // Akri_ContourElement_h diff --git a/packages/krino/krino/krino_lib/Akri_ContourSubElement.cpp b/packages/krino/krino/krino_lib/Akri_ContourSubElement.cpp new file mode 100644 index 000000000000..2ef3e52bf7c1 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ContourSubElement.cpp @@ -0,0 +1,2565 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +#include + +#include + +#include + +namespace krino{ + +bool ContourSubElement::is_more(const Vector3d & x, const Vector3d & y) +{ + // note that in the case of x==y, this will return false + if (utility::is_more(x[0],y[0]) || (!utility::is_less(x[0],y[0]) && + (utility::is_more(x[1],y[1]) || (!utility::is_less(x[1],y[1]) && + (utility::is_more(x[2],y[2])))))) + { + return true; + } + return false; +} + +ContourSubElement::ContourSubElement( const stk::topology topo, + const PointVec & coords, + const std::vector & side_ids, + const ContourElement *in_owner, + const int in_subelement_depth, + const int subelement_sign ) + : my_master_element( MasterElementDeterminer::getMasterElement(topo) ), + my_side_master_element( MasterElementDeterminer::getMasterElement(topo.side_topology()) ), + my_coords( coords ), + my_side_ids( side_ids ), + my_owner( in_owner ), + my_subelement_depth( in_subelement_depth ), + my_sign( subelement_sign ) +{ /* %TRACE% */ /* %TRACE% */ + my_num_nodes = my_coords.size(); + ThrowAssert( (unsigned)my_num_nodes == topology().num_nodes() ); + my_num_sides = my_side_ids.size(); + ThrowAssert( (unsigned)my_num_sides == topology().num_sides() ); + + // compute distance at each node + my_dist.clear(); + my_dist.reserve(my_num_nodes); + for ( int i = 0; i < my_num_nodes; i++ ) + { + double nodal_dist = my_owner->distance( my_coords[i] ); + my_dist.push_back(nodal_dist); + } +} + +int +ContourSubElement::build_facets( Faceted_Surface & facets ) +{ /* %TRACE% */ /* %TRACE% */ + int start_size = facets.size(); + + if ( !my_subelements.empty() ) + { + for ( auto && subelem : my_subelements ) + { + subelem->build_facets( facets ); + } + } + else + { + for ( int iside = 0; iside < my_num_sides; iside++ ) + { + // side_ids == -2 indicates that sides is on interface + if ( my_side_ids[iside] == -2 ) + { + const int subelem_num_facets = side_facets( facets, iside ); + if ( krinolog.shouldPrint(LOG_SUBELEMENT) ) + { + krinolog << "Subelement with area = " << side_relative_area(iside) + << " added " << subelem_num_facets << " facets." << std::endl; + } + } + } + } + + int added_facets = facets.size() - start_size; + return added_facets; +} + +void +ContourSubElement::dump_structure() const +{ /* %TRACE% */ /* %TRACE% */ + + if ( !my_subelements.empty() ) + { + for ( int i = 0; i < my_subelement_depth; i++ ) + { + krinolog << " "; + } + krinolog << "my subelement type = " << topology().name() << ", my # of subelements = " << my_subelements.size() << std::endl; + for ( auto && subelem : my_subelements ) + { + subelem->dump_structure(); + } + } + else + { + for ( int i = 0; i < my_subelement_depth; i++ ) + { + krinolog << " "; + } + krinolog << "my subelement type = " << topology().name() << std::endl; + } +} + +void +ContourSubElement::dump_details() const +{ /* %TRACE% */ /* %TRACE% */ + if ( !my_subelements.empty() ) + { + krinolog << "my subelement type = " << topology().name() << ", my # of subelements = " << my_subelements.size() << std::endl; + for ( auto && subelem : my_subelements ) + { + subelem->dump_details(); + } + } + else + { + krinolog << "--------------------begin subelement definition--------------------" << std::endl; + krinolog << *this; + krinolog << "---------------------end subelement definition---------------------" << std::endl; + } +} + +int +ContourSubElement::side_facets( Faceted_Surface & facets, int side ) const +{ /* %TRACE% */ /* %TRACE% */ + const std::string & owner_type = my_owner->dist_topology().name(); + const std::string & sub_type = topology().name(); + ThrowRuntimeError("Subelement decomposition for subelement of type '" << sub_type + << "' which was generated from owning element of type '" << owner_type + << "' is missing the capability to generate conformal facets."); + return -1; +} + +std::ostream & +ContourSubElement::put( std::ostream& os ) const +{ /* %TRACE% */ /* %TRACE% */ + os << "Subelement description:" << std::endl; + os << " type = " << topology().name() + << ", relative volume = " << relative_volume() + << ", parametric_quality = " << parametric_quality() + << ", physical_quality = " << physical_quality() << std::endl; + for ( int i = 0; i < my_num_nodes; i++ ) + { + Vector3d x = my_owner->coordinates( my_coords[i] ); + os << " coords[" << i << "] = (" + << my_coords[i][0] << "," + << my_coords[i][1] << "," + << my_coords[i][2] << ")" + << ", x = (" + << x[0] << "," + << x[1] << "," + << x[2] << ")" + << ", dist = " << my_dist[i] + << ", sign = " << -1 + 2*LevelSet::sign_change(my_dist[i],-1.) << std::endl; + } + for ( int i = 0; i < my_num_sides; i++ ) + { + os << " side_ids[" << i << "] = " << my_side_ids[i] + << ", side_relative_area[" << i << "] = " << side_relative_area(i) + << ", side_quality[" << i << "] = " << side_quality(i) << std::endl; + } + // matlab visualization + os << " matlabvertices = ["; + for ( int i = 0; i < my_num_nodes; i++ ) + { + os << my_coords[i][0] << " " + << my_coords[i][1] << " " + << my_coords[i][2] << "; "; + } + os << "];" << std::endl; + os << " physical space matlabvertices = ["; + for ( int i = 0; i < my_num_nodes; i++ ) + { + Vector3d x = my_owner->coordinates( my_coords[i] ); + os << x[0] << " " + << x[1] << " " + << x[2] << "; "; + } + os << "];" << std::endl; + + return os ; +} + +double +ContourSubElement::relative_volume() const +{ /* %TRACE% */ /* %TRACE% */ + // This is a relative volume compared to the owner volume. + // Actually this is a relative volume if the "parametric" volume of the element is unity. + // Otherwise, it is off by a factor. + const int nelem = 1; + const int dim = spatial_dim(); + const int nint = my_master_element.num_intg_pts(); + std::vector coords(my_num_nodes * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + + // integration weights + const double * intg_weights = my_master_element.intg_weights(); + + // load coords + int count = 0; + for ( int i = 0; i < my_num_nodes; i++ ) + { + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = my_coords[i][j]; + } + } + + // determinant at integration points + my_master_element.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double elem_volume = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + elem_volume += det_J[ip] * intg_weights[ip]; + } + + return elem_volume; +} + +double +ContourSubElement::side_relative_area( const int side ) const +{ /* %TRACE% */ /* %TRACE% */ + // This is a relative volume compared to the owner volume. + // Actually this is a relative volume if the "parametric" volume of the element is unity. + // Otherwise, it is off by a factor. + const int nelem = 1; + const int dim = spatial_dim(); + const int nint = my_side_master_element.num_intg_pts(); + const stk::topology Top = topology(); + const stk::topology sideTop = Top.side_topology(side); + const int side_num_nodes = sideTop.num_nodes(); + const unsigned * const lnn = get_side_node_ordinals(Top, side); + + std::vector coords(side_num_nodes * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + + // integration weights + const double * intg_weights = my_side_master_element.intg_weights(); + + // load coords + int count = 0; + for ( int i = 0; i < side_num_nodes; i++ ) + { + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = my_coords[lnn[i]][j]; + } + } + + // determinant at integration points + my_side_master_element.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double elem_side_area = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + elem_side_area += det_J[ip] * intg_weights[ip]; + } + + return elem_side_area; +} + +bool +ContourSubElement::have_interface_sides() const +{ + if ( !my_subelements.empty()) + { + for ( auto && subelem : my_subelements ) + { + if (subelem->have_interface_sides()) + { + return true; + } + } + } + else + { + for ( int iside = 0; iside < my_num_sides; iside++ ) + { + // side_ids == -2 indicates that sides is on interface + if ( my_side_ids[iside] == -2 ) + { + return true; + } + } + } + return false; +} + +ContourSubElement::~ContourSubElement() +{ /* %TRACE% */ /* %TRACE% */ + for ( auto && subelem : my_subelements ) + delete subelem; +} + +int +ContourSubElement::num_intg_pts(const int intg_pt_sign) +{ /* %TRACE% */ /* %TRACE% */ + int num_pts = 0; + + if ( !my_subelements.empty() ) + { + for ( auto && subelem : my_subelements ) + { + num_pts += subelem->num_intg_pts(intg_pt_sign); + } + } + else + { + if ( 0 == intg_pt_sign ) // interface points + { + for ( int iside = 0; iside < my_num_sides; iside++ ) + { + // side_ids == -2 indicates that side is on interface + if ( my_side_ids[iside] == -2 ) + { + num_pts += my_side_master_element.num_intg_pts(); + } + } + } + else // volume points + { + if ( intg_pt_sign != my_sign ) + { + return(0); + } + else + { + return ( my_master_element.num_intg_pts() ); + } + } + } + + return num_pts; +} + +int +ContourSubElement::gather_intg_pts( const int intg_pt_sign, + sierra::ArrayContainer & intg_pt_locations, + sierra::ArrayContainer & intg_weights, + sierra::ArrayContainer & determinant, + int index ) +{ /* %TRACE% */ /* %TRACE% */ + if ( !my_subelements.empty() ) + { + for ( auto && subelem : my_subelements ) + { + index = subelem->gather_intg_pts( intg_pt_sign, + intg_pt_locations, + intg_weights, + determinant, + index ); + } + } + else + { + if ( 0 == intg_pt_sign ) // interface points + { + for ( int iside = 0; iside < my_num_sides; iside++ ) + { + // side_ids == -2 indicates that side is on interface + if ( my_side_ids[iside] == -2 ) + { + const int nelem = 1; + const int dim = spatial_dim(); + const stk::topology Top = topology(); + const stk::topology sideTop = Top.side_topology(iside); + const int side_num_intg_pts = my_side_master_element.num_intg_pts(); + const int side_num_nodes = sideTop.num_nodes(); + const unsigned * const lnn = get_side_node_ordinals(Top, iside ); + double error; + + // temp arrays + sierra::ArrayContainer coords(dim,side_num_nodes); + sierra::ArrayContainer det_J(side_num_intg_pts); + + // load coords + for ( int i = 0; i < side_num_nodes; i++ ) + { + Vector3d coordinates = my_owner->coordinates( my_coords[lnn[i]] ); + for ( int d = 0; d < dim; d++ ) coords(d,i) = coordinates[d]; + } + + // determinant at integration points + my_side_master_element.determinant( dim, nelem, coords.ptr(), det_J.ptr(), &error ); + + // integration weights + const double * intg_wts_ptr = my_side_master_element.intg_weights(); + const sierra::Array intg_wts(intg_wts_ptr,side_num_intg_pts); + + // basis fns at integration point locations + const double * bf_ptr = my_side_master_element.shape_fcn(); + const sierra::Array bf(bf_ptr,side_num_nodes,side_num_intg_pts); + + for ( int ip = 0; ip < side_num_intg_pts; ++ip) + { + determinant(index) = det_J(ip); + intg_weights(index) = intg_wts(ip); + + Vector3d xi(Vector3d::ZERO); + for ( int i = 0; i < side_num_nodes; i++ ) + xi += bf(i,ip) * my_coords[lnn[i]]; + + for ( int d = 0; d < dim; ++d ) + intg_pt_locations(d,index) = xi[d]; + + index++; + } + } + } + } + else // volume points + { + ThrowAssert(-1 == intg_pt_sign || 1 == intg_pt_sign); + + if ( intg_pt_sign != my_sign ) + { + return(index); + } + + const int nelem = 1; + const int dim = spatial_dim(); + const int vol_num_intg_pts = my_master_element.num_intg_pts(); + + // temp arrays + sierra::ArrayContainer coords(dim,my_num_nodes); + sierra::ArrayContainer det_J(vol_num_intg_pts); + + double error; + + // integration weights + const double * intg_wts_ptr = my_master_element.intg_weights(); + const sierra::Array intg_wts(intg_wts_ptr,vol_num_intg_pts); + + // load coords + for ( int i = 0; i < my_num_nodes; i++ ) + { + for ( int d = 0; d < dim; d++ ) coords(d,i) = my_coords[i][d]; + } + + // determinant at integration points + my_master_element.determinant( dim, nelem, coords.ptr(), det_J.ptr(), &error ); + + // basis fns at integration point locations + const double * bf_ptr = my_master_element.shape_fcn(); + const sierra::Array bf(bf_ptr,my_num_nodes,vol_num_intg_pts); + + for ( int ip = 0; ip < vol_num_intg_pts; ++ip) + { + determinant(index) = det_J(ip); + intg_weights(index) = intg_wts(ip); + + Vector3d xi(Vector3d::ZERO); + for ( int i = 0; i < my_num_nodes; i++ ) + xi += bf(i,ip) * my_coords[i]; + + for ( int d = 0; d < dim; d++ ) + intg_pt_locations(d,index) = xi[d]; + + index++; + } + } + } + return(index); +} + +double +ContourSubElement::parametric_quality() const +{ /* %TRACE% */ /* %TRACE% */ + const int nelem = 1; + const int nint = my_master_element.num_intg_pts(); + const int dim = spatial_dim(); + std::vector coords(my_num_nodes * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + double sub_quality = 0.; + + // load coords + int count = 0; + for ( int i = 0; i < my_num_nodes; i++ ) + { + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = my_coords[i][j]; + } + } + + // determinant at integration points + my_master_element.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double min_det_J = 0., sum_det_J = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + if ( ip == 0 || det_J[ip] < min_det_J ) + min_det_J = det_J[ip]; + sum_det_J += std::fabs( det_J[ip] ); + } + + if ( sum_det_J < std::pow(std::numeric_limits::epsilon(),1./dim) ) + sub_quality = 1.; // element too small to consider + else + sub_quality = min_det_J * nint / sum_det_J; + + return sub_quality; +} + +double +ContourSubElement::physical_quality() const +{ /* %TRACE% */ /* %TRACE% */ + const int nelem = 1; + const int nint = my_master_element.num_intg_pts(); + const int dim = spatial_dim(); + std::vector coords(my_num_nodes * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + double sub_quality = 0.; + + // load coords + int count = 0; + for ( int i = 0; i < my_num_nodes; i++ ) + { + const Vector3d phys_coords = my_owner->coordinates(my_coords[i]); + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = phys_coords[j]; + } + } + + // determinant at integration points + my_master_element.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double min_det_J = 0., sum_det_J = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + if ( ip == 0 || det_J[ip] < min_det_J ) + min_det_J = det_J[ip]; + sum_det_J += std::fabs( det_J[ip] ); + } + + if ( sum_det_J < std::pow(std::numeric_limits::epsilon(),1./dim) * std::pow(my_owner->length_scale(),1.*dim) ) + sub_quality = 1.; // element too small to consider + else + sub_quality = min_det_J * nint / sum_det_J; + + return sub_quality; +} + +double +ContourSubElement::side_quality(const int side) const +{ /* %TRACE% */ /* %TRACE% */ + const int nelem = 1; + const int nint = my_side_master_element.num_intg_pts(); + const stk::topology Top = topology(); + const stk::topology sideTop = Top.side_topology(side); + const int side_num_nodes = sideTop.num_nodes(); + const unsigned * const lnn = get_side_node_ordinals(Top, side); + const int dim = spatial_dim(); + std::vector coords(side_num_nodes * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + double quality = 0.; + + // load coords on side + int count = 0; + for ( int i = 0; i < side_num_nodes; i++ ) + { + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = my_coords[lnn[i]][j]; + } + } + + // determinant at integration points + my_side_master_element.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double min_det_J = 0., sum_det_J = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + if ( ip == 0 || det_J[ip] < min_det_J ) + min_det_J = det_J[ip]; + sum_det_J += std::fabs( det_J[ip] ); + } + + if ( sum_det_J < std::pow(std::numeric_limits::epsilon(),1./dim) ) + quality = 1.; // element too small to consider + else + quality = min_det_J * nint / sum_det_J; + + return quality; +} + +double +ContourSubElement::find_quadratic_crossing( double d0, + double d1, + double d2 ) +{ /* %TRACE% */ /* %TRACE% */ + const double epsilon = std::numeric_limits::epsilon()*std::sqrt(d0*d0 + d1*d1 + d2*d2); + if ( std::fabs(d0) < epsilon ) return 0.0; + if ( std::fabs(d1) < epsilon ) return 1.0; + if ( std::fabs(d2) < epsilon ) return 0.5; + + ThrowAssert(d0*d1 < 0.0 && (d0*d2 < 0.0 || d1*d2 < 0.0)); // Insist on one and only one crossing + + const double a = 2.0*(d0 - 2.0*d2 + d1); + const double b = -3.0*d0 - d1 + 4.0*d2; + const double c = d0; + const int sign_b = ( b < 0.0 ) ? -1 : 1; + const double q = -0.5*(b + sign_b*std::sqrt(b*b-4.0*a*c)); + + const int sign_a = ( a < 0.0 ) ? -1 : 1; + + if (q*sign_a > 0.0 && q*sign_a < a*sign_a) + { + ThrowAssert(!(c*(( q < 0.0 ) ? -1 : 1) > 0.0 && c*(( q < 0.0 ) ? -1 : 1) < q*(( q < 0.0 ) ? -1 : 1))); // Insist on only one crossing + return (q/a); + } + else + { + ThrowAssert(c*(( q < 0.0 ) ? -1 : 1) > 0.0 && c*(( q < 0.0 ) ? -1 : 1) < q*(( q < 0.0 ) ? -1 : 1)); + return (c/q); + } +} + +ContourSubElement_Quad_4::ContourSubElement_Quad_4( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ) + : ContourSubElement( stk::topology::QUADRILATERAL_4_2D, + coords, + side_ids, + in_owner, + 0, /* in_subelement_depth*/ + 0 /* subelement_sign=0 for now, correct this below if this element is entirely on one side */ ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + non_conformal_decomposition(); +} + +int +ContourSubElement_Quad_4::non_conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + + // create 4, 3-noded, adaptive triangles + my_subelements.reserve(4); + ContourSubElement *sub = NULL; + PointVec sub_coords(3,Vector3d::ZERO); + std::vector sub_ids(3); + + Vector3d center = 0.25*(my_coords[0]+my_coords[1]+my_coords[2]+my_coords[3]); + + // triangle #1 + sub_coords[0] = my_coords[0]; + sub_coords[1] = my_coords[1]; + sub_coords[2] = center; + sub_ids[0] = my_side_ids[0]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #2 + sub_coords[0] = my_coords[1]; + sub_coords[1] = my_coords[2]; + sub_coords[2] = center; + sub_ids[0] = my_side_ids[1]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #3 + sub_coords[0] = my_coords[2]; + sub_coords[1] = my_coords[3]; + sub_ids[0] = my_side_ids[2]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #4 + sub_coords[0] = my_coords[3]; + sub_coords[1] = my_coords[0]; + sub_coords[2] = center; + sub_ids[0] = my_side_ids[3]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + return success; +} + +ContourSubElement_Quad_9::ContourSubElement_Quad_9( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement *in_owner ) + : ContourSubElement( stk::topology::QUADRILATERAL_9_2D, + coords, + side_ids, + in_owner, + 0, /* in_subelement_depth*/ + 0 /* subelement_sign=0 for now, correct this below if this element is entirely on one side */ ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + non_conformal_decomposition(); +} + +int +ContourSubElement_Quad_9::non_conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + + // create 4, 3-noded, adaptive triangles + my_subelements.reserve(4); + ContourSubElement *sub = NULL; + PointVec sub_coords(3,Vector3d::ZERO); + std::vector sub_ids(3); + + // triangle #1 + sub_coords[0] = my_coords[0]; + sub_coords[1] = my_coords[1]; + sub_coords[2] = my_coords[8]; + sub_ids[0] = my_side_ids[0]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #2 + sub_coords[0] = my_coords[1]; + sub_coords[1] = my_coords[2]; + sub_coords[2] = my_coords[8]; + sub_ids[0] = my_side_ids[1]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #3 + sub_coords[0] = my_coords[2]; + sub_coords[1] = my_coords[3]; + sub_coords[2] = my_coords[8]; + sub_ids[0] = my_side_ids[2]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // triangle #4 + sub_coords[0] = my_coords[3]; + sub_coords[1] = my_coords[0]; + sub_coords[2] = my_coords[8]; + sub_ids[0] = my_side_ids[3]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + return success; +} + +ContourSubElement_Tri_3::ContourSubElement_Tri_3( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth, + const int subelement_sign ) + : ContourSubElement( stk::topology::TRIANGLE_3_2D, + coords, + side_ids, + in_owner, + in_subelement_depth, + subelement_sign ) +{ /* %TRACE% */ /* %TRACE% */ + // if this is a conformal element, return quickly + if ( subelement_sign != 0 ) + { + return; + } + + // snap to mesh + for (int n = 0; n < 3; ++n) + { + if (std::fabs(my_dist[n]) < my_owner->edge_linear_tolerance() * my_owner->length_scale() ) + { + my_dist[n] = 0.0; + } + } + + // see if there is a crossing + bool have_crossing = false; + for ( int i = 1; i < my_num_nodes; i++ ) + { + if ( LevelSet::sign_change(my_dist[0], my_dist[i]) ) have_crossing = true; + } + + if ( have_crossing ) + { + // attempt conformal decomposition + int success = conformal_decomposition(); + ThrowErrorMsgIf(!success, " Conformal decomposition failed.\n"); + } + else + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + } +} + +int +ContourSubElement_Tri_3::conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + + // create 4 conforming triangular subelements + + // create 4, 3-noded tris + my_subelements.clear(); + my_subelements.reserve(4); + ContourSubElement *sub = NULL; + PointVec sub_coords(3,Vector3d::ZERO); + + // For any edge with a crossing, we will move the + // mid side node for that egdge to the crossing + // we will keep the modified locations of the nodes + // in a local vector of nodes (lcoords). + // We will also create local vectors for the distance and side_ids + // so that we can reorient the tri as discussed below. + PointVec lcoords = my_coords; + lcoords.resize(6,Vector3d::ZERO); + std::vector sub_ids(3); + std::vector is_on_surf(6); // initializes to 0 (false) + int sub_sign; + std::vector edge_node_ids(6); + + // find edge crossings + edge_node_ids[0] = 0; + edge_node_ids[1] = 1; + edge_node_ids[2] = 2; + edge_node_ids[3] = process_edge( 0, 1, 3, is_on_surf, lcoords, my_dist ); + edge_node_ids[4] = process_edge( 1, 2, 4, is_on_surf, lcoords, my_dist ); + edge_node_ids[5] = process_edge( 2, 0, 5, is_on_surf, lcoords, my_dist ); + + const int zero_sign = LevelSet::sign(0.0); + std::vector sub_degenerate(4); // initializes to zero (false) + + sub_degenerate[0] = is_degenerate(edge_node_ids,0,3,5); + sub_degenerate[1] = is_degenerate(edge_node_ids,3,1,4); + sub_degenerate[2] = is_degenerate(edge_node_ids,5,4,2); + sub_degenerate[3] = is_degenerate(edge_node_ids,3,4,5); + + // tri #1 + if (!sub_degenerate[0]) + { + sub_coords[0] = lcoords[0]; + sub_coords[1] = lcoords[3]; + sub_coords[2] = lcoords[5]; + sub_sign = LevelSet::sign(my_dist[0]); + sub_ids[0] = my_side_ids[0]; + sub_ids[1] = ((is_on_surf[3] && is_on_surf[5]) && (zero_sign != sub_sign || sub_degenerate[3])) ? -2 : -1; + sub_ids[2] = my_side_ids[2]; + sub = new ContourSubElement_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tri #2 + if (!sub_degenerate[1]) + { + sub_coords[0] = lcoords[3]; + sub_coords[1] = lcoords[1]; + sub_coords[2] = lcoords[4]; + sub_sign = LevelSet::sign(my_dist[1]); + sub_ids[0] = my_side_ids[0]; + sub_ids[1] = my_side_ids[1]; + sub_ids[2] = ((is_on_surf[3] && is_on_surf[4]) && (zero_sign != sub_sign || sub_degenerate[3])) ? -2 : -1; + sub = new ContourSubElement_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tri #3 + if (!sub_degenerate[2]) + { + sub_coords[0] = lcoords[5]; + sub_coords[1] = lcoords[4]; + sub_coords[2] = lcoords[2]; + sub_sign = LevelSet::sign(my_dist[2]); + sub_ids[0] = ((is_on_surf[5] && is_on_surf[4]) && (zero_sign != sub_sign || sub_degenerate[3])) ? -2 : -1; + sub_ids[1] = my_side_ids[1]; + sub_ids[2] = my_side_ids[2]; + sub = new ContourSubElement_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tri #4 + if (!sub_degenerate[3]) + { + sub_coords[0] = lcoords[3]; + sub_coords[1] = lcoords[4]; + sub_coords[2] = lcoords[5]; + sub_sign = LevelSet::sign( (is_on_surf[3] ? 0.0 : my_dist[0]+my_dist[1]) + + (is_on_surf[4] ? 0.0 : my_dist[1]+my_dist[2]) + + (is_on_surf[5] ? 0.0 : my_dist[2]+my_dist[0]) ); + sub_ids[0] = ((is_on_surf[3] && is_on_surf[4]) && (zero_sign != sub_sign || sub_degenerate[1])) ? -2 : -1; + sub_ids[1] = ((is_on_surf[4] && is_on_surf[5]) && (zero_sign != sub_sign || sub_degenerate[2])) ? -2 : -1; + sub_ids[2] = ((is_on_surf[5] && is_on_surf[3]) && (zero_sign != sub_sign || sub_degenerate[0])) ? -2 : -1; + sub = new ContourSubElement_Tri_3( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // check quality of subelements + // Here we assume that the linear tri is always decomposed into reasonable quality sub-tris + int success = true; + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + for ( unsigned i=0; iphysical_quality() < 0.0 ) + { + krinolog << "low quality subelement: " << i << "\n" + << *my_subelements[i] << "\n" + << "parent:" << "\n" + << *this << "\n"; + } + } + } + + return success; +} + +int +ContourSubElement_Tri_3::process_edge( const int i0, + const int i1, + const int i2, + std::vector & is_on_surf, + PointVec & lcoords, + const std::vector & ldist ) +{ /* %TRACE% */ /* %TRACE% */ + int edge_node_id = i2; + is_on_surf[i2] = LevelSet::sign_change( ldist[i0], ldist[i1] ); + if ( is_on_surf[i2] ) + { + // tolerance chosen very small since degeneracies should already be eliminated + const double tol = std::numeric_limits::epsilon(); + + const double d0 = std::fabs(ldist[i0]); + const double d1 = std::fabs(ldist[i1]); + + // make calculation completely symmetric + if (d0 < d1) + { + const double alpha = my_owner->dist_is_linear() ? d0/(d0+d1) : find_quadratic_crossing(ldist[i0],ldist[i1],my_owner->distance(0.5*(lcoords[i0]+lcoords[i1]))); + if (alpha < tol) + { + edge_node_id = i0; + lcoords[i2] = lcoords[edge_node_id]; + } + else + { + lcoords[i2] = (1.-alpha) * lcoords[i0] + alpha * lcoords[i1]; + } + } + else + { + const double alpha = my_owner->dist_is_linear() ? d1/(d1+d0) : find_quadratic_crossing(ldist[i1],ldist[i0],my_owner->distance(0.5*(lcoords[i1]+lcoords[i0]))); + if (alpha < tol) + { + edge_node_id = i1; + lcoords[i2] = lcoords[edge_node_id]; + } + else + { + lcoords[i2] = (1.-alpha) * lcoords[i1] + alpha * lcoords[i0]; + } + } + } + else + { + // eliminate side node by sliding to one end or the other + const double d0 = std::fabs(ldist[i0]); + const double d1 = std::fabs(ldist[i1]); + const double epsilon = std::sqrt(std::numeric_limits::epsilon()) * (d0 + d1); + + if ( d0 > d1 + epsilon ) + { + edge_node_id = i0; + } + else if ( d1 > d0 + epsilon ) + { + edge_node_id = i1; + } + else + { + // tie breaker + const Vector3d phys0 = my_owner->coordinates(lcoords[i0]); + const Vector3d phys1 = my_owner->coordinates(lcoords[i1]); + + if ( is_more(phys1,phys0) ) + { + edge_node_id = i0; + } + else + { + edge_node_id = i1; + } + } + lcoords[i2] = lcoords[edge_node_id]; + } + return edge_node_id; +} + +bool +ContourSubElement_Tri_3::is_degenerate( const std::vector & edge_node_ids, + const int i0, const int i1, const int i2 ) +{ /* %TRACE% */ /* %TRACE% */ + + // DRN: This is really ugly, hand-optimized code for looking for degenerate tris + // Basically, it checks if any of the edges are degenerate. Then it has to look for + // the entire tri being degerate because it consists of 3 colinear points. + // This is handled by checking against the 3 specific bad cases. + + if ( edge_node_ids[i0] == edge_node_ids[i1] || + edge_node_ids[i0] == edge_node_ids[i2] || + edge_node_ids[i1] == edge_node_ids[i2] ) + { + // this tri is degenerate with two coincident nodes + return true; + } + + if ( edge_node_ids[i0]==i0 && + edge_node_ids[i1]==i1 && + edge_node_ids[i2]==i2 ) + { + // this tri is not degenerate since is has no degenerate nodes + return false; + } + + // look for a colinear triangle + std::vector is_used(6); // initializes to zero (false); + is_used[edge_node_ids[i0]] = true; + is_used[edge_node_ids[i1]] = true; + is_used[edge_node_ids[i2]] = true; + + if ((is_used[0] && ((is_used[1] && is_used[3]) || (is_used[2] && is_used[5]))) || + (is_used[1] && is_used[2] && is_used[4])) + { + // this tri is colinear + return true; + } + + return false; +} + +int +ContourSubElement_Tri_3::side_facets( Faceted_Surface & facets, + int side ) const +{ /* %TRACE% */ /* %TRACE% */ + ThrowAssert( my_side_ids[side] == -2 ); + + // just one linear facet per side + const int num_facets = 1; + + const unsigned * const lnn = get_side_node_ordinals(topology(), side); + + if ( LevelSet::sign_change(0.0, (double) my_sign) ) + { + std::unique_ptr facet = std::make_unique( my_owner->coordinates(my_coords[lnn[0]]), my_owner->coordinates(my_coords[lnn[1]]) ); + facets.add( std::move(facet) ); + } + else + { + std::unique_ptr facet = std::make_unique( my_owner->coordinates(my_coords[lnn[1]]), my_owner->coordinates(my_coords[lnn[0]]) ); + facets.add( std::move(facet) ); + } + + return( num_facets ); +} + +const int ContourSubElement_Adaptive_Tri_3::MAX_REFINMENT_LEVELS = 6; + +ContourSubElement_Adaptive_Tri_3::ContourSubElement_Adaptive_Tri_3( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth ) + : ContourSubElement( stk::topology::TRIANGLE_3_2D, + coords, + side_ids, + in_owner, + in_subelement_depth, + 0 ) +{ /* %TRACE% */ /* %TRACE% */ + my_edge_age.resize(3); // initializes to zero + non_conformal_decomposition(); +} + +ContourSubElement_Adaptive_Tri_3::ContourSubElement_Adaptive_Tri_3( + const PointVec & coords, + const std::vector & side_ids, + const std::vector & edge_age, + const ContourElement * in_owner, + const int in_subelement_depth ) + : ContourSubElement( stk::topology::TRIANGLE_3_2D, + coords, + side_ids, + in_owner, + in_subelement_depth, + 0 ) +{ /* %TRACE% */ /* %TRACE% */ + my_edge_age = edge_age; + non_conformal_decomposition(); +} + +int +ContourSubElement_Adaptive_Tri_3::non_conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return success; + } + + int longest_bad_edge = -1; + + // use temporary storage for vertex and side nodes + PointVec lcoords = my_coords; + lcoords.resize(6,Vector3d::ZERO); + lcoords[3] = 0.5 * (my_coords[0] + my_coords[1]); + lcoords[4] = 0.5 * (my_coords[1] + my_coords[2]); + lcoords[5] = 0.5 * (my_coords[2] + my_coords[0]); + + PointVec lphyscoords(6); + for (int n = 0; n < 6; ++n) + { + lphyscoords[n] = my_owner->coordinates( lcoords[n] ); + } + + std::vector ldist = my_dist; + ldist.resize(6); + for (int n = 3; n < 6; ++n) + { + ldist[n] = my_owner->distance( lcoords[n] ); + } + + const stk::topology Top = stk::topology::TRIANGLE_6_2D; + int num_edges = Top.num_edges(); + + std::vector bad_edges; + bad_edges.reserve(num_edges); + + std::vector edge_lengths(num_edges); + + for ( int edge = 0; edge < num_edges; edge++ ) + { + const unsigned * const lnn = get_edge_node_ordinals(Top, edge); + + ThrowAssert(Top.edge_topology(edge).num_nodes() == 3); + + const double edge_straight_length = (lphyscoords[lnn[0]] - lphyscoords[lnn[1]]).length(); + ThrowRequire(edge_straight_length > 0.0); + edge_lengths[edge] = edge_straight_length; + + const double edge_curve_error = (lphyscoords[lnn[2]] - 0.5*(lphyscoords[lnn[0]] + lphyscoords[lnn[1]])).length(); + + const double edge_dist_error = std::fabs(ldist[lnn[2]] - 0.5*(ldist[lnn[0]]+ldist[lnn[1]])); + + const double scale = std::min(std::sqrt(std::numeric_limits::max()),std::fabs(ldist[lnn[0]]) + std::fabs(ldist[lnn[1]]) + my_owner->length_scale()); + + const double edge_error = (edge_curve_error + edge_dist_error)*edge_straight_length/(scale*scale); + + if (edge_error > my_owner->edge_nonlinear_tolerance() && my_edge_age[edge] < MAX_REFINMENT_LEVELS) + { + bad_edges.push_back(edge); + } + } + + double max_length = 0.0; + for (auto edge : bad_edges) + { + const double edge_length = edge_lengths[edge]; + ThrowRequire(edge_length > 0.0); + + // we need an absolute mechanism for selecting the edge to bisect so that all elements that share + // common edges will make the same decisions + if (utility::is_more(edge_length,max_length)) + { + longest_bad_edge = edge; + max_length = edge_length; + } + else if (!utility::is_less(edge_length,max_length)) // tie breaker + { + const Vector3d & edge_midside_coords = lphyscoords[get_edge_node_ordinals(Top, edge)[2]]; + // note that it is safe to assume that longest_bad_edge is already assigned if edge_length == max_length + const Vector3d longest_edge_midside_coords = lphyscoords[get_edge_node_ordinals(Top, longest_bad_edge)[2]]; + + ThrowAssert((utility::is_not_equal(edge_midside_coords[0],longest_edge_midside_coords[0]) || + utility::is_not_equal(edge_midside_coords[1],longest_edge_midside_coords[1]))); + + if (utility::is_more(edge_midside_coords[0],longest_edge_midside_coords[0]) || + (!utility::is_less(edge_midside_coords[0],longest_edge_midside_coords[0]) && + (utility::is_more(edge_midside_coords[1],longest_edge_midside_coords[1])))) + { + longest_bad_edge = edge; + max_length = edge_length; + } + } + } + + if ( longest_bad_edge == -1 ) + { + // no bad edges + + // use a single nonconformal linear tet subelement + my_subelements.clear(); + my_subelements.reserve(1); + + ContourSubElement *sub = new ContourSubElement_Tri_3( my_coords, my_side_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + } + else + { + // + // create 2, adaptive, 3-noded triangles by cutting the longest_bad_edge + // + + my_subelements.clear(); + my_subelements.reserve(2); + ContourSubElement *sub = NULL; + PointVec sub_coords(3,Vector3d::ZERO); + std::vector sub_ids(3); + std::vector sub_edge_age(3); + + static const unsigned permute_0[] = { 0,1,2 }; + static const unsigned permute_1[] = { 1,2,0 }; + static const unsigned permute_2[] = { 2,0,1 }; + static const unsigned * permute_table[] = { permute_0, permute_1, permute_2 }; + + const unsigned * lnn = permute_table[longest_bad_edge]; + const unsigned * lsn = lnn; // side permutation mirrors node permutation + + const Vector3d edge_node = 0.5 * (my_coords[lnn[0]] + my_coords[lnn[1]]); + + // tri #1 + sub_coords[0] = my_coords[lnn[0]]; + sub_coords[1] = edge_node; + sub_coords[2] = my_coords[lnn[2]]; + sub_ids[0] = my_side_ids[lsn[0]]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = my_side_ids[lsn[2]]; + sub_edge_age[0] = my_edge_age[lsn[0]]+1; + sub_edge_age[1] = my_edge_age[lsn[0]]+1; + sub_edge_age[2] = my_edge_age[lsn[2]]; + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, sub_edge_age, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tri #2 + sub_coords[0] = edge_node; + sub_coords[1] = my_coords[lnn[1]]; + sub_coords[2] = my_coords[lnn[2]]; + sub_ids[0] = my_side_ids[lsn[0]]; + sub_ids[1] = my_side_ids[lsn[1]]; + sub_edge_age[0] = my_edge_age[lsn[0]]+1; + sub_edge_age[1] = my_edge_age[lsn[1]]; + sub_edge_age[2] = my_edge_age[lsn[0]]+1; + sub_ids[2] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, sub_ids, sub_edge_age, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + } + + return success; +} + +ContourSubElement_Tri_6::ContourSubElement_Tri_6( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth, + const int subelement_sign ) + : ContourSubElement( stk::topology::TRIANGLE_6_2D, + coords, + side_ids, + in_owner, + in_subelement_depth, + subelement_sign ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + // use a single non-conformal, adaptive 4-noded tet + my_subelements.clear(); + my_subelements.reserve(1); + ContourSubElement *sub = NULL; + PointVec sub_coords(3,Vector3d::ZERO); + + sub_coords[0] = my_coords[0]; + sub_coords[1] = my_coords[1]; + sub_coords[2] = my_coords[2]; + + sub = new ContourSubElement_Adaptive_Tri_3( sub_coords, my_side_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); +} + +ContourSubElement_Hex_8::ContourSubElement_Hex_8( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ) + : ContourSubElement( stk::topology::HEXAHEDRON_8, + coords, + side_ids, + in_owner, + 0, /* in_subelement_depth*/ + 0 /* subelement_sign=0 for now, correct this below if this element is entirely on one side */ ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + // create 24, 4-noded, adaptive tetrahedra + my_subelements.reserve(24); + + // Conceptually, hex is broken into 6 prisms, with the + // bases of the prisms corresponding to a face of the hex. + int success = true; // optimism + for ( int face = 0; face < 6 && success; ++face ) + { + success &= subpyramid_non_conformal_decomposition( face ); + } +} + +int +ContourSubElement_Hex_8::subpyramid_non_conformal_decomposition( const int face ) +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + std::vector sub_ids(4); + + static const unsigned face_0[] = { 0,1,5,4 }; + static const unsigned face_1[] = { 1,2,6,5 }; + static const unsigned face_2[] = { 2,3,7,6 }; + static const unsigned face_3[] = { 0,4,7,3 }; + static const unsigned face_4[] = { 0,3,2,1 }; + static const unsigned face_5[] = { 4,5,6,7 }; + + static const unsigned * face_table[] = { face_0 , face_1 , face_2 , face_3 , face_4 , face_5 }; + + const unsigned * lnn = face_table[face]; + + // + // create 4, 4-noded adaptive tetrahedra + // + // The advantage of 4 tets per face over 2 tets per face is that all corners + // will be bisected. This eliminates some of the pathologies that occur when + // 3 nodes have the same value while the 4th node on the face has a different + // sign. Note that this problem can be mitigated, however, if the non-conformal + // refinement of the sub-tets will do longest edge bisection rather than the + // self-similar 8 subtet refinement. + + Vector3d vol_center = 0.125*(my_coords[0]+my_coords[1]+my_coords[2]+my_coords[3]+ + my_coords[4]+my_coords[5]+my_coords[6]+my_coords[7]); + Vector3d face_center = 0.25*(my_coords[lnn[0]]+my_coords[lnn[1]]+my_coords[lnn[2]]+my_coords[lnn[3]]); + + // tet #1 + sub_coords[0] = my_coords[lnn[0]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[1]]; + sub_coords[3] = vol_center; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #2 + sub_coords[0] = my_coords[lnn[1]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[2]]; + sub_coords[3] = vol_center; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #3 + sub_coords[0] = my_coords[lnn[2]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[3]]; + sub_coords[3] = vol_center; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #4 + sub_coords[0] = my_coords[lnn[3]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[0]]; + sub_coords[3] = vol_center; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + return success; +} + +ContourSubElement_Hex_27::ContourSubElement_Hex_27( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ) + : ContourSubElement( stk::topology::HEXAHEDRON_27, + coords, + side_ids, + in_owner, + 0, /* in_subelement_depth*/ + 0 /* subelement_sign=0 for now, correct this below if this element is entirely on one side */ ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + // create 24, 4-noded, adaptive tetrahedra + my_subelements.reserve(24); + + // Conceptually, hex is broken into 6 prisms, with the + // bases of the prisms corresponding to a face of the hex. + int success = true; // optimism + for ( int face = 0; face < 6 && success; ++face ) + { + success &= subpyramid_non_conformal_decomposition( face ); + } +} + +int +ContourSubElement_Hex_27::subpyramid_non_conformal_decomposition( const int face ) +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + std::vector sub_ids(4); + + static const unsigned face_0[] = { 0,1,5,4, 25 }; + static const unsigned face_1[] = { 1,2,6,5, 24 }; + static const unsigned face_2[] = { 2,3,7,6, 26 }; + static const unsigned face_3[] = { 0,4,7,3, 23 }; + static const unsigned face_4[] = { 0,3,2,1, 21 }; + static const unsigned face_5[] = { 4,5,6,7, 22 }; + + static const unsigned * face_table[] = { face_0 , face_1 , face_2 , face_3 , face_4 , face_5 }; + + const unsigned * lnn = face_table[face]; + + // + // create 4, 4-noded adaptive tetrahedra + // + // The advantage of 4 tets per face over 2 tets per face is that all corners + // will be bisected. This eliminates some of the pathologies that occur when + // 3 nodes have the same value while the 4th node on the face has a different + // sign. Note that this problem can be mitigated, however, if the non-conformal + // refinement of the sub-tets will do longest edge bisection rather than the + // self-similar 8 subtet refinement. + + // tet #1 + sub_coords[0] = my_coords[lnn[0]]; + sub_coords[1] = my_coords[lnn[4]]; + sub_coords[2] = my_coords[lnn[1]]; + sub_coords[3] = my_coords[20]; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #2 + sub_coords[0] = my_coords[lnn[1]]; + sub_coords[1] = my_coords[lnn[4]]; + sub_coords[2] = my_coords[lnn[2]]; + sub_coords[3] = my_coords[20]; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #3 + sub_coords[0] = my_coords[lnn[2]]; + sub_coords[1] = my_coords[lnn[4]]; + sub_coords[2] = my_coords[lnn[3]]; + sub_coords[3] = my_coords[20]; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #4 + sub_coords[0] = my_coords[lnn[3]]; + sub_coords[1] = my_coords[lnn[4]]; + sub_coords[2] = my_coords[lnn[0]]; + sub_coords[3] = my_coords[20]; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + return success; +} + +ContourSubElement_Wedge_6::ContourSubElement_Wedge_6( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ) + : ContourSubElement( stk::topology::WEDGE_6, + coords, + side_ids, + in_owner, + 0, /* in_subelement_depth*/ + 0 /* subelement_sign=0 for now, correct this below if this element is entirely on one side */ ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + // create 12, 4-noded, adaptive tetrahedra + my_subelements.reserve(12); + + int success = true; // optimism + for ( int face = 0; face < 3 && success; ++face ) + { + success &= subpyramid_non_conformal_decomposition( face ); + } +} + +int +ContourSubElement_Wedge_6::subpyramid_non_conformal_decomposition( const int face ) +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + std::vector sub_ids(4); + + static const unsigned face_0[] = {0, 1, 4, 3}; + static const unsigned face_1[] = {1, 2, 5, 4}; + static const unsigned face_2[] = {0, 3, 5, 2}; + static const unsigned * face_table[] = { face_0 , face_1 , face_2 }; + + const unsigned * lnn = face_table[face]; + + // + // create 4, 4-noded adaptive tetrahedra + // + // The advantage of 4 tets per face over 2 tets per face is that all corners + // will be bisected. This eliminates some of the pathologies that occur when + // 3 nodes have the same value while the 4th node on the face has a different + // sign. Note that this problem can be mitigated, however, if the non-conformal + // refinement of the sub-tets will do longest edge bisection rather than the + // self-similar 8 subtet refinement. + + // Not guaranteed to be within a highly deformed wedge + const Vector3d centroid = (my_coords[0]+my_coords[1]+my_coords[2]+my_coords[3]+my_coords[4]+my_coords[5])/6.; + const Vector3d face_center = 0.25*(my_coords[lnn[0]]+my_coords[lnn[1]]+my_coords[lnn[2]]+my_coords[lnn[3]]); + + // tet #1 + sub_coords[0] = my_coords[lnn[0]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[1]]; + sub_coords[3] = centroid; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #2 + sub_coords[0] = my_coords[lnn[1]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[2]]; + sub_coords[3] = centroid; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #3 + sub_coords[0] = my_coords[lnn[2]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[3]]; + sub_coords[3] = centroid; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #4 + sub_coords[0] = my_coords[lnn[3]]; + sub_coords[1] = face_center; + sub_coords[2] = my_coords[lnn[0]]; + sub_coords[3] = centroid; + sub_ids[0] = my_side_ids[face]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = -1; /* not on any parent side */ + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + return success; +} + +ContourSubElement_Tet_4::ContourSubElement_Tet_4( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth, + const int subelement_sign ) + : ContourSubElement( stk::topology::TETRAHEDRON_4, + coords, + side_ids, + in_owner, + in_subelement_depth, + subelement_sign ) +{ /* %TRACE% */ /* %TRACE% */ + // if this is a conformal element, return quickly + if ( subelement_sign != 0 ) + { + return; + } + + // snap to mesh + for (int n = 0; n < 4; ++n) + { + if (std::fabs(my_dist[n]) < my_owner->edge_linear_tolerance() * my_owner->length_scale()) + { + my_dist[n] = 0.0; + } + } + + // see if there is a crossing + bool have_crossing = false; + for ( int i = 1; i < my_num_nodes; i++ ) + { + if ( LevelSet::sign_change(my_dist[0], my_dist[i]) ) have_crossing = true; + } + + if ( have_crossing ) + { + // attempt conformal decomposition + int success = conformal_decomposition(); + ThrowErrorMsgIf(!success, " Conformal decomposition failed.\n"); + } + else + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + } +} + +int +ContourSubElement_Tet_4::conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + + // attempt to create 8 conforming tetrahedral subelements + // This attempt may unsuccessful if the resulting subelements + // are of poor quality + int success = true; // optimism + + // create 8, 4-noded tets + my_subelements.clear(); + my_subelements.reserve(8); + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + + // For any edge with a crossing, we will move the + // mid side node for that egdge to the crossing + // we will keep the modified locations of the nodes + // in a local vector of nodes (lcoords). + // We will also create local vectors for the distance and side_ids + // so that we can reorient the tet as discussed below. + PointVec lcoords = my_coords; + lcoords.resize(10,Vector3d::ZERO); + std::vector lsides = my_side_ids; + std::vector ldist = my_dist; + std::vector sub_ids(4); + std::vector is_on_surf(10); // initializes to 0 (false) + int sub_sign; + + // Find orientation of tet + // Specifically, orient such that we don't have nodes 0 and 2 on one side and + // nodes 1 and 3 on the other + if ( LevelSet::sign_change(my_dist[0],my_dist[1]) && + LevelSet::sign_change(my_dist[1],my_dist[2]) && + LevelSet::sign_change(my_dist[2],my_dist[3]) ) + { + lcoords[0] = my_coords[0]; + lcoords[1] = my_coords[3]; + lcoords[2] = my_coords[1]; + lcoords[3] = my_coords[2]; + ldist[0] = my_dist[0]; + ldist[1] = my_dist[3]; + ldist[2] = my_dist[1]; + ldist[3] = my_dist[2]; + lsides[0] = my_side_ids[2]; + lsides[1] = my_side_ids[1]; + lsides[2] = my_side_ids[3]; + lsides[3] = my_side_ids[0]; + } + + std::vector edge_node_ids(10); + edge_node_ids[0] = 0; + edge_node_ids[1] = 1; + edge_node_ids[2] = 2; + edge_node_ids[3] = 3; + edge_node_ids[4] = process_edge( 0, 1, 4, is_on_surf, lcoords, ldist ); + edge_node_ids[5] = process_edge( 1, 2, 5, is_on_surf, lcoords, ldist ); + edge_node_ids[6] = process_edge( 2, 0, 6, is_on_surf, lcoords, ldist ); + edge_node_ids[7] = process_edge( 0, 3, 7, is_on_surf, lcoords, ldist ); + edge_node_ids[8] = process_edge( 1, 3, 8, is_on_surf, lcoords, ldist ); + edge_node_ids[9] = process_edge( 2, 3, 9, is_on_surf, lcoords, ldist ); + + const int zero_sign = LevelSet::sign(0.0); + std::vector sub_degenerate(8); // initializes to zero (false) + + sub_degenerate[0] = is_degenerate(edge_node_ids,0,4,6,7); + sub_degenerate[1] = is_degenerate(edge_node_ids,4,1,5,8); + sub_degenerate[2] = is_degenerate(edge_node_ids,6,5,2,9); + sub_degenerate[3] = is_degenerate(edge_node_ids,7,8,9,3); + sub_degenerate[4] = is_degenerate(edge_node_ids,8,7,6,4); + sub_degenerate[5] = is_degenerate(edge_node_ids,6,9,8,5); + sub_degenerate[6] = is_degenerate(edge_node_ids,9,8,7,6); + sub_degenerate[7] = is_degenerate(edge_node_ids,5,6,4,8); + + // tet #1 + if (!sub_degenerate[0]) + { + sub_coords[0] = lcoords[0]; + sub_coords[1] = lcoords[4]; + sub_coords[2] = lcoords[6]; + sub_coords[3] = lcoords[7]; + sub_sign = LevelSet::sign(ldist[0]); + sub_ids[0] = lsides[0]; + sub_ids[1] = ((is_on_surf[4] && is_on_surf[6] && is_on_surf[7]) && (zero_sign != sub_sign || sub_degenerate[4])) ? -2 : -1; + sub_ids[2] = lsides[2]; + sub_ids[3] = lsides[3]; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #2 + if (!sub_degenerate[1]) + { + sub_coords[0] = lcoords[4]; + sub_coords[1] = lcoords[1]; + sub_coords[2] = lcoords[5]; + sub_coords[3] = lcoords[8]; + sub_sign = LevelSet::sign(ldist[1]); + sub_ids[0] = lsides[0]; + sub_ids[1] = lsides[1]; + sub_ids[2] = ((is_on_surf[4] && is_on_surf[5] && is_on_surf[8]) && (zero_sign != sub_sign || sub_degenerate[7])) ? -2 : -1; + sub_ids[3] = lsides[3]; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #3 + if (!sub_degenerate[2]) + { + sub_coords[0] = lcoords[6]; + sub_coords[1] = lcoords[5]; + sub_coords[2] = lcoords[2]; + sub_coords[3] = lcoords[9]; + sub_sign = LevelSet::sign(ldist[2]); + sub_ids[0] = ((is_on_surf[5] && is_on_surf[6] && is_on_surf[9]) && (zero_sign != sub_sign || sub_degenerate[5])) ? -2 : -1; + sub_ids[1] = lsides[1]; + sub_ids[2] = lsides[2]; + sub_ids[3] = lsides[3]; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #4 + if (!sub_degenerate[3]) + { + sub_coords[0] = lcoords[7]; + sub_coords[1] = lcoords[8]; + sub_coords[2] = lcoords[9]; + sub_coords[3] = lcoords[3]; + sub_sign = LevelSet::sign(ldist[3]); + sub_ids[0] = lsides[0]; + sub_ids[1] = lsides[1]; + sub_ids[2] = lsides[2]; + sub_ids[3] = ((is_on_surf[7] && is_on_surf[8] && is_on_surf[9]) && (zero_sign != sub_sign || sub_degenerate[6])) ? -2 : -1; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #5 + if (!sub_degenerate[4]) + { + sub_coords[0] = lcoords[8]; + sub_coords[1] = lcoords[7]; + sub_coords[2] = lcoords[6]; + sub_coords[3] = lcoords[4]; + sub_sign = LevelSet::sign( (is_on_surf[8] ? 0.0 : ldist[1]+ldist[3]) + + (is_on_surf[7] ? 0.0 : ldist[0]+ldist[3]) + + (is_on_surf[6] ? 0.0 : ldist[0]+ldist[2]) + + (is_on_surf[4] ? 0.0 : ldist[0]+ldist[1]) ); + sub_ids[0] = lsides[0]; // 8-7-4 + sub_ids[1] = ((is_on_surf[7] && is_on_surf[6] && is_on_surf[4]) && (zero_sign != sub_sign || sub_degenerate[0])) ? -2 : -1; + sub_ids[2] = ((is_on_surf[8] && is_on_surf[6] && is_on_surf[4]) && (zero_sign != sub_sign || sub_degenerate[7])) ? -2 : -1; + sub_ids[3] = ((is_on_surf[8] && is_on_surf[7] && is_on_surf[6]) && (zero_sign != sub_sign || sub_degenerate[6])) ? -2 : -1; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #6 + if (!sub_degenerate[5]) + { + sub_coords[0] = lcoords[6]; + sub_coords[1] = lcoords[9]; + sub_coords[2] = lcoords[8]; + sub_coords[3] = lcoords[5]; + sub_sign = LevelSet::sign( (is_on_surf[6] ? 0.0 : ldist[0]+ldist[2]) + + (is_on_surf[9] ? 0.0 : ldist[2]+ldist[3]) + + (is_on_surf[8] ? 0.0 : ldist[1]+ldist[3]) + + (is_on_surf[5] ? 0.0 : ldist[1]+ldist[2]) ); + sub_ids[0] = ((is_on_surf[6] && is_on_surf[9] && is_on_surf[5]) && (zero_sign != sub_sign || sub_degenerate[2])) ? -2 : -1; + sub_ids[1] = lsides[1]; // 8-9-5 + sub_ids[2] = ((is_on_surf[6] && is_on_surf[8] && is_on_surf[5]) && (zero_sign != sub_sign || sub_degenerate[7])) ? -2 : -1; + sub_ids[3] = ((is_on_surf[6] && is_on_surf[9] && is_on_surf[8]) && (zero_sign != sub_sign || sub_degenerate[6])) ? -2 : -1; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #7 + if (!sub_degenerate[6]) + { + sub_coords[0] = lcoords[9]; + sub_coords[1] = lcoords[8]; + sub_coords[2] = lcoords[7]; + sub_coords[3] = lcoords[6]; + sub_sign = LevelSet::sign( (is_on_surf[9] ? 0.0 : ldist[2]+ldist[3]) + + (is_on_surf[8] ? 0.0 : ldist[1]+ldist[3]) + + (is_on_surf[7] ? 0.0 : ldist[0]+ldist[3]) + + (is_on_surf[6] ? 0.0 : ldist[0]+ldist[2]) ); + sub_ids[0] = ((is_on_surf[9] && is_on_surf[8] && is_on_surf[6]) && (zero_sign != sub_sign || sub_degenerate[5])) ? -2 : -1; + sub_ids[1] = ((is_on_surf[8] && is_on_surf[7] && is_on_surf[6]) && (zero_sign != sub_sign || sub_degenerate[4])) ? -2 : -1; + sub_ids[2] = lsides[2]; // 9-7-6 + sub_ids[3] = ((is_on_surf[9] && is_on_surf[8] && is_on_surf[7]) && (zero_sign != sub_sign || sub_degenerate[3])) ? -2 : -1; + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // tet #8 + if (!sub_degenerate[7]) + { + sub_coords[0] = lcoords[5]; + sub_coords[1] = lcoords[6]; + sub_coords[2] = lcoords[4]; + sub_coords[3] = lcoords[8]; + sub_sign = LevelSet::sign( (is_on_surf[5] ? 0.0 : ldist[1]+ldist[2]) + + (is_on_surf[6] ? 0.0 : ldist[0]+ldist[2]) + + (is_on_surf[4] ? 0.0 : ldist[0]+ldist[1]) + + (is_on_surf[8] ? 0.0 : ldist[1]+ldist[3]) ); + sub_ids[0] = ((is_on_surf[5] && is_on_surf[6] && is_on_surf[8]) && (zero_sign != sub_sign || sub_degenerate[5])) ? -2 : -1; + sub_ids[1] = ((is_on_surf[6] && is_on_surf[4] && is_on_surf[8]) && (zero_sign != sub_sign || sub_degenerate[4])) ? -2 : -1; + sub_ids[2] = ((is_on_surf[5] && is_on_surf[4] && is_on_surf[8]) && (zero_sign != sub_sign || sub_degenerate[1])) ? -2 : -1; + sub_ids[3] = lsides[3]; // 4-5-6 + sub = new ContourSubElement_Tet_4( sub_coords, sub_ids, my_owner, my_subelement_depth+1, sub_sign ); + my_subelements.push_back( sub ); + } + + // check quality of subelements + // Here we assume that the linear tet is always decomposed into reasonable quality sub-tets + success = true; + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + for ( unsigned i=0; iphysical_quality() < 0.0 ) + { + krinolog << "low quality subelement: " << i << "\n" + << *my_subelements[i] << "\n" + << "parent:" << "\n" + << *this << "\n"; + } + } + } + + return success; +} + +int +ContourSubElement_Tet_4::process_edge( const int i0, + const int i1, + const int i2, + std::vector & is_on_surf, + PointVec & lcoords, + const std::vector & ldist ) +{ /* %TRACE% */ /* %TRACE% */ + int edge_node_id = i2; + is_on_surf[i2] = LevelSet::sign_change( ldist[i0], ldist[i1] ); + if ( is_on_surf[i2] ) + { + // tolerance chosen very small since degeneracies should already be eliminated + const double tol = std::numeric_limits::epsilon(); + + const double d0 = std::fabs(ldist[i0]); + const double d1 = std::fabs(ldist[i1]); + + // make calculation completely symmetric + if (d0 < d1) + { + const double linear_alpha = d0/(d0+d1); + + if (linear_alpha < tol) + { + edge_node_id = i0; + lcoords[i2] = lcoords[edge_node_id]; + } + else + { + const double alpha = my_owner->dist_is_linear() ? linear_alpha : + find_quadratic_crossing(ldist[i0],ldist[i1],my_owner->distance(0.5*(lcoords[i0]+lcoords[i1]))); + lcoords[i2] = (1.-alpha) * lcoords[i0] + alpha * lcoords[i1]; + } + } + else + { + const double linear_alpha = d1/(d1+d0); + + if (linear_alpha < tol) + { + edge_node_id = i1; + lcoords[i2] = lcoords[edge_node_id]; + } + else + { + const double alpha = my_owner->dist_is_linear() ? linear_alpha : + find_quadratic_crossing(ldist[i1],ldist[i0],my_owner->distance(0.5*(lcoords[i1]+lcoords[i0]))); + lcoords[i2] = (1.-alpha) * lcoords[i1] + alpha * lcoords[i0]; + } + } + } + else + { + // eliminate side node by sliding to one end or the other + const double d0 = std::fabs(ldist[i0]); + const double d1 = std::fabs(ldist[i1]); + const double epsilon = std::sqrt(std::numeric_limits::epsilon()) * (d0 + d1); + + if ( d0 > d1 + epsilon ) + { + edge_node_id = i0; + } + else if ( d1 > d0 + epsilon ) + { + edge_node_id = i1; + } + else + { + // tie breaker + const Vector3d phys0 = my_owner->coordinates(lcoords[i0]); + const Vector3d phys1 = my_owner->coordinates(lcoords[i1]); + + if ( is_more(phys1,phys0) ) + { + edge_node_id = i0; + } + else + { + edge_node_id = i1; + } + } + lcoords[i2] = lcoords[edge_node_id]; + } + + return edge_node_id; +} + +bool +ContourSubElement_Tet_4::is_degenerate( const std::vector & edge_node_ids, + const int i0, const int i1, const int i2, const int i3 ) +{ /* %TRACE% */ /* %TRACE% */ + + // DRN: This is really ugly, hand-optimized code for looking for degenerate tets + // Basically, it checks if any of the edges are degenerate. Then it has to look for degenerate + // faces that consist of 3 colinear points. These are handled by checking against + // the 6 specific bad cases. + + if ( edge_node_ids[i0] == edge_node_ids[i1] || + edge_node_ids[i0] == edge_node_ids[i2] || + edge_node_ids[i0] == edge_node_ids[i3] || + edge_node_ids[i1] == edge_node_ids[i2] || + edge_node_ids[i1] == edge_node_ids[i3] || + edge_node_ids[i2] == edge_node_ids[i3] ) + { + // this tet is degenerate with two coincident nodes + return true; + } + + if ( edge_node_ids[i0]==i0 && + edge_node_ids[i1]==i1 && + edge_node_ids[i2]==i2 && + edge_node_ids[i3]==i3 ) + { + // this tet is not degenerate since is has no degenerate nodes + return false; + } + + // look for a colinear face + std::vector is_used(10); // initializes to zero (false); + is_used[edge_node_ids[i0]] = true; + is_used[edge_node_ids[i1]] = true; + is_used[edge_node_ids[i2]] = true; + is_used[edge_node_ids[i3]] = true; + + if ((is_used[0] && ((is_used[1] && is_used[4]) || (is_used[2] && is_used[6]) || (is_used[3] && is_used[7]))) || + (is_used[1] && ((is_used[2] && is_used[5]) || (is_used[3] && is_used[8]))) || + (is_used[2] && is_used[3] && is_used[9])) + { + // this tet has a colinear face + return true; + } + + // look for all nodes on the same face + if ((!is_used[0] && !is_used[4] && !is_used[6] && !is_used[7]) || // all on face 1 + (!is_used[4] && !is_used[1] && !is_used[5] && !is_used[8]) || // all on face 2 + (!is_used[6] && !is_used[5] && !is_used[2] && !is_used[9]) || // all on face 0 + (!is_used[7] && !is_used[8] && !is_used[9] && !is_used[3])) // all on face 3 + { + // this tet has all nodes on one face + return true; + } + + return false; +} + +int +ContourSubElement_Tet_4::side_facets( Faceted_Surface & facets, + int side ) const +{ /* %TRACE% */ /* %TRACE% */ + ThrowAssert( my_side_ids[side] == -2 ); + + // just one linear facet per linear triangle + const int num_facets = 1; + + const unsigned * const lnn = get_side_node_ordinals(topology(), side); + + if ( LevelSet::sign_change(0.0, (double) my_sign) ) + { + std::unique_ptr facet = std::make_unique( my_owner->coordinates(my_coords[lnn[0]]), my_owner->coordinates(my_coords[lnn[1]]), my_owner->coordinates(my_coords[lnn[2]]) ); + facets.add( std::move(facet) ); + } + else + { + std::unique_ptr facet = std::make_unique( my_owner->coordinates(my_coords[lnn[0]]), my_owner->coordinates(my_coords[lnn[2]]), my_owner->coordinates(my_coords[lnn[1]]) ); + facets.add( std::move(facet) ); + } + + return( num_facets ); +} + +ContourSubElement_Tet_10::ContourSubElement_Tet_10( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth, + const int subelement_sign ) + : ContourSubElement( stk::topology::TETRAHEDRON_10, + coords, + side_ids, + in_owner, + in_subelement_depth, + subelement_sign ) +{ /* %TRACE% */ /* %TRACE% */ + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return; + } + + // use a single non-conformal, adaptive 4-noded tet + my_subelements.clear(); + my_subelements.reserve(1); + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + + sub_coords[0] = my_coords[0]; + sub_coords[1] = my_coords[1]; + sub_coords[2] = my_coords[2]; + sub_coords[3] = my_coords[3]; + + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, my_side_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); +} + +const int ContourSubElement_Adaptive_Tet_4::MAX_REFINMENT_LEVELS = 6; + +ContourSubElement_Adaptive_Tet_4::ContourSubElement_Adaptive_Tet_4( + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth ) + : ContourSubElement( stk::topology::TETRAHEDRON_4, + coords, + side_ids, + in_owner, + in_subelement_depth, + 0 ) +{ /* %TRACE% */ /* %TRACE% */ + my_edge_age.resize(6); // initializes to zero + non_conformal_decomposition(); +} + +ContourSubElement_Adaptive_Tet_4::ContourSubElement_Adaptive_Tet_4( + const PointVec & coords, + const std::vector & side_ids, + const std::vector & edge_age, + const ContourElement * in_owner, + const int in_subelement_depth ) + : ContourSubElement( stk::topology::TETRAHEDRON_4, + coords, + side_ids, + in_owner, + in_subelement_depth, + 0 ) +{ /* %TRACE% */ /* %TRACE% */ + my_edge_age = edge_age; + non_conformal_decomposition(); +} + +int +ContourSubElement_Adaptive_Tet_4::non_conformal_decomposition() +{ /* %TRACE% */ /* %TRACE% */ + int success = true; // optimism + + // Determine if we will continue to look for crossing within this element. + // This test should be conservative, proceeding to look for crossings if there + // is even a remote chance of a crossing (To avoid cracks in the surface). + + // find extrema + double max_dist = -std::numeric_limits::max(); + double min_dist = std::numeric_limits::max(); + for ( int n = 0; n < my_num_nodes; n++ ) + { + if (my_dist[n] < min_dist) min_dist = my_dist[n]; + if (my_dist[n] > max_dist) max_dist = my_dist[n]; + } + + const double variation = max_dist - min_dist; + + const bool all_hi = (min_dist - variation) > 0.0; + const bool all_lo = (max_dist + variation) < 0.0; + + if (all_hi || all_lo) + { + // correct the sign since we lie entirely on one side of the interface + my_sign = LevelSet::sign(my_dist[0]); + return success; + } + + int longest_bad_edge = -1; + + // use temporary storage for vertex and side nodes + PointVec lcoords = my_coords; + lcoords.resize(10,Vector3d::ZERO); + lcoords[4] = 0.5 * (my_coords[0] + my_coords[1]); + lcoords[5] = 0.5 * (my_coords[1] + my_coords[2]); + lcoords[6] = 0.5 * (my_coords[2] + my_coords[0]); + lcoords[7] = 0.5 * (my_coords[0] + my_coords[3]); + lcoords[8] = 0.5 * (my_coords[1] + my_coords[3]); + lcoords[9] = 0.5 * (my_coords[2] + my_coords[3]); + + PointVec lphyscoords(10); + for (int n = 0; n < 10; ++n) + { + lphyscoords[n] = my_owner->coordinates( lcoords[n] ); + } + + std::vector ldist = my_dist; + ldist.resize(10); + for (int n = 4; n < 10; ++n) + { + ldist[n] = my_owner->distance( lcoords[n] ); + } + + const stk::topology Top = stk::topology::TETRAHEDRON_10; + int num_edges = Top.num_edges(); + + std::vector bad_edges; + bad_edges.reserve(num_edges); + + std::vector edge_lengths(num_edges); + + for ( int edge = 0; edge < num_edges; edge++ ) + { + const unsigned * const lnn = get_edge_node_ordinals(Top, edge); + + ThrowAssert(Top.edge_topology(edge).num_nodes() == 3); + + const double edge_straight_length = (lphyscoords[lnn[0]] - lphyscoords[lnn[1]]).length(); + ThrowRequire(edge_straight_length > 0.0); + edge_lengths[edge] = edge_straight_length; + + const double edge_curve_error = (lphyscoords[lnn[2]] - 0.5*(lphyscoords[lnn[0]] + lphyscoords[lnn[1]])).length(); + + const double edge_dist_error = std::fabs(ldist[lnn[2]] - 0.5*(ldist[lnn[0]]+ldist[lnn[1]])); + + const double scale = std::min(std::sqrt(std::numeric_limits::max()),std::fabs(ldist[lnn[0]]) + std::fabs(ldist[lnn[1]]) + my_owner->length_scale()); + + const double edge_error = (edge_curve_error + edge_dist_error)*edge_straight_length/(scale*scale); + + if (edge_error > my_owner->edge_nonlinear_tolerance() && my_edge_age[edge] < MAX_REFINMENT_LEVELS) + { + bad_edges.push_back(edge); + } + } + + double max_length = 0.0; + for (auto edge : bad_edges) + { + const double edge_length = edge_lengths[edge]; + ThrowRequire(edge_length > 0.0); + + // we need an absolute mechanism for selecting the edge to bisect so that all elements that share + // common edges will make the same decisions + if (utility::is_more(edge_length,max_length)) + { + longest_bad_edge = edge; + max_length = edge_length; + } + else if (!utility::is_less(edge_length,max_length)) // tie breaker + { + const Vector3d & edge_midside_coords = lphyscoords[get_edge_node_ordinals(Top, edge)[2]]; + // note that it is safe to assume that longest_bad_edge is already assigned if edge_length == max_length + const Vector3d longest_edge_midside_coords = lphyscoords[get_edge_node_ordinals(Top, longest_bad_edge)[2]]; + + ThrowAssert((utility::is_not_equal(edge_midside_coords[0],longest_edge_midside_coords[0]) || + utility::is_not_equal(edge_midside_coords[1],longest_edge_midside_coords[1]) || + utility::is_not_equal(edge_midside_coords[2],longest_edge_midside_coords[2]))); + + if (utility::is_more(edge_midside_coords[0],longest_edge_midside_coords[0]) || + (!utility::is_less(edge_midside_coords[0],longest_edge_midside_coords[0]) && + (utility::is_more(edge_midside_coords[1],longest_edge_midside_coords[1]) || + (!utility::is_less(edge_midside_coords[1],longest_edge_midside_coords[1]) && + (utility::is_more(edge_midside_coords[2],longest_edge_midside_coords[2])))))) + { + longest_bad_edge = edge; + max_length = edge_length; + } + } + } + + if ( longest_bad_edge == -1 ) + { + // no bad edges + + // use a single nonconformal linear tet subelement + my_subelements.clear(); + my_subelements.reserve(1); + + ContourSubElement *sub = new ContourSubElement_Tet_4( my_coords, my_side_ids, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + } + else + { + // + // create 2, adaptive, 4-noded tetrahedra by cutting the longest_bad_edge + // + + my_subelements.clear(); + my_subelements.reserve(2); + ContourSubElement *sub = NULL; + PointVec sub_coords(4,Vector3d::ZERO); + std::vector sub_ids(4); + std::vector sub_edge_age(6); + + static const unsigned node_permute_0[] = { 0,1,2,3 }; + static const unsigned node_permute_1[] = { 1,2,0,3 }; + static const unsigned node_permute_2[] = { 2,0,1,3 }; + static const unsigned node_permute_3[] = { 3,0,2,1 }; + static const unsigned node_permute_4[] = { 1,3,2,0 }; + static const unsigned node_permute_5[] = { 3,2,1,0 }; + static const unsigned side_permute_0[] = { 0,1,2,3 }; + static const unsigned side_permute_1[] = { 1,2,0,3 }; + static const unsigned side_permute_2[] = { 2,0,1,3 }; + static const unsigned side_permute_3[] = { 0,3,1,2 }; + static const unsigned side_permute_4[] = { 0,2,3,1 }; + static const unsigned side_permute_5[] = { 2,3,0,1 }; + static const unsigned edge_permute_0[] = { 0,1,2,3,4,5 }; + static const unsigned edge_permute_1[] = { 1,2,0,4,5,3 }; + static const unsigned edge_permute_2[] = { 2,0,1,5,3,4 }; + static const unsigned edge_permute_3[] = { 3,2,5,4,0,1 }; + static const unsigned edge_permute_4[] = { 4,5,1,0,3,2 }; + static const unsigned edge_permute_5[] = { 5,1,4,3,2,0 }; + static const unsigned * node_permute_table[] = { node_permute_0, node_permute_1, node_permute_2, node_permute_3, node_permute_4, node_permute_5 }; + static const unsigned * side_permute_table[] = { side_permute_0, side_permute_1, side_permute_2, side_permute_3, side_permute_4, side_permute_5 }; + static const unsigned * edge_permute_table[] = { edge_permute_0, edge_permute_1, edge_permute_2, edge_permute_3, edge_permute_4, edge_permute_5 }; + + const unsigned * lnn = node_permute_table[longest_bad_edge]; + const unsigned * lsn = side_permute_table[longest_bad_edge]; + const unsigned * len = edge_permute_table[longest_bad_edge]; + + const Vector3d edge_node = 0.5 * (my_coords[lnn[0]] + my_coords[lnn[1]]); + + // tet #1 + sub_coords[0] = my_coords[lnn[0]]; + sub_coords[1] = edge_node; + sub_coords[2] = my_coords[lnn[2]]; + sub_coords[3] = my_coords[lnn[3]]; + sub_ids[0] = my_side_ids[lsn[0]]; + sub_ids[1] = -1; /* not on any parent side */ + sub_ids[2] = my_side_ids[lsn[2]]; + sub_ids[3] = my_side_ids[lsn[3]]; + sub_edge_age[0] = my_edge_age[len[0]]+1; + sub_edge_age[1] = my_edge_age[len[0]]+1; + sub_edge_age[2] = my_edge_age[len[2]]; + sub_edge_age[3] = my_edge_age[len[3]]; + sub_edge_age[4] = my_edge_age[len[0]]+1; + sub_edge_age[5] = my_edge_age[len[5]]; + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, sub_edge_age, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + + // tet #2 + sub_coords[0] = edge_node; + sub_coords[1] = my_coords[lnn[1]]; + sub_coords[2] = my_coords[lnn[2]]; + sub_coords[3] = my_coords[lnn[3]]; + sub_ids[0] = my_side_ids[lsn[0]]; + sub_ids[1] = my_side_ids[lsn[1]]; + sub_ids[2] = -1; /* not on any parent side */ + sub_ids[3] = my_side_ids[lsn[3]]; + sub_edge_age[0] = my_edge_age[len[0]]+1; + sub_edge_age[1] = my_edge_age[len[1]]; + sub_edge_age[2] = my_edge_age[len[0]]+1; + sub_edge_age[3] = my_edge_age[len[0]]+1; + sub_edge_age[4] = my_edge_age[len[4]]; + sub_edge_age[5] = my_edge_age[len[5]]; + sub = new ContourSubElement_Adaptive_Tet_4( sub_coords, sub_ids, sub_edge_age, my_owner, my_subelement_depth+1 ); + my_subelements.push_back( sub ); + } + + return success; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_ContourSubElement.hpp b/packages/krino/krino/krino_lib/Akri_ContourSubElement.hpp new file mode 100644 index 000000000000..b00b27325508 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ContourSubElement.hpp @@ -0,0 +1,311 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_ContourSubElement_h +#define Akri_ContourSubElement_h + +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +namespace krino { + +template +bool compare_ptr_by_global_id (const T* i, const T* j) { return (i->global_id() < j->global_id()); } + +class ContourSubElement { +public: + + ContourSubElement( const stk::topology topo, + const PointVec & coords, + const std::vector & side_ids, + const ContourElement * owner, + const int in_subelement_depth, + const int subelement_sign ); + + virtual ~ContourSubElement(); + + static bool is_more(const Vector3d & v1, const Vector3d & v2); + + double relative_volume() const; + double side_relative_area( const int side ) const; + double parametric_quality() const; + double physical_quality() const; + double side_quality(const int side) const; + + int num_intg_pts( const int intg_pt_sign ); + + int gather_intg_pts( const int intg_pt_sign, + sierra::ArrayContainer & intg_pt_locations, + sierra::ArrayContainer & intg_weights, + sierra::ArrayContainer & determinants, + int index = 0 ); + + int build_facets( Faceted_Surface & facets ); + + // default implementation + virtual int side_facets( Faceted_Surface & facets, int side ) const; + + stk::topology topology() const { return my_master_element.get_topology(); } + + int spatial_dim() const { return my_owner->spatial_dim(); } + int num_subelements() const { return my_subelements.size(); } + + std::vector & get_side_ids() { return my_side_ids; } + const std::vector & get_side_ids() const { return my_side_ids; } + + const PointVec & get_coords() const { return my_coords; } + const ContourElement * owner() const { return my_owner; } + int subelement_depth() const { return my_subelement_depth; } + + void dump_structure() const; + void dump_details() const; + + bool have_interface_sides() const; + + virtual std::ostream & put( std::ostream& os ) const; + + friend std::ostream & operator << ( std::ostream &os , const ContourSubElement &s ) { + return s.put(os); + } + + static double find_quadratic_crossing( const double d0, + const double d1, + const double d2 ); + +protected: + + const MasterElement& my_master_element; + const MasterElement& my_side_master_element; + int my_num_nodes; + int my_num_sides; + PointVec my_coords; + std::vector my_side_ids; + std::vector my_dist; + std::vector< ContourSubElement * > my_subelements; + const ContourElement * my_owner; + int my_subelement_depth; // depth down the tree of subelements (0 for the base_subelement) + int my_sign; // -1 for elements on negative side, +1 for positive side, 0 for non-conformal elements spanning interface + +private: + //: Default constructor not allowed + ContourSubElement(); +}; + +class ContourSubElement_Quad_4 : public ContourSubElement { +public: + ContourSubElement_Quad_4( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ); + virtual ~ContourSubElement_Quad_4() {} + +private: + //: Default constructor not allowed + ContourSubElement_Quad_4(); + + int non_conformal_decomposition(); +}; + +class ContourSubElement_Quad_9 : public ContourSubElement { +public: + ContourSubElement_Quad_9( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ); + + virtual ~ContourSubElement_Quad_9() {} + +private: + //: Default constructor not allowed + ContourSubElement_Quad_9(); + + int non_conformal_decomposition(); +}; + +class ContourSubElement_Hex_8 : public ContourSubElement { +public: + ContourSubElement_Hex_8( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ); + virtual ~ContourSubElement_Hex_8() {} + +private: + //: Default constructor not allowed + ContourSubElement_Hex_8(); + + int subpyramid_non_conformal_decomposition( const int face ); +}; + +class ContourSubElement_Hex_27 : public ContourSubElement { +public: + ContourSubElement_Hex_27( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ); + virtual ~ContourSubElement_Hex_27() {} + +private: + //: Default constructor not allowed + ContourSubElement_Hex_27(); + + int subpyramid_non_conformal_decomposition( const int face ); +}; + +class ContourSubElement_Wedge_6 : public ContourSubElement { +public: + ContourSubElement_Wedge_6( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner ); + virtual ~ContourSubElement_Wedge_6() {} + +private: + int subpyramid_non_conformal_decomposition( const int face ); +}; + +class ContourSubElement_Tri_3 : public ContourSubElement { +public: + ContourSubElement_Tri_3( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0, + const int subelement_sign = 0 ); + virtual ~ContourSubElement_Tri_3() {} + + virtual int side_facets( Faceted_Surface & facets, int side ) const; + +private: + //: Default constructor not allowed + ContourSubElement_Tri_3(); + + int conformal_decomposition(); + + int process_edge( const int i0, + const int i1, + const int i2, + std::vector & is_on_surf, + PointVec & lnodes, + const std::vector & ldist ); + + bool is_degenerate( const std::vector & edge_node_ids, + const int i0, const int i1, const int i2 ); +}; + +class ContourSubElement_Adaptive_Tri_3 : public ContourSubElement { +public: + ContourSubElement_Adaptive_Tri_3( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0); + ContourSubElement_Adaptive_Tri_3( const PointVec & coords, + const std::vector & side_ids, + const std::vector & edge_age, + const ContourElement * in_owner, + const int in_subelement_depth = 0); + virtual ~ContourSubElement_Adaptive_Tri_3() {} + +private: + //: Default constructor not allowed + ContourSubElement_Adaptive_Tri_3(); + + static const int MAX_REFINMENT_LEVELS; + + int non_conformal_decomposition(); + + std::vector my_edge_age; +}; + +class ContourSubElement_Tri_6 : public ContourSubElement { +public: + ContourSubElement_Tri_6( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0, + const int subelement_sign = 0 ); + virtual ~ContourSubElement_Tri_6() {} + +private: + //: Default constructor not allowed + ContourSubElement_Tri_6(); +}; + +class ContourSubElement_Tet_4 : public ContourSubElement { +public: + ContourSubElement_Tet_4( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0, + const int subelement_sign = 0 ); + virtual ~ContourSubElement_Tet_4() {} + + virtual int side_facets( Faceted_Surface & facets, int side ) const; + +private: + //: Default constructor not allowed + ContourSubElement_Tet_4(); + + int conformal_decomposition(); + + int process_edge( const int i0, + const int i1, + const int i2, + std::vector & is_on_surf, + PointVec & lnodes, + const std::vector & ldist ); + + bool is_degenerate( const std::vector & edge_node_ids, + const int i0, const int i1, const int i2, const int i3 ); +}; + +class ContourSubElement_Adaptive_Tet_4 : public ContourSubElement { +public: + ContourSubElement_Adaptive_Tet_4( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0); + ContourSubElement_Adaptive_Tet_4( const PointVec & coords, + const std::vector & side_ids, + const std::vector & edge_age, + const ContourElement * in_owner, + const int in_subelement_depth = 0); + virtual ~ContourSubElement_Adaptive_Tet_4() {} + +private: + //: Default constructor not allowed + ContourSubElement_Adaptive_Tet_4(); + + static const int MAX_REFINMENT_LEVELS; + + int non_conformal_decomposition(); + + std::vector my_edge_age; +}; + +class ContourSubElement_Tet_10 : public ContourSubElement { +public: + ContourSubElement_Tet_10( const PointVec & coords, + const std::vector & side_ids, + const ContourElement * in_owner, + const int in_subelement_depth = 0, + const int subelement_sign = 0 ); + virtual ~ContourSubElement_Tet_10() {} + +private: + //: Default constructor not allowed + ContourSubElement_Tet_10(); +}; + +} // namespace krino + +#endif // Akri_ContourSubElement_h diff --git a/packages/krino/krino/krino_lib/Akri_Cutting_Surface.cpp b/packages/krino/krino/krino_lib/Akri_Cutting_Surface.cpp new file mode 100644 index 000000000000..2cef540c7dd0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Cutting_Surface.cpp @@ -0,0 +1,170 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +#include +#include + +namespace krino{ + +int +Plane_Cutting_Surface::sign_at_position(const Vector3d & p_coords) const +{ + return my_plane.signed_distance(p_coords) < 0. ? -1 : 1; +} + +bool +Plane_Cutting_Surface::on_surface(const Vector3d & p_coords, const double tol) const +{ + return std::abs(my_plane.signed_distance(p_coords)) < tol; +} + +double +Plane_Cutting_Surface::interface_crossing_position(const Segment3d & edge) const +{ + const double signed_dist_node0 = my_plane.signed_distance(edge.GetNode(0)); + const double signed_dist_node1 = my_plane.signed_distance(edge.GetNode(1)); + + if((signed_dist_node0 < 0) == (signed_dist_node1 < 0)) + { + std::stringstream str; + str << "Failed to find intersection of plane " << my_plane << " with segment " << edge; + throw std::runtime_error(str.str()); + } + + const double pos = signed_dist_node0 / (signed_dist_node0-signed_dist_node1); + + return pos; +} + +std::string Plane_Cutting_Surface::print() const +{ + std::ostringstream os; + os << "Plane cutting surface, plane = " << my_plane; + return os.str(); +} + +Intersecting_Planes_Cutting_Surface::Intersecting_Planes_Cutting_Surface(const Vector3d & p0, const Vector3d & p1, const Vector3d & p2, const Vector3d & p3) +: Cutting_Surface() +{ + // Points p0 and p2 lie on the line common to the two planes + my_plane0.set_from_most_orthogonal_angle_of_triangle(p0,p1,p2); + my_plane1.set_from_most_orthogonal_angle_of_triangle(p2,p3,p0); + + myTriangleForPlane0IsLarger = Cross(p2-p0, p1-p0).length_squared() > Cross(p2-p0, p3-p0).length_squared(); + + // Need to keep track of whether the normals to the plane point "toward" each other (positive_dihedral = true) + // or "away" from each other (positive_dihedral = false). + // We check this by seeing if p1 and p2 are on the positive side of the other plane. + const double dist1 = my_plane1.signed_distance(p1); + const double dist3 = my_plane0.signed_distance(p3); + my_positive_dihedral = (std::abs(dist1) > std::abs(dist3)) ? (dist1>0) : (dist3>0); +} + +int +Intersecting_Planes_Cutting_Surface::sign_at_position(const Vector3d & p_coords) const +{ + const double signed_dist0 = my_plane0.signed_distance(p_coords); + const double signed_dist1 = my_plane1.signed_distance(p_coords); + if (my_positive_dihedral) + { + const double min = std::min(signed_dist0,signed_dist1); + return min < 0. ? -1 : 1; + } + const double max = std::max(signed_dist0,signed_dist1); + return max < 0. ? -1 : 1; +} + +bool +Intersecting_Planes_Cutting_Surface::on_surface(const Vector3d & p_coords, const double tol) const +{ + const double signed_dist0 = my_plane0.signed_distance(p_coords); + const double signed_dist1 = my_plane1.signed_distance(p_coords); + if (my_positive_dihedral) + { + return (signed_dist0 > -tol && std::abs(signed_dist1) < tol) || + (signed_dist1 > -tol && std::abs(signed_dist0) < tol); + } + return (signed_dist0 < tol && std::abs(signed_dist1) < tol) || + (signed_dist1 < tol && std::abs(signed_dist0) < tol); +} + +double +Intersecting_Planes_Cutting_Surface::interface_crossing_position(const Segment3d & edge) const +{ + const double signed_dist0_node0 = my_plane0.signed_distance(edge.GetNode(0)); + const double signed_dist0_node1 = my_plane0.signed_distance(edge.GetNode(1)); + const double signed_dist1_node0 = my_plane1.signed_distance(edge.GetNode(0)); + const double signed_dist1_node1 = my_plane1.signed_distance(edge.GetNode(1)); + + double pos0 = signed_dist0_node0 / (signed_dist0_node0-signed_dist0_node1); + double pos1 = signed_dist1_node0 / (signed_dist1_node0-signed_dist1_node1); + + const int sign_case_id = + (((signed_dist0_node0 < 0) == my_positive_dihedral) ? 0 : 1) + + (((signed_dist1_node0 < 0) == my_positive_dihedral) ? 0 : 2) + + (((signed_dist0_node1 < 0) == my_positive_dihedral) ? 0 : 4) + + (((signed_dist1_node1 < 0) == my_positive_dihedral) ? 0 : 8); + static const int case_id_from_sign_case_id [] = {-1,-1,-1, 2,-1,-1,-1, 1,-1,-1,-1, 0, 3, 1, 0,-1}; + + const int case_id = case_id_from_sign_case_id[sign_case_id]; + switch (case_id) + { + case 0: return pos0; + case 1: return pos1; + case 2: return (pos0 < pos1) ? pos0 : pos1; + case 3: return (pos0 < pos1) ? pos1 : pos0; + } + + // Either 0 or 2 true crossings. Not ok. + std::stringstream str; + str << "Failed to find intersection of Intersecting_Planes_Cutting_Surface with planes " + << my_plane0 << " and " << my_plane1 + << " with segment " << edge + << " with crossings " << pos0 << " and " << pos1 << " with diff " << pos0-pos1 << " sign_case_id " << sign_case_id; + throw std::runtime_error(str.str()); +} + +std::string Intersecting_Planes_Cutting_Surface::print() const +{ + std::ostringstream os; + os << "Intersecting planes cutting surface. Plane 0 = " << my_plane0 << " Plane 1 = " << my_plane1 + << " positive dihedral = " << std::boolalpha << my_positive_dihedral; + return os.str(); +} + +std::string print_plane_visualization(const Plane3d & plane, std::array & geomIds, const std::string & description) +{ + std::ostringstream os; + const Vector3d x0 = plane.constant() * plane.normal(); + const Vector3d x1 = x0 + plane.normal(); + os << "Create vertex " << x0[0] << " " << x0[1] << " " << x0[2] << std::endl; + os << "Create vertex " << x1[0] << " " << x1[1] << " " << x1[2] << std::endl; + os << "Create curve vertex " << ++geomIds[0] << " " << ++geomIds[0] << std::endl; + os << "Create planar surface curve " << ++geomIds[1] << " distance 0. # Plane " << ++geomIds[2] << ": " << description << std::endl; + geomIds[0] += 4; // 4 vertices created for plane + geomIds[1] += 4; // 4 curves created for plane + return os.str(); +} + +std::string Plane_Cutting_Surface::print_visualization(std::array & geomIds, const std::string & description) const +{ + return print_plane_visualization(my_plane, geomIds, description); +} + +std::string Intersecting_Planes_Cutting_Surface::print_visualization(std::array & geomIds, const std::string & description) const +{ + const std::string viz0 = print_plane_visualization(my_plane0, geomIds, description+", plane 1/2"); + const std::string viz1 = print_plane_visualization(my_plane1, geomIds, description+", plane 2/2"); + return viz0 + viz1; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Cutting_Surface.hpp b/packages/krino/krino/krino_lib/Akri_Cutting_Surface.hpp new file mode 100644 index 000000000000..51e764864f50 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Cutting_Surface.hpp @@ -0,0 +1,81 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Cutting_Surface_h +#define Akri_Cutting_Surface_h + +#include +#include +#include +#include +#include + +namespace krino { + +class Cutting_Surface +{ +public: + Cutting_Surface() {} + virtual ~Cutting_Surface() {} + virtual bool on_surface(const Vector3d & p_coords, const double tol) const = 0; + virtual int sign_at_position(const Vector3d & p_coords) const = 0; + virtual double interface_crossing_position(const Segment3d & edge) const = 0; + virtual std::string print() const = 0; + virtual std::string print_visualization(std::array & geomIds, const std::string & description) const = 0; + virtual const Plane3d & get_plane() const = 0; +}; + +class Plane_Cutting_Surface : public Cutting_Surface +{ +public: + // for 3D from 3 points on plane + Plane_Cutting_Surface(const Vector3d & p0, const Vector3d & p1, const Vector3d & p2) : Cutting_Surface() {my_plane.set_from_most_orthogonal_angle_of_triangle(p0,p1,p2);} + // for 2D or 3D from direction and point on plane + Plane_Cutting_Surface(const Vector3d & direction, const Vector3d & p0) : my_plane(direction,p0) {} + virtual ~Plane_Cutting_Surface() {} + virtual bool on_surface(const Vector3d & p_coords, const double tol) const override; + int sign_at_position(const Vector3d & p_coords) const override; + double interface_crossing_position(const Segment3d & edge) const override; + std::string print() const override; + virtual std::string print_visualization(std::array & geomIds, const std::string & description) const override; + virtual const Plane3d & get_plane() const override { return my_plane; } +private: + Plane3d my_plane; +}; + +class Plane_Cutting_Surface_2D : public Plane_Cutting_Surface +{ +public: + // for 2D from 2 points on line + Plane_Cutting_Surface_2D(const Vector3d & p0, const Vector3d & p1) : Plane_Cutting_Surface(Vector3d(p1[1]-p0[1],p0[0]-p1[0],0),p0) {} + virtual ~Plane_Cutting_Surface_2D() {} +private: +}; + + +class Intersecting_Planes_Cutting_Surface : public Cutting_Surface +{ +public: + Intersecting_Planes_Cutting_Surface(const Vector3d & p0, const Vector3d & p1, const Vector3d & p2, const Vector3d & p3); // 3D + virtual ~Intersecting_Planes_Cutting_Surface() {} + virtual bool on_surface(const Vector3d & p_coords, const double tol) const override; + int sign_at_position(const Vector3d & p_coords) const override; + double interface_crossing_position(const Segment3d & edge) const override; + std::string print() const override; + virtual std::string print_visualization(std::array & geomIds, const std::string & description) const override; + virtual const Plane3d & get_plane() const override { /* THIS IS A BAD IDEA. SHOULD WE TEST PLANARITY? */ return myTriangleForPlane0IsLarger ? my_plane0 : my_plane1; } +private: + bool myTriangleForPlane0IsLarger; + Plane3d my_plane0; + Plane3d my_plane1; + bool my_positive_dihedral; +}; + +} // namespace krino + +#endif // Akri_Cutting_Surface_h diff --git a/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.cpp b/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.cpp new file mode 100644 index 000000000000..71bc5488dd90 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.cpp @@ -0,0 +1,302 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +static bool owned_nodes_are_handled_by_other_procs(const stk::mesh::BulkData & mesh, + const std::vector & interfaceNodesWithoutMatchingCrossing, + const std::vector & interfaceNodesWithMatchingCrossing) +{ + stk::CommSparse commSparse(mesh.parallel()); + pack_entities_for_owning_proc(mesh, interfaceNodesWithMatchingCrossing, commSparse); + std::set ownedNodesWithRemoteMatchingCrossing; + unpack_entities_from_other_procs(mesh, ownedNodesWithRemoteMatchingCrossing, commSparse); + + for (auto node : interfaceNodesWithoutMatchingCrossing) + if (mesh.bucket(node).owned() && ownedNodesWithRemoteMatchingCrossing.count(node) == 0) + return false; + + return true; +} + +static bool any_node_of_edge_including_children_is_on_interface(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const ParentsToChildMapper & parentToChildMapper, + const EdgeIntersection & edgeCrossing) +{ + std::vector edgeNodesIncludingChildren; + fill_edge_nodes(mesh, edgeCrossing.nodes[0], edgeCrossing.nodes[1], parentToChildMapper, edgeNodesIncludingChildren); + for (auto node : edgeNodesIncludingChildren) + if (node_is_on_interface(mesh, cdfemSupport, phaseSupport, node, edgeCrossing.interface)) + return true; + return false; +} + +static bool edge_crossings_have_matching_interface_node(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const ParentsToChildMapper & parentToChildMapper, + const EdgeIntersection & edgeCrossing, + const double snapTol) +{ + const auto & edgeNodes = edgeCrossing.nodes; + const auto & crossingInterface = edgeCrossing.interface; + const double crossingPosition = edgeCrossing.crossingLocation; + if (crossingPosition < snapTol) + { + if (!node_is_on_interface(mesh, cdfemSupport, phaseSupport, edgeNodes[0], crossingInterface)) + return false; + } + else if (crossingPosition > 1.-snapTol) + { + if (!node_is_on_interface(mesh, cdfemSupport, phaseSupport, edgeNodes[1], crossingInterface)) + return false; + } + else if (!any_node_of_edge_including_children_is_on_interface(mesh, cdfemSupport, phaseSupport, parentToChildMapper, edgeCrossing)) + { + return false; + } + return true; +} + +static bool edges_with_crossings_have_matching_interface_nodes(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const ParentsToChildMapper & parentToChildMapper, + const std::vector & edgeIntersections) +{ + const double snapTol = cdfemSupport.get_snapper().get_edge_tolerance(); + bool edgesWithCrossingHaveMatchingInterfaceNodes = true; + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edge(edgeIntersection); + if (!edge_crossings_have_matching_interface_node(mesh, cdfemSupport, phaseSupport, parentToChildMapper, edge, snapTol)) + { + edgesWithCrossingHaveMatchingInterfaceNodes = false; + break; + } + } + return stk::is_true_on_all_procs(mesh.parallel(), edgesWithCrossingHaveMatchingInterfaceNodes); +} + +static std::map> build_nodes_to_interfaces_within_tolerance(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const std::vector & edgeIntersections, + const ParentsToChildMapper & parentToChildMapper) +{ + + const double snapTol = cdfemSupport.get_snapper().get_edge_tolerance(); + std::vector parentEdgeNodes; + std::vector parentEdgeNodePositions; + + std::map> nodesToInterfacesWithinTolerance; + for (auto && edgeIntersection : edgeIntersections) + { + const EdgeIntersection edgeCrossing(edgeIntersection); + const auto & crossingInterface = edgeCrossing.interface; + const double crossingPosition = edgeCrossing.crossingLocation; + + parentEdgeNodes.clear(); + parentEdgeNodePositions.clear(); + fill_edge_nodes_and_positions(mesh, edgeCrossing.nodes[0], edgeCrossing.nodes[1], parentToChildMapper, parentEdgeNodes, parentEdgeNodePositions); + + for (size_t iNode=0; iNode> & nodesToInterfacesWithinTolerance) +{ + const auto mapIter = nodesToInterfacesWithinTolerance.find(node); + if (mapIter == nodesToInterfacesWithinTolerance.end()) + return false; + + const PhaseTag nodePhase = determine_phase_for_entity(mesh, node, phaseSupport); + const auto & nodeInterfacesWithinTolerance = mapIter->second; + for (auto && interfaceWithinTolerance : nodeInterfacesWithinTolerance) + if (phase_matches_interface(cdfemSupport, nodePhase, interfaceWithinTolerance)) + return true; + + return false; +} + +static void fill_interface_nodes_with_and_without_matching_crossing(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const ParentsToChildMapper & parentToChildMapper, + const std::vector & edgeIntersections, + std::vector & interfaceNodesWithMatchingCrossing, + std::vector & interfaceNodesWithoutMatchingCrossing) +{ + interfaceNodesWithMatchingCrossing.clear(); + interfaceNodesWithoutMatchingCrossing.clear(); + + const std::map> nodesToInterfacesWithinTolerance = build_nodes_to_interfaces_within_tolerance(mesh, cdfemSupport, edgeIntersections, parentToChildMapper); + + for ( auto && bucket : mesh.buckets(stk::topology::NODE_RANK) ) + { + if (nodes_are_on_any_interface(mesh, phaseSupport, *bucket)) + { + for ( auto && node : *bucket ) + { + if (node_has_matching_interface_within_tolerance(mesh, cdfemSupport, phaseSupport, node, nodesToInterfacesWithinTolerance)) + interfaceNodesWithMatchingCrossing.push_back(node); + else + interfaceNodesWithoutMatchingCrossing.push_back(node); + } + } + } +} + +static bool interface_nodes_have_matching_edge_crossing(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + const ParentsToChildMapper & parentToChildMapper, + const std::vector & edgeIntersections) +{ + std::vector interfaceNodesWithMatchingCrossing; + std::vector interfaceNodesWithoutMatchingCrossing; + fill_interface_nodes_with_and_without_matching_crossing(mesh, cdfemSupport, phaseSupport, parentToChildMapper, edgeIntersections, interfaceNodesWithMatchingCrossing, interfaceNodesWithoutMatchingCrossing); + + if (stk::is_true_on_all_procs(mesh.parallel(), interfaceNodesWithoutMatchingCrossing.empty())) + return true; + + bool allOwnedNotSharedInterfaceNodesHaveMatchingEdgeCrossing = true; + for (auto node : interfaceNodesWithoutMatchingCrossing) + { + if (mesh.bucket(node).owned() && !mesh.bucket(node).shared()) + { + allOwnedNotSharedInterfaceNodesHaveMatchingEdgeCrossing = false; + break; + } + } + + if (!stk::is_true_on_all_procs(mesh.parallel(), allOwnedNotSharedInterfaceNodesHaveMatchingEdgeCrossing)) + return false; + + const bool allInterfaceNodesHaveMatchingEdgeCrossing = + owned_nodes_are_handled_by_other_procs(mesh, interfaceNodesWithoutMatchingCrossing, interfaceNodesWithMatchingCrossing); + + return stk::is_true_on_all_procs(mesh.parallel(), allInterfaceNodesHaveMatchingEdgeCrossing); +} + +void fill_neighbor_nodes(const stk::mesh::BulkData & mesh, + stk::mesh::Entity node, + const stk::mesh::Selector & elementSelector, + std::vector & neighborNodes) +{ + neighborNodes.clear(); + for (auto element : StkMeshEntities{mesh.begin_elements(node), mesh.end_elements(node)}) + if (elementSelector(mesh.bucket(element))) + for (auto nbr : StkMeshEntities{mesh.begin_nodes(element), mesh.end_nodes(element)}) + if (nbr != node) + neighborNodes.push_back(nbr); + stk::util::sort_and_unique(neighborNodes); +} + +static bool snap_displacements_at_node_are_small_compared_to_parent_edges(const stk::mesh::BulkData & mesh, + stk::mesh::Entity node, + FieldRef cdfemSnapField, + FieldRef coordsField, + const stk::mesh::Selector & parentElementSelector, + const double snapTol) +{ + const Vector3d snapDisplacements(field_data(cdfemSnapField, node), mesh.mesh_meta_data().spatial_dimension()); + const double snapDisplacmentsSqrLength = snapDisplacements.length_squared(); + const Vector3d nodeCoords(field_data(coordsField, node), mesh.mesh_meta_data().spatial_dimension()); + std::vector neighborNodes; + fill_neighbor_nodes(mesh, node, parentElementSelector, neighborNodes); + for (auto && nbr : neighborNodes) + { + const Vector3d nbrCoords(field_data(coordsField, nbr), mesh.mesh_meta_data().spatial_dimension()); + const double edgeSqrLength = (nbrCoords-nodeCoords).length_squared(); + if (snapDisplacmentsSqrLength > snapTol*snapTol * edgeSqrLength) + return false; + } + return true; +} + +static bool locally_snap_displacements_are_small_on_nodes_with_interfaces(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + FieldRef cdfemSnapField = cdfemSupport.get_cdfem_snap_displacements_field(); + if (cdfemSnapField.valid()) + { + const double snapTol = cdfemSupport.get_snapper().get_edge_tolerance(); + FieldRef oldCdfemSnapField = cdfemSupport.get_cdfem_snap_displacements_field().field_state(stk::mesh::StateOld); + const stk::mesh::Selector parentElementSelector = get_owned_parent_element_selector(mesh, activePart, cdfemSupport, phaseSupport); + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + for ( auto && bucket : mesh.buckets(stk::topology::NODE_RANK) ) + if (bucket->field_data_is_allocated(oldCdfemSnapField) && nodes_are_on_any_interface(mesh, phaseSupport, *bucket)) + for ( auto && node : *bucket ) + if (!snap_displacements_at_node_are_small_compared_to_parent_edges(mesh, node, oldCdfemSnapField, coordsField, parentElementSelector, snapTol)) + return false; + } + return true; +} + +static bool snap_displacements_are_small_on_nodes_with_interfaces(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + return stk::is_true_on_all_procs(mesh.parallel(), locally_snap_displacements_are_small_on_nodes_with_interfaces(mesh, activePart, cdfemSupport, phaseSupport)); +} + +bool decomposition_has_changed(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + if (!snap_displacements_are_small_on_nodes_with_interfaces(mesh, activePart, cdfemSupport, phaseSupport)) + return true; + + const NodeToCapturedDomainsMap nodesToCapturedDomains; + const std::vector edgeIntersections = interfaceGeometry.get_edge_intersection_points(mesh, nodesToCapturedDomains); + + ParentsToChildMapper parentToChildMapper; + parentToChildMapper.build_map(mesh, activePart, cdfemSupport, phaseSupport); + + if (edges_with_crossings_have_matching_interface_nodes(mesh, cdfemSupport, phaseSupport, parentToChildMapper, edgeIntersections) && + interface_nodes_have_matching_edge_crossing(mesh, cdfemSupport, phaseSupport, parentToChildMapper, edgeIntersections)) + { + return false; + } + + return true; +} + + +} // namespace diff --git a/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.hpp b/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.hpp new file mode 100644 index 000000000000..f6aedb4fe6ad --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DecompositionHasChanged.hpp @@ -0,0 +1,25 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_DECOMPOSITIONHASCHANGED_H_ +#define KRINO_INCLUDE_AKRI_DECOMPOSITIONHASCHANGED_H_ +#include +#include +#include +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" +namespace krino { + +bool decomposition_has_changed(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport); + +} + +#endif /* KRINO_INCLUDE_AKRI_DECOMPOSITIONHASCHANGED_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_DiagWriter.cpp b/packages/krino/krino/krino_lib/Akri_DiagWriter.cpp new file mode 100644 index 000000000000..6135a722231b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DiagWriter.cpp @@ -0,0 +1,54 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include + +#include + +namespace krino { + +DiagWriterParser & +theDiagWriterParser() +{ + /* %TRACE% */ /* %TRACE% */ + static DiagWriterParser parser; + return parser; +} + + +stk::diag::Writer & +theDiagWriter() +{ + /* %TRACE[NONE]% */ /* %TRACE% */ + static stk::diag::Writer s_diagWriter(sierra::dwout().rdbuf(), theDiagWriterParser().parse(std::getenv("KRINOLOG"))); + + return s_diagWriter; +} + +DiagWriterParser::DiagWriterParser() + : stk::diag::WriterParser() +{ + /* %TRACE% */ /* %TRACE% */ + mask("debug", (unsigned long) (LOG_DEBUG), "Display debug diagnostic information"); + mask("subelement", (unsigned long) (LOG_SUBELEMENT), "Display subelement decomposition diagnostic information"); + mask("facets", (unsigned long) (LOG_FACETS), "Output exodus file with facets data"); + mask("parts", (unsigned long) (LOG_PARTS), "Display CDFEM parts diagnostic information"); +} + +namespace +{ + +void bootstrap() { sierra::Diag::registerWriter("krinolog", krinolog, theDiagWriterParser()); } + +stk::Bootstrap x(&bootstrap); +} // namespace + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_DiagWriter.hpp b/packages/krino/krino/krino_lib/Akri_DiagWriter.hpp new file mode 100644 index 000000000000..915dd4b42ae7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DiagWriter.hpp @@ -0,0 +1,63 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_DiagWriter_h +#define Akri_DiagWriter_h + +#include +#include +#include +#include + +#include + +namespace krino +{ + class DiagWriterParser : public stk::diag::WriterParser + { + public: + DiagWriterParser(); + }; + + stk::diag::Writer &theDiagWriter(); + DiagWriterParser &theDiagWriterParser(); + +#define krinolog krino::theDiagWriter() + +#ifdef KRINO_TRACE_ENABLED + typedef stk::diag::Tracespec Tracespec; + typedef stk::diag::Traceback Traceback; + + class Trace : public stk::diag::Trace + { + public: + Trace(const char *message) + : stk::diag::Trace(krinolog, message) + {} + }; + +#elif defined(KRINO_TRACE_TRACEBACK) + typedef stk::diag::Tracespec Tracespec; + typedef stk::diag::Traceback Traceback; + typedef stk::diag::Traceback Trace; + +#else + typedef stk::diag::Tracespec Tracespec; + typedef stk::diag::Tracespec Traceback; + typedef stk::diag::Tracespec Trace; +#endif + +#define ThrowRuntimeError(message) \ +{ \ + std::ostringstream internal_throw_runtime_message; \ + internal_throw_runtime_message << message; \ + throw std::runtime_error(internal_throw_runtime_message.str()); \ +} +} // namespace krino + +#endif // Akri_DiagWriter_h diff --git a/packages/krino/krino/krino_lib/Akri_DiagWriter_fwd.hpp b/packages/krino/krino/krino_lib/Akri_DiagWriter_fwd.hpp new file mode 100644 index 000000000000..d5aa04dc9174 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DiagWriter_fwd.hpp @@ -0,0 +1,37 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_DiagWriter_fwd_h +#define Akri_DiagWriter_fwd_h + +#define KRINO_TRACE_ENABLED +// #define KRINO_TRACE_TRACEBACK + +#include + +namespace krino +{ + class DebugOut; + + enum + { + LOG_ALWAYS = stk::LOG_ALWAYS, + LOG_MEMBERS = stk::LOG_MEMBERS, + LOG_TRACE = stk::LOG_TRACE, + LOG_TRACE_STATS = stk::LOG_TRACE_STATS, + LOG_TRACE_SUB_CALLS = stk::LOG_TRACE_SUB_CALLS, + + LOG_DEBUG = 0x00010000, + LOG_SUBELEMENT = 0x00020000, + LOG_FACETS = 0x00040000, + LOG_PARTS = 0x00080000 + }; + +} // namespace krino + +#endif // Akri_DiagWriter_fwd_h diff --git a/packages/krino/krino/krino_lib/Akri_DistanceSweeper.cpp b/packages/krino/krino/krino_lib/Akri_DistanceSweeper.cpp new file mode 100644 index 000000000000..49a96dc635ea --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DistanceSweeper.cpp @@ -0,0 +1,177 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +namespace krino{ + +namespace { + +bool node_has_other_sign(stk::mesh::Entity node, const FieldRef distance_field, const double signed_narrow_band) +{ + double * distance = field_data(distance_field, node); + ThrowAssert(nullptr != distance); + return (signed_narrow_band < 0.) ? (*distance > 0.) : (*distance < 0.); +} + +bool node_is_inside_narrow_band(stk::mesh::Entity node, const FieldRef distance_field, const double signed_narrow_band) +{ + double * distance = field_data(distance_field, node); + ThrowAssert(nullptr != distance); + return (signed_narrow_band < 0.) ? (*distance > signed_narrow_band) : (*distance < signed_narrow_band); +} + +void get_nodes_ready_to_update(const AuxMetaData & aux_meta, const stk::mesh::BulkData& mesh, const FieldRef distance_field, const double signed_narrow_band, std::set & nodes_ready_to_update) +{ + stk::mesh::Selector field_not_ghost = aux_meta.active_not_ghost_selector() & stk::mesh::selectField(distance_field); + const stk::mesh::BucketVector & buckets = mesh.get_buckets( stk::topology::ELEMENT_RANK, field_not_ghost ); + std::vector elem_nodes_to_update; + + for ( auto && bucket : buckets ) + { + stk::topology elem_topology = bucket->topology(); + const unsigned num_nodes = elem_topology.num_nodes(); + + for ( auto && elem : *bucket ) + { + elem_nodes_to_update.clear(); + const stk::mesh::Entity* nodes = mesh.begin_nodes(elem); + bool have_node_with_other_sign = false; + for ( unsigned i = 0; i < num_nodes; ++i ) + { + stk::mesh::Entity node = nodes[i]; + if (has_field_data(distance_field, node)) + { + if (node_has_other_sign(node, distance_field, signed_narrow_band)) + { + have_node_with_other_sign = true; + } + else if (!node_is_inside_narrow_band(node, distance_field, signed_narrow_band)) + { + elem_nodes_to_update.push_back(node); + } + } + } + if (have_node_with_other_sign) + { + nodes_ready_to_update.insert(elem_nodes_to_update.begin(), elem_nodes_to_update.end()); + } + } + } +} + +void get_neighbor_nodes_ready_to_update(const AuxMetaData & aux_meta, + const stk::mesh::BulkData& mesh, + const FieldRef distance_field, + const double signed_narrow_band, + const bool check_if_nbr_is_outside_band, + stk::mesh::Entity node, + std::set & nodes_ready_to_update) +{ + const stk::mesh::Entity* node_elems = mesh.begin_elements(node); + const unsigned num_node_elements = mesh.num_elements(node); + + for (unsigned ielem = 0; ielem < num_node_elements; ++ ielem) + { + stk::mesh::Entity elem = node_elems[ielem]; + const unsigned num_nodes = mesh.num_nodes(elem); + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(elem); + for ( unsigned inode = 0; inode < num_nodes; ++inode ) + { + stk::mesh::Entity nbr_node = elem_nodes[inode]; + if (nbr_node != node && + has_field_data(distance_field, nbr_node) && + !node_has_other_sign(nbr_node, distance_field, signed_narrow_band) && + (!check_if_nbr_is_outside_band || !node_is_inside_narrow_band(nbr_node, distance_field, signed_narrow_band))) + { + nodes_ready_to_update.insert(nbr_node); + } + } + } +} + +void get_shared_nodes_ready_to_update(const AuxMetaData & aux_meta, const stk::mesh::BulkData& mesh, const FieldRef distance_field, const double signed_narrow_band, std::set & nodes_ready_to_update) +{ + stk::mesh::Selector field_globally_shared = mesh.mesh_meta_data().globally_shared_part() & stk::mesh::selectField(distance_field); + std::vector< stk::mesh::Entity> shared_nodes; + stk::mesh::get_selected_entities( field_globally_shared, mesh.buckets( stk::topology::NODE_RANK ), shared_nodes ); + const bool check_if_nbr_is_outside_band = true; + + for (auto && node : shared_nodes) + { + if (node_has_other_sign(node, distance_field, signed_narrow_band)) + { + get_neighbor_nodes_ready_to_update(aux_meta, mesh, distance_field, signed_narrow_band, check_if_nbr_is_outside_band, node, nodes_ready_to_update); + } + } +} + +} // anonymous + +void DistanceSweeper::fix_sign_by_sweeping(const stk::mesh::BulkData& mesh, const FieldRef distance_field, const double signed_narrow_band) +{ + const AuxMetaData & aux_meta = AuxMetaData::get(mesh.mesh_meta_data()); + if (signed_narrow_band == 0.0) return; + const int sign_to_fix = (signed_narrow_band < 0.) ? -1 : 1; + + std::set nodes_ready_to_update; + + get_nodes_ready_to_update(aux_meta, mesh, distance_field, signed_narrow_band, nodes_ready_to_update); + + bool done = false; + while (!done) + { + size_t num_nodes_updated = 0; + + const bool check_if_nbr_is_outside_band = false; + while (!nodes_ready_to_update.empty()) + { + ++num_nodes_updated; + stk::mesh::Entity node = *nodes_ready_to_update.begin(); + nodes_ready_to_update.erase(nodes_ready_to_update.begin()); + + double * distance = field_data(distance_field, node); + ThrowAssert(nullptr != distance); + *distance = -signed_narrow_band; + + get_neighbor_nodes_ready_to_update(aux_meta, mesh, distance_field, signed_narrow_band, check_if_nbr_is_outside_band, node, nodes_ready_to_update); + } + + done = true; + if (mesh.parallel_size() > 1) + { + const size_t local_num_nodes_updated = num_nodes_updated; + stk::all_reduce_sum(mesh.parallel(), &local_num_nodes_updated, &num_nodes_updated, 1); + + if (num_nodes_updated > 0) + { + done = false; + + std::vector parallel_fields(1, &distance_field.field()); + if (sign_to_fix > 0) stk::mesh::parallel_min(mesh, parallel_fields); + else stk::mesh::parallel_max(mesh, parallel_fields); + + get_shared_nodes_ready_to_update(aux_meta, mesh, distance_field, signed_narrow_band, nodes_ready_to_update); + } + } + } +} + +//---------------------------------------------------------------- +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_DistanceSweeper.hpp b/packages/krino/krino/krino_lib/Akri_DistanceSweeper.hpp new file mode 100644 index 000000000000..051cf9dc37cb --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_DistanceSweeper.hpp @@ -0,0 +1,22 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_DistanceSweeper_h +#define Akri_DistanceSweeper_h + +namespace stk { namespace mesh { class BulkData; } } +namespace krino { class FieldRef; } + +namespace krino { +namespace DistanceSweeper { + + void fix_sign_by_sweeping(const stk::mesh::BulkData& mesh, const FieldRef distance_field, const double signed_narrow_band); + +}} + +#endif // Akri_DistanceSweeper_h diff --git a/packages/krino/krino/krino_lib/Akri_Element.cpp b/packages/krino/krino/krino_lib/Akri_Element.cpp new file mode 100644 index 000000000000..3eb348e43e1a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element.cpp @@ -0,0 +1,1077 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" +#include +namespace krino{ + +ElementObj::ElementObj(const stk::mesh::BulkData & stkMesh, stk::mesh::Entity elemEntity) + : my_master_elem(MasterElementDeterminer::getMasterElement(stkMesh.bucket(elemEntity).topology())), + my_entity(elemEntity), + my_entityId(stkMesh.identifier(elemEntity)), + my_prolongation_data(NULL) +{ +} + +ElementObj::ElementObj(const stk::topology elem_topology, const NodeVec & nodes) + : my_master_elem(MasterElementDeterminer::getMasterElement(elem_topology)), + my_nodes(nodes), + my_entity(), + my_entityId(0), + my_prolongation_data(NULL) +{ +} + +ElementObj::~ElementObj() {} + +void +ElementObj::integration_locations( + std::vector & intg_pt_locations, + const MasterElement & me) +{ + const unsigned num_intg_pts = me.num_intg_pts(); + const double * intg_pt_loc_ptr = me.intg_pt_locations(); + const unsigned dim = me.topology_dimension(); + + intg_pt_locations.resize(num_intg_pts); + for(unsigned i=0; i & intg_weights, // includes both gauss point weight and detJ + const int numCoordDims, + const std::vector & mesh_coords, + const MasterElement & me, + const MasterElement & mesh_me) +{ + const unsigned num_intg_pts = me.num_intg_pts(); + const unsigned dim = me.topology_dimension(); + + std::vector det_J(num_intg_pts); + double det_J_error; + + if ( me.get_topology() == mesh_me.get_topology() ) + { + mesh_me.determinant( numCoordDims, 1, mesh_coords.data(), det_J.data(), &det_J_error ); + } + else + { + const int num_coord_dofs = mesh_me.get_topology().num_nodes(); + const double * intg_pt_loc_ptr = me.intg_pt_locations(); + std::vector d_shapef_coords(num_coord_dofs*dim*num_intg_pts); + mesh_me.shape_fcn_deriv(num_intg_pts, intg_pt_loc_ptr, d_shapef_coords.data()); + mesh_me.determinant( + numCoordDims, // Number of coordinate dimensions + num_intg_pts, // Number of target points + num_coord_dofs, // Number of coord shape functions + d_shapef_coords.data(), // Mesh shape function derivatives + 1, // Number of elements + mesh_coords.data(), // Mesh coordinate values + det_J.data(), // Determinant of the transformation Jacobian for each element (output) + &det_J_error ); // Determinant error (output) + } + + const double * intg_wt_ptr = me.intg_weights(); + + intg_weights.resize(num_intg_pts); + for(unsigned i=0; i & result, unsigned dim, unsigned npe) +{ + if (npe == 0) + { + npe = mesh.bucket(element).topology().num_nodes(); + } + result.resize(npe*dim); + + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(element); + + for (unsigned n=0; n(field, elem_nodes[n]); + for (unsigned d=0; d coords; + ElementObj::gather_nodal_field(mesh, element, coords_field, coords, dim); + + const MasterElement& master_elem = MasterElementDeterminer::getMasterElement(mesh.bucket(element).topology()); + + std::vector intg_weights; + ElementObj::integration_weights( intg_weights, dim, coords, master_elem ); + + double vol = 0.0; + for ( double intg_wt : intg_weights ) + { + vol += intg_wt; + } + return vol; +} + +PhaseTag +ElementObj::update_phase(const CDMesh & mesh, const PhaseTag & startPhase, const InterfaceID interface_key, const int sign) +{ + PhaseTag phase = startPhase; + if (sign == -1 || sign == 1) + { + if (interface_key.is_single_ls()) + { + phase.add(mesh.ls_field(interface_key.first_ls()).identifier,sign); + } + else + { + const int other_ls_id = (sign < 0) ? interface_key.second_ls() : interface_key.first_ls(); + if (phase.contain(mesh.ls_field(other_ls_id).identifier, -1)) + { + const int ls_id = (sign < 0) ? interface_key.first_ls() : interface_key.second_ls(); + + phase.clear(); + phase.add(mesh.ls_field(ls_id).identifier, -1); + } + } + } + + return phase; +} + +PhaseTag +ElementObj::update_phase(const CDMesh & mesh, const PhaseTag & startPhase, const std::vector & interfaces, const std::vector & interfaceSigns) +{ + PhaseTag phase = startPhase; + const int numInterfaces = interfaces.size(); + ThrowRequire((int)interfaceSigns.size() == numInterfaces); + + if (numInterfaces > 0) + { + bool badConfig = false; + int iterCount = 0; + while (true) + { + PhaseTag iterationPhase = phase; + for (int i=0; i numInterfaces) + { + krinolog << "BAD INTERFACE CROSSING CONFIG WITH STARTING PHASE: " << startPhase << stk::diag::dendl; + for (int i=0; i & nodeOwnerCoords) const +{ + nodeOwnerCoords.clear(); + nodeOwnerCoords.reserve(my_nodes.size()); + + for ( auto && node : my_nodes ) + nodeOwnerCoords.push_back(node->owner_coords(owner)); +} + +Vector3d +ElementObj::compute_local_coords_from_owner_coordinates(const Mesh_Element * owner, const Vector3d & ptOwnerCoords) const +{ + std::vector nodeOwnerCoords; + fill_node_owner_coords(owner, nodeOwnerCoords); + + ThrowAssert((spatial_dim() == 2 && (nodeOwnerCoords.size() == 3 || nodeOwnerCoords.size() == 6)) || + (spatial_dim() == 3 && (nodeOwnerCoords.size() == 4 || nodeOwnerCoords.size() == 10))); + if (spatial_dim() == 2 && nodeOwnerCoords.size() == 6) + nodeOwnerCoords.resize(3); + else if (spatial_dim() == 3 && nodeOwnerCoords.size() == 10) + nodeOwnerCoords.resize(4); + + return get_parametric_coordinates_of_point(nodeOwnerCoords, ptOwnerCoords); +} + +void +ElementObj::integration_weights( + std::vector & intg_weights, // includes both gauss point weight and detJ + const MasterElement & me ) const +{ + const unsigned dim = spatial_dim(); + const unsigned nnodes = my_nodes.size(); + std::vector flat_coords(nnodes*dim); + for ( unsigned n = 0; n < nnodes; n++ ) + { + const Vector3d & node_coords = my_nodes[n]->coordinates(); + for (unsigned d=0; d intg_weights; + integration_weights( intg_weights, my_master_elem ); + + double vol = 0.0; + + for ( double intg_weight : intg_weights ) + { + vol += intg_weight; + } + return vol; +} + +void ElementObj::add_subelement(std::unique_ptr subelem) +{ + my_subelements.emplace_back(std::move(subelem)); +} + +void ElementObj::get_subelements( std::vector & subelems ) const +{ + if ( !my_subelements.empty() ) + { + for ( auto && subelem : my_subelements ) + { + subelem->get_subelements(subelems); + } + return; + } + + const SubElement * subelem = dynamic_cast( this ); + if (NULL != subelem) subelems.push_back(subelem); +} + +void ElementObj::get_subelements( std::vector & subelems ) +{ + if ( !my_subelements.empty() ) + { + for ( auto && subelem : my_subelements ) + { + subelem->get_subelements(subelems); + } + return; + } + + SubElement * subelem = dynamic_cast( this ); + if (NULL != subelem) subelems.push_back(subelem); +} + +bool +ElementObj::have_refined_edges() const +{ /* %TRACE% */ /* %TRACE% */ + + const stk::topology Top = topology(); + const int num_edges = Top.num_edges(); + + for ( int edge = 0; edge < num_edges; edge++ ) + { + const unsigned * const lnn = get_edge_node_ordinals(Top, edge); + + const int num_edge_nodes = Top.edge_topology(edge).num_nodes(); + ThrowRequire(2 == num_edge_nodes || 3 == num_edge_nodes); + + if ((2 == num_edge_nodes && + NULL != SubElementNode::common_child({my_nodes[lnn[0]], my_nodes[lnn[1]]})) || + (3 == num_edge_nodes && + (NULL != SubElementNode::common_child({my_nodes[lnn[0]], my_nodes[lnn[2]]}) || + NULL != SubElementNode::common_child({my_nodes[lnn[1]], my_nodes[lnn[2]]})))) + { + return true; + } + } + return false; +} + +void ElementObj::cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains) +{ + throw std::runtime_error("Incorrect usage of ElementObj. The type of element cannot cut_interior_intersection_point."); +} + +void ElementObj::cut_face_intersection_point(const int iFace, const Vector3d & pCoords, const std::vector & sortedDomains) +{ + throw std::runtime_error("Incorrect usage of ElementObj. The type of element cannot cut_face_intersection_point."); +} + +bool ElementObj::captures_intersection_point_domains(const std::vector & intersectionPointDomains) const +{ + for (auto && node : my_nodes) + if (node->captures_intersection_point_domains(intersectionPointDomains)) + return true; + return false; +} + +void +ElementObj::prolongate_fields(const CDMesh & mesh) const +{ + const CDMesh* old_mesh = mesh.get_old_mesh(); + if (nullptr != old_mesh) + { + const FieldSet & element_fields = mesh.get_element_fields(); + if (element_fields.empty()) return; + + const ProlongationElementData * prolong_element = NULL; + const SubElement * subelem = dynamic_cast(this); + if (NULL == subelem) + { + prolong_element = old_mesh->fetch_prolong_element(entityId()); + } + else + { + prolong_element = old_mesh->fetch_prolong_element(subelem->get_owner().entityId()); + } + + //I think that adaptivity currently can lead to prolong_element == NULL: ThrowAssert(NULL != prolong_element); + + for(FieldSet::const_iterator it = element_fields.begin(); it != element_fields.end(); ++it) + { + const FieldRef field = *it; + + double * val = field_data(field, entity()); + if (NULL == val) continue; + + const unsigned field_length = field.length(); + + const double * owner_val = (NULL == prolong_element) ? NULL : prolong_element->get_field_data(field); + if (NULL == owner_val) + { + std::fill(val, val+field_length, 0.); + } + else + { + std::copy(owner_val, owner_val+field_length, val); + } + } + } +} + +const MasterElement* +ElementObj::get_evaluation_master_element(const FieldRef field) const +{ /* %TRACE% */ /* %TRACE% */ + // Supports Q1Q1, Q2Q2, and Q2Q1 cases + const MasterElement* calc_master_elem = &master_elem(); + const unsigned full_npe = master_elem().get_topology().num_nodes(); + ThrowAssert(field.type_is()); + + for ( unsigned n = 0; n < full_npe; n++ ) + { + double * data = field_data(field, my_nodes[n]->entity()); + if (nullptr == data) + { + calc_master_elem = &MasterElementDeterminer::getMasterElement(master_elem().get_topology().base()); + ThrowRequire(n >= calc_master_elem->num_nodes()); + break; + } + } + return calc_master_elem; +} + +void +ElementObj::evaluate_prolongation_field(const CDMesh & mesh, const FieldRef field, const unsigned field_length, const Vector3d & p_coords, double * result) const +{ /* %TRACE% */ /* %TRACE% */ + + // Figuring out the field master element here is actually quite hard since the entity may not exist any more. + // We'll assume that the field master element is the master_elem or the one with topology master_elem->get_topology().base(). + // This will handle the Q2Q1 case. + + for (unsigned i=0; i node_data(full_npe, nullptr); + const std::vector zeros(field_length,0.0); + + for ( int n = 0; n < full_npe; n++ ) + { + const ProlongationNodeData * prolong_data = mesh.fetch_prolong_node(my_nodes[n]->entityId()); + if (nullptr != prolong_data) node_data[n] = prolong_data->get_field_data(field); + if (node_data[n] == nullptr) + { + if (!initial_field.valid()) + { + initial_field = mesh.get_cdfem_support().get_initial_prolongation_field( field ); + } + if (initial_field.valid()) + { + node_data[n] = prolong_data->get_field_data(initial_field); + } + } + if (node_data[n] == nullptr) + { + calc_master_elem = &MasterElementDeterminer::getMasterElement(master_elem().get_topology().base()); + node_data[n] = zeros.data(); + } + } + + const int npe = calc_master_elem->get_topology().num_nodes(); + std::vector shapefcn (npe,0.); + calc_master_elem->shape_fcn(1, p_coords.data(), shapefcn.data()); + + for ( int n = 0; n < npe; n++ ) + { + ThrowRequire(nullptr != node_data[n]); + for (unsigned i=0; idetermine_decomposed_elem_phase(mesh); + } + // Phase for Mesh_Element with subelements is left empty + return; + } +} + +static std::function &)> +cut_element_intersecting_planes_diagonal_picker(const NodeVec & cutElemNodes) +{ + auto intersectingPlanesDiagonalPicker = + [&cutElemNodes](const std::array & faceNodes) + { + return ElementObj::determine_diagonal_for_internal_quad_of_cut_tet_from_owner_nodes(cutElemNodes[faceNodes[0]], cutElemNodes[faceNodes[1]], cutElemNodes[faceNodes[2]], cutElemNodes[faceNodes[3]]); + }; + return intersectingPlanesDiagonalPicker; +} + +std::function &)> +Mesh_Element::get_diagonal_picker() const +{ + return cut_element_intersecting_planes_diagonal_picker(my_nodes); +} + + +bool +Mesh_Element::is_single_coincident() const +{ + std::vector conformal_subelems; + get_subelements(conformal_subelems); + if(conformal_subelems.size() != 1) return false; + + const SubElement * subelem = conformal_subelems[0]; + if(subelem->topology() != coord_topology()) return false; + if (get_nodes() != subelem->get_nodes()) return false; + return true; +} + +Mesh_Element::~Mesh_Element() {} + +Mesh_Element::Mesh_Element(CDMesh & mesh, + stk::mesh::Entity elemEntity) + : ElementObj(mesh.stk_bulk(), elemEntity), + my_subelement_order(0), + my_have_interface(false) +{ + // set subelement specs + const stk::topology me_topology = my_master_elem.get_topology(); + + std::tie(my_subelement_topology, my_subelement_order) = determine_subelement_topology(me_topology); + ThrowRequire(stk::topology::INVALID_TOPOLOGY != my_subelement_topology); + + const unsigned npe_coords = me_topology.num_nodes(); + const stk::mesh::Entity* elem_nodes = mesh.stk_bulk().begin_nodes(my_entity); + + my_nodes.reserve(npe_coords); + const unsigned npe_base = me_topology.base().num_nodes(); + for (unsigned i=0; i npe_base) + { + my_nodes.resize(npe_coords); + ThrowRequireMsg(npe_coords == npe_base + me_topology.num_edges(), "Unexpected topology"); + for (unsigned edge_i=0; edge_i= npe_base && inode +Mesh_Element::determine_subelement_topology(stk::topology elem_topology) +{ + switch(elem_topology()) + { + case stk::topology::TRIANGLE_3_2D: + return std::pair(stk::topology::TRIANGLE_3_2D, 1); + case stk::topology::TRIANGLE_6_2D: + return std::pair(stk::topology::TRIANGLE_6_2D, 2); + case stk::topology::TETRAHEDRON_4: + return std::pair(stk::topology::TETRAHEDRON_4, 1); + case stk::topology::TETRAHEDRON_10: + return std::pair(stk::topology::TETRAHEDRON_10, 2); + default: + return std::pair(stk::topology::INVALID_TOPOLOGY, 0); + } +} + +Vector3d +Mesh_Element::get_node_parametric_coords( const int lnn ) const +{ + const double * nodal_parametric_coordinates = my_master_elem.nodal_parametric_coordinates(); + const int dim = spatial_dim(); + return Vector3d(&nodal_parametric_coordinates[lnn*dim],dim); +} + +static int get_local_node_number( const NodeVec & nodes, const SubElementNode * node ) +{ + for (size_t iNode=0; iNode conformal_subelems; + get_subelements(conformal_subelems); + + double minSqrDist = std::numeric_limits::max(); + for ( auto&& subelement : conformal_subelems ) + { + const Vector3d currentChildPCoords = subelement->compute_local_coords_from_owner_coordinates(this, ownerCoordinates); + const double currentChildSqrDist = compute_parametric_square_distance(currentChildPCoords); + if (currentChildSqrDist < minSqrDist) + { + minSqrDist = currentChildSqrDist; + child = subelement; + childPCoords = currentChildPCoords; + } + } +} + +Vector3d +Mesh_Element::coordinates( const Vector3d & p_coords ) const +{ /* %TRACE% */ /* %TRACE% */ + + const int npeCoords = my_nodes.size(); + std::vector shapeFcn(npeCoords); + my_master_elem.shape_fcn(1, p_coords.data(), shapeFcn.data()); + + Vector3d coords(Vector3d::ZERO); + for ( int n = 0; n < npeCoords; n++ ) + coords += shapeFcn[n] * my_nodes[n]->coordinates(); + + return coords; +} + +std::string Mesh_Element::visualize(const CDMesh & mesh) const +{ + std::ostringstream os; + os << "Debugging mesh element " << entityId() << " with cutter:\n" << myCutter->visualize(mesh.stk_bulk()) << "\n"; + return os.str(); +} + +double +Mesh_Element::interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const +{ + ThrowRequire(get_cutter()); + return get_cutter()->interface_crossing_position(interface, edge); +} + +static ElementIntersectionPointFilter build_element_intersection_filter(const NodeVec & nodes) +{ + auto filter = + [&nodes](const std::vector & intersectionPointDomains) + { + for (auto && node : nodes) + if (node->captures_intersection_point_domains(intersectionPointDomains)) + return false; + return true; + }; + return filter; +} + +void +Mesh_Element::fill_face_interior_intersections(const NodeVec & faceNodes, const InterfaceID & interface1, const InterfaceID & interface2, std::vector & faceIntersectionPoints) const +{ + ThrowRequire(get_cutter() && faceNodes.size() == 3); + const std::array faceNodeOwnerCoords = {{faceNodes[0]->owner_coords(this), faceNodes[1]->owner_coords(this), faceNodes[2]->owner_coords(this)}}; + const ElementIntersectionPointFilter intersectionPointFilter = build_element_intersection_filter(faceNodes); + get_cutter()->fill_tetrahedron_face_interior_intersections(faceNodeOwnerCoords, interface1, interface2, intersectionPointFilter, faceIntersectionPoints); +} + +int +Mesh_Element::interface_node_sign(const InterfaceID interface, const SubElementNode * node) const +{ + ThrowRequire(get_cutter()); + return get_cutter()->sign_at_position(interface, node->owner_coords(this)); +} + +double +Mesh_Element::interface_crossing_position(const InterfaceID interface, const SubElementNode * node1, const SubElementNode * node2) const +{ + ThrowRequire(get_cutter()); + Segment3d edge(node1->owner_coords(this), node2->owner_coords(this)); + return get_cutter()->interface_crossing_position(interface, edge); +} + +bool +Mesh_Element::is_prolonged() const +{ /* %TRACE% */ /* %TRACE% */ + for (auto && node : my_nodes) + { + if (!(node->is_prolonged())) return false; + } + return true; +} + +int Mesh_Element::get_interface_index(const InterfaceID interface) const +{ + ThrowAssert(have_interface(interface)); + const auto iter = std::lower_bound(myCuttingInterfaces.begin(), myCuttingInterfaces.end(), interface); + return std::distance(myCuttingInterfaces.begin(), iter); +} + +bool +Mesh_Element::triangulate(const CDMesh & mesh, const InterfaceGeometry & interfaceGeometry) +{ /* %TRACE% */ /* %TRACE% */ + + const auto & decomposedBlocksSelector = mesh.get_phase_support().get_all_decomposed_blocks_selector(); + const bool inDecomposedBlock = decomposedBlocksSelector(mesh.stk_bulk().bucket(entity())); + if (inDecomposedBlock) + { + create_cutter(mesh, interfaceGeometry); + + if (!myCuttingInterfaces.empty()) + my_have_interface = true; + + if (my_phase.empty()) + my_phase = interfaceGeometry.get_starting_phase(myCutter.get()); + else + my_have_interface = false; // uncut element with phase already set + } + + if (!have_subelements() && (have_interface() || have_refined_edges())) + { + create_base_subelement(); + } + + return false; +} + +const SubElementNode * get_node_matching_entity(const std::vector & nodes, stk::mesh::Entity stkNode) +{ + for (auto && node : nodes) + if (stkNode == node->entity()) + return node; + return nullptr; +} + +static IntersectionPointFilter +keep_all_intersecion_points_filter() +{ + auto filter = + [](const std::vector & intersectionPointNodes, const std::vector & intersectionPointSortedDomains) + { + return true; + }; + return filter; +} + +Vector3d Mesh_Element::get_intersection_point_parametric_coordinates(const IntersectionPoint & intersectionPoint) const +{ + Vector3d pCoords(Vector3d::ZERO); + const auto & intersectionPointNodes = intersectionPoint.get_nodes(); + const auto & intersectionPointWeights = intersectionPoint.get_weights(); + const size_t numIntersectionPointNodes = intersectionPointNodes.size(); + for (size_t iNode=0; iNodeowner_coords(this); + } + return pCoords; +} + +std::vector +Mesh_Element::get_interface_signs_based_on_crossings(const NodeVec & nodes) const +{ + std::vector nodeCoords; + std::vector*> nodeDomains; + + nodeCoords.clear(); + nodeDomains.clear(); + nodeCoords.reserve(nodes.size()); + nodeDomains.reserve(nodes.size()); + for (auto && node : nodes) + { + nodeCoords.push_back(node->owner_coords(this)); + nodeDomains.push_back(&node->get_sorted_node_domains()); + } + return get_cutter()->get_interface_signs_based_on_crossings(nodeCoords, nodeDomains); +} + +void +Mesh_Element::cut_interior_intersection_points(CDMesh & mesh) +{ /* %TRACE% */ /* %TRACE% */ + if (!have_interface()) + return; + + std::vector intersectionPoints; + stk::topology elementTopology = mesh.stk_bulk().bucket(entity()).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + const std::vector elementNodes(mesh.stk_bulk().begin_nodes(entity()), mesh.stk_bulk().end_nodes(entity())); + append_intersection_points_from_element_interior(masterElement, elementNodes, *myCutter, keep_all_intersecion_points_filter(), intersectionPoints); + + for (auto && intersectionPoint : intersectionPoints) + { + const Vector3d pCoords = get_intersection_point_parametric_coordinates(intersectionPoint); + + const ElementObj * containingElem = nullptr; + Vector3d containingElemPCoords; + find_child_coordinates_at_owner_coordinates(pCoords, containingElem, containingElemPCoords); + ThrowAssert(containingElem); + + ElementObj * elem = const_cast(containingElem); + if (!elem->captures_intersection_point_domains(intersectionPoint.get_sorted_domains())) + elem->cut_interior_intersection_point(mesh, containingElemPCoords, intersectionPoint.get_sorted_domains()); + } + + const std::vector interfaces = get_sorted_cutting_interfaces(); + for (size_t i1=0; i1cut_face_interior_intersection_points(mesh, interfaces[i1], interfaces[i2]); + } + } + + std::vector leafSubElements; + get_subelements(leafSubElements); + for (auto && leafSubElement : leafSubElements) + { + SubElement * subElem = const_cast(leafSubElement); + const std::vector interfaceSigns = get_interface_signs_based_on_crossings(subElem->get_nodes()); + subElem->set_interface_signs(interfaceSigns); + } +} + +void +Mesh_Element::create_cutter(const CDMesh & mesh, const InterfaceGeometry & interfaceGeometry) +{ /* %TRACE% */ /* %TRACE% */ + const auto intersectingPlanesDiagonalPicker = get_diagonal_picker(); + myCutter = interfaceGeometry.build_element_cutter(mesh.stk_bulk(), entity(), intersectingPlanesDiagonalPicker); + myCuttingInterfaces = myCutter->get_sorted_cutting_interfaces(); +} + +void +Mesh_Element::create_base_subelement() +{ /* %TRACE% */ /* %TRACE% */ + + stk::topology base_topology = coord_topology(); + + const unsigned num_sides = base_topology.num_sides(); + + std::vector parent_side_ids(num_sides); + for (unsigned i=0; i base_subelement; + if (stk::topology::TETRAHEDRON_4 == base_topology) + { + base_subelement = std::make_unique( my_nodes, parent_side_ids, this); + } + else if (stk::topology::TETRAHEDRON_10 == base_topology) + { + // purposely use lower order base subelement + std::vector sub_nodes(my_nodes.begin(), my_nodes.begin()+4); + base_subelement = std::make_unique( sub_nodes, parent_side_ids, this); + } + else if (stk::topology::TRIANGLE_3_2D == base_topology) + { + base_subelement = std::make_unique( my_nodes, parent_side_ids, this); + } + else if (stk::topology::TRIANGLE_6_2D == base_topology) + { + // purposely use lower order base subelement + std::vector sub_nodes(my_nodes.begin(), my_nodes.begin()+3); + base_subelement = std::make_unique( sub_nodes, parent_side_ids, this); + } + ThrowErrorMsgIf(!base_subelement, "Elements with topology " << base_topology.name() << " not supported for CDFEM."); + + base_subelement->initialize_interface_signs(); + add_subelement(std::move(base_subelement)); +} + +void +Mesh_Element::determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) +{ + if (have_interface(interface_key)) + { + for(auto && subelement : my_subelements) + { + subelement->SubElement::determine_node_signs(mesh, interface_key); + } + } +} + +void +Mesh_Element::determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) +{ + if (have_interface(interface_key)) + { + for(auto && subelement : my_subelements) + { + subelement->SubElement::determine_node_scores(mesh, interface_key); + } + } +} + +void +Mesh_Element::decompose(CDMesh & mesh, const InterfaceID interface_key) +{ + if (have_interface(interface_key)) + { + for(auto && subelement : my_subelements) + { + subelement->decompose(mesh, interface_key); + } + } +} + +void +Mesh_Element::handle_hanging_children(CDMesh & mesh, const InterfaceID & interface) +{ + if (!have_subelements() && have_edges_with_children()) + { + create_base_subelement(); + } + + for(auto && subelement : my_subelements) + { + subelement->handle_hanging_children(mesh, interface); + } +} + +void +Mesh_Element::build_quadratic_subelements(CDMesh & mesh) +{ + if (2 == subelement_order()) + { + for (auto && subelement : my_subelements) + { + subelement->build_quadratic_subelements(mesh); + } + } +} + +int +ElementObj::evaluate_quad(const SubElementNode * n0, const SubElementNode * n1, const SubElementNode * n2, const SubElementNode * n3) +{ /* %TRACE% */ /* %TRACE% */ + return evaluate_quad(n0->coordinates(), n1->coordinates(), n2->coordinates(), n3->coordinates()); +} + +int +ElementObj::evaluate_quad(const Vector3d & x0, const Vector3d & x1, const Vector3d & x2, const Vector3d & x3) +{ /* %TRACE% */ /* %TRACE% */ + // given 4 angles + // angle0 - angle subtended by (x3-x0) and (x1-x0) + // angle1 - angle subtended by (x0-x1) and (x2-x1) + // angle2 - angle subtended by (x1-x2) and (x3-x2) + // angle3 - angle subtended by (x2-x3) and (x0-x3) + // returns -1 if the max of angle 0 and angle 2 is significant larger than the max of angle 1 and angle 3 + // returns +1 if the opposite is true + // returns 0 if neither is true (the max angles are basically the same) OR one of the sides is degenerate + + const Vector3d side0 = x1 - x0; + const Vector3d side1 = x2 - x1; + const Vector3d side2 = x3 - x2; + const Vector3d side3 = x0 - x3; + + const double side_len0 = side0.length(); + const double side_len1 = side1.length(); + const double side_len2 = side2.length(); + const double side_len3 = side3.length(); + + // here, meas0 = -cos(angle0) * side_len0*side_len1*side_len2*side_len3 + const double meas0 = Dot(side3,side0) * side_len1*side_len2; + const double meas1 = Dot(side0,side1) * side_len2*side_len3; + const double meas2 = Dot(side1,side2) * side_len3*side_len0; + const double meas3 = Dot(side2,side3) * side_len0*side_len1; + + if ( krinolog.shouldPrint(LOG_DEBUG) ) + { + krinolog << "Lengths: " << side_len0 << ", " << side_len1 << ", " << side_len2 << ", " << side_len3 << "\n"; + krinolog << "Angle measures: " << meas0 << ", " << meas1 << ", " << meas2 << ", " << meas3 << "\n"; + krinolog << "Angles: " << std::acos(-meas0/(side_len0*side_len1*side_len2*side_len3))*180.0/3.141592654 << ", " + << std::acos(-meas1/(side_len0*side_len1*side_len2*side_len3))*180.0/3.141592654 << ", " + << std::acos(-meas2/(side_len0*side_len1*side_len2*side_len3))*180.0/3.141592654 << ", " + << std::acos(-meas3/(side_len0*side_len1*side_len2*side_len3))*180.0/3.141592654 << "\n"; + } + + const double meas02 = std::max(meas0,meas2); + const double meas13 = std::max(meas1,meas3); + + const double tol = std::numeric_limits::epsilon()*(side_len0*side_len1*side_len2*side_len3); + + if (meas02 > (meas13 + tol)) + { + return -1; + } + else if (meas13 > (meas02 + tol)) + { + return +1; + } + else + { + return 0; + } +} + +bool +ElementObj::have_edges_with_children() const +{ /* %TRACE% */ /* %TRACE% */ + const int num_edges = topology().num_edges(); + + // Iterate edges looking for any common children of the edge nodes + for ( int edge = 0; edge < num_edges; ++edge ) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topology(), edge); + + const SubElementNode * node0 = my_nodes[edge_node_ordinals[0]]; + const SubElementNode * node1 = my_nodes[edge_node_ordinals[1]]; + const SubElementNode * child = SubElementNode::common_child({node0, node1}); + if( child ) + { + return true; + } + } + return false; +} + +bool +ElementObj::determine_diagonal_for_internal_quad_of_cut_tet_from_owner_nodes(const SubElementNode * pn0, const SubElementNode * pn1, const SubElementNode * pn2, const SubElementNode * pn3) +{ + // true: connect child of pn0 and pn2 (n0) to child of pn1 and pn3 (n2) + // false: connect child of pn1 and pn2 (n1) to child of pn0 and pn3 (n3) + + // This method is used for the cutter. For CUT_QUADS_BY_GLOBAL_IDENTIFIER, use logic that is consistent with the way elements are cut. + // For other strategies, still use id based logic because this is only being used for the cutter, and it will be removed when + // we use the actual facets instead of the cutter. + + stk::mesh::EntityId pn0_id = pn0->entityId(); + stk::mesh::EntityId pn1_id = pn1->entityId(); + stk::mesh::EntityId pn2_id = pn2->entityId(); + stk::mesh::EntityId pn3_id = pn3->entityId(); + + ThrowAssert(pn0_id != 0 && pn1_id != 0 && pn2_id != 0 && pn3_id != 0); + + if ((pn0_id < pn1_id) == (pn2_id < pn3_id)) + { + return true; + } + return false; +} + +bool +ElementObj::determine_diagonal_for_internal_quad_of_cut_tet_from_edge_nodes(const Simplex_Generation_Method simplexMethod, const SubElementNode * n0, const SubElementNode * n1, const SubElementNode * n2, const SubElementNode * n3, + const bool face0, const bool face1, const bool face2, const bool face3) +{ + // true: connect n0 and n2, false: connect n1 and n3 + + if (simplexMethod == CUT_QUADS_BY_GLOBAL_IDENTIFIER) + { + SubElementNodeAncestry ancestry0 = n0->get_ancestry(); + SubElementNodeAncestry ancestry1 = n1->get_ancestry(); + SubElementNodeAncestry ancestry2 = n2->get_ancestry(); + SubElementNodeAncestry ancestry3 = n3->get_ancestry(); + + SubElementNodeAncestry ancestry02 = std::min(ancestry0, ancestry2); + SubElementNodeAncestry ancestry13 = std::min(ancestry1, ancestry3); + + return (ancestry02 < ancestry13); + } + + // Make sure that diagonal can be picked either way and still avoid Steiner point + const int caseId = (face0 ? 1 : 0) + (face1 ? 2 : 0) + (face2 ? 4 : 0) + (face3 ? 8 : 0); + ThrowRequire(caseId == 3 || caseId == 5 || caseId == 10 || caseId == 12); + + return (evaluate_quad(n0,n1,n2,n3) == -1); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Element.hpp b/packages/krino/krino/krino_lib/Akri_Element.hpp new file mode 100644 index 000000000000..10f0f06a1da5 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element.hpp @@ -0,0 +1,207 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Element_h +#define Akri_Element_h + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" +namespace krino { + +class SubElement; +class SubElementNode; +class ProlongationElementData; +class IntersectionPoint; +class ElementIntersection; + +class ElementObj { +public: + + ElementObj(const stk::mesh::BulkData & stkMesh, stk::mesh::Entity elemEntity); + ElementObj(const stk::topology elem_topology, const NodeVec & nodes); + + virtual ~ElementObj(); // Definition must in implementation file because SubElement is incomplete + + static bool is_less(const ElementObj * elem0,const ElementObj * elem1) { return (elem0->entityId() < elem1->entityId()); } + + static int evaluate_quad(const SubElementNode * n0, const SubElementNode * n1, const SubElementNode * n2, const SubElementNode * n3); + static int evaluate_quad(const Vector3d & x0, const Vector3d & x1, const Vector3d & x2, const Vector3d & x3); + static bool determine_diagonal_for_internal_quad_of_cut_tet_from_owner_nodes(const SubElementNode * pn0, const SubElementNode * pn1, const SubElementNode * pn2, const SubElementNode * pn3); + static bool determine_diagonal_for_internal_quad_of_cut_tet_from_edge_nodes(const Simplex_Generation_Method simplexMethod, const SubElementNode * n0, const SubElementNode * n1, const SubElementNode * n2, const SubElementNode * n3, + const bool face0, const bool face1, const bool face2, const bool face3); + + int spatial_dim() const { return my_master_elem.topology_dimension(); } + const NodeVec & get_nodes() const { return my_nodes; } + unsigned num_nodes() const { return my_nodes.size(); } + const PhaseTag & get_phase() const { return my_phase; } + void set_phase(const PhaseTag & phase) { my_phase = phase; } + stk::mesh::EntityId entityId() const { return my_entityId; } + bool check_entity(const stk::mesh::BulkData & mesh) const { return (my_entityId == 0) ? (my_entity == stk::mesh::Entity()) : (mesh.is_valid(my_entity) && my_entityId == mesh.identifier(my_entity)); } + stk::mesh::Entity entity() const { return my_entity; } + void set_entity( const stk::mesh::BulkData & mesh, stk::mesh::Entity meshEntity ) const { my_entity = meshEntity; my_entityId = mesh.identifier(my_entity); } + + const MasterElement & master_elem() const { return my_master_elem; } + stk::topology topology() const { return my_master_elem.get_topology(); } + void std_intg_pts( sierra::Array & intg_pt_locations, + sierra::Array & intg_weights, + sierra::ArrayContainer & det_J, + const sierra::ArrayContainer & coords, + const MasterElement & me ) const; + void std_intg_pts( sierra::Array & intg_pt_locations, + sierra::Array & intg_weights, + sierra::ArrayContainer & det_J, + const sierra::ArrayContainer & coords ) const { std_intg_pts(intg_pt_locations, intg_weights, det_J, coords, my_master_elem); } + + void fill_node_owner_coords(const Mesh_Element * owner, std::vector & coords) const; + Vector3d compute_local_coords_from_owner_coordinates(const Mesh_Element * owner, const Vector3d & coords) const; + + void integration_weights( + std::vector & intg_weights, // includes both gauss point weight and detJ + const MasterElement & me ) const; + void integration_weights( + std::vector & intg_weights ) const { return integration_weights(intg_weights, my_master_elem); } + static void integration_weights( + std::vector & intg_weights, // includes both gauss point weight and detJ + const int numCoordDims, + const std::vector & mesh_coords, + const MasterElement & me, + const MasterElement & mesh_me); + static void integration_weights( + std::vector & intg_weights, // includes both gauss point weight and detJ + const int numCoordDims, + const std::vector & mesh_coords, + const MasterElement & me) { integration_weights(intg_weights, numCoordDims, mesh_coords, me, me); } + static void integration_locations( + std::vector & intg_pt_locations, + const MasterElement & me); + static void gather_nodal_field(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef field, std::vector & result, unsigned dim = 1, unsigned npe = 0); + static double volume(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coords_field); + static PhaseTag update_phase(const CDMesh & mesh, const PhaseTag & startPhase, const InterfaceID interface_key, const int sign); + static PhaseTag update_phase(const CDMesh & mesh, const PhaseTag & startPhase, const std::vector & interfaces, const std::vector & interfaceSigns); + + const MasterElement* get_evaluation_master_element(const FieldRef field) const; + void evaluate_prolongation_field(const CDMesh & mesh, const FieldRef field, const unsigned field_length, const Vector3d & p_coords, double * result) const; + + void add_subelement(std::unique_ptr subelem); + void get_subelements( std::vector & subelems ) const; + void get_subelements( std::vector & subelems ); + bool have_subelements() const { return !my_subelements.empty(); } + unsigned num_subelements() const { return my_subelements.size(); } + bool have_refined_edges() const; + + virtual void determine_decomposed_elem_phase(const CDMesh & mesh) { ThrowRequire(false); } + virtual void cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains); + virtual void cut_face_intersection_point(const int iFace, const Vector3d & pCoords, const std::vector & sortedDomains); + bool have_edges_with_children() const; + bool captures_intersection_point_domains(const std::vector & intersectionPointDomains) const; + bool face_captures_intersection_point_domains(const int iFace, const std::vector & intersectionPointDomains) const; + + ProlongationElementData * get_prolongation_data() const { return my_prolongation_data; } + void set_prolongation_data( ProlongationElementData * data ) const { my_prolongation_data = data; } + + void prolongate_fields(const CDMesh & mesh) const; + +protected: + const MasterElement& my_master_elem; + std::vector my_nodes; + std::vector> my_subelements; + PhaseTag my_phase; + mutable stk::mesh::Entity my_entity; + mutable stk::mesh::EntityId my_entityId; + mutable ProlongationElementData * my_prolongation_data; + +private: + //: Default constructor not allowed + ElementObj(); +}; + +class Mesh_Element : public ElementObj { +public: + + Mesh_Element(CDMesh & mesh, stk::mesh::Entity elemEntity); + + virtual ~Mesh_Element(); + + static bool is_supported_topology(stk::topology elem_topology) { return determine_subelement_topology(elem_topology).first != stk::topology::INVALID_TOPOLOGY; } + static std::pair determine_subelement_topology(stk::topology elem_topology); + + Vector3d get_node_parametric_coords( const int lnn ) const; + Vector3d get_node_parametric_coords( const SubElementNode * node ) const; + + const MasterElement & coord_master_elem() const { return my_master_elem; } + + stk::topology coord_topology() const { return my_master_elem.get_topology(); } + + const stk::topology & subelement_topology() const { return my_subelement_topology; } + int subelement_order() const { return my_subelement_order; } + + std::string visualize(const CDMesh & mesh) const; + double interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const; + int interface_node_sign(const InterfaceID interface, const SubElementNode * node) const; + void fill_face_interior_intersections(const NodeVec & faceNodes, const InterfaceID & interface1, const InterfaceID & interface2, std::vector & faceIntersectionPoints) const; + double interface_crossing_position(const InterfaceID interface, const SubElementNode * node1, const SubElementNode * node2) const; + std::function &)> get_diagonal_picker() const; + + const ElementCutter * get_cutter() const { return myCutter.get(); } + ElementCutter * get_cutter() { return myCutter.get(); } + + bool is_prolonged() const; + Vector3d coordinates( const Vector3d & p_coords ) const; + + PhaseTag determine_phase_at_location(const Vector3d & location) const; + bool have_interface() const { return my_have_interface; } + bool have_interface(const InterfaceID interface) const { return std::binary_search(myCuttingInterfaces.begin(), myCuttingInterfaces.end(), interface); } + int get_num_interfaces() const { return myCuttingInterfaces.size(); } + int get_interface_index(const InterfaceID interface) const; + const std::vector & get_sorted_cutting_interfaces() const { return myCuttingInterfaces; } + virtual void determine_decomposed_elem_phase(const CDMesh & mesh) override; + + bool triangulate(const CDMesh & mesh, const InterfaceGeometry & interfaceGeometry); //return value indicates if any changes were made + void create_cutter(const CDMesh & mesh, const InterfaceGeometry & interfaceGeometry); + void create_base_subelement(); + void determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key); + void determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key); + void decompose(CDMesh & mesh, const InterfaceID interface_key); + void handle_hanging_children(CDMesh & mesh, const InterfaceID & interface); + void build_quadratic_subelements(CDMesh & mesh); + std::vector get_interface_signs_based_on_crossings(const NodeVec & nodes) const; + void cut_interior_intersection_points(CDMesh & mesh); + + void find_child_coordinates_at_owner_coordinates(const Vector3d & ownerCoordinates, const ElementObj *& child, Vector3d & child_p_coords) const; + + double volume() const; + + bool is_single_coincident() const; + +private: + Mesh_Element() = delete; + Vector3d get_intersection_point_parametric_coordinates(const IntersectionPoint & intersectionPoint) const; + std::vector gather_nodal_coordinates() const; + + int my_subelement_order; + stk::topology my_subelement_topology; + bool my_have_interface; + + std::unique_ptr myCutter; + std::vector myCuttingInterfaces; +}; + +} // namespace krino + +#endif // Akri_Element_h diff --git a/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.cpp b/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.cpp new file mode 100644 index 000000000000..e640df211435 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.cpp @@ -0,0 +1,184 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" +#include + +namespace krino { + +static void fill_nodal_shape_functions(const MasterElement & masterElement, const Vector3d & elementParametricCoords, std::vector & nodalShapeFunctions) +{ + const int npe = masterElement.num_nodes(); + nodalShapeFunctions.resize(npe); + masterElement.shape_fcn(1, elementParametricCoords.data(), nodalShapeFunctions.data()); +} + +static ElementIntersectionPointFilter build_element_intersection_filter(const std::vector & nodes, + const IntersectionPointFilter & intersectionPointFilter) +{ + auto filter = + [&nodes, &intersectionPointFilter](const std::vector & intersectionPointSortedDomains) + { + return intersectionPointFilter(nodes, intersectionPointSortedDomains); + }; + return filter; +} + +static void append_intersection_points_from_interior(const MasterElement & masterElement, + const std::vector & intersectionPointNodes, + const std::vector & interiorIntersections, + std::vector & intersectionPoints) +{ + if (interiorIntersections.empty()) + return; + + const bool intersectionPointIsOwned = true; + + std::vector intersectionPointWeights; + for (auto & interiorIntersection : interiorIntersections) + { + fill_nodal_shape_functions(masterElement, interiorIntersection.parametricCoords, intersectionPointWeights); + intersectionPoints.emplace_back(intersectionPointIsOwned, intersectionPointNodes, intersectionPointWeights, interiorIntersection.sortedDomains); + } +} + +static void append_intersection_points_from_element_face(const MasterElement & elementMasterElement, + const std::vector & elementNodes, + const int iFace, + const ElementCutter & elementCutter, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) +{ + std::vector interiorIntersections; + + const std::vector interfaces = elementCutter.get_sorted_cutting_interfaces(); + + std::array faceNodeOrdinals; + elementMasterElement.get_topology().face_node_ordinals(iFace, faceNodeOrdinals.data()); + const std::vector faceNodes{elementNodes[faceNodeOrdinals[0]], elementNodes[faceNodeOrdinals[1]], elementNodes[faceNodeOrdinals[2]]}; + const double * elemNodeParamCoords = elementMasterElement.nodal_parametric_coordinates(); + const std::array faceNodeCoordinates = {{Vector3d(elemNodeParamCoords+3*faceNodeOrdinals[0]), Vector3d(elemNodeParamCoords+3*faceNodeOrdinals[1]), Vector3d(elemNodeParamCoords+3*faceNodeOrdinals[2])}}; + + const MasterElement & faceMasterElement = MasterElementDeterminer::getMasterElement(elementMasterElement.get_topology().face_topology(iFace)); + const ElementIntersectionPointFilter faceIntersectionPointFilter = build_element_intersection_filter(faceNodes, intersectionPointFilter); + + std::vector sortedDomains; + for (size_t i1=0; i1 & elementNodes, + const int iFace) +{ + stk::mesh::EntityId elementId = mesh.identifier(element); + std::vector faceNodes(elementTopology.face_topology(iFace).num_nodes()); + std::vector faceElements; + elementTopology.face_nodes(elementNodes, iFace, faceNodes.data()); + stk::mesh::get_entities_through_relations(mesh, faceNodes, stk::topology::ELEMENT_RANK, faceElements); + + for (auto faceElement : faceElements) + if (mesh.identifier(faceElement) < elementId && elementSelector(mesh.bucket(faceElement))) + return false; + return true; +} + +static void append_intersection_points_from_within_element_and_owned_faces(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & parentElementSelector, + const stk::mesh::Entity element, + const InterfaceGeometry & geometry, + const std::function &)> & diagonalPicker, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) +{ + stk::topology elementTopology = mesh.bucket(element).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + const std::vector elementNodes(mesh.begin_nodes(element), mesh.end_nodes(element)); + + std::unique_ptr elementCutter = geometry.build_element_cutter(mesh, element, diagonalPicker); + if (elementCutter->might_have_interior_or_face_intersections()) + { + append_intersection_points_from_element_interior(masterElement, elementNodes, *elementCutter, intersectionPointFilter, intersectionPoints); + + const int numFaces = masterElement.get_topology().num_faces(); + if (numFaces > 0) + { + for (int iFace=0; iFace &)> +temporary_build_always_true_diagonal_picker() +{ + auto diagonalPicker = + [](const std::array & faceNodes) + { + return true; + }; + return diagonalPicker; +} + +void append_intersection_points_from_within_elements_and_owned_faces(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & parentElementSelector, + const std::vector & elements, + const InterfaceGeometry & geometry, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) +{ + const auto diagonalPicker = temporary_build_always_true_diagonal_picker(); + + for (auto element : elements) + { + if (parentElementSelector(mesh.bucket(element))) + { + append_intersection_points_from_within_element_and_owned_faces(mesh, + parentElementSelector, + element, + geometry, + diagonalPicker, + intersectionPointFilter, + intersectionPoints); + } + } +} + +void append_intersection_points_from_element_interior(const MasterElement & masterElement, + const std::vector & nodes, + const ElementCutter & elementCutter, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) +{ + std::vector interiorIntersections; + const ElementIntersectionPointFilter elementIntersectionPointFilter = build_element_intersection_filter(nodes, intersectionPointFilter); + elementCutter.fill_interior_intersections(elementIntersectionPointFilter, interiorIntersections); + append_intersection_points_from_interior(masterElement, nodes, interiorIntersections, intersectionPoints); +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.hpp b/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.hpp new file mode 100644 index 000000000000..051f02e028fd --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ElementCutterUtils.hpp @@ -0,0 +1,37 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_ELEMENTCUTTERUTILS_H_ +#define KRINO_INCLUDE_AKRI_ELEMENTCUTTERUTILS_H_ +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +void append_intersection_points_from_element_interior(const MasterElement & masterElement, + const std::vector & nodes, + const ElementCutter & elementCutter, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints); + +void append_intersection_points_from_within_elements_and_owned_faces(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & parentElementSelector, + const std::vector & elements, + const InterfaceGeometry & geometry, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints); + +} + +#endif /* KRINO_INCLUDE_AKRI_ELEMENTCUTTERUTILS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_Element_Cutter.cpp b/packages/krino/krino/krino_lib/Akri_Element_Cutter.cpp new file mode 100644 index 000000000000..bea70cbe6fdb --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element_Cutter.cpp @@ -0,0 +1,1064 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "Akri_MasterElementDeterminer.hpp" + +namespace krino { + +bool all_interfaces_have_single_level_set(const std::vector &interfaces) +{ + for (auto && interface : interfaces) + if (interface.first_ls() != interface.second_ls()) + return false; + return true; +} + +void fill_sorted_domains(const bool isOneLSPerPhase,const InterfaceID & interface0, const InterfaceID & interface1, std::vector & sortedDomains) +{ + sortedDomains.clear(); + if (isOneLSPerPhase) + { + + sortedDomains = {interface0.first_ls(), interface0.second_ls(), interface1.first_ls(), interface1.second_ls()}; + stk::util::sort_and_unique(sortedDomains); + } + else + { + ThrowAssert(all_interfaces_have_single_level_set({interface0, interface1})); + sortedDomains = {interface0.first_ls(), interface1.first_ls()}; + } +} + +void fill_sorted_domains(const bool isOneLSPerPhase,const InterfaceID & interface0, const InterfaceID & interface1, const InterfaceID & interface2, std::vector & sortedDomains) +{ + sortedDomains.clear(); + if (isOneLSPerPhase) + { + + sortedDomains = {interface0.first_ls(), interface0.second_ls(), interface1.first_ls(), interface1.second_ls(), interface2.first_ls(), interface2.second_ls()}; + stk::util::sort_and_unique(sortedDomains); + } + else + { + ThrowAssert(all_interfaces_have_single_level_set({interface0, interface1, interface2})); + sortedDomains = {interface0.first_ls(), interface1.first_ls(), interface2.first_ls()}; + } +} + +bool sorted_domains_form_triple_point(const bool is_one_interface_per_phase, const std::vector & sortedDomains) +{ + return !is_one_interface_per_phase || sortedDomains.size() == 3; +} + +bool sorted_domains_form_quadruple_point(const bool is_one_interface_per_phase, const std::vector & sortedDomains) +{ + return !is_one_interface_per_phase || sortedDomains.size() == 4; +} + +void fill_tetrahedron_face_surface_intersection_points(const int iFace, const Cutting_Surface * surf0, const Cutting_Surface * surf1, const std::vector & sortedDomains, std::vector & intersections) +{ + Vector3d intersectionPoint; + if (find_intersection_of_two_planes_and_side_of_tet(iFace, surf0->get_plane(), surf1->get_plane(), intersectionPoint)) + intersections.emplace_back(intersectionPoint, sortedDomains); +} + +void fill_tetrahedron_interior_surface_intersection_points(const Cutting_Surface * surf0, const Cutting_Surface * surf1, const Cutting_Surface * surf2, const std::vector & sortedDomains, std::vector & intersections) +{ + Vector3d intersectionPoint; + if (find_intersection_of_three_planes_within_tet(surf0->get_plane(), surf1->get_plane(), surf2->get_plane(), intersectionPoint)) + intersections.emplace_back(intersectionPoint, sortedDomains); +} + +std::string visualize_element(const stk::topology & topology, std::array & usedGeomIds) +{ + const auto & masterElem = MasterElementDeterminer::getMasterElement(topology); + const double * elemNodeParamCoords = masterElem.nodal_parametric_coordinates(); + + const unsigned numNodes = topology.num_nodes(); + const int dim = topology.dimension(); + + std::ostringstream os; + for (unsigned n=0; n usedGeomIds{0,0,0,0}; + std::string viz = visualize_element(topology, usedGeomIds); + for (auto && cuttingSurf : cuttingSurfaces) + { + std::ostringstream os; + os << cuttingSurf.first; + const std::string interfaceDesc = "on interface " + os.str(); + viz += cuttingSurf.second->print_visualization(usedGeomIds, interfaceDesc); + } + return viz; +} + + +void Element_Cutter::fill_triangle_interior_intersection_points(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const +{ + std::vector interfacesWithCuttingSurface; + fill_interfaces_with_cutting_surface(interfacesWithCuttingSurface); + + std::vector sortedDomains; + std::set> alreadyFound; + Vector3d intersectionPoint; + + intersections.clear(); + for (size_t index0=0; index0get_plane(); + const Plane3d & plane1 = cutting_surfaces.at(interfacesWithCuttingSurface[index1])->get_plane(); + if (find_intersection_of_two_2D_planes_within_tri(plane0, plane1, intersectionPoint) && + intersection_point_is_real(intersectionPoint, sortedDomains)) + { + intersections.emplace_back(intersectionPoint, sortedDomains); + } + } + } + } +} + +void Element_Cutter::fill_tetrahedron_face_interior_intersections(const std::array & faceNodes, + const InterfaceID & interface1, + const InterfaceID & interface2, + const ElementIntersectionPointFilter & intersectionPointFilter, + std::vector & intersections) const +{ + const Plane3d facePlane{faceNodes[0], faceNodes[1], faceNodes[2]}; + + std::vector sortedDomains; + Vector3d intersectionPoint; + + intersections.clear(); + fill_sorted_domains(is_one_ls_per_phase(), interface1, interface2, sortedDomains); + if (sorted_domains_form_triple_point(is_one_ls_per_phase(), sortedDomains)) + { + const Plane3d & plane0 = cutting_surfaces.at(interface1)->get_plane(); + const Plane3d & plane1 = cutting_surfaces.at(interface2)->get_plane(); + if (intersectionPointFilter(sortedDomains) && + find_intersection_of_three_planes(plane0, plane1, facePlane, intersectionPoint) && + intersection_point_is_real(intersectionPoint, sortedDomains)) + { + const Vector3d faceCoords = triangle_parametric_coordinates_of_projected_point(faceNodes, intersectionPoint); + if (within_tri_bounds(faceCoords)) + intersections.emplace_back(faceCoords, sortedDomains); + } + } +} + +void Element_Cutter::fill_tetrahedron_interior_intersection_points(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const +{ + std::vector interfacesWithCuttingSurface; + fill_interfaces_with_cutting_surface(interfacesWithCuttingSurface); + + std::vector sortedDomains; + std::set> alreadyFound; + Vector3d intersectionPoint; + + intersections.clear(); + for (size_t index0=0; index0get_plane(); + const Plane3d & plane1 = cutting_surfaces.at(interfacesWithCuttingSurface[index1])->get_plane(); + const Plane3d & plane2 = cutting_surfaces.at(interfacesWithCuttingSurface[index2])->get_plane(); + if (find_intersection_of_three_planes_within_tet(plane0, plane1, plane2, intersectionPoint) && + intersection_point_is_real(intersectionPoint, sortedDomains)) + { + intersections.emplace_back(intersectionPoint, sortedDomains); + } + } + } + } + } +} + +static ElementIntersectionPointFilter +keep_all_intersecion_points_filter() +{ + auto filter = + [](const std::vector & intersectionPointSortedDomains) + { + return true; + }; + return filter; +} + +void Element_Cutter::fill_interior_intersections(std::vector & intersections) const +{ + fill_interior_intersections(keep_all_intersecion_points_filter(), intersections); +} + +void Element_Cutter::fill_interior_intersections(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const +{ + if (myTopology.base() == stk::topology::TETRAHEDRON_4) + fill_tetrahedron_interior_intersection_points(intersectionPointFilter, intersections); + else if (myTopology.base() == stk::topology::TRIANGLE_3_2D || myTopology.base() == stk::topology::TRIANGLE_3) + fill_triangle_interior_intersection_points(intersectionPointFilter, intersections); + else + ThrowErrorMsg("Unexepected topology " << myTopology.name()); +} + +std::unique_ptr create_element_cutter(const bool oneLSPerPhase, + const MasterElement & masterElem, + const std::vector & elementParentEdges, + const std::vector & areParentEdgesAreOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker) +{ + std::unique_ptr cutter; + if(oneLSPerPhase) + cutter.reset(new One_LS_Per_Phase_Cutter(masterElem, elementParentEdges, areParentEdgesAreOrientedSameAsElementEdges, intersectingPlanesDiagonalPicker)); + else + cutter.reset(new LS_Per_Interface_Cutter(masterElem, elementParentEdges, areParentEdgesAreOrientedSameAsElementEdges, intersectingPlanesDiagonalPicker)); + + return cutter; +} + + +int +Element_Cutter::sign_at_position(const InterfaceID interface, const Vector3d & p_coords) const +{ + const auto iter = cutting_surfaces.find(interface); + if(iter == cutting_surfaces.end()) + { + // Right now, One_LS_Per_Phase_Cutter does not build up the cutting surfaces for the single_phase case. So + // we need a "default" answer. + return +1; + } + const Cutting_Surface & interface_surface = *(iter->second); + + return interface_surface.sign_at_position(p_coords); +} + +double +Element_Cutter::interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const +{ + ThrowErrorMsgIf(cutting_surfaces.find(interface) == cutting_surfaces.end(), + "No cutting surface found for interface " << interface); + const Cutting_Surface & interface_surface = *(cutting_surfaces.find(interface)->second); + return interface_surface.interface_crossing_position(edge); +} + +void +Element_Cutter::fill_interfaces_with_cutting_surface(std::vector & interfaces) const +{ + interfaces.clear(); + for (auto && entry : cutting_surfaces) + interfaces.push_back(entry.first); +} + +int +Element_Cutter::get_starting_phase_for_cutting_surfaces() const +{ + if (cutting_surfaces.empty()) + return -1; + return cutting_surfaces.begin()->first.first_ls(); +} + +bool +Element_Cutter::have_cutting_surface(const InterfaceID interface) const +{ + return cutting_surfaces.find(interface) != cutting_surfaces.end(); +} + +Cutting_Surface * +Element_Cutter::get_cutting_surface(const InterfaceID interface) const +{ + const auto iter = cutting_surfaces.find(interface); + if (iter != cutting_surfaces.end()) + return iter->second.get(); + return nullptr; +} + +static std::vector< std::array > get_element_edge_node_ordinals(const stk::topology baseTopology) +{ + const unsigned numEdges = baseTopology.num_edges(); + std::vector< std::array > elemEdgeNodeOrdinals(numEdges); + for(unsigned i=0; i < numEdges; ++i) + { + const unsigned * node_ordinals = get_edge_node_ordinals(baseTopology, i); + elemEdgeNodeOrdinals[i][0] = node_ordinals[0]; + elemEdgeNodeOrdinals[i][1] = node_ordinals[1]; + } + return elemEdgeNodeOrdinals; +} + +static std::vector +get_parametric_node_coords_on_element_nodes_and_cut_edges(const MasterElement & masterElem, + const std::vector & cutEdges, + const std::vector< std::array > elemEdgeNodeOrdinals) +{ + const stk::topology baseTopology = masterElem.get_topology().base(); + const double * elemNodeParamCoords = masterElem.nodal_parametric_coordinates(); + + const unsigned numNodes = baseTopology.num_nodes(); + const unsigned numEdges = baseTopology.num_edges(); + const int dim = baseTopology.dimension(); + + std::vector nodeParamCoords(numNodes+numEdges); + + for (unsigned n=0; n +get_node_signs_on_element_nodes(const stk::topology baseTopology, + const std::vector & cutEdges, + const std::vector< std::array > elemEdgeNodeOrdinals) +{ + const unsigned numNodes = baseTopology.num_nodes(); + std::vector nodeSigns(numNodes,-2); + + unsigned edge_error = 0; + for (auto && cut_edge : cutEdges) + { + const unsigned edge = cut_edge.edge; + const unsigned node0_ord = elemEdgeNodeOrdinals[edge][0]; + const unsigned node1_ord = elemEdgeNodeOrdinals[edge][1]; + + int node0_sign = -cut_edge.sign; + int node1_sign = cut_edge.sign; + + if (cut_edge.pos < Element_Cutter::theSnapToNodeTol) + node0_sign = 0; + else if (cut_edge.pos > 1.-Element_Cutter::theSnapToNodeTol) + node1_sign = 0; + + if ((nodeSigns[node0_ord]*node0_sign == -1) || + (nodeSigns[node1_ord]*node1_sign == -1)) + edge_error += 1< 0) + { + std::ostringstream err_msg; + err_msg << "Edge crossings are not consistent: " << std::endl; + for(auto && cut_edge : cutEdges) + { + const unsigned edge = cut_edge.edge; + const double pos = cut_edge.pos; + const int sign = cut_edge.sign; + const unsigned node0_ord = elemEdgeNodeOrdinals[edge][0]; + const unsigned node1_ord = elemEdgeNodeOrdinals[edge][1]; + err_msg << " Edge: " << edge << " error = " << ((edge_error & (1< 0) << " pos = " << pos << " sign = " << sign << " node0_ord = " << node0_ord << " node1_ord = " << node1_ord << std::endl; + } + krinolog << err_msg.str(); + throw std::runtime_error(err_msg.str()); + } + + return nodeSigns; +} + +static std::shared_ptr +build_triangle_cutting_surface(const std::vector & nodeSigns, const std::vector & nodeParamCoords) +{ + const int case_id = (nodeSigns[0]+1) + + (nodeSigns[1]+1)*3 + + (nodeSigns[2]+1)*9; + + static const unsigned case_permutations[] = + { 0, 0, 0, 2, 0, 0, 2, 1, 1, 1, // 0-9 + 1, 2, 2, 0, 2, 2, 1, 1, 1, 1, // 10-19 + 2, 0, 0, 2, 0, 0, 0 }; // 20-26 + + stk::topology topo = stk::topology::TRIANGLE_6_2D; + std::vector permute(6); + topo.permutation_node_ordinals(case_permutations[case_id], permute.begin()); + + const unsigned i0 = permute[0]; + const unsigned i1 = permute[1]; + const unsigned i2 = permute[2]; + const unsigned i3 = permute[3]; + const unsigned i5 = permute[5]; + + const int permute_case_id = + (nodeSigns[i0]+1) + + (nodeSigns[i1]+1)*3 + + (nodeSigns[i2]+1)*9; + + switch (permute_case_id) + { + case 1: // ls[0]==0 && ls[1]<0 && ls[2]<0 + case 25: // ls[0]==0 && ls[1]>0 && ls[2]>0 + { + ThrowAssert((nodeSigns[i0] == 0 && nodeSigns[i1] < 0 && nodeSigns[i2] < 0) || (nodeSigns[i0] == 0 && nodeSigns[i1] > 0 && nodeSigns[i2] > 0)); + return (permute_case_id==1) ? + (std::make_shared(nodeParamCoords[i0], (nodeParamCoords[i0] + nodeParamCoords[i1] - nodeParamCoords[i2]))) : + (std::make_shared(nodeParamCoords[i0], (nodeParamCoords[i0] + nodeParamCoords[i2] - nodeParamCoords[i1]))); + } + break; + + case 2: // ls[0]>0 && ls[1]<0 && ls[2]<0 + case 24: // ls[0]<0 && ls[1]>0 && ls[2]>0) + { + ThrowAssert((nodeSigns[i0] > 0 && nodeSigns[i1] < 0 && nodeSigns[i2] < 0) || (nodeSigns[i0] < 0 && nodeSigns[i1] > 0 && nodeSigns[i2] > 0)); + return (permute_case_id==2) ? + (std::make_shared(nodeParamCoords[i5], nodeParamCoords[i3])) : + (std::make_shared(nodeParamCoords[i3], nodeParamCoords[i5])); + } + break; + + case 5: // ls[0]>0 && ls[1]==0 && ls[2]<0 + case 21: // ls[0]<0 && ls[1]==0 && ls[2]>0 + { + ThrowAssert((nodeSigns[i0] > 0 && nodeSigns[i1] == 0 && nodeSigns[i2] < 0) || (nodeSigns[i0] < 0 && nodeSigns[i1] == 0 && nodeSigns[i2] > 0)); + return (permute_case_id==5) ? + (std::make_shared(nodeParamCoords[i5], nodeParamCoords[i1])) : + (std::make_shared(nodeParamCoords[i1], nodeParamCoords[i5])); + } + break; + + case 4: // ls[0]==0 && ls[1]==0 && ls[2]<0 + case 22: // ls[0]==0 && ls[1]==0 && ls[2]>0 + { + ThrowAssert((nodeSigns[i0] == 0 && nodeSigns[i1] == 0 && nodeSigns[i2] < 0) || (nodeSigns[i0] == 0 && nodeSigns[i1] == 0 && nodeSigns[i2] > 0)); + return (permute_case_id==4) ? + (std::make_shared(nodeParamCoords[i0], nodeParamCoords[i1])) : + (std::make_shared(nodeParamCoords[i1], nodeParamCoords[i0])); + } + break; + + default: + { + krinolog << "Case id " << case_id << " " << permute_case_id << stk::diag::dendl; + ThrowRuntimeError("Subelement decomposition error."); + } + } + + ThrowRuntimeError("Subelement decomposition error."); +} + +static std::shared_ptr +build_tetrahedral_cutting_surface(const std::vector & nodeSigns, + const std::vector & nodeParamCoords, + const std::function &)> & intersectingPlanesDiagonalPicker) +{ + const int case_id = (nodeSigns[0]+1) + + (nodeSigns[1]+1)*3 + + (nodeSigns[2]+1)*9 + + (nodeSigns[3]+1)*27; + + static const unsigned case_permutations[] = + { 0, 0, 0, 1, 0, 0, 1, 5, 0, 2, // 0-9 + 2, 6, 1, 0, 0, 1, 1,10, 2, 2, // 10-19 + 2,11, 2, 4, 1, 8, 4, 4, 3, 3, // 20-29 + 4, 3, 3, 9, 5, 7, 7, 6, 6, 9, // 30-39 + 0, 9, 9, 6, 7, 7, 7, 9,11, 3, // 40-49 + 4, 3, 3, 4, 4, 8, 3, 4, 4,11, // 50-59 + 4, 2, 2,10, 8, 1,10, 0, 1, 6, // 60-69 + 2, 2, 7, 5, 1, 0, 0, 1, 0, 0, // 70-79 + 0 }; + + stk::topology full_topology = stk::topology::TETRAHEDRON_10; + std::vector permute_node_ordinals(10); + full_topology.permutation_node_ordinals(case_permutations[case_id], permute_node_ordinals.begin()); + + const unsigned i0 = permute_node_ordinals[0]; + const unsigned i1 = permute_node_ordinals[1]; + const unsigned i2 = permute_node_ordinals[2]; + const unsigned i3 = permute_node_ordinals[3]; + const unsigned i4 = permute_node_ordinals[4]; + const unsigned i5 = permute_node_ordinals[5]; + const unsigned i6 = permute_node_ordinals[6]; + const unsigned i7 = permute_node_ordinals[7]; + const unsigned i8 = permute_node_ordinals[8]; + + const int permute_case_id = (nodeSigns[i0]+1) + + (nodeSigns[i1]+1)*3 + + (nodeSigns[i2]+1)*9 + + (nodeSigns[i3]+1)*27; + + switch (permute_case_id) + { + case 1: // ls[0]=0 && ls[1]<0 && ls[2]<0 && ls[3]<0 + case 79: // ls[0]=0 && ls[1]>0 && ls[2]>0 && ls[3]>0 + { + const Vector3d x0p13 = nodeParamCoords[i0] + nodeParamCoords[i3]-nodeParamCoords[i1]; + const Vector3d x0p12 = nodeParamCoords[i0] + nodeParamCoords[i2]-nodeParamCoords[i1]; + return (permute_case_id==1) ? + (std::make_shared(nodeParamCoords[i0],x0p13,x0p12)) : + (std::make_shared(nodeParamCoords[i0],x0p12,x0p13)); + } + break; + + case 4: // ls[0]=0 && ls[1]=0 && ls[2]<0 && ls[3]<0 + case 76: // ls[0]=0 && ls[1]=0 && ls[2]>0 && ls[3]>0 + { + const Vector3d x0p23 = nodeParamCoords[i0] + nodeParamCoords[i3]-nodeParamCoords[i2]; + return (permute_case_id==4) ? + (std::make_shared(nodeParamCoords[i0],nodeParamCoords[i1],x0p23)) : + (std::make_shared(nodeParamCoords[i1],nodeParamCoords[i0],x0p23)); + } + break; + + case 2: // ls[0]>0 && ls[1]<0 && ls[2]<0 && ls[3]<0 + case 78: // ls[0]<0 && ls[1]>0 && ls[2]>0 && ls[3]>0 + { + ThrowAssert((nodeSigns[i0] > 0 && nodeSigns[i1] < 0 && nodeSigns[i2] < 0 && nodeSigns[i3] < 0) || (nodeSigns[i0] < 0 && nodeSigns[i1] > 0 && nodeSigns[i2] > 0 && nodeSigns[i3] > 0)); + + return (permute_case_id==2) ? + (std::make_shared(nodeParamCoords[i4],nodeParamCoords[i7],nodeParamCoords[i6])) : + (std::make_shared(nodeParamCoords[i4],nodeParamCoords[i6],nodeParamCoords[i7])); + } + break; + + case 5: // ls[0]>0 && ls[1]=0 && ls[2]<0 && ls[3]<0 + case 75: // ls[0]<0 && ls[1]=0 && ls[2]>0 && ls[3]>0 + { + return (permute_case_id==5) ? + (std::make_shared(nodeParamCoords[i1],nodeParamCoords[i7],nodeParamCoords[i6])) : + (std::make_shared(nodeParamCoords[i1],nodeParamCoords[i6],nodeParamCoords[i7])); + } + break; + + case 8: // ls[0]>0 && ls[1]>0 && ls[2]<0 && ls[3]<0 + { + const bool face_diag = intersectingPlanesDiagonalPicker({{i0,i1,i2,i3}}); + return (face_diag) ? + (std::make_shared(nodeParamCoords[i8],nodeParamCoords[i7],nodeParamCoords[i6],nodeParamCoords[i5])) : + (std::make_shared(nodeParamCoords[i7],nodeParamCoords[i6],nodeParamCoords[i5],nodeParamCoords[i8])); + } + break; + + case 13: // ls[0]=0 && ls[1]=0 && ls[2]=0 && ls[3]<0 + case 67: // ls[0]=0 && ls[1]=0 && ls[2]=0 && ls[3]>0 + { + return (permute_case_id==13) ? + (std::make_shared(nodeParamCoords[i0],nodeParamCoords[i2],nodeParamCoords[i1])) : + (std::make_shared(nodeParamCoords[i0],nodeParamCoords[i1],nodeParamCoords[i2])); + } + break; + + case 14: // ls[0]>0 && ls[1]=0 && ls[2]=0 && ls[3]<0 + { + ThrowAssert(nodeSigns[i0] > 0 && nodeSigns[i1] == 0 && nodeSigns[i2] == 0 && nodeSigns[i3] < 0); + return std::make_shared(nodeParamCoords[i2],nodeParamCoords[i1],nodeParamCoords[i7]); + } + break; + + default: + { + krinolog << "Case id " << case_id << " " << permute_case_id << stk::diag::dendl; + ThrowRuntimeError("Subelement decomposition error."); + } + } + + ThrowRuntimeError("Subelement decomposition error."); +} + +static std::shared_ptr +build_cutting_surface(const MasterElement & masterElem, + const std::vector & cutEdges, + const std::function &)> & intersectingPlanesDiagonalPicker) +{ + const stk::topology baseTopology = masterElem.get_topology().base(); + const std::vector< std::array > elemEdgeNodeOrdinals = get_element_edge_node_ordinals(baseTopology); + + const auto nodeParamCoords = get_parametric_node_coords_on_element_nodes_and_cut_edges(masterElem, cutEdges, elemEdgeNodeOrdinals); + const auto nodeSigns = get_node_signs_on_element_nodes(baseTopology, cutEdges, elemEdgeNodeOrdinals); + + if (baseTopology == stk::topology::TRIANGLE_3_2D || baseTopology == stk::topology::TRIANGLE_3) + { + ThrowRequire(cutEdges.size() == 2); + return build_triangle_cutting_surface(nodeSigns, nodeParamCoords); + } + + ThrowRequireMsg(baseTopology == stk::topology::TETRAHEDRON_4, "Unsupported base topology: " << baseTopology.name()); + ThrowRequire(cutEdges.size() == 3 || cutEdges.size() == 4); + return build_tetrahedral_cutting_surface(nodeSigns, nodeParamCoords, intersectingPlanesDiagonalPicker); +} + +bool node_captures_intersection_point_domains(const std::vector & nodeDomains, const std::vector & intersectionPointDomains) +{ + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(nodeDomains, intersectionPointDomains); +} + +template +bool any_node_captures_intersection_point_domains(const NODEDOMAINS & nodesSnappedDomains, const std::vector & intersectionPointDomains) +{ + if (nodesSnappedDomains.empty()) + return false; + for (auto && nodeSnappedDomains : nodesSnappedDomains) + if (node_captures_intersection_point_domains(*nodeSnappedDomains, intersectionPointDomains)) + return true; + return false; +} + +bool intersection_is_already_captured(const std::vector*> & elementNodesSnappedDomains, const std::vector & nodes, const std::vector & intersectionPointDomains) +{ + if (elementNodesSnappedDomains.empty()) + return false; + for (auto && node : nodes) + if (node_captures_intersection_point_domains(*elementNodesSnappedDomains[node], intersectionPointDomains)) + return true; + return false; +} + +LS_Per_Interface_Cutter::LS_Per_Interface_Cutter(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker) + : Element_Cutter(masterElem) +{ + for(auto && interface : get_interfaces_present(parentEdges)) + { + const std::vector cutEdges = build_cut_edges(interface, parentEdges, areParentEdgesOrientedSameAsElementEdges); + ThrowRequire(!cutEdges.empty()); + + cutting_surfaces[interface] = build_cutting_surface(masterElem, cutEdges, intersectingPlanesDiagonalPicker); + } +} + +bool +LS_Per_Interface_Cutter::have_crossing(const InterfaceID interface, const Segment3d & edge) const +{ + const auto iter = cutting_surfaces.find(interface); + ThrowRequire(iter != cutting_surfaces.end()); + const Cutting_Surface & interface_surface = *(iter->second); + return interface_surface.sign_at_position(edge.GetNode(0)) == -interface_surface.sign_at_position(edge.GetNode(1)); +} + +int LS_Per_Interface_Cutter::get_ls_per_interface_phase_at_location(const Vector3d & pCoords) const +{ + ThrowRequireMsg(false, "Improper usage of LS_Per_Interface_Cutter."); + return -1; +} + +void LS_Per_Interface_Cutter::add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const +{ + // For LS_Per_Interface_Cutter, internal intersections only happen if there are edge intersections so nothing to do here. +} + +std::vector +LS_Per_Interface_Cutter::build_cut_edges(const InterfaceID & interface, + const std::vector & parentEdges, + const std::vector & parentEdgeIsOrientedSameAsElementEdge) +{ + std::vector cutEdges; + + for(unsigned i=0; i < parentEdges.size(); ++i) + { + const CDFEM_Parent_Edge * parent_edge = parentEdges[i]; + if(parent_edge) + { + const int crossing_sign = parent_edge->get_crossing_sign(interface); + const double crossing_pos = parent_edge->get_crossing_position(interface); + + if( crossing_pos >= 0. ) + { + const double pos = parentEdgeIsOrientedSameAsElementEdge[i] ? crossing_pos : (1 -crossing_pos); + const int sign = parentEdgeIsOrientedSameAsElementEdge[i] ? crossing_sign : (-crossing_sign); + cutEdges.push_back(Edge_Crossing(i,pos,sign)); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Crossing of edge " << i << " at position " << pos << "\n"; + } + } + } + return cutEdges; +} + +std::vector +One_LS_Per_Phase_Cutter::build_cut_edges(const InterfaceID & interface, + const std::vector & parentEdges, + const std::vector & parentEdgeIsOrientedSameAsElementEdge) +{ + std::vector cutEdges; + + for(unsigned i=0; i < parentEdges.size(); ++i) + { + const CDFEM_Parent_Edge * parent_edge = parentEdges[i]; + if(parent_edge) + { + double crossing_pos; + int crossing_sign; + bool is_fake; + std::tie(crossing_pos, crossing_sign, is_fake) = parent_edge->get_crossing_position_and_sign(interface); + + if( crossing_pos >= 0. ) + { + const double pos = parentEdgeIsOrientedSameAsElementEdge[i] ? crossing_pos : (1 -crossing_pos); + const int sign = parentEdgeIsOrientedSameAsElementEdge[i] ? crossing_sign : (-crossing_sign); + cutEdges.push_back(Edge_Crossing(i,pos,sign)); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Crossing of edge " << i << " for interface " << interface << " at position " << pos << " fake = " << std::boolalpha << is_fake << "\n"; + } + } + } + return cutEdges; +} + +std::shared_ptr One_LS_Per_Phase_Cutter::attempt_to_build_cutting_surface(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker, + const InterfaceID& interface) +{ + std::shared_ptr cuttingSurface; + try + { + const std::vector cutEdges = build_cut_edges(interface, parentEdges, areParentEdgesOrientedSameAsElementEdges); + ThrowRequire(!cutEdges.empty()); + cuttingSurface = build_cutting_surface(masterElem, cutEdges, intersectingPlanesDiagonalPicker); + } + catch (const std::exception & err) + { + std::stringstream err_msg; + err_msg << "Error while cutting element with interface " << interface << std::endl; + err_msg << err.what() << std::endl; + throw std::runtime_error(err_msg.str()); + } + return cuttingSurface; +} + +static std::set determine_optimal_phases_at_location(const Vector3d & location, + const InterfaceToSurface & allSurfaces) +{ + // optimal phases are phases those that are on the "right" side of at least one surface, + // and never on the "wrong" side of an interface + std::set toPhases; + std::set fromPhases; + + for (auto && surface : allSurfaces) + { + const int sign = surface.second->sign_at_position(location); + const int toPhase = (sign < 0) ? surface.first.first_ls() : surface.first.second_ls(); + const int fromPhase = (sign < 0) ? surface.first.second_ls() : surface.first.first_ls(); + toPhases.insert(toPhase); + fromPhases.insert(fromPhase); + } + + for (int phase : fromPhases) + toPhases.erase(phase); + + return toPhases; +} + +bool intersection_point_is_real(const Vector3d & intersectionPoint, + const InterfaceToSurface & allSurfaces, + const std::vector & sortedDomains) +{ + for (auto && surface : allSurfaces) + { + if (!surface.second->on_surface(intersectionPoint, Element_Cutter::theSnapToNodeTol)) + { + const int sign = surface.second->sign_at_position(intersectionPoint); + const int toPhase = (sign < 0) ? surface.first.first_ls() : surface.first.second_ls(); + const int fromPhase = (sign < 0) ? surface.first.second_ls() : surface.first.first_ls(); + const bool toPhaseIsInDomains = std::binary_search(sortedDomains.begin(), sortedDomains.end(), toPhase); + const bool fromPhaseIsInDomains = std::binary_search(sortedDomains.begin(), sortedDomains.end(), fromPhase); + if (!toPhaseIsInDomains && fromPhaseIsInDomains) + return false; + } + } + return true; +} + +static void add_triple_point_interfaces(const bool isOneLSPerPhase, const std::vector & triplePointDomains, std::set & interfaces) +{ + ThrowRequire(triplePointDomains.size() == 3); + if (isOneLSPerPhase) + { + interfaces.insert(InterfaceID(triplePointDomains[0],triplePointDomains[1])); + interfaces.insert(InterfaceID(triplePointDomains[1],triplePointDomains[2])); + interfaces.insert(InterfaceID(triplePointDomains[0],triplePointDomains[2])); + } + else + { + interfaces.insert(InterfaceID(triplePointDomains[0],triplePointDomains[0])); + interfaces.insert(InterfaceID(triplePointDomains[1],triplePointDomains[1])); + interfaces.insert(InterfaceID(triplePointDomains[2],triplePointDomains[2])); + } +} + +static void add_interfaces_that_have_uncaptured_intersection_within_sides_of_tet(const std::vector & elemNodesCoords, + const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface & allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + Vector3d intersectionPoint; + std::vector sortedDomains; + constexpr bool oneLSPerPhase(true); + + stk::topology topology = stk::topology::TETRAHEDRON_4; + std::vector faceNodes(3); + + for (auto && surface1 : allSurfaces) + { + for (auto && surface2 : allSurfaces) + { + if (surface1.first < surface2.first && + (interfacesWithUncapturedCrossings.count(surface1.first) == 0 || interfacesWithUncapturedCrossings.count(surface2.first))) + { + fill_sorted_domains(oneLSPerPhase, surface1.first, surface2.first, sortedDomains); + + if (sorted_domains_form_triple_point(oneLSPerPhase, sortedDomains)) + { + for (int iFace=0; iFace<4; ++iFace) + { + topology.face_node_ordinals(iFace, faceNodes); + const std::array faceNodeCoords{elemNodesCoords[faceNodes[0]], elemNodesCoords[faceNodes[1]], elemNodesCoords[faceNodes[2]]}; + const Plane3d facePlane{elemNodesCoords[faceNodes[0]], elemNodesCoords[faceNodes[1]], elemNodesCoords[faceNodes[2]]}; + if (!intersection_is_already_captured(nodesSnappedDomains, faceNodes, sortedDomains) && + find_intersection_of_three_planes(facePlane, surface1.second->get_plane(), surface2.second->get_plane(), intersectionPoint) && + intersection_point_is_real(intersectionPoint, allSurfaces, sortedDomains)) + { + const Vector3d faceCoords = triangle_parametric_coordinates_of_projected_point(faceNodeCoords, intersectionPoint); + if (within_tri_bounds(faceCoords)) + add_triple_point_interfaces(oneLSPerPhase, sortedDomains, interfacesWithUncapturedCrossings); + } + } + } + } + } + } +} + +static void add_interfaces_that_have_uncaptured_intersection_within_sides_of_tet(const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface & allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + Vector3d intersectionPoint; + std::vector sortedDomains; + constexpr bool oneLSPerPhase(true); + + stk::topology topology = stk::topology::TETRAHEDRON_4; + std::vector faceNodes(3); + + for (auto && surface1 : allSurfaces) + { + for (auto && surface2 : allSurfaces) + { + if (surface1.first < surface2.first && + (interfacesWithUncapturedCrossings.count(surface1.first) == 0 || interfacesWithUncapturedCrossings.count(surface2.first))) + { + fill_sorted_domains(oneLSPerPhase, surface1.first, surface2.first, sortedDomains); + if (sorted_domains_form_triple_point(oneLSPerPhase, sortedDomains)) + { + for (int iFace=0; iFace<4; ++iFace) + { + topology.face_node_ordinals(iFace, faceNodes); + if (!intersection_is_already_captured(nodesSnappedDomains, faceNodes, sortedDomains) && + find_intersection_of_two_planes_and_side_of_tet(iFace, surface1.second->get_plane(), surface2.second->get_plane(), intersectionPoint) && + intersection_point_is_real(intersectionPoint, allSurfaces, sortedDomains)) + add_triple_point_interfaces(oneLSPerPhase, sortedDomains, interfacesWithUncapturedCrossings); + } + } + } + } + } +} + +static void add_interfaces_that_have_uncaptured_intersection_within_tri(const std::vector & elemNodesCoords, + const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface & allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + Vector3d intersectionPoint; + std::vector sortedDomains; + constexpr bool oneLSPerPhase(true); + const std::vector triNodes = {0,1,2}; + + for (auto && surface1 : allSurfaces) + { + for (auto && surface2 : allSurfaces) + { + if (surface1.first < surface2.first && + (interfacesWithUncapturedCrossings.count(surface1.first) == 0 || interfacesWithUncapturedCrossings.count(surface2.first))) + { + fill_sorted_domains(oneLSPerPhase, surface1.first, surface2.first, sortedDomains); + if (sorted_domains_form_triple_point(oneLSPerPhase, sortedDomains) && + !intersection_is_already_captured(nodesSnappedDomains, triNodes, sortedDomains) && + find_intersection_of_two_2D_planes_within_tri(surface1.second->get_plane(), surface2.second->get_plane(), intersectionPoint) && // ASSUME THAT PROVIDED TRIANGLE CONTAINED WITHIN PARENT TRIANGLE + intersection_point_is_real(intersectionPoint, allSurfaces, sortedDomains)) + { + const std::array triNodeCoords{elemNodesCoords[0], elemNodesCoords[1], elemNodesCoords[2]}; + const Vector3d triCoords = triangle_parametric_coordinates_of_projected_point(triNodeCoords, intersectionPoint); + if (within_tri_bounds(triCoords)) + add_triple_point_interfaces(oneLSPerPhase, sortedDomains, interfacesWithUncapturedCrossings); + } + } + } + } +} + +static void add_interfaces_that_have_uncaptured_intersection_within_tri(const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface& allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + Vector3d intersectionPoint; + std::vector sortedDomains; + constexpr bool oneLSPerPhase(true); + const std::vector triNodes = {0,1,2}; + + for (auto && surface1 : allSurfaces) + { + for (auto && surface2 : allSurfaces) + { + if (surface1.first < surface2.first && + (interfacesWithUncapturedCrossings.count(surface1.first) == 0 || interfacesWithUncapturedCrossings.count(surface2.first))) + { + fill_sorted_domains(oneLSPerPhase, surface1.first, surface2.first, sortedDomains); + if (sorted_domains_form_triple_point(oneLSPerPhase, sortedDomains) && + !intersection_is_already_captured(nodesSnappedDomains, triNodes, sortedDomains) && + find_intersection_of_two_2D_planes_within_tri(surface1.second->get_plane(), surface2.second->get_plane(), intersectionPoint) && + intersection_point_is_real(intersectionPoint, allSurfaces, sortedDomains)) + add_triple_point_interfaces(oneLSPerPhase, sortedDomains, interfacesWithUncapturedCrossings); + } + } + } +} + +static void add_interfaces_that_have_uncaptured_intersection_within_element(const stk::topology & baseTopology, + const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface & allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + if (baseTopology == stk::topology::TETRAHEDRON_4) + add_interfaces_that_have_uncaptured_intersection_within_sides_of_tet(nodesSnappedDomains, allSurfaces, interfacesWithUncapturedCrossings); + else if (baseTopology == stk::topology::TRIANGLE_3 || baseTopology == stk::topology::TRIANGLE_3_2D) + add_interfaces_that_have_uncaptured_intersection_within_tri(nodesSnappedDomains, allSurfaces, interfacesWithUncapturedCrossings); + else + ThrowRequireMsg(false, "Unsupported topology " << baseTopology); +} + +static void add_interfaces_that_have_uncaptured_intersection_within_element(const stk::topology & baseTopology, + const std::vector & elemNodesCoords, + const std::vector*> & nodesSnappedDomains, + const InterfaceToSurface & allSurfaces, + std::set & interfacesWithUncapturedCrossings) +{ + if (baseTopology == stk::topology::TETRAHEDRON_4) + add_interfaces_that_have_uncaptured_intersection_within_sides_of_tet(elemNodesCoords, nodesSnappedDomains, allSurfaces, interfacesWithUncapturedCrossings); + else if (baseTopology == stk::topology::TRIANGLE_3 || baseTopology == stk::topology::TRIANGLE_3_2D) + add_interfaces_that_have_uncaptured_intersection_within_tri(elemNodesCoords, nodesSnappedDomains, allSurfaces, interfacesWithUncapturedCrossings); + else + ThrowRequireMsg(false, "Unsupported topology " << baseTopology); +} + +void One_LS_Per_Phase_Cutter::add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const +{ + // Does not consider uncaptured edge crossings, these should be considered already + add_interfaces_that_have_uncaptured_intersection_within_element(myTopology.base(), elemNodesCoords, elemNodesSnappedDomains, all_cutting_surfaces, interfacesWithUncapturedCrossings); +} + +bool +One_LS_Per_Phase_Cutter::have_crossing(const InterfaceID interface, const Segment3d & edge) const +{ + const auto iter = cutting_surfaces.find(interface); + ThrowRequire(iter != cutting_surfaces.end()); + const Cutting_Surface & interface_surface = *(iter->second); + if (interface_surface.sign_at_position(edge.GetNode(0)) == -interface_surface.sign_at_position(edge.GetNode(1))) + { + const double loc = interface_crossing_position(interface, edge); + const Vector3d intersectionPoint = (1.-loc)*edge.GetNode(0) + loc*edge.GetNode(1); + return krino::intersection_point_is_real(intersectionPoint, all_cutting_surfaces, {interface.first_ls(), interface.second_ls()}); + } + return false; +} + +int One_LS_Per_Phase_Cutter::get_ls_per_interface_phase_at_location(const Vector3d & pCoords) const +{ + const std::set optimalPhases = determine_optimal_phases_at_location(pCoords, all_cutting_surfaces); + ThrowRequireMsg(optimalPhases.size()==1, "Unexpected phase configuration with " << optimalPhases.size() << " optimal phases when evaluated phase at " << pCoords << "\n" << visualize()); + return *optimalPhases.begin(); +} + +bool One_LS_Per_Phase_Cutter::intersection_point_is_real(const Vector3d & intersectionPoint, + const std::vector & sortedDomains) const +{ + return krino::intersection_point_is_real(intersectionPoint, all_cutting_surfaces, sortedDomains); +} + +One_LS_Per_Phase_Cutter::One_LS_Per_Phase_Cutter(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker) + : Element_Cutter(masterElem) +{ + std::set edgePhases = get_phases_present_on_edges_and_interior(parentEdges); + for (int phase1 : edgePhases) + { + for (int phase2 : edgePhases) + { + if (phase2 > phase1) + { + const InterfaceID interface(phase1, phase2); + all_cutting_surfaces[interface] = attempt_to_build_cutting_surface(masterElem, parentEdges, areParentEdgesOrientedSameAsElementEdges, intersectingPlanesDiagonalPicker, interface); + } + } + } + + std::set interfacesWithRealCrossings; + for (auto && interface : get_interfaces_present(parentEdges)) + interfacesWithRealCrossings.insert(interface); + + const std::vector*> emptyNodesSnappedDomains; + add_interfaces_that_have_uncaptured_intersection_within_element(myTopology.base(), emptyNodesSnappedDomains, all_cutting_surfaces, interfacesWithRealCrossings); + + for (auto && interface : interfacesWithRealCrossings) + cutting_surfaces[interface] = all_cutting_surfaces.at(interface); +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_Element_Cutter.hpp b/packages/krino/krino/krino_lib/Akri_Element_Cutter.hpp new file mode 100644 index 000000000000..0d5a0c2e907f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element_Cutter.hpp @@ -0,0 +1,132 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_ELEMENT_CUTTER_H_ +#define KRINO_INCLUDE_AKRI_ELEMENT_CUTTER_H_ +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +class Cutting_Surface; +class CDFEM_Parent_Edge; +class ElementIntersection; + +typedef std::function &)> ElementIntersectionPointFilter; +typedef std::map> InterfaceToSurface; + +class Element_Cutter +{ +public: + Element_Cutter(const MasterElement & masterElement) : myTopology(masterElement.get_topology()) {} + virtual ~Element_Cutter() {} + double interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const; + int sign_at_position(const InterfaceID interface, const Vector3d & p_coords) const; + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const = 0; + virtual int get_ls_per_interface_phase_at_location(const Vector3d & pCoords) const = 0; + virtual void add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const = 0; + + int get_num_cutting_surfaces() const {return cutting_surfaces.size(); } + bool have_cutting_surface(const InterfaceID interface) const; + void fill_interfaces_with_cutting_surface(std::vector & interfaces) const; + Cutting_Surface * get_cutting_surface(const InterfaceID interface) const; + + virtual bool is_one_ls_per_phase() const = 0; + void fill_interior_intersections(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const; + void fill_interior_intersections(std::vector & intersections) const; + void fill_tetrahedron_face_interior_intersections(const std::array & faceNodes, const InterfaceID & interface1, const InterfaceID & interface2, const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const; + static std::string visualize_cutting_surfaces(const stk::topology & topology, const InterfaceToSurface & cuttingSurfaces); + virtual std::string visualize() const { return visualize_cutting_surfaces(myTopology, cutting_surfaces); } + + int get_starting_phase_for_cutting_surfaces() const; + + struct Edge_Crossing { + Edge_Crossing(unsigned e, double p, int s) : edge(e), pos(p), sign(s) {} + unsigned edge; + double pos; + int sign; + }; + + static constexpr double theSnapToNodeTol{1.e-12}; + +protected: + stk::topology myTopology; + InterfaceToSurface cutting_surfaces; + +private: + virtual bool intersection_point_is_real(const Vector3d & intersection, const std::vector & sortedDomains) const = 0; + void fill_triangle_interior_intersection_points(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const; + void fill_tetrahedron_interior_intersection_points(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const; +}; + +class LS_Per_Interface_Cutter : public Element_Cutter +{ +public: + LS_Per_Interface_Cutter(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker); + virtual bool is_one_ls_per_phase() const override { return false; } + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const override; + virtual int get_ls_per_interface_phase_at_location(const Vector3d & pCoords) const override; + virtual void add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const override; +private: + virtual bool intersection_point_is_real(const Vector3d & intersection, const std::vector & sortedDomains) const override { return true; } + static std::vector build_cut_edges(const InterfaceID & interface, + const std::vector & parentEdges, + const std::vector & parentEdgeIsOrientedSameAsElementEdge); +}; + +class One_LS_Per_Phase_Cutter : public Element_Cutter +{ +public: + One_LS_Per_Phase_Cutter(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker); + virtual bool is_one_ls_per_phase() const override { return true; } + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const override; + virtual int get_ls_per_interface_phase_at_location(const Vector3d & pCoords) const override; + virtual void add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const override; + virtual std::string visualize() const override { return visualize_cutting_surfaces(myTopology, all_cutting_surfaces); } + +private: + virtual bool intersection_point_is_real(const Vector3d & intersection, const std::vector & sortedDomains) const override; + static std::vector build_cut_edges(const InterfaceID & interface, + const std::vector & parentEdges, + const std::vector & parentEdgeIsOrientedSameAsElementEdge); + static std::shared_ptr attempt_to_build_cutting_surface(const MasterElement & masterElem, + const std::vector & parentEdges, + const std::vector & areParentEdgesOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker, + const InterfaceID& interface); + + InterfaceToSurface all_cutting_surfaces; +}; + +std::unique_ptr create_element_cutter(const bool oneLSPerPhase, + const MasterElement & masterElem, + const std::vector & elementParentEdges, + const std::vector & areParentEdgesAreOrientedSameAsElementEdges, + const std::function &)> & intersectingPlanesDiagonalPicker); + +} + +#endif /* KRINO_INCLUDE_AKRI_ELEMENT_CUTTER_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_Element_Intersections.cpp b/packages/krino/krino/krino_lib/Akri_Element_Intersections.cpp new file mode 100644 index 000000000000..04d59b4e3da8 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element_Intersections.cpp @@ -0,0 +1,28 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + + +namespace krino { + +std::ostream & operator<<(std::ostream & os, const ElementIntersection & elementIntersection) +{ + os << elementIntersection.parametricCoords << ", interfaces={ "; + for (int domain : elementIntersection.sortedDomains) + os << domain << " "; + os << "}"; + return os; +} + +} + diff --git a/packages/krino/krino/krino_lib/Akri_Element_Intersections.hpp b/packages/krino/krino/krino_lib/Akri_Element_Intersections.hpp new file mode 100644 index 000000000000..2931938ffc81 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Element_Intersections.hpp @@ -0,0 +1,34 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_ELEMENT_INTERSECTIONS_H_ +#define KRINO_INCLUDE_AKRI_ELEMENT_INTERSECTIONS_H_ + +#include +#include +#include + +namespace krino { + +class Element_Cutter; + +struct ElementIntersection +{ + ElementIntersection(const Vector3d & coords, const std::vector & domains) + : parametricCoords(coords), + sortedDomains(domains) {} + + Vector3d parametricCoords; + std::vector sortedDomains; +}; + +std::ostream & operator<<(std::ostream & os, const ElementIntersection& elementIntersection); + +} + +#endif /* KRINO_INCLUDE_AKRI_ELEMENT_INTERSECTIONS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_EntityIdPool.cpp b/packages/krino/krino/krino_lib/Akri_EntityIdPool.cpp new file mode 100644 index 000000000000..6fcebc0157f7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_EntityIdPool.cpp @@ -0,0 +1,92 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino{ + +EntityIdPool::EntityIdPool(stk::mesh::MetaData & meta_data) + : my_meta_data(meta_data), + my_entity_id_pool(meta_data.entity_rank_count()) +{ +} + +stk::mesh::EntityId +EntityIdPool::get_EntityId(stk::mesh::EntityRank rank) +{ + ThrowAssert(static_cast(rank) < my_entity_id_pool.size()); + ThrowRequireMsg(!my_entity_id_pool[rank].empty(), "EntityIdPool is empty for " << rank << "."); + + stk::mesh::EntityId entity_id = my_entity_id_pool[rank].back(); + my_entity_id_pool[rank].pop_back(); + return entity_id; +} + +void +EntityIdPool::reserve(stk::mesh::EntityRank rank, size_t count, bool assert_32bit_ids, bool make_64bit_ids) +{ + my_meta_data.mesh_bulk_data().generate_new_ids( rank, count, my_entity_id_pool[rank] ); + ThrowAssert(!make_64bit_ids || !assert_32bit_ids); + if (make_64bit_ids) + { + push_ids_to_64_bit(my_entity_id_pool[rank]); + } + if (assert_32bit_ids && (rank == stk::topology::NODE_RANK || rank == stk::topology::ELEMENT_RANK)) // Only worry about node and elements since they are output + { + check_ids_are_32_bit(rank, my_entity_id_pool[rank]); + } +} + +void +EntityIdPool::generate_new_ids(stk::mesh::BulkData & mesh, stk::mesh::EntityRank rank, size_t count, std::vector & ids, bool assert_32bit_ids, bool make_64bit_ids) +{ + mesh.generate_new_ids( rank, count, ids ); + ThrowAssert(!make_64bit_ids || !assert_32bit_ids); + if (make_64bit_ids) + { + push_ids_to_64_bit(ids); + } + if (assert_32bit_ids && (rank == stk::topology::NODE_RANK || rank == stk::topology::ELEMENT_RANK)) // Only worry about node and elements since they are output + { + check_ids_are_32_bit(rank, ids); + } +} + +void +EntityIdPool::push_ids_to_64_bit(std::vector & ids) +{ + const uint64_t max_32_bit_id = std::numeric_limits::max(); + const bool ids_are_32_bit = !ids.empty() && ids[0] <= max_32_bit_id; + if (ids_are_32_bit) + { + for (auto && id : ids) + { + ThrowRequireMsg(id <= max_32_bit_id, "Mixture of ids above and below 32 bit limit not allowed in push_ids_to_64_bit."); + id += max_32_bit_id; + } + } +} + +void +EntityIdPool::check_ids_are_32_bit(stk::mesh::EntityRank rank, std::vector & ids) +{ + static const uint64_t max_allowed_id = std::numeric_limits::max(); + bool have_bad_id = false; + for (auto && id : ids) + { + if (id > max_allowed_id) + { + have_bad_id = true; + break; + } + } + ThrowRequireMsg(!have_bad_id, "Exhausted valid ids for rank " << rank << "!"); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_EntityIdPool.hpp b/packages/krino/krino/krino_lib/Akri_EntityIdPool.hpp new file mode 100644 index 000000000000..4ecea3088548 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_EntityIdPool.hpp @@ -0,0 +1,39 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_EntityIdPool_h +#define Akri_EntityIdPool_h + +#include +#include + +namespace stk { namespace mesh { class BulkData; } } + +namespace krino { + +class EntityIdPool { +public: + EntityIdPool(stk::mesh::MetaData & meta_data); + ~EntityIdPool() {} + + static void generate_new_ids(stk::mesh::BulkData & mesh, stk::mesh::EntityRank rank, size_t count, std::vector & ids, bool assert_32bit_ids, bool make_64bit_ids); + + void reserve(stk::mesh::EntityRank rank, size_t count, bool assert_32bit_ids, bool make_64bit_ids); + stk::mesh::EntityId get_EntityId(stk::mesh::EntityRank rank); +private: + static void push_ids_to_64_bit(std::vector & ids); + static void check_ids_are_32_bit(stk::mesh::EntityRank rank, std::vector & ids); + +protected: + stk::mesh::MetaData & my_meta_data; + std::vector< std::vector > my_entity_id_pool; +}; + +} // namespace krino + +#endif // Akri_EntityIdPool_h diff --git a/packages/krino/krino/krino_lib/Akri_Facet.cpp b/packages/krino/krino/krino_lib/Akri_Facet.cpp new file mode 100644 index 000000000000..9744abd1fca0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Facet.cpp @@ -0,0 +1,197 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino{ + +// +//-------------------------------------------------------------------------------- + +std::unique_ptr +Facet::unpack_from_buffer( stk::CommBuffer & b ) +{ /* %TRACE% */ /* %TRACE% */ + std::unique_ptr facet; + + int dim = 0; + b.unpack(dim); + + switch(dim) + { + case 2: facet = Facet2d::unpack_from_buffer(b); break; + case 3: facet = Facet3d::unpack_from_buffer(b); break; + default: ThrowRuntimeError("Unrecognized facet dimension."); + } + + ThrowRequire(facet); + return facet; +} + +//-------------------------------------------------------------------------------- + +void +Facet2d::pack_into_buffer(stk::CommBuffer & b) const +{ + const int dim = 2; + b.pack(dim); + for (int n = 0; n < 2; ++n ) + { + const Vector3d & pt = facet_vertex(n); + b.pack(pt[0]); + b.pack(pt[1]); + } +} + +std::unique_ptr +Facet2d::unpack_from_buffer( stk::CommBuffer & b ) +{ /* %TRACE% */ /* %TRACE% */ + std::unique_ptr facet; + + double vx, vy; + b.unpack(vx); + b.unpack(vy); + Vector3d x0( vx, vy, 0.0 ); + b.unpack(vx); + b.unpack(vy); + Vector3d x1( vx, vy, 0.0 ); + + facet = std::make_unique( x0, x1 ); + return facet; +} + +void +Facet3d::pack_into_buffer(stk::CommBuffer & b) const +{ + const int dim = 3; + b.pack(dim); + for (int n = 0; n < 3; ++n ) + { + const Vector3d & pt = facet_vertex(n); + b.pack(pt[0]); + b.pack(pt[1]); + b.pack(pt[2]); + } +} + +std::unique_ptr +Facet3d::unpack_from_buffer( stk::CommBuffer & b ) +{ /* %TRACE% */ /* %TRACE% */ + std::unique_ptr facet; + + double vx, vy, vz; + b.unpack(vx); + b.unpack(vy); + b.unpack(vz); + Vector3d x0( vx, vy, vz ); + b.unpack(vx); + b.unpack(vy); + b.unpack(vz); + Vector3d x1( vx, vy, vz ); + b.unpack(vx); + b.unpack(vy); + b.unpack(vz); + Vector3d x2( vx, vy, vz ); + + facet = std::make_unique( x0, x1, x2 ); + return facet; +} + +std::ostream & Facet3d::put( std::ostream & os ) const +{ /* %TRACE% */ /* %TRACE% */ + // facet info + os << ": facet description: " << std::endl + << " facet point 0 = (" + << facet_vertex(0)[0] << "," + << facet_vertex(0)[1] << "," + << facet_vertex(0)[2] << ")" << std::endl + << " facet point 1 = (" + << facet_vertex(1)[0] << "," + << facet_vertex(1)[1] << "," + << facet_vertex(1)[2] << ")" << std::endl + << " facet point 2 = (" + << facet_vertex(2)[0] << "," + << facet_vertex(2)[1] << "," + << facet_vertex(2)[2] << ")" << std::endl + << " facet area = " << facet_area() << std::endl; + + return os ; +} + +void Facet3d::apply_transformation(const Transformation & transformation) +{ + Vector3d pt0 = facet_vertex(0); + Vector3d pt1 = facet_vertex(1); + Vector3d pt2 = facet_vertex(2); + + transformation.apply(pt0); + transformation.apply(pt1); + transformation.apply(pt2); + + my_facet_tri = Triangle3d( pt0, pt1 , pt2 ); + + my_bounding_box.clear(); + my_bounding_box.accommodate(pt0); + my_bounding_box.accommodate(pt1); + my_bounding_box.accommodate(pt2); +} + +void Facet2d::apply_transformation(const Transformation & transformation) +{ + Vector3d pt0 = facet_vertex(0); + Vector3d pt1 = facet_vertex(1); + + transformation.apply(pt0); + transformation.apply(pt1); + + // create facet segment + my_facet_segment = Segment3d( pt0, pt1 ); + + my_bounding_box.clear(); + my_bounding_box.accommodate(pt0); + my_bounding_box.accommodate(pt1); +} + +std::ostream & Facet2d::put( std::ostream & os ) const +{ /* %TRACE% */ /* %TRACE% */ + // facet info + os << ": facet description: " << std::endl + << " facet point 0 = (" + << facet_vertex(0)[0] << "," + << facet_vertex(0)[1] << ")" << std::endl + << " facet point 1 = (" + << facet_vertex(1)[0] << "," + << facet_vertex(1)[1] << ")" << std::endl + << " facet area = " << facet_area() << std::endl; + + return os ; +} + +Facet3d::Facet3d( const Vector3d & pt0, + const Vector3d & pt1, + const Vector3d & pt2 ) + : Facet(), + my_facet_tri( pt0, pt1, pt2 ) +{ /* %TRACE% */ /* %TRACE% */ + my_bounding_box.accommodate(pt0); + my_bounding_box.accommodate(pt1); + my_bounding_box.accommodate(pt2); +} + +Facet2d::Facet2d( const Vector3d & pt0, + const Vector3d & pt1 ) + : Facet(), + my_facet_segment(pt0, pt1) +{ /* %TRACE% */ /* %TRACE% */ + my_bounding_box.accommodate(pt0); + my_bounding_box.accommodate(pt1); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Facet.hpp b/packages/krino/krino/krino_lib/Akri_Facet.hpp new file mode 100644 index 000000000000..b9da02cdb513 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Facet.hpp @@ -0,0 +1,158 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Facet_h +#define Akri_Facet_h + +#include +#include +#include + +#include + +#include +#include +#include +#include + +namespace stk { class CommBuffer; } + +namespace krino { + +class Facet; +class Transformation; + +typedef std::vector< Facet * > FacetVec; +typedef std::vector< std::unique_ptr > FacetOwningVec; + +class Facet { +public: + Facet() {} + virtual ~Facet() {} + + // for debugging memory usage + virtual size_t storage_size() const = 0; + + virtual std::ostream & put( std::ostream& os ) const = 0; + friend std::ostream & operator << ( std::ostream &os , const Facet &f ) { return f.put(os); } + + // methods for off-processor communication + static std::unique_ptr unpack_from_buffer( stk::CommBuffer & b ); // static method that builds facet from data in buffer for off-processor communication + virtual void pack_into_buffer(stk::CommBuffer & b) const = 0; // pack into buffer for off-processor communication + + virtual Vector3d facet_vertex(const int i) const = 0; + virtual double facet_area() const = 0; + virtual Vector3d facet_normal() const = 0; + virtual bool degenerate() const = 0; + + virtual double point_distance_squared( const Vector3d & x ) const = 0; + virtual double point_distance_squared( const Vector3d & x, Vector2d & parametric_coords ) const = 0; + virtual int point_distance_sign( const Vector3d & x ) const = 0; + virtual Vector3d real_coordinates(const Vector2d & parametric_coords) const = 0; + virtual Vector3d weights(const Vector2d & parametric_coords) const = 0; + + virtual void apply_transformation(const Transformation & transformation) = 0; + + const BoundingBox & bounding_box() const { ThrowAssert (my_bounding_box.valid()); return my_bounding_box; } + static const BoundingBox & get_bounding_box(const Facet * facet) { return facet->bounding_box(); } + +protected: + BoundingBox my_bounding_box; +}; + +class Facet3d : public Facet { +public: + Facet3d( const Vector3d & x0, + const Vector3d & x1, + const Vector3d & x2 ); + Facet3d() = delete; + virtual ~Facet3d() {} + + virtual size_t storage_size() const { return sizeof(Facet3d); } + virtual std::ostream & put( std::ostream& os ) const; + + static std::unique_ptr unpack_from_buffer( stk::CommBuffer & b ); // static method that builds facet from data in buffer for off-processor communication + virtual void pack_into_buffer(stk::CommBuffer & b) const; + + virtual Vector3d facet_vertex(const int i) const { return my_facet_tri.GetNode(i); } + virtual double facet_area() const { return my_facet_tri.area(); } + virtual Vector3d facet_normal() const { return my_facet_tri.normal(); } + virtual bool degenerate() const { return my_facet_tri.normal_dir().zero_length(); } + virtual double point_distance_squared( const Vector3d & x ) const + { return my_facet_tri.DistanceSquared( x ); } + virtual double point_distance_squared( const Vector3d & x, Vector2d & parametric_coords ) const + { return my_facet_tri.DistanceSquared( x, parametric_coords ); } + virtual int point_distance_sign( const Vector3d & x ) const + { return (Dot(my_facet_tri.normal_dir(),x-facet_vertex(0)) < 0.0) ? -1 : 1; } + virtual Vector3d real_coordinates(const Vector2d & parametric_coords) const + { return my_facet_tri.ParametricToRealCoords(parametric_coords); } + virtual Vector3d weights(const Vector2d & parametric_coords) const + { return Vector3d(1.0-parametric_coords[0]-parametric_coords[1],parametric_coords[0],parametric_coords[1]); } + virtual void apply_transformation(const Transformation & transformation); +private: + Triangle3d my_facet_tri; +}; + +class Facet2d : public Facet { +public: + Facet2d( const Vector3d & x0, + const Vector3d & x1 ); + Facet2d() = delete; + virtual ~Facet2d() {} + + virtual size_t storage_size() const { return sizeof(Facet2d); } + virtual std::ostream & put( std::ostream& os ) const; + + static std::unique_ptr unpack_from_buffer( stk::CommBuffer & b ); // static method that builds facet from data in buffer for off-processor communication + virtual void pack_into_buffer(stk::CommBuffer & b) const; + + virtual Vector3d facet_vertex(const int i) const { return my_facet_segment.GetNode(i); } + virtual double facet_area() const { return my_facet_segment.Length(); } + virtual Vector3d facet_normal() const + { return (crossZ(facet_vertex(1)-facet_vertex(0))).unit_vector(); } + virtual bool degenerate() const { return (0.0 == my_facet_segment.Length()); } + virtual double point_distance_squared( const Vector3d & x ) const + { return my_facet_segment.DistanceSquared(x); } + virtual double point_distance_squared( const Vector3d & x, Vector2d & parametric_coords ) const + { return my_facet_segment.DistanceSquared(x, parametric_coords[0]); } + virtual int point_distance_sign( const Vector3d & x ) const + { return (Dot(crossZ(facet_vertex(1)-facet_vertex(0)), x-facet_vertex(0)) < 0.0) ? -1 : 1; } + virtual Vector3d real_coordinates(const Vector2d & parametric_coords) const + { return (1.0-parametric_coords[0])*my_facet_segment.GetNode(0) + parametric_coords[0]*my_facet_segment.GetNode(1); } + virtual Vector3d weights(const Vector2d & parametric_coords) const + { return Vector3d(1.0-parametric_coords[0],parametric_coords[0],0.0); } + virtual void apply_transformation(const Transformation & transformation); +private: + Segment3d my_facet_segment; +}; + +class FacetDistanceQuery { +public: + FacetDistanceQuery() : my_facet(nullptr), my_sqr_distance(0.0) {} + FacetDistanceQuery(const Facet & in_facet, const Vector3d & x) : my_facet(&in_facet), my_query_pt(x) + { + my_sqr_distance = my_facet->point_distance_squared(x, my_parametric_coords); + } + + bool empty() const { return my_facet == nullptr; } + const Facet & facet() const { return *my_facet; } + double distance_squared() const { return my_sqr_distance; } + Vector3d closest_point() const { return my_facet->real_coordinates(my_parametric_coords); } + double signed_distance() const { return std::sqrt(my_sqr_distance)*my_facet->point_distance_sign(my_query_pt); } + Vector3d closest_point_weights() const { return my_facet->weights(my_parametric_coords); } + +private: + const Facet* my_facet; + Vector3d my_query_pt; + double my_sqr_distance; + Vector2d my_parametric_coords; +}; + +} // namespace krino + +#endif // Akri_Facet_h diff --git a/packages/krino/krino/krino_lib/Akri_Faceted_Surface.cpp b/packages/krino/krino/krino_lib/Akri_Faceted_Surface.cpp new file mode 100644 index 000000000000..1c8eca3243f1 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Faceted_Surface.cpp @@ -0,0 +1,494 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include + +namespace krino{ + +Faceted_Surface::Faceted_Surface(const std::string & sn) + : SurfaceThatTakesAdvantageOfNarrowBandAndThereforeMightHaveWrongSign(), + my_name(sn) {} + +void +Faceted_Surface::parallel_distribute_facets(const size_t batch_size, const std::vector & proc_bboxes) +{ + const int num_procs = stk::EnvData::parallel_size(); + if ( num_procs == 1 ) return; + + const int me = stk::EnvData::parallel_rank(); + ThrowRequire(me != 0 || batch_size <= my_local_facets.size()); + + stk::CommSparse comm_sparse(stk::EnvData::parallel_comm()); + + std::vector dest_procs; + std::vector proc_facet_counts; + size_t start = 0; + if (me == 0) + { + dest_procs.resize(batch_size, 0); + proc_facet_counts.resize(num_procs, 0); + start = my_local_facets.size() - batch_size; + for ( size_t index = 0; index < batch_size; ++index ) + { + const Facet * facet = my_local_facets[start+index].get(); + for ( int dest_proc = 1; dest_proc < num_procs; ++dest_proc ) + { + if ( proc_bboxes[dest_proc].intersects(facet->bounding_box()) ) + { + dest_procs[index] = dest_proc; + ++(proc_facet_counts[dest_proc]); + break; + } + } + if (dest_procs[index] == 0) + { + ++(proc_facet_counts[0]); + } + } + } + + // Communication involves two steps, the first one sizes the messages, the second one actually packs and sends the messages + for ( int comm_step = 0; comm_step < 2; ++comm_step) + { + if (me == 0) + { + for ( int dest_proc = 0; dest_proc < num_procs; ++dest_proc ) + { + if (comm_step == 0 && krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "P" << me << ":" + << " Packaging " << proc_facet_counts[dest_proc] + << " facets for proc#" << dest_proc << stk::diag::dendl; + } + + stk::CommBuffer & b = comm_sparse.send_buffer(dest_proc); + b.pack(proc_facet_counts[dest_proc]); + + for ( size_t index = 0; index < batch_size; ++index ) + { + if (dest_procs[index] == dest_proc) + { + const Facet * facet = my_local_facets[start+index].get(); + facet->pack_into_buffer(b); + } + } + } + } + if (comm_step == 0) + { //allocation step + comm_sparse.allocate_buffers(); + } + else + { //communication step + comm_sparse.communicate(); + } + } + + if (me == 0) + { + // delete facets that have been sent away (even if they are headed back to 0) + my_local_facets.erase(my_local_facets.begin()+start, my_local_facets.end()); + } + + // unload, creating locally owned copy of facet + const int recv_proc = 0; + stk::CommBuffer & b = comm_sparse.recv_buffer(recv_proc); + + size_t proc_num_facets_recvd = 0; + b.unpack(proc_num_facets_recvd); + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "P" << stk::EnvData::parallel_rank() << ":" << " Receiving " << proc_num_facets_recvd << " facets from proc#" << recv_proc << stk::diag::dendl; + + for ( size_t n = 0; n < proc_num_facets_recvd; ++n ) + { + std::unique_ptr facet = Facet::unpack_from_buffer( b ); + my_local_facets.emplace_back( std::move(facet) ); + } + ThrowAssert( 0 == b.remaining() ); +} + +void +Faceted_Surface::pack_into_buffer(stk::CommBuffer & b) const +{ + ThrowRuntimeError("pack_into_buffer should not be called for a Faceted_Surface."); +} + +void +Faceted_Surface::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) +{ /* %TRACE[ON]% */ Trace trace__("krino::Faceted_Surface::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length)"); /* %TRACE% */ + + build_local_facets(point_bbox); + + if (my_transformation != nullptr) + { + for ( auto&& facet : my_local_facets ) + { + facet->apply_transformation(*my_transformation); + } + } + + my_bounding_box.clear(); + for (auto && facet : my_local_facets) + { + my_bounding_box.accommodate(facet->bounding_box()); + } + + my_all_facets.clear(); + for ( auto&& facet : my_local_facets ) + { + my_all_facets.push_back(facet.get()); + } + + // Get all remote facets that might be closest to this processors query points + gather_nonlocal_facets(point_bbox, truncation_length); + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "P" << stk::EnvData::parallel_rank() << ":" << " Building facet tree for " << my_all_facets.size() << " facets." << stk::diag::dendl; + + my_facet_tree = std::make_unique>( my_all_facets, Facet::get_bounding_box ); + + if ( krinolog.shouldPrint(LOG_DEBUG) ) + krinolog << "P" << stk::EnvData::parallel_rank() << ": After building search tree, storage size is " << storage_size()/(1024.*1024.) << " Mb." << stk::diag::dendl; +} + +void +Faceted_Surface::gather_nonlocal_facets(const BoundingBox & point_bbox, const double truncation_length) +{ /* %TRACE[ON]% */ Trace trace__("krino::Faceted_Surface::get_nonlocal_descendants(const BoundingBox & point_bbox, const double truncation_length)"); /* %TRACE% */ + + // If truncation length is specified, get all of the facets that are within + // our padded processor's bounding box. + // To do this, see if any local facets lie in the padded nodal bounding box + // of another proc. if so, send them a copy of those facets. + + my_nonlocal_facets.clear(); + + const int num_procs = stk::EnvData::parallel_size(); + if ( num_procs == 1) return; + + // We estimate the padding based on the uppoer bound of the distance from this processor's nodal bounding box + // to the other processors bounding box of facets. This calculation requires that that local + // descendants are already gathered. + + std::vector facet_bboxes; + BoundingBox::gather_bboxes( my_bounding_box, facet_bboxes ); + + double bbox_padding = std::numeric_limits::max(); + for ( int p = 0; p < num_procs; ++p ) + { + const BoundingBox & proc_facet_bbox = facet_bboxes[p]; + if (proc_facet_bbox.valid()) + { + const double upperBnd = std::sqrt(proc_facet_bbox.SqrDistUpperBnd(point_bbox)); + bbox_padding = std::min(bbox_padding,upperBnd); + } + } + if (std::numeric_limits::max() == bbox_padding) + { + bbox_padding = truncation_length; // only should happen for no facets anywhere + } + if (truncation_length > 0.0) + { + bbox_padding = std::min(bbox_padding, truncation_length); + } + + // gather the bounding box sizes for all procs + BoundingBox local_bbox = point_bbox; + std::vector bboxes; + local_bbox.pad(bbox_padding); + BoundingBox::gather_bboxes( local_bbox, bboxes ); + + // determine which facets will be sent to each processor and formulate message sizes + const int me = stk::EnvData::parallel_rank(); + size_t me_intersecting_facet_counts = 0; + std::vector intersecting_facets; + intersecting_facets.reserve(my_all_facets.size()); + + // Perform communication in stages. In the nth stage, processor, p, + // sends facets to processor p+n and receives from p-n. + // In the 0th stage, each processor count how many of its own facets are + // are within that processor's nodal bounding box. + for ( int comm_partner = 0; comm_partner < num_procs; ++comm_partner ) + { + stk::CommSparse comm_sparse(stk::EnvData::parallel_comm()); + + const int dest_proc = (me+comm_partner) % num_procs; + + // Communication involves two steps, the first one sizes the messages, the second one actually packs and sends the messages + for ( int comm_step = 0; comm_step < 2; ++comm_step) + { + if (comm_step == 0) + { + const BoundingBox & proc_bbox = bboxes[dest_proc]; + intersecting_facets.clear(); + if (proc_bbox.intersects(my_bounding_box)) + { + for ( auto&& facet : my_all_facets ) + { + if ( proc_bbox.intersects(facet->bounding_box()) ) + { + intersecting_facets.push_back(facet); + } + } + } + if (dest_proc == me) me_intersecting_facet_counts = intersecting_facets.size(); + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "P" << me << ":" << " Packaging " << intersecting_facets.size() << " facets for proc#" << dest_proc << stk::diag::dendl; + } + + stk::CommBuffer & b = comm_sparse.send_buffer(dest_proc); + if (dest_proc != me) // Don't talk to yourself, it's embarrassing + { + const size_t intersecting_facets_size = intersecting_facets.size(); + b.pack(intersecting_facets_size); + for ( auto&& facet : intersecting_facets ) + { + facet->pack_into_buffer(b); + } + } + + if (comm_step == 0) + { //allocation step + comm_sparse.allocate_buffers(); + } + else + { //communication step + comm_sparse.communicate(); + } + } + + // unload, creating local copies of nonlocal facets + + const int recv_proc = (me+num_procs-comm_partner) % num_procs; + + if (recv_proc != me) + { + stk::CommBuffer & b = comm_sparse.recv_buffer(recv_proc); + + size_t proc_num_facets_recvd = 0; + b.unpack(proc_num_facets_recvd); + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "P" << stk::EnvData::parallel_rank() << ":" << " Receiving " << proc_num_facets_recvd << " facets from proc#" << recv_proc << stk::diag::dendl; + + for ( size_t n = 0; n < proc_num_facets_recvd; ++n ) + { + std::unique_ptr facet = Facet::unpack_from_buffer( b ); + my_nonlocal_facets.emplace_back( std::move(facet) ); + } + ThrowAssert( 0 == b.remaining() ); + } + } + + // only retain intersecting local descendants + if (my_all_facets.size() != me_intersecting_facet_counts) + { + FacetVec local_descendants; + local_descendants.reserve(me_intersecting_facet_counts); + for ( auto&& facet : my_all_facets ) + { + if ( local_bbox.intersects(facet->bounding_box()) ) + { + local_descendants.push_back( facet ); + } + } + my_all_facets.swap(local_descendants); + } + + // copy nonlocal facets into my_descendants + my_all_facets.reserve(my_all_facets.size()+ my_nonlocal_facets.size()); + for (auto && nonlocal_descendant : my_nonlocal_facets) { my_all_facets.push_back(nonlocal_descendant.get()); } +} + +double +Faceted_Surface::point_distance(const Vector3d &x, const double narrow_band_size, const double far_field_value, const bool compute_signed_distance) const +{ /* %TRACE% */ /* %TRACE% */ + ThrowAssertMsg(my_facet_tree, "ERROR: Empty facet tree"); + + // get all facets we need to check + FacetVec facets; + my_facet_tree->find_closest_entities( x, facets, narrow_band_size ); + + if (facets.empty()) + { + ThrowRequire( 0.0 != narrow_band_size || my_facet_tree->empty() ); + return far_field_value; + } + + double dist = 0.0; + if (compute_signed_distance) + { + dist = compute_point_to_facets_distance_by_average_normal(x, facets); + if (0.0 != narrow_band_size && std::abs(dist) > narrow_band_size) + { + dist = far_field_value; + } + } + else + { + double min_sqr_dist = std::numeric_limits::max(); + for ( auto&& facet : facets ) + { + const double sqr_dist = facet->point_distance_squared(x); + if (sqr_dist < min_sqr_dist) + { + min_sqr_dist = sqr_dist; + } + } + if (0.0 != narrow_band_size && min_sqr_dist > narrow_band_size*narrow_band_size) + { + dist = far_field_value; + } + else + { + dist = std::sqrt(min_sqr_dist); + } + } + + return dist; +} + +double +Faceted_Surface::compute_point_to_facets_distance_by_average_normal(const Vector3d &x, const FacetVec & facets) const +{ /* %TRACE% */ /* %TRACE% */ + + // If the closest_point weights are all larger than this value, then the closest point + // is considered to be on the face of the closest facet rather than on the edges of the facet, and + // therefore only the closest facet is considered in the distance calculation. Otherwise, all of the + // facets are considered to compute an average normal in order to compute the distance. + const double edge_tol = 1.e-6; + + std::vector facet_queries; + facet_queries.reserve(facets.size()); + for ( auto&& facet : facets ) + { + if (facet->degenerate()) continue; // Skip zero-sized facets + facet_queries.emplace_back(*facet, x); + } + + ThrowRequireMsg(!facet_queries.empty(), "All facets are degenerate in compute_point_to_facets_distance_by_average_normal."); + + unsigned nearest = 0; + for ( unsigned index=0; index(facets[nearest]) ? 3 : 2; + + bool closest_point_on_edge = false; + for (int d=0; d 0) + { + return std::sqrt(min_sqr_dist); + } + else + { + return -std::sqrt(min_sqr_dist); + } + } +} + +Vector3d +Faceted_Surface::compute_pseudo_normal(const unsigned dim, const std::vector & facet_queries, const unsigned nearest) const +{ + const double tol = 1.e-6; + Vector3d pseudo_normal = Vector3d::ZERO; + Vector3d average_normal = Vector3d::ZERO; + + const Vector3d nearest_closest_point = facet_queries[nearest].closest_point(); + const double nearest_size2 = facet_queries[nearest].facet().bounding_box().SqrSize(); + unsigned close_count = 0; + for ( auto&& query : facet_queries ) + { + const Vector3d closest_point = query.closest_point(); + const double dist2_from_nearest = (closest_point-nearest_closest_point).length_squared(); + if (dist2_from_nearest < tol*tol*nearest_size2) + { + ++close_count; + const Facet & facet = query.facet(); + + average_normal += facet.facet_normal(); + + if (3 == dim) + { + const Vector3d closest_pt_wts = query.closest_point_weights(); + const int closest_node = (closest_pt_wts[0] > closest_pt_wts[1]) ? ((closest_pt_wts[0] > closest_pt_wts[2]) ? 0 : 2) : ((closest_pt_wts[1] > closest_pt_wts[2]) ? 1 : 2); + + const int n0 = closest_node; + const int n1 = (n0<2) ? (n0+1) : 0; + const int n2 = (n1<2) ? (n1+1) : 0; + const Vector3d edge0 = facet.facet_vertex(n1) - facet.facet_vertex(n0); + const Vector3d edge1 = facet.facet_vertex(n2) - facet.facet_vertex(n0); + const double facet_angle = std::acos(Dot(edge0, edge1)/(edge0.length()*edge1.length())); + + pseudo_normal += facet.facet_normal()*facet_angle; + } + } + } + ThrowRequireMsg(close_count>0,"Issue with tolerance in compute_pseudo_normal. No facet found within tolerance of closest point."); + + return (3 == dim && close_count > 2) ? pseudo_normal : average_normal; +} + +size_t +Faceted_Surface::storage_size() const +{ + size_t store_size = sizeof(Faceted_Surface); + if (my_facet_tree) + { + store_size += my_facet_tree->storage_size(); + } + + store_size += utility::storage_size(my_local_facets); + store_size += utility::storage_size(my_nonlocal_facets); + store_size += utility::storage_size(my_all_facets); + + return store_size; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Faceted_Surface.hpp b/packages/krino/krino/krino_lib/Akri_Faceted_Surface.hpp new file mode 100644 index 000000000000..9ff26e6f0142 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Faceted_Surface.hpp @@ -0,0 +1,69 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Faceted_Surface_h +#define Akri_Faceted_Surface_h + +#include +#include +#include + +namespace krino { + +class Faceted_Surface : public SurfaceThatTakesAdvantageOfNarrowBandAndThereforeMightHaveWrongSign { + +public: + Faceted_Surface(const std::string & sn); + + virtual Surface_Type type() const override { return FACETED_SURFACE; } + virtual size_t storage_size() const override; + virtual void pack_into_buffer(stk::CommBuffer & b) const; // pack into buffer for off-processor communication + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) override; + virtual double truncated_point_signed_distance(const Vector3d &x, const double narrow_band_size, const double far_field_value) const override + { + return point_distance(x, narrow_band_size, far_field_value, true); + } + + // query/modify facets + void add( std::unique_ptr facet ) { my_local_facets.emplace_back(std::move(facet)); } + void reserve(unsigned size_) { my_local_facets.reserve(size_); } + unsigned size() const { return my_local_facets.size(); } + unsigned nonlocal_size() const { return my_nonlocal_facets.size(); } + Facet * operator()( const unsigned index ) const { return my_local_facets[index].get(); } + void clear() { my_local_facets.clear(); } + void swap(Faceted_Surface & other) { my_local_facets.swap(other.my_local_facets); } + const FacetOwningVec & get_facets() const { return my_local_facets; } + void parallel_distribute_facets(const size_t batch_size, const std::vector & proc_bboxes); + +public: + void prepare_to_compute(const BoundingBox & point_bbox, const double truncation_length) + { ThrowAssert(nullptr == my_transformation); prepare_to_compute(0.0, point_bbox, truncation_length); } + double point_unsigned_distance(const Vector3d &x, const double narrow_band_size, const double far_field_value) const + { + return point_distance(x, narrow_band_size, far_field_value, false); + } + +private: + virtual void build_local_facets(const BoundingBox & proc_bbox) {} + double point_distance(const Vector3d &x, const double narrow_band_size, const double far_field_value, const bool compute_signed_distance) const; + double compute_point_to_facets_distance_by_average_normal(const Vector3d &x, const FacetVec & facets) const; + Vector3d compute_pseudo_normal(const unsigned dim, const std::vector & facet_queries, const unsigned nearest) const; + void gather_nonlocal_facets(const BoundingBox & local_bbox, const double truncation_length); + + std::string my_name; + FacetOwningVec my_local_facets; + + mutable std::unique_ptr> my_facet_tree; + mutable FacetOwningVec my_nonlocal_facets; + mutable FacetVec my_all_facets; + BoundingBox my_bounding_box; +}; + +} // namespace krino + +#endif // Akri_Faceted_Surface_h diff --git a/packages/krino/krino/krino_lib/Akri_Fast_Marching.cpp b/packages/krino/krino/krino_lib/Akri_Fast_Marching.cpp new file mode 100644 index 000000000000..2a09003eaf2c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Fast_Marching.cpp @@ -0,0 +1,726 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +namespace krino{ + +Fast_Marching::Fast_Marching(LevelSet & ls, const stk::mesh::Selector & selector, stk::diag::Timer & parent_timer) + : my_ls(ls), + my_selector(selector), + my_timer("Fast Marching", parent_timer), + my_tri_timer("Update Triangle", my_timer), + my_tet_timer("Update Tetrahedron", my_timer), + my_fm_node_less(ls.mesh()), + trial_nodes(my_fm_node_less) +{ + ParallelErrorMessage err(mesh().parallel()); + stk::mesh::Selector fieldSelector(my_ls.get_distance_field()); + const stk::mesh::BucketVector& buckets = selector.get_buckets(stk::topology::ELEMENT_RANK); + for (auto && bucket : buckets) + { + if (fieldSelector(*bucket) && + bucket->topology() != stk::topology::TRIANGLE_3_2D && + bucket->topology() != stk::topology::TETRAHEDRON_4) + { + err << "Topology " << bucket->topology().name() << " is not supported in Fast_Marching.\n"; + } + } + check_error(err, "Checking topology"); +} + +void +Fast_Marching::check_error(const ParallelErrorMessage& err, const std::string & context) const +{ + auto globalError = err.gather_message(); + if (globalError.first) + { + krinolog<< "Error in " << context << ":" << stk::diag::dendl; + krinolog << globalError.second << stk::diag::dendl; + } + ThrowRequireMsg(!globalError.first, "Error in " << context << "."); +} + +void Fast_Marching::redistance() +{ + stk::diag::TimeBlock timer__(my_timer); + const FieldRef& dRef = my_ls.get_distance_field(); + const FieldRef& olddRef = my_ls.get_old_distance_field(); + + // make sure field is parallel consistent to start out + { + std::vector parallel_fields(1, &dRef.field()); + stk::mesh::copy_owned_to_shared(mesh(), parallel_fields); + } + + ParallelErrorMessage err(mesh().parallel()); + + initialize(err); + + // neighbors of initial nodes are trial nodes + for ( auto && fm_node : fm_nodes ) + { + if (fm_node.status() == STATUS_INITIAL) + { + update_neighbors(fm_node, err); + } + } + + check_error(err, "Fast Marching Initialization"); + + stk::mesh::Selector globally_shared_selector = my_selector & mesh().mesh_meta_data().globally_shared_part(); + std::vector< stk::mesh::Entity> shared_nodes; + stk::mesh::get_selected_entities( globally_shared_selector, mesh().buckets( stk::topology::NODE_RANK ), shared_nodes ); + + bool done = false; + + const size_t local_num_nodes = fm_nodes.size(); + size_t max_num_nodes = 0; + stk::all_reduce_max(mesh().parallel(), &local_num_nodes, &max_num_nodes, 1); + + const unsigned max_outer_steps = max_num_nodes; // should be overkill + unsigned num_outer_steps = 0; + while (!done) + { + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "num_trial nodes = " << trial_nodes.size() << "\n"; + + if (num_outer_steps++ > max_outer_steps) + { + err << "Error: Outer loop of Fast_Marching::redistance did not converge!\n"; + break; + } + + const unsigned max_inner_steps = 10*max_outer_steps; // should be overkill + unsigned num_inner_steps = 0; + while(!trial_nodes.empty()) + { + auto begin = trial_nodes.begin(); + Fast_Marching_Node & fm_node = **begin; + trial_nodes.erase(begin); + fm_node.set_status(STATUS_ACCEPTED); + update_neighbors(fm_node, err); + if (num_inner_steps++ > max_inner_steps) + { + err << "Error: Inner loop of Fast_Marching::redistance did not converge! Number of trial nodes = " << trial_nodes.size() << "\n"; + } + if (err.have_local_error()) break; + } + + check_error(err, "Fast Marching Iteration"); + + unsigned num_locally_updated = 0; + if (mesh().parallel_size() > 1) + { + for ( auto && shared_node : shared_nodes ) + { + Fast_Marching_Node * fm_node = get_fm_node(shared_node); + if (nullptr != fm_node && fm_node->status() != STATUS_UNUSED) + { + double & node_dist = *field_data(dRef, fm_node->node()); + node_dist = fm_node->signed_dist()*fm_node->sign(); + } + } + stk::mesh::parallel_min(mesh(), {&dRef.field()}); + + for ( auto && shared_node : shared_nodes ) + { + Fast_Marching_Node * fm_node = get_fm_node(shared_node); + if (nullptr != fm_node && fm_node->status() != STATUS_UNUSED) + { + stk::mesh::Entity node = fm_node->node(); + const double min_node_unsigned_dist = *field_data(dRef, node); + const double fm_node_unsigned_dist = fm_node->signed_dist()*fm_node->sign(); + if(min_node_unsigned_dist < fm_node_unsigned_dist) + { + ThrowAssertMsg(fm_node->status() != STATUS_INITIAL || fm_node->status() != STATUS_TRIAL, "Unexpected node to have INITIAL or TRIAL status."); + fm_node->set_signed_dist(min_node_unsigned_dist*fm_node->sign()); + add_trial_node(*fm_node); + ++num_locally_updated; + } + } + } + } + + unsigned num_globally_updated = 0; + stk::all_reduce_sum(mesh().parallel(), &num_locally_updated, &num_globally_updated, 1); + + done = (num_globally_updated == 0); + } + + for ( auto && fm_node : fm_nodes ) + { + if (fm_node.status() == STATUS_TRIAL || fm_node.status() == STATUS_FAR) + { + err << "Node " << mesh().identifier(fm_node.node()) << " with status " << fm_node.status() << " with distance " << fm_node.signed_dist() << " did not get updated!\n"; + } + if (fm_node.status() != STATUS_UNUSED) + { + double & node_dist = *field_data(dRef, fm_node.node()); + node_dist = fm_node.signed_dist(); + } + } + + check_error(err, "Fast Marching Update"); + stk::mesh::field_copy(dRef, olddRef); +} + +Fast_Marching_Node * Fast_Marching::get_fm_node(stk::mesh::Entity node) +{ + if (mesh().is_valid(node) && mesh().local_id(node) < fm_nodes.size()) + { + return &fm_nodes[mesh().local_id(node)]; + } + else + { + return nullptr; + } +} + +void Fast_Marching::initialize(ParallelErrorMessage& err) +{ + stk::mesh::BulkData& stk_mesh = mesh(); + const FieldRef xRef = my_ls.get_coordinates_field(); + const FieldRef dRef = my_ls.get_distance_field(); + + const int dim = mesh().mesh_meta_data().spatial_dimension(); + + fm_nodes.clear(); + fm_nodes.resize(stk::mesh::count_selected_entities(stk_mesh.mesh_meta_data().universal_part(), stk_mesh.buckets(stk::topology::NODE_RANK))); + + std::vector field_nodes; + stk::mesh::Selector field_not_ghost = aux_meta().active_not_ghost_selector() & my_selector & stk::mesh::selectField(dRef); + stk::mesh::get_selected_entities( field_not_ghost, stk_mesh.buckets( stk::topology::NODE_RANK ), field_nodes ); + + for ( auto&& node : field_nodes ) + { + const double * curr_node_dist = field_data(dRef, node); + ThrowAssert(nullptr != curr_node_dist); + + Vector3d coords = Vector3d::ZERO; + const double * xptr = field_data(xRef, node); + ThrowAssert(nullptr != xptr); + for ( int d = 0; d < dim; d++ ) + { + coords[d] = xptr[d]; + } + + Fast_Marching_Node * fm_node = get_fm_node(node); + ThrowAssert(nullptr != fm_node); + *fm_node = Fast_Marching_Node(node,STATUS_FAR,LevelSet::sign(*curr_node_dist) * std::numeric_limits::max(),LevelSet::sign(*curr_node_dist),coords); + } + + // To start the nodes of elements that have interfaces will be redistanced. + // I have tried a few different methods for this distance calculation with varying success. + // We can: + // 1. Use only local facets to redistance the nodes of the element. This appears to not work too + // well because the closest facet to a node might be in an element that does not support the node. + // 2. Use local facets, but use the normal distance instead of the facet distance. This seems to work + // better than (1) usually. However, it seems prone to pathalogical behavior when small facets run + // parallel to an element side, producing inaccurate distance measures on this side. + // 3. Use the standard parallel redistance calculation used in "normal" redistancing. This is susceptible + // to seeing through walls if the walls are thinner than the distance of the nodes of the cut element to + // the surface. + // 4. Start the redistancing from the subelement facets, progressing through the subelements. + // Somewhat surprisingly, this does not work too well. I think this may be due to the obtuse angles + // in the subelement decomposition. The results are very similar to that produced by local redistancing (#1). + // 5. Rescale each cut element so that it has a unit gradient (or prescribed gradient) and set the nodal + // distance to the minimum (magnitude) from all of the supporting elements. This seems to work pretty + // well in the test cases and is completely local, and is not susceptible to seeing through walls. + + { + // Initialize using method #5 (element rescaling) + std::vector field_elems; + stk::mesh::get_selected_entities( field_not_ghost, stk_mesh.buckets( stk::topology::ELEMENT_RANK ), field_elems ); + for (auto&& elem : field_elems) + { + if (have_crossing(elem)) + { + const double speed = my_ls.get_time_of_arrival_speed(elem, err); + initialize_element(elem, speed); + } + } + + if (mesh().parallel_size() > 1) + { + stk::mesh::Selector globally_shared_selector = my_selector & mesh().mesh_meta_data().globally_shared_part(); + std::vector< stk::mesh::Entity> shared_nodes; + stk::mesh::get_selected_entities( globally_shared_selector, stk_mesh.buckets( stk::topology::NODE_RANK ), shared_nodes ); + + for ( auto && shared_node : shared_nodes ) + { + Fast_Marching_Node * fm_node = get_fm_node(shared_node); + if (nullptr != fm_node && fm_node->status() != STATUS_UNUSED) + { + double & node_dist = *field_data(dRef, fm_node->node()); + node_dist = fm_node->signed_dist()*fm_node->sign(); + } + } + stk::mesh::parallel_min(mesh(), {&dRef.field()}); + + for ( auto && shared_node : shared_nodes ) + { + Fast_Marching_Node * fm_node = get_fm_node(shared_node); + if (nullptr != fm_node && fm_node->status() != STATUS_UNUSED) + { + stk::mesh::Entity node = fm_node->node(); + const double min_node_unsigned_dist = *field_data(dRef, node); + const double fm_node_unsigned_dist = fm_node->signed_dist()*fm_node->sign(); + fm_node->set_signed_dist(min_node_unsigned_dist*fm_node->sign()); + if (min_node_unsigned_dist < fm_node_unsigned_dist) + { + fm_node->set_status(STATUS_INITIAL); + } + } + } + } + } +} + +bool +Fast_Marching::have_crossing(const stk::mesh::Entity & elem) const +{ + const FieldRef dRef = my_ls.get_distance_field(); + const unsigned npe = mesh().bucket(elem).topology().num_nodes(); + ThrowAssert(npe > 0); + + const stk::mesh::Entity * elem_nodes = mesh().begin(elem, stk::topology::NODE_RANK); + const double * dist0 = field_data(dRef, elem_nodes[0]); + ThrowAssert(nullptr != dist0); + for (unsigned n=1; n(dRef, elem_nodes[n]); + ThrowAssert(nullptr != dist); + if (LevelSet::sign_change(*dist0, *dist)) + { + return true; + } + } + return false; +} + +static std::function build_get_fm_node_coordinates(Fast_Marching * fm) +{ + return [fm](stk::mesh::Entity node) -> const Vector3d & + { + Fast_Marching_Node * fm_node = fm->get_fm_node(node); + ThrowAssert(fm_node); + return fm_node->coords(); + }; +} + +static double calculate_gradient_magnitude(const int npe, + const stk::mesh::Entity * elem_nodes, + const FieldRef dRef, + const std::function & get_coordinates) +{ + double mag_grad = 1.0; + + if (3 == npe) + { + const double d0 = *field_data(dRef, elem_nodes[0]); + const double d10 = *field_data(dRef, elem_nodes[1])-d0; + const double d20 = *field_data(dRef, elem_nodes[2])-d0; + + const Vector3d x0 = get_coordinates(elem_nodes[0]); + const Vector3d x10 = get_coordinates(elem_nodes[1]) - x0; + const Vector3d x20 = get_coordinates(elem_nodes[2]) - x0; + + const double detJ = (x10[0]*x20[1]-x20[0]*x10[1]); + const Vector3d grad = d10*Vector3d(x20[1],-x20[0],0.0) + d20*Vector3d(-x10[1],x10[0],0.0); + mag_grad = grad.length()/detJ; + } + else + { + ThrowAssert(4 == npe); + + const double d0 = *field_data(dRef, elem_nodes[0]); + const double d10 = *field_data(dRef, elem_nodes[1])-d0; + const double d20 = *field_data(dRef, elem_nodes[2])-d0; + const double d30 = *field_data(dRef, elem_nodes[3])-d0; + + const Vector3d x0 = get_coordinates(elem_nodes[0]); + const Vector3d x10 = get_coordinates(elem_nodes[1]) - x0; + const Vector3d x20 = get_coordinates(elem_nodes[2]) - x0; + const Vector3d x30 = get_coordinates(elem_nodes[3]) - x0; + + const Vector3d x10_x_x20 = Cross(x10,x20); + const Vector3d x20_x_x30 = Cross(x20,x30); + const Vector3d x30_x_x10 = Cross(x30,x10); + + const double detJ = Dot(x30,x10_x_x20); + const Vector3d grad = d10*x20_x_x30 + d20*x30_x_x10 + d30*x10_x_x20; + mag_grad = grad.length()/detJ; + } + + return mag_grad; +} + +void +Fast_Marching::initialize_element(const stk::mesh::Entity & elem, const double speed) +{ + // Still another way to initialize fast marching. + // Here we go to each cut element and find the current distance gradient. + // By comparing this to the desired gradient, we rescale each element. The nodal + // distance is set to the minimum (magnitude) for each of the rescaled elements that + // support the node. + const FieldRef dRef = my_ls.get_distance_field(); + const stk::mesh::Entity * elem_nodes = mesh().begin(elem, stk::topology::NODE_RANK); + const int npe = mesh().bucket(elem).topology().num_nodes(); + + auto get_coordinates = build_get_fm_node_coordinates(this); + + const double mag_grad = calculate_gradient_magnitude(npe, elem_nodes, dRef, get_coordinates); + + for (int inode=0; inodestatus() != STATUS_UNUSED); + const double elem_node_dist = *field_data(dRef, elem_nodes[inode]) / (mag_grad * speed); + const int sign = LevelSet::sign(fm_node->signed_dist()); + fm_node->set_signed_dist(sign * std::min(std::abs(fm_node->signed_dist()), std::abs(elem_node_dist))); + fm_node->set_status(STATUS_INITIAL); + fm_node->set_sign(sign); + } +} + +void +Fast_Marching::update_neighbors(Fast_Marching_Node & accepted_node, ParallelErrorMessage& err) +{ + const FieldRef dRef = my_ls.get_distance_field(); + const stk::mesh::Selector active_field_not_aura = my_selector & aux_meta().active_not_ghost_selector() & stk::mesh::selectField(dRef); + + stk::mesh::Entity node = accepted_node.node(); + + ThrowAssertMsg(STATUS_ACCEPTED == accepted_node.status() || STATUS_INITIAL == accepted_node.status(), "Expected ACCEPTED OR INITIAL status"); + + const int dim = mesh().mesh_meta_data().spatial_dimension(); + ThrowAssert(2 == dim || 3 == dim); + const int npe_dist = (2==dim) ? 3 : 4; + std::vector elem_nodes(npe_dist); + + const unsigned num_node_elems = mesh().num_elements(node); + const stk::mesh::Entity* node_elems = mesh().begin_elements(node); + for (unsigned node_elem_index=0; node_elem_indexstatus() || STATUS_ACCEPTED == fm_nbr->status() || STATUS_FAR == fm_nbr->status() || STATUS_TRIAL == fm_nbr->status()), "Unexpected node status."); + elem_nodes[i] = fm_nbr; + bool do_add_trial_node = fm_nbr->status() == STATUS_FAR; + if (fm_nbr->status() == STATUS_ACCEPTED) + { + const double accepted_node_unsigned_dist = accepted_node.signed_dist()*accepted_node.sign(); + const double nbr_unsigned_dist = fm_nbr->signed_dist()*fm_nbr->sign(); + if(nbr_unsigned_dist > accepted_node_unsigned_dist) + { + do_add_trial_node = true; + } + } + if (do_add_trial_node) + { + add_trial_node(*fm_nbr); + } + if (fm_nbr->status() == STATUS_TRIAL) + { + ++num_trial; + node_to_update = i; + } + } + + if (1 == num_trial) + { + update_node(elem_nodes, node_to_update, speed); + } + } +} + +void +Fast_Marching::add_trial_node(Fast_Marching_Node & trial_node) +{ + ThrowAssertMsg(trial_node.status() == STATUS_ACCEPTED || trial_node.status() == STATUS_FAR, "Expected ACCEPTED or FAR when adding trial node"); + trial_nodes.insert(&trial_node); + trial_node.set_status(STATUS_TRIAL); +} + +void +Fast_Marching::update_trial_node(Fast_Marching_Node & trial_node, const double dist) +{ + ThrowAssertMsg(trial_node.status() == STATUS_TRIAL, "Unexpected node status when updating trial node"); + + auto it = trial_nodes.find(&trial_node); + ThrowAssertMsg(it != trial_nodes.end(), "Can't find trial node"); + + trial_nodes.erase(it); + + trial_node.set_signed_dist(dist); + trial_nodes.insert(&trial_node); +} + +void +Fast_Marching::update_node(std::vector & elem_nodes, int node_to_update, const double speed) +{ + // update distance + double dist = std::numeric_limits::max(); + const int npe_dist = elem_nodes.size(); + + if (3 == npe_dist) + { + dist = update_triangle(elem_nodes, node_to_update, speed); + } + else if (4 == npe_dist) + { + dist = update_tetrahedron(elem_nodes, node_to_update, speed); + } + else + { + ThrowAssertMsg(false, "Unexpected number of nodes per element: " << npe_dist); + } + + Fast_Marching_Node & fm_node = *elem_nodes[node_to_update]; + if (dist*fm_node.sign() < fm_node.signed_dist()*fm_node.sign()) + { + update_trial_node(fm_node, dist); + } +} + +double +Fast_Marching::update_triangle(std::vector & elem_nodes, int node_to_update, const double speed, int side_to_update) +{ + stk::diag::TimeBlock timer__(my_tri_timer); + const int dim = mesh().mesh_meta_data().spatial_dimension(); + ThrowAssert(2 == dim || 3 == dim); + + int lnn[3]; + if (2 == dim) + { + ThrowAssert(-1 == side_to_update); + lnn[0] = (node_to_update + 1) % 3; + lnn[1] = (node_to_update + 2) % 3; + lnn[2] = node_to_update; + } + else // (3 == dim) + { + const stk::topology tet4_topology = stk::topology::TETRAHEDRON_4; + const unsigned * side_node_ordinals = get_side_node_ordinals(tet4_topology, side_to_update); + lnn[0] = side_node_ordinals[(node_to_update + 1) % 3]; + lnn[1] = side_node_ordinals[(node_to_update + 2) % 3]; + lnn[2] = side_node_ordinals[node_to_update]; + } + + const double dist_0 = elem_nodes[lnn[0]]->signed_dist(); + const double dist_1 = elem_nodes[lnn[1]]->signed_dist(); + double dist_2 = elem_nodes[lnn[2]]->signed_dist(); + + const int sign = elem_nodes[lnn[2]]->sign(); + if (sign*(dist_2-dist_0) < 0 || sign*(dist_2-dist_1) < 0) + { + return dist_2; + } + + const Vector3d & coords_0 = elem_nodes[lnn[0]]->coords(); + const Vector3d & coords_1 = elem_nodes[lnn[1]]->coords(); + const Vector3d & coords_2 = elem_nodes[lnn[2]]->coords(); + + const double sqr_speed = speed*speed; + const double d10 = dist_1 - dist_0; + const Vector3d x10 = coords_1 - coords_0; + const Vector3d x20 = coords_2 - coords_0; + const double h10 = x10.length(); + const double h20 = x20.length(); + + double detJ = 0; + if (2 == dim) + { + detJ = (x10[0]*x20[1]-x20[0]*x10[1]); + } + else // (3 == dim) + { + detJ = Cross(x10,x20).length(); + } + ThrowAssert(detJ > 0.0); + + const double a = h10*h10; + const double b = -2.0 * sign*d10 * Dot(x10,x20); + const double c = d10*d10 * h20*h20 - detJ*detJ/sqr_speed; + + bool elem_is_defining = false; + + const double det = b*b-4.0*a*c; + if (det > 0.0) + { + // solve quadratic equation, roots are q/a and c/q + const int sign_b = ( b < 0.0 ) ? -1 : 1; + const double q = -0.5*(b + sign_b*std::sqrt(det)); + + const double d20 = sign*std::max(c/q,q/a); + + const bool causal = (sign*d20 > 0.0 && sign*(d20-d10) > 0.0); + + if (causal) + { + const double loc = (Dot(x10,x20) - sqr_speed*d10*d20) / (h10*h10 - sqr_speed*d10*d10); + elem_is_defining = (loc > 0.0 && loc < 1.0); + + if (elem_is_defining) + { + dist_2 = sign * std::min(sign*dist_2,sign*(dist_0 + d20)); + } + } + } + + if (!elem_is_defining) + { + const double h21 = (coords_2 - coords_1).length(); + dist_2 = sign * std::min(sign*dist_2,std::min(sign*dist_0+h20/speed,sign*dist_1+h21/speed)); + // Enforce causality - This is to catch the corner case (literally) where the characteristic is marching along the edges of the element + dist_2 = sign * std::max(sign*dist_2,std::max(sign*dist_0,sign*dist_1)); + } + + ThrowAssert(sign*(dist_2-dist_0)>=0 && sign*(dist_2-dist_1)>=0); + + return dist_2; +} + +double +Fast_Marching::update_tetrahedron(std::vector & elem_nodes, int node_to_update, const double speed) +{ + stk::diag::TimeBlock timer__(my_tet_timer); + static const unsigned node_permute_0[] = { 1,3,2,0 }; + static const unsigned node_permute_1[] = { 0,2,3,1 }; + static const unsigned node_permute_2[] = { 0,3,1,2 }; + static const unsigned node_permute_3[] = { 0,1,2,3 }; + static const unsigned * node_permute_table[] = { node_permute_0, node_permute_1, node_permute_2, node_permute_3 }; + + int lnn[4]; + lnn[0] = node_permute_table[node_to_update][0]; + lnn[1] = node_permute_table[node_to_update][1]; + lnn[2] = node_permute_table[node_to_update][2]; + lnn[3] = node_permute_table[node_to_update][3]; + + const double dist_0 = elem_nodes[lnn[0]]->signed_dist(); + const double dist_1 = elem_nodes[lnn[1]]->signed_dist(); + const double dist_2 = elem_nodes[lnn[2]]->signed_dist(); + double dist_3 = elem_nodes[lnn[3]]->signed_dist(); + + const int sign = elem_nodes[lnn[3]]->sign(); + if (sign*(dist_3-dist_0) < 0 || sign*(dist_3-dist_1) < 0 || sign*(dist_3-dist_2) < 0) + { + return dist_3; + } + + const Vector3d & coords_0 = elem_nodes[lnn[0]]->coords(); + const Vector3d & coords_1 = elem_nodes[lnn[1]]->coords(); + const Vector3d & coords_2 = elem_nodes[lnn[2]]->coords(); + const Vector3d & coords_3 = elem_nodes[lnn[3]]->coords(); + + const double sqr_speed = speed*speed; + const double d10 = dist_1-dist_0; + const double d20 = dist_2-dist_0; + + const Vector3d x10 = coords_1 - coords_0; + const Vector3d x20 = coords_2 - coords_0; + const Vector3d x30 = coords_3 - coords_0; + + const Vector3d x10_x_x20 = Cross(x10,x20); + const Vector3d x20_x_x30 = Cross(x20,x30); + const Vector3d x30_x_x10 = Cross(x30,x10); + + const double detJ = Dot(x30,x10_x_x20); + ThrowAssert(detJ > 0); + + const Vector3d contrib12 = sign * (d10*x20_x_x30 + d20*x30_x_x10); + + const double a = x10_x_x20.length_squared(); + const double b = 2.0 * Dot(x10_x_x20,contrib12); + const double c = contrib12.length_squared() - detJ*detJ/sqr_speed; + + bool elem_is_defining = false; + + const double det = b*b-4.0*a*c; + if (det > 0.0) + { + // solve quadratic equation, roots are q/a and c/q + const int sign_b = ( b < 0.0 ) ? -1 : 1; + const double q = -0.5*(b + sign_b*std::sqrt(det)); + + const double d30 = sign*std::max(c/q,q/a); + + const bool causal = (sign*d30 > 0.0 && sign*(d30-d10) > 0.0 && sign*(d30-d20) > 0.0); + + if (causal) + { + // Solve 2x2 system for parametric coords of intersection of gradient and 0-1-2 + // A1 r + B1 s == C1 + // A2 r + B2 s == C2 + const double A1 = x10.length_squared() - sqr_speed*d10*d10; + const double B1 = Dot(x10,x20) - sqr_speed*d10*d20; + const double C1 = Dot(x10,x30) - sqr_speed*d10*d30; + const double A2 = B1; + const double B2 = x20.length_squared() - sqr_speed*d20*d20; + const double C2 = Dot(x20,x30) - sqr_speed*d20*d30; + const double denom = A2*B1 - A1*B2; + const double loc_r = (C2*B1 - C1*B2)/denom; + const double loc_s = (A2*C1 - A1*C2)/denom; + const double loc_t = 1.0 - loc_r - loc_s; + elem_is_defining = (loc_r > 0.0 && loc_s > 0.0 && loc_t > 0.0); + + if (elem_is_defining) + { + dist_3 = sign * std::min(sign*dist_3,sign*(dist_0 + d30)); + } + } + } + + if (!elem_is_defining) + { + const stk::topology tet4_topology = stk::topology::TETRAHEDRON_4; + for (int iside=0; iside<4; ++iside) + { + const unsigned * side_node_lnn = get_side_node_ordinals(tet4_topology, iside); + for (int inode=0; inode<3; ++inode) + { + if (node_to_update == (int)side_node_lnn[inode]) + { + dist_3 = sign * std::min(sign*dist_3, sign*update_triangle(elem_nodes,inode,speed,iside)); + } + } + } + // Enforce causality - This is to catch the corner case (literally) where the characteristic is marching along the edges of the element + // This is not completely covered by the 2d check because 1 face might still predict a value that is less than the neighbors. + dist_3 = sign * std::max(sign*dist_3,std::max(sign*dist_2,std::max(sign*dist_1,sign*dist_0))); + } + + ThrowAssert(sign*(dist_3-dist_0)>=0 && sign*(dist_3-dist_1)>=0 && sign*(dist_3-dist_2)>=0); + + return dist_3; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Fast_Marching.hpp b/packages/krino/krino/krino_lib/Akri_Fast_Marching.hpp new file mode 100644 index 000000000000..233bec1d38a7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Fast_Marching.hpp @@ -0,0 +1,104 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Fast_Marching_h +#define Akri_Fast_Marching_h + +#include +#include +#include + +namespace krino { + +class SubElement; +class Mesh_Element; +class AuxMetaData; +class ParallelErrorMessage; + +enum Enum_Fast_Marching_Node_Status{STATUS_UNUSED=0, STATUS_INITIAL, STATUS_ACCEPTED, STATUS_TRIAL, STATUS_FAR}; + +class Fast_Marching_Node +{ +public: + Fast_Marching_Node() + : my_node(), my_status(STATUS_UNUSED), my_signed_dist(std::numeric_limits::max()), my_on_neg_side(false) {} + Fast_Marching_Node(stk::mesh::Entity in_node, Enum_Fast_Marching_Node_Status in_status, double in_dist, int in_sign, Vector3d in_coords) + : my_node(in_node), my_status(in_status), my_signed_dist(in_dist), my_on_neg_side(in_sign<0), my_coords(in_coords) {} + + int sign() const { return (my_on_neg_side ? (-1) : 1); } + void set_sign(const int in_sign) { my_on_neg_side = (in_sign<0); } + stk::mesh::Entity node() const { return my_node; } + Enum_Fast_Marching_Node_Status status() const { return my_status; } + const Vector3d & coords() const { return my_coords; } + double signed_dist() const { return my_signed_dist; } + void set_signed_dist(double dist) { my_signed_dist = dist; } + void set_status(Enum_Fast_Marching_Node_Status status) { my_status = status; } + +private: + stk::mesh::Entity my_node; + Enum_Fast_Marching_Node_Status my_status; + double my_signed_dist; + bool my_on_neg_side; + Vector3d my_coords; +}; + +class Fast_Marching_Node_Less +{ +public: + Fast_Marching_Node_Less(const stk::mesh::BulkData & mesh) : mMesh(mesh) {} + bool operator() (const Fast_Marching_Node *a, const Fast_Marching_Node *b) const + { + const double unsignedDistA = a->signed_dist()*a->sign(); + const double unsignedDistB = b->signed_dist()*b->sign(); + if (unsignedDistA < unsignedDistB) return true; + if (unsignedDistB < unsignedDistA) return false; + return mMesh.identifier(a->node()) < mMesh.identifier(b->node()); + } +private: + const stk::mesh::BulkData & mMesh; +}; + +class Fast_Marching { +public: + Fast_Marching(LevelSet & ls, const stk::mesh::Selector & selector, stk::diag::Timer & parent_timer); + + void redistance(); + void initialize(ParallelErrorMessage& err); + void update_neighbors(Fast_Marching_Node & accepted_node, ParallelErrorMessage & err); + void update_node(std::vector & elem_nodes, int node_to_update, const double speed); + + bool have_crossing(const stk::mesh::Entity & elem) const; + void initialize_subelement(const SubElement & subelem, const int side, const double speed); + void initialize_element(const stk::mesh::Entity & elem, const double speed); + double update_triangle(std::vector & elem_nodes, int node_to_update, const double speed, int side_to_update=-1); + double update_tetrahedron(std::vector & elem_nodes, int node_to_update, const double speed); + + void add_trial_node(Fast_Marching_Node & add_trial_node); + void update_trial_node(Fast_Marching_Node & add_trial_node, const double dist); + Fast_Marching_Node * get_fm_node(stk::mesh::Entity node); + + const AuxMetaData& aux_meta() const { return my_ls.aux_meta(); } + AuxMetaData& aux_meta() { return my_ls.aux_meta(); } + const stk::mesh::BulkData& mesh() const { return my_ls.mesh(); } + stk::mesh::BulkData& mesh() { return my_ls.mesh(); } +private: + LevelSet & my_ls; + stk::mesh::Selector my_selector; + stk::diag::Timer my_timer; + stk::diag::Timer my_tri_timer; + stk::diag::Timer my_tet_timer; + std::vector fm_nodes; + Fast_Marching_Node_Less my_fm_node_less; + std::set trial_nodes; //set sorted by distance, then by id to break "ties" + + void check_error(const ParallelErrorMessage& err, const std::string & context) const; +}; + +} // namespace krino + +#endif // Akri_Fast_Marching_h diff --git a/packages/krino/krino/krino_lib/Akri_FieldRef.cpp b/packages/krino/krino/krino_lib/Akri_FieldRef.cpp new file mode 100644 index 000000000000..c10c1dd8a22f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_FieldRef.cpp @@ -0,0 +1,54 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include // for operator<<, stringstream, etc + +namespace krino{ + +bool FieldRef::operator < ( const FieldRef & rhs ) const +{ + if ( my_field == rhs.my_field || rhs.my_field == NULL ) + { + return false; // identical + } + else if (my_field == NULL) + { + return true; + } + else if ( my_field->field_state(stk::mesh::StateNone) == rhs.field().field_state(stk::mesh::StateNone) ) + { + return my_field->state() < rhs.state(); + } + return name() < rhs.name(); +} + +std::string +state_string(stk::mesh::FieldState state) +{ + static const char * const local_state_name[] = { + "STATE_NONE/NEW/NP1", + "STATE_OLD/N", + "STATE_NM1", + "STATE_NM2", + "STATE_NM3", + "STATE_NM4" + }; + + if ((unsigned) state < (unsigned)sizeof(local_state_name)/(unsigned)sizeof(local_state_name[0])) + return local_state_name[state]; + else { + std::stringstream strout; + strout << "(" << (unsigned) state << ")"; + return strout.str().c_str(); + } +} + +//---------------------------------------------------------------------- + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_FieldRef.hpp b/packages/krino/krino/krino_lib/Akri_FieldRef.hpp new file mode 100644 index 000000000000..b64fcdf37f36 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_FieldRef.hpp @@ -0,0 +1,168 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_FieldRef_h +#define Akri_FieldRef_h + +#include // for NULL +#include // for string +#include "stk_mesh/base/DataTraits.hpp" // for DataTraits +#include "stk_mesh/base/Entity.hpp" // for Entity +#include "stk_mesh/base/Field.hpp" // for Field +#include "stk_mesh/base/FieldBase.hpp" // for FieldBase, etc +#include "stk_mesh/base/FieldState.hpp" // for FieldState, etc +#include "stk_mesh/base/Types.hpp" // for EntityRank +#include "stk_util/util/ReportHandler.hpp" // for ThrowAssertMsg, etc +namespace stk { namespace mesh { class Bucket; } } + +namespace krino{ + +std::string +state_string(stk::mesh::FieldState state); + +class FieldRef +{ +public: + // Only default constructed FieldRef (or copies of a default constructed FieldRef) should ever have my_field==NULL + FieldRef() : my_field(NULL) {} + + FieldRef(const FieldRef &) = default; + FieldRef & operator= (const FieldRef &) = default; + + FieldRef(const stk::mesh::FieldBase * in_field) + : my_field(in_field) + { + ThrowAssertMsg(NULL != in_field, "Cannot set FieldRef with NULL field."); + } + FieldRef(const stk::mesh::FieldBase * in_field, const stk::mesh::FieldState in_state) + : my_field(in_field) + { + ThrowAssertMsg(NULL != in_field, "Cannot set FieldRef with NULL field."); + my_field = in_field->field_state(in_state); + ThrowAssertMsg(NULL != my_field, "Invalid state."); + } + FieldRef(const stk::mesh::FieldBase & in_fieldref) + { + my_field = &in_fieldref; + } + FieldRef(const FieldRef in_fieldref, const stk::mesh::FieldState in_state) + { + ThrowAssertMsg(NULL != in_fieldref.my_field, "Cannot set FieldRef with NULL field."); + my_field = in_fieldref.my_field->field_state(in_state); + } + + FieldRef field_state(stk::mesh::FieldState in_state) const + { + return FieldRef(my_field, in_state); + } + + // assignment operators + FieldRef& operator=( const stk::mesh::FieldBase * in_field ) + { + ThrowAssertMsg(NULL != in_field, "Cannot set FieldRef with NULL field."); + my_field = in_field; + return *this; + } + FieldRef& operator=( const stk::mesh::FieldBase & in_field ) + { + my_field = &in_field; + return *this; + } + + bool valid() const { return NULL != my_field; } + bool valid_restriction_size() const { return NULL != my_field && 0 != my_field->restrictions().size(); } + void assert_valid() const { ThrowAssertMsg(NULL != my_field, "Attempt to access field of uninitialized FieldRef."); } + + // stk access + const stk::mesh::FieldBase & field() const { assert_valid(); return *my_field; } + stk::mesh::FieldBase & field() { assert_valid(); return const_cast(*my_field); } + operator const stk::mesh::FieldBase &() const { assert_valid(); return *my_field; } + + // pass through methods + unsigned number_of_states() const { assert_valid(); return my_field->number_of_states(); } + stk::mesh::FieldState state() const { assert_valid(); return my_field->state(); } + stk::mesh::EntityRank entity_rank() const { assert_valid(); return my_field->entity_rank(); } + + template bool type_is() const + { return my_field->type_is(); } + + // name_with_state() includes any suffix indicating the state, ie "_STKFS_OLD" + const std::string & name_with_state() const { assert_valid(); return my_field->name(); } + // name() is the basic field name without any suffix for state, regardless of the state of the field + std::string name() const { assert_valid(); return my_field->field_state(stk::mesh::StateNone)->name(); } + + unsigned length(const stk::mesh::Bucket& b) const + { + assert_valid(); + const unsigned type_stride = my_field->data_traits().stride_of; + const unsigned fieldSize = stk::mesh::field_bytes_per_entity(*my_field, b) / type_stride; + return fieldSize; + } + + unsigned length(stk::mesh::Entity e) const + { + assert_valid(); + const unsigned type_stride = my_field->data_traits().stride_of; + const unsigned fieldSize = stk::mesh::field_bytes_per_entity(*my_field, e) / type_stride; + return fieldSize; + } + + // Only safe if field has same length on all entities + unsigned length() const + { + ThrowAssert(valid()); + return my_field->max_size(my_field->entity_rank()); + } + + // testing + bool operator ==(const FieldRef & rhs) const { return my_field == rhs.my_field; } + bool operator !=(const FieldRef & rhs) const { return my_field != rhs.my_field; } + bool operator < (const FieldRef & rhs) const; + +private: + const stk::mesh::FieldBase * my_field; +}; + +typedef std::set FieldSet; + +inline std::ostream & operator << (std::ostream & os, const FieldRef & field_ref) +{ + const bool valid = field_ref.valid(); + os << "FieldRef valid = " << std::boolalpha << valid; + if(valid) + { + os << " field = " << field_ref.name_with_state(); + } + return os; +} + +template< class pod_type > +pod_type * field_data( const stk::mesh::FieldBase & field, stk::mesh::Entity entity ) +{ + return stk::mesh::field_data(static_cast< const stk::mesh::Field& >(field), entity); +} + +template< class pod_type > +pod_type * field_data( const stk::mesh::FieldBase & field, const stk::mesh::Bucket & bucket ) +{ + return stk::mesh::field_data(static_cast< const stk::mesh::Field& >(field), bucket); +} + +inline bool has_field_data( const FieldRef fieldref, stk::mesh::Entity entity ) +{ + return stk::mesh::field_is_allocated_for_bucket(fieldref.field(), fieldref.field().get_mesh().bucket(entity)); +} + +inline bool has_field_data( const FieldRef fieldref, const stk::mesh::Bucket & bucket ) +{ + return stk::mesh::field_is_allocated_for_bucket(fieldref.field(), bucket); +} + +} // namespace krino + +#endif // Akri_FieldRef_h diff --git a/packages/krino/krino/krino_lib/Akri_IC_Alg.cpp b/packages/krino/krino/krino_lib/Akri_IC_Alg.cpp new file mode 100644 index 000000000000..0050bcc786fc --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_IC_Alg.cpp @@ -0,0 +1,225 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include + +#include +#include + +namespace krino{ + +namespace { +double relative_crossing_position(const double ls0, const double ls1) +{ + return LevelSet::sign_change(ls0, ls1) ? ls0 / ( ls0 - ls1 ) : -10.; +} +} + +//---------------------------------------------------------------- +void IC_Alg::execute(const double time, const bool requires_additional_initialization) +{ /* %TRACE[ON]% */ Trace trace__("krino::IC_Analytic_Alg::execute()"); /* %TRACE% */ + + if (surface_list.size() == 0 && my_calculators.empty()) + { + return; + } + + const stk::mesh::BulkData& mesh = levelSet.mesh(); + const stk::mesh::MetaData& meta = mesh.mesh_meta_data(); + const FieldRef xField = levelSet.get_coordinates_field(); + const FieldRef dField = levelSet.get_distance_field(); + const int spatial_dim = meta.spatial_dimension(); + + BoundingBox node_bbox; + levelSet.compute_nodal_bbox( mesh.mesh_meta_data().universal_part(), node_bbox ); + surface_list.prepare_to_compute(time, node_bbox, levelSet.narrow_band_size()); + + stk::mesh::BucketVector const& buckets = mesh.get_buckets( stk::topology::NODE_RANK, stk::mesh::selectField(dField) ); + + for ( auto && bucket_ptr : buckets ) + { + const stk::mesh::Bucket & b = *bucket_ptr; + const int length = b.size(); + double *dist = field_data(dField, b); + double * coord = field_data(xField, b); + + for (int n = 0; n < length; ++n) + { + ThrowAssert(&(dist[n]) != NULL); + + const Vector3d x(&coord[spatial_dim*n], spatial_dim); + + dist[n] = surface_list.point_signed_distance_with_narrow_band(x, levelSet.narrow_band_size()); + } + } + + stk::mesh::communicate_field_data(mesh, {&dField.field()}); + + if (levelSet.narrow_band_size() > 0. && surface_list.truncated_distance_may_have_wrong_sign()) + { + DistanceSweeper::fix_sign_by_sweeping(mesh, dField, surface_list.get_signed_narrow_band_size(levelSet.narrow_band_size())); + } + + if(CDFEM_Support::get(meta).get_nonconformal_adapt_target_count() > 0) + { + compute_IC_error_indicator(); + } + + for (auto && calc : my_calculators) + { + calc->compute_signed_distance(levelSet); + } + + if (!levelSet.get_keep_IC_surfaces() && !requires_additional_initialization) + { + clear(); + } +} + +void IC_Alg::compute_IC_error_indicator() +{ + const stk::mesh::BulkData& mesh = levelSet.mesh(); + const stk::mesh::MetaData& meta = mesh.mesh_meta_data(); + const FieldRef xField = levelSet.get_coordinates_field(); + const FieldRef dField = levelSet.get_distance_field(); + stk::mesh::Selector fieldSelector(dField); + const int spatial_dim = meta.spatial_dimension(); + const auto & cdfem_support = CDFEM_Support::get(meta); + + const auto & aux_meta = AuxMetaData::get(meta); + const auto & indicator_field_name = cdfem_support.get_nonconformal_adapt_indicator_name(); + auto indicator_field = + aux_meta.get_field(stk::topology::ELEMENT_RANK, indicator_field_name); + const auto & elem_buckets = + mesh.get_buckets(stk::topology::ELEMENT_RANK, meta.locally_owned_part() & fieldSelector); + + std::vector nodal_signed_distances; + std::vector nodal_coordinates; + std::vector edge_midpoints; + std::vector midpoint_signed_distances, midpoint_interp_signed_distances; + int edge_nodes[] = {0, 0}; + + for(auto && b_ptr : elem_buckets) + { + const auto & b = *b_ptr; + + const int size = b.size(); + double * indicator_data = field_data(indicator_field, b); + + const stk::topology & topo = b.topology(); + + const auto & master_elem = MasterElementDeterminer::getMasterElement(*b_ptr, xField); + const int num_nodes = master_elem.num_nodes(); + + nodal_signed_distances.resize(num_nodes); + nodal_coordinates.resize(num_nodes); + + for(int el=0; el < size; ++el) + { + const auto * nodes = mesh.begin_nodes(b[el]); + for(int n=0; n < num_nodes; ++n) + { + auto node = nodes[n]; + nodal_signed_distances[n] = *field_data(dField, node); + const double * coords_data = field_data(xField, node); + nodal_coordinates[n] = Vector3d(coords_data, spatial_dim); + } + + // Iterate edges, find location of crossing on the edge and compare to location of crossing + // if we add a node at the midpoint with the exact signed distance there. + const int num_edges = topo.num_edges(); + edge_midpoints.resize(num_edges); + midpoint_signed_distances.resize(num_edges); + midpoint_interp_signed_distances.resize(num_edges); + double err = 0.; + for (int e=0; e < num_edges; ++e) + { + ThrowAssert(topo.edge_topology(e).num_nodes() == 2); + topo.edge_node_ordinals(e, edge_nodes); + + const Vector3d & x0 = nodal_coordinates[edge_nodes[0]]; + const Vector3d & x1 = nodal_coordinates[edge_nodes[1]]; + edge_midpoints[e] = 0.5*(x0+x1); + const double edge_length_sqr = (x1-x0).length_squared(); + + double midpoint_signed_distance = + surface_list.point_signed_distance_with_narrow_band(edge_midpoints[e], levelSet.narrow_band_size()); + midpoint_signed_distances[e] = midpoint_signed_distance; + + const double ls0 = nodal_signed_distances[edge_nodes[0]]; + const double ls1 = nodal_signed_distances[edge_nodes[1]]; + midpoint_interp_signed_distances[e] = 0.5 * (ls0 + ls1); + const double orig_crossing_pos = relative_crossing_position(ls0, ls1); + const double left_half_crossing_pos = + 0.5 * relative_crossing_position(ls0, midpoint_signed_distance); + const double right_half_crossing_pos = + 0.5 * (1. + relative_crossing_position(midpoint_signed_distance, ls1)); + + if(orig_crossing_pos >= 0.) + { + if(left_half_crossing_pos >= 0.) + { + const double delta = orig_crossing_pos - left_half_crossing_pos; + err += edge_length_sqr * delta * delta; + } + if(right_half_crossing_pos >= 0.) + { + const double delta = orig_crossing_pos - right_half_crossing_pos; + err += edge_length_sqr * delta * delta; + } + } + else + { + if(left_half_crossing_pos >= 0. || right_half_crossing_pos >= 0.) + { + err += edge_length_sqr; + } + } + } + + for(int ei=0; ei < num_edges; ++ei) + { + for(int ej=ei+1; ej < num_edges; ++ej) + { + const double edge_length_sqr = (edge_midpoints[ei] - edge_midpoints[ej]).length_squared(); + const double interp_crossing_pos = + relative_crossing_position(midpoint_interp_signed_distances[ei], + midpoint_interp_signed_distances[ej]); + const double crossing_pos = + relative_crossing_position(midpoint_signed_distances[ei], + midpoint_signed_distances[ej]); + + const bool has_interp_crossing = interp_crossing_pos >= 0.; + const bool has_crossing = crossing_pos >= 0.; + if(has_interp_crossing != has_crossing) err += edge_length_sqr; + if(has_crossing && has_interp_crossing) + { + const double delta = crossing_pos - interp_crossing_pos; + err += edge_length_sqr * delta * delta; + } + } + } + indicator_data[el] += err; + } + } +} + +//---------------------------------------------------------------- +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_IC_Alg.hpp b/packages/krino/krino/krino_lib/Akri_IC_Alg.hpp new file mode 100644 index 000000000000..b74bb2ebf174 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_IC_Alg.hpp @@ -0,0 +1,55 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_IC_Alg_h +#define Akri_IC_Alg_h + +#include +#include +#include + +namespace krino { class LevelSet; } + +namespace krino { + +//---------------------------------------------------------------- +class IC_Alg { + +public: + IC_Alg( LevelSet & ls ) : levelSet( ls ), surface_list("IC Surface List") {} + ~IC_Alg() {} + + void set_composition_method(Composite_Surface::CompositionMethod composition_method) { + surface_list.set_composition_method(composition_method); + } + + // query number of surfaces + unsigned numberSurfaces() { return surface_list.size();} + + // push a surface onto our container + void addSurface(Surface * surf) { surface_list.add(surf); } + + // remove all surfaces and calculators + void clear() { surface_list.clear(); my_calculators.clear(); } + + void addCalculator(std::unique_ptr calc) { my_calculators.emplace_back(std::move(calc)); } + + BoundingBox get_surface_bounding_box() { return surface_list.get_bounding_box(); } + + void execute(const double time, const bool requires_additional_initialization); +private: + void compute_IC_error_indicator(); +private: + LevelSet & levelSet; + Composite_Surface surface_list; + std::vector> my_calculators; +}; +//---------------------------------------------------------------- +} // namespace krino + +#endif // Akri_IC_Alg_h diff --git a/packages/krino/krino/krino_lib/Akri_IC_Calculator.cpp b/packages/krino/krino/krino_lib/Akri_IC_Calculator.cpp new file mode 100644 index 000000000000..6ff101371964 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_IC_Calculator.cpp @@ -0,0 +1,100 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include + +#include + +namespace krino{ + +void IC_Binder::compute_signed_distance(const LevelSet &ls) const +{ + const stk::mesh::MetaData & meta = ls.meta(); + const stk::mesh::BulkData & mesh = ls.mesh(); + const FieldRef distRef = ls.get_distance_field(); + + const stk::mesh::Selector selector = stk::mesh::selectField(distRef); + + const LevelSetManager & region_ls = LevelSetManager::get(meta); + const unsigned num_ls = region_ls.numberLevelSets(); + + std::vector otherDistRefs; + for (unsigned i=0; i otherDist(num_other_dist, nullptr); + for ( auto && bucket : mesh.get_buckets( stk::topology::NODE_RANK, selector) ) + { + const stk::mesh::Bucket & b = *bucket; + const size_t length = b.size(); + + double * dist = field_data(distRef, b); + for (unsigned i=0; i(otherDistRefs[i], b); + } + + for ( size_t n = 0; n < length; ++n ) + { + dist[n] = std::numeric_limits::max(); + for (unsigned i=0; i<(num_other_dist-my_binder_type); ++i) + { + for (unsigned j=i+1; j<(num_other_dist-my_binder_type); ++j) + { + //ensure binder separates particles by a distance of my_interface_size + if (my_binder_type==0) + { + dist[n] = std::min(dist[n], std::max(otherDist[i][n]-my_interface_size, otherDist[j][n]-my_interface_size)); + } + + //create smooth connection between particles if bridge size specified + //take the product of two offset particle level sets and move the zero crossing by bridge_size + if (my_binder_type==1) + { + if (my_smooth_bridge_size > 0.0) + { + double bridge = (otherDist[i][n]+my_smooth_bridge_offset)*(otherDist[j][n]+my_smooth_bridge_offset)-my_smooth_bridge_size; + if (my_root_smooth_bridge) + { + //root the level set product to bring it back to distance function magnitudes + const int sign = (bridge >= 0.0) ? 1 : -1; + bridge = sign*std::sqrt(std::abs(bridge)); + } + dist[n] = std::min(dist[n], bridge); + } + } + } + } + for (unsigned i=0; i + +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +namespace krino{ + +Block_Surface_Connectivity::Block_Surface_Connectivity(const stk::mesh::MetaData & meta) +{ + /* %TRACE[ON]% */ + Trace trace__("Block_Surface_Connectivity::Block_Surface_Connectivity(const stk::mesh::MetaData & meta)"); /* %TRACE% */ + + std::vector surfacesInMap = meta.get_surfaces_in_surface_to_block_map(); + for(auto && surfaceInMap : surfacesInMap) + { + std::set touching_block_ordinals; + for (auto && touching_part : meta.get_blocks_touching_surface(surfaceInMap)) + { + touching_block_ordinals.insert(touching_part->mesh_meta_data_ordinal()); + } + add_surface(surfaceInMap->mesh_meta_data_ordinal(), touching_block_ordinals); + } +} + +Block_Surface_Connectivity::Block_Surface_Connectivity(const stk::mesh::MetaData & meta, const Ioss::Region & io_region) +{ + /* %TRACE[ON]% */ + Trace trace__("Block_Surface_Connectivity::Block_Surface_Connectivity(const Ioss::Region & reg)"); /* %TRACE% */ + + std::vector side_block_names; + std::vector side_block_ordinals; + + for(auto sideset : io_region.get_sidesets()) + { + side_block_names.clear(); + sideset->block_membership(side_block_names); + side_block_ordinals.clear(); + for (auto && block_name : side_block_names) + { + const stk::mesh::Part * side_block_part = meta.get_part(block_name); + ThrowRequire(nullptr != side_block_part); + side_block_ordinals.push_back(side_block_part->mesh_meta_data_ordinal()); + } + const stk::mesh::Part * side_part = meta.get_part(sideset->name()); + ThrowRequire(nullptr != side_part); + add_surface(side_part->mesh_meta_data_ordinal(), std::set(side_block_ordinals.begin(), side_block_ordinals.end())); + + if (!sideset->get_side_blocks().empty()) + { + for (auto&& side_subset : sideset->get_side_blocks()) + { + // Fmwk only creates subset if more than 1 sideblock, but stk always creates them, so just check. + const stk::mesh::Part * side_subset_part = meta.get_part(side_subset->name()); + if (nullptr == side_subset_part) continue; + side_block_names.clear(); + side_subset->block_membership(side_block_names); + side_block_ordinals.clear(); + for (auto && block_name : side_block_names) + { + const stk::mesh::Part * side_block_part = meta.get_part(block_name); + ThrowRequire(nullptr != side_block_part); + side_block_ordinals.push_back(side_block_part->mesh_meta_data_ordinal()); + } + add_surface(side_subset_part->mesh_meta_data_ordinal(), std::set(side_block_ordinals.begin(), side_block_ordinals.end())); + } + } + } +} + +std::vector +get_input_mesh_block_names( const Ioss::Region & io_region ) +{ + std::vector mesh_elem_blocks; + for(auto && elem_block : io_region.get_element_blocks()) + { + if (stk::io::include_entity(elem_block)) + { + mesh_elem_blocks.push_back(elem_block->name()); + } + } + return mesh_elem_blocks; +} + // namespace krino +} diff --git a/packages/krino/krino/krino_lib/Akri_IO_Helpers.hpp b/packages/krino/krino/krino_lib/Akri_IO_Helpers.hpp new file mode 100644 index 000000000000..2ec5005ffd08 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_IO_Helpers.hpp @@ -0,0 +1,66 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_IO_Helpers_h +#define Akri_IO_Helpers_h +// +#include +#include + +#include + +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace diag { class Timer; } } +namespace Ioss { class Region; } + +namespace krino { + +class AuxMetaData; + +class Block_Surface_Connectivity +{ +public: + Block_Surface_Connectivity() {} + Block_Surface_Connectivity(const stk::mesh::MetaData & meta); + Block_Surface_Connectivity(const stk::mesh::MetaData & meta, const Ioss::Region & io_region); + void get_surfaces_touching_block(const stk::mesh::PartOrdinal & block_ordinal, + std::set & surface_ordinals) const + { + auto it = block_to_surface_map.find(block_ordinal); + if(it == block_to_surface_map.end()) return; + surface_ordinals.insert(it->second.begin(), it->second.end()); + } + void get_blocks_touching_surface(const stk::mesh::PartOrdinal & surface_ordinal, + std::set & block_ordinals) const + { + block_ordinals.clear(); + auto it = surface_to_block_map.find(surface_ordinal); + if(it == surface_to_block_map.end()) return; + block_ordinals.insert(it->second.begin(), it->second.end()); + } + + void add_surface(const stk::mesh::PartOrdinal & surf_ordinal, const std::set touching_blocks) + { + surface_to_block_map[surf_ordinal].insert(touching_blocks.begin(), touching_blocks.end()); + for(auto && block : touching_blocks) + { + block_to_surface_map[block].insert(surf_ordinal); + } + } +private: + std::map< stk::mesh::PartOrdinal, std::set > block_to_surface_map; + std::map< stk::mesh::PartOrdinal, std::set > surface_to_block_map; +}; + +std::vector get_input_mesh_block_names( const Ioss::Region & io_region ); +} // namespace krino + +#endif // Akri_IO_Helpers_h diff --git a/packages/krino/krino/krino_lib/Akri_InterfaceID.hpp b/packages/krino/krino/krino_lib/Akri_InterfaceID.hpp new file mode 100644 index 000000000000..a72328ac6b8b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_InterfaceID.hpp @@ -0,0 +1,98 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_INTERFACEID_H_ +#define AKRI_INTERFACEID_H_ + +#include +#include +#include +#include + +#include + +namespace krino { + +class InterfaceID; +typedef std::map CrossingMap; +typedef std::map CrossingSignMap; + +class InterfaceID +{ +public: + InterfaceID() : ls_1(-1), ls_2(-1) {} + InterfaceID(const int first, const int second) : ls_1(std::min(first, second)), + ls_2(std::max(first, second)) {} + + bool is_single_ls() const { return ls_1 == ls_2; } + int first_ls() const { return ls_1; } + int second_ls() const {return ls_2; } + void fill_sorted_domains(std::vector & sortedDomains) const; + + static std::vector all_phase_pairs(const std::set & phases); +private: + int ls_1; + int ls_2; +}; + +inline bool operator<(const InterfaceID lhs, const InterfaceID rhs) +{ + if(lhs.first_ls() < rhs.first_ls()) return true; + if(rhs.first_ls() < lhs.first_ls()) return false; + if(lhs.second_ls() < rhs.second_ls()) return true; + return false; +} + +inline bool operator==(const InterfaceID lhs, const InterfaceID rhs) +{ + return (lhs.first_ls() == rhs.first_ls()) && (lhs.second_ls() == rhs.second_ls()); +} + +inline bool operator!=(const InterfaceID lhs, const InterfaceID rhs) +{ + return !(lhs == rhs); +} + +inline std::ostream & operator<<(std::ostream &os, const InterfaceID lhs) +{ + os << "InterfaceID(" << lhs.first_ls() << ", " << lhs.second_ls() << ")"; + return os; +} + +inline std::vector InterfaceID::all_phase_pairs(const std::set & phases) +{ + std::vector result; + std::set::const_iterator end_phase = phases.end(); + for(std::set::const_iterator it = phases.begin(); it != end_phase; ++it) + { + std::set::const_iterator it2 = it; + for(++it2; it2 != end_phase; ++it2) + { + result.push_back(InterfaceID(*it, *it2)); + } + } + return result; +} + +inline void InterfaceID::fill_sorted_domains(std::vector & sortedDomains) const +{ + sortedDomains.clear(); + if (first_ls() == second_ls()) + { + sortedDomains.push_back(first_ls()); + } + else + { + sortedDomains.push_back(first_ls()); + sortedDomains.push_back(second_ls()); + } +} + +} // namespace krino + +#endif /* AKRI_INTERFACEID_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_Interface_Name_Generator.hpp b/packages/krino/krino/krino_lib/Akri_Interface_Name_Generator.hpp new file mode 100644 index 000000000000..98e9bde5c0e7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Interface_Name_Generator.hpp @@ -0,0 +1,71 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Interface_Name_Generator_h +#define Akri_Interface_Name_Generator_h +// + +#include + +namespace krino { + +// Interface_Name_Generator are used in Phase_Support::decompose_blocks() to determine the name of the +// interface sideset within a block so that cdfem death and LS-like problems can have different naming conventions +// that are more user-friendly for each case. +class Interface_Name_Generator +{ +public: + virtual ~Interface_Name_Generator() {} + virtual std::string interface_name(const std::string & io_part_name, const std::string & phase_name) const = 0; + virtual std::string interface_superset_name(const std::string & phase_name) const = 0; + virtual std::string interface_subset_name(const std::string & io_part_name, const std::string & phase_name) const = 0; +}; + +class LS_Name_Generator : public Interface_Name_Generator +{ +public: + virtual ~LS_Name_Generator() {} + virtual std::string interface_name(const std::string & io_part_name, const std::string & phase_name) const + { + return "surface_"+io_part_name+"_"+phase_name; + } + virtual std::string interface_superset_name(const std::string & phase_name) const + { + return "surface_"+phase_name; + } + virtual std::string interface_subset_name(const std::string & io_part_name, const std::string & phase_name) const + { + return "surface_"+io_part_name+"_"+phase_name; + } +}; + +class Death_Name_Generator : public Interface_Name_Generator +{ +public: + Death_Name_Generator(std::string spec_name) : death_spec_name(spec_name) {} + virtual ~Death_Name_Generator() {} + virtual std::string interface_name(const std::string & io_part_name, const std::string & phase_name) const + { + return "surface_"+io_part_name+"_"+death_spec_name; + } + virtual std::string interface_superset_name(const std::string & phase_name) const + { + return "surface_"+death_spec_name; + } + virtual std::string interface_subset_name(const std::string & io_part_name, const std::string & phase_name) const + { + return "surface_"+io_part_name+"_"+death_spec_name; + } +private: + std::string death_spec_name; +}; + + +} // namespace krino + +#endif // Akri_Interface_Name_Generator_h diff --git a/packages/krino/krino/krino_lib/Akri_Intersection_Points.cpp b/packages/krino/krino/krino_lib/Akri_Intersection_Points.cpp new file mode 100644 index 000000000000..f75cfc998e3c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Intersection_Points.cpp @@ -0,0 +1,267 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include + +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +EdgeIntersection::EdgeIntersection(const IntersectionPoint & intersectionPt) +{ + const std::vector & intPtNodes = intersectionPt.get_nodes(); + ThrowAssert(intPtNodes.size() == 2); + nodes = {intPtNodes[0], intPtNodes[1]}; + crossingLocation = intersectionPt.get_weights()[1]; + const auto & domains = intersectionPt.get_sorted_domains(); + ThrowAssert(domains.size() == 1 || domains.size() == 2); + interface = (domains.size() == 1) ? InterfaceID(domains[0],domains[0]) : InterfaceID(domains[0], domains[1]); +} + +std::string debug_output(const stk::mesh::BulkData & mesh, const IntersectionPoint & intersectionPoint) +{ + const std::vector & nodes = intersectionPoint.get_nodes(); + const std::vector & weights = intersectionPoint.get_weights(); + const std::vector & domains = intersectionPoint.get_sorted_domains(); + std::ostringstream os; + os << "intersection point domains={ "; + for (int domain : domains) + os << domain << " "; + os << "} stencil={ "; + for (size_t i=0; i & firstVec, const std::vector & secondVec) +{ + for (int domain : secondVec) + if (!std::binary_search(firstVec.begin(), firstVec.end(), domain)) + return false; + return true; +} + +bool any_node_already_captures_intersection_point(const std::vector & nodes, + const std::vector & intersectionPointSortedDomains, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + for (auto node : nodes) + { + auto iter = nodesToCapturedDomains.find(node); + if (iter != nodesToCapturedDomains.end()) + { + const std::vector & nodeSortedDomains = iter->second; + if (first_sorted_vector_of_domains_contains_all_domains_in_second_vector(nodeSortedDomains, intersectionPointSortedDomains)) + return true; + } + } + return false; +} + +bool domains_already_snapped_to_node_are_also_at_intersection_point(const NodeToCapturedDomainsMap & nodesToCapturedDomains, stk::mesh::Entity node, const std::vector & intersectionPointDomains) +{ + const auto iter = nodesToCapturedDomains.find(node); + if (iter == nodesToCapturedDomains.end()) + return true; + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(intersectionPointDomains, iter->second); +} + +static bool any_entity_in_first_vector_is_contained_in_second_sorted_vector(const std::vector & firstVec, const std::vector & secondVec) +{ + for (auto && first : firstVec) + if (std::binary_search(secondVec.begin(), secondVec.end(), first)) + return true; + return false; +} + +IntersectionPointFilter +keep_all_intersection_points_filter() +{ + auto filter = + [](const std::vector & intersectionPointNodes, const std::vector & intersectionPointSortedDomains) + { + return true; + }; + return filter; +} + +static +void pack_intersection_points_for_owners_of_nodes(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + stk::CommSparse &commSparse) +{ + std::vector intersectionPointNodeOwners; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto && intersectionPoint : intersectionPoints) + { + intersectionPointNodeOwners.clear(); + for (auto && node : intersectionPoint.get_nodes()) + { + const int procId = mesh.parallel_owner_rank(node); + if (procId != commSparse.parallel_rank()) + intersectionPointNodeOwners.push_back(procId); + } + stk::util::sort_and_unique(intersectionPointNodeOwners); + for (int procId : intersectionPointNodeOwners) + { + commSparse.send_buffer(procId).pack(intersectionPoint.get_nodes().size()); + for (auto && node : intersectionPoint.get_nodes()) + commSparse.send_buffer(procId).pack(mesh.identifier(node)); + for (auto && weight : intersectionPoint.get_weights()) + commSparse.send_buffer(procId).pack(weight); + commSparse.send_buffer(procId).pack(intersectionPoint.get_sorted_domains().size()); + for (auto && domain : intersectionPoint.get_sorted_domains()) + commSparse.send_buffer(procId).pack(domain); + } + } + }); +} + +static +void unpack_intersection_points(const stk::mesh::BulkData & mesh, + std::vector & intersectionPoints, + stk::CommSparse &commSparse) +{ + std::vector intersectionPointNodes; + std::vector intersectionPointWeights; + std::vector intersectionPointDomains; + stk::mesh::EntityId nodeId; + const bool intersectionPointIsOwned = false; + + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + size_t numNodes; + commSparse.recv_buffer(procId).unpack(numNodes); + intersectionPointNodes.resize(numNodes); + for (auto && node : intersectionPointNodes) + { + commSparse.recv_buffer(procId).unpack(nodeId); + node = mesh.get_entity(stk::topology::NODE_RANK, nodeId); + } + intersectionPointWeights.resize(numNodes); + for (auto && weight : intersectionPointWeights) + commSparse.recv_buffer(procId).unpack(weight); + size_t numDomains; + commSparse.recv_buffer(procId).unpack(numDomains); + intersectionPointDomains.resize(numDomains); + for (auto && domain : intersectionPointDomains) + { + commSparse.recv_buffer(procId).unpack(domain); + } + intersectionPoints.emplace_back(intersectionPointIsOwned, intersectionPointNodes, intersectionPointWeights, intersectionPointDomains); + } + }); +} + +void communicate_intersection_points(const stk::mesh::BulkData & mesh, std::vector & intersectionPoints) +{ + stk::CommSparse commSparse(mesh.parallel()); + pack_intersection_points_for_owners_of_nodes(mesh, intersectionPoints, commSparse); + unpack_intersection_points(mesh, intersectionPoints, commSparse); +} + +static std::vector build_intersection_points(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const IntersectionPointFilter & intersectionPointFilter) +{ + std::vector elementsToIntersect; + stk::mesh::get_entities( mesh, stk::topology::ELEMENT_RANK, mesh.mesh_meta_data().locally_owned_part(), elementsToIntersect, false); + + std::vector intersectionPoints; + geometry.append_element_intersection_points(mesh, nodesToCapturedDomains, elementsToIntersect, intersectionPointFilter, intersectionPoints); + communicate_intersection_points(mesh, intersectionPoints); + + return intersectionPoints; +} + +std::vector build_all_intersection_points(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + const IntersectionPointFilter intersectionPointFilter = keep_all_intersection_points_filter(); + return build_intersection_points(mesh, geometry, nodesToCapturedDomains, intersectionPointFilter); +} + +static IntersectionPointFilter +filter_intersection_points_to_those_not_already_handled(const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + auto filter = + [&nodesToCapturedDomains](const std::vector & intersectionPointNodes, const std::vector & intersectionPointSortedDomains) + { + return !any_node_already_captures_intersection_point(intersectionPointNodes, intersectionPointSortedDomains, nodesToCapturedDomains); + }; + return filter; +} + +std::vector build_uncaptured_intersection_points(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + IntersectionPointFilter intersectionPointFilter = filter_intersection_points_to_those_not_already_handled(nodesToCapturedDomains); + + return build_intersection_points(mesh, geometry, nodesToCapturedDomains, intersectionPointFilter); +} + +static IntersectionPointFilter +filter_intersection_points_to_those_using_previous_iteration_snap_nodes_but_not_already_handled(const NodeToCapturedDomainsMap & nodesToCapturedDomains, const std::vector & iterationSortedSnapNodes) +{ + auto filter = + [&nodesToCapturedDomains, &iterationSortedSnapNodes](const std::vector & intersectionPointNodes, const std::vector & intersectionPointSortedDomains) + { + return any_entity_in_first_vector_is_contained_in_second_sorted_vector(intersectionPointNodes, iterationSortedSnapNodes) && + !any_node_already_captures_intersection_point(intersectionPointNodes, intersectionPointSortedDomains, nodesToCapturedDomains); + }; + return filter; +} + +std::vector get_owned_elements_using_nodes_knowing_that_nodes_dont_have_common_elements(const stk::mesh::BulkData & mesh, + const std::vector & nodes) +{ + std::vector nodeElements; + for (auto node : nodes) + for (auto element : StkMeshEntities{mesh.begin_elements(node), mesh.end_elements(node)}) + if (mesh.bucket(element).owned()) + nodeElements.push_back(element); + return nodeElements; +} + +void update_intersection_points_after_snap_iteration(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const std::vector & iterationSortedSnapNodes, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + std::vector & intersectionPoints) +{ + const auto intersectionPointFilter = filter_intersection_points_to_those_using_previous_iteration_snap_nodes_but_not_already_handled(nodesToCapturedDomains, iterationSortedSnapNodes); + + size_t newSize=0; + for (auto && intersectionPoint : intersectionPoints) + { + if (intersectionPoint.is_owned() && !any_entity_in_first_vector_is_contained_in_second_sorted_vector(intersectionPoint.get_nodes(), iterationSortedSnapNodes)) + intersectionPoints[newSize++] = intersectionPoint; // FIXME use custom swap? + } + intersectionPoints.erase(intersectionPoints.begin()+newSize, intersectionPoints.end()); + + const std::vector updateElements = get_owned_elements_using_nodes_knowing_that_nodes_dont_have_common_elements(mesh, iterationSortedSnapNodes); + geometry.append_element_intersection_points(mesh, nodesToCapturedDomains, updateElements, intersectionPointFilter, intersectionPoints); + communicate_intersection_points(mesh, intersectionPoints); +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_Intersection_Points.hpp b/packages/krino/krino/krino_lib/Akri_Intersection_Points.hpp new file mode 100644 index 000000000000..0f7c07da5832 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Intersection_Points.hpp @@ -0,0 +1,75 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_INTERSECTION_POINTS_H_ +#define KRINO_INCLUDE_AKRI_INTERSECTION_POINTS_H_ + +#include +#include +#include +#include +#include + +namespace krino { + +class CDFEM_Support; +class Phase_Support; +class CDFEM_Parent_Edge; +class InterfaceGeometry; + +class IntersectionPoint +{ +public: + IntersectionPoint(const bool owned, const std::vector & nodes, const std::vector & weights, const std::vector & sortedDomains) + : mOwned(owned), mNodes(nodes), mWeights(weights), mSortedDomains(sortedDomains) {ThrowAssert(mNodes.size() == mWeights.size());} + bool is_owned() const { return mOwned; } + const std::vector & get_nodes() const { return mNodes; } + const std::vector & get_weights() const { return mWeights; } + const std::vector & get_sorted_domains() const { return mSortedDomains; } +private: + bool mOwned; + std::vector mNodes; + std::vector mWeights; + std::vector mSortedDomains; +}; + +struct EdgeIntersection +{ + EdgeIntersection(const IntersectionPoint & intersectionPt); + std::array nodes; + double crossingLocation; + InterfaceID interface; +}; + +void communicate_intersection_points(const stk::mesh::BulkData & mesh, std::vector & intersectionPoints); + +typedef std::function &, const std::vector &)> IntersectionPointFilter; + +bool first_sorted_vector_of_domains_contains_all_domains_in_second_vector(const std::vector & firstVec, const std::vector & secondVec); +bool domains_already_snapped_to_node_are_also_at_intersection_point(const NodeToCapturedDomainsMap & nodesToCapturedDomains, stk::mesh::Entity node, const std::vector & intersectionPointDomains); +std::string debug_output(const stk::mesh::BulkData & mesh, const IntersectionPoint & intersectionPoint); + +IntersectionPointFilter keep_all_intersection_points_filter(); + +std::vector build_all_intersection_points(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const NodeToCapturedDomainsMap & nodesToCapturedDomains); + +std::vector build_uncaptured_intersection_points(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const NodeToCapturedDomainsMap & nodesToCapturedDomains); + +void update_intersection_points_after_snap_iteration(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & geometry, + const std::vector & iterationSortedSnapNodes, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + std::vector & intersectionPoints); + +} + +#endif /* KRINO_INCLUDE_AKRI_INTERSECTION_POINTS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_LevelSet.cpp b/packages/krino/krino/krino_lib/Akri_LevelSet.cpp new file mode 100644 index 000000000000..64dc628a7d55 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LevelSet.cpp @@ -0,0 +1,1822 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +namespace krino { + +bool all_nodes_have_field_data(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, const stk::mesh::FieldBase& field) +{ + const unsigned nnodes = stk_bulk.num_nodes(entity); + const stk::mesh::Entity* nodes = stk_bulk.begin_nodes(entity); + for (unsigned i = 0; i < nnodes; ++i ) + { + if (field_bytes_per_entity(field, nodes[i]) == 0) + { + return false; + } + } + return true; +} + +std::vector LevelSet::the_levelSet_names; + +LevelSet_Identifier LevelSet::get_identifier(const std::string & name) +{ + std::string upper_name = name; + std::transform(upper_name.begin(), upper_name.end(), upper_name.begin(), ::toupper); + for (unsigned i=0; i 0; +} + +BoundingBox LevelSet::get_IC_surface_bounding_box() +{ + IC_Alg& ic_alg = get_IC_alg(); + return ic_alg.get_surface_bounding_box(); +} + +IC_Alg& LevelSet::get_IC_alg() +{ + if (!my_IC_alg) + { + my_IC_alg = std::make_unique(*this); + } + return *my_IC_alg; +} + +void LevelSet::set_current_coordinates(stk::mesh::MetaData & meta, const FieldRef ref) +{ + LevelSetManager & ls_manager = LevelSetManager::get(meta); + ls_manager.set_current_coordinates(ref); +} + +FieldRef LevelSet::get_current_coordinates(stk::mesh::MetaData & meta) +{ + LevelSetManager & ls_manager = LevelSetManager::get(meta); + FieldRef current_coords = ls_manager.get_current_coordinates(); + if (!current_coords.valid()) + { + const stk::mesh::FieldBase * meta_coords = meta.coordinate_field(); + ThrowRequireMsg(nullptr != meta_coords, "Coordinates must be defined before calling LevelSet::get_current_coordinates()."); + ls_manager.set_current_coordinates(meta_coords); + current_coords = ls_manager.get_current_coordinates(); + } + return current_coords; +} + +void LevelSet::setup(stk::mesh::MetaData & meta) +{ + const LevelSetManager & region_ls = LevelSetManager::get(meta); + for (auto&& ls : region_ls) + { + ls->setup(); + } +} + +void LevelSet::post_commit_setup(stk::mesh::MetaData & meta) +{ + const double max_elem_size = compute_maximum_element_size(meta.mesh_bulk_data()); + + const LevelSetManager & region_ls = LevelSetManager::get(meta); + for (auto&& ls : region_ls) + { + ls->setup(); + if (ls->my_narrow_band_multiplier > 0.) + { + ls->narrow_band_size(ls->my_narrow_band_multiplier * max_elem_size); + } + else if (ls->narrow_band_size() > 0.) + { + const double narrow_band = ls->narrow_band_size(); + ThrowErrorMsgIf(!(narrow_band > max_elem_size), + "Currently, narrow_band_size must be greater than the maximum element size of " << max_elem_size << std::endl + << "in order to avoid unintentional accuracy degradation. If this feature is needed, please contact krino developers."); + } + } +} + + +void LevelSet::setup(void) +{ + register_fields(); + + facets.reset(new Faceted_Surface("current_facets")); + facets_old.reset(new Faceted_Surface("old_facets")); + + // initializes CDFEM_Support + if (!meta().is_commit()) + { + CDFEM_Support::get(my_meta); + } +} +//-------------------------------------------------------------------------------- +void LevelSet::register_fields(void) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::register_fields(void)"); /* %TRACE% */ + + if (trackIsoSurface || aux_meta().has_field(stk::topology::NODE_RANK, my_distance_name)) + { + // non-krino region + if (trackIsoSurface) + { + if (aux_meta().has_field(stk::topology::NODE_RANK, my_isovar_name)) + { + set_isovar_field( aux_meta().get_field(stk::topology::NODE_RANK, my_isovar_name) ); + } + else if (aux_meta().has_field(stk::topology::ELEMENT_RANK, my_isovar_name)) + { + set_isovar_field( aux_meta().get_field(stk::topology::ELEMENT_RANK, my_isovar_name) ); + } + else + { + ThrowErrorMsgIf( + true, "Isosurface variable '" << my_isovar_name << "' should already be registered."); + } + } + else + { + const FieldRef distance_ref = aux_meta().get_field(stk::topology::NODE_RANK, my_distance_name); + if ( distance_ref.number_of_states() == 1 ) + { + set_distance_field( distance_ref ); + set_old_distance_field( distance_ref ); + } + else + { + set_distance_field( distance_ref.field_state(stk::mesh::StateNew) ); + set_old_distance_field( distance_ref.field_state(stk::mesh::StateOld) ); + } + + set_isovar_field( my_distance_field ); + } + } + else + { + if (aux_meta().using_fmwk()) + { + ThrowRuntimeError("ERROR: field " << my_distance_name << " is not registered for level set " << name() << ". " + << "This can be caused by an incorrect Distance Variable. " + << "Or, in aria, there could be a conflict between the specified subindex and the named species. " + << "If so, try using a subindex greater than the number of species for your level set."); + } + + // krino region + const FieldType & type_double = FieldType::REAL; + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "KRINO: Registering distance variable with name '" << my_distance_name << "'." << stk::diag::dendl; + + const bool cdfem_is_active = krino::CDFEM_Support::is_active(meta()); + if (cdfem_is_active) + { + Phase_Support phase_support = Phase_Support::get(meta()); + for (auto partPtr : meta().get_mesh_parts()) + { + if (partPtr->primary_entity_rank() == stk::topology::ELEMENT_RANK && + phase_support.level_set_is_used_by_nonconformal_part(this, phase_support.find_nonconformal_part(*partPtr))) + { + FieldRef distance_ref = aux_meta().register_field( my_distance_name, type_double, stk::topology::NODE_RANK, 1, 1, *partPtr ); + set_old_distance_field( distance_ref ); + set_distance_field( distance_ref ); + } + } + } + else + { + FieldRef distance_ref = aux_meta().register_field( my_distance_name, type_double, stk::topology::NODE_RANK, 2, 1, meta().universal_part() ); + set_old_distance_field( FieldRef( distance_ref, stk::mesh::StateOld ) ); + set_distance_field( FieldRef( distance_ref, stk::mesh::StateNew ) ); + } + + set_isovar_field( my_distance_field ); + } + + if (!myTimeOfArrivalBlockSpeedsByName.empty()) + { + myTimeOfArrivalBlockSpeeds.resize(my_meta.get_parts().size()); + for (auto entry : myTimeOfArrivalBlockSpeedsByName) + { + if (my_aux_meta.has_part(entry.first)) + { + myTimeOfArrivalBlockSpeeds[my_aux_meta.get_part(entry.first).mesh_meta_data_ordinal()] = entry.second; + } + else + { + ThrowErrorMsgIf(true, "Could not find block " << entry.first << " when setting speed for computing time-of-arrival."); + } + } + } + + if (!my_time_of_arrival_element_speed_field_name.empty()) + { + const bool hasSpeedField = aux_meta().has_field(stk::topology::ELEMENT_RANK, my_time_of_arrival_element_speed_field_name); + ThrowErrorMsgIf(!hasSpeedField, "Could not find element speed field " << my_time_of_arrival_element_speed_field_name << " for computing time-of-arrival."); + myTimeOfArrivalElementSpeedField = aux_meta().get_field(stk::topology::ELEMENT_RANK, my_time_of_arrival_element_speed_field_name); + ThrowRequireMsg(myTimeOfArrivalBlockSpeeds.empty(), "Speed for time-of-arrival calculation should be specified via element speed or block speed (not both)."); + } +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::set_time_of_arrival_block_speed(const std::string & blockName, const double blockSpeed) +{ + std::string lowerBlockName = blockName; + std::transform(lowerBlockName.begin(), lowerBlockName.end(), lowerBlockName.begin(), ::tolower); + auto entry = myTimeOfArrivalBlockSpeedsByName.find(lowerBlockName); + ThrowRequireMsg(entry == myTimeOfArrivalBlockSpeedsByName.end(), "Speed for block " << blockName << " specified more than once."); + myTimeOfArrivalBlockSpeedsByName[lowerBlockName] = blockSpeed; +} + +//----------------------------------------------------------------------------------- +void +LevelSet::facets_exoii(void) +{ + /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::facets_exoii(void)"); /* %TRACE% */ + Faceted_Surface & f = *facets; + facets_exoii(f); +} + + +void +LevelSet::facets_exoii(Faceted_Surface & cs) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::facets_exoii(Faceted_Surface & cs)"); /* %TRACE% */ + + int nfaces = cs.size(); + const int nodes_per_elem = spatial_dimension; + const int nnodes = nfaces * nodes_per_elem; + const int nelems = nfaces * 1; //writing out faces as elements + + // construct file name + ThrowAssert(my_facetFileIndex <= 99999); + char counterChar[6]; + std::sprintf(counterChar, "%.5d", my_facetFileIndex); + std::string fn = std::string("facets.") + name() + ".e-s" + std::string(counterChar); + + // Type (ExodusII) is hard-wired at this time. + Ioss::DatabaseIO *db = Ioss::IOFactory::create("exodusII", fn, Ioss::WRITE_RESULTS); + Ioss::Region io(db, "FacetRegion"); + + // find offsets for consistent global numbering + int elem_start = 0; + if ( mesh().parallel_size() > 1 ) { + std::vector< int > num_faces; + num_faces.resize( mesh().parallel_size() ); + + // Gather everyone's facet list sizes + // I don't think there is a framework call for this... + MPI_Allgather( &nfaces, 1, MPI_INT, + &(num_faces[0]), 1, MPI_INT, mesh().parallel() ); + for (int i = 0; i< mesh().parallel_rank(); ++i) { + elem_start += num_faces[i]; + } + } + + const std::string description = "level set interface facets"; + io.property_add(Ioss::Property("title", description)); + io.begin_mode(Ioss::STATE_DEFINE_MODEL); + + // if we have no elements bail now + if ( 0 == nelems ) { + io.end_mode(Ioss::STATE_DEFINE_MODEL); + my_facetFileIndex++; + return; + } + + Ioss::NodeBlock *nb = new Ioss::NodeBlock(db, "nodeblock_1", nnodes, spatial_dimension); + io.add(nb); + + std::string el_type; + if (spatial_dimension == 3) + el_type = "trishell3"; + else + el_type = "shellline2d2"; + + Ioss::ElementBlock *eb = new Ioss::ElementBlock(db, "block_1", el_type, nelems); + io.add(eb); + + io.end_mode(Ioss::STATE_DEFINE_MODEL); + io.begin_mode(Ioss::STATE_MODEL); + + const FacetOwningVec & cs_surfaces = cs.get_facets(); + + // loop over elements and node to create maps + { + std::vector< int > nmap, emap; + nmap.reserve(nnodes); + emap.reserve(nelems); + + for ( unsigned n=0, e=0; eput_field_data("ids", nmap); + eb->put_field_data("ids", emap); + } + + // generate coordinates + { + std::vector< double > xyz; + xyz.reserve(spatial_dimension*nnodes); + + for ( auto&& cs_surface : cs_surfaces ) { + for ( int j = 0; j < nodes_per_elem; ++j ) { + const Vector3d & vert = cs_surface->facet_vertex(j); + xyz.push_back(vert[0]); + xyz.push_back(vert[1]); + if (3 == spatial_dimension) xyz.push_back(vert[2]); + } + } + nb->put_field_data("mesh_model_coordinates", xyz); + } + + // generate connectivity + { + std::vector< int > conn; + conn.reserve(nnodes); + for ( int n = 0; n < nnodes; ++n ) { + conn.push_back(nodes_per_elem*elem_start + n+1); + } + eb->put_field_data("connectivity", conn); + } + + io.end_mode(Ioss::STATE_MODEL); + my_facetFileIndex++; +} + +//----------------------------------------------------------------------------------- +void +LevelSet::compute_surface_distance(const double narrowBandSize, const double farFieldValue) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::compute_surface_distance(void)"); /* %TRACE% */ + + stk::mesh::Selector surface_selector = selectUnion(my_compute_surface_distance_parts); + + if (narrowBandSize > 0.0) + { + my_narrow_band_size = narrowBandSize; + } + + const stk::mesh::Field& coords = reinterpret_cast&>(get_coordinates_field().field()); + const stk::mesh::Field& dist = reinterpret_cast&>(get_distance_field().field()); + + Compute_Surface_Distance::calculate( + mesh(), + get_timer(), + coords, + dist, + surface_selector, + my_narrow_band_size, + farFieldValue); + + // output for time 0 is from old + if (!(my_distance_field == my_old_distance_field)) + { + stk::mesh::field_copy(my_distance_field, my_old_distance_field); + } + +} + +//----------------------------------------------------------------------------------- +void +LevelSet::set_surface_distance(std::vector surfaces, const double in_distance) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::compute_surface_distance(void)"); /* %TRACE% */ + + const FieldRef dField = get_distance_field(); + + const stk::mesh::Selector selector = stk::mesh::selectField(dField) & selectUnion(surfaces); + stk::mesh::BucketVector const& buckets = mesh().get_buckets( stk::topology::NODE_RANK, selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const size_t length = b.size(); + double *dist = field_data(dField , b); + + for ( size_t n = 0; n < length; ++n ) + { + dist[n] = in_distance; + } + } +} + +//----------------------------------------------------------------------------------- +void +LevelSet::advance_semilagrangian(const double deltaTime) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::advance_semilagrangian(const double deltaTime)"); /* %TRACE% */ + + if(trackIsoSurface) + { + redistance(); + } + else + { + stk::mesh::Selector selector(my_meta.universal_part()); + + // store existing facets in facets_old + facets->swap( *facets_old ); + + // get non-local facets such that we have copies of all old facets + // within the range of this proc's nodes + prepare_to_compute_distance( deltaTime, selector ); + + // compute nodal distances with semi-lagrangian step + stk::mesh::field_copy(my_old_distance_field, my_distance_field); + compute_distance_semilagrangian( deltaTime, selector ); + + // build local facet list + build_facets_locally(my_meta.universal_part()); + + // debugging + if (krinolog.shouldPrint(LOG_FACETS)) + { + facets_exoii(); + } + } +} + +//----------------------------------------------------------------------------------- +void +LevelSet::initialize(stk::mesh::MetaData & meta, const bool requires_additional_initialization) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::initialize(void)"); /* %TRACE% */ + + const LevelSetManager & region_ls = LevelSetManager::get(meta); + for (auto&& ls : region_ls) + { + ls->initialize(0., requires_additional_initialization); + } +} + +//----------------------------------------------------------------------------------- +void +LevelSet::initialize(const double time, const bool requires_additional_initialization) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::initialize(void)"); /* %TRACE% */ + + if (trackIsoSurface) + { + return; + } + + if(get_isovar_field().valid()) get_isovar_field().field().sync_to_host(); + if(get_distance_field().valid()) get_distance_field().field().sync_to_host(); + if(get_old_distance_field().valid()) get_old_distance_field().field().sync_to_host(); + + if(get_isovar_field().valid()) get_isovar_field().field().modify_on_host(); + if(get_distance_field().valid()) get_distance_field().field().modify_on_host(); + if(get_old_distance_field().valid()) get_old_distance_field().field().modify_on_host(); + + if (!my_compute_surface_distance_parts.empty()) + { + compute_surface_distance(); + return; + } + + krinolog << "Initializing levelset " << name() << "..." << stk::diag::dendl; + + /* process analytic surfaces */ + if (my_IC_alg) + { + my_IC_alg->execute(time, requires_additional_initialization); + } + + if (compute_time_of_arrival()) + { + fast_marching_redistance(my_meta.universal_part(), true); + } + else if (my_perform_initial_redistance) + { + constrained_redistance(); + } + + // Offset initialized LS if requested + if (my_ic_offset != 0.0) increment_distance(my_ic_offset, false); + + // Scale initialized LS if requested + if (my_ic_scale != 1.0) scale_distance(my_ic_scale); + + stk::mesh::field_copy(get_distance_field(), get_old_distance_field()); +} + +double LevelSet::constrained_redistance(const bool use_initial_vol) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::constrained_redistance(const bool use_initial_vol)"); /* %TRACE% */ + + // Steps: + // 1. measure current volume + // 2. perform regular redistance + // 3. find offset needed to conserve volume + // 4. increment nodal distance by this amount + + if (get_isovar_field().valid()) get_isovar_field().field().sync_to_host(); + if (get_distance_field().valid()) get_distance_field().field().sync_to_host(); + if (get_old_distance_field().valid()) get_old_distance_field().field().sync_to_host(); + + if (get_isovar_field().valid()) get_isovar_field().field().modify_on_host(); + if (get_distance_field().valid()) get_distance_field().field().modify_on_host(); + if (get_old_distance_field().valid()) get_old_distance_field().field().modify_on_host(); + + // measure current area and volumes + double start_area, start_neg_vol, start_pos_vol; + compute_sizes( start_area,start_neg_vol, start_pos_vol, 0. ); + if ( 0. == start_neg_vol || 0. == start_area ) + { + krinolog << "Skipping redistancing operation. Volume and/or area have zero value. Area: " + << start_area << " Volume: " << start_neg_vol << stk::diag::dendl; + return 0.; + } + + if (use_initial_vol) + { + krinolog << "Performing conserved redistancing..." << stk::diag::dendl; + + if (my_initial_neg_vol <= 0.0) + { + my_initial_neg_vol = start_neg_vol; + } + start_pos_vol = start_neg_vol + start_pos_vol - my_initial_neg_vol; + start_neg_vol = my_initial_neg_vol; + } + else + { + krinolog << "Performing constrained redistancing..." << stk::diag::dendl; + } + + // perform regular redistance + redistance(); + + krinolog << "Correcting for volume change:" << stk::diag::dendl; + + // find correction needed to conserve volume + const double correction = find_redistance_correction( start_area, start_neg_vol, start_pos_vol ); + + // update nodal distance field + increment_distance( -correction, true ); + + return my_initial_neg_vol; +} + +//-------------------------------------------------------------------------------- + +static std::function(const double)> build_volume_error_function_with_derivative(LevelSet & ls, const double startingNegVol, const double startingPosVol) +{ + auto volume_error_function_with_derivative = [&ls, startingNegVol, startingPosVol](const double x) + { + double area, negVol, posVol; + ls.compute_sizes( area, negVol, posVol, x ); + const double totVol = startingNegVol+startingPosVol; + const double relativeError = (negVol - startingNegVol) / totVol; + krinolog << " Correction = " << x + << ", Current volume = " << negVol + << ", Target volume = " << startingNegVol + << ", Relative Error = " << std::abs(relativeError) + << stk::diag::dendl; + const double derivative = area/totVol; + return std::make_pair(relativeError, derivative); + }; + return volume_error_function_with_derivative; +} + +double +LevelSet::find_redistance_correction( const double start_area, + const double start_neg_vol, + const double start_pos_vol, + const int max_iterations, + const double tol ) +{ /* %TRACE% */ /* %TRACE% */ + auto volume_error_function_with_derivative = build_volume_error_function_with_derivative(*this, start_neg_vol, start_pos_vol); + const auto result = find_root_newton_raphson(volume_error_function_with_derivative, 0., max_iterations, tol); + + if (!result.first) + { + stk::RuntimeWarningAdHoc() << "\nConstrained renormalization failed to converge to root within " + << max_iterations << " iterations. Continuing with correction " << result.second << "\n"; + } + return result.second; +} + +void +LevelSet::redistance() +{ + redistance(my_meta.universal_part()); +} + +void +LevelSet::redistance(const stk::mesh::Selector & selector) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::redistance(void)"); /* %TRACE% */ + + ThrowErrorMsgIf(!my_time_of_arrival_element_speed_field_name.empty(), "Redistancing a time-of-arrival field will corrupt it."); + + if (get_isovar_field().valid()) get_isovar_field().field().sync_to_host(); + if (get_distance_field().valid()) get_distance_field().field().sync_to_host(); + if (get_old_distance_field().valid()) get_old_distance_field().field().sync_to_host(); + + if (get_isovar_field().valid()) get_isovar_field().field().modify_on_host(); + if (get_distance_field().valid()) get_distance_field().field().modify_on_host(); + if (get_old_distance_field().valid()) get_old_distance_field().field().modify_on_host(); + + if (FAST_MARCHING == my_redistance_method) + { + fast_marching_redistance(selector); + return; + } + ThrowRequire(CLOSEST_POINT == my_redistance_method); + + krinolog << "Redistancing the level set field..." << stk::diag::dendl; + + // our starting point is a nodal variable (like distance or temperature) + // that needs to be contoured to form the surface + // after forming the surface, the nodal distance needs to be calculated + // the newly formed surface should be remain in the vector facets + build_facets_locally(selector); + + // debugging + if (krinolog.shouldPrint(LOG_FACETS)) + { + facets_exoii(); + } + + // swap these facets into facet_old to take advantage of routines + // that are expecting the facets there + facets->swap( *facets_old ); + + // get non-local facets such that we have copies of all "old" facets + // within the range of this proc's nodes + prepare_to_compute_distance( 0., selector ); + + // compute nodal distances with semi-lagrangian step + compute_distance_semilagrangian( 0., selector ); + + // swap so that the facets that were formed remain in the vector facets + facets->swap( *facets_old ); + +} + +double +LevelSet::get_time_of_arrival_speed(stk::mesh::Entity elem, ParallelErrorMessage& err) const +{ + double speed = 1.0; + if (myTimeOfArrivalBlockSpeeds.empty()) + { + if (myTimeOfArrivalElementSpeedField.valid()) + { + const double * speedFieldData = field_data(myTimeOfArrivalElementSpeedField, elem); + if (!speedFieldData) err << "Missing element speed on element " << mesh().identifier(elem) << "\n"; + else speed = *speedFieldData; + + if (speed <= 0.0) + { + err << "Non positive-definite speed " << speed << " found on element " << mesh().identifier(elem) << "\n"; + } + } + } + else + { + const stk::mesh::Part & elemPart = find_element_part(mesh(), elem); + speed = myTimeOfArrivalBlockSpeeds[elemPart.mesh_meta_data_ordinal()]; + ThrowAssert(speed >= 0.0); // Negative speeds should have already been caught and generated error. + if (speed == 0.0) + err << "Speed not specified for block " << elemPart.name() << "\n"; + } + + return speed; +} + +void +LevelSet::fast_marching_redistance(const stk::mesh::Selector & selector, const bool compute_time_of_arrival) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::fast_marching_redistance(const stk::mesh::Selector & selector)"); /* %TRACE% */ + + // Unlike redistance() this method provides an approximate (not exact) distance to the isosurface. + // On the other hand, this method provide solve the Eikonal equation on the mesh. This is slightly + // different than a pure distance function because it provides the distance through domain. It can't see + // through walls like the redistance() method does. + + if (compute_time_of_arrival) krinolog << "Initializing the level set field to be the time-of-arrival using a fast marching method..." << stk::diag::dendl; + else krinolog << "Redistancing the level set field using a fast marching method..." << stk::diag::dendl; + Fast_Marching fm(*this, selector, get_timer()); + fm.redistance(); +} + +//-------------------------------------------------------------------------------- + +void +LevelSet::set_distance( const double & in_distance ) const +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::set_distance( const double & in_distance ) const"); /* %TRACE% */ + + stk::mesh::field_fill(in_distance, get_distance_field()); +} + +void +LevelSet::increment_distance( const double increment, const bool enforce_sign ) const +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::increment_distance( const double & increment ) const"); /* %TRACE% */ + // + // increment the distance everywhere by the given value + // + + const FieldRef dField = get_distance_field(); + + const stk::mesh::Selector active_field_selector = aux_meta().active_not_ghost_selector() & stk::mesh::selectField(dField); + stk::mesh::BucketVector const& buckets = mesh().get_buckets( stk::topology::NODE_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const size_t length = b.size(); + + double *d = field_data(dField , b); + + for (size_t i = 0; i < length; ++i) + { + const double change = (enforce_sign && sign_change(d[i],d[i]+increment)) ? -0.5*d[i] : increment; + d[i] += change; + } + } // end bucket loop +} + +void +LevelSet::scale_distance( const double scale) const +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::scale_distance( const double & scale ) const"); /* %TRACE% */ + // + // increment the distance everywhere by the given value + // + + const FieldRef dField = get_distance_field(); + + const stk::mesh::Selector active_field_selector = aux_meta().active_not_ghost_selector() & stk::mesh::selectField(dField); + stk::mesh::BucketVector const& buckets = mesh().get_buckets( stk::topology::NODE_RANK, active_field_selector); + + stk::mesh::BucketVector::const_iterator ib = buckets.begin(); + stk::mesh::BucketVector::const_iterator ib_end = buckets.end(); + + // iterate nodes, by buckets, and set distance + for ( ; ib != ib_end ; ++ib ) + { + const stk::mesh::Bucket & b = **ib; + + const size_t length = b.size(); + + double *d = field_data(dField , b); + + for (size_t i = 0; i < length; ++i) + { + d[i] *= scale; + } + } // end bucket loop +} + +void +LevelSet::negate_distance() const +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::increment_distance( const double & increment ) const"); /* %TRACE% */ + + const FieldRef dRef = get_distance_field(); + stk::mesh::field_scale(-1.0, dRef); +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::compute_continuous_gradient() const +{ /* %TRACE[ON]% */ /* %TRACE% */ + // + // Compute a mass-lumped continuous distance gradient + // + + const int dim = mesh().mesh_meta_data().spatial_dimension(); + + const FieldRef contGradRef = aux_meta().get_field(stk::topology::NODE_RANK, "CONT_GRAD"); + const FieldRef nodeAreaRef = aux_meta().get_field(stk::topology::NODE_RANK, "NODE_AREA"); + + + // initialize + stk::mesh::field_fill(0.0, contGradRef); + stk::mesh::field_fill(0.0, nodeAreaRef); + + // intg_pt_locations and intg_weights are just wrappers for framework data + // determinants and grad_distance are arrays containing data that are resized + // only as needed + sierra::Array intg_pt_locations; + sierra::Array intg_weights; + sierra::ArrayContainer determinants; + sierra::ArrayContainer grad_distance; + + // ************************** + // Not-covered-in-nightly RWH + // ************************** + + const FieldRef xField = get_coordinates_field(); + const FieldRef isoField = get_isovar_field(); + + stk::mesh::Selector active_field_selector = stk::mesh::selectField(contGradRef) & aux_meta().active_not_ghost_selector(); + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities( active_field_selector, mesh().buckets( stk::topology::ELEMENT_RANK ), objs ); + + for ( auto && elem : objs ) + { + // create element + ContourElement ls_elem( mesh(), elem, xField, isoField ); + + ls_elem.std_intg_pts( intg_pt_locations, intg_weights, determinants, + ls_elem.dist_master_elem() ); + ls_elem.compute_distance_gradient( intg_pt_locations, grad_distance ); + + const unsigned num_intg_pts = intg_pt_locations.dimension(); + const int npe = ls_elem.dist_topology().num_nodes(); + + const double * shape_fcn_ptr = ls_elem.dist_master_elem().shape_fcn(); + const sierra::Array shape_fcn(shape_fcn_ptr,npe,num_intg_pts); + + const stk::mesh::Entity* elem_nodes = mesh().begin_nodes(elem); + + for ( int i = 0; i < npe; ++i ) + { + double * cont_grad = field_data(contGradRef, elem_nodes[i]); + double * area_ptr = field_data(nodeAreaRef, elem_nodes[i]); + double & area = *area_ptr; + + for (unsigned ip = 0; ip < num_intg_pts; ++ip ) + { + const double NdV = shape_fcn(i,ip) * intg_weights(ip) * determinants(ip); + area += NdV; + + for ( int d = 0; d < dim; d++ ) + { + cont_grad[d] += grad_distance(d,ip) * NdV; + //krinolog << "grad_distance(" << d << "," << ip << ") = " << grad_distance(d,ip) << stk::diag::dendl; + } + } + } + } + + // iterate nodes, by buckets, and calculate average gradient + + stk::mesh::BucketVector const& buckets = mesh().get_buckets(stk::topology::NODE_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const size_t length = b.size(); + + double * cont_grad = field_data(contGradRef, b); + double * area = field_data(nodeAreaRef, b); + + for (size_t i = 0; i < length; ++i) + { + for ( int d = 0; d < dim; d++ ) + { + cont_grad[dim*i+d] = cont_grad[dim*i+d] / area[i]; + } + } + } +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::compute_nodal_bbox( const stk::mesh::Selector & selector, + BoundingBox & node_bbox, + const Vector3d & displacement ) const +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::compute_nodal_bbox( BoundingBox & node_bboxes, const double & deltaTime ) const"); /* %TRACE% */ + + // find the local nodal bounding box + + const FieldRef xField = get_coordinates_field(); + const FieldRef dField = get_distance_field(); + + const stk::mesh::Selector active_field_selector = aux_meta().active_not_ghost_selector() & selector & stk::mesh::selectField(dField); + stk::mesh::BucketVector const& buckets = mesh().get_buckets( stk::topology::NODE_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const size_t length = b.size(); + + double *x = field_data(xField, b); + + for (size_t i = 0; i < length; ++i) + { + + Vector3d x_bw(Vector3d::ZERO); + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) + { + int index = i*spatial_dimension+dim; + x_bw[dim] = x[index] - displacement[dim]; + } + + // incrementally size bounding box + node_bbox.accommodate( x_bw ); + } + } // end bucket loop +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::prepare_to_compute_distance( const double & deltaTime, const stk::mesh::Selector & selector ) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::get_nonlocal_facets( const double & deltaTime )"); /* %TRACE% */ + + // Get all of the facets that are within our processor's bounding box + // To do this, see if any local facets lie in the nodal bounding box + // of another proc. if so, send them a copy of those facets + + // First, find the bounding box for each proc that contains all of the + // nodes on that proc plus the narrow_band size + + BoundingBox node_bbox; + const Vector3d displacement = deltaTime * get_extension_velocity(); + compute_nodal_bbox( selector, node_bbox, displacement ); + + facets_old->prepare_to_compute(node_bbox, my_narrow_band_size); +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::compute_distance_semilagrangian( const double & deltaTime, const stk::mesh::Selector & selector ) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::compute_distance_semilagrangian( const double & deltaTime ) const"); /* %TRACE% */ + + const double h_avg = compute_average_edge_length(); + + const FieldRef xField = get_coordinates_field(); + const FieldRef dField = get_distance_field(); + const Vector3d extv = get_extension_velocity(); + + const stk::mesh::Selector active_field_selector = aux_meta().active_not_ghost_selector() & selector & stk::mesh::selectField(dField); + stk::mesh::BucketVector const& buckets = mesh().get_buckets(stk::topology::NODE_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const size_t length = b.size(); + + double *d = field_data( dField , b); + double *x = field_data( xField , b); + + // Handle special case of ( deltaTime == 0. ) so that we + // can handle situation where velocity is not defined at all + // nodes where distance is defined. (This is currently a requirement + // for regular semilagrangian advancement). + if ( deltaTime == 0. ) + { + for (size_t i = 0; i < length; ++i) + { + Vector3d x_node(Vector3d::ZERO); + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) + { + int index = i*spatial_dimension+dim; + x_node[dim] = x[index]; + } + + int previous_sign = LevelSet::sign(d[i]); + // If this is too large, then sharp edges can propagate incorrect signs + // (even through walls, etc). + // If this is too small, then a phase can't disappear because the sign + // preservation will prevent it even if the subelement contouring process + // neglects it. So this should be slightly larger than the tolerance in + // compute_subelement_decomposition. + bool enforce_sign = (std::abs(d[i]) > 5.e-4*h_avg); + + d[i] = distance( x_node, previous_sign, enforce_sign ); + } + } + else + { + for (size_t i = 0; i < length; ++i) + { + Vector3d x_bw(Vector3d::ZERO); + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) + { + int index = i*spatial_dimension+dim; + x_bw[dim] = x[index] - extv[dim] * deltaTime; + } + + int previous_sign = LevelSet::sign(d[i]); + + d[i] = distance( x_bw, previous_sign, false ); + } + } + } // end bucket loop +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::compute_distance( stk::mesh::Entity n, + const double & deltaTime ) const +{ /* %TRACE% */ /* %TRACE% */ + + // use the facet cell array to compute the distance to a node n + + const FieldRef xField = get_coordinates_field(); + const FieldRef dField = get_distance_field(); + const Vector3d extv = get_extension_velocity(); + + double *x = field_data( xField , n); + double *d = field_data( dField , n); + + // Handle special case of ( deltaTime == 0. ) so that we + // can handle situation where velocity is not defined at all + // nodes where distance is defined. (This is currently a requirement + // for regular semilagrangian advancement). + if ( deltaTime == 0. ) + { + Vector3d x_node(Vector3d::ZERO); + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) + { + x_node[dim] = x[dim]; + } + + int previous_sign = LevelSet::sign(*d); + *d = distance( x_node, previous_sign, true ); + } + else + { + Vector3d x_bw(Vector3d::ZERO); + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) + { + x_bw[dim] = x[dim] - extv[dim] * deltaTime; + } + + int previous_sign = LevelSet::sign(*d); + *d = distance( x_bw, previous_sign, false ); + } +} + +//----------------------------------------------------------------------------------- + +double +LevelSet::distance( const Vector3d & x, + const int previous_sign, + const bool enforce_sign ) const +{ /* %TRACE% */ /* %TRACE% */ + + if (enforce_sign) + { + return previous_sign * facets_old->point_unsigned_distance(x, my_narrow_band_size, my_narrow_band_size); + } + return facets_old->truncated_point_signed_distance(x, my_narrow_band_size, previous_sign*my_narrow_band_size); +} + +//----------------------------------------------------------------------------------- + +void +LevelSet::snap_to_mesh() const +{ /* %TRACE[ON]% */ Trace trace__("LevelSet::snap_to_mesh()"); /* %TRACE% */ + const double tol = 1.0e-2; + + // Remove sliver subelements by setting nodal values near zero to zero exactly. + // This should probably be an edge-based check. But this poses a problem for higher order + // elements, which we are going to decompose into lower order elements. So we make it + // simpler by compare ALL pairs of nodes within the element. If the crossing between any + // pair of nodes is is within a relative distance of tol, the distance at the nearest node + // is set to zero. + + // This seems like a great way to consistently handle degeneracies. + // One problem, however, is this only handles the near zero's on the original elements. + // We will generate others as we decompose into non-conformal subelements. This won't fix + // those degenerate situations. + + std::vector dist; + + const FieldRef dField = get_distance_field(); + + const stk::mesh::Selector active_field_selector = stk::mesh::selectField(dField) & aux_meta().active_locally_owned_selector(); + stk::mesh::BucketVector const& buckets = mesh().get_buckets(stk::topology::ELEMENT_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const stk::topology dist_topology = MasterElementDeterminer::get_field_topology(b, dField); + const int npe_dist = dist_topology.num_nodes(); + dist.resize( npe_dist ); + + const size_t length = b.size(); + for (size_t i = 0; i < length; ++i) + { + stk::mesh::Entity elem = b[i]; + + if (!elem_on_interface(elem)) continue; + + const stk::mesh::Entity* elem_nodes = mesh().begin_nodes(elem); + + for ( int n = 0; n < npe_dist; ++n ) + { + dist[n] = *field_data(dField, elem_nodes[n]); + } + + for ( int n = 0; n < npe_dist; ++n ) + { + for ( int np = n+1; np < npe_dist; ++np ) + { + if (sign_change(dist[n],dist[np])) + { + const double d0 = std::fabs(dist[n]); + const double d1 = std::fabs(dist[np]); + if (d0 < d1) + { + if (d0 / (d0+d1) < tol) + { + *field_data(dField, elem_nodes[n]) = 0.0; + } + } + else + { + if (d1 / (d1+d0) < tol) + { + *field_data(dField, elem_nodes[np]) = 0.0; + } + } + } + } + } + } + } +} + +//----------------------------------------------------------------------------------- + +bool +LevelSet::remove_wall_features() const +{ /* %TRACE[ON]% */ Trace trace__("LevelSet::remove_wall_features()"); /* %TRACE% */ + + std::vector dist; + std::vector coords; + int small_feature_removed = false; + + const FieldRef dField = get_distance_field(); + const FieldRef coordinates_field = get_coordinates_field(); + + stk::mesh::Selector surface_selector = selectUnion(my_surface_parts); + + const stk::mesh::Selector active_field_selector = stk::mesh::selectField(dField) & aux_meta().active_locally_owned_selector() & surface_selector; + stk::mesh::BucketVector const& buckets = mesh().get_buckets(meta().side_rank(), active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + + const stk::topology dist_topology = MasterElementDeterminer::get_field_topology(b, dField); + const int npe_dist = dist_topology.num_nodes(); + dist.resize( npe_dist ); + coords.resize( npe_dist ); + + const size_t length = b.size(); + for (size_t i = 0; i < length; ++i) + { + stk::mesh::Entity side = b[i]; + + const stk::mesh::Entity* side_nodes = mesh().begin_nodes(side); + + for ( int n = 0; n < npe_dist; ++n ) + { + dist[n] = *field_data(dField, side_nodes[n]); + + double *coord_data = field_data(coordinates_field,side_nodes[n]); + coords[n] = coord_data; + } + + for ( int n = 0; n < npe_dist; ++n ) + { + const stk::mesh::Entity *elems = mesh().begin_elements(side); //get the element + const int num_elems = mesh().num_elements(side); + + for (int l = 0; l < num_elems; ++l ) + { + const stk::mesh::Entity elem = elems[l]; + + //make sure we have the right element (active) and has the distance function + //at every point in the element (to take gradient) + + if(!aux_meta().active_locally_owned_selector()(mesh().bucket(elem))) continue; + if(!elem_has_field_data(dField, elem)) continue; + + //const double elem_len = calc_elem_len_normal(elem, side, coordinates_field); + + if(std::fabs(dist[n]) > my_max_feature_size) continue; + + ContourElement ls_elem( mesh(), elem, coordinates_field, dField ); + const Vector3d p_coords(1/3., 1/3., 1/3.); + const Vector3d grad_dist_vec = ls_elem.distance_gradient(p_coords); + + Vector3d face_normal; + + //assume linear tet or tri elements! + if(spatial_dimension == 2) + { + face_normal = {-coords[1][1]+coords[0][1], coords[1][0]-coords[0][0], 0}; //simple 90 deg rotation + const stk::mesh::Entity* elem_nodes = mesh().begin_nodes(elem); + + int num_elem_nodes = mesh().num_nodes(elem); + + for (int j = 0; j < num_elem_nodes; ++j) //find node in elem not part of side part, confirm normal points into elem + { + if(elem_nodes[j] != side_nodes[0] && elem_nodes[j] != side_nodes[spatial_dimension-1]) + { + double *coord = field_data(coordinates_field,elem_nodes[j]); + const Vector3d vec_check(coord[0]-coords[0][0], coord[1]-coords[0][1], 0); + + if(Dot(face_normal, vec_check) < 0) + { + face_normal *= -1; + break; + } + } + } + } + else + { + const Vector3d x1 (coords[1][0]-coords[0][0], coords[1][1]-coords[0][1],coords[1][2]-coords[0][2]); + const Vector3d x2 (coords[2][0]-coords[0][0], coords[2][1]-coords[0][1],coords[2][2]-coords[0][2]); + face_normal = -1.0*Cross(x1,x2); + } + + face_normal.unitize(); + const double eta = -dist[n]/(Dot(grad_dist_vec, face_normal)); + + if(eta < my_max_feature_size && eta > 0) + { + *field_data(dField, side_nodes[n]) = -1.0 * dist[n]; + small_feature_removed = true; + } + } + } + } + } + + int global_small_feature_removed = false; + stk::all_reduce_sum(mesh().parallel(), &small_feature_removed, &global_small_feature_removed, 1); + + if (global_small_feature_removed) + { + stk::mesh::communicate_field_data(mesh(), {&dField.field()}); + return true; + } + + return false; +} +//-------------------------------------------------------------------------------- + +bool +LevelSet::simple_remove_wall_features() const +{ /* %TRACE[ON]% */ Trace trace__("LevelSet::remove_wall_features()"); /* %TRACE% */ + + int small_feature_removed = false; + const FieldRef dField = get_distance_field(); + + stk::mesh::Selector surface_selector = selectUnion(my_surface_parts); + + const stk::mesh::Selector active_field_selector = stk::mesh::selectField(dField) & aux_meta().active_part() & surface_selector; + stk::mesh::BucketVector const& buckets = mesh().get_buckets(stk::topology::NODE_RANK, active_field_selector); + + for ( auto && bucket : buckets ) + { + const stk::mesh::Bucket & b = *bucket; + const size_t length = b.size(); + for (size_t i = 0; i < length; ++i) + { + stk::mesh::Entity node = b[i]; + double & dist = *field_data(dField, node); + + if(std::fabs(dist) < my_max_feature_size) + { + dist*=-1; + small_feature_removed = true; + } + } + } + + return small_feature_removed; +} +//-------------------------------------------------------------------------------- + +void +LevelSet::set_surface_parts_vector() +{ + Phase_Support my_phase_support = Phase_Support::get(meta()); + + std::vector conformal_parts = my_phase_support.get_conformal_parts(); + + krinolog << "Removing small features less than " << my_max_feature_size << " on surfaces: "; + for (auto && mypart : conformal_parts) + { + if(mypart->primary_entity_rank() == meta().side_rank() && !my_phase_support.is_interface(mypart)) + { + my_surface_parts.push_back(mypart); + krinolog << mypart->name() << " "; + } + } + + krinolog << stk::diag::dendl; +} + +//-------------------------------------------------------------------------------- + +bool +LevelSet::elem_has_field_data(const FieldRef &myField, const stk::mesh::Entity &elem) const +{ + const stk::mesh::Entity* elem_nodes = mesh().begin_nodes(elem); + int num_nodes = mesh().num_nodes(elem); + + for (int k = 0; k < num_nodes; ++k) + { + if(!has_field_data(myField, elem_nodes[k])) return false; + } + + return true; +} +//-------------------------------------------------------------------------------- + +bool +LevelSet::elem_on_interface(stk::mesh::Entity e) const +{ /* %TRACE% */ /* %TRACE% */ + + const FieldRef isoField = get_isovar_field(); + + const unsigned nnodes = mesh().num_nodes(e); + ThrowAssert( 0 < nnodes ); + const stk::mesh::Entity* nodes = mesh().begin_nodes(e); + + // guilty till proven innocent here + bool on_interface = false; + bool have_crossing = false; + + double *d = field_data(isoField, nodes[0]); + double first_value = *d - my_threshold; + bool inside_narrow_band = fabs(first_value) < 0.5*my_narrow_band_size; + + for (unsigned i = 1; i < nnodes; ++i ) + { + d = field_data(isoField, nodes[i]); + if ( NULL == d ) continue; // account for lower order interpolation + double value = *d - my_threshold; + + have_crossing |= sign_change(value, first_value); + inside_narrow_band |= (fabs(value) < 0.5*my_narrow_band_size); + } + + // It is the user's job to make sure that the narrow band is sufficiently + // large that we don't to test if this crossing is within the narrow band + if ( have_crossing ) + on_interface = true; + + return on_interface; +} + +//-------------------------------------------------------------------------------- +void +LevelSet::compute_sizes( double & area, double & neg_vol, double & pos_vol, const double iso_val ) +{ /* %TRACE[ON]% */ /* %TRACE% */ + + // initialize + area = 0.0; + neg_vol = 0.0; + pos_vol = 0.0; + + const double h_avg = compute_average_edge_length(); + + sierra::ArrayContainer intg_pt_locations; + sierra::ArrayContainer intg_weights; + sierra::ArrayContainer determinants; + + const FieldRef xField = get_coordinates_field(); + const FieldRef isoField = get_isovar_field(); + //const Vector3d extv = get_extension_velocity(); + + stk::mesh::Selector active_field_selector = stk::mesh::selectField(isoField) & aux_meta().active_locally_owned_selector(); + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities(active_field_selector, mesh().buckets( stk::topology::ELEMENT_RANK ), objs); + + for ( auto && elem : objs ) + { + // create element that is decomposed into subelements + ContourElement ls_elem( mesh(), elem, xField, isoField, iso_val ); + + ls_elem.compute_subelement_decomposition(h_avg); + + // get integration point locations, weights, and determinants for surface + int num_intg_pts = ls_elem.gather_intg_pts( 0, // interface + intg_pt_locations,// gauss pt locations + intg_weights, // integration wts at gauss pts + determinants, // determinant at gauss pts + true ); // map_to_real_coords + for ( int ip = 0; ip < num_intg_pts; ++ip ) + { + area += intg_weights(ip) * determinants(ip); + } + + // get integration point locations, weights, and determinants for negative volume + num_intg_pts = ls_elem.gather_intg_pts( -1, // negative side of interface + intg_pt_locations, // gauss pt locations + intg_weights, // integration wts at gauss pts + determinants, // determinant at gauss pts + true ); // map_to_real_coords + for ( int ip = 0; ip < num_intg_pts; ++ip ) + { + neg_vol += intg_weights(ip) * determinants(ip); + } + + // get integration point locations, weights, and determinants for positive volume + num_intg_pts = ls_elem.gather_intg_pts( 1, // positive side of interface + intg_pt_locations, // gauss pt locations + intg_weights, // integration wts at gauss pts + determinants, // determinant at gauss pts + true ); // map_to_real_coords + for ( int ip = 0; ip < num_intg_pts; ++ip ) + { + pos_vol += intg_weights(ip) * determinants(ip); + } + } + + // communicate global sums + const int vec_length = 3; + std::vector local_sum( vec_length ); + std::vector global_sum( vec_length ); + local_sum[0] = area; + local_sum[1] = neg_vol; + local_sum[2] = pos_vol; + + stk::all_reduce_sum(mesh().parallel(), &local_sum[0], &global_sum[0], vec_length); + + area = global_sum[0]; + neg_vol = global_sum[1]; + pos_vol = global_sum[2]; + +} +//-------------------------------------------------------------------------------- +double +LevelSet::gradient_magnitude_error(void) +{ /* %TRACE[ON]% */ /* %TRACE% */ + + double area = 0., sum_L2 = 0., global_L2 = 0., local_Loo = 0., global_Loo = 0.; + + sierra::ArrayContainer intg_pt_locations; + sierra::ArrayContainer intg_weights; + sierra::ArrayContainer determinants; + sierra::ArrayContainer grad_dist; + + const double h_avg = compute_average_edge_length(); + + const FieldRef xField = get_coordinates_field(); + const FieldRef isoField = get_isovar_field(); + //const Vector3d extv = get_extension_velocity(); + + stk::mesh::Selector active_field_selector = stk::mesh::selectField(isoField) & aux_meta().active_locally_owned_selector(); + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities( active_field_selector, mesh().buckets( stk::topology::ELEMENT_RANK ), objs ); + + for ( auto && elem : objs ) + { + // create element that is decomposed into subelements + ContourElement ls_elem( mesh(), elem, xField, isoField ); + + ls_elem.compute_subelement_decomposition(h_avg); + + // get integration point locations, weights, and determinants for surface + int num_intg_pts = ls_elem.gather_intg_pts( 0, // interface + intg_pt_locations,// gauss pt locations + intg_weights, // integration wts at gauss pts + determinants, // determinant at gauss pts + true ); // map_to_real_coords + + ls_elem.compute_distance_gradient( intg_pt_locations, grad_dist ); + for ( int ip = 0; ip < num_intg_pts; ++ip ) + { + double mag_grad_phi = 0.; + for ( unsigned dim = 0; dim < spatial_dimension; ++dim ) mag_grad_phi += grad_dist(dim,ip) * grad_dist(dim,ip); + mag_grad_phi = sqrt(mag_grad_phi); + + sum_L2 += (mag_grad_phi - 1.) * (mag_grad_phi - 1.) * intg_weights(ip) * determinants(ip); + area += intg_weights(ip) * determinants(ip); + + if ( fabs(mag_grad_phi - 1.) > local_Loo ) local_Loo = fabs(mag_grad_phi - 1.); + } + } + + // communicate global norms + const int vec_length = 2; + std::vector local_sum( vec_length ); + std::vector global_sum( vec_length ); + local_sum[0] = sum_L2; + local_sum[1] = area; + + stk::all_reduce_sum(mesh().parallel(), &local_sum[0], &global_sum[0], vec_length); + stk::all_reduce_max(mesh().parallel(), &local_Loo, &global_Loo, 1); + + if ( global_sum[1] > 0. ) + { + global_L2 = global_sum[0] / global_sum[1]; + } + + krinolog << "Gradient norm error for " << name() << ": L2 = " << global_L2 << ", Loo = " << global_Loo << stk::diag::dendl; + + // L2 is the standard now, maybe Loo would be better? + return global_L2; +} +//-------------------------------------------------------------------------------- +double +LevelSet::compute_average_edge_length() const +{ /* %TRACE[ON]% */ /* %TRACE% */ + + double sum_avg_edge_lengths = 0.0; + int num_elems = 0; + + const FieldRef xField = get_coordinates_field(); + const FieldRef isoField = get_isovar_field(); + + stk::mesh::Selector active_field_selector = stk::mesh::selectField(isoField) & aux_meta().active_locally_owned_selector(); + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities( active_field_selector, mesh().buckets( stk::topology::ELEMENT_RANK ), objs ); + + for ( auto && elem : objs ) + { + ++num_elems; + + // create element + ContourElement ls_elem( mesh(), elem, xField, isoField ); + + sum_avg_edge_lengths += ls_elem.average_edge_length(); + } + + // communicate global sums + const int vec_length = 2; + std::vector local_sum( vec_length ); + std::vector global_sum( vec_length ); + local_sum[0] = sum_avg_edge_lengths; + local_sum[1] = 1.0*num_elems; + + stk::all_reduce_sum(mesh().parallel(), &local_sum[0], &global_sum[0], vec_length); + + const double h_avg = ( global_sum[1] != 0.0 ) ? global_sum[0]/global_sum[1] : 0.0; + + return h_avg; +} + +//-------------------------------------------------------------------------------- + +void +LevelSet::build_facets_locally(const stk::mesh::Selector & selector) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::build_facets_locally(void)"); /* %TRACE% */ + + // clear vector of facets + facets->clear(); + + const double h_avg = compute_average_edge_length(); + + const FieldRef xField = get_coordinates_field(); + const FieldRef isoField = get_isovar_field(); + + stk::mesh::Selector active_field_selector = selector & stk::mesh::selectField(isoField) & aux_meta().active_locally_owned_selector(); + std::vector< stk::mesh::Entity> objs; + stk::mesh::get_selected_entities( active_field_selector, mesh().buckets( stk::topology::ELEMENT_RANK ), objs ); + + for ( auto && elem : objs ) + { + // create element that is decomposed into subelements + ContourElement ls_elem( mesh(), elem, xField, isoField ); + ls_elem.compute_subelement_decomposition(h_avg); + + ls_elem.build_subelement_facets( *facets ); + } +} + +LevelSet & +LevelSet::build( + stk::mesh::MetaData & in_meta, + const std::string & ls_name, + stk::diag::Timer & parent_timer ) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::build(stk::mesh::MetaData & in_meta, const std::string & ls_name, stk::diag::Timer & parent_timer)"); /* %TRACE% */ + LevelSetManager & region_ls = LevelSetManager::get(in_meta); + + ThrowRequire(!region_ls.has_levelSet(ls_name)); + LevelSet * ls = new LevelSet(in_meta, ls_name, parent_timer); + region_ls.add(ls); + return *ls; +} + +//-------------------------------------------------------------------------------- +LevelSet::LevelSet( + stk::mesh::MetaData & in_meta, + const std::string & in_name, + stk::diag::Timer & parent_timer ) : + my_meta(in_meta), + my_aux_meta(AuxMetaData::get(in_meta)), + my_identifier(LevelSet::get_identifier(in_name)), + my_name(LevelSet::get_name(my_identifier)), + my_parent_timer(parent_timer), + my_timer("LevelSet", parent_timer), + spatial_dimension(in_meta.spatial_dimension()), + my_narrow_band_multiplier(0.0), + my_narrow_band_size(0.0), + my_max_feature_size(-1.0), + my_ic_offset(0.0), + my_ic_scale(1.0), + my_perform_initial_redistance(false), + my_keep_IC_surfaces(false), + my_threshold(0.0), + my_redistance_method(CLOSEST_POINT), + epsilon(1.0e-16), + trackIsoSurface(false), + my_facetFileIndex(1), + my_initial_neg_vol(0.0), + my_needs_reinitialize_every_step(false) +{ /* %TRACE[ON]% */ Trace trace__("krino::LevelSet::LevelSet(stk::mesh::MetaData & in_meta, const std::string & ls_name, stk::diag::Timer & parent_timer)"); /* %TRACE% */ + my_coordinates_field = get_current_coordinates(in_meta); + + // default names for distance and velocity + // line commands are available for overriding these names + const std::string distName = "D_" + name(); + set_distance_name(distName); +} + +LevelSet::~LevelSet() +{ +} + +//----------------------------------------------------------------------------------- +void +LevelSet::gather_nodal_field( + const stk::mesh::BulkData& stk_mesh, + stk::mesh::Entity obj, + const FieldRef & field, + double * gathered_field_data ) +{ /* %TRACE% */ /* %TRACE% */ + + int ncomp_field = field.length(); + + // Gather obj's nodal field into a single flat array + // of dimension (ncomp_field,num_nodes) + + int j = 0; + const unsigned num_nodes = stk_mesh.num_nodes(obj); + const stk::mesh::Entity* nodes = stk_mesh.begin_nodes(obj); + for (unsigned node_index=0; node_index(field, node); + for ( int i = 0; i < ncomp_field; ++i ) + { + gathered_field_data[j++] = var[i]; + } + } + + ThrowAssert( (unsigned)j == ncomp_field * stk_mesh.num_nodes(obj)); +} +//-------------------------------------------------------------------------------- +LevelSetManager & +LevelSetManager::get(stk::mesh::MetaData & meta) +{ + LevelSetManager * mgr = const_cast(meta.get_attribute()); + if (nullptr == mgr) + { + mgr = new LevelSetManager; + meta.declare_attribute_with_delete(mgr); + } + return *mgr; +} +//-------------------------------------------------------------------------------- +LevelSetManager & +LevelSetManager::get(const stk::mesh::MetaData & meta) +{ + LevelSetManager * mgr = const_cast(meta.get_attribute()); + ThrowRequireMsg(nullptr != mgr, "No LevelSetManager found for MetaData."); + return *mgr; +} +//-------------------------------------------------------------------------------- +bool LevelSetManager::has_levelSet(const std::string & ls_name) const +{ + for (auto&& ls : my_level_sets) + { + if (ls->name() == ls_name || ls->get_composite_name() == ls_name) + { + return true; + } + } + return false; +} +//-------------------------------------------------------------------------------- +std::string +print_sizes(const LevelSet & ls) +{ /* %TRACE[ON]% */ Trace trace__("krino::print_sizes(const LevelSet & levelSet)"); /* %TRACE% */ + + // + // find sizes of facets stored in vector of facet descriptions + // + + const auto & ls_surfaces = ls.get_facets().get_facets(); + unsigned local_facet_num = ls_surfaces.size(); + unsigned global_facet_num = 0; + stk::all_reduce_sum(ls.mesh().parallel(), &local_facet_num , &global_facet_num, 1); + + // iterate local facets and calc area + + double local_facets_totalArea = 0.0; // total surface area of interface from facets + double local_facets_maxArea = -1.0; // area of largest facet on interface + double local_facets_minArea = std::numeric_limits::max(); // area of smallest facet on interface + + // loop over facets + for ( auto&& surface : ls_surfaces ) + { + double area = surface->facet_area(); + local_facets_totalArea += area; + + local_facets_maxArea = std::min(area, local_facets_maxArea); + local_facets_minArea = std::max(area, local_facets_maxArea); + } + + double global_facets_totalArea = 0.0; + double global_facets_maxArea = 0.0; + double global_facets_minArea = 0.0; + + stk::all_reduce_min(ls.mesh().parallel(), &local_facets_minArea, &global_facets_minArea, 1); + stk::all_reduce_max(ls.mesh().parallel(), &local_facets_maxArea, &global_facets_maxArea, 1); + stk::all_reduce_sum(ls.mesh().parallel(), &local_facets_totalArea, &global_facets_totalArea, 1); + + std::ostringstream out; + + // facet info + out << "P" << ls.mesh().parallel_rank() << ": facets for level set '" << ls.name() << "' " << std::endl ; + out << "\t " << "Global sizes: { " << global_facet_num << " facets on }" << std::endl; + out << "\t " << "Local sizes: { " << local_facet_num << " facets on }" << std::endl; + out << "\t Global areas: { Min = " << global_facets_minArea << ", Max = " << global_facets_maxArea + << ", Total = " << global_facets_totalArea << " }" << std::endl; + return out.str(); +} +//-------------------------------------------------------------------------------- + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_LevelSet.hpp b/packages/krino/krino/krino_lib/Akri_LevelSet.hpp new file mode 100644 index 000000000000..609e13728396 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LevelSet.hpp @@ -0,0 +1,339 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_LevelSet_h +#define Akri_LevelSet_h + +/** + + Create one of these for every interface you want to capture. + + */ +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class MetaData; } } +namespace sierra { namespace Sctl { class Event; } } +namespace krino { class AuxMetaData; } +namespace krino { class IC_Alg; } +namespace krino { class ParallelErrorMessage; } + +namespace krino { + +enum Redistance_Method +{ + CLOSEST_POINT=0, + FAST_MARCHING, + MAX_REDISTANCE_METHOD_TYPE +}; + +/// Return true if field-data exists for the specified meshobj and field. +bool all_nodes_have_field_data(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, const stk::mesh::FieldBase& field); + +class LevelSet { +friend class LevelSet_Size; +public: + stk::mesh::MetaData & meta(); + const stk::mesh::MetaData & meta() const; + stk::mesh::BulkData & mesh(); + const stk::mesh::BulkData & mesh() const; + AuxMetaData & aux_meta(); + const AuxMetaData & aux_meta() const; + + const std::string & name() const { return my_name; } + LevelSet_Identifier get_identifier() const {return my_identifier; } + stk::diag::Timer & get_timer() const { return my_timer; } + stk::diag::Timer & get_parent_timer() const { return my_parent_timer; } + + // finalize setup + static void setup(stk::mesh::MetaData & meta); + static void post_commit_setup(stk::mesh::MetaData & meta); + virtual void setup(); + + static void set_current_coordinates(stk::mesh::MetaData & meta, const FieldRef ref); + static FieldRef get_current_coordinates(stk::mesh::MetaData & meta); + + void register_fields(); + + void advance_semilagrangian(const double deltaTime); + + static void gather_nodal_field( + const stk::mesh::BulkData& stk_mesh, + stk::mesh::Entity obj, + const FieldRef & field_ref, + double * field); + + double compute_average_edge_length() const; + + void build_facets_locally(const stk::mesh::Selector & selector); + + void compute_sizes( double & area, double & neg_vol, double & pos_vol, const double distance = 0.0 ); + double gradient_magnitude_error(); + void compute_continuous_gradient() const; + + void compute_distance( stk::mesh::Entity n, + const double & deltaTime ) const; + void estimate_error(); + + // hack to dump facet list to exoii databse. + void facets_exoii(); + void facets_exoii(Faceted_Surface & cs); + + bool elem_on_interface(stk::mesh::Entity e) const; + + void snap_to_mesh() const; + bool remove_wall_features() const; + bool simple_remove_wall_features() const; + bool elem_has_field_data(const FieldRef &myField, const stk::mesh::Entity &elem) const; + double calc_elem_len_normal(const stk::mesh::Entity &elem, const stk::mesh::Entity &side, const FieldRef &coordinates_field) const; + + + //-------------------------------------------------------------------------------- + // queries + //-------------------------------------------------------------------------------- + + const std::string & get_distance_name() const { return my_distance_name; } + void set_distance_name( const std::string & distance_name ) { my_distance_name = distance_name; } + + const FieldRef & get_distance_field() const { return my_distance_field; } + void set_distance_field( const FieldRef & ref ) { my_distance_field = ref; } + + const FieldRef & get_old_distance_field() const { return my_old_distance_field; } + void set_old_distance_field( const FieldRef & ref ) { my_old_distance_field = ref; } + + void set_extension_velocity( const Vector3d & extension_velocity ) { my_extension_velocity = extension_velocity; } + const Vector3d & get_extension_velocity() const { return my_extension_velocity; } + + const FieldRef & get_coordinates_field() const { return my_coordinates_field; } + + const std::string & get_isovar_name() const { return my_isovar_name; } + + const std::string & get_composite_name() const { return my_composite_name; } + void set_composite_name( const std::string & composite_name ) { + my_composite_name = composite_name; + std::transform(my_composite_name.begin(), my_composite_name.end(), my_composite_name.begin(), ::toupper); + } + + const FieldRef & get_isovar_field() const { return my_isovar_field; } + void set_isovar_field( const FieldRef & ref ) { my_isovar_field = ref; } + + double get_time_of_arrival_speed(stk::mesh::Entity elem, ParallelErrorMessage& err) const; + + void set_isovar(const std::string & isovar_name, const double isoval) { my_isovar_name = isovar_name; my_threshold = isoval; trackIsoSurface = true; } + const double & get_isoval() const { return my_threshold; } + + bool get_reinitialize_every_step() const { return my_needs_reinitialize_every_step; } + void set_reinitialize_every_step(const bool reinit) { set_keep_IC_surfaces(); my_needs_reinitialize_every_step = true; } + + Redistance_Method get_redistance_method() const { return my_redistance_method; } + void set_redistance_method( const Redistance_Method type ) { my_redistance_method = type; } + void set_time_of_arrival_element_speed_field_name( const std::string & time_of_arrival_speed_field_name) { my_time_of_arrival_element_speed_field_name = time_of_arrival_speed_field_name; } + void set_time_of_arrival_block_speed(const std::string & blockName, const double blockSpeed); + Faceted_Surface & get_facets() { return *facets; } + const Faceted_Surface & get_facets() const { return *facets; } + + static std::vector the_levelSet_names; + static LevelSet_Identifier get_identifier(const std::string & name); + static std::string & get_name(const LevelSet_Identifier identifier) { ThrowAssert(identifier.get() < the_levelSet_names.size()); return the_levelSet_names[identifier.get()]; } + + void narrow_band_multiplier( double multiplier ) { my_narrow_band_multiplier = multiplier; } + const double & narrow_band_size() const { return my_narrow_band_size; } + void narrow_band_size( double size ) { my_narrow_band_size = size; } // publicly deprecated, make private + + void max_feature_size( double size ) { my_max_feature_size= size; } + void use_simple_remove_feature( bool is_simple ) {my_use_simple_remove_feature = is_simple; } + + double max_feature_size() { return my_max_feature_size; } + bool use_simple_remove_feature() { return my_use_simple_remove_feature; } + + void set_surface_parts_vector(); + + void set_ic_offset (const double offset) { + my_ic_offset = offset; + } + void set_ic_scale (const double scale) { + my_ic_scale = scale; + } + void perform_initial_redistance(const bool flag) { + my_perform_initial_redistance = flag; + } + + void set_keep_IC_surfaces() { my_keep_IC_surfaces = true; } + bool get_keep_IC_surfaces() const { return my_keep_IC_surfaces; } + + static bool sign_change( double f1, double f2 ) { + return ( (f1 < 0.) ? (f2 >= 0.) : (f2 < 0.) ); // GOMA sign convention + //return ( (f1 > 0.) ? (f2 <= 0.) : (f2 > 0.) ); // Marching cubes sign convention + } + + static int sign( double f ) { + return ( (f < 0.) ? -1 : 1 ); // GOMA sign convention + //return ( (f > 0.) ? 1 : -1 ); // Marching cubes sign convention + } + + const std::vector & get_compute_surface_distance_parts() const { return my_compute_surface_distance_parts; } + std::vector & get_compute_surface_distance_parts() { return my_compute_surface_distance_parts; } + void set_surface_distance(std::vector surfaces, const double in_distance); + void compute_surface_distance(const double narrowBandSize=0.0, const double farFieldValue=0.0); + static void initialize(stk::mesh::MetaData & meta, const bool requires_additional_initialization); + void initialize(const double time = 0.0, const bool requires_additional_initialization = false); + void redistance(); + void redistance(const stk::mesh::Selector & selector); + void fast_marching_redistance(const stk::mesh::Selector & selector, const bool compute_time_of_arrival = false); + + void set_initial_volume(const double v) { my_initial_neg_vol = v; } + double constrained_redistance(const bool use_initial_vol = false); + + void compute_nodal_bbox( const stk::mesh::Selector & selector, + BoundingBox & node_bbox, + const Vector3d & displacement = Vector3d::ZERO ) const; + + double find_redistance_correction( const double start_area, + const double start_neg_vol, + const double start_pos_vol, + const int max_iterations = 100, + const double tol = 1.e-6 ); + + bool has_IC_surfaces(); + BoundingBox get_IC_surface_bounding_box(); + IC_Alg& get_IC_alg(); + + static LevelSet & build(stk::mesh::MetaData & in_meta, const std::string & ls_name, stk::diag::Timer & parent_timer); + + virtual ~LevelSet(); + +private: + LevelSet(stk::mesh::MetaData & in_meta, const std::string & in_name, stk::diag::Timer & parent_timer); + +private: + stk::mesh::MetaData & my_meta; + AuxMetaData & my_aux_meta; + const LevelSet_Identifier my_identifier; + const std::string my_name; + mutable stk::diag::Timer my_parent_timer; + mutable stk::diag::Timer my_timer; + +public: + const unsigned spatial_dimension; + +private: + + FieldRef my_coordinates_field; + FieldRef my_distance_field; + FieldRef my_old_distance_field; + FieldRef my_isovar_field; + FieldRef myTimeOfArrivalElementSpeedField; + + std::string my_distance_name; + std::string my_isovar_name; + + std::string my_composite_name; + + double my_narrow_band_multiplier; + double my_narrow_band_size; + + double my_max_feature_size; + bool my_use_simple_remove_feature = false; + + + double my_ic_offset; + double my_ic_scale; + bool my_perform_initial_redistance; + bool my_keep_IC_surfaces; + + double my_threshold; + Redistance_Method my_redistance_method; + std::string my_time_of_arrival_element_speed_field_name; + std::map myTimeOfArrivalBlockSpeedsByName; + std::vector myTimeOfArrivalBlockSpeeds; + + std::unique_ptr my_IC_alg; + + // vector of previous facets + std::unique_ptr facets_old; + + // vector of current facets + std::unique_ptr facets; + + Vector3d my_extension_velocity; + const double epsilon; + + bool trackIsoSurface; + + // used to increment file name for facet exoii database hack + int my_facetFileIndex; + + double my_initial_neg_vol; + + bool my_needs_reinitialize_every_step; + + std::vector my_compute_surface_distance_parts; + std::vector my_surface_parts; + + + void set_distance(const double & distance) const; + void increment_distance(const double increment, const bool enforce_sign = false) const; + void scale_distance(const double scale) const; + void negate_distance() const; + + void time_integrate(const double deltaTime); + + void prepare_to_compute_distance( const double & deltaTime, const stk::mesh::Selector & selector ); + + void compute_distance_semilagrangian(const double & deltaTime, const stk::mesh::Selector & selector ); + + double distance( const Vector3d & x, + const int previous_sign, + const bool enforce_sign ) const; + + bool compute_time_of_arrival() const { return !my_time_of_arrival_element_speed_field_name.empty() || !myTimeOfArrivalBlockSpeeds.empty(); } +}; + +class LevelSetManager { +public: + LevelSetManager() {} + LevelSetManager(LevelSetManager const&) = delete; + LevelSetManager& operator=(LevelSetManager const&) = delete; + + static LevelSetManager & get(stk::mesh::MetaData & meta); + static LevelSetManager & get(const stk::mesh::MetaData & meta); + + int numberLevelSets() const { return my_level_sets.size(); } + LevelSet & levelSet(const unsigned ordinal) const { ThrowAssert(ordinal < my_level_sets.size()); return *my_level_sets[ordinal]; } + bool has_levelSet(const std::string & ls_name) const; + void add(LevelSet * ls) { my_level_sets.emplace_back(ls); } + + std::vector< std::unique_ptr >::const_iterator begin() const { return my_level_sets.begin(); } + std::vector< std::unique_ptr >::const_iterator end() const { return my_level_sets.end(); } + + void set_current_coordinates(FieldRef current_coords) { my_current_coordinates = current_coords; } + FieldRef get_current_coordinates() const { return my_current_coordinates; } +private: + std::vector< std::unique_ptr > my_level_sets; + FieldRef my_current_coordinates; +}; + +std::string print_sizes(const LevelSet & ls); + +} // namespace krino + +#endif // Akri_LevelSet_h diff --git a/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.cpp b/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.cpp new file mode 100644 index 000000000000..9f2cfdda6005 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.cpp @@ -0,0 +1,931 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +std::unique_ptr create_element_cutter_with_error_handling(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::vector & elementParentEdges, + const std::vector & areParentEdgesAreOrientedSameAsElementEdges, + const Phase_Support & phaseSupport, + const std::function &)> & intersectingPlanesDiagonalPicker) +{ + if (krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "Building cutting planes for element global_id=" << mesh.identifier(element) << "\n"; + + stk::topology elementTopology = mesh.bucket(element).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + const bool oneLSPerPhase = phaseSupport.has_one_levelset_per_phase(); + + std::unique_ptr cutter; + + try + { + cutter = create_element_cutter(oneLSPerPhase, masterElement, elementParentEdges, areParentEdgesAreOrientedSameAsElementEdges, intersectingPlanesDiagonalPicker); + } + catch(const std::exception & err) + { + krinolog << "Error constructing cutting surfaces for Mesh_Element " << mesh.identifier(element) << stk::diag::push << stk::diag::dendl; + for(unsigned i=0; i < elementParentEdges.size(); ++i) + { + krinolog << "Edge " << i; + if(elementParentEdges[i]) { + krinolog << " node ids = "; + for(auto && node : elementParentEdges[i]->get_nodes()) krinolog << mesh.identifier(node) << " "; + krinolog << stk::diag::push << stk::diag::dendl; + krinolog << *elementParentEdges[i] << stk::diag::pop << stk::diag::dendl; + } + else + { + krinolog << " No parent edge." << stk::diag::dendl; + } + } + krinolog << stk::diag::pop << stk::diag::dendl; + krinolog << err.what() << stk::diag::dendl; + throw err; + } + + return cutter; +} + +LevelSetElementCutter::LevelSetElementCutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const ParentEdgeMap & parentEdges, + const Phase_Support & phaseSupport, + const std::function &)> & intersectingPlanesDiagonalPicker) +{ + fill_element_parent_edges(mesh, element, parentEdges, myParentEdges, myParentEdgesAreOrientedSameAsElementEdges); + myElementInterfaceCutter = create_element_cutter_with_error_handling(mesh, element, myParentEdges, myParentEdgesAreOrientedSameAsElementEdges, phaseSupport, intersectingPlanesDiagonalPicker); +} + +std::string LevelSetElementCutter::visualize(const stk::mesh::BulkData & mesh) const +{ + std::ostringstream os; + + std::vector interiorIntersections; + myElementInterfaceCutter->fill_interior_intersections(interiorIntersections); + + os << "Interior intersections " << interiorIntersections.size() << ": \n"; + for (auto && intersection : interiorIntersections) + { + os << "Interior intersection at " << intersection.parametricCoords << " with domains { "; + for (int domain : intersection.sortedDomains) os<< domain << " "; + os << "}\n"; + } + + os << "Parent edges: \n"; + for (auto && edge : myParentEdges) + { + os << "Edge with nodes " << mesh.identifier(edge->get_parent_nodes().first) << " and " << mesh.identifier(edge->get_parent_nodes().second) << ":\n"; + if (edge) os << *edge; + } + + os << myElementInterfaceCutter->visualize() << "\n"; + + return os.str(); +} + +std::unique_ptr LevelSetInterfaceGeometry::build_element_cutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::function &)> & intersectingPlanesDiagonalPicker) const +{ + std::unique_ptr cutter; + cutter.reset( new LevelSetElementCutter(mesh, element, myParentEdges, myPhaseSupport, intersectingPlanesDiagonalPicker) ); + return cutter; +} + +PhaseTag LevelSetInterfaceGeometry::get_starting_phase(const ElementCutter * cutter) const +{ + const LevelSetElementCutter * LSCutter = dynamic_cast(cutter); + ThrowRequire(LSCutter); + return LSCutter->get_starting_phase(myCdfemSupport, myPhaseSupport); +} + +PhaseTag LevelSetElementCutter::get_starting_phase(const CDFEM_Support & cdfemSupport, const Phase_Support & phaseSupport) const +{ + PhaseTag phase; + + // For elements with no interfaces, this will be the uncrossed phase of the mesh element. + // For elements with interface, this is the starting phase that will be inherited by the + // subelements and then incrementally updated as we process the interfaces. + if (cdfemSupport.num_ls_fields() > 1 && Phase_Support::has_one_levelset_per_phase()) + { + int LSphase = myElementInterfaceCutter->get_starting_phase_for_cutting_surfaces(); + if (LSphase == -1) + { + const auto & phasesPresent = get_phases_present_on_edges(myParentEdges); + ThrowRequire(!phasesPresent.empty() && (myElementInterfaceCutter->get_num_cutting_surfaces() > 0 || 1 == phasesPresent.size())); + LSphase = *phasesPresent.begin(); + } + phase.add(cdfemSupport.ls_field(LSphase).identifier, -1); + } + else + { + const int num_ls = cdfemSupport.num_ls_fields(); + for(int ls_index=0; ls_index < num_ls; ++ls_index) + { + const InterfaceID interface(ls_index,ls_index); + int sign = 0; + bool shouldSetPhase = false; + for(auto && edge : myParentEdges) + { + if (edge) + { + shouldSetPhase = true; + if (edge->have_crossing(InterfaceID(ls_index,ls_index))) + { + shouldSetPhase = false; + break; + } + else + sign = edge->get_crossing_sign(interface); + } + } + if (shouldSetPhase) + phase.add(cdfemSupport.ls_field(ls_index).identifier, sign); + } + } + + return phase; +} + +static std::vector find_next_phase_candidates(const std::vector & interfaces, + const std::vector & pathSoFar) +{ + const int currentPhase = pathSoFar.back(); + std::vector nextPhaseCandidates; + for (auto && interface : interfaces) + { + if (interface.first_ls() == currentPhase) + { + if (std::find(pathSoFar.begin(), pathSoFar.end(), interface.second_ls()) == pathSoFar.end()) + nextPhaseCandidates.push_back(interface.second_ls()); + } + else if (interface.second_ls() == currentPhase) + { + if (std::find(pathSoFar.begin(), pathSoFar.end(), interface.first_ls()) == pathSoFar.end()) + nextPhaseCandidates.push_back(interface.first_ls()); + } + } + return nextPhaseCandidates; +} + +static std::vector shortest_path_to_end(const std::vector & pathSoFar, + const std::vector & interfaces, + const std::set & endPhases) +{ + if (endPhases.count(pathSoFar.back()) > 0) + return pathSoFar; + + const std::vector nextPhaseCandidates = find_next_phase_candidates(interfaces, pathSoFar); + if (nextPhaseCandidates.empty()) + { + return {}; + } + + std::vector shortestPath; + size_t shortestPathSize = std::numeric_limits::max(); + for (int nextPhase : nextPhaseCandidates) + { + std::vector path = pathSoFar; + path.push_back(nextPhase); + const auto fullPath = shortest_path_to_end(path, interfaces, endPhases); + if (!fullPath.empty() && fullPath.size() < shortestPathSize) + { + shortestPath = fullPath; + shortestPathSize = fullPath.size(); + } + } + return shortestPath; +} + +std::vector shortest_path_from_begin_to_end(const std::vector & interfaces, + const int beginPhase, + const std::set & endPhases) +{ + std::vector startPath; + startPath.push_back(beginPhase); + return shortest_path_to_end(startPath, interfaces, endPhases); +} + +static bool captures_interface(const std::vector * sortedDomains, const InterfaceID & interface) +{ + if (sortedDomains == nullptr) + return false; + if (interface.first_ls() == interface.second_ls()) + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(*sortedDomains, {interface.first_ls()}); + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(*sortedDomains, {interface.first_ls(),interface.second_ls()}); +} + +static bool interface_has_uncaptured_edge_intersection(const LevelSetElementCutter & cutter, + const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + const InterfaceID & interface) +{ + ThrowRequire(elemNodesCoords.size() == 4 || elemNodesCoords.size() == 3); + const stk::topology topology = (elemNodesCoords.size() == 4)? stk::topology::TETRAHEDRON_4 : stk::topology::TRIANGLE_3_2D; + + const unsigned numEdges = topology.num_edges(); + for(unsigned i=0; i < numEdges; ++i) + { + const unsigned * edgeNodeOrdinals = get_edge_node_ordinals(topology, i); + const int n0 = edgeNodeOrdinals[0]; + const int n1 = edgeNodeOrdinals[1]; + if (!captures_interface(elemNodesSnappedDomains[n0], interface) && !captures_interface(elemNodesSnappedDomains[n1], interface)) + { + const Segment3d edge(elemNodesCoords[n0], elemNodesCoords[n1]); + if (cutter.have_crossing(interface, edge)) + return true; + } + } + return false; +} + +static std::vector +get_sorted_cutting_interfaces_with_uncaptured_intersections(const LevelSetElementCutter & cutter, + const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains) +{ + std::set interfacesWithUncapturedCrossings; + for (auto && interface : cutter.get_sorted_cutting_interfaces()) + if (interface_has_uncaptured_edge_intersection(cutter, elemNodesCoords, elemNodesSnappedDomains, interface)) + interfacesWithUncapturedCrossings.insert(interface); + + cutter.add_interfaces_with_uncaptured_intersection_within_element(elemNodesCoords, elemNodesSnappedDomains, interfacesWithUncapturedCrossings); + + std::vector interfaces(interfacesWithUncapturedCrossings.begin(), interfacesWithUncapturedCrossings.end()); + return interfaces; +} + +static int get_interface_index(const std::vector & sortedInterfaces, const InterfaceID interface) +{ + const auto iter = std::lower_bound(sortedInterfaces.begin(), sortedInterfaces.end(), interface); + return std::distance(sortedInterfaces.begin(), iter); +} + +static Vector3d get_centroid(const std::vector & elemNodesCoords) +{ + Vector3d centroid = Vector3d::ZERO; + for(auto && nodeCoords : elemNodesCoords) + { + centroid += nodeCoords; + } + centroid *= 1./elemNodesCoords.size(); + return centroid; +} + +std::vector +LevelSetElementCutter::get_interface_signs_based_on_crossings(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains) const +{ + const auto allInterfaces = get_sorted_cutting_interfaces(); + std::vector interfaceSigns(allInterfaces.size(), 0); + + const auto intersectingInterfaces = get_sorted_cutting_interfaces_with_uncaptured_intersections(*this, elemNodesCoords, elemNodesSnappedDomains); + const Vector3d centroid = get_centroid(elemNodesCoords); + + const bool oneLSPerPhase = Phase_Support::has_one_levelset_per_phase(); + if (oneLSPerPhase) + { + std::set subPhases; + const int ownerStartPhase = get_starting_phase_for_cutting_surfaces(); + + for (auto && interface : allInterfaces) + { + if (std::binary_search(intersectingInterfaces.begin(), intersectingInterfaces.end(), interface)) + { + subPhases.insert(interface.first_ls()); + subPhases.insert(interface.second_ls()); + } + else + { + interfaceSigns[get_interface_index(allInterfaces, interface)] = -2; + } + } + if (subPhases.empty()) + { + subPhases.insert(myElementInterfaceCutter->get_ls_per_interface_phase_at_location(centroid)); + } + + if (subPhases.count(ownerStartPhase) == 0) + { + std::vector fixPath = shortest_path_from_begin_to_end(allInterfaces, ownerStartPhase, subPhases); + ThrowRequireMsg(!fixPath.empty(), "Cannot fix starting phase."); + for (unsigned i=1; i fixPath[i-1]) ? 1 : -1; + interfaceSigns[get_interface_index(allInterfaces, interface)] = sign; + } + } + } + else + { + for (auto && interface : allInterfaces) + if (!std::binary_search(intersectingInterfaces.begin(), intersectingInterfaces.end(), interface)) + interfaceSigns[get_interface_index(allInterfaces, interface)] = sign_at_position(interface, centroid); + } + + return interfaceSigns; +} + +void LevelSetElementCutter::update_edge_crossings(const unsigned iEdge, const std::vector> & nodesIsovar) +{ + ThrowRequire(iEdge < myParentEdges.size()); + CDFEM_Parent_Edge * parentEdge = const_cast(myParentEdges[iEdge]); + ThrowRequire(parentEdge); + if (myParentEdgesAreOrientedSameAsElementEdges[iEdge]) + { + parentEdge->find_crossings(nodesIsovar); + } + else + { + const std::vector> orientedIsovar = {nodesIsovar[1], nodesIsovar[0]}; + parentEdge->find_crossings(orientedIsovar); + } +} + +static std::function &)> +temporary_build_always_true_diagonal_picker() +{ + auto diagonalPicker = + [](const std::array & faceNodes) + { + return true; + }; + return diagonalPicker; +} + +typedef std::function ParentEdgeFilter; + +static ParentEdgeFilter keep_owned_edges_filter(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & parentElementSelector) +{ + const auto filter = [&mesh, &parentElementSelector](const CDFEM_Parent_Edge & edge) + { + const std::pair edgeNodes = edge.get_parent_nodes(); + std::vector edgeElems; + stk::mesh::get_entities_through_relations(mesh, {edgeNodes.first, edgeNodes.second}, stk::topology::ELEMENT_RANK, edgeElems); + { + bool foundOwnedElement = false; + for (auto && edgeElem : edgeElems) + if (parentElementSelector(mesh.bucket(edgeElem)) && mesh.parallel_owner_rank(edgeElem) == mesh.parallel_rank()) + foundOwnedElement = true; + ThrowRequire(foundOwnedElement); + } + const int parallelRank = mesh.parallel_rank(); // Assumes local proc owns at least one selected element of edge + for (auto && edgeElem : edgeElems) + if (mesh.parallel_owner_rank(edgeElem) < parallelRank && parentElementSelector(mesh.bucket(edgeElem))) + return false; + return true; + }; + return filter; +} + +static ParentEdgeFilter keep_all_edges_filter() +{ + const auto filter = [](const CDFEM_Parent_Edge & edge) + { + return true; + }; + return filter; +} + +static void append_intersection_points_from_filtered_parent_edges(std::vector & intersectionPoints, + const ParentEdgeMap & parentEdges, + const IntersectionPointFilter & intersectionPointFilter, + const ParentEdgeFilter edgeFilter) +{ + const bool intersectionPointIsOwned = true; + std::vector intersectionPointSortedDomains; + for (auto && mapEntry : parentEdges) + { + const CDFEM_Parent_Edge & edge = mapEntry.second; + const auto & edgeCrossings = edge.get_crossings(); + if (!edgeCrossings.empty() && edgeFilter(edge)) + { + const std::pair edgeNodes = edge.get_parent_nodes(); + for (auto & crossing : edgeCrossings) + { + const InterfaceID & interface = crossing.first; + const double location = crossing.second; + interface.fill_sorted_domains(intersectionPointSortedDomains); + std::vector intersectionPointNodes{edgeNodes.first, edgeNodes.second}; + if (intersectionPointFilter(intersectionPointNodes, intersectionPointSortedDomains)) + intersectionPoints.emplace_back(intersectionPointIsOwned, intersectionPointNodes, std::vector{1.-location, location}, intersectionPointSortedDomains); + } + } + } +} + +static void append_intersection_points_from_owned_parent_edges(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & parentElementSelector, + std::vector & intersectionPoints, + const ParentEdgeMap & parentEdges, + const IntersectionPointFilter & intersectionPointFilter) +{ + append_intersection_points_from_filtered_parent_edges(intersectionPoints, parentEdges, intersectionPointFilter, keep_owned_edges_filter(mesh, parentElementSelector)); +} + +static void append_intersection_points_from_all_parent_edges(std::vector & intersectionPoints, + const ParentEdgeMap & parentEdges, + const IntersectionPointFilter & intersectionPointFilter) +{ + append_intersection_points_from_filtered_parent_edges(intersectionPoints, parentEdges, intersectionPointFilter, keep_all_edges_filter()); +} + +LevelSetInterfaceGeometry::LevelSetInterfaceGeometry(const stk::mesh::MetaData & meta) +: LevelSetInterfaceGeometry(AuxMetaData::get(meta).active_part(), CDFEM_Support::get(meta), Phase_Support::get(meta)) {} + +void LevelSetInterfaceGeometry::prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + myParentsToChildMapper.build_map(mesh, myActivePart, myCdfemSupport, myPhaseSupport); + const auto should_build_linearized_edge = build_no_linearized_edges_function(); + myParentEdges = build_parent_edges(mesh, myParentsToChildMapper, should_build_linearized_edge, myActivePart, myCdfemSupport, myPhaseSupport); +} + +void LevelSetInterfaceGeometry::prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const std::vector & elementsToIntersect, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + myParentsToChildMapper.build_map(mesh, myActivePart, myCdfemSupport, myPhaseSupport); + const auto should_build_linearized_edge = build_no_linearized_edges_function(); + myParentEdges = build_parent_edges_using_elements(mesh, myParentsToChildMapper, should_build_linearized_edge, elementsToIntersect, myActivePart, myCdfemSupport, myPhaseSupport); +} + +std::vector LevelSetInterfaceGeometry::get_edge_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + std::vector intersectionPoints; + prepare_to_process_elements(mesh, nodesToCapturedDomains); + const IntersectionPointFilter intersectionPointFilter = keep_all_intersection_points_filter(); + append_intersection_points_from_all_parent_edges(intersectionPoints, myParentEdges, intersectionPointFilter); + return intersectionPoints; +} + +void LevelSetInterfaceGeometry::append_element_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const std::vector & elementsToIntersect, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) const +{ + const stk::mesh::Selector parentElementSelector = get_parent_element_selector(myActivePart, myCdfemSupport, myPhaseSupport); + prepare_to_process_elements(mesh, elementsToIntersect, nodesToCapturedDomains); + append_intersection_points_from_owned_parent_edges(mesh, parentElementSelector, intersectionPoints, myParentEdges, intersectionPointFilter); + append_intersection_points_from_within_elements_and_owned_faces(mesh, parentElementSelector, elementsToIntersect, *this, intersectionPointFilter, intersectionPoints); +} + +static int get_domain_for_uncut_element(const stk::mesh::BulkData & mesh, + const stk::mesh::Entity element, + const std::vector & elementParentEdges, + const bool oneLSPerPhase) +{ + if (oneLSPerPhase) + { + const auto edgePhases = get_phases_present_on_edges_and_interior(elementParentEdges); + if (edgePhases.size() == 1) + return *edgePhases.begin(); + } + return -1; +} + +void LevelSetInterfaceGeometry::store_phase_for_uncut_elements(const stk::mesh::BulkData & mesh) const +{ + std::vector elementsToIntersect; + stk::mesh::get_entities( mesh, stk::topology::ELEMENT_RANK, elementsToIntersect, false); + + myParentsToChildMapper.build_map(mesh, myActivePart, myCdfemSupport, myPhaseSupport); + const auto linearize_all_edges = build_all_linearized_edges_function(); + ParentEdgeMap parentEdges = build_parent_edges_using_elements(mesh, myParentsToChildMapper, linearize_all_edges, elementsToIntersect, myActivePart, myCdfemSupport, myPhaseSupport); + + const bool oneLSPerPhase = myCdfemSupport.num_ls_fields() > 1 && Phase_Support::has_one_levelset_per_phase(); + std::vector elementParentEdges; + std::vector areParentEdgesOrientedSameAsElementEdges; + + const std::vector parentElements = get_owned_parent_elements(mesh, myActivePart, myCdfemSupport, myPhaseSupport); + for (auto element : parentElements) + { + fill_element_parent_edges(mesh, element, parentEdges, elementParentEdges, areParentEdgesOrientedSameAsElementEdges); + const int elementDomain = get_domain_for_uncut_element(mesh, + element, + elementParentEdges, + oneLSPerPhase); + if (elementDomain >= 0) + myUncutElementPhases[element] = elementDomain; + } +} + +static NodeToCapturedDomainsMap store_and_communicate_new_snap_node_domains(const stk::mesh::BulkData & mesh, const std::vector & intersectionPoints, const std::vector & snapInfos) +{ + std::vector snapNodes; + NodeToCapturedDomainsMap newSnapnodesToCapturedDomains; + for (auto && snapInfo : snapInfos) + { + if (snapInfo.get_owner() == mesh.parallel_rank()) + { + const size_t intersectionPointIndex = snapInfo.get_intersection_point_index(); + stk::mesh::Entity snapNode = mesh.get_entity(stk::topology::NODE_RANK, snapInfo.get_node_global_id()); + snapNodes.push_back(snapNode); + const IntersectionPoint & intersectionPoint = intersectionPoints[intersectionPointIndex]; + + newSnapnodesToCapturedDomains[snapNode] = intersectionPoint.get_sorted_domains(); + } + } + + communicate_node_captured_domains_for_given_nodes(mesh, snapNodes, newSnapnodesToCapturedDomains); + + return newSnapnodesToCapturedDomains; +} + +static std::vector get_node_parametric_coords_after_snapping(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const Vector3d snapNodeLocation) +{ + stk::topology elementTopology = mesh.bucket(element).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + const double * elemNodeParamCoords = masterElement.nodal_parametric_coordinates(); + const int dim = mesh.mesh_meta_data().spatial_dimension(); + const StkMeshEntities elementNodes{mesh.begin_nodes(element), mesh.end_nodes(element)}; + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + + std::vector nodeLocations; + fill_element_node_coordinates(mesh, element, coordsField, nodeLocations); + + std::vector nodesCoords; + for (unsigned n=0; n= baseShapeFcn) + return 1.; + return baseShapeFcn/(baseShapeFcn-shapeFcn); +} + +static Vector3d find_point_within_deformed_and_undeformed_tet(const std::vector & deformedElementParamCoords, + const int lnn) +{ + stk::topology topology = stk::topology::TETRAHEDRON_4; + std::array permutations{0, 1, 2, 4}; + std::array permuteNodes; + topology.permutation_node_ordinals(permutations[lnn], permuteNodes.data()); + ThrowAssert(permuteNodes[0] == lnn); + const Vector3d & pt = deformedElementParamCoords[lnn]; + const Vector3d oppositePt = 1./3.*(deformedElementParamCoords[permuteNodes[1]] + deformedElementParamCoords[permuteNodes[2]] + deformedElementParamCoords[permuteNodes[3]]); + double fraction = 1.0; + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(pt[0], oppositePt[0])); + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(pt[1], oppositePt[1])); + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(pt[2], oppositePt[2])); + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(1.-pt[0]-pt[1]-pt[2], 1.-oppositePt[0]-oppositePt[1]-oppositePt[2])); + const double centroidWt = 0.25*fraction; + return centroidWt*pt + (1.-centroidWt)*oppositePt; +} + +static Vector3d find_point_within_deformed_and_undeformed_tri(const std::vector & deformedElementParamCoords, + const int lnn) +{ + stk::topology topology = stk::topology::TRIANGLE_3_2D; + std::array permutations{0, 2, 1}; + std::array permuteNodes; + topology.permutation_node_ordinals(permutations[lnn], permuteNodes.data()); + ThrowAssert(permuteNodes[0] == lnn); + const Vector3d & pt = deformedElementParamCoords[lnn]; + const Vector3d oppositePt = 0.5*(deformedElementParamCoords[permuteNodes[1]] + deformedElementParamCoords[permuteNodes[2]]); + double fraction = 1.0; + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(pt[0], oppositePt[0])); + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(pt[1], oppositePt[1])); + fraction = std::min(fraction, truncate_to_maintain_positive_shape_function(1.-pt[0]-pt[1], 1.-oppositePt[0]-oppositePt[1])); + const double centroidWt = 1./3.*fraction; + return centroidWt*pt + (1.-centroidWt)*oppositePt; +} + +static int get_node_of_element(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + stk::mesh::Entity node) +{ + const StkMeshEntities elementNodes{mesh.begin_nodes(element), mesh.end_nodes(element)}; + for (unsigned n=0; n & deformedElementParamCoords) +{ + const int lnn = get_node_of_element(mesh, element, snapNode); + + stk::topology elementTopology = mesh.bucket(element).topology(); + if (elementTopology.base() == stk::topology::TETRAHEDRON_4) + return find_point_within_deformed_and_undeformed_tet(deformedElementParamCoords, lnn); + ThrowRequire(elementTopology.base() == stk::topology::TRIANGLE_3_2D); + return find_point_within_deformed_and_undeformed_tri(deformedElementParamCoords, lnn); +} + +static std::vector*> get_node_snap_domains(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const std::vector & snapNodeDomains, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + const StkMeshEntities elementNodes{mesh.begin_nodes(element), mesh.end_nodes(element)}; + std::vector*> nodeDomains; + nodeDomains.reserve(elementNodes.size()); + for (auto node : StkMeshEntities{mesh.begin_nodes(element), mesh.end_nodes(element)}) + { + if (node == snapNode) + { + nodeDomains.push_back(&snapNodeDomains); + } + else + { + const auto iter = nodesToCapturedDomains.find(node); + if (iter == nodesToCapturedDomains.end()) + nodeDomains.push_back(nullptr); + else + nodeDomains.push_back(&(iter->second)); + } + } + + return nodeDomains; +} + +static bool domain_is_common_to_all_entities(const int domain, const std::vector*> & entitiesDomains) +{ + for (auto && domains : entitiesDomains) + if (!std::binary_search(domains->begin(), domains->end(), domain)) + return false; + return true; +} + +static std::set get_common_domains(std::vector*> entitiesDomains) +{ + std::set commonDomains; + + if (entitiesDomains.empty()) + return commonDomains; + + for (auto & entityDomains : entitiesDomains) + if (!entityDomains) + return commonDomains; + + for (int domain : *entitiesDomains[0]) + if (domain_is_common_to_all_entities(domain, entitiesDomains)) + commonDomains.insert(domain); + + return commonDomains; +} + +static bool will_have_uncaptured_edge_intersection_after_snapping(const Element_Cutter & cutter, stk::topology elementTopology, const std::vector nodeCoords, + const std::vector*> & nodeDomains) +{ + std::vector interfacesWithCuttingSurface; + cutter.fill_interfaces_with_cutting_surface(interfacesWithCuttingSurface); + + const unsigned numEdges = elementTopology.num_edges(); + for(unsigned i=0; i < numEdges; ++i) + { + const unsigned * edgeNodeOrdinals = get_edge_node_ordinals(elementTopology(), i); + const std::vector* node0Domains = nodeDomains[edgeNodeOrdinals[0]]; + const std::vector* node1Domains = nodeDomains[edgeNodeOrdinals[1]]; + + for (auto && interface : interfacesWithCuttingSurface) + { + if (!captures_interface(node0Domains, interface) && !captures_interface(node1Domains, interface)) + { + const Segment3d edge(nodeCoords[edgeNodeOrdinals[0]], nodeCoords[edgeNodeOrdinals[1]]); + if (cutter.have_crossing(interface, edge)) + return true; + } + } + } + return false; +} + +static int get_domain_of_element_if_it_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper parentsToChildMapper, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const Vector3d & snapNodeLocation, + const std::vector*> & elementNodeDomains) +{ + const auto diagonalPicker = temporary_build_always_true_diagonal_picker(); + const bool oneLSPerPhase = true; + + ParentEdgeMap parentEdges = build_parent_edges_using_elements(mesh, parentsToChildMapper, build_all_linearized_edges_function(), {element}, activePart, cdfemSupport, phaseSupport); + if (parentEdges.empty()) + return -1; // not parent element + + std::vector elementParentEdges; + std::vector areParentEdgesOrientedSameAsElementEdges; + fill_element_parent_edges(mesh, element, parentEdges, elementParentEdges, areParentEdgesOrientedSameAsElementEdges); + + const auto edgePhases = get_phases_present_on_edges_and_interior(elementParentEdges); + if (edgePhases.size() == 1) + return *edgePhases.begin(); + + stk::topology elementTopology = mesh.bucket(element).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + std::unique_ptr elementCutter = create_element_cutter(oneLSPerPhase, masterElement, elementParentEdges, areParentEdgesOrientedSameAsElementEdges, diagonalPicker); + + const std::vector nodeParamCoordsAfterSnapping = get_node_parametric_coords_after_snapping(mesh, element, snapNode, snapNodeLocation); + if (!will_have_uncaptured_edge_intersection_after_snapping(*elementCutter, elementTopology, nodeParamCoordsAfterSnapping, elementNodeDomains)) + { + const Vector3d evaluationPt = find_point_within_deformed_and_undeformed_element(mesh, element, snapNode, nodeParamCoordsAfterSnapping); + return elementCutter->get_ls_per_interface_phase_at_location(evaluationPt); + } + + return -1; +} + +static int get_sign_of_uncrossed_edges(const InterfaceID interface, const std::vector & elementParentEdges) +{ + int uncrossedSign = 0; + for (auto && edge : elementParentEdges) + { + if (edge->have_crossing(interface)) + { + return 0; + } + else + { + const int edgeSign = edge->get_crossing_sign(interface); + if (edgeSign == -uncrossedSign) + return 0; + uncrossedSign = edgeSign; + } + } + return uncrossedSign; +} + +static int get_sign_of_element_if_it_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper parentsToChildMapper, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const Vector3d & snapNodeLocation, + const InterfaceID & interface) +{ + const auto diagonalPicker = temporary_build_always_true_diagonal_picker(); + const bool oneLSPerPhase = false; + + ParentEdgeMap parentEdges = build_parent_edges_using_elements(mesh, parentsToChildMapper, build_all_linearized_edges_function(), {element}, activePart, cdfemSupport, phaseSupport); + if (parentEdges.empty()) + return -1; // not parent element + + std::vector elementParentEdges; + std::vector areParentEdgesOrientedSameAsElementEdges; + fill_element_parent_edges(mesh, element, parentEdges, elementParentEdges, areParentEdgesOrientedSameAsElementEdges); + + const int uncrossedSign = get_sign_of_uncrossed_edges(interface, elementParentEdges); + if (uncrossedSign != 0) + return uncrossedSign; + + stk::topology elementTopology = mesh.bucket(element).topology(); + const MasterElement & masterElement = MasterElementDeterminer::getMasterElement(elementTopology); + std::unique_ptr elementCutter = create_element_cutter(oneLSPerPhase, masterElement, elementParentEdges, areParentEdgesOrientedSameAsElementEdges, diagonalPicker); + + const std::vector nodeParamCoordsAfterSnapping = get_node_parametric_coords_after_snapping(mesh, element, snapNode, snapNodeLocation); + const Vector3d evaluationPt = find_point_within_deformed_and_undeformed_element(mesh, element, snapNode, nodeParamCoordsAfterSnapping); + return elementCutter->sign_at_position(interface, evaluationPt); +} + +static void set_domains_for_element_if_it_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper parentsToChildMapper, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const std::vector & snapNodeDomains, + const Vector3d & snapNodeLocation, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + ElementToDomainMap & elementsToDomain ) +{ + auto iter = elementsToDomain.lower_bound(element); + if (iter == elementsToDomain.end() || iter->first != element) + { + const std::vector*> nodeDomains = get_node_snap_domains(mesh, element, snapNode, snapNodeDomains, nodesToCapturedDomains); + + const std::set commonDomains = get_common_domains(nodeDomains); + + int elementDomain = -1; + if (commonDomains.size() == 1) + { + elementDomain = *commonDomains.begin(); + } + else if (commonDomains.size() > 1) + { + elementDomain = get_domain_of_element_if_it_will_be_uncut_after_snapping(mesh, parentsToChildMapper, activePart, cdfemSupport, phaseSupport, element, snapNode, snapNodeLocation, nodeDomains); + } + + if (elementDomain >= 0) + elementsToDomain.emplace_hint(iter, element, elementDomain); + } +} + +static void set_sign_for_element_if_it_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const ParentsToChildMapper parentsToChildMapper, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport, + stk::mesh::Entity element, + stk::mesh::Entity snapNode, + const std::vector & snapNodeDomains, + const Vector3d & snapNodeLocation, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + ElementToDomainMap & elementsToDomain ) +{ + auto iter = elementsToDomain.lower_bound(element); + if (iter == elementsToDomain.end() || iter->first != element) + { + const std::vector*> nodeDomains = get_node_snap_domains(mesh, element, snapNode, snapNodeDomains, nodesToCapturedDomains); + + const std::set commonDomains = get_common_domains(nodeDomains); + + int elementSign = 0; + if (commonDomains.size() == 1) + { + const int lsIndex = *commonDomains.begin(); + const InterfaceID interface(lsIndex,lsIndex); + elementSign = get_sign_of_element_if_it_will_be_uncut_after_snapping(mesh, parentsToChildMapper, activePart, cdfemSupport, phaseSupport, element, snapNode, snapNodeLocation, interface); + } + + if (elementSign != 0) + elementsToDomain.emplace_hint(iter, element, elementSign); + } +} + +void LevelSetInterfaceGeometry::store_phase_for_elements_that_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + const std::vector & snapInfos, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const +{ + const bool oneLSPerPhase = myCdfemSupport.num_ls_fields() > 1 && Phase_Support::has_one_levelset_per_phase(); + if (!oneLSPerPhase && myCdfemSupport.num_ls_fields() > 1) + return; //FIXME: Fix for more than one ls per interface + + const NodeToCapturedDomainsMap newSnapnodesToCapturedDomains = store_and_communicate_new_snap_node_domains(mesh, intersectionPoints, snapInfos); + + for (auto && snapInfo : snapInfos) + { + stk::mesh::Entity snapNode = mesh.get_entity(stk::topology::NODE_RANK, snapInfo.get_node_global_id()); + const stk::math::Vector3d snapLocation = snapInfo.get_snap_location(); + const auto & newSnapNodeDomains = newSnapnodesToCapturedDomains.at(snapNode); + for (auto elem : StkMeshEntities{mesh.begin_elements(snapNode), mesh.end_elements(snapNode)}) + { + if (mesh.bucket(elem).owned() && mesh.bucket(elem).member(myActivePart)) + { + if (oneLSPerPhase) + set_domains_for_element_if_it_will_be_uncut_after_snapping(mesh, myParentsToChildMapper, myActivePart, myCdfemSupport, myPhaseSupport, elem, snapNode, newSnapNodeDomains, snapLocation, nodesToCapturedDomains, myUncutElementPhases); + else + set_sign_for_element_if_it_will_be_uncut_after_snapping(mesh, myParentsToChildMapper, myActivePart, myCdfemSupport, myPhaseSupport, elem, snapNode, newSnapNodeDomains, snapLocation, nodesToCapturedDomains, myUncutElementPhases); + } + } + } +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.hpp b/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.hpp new file mode 100644 index 000000000000..393c97c3e622 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LevelSetInterfaceGeometry.hpp @@ -0,0 +1,122 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_LEVELSETINTERFACEGEOMETRY_H_ +#define KRINO_INCLUDE_AKRI_LEVELSETINTERFACEGEOMETRY_H_ +#include +#include +#include +#include +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +class CDFEM_Support; +class Phase_Support; + +class LevelSetElementCutter : public ElementCutter +{ +public: + LevelSetElementCutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const ParentEdgeMap & parentEdges, + const Phase_Support & phaseSupport, + const std::function &)> & intersectingPlanesDiagonalPicker); + virtual ~LevelSetElementCutter() {} + + virtual bool might_have_interior_or_face_intersections() const override + { return myElementInterfaceCutter->get_num_cutting_surfaces() > 1; } + virtual void fill_interior_intersections(const ElementIntersectionPointFilter & intersectionPointFilter, std::vector & intersections) const override + { myElementInterfaceCutter->fill_interior_intersections(intersectionPointFilter, intersections); } + virtual std::vector get_sorted_cutting_interfaces() const override + { std::vector interfaces; myElementInterfaceCutter->fill_interfaces_with_cutting_surface(interfaces); return interfaces; } + virtual std::vector get_interface_signs_based_on_crossings(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains) const override; + virtual void fill_tetrahedron_face_interior_intersections(const std::array & faceNodes, + const InterfaceID & interface1, + const InterfaceID & interface2, + const ElementIntersectionPointFilter & intersectionPointFilter, + std::vector & intersections) const override + { myElementInterfaceCutter->fill_tetrahedron_face_interior_intersections(faceNodes, interface1, interface2, intersectionPointFilter, intersections); } + virtual std::string visualize(const stk::mesh::BulkData & mesh) const override; + virtual bool have_crossing(const InterfaceID interface, const Segment3d & edge) const override + { return myElementInterfaceCutter->have_crossing(interface, edge); } + virtual double interface_crossing_position(const InterfaceID interface, const Segment3d & edge) const override + { return myElementInterfaceCutter->interface_crossing_position(interface, edge); } + virtual int sign_at_position(const InterfaceID interface, const Vector3d & paramCoords) const override + { return myElementInterfaceCutter->sign_at_position(interface, paramCoords); } + virtual int get_starting_phase_for_cutting_surfaces() const override + { return myElementInterfaceCutter->get_starting_phase_for_cutting_surfaces(); } + + PhaseTag get_starting_phase(const CDFEM_Support & cdfemSupport, const Phase_Support & phaseSupport) const; + void update_edge_crossings(const unsigned iEdge, const std::vector> & nodesIsovar); + void add_interfaces_with_uncaptured_intersection_within_element(const std::vector & elemNodesCoords, + const std::vector *> & elemNodesSnappedDomains, + std::set & interfacesWithUncapturedCrossings) const + { return myElementInterfaceCutter->add_interfaces_with_uncaptured_intersection_within_element(elemNodesCoords, elemNodesSnappedDomains, interfacesWithUncapturedCrossings); } + +private: + std::vector myParentEdges; + std::vector myParentEdgesAreOrientedSameAsElementEdges; + std::unique_ptr myElementInterfaceCutter; +}; + +class LevelSetInterfaceGeometry : public InterfaceGeometry { + +public: + LevelSetInterfaceGeometry(const stk::mesh::MetaData & meta); + LevelSetInterfaceGeometry(const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +: myActivePart(activePart), + myCdfemSupport(cdfemSupport), + myPhaseSupport(phaseSupport) {} + virtual ~LevelSetInterfaceGeometry() {} + + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const override; + virtual void prepare_to_process_elements(const stk::mesh::BulkData & mesh, + const std::vector & elementsToIntersect, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const override; + + virtual std::vector get_edge_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const override; + virtual void append_element_intersection_points(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const std::vector & elementsToIntersect, + const IntersectionPointFilter & intersectionPointFilter, + std::vector & intersectionPoints) const override; + + // FIXME: Temporary methods + virtual void store_phase_for_uncut_elements(const stk::mesh::BulkData & mesh) const override; + virtual void store_phase_for_elements_that_will_be_uncut_after_snapping(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + const std::vector & independentSnapInfos, + const NodeToCapturedDomainsMap & nodesToCapturedDomains) const override; + + virtual const ElementToDomainMap & get_phase_for_uncut_elements() const override { return myUncutElementPhases; } + + virtual std::unique_ptr build_element_cutter(const stk::mesh::BulkData & mesh, + stk::mesh::Entity element, + const std::function &)> & intersectingPlanesDiagonalPicker) const override; + + virtual PhaseTag get_starting_phase(const ElementCutter * cutter) const override; + +private: + const stk::mesh::Part & myActivePart; + const CDFEM_Support & myCdfemSupport; + const Phase_Support & myPhaseSupport; + mutable ParentEdgeMap myParentEdges; + mutable ParentsToChildMapper myParentsToChildMapper; + mutable ElementToDomainMap myUncutElementPhases; +}; + +} + + +#endif /* KRINO_INCLUDE_AKRI_LEVELSETINTERFACEGEOMETRY_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_LevelSet_Identifier.hpp b/packages/krino/krino/krino_lib/Akri_LevelSet_Identifier.hpp new file mode 100644 index 000000000000..4de543ea1156 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LevelSet_Identifier.hpp @@ -0,0 +1,37 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_LevelSet_Identifier_h +#define Akri_LevelSet_Identifier_h + +#include + +namespace krino { + +class LevelSet_Identifier { +public: + explicit LevelSet_Identifier(const unsigned id) : my_id(id) {} + + bool operator < ( const LevelSet_Identifier & RHS ) const { return my_id < RHS.my_id; } + bool operator == ( const LevelSet_Identifier & RHS ) const { return my_id == RHS.my_id; } + bool operator != ( const LevelSet_Identifier & RHS ) const { return my_id != RHS.my_id; } + + unsigned get() const { return my_id; } + + friend std::ostream& operator<<(std::ostream & os, const LevelSet_Identifier & id) + { + os << id.get(); + return os; + } +private: + unsigned my_id; +}; + +} // namespace krino + +#endif // Akri_LevelSet_Identifier_h diff --git a/packages/krino/krino/krino_lib/Akri_LowerEnvelope.cpp b/packages/krino/krino/krino_lib/Akri_LowerEnvelope.cpp new file mode 100644 index 000000000000..0f660042073a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LowerEnvelope.cpp @@ -0,0 +1,317 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include + +namespace krino{ + +LS_Segment::LS_Segment(const double xL, const double xR, int id_) +: x_left(xL), x_right(xR), LS_index(id_) +{ +} + +int +get_min(const std::vector & phi) +{ + double min_value = 0.0; + int min_index = -1; + for (unsigned i=0; i +find_crossing_position_and_sign(const InterfaceID key, const std::vector & pos, const std::vector> & phi) +{ + const int num_nodes = pos.size(); + std::vector key_isovar(num_nodes); + for ( int node = 0; node < num_nodes; ++node ) + { + key_isovar[node] = phi[node][key.first_ls()]-phi[node][key.second_ls()]; + } + + if ( LevelSet::sign_change(key_isovar[0], key_isovar[num_nodes-1]) ) + { + for ( int s = 0; s < num_nodes-1; ++s ) + { + const double ls0 = key_isovar[s]; + const double ls1 = key_isovar[s+1]; + if ( LevelSet::sign_change(ls0, ls1) ) + { + const double interval_position = ls0 / ( ls0 - ls1 ); + const double abs_position = (1.-interval_position)*pos[s] + interval_position*pos[s+1]; + return std::make_pair(abs_position, LevelSet::sign(ls1)); + } + } + } + + const int node0_sign = LevelSet::sign(key_isovar[0]); + const int node1_sign = LevelSet::sign(key_isovar[num_nodes-1]); + ThrowRequire(node0_sign == node1_sign); + return std::make_pair(-1., node0_sign); +} + +bool +find_lower_envelope_crossing_point( const std::array,2> & phi, double & x) +{ + const int id0 = get_min(phi[0]); + const int id1 = get_min(phi[1]); + + if ( id0 != id1 ) + { + const double ls0 = (phi[0][id0]-phi[0][id1]); + const double ls1 = (phi[1][id0]-phi[1][id1]); + + x = ls0 / ( ls0 - ls1 ); + return true; + } + + return false; +} + +bool +find_lower_envelope_crossing_point(const std::array,3> & phi, std::array & point) +{ + const int id0 = get_min(phi[0]); + const int id1 = get_min(phi[1]); + const int id2 = get_min(phi[2]); + + if (id0 != id1 && id1 != id2 && id0 != id2) + { + const double d10 = (phi[0][id1]-phi[0][id0]); + const double d11 = (phi[1][id1]-phi[1][id0]); + const double d12 = (phi[2][id1]-phi[2][id0]); + const double d20 = (phi[0][id2]-phi[0][id0]); + const double d21 = (phi[1][id2]-phi[1][id0]); + const double d22 = (phi[2][id2]-phi[2][id0]); + + const double a00 = d11-d10; + const double a01 = d12-d10; + const double a10 = d21-d20; + const double a11 = d22-d20; + + const double b0 = -d10; + const double b1 = -d20; + + const double det = a00*a11-a01*a10; + if (det == 0.) return false; + + const double x = (b0*a11-b1*a01)/det; + const double y = (-b0*a10+b1*a00)/det; + if (x < 0. || y < 0. || 1.-x-y < 0.) return false; + + point = {{x,y}}; + return true; + } + + return false; +} + +bool +find_lower_envelope_crossing_point(const std::array,4> & phi, std::array & point) +{ + const int id0 = get_min(phi[0]); + const int id1 = get_min(phi[1]); + const int id2 = get_min(phi[2]); + const int id3 = get_min(phi[3]); + + if (id0 != id1 && id0 != id2 && id0 != id3 && id1 != id2 && id1 != id3 && id2 != id3) + { + const double d10 = (phi[0][id1]-phi[0][id0]); + const double d11 = (phi[1][id1]-phi[1][id0]); + const double d12 = (phi[2][id1]-phi[2][id0]); + const double d13 = (phi[3][id1]-phi[3][id0]); + const double d20 = (phi[0][id2]-phi[0][id0]); + const double d21 = (phi[1][id2]-phi[1][id0]); + const double d22 = (phi[2][id2]-phi[2][id0]); + const double d23 = (phi[3][id2]-phi[3][id0]); + const double d30 = (phi[0][id3]-phi[0][id0]); + const double d31 = (phi[1][id3]-phi[1][id0]); + const double d32 = (phi[2][id3]-phi[2][id0]); + const double d33 = (phi[3][id3]-phi[3][id0]); + + const double a00 = d11-d10; + const double a01 = d12-d10; + const double a02 = d13-d10; + const double a10 = d21-d20; + const double a11 = d22-d20; + const double a12 = d23-d20; + const double a20 = d31-d30; + const double a21 = d32-d30; + const double a22 = d33-d30; + const double b0 = -d10; + const double b1 = -d20; + const double b2 = -d30; + const double det = a00*(a22*a11-a21*a12)-a10*(a22*a01-a21*a02)+a20*(a12*a01-a11*a02); + const double x =( b0*(a22*a11-a21*a12)-b1*(a22*a01-a21*a02)+b2*(a12*a01-a11*a02))/det; + const double y =(-b0*(a22*a10-a20*a12)+b1*(a22*a00-a20*a02)-b2*(a12*a00-a10*a02))/det; + const double z =( b0*(a21*a10-a20*a11)-b1*(a21*a00-a20*a01)+b2*(a11*a00-a10*a01))/det; + + point = {{x,y,z}}; + return true; + } + + return false; +} + +void +SegmentLowerEnvelope::adjust_piecewise_linear_positions(Segment_Vector & segments, const std::vector & pos, const std::vector> & phi) +{ + if (pos.size() > 2) + { + // Even for piecewise edges, the structure of the phases must be no more complicated than that + // given by the linear version of the edge. So adjust the linear locations and then remove + // the degenerate, inverted segements. + + // Use piecewise approximation to find actual transition locations + for(Segment_Vector::iterator it = segments.begin(); it != segments.end()-1; ++it) + { + LS_Segment & cur = *it; + LS_Segment & next = *(it+1); + if (cur.ls_index() == next.ls_index()) continue; + InterfaceID iface(cur.ls_index(), next.ls_index()); + + const double crossing_pos = (find_crossing_position_and_sign(iface, pos, phi)).first; + ThrowRequire(crossing_pos >= 0.); + cur = LS_Segment(cur.left_endpoint(), crossing_pos, cur.ls_index()); + next = LS_Segment(crossing_pos, next.right_endpoint(), next.ls_index()); + } + + // Now remove inverted segments + if (segments.size() > 2) + { + for(Segment_Vector::iterator it = segments.begin()+1; it != segments.end()-1; ++it) + { + LS_Segment & prev = *(it-1); + LS_Segment & cur = *it; + LS_Segment & next = *(it+1); + + if (cur.right_endpoint() < cur.left_endpoint()) + { + InterfaceID iface(prev.ls_index(), next.ls_index()); + + const double crossing_pos = (find_crossing_position_and_sign(iface, pos, phi)).first; + ThrowRequire(crossing_pos >= 0.); + prev = LS_Segment(prev.left_endpoint(), cur.right_endpoint(), prev.ls_index()); + cur = LS_Segment(cur.right_endpoint(), crossing_pos, prev.ls_index()); + next = LS_Segment(crossing_pos, next.right_endpoint(), next.ls_index()); + } + } + } + } +} + +void +SegmentLowerEnvelope::collapse_identical_segments(Segment_Vector & segments) +{ + if (segments.size() > 1) + { + Segment_Vector uncollapsed; + uncollapsed.swap(segments); + segments.push_back(uncollapsed.front()); + for(Segment_Vector::const_iterator it = uncollapsed.begin()+1; it != uncollapsed.end(); ++it) + { + const LS_Segment & prev = *(it-1); + const LS_Segment & curr = *it; + if (prev.ls_index() == curr.ls_index()) + { + segments.back() = LS_Segment(segments.back().left_endpoint(), curr.right_endpoint(), prev.ls_index()); + } + else + { + segments.push_back(curr); + } + } + } +} + +void +SegmentLowerEnvelope::add_segment(Segment_Vector & segments, + const double x0, const std::vector & phi0, const int min0, + const double x1, const std::vector & phi1, const int min1) +{ + if (min0 == min1) + { + const LS_Segment segment(x0, x1, min0); + segments.push_back(segment); + return; + } + else + { + InterfaceID key(min0, min1); + const double ls0 = (phi0[key.first_ls()]-phi0[key.second_ls()]); // ls >= 0 for phi2 >= phi1 + const double ls1 = (phi1[key.first_ls()]-phi1[key.second_ls()]); + ThrowRequire(ls0*ls1 <= 0.); + const double cut = ls0 / (ls0 - ls1); + + { + const double x_cut = (1.-cut)*x0 + cut*x1; + ThrowAssert(phi0.size() == phi1.size()); + std::vector phiAtCut(phi0.size()); + for (unsigned i=0; i 1.-tol; + + if (isInfinitesmalCutAt0) + { + if (segments.empty()) + segments.emplace_back(0., 0., min0); + if (minCutMatchesEndPoint) + segments.emplace_back(x0, x1, min1); + else + add_segment(segments, x0, phiAtCut, minAtCut, x1, phi1, min1); + } + else if (isInfinitesmalCutAt1) + { + if (minCutMatchesEndPoint) + segments.emplace_back(x0, x1, min0); + else + add_segment(segments, x0, phi0, min0, x1, phiAtCut, minAtCut); + if (x1 == 1.) + { + if (segments.back().left_endpoint() == 1.) + segments.pop_back(); + segments.emplace_back(1., 1., min1); + } + } + else + { + if (minCutMatchesEndPoint) + segments.emplace_back(x0, x_cut, min0); + else + add_segment(segments, x0, phi0, min0, x_cut, phiAtCut, minAtCut); + + if (minCutMatchesEndPoint) + segments.emplace_back(x_cut, x1, min1); + else + add_segment(segments, x_cut, phiAtCut, minAtCut, x1, phi1, min1); + } + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_LowerEnvelope.hpp b/packages/krino/krino/krino_lib/Akri_LowerEnvelope.hpp new file mode 100644 index 000000000000..88cd8f6e6210 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_LowerEnvelope.hpp @@ -0,0 +1,120 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_LowerEnvelope_h +#define Akri_LowerEnvelope_h + +#include +#include + +#include + +namespace krino { + +class LS_Segment +{ +public: + LS_Segment(const double xL, const double xR, int id); + + double length() const { return x_right - x_left; } + int ls_index() const { return LS_index; } + double left_endpoint() const { return x_left; } + double right_endpoint() const { return x_right; } + + friend bool operator==(const LS_Segment & lhs, const LS_Segment & rhs); + friend std::ostream & operator << (std::ostream &os, const LS_Segment & segment); + +private: + double x_left; + double x_right; + int LS_index; +}; +typedef std::vector Segment_Vector; + +inline std::ostream & operator << (std::ostream &os, const LS_Segment & segment) +{ + os << "segment LS id = " << segment.LS_index + << " left point = " << segment.x_left + << " right point = " << segment.x_right; + return os; +} + +inline std::ostream & operator << (std::ostream &os, const Segment_Vector & segmentVec) +{ + os << "Segments: "; + for (auto && segment : segmentVec) + os << "{" << segment << "} "; + return os; +} + +std::pair +find_crossing_position_and_sign(const InterfaceID key, const std::vector & pos, const std::vector> & phi); + +bool find_lower_envelope_crossing_point(const std::array,2> & phi, double & x); + +bool find_lower_envelope_crossing_point(const std::array,3> & phi, std::array & point); + +bool find_lower_envelope_crossing_point(const std::array,4> & phi, std::array & point); + +int get_min(const std::vector & phi); + +class SegmentLowerEnvelope +{ +public: + // Must be larger than machine epsilon, but puts limit on smallest effective snap tolerance + static constexpr double MinSize() {return 1.e-12;}; + + // linear (2 points) + static Segment_Vector find_lower_envelope(const std::vector & phi0, + const std::vector & phi1) { SegmentLowerEnvelope env(0., phi0, 1., phi1); return env.get_segments(); } + static Segment_Vector find_lower_envelope(const double x0, const std::vector & phi0, + const double x1, const std::vector & phi1) { SegmentLowerEnvelope env(x0, phi0, x1, phi1); return env.get_segments(); } + // piecewise linear (>2 points) + static Segment_Vector find_lower_envelope(const std::vector & pos, const std::vector> & phi) + { SegmentLowerEnvelope env(pos,phi); return env.get_segments(); } + + SegmentLowerEnvelope(const std::vector & phi0, const std::vector & phi1) : SegmentLowerEnvelope(0., phi0, 1., phi1) {} + SegmentLowerEnvelope(const double x0, const std::vector & phi0, + const double x1, const std::vector & phi1) + { + add_segment(mySegments, x0, phi0, x1, phi1); + collapse_identical_segments(mySegments); + } + SegmentLowerEnvelope(const std::vector & pos, const std::vector> & phi) + { + ThrowRequire(pos.size() == phi.size() && pos.size() > 1); + add_segment(mySegments, pos.front(), phi.front(), pos.back(), phi.back()); + collapse_identical_segments(mySegments); + adjust_piecewise_linear_positions(mySegments, pos, phi); + } + const Segment_Vector & get_segments() const { return mySegments; } + +private: + static void add_segment(Segment_Vector & segments, + const double x0, const std::vector & phi0, + const double x1, const std::vector & phi1) + { + const int min0 = get_min(phi0); + const int min1 = get_min(phi1); + return add_segment(segments, x0, phi0, min0, x1, phi1, min1); + } + + static void add_segment(Segment_Vector & segments, + const double x0, const std::vector & phi0, const int min0, + const double x1, const std::vector & phi1, const int min1); + + static void collapse_identical_segments(Segment_Vector & segments); + + static void adjust_piecewise_linear_positions(Segment_Vector & segments, const std::vector & pos, const std::vector> & phi); + + Segment_Vector mySegments; +}; + +} // namespace krino + +#endif // Akri_LowerEnvelope_h diff --git a/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.cpp b/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.cpp new file mode 100644 index 000000000000..dad407903149 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.cpp @@ -0,0 +1,105 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +#include +#include +#include +#include + +namespace krino { + +const MasterElement& +MasterElementDeterminer::getMasterElement(stk::mesh::Bucket & bucket, FieldRef field) +{ + stk::topology field_topology = get_field_topology(bucket, field); + return MasterElementDeterminer::getMasterElement(field_topology); +} + +stk::topology +MasterElementDeterminer::get_field_topology(const stk::mesh::Bucket & b, const FieldRef field) +{ + // As an optimization, assume there is only 1 field topology active for a given mesh topology and field + typedef std::map, stk::topology> FieldAndMeshTopoToFieldTopoMap; + static FieldAndMeshTopoToFieldTopoMap field_topo_map; + + const stk::topology mesh_topology = b.topology(); + const unsigned field_ordinal = field.field().mesh_meta_data_ordinal(); + FieldAndMeshTopoToFieldTopoMap::iterator it = field_topo_map.find(std::make_pair(field_ordinal, mesh_topology)); + if (it != field_topo_map.end()) + { + return it->second; + } + + stk::mesh::MetaData & meta = field.field().mesh_meta_data(); + stk::topology field_topology = AuxMetaData::get(meta).get_nodal_field_topology(field, b); + + field_topo_map.insert(FieldAndMeshTopoToFieldTopoMap::value_type(std::make_pair(field_ordinal, mesh_topology), field_topology)); + return field_topology; +} + +const MasterElement & +MasterElementDeterminer::getMasterElement(stk::topology t) +{ + static std::vector> all_master_elems(stk::topology::BEGIN_TOPOLOGY + stk::topology::NUM_TOPOLOGIES); + std::unique_ptr & master_elem = all_master_elems[t()]; + if (nullptr == master_elem.get()) + { + std::unique_ptr basis; + switch(t()) + { + case stk::topology::LINE_2: + basis = std::make_unique(); + break; + case stk::topology::LINE_3: + basis = std::make_unique(); + break; + case stk::topology::TRI_3: + case stk::topology::TRI_3_2D: + basis = std::make_unique(); + break; + case stk::topology::TRI_6: + case stk::topology::TRI_6_2D: + basis = std::make_unique(); + break; + case stk::topology::QUAD_4: + case stk::topology::QUAD_4_2D: + basis = std::make_unique(); + break; + case stk::topology::QUAD_9: + case stk::topology::QUAD_9_2D: + basis = std::make_unique(); + break; + case stk::topology::TET_4: + basis = std::make_unique(); + break; + case stk::topology::TET_10: + basis = std::make_unique(); + break; + case stk::topology::HEX_8: + basis = std::make_unique(); + break; + case stk::topology::HEX_27: + basis = std::make_unique(); + break; + case stk::topology::WEDGE_6: + basis = std::make_unique(); + break; + default: + ThrowRuntimeError("Element topology not found in MasterElementDeterminer::getMasterElement: " << t.name()); + break; + } + master_elem = std::make_unique(t, std::move(basis)); + } + return *master_elem; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.hpp b/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.hpp new file mode 100644 index 000000000000..af84aaea85f2 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MasterElementDeterminer.hpp @@ -0,0 +1,30 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElementDeterminer_h +#define Akri_MasterElementDeterminer_h + +#include + +namespace krino { class FieldRef; } +namespace stk { namespace mesh { class Bucket; } } +namespace stk { class topology; } + +namespace krino { + +class MasterElementDeterminer +{ +public: + static const MasterElement& getMasterElement(stk::mesh::Bucket & bucket, FieldRef field); + static const MasterElement& getMasterElement(stk::topology topology); + static stk::topology get_field_topology(const stk::mesh::Bucket & b, const FieldRef field); +}; + +} // end namespace krino + +#endif // Akri_MasterElementDeterminer_h diff --git a/packages/krino/krino/krino_lib/Akri_MathUtil.cpp b/packages/krino/krino/krino_lib/Akri_MathUtil.cpp new file mode 100644 index 000000000000..f2a7d53a2b6f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MathUtil.cpp @@ -0,0 +1,233 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +namespace krino { + +Vector3d +get_parametric_coordinates_of_point(const std::vector & nodeCoords, const Vector3d & pt) +{ + if (nodeCoords.size() == 3) + { + const Vector3d relativeCoords1 = nodeCoords[1] - nodeCoords[0]; + const Vector3d relativeCoords2 = nodeCoords[2] - nodeCoords[0]; + const Vector3d relativeCoords = pt - nodeCoords[0]; + + const double a00 = relativeCoords1[0]; + const double a01 = relativeCoords2[0]; + const double a10 = relativeCoords1[1]; + const double a11 = relativeCoords2[1]; + const double b0 = relativeCoords[0]; + const double b1 = relativeCoords[1]; + const double det = a00*a11-a01*a10; + const double x = (b0*a11-b1*a01)/det; + const double y = (-b0*a10+b1*a00)/det; + return Vector3d(x,y,0.); + } + else + { + const Vector3d relativeCoords1 = nodeCoords[1] - nodeCoords[0]; + const Vector3d relativeCoords2 = nodeCoords[2] - nodeCoords[0]; + const Vector3d relativeCoords3 = nodeCoords[3] - nodeCoords[0]; + const Vector3d relativeCoords = pt - nodeCoords[0]; + const double a00 = relativeCoords1[0]; + const double a01 = relativeCoords2[0]; + const double a02 = relativeCoords3[0]; + const double a10 = relativeCoords1[1]; + const double a11 = relativeCoords2[1]; + const double a12 = relativeCoords3[1]; + const double a20 = relativeCoords1[2]; + const double a21 = relativeCoords2[2]; + const double a22 = relativeCoords3[2]; + const double b0 = relativeCoords[0]; + const double b1 = relativeCoords[1]; + const double b2 = relativeCoords[2]; + const double det = a00*(a22*a11-a21*a12)-a10*(a22*a01-a21*a02)+a20*(a12*a01-a11*a02); + const double x =( b0*(a22*a11-a21*a12)-b1*(a22*a01-a21*a02)+b2*(a12*a01-a11*a02))/det; + const double y =(-b0*(a22*a10-a20*a12)+b1*(a22*a00-a20*a02)-b2*(a12*a00-a10*a02))/det; + const double z =( b0*(a21*a10-a20*a11)-b1*(a21*a00-a20*a01)+b2*(a11*a00-a10*a01))/det; + return Vector3d(x,y,z); + } +} + +std::pair find_root( const std::function & f, + const double xa, + const double xb, + const double fa, + const double fb, + const unsigned maxIters, + const double xTol) +{ + boost::uintmax_t iterCount = maxIters; + auto tol_function = [&xTol](const double a, const double b) { return std::abs(b-a) <= xTol; }; + auto result = boost::math::tools::toms748_solve(f, xa, xb, fa, fb, tol_function, iterCount); + const bool success = iterCount < maxIters; + return {success, 0.5*(result.first+result.second)}; +} + +std::pair find_bracketed_root_newton_raphson( const std::function(const double)> & f, + double x, + double fx, + double dfx, + double xa, + double xb, + double fa, + double fb, + const unsigned maxIters, + const double fTol) +{ + unsigned iter = 0; + while (iter++ < maxIters) + { + if (dfx == 0.) + { + x = 0.5*(xa+xb); // zero slope so use bisection + } + else + { + x -= fx / dfx; + if (x < xa || x > xb) + x = 0.5*(xa+xb); // Newton-Raphson step went out of bounds so use bisection + } + + std::tie(fx, dfx) = f(x); + + if (std::abs(fx) <= fTol) + return {true, x}; + + if (fx*fb < 0.) + { + xa = x; + fa = fx; + } + else + { + xb = x; + fb = fx; + } + + const double xTol = 4*std::numeric_limits::epsilon()*(fabs(xa)+fabs(xb)); + if (xb-xa < xTol) + return {false, x}; + } + return {true, x}; +} + +void attempt_to_bracket_root_newton_raphson( const std::function(const double)> & f, + const double guess, + double & x, + double & fx, + double & dfx, + double & xa, + double & xb, + double & fa, + double & fb, + bool & solnIsConvergedAtX, + bool & solnIsBracketed, + const unsigned maxIters, + const double fTol) +{ + x = guess; + std::tie(fx,dfx) = f(x); + + if (std::abs(fx) <= fTol) + { + solnIsConvergedAtX = true; + solnIsBracketed = false; + return; + } + + xa = x; + xb = x; + fa = fx; + fb = fx; + + unsigned iter = 0; + while (iter++ < maxIters) + { + if (dfx == 0.) + { + // FAILED: zero slope + solnIsConvergedAtX = false; + solnIsBracketed = false; + return; + } + + xa = x; + fa = fx; + + x -= fx / dfx; + std::tie(fx,dfx) = f(x); + + if (std::abs(fx) <= fTol) + { + solnIsConvergedAtX = true; + solnIsBracketed = false; + return; + } + + if (fa*fx > 0. && std::abs(fx) > std::abs(fa)) + { + // Jacobian is poor, try line search + const double tau = 0.5; + const int maxLineSearchIters = 5; + unsigned lineSearchIters = 0; + while (lineSearchIters++ < maxLineSearchIters && fa*fx > 0. && std::abs(fx) > std::abs(fa)) + { + x = xa + tau*(x-xa); + std::tie(fx,dfx) = f(x); + } + } + + if (fa*fx < 0.) + { + solnIsConvergedAtX = false; + solnIsBracketed = true; + xb = x; + fb = fx; + if (xa > xb) + { + std::swap(xa,xb); + std::swap(fa,fb); + } + return; + } + } + + //FAILED: did not bracket root + solnIsConvergedAtX = false; + solnIsBracketed = false; +} + +std::pair find_root_newton_raphson( const std::function(const double)> & f, + const double guess, + const unsigned maxIters, + const double fTol) +{ + double x, fx, dfx, xa, xb, fa, fb; + bool solnIsConvergedAtX, solnIsBracketed; + attempt_to_bracket_root_newton_raphson(f, guess, x, fx, dfx, xa, xb, fa, fb, solnIsConvergedAtX, solnIsBracketed, maxIters, fTol); + + if (solnIsConvergedAtX) + return {true, x}; + + if (!solnIsBracketed) + return {false, guess}; + + return find_bracketed_root_newton_raphson(f, x, fx, dfx, xa, xb, fa, fb, maxIters, fTol); +} + +} + + diff --git a/packages/krino/krino/krino_lib/Akri_MathUtil.hpp b/packages/krino/krino/krino_lib/Akri_MathUtil.hpp new file mode 100644 index 000000000000..6741d5bd9eac --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MathUtil.hpp @@ -0,0 +1,35 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_MATHUTIL_H_ +#define KRINO_INCLUDE_AKRI_MATHUTIL_H_ +#include +#include +#include + +namespace krino { + +Vector3d get_parametric_coordinates_of_point(const std::vector & nodeCoords, const Vector3d & pt); + +std::pair find_root( const std::function & f, + const double xa, + const double xb, + const double fa, + const double fb, + const unsigned maxIters = 100, + const double tol = 1.e-4); + +std::pair find_root_newton_raphson( const std::function(const double)> & f, + const double guess, + const unsigned maxIters = 100, + const double fTol = 1.e-4); + +} + + +#endif /* KRINO_INCLUDE_AKRI_MATHUTIL_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_MeshClone.cpp b/packages/krino/krino/krino_lib/Akri_MeshClone.cpp new file mode 100644 index 000000000000..49d9abaea644 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshClone.cpp @@ -0,0 +1,629 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace krino{ + +bool +MeshClone::stash_or_restore_mesh(stk::mesh::BulkData & mesh, const unsigned step_count) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::stash_or_restore_mesh(tftk::mesh::Mesh &mesh)"); /* %TRACE% */ + + const auto empty_function = []() {}; + return stash_or_restore_mesh(mesh, step_count, empty_function, empty_function); +} + +bool +MeshClone::stash_or_restore_mesh(stk::mesh::BulkData & mesh, const unsigned step_count, + const std::function & notify_of_pre_mesh_modification, + const std::function & notify_of_post_mesh_modification) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::stash_or_restore_mesh(tftk::mesh::Mesh &mesh)"); /* %TRACE% */ + bool restored_mesh = false; + MeshClone * clone = const_cast(mesh.mesh_meta_data().get_attribute()); + if (!clone) + { + clone = new MeshClone(mesh, sierra::Diag::sierraTimer(), step_count); + mesh.mesh_meta_data().declare_attribute_with_delete(clone); + } + else + { + if (step_count > clone->my_step_count) + { + if (!clone->mesh_is_up_to_date()) + { + clone->update(step_count); + } + } + else if (!clone->mesh_is_up_to_date()) + { + notify_of_pre_mesh_modification(); + clone->restore(step_count); + notify_of_post_mesh_modification(); + restored_mesh = true; + } + } + return restored_mesh; +} + +bool +MeshClone::exists(const stk::mesh::BulkData & mesh) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::exists(stk::mesh::BulkData & mesh)"); /* %TRACE% */ + MeshClone * clone = const_cast(mesh.mesh_meta_data().get_attribute()); + return (clone != nullptr); +} + +MeshClone & +MeshClone::get(const stk::mesh::BulkData & mesh) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::update_cloned_fields(stk::mesh::BulkData & mesh)"); /* %TRACE% */ + MeshClone * clone = const_cast(mesh.mesh_meta_data().get_attribute()); + ThrowRequireMsg(clone != nullptr, "Could not find MeshClone."); + return *clone; +} + +MeshClone::MeshClone( stk::mesh::BulkData & orig_mesh, stk::diag::Timer parent_timer, const unsigned step_count ) +: my_orig_mesh(&orig_mesh), + my_timer("Clone mesh", parent_timer), + my_step_count(step_count), + my_synchronized_count(orig_mesh.synchronized_count()) +{ + stk::diag::TimeBlock timer__(my_timer); + const stk::mesh::MetaData & in_meta = my_orig_mesh->mesh_meta_data(); + my_meta = std::make_unique(); + clone_meta_data_parts_and_fields(in_meta, *my_meta); + + my_mesh = std::make_unique(*my_meta, + my_orig_mesh->parallel(), + stk::mesh::BulkData::NO_AUTO_AURA +#ifdef SIERRA_MIGRATION + ,my_orig_mesh->add_fmwk_data() +#endif + ); + + my_meta->commit(); + + my_mesh->modification_begin(); + clone_bulk_data_entities(*my_orig_mesh, *my_mesh, false); + my_mesh->modification_end(); + + copy_field_data(*my_orig_mesh, *my_mesh); +} + +void MeshClone::update(const unsigned step_count) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::update(const unsigned step_count)"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer); + + const stk::mesh::BulkData & in_mesh = *my_orig_mesh; + stk::mesh::BulkData & out_mesh = *my_mesh; + + clone_mesh(in_mesh, out_mesh, false); + + my_step_count = step_count; + mark_mesh_as_up_to_date(); +} + +void MeshClone::restore(const unsigned step_count) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::restore(const unsigned step_count)"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer); + krinolog << "Restoring mesh from clone." << stk::diag::dendl; + + const stk::mesh::BulkData & in_mesh = *my_mesh; + stk::mesh::BulkData & out_mesh = *my_orig_mesh; + + clone_mesh(in_mesh, out_mesh, false); + + ThrowRequire(step_count == my_step_count); + mark_mesh_as_up_to_date(); +} + +void MeshClone::clone_mesh(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const bool full_overwrite) +{ /* %TRACE[ON]% */ Trace trace__("krino::MeshClone::clone_mesh(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const bool full_overwrite)"); /* %TRACE% */ + if (full_overwrite) + { + // Ugly, but legal and effective. + stk::mesh::MetaData & out_meta = out_mesh.mesh_meta_data(); + out_mesh.~BulkData(); + + const stk::mesh::BulkData::AutomaticAuraOption aura_option = + in_mesh.is_automatic_aura_on() ? + stk::mesh::BulkData::AUTO_AURA : + stk::mesh::BulkData::NO_AUTO_AURA; + + new (&out_mesh) stk::mesh::BulkData(out_meta, + in_mesh.parallel(), + aura_option +#ifdef SIERRA_MIGRATION + ,in_mesh.add_fmwk_data() +#endif + ); + + out_mesh.modification_begin(); + clone_bulk_data_entities(in_mesh, out_mesh, false); + out_mesh.modification_end(); + } + else + { + // I don't think you can start with clone_parallel because you can't know where something goes unless you know about it locally. + // Therefore I don't think that creation can go before deletion because you can't know if it already exists. + // Best to just delete everything wrong and then rebuild. + ThrowRequireMsg(out_mesh.modification_begin(), "MeshClone::restore must not be called within a modification cycle."); + delete_extraneous_entities(in_mesh, out_mesh); + // Occasionally, there is an issue with deleting and recreating the same entity within the same modification cycle, + // so we need to end here and begin again for the creation. + out_mesh.modification_end(); + + //Delete graph because the following mod cycle creates elements and faces in the same mode cycle. + out_mesh.delete_face_adjacent_element_graph(); + + out_mesh.modification_begin(); + clone_bulk_data_entities(in_mesh, out_mesh, true); + out_mesh.modification_end(); + } + + copy_field_data(in_mesh, out_mesh); +} + + +void +MeshClone::clone_meta_data_parts_and_fields(const stk::mesh::MetaData & in_meta, stk::mesh::MetaData & out_meta) +{ + /* %TRACE[ON]% */ Trace trace__("void MeshClone::clone_meta_data(stk::mesh::MetaData & in_meta)"); /* %TRACE% */ + + // This is pretty nasty. We want the part.mesh_meta_data_ordinal to be the same for the in_meta and out_meta. + // To accomplish this, we must be careful about the order of the part creation. + // Specifically, we must clone the parts that were created before in_meta.initialize() were called, then + // call out_meta.initialize(), then clone the rest. + + const stk::mesh::PartVector & in_parts = in_meta.get_parts(); + + unsigned ipart = 0; + bool more_to_do = ipart < in_parts.size(); + while (more_to_do) + { + stk::mesh::Part * in_part = in_parts[ipart++]; + if (stk::mesh::is_topology_root_part(*in_part)) + { + more_to_do = false; + } + else + { + more_to_do = ipart < in_parts.size(); + ThrowRequire(in_part->primary_entity_rank() == stk::topology::INVALID_RANK); + stk::mesh::Part & out_part = out_meta.declare_part(in_part->name()); + ThrowRequire(out_part.mesh_meta_data_ordinal() == in_part->mesh_meta_data_ordinal()); + } + } + + out_meta.initialize(in_meta.spatial_dimension(), in_meta.entity_rank_names()); + + for ( auto&& in_part : in_parts ) + { + stk::mesh::Part & out_part = + (in_part->primary_entity_rank() == stk::topology::INVALID_RANK) ? + out_meta.declare_part(in_part->name()) : + out_meta.declare_part(in_part->name(), in_part->primary_entity_rank(), in_part->force_no_induce()); + ThrowRequire(out_part.mesh_meta_data_ordinal() == in_part->mesh_meta_data_ordinal()); + if (stk::io::is_part_io_part(*in_part)) + { + stk::io::put_io_part_attribute(out_part); + } + } + + for ( auto&& in_part : in_parts ) + { + stk::mesh::Part & out_part = out_meta.get_part(in_part->mesh_meta_data_ordinal()); + const stk::mesh::PartVector & in_subsets = in_part->subsets(); + for (auto && in_subset : in_subsets) + { + stk::mesh::Part & out_subset = out_meta.get_part(in_subset->mesh_meta_data_ordinal()); + out_meta.declare_part_subset(out_part, out_subset); + } + } + + const stk::mesh::FieldVector & in_fields = in_meta.get_fields(); + for ( auto&& in_field : in_fields ) + { + if (in_field->state() == stk::mesh::StateNone) + { + stk::topology::rank_t entity_rank = static_cast(in_field->entity_rank()); + stk::mesh::FieldBase * out_field = out_meta.declare_field_base(in_field->name(), entity_rank, in_field->data_traits(), in_field->field_array_rank(), in_field->dimension_tags(), in_field->number_of_states()); + + for ( auto&& in_restriction : in_field->restrictions() ) + { + const stk::mesh::Selector out_selector = MeshClone::translate_selector(in_restriction.selector(), out_meta); + + out_meta.declare_field_restriction( *out_field, out_selector, in_restriction.num_scalars_per_entity(), in_restriction.dimension() ); + } + } + } +} + +void +MeshClone::delete_extraneous_entities(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh) +{ + /* %TRACE[ON]% */ Trace trace__("void MeshClone::delete_extraneous_entities(stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh)"); /* %TRACE% */ + + std::vector entities; + std::vector relatives; + std::vector relative_ordinals; + std::vector in_mesh_comm_procs; + std::vector out_mesh_comm_procs; + + const stk::mesh::EntityRank highest_entity_rank = static_cast(in_mesh.mesh_meta_data().entity_rank_count()-1); + for (stk::mesh::EntityRank entity_rank = highest_entity_rank; entity_rank >= stk::topology::NODE_RANK; --entity_rank) + { + stk::mesh::get_entities( out_mesh, entity_rank, entities ); + + for (auto&& out_entity : entities) + { + // Delete all entities for which any of the following are true: + // 1. There is no corresponding entity in in_mesh + // 2. The parallel owner changed. + // 3. The comm procs or comm shared procs differ. (Ugh. This is to work around strange corner case issues.) + // 4. The entity has invalid nodes (due to the nodes violating 1 or 2). + + stk::mesh::Entity in_entity = get_entity_on_other_mesh(out_mesh, out_entity, in_mesh); + bool delete_entity = !in_mesh.is_valid(in_entity); + + if (!delete_entity) + { + delete_entity = + in_mesh.parallel_owner_rank(in_entity) != out_mesh.parallel_owner_rank(out_entity); + } + + if (!delete_entity) + { + in_mesh.comm_procs(in_mesh.entity_key(in_entity), in_mesh_comm_procs); + out_mesh.comm_procs(out_mesh.entity_key(out_entity), out_mesh_comm_procs); + delete_entity = in_mesh_comm_procs != out_mesh_comm_procs; + } + + if (!delete_entity) + { + in_mesh.comm_shared_procs(in_entity, in_mesh_comm_procs); + out_mesh.comm_shared_procs(out_entity, out_mesh_comm_procs); + delete_entity = in_mesh_comm_procs != out_mesh_comm_procs; + } + + if (delete_entity) + { + ThrowRequireMsg(disconnect_and_destroy_entity(out_mesh, out_entity), "Could not destroy entity " << out_mesh.entity_key(out_entity) << debug_entity(out_mesh, out_entity)); + } + } + } + + for (stk::mesh::EntityRank entity_rank = stk::topology::ELEMENT_RANK; entity_rank > stk::topology::NODE_RANK; --entity_rank) + { + stk::mesh::get_entities( out_mesh, entity_rank, entities ); + + for (auto&& out_entity : entities) + { + const unsigned num_nodes = out_mesh.bucket(out_entity).topology().num_nodes(); + if (out_mesh.count_valid_connectivity(out_entity, stk::topology::NODE_RANK) != num_nodes) + { + ThrowRequireMsg(disconnect_and_destroy_entity(out_mesh, out_entity), "Could not destroy entity " << out_mesh.entity_key(out_entity)); + } + } + } +} + +void +MeshClone::delete_all_entities(stk::mesh::BulkData & mesh) +{ + /* %TRACE[ON]% */ Trace trace__("void MeshClone::delete_extraneous_entities(stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh)"); /* %TRACE% */ + + std::vector entities; + + const stk::mesh::EntityRank highest_entity_rank = static_cast(mesh.mesh_meta_data().entity_rank_count()-1); + for (stk::mesh::EntityRank entity_rank = highest_entity_rank; entity_rank >= stk::topology::NODE_RANK; --entity_rank) + { + stk::mesh::get_entities( mesh, entity_rank, entities ); + + for (auto && entity : entities) + { + ThrowRequireMsg(mesh.destroy_entity(entity), "Could not destroy entity " << mesh.entity_key(entity)); + } + } +} + +void +MeshClone::clone_bulk_data_entities(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const bool search_for_existing) +{ + /* %TRACE[ON]% */ Trace trace__("void MeshClone::clone_bulk_data(stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh)"); /* %TRACE% */ + + const bool debug = false; + + const stk::mesh::MetaData & in_meta = in_mesh.mesh_meta_data(); + const stk::mesh::MetaData & out_meta = out_mesh.mesh_meta_data(); + + std::vector sharing; + + const stk::mesh::EntityRank highest_entity_rank = static_cast(in_meta.entity_rank_count()-1); + for (stk::mesh::EntityRank entity_rank = stk::topology::NODE_RANK; entity_rank <= highest_entity_rank; ++entity_rank) + { + stk::mesh::Selector not_ghost = in_meta.locally_owned_part() | in_meta.globally_shared_part(); + const stk::mesh::BucketVector & buckets = in_mesh.get_buckets(entity_rank, not_ghost); + + for ( auto&& bucket_ptr : buckets ) + { + const stk::mesh::Bucket & b = *bucket_ptr; + + stk::mesh::PartVector in_bucket_parts, out_bucket_parts; + get_bucket_parts(b,in_bucket_parts); + + translate_parts(in_bucket_parts, out_meta, out_bucket_parts); + + const bool bucket_is_locally_owned = b.member(in_meta.locally_owned_part()); + + + const int length = b.size(); + for (int i = 0; i < length; ++i) + { + stk::mesh::Entity in_entity = b[i]; + + stk::mesh::Entity out_entity; + if (search_for_existing) + { + out_entity = out_mesh.get_entity( entity_rank, in_mesh.identifier(in_entity) ); + if (out_mesh.is_valid(out_entity) && + out_mesh.bucket(out_entity).member(out_meta.locally_owned_part())) + { + // make sure parts are right + stk::mesh::PartVector current_parts; + get_bucket_parts(out_mesh.bucket(out_entity), current_parts); + out_mesh.change_entity_parts(out_entity, out_bucket_parts, current_parts); + } + } + + // Unfortunately, there is a subtle bug that may be present in the input mesh that can cause a face to be present on + // this processor even when there are no locally owned elements using that face. We will skip these faces. + if (!bucket_is_locally_owned && entity_rank == in_meta.side_rank()) + { + bool found_locally_owned_elem = false; + const unsigned num_elems = in_mesh.num_elements(in_entity); + const stk::mesh::Entity* elems = in_mesh.begin_elements(in_entity); + for (unsigned ielem=0; ielem 1) + { + in_mesh.comm_shared_procs(in_entity,sharing); + for ( size_t k = 0 ; k < sharing.size() ; ++k ) + { + out_mesh.add_node_sharing(out_entity, sharing[k]); + } + } + + for (stk::mesh::EntityRank relative_rank = stk::topology::NODE_RANK; relative_rank < entity_rank; ++relative_rank) + { + const unsigned num_relatives = in_mesh.num_connectivity(in_entity, relative_rank); + const stk::mesh::Entity* in_relatives = in_mesh.begin(in_entity, relative_rank); + const stk::mesh::ConnectivityOrdinal * relative_ordinals = in_mesh.begin_ordinals(in_entity, relative_rank); + const stk::mesh::Permutation * relative_permutations = in_mesh.begin_permutations(in_entity, relative_rank); + + for (unsigned relative_index=0; relative_index( stk::mesh::field_data( out_field, b ) ); + + for (unsigned ib=0; ib( stk::mesh::field_data( in_field, in_entity ) ); + for ( unsigned i = 0; i < out_length; i++ ) out_data[i] = in_data[i]; + } + } +} + +void +MeshClone::copy_field_data(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh) +{ + /* %TRACE[ON]% */ Trace trace__("void MeshClone::copy_field_data(stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh)"); /* %TRACE% */ + + const stk::mesh::MetaData & in_meta = in_mesh.mesh_meta_data(); + stk::mesh::MetaData & out_meta = out_mesh.mesh_meta_data(); + + const stk::mesh::FieldVector & in_fields = in_meta.get_fields(); + const stk::mesh::FieldVector & out_fields = out_meta.get_fields(); + ThrowAssert(in_fields.size() == out_fields.size()); + + const bool out_mesh_aura_from_communication = out_mesh.is_automatic_aura_on() && !in_mesh.is_automatic_aura_on(); + + for ( unsigned field_index=0; field_index < in_fields.size(); ++field_index ) + { + const stk::mesh::FieldBase & in_field = *in_fields[field_index]; + const stk::mesh::FieldBase & out_field = *out_fields[field_index]; + copy_field_data(in_mesh, out_mesh, in_field, out_field, out_mesh_aura_from_communication); + } + + if (out_mesh_aura_from_communication) + { + const std::vector ghostings = out_mesh.ghostings(); + const std::vector const_fields(out_fields.begin(), out_fields.end()); + stk::mesh::communicate_field_data(*ghostings[stk::mesh::BulkData::AURA], const_fields); + } +} + +void +MeshClone::translate_parts(const stk::mesh::PartVector & in_parts, const stk::mesh::MetaData & out_meta, stk::mesh::PartVector & out_parts) +{ + out_parts.clear(); + for ( auto&& in_part : in_parts ) + { + stk::mesh::Part & out_part = out_meta.get_part(in_part->mesh_meta_data_ordinal()); + stk::mesh::insert(out_parts, out_part); + } +} + +stk::mesh::Selector +MeshClone::translate_selector(const stk::mesh::Selector & in_selector, const stk::mesh::MetaData & out_meta) +{ + if (in_selector == stk::mesh::Selector()) + { + return in_selector; + } + ThrowRequireMsg(in_selector.is_all_unions(), "Cannot translate selector " << in_selector); + stk::mesh::PartVector in_parts, out_parts; + in_selector.get_parts(in_parts); + translate_parts(in_parts, out_meta, out_parts); + return stk::mesh::selectUnion(out_parts); +} + +stk::mesh::Part * +MeshClone::translate_part(const stk::mesh::Part & in_part, const stk::mesh::MetaData & out_meta) +{ + return &out_meta.get_part(in_part.mesh_meta_data_ordinal()); +} + +void +MeshClone::get_bucket_parts(const stk::mesh::Bucket & bucket, stk::mesh::PartVector & parts) +{ + parts.clear(); + + stk::mesh::PartVector const& bucket_parts = bucket.supersets(); + for ( stk::mesh::PartVector::const_iterator ip = bucket_parts.begin(); ip != bucket_parts.end(); ++ip ) + { + stk::mesh::Part & bucket_part = **ip; + if (bucket_part.primary_entity_rank() != stk::topology::INVALID_RANK && bucket_part.primary_entity_rank() != bucket.entity_rank()) + { + continue; + } + if (stk::mesh::is_auto_declared_part(bucket_part) && !stk::mesh::is_topology_root_part(bucket_part)) + { + continue; + } + + parts.push_back(&bucket_part); + } + std::sort( parts.begin(), parts.end(), stk::mesh::PartLess() ); +} + +stk::mesh::Entity +MeshClone::get_entity_on_other_mesh(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const stk::mesh::BulkData & other_mesh) +{ + stk::mesh::EntityRank entity_rank = mesh.entity_rank(entity); + stk::mesh::Entity other_entity = other_mesh.get_entity( entity_rank, mesh.identifier(entity) ); + + if (other_mesh.is_valid(other_entity) && entity_rank != stk::topology::NODE_RANK) + { + // check if nodes are the same + const unsigned num_entity_nodes = mesh.num_nodes(entity); + const unsigned num_other_entity_nodes = other_mesh.num_nodes(other_entity); + if (num_entity_nodes != num_other_entity_nodes) + { + return stk::mesh::Entity(); + } + const stk::mesh::Entity* entity_nodes = mesh.begin_nodes(entity); + const stk::mesh::Entity* other_entity_nodes = other_mesh.begin_nodes(other_entity); + for (unsigned n=0; n +#include +#include +#include + +namespace krino { + +class MeshClone { +public: + + MeshClone( stk::mesh::BulkData & orig_mesh, stk::diag::Timer parent_timer, const unsigned step_count = 0 ); + + static bool exists(const stk::mesh::BulkData & mesh); + static MeshClone & get(const stk::mesh::BulkData & mesh); + static bool stash_or_restore_mesh(stk::mesh::BulkData & mesh, const unsigned step_count); + static bool stash_or_restore_mesh(stk::mesh::BulkData & mesh, + const unsigned step_count, + const std::function & notify_of_pre_mesh_modification, + const std::function & notify_of_post_mesh_modification); + bool mesh_is_up_to_date() const {return my_orig_mesh->synchronized_count() == my_synchronized_count;} + void mark_mesh_as_up_to_date() {my_synchronized_count = my_orig_mesh->synchronized_count();} + void mark_mesh_as_out_of_date() {--my_synchronized_count;} + +private: + void update(const unsigned step_count = 0); + void restore(const unsigned step_count = 0); + + static void clone_meta_data_parts_and_fields(const stk::mesh::MetaData & in_meta, stk::mesh::MetaData & out_meta); + static void translate_parts(const stk::mesh::PartVector & in_parts, const stk::mesh::MetaData & out_meta, stk::mesh::PartVector & out_parts); + static stk::mesh::Part * translate_part(const stk::mesh::Part & in_part, const stk::mesh::MetaData & out_meta); + static stk::mesh::Selector translate_selector(const stk::mesh::Selector & in_selector, const stk::mesh::MetaData & out_meta); + static void get_bucket_parts(const stk::mesh::Bucket & bucket, stk::mesh::PartVector & parts); + + static void clone_mesh(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const bool full_overwrite=false); + static void clone_bulk_data(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh); + static void copy_field_data(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const stk::mesh::FieldBase & in_field, const stk::mesh::FieldBase & out_field, const bool out_mesh_aura_from_communication); + static void copy_field_data(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh); + + static void delete_extraneous_entities(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh); + static void delete_all_entities(stk::mesh::BulkData & mesh); + static void clone_bulk_data_entities(const stk::mesh::BulkData & in_mesh, stk::mesh::BulkData & out_mesh, const bool search_for_existing); + + static stk::mesh::Entity get_entity_on_other_mesh(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const stk::mesh::BulkData & other_mesh); + + stk::mesh::BulkData* my_orig_mesh; + std::unique_ptr my_meta; + std::unique_ptr my_mesh; + + mutable stk::diag::Timer my_timer; + unsigned my_step_count; + size_t my_synchronized_count; +}; + +} // namespace krino + +#endif // Akri_MeshClone_h diff --git a/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.cpp b/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.cpp new file mode 100644 index 000000000000..e030340d2567 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.cpp @@ -0,0 +1,70 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include +#include +#include + +namespace krino{ + +void print_volume_or_surface_area(const stk::mesh::BulkData& mesh, const stk::mesh::EntityRank entity_rank, const stk::mesh::Selector & active_selector, const stk::mesh::PartVector & parts) +{ + double overall_sum = 0.; + + const std::string label = (entity_rank == stk::topology::ELEMENT_RANK) ? "Volume" : "Surface Area"; + + krinolog << stk::diag::dendl; + + for (auto && part : parts) + { + const stk::mesh::Selector selector = mesh.mesh_meta_data().locally_owned_part() & active_selector & *part; + const double local_part_sum = compute_volume_or_surface_area(mesh, entity_rank, selector); + double global_part_sum = 0.; + + stk::all_reduce_sum(mesh.parallel(), &local_part_sum, &global_part_sum, 1); + overall_sum += global_part_sum; + + krinolog << label << " for part " << part->name() << " = " << global_part_sum << stk::diag::dendl; + } + + krinolog << "Sum of " << label << " for all parts (which may overlap) = " << overall_sum << stk::diag::dendl; +} + +double +compute_volume_or_surface_area(const stk::mesh::BulkData& mesh, const stk::mesh::EntityRank entity_rank, const stk::mesh::Selector & selector) +{ + const FieldRef coords_field(mesh.mesh_meta_data().coordinate_field()); + const unsigned dim = mesh.mesh_meta_data().spatial_dimension(); + + std::vector coords; + std::vector intg_weights; + + double volume_or_area = 0.; + for ( auto && bucket : mesh.get_buckets( entity_rank, selector ) ) + { + const krino::MasterElement& master_elem = MasterElementDeterminer::getMasterElement(bucket->topology()); + + for ( auto && entity : *bucket ) + { + ElementObj::gather_nodal_field(mesh, entity, coords_field, coords, dim); + ElementObj::integration_weights( intg_weights, dim, coords, master_elem ); + + for ( double intg_wt : intg_weights ) volume_or_area += intg_wt; + } + } + return volume_or_area; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.hpp b/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.hpp new file mode 100644 index 000000000000..668e904d417f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshDiagnostics.hpp @@ -0,0 +1,23 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MeshDiagnostics_h +#define Akri_MeshDiagnostics_h + +#include +#include +#include + +namespace krino { + +void print_volume_or_surface_area(const stk::mesh::BulkData& mesh, const stk::mesh::EntityRank entity_rank, const stk::mesh::Selector & active_selector, const stk::mesh::PartVector & parts); +double compute_volume_or_surface_area(const stk::mesh::BulkData& mesh, const stk::mesh::EntityRank entity_rank, const stk::mesh::Selector & selector); + +} // namespace krino + +#endif // Akri_MeshDiagnostics_h diff --git a/packages/krino/krino/krino_lib/Akri_MeshHelpers.cpp b/packages/krino/krino/krino_lib/Akri_MeshHelpers.cpp new file mode 100644 index 000000000000..f701face6949 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshHelpers.cpp @@ -0,0 +1,2560 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include // Needed for all_reduce_max +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino{ + +template +class ContainerResizer +{ +public: + ContainerResizer(CONTAINER & container) : myContainer(container) {} + void resize(size_t size) { myContainer.resize(size); } +private: + CONTAINER & myContainer; +}; + +template +class ContainerResizer> +{ +public: + ContainerResizer(std::array & container) : myContainer(container) {} + void resize(size_t size) { ThrowRequire(SIZE == size); } +private: + std::array & myContainer; +}; + +template +void resize_container(CONTAINER & container, size_t size) +{ + ContainerResizer resizer(container); + resizer.resize(size); +} + +void fill_procs_owning_or_sharing_or_ghosting_node(const stk::mesh::BulkData& bulkData, stk::mesh::Entity node, std::vector & procsOwningSharingOrGhostingNode) +{ + ThrowAssert(bulkData.parallel_owner_rank(node)==bulkData.parallel_rank()); + bulkData.comm_procs(bulkData.entity_key(node), procsOwningSharingOrGhostingNode); + procsOwningSharingOrGhostingNode.push_back(bulkData.parallel_rank()); +} + +//-------------------------------------------------------------------------------- + +template +void fill_element_node_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField, CONTAINER & elementNodeCoords) +{ + StkMeshEntities elementNodes{mesh.begin_nodes(element), mesh.end_nodes(element)}; + resize_container(elementNodeCoords, elementNodes.size()); + for (size_t n=0; n(coordsField, elementNodes[n]); + for ( int d = 0; d < DIM; ++d ) + elementNodeCoords[n][d] = coords[d]; + } +} + +void fill_element_node_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField, const int dim, std::vector & elementNodeCoords) +{ + ThrowAssert(dim == 3 || dim == 2); + if (dim == 2) + fill_element_node_coordinates<2>(mesh, element, coordsField, elementNodeCoords); + else + fill_element_node_coordinates<3>(mesh, element, coordsField, elementNodeCoords); +} + +void fill_element_node_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField, std::vector & elementNodeCoords) +{ + const int dim = mesh.mesh_meta_data().spatial_dimension(); + elementNodeCoords.clear(); + for (auto node : StkMeshEntities{mesh.begin_nodes(element), mesh.end_nodes(element)}) + elementNodeCoords.emplace_back(field_data(coordsField, node), dim); +} + +static std::array gather_tet_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField) +{ + ThrowAssert(mesh.bucket(element).topology() == stk::topology::TETRAHEDRON_4); + std::array elementNodeCoords; + fill_element_node_coordinates<3>(mesh, element, coordsField, elementNodeCoords); + return elementNodeCoords; +} + +static std::array gather_tri_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField) +{ + ThrowAssert(mesh.bucket(element).topology() == stk::topology::TRIANGLE_3_2D); + std::array elementNodeCoords; + fill_element_node_coordinates<2>(mesh, element, coordsField, elementNodeCoords); + return elementNodeCoords; +} + +static double compute_tri_volume(const std::array & elementNodeCoords) +{ + return 0.5*(Cross(elementNodeCoords[1]-elementNodeCoords[0], elementNodeCoords[2]-elementNodeCoords[0]).length()); +} + +static double compute_tet_volume(const std::array & elementNodeCoords) +{ + return Dot(elementNodeCoords[3]-elementNodeCoords[0],Cross(elementNodeCoords[1]-elementNodeCoords[0], elementNodeCoords[2]-elementNodeCoords[0]))/6.0; +} + +static double compute_tri_or_tet_volume(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField) +{ + stk::topology elemTopology = mesh.bucket(element).topology(); + + if (elemTopology == stk::topology::TETRAHEDRON_4) + { + const auto elementNodeCoords = gather_tet_coordinates(mesh, element, coordsField); + return compute_tet_volume(elementNodeCoords); + } + + ThrowRequireMsg(elemTopology == stk::topology::TRIANGLE_3_2D, "Topology " << elemTopology << " not supported in compute_tri_or_tet_volume."); + const auto elementNodeCoords = gather_tri_coordinates(mesh, element, coordsField); + return compute_tri_volume(elementNodeCoords); +} + +static void update_min_max_values(const double currentValue, double & minValue, double & maxValue) +{ + minValue = std::min(minValue, currentValue); + maxValue = std::max(maxValue, currentValue); +} + +template +void update_min_max_edge_lengths_squared(const CONTAINER & elementNodeCoords, double & minEdgeLengthSqr, double & maxEdgeLengthSqr) +{ + for ( size_t inode = 0; inode < elementNodeCoords.size(); ++inode ) + for ( size_t jnode = inode+1; jnode < elementNodeCoords.size(); ++jnode ) + update_min_max_values((elementNodeCoords[inode] - elementNodeCoords[jnode]).length_squared(), minEdgeLengthSqr, maxEdgeLengthSqr); +} + +template +void update_max_edge_lengths_squared(const CONTAINER & elementNodeCoords, double & maxEdgeLengthSqr) +{ + // This is a little strange for non-simplex elements since it goes from each node to every other node + for ( size_t inode = 0; inode < elementNodeCoords.size(); ++inode ) + for ( size_t jnode = inode+1; jnode < elementNodeCoords.size(); ++jnode ) + maxEdgeLengthSqr = std::max(maxEdgeLengthSqr, (elementNodeCoords[inode] - elementNodeCoords[jnode]).length_squared()); +} + +//-------------------------------------------------------------------------------- + +double +compute_maximum_element_size(stk::mesh::BulkData& mesh) +{ + const unsigned ndim = mesh.mesh_meta_data().spatial_dimension(); + double max_sqr_edge_length = 0.0; + + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + + stk::mesh::Selector locally_owned_selector = mesh.mesh_meta_data().locally_owned_part(); + + const stk::mesh::BucketVector & buckets = mesh.get_buckets( stk::topology::ELEMENT_RANK, locally_owned_selector ); + std::vector elementNodeCoords; + + for ( auto && bucket : buckets ) + { + for ( auto && elem : *bucket ) + { + fill_element_node_coordinates(mesh, elem, coordsField, ndim, elementNodeCoords); + update_max_edge_lengths_squared(elementNodeCoords, max_sqr_edge_length); + } + } + + const double local_max = max_sqr_edge_length; + stk::all_reduce_max(mesh.parallel(), &local_max, &max_sqr_edge_length, 1); + + return std::sqrt(max_sqr_edge_length); +} + +//-------------------------------------------------------------------------------- + +void compute_element_quality(const stk::mesh::BulkData & mesh, double & minEdgeLength, double & maxEdgeLength, double & minVolume, double & maxVolume) +{ + double minEdgeLengthSqr = std::numeric_limits::max(); + double maxEdgeLengthSqr = -std::numeric_limits::max(); + minVolume = std::numeric_limits::max(); + maxVolume = std::numeric_limits::lowest(); + + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + + stk::mesh::Selector locally_owned_selector = mesh.mesh_meta_data().locally_owned_part(); + + const stk::mesh::BucketVector & buckets = mesh.get_buckets( stk::topology::ELEMENT_RANK, locally_owned_selector ); + + for ( auto && bucket : buckets ) + { + stk::topology elem_topology = bucket->topology(); + const unsigned num_nodes = elem_topology.num_nodes(); + std::vector elem_node_coords(num_nodes); + + for ( auto && elem : *bucket ) + { + if (elem_topology == stk::topology::TETRAHEDRON_4) + { + const auto elementNodeCoords = gather_tet_coordinates(mesh, elem, coordsField); + update_min_max_values(compute_tet_volume(elementNodeCoords), minVolume, maxVolume); + update_min_max_edge_lengths_squared(elementNodeCoords, minEdgeLengthSqr, maxEdgeLengthSqr); + } + else if (elem_topology == stk::topology::TRIANGLE_3_2D) + { + const auto elementNodeCoords = gather_tri_coordinates(mesh, elem, coordsField); + update_min_max_values(compute_tri_volume(elementNodeCoords), minVolume, maxVolume); + update_min_max_edge_lengths_squared(elementNodeCoords, minEdgeLengthSqr, maxEdgeLengthSqr); + } + else + { + ThrowRuntimeError("Topology " << elem_topology << " not supported in compute_element_quality."); + } + } + } + + const double localMinEdgeLength = std::sqrt(minEdgeLengthSqr); + stk::all_reduce_min(mesh.parallel(), &localMinEdgeLength, &minEdgeLength, 1); + const double localMaxEdgeLength = std::sqrt(maxEdgeLengthSqr); + stk::all_reduce_max(mesh.parallel(), &localMaxEdgeLength, &maxEdgeLength, 1); + const double localMinVolume = minVolume; + stk::all_reduce_min(mesh.parallel(), &localMinVolume, &minVolume, 1); + const double localMaxVolume = maxVolume; + stk::all_reduce_max(mesh.parallel(), &localMaxVolume, &maxVolume, 1); +} + +static std::vector get_owned_nodes_with_nodal_volume_below_threshold(const stk::mesh::BulkData & mesh, const stk::mesh::Selector & blockSelector, const double threshold) +{ + ThrowRequireMsg(mesh.is_automatic_aura_on() || mesh.parallel_size() == 1, "Method requires automatic aura."); + + // This would be more efficient if a nodal field was used because it could compute the element volume only once. + std::vector ownedNodesWithNodalVolBelowThreshold; + + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + std::vector elementNodeCoords; + + stk::mesh::Selector ownedBlockSelector = mesh.mesh_meta_data().locally_owned_part() & blockSelector; + + const stk::mesh::BucketVector & buckets = mesh.get_buckets( stk::topology::NODE_RANK, ownedBlockSelector ); + + for ( auto && bucket : buckets ) + { + for ( auto && node : *bucket ) + { + double nodalVolume = 0.; + for (auto && element : StkMeshEntities{mesh.begin_elements(node), mesh.end_elements(node)}) + { + if (blockSelector(mesh.bucket(element))) + nodalVolume += compute_tri_or_tet_volume(mesh, element, coordsField); + + if (nodalVolume >= threshold) + break; + } + if (nodalVolume < threshold) + ownedNodesWithNodalVolBelowThreshold.push_back(node); + } + } + return ownedNodesWithNodalVolBelowThreshold; +} + +static std::vector get_nodes_with_no_attached_elements(const stk::mesh::BulkData & mesh) +{ + ThrowRequireMsg(mesh.is_automatic_aura_on() || mesh.parallel_size() == 1, "Method requires automatic aura."); + + std::vector nodesWithNoAttachedElements; + + for ( auto && bucket : mesh.buckets(stk::topology::NODE_RANK) ) + for ( auto && node : *bucket ) + if (mesh.num_elements(node) == 0) + nodesWithNoAttachedElements.push_back(node); + + return nodesWithNoAttachedElements; +} + +static +void pack_entities_for_sharing_procs(const stk::mesh::BulkData & mesh, + const std::vector & entities, + stk::CommSparse &commSparse) +{ + std::vector sharingProcs; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto entity : entities) + { + if (mesh.bucket(entity).shared()) + { + mesh.comm_shared_procs(entity, sharingProcs); + for (int procId : sharingProcs) + commSparse.send_buffer(procId).pack(mesh.entity_key(entity)); + } + } + }); +} + +static +void unpack_shared_entities(const stk::mesh::BulkData & mesh, + std::vector & sharedEntities, + stk::CommSparse &commSparse) +{ + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + stk::mesh::EntityKey entityKey; + commSparse.recv_buffer(procId).unpack(entityKey); + stk::mesh::Entity entity = mesh.get_entity(entityKey); + ThrowAssert(mesh.is_valid(entity)); + sharedEntities.push_back(entity); + } + }); +} + +static +void append_shared_entities_to_owned_ones(const stk::mesh::BulkData & mesh, + std::vector & entities) +{ + stk::CommSparse commSparse(mesh.parallel()); + pack_entities_for_sharing_procs(mesh, entities, commSparse); + + std::vector sharedEntities; + unpack_shared_entities(mesh, sharedEntities, commSparse); + entities.insert(entities.end(), sharedEntities.begin(), sharedEntities.end()); +} + +//-------------------------------------------------------------------------------- + +void delete_node_and_all_entities_using_it(stk::mesh::BulkData & mesh, const stk::mesh::Entity node) +{ + std::vector relatives; + + const stk::mesh::EntityRank highestEntityRank = static_cast(mesh.mesh_meta_data().entity_rank_count()-1); + for (stk::mesh::EntityRank irank = highestEntityRank; irank != stk::topology::NODE_RANK; --irank) + { + relatives.assign(mesh.begin(node, irank), mesh.end(node, irank)); + for (auto && relative : relatives) + ThrowRequire(mesh.destroy_entity(relative)); + } + ThrowRequire(mesh.destroy_entity(node)); +} + +static void delete_nodes_and_all_entities_using_them(stk::mesh::BulkData & mesh, const std::vector & nodesToDelete) +{ + mesh.modification_begin(); + for (auto && node : nodesToDelete) + delete_node_and_all_entities_using_it(mesh, node); + mesh.modification_end(); +} + +static size_t delete_nodes_with_nodal_volume_below_threshold_and_all_entities_using_them(stk::mesh::BulkData & mesh, const stk::mesh::Selector & blockSelector, const double threshold) +{ + std::vector nodesToDelete = get_owned_nodes_with_nodal_volume_below_threshold(mesh, blockSelector, threshold); + const size_t globalNumNodesToDelete = stk::get_global_sum(mesh.parallel(), nodesToDelete.size()); + + if (globalNumNodesToDelete > 0) + { + append_shared_entities_to_owned_ones(mesh, nodesToDelete); + delete_nodes_and_all_entities_using_them(mesh, nodesToDelete); + } + return globalNumNodesToDelete; +} + +static size_t delete_nodes_with_no_attached_elements(stk::mesh::BulkData & mesh) +{ + const std::vector nodesToDelete = get_nodes_with_no_attached_elements(mesh); + const size_t globalNumNodesToDelete = stk::get_global_sum(mesh.parallel(), nodesToDelete.size()); + + if (globalNumNodesToDelete > 0) + delete_nodes_and_all_entities_using_them(mesh, nodesToDelete); + + return globalNumNodesToDelete; +} + +void delete_all_entities_using_nodes_with_nodal_volume_below_threshold(stk::mesh::BulkData & mesh, const stk::mesh::Selector & blockSelector, const double threshold) +{ + const int maxIterations = 10; + int iteration = 0; + while (++iteration <= maxIterations) + { + const size_t numNodesDeletedWithSmallVolume = delete_nodes_with_nodal_volume_below_threshold_and_all_entities_using_them(mesh, blockSelector, threshold); + if (numNodesDeletedWithSmallVolume > 0) + { + sierra::Env::outputP0() << "Iteration " << iteration << ":" << std::endl; + sierra::Env::outputP0() << " Deleted " << numNodesDeletedWithSmallVolume << " node(s) with a nodal volume less than " << threshold << " (and all attached entities)." << std::endl; + const size_t numNodesDeletedWithNoElements = delete_nodes_with_no_attached_elements(mesh); + sierra::Env::outputP0() << " Deleted " << numNodesDeletedWithNoElements << " node(s) that have no attached elements." << std::endl; + } + else + break; + } + if (iteration < maxIterations) + sierra::Env::outputP0() << "Successfully deleted all nodes with a nodal volume less than " << threshold << "." << std::endl; + else + sierra::Env::outputP0() << "Terminating after performing max iterations. There still may be nodes with a nodal volume less than " << threshold << "." << std::endl; +} + +//-------------------------------------------------------------------------------- + +struct ActiveChildNodeRequest +{ + std::vector m_parents; + std::vector m_sharing_procs; + std::vector > m_id_proc_pairs_from_all_procs; + bool m_id_procs_pairs_have_been_sorted; + stk::mesh::Entity *m_node_entity; + + ActiveChildNodeRequest(const std::vector & parents, stk::mesh::Entity *entity_place_holder=NULL) + : m_parents(parents), m_sharing_procs(), m_id_proc_pairs_from_all_procs(), + m_id_procs_pairs_have_been_sorted(false), m_node_entity(entity_place_holder) + { + std::sort(m_parents.begin(), m_parents.end()); + } + + void add_proc_id_pair(int proc_id, stk::mesh::EntityId id) + { + m_id_proc_pairs_from_all_procs.push_back(std::make_pair(proc_id, id)); + } + + void calculate_sharing_procs(stk::mesh::BulkData& mesh) + { + ThrowRequire(!m_parents.empty()); + + stk::mesh::EntityKey key0(stk::topology::NODE_RANK, m_parents[0]); + mesh.comm_shared_procs(key0, m_sharing_procs); + std::sort(m_sharing_procs.begin(), m_sharing_procs.end()); + + std::vector sharingProcs; + for (unsigned i=1; i working_set; + m_sharing_procs.swap(working_set); + std::set_intersection(working_set.begin(),working_set.end(),sharingProcs.begin(),sharingProcs.end(),std::back_inserter(m_sharing_procs)); + } + } + + size_t num_sharing_procs() const + { + return m_sharing_procs.size(); + } + + int sharing_proc(int index) const + { + return m_sharing_procs[index]; + } + + stk::mesh::EntityId suggested_node_id() const + { + ThrowRequireMsg(!m_id_procs_pairs_have_been_sorted, "Invalid use of child node calculation. Contact sierra-help"); + return m_id_proc_pairs_from_all_procs[0].second; + } + + void sort_id_proc_pairs() + { + m_id_procs_pairs_have_been_sorted = true; + std::sort(m_id_proc_pairs_from_all_procs.begin(), m_id_proc_pairs_from_all_procs.end()); + } + + stk::mesh::EntityId get_id_for_child() const + { + ThrowRequireMsg(m_id_procs_pairs_have_been_sorted, "Invalid use of child node calculation. Contact sierra-help"); + return m_id_proc_pairs_from_all_procs[0].second; + } + + void set_node_entity_for_request(stk::mesh::BulkData& mesh, const stk::mesh::PartVector & node_parts) + { + this->sort_id_proc_pairs(); + stk::mesh::EntityId id_for_child = get_id_for_child(); + *m_node_entity = mesh.declare_node(id_for_child, node_parts); + for (size_t i=0;i & child_node_requests, const stk::mesh::PartVector & node_parts, bool assert_32bit_ids, bool make_64bit_ids) +{ + std::vector communicate_request(child_node_requests.size(), false); + + unsigned num_nodes_requested = child_node_requests.size(); + std::vector available_node_ids; + + EntityIdPool::generate_new_ids(mesh, stk::topology::NODE_RANK, num_nodes_requested, available_node_ids, assert_32bit_ids, make_64bit_ids); + + while ( true ) + { + int more_work_to_be_done = false; + + std::vector active_child_node_requests; + + for (unsigned it_req=0; it_req & request_parents = request.parents; + + bool request_is_ready = true; + for (auto && request_parent : request_parents) + { + if (!mesh.is_valid(*request_parent)) + { + request_is_ready = false; + } + } + + if (request_is_ready) + { + stk::mesh::Entity *request_child = request.child; + + communicate_request[it_req] = true; + more_work_to_be_done = true; + + std::vector parent_ids(request_parents.size()); + for (size_t parent_index=0; parent_index & request_parents = active_child_node_requests[request_index].m_parents; + const stk::mesh::EntityId this_procs_suggested_id = active_child_node_requests[request_index].suggested_node_id(); + const size_t num_parents = request_parents.size(); + comm_spec.send_buffer(other_proc).pack(num_parents); + for (size_t parent_index=0; parent_index request_parents(num_parents); + for (size_t parent_index=0; parent_index::iterator iter = std::lower_bound(active_child_node_requests.begin(), active_child_node_requests.end(), from_other_proc); + + if ( iter != active_child_node_requests.end() && *iter == from_other_proc) + { + iter->add_proc_id_pair(i, suggested_node_id); + } + } + } + } + + for (size_t request_index=0;request_index::iterator iter = std::find(communicate_request.begin(), communicate_request.end(), false); + ThrowRequireMsg(iter == communicate_request.end(), "Invalid child node request. Contact sierra-help."); +} + +//-------------------------------------------------------------------------------- + +void +batch_create_sides(stk::mesh::BulkData & mesh, const std::vector & side_requests) +{ + const stk::mesh::EntityRank side_rank = mesh.mesh_meta_data().side_rank(); + + if (!mesh.has_face_adjacent_element_graph()) + { + mesh.initialize_face_adjacent_element_graph(); + } + + mesh.modification_begin(); + for (auto && side_request : side_requests) + { + stk::mesh::Entity element = side_request.element; + const unsigned element_side_ord = side_request.element_side_ordinal; + + stk::mesh::Entity existing_element_side = find_entity_by_ordinal(mesh, element, side_rank, element_side_ord); + if (mesh.is_valid(existing_element_side)) + { + continue; + } + + mesh.declare_element_side(element, element_side_ord, side_request.side_parts); + } + mesh.modification_end(); + + ThrowAssert(check_face_and_edge_ownership(mesh)); + ThrowAssert(check_face_and_edge_relations(mesh)); +} + +//-------------------------------------------------------------------------------- + +void +make_side_ids_consistent_with_stk_convention(stk::mesh::BulkData & mesh) +{ + const stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + const stk::mesh::EntityRank side_rank = meta.side_rank(); + stk::mesh::Selector not_ghost_selector(meta.locally_owned_part() | meta.globally_shared_part()); + + std::vector sides; + stk::mesh::get_selected_entities( not_ghost_selector, mesh.buckets(side_rank), sides ); + + std::vector side_requests; + + mesh.modification_begin(); + for (auto&& side : sides) + { + const unsigned num_side_elems = mesh.num_elements(side); + const stk::mesh::Entity* side_elems = mesh.begin_elements(side); + const stk::mesh::ConnectivityOrdinal* side_elem_ordinals = mesh.begin_element_ordinals(side); + ThrowRequire(num_side_elems > 0); + stk::mesh::EntityId newId = 0; + for (unsigned i=0; i * const coordsField) +{ + stk::topology elem_topology = mesh.bucket(element).topology(); + if (elem_topology == stk::topology::TETRAHEDRON_4) + { + const std::array nodes = gather_tet_coordinates(mesh, element, coordsField); + const double vol = compute_tet_volume(nodes); + compute_tri_or_tet_volume(mesh, element, *coordsField); + const double edge_rms = std::sqrt( + ((nodes[1]-nodes[0]).length_squared() + + (nodes[2]-nodes[0]).length_squared() + + (nodes[3]-nodes[0]).length_squared() + + (nodes[3]-nodes[1]).length_squared() + + (nodes[3]-nodes[2]).length_squared() + + (nodes[2]-nodes[1]).length_squared())/6.); + return vol/(edge_rms*edge_rms*edge_rms); + } + ThrowRuntimeError("Topology " << elem_topology << " not supported in compute_element_volume_to_edge_ratio."); +} + +//-------------------------------------------------------------------------------- + +static void +debug_entity(std::ostream & output, const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const bool includeFields) +{ + if (!mesh.is_valid(entity)) + { + output << "Invalid entity: " << mesh.entity_key(entity) << std::endl; + return; + } + output << mesh.entity_key(entity) << ", parallel owner = " << mesh.parallel_owner_rank(entity) << " {" << std::endl; + output << " Connectivity:" << std::endl; + const stk::mesh::EntityRank end_rank = static_cast(mesh.mesh_meta_data().entity_rank_count()); + for (stk::mesh::EntityRank r = stk::topology::BEGIN_RANK; r < end_rank; ++r) { + unsigned num_rels = mesh.num_connectivity(entity, r); + stk::mesh::Entity const *rel_entities = mesh.begin(entity, r); + stk::mesh::ConnectivityOrdinal const *rel_ordinals = mesh.begin_ordinals(entity, r); + stk::mesh::Permutation const *rel_permutations = mesh.begin_permutations(entity, r); + for (unsigned i = 0; i < num_rels; ++i) { + output << " " << mesh.entity_key(rel_entities[i]) + << " @" << rel_ordinals[i]; + if (rel_permutations) output << ":" << (int)rel_permutations[i]; + output << std::endl; + } + } + output << " Parts: "; + const stk::mesh::PartVector & parts = mesh.bucket(entity).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = parts.begin(); part_iter != parts.end(); ++part_iter) + { + const stk::mesh::Part * const part = *part_iter; + output << part->name() << " "; + } + output << std::endl; + + if (includeFields) + { + const stk::mesh::FieldVector & all_fields = mesh.mesh_meta_data().get_fields(); + for ( stk::mesh::FieldVector::const_iterator it = all_fields.begin(); it != all_fields.end() ; ++it ) + { + const FieldRef field = (const FieldRef)(**it); + + if(field.entity_rank()!=mesh.entity_rank(entity)) continue; + + const unsigned field_length = field.length(); + + field.field().sync_to_host(); + if (field.type_is()) + { + const double * data = field_data(field, entity); + if (NULL != data) + { + if (1 == field_length) + { + output << " Field: field_name=" << field.name() << ", field_state=" << field.state() << ", value=" << *data << std::endl; + } + else + { + for (unsigned i = 0; i < field_length; ++i) + { + output << " Field: field_name=" << field.name() << ", field_state=" << field.state() << ", value[" << i << "]=" << data[i] << std::endl; + } + } + } + } + else if (field.type_is()) + { + const int * data = field_data(field, entity); + if (NULL != data) + { + if (1 == field_length) + { + output << " Field: field_name=" << field.name() << ", field_state=" << field.state() << ", value=" << *data << std::endl; + } + else + { + for (unsigned i = 0; i < field_length; ++i) + { + output << " Field: field_name=" << field.name() << ", field_state=" << field.state() << ", value[" << i << "]=" << data[i] << std::endl; + } + } + } + } + } + output << std::endl; + } +} + +std::string +debug_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const bool includeFields) +{ + std::ostringstream out; + debug_entity(out, mesh, entity, includeFields); + return out.str(); +} + +std::string +debug_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity) +{ + return debug_entity(mesh, entity, false); +} + +//-------------------------------------------------------------------------------- + +std::vector +get_side_permutation(stk::topology topology, stk::mesh::Permutation node_permutation) +{ + const unsigned perm = node_permutation; + switch (topology) + { + case stk::topology::TRIANGLE_3_2D: + case stk::topology::TRIANGLE_6_2D: + switch (perm) + { + case 0: return {0, 1, 2}; + case 1: return {2, 0, 1}; + case 2: return {1, 2, 0}; + default: ThrowRuntimeError("find_side_permutation error, invalid triangle permutation."); + } + break; + case stk::topology::TETRAHEDRON_4: + case stk::topology::TETRAHEDRON_10: + switch (perm) + { + case 0: return {0, 1, 2, 3}; + case 1: return {1, 2, 0, 3}; + case 2: return {2, 0, 1, 3}; + case 3: return {2, 1, 3, 0}; + case 4: return {1, 3, 2, 0}; + case 5: return {3, 2, 1, 0}; + case 6: return {3, 1, 0, 2}; + case 7: return {1, 0, 3, 2}; + case 8: return {0, 3, 1, 2}; + case 9: return {0, 2, 3, 1}; + case 10: return {2, 3, 0, 1}; + case 11: return {3, 0, 2, 1}; + default: ThrowRuntimeError("find_side_permutation error, invalid tetrahedron permutation."); + } + break; + default: ThrowRuntimeError("find_side_permutation error, unsupported topology."); + } +} + +//-------------------------------------------------------------------------------- + +const stk::mesh::Part & +find_element_part(const stk::mesh::BulkData& mesh, stk::mesh::Entity elem) +{ + ThrowAssert(mesh.entity_rank(elem) == stk::topology::ELEMENT_RANK); + const stk::mesh::Part * elem_io_part = nullptr; + + const stk::mesh::PartVector & elem_parts = mesh.bucket(elem).supersets(); + for(stk::mesh::PartVector::const_iterator part_iter = elem_parts.begin(); part_iter != elem_parts.end(); ++part_iter) + { + const stk::mesh::Part * const part = *part_iter; + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK && part->subsets().empty() && part->topology() != stk::topology::INVALID_TOPOLOGY) + { + // there should only be one element rank part without subsets with topology on the element + ThrowRequireMsg(nullptr == elem_io_part, "For element " << mesh.identifier(elem) << ", more than one element rank part was found: " << elem_io_part->name() << " " << part->name()); + elem_io_part = part; + } + } + ThrowRequire(NULL != elem_io_part); + + return *elem_io_part; +} + +//-------------------------------------------------------------------------------- + +void +disconnect_entity(stk::mesh::BulkData & mesh, stk::mesh::Entity entity) +{ + stk::mesh::EntityRank entity_rank = mesh.entity_rank(entity); + std::vector relatives; + std::vector relative_ordinals; + + const stk::mesh::EntityRank highest_entity_rank = static_cast(mesh.mesh_meta_data().entity_rank_count()-1); + for (stk::mesh::EntityRank irank = highest_entity_rank; irank != entity_rank; --irank) + { + // Previously this attempted to delete forward or backward and still the list got corrupted, + // so just copy into vector and delete from there. + relatives.assign(mesh.begin(entity, irank),mesh.end(entity, irank)); + relative_ordinals.assign(mesh.begin_ordinals(entity, irank), mesh.end_ordinals(entity, irank)); + + for (size_t irel = 0; irel < relatives.size(); ++irel) + { + mesh.destroy_relation( relatives[irel], entity, relative_ordinals[irel]); + } + } +} + +//-------------------------------------------------------------------------------- + +bool +disconnect_and_destroy_entity(stk::mesh::BulkData & mesh, stk::mesh::Entity entity) +{ + disconnect_entity(mesh, entity); + return mesh.destroy_entity(entity); +} + +//-------------------------------------------------------------------------------- + +bool +check_induced_parts(const stk::mesh::BulkData & mesh) +{ /* %TRACE[ON]% */ Trace trace__("krino::debug_induced_parts()"); /* %TRACE% */ + + // This method requires aura to work correctly. + if (!mesh.is_automatic_aura_on() && mesh.parallel_size() > 1) + { + // Skip check if we don't have aura + return true; + } + + bool success = true; + + const stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::mesh::Selector not_ghost_selector(meta.locally_owned_part() | meta.globally_shared_part()); + + std::vector< stk::mesh::Entity> entities; + + for (stk::mesh::EntityRank entity_rank = stk::topology::NODE_RANK; entity_rank <= stk::topology::ELEMENT_RANK; ++entity_rank) + { + stk::mesh::get_selected_entities( not_ghost_selector, mesh.buckets(entity_rank), entities ); + + for (unsigned i=0; iprimary_entity_rank() == entity_rank) + { + bool have_relative_missing_part = false; + const unsigned num_relatives = mesh.num_connectivity(entity, relative_rank); + const stk::mesh::Entity* relatives = mesh.begin(entity, relative_rank); + for (unsigned it_rel=0; it_relname() << " is found on " << mesh.entity_key(entity) << " but is missing from relatives: "; + for (unsigned it_rel=0; it_relprimary_entity_rank() == relative_rank) + { + bool found_relative_with_part = false; + const unsigned num_relatives = mesh.num_connectivity(entity, relative_rank); + const stk::mesh::Entity* relatives = mesh.begin(entity, relative_rank); + for (unsigned it_rel=0; it_relname() << " is found on " << mesh.entity_key(entity) << " but not on any of its relatives: "; + for (unsigned it_rel=0; it_rel & remote_entity_node_ids) +{ + stk::mesh::Entity entity = mesh.get_entity(remote_entity_key); + if (!mesh.is_valid(entity)) + { + krinolog << "Shared entity error, local entity does not exist, remote entity: " << remote_entity_key << stk::diag::dendl; + return false; + } + + std::vector entity_nodes(mesh.begin_nodes(entity), mesh.end_nodes(entity)); + if (entity_nodes.size() != remote_entity_node_ids.size()) + { + krinolog << "Shared entity error, number_of nodes don't match, number of remote nodes = " << remote_entity_node_ids.size() << stk::diag::dendl; + krinolog << "Local entity: " << debug_entity(mesh, entity) << stk::diag::dendl; + return false; + } + + bool nodes_match = true; + for (size_t node_index=0;node_index & entities) +{ + bool success = true; + + std::vector sharing_procs; + stk::CommSparse comm_spec(mesh.parallel()); + + for (int phase=0;phase<2;++phase) + { + for (std::vector::iterator it_entity = entities.begin(); it_entity != entities.end(); ++it_entity) + { + stk::mesh::Entity entity = *it_entity; + std::vector entity_nodes(mesh.begin_nodes(entity), mesh.end_nodes(entity)); + stk::mesh::EntityKey entity_key = mesh.entity_key(entity); + ThrowRequire(mesh.bucket(entity).shared()); + + mesh.shared_procs_intersection(entity_nodes, sharing_procs); + for (size_t proc_index=0;proc_index entity_node_ids(num_nodes); + for (size_t node_index=0; node_index sharing_procs; + stk::CommSparse comm_spec(mesh.parallel()); + + bool success = true; + stk::mesh::Selector shared_selector = meta.globally_shared_part(); + std::vector entities; + + for (stk::mesh::EntityRank entity_rank = stk::topology::EDGE_RANK; entity_rank < stk::topology::ELEMENT_RANK; ++entity_rank) + { + stk::mesh::get_selected_entities( shared_selector, mesh.buckets( entity_rank ), entities ); + + if (!check_shared_entity_nodes(mesh, entities)) success = false; + } + return success; +} + +//-------------------------------------------------------------------------------- + +bool +check_face_and_edge_relations(const stk::mesh::BulkData & mesh) +{ + const stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + + bool success = true; + stk::mesh::Selector not_ghost_selector = meta.locally_owned_part() | meta.globally_shared_part(); + + for (stk::mesh::EntityRank entity_rank = stk::topology::EDGE_RANK; entity_rank <= stk::topology::FACE_RANK; ++entity_rank) + { + const stk::mesh::BucketVector & buckets = mesh.get_buckets( entity_rank, not_ghost_selector ); + + stk::mesh::BucketVector::const_iterator ib = buckets.begin(); + stk::mesh::BucketVector::const_iterator ib_end = buckets.end(); + + for ( ; ib != ib_end; ++ib ) + { + const stk::mesh::Bucket & b = **ib; + const size_t length = b.size(); + for (size_t it_entity = 0; it_entity < length; ++it_entity) + { + stk::mesh::Entity entity = b[it_entity]; + stk::topology entity_topology = mesh.bucket(entity).topology(); + std::vector entity_nodes(mesh.begin_nodes(entity), mesh.end_nodes(entity)); + std::vector entity_elems; + stk::mesh::get_entities_through_relations(mesh, entity_nodes, stk::topology::ELEMENT_RANK, entity_elems); + + if (entity_elems.empty()) + { + krinolog << "Relation error, entity not attached to any elements: " << stk::diag::dendl; + krinolog << "Entity: " << debug_entity(mesh, entity) << stk::diag::dendl; + success = false; + } + + bool have_coincident_shell = false; + std::pair shell_relationship(stk::mesh::INVALID_CONNECTIVITY_ORDINAL, stk::mesh::INVALID_PERMUTATION); + for (auto&& elem : entity_elems) + { + stk::topology elem_topology = mesh.bucket(elem).topology(); + if (elem_topology.is_shell() && elem_topology.num_nodes() == entity_topology.num_nodes()) + { + have_coincident_shell = true; + shell_relationship = determine_shell_side_ordinal_and_permutation(mesh, elem, entity); + break; + } + } + + for (auto&& elem : entity_elems) + { + stk::topology elem_topology = mesh.bucket(elem).topology(); + const bool is_coincident_shell = (elem_topology.is_shell() && elem_topology.num_nodes() == entity_topology.num_nodes()); + bool should_be_attached = true; + if (have_coincident_shell && !is_coincident_shell) + { + // Volume elements should only be attached to inward pointing faces when the surface has a shell. + std::pair relationship = determine_ordinal_and_permutation(mesh, elem, entity); + const bool elem_polarity = entity_topology.is_positive_polarity(relationship.second); + const bool shell_polarity = entity_topology.is_positive_polarity(shell_relationship.second); + should_be_attached = elem_polarity != shell_polarity; + } + + const unsigned num_elem_entities = mesh.num_connectivity(elem, entity_rank); + const stk::mesh::Entity* elem_entities = mesh.begin(elem, entity_rank); + const stk::mesh::ConnectivityOrdinal * elem_ordinals = mesh.begin_ordinals(elem, entity_rank); + const stk::mesh::Permutation * elem_permutations = mesh.begin_permutations(elem, entity_rank); + bool already_attached = false; + for (unsigned it_s=0; it_s relationship = + is_coincident_shell ? + shell_relationship : + determine_ordinal_and_permutation(mesh, elem, entity); + if (relationship.first != elem_ordinals[it_s]) + { + krinolog << "Relation error, ordinal is incorrect: " << relationship.first << "!=" << elem_ordinals[it_s] << stk::diag::dendl; + krinolog << "Entity: " << debug_entity(mesh, entity) << stk::diag::dendl; + krinolog << "Element: " << debug_entity(mesh, elem) << stk::diag::dendl; + success = false; + } + if (relationship.second != elem_permutations[it_s]) + { + krinolog << "Relation error, permutation is incorrect: " << relationship.second << "!=" << elem_permutations[it_s] << stk::diag::dendl; + krinolog << "Entity: " << debug_entity(mesh, entity) << stk::diag::dendl; + krinolog << "Element: " << debug_entity(mesh, elem) << stk::diag::dendl; + success = false; + } + } + } + } + if (!already_attached && should_be_attached) + { + + krinolog << "Relation error, entity is not attached to element: " << stk::diag::dendl; + krinolog << "Entity: " << debug_entity(mesh, entity) << stk::diag::dendl; + krinolog << "Element: " << debug_entity(mesh, elem) << stk::diag::dendl; + std::pair relationship = determine_ordinal_and_permutation(mesh, elem, entity); + for (unsigned it_s=0; it_s entities; + stk::mesh::get_entities( mesh, meta.side_rank(), entities ); + + mesh.modification_begin(); + for (auto&& entity : entities) + { + attach_entity_to_elements(mesh, entity); + } + mesh.modification_end(); +} + +void +attach_entity_to_elements(stk::mesh::BulkData & mesh, stk::mesh::Entity entity) +{ + //Sorry! Passing these scratch vectors into stk's declare_relation function is + //a performance improvement (fewer allocations). But stk will try to clean up + //this ugliness soon. (i.e., find a better way to get the performance.) + stk::mesh::OrdinalVector scratch1, scratch2, scratch3; + + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::topology entity_topology = mesh.bucket(entity).topology(); + stk::mesh::EntityRank entity_rank = entity_topology.rank(); + std::vector entity_nodes(mesh.begin_nodes(entity), mesh.end_nodes(entity)); + std::vector entity_elems; + stk::mesh::get_entities_through_relations(mesh, entity_nodes, stk::topology::ELEMENT_RANK, entity_elems); + + bool have_coincident_shell = false; + std::pair shell_relationship(stk::mesh::INVALID_CONNECTIVITY_ORDINAL, stk::mesh::INVALID_PERMUTATION); + for (auto&& elem : entity_elems) + { + stk::topology elem_topology = mesh.bucket(elem).topology(); + if (elem_topology.is_shell() && elem_topology.num_nodes() == entity_topology.num_nodes()) + { + have_coincident_shell = true; + shell_relationship = determine_shell_side_ordinal_and_permutation(mesh, elem, entity); + break; + } + } + + for (auto&& elem : entity_elems) + { + if (!mesh.bucket(elem).member(meta.locally_owned_part())) + { + continue; + } + bool already_attached = false; + const unsigned num_elem_entities = mesh.num_connectivity(elem, entity_rank); + const stk::mesh::Entity* elem_entities = mesh.begin(elem, entity_rank); + for (unsigned it_s=0; it_s relationship(stk::mesh::INVALID_CONNECTIVITY_ORDINAL, stk::mesh::INVALID_PERMUTATION); + if (!have_coincident_shell) + { + relationship = determine_ordinal_and_permutation(mesh, elem, entity); + } + else + { + stk::topology elem_topology = mesh.bucket(elem).topology(); + if (elem_topology.is_shell() && elem_topology.num_nodes() == entity_topology.num_nodes()) + { + ThrowAssertMsg(shell_relationship.second == determine_permutation(mesh, elem, entity, shell_relationship.first), "All shells should have same permutation for side."); + relationship = shell_relationship; + } + else + { + relationship = determine_ordinal_and_permutation(mesh, elem, entity); + const bool elem_polarity = entity_topology.is_positive_polarity(relationship.second); + const bool shell_polarity = entity_topology.is_positive_polarity(shell_relationship.second); + if (elem_polarity == shell_polarity) + { + // Side does not touch volume element; + continue; + } + } + } + + mesh.declare_relation( elem, entity, relationship.first, relationship.second, scratch1, scratch2, scratch3 ); + const bool successfully_attached = (find_entity_by_ordinal(mesh, elem, entity_rank, relationship.first) == entity); + if (!successfully_attached) + { + krinolog << "Could not attach " << debug_entity(mesh,entity) << " to element " << debug_entity(mesh,elem) << stk::diag::dendl; + krinolog << "Existing attached entities:" << stk::diag::dendl; + for (unsigned it_s=0; it_s & entities, + stk::CommSparse &commSparse) +{ + entities.clear(); + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + stk::mesh::EntityKey entityKey; + commSparse.recv_buffer(procId).unpack(entityKey); + entities.insert(mesh.get_entity(entityKey)); + } + }); +} + +void +update_node_activation(stk::mesh::BulkData & mesh, stk::mesh::Part & active_part) +{ + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + + stk::mesh::PartVector active_part_vec(1, &active_part); + stk::mesh::PartVector inactive_part_vec; + + std::vector entities; + stk::mesh::Selector locally_owned(meta.locally_owned_part()); + stk::mesh::get_selected_entities( locally_owned, mesh.buckets( stk::topology::NODE_RANK ), entities ); + + for (std::vector::iterator i_node = entities.begin(); i_node != entities.end(); ++i_node) + { + stk::mesh::Entity node = *i_node; + + const unsigned num_node_elems = mesh.num_elements(node); + const stk::mesh::Entity* node_elems = mesh.begin_elements(node); + bool have_active_elems = false; + for (unsigned node_elem_index=0; node_elem_index add_parts; + std::vector remove_parts; + std::vector entities; + + stk::mesh::Selector inactive_locally_owned = mesh.mesh_meta_data().locally_owned_part() & !active_part; + + for (stk::mesh::EntityRank entity_rank = stk::topology::NODE_RANK; entity_rank <= stk::topology::ELEMENT_RANK; ++entity_rank) + { + const stk::mesh::BucketVector & buckets = mesh.get_buckets(entity_rank, inactive_locally_owned); + for (auto&& bucket_ptr : buckets) + { + entities.insert(entities.end(), bucket_ptr->begin(), bucket_ptr->end()); + } + } + add_parts.assign(entities.size(), {&active_part}); + remove_parts.resize(entities.size()); + + mesh.batch_change_entity_parts(entities, add_parts, remove_parts); +} + +//-------------------------------------------------------------------------------- + +void destroy_custom_ghostings(stk::mesh::BulkData & mesh) +{ + const std::vector & ghostings = mesh.ghostings(); + for(unsigned i = stk::mesh::BulkData::AURA+1; i < ghostings.size(); ++i) + { + mesh.destroy_ghosting(*ghostings[i]); + } +} + +//-------------------------------------------------------------------------------- + +void +delete_mesh_entities(stk::mesh::BulkData & mesh, std::vector & child_elems) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::delete_old_mesh_entities(void)"); /* %TRACE% */ + + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + + stk::mesh::Selector not_ghost_selector = meta.locally_owned_part() | meta.globally_shared_part(); + stk::mesh::Selector universal_selector = meta.universal_part(); + + std::vector child_sides; + std::vector child_edges; + std::vector child_nodes; + + for (unsigned i=0; i * const coords_field = reinterpret_cast*>(mesh.mesh_meta_data().coordinate_field()); + ThrowRequireMsg(nullptr != coords_field, "Coordinates must be defined."); + + double * child_coords = stk::mesh::field_data(*coords_field, child); + double * parent0_coords = stk::mesh::field_data(*coords_field, parent0); + double * parent1_coords = stk::mesh::field_data(*coords_field, parent1); + + const unsigned ndim = mesh.mesh_meta_data().spatial_dimension(); + unsigned best_dim = 0; + double best_extent = std::abs(parent1_coords[0] - parent0_coords[0]); + for (unsigned dim = 1; dim < ndim; ++dim) + { + const double extent = std::abs(parent1_coords[dim] - parent0_coords[dim]); + if (extent > best_extent) + { + best_dim = dim; + best_extent = extent; + } + } + return std::abs(child_coords[best_dim] - parent0_coords[best_dim])/best_extent; +} + +//-------------------------------------------------------------------------------- + +void +store_edge_node_parent_ids(const stk::mesh::BulkData & mesh, + const FieldRef & parent_id_field, + stk::mesh::Entity edge_node_entity, + stk::mesh::EntityId parent0_id, + stk::mesh::EntityId parent1_id) +{ + if (parent_id_field.type_is()) + { + auto * stored_parent_ids = field_data(parent_id_field, edge_node_entity); + ThrowAssertMsg(stored_parent_ids, "Node " << mesh.identifier(edge_node_entity) + << " does not have the parent_ids field suggesting it is a mesh node."); + stored_parent_ids[0] = parent0_id; + stored_parent_ids[1] = parent1_id; + } + else if (parent_id_field.type_is()) + { + auto * stored_parent_ids = field_data(parent_id_field, edge_node_entity); + ThrowAssertMsg(stored_parent_ids, "Node " << mesh.identifier(edge_node_entity) + << " does not have the parent_ids field suggesting it is a mesh node."); + stored_parent_ids[0] = parent0_id; + stored_parent_ids[1] = parent1_id; + } + else + { + ThrowRequireMsg(false, "Unsupported field type for parent_node_ids_field"); + } +} + +//-------------------------------------------------------------------------------- + +std::array +get_edge_node_parent_ids(const stk::mesh::BulkData & mesh, + const FieldRef & parent_id_field, + const stk::mesh::Entity edge_node_entity) +{ + std::array parent_ids; + + if (parent_id_field.type_is()) + { + const auto * stored_parent_ids = field_data(parent_id_field, edge_node_entity); + ThrowAssertMsg(stored_parent_ids, "No SubElementNode found for node " << mesh.identifier(edge_node_entity) + << ", but it does not have the parent_ids field suggesting it is a mesh node."); + parent_ids[0] = stored_parent_ids[0]; + parent_ids[1] = stored_parent_ids[1]; + } + else if (parent_id_field.type_is()) + { + const auto * stored_parent_ids = field_data(parent_id_field, edge_node_entity); + ThrowAssertMsg(stored_parent_ids, "No SubElementNode found for node " << mesh.identifier(edge_node_entity) + << ", but it does not have the parent_ids field suggesting it is a mesh node."); + parent_ids[0] = stored_parent_ids[0]; + parent_ids[1] = stored_parent_ids[1]; + } + else + { + ThrowRequireMsg(false, "Unsupported field type for parent_node_ids_field"); + } + return parent_ids; +} + +//-------------------------------------------------------------------------------- + +void get_parent_nodes_from_child(const stk::mesh::BulkData & mesh, + stk::mesh::Entity child, const FieldRef & parent_id_field, + std::set & parent_nodes) +{ + if (has_field_data(parent_id_field, child)) + { + auto parent_ids = get_edge_node_parent_ids(mesh, parent_id_field, child); + const stk::mesh::Entity parent0 = mesh.get_entity(stk::topology::NODE_RANK, parent_ids[0]); + const stk::mesh::Entity parent1 = mesh.get_entity(stk::topology::NODE_RANK, parent_ids[1]); + ThrowAssert(mesh.is_valid(parent0) && mesh.is_valid(parent1)); + get_parent_nodes_from_child(mesh, parent0, parent_id_field, parent_nodes); + get_parent_nodes_from_child(mesh, parent1, parent_id_field, parent_nodes); + } + else + { + parent_nodes.insert(child); + } +} + +//-------------------------------------------------------------------------------- + +void debug_print_selector_parts(const stk::mesh::Selector & selector) +{ + stk::mesh::PartVector parts; + selector.get_parts(parts); + krinolog << "Selector contains parts: " << stk::diag::push << stk::diag::dendl; + for(stk::mesh::PartVector::const_iterator it = parts.begin(); it != parts.end(); ++it) + { + krinolog << (*it)->name() << stk::diag::dendl; + } + krinolog << stk::diag::pop << stk::diag::dendl; +} + +//-------------------------------------------------------------------------------- + +stk::mesh::PartVector filter_non_io_parts(const stk::mesh::PartVector & all_parts) +{ + stk::mesh::PartVector io_parts; + + for(stk::mesh::PartVector::const_iterator it = all_parts.begin(); it != all_parts.end(); ++it) + { + if( stk::io::is_part_io_part(**it) ) + { + io_parts.push_back(*it); + } + } + + return io_parts; +} + +void +activate_selected_sides_touching_active_elements(stk::mesh::BulkData & mesh, const stk::mesh::Selector & side_selector, stk::mesh::Part & active_part) +{ + // This method requires AURA + ThrowRequire(mesh.is_automatic_aura_on()); + + mesh.modification_begin(); + stk::mesh::PartVector active_part_vec(1, &active_part); + stk::mesh::PartVector inactive_part_vec; + stk::mesh::Selector select_locally_owned = side_selector & mesh.mesh_meta_data().locally_owned_part(); + + std::vector sides; + stk::mesh::get_selected_entities( select_locally_owned, mesh.buckets( mesh.mesh_meta_data().side_rank() ), sides ); + for (auto && side : sides) + { + bool have_active_elem = false; + const stk::mesh::Entity* side_elems = mesh.begin_elements(side); + const unsigned num_side_elems = mesh.num_elements(side); + for (unsigned ielem=0; ielem & coincident_elems) +{ + stk::topology elem_topology = mesh.bucket(elem).topology(); + const stk::mesh::Entity* elem_nodes = mesh.begin_nodes(elem); + std::vector elem_side_nodes; + std::vector elem_nbrs; + std::vector nbr_side_nodes; + + coincident_elems.clear(); + const unsigned num_sides = elem_topology.num_sides(); + for (unsigned iside=0; iside sorted_elem_side_nodes = elem_side_nodes; + std::sort(sorted_elem_side_nodes.begin(), sorted_elem_side_nodes.end(), stk::mesh::EntityLess(mesh)); + const unsigned unique_len = std::distance(sorted_elem_side_nodes.begin(), std::unique( sorted_elem_side_nodes.begin(), sorted_elem_side_nodes.end() )); + const bool is_degenerate_side = unique_len < mesh.mesh_meta_data().spatial_dimension(); + if (is_degenerate_side) continue; + + stk::mesh::get_entities_through_relations(mesh, elem_side_nodes, stk::topology::ELEMENT_RANK, elem_nbrs); + ThrowRequire(!elem_nbrs.empty()); + + for (auto && nbr : elem_nbrs) + { + if (nbr == elem) continue; + + stk::topology nbr_topology = mesh.bucket(nbr).topology(); + const stk::mesh::Entity* nbr_nodes = mesh.begin_nodes(nbr); + const unsigned num_nbr_sides = nbr_topology.num_sides(); + for (unsigned inbr_side=0; inbr_side 1) + { + // Skip check if we don't have aura + return true; + } + + bool found_mismatched_side = false; + + std::vector element_nodes; + std::vector element_side_nodes; + std::vector side_elements; + std::vector active_side_elements; + + const stk::mesh::BucketVector & buckets = mesh.get_buckets( stk::topology::ELEMENT_RANK, active_part & mesh.mesh_meta_data().locally_owned_part() ); + + for ( auto && bucket : buckets ) + { + stk::topology element_topology = bucket->topology(); + if (element_topology.is_shell()) continue; + const unsigned num_sides = element_topology.num_sides(); + + for ( auto && element : *bucket ) + { + element_nodes.assign(mesh.begin_nodes(element), mesh.end_nodes(element)); + for (unsigned iside=0; iside elements; + std::vector< stk::mesh::Entity> coincident_elements; + std::vector< stk::mesh::Entity> element_nodes; + + ParallelErrorMessage err(mesh.parallel()); + + stk::mesh::get_entities( mesh, stk::topology::ELEMENT_RANK, elements ); + for (auto && element : elements) + { + element_nodes.assign(mesh.begin_nodes(element), mesh.end_nodes(element)); + stk::mesh::get_entities_through_relations(mesh, element_nodes, stk::topology::ELEMENT_RANK, coincident_elements); + ThrowRequire(!coincident_elements.empty()); + stk::topology element_topology = mesh.bucket(element).topology(); + + bool coincident_element_error = false; + for (auto && coincident : coincident_elements) + { + if (coincident == element || element_topology != mesh.bucket(coincident).topology()) continue; + if (!element_topology.is_shell()) + { + err << "Non-shell elements " << mesh.entity_key(element) << " and " + << mesh.entity_key(coincident) << " are fully coincident (overlapping).\n"; + coincident_element_error = true; + } + else + { + stk::EquivalentPermutation result = element_topology.is_equivalent(mesh.begin_nodes(coincident), element_nodes.data()); + ThrowRequire(result.is_equivalent); + if (result.permutation_number != stk::mesh::DEFAULT_PERMUTATION) + { + err << "Elements " << mesh.entity_key(element) << " and " << mesh.entity_key(coincident) + << " are fully coincident shell elements but have different node order.\n"; + coincident_element_error = true; + } + } + } + + // Detect partially coincident, non-shell elements that are both active + if (!coincident_element_error && mesh.bucket(element).member(active_part) && !element_topology.is_shell() && element_topology.base() != stk::topology::BEAM_2) + { + get_partially_and_fully_coincident_elements(mesh, element, coincident_elements); + + for (auto && coincident : coincident_elements) + { + if (mesh.bucket(coincident).member(active_part) && !mesh.bucket(coincident).topology().is_shell() && + mesh.bucket(coincident).topology().base() != stk::topology::BEAM_2) + { + err << "Non-shell elements " << mesh.entity_key(element) << " with topology " + << element_topology.name() << " and " << mesh.entity_key(coincident) + << " with topology " << mesh.bucket(coincident).topology().name() + << " are partially coincident (overlapping) and active.\n"; + coincident_element_error = true; + } + } + } + } + auto err_msg = err.gather_message(); + krinolog << err_msg.second; + return !err_msg.first; +} + +bool +fix_coincident_element_ownership(stk::mesh::BulkData & mesh) +{ + // This method exploits aura to choose which processor the faces and edges should be owned by + if (!mesh.is_automatic_aura_on()) + { + // Make no changes, hope for the best. + return false; + } + + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::mesh::Selector locally_owned_selector(meta.locally_owned_part()); + + std::vector elems; + std::vector coincident_elems; + + std::vector entities_to_move; + + stk::mesh::get_selected_entities( locally_owned_selector, mesh.buckets(stk::topology::ELEMENT_RANK), elems ); + + for (auto && elem : elems) + { + get_partially_and_fully_coincident_elements(mesh, elem, coincident_elems); + + int new_owner = mesh.parallel_owner_rank(elem); + for (auto && nbr : coincident_elems) + { + const int elem_owner = mesh.parallel_owner_rank(nbr); + if (elem_owner < new_owner) new_owner = elem_owner; + } + + if (new_owner != mesh.parallel_owner_rank(elem)) + { + entities_to_move.push_back(stk::mesh::EntityProc(elem, new_owner)); + } + } + + const int local_made_moves = !entities_to_move.empty(); + int global_made_moves = false; + stk::all_reduce_max(mesh.parallel(), &local_made_moves, &global_made_moves, 1); + + if (global_made_moves) + { + mesh.change_entity_owner(entities_to_move); + } + return global_made_moves; +} + +bool +fix_face_and_edge_ownership(stk::mesh::BulkData & mesh) +{ + // This method exploits aura to choose which processor the faces and edges should be owned by + if (!mesh.is_automatic_aura_on()) + { + // Make no changes, hope for the best. + return false; + } + + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::mesh::Selector locally_owned_selector(meta.locally_owned_part()); + + std::vector< stk::mesh::Entity> entities; + std::vector< stk::mesh::Entity> entity_elems; + + std::vector entities_to_move; + + for (stk::mesh::EntityRank entity_rank = stk::topology::EDGE_RANK; entity_rank <= stk::topology::FACE_RANK; ++entity_rank) + { + stk::mesh::get_selected_entities( locally_owned_selector, mesh.buckets(entity_rank), entities ); + + for (auto && entity : entities) + { + entity_elems.assign(mesh.begin_elements(entity), mesh.end_elements(entity)); + ThrowRequire(!entity_elems.empty()); + + int new_owner = mesh.parallel_size(); + for (auto && entity_elem : entity_elems) + { + const int elem_owner = mesh.parallel_owner_rank(entity_elem); + if (elem_owner < new_owner) new_owner = elem_owner; + } + + if (new_owner != mesh.parallel_owner_rank(entity)) + { + entities_to_move.push_back(stk::mesh::EntityProc(entity, new_owner)); + } + } + } + + const int local_made_moves = !entities_to_move.empty(); + int global_made_moves = false; + stk::all_reduce_max(mesh.parallel(), &local_made_moves, &global_made_moves, 1); + + if (global_made_moves) + { + mesh.change_entity_owner(entities_to_move); + } + return global_made_moves; +} + +bool +check_face_and_edge_ownership(const stk::mesh::BulkData & mesh) +{ + // This method exploits aura to choose which processor the faces and edges should be owned by + if (!mesh.is_automatic_aura_on()) + { + // Skip check if we don't have aura + return true; + } + + const stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + stk::mesh::Selector locally_owned_selector(meta.locally_owned_part()); + + std::vector< stk::mesh::Entity> entities; + std::vector< stk::mesh::Entity> entity_elems; + std::vector< stk::mesh::Entity> entity_nodes; + + for (stk::mesh::EntityRank entity_rank = stk::topology::EDGE_RANK; entity_rank <= stk::topology::FACE_RANK; ++entity_rank) + { + const stk::mesh::BucketVector & buckets = mesh.get_buckets( entity_rank, locally_owned_selector ); + + stk::mesh::BucketVector::const_iterator ib = buckets.begin(); + stk::mesh::BucketVector::const_iterator ib_end = buckets.end(); + + for ( ; ib != ib_end; ++ib ) + { + const stk::mesh::Bucket & b = **ib; + const size_t length = b.size(); + for (size_t it_entity = 0; it_entity < length; ++it_entity) + { + stk::mesh::Entity entity = b[it_entity]; + const int entity_owner = mesh.parallel_owner_rank(entity); + + entity_nodes.assign(mesh.begin_nodes(entity), mesh.end_nodes(entity)); + entity_elems.assign(mesh.begin_elements(entity), mesh.end_elements(entity)); + + bool have_element_on_owning_proc = false; + for (std::vector::iterator it_elem = entity_elems.begin(); it_elem != entity_elems.end(); ++it_elem) + { + if (mesh.parallel_owner_rank(*it_elem) == entity_owner) + { + have_element_on_owning_proc = true; + break; + } + } + ThrowRequireMsg(have_element_on_owning_proc, "Error: " << mesh.entity_key(entity) + << " is owned on processor " << entity_owner + << " but does not have any elements that are owned on this processor."); + } + } + } + const bool success = true; + return success; +} + +bool +set_region_id_on_unset_entity_and_neighbors(stk::mesh::BulkData & mesh, stk::mesh::Entity & entity, stk::mesh::EntityRank entity_rank, stk::mesh::FieldBase & region_id_field, const unsigned region_id) +{ + unsigned * region_id_data = stk::mesh::field_data(reinterpret_cast&>(region_id_field), entity); + ThrowAssert(NULL != region_id_data); + if (*region_id_data != 0) + { + ThrowAssert(*region_id_data == region_id); + return false; + } + + *region_id_data = region_id; + + // now visit neighbors + const stk::mesh::Entity* begin_nodes = mesh.begin_nodes(entity); + const stk::mesh::Entity* end_nodes = mesh.end_nodes(entity); + + for (const stk::mesh::Entity* it_node = begin_nodes; it_node != end_nodes; ++it_node) + { + stk::mesh::Entity node = *it_node; + + const stk::mesh::Entity* node_entities_begin = mesh.begin(node, entity_rank); + const stk::mesh::Entity* node_entities_end = mesh.end(node, entity_rank); + + for (const stk::mesh::Entity* it_nbr = node_entities_begin; it_nbr != node_entities_end; ++it_nbr) + { + stk::mesh::Entity neighbor = *it_nbr; + set_region_id_on_unset_entity_and_neighbors(mesh, neighbor, entity_rank, region_id_field, region_id); + } + } + + return true; +} + +void +identify_isolated_regions(stk::mesh::Part & part, stk::mesh::FieldBase & region_id_field) +{ /* %TRACE[ON]% */ Trace trace__("krino::Mesh::identify_isolated_portions_of_part(stk::mesh::Part & part)"); /* %TRACE% */ + stk::mesh::BulkData & mesh = part.mesh_bulk_data(); + stk::mesh::MetaData & meta = mesh.mesh_meta_data(); + + stk::mesh::EntityRank entity_rank = part.primary_entity_rank(); + stk::mesh::Selector selector = part & meta.locally_owned_part(); + + std::vector entities; + stk::mesh::get_selected_entities( selector, mesh.buckets(entity_rank), entities ); + + // initialize region id + const stk::mesh::BucketVector & buckets = mesh.get_buckets(entity_rank, selector); + for (stk::mesh::BucketVector::const_iterator ib = buckets.begin(); ib != buckets.end(); ++ib ) + { + const stk::mesh::Bucket & b = **ib; + const size_t length = b.size(); + unsigned * region_id = stk::mesh::field_data(reinterpret_cast&>(region_id_field), b); + ThrowAssert(NULL != region_id); + std::fill(region_id, region_id+length, 0); + } + + unsigned local_region_counter = 0; + unsigned region_id = 1 + local_region_counter*mesh.parallel_size() + mesh.parallel_rank(); + + for (std::vector::iterator it_entity=entities.begin(); it_entity!=entities.end(); ++it_entity) + { + stk::mesh::Entity entity = *it_entity; + + const bool made_changes = set_region_id_on_unset_entity_and_neighbors(mesh, entity, entity_rank, region_id_field, region_id); + if (made_changes) + { + ++local_region_counter; + region_id = 1 + local_region_counter*mesh.parallel_size() + mesh.parallel_rank(); + } + } +} + +const unsigned * get_side_node_ordinals(stk::topology topology, unsigned side_ordinal) +{ + static std::vector< std::vector< std::vector > > all_side_node_ordinals(stk::topology::BEGIN_TOPOLOGY + stk::topology::NUM_TOPOLOGIES); + std::vector< std::vector > & topology_side_node_ordinals = all_side_node_ordinals[topology.value()]; + if (topology_side_node_ordinals.empty()) + { + const size_t num_sides = topology.num_sides(); + topology_side_node_ordinals.resize(num_sides); + for (size_t side_index = 0; side_index < num_sides; ++side_index) + { + std::vector & side_node_ordinals = topology_side_node_ordinals[side_index]; + side_node_ordinals.resize(topology.side_topology(side_index).num_nodes()); + topology.side_node_ordinals(side_index, side_node_ordinals.begin()); + } + } + return &topology_side_node_ordinals[side_ordinal][0]; +} + +const unsigned * get_edge_node_ordinals(stk::topology topology, unsigned edge_ordinal) +{ + static std::vector< std::vector< std::vector > > all_edge_node_ordinals(stk::topology::BEGIN_TOPOLOGY + stk::topology::NUM_TOPOLOGIES); + std::vector< std::vector > & topology_edge_node_ordinals = all_edge_node_ordinals[topology.value()]; + if (topology_edge_node_ordinals.empty()) + { + const size_t num_edges = topology.num_edges(); + topology_edge_node_ordinals.resize(num_edges); + for (size_t edge_index = 0; edge_index < num_edges; ++edge_index) + { + std::vector & edge_node_ordinals = topology_edge_node_ordinals[edge_index]; + edge_node_ordinals.resize(topology.edge_topology(edge_index).num_nodes()); + topology.edge_node_ordinals(edge_index, edge_node_ordinals.begin()); + } + } + return &topology_edge_node_ordinals[edge_ordinal][0]; +} + +stk::mesh::PartVector get_common_io_parts(const stk::mesh::BulkData & mesh, const std::vector entities) +{ + stk::mesh::PartVector common_io_parts; + + bool first = true; + for (auto&& entity : entities) + { + stk::mesh::PartVector entity_io_parts = filter_non_io_parts(mesh.bucket(entity).supersets()); + std::sort(entity_io_parts.begin(), entity_io_parts.end()); + if (first) + { + first = false; + common_io_parts.swap(entity_io_parts); + } + else + { + stk::mesh::PartVector working_set; + working_set.swap(common_io_parts); + std::set_intersection(working_set.begin(),working_set.end(),entity_io_parts.begin(),entity_io_parts.end(),std::back_inserter(common_io_parts)); + } + } + return common_io_parts; +} + +stk::mesh::PartVector get_removable_parts(const stk::mesh::BulkData & mesh, const stk::mesh::Bucket & bucket) +{ + stk::mesh::PartVector removable_parts; + for ( auto&& part : bucket.supersets() ) + { + stk::mesh::EntityRank part_rank = part->primary_entity_rank(); + if ((part_rank == stk::topology::INVALID_RANK || part_rank == bucket.entity_rank()) && + (!stk::mesh::is_auto_declared_part(*part) || stk::mesh::is_topology_root_part(*part))) + { + removable_parts.push_back(part); + } + } + return removable_parts; +} + +stk::mesh::PartVector get_removable_parts(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity) +{ + return get_removable_parts(mesh, mesh.bucket(entity)); +} + +//-------------------------------------------------------------------------------- +bool is_refinement_child(const stk::mesh::BulkData & stk_bulk, const stk::mesh::Entity entity) +{ + const stk::mesh::EntityRank entity_rank = stk_bulk.entity_rank(entity); + const unsigned num_family_trees = stk_bulk.num_connectivity(entity, stk::topology::CONSTRAINT_RANK); + const stk::mesh::Entity* family_trees = stk_bulk.begin(entity, stk::topology::CONSTRAINT_RANK); + for (unsigned ifamily=0; ifamily < num_family_trees; ++ifamily) + { + const stk::mesh::Entity ft = family_trees[ifamily]; + const stk::mesh::Entity* family_tree_entities = stk_bulk.begin(ft, entity_rank); + if(family_tree_entities[0] != entity) return true; + } + return false; +} + +void +get_refinement_immediate_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity parent, std::vector & children) +{ + children.clear(); + stk::mesh::EntityRank entity_rank = stk_bulk.entity_rank(parent); + const unsigned num_family_trees = stk_bulk.num_connectivity(parent, stk::topology::CONSTRAINT_RANK); + const stk::mesh::Entity* family_trees = stk_bulk.begin(parent, stk::topology::CONSTRAINT_RANK); + for (unsigned ifamily=0; ifamily < num_family_trees; ++ifamily) + { + const stk::mesh::Entity* family_tree_entities = stk_bulk.begin(family_trees[ifamily], entity_rank); + const stk::mesh::Entity tree_parent = family_tree_entities[0]; // 0th entry in the family_tree is the parent + if (parent == tree_parent) // I am the parent + { + const unsigned num_family_tree_entities = stk_bulk.num_connectivity(family_trees[ifamily], entity_rank); + for (unsigned ichild=1; ichild < num_family_tree_entities; ++ichild) + { + children.push_back(family_tree_entities[ichild]); + } + } + } +} + +//-------------------------------------------------------------------------------- + +bool +has_refinement_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity parent) +{ + stk::mesh::EntityRank entity_rank = stk_bulk.entity_rank(parent); + const unsigned num_family_trees = stk_bulk.num_connectivity(parent, stk::topology::CONSTRAINT_RANK); + const stk::mesh::Entity* family_trees = stk_bulk.begin(parent, stk::topology::CONSTRAINT_RANK); + for (unsigned ifamily=0; ifamily < num_family_trees; ++ifamily) + { + const stk::mesh::Entity* family_tree_entities = stk_bulk.begin(family_trees[ifamily], entity_rank); + const stk::mesh::Entity tree_parent = family_tree_entities[0]; // 0th entry in the family_tree is the parent + if (parent == tree_parent) // I am the parent + { + return true; + } + } + return false; +} + +//-------------------------------------------------------------------------------- + +namespace { +void +get_refinement_leaf_children(const stk::mesh::BulkData& stk_bulk, const std::vector & children, std::vector & leaf_children) +{ + std::vector grand_children; + for (auto&& child : children) + { + get_refinement_immediate_children(stk_bulk, child, grand_children); + if (grand_children.empty()) + { + leaf_children.push_back(child); + } + else + { + get_refinement_leaf_children(stk_bulk, grand_children, leaf_children); + } + } +} + +void +get_refinement_all_children(const stk::mesh::BulkData& stk_bulk, const std::vector & children, std::vector & all_children) +{ + std::vector grand_children; + for (auto&& child : children) + { + get_refinement_immediate_children(stk_bulk, child, grand_children); + all_children.insert(all_children.end(), grand_children.begin(), grand_children.end()); + get_refinement_all_children(stk_bulk, grand_children, all_children); + } +} +} + +//-------------------------------------------------------------------------------- + +void +get_refinement_leaf_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, std::vector & leaf_children) +{ + leaf_children.clear(); + std::vector children; + get_refinement_immediate_children(stk_bulk, entity, children); + get_refinement_leaf_children(stk_bulk, children, leaf_children); +} + +void +get_refinement_all_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, std::vector & all_children) +{ + std::vector children; + get_refinement_immediate_children(stk_bulk, entity, children); + all_children = children; + get_refinement_all_children(stk_bulk, children, all_children); +} + +void set_relation_permutation(stk::mesh::BulkData & mesh, stk::mesh::Entity from, stk::mesh::Entity to, stk::mesh::ConnectivityOrdinal to_ord, stk::mesh::Permutation to_permutation) +{ + const stk::mesh::EntityRank from_rank = mesh.entity_rank(from); + const stk::mesh::EntityRank to_rank = mesh.entity_rank(to); + + stk::mesh::Entity const* fwd_rels = mesh.begin(from, to_rank); + stk::mesh::ConnectivityOrdinal const* fwd_ords = mesh.begin_ordinals(from, to_rank); + stk::mesh::Permutation * fwd_perms = const_cast(mesh.begin_permutations(from, to_rank)); + const int num_fwd = mesh.num_connectivity(from, to_rank); + + stk::mesh::Entity const* back_rels = mesh.begin(to, from_rank); + stk::mesh::ConnectivityOrdinal const* back_ords = mesh.begin_ordinals(to, from_rank); + stk::mesh::Permutation * back_perms = const_cast(mesh.begin_permutations(to, from_rank)); + const int num_back = mesh.num_connectivity(to,from_rank); + + // Find and change fwd connectivity + for (int i = 0; i < num_fwd; ++i, ++fwd_rels, ++fwd_ords, ++fwd_perms) { + // Allow clients to make changes to permutation + // Permutations do not affect Relation ordering, so this is safe. + if (*fwd_rels == to && *fwd_ords == to_ord) { + *fwd_perms = to_permutation; + } + } + + // Find and change back connectivity + for (int i = 0; i < num_back; ++i, ++back_rels, ++back_ords, ++back_perms) { + // Allow clients to make changes to permutation + // Permutations do not affect Relation ordering, so this is safe. + if (*back_rels == from && *back_ords == to_ord) { + *back_perms = to_permutation; + } + } +} + +std::pair +determine_shell_side_ordinal_and_permutation(const stk::mesh::BulkData & mesh, stk::mesh::Entity shell, stk::mesh::Entity side) +{ + // The input shell may or may not be attached to side, but should be coincident with the side. + // We will figure out what the ordinal for this shell-side relation based on the existing + // connectivity of the side. + const unsigned num_side_elems = mesh.num_elements(side); + ThrowRequireMsg(num_side_elems > 0, "Cannot determine shell_side_ordinal for completely disconnected side."); + + stk::mesh::EntityRank side_rank = mesh.mesh_meta_data().side_rank(); + stk::topology side_topology = mesh.bucket(side).topology(); + const stk::mesh::Entity * side_elems = mesh.begin_elements(side); + const stk::mesh::ConnectivityOrdinal * side_elem_ordinals = mesh.begin_element_ordinals(side); + const stk::mesh::Permutation * side_elem_permutations = mesh.begin_element_permutations(side); + + std::pair result(stk::mesh::INVALID_CONNECTIVITY_ORDINAL, stk::mesh::INVALID_PERMUTATION); + for (unsigned it = 0; it relative_rank); + + const stk::mesh::Entity * relative_nodes = mesh.begin_nodes(relative); + + const stk::EquivalentPermutation equiv = stk::mesh::sub_rank_equivalent(mesh, entity, ordinal, relative_rank, relative_nodes); + if(!equiv.is_equivalent) + { + ThrowErrorMsg("Could not find connection between " << mesh.entity_key(entity) <<" and " + << mesh.entity_key(relative) << " with ordinal " << ordinal + << debug_entity(mesh, entity) << debug_entity(mesh, relative)); + } + + return static_cast(equiv.permutation_number); +} + +std::pair +determine_ordinal_and_permutation(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity, const stk::mesh::Entity relative) +{ + const stk::mesh::EntityRank relative_rank = mesh.entity_rank(relative); + ThrowAssert(mesh.entity_rank(entity) > relative_rank); + stk::topology relative_topology = mesh.bucket(relative).topology(); + ThrowAssert(relative_topology.num_nodes() == mesh.num_nodes(relative)); + + const stk::mesh::Entity * relative_nodes = mesh.begin_nodes(relative); + + stk::topology entity_topology = mesh.bucket(entity).topology(); + const bool looking_for_shell_side = entity_topology.is_shell() && relative_rank == mesh.mesh_meta_data().side_rank(); + + for(size_t i = 0; i < entity_topology.num_sub_topology(relative_rank); ++i) + { + if (entity_topology.sub_topology(relative_rank, i) == relative_topology) + { + const stk::EquivalentPermutation equiv = stk::mesh::sub_rank_equivalent(mesh, entity, stk::mesh::ConnectivityOrdinal(i), relative_rank, relative_nodes); + const bool match = equiv.is_equivalent && (!looking_for_shell_side || equiv.permutation_number < relative_topology.num_positive_permutations()); + if(match) + { + return std::pair(static_cast(i), static_cast(equiv.permutation_number)); + } + } + } + ThrowRuntimeError("Could not find connection between " << mesh.entity_key(entity) << " and " << mesh.entity_key(relative) << debug_entity(mesh, entity) << debug_entity(mesh, relative)); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_MeshHelpers.hpp b/packages/krino/krino/krino_lib/Akri_MeshHelpers.hpp new file mode 100644 index 000000000000..563be698eaf4 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshHelpers.hpp @@ -0,0 +1,182 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MeshHelpers_h +#define Akri_MeshHelpers_h + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { class FieldRef; } + +namespace krino { + +typedef std::pair TopologyPartPair; +typedef std::vector TopologyPartVector; + +struct StkMeshEntities +{ + typedef stk::mesh::Entity value_type; + const value_type *mBegin; + const value_type *mEnd; + const value_type * begin() const { return mBegin; } + const value_type * end() const { return mEnd; } + size_t size() const { return mEnd - mBegin; } + bool empty() const { return mEnd == mBegin; } + value_type operator[](int i) const { return *(mBegin + i); } +}; + +void fill_element_node_coordinates(const stk::mesh::BulkData & mesh, stk::mesh::Entity element, const FieldRef coordsField, std::vector & elementNodeCoords); +void fill_procs_owning_or_sharing_or_ghosting_node(const stk::mesh::BulkData& bulkData, stk::mesh::Entity node, std::vector & procsOwningSharingOrGhostingNode); +double compute_maximum_element_size(stk::mesh::BulkData& mesh); +void compute_element_quality(const stk::mesh::BulkData & mesh, double & minEdgeLength, double & maxEdgeLength, double & minVolume, double & maxVolume); +void delete_all_entities_using_nodes_with_nodal_volume_below_threshold(stk::mesh::BulkData & mesh, const stk::mesh::Selector & blockSelector, const double threshold); +std::vector get_side_permutation(stk::topology topology, stk::mesh::Permutation node_permutation); +const stk::mesh::Part & find_element_part(const stk::mesh::BulkData& mesh, stk::mesh::Entity elem); +bool check_induced_parts(const stk::mesh::BulkData & mesh); +void attach_sides_to_elements(stk::mesh::BulkData & mesh); +void attach_entity_to_elements(stk::mesh::BulkData & mesh, stk::mesh::Entity entity); +void unpack_entities_from_other_procs(const stk::mesh::BulkData & mesh, std::set & entities, stk::CommSparse &commSparse); +void update_node_activation(stk::mesh::BulkData & mesh, stk::mesh::Part & active_part); +void activate_all_entities(stk::mesh::BulkData & mesh, stk::mesh::Part & active_part); +void destroy_custom_ghostings(stk::mesh::BulkData & mesh); +void delete_mesh_entities(stk::mesh::BulkData & mesh, std::vector & child_elems); +void debug_print_selector_parts(const stk::mesh::Selector & selector); +stk::mesh::PartVector filter_non_io_parts(const stk::mesh::PartVector & all_parts); +void activate_selected_sides_touching_active_elements(stk::mesh::BulkData & mesh, const stk::mesh::Selector & side_selector, stk::mesh::Part & active_part); +void get_partially_and_fully_coincident_elements(const stk::mesh::BulkData & mesh, stk::mesh::Entity elem, std::vector & coincident_elems); +bool check_element_side_connectivity(const stk::mesh::BulkData & mesh, const stk::mesh::Part & exterior_boundary_part, const stk::mesh::Part & active_part); +bool check_coincident_elements(const stk::mesh::BulkData & mesh, const stk::mesh::Part & active_part); +bool fix_coincident_element_ownership(stk::mesh::BulkData & mesh); +bool fix_face_and_edge_ownership(stk::mesh::BulkData & mesh); +bool check_face_and_edge_ownership(const stk::mesh::BulkData & mesh); +bool check_face_and_edge_relations(const stk::mesh::BulkData & mesh); +bool check_shared_entity_nodes(const stk::mesh::BulkData & mesh, stk::mesh::EntityKey remote_entity_key, std::vector & remote_entity_node_ids); +bool check_shared_entity_nodes(const stk::mesh::BulkData & mesh, std::vector & entities); +bool check_shared_entity_nodes(const stk::mesh::BulkData & mesh); +void disconnect_entity(stk::mesh::BulkData & mesh, stk::mesh::Entity entity); +bool disconnect_and_destroy_entity(stk::mesh::BulkData & mesh, stk::mesh::Entity entity); + +stk::mesh::PartVector get_common_io_parts(const stk::mesh::BulkData & mesh, const std::vector entities); +stk::mesh::PartVector get_removable_parts(const stk::mesh::BulkData & mesh, const stk::mesh::Bucket & bucket); +stk::mesh::PartVector get_removable_parts(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity); + +void +store_edge_node_parent_ids(const stk::mesh::BulkData & mesh, + const FieldRef & parent_id_field, + stk::mesh::Entity edge_node_entity, + stk::mesh::EntityId parent0_id, + stk::mesh::EntityId parent1_id); + +std::array +get_edge_node_parent_ids(const stk::mesh::BulkData & mesh, + const FieldRef & parent_id_field, + const stk::mesh::Entity edge_node_entity); + +void get_parent_nodes_from_child(const stk::mesh::BulkData & mesh, + stk::mesh::Entity child, const FieldRef & parent_id_field, + std::set & parent_nodes); + +double compute_child_position(const stk::mesh::BulkData & mesh, stk::mesh::Entity child, stk::mesh::Entity parent0, stk::mesh::Entity parent1); + +// topology helpers +// NOTE: These use static storage, but it does not depend on anything so it should be ok for nested or multithreaded usage. +const unsigned * get_side_node_ordinals(stk::topology topology, unsigned side_ordinal); +const unsigned * get_edge_node_ordinals(stk::topology topology, unsigned edge_ordinal); + +std::string debug_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity); +std::string debug_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity entity, const bool includeFields); + +struct ChildNodeRequest +{ + std::vector parents; + stk::mesh::Entity* child; + + ChildNodeRequest(const std::vector & in_parents, stk::mesh::Entity *in_child) + : parents(in_parents), child(in_child) {} +}; +struct SideRequest +{ + stk::mesh::Entity element; + unsigned element_side_ordinal; + stk::mesh::PartVector side_parts; + + SideRequest(stk::mesh::Entity in_element, unsigned in_element_side_ordinal, const stk::mesh::PartVector & in_side_parts) + : element(in_element), element_side_ordinal(in_element_side_ordinal), side_parts(in_side_parts) {} +}; + +void batch_create_child_nodes(stk::mesh::BulkData & mesh, const std::vector< ChildNodeRequest > & child_node_requests, const stk::mesh::PartVector & node_parts, bool assert_32bit_ids, bool make_64bit_ids); +void batch_create_sides(stk::mesh::BulkData & mesh, const std::vector< SideRequest > & side_requests); +void make_side_ids_consistent_with_stk_convention(stk::mesh::BulkData & mesh); + +double compute_element_volume_to_edge_ratio(stk::mesh::BulkData & mesh, stk::mesh::Entity element, const stk::mesh::Field * const coords_field); + +bool is_refinement_child(const stk::mesh::BulkData & stk_bulk, stk::mesh::Entity entity); +bool has_refinement_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity parent); +void get_refinement_immediate_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity parent, std::vector & children); +void get_refinement_leaf_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, std::vector & leaf_children); +void get_refinement_all_children(const stk::mesh::BulkData& stk_bulk, stk::mesh::Entity entity, std::vector & children); + +// Temporary method for manually correcting the relation permutation +void set_relation_permutation(stk::mesh::BulkData & mesh, stk::mesh::Entity from, stk::mesh::Entity to, stk::mesh::ConnectivityOrdinal to_ord, stk::mesh::Permutation to_permutation); + +std::pair +determine_shell_side_ordinal_and_permutation(const stk::mesh::BulkData & mesh, stk::mesh::Entity shell, stk::mesh::Entity side); + +stk::mesh::Permutation +determine_permutation(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity, const stk::mesh::Entity relative, const stk::mesh::ConnectivityOrdinal ordinal); + +std::pair +determine_ordinal_and_permutation(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity, const stk::mesh::Entity relative); + +inline stk::mesh::Entity find_entity_by_ordinal(const stk::mesh::BulkData &mesh, stk::mesh::Entity entity, stk::mesh::EntityRank rank, const unsigned ordinal) +{ + stk::mesh::ConnectivityOrdinal const* relative_ordinals = mesh.begin_ordinals(entity, rank); + stk::mesh::Entity const* relatives = mesh.begin(entity, rank); + const int num_relatives = mesh.num_connectivity(entity, rank); + for (int i = 0; i < num_relatives; ++i) + { + if (relative_ordinals[i] == ordinal) { + return relatives[i]; + } + } + return stk::mesh::Entity(); +} + +template +void pack_entities_for_owning_proc(const stk::mesh::BulkData & mesh, + const CONTAINER & entities, + stk::CommSparse &commSparse) +{ + stk::pack_and_communicate(commSparse,[&]() + { + for (auto entity : entities) + { + const int entityOwner = mesh.parallel_owner_rank(entity); + if (commSparse.parallel_rank() != entityOwner) + commSparse.send_buffer(entityOwner).pack(mesh.entity_key(entity)); + } + }); +} + +} // namespace krino + +#endif // Akri_MeshHelpers_h diff --git a/packages/krino/krino/krino_lib/Akri_MeshInputOptions.cpp b/packages/krino/krino/krino_lib/Akri_MeshInputOptions.cpp new file mode 100644 index 000000000000..aeda2c5e95eb --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshInputOptions.cpp @@ -0,0 +1,52 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino { + +MeshInputOptions::Registry MeshInputOptions::the_registry; + +std::shared_ptr +MeshInputOptions::get_or_create(const std::string & model_name) +{ + std::shared_ptr options = std::make_shared(model_name); + std::pair result = the_registry.insert(options); + + if ( ! result.second ) { + stk::RuntimeWarningAdHoc() << "A mesh database named '" << model_name + << "' has already been defined and will be reused"; + } + + return *result.first; +} + +MeshInputOptions * +MeshInputOptions::get(const std::string &model_name) +{ + MeshInputOptions *options = nullptr; + std::shared_ptr tmp = std::make_shared(model_name); + + Registry::iterator iter = the_registry.find(tmp); + + if ( iter != the_registry.end() ) + options = iter->get() ; + + return options; +} + +int MeshInputOptions::get_generated_mesh_spatial_dimension() const +{ + ThrowRequire(use_generated_mesh()); + return (my_generated_mesh_domain_type == GENERATED_2D_MESH_FOR_INTERFACE_BOUNDING_BOX || my_generated_mesh_domain.size() == 4) ? 2 : 3; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_MeshInputOptions.hpp b/packages/krino/krino/krino_lib/Akri_MeshInputOptions.hpp new file mode 100644 index 000000000000..203d4ee5d6bd --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshInputOptions.hpp @@ -0,0 +1,112 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MeshInputOptions_h +#define Akri_MeshInputOptions_h + +#include +#include +#include +#include +#include +#include + +namespace krino { + + class MeshInputOptions { + + public: + static std::shared_ptr get_or_create(const std::string & model_name); + static MeshInputOptions * get(const std::string & model_name); + + enum GeneratedMeshDomainType + { + NO_GENERATED_MESH=0, + GENERATED_MESH_FOR_SPECIFIED_DOMAIN, + GENERATED_2D_MESH_FOR_INTERFACE_BOUNDING_BOX, + GENERATED_3D_MESH_FOR_INTERFACE_BOUNDING_BOX + }; + + MeshInputOptions(const std::string & name) : + my_name(name), + my_filename("%B.g"), + my_filetype("exodusII"), + my_generated_mesh_domain_type(NO_GENERATED_MESH), + myGeneratedMeshStructureType(BoundingBoxMeshStructureType::CUBIC_BOUNDING_BOX_MESH), + my_generated_mesh_size(-1.0) {} + + const std::string & get_name() const { return my_name; } + bool is_valid() const + { + return !my_name.empty() && ((! my_filetype.empty() && ! my_filename.empty()) || use_generated_mesh()) ; + } + + void set_generated_mesh_structure_type(BoundingBoxMeshStructureType type) { myGeneratedMeshStructureType = type; } + BoundingBoxMeshStructureType get_generated_mesh_structure_type() const { return myGeneratedMeshStructureType; } + + bool use_generated_mesh() const { return my_generated_mesh_domain_type != NO_GENERATED_MESH; } + + void set_generated_mesh_domain_type(GeneratedMeshDomainType type) { my_generated_mesh_domain_type = type; } + GeneratedMeshDomainType get_generated_mesh_domain_type() const { return my_generated_mesh_domain_type; } + + int get_generated_mesh_spatial_dimension() const; + + void set_generated_mesh_size(double size) { my_generated_mesh_size = size; } + double get_generated_mesh_size() const { return my_generated_mesh_size; } + + void set_generated_mesh_element_type(stk::topology top) { my_generated_mesh_element_type = top; } + stk::topology get_generated_mesh_element_type() const { return my_generated_mesh_element_type; } + + void set_generated_mesh_domain(const std::vector & domain) { my_generated_mesh_domain = domain; } + const std::vector & get_generated_mesh_domain() const { return my_generated_mesh_domain; } + + void set_filename(std::string filename) { my_filename = filename; } + const std::string & get_filename() const { return my_filename; } + + void set_filetype(std::string type) { my_filetype = type; } + const std::string & get_filetype() const { return my_filetype; } + + void set_decomposition_method(std::string decomposition_method) { my_decomposition_method = decomposition_method; } + const std::string & get_decomposition_method() const { return my_decomposition_method; } + + void set_coordinate_system(std::string coordinate_system) { my_coordinate_system = coordinate_system; } + const std::string & get_coordinate_system() const { return my_coordinate_system; } + + void add_property(const Ioss::Property & property) { my_properties.add(property); } + Ioss::PropertyManager & get_properties() { return my_properties; } + + private: + struct compare_ptr { + bool operator()( std::shared_ptr const lhs , + std::shared_ptr const rhs ) const + { + return lhs.get() == nullptr ? rhs.get() != nullptr : + ( rhs.get() == nullptr ? false : lhs->get_name() < rhs->get_name() ); + } + }; + + typedef std::set, compare_ptr> Registry; + static Registry the_registry; + + private: + std::string my_name; + std::string my_filename; + std::string my_filetype; + GeneratedMeshDomainType my_generated_mesh_domain_type; + BoundingBoxMeshStructureType myGeneratedMeshStructureType; + std::vector my_generated_mesh_domain; + stk::topology my_generated_mesh_element_type = stk::topology::INVALID_TOPOLOGY; + double my_generated_mesh_size; + std::string my_decomposition_method; + std::string my_coordinate_system; + Ioss::PropertyManager my_properties; + }; + +} // namespace krino + +#endif /* Akri_MeshInputOptions_h */ diff --git a/packages/krino/krino/krino_lib/Akri_MeshSurface.cpp b/packages/krino/krino/krino_lib/Akri_MeshSurface.cpp new file mode 100644 index 000000000000..36a535fb3da4 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshSurface.cpp @@ -0,0 +1,1019 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace krino{ + +void Parallel_Facet_File_Reader::read(const std::string & read_description, const std::function & read_function) +{ + bool ok_locally = true; + + if (0 == stk::EnvData::parallel_rank() ) + { + my_input.exceptions(std::ifstream::failbit | std::ifstream::badbit); + try + { + read_function(); + } + catch (std::ifstream::failure & e) + { + ok_locally = false; + } + } + const bool ok_globally = stk::is_true_on_all_procs(stk::EnvData::parallel_comm(), ok_locally); + if (!ok_globally) + { + ThrowRuntimeError("Error " << read_description << " for file " << my_filename); + } +} + +void Parallel_Facet_File_Reader::open_file() +{ + read("opening file", [this](){my_input.open(my_filename.c_str());}); +} + +void Parallel_Facet_File_Reader::get_batch_size(const int local_num_facets, int & batch_size, int & num_batches) +{ + int num_facets = 0; + stk::all_reduce_sum( stk::EnvData::parallel_comm(), &local_num_facets, &num_facets, 1 ); + + const int min_batch_size = std::min(2048, num_facets); + batch_size = std::max(min_batch_size, 1+num_facets/stk::EnvData::parallel_size()); + num_batches = 1+num_facets/batch_size; + + if(krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "Reading " << num_facets << " facets, using " << num_batches << " batches of " << batch_size << "." << stk::diag::dendl; +} + +Faceted_Surface_From_File::Faceted_Surface_From_File(const std::string & surface_name, const stk::diag::Timer &parent_timer) +: Faceted_Surface(surface_name), + my_timer("Facet File Reader", parent_timer), + my_built_local_facets(false) +{ +} + +void Faceted_Surface_From_File::build_local_facets(const BoundingBox & proc_bbox) +{ + stk::diag::TimeBlock timer_(my_timer); + + if(my_built_local_facets) return; + + std::vector proc_bboxes; + BoundingBox::gather_bboxes( proc_bbox, proc_bboxes ); + + read_file(proc_bboxes); + my_built_local_facets = true; +} + +void Parallel_Facet_File_Reader::close_file() +{ + read("closing file", [this](){my_input.close();}); +} + +FACSurface::FACSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale) + : Faceted_Surface_From_File(surface_name, parent_timer), + my_reader(filename), + my_dist_sign(sign), + my_scale(scale) +{ + // Make sure the file is openable, but close it for now to avoid ulimit restrictions. + my_reader.open_file(); + my_reader.close_file(); +} + +BoundingBox +FACSurface::get_bounding_box() +{ + BoundingBox bbox; + + my_reader.open_file(); + + std::vector points; + my_reader.read("reading points", [this, &points](){read_points(points);}); + + for (auto && point : points) + { + bbox.accommodate(point); + } + + my_reader.close_file(); + + bbox.global_reduce(); + return bbox; +} + +void FACSurface::read_file(const std::vector & proc_bboxes) +{ + my_reader.open_file(); + + std::ifstream & input = my_reader.input(); + std::vector points; + my_reader.read("reading points", [this, &points](){read_points(points);}); + + int num_facets = 0; + my_reader.read("reading number of facets", [&input, &num_facets](){input >> num_facets; ThrowRequire(num_facets > 0);}); + + int batch_size = 0; + int num_batches = 0; + my_reader.get_batch_size(num_facets, batch_size, num_batches); + + for (int batch = 0; batch < num_batches; ++batch) + { + const int current_batch_size = std::min(batch_size, num_facets-batch*batch_size); + my_reader.read("reading facets", [this, &points, current_batch_size, num_facets](){read_facets(current_batch_size, num_facets, points);}); + parallel_distribute_facets(current_batch_size, proc_bboxes); + } + + my_reader.close_file(); +} + +void FACSurface::read_points(std::vector & points) +{ + std::ifstream & input = my_reader.input(); + int num_points; + input >> num_points; + ThrowRequire(num_points > 0); + points.reserve(num_points); + for ( int i = 0; i < num_points; i++ ) + { + int id; + double X, Y, Z; + input >> id; + ThrowRequire(id >= 0 && id < num_points); + input >> X >> Y >> Z; + points.emplace_back(X*my_scale[0], Y*my_scale[1], Z*my_scale[2]); + } +} + +void FACSurface::read_facets(const int batch_size, const int num_facets, const std::vector & points) +{ + std::ifstream & input = my_reader.input(); + const int num_points = points.size(); + for ( int i = 0; i < batch_size; ++i ) + { + int id; + int p1, p2, p3; + input >> id; + ThrowRequire(id >= 0 && id < num_facets); + input >> p1 >> p2 >> p3; + + ThrowRequire(p1 >= 0 && p1 < num_points); + ThrowRequire(p2 >= 0 && p2 < num_points); + ThrowRequire(p3 >= 0 && p3 < num_points); + + if (my_dist_sign == -1) + { + // permute to flip normal direction + int tmp = p1; + p1 = p2; + p2 = tmp; + } + std::unique_ptr facet = std::make_unique( points[p1], points[p2], points[p3] ); + add( std::move(facet) ); + } +} + +PLYSurface::PLYSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale) + : Faceted_Surface_From_File(surface_name, parent_timer), + my_reader(filename), + my_dist_sign(sign), + my_scale(scale) +{ + // Make sure the file is openable, but close it for now to avoid ulimit restrictions. + my_reader.open_file(); + my_reader.close_file(); +} + +BoundingBox PLYSurface::get_bounding_box() +{ + BoundingBox bbox; + + my_reader.open_file(); + + int num_points = 0; + int num_facets = 0; + + my_reader.read("reading file header", [this, &num_points, &num_facets](){read_header(num_points, num_facets);}); + + std::vector points; + my_reader.read("reading points", [this, num_points, &points](){read_points(num_points, points);}); + + for (auto && point : points) + { + bbox.accommodate(point); + } + + my_reader.close_file(); + + bbox.global_reduce(); + + return bbox; +} + +void PLYSurface::read_file(const std::vector & proc_bboxes) +{ + my_reader.open_file(); + + int num_points = 0; + int num_facets = 0; + + my_reader.read("reading file header", [this, &num_points, &num_facets](){read_header(num_points, num_facets);}); + + std::vector points; + my_reader.read("reading points", [this, num_points, &points](){read_points(num_points, points);}); + + int batch_size = 0; + int num_batches = 0; + my_reader.get_batch_size(num_facets, batch_size, num_batches); + + for (int batch = 0; batch < num_batches; ++batch) + { + const int current_batch_size = std::min(batch_size, num_facets-batch*batch_size); + my_reader.read("reading facets", + [this, &points, current_batch_size]() { read_facets(current_batch_size, points); }); + parallel_distribute_facets(current_batch_size, proc_bboxes); + } + + my_reader.close_file(); +} + +void PLYSurface::read_header(int & num_points, int & num_facets) +{ + std::ifstream & input = my_reader.input(); + num_points = 0; + num_facets = 0; + + // Read in the file identifier + std::string symbol; + input >> symbol; + ThrowRequire(symbol.compare("ply") == 0); + + while (symbol.compare("end_header") != 0) + { + ThrowErrorMsgIf(input.eof(), "Problem reading PLY file, reached end of file."); + input >> symbol; + if (symbol.compare("element") == 0) + { + input >> symbol; + if (symbol.compare("vertex") == 0) + { + input >> num_points; + } + else if (symbol.compare("face") == 0) + { + input >> num_facets; + } + } + } +} + +void PLYSurface::read_points(const int num_points, std::vector & points) +{ + std::ifstream & input = my_reader.input(); + points.clear(); + points.reserve(num_points); + for ( int i = 0; i < num_points; i++ ) + { + double X, Y, Z; + input >> X >> Y >> Z; + points.emplace_back(X*my_scale[0], Y*my_scale[1], Z*my_scale[2]); + } + // Move to start of next line to prepare for reading facets + std::string line; + std::getline(input,line); +} + +void PLYSurface::read_facets(const int batch_size, const std::vector & points) +{ + std::ifstream & input = my_reader.input(); + const unsigned num_points = points.size(); + std::string line; + for ( int i = 0; i < batch_size; ++i ) + { + unsigned num_facet_nodes; + unsigned p1, p2, p3; + std::getline(input,line); + std::stringstream linestream(line); + linestream >> num_facet_nodes; + ThrowRequireMsg(num_facet_nodes == 3, "Failed to read face connectivity correctly."); + linestream >> p1 >> p2 >> p3; + ThrowRequire(p1 < num_points); + ThrowRequire(p2 < num_points); + ThrowRequire(p3 < num_points); + + if (my_dist_sign == -1) + { + // permute to flip normal direction + int tmp = p1; + p1 = p2; + p2 = tmp; + } + std::unique_ptr facet = std::make_unique( points[p1], points[p2], points[p3] ); + add( std::move(facet) ); + } +} + +STLSurface::STLSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale) + : Faceted_Surface_From_File(surface_name, parent_timer), + my_is_ascii(true), + my_reader(filename), + my_dist_sign(sign), + my_scale(scale) +{ + // Make sure the file is openable, but close it for now to avoid ulimit restrictions. + my_reader.open_file(); + my_reader.close_file(); +} + +static std::unique_ptr build_facet(const std::array & pts, const int sign) +{ + unsigned p0 = 0; + unsigned p1 = 1; + unsigned p2 = 2; + if (sign == -1) + { + // permute to flip normal direction + p1 = 2; + p2 = 1; + } + + std::unique_ptr facet = std::make_unique( pts[p0], pts[p1], pts[p2] ); + return facet; +} + +static bool is_finite_normal(const Vector3d normal) +{ + bool finiteFlag = true; + if (!std::isfinite(normal[0]) || + !std::isfinite(normal[1]) || + !std::isfinite(normal[2]) ) + { + finiteFlag = false; + krinolog << "Krino::STLSurface found an invalid facet and is skipping." << std::endl; + krinolog << " facet normal " << normal[0] << " " << normal[1] << " " << normal[2] << std::endl; + } + return finiteFlag; +} + +static std::unique_ptr read_ascii_facet(std::ifstream & input, const Vector3d & scale, const int sign) +{ + std::string symbol, nx, ny, nz; + double X, Y, Z; + + // Read in the facet normal + input >> symbol; + ThrowRequire(symbol.compare("normal") == 0); + input >> nx >> ny >> nz; + const Vector3d normal(std::atof(nx.c_str()), std::atof(ny.c_str()), std::atof(nz.c_str())); + + // Read in the "outer loop" line + input >> symbol; + ThrowRequire(symbol.compare("outer") == 0); + input >> symbol; + ThrowRequire(symbol.compare("loop") == 0); + + // Read in the vertices + std::array pts; + for (int i=0; i<3; i++) { + input >> symbol; + ThrowRequire(symbol.compare("vertex") == 0); + input >> X >> Y >> Z; + + pts[i] = Vector3d(X*scale[0], Y*scale[1], Z*scale[2]); + } + + // Read in the "endloop" and "endfacet" lines + input >> symbol; + ThrowRequire(symbol.compare("endloop") == 0); + input >> symbol; + ThrowRequire(symbol.compare("endfacet") == 0); + + std::unique_ptr facet; + if (is_finite_normal(normal)) + { + facet = build_facet(pts, sign); + if (facet->degenerate()) + facet.reset(); + } + + return facet; +} + +static bool read_start_of_next_ascii_facet(std::ifstream & input) +{ + // Read the next line + std::string symbol; + input >> symbol; + return symbol.compare("facet") == 0; +} + +static float read_binary_float(std::ifstream& input) +{ + float val = 0; + input.read((char *) &val, sizeof(val)); + return val; +} + +static Vector3d read_binary_vector(std::ifstream& input) +{ + float x = read_binary_float(input); + float y = read_binary_float(input); + float z = read_binary_float(input); + return Vector3d(x, y, z); +} + +static std::unique_ptr read_binary_facet(std::ifstream & input, const Vector3d & scale, const int sign) +{ + const Vector3d normal = read_binary_vector(input); + + std::array pts; + for (auto && pt : pts) + { + const Vector3d vec = read_binary_vector(input); + pt = Vector3d(vec[0]*scale[0], vec[1]*scale[1], vec[2]*scale[2]); + } + + char dummy[2]; + input.read(dummy, 2); + + std::unique_ptr facet; + if (is_finite_normal(normal)) + { + facet = build_facet(pts, sign); + if (facet->degenerate()) + facet.reset(); + } + + return facet; +} + +BoundingBox +STLSurface::get_bounding_box() +{ + BoundingBox bbox; + + my_reader.open_file(); + + my_reader.read("reading file header", [this](){read_header();}); + my_is_ascii = stk::is_true_on_all_procs(stk::EnvData::parallel_comm(), my_is_ascii); + + if (my_is_ascii) + { + my_reader.read("reading facets", [this, &bbox](){bbox = get_ascii_facet_bounding_box();}); + } + else + { + unsigned numFacets = 0; + my_reader.read("reading num facets", [this, &numFacets](){numFacets = read_num_binary_facets();}); + my_reader.read("reading facets", [this, &bbox, numFacets](){bbox = get_binary_facet_bounding_box(numFacets);}); + } + + my_reader.close_file(); + + bbox.global_reduce(); + return bbox; +} + +void +STLSurface::read_file(const std::vector & proc_bboxes) +{ + my_reader.open_file(); + + my_reader.read("reading file header", [this](){read_header();}); + my_is_ascii = stk::is_true_on_all_procs(stk::EnvData::parallel_comm(), my_is_ascii); + + unsigned numBinaryFacets = 0; + if (!my_is_ascii) + my_reader.read("reading num facets", [this, &numBinaryFacets](){numBinaryFacets = read_num_binary_facets();}); + + const unsigned maxBatchSize = 8192; + + unsigned numValidFacetsRead = 0; + bool done = false; + while (!done) + { + unsigned batchSize = 0; + + if (my_is_ascii) + { + my_reader.read("reading facets", [this, &batchSize](){batchSize = read_ascii_facets(maxBatchSize);}); + } + else + { + my_reader.read("reading facets", [this, &batchSize, &numBinaryFacets](){batchSize = read_binary_facets(maxBatchSize, numBinaryFacets);}); + } + + const unsigned localBatchSize = batchSize; + stk::all_reduce_max( stk::EnvData::parallel_comm(), &localBatchSize, &batchSize, 1 ); + numValidFacetsRead += batchSize; + + parallel_distribute_facets(batchSize, proc_bboxes); + + done = batchSize < maxBatchSize; + } + + my_reader.close_file(); + + krinolog << "Read " << (my_is_ascii ? "ASCII" : "binary") << " STL file " << my_reader.filename() << " with " << numValidFacetsRead << " valid facets." << stk::diag::dendl; +} + +void +STLSurface::read_header() +{ + std::ifstream & input = my_reader.input(); + + std::string symbol; + input >> symbol; + my_is_ascii = symbol.compare("solid") == 0; + + if (my_is_ascii) + { + // Read in strings until you get to facet + while (symbol.compare("facet") != 0) + { + ThrowErrorMsgIf(input.eof(), "Problem reading STL file, no facets found."); + input >> symbol; + } + krinolog << "Reading ASCII STL file." << stk::diag::dendl; + } + else + { + char header_info[80] = ""; + input.clear(); + input.seekg(0); + input.read(header_info, 80); + ThrowErrorMsgIf(!input.good(), "Problem reading STL file, cannot read binary file header."); + } +} + +unsigned STLSurface::read_num_binary_facets() +{ + ThrowAssert(!my_is_ascii); + std::ifstream & input = my_reader.input(); + unsigned numFacets = 0; + input.read((char *) &numFacets, sizeof(numFacets)); + ThrowErrorMsgIf(!input.good(), "Problem reading STL file, cannot read number of facets."); + krinolog << "Reading binary STL file with " << numFacets << " facets." << stk::diag::dendl; + return numFacets; +} + +unsigned STLSurface::read_ascii_facets(const unsigned max_batch_size) +{ + std::ifstream & input = my_reader.input(); + + unsigned count = 0; + bool done = false; + while (!done) + { + std::unique_ptr facet = read_ascii_facet(input, my_scale, my_dist_sign); + if (facet) + { + add(std::move(facet)); + ++count; + } + done = (!read_start_of_next_ascii_facet(input) || count >= max_batch_size); + } + return count; +} + +unsigned STLSurface::read_binary_facets(const unsigned maxBatchSize, unsigned & numRemainingInFile) +{ + std::ifstream & input = my_reader.input(); + + unsigned count = 0; + bool done = numRemainingInFile == 0; + while (!done) + { + std::unique_ptr facet = read_binary_facet(input, my_scale, my_dist_sign); + if (facet) + { + add(std::move(facet)); + ++count; + } + done = (--numRemainingInFile == 0 || count >= maxBatchSize); + } + + return count; +} + +BoundingBox STLSurface::get_ascii_facet_bounding_box() +{ + std::ifstream & input = my_reader.input(); + + BoundingBox bbox; + + bool done = false; + while (!done) + { + std::unique_ptr facet = read_ascii_facet(input, my_scale, my_dist_sign); + if (facet) + bbox.accommodate(facet->bounding_box()); + done = !read_start_of_next_ascii_facet(input); + } + return bbox; +} + +BoundingBox STLSurface::get_binary_facet_bounding_box(const unsigned numFacets) +{ + std::ifstream & input = my_reader.input(); + + BoundingBox bbox; + + for (unsigned count=0; count facet = read_binary_facet(input, my_scale, my_dist_sign); + if (facet) + bbox.accommodate(facet->bounding_box()); + } + return bbox; +} + +EXOSurface::EXOSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale) + : Faceted_Surface_From_File(surface_name, parent_timer), + my_filename(filename), + my_dist_sign(sign), + my_scale(scale) +{ +} + +BoundingBox +EXOSurface::get_bounding_box() +{ + BoundingBox bbox; + + std::vector xyz; + std::unique_ptr io; + if ( 0 == stk::EnvData::parallel_rank() ) + { + /* open file */ + Ioss::DatabaseIO *db = Ioss::IOFactory::create("exodusII", my_filename.c_str(), Ioss::READ_MODEL, MPI_COMM_SELF); + if ( !db ) { + ThrowRuntimeError("error reading file " << my_filename); + } + io = std::make_unique(db, "EXOSurface IC Region"); + + /* exodus description */ + int num_dim = io->get_property("spatial_dimension").get_int(); + int num_nodes = io->get_property("node_count").get_int(); + + ThrowAssert( 3 == num_dim ); + + /* generate coordinates */ + xyz.resize(num_nodes*num_dim); + + Ioss::NodeBlock *nb = io->get_node_blocks()[0]; + nb->get_field_data("mesh_model_coordinates", xyz); + + for (int n = 0; n & proc_bboxes) +{ + const int nodes_per_elem = 3; + int num_elem_blk = 0; + std::vector xyz; + std::vector nmap; + std::unique_ptr io; + if ( 0 == stk::EnvData::parallel_rank() ) + { + /* open file */ + Ioss::DatabaseIO *db = Ioss::IOFactory::create("exodusII", my_filename.c_str(), Ioss::READ_MODEL, MPI_COMM_SELF); + if ( !db ) { + ThrowRuntimeError("error reading file " << my_filename); + } + io = std::make_unique(db, "EXOSurface IC Region"); + + krinolog << "opened file " << my_filename << " for reading..." << std::endl; + + /* exodus description */ + int num_dim = io->get_property("spatial_dimension").get_int(); + int num_nodes = io->get_property("node_count").get_int(); + int num_elem = io->get_property("element_count").get_int(); + num_elem_blk = io->get_property("element_block_count").get_int(); + + krinolog + << "num dim = " << num_dim + << ", num nodes = " << num_nodes + << ", num elems = " << num_elem + << ", num elem blks = " << num_elem_blk << std::endl; + + ThrowAssert( 3 == num_dim ); + + /* generate coordinates */ + xyz.resize(num_nodes*num_dim); + nmap.resize(num_nodes); + + Ioss::NodeBlock *nb = io->get_node_blocks()[0]; + nb->get_field_data("mesh_model_coordinates", xyz); + nb->get_field_data("ids", nmap); + } + + const int local_num_elem_blk = num_elem_blk; + stk::all_reduce_max( stk::EnvData::parallel_comm(), &local_num_elem_blk, &num_elem_blk, 1 ); + + + for (int blk = 0; blk < num_elem_blk; blk++ ) + { + int num_elem_in_blk = 0; + std::vector conn; + + if ( 0 == stk::EnvData::parallel_rank() ) + { + Ioss::ElementBlockContainer ebs = io->get_element_blocks(); + Ioss::ElementBlock *eb = ebs[blk]; + num_elem_in_blk = eb->get_property("entity_count").get_int(); + + std::string eb_name = eb->name(); + krinolog + << "Reading elem blk #" << blk+1 + << " with name " << eb_name << "..." << std::endl; + + int nodes_per_elem_in_blk = eb->get_property("topology_node_count").get_int(); + ThrowAssert( nodes_per_elem_in_blk == nodes_per_elem ); + + conn.resize(num_elem_in_blk*nodes_per_elem_in_blk); + + krinolog + << " num elem in blk = " << num_elem_in_blk + << ", nodes per elem in blk = " << nodes_per_elem_in_blk << std::endl; + + eb->get_field_data("connectivity", conn); + } + + int batch_size = 0; + int num_batches = 0; + Parallel_Facet_File_Reader::get_batch_size(num_elem_in_blk, batch_size, num_batches); + + for (int batch = 0; batch < num_batches; ++batch) + { + const int current_batch_size = std::min(batch_size, num_elem_in_blk-batch*batch_size); + if ( 0 == stk::EnvData::parallel_rank() ) + { + Vector3d pt[3]; + for ( int e = 0; e < current_batch_size; e++ ) + { + for ( int j = 0; j < nodes_per_elem; j++ ) + { + const int nodeid = conn[e*nodes_per_elem + j]; + const int n = std::distance(nmap.begin(), std::find(nmap.begin(), nmap.end(), nodeid)); + double nodeX = xyz[3*n+0]; + double nodeY = xyz[3*n+1]; + double nodeZ = xyz[3*n+2]; + pt[j] = Vector3d( nodeX*my_scale[0], nodeY*my_scale[1], nodeZ*my_scale[2] ); + } + + unsigned p0 = 0; + unsigned p1 = 1; + unsigned p2 = 2; + if (my_dist_sign == -1) + { + // permute to flip normal direction + p1 = 2; + p2 = 1; + } + + std::unique_ptr facet = std::make_unique( pt[p0], pt[p1], pt[p2] ); + add( std::move(facet) ); + } + } + parallel_distribute_facets(current_batch_size, proc_bboxes); + } + } +} + +MeshSurface::MeshSurface(const stk::mesh::MetaData & meta, + const stk::mesh::Field& coord_ref, + const stk::mesh::Selector & surface_selector, + const int sign) + : Faceted_Surface("Mesh surface"), + my_sign(sign), + my_mesh_meta(meta), + my_coord_ref(coord_ref), + my_surface_selector(surface_selector) +{ +} + +void +MeshSurface::build_local_facets(const BoundingBox & proc_bbox) +{ + /* %TRACE[ON]% */ Trace trace__("krino::MeshSurface::build_local_facets()"); /* %TRACE% */ + const stk::mesh::BulkData & mesh = my_mesh_meta.mesh_bulk_data(); + stk::mesh::Selector active_locally_owned_selector = + (NULL != my_mesh_meta.get_part("ACTIVE_CONTEXT_BIT")) ? + (*my_mesh_meta.get_part("ACTIVE_CONTEXT_BIT") & my_mesh_meta.locally_owned_part()) : + stk::mesh::Selector(my_mesh_meta.locally_owned_part()); + + stk::mesh::Selector active_locally_owned_part_selector = active_locally_owned_selector & my_surface_selector; + + stk::mesh::BucketVector const& buckets = mesh.get_buckets( my_mesh_meta.side_rank(), active_locally_owned_part_selector); + + clear(); + + stk::mesh::BucketVector::const_iterator ib = buckets.begin(); + stk::mesh::BucketVector::const_iterator ib_end = buckets.end(); + + for ( ; ib != ib_end ; ++ib ) + { + const stk::mesh::Bucket & b = **ib; + const unsigned length = b.size(); + + for ( unsigned iSide = 0; iSide < length; ++iSide ) + { + stk::mesh::Entity side = b[iSide]; + + stk::topology side_topology = mesh.bucket(side).topology(); + if (stk::topology::TRI_3 == side_topology) + { + add_facet3d(mesh,side,0,1,2); + } + else if (stk::topology::QUAD_4 == side_topology) + { + add_quad3d(mesh,side,0,1,2,3); + } + else if (stk::topology::TRI_6 == side_topology) + { + add_facet3d(mesh,side,0,3,5); + add_facet3d(mesh,side,1,4,3); + add_facet3d(mesh,side,2,5,4); + add_facet3d(mesh,side,3,4,5); + } + else if (stk::topology::LINE_2 == side_topology) + { + add_facet2d(mesh,side,0,1); + } + else if (stk::topology::LINE_3 == side_topology) + { + add_facet2d(mesh,side,0,2); + add_facet2d(mesh,side,2,1); + } + else + { + ThrowRuntimeError("Elements with side topology " << side_topology.name() << " not supported for mesh surface initialization."); + } + } + } +} + +void +MeshSurface::add_facet2d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1) +{ + ThrowAssert(2 == my_mesh_meta.spatial_dimension()); + Vector3d pt[2]; + + if (my_sign == -1) + { + // permute to flip normal direction + const unsigned tmp = p0; + p0 = p1; + p1 = tmp; + } + + const stk::mesh::Entity* side_nodes = mesh.begin_nodes(side); + + const double * pt0 = stk::mesh::field_data(my_coord_ref, side_nodes[p0]); + const double * pt1 = stk::mesh::field_data(my_coord_ref, side_nodes[p1]); + + pt[0][0] = pt0[0]; + pt[0][1] = pt0[1]; + pt[0][2] = 0.0; + pt[1][0] = pt1[0]; + pt[1][1] = pt1[1]; + pt[1][2] = 0.0; + + add_facet2d(pt[0], pt[1]); +} + +void +MeshSurface::add_facet3d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1, unsigned p2) +{ + ThrowAssert(3 == my_mesh_meta.spatial_dimension()); + Vector3d pt[3]; + + if (my_sign == -1) + { + // permute to flip normal direction + const unsigned tmp = p1; + p1 = p2; + p2 = tmp; + } + + const stk::mesh::Entity* side_nodes = mesh.begin_nodes(side); + + pt[0] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p0])); + pt[1] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p1])); + pt[2] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p2])); + + add_facet3d(pt[0], pt[1], pt[2]); +} + +void +MeshSurface::add_quad3d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1, unsigned p2, unsigned p3) +{ + ThrowAssert(3 == my_mesh_meta.spatial_dimension()); + Vector3d pt[5]; + + if (my_sign == -1) + { + // permute to flip normal direction + const unsigned tmp = p1; + p1 = p3; + p3 = tmp; + } + + const stk::mesh::Entity* side_nodes = mesh.begin_nodes(side); + + pt[0] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p0])); + pt[1] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p1])); + pt[2] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p2])); + pt[3] = Vector3d(stk::mesh::field_data(my_coord_ref, side_nodes[p3])); + + // scale is the RMS of the diagonal lengths, sqr_scale is scale*scale, or the average of the lengths squared + const double sqr_scale = 0.5*((pt[0]-pt[2]).length_squared()+(pt[1]-pt[3]).length_squared()); + // tol is 1e-4, sqr_tol is 1e-8 + const double sqr_tol = 1.e-8; + // Test is that the distance between the midpoints of the 2 diagonals is less than tol*scale + const bool is_planar = (0.5*(pt[0]+pt[2])-0.5*(pt[1]+pt[3])).length_squared() < sqr_tol*sqr_scale; + //const bool is_planar = false; // conservative approach, forces 4 facets per quad + + if (is_planar) + { + add_facet3d(pt[0], pt[1], pt[2]); + add_facet3d(pt[0], pt[2], pt[3]); + } + else + { + pt[4] = 0.25 * (pt[0]+pt[1]+pt[2]+pt[3]); + add_facet3d(pt[0], pt[1], pt[4]); + add_facet3d(pt[1], pt[2], pt[4]); + add_facet3d(pt[2], pt[3], pt[4]); + add_facet3d(pt[3], pt[0], pt[4]); + } +} + +void +MeshSurface::add_facet2d(Vector3d & p0, Vector3d & p1) +{ + ThrowAssert(2 == my_mesh_meta.spatial_dimension()); + + std::unique_ptr facet = std::make_unique( p0, p1 ); + add( std::move(facet) ); +} + +void +MeshSurface::add_facet3d(Vector3d & p0, Vector3d & p1, Vector3d & p2) +{ + ThrowAssert(3 == my_mesh_meta.spatial_dimension()); + + std::unique_ptr facet = std::make_unique( p0, p1, p2 ); + add( std::move(facet) ); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_MeshSurface.hpp b/packages/krino/krino/krino_lib/Akri_MeshSurface.hpp new file mode 100644 index 000000000000..7f2ec3c199c7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MeshSurface.hpp @@ -0,0 +1,177 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MeshSurface_h +#define Akri_MeshSurface_h + +#include + +#include +#include + +#include +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class Entity; } } +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace mesh { class Selector; } } + +namespace krino { + +class MeshSurface : public Faceted_Surface { +public: + MeshSurface(const stk::mesh::MetaData & meta, + const stk::mesh::Field& coord_ref, + const stk::mesh::Selector & surface_selector, + const int sign); + + virtual ~MeshSurface() {} + virtual void build_local_facets(const BoundingBox & proc_bbox) override; + +protected: + void add_facet2d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1); + void add_facet3d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1, unsigned p2); + void add_quad3d(const stk::mesh::BulkData& mesh, stk::mesh::Entity side, unsigned p0, unsigned p1, unsigned p2, unsigned p3); + void add_facet2d(Vector3d & p0, Vector3d & p1); + void add_facet3d(Vector3d & p0, Vector3d & p1, Vector3d & p2); + +private: + int my_sign; + const stk::mesh::MetaData & my_mesh_meta; + const stk::mesh::Field& my_coord_ref; + const stk::mesh::Selector my_surface_selector; +}; + +class Parallel_Facet_File_Reader { +public: + Parallel_Facet_File_Reader(const std::string & in_filename) : my_filename(in_filename) {} + + static void get_batch_size(const int local_num_facets, int & batch_size, int & num_batches); + + std::ifstream & input() { return my_input; } + const std::string & filename() const { return my_filename; } + + void open_file(); + void close_file(); + void read(const std::string & read_description, const std::function & read_function); + +private: + std::string my_filename; + std::ifstream my_input; +}; + +class Faceted_Surface_From_File : public Faceted_Surface { +public: + Faceted_Surface_From_File(const std::string & surface_name, const stk::diag::Timer &parent_timer); + virtual ~Faceted_Surface_From_File() {} + virtual void build_local_facets(const BoundingBox & proc_bbox) override; + virtual BoundingBox get_bounding_box() override = 0; + +protected: + virtual void read_file(const std::vector & proc_bboxes) = 0; +private: + stk::diag::Timer my_timer; + bool my_built_local_facets; +}; + +class STLSurface : public Faceted_Surface_From_File { +public: + STLSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale); + + virtual ~STLSurface() {} + virtual BoundingBox get_bounding_box() override; + +private: + virtual void read_file(const std::vector & proc_bboxes) override; + void read_header(); + unsigned read_num_binary_facets(); + unsigned read_ascii_facets(const unsigned max_batch_size); + unsigned read_binary_facets(const unsigned maxBatchSize, unsigned & numRemainingInFile); + BoundingBox get_ascii_facet_bounding_box(); + BoundingBox get_binary_facet_bounding_box(const unsigned numFacets); + +private: + bool my_is_ascii; + Parallel_Facet_File_Reader my_reader; + int my_dist_sign; + Vector3d my_scale; +}; + +class FACSurface : public Faceted_Surface_From_File { +public: + FACSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale); + + virtual ~FACSurface() {} + virtual BoundingBox get_bounding_box() override; + +private: + virtual void read_file(const std::vector & proc_bboxes) override; + void read_points(std::vector & points); + void read_facets(const int batch_size, const int num_facets, const std::vector & points); + +private: + Parallel_Facet_File_Reader my_reader; + int my_dist_sign; + Vector3d my_scale; +}; + +class PLYSurface : public Faceted_Surface_From_File { +public: + PLYSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale); + + virtual ~PLYSurface() {} + virtual BoundingBox get_bounding_box() override; + +private: + Parallel_Facet_File_Reader my_reader; + virtual void read_file(const std::vector & proc_bboxes) override; + void read_header(int & num_points, int & num_facets); + void read_points(const int num_points, std::vector & points); + void read_facets(const int batch_size, const std::vector & points); + +private: + int my_dist_sign; + Vector3d my_scale; +}; + +class EXOSurface : public Faceted_Surface_From_File { +public: + EXOSurface(const std::string & surface_name, + const stk::diag::Timer &parent_timer, + const std::string & filename, + const int sign, + const Vector3d & scale); + + virtual ~EXOSurface() {} + virtual BoundingBox get_bounding_box() override; + +private: + virtual void read_file(const std::vector & proc_bboxes) override; + +private: + std::string my_filename; + int my_dist_sign; + Vector3d my_scale; +}; + +} // namespace krino + +#endif // Akri_MeshSurface_h diff --git a/packages/krino/krino/krino_lib/Akri_MortonIndex.hpp b/packages/krino/krino/krino_lib/Akri_MortonIndex.hpp new file mode 100644 index 000000000000..4d811bbf1218 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_MortonIndex.hpp @@ -0,0 +1,58 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MortonIndex_h +#define Akri_MortonIndex_h + +#include +#include + +namespace krino { + +constexpr int MAX_VALID_MORTON3D_INDEX = 0x1fffff; + +uint64_t morton3d_encode_index(const int i) +{ + ThrowAssertMsg(i >= 0, "Index must be >= 0 to encode: " << i); + ThrowAssertMsg(i <= MAX_VALID_MORTON3D_INDEX, "Index must be <= " << MAX_VALID_MORTON3D_INDEX << " to encode: " << i); + uint64_t m = i & 0x1fffff; + m = (m | m << 32) & 0x001f00000000ffff; + m = (m | m << 16) & 0x001f0000ff0000ff; + m = (m | m << 8) & 0x100f00f00f00f00f; + m = (m | m << 4) & 0x10c30c30c30c30c3; + m = (m | m << 2) & 0x1249249249249249; + return m; +} + +int morton3d_decode_index(uint64_t m) +{ + m &= 0x1249249249249249; + m = (m ^ (m >> 2)) & 0x10c30c30c30c30c3; + m = (m ^ (m >> 4)) & 0x100f00f00f00f00f; + m = (m ^ (m >> 8)) & 0x001f0000ff0000ff; + m = (m ^ (m >> 16)) & 0x001f00000000ffff; + m = (m ^ (m >> 32)) & 0x1fffff; + return static_cast(m); +} + +uint64_t morton3d_encode_indices(const std::array & indices) +{ + return morton3d_encode_index(indices[2]) * 4 + morton3d_encode_index(indices[1]) * 2 + morton3d_encode_index(indices[0]); +} + +std::array morton3d_decode_indices(const uint64_t m) +{ + const int ix = morton3d_decode_index(m); + const int iy = morton3d_decode_index(m >> 1); + const int iz = morton3d_decode_index(m >> 2); + return {{ix,iy,iz}}; +} + +} // namespace krino + +#endif // Akri_MortonIndex_h diff --git a/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.cpp b/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.cpp new file mode 100644 index 000000000000..6f1f5d091d5c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.cpp @@ -0,0 +1,121 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino { + +static void pack_node_captured_domains_for_sharing_or_ghosting_procs(const stk::mesh::BulkData & mesh, + const stk::mesh::Entity node, + const std::vector & nodeCapturedDomains, + std::vector procsThatNeedToKnowAboutNode, + stk::CommSparse &commSparse) +{ + fill_procs_owning_or_sharing_or_ghosting_node(mesh, node, procsThatNeedToKnowAboutNode); + for (int procId : procsThatNeedToKnowAboutNode) + { + if (procId != mesh.parallel_rank()) + { + commSparse.send_buffer(procId).pack(mesh.identifier(node)); + commSparse.send_buffer(procId).pack(nodeCapturedDomains.size()); + for (int domain : nodeCapturedDomains) + commSparse.send_buffer(procId).pack(domain); + } + } +} + +static +void pack_all_node_captured_domains_for_sharing_or_ghosting_procs(const stk::mesh::BulkData & mesh, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + stk::CommSparse &commSparse) +{ + std::vector scratchVec; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto && entry : nodesToCapturedDomains) + { + stk::mesh::Entity node = entry.first; + if (mesh.parallel_owner_rank(node) == mesh.parallel_rank()) + { + const auto & nodeCapturedDomains = entry.second; + pack_node_captured_domains_for_sharing_or_ghosting_procs(mesh, node, nodeCapturedDomains, scratchVec, commSparse); + } + } + }); +} + +static +void pack_node_captured_domains_of_given_nodes_for_sharing_or_ghosting_procs(const stk::mesh::BulkData & mesh, + const std::vector & nodes, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + stk::CommSparse &commSparse) +{ + std::vector scratchVec; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto node : nodes) + { + if (mesh.parallel_owner_rank(node) == mesh.parallel_rank()) + { + const auto nodeCapturedDomains = nodesToCapturedDomains.at(node); + pack_node_captured_domains_for_sharing_or_ghosting_procs(mesh, node, nodeCapturedDomains, scratchVec, commSparse); + } + } + }); +} + +static +void unpack_snap_node_domains(const stk::mesh::BulkData & mesh, + NodeToCapturedDomainsMap & nodesToSnappedDomains, + stk::CommSparse &commSparse) +{ + std::vector nodeSnappedDomains; + + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + stk::mesh::EntityId nodeId; + commSparse.recv_buffer(procId).unpack(nodeId); + size_t numNodes; + commSparse.recv_buffer(procId).unpack(numNodes); + nodeSnappedDomains.resize(numNodes); + for (auto && domain : nodeSnappedDomains) + commSparse.recv_buffer(procId).unpack(domain); + + stk::mesh::Entity snapNode = mesh.get_entity(stk::topology::NODE_RANK, nodeId); + nodesToSnappedDomains[snapNode] = nodeSnappedDomains; + } + }); +} + +void communicate_node_captured_domains_for_given_nodes(const stk::mesh::BulkData & mesh, + const std::vector & nodes, + NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + stk::CommSparse commSparse(mesh.parallel()); + pack_node_captured_domains_of_given_nodes_for_sharing_or_ghosting_procs(mesh, nodes, nodesToCapturedDomains, commSparse); + unpack_snap_node_domains(mesh, nodesToCapturedDomains, commSparse); +} + +void communicate_node_captured_domains_for_all_nodes(const stk::mesh::BulkData & mesh, + NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + stk::CommSparse commSparse(mesh.parallel()); + pack_all_node_captured_domains_for_sharing_or_ghosting_procs(mesh, nodesToCapturedDomains, commSparse); + unpack_snap_node_domains(mesh, nodesToCapturedDomains, commSparse); +} + +} + + diff --git a/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.hpp b/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.hpp new file mode 100644 index 000000000000..7245a6e9398c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_NodeToCapturedDomains.hpp @@ -0,0 +1,31 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_NODETOCAPTUREDDOMAINS_H_ +#define KRINO_INCLUDE_AKRI_NODETOCAPTUREDDOMAINS_H_ +#include +#include +#include +#include + +namespace krino { + +typedef std::map> NodeToCapturedDomainsMap; + +void communicate_node_captured_domains_for_given_nodes(const stk::mesh::BulkData & mesh, + const std::vector & nodes, + NodeToCapturedDomainsMap & nodesToCapturedDomains); + +void communicate_node_captured_domains_for_all_nodes(const stk::mesh::BulkData & mesh, + NodeToCapturedDomainsMap & nodesToCapturedDomains); + +typedef std::map ElementToDomainMap; + +} + +#endif /* KRINO_INCLUDE_AKRI_NODETOCAPTUREDDOMAINS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_OrderedIdPair.hpp b/packages/krino/krino/krino_lib/Akri_OrderedIdPair.hpp new file mode 100644 index 000000000000..9f89f71a210a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_OrderedIdPair.hpp @@ -0,0 +1,50 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_ORDEREDIDPAIR_H_ +#define AKRI_ORDEREDIDPAIR_H_ + +#include +#include + +namespace krino { + +class OrderedIdPair { +public: + OrderedIdPair(stk::mesh::EntityId id0, stk::mesh::EntityId id1) + : my_ids(id0 < id1 ? id0 : id1, id0 < id1 ? id1 : id0) {} + + stk::mesh::EntityId first() const { return my_ids.first; } + stk::mesh::EntityId second() const { return my_ids.second; } + +private: + std::pair my_ids; +}; + +inline bool operator<(const OrderedIdPair lhs, const OrderedIdPair rhs) +{ + if(lhs.first() < rhs.first()) return true; + if(rhs.first() < lhs.first()) return false; + if(lhs.second() < rhs.second()) return true; + return false; +} + +inline bool operator==(const OrderedIdPair lhs, const OrderedIdPair rhs) +{ + return (lhs.first() == rhs.first()) && (lhs.second() == rhs.second()); +} + +inline bool operator!=(const OrderedIdPair lhs, const OrderedIdPair rhs) +{ + return !(lhs == rhs); +} + +} + + +#endif /* AKRI_ORDEREDIDPAIR_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_ParallelCommHelpers.hpp b/packages/krino/krino/krino_lib/Akri_ParallelCommHelpers.hpp new file mode 100644 index 000000000000..273e4ab441b7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ParallelCommHelpers.hpp @@ -0,0 +1,77 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_PARALLELCOMMHELPERS_H_ +#define KRINO_INCLUDE_AKRI_PARALLELCOMMHELPERS_H_ + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +// PACK_OP shoudl have an operator()(stk::CommBuffer & buffer, const stk::mesh::EntityKey & entity_key) +// UNPACK_OP should have an operator()(CommBuffer & buffer) +template +void communicate_with_shared_procs(const stk::mesh::BulkData& mesh, + const std::vector & local_entities, + PACK_OP pack_op, + UNPACK_OP unpack_op) +{ + // The input vector, local_entities, must only contain entities that are locally_owned or globally_shared (or both). + + stk::CommSparse comm_spec(mesh.parallel()); + std::vector sharing_procs; + + for (int phase=0;phase<2;++phase) + { + for (auto&& local_entity : local_entities) + { + ThrowAssert(mesh.bucket(local_entity).owned() || mesh.bucket(local_entity).shared()); + mesh.comm_shared_procs(local_entity, sharing_procs); + for (auto&& sharing_proc : sharing_procs) + { + if (sharing_proc != mesh.parallel_rank()) + { + pack_op(comm_spec.send_buffer(sharing_proc), mesh.entity_key(local_entity)); + } + } + } + + if ( phase == 0 ) + { + comm_spec.allocate_buffers(); + } + else + { + comm_spec.communicate(); + } + } + + for(int i = 0; i < mesh.parallel_size(); ++i) + { + if(i != mesh.parallel_rank()) + { + auto & recv_buffer = comm_spec.recv_buffer(i); + while(recv_buffer.remaining()) + { + unpack_op(recv_buffer); + } + } + } +} + +} + +#endif /* KRINO_INCLUDE_AKRI_PARALLELCOMMHELPERS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.cpp b/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.cpp new file mode 100644 index 000000000000..4881453ec8a3 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.cpp @@ -0,0 +1,30 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino +{ + +ParallelErrorMessage::ParallelErrorMessage(const stk::Parallel & c) : comm(c) {} + +std::pair ParallelErrorMessage::gather_message() const +{ + const std::string & local_str = local_message.str(); + + std::ostringstream result; + stk::all_write_string(comm.parallel(), result, local_str); + + int err = result.str().size(); + int global_err; + stk::all_reduce_sum(comm.parallel(), &err, &global_err, 1); + + return make_pair(static_cast(global_err), result.str()); +} +} diff --git a/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.hpp b/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.hpp new file mode 100644 index 000000000000..b2b76e3a4ee0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ParallelErrorMessage.hpp @@ -0,0 +1,43 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_PARALLELERRORMESSAGE_H_ +#define KRINO_INCLUDE_AKRI_PARALLELERRORMESSAGE_H_ + +#include +#include +#include + +namespace krino +{ + +class ParallelErrorMessage +{ +public: + ParallelErrorMessage(const stk::Parallel & c); + + template ParallelErrorMessage & operator<<(const T & t) + { + local_message << t; + return *this; + } + + // This will gather the messages from all ranks to rank 0 where it can be output. + // and additionally return a parallel-consistent bool for whether or not any errors + // were logged. + std::pair gather_message() const; + + bool have_local_error() const { return !local_message.str().empty(); } + +private: + const stk::Parallel comm; + std::ostringstream local_message; +}; +} + +#endif /* KRINO_INCLUDE_AKRI_PARALLELERRORMESSAGE_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_ParentsToChildMapper.cpp b/packages/krino/krino/krino_lib/Akri_ParentsToChildMapper.cpp new file mode 100644 index 000000000000..6f217818262f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ParentsToChildMapper.cpp @@ -0,0 +1,188 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +static bool determine_if_mesh_has_higher_order_midside_nodes_with_level_set_locally(const stk::mesh::BulkData & mesh, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + // Assume we can check master element on one bucket and get the right answer + + for ( auto && bucket_ptr : mesh.get_buckets(stk::topology::ELEMENT_RANK, phaseSupport.get_all_decomposed_blocks_selector()) ) + { + if (bucket_ptr->topology() != bucket_ptr->topology().base()) + { + for (int ls_index = 0; ls_index < cdfemSupport.num_ls_fields(); ++ls_index) + { + stk::topology fieldTopology = MasterElementDeterminer::get_field_topology(*bucket_ptr, cdfemSupport.ls_field(ls_index).isovar); + if (fieldTopology != fieldTopology.base()) + return true; + } + } + } + return false; +} + +void fill_edge_nodes( + const stk::mesh::BulkData & mesh, + const stk::mesh::Entity node0, + const stk::mesh::Entity node1, + const ParentsToChildMapper & parentToChildMapper, + std::vector & edgeNodes) +{ + stk::mesh::Entity child = parentToChildMapper.get_child(mesh, node0, node1); + + if (mesh.is_valid(child)) + { + ThrowRequire(child != node0); + ThrowRequire(child != node1); + fill_edge_nodes(mesh, node0,child, parentToChildMapper, edgeNodes); + fill_edge_nodes(mesh, child,node1, parentToChildMapper, edgeNodes); + } + else + { + if (edgeNodes.empty()) + { + edgeNodes.push_back(node0); + } + edgeNodes.push_back(node1); + } +} + +static void fill_edge_nodes_and_positions( + const double pos0, stk::mesh::Entity node0, + const double pos1, stk::mesh::Entity node1, + std::vector & edgeNodes, + std::vector & edgeNodePositions) +{ + if (edgeNodePositions.empty()) + { + edgeNodePositions.push_back(pos0); + edgeNodes.push_back(node0); + } + edgeNodePositions.push_back(pos1); + edgeNodes.push_back(node1); +} + +static void fill_edge_nodes_and_positions( + const stk::mesh::BulkData & mesh, + const double pos0, stk::mesh::Entity node0, + const double pos1, stk::mesh::Entity node1, + const ParentsToChildMapper & parent_child_mapper, + std::vector & edgeNodes, + std::vector & edgeNodePositions) +{ + stk::mesh::Entity child = parent_child_mapper.get_child(mesh, node0, node1); + + if (mesh.is_valid(child)) + { + ThrowRequire(child != node0); + ThrowRequire(child != node1); + const double child_rel_pos = compute_child_position(mesh, child, node0, node1); + const double child_abs_pos = pos0 * (1.-child_rel_pos) + pos1 * child_rel_pos; + fill_edge_nodes_and_positions(mesh,pos0,node0,child_abs_pos,child, parent_child_mapper, edgeNodes, edgeNodePositions); + fill_edge_nodes_and_positions(mesh,child_abs_pos,child,pos1,node1, parent_child_mapper, edgeNodes, edgeNodePositions); + } + else + { + fill_edge_nodes_and_positions(pos0, node0, pos1, node1, edgeNodes, edgeNodePositions); + } +} + +void fill_edge_nodes_and_positions(const stk::mesh::BulkData & mesh, + stk::mesh::Entity node0, stk::mesh::Entity node1, + const ParentsToChildMapper & parent_child_mapper, + std::vector & edgeNodes, + std::vector & edgeNodePositions) +{ + edgeNodes.clear(); + edgeNodePositions.clear(); + fill_edge_nodes_and_positions(mesh, 0.0, node0, 1.0, node1, parent_child_mapper, edgeNodes, edgeNodePositions); +} + +void fill_linear_edge_nodes_and_positions(stk::mesh::Entity node0, stk::mesh::Entity node1, + std::vector & edgeNodes, + std::vector & edgeNodePositions) +{ + edgeNodes.clear(); + edgeNodePositions.clear(); + fill_edge_nodes_and_positions(0.0, node0, 1.0, node1, edgeNodes, edgeNodePositions); +} + + +void ParentsToChildMapper::build_map(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & activePart, + const CDFEM_Support & cdfemSupport, + const Phase_Support & phaseSupport) +{ + const bool addHigherOrderMidsideNodes = stk::is_true_on_any_proc(mesh.parallel(), determine_if_mesh_has_higher_order_midside_nodes_with_level_set_locally(mesh, cdfemSupport, phaseSupport)); + + stk::mesh::Selector elementSelectorForParentChildMapper = activePart & mesh.mesh_meta_data().locally_owned_part(); + + build_map(mesh, cdfemSupport.get_parent_node_ids_field(), elementSelectorForParentChildMapper, addHigherOrderMidsideNodes); +} + +void ParentsToChildMapper::build_map(const stk::mesh::BulkData & mesh, const FieldRef & parent_ids_field, const stk::mesh::Selector & elementSelector, bool add_higher_order_midside_nodes) +{ + my_parents_to_child_map.clear(); + + if (parent_ids_field.valid()) + { + const auto & field_selector = stk::mesh::selectField(parent_ids_field); + + ThrowRequire(!mesh.in_modifiable_state()); + + const auto & buckets = mesh.get_buckets(stk::topology::NODE_RANK, field_selector); + for(auto && b_ptr : buckets) + { + for(unsigned i=0; i < b_ptr->size(); ++i) + { + const stk::mesh::Entity child_node = (*b_ptr)[i]; + const auto parent_ids = get_edge_node_parent_ids(mesh, parent_ids_field, child_node); + my_parents_to_child_map[{parent_ids[0], parent_ids[1]}] = mesh.identifier(child_node); + } + } + } + + if (add_higher_order_midside_nodes) + { + // Add higher order edge "children" + for(auto && b_ptr : mesh.get_buckets(stk::topology::ELEMENT_RANK, elementSelector)) + { + const stk::topology elem_topology = b_ptr->topology(); + if (elem_topology == stk::topology::TRIANGLE_6_2D || elem_topology == stk::topology::TETRAHEDRON_10) + { + for (auto elem : *b_ptr) + { + const stk::mesh::Entity * elem_nodes = mesh.begin_nodes(elem); + for (unsigned edge_i=0; edge_i + +#include +#include +#include + +namespace krino { class FieldRef; } + +namespace krino { + +class CDFEM_Support; +class Phase_Support; + +class ParentsToChildMapper +{ +public: + ParentsToChildMapper() = default; + + void build_map(const stk::mesh::BulkData & mesh, const stk::mesh::Part & activePart, const CDFEM_Support & cdfemSupport, const Phase_Support & phaseSupport); + void build_map(const stk::mesh::BulkData & mesh, const FieldRef & parent_ids_field, const stk::mesh::Selector & elementSelector, bool add_higher_order_midside_nodes); + + bool get_child_id(const stk::mesh::EntityId parent0, + const stk::mesh::EntityId parent1, + stk::mesh::EntityId & child) const + { + const auto it = my_parents_to_child_map.find({parent0, parent1}); + if(it == my_parents_to_child_map.end()) return false; + child = it->second; + return true; + } + + stk::mesh::Entity get_child(const stk::mesh::BulkData & mesh, const stk::mesh::Entity parent0, + const stk::mesh::Entity parent1) const + { + const auto it = + my_parents_to_child_map.find({mesh.identifier(parent0), mesh.identifier(parent1)}); + if(it == my_parents_to_child_map.end()) return stk::mesh::Entity(); + return mesh.get_entity(stk::topology::NODE_RANK, it->second); + } + +private: + typedef OrderedIdPair ParentsToChildKey; + typedef std::map ParentsToChildMap; + ParentsToChildMap my_parents_to_child_map; +}; + +void fill_edge_nodes( + const stk::mesh::BulkData & mesh, + const stk::mesh::Entity node0, + const stk::mesh::Entity node1, + const ParentsToChildMapper & parentToChildMapper, + std::vector & edgeNodes); + +void fill_edge_nodes_and_positions(const stk::mesh::BulkData & mesh, + stk::mesh::Entity node0, stk::mesh::Entity node1, + const ParentsToChildMapper & parent_child_mapper, + std::vector & edgeNodes, + std::vector & edgeNodePositions); + +void fill_linear_edge_nodes_and_positions(stk::mesh::Entity node0, + stk::mesh::Entity node1, + std::vector & edgeNodes, + std::vector & edgeNodePositions); + +} // namespace krino + +#endif /* AKRI_PARENTSTOCHILDMAPPER_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_PhaseTag.cpp b/packages/krino/krino/krino_lib/Akri_PhaseTag.cpp new file mode 100644 index 000000000000..5f029c295be4 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_PhaseTag.cpp @@ -0,0 +1,112 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +namespace krino{ + +std::map LS_SideTag::the_composite_ls_map; + +void LS_SideTag::declare_composite(const LevelSet_Identifier constituent, const LevelSet_Identifier composite) +{ + LS_SideTag constituent_tag(constituent,0); + LS_SideTag composite_tag(composite,0); + + // verbose version of operator[] to avoid needing default constructor for LevelSet_Interface + auto existing_entry = the_composite_ls_map.find(constituent_tag.my_ls_identifier); + if (existing_entry != the_composite_ls_map.end()) + { + existing_entry->second = composite_tag.my_ls_identifier; + } + else + { + the_composite_ls_map.insert(std::make_pair(constituent_tag.my_ls_identifier, composite_tag.my_ls_identifier)); + } + +} + +std::ostream& +operator<<(std::ostream & os, const LS_SideTag & ls_side) +{ + /* %TRACE[NONE]% */ /* %TRACE% */ + os << "(" << ls_side.my_ls_identifier << "," << ls_side.my_ls_sign << ")"; + return os; +} + +std::ostream& +operator<<(std::ostream & os, const PhaseTag & phase) +{ + /* %TRACE[NONE]% */ /* %TRACE% */ + os << " with ls sides: "; + const std::set & ls_sides = phase.ls_sides(); + for (std::set::const_iterator it = ls_sides.begin(); it != ls_sides.end(); ++it) + { + os << *it << " "; + } + return os; +} + +bool PhaseTag::contain(const PhaseTag & phase) const +{ + // This phase is considered to contain "phase" if every phase in "phase" is contained. + // Example: "this": (LS1,-1), (LS2,-1) + // "phase": (LS1,-1) + // Then "this" contains "phase", but "phase" doesn't contain "this" + for (std::set::const_iterator it=phase.my_ls_sides.begin(); it != phase.my_ls_sides.end(); ++it) + { + if (!contain(*it)) return false; + } + return true; +} + +bool +PhaseTag::is_nonconformal() const +{ + for (std::set::const_iterator it=my_ls_sides.begin(); it != my_ls_sides.end(); ++it) + { + const LS_SideTag & ls_side = *it; + + if (ls_side.is_interface()) + { + return true; + } + } + return false; +} + +bool +PhaseTag::operator== (const PhaseTag & rhs) const +{ + if (my_ls_sides.size() != rhs.my_ls_sides.size()) return false; + for (std::set::const_iterator it=my_ls_sides.begin(); it != my_ls_sides.end(); ++it) + { + const LS_SideTag & ls_side = *it; + + if (!rhs.contain(ls_side)) return false; + } + return true; +} + +PhaseTag & +PhaseTag::operator &= ( const PhaseTag & rhs ) +{ + for (std::set::const_iterator it=my_ls_sides.begin(); it != my_ls_sides.end();) + { + if (!rhs.contain(*it)) + { + my_ls_sides.erase(it++); + } + else + { + ++it; + } + } + return *this; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_PhaseTag.hpp b/packages/krino/krino/krino_lib/Akri_PhaseTag.hpp new file mode 100644 index 000000000000..94fa63b58f18 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_PhaseTag.hpp @@ -0,0 +1,171 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_PhaseTag_h +#define Akri_PhaseTag_h + +#include +#include + +#include +#include +#include + +namespace krino { + +class LS_SideTag { +public: + LS_SideTag(const LevelSet_Identifier ls_identifier, const int ls_sign) : my_ls_identifier(ls_identifier), my_ls_sign(ls_sign) {} + LS_SideTag(const LS_SideTag & orig, const int ls_sign) : my_ls_identifier(orig.my_ls_identifier), my_ls_sign(ls_sign) {} + ~LS_SideTag() {} +public: + static void declare_composite(const LevelSet_Identifier constituent, const LevelSet_Identifier composite); + LS_SideTag opposite_side() const {return LS_SideTag(my_ls_identifier,-1*my_ls_sign);} + LS_SideTag composite() const + { + auto it = the_composite_ls_map.find(my_ls_identifier); + if (it != the_composite_ls_map.end()) + { + return LS_SideTag(it->second, my_ls_sign); + } + else + { + return *this; + } + } + bool is_interface() const {return (0 == my_ls_sign);} + int get_ls_sign() const {return my_ls_sign;} + LevelSet_Identifier get_ls_identifier() const {return my_ls_identifier;} + bool operator < ( const LS_SideTag & RHS ) const { return my_ls_identifier < RHS.my_ls_identifier || (my_ls_identifier == RHS.my_ls_identifier && my_ls_sign < RHS.my_ls_sign); } + bool operator == ( const LS_SideTag & RHS ) const { return (my_ls_identifier == RHS.my_ls_identifier && my_ls_sign == RHS.my_ls_sign); } + bool operator != ( const LS_SideTag & RHS ) const { return (my_ls_identifier != RHS.my_ls_identifier || my_ls_sign != RHS.my_ls_sign); } + friend std::ostream& operator<<(std::ostream & os, const LS_SideTag & phase); +protected: + const LevelSet_Identifier my_ls_identifier; + const int my_ls_sign; + static std::map the_composite_ls_map; +}; + +class PhaseTag { +public: + PhaseTag() {} + ~PhaseTag() {} +public: + bool empty() const { return my_ls_sides.empty(); } + void clear() { my_ls_sides.clear(); } + const std::set & ls_sides() const { return my_ls_sides; } + void add(const LevelSet_Identifier ls_identifier, const int ls_sign) { add(LS_SideTag(ls_identifier, ls_sign)); } + void add(const PhaseTag & phase) { for (auto && ls_side : phase.my_ls_sides) add(ls_side); } + void add_opposite_sides(const PhaseTag & phase) { for (auto && ls_side : phase.my_ls_sides) add(ls_side.opposite_side()); } + void add(const LS_SideTag & ls_side) + { + const LS_SideTag ls_side_composite = ls_side.composite(); + my_ls_sides.insert(ls_side_composite); + if (ls_side_composite != ls_side) + { + // Apply priority rule. -1 (inside) beats +1 (outside) + if (my_ls_sides.count(LS_SideTag(ls_side_composite.get_ls_identifier(),-1))) + { + my_ls_sides.erase(LS_SideTag(ls_side_composite.get_ls_identifier(),+1)); + } + } + } + void remove(const LevelSet_Identifier ls_identifier, const int ls_sign){ remove(LS_SideTag(ls_identifier,ls_sign)); } + void remove(const LS_SideTag & ls_side) { my_ls_sides.erase(ls_side.composite()); } + + bool contain(const PhaseTag & phase) const; + bool contain(const LevelSet_Identifier ls_identifier, const int ls_sign) const { return contain(LS_SideTag(ls_identifier,ls_sign)); } + bool contain(const LS_SideTag & ls_side) const { return my_ls_sides.count(ls_side.composite()); } + + bool is_nonconformal() const; + bool operator!= (const PhaseTag & rhs) const { return !operator==(rhs); } + bool operator== (const PhaseTag & rhs) const; + bool operator < ( const PhaseTag & RHS ) const { return (my_ls_sides < RHS.my_ls_sides); } + friend std::ostream& operator<<(std::ostream & os, const PhaseTag & phase); + /** \brief Intersection: this = this INTERSECT ( expression ) */ + PhaseTag & operator &= ( const PhaseTag & rhs); + + void get_data(std::vector & phase_data) const + { + for (std::set::const_iterator side_it = ls_sides().begin(); side_it != ls_sides().end(); ++side_it) + { + phase_data.push_back(side_it->get_ls_identifier().get()); + phase_data.push_back(side_it->get_ls_sign()); + } + } + void set_from_data(const std::vector & phase_data) + { + clear(); + ThrowAssert(phase_data.size() % 2 == 0); + const unsigned num_phases = phase_data.size() / 2; + for (unsigned phase_index=0; phase_index my_ls_sides; +}; + +class NamedPhase +{ +public: + NamedPhase(std::string in_name) : my_name(in_name) {} + NamedPhase(std::string in_name, const PhaseTag & in_tag) : my_name(in_name), my_tag(in_tag) {} + const std::string & name() const { return my_name; } + const PhaseTag & tag() const { return my_tag; } + PhaseTag & tag() { return my_tag; } +protected: + std::string my_name; + PhaseTag my_tag; +}; +typedef std::vector< NamedPhase > PhaseVec; + +class PhasePartTag { +public: + // For non-interface phase parts + PhasePartTag(const unsigned & conformal_part_ordinal, const unsigned & nonconformal_part_ordinal, const unsigned & original_part_ordinal, const PhaseTag & vol_phase) + : my_conformal_part_ordinal(conformal_part_ordinal), + my_nonconformal_part_ordinal(nonconformal_part_ordinal), + my_original_part_ordinal(original_part_ordinal), + my_touching_vol_phase(vol_phase) { ThrowRequire(!vol_phase.empty()); } + // For interface phase parts defined as intersection of touching_vol_phase and opposite_vol_phase + PhasePartTag(const unsigned & conformal_part_ordinal, const unsigned & nonconformal_part_ordinal, const unsigned & original_part_ordinal, const PhaseTag & touching_vol_phase, const PhaseTag & opposite_vol_phase) + : my_conformal_part_ordinal(conformal_part_ordinal), + my_nonconformal_part_ordinal(nonconformal_part_ordinal), + my_original_part_ordinal(original_part_ordinal), + my_touching_vol_phase(touching_vol_phase), + my_opposite_vol_phase(opposite_vol_phase) { ThrowRequire(!touching_vol_phase.empty() && !opposite_vol_phase.empty()); } + ~PhasePartTag() {} +public: + unsigned get_conformal_part_ordinal() const { return my_conformal_part_ordinal; } + unsigned get_nonconformal_part_ordinal() const { return my_nonconformal_part_ordinal; } + unsigned get_original_part_ordinal() const { return my_original_part_ordinal; } + bool is_interface() const { return !my_opposite_vol_phase.empty(); } + const PhaseTag & get_phase() const { ThrowRequire(!is_interface()); return my_touching_vol_phase; } + const PhaseTag & get_touching_phase() const { ThrowRequire(is_interface()); return my_touching_vol_phase; } + const PhaseTag & get_opposite_phase() const { ThrowRequire(is_interface()); return my_opposite_vol_phase; } + bool operator<(PhasePartTag rhs) const + { + // There must be a 1-1 mapping between conformal parts and PhasePartTags + // therefore the conformal part ordinal must be a unique identifier for the PhasePartTag and + // we can sort on just it. + return my_conformal_part_ordinal < rhs.my_conformal_part_ordinal; + } +protected: + unsigned my_conformal_part_ordinal; + unsigned my_nonconformal_part_ordinal; + unsigned my_original_part_ordinal; + PhaseTag my_touching_vol_phase; + PhaseTag my_opposite_vol_phase; +}; +typedef std::set< PhasePartTag > PhasePartSet; + +} // namespace krino + +#endif // Akri_PhaseTag_h diff --git a/packages/krino/krino/krino_lib/Akri_Phase_Support.cpp b/packages/krino/krino/krino_lib/Akri_Phase_Support.cpp new file mode 100644 index 000000000000..e611f2649c5e --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Phase_Support.cpp @@ -0,0 +1,961 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include + +namespace krino{ + +bool Phase_Support::oneLevelSetPerPhase = false; +std::map Phase_Support::the_mesh_phases; +std::map Phase_Support::the_mesh_block_phases_by_name; + +void Phase_Support::check_phase_parts() const +{ + const LevelSetManager & region_ls = LevelSetManager::get(my_meta); + bool error = false; + for (auto&& phase_part : my_phase_parts) + { + const PhaseTag & part_phase = (phase_part.is_interface()) ? phase_part.get_touching_phase() : phase_part.get_phase(); + const std::set & phase_ls_sides = part_phase.ls_sides(); + for (std::set::const_iterator side_it = phase_ls_sides.begin(); side_it != phase_ls_sides.end(); ++side_it) + { + const std::string phase_ls_name = LevelSet::get_name(side_it->get_ls_identifier()); + if (!region_ls.has_levelSet(phase_ls_name)) + { + error = true; + stk::mesh::Part & conformal_part = my_meta.get_part(phase_part.get_conformal_part_ordinal()); + krinolog << "Error: Phase \"" << conformal_part.name() << "\" uses level set \"" << phase_ls_name << "\" but no such level set exists." << stk::diag::dendl; + } + } + } + ThrowErrorMsgIf(error, "Error: Phases are not defined correctly."); +} + +Phase_Support::Phase_Support(stk::mesh::MetaData & meta) +: my_meta(meta), + my_aux_meta(AuxMetaData::get(meta)), + nonconformalLsMapsAreFilled_(false) {} + +Phase_Support & +Phase_Support::get(stk::mesh::MetaData & meta) +{ + Phase_Support * support = const_cast(meta.get_attribute()); + if (nullptr == support) + { + support = new Phase_Support(meta); + ThrowAssert(nullptr != support); + meta.declare_attribute_with_delete(support); + } + return *support; +} + +Phase_Support & +Phase_Support::get(const stk::mesh::MetaData & meta) +{ + Phase_Support * support = const_cast(meta.get_attribute()); + ThrowRequireMsg(nullptr != support, "No Phase_Support found for MetaData."); + return *support; +} + +bool +Phase_Support::exists_and_has_phases_defined(const stk::mesh::MetaData & meta) +{ + Phase_Support * support = const_cast(meta.get_attribute()); + return support != nullptr && support->phases_defined(); +} + +stk::mesh::Selector Phase_Support::get_all_conformal_surfaces_selector() const +{ + std::vector surfaceParts; + for (auto && part : get_conformal_parts()) + if(is_interface(part)) + surfaceParts.push_back(part); + return selectUnion(surfaceParts); +} + +void +Phase_Support::addPhasePart(stk::mesh::Part & io_part, PhasePartSet & phase_parts, const NamedPhase & ls_phase) +{ + const std::string & phase_name = ls_phase.name(); + std::string phase_part_name = io_part.name(); + if(phase_name != "") // The alive phase for death problems just uses the io part as the conformal part + { + phase_part_name += "_" + phase_name; + } + + stk::mesh::Part & conformal_io_part = my_aux_meta.declare_io_part(phase_part_name, io_part.primary_entity_rank()); + ThrowAssert(phase_name != "" || conformal_io_part.mesh_meta_data_ordinal() == io_part.mesh_meta_data_ordinal()); + std::string topology_name = "INVALID_TOPOLOGY"; + if (stk::topology::INVALID_TOPOLOGY != io_part.topology()) + { + stk::mesh::set_topology(conformal_io_part, io_part.topology()); + topology_name = conformal_io_part.topology().name(); + } + + const std::string nonconf_name = io_part.name() + "_nonconformal"; + if(krinolog.shouldPrint(LOG_PARTS)) + { + krinolog << "Created conformal IO part " << conformal_io_part.name() << " with topology " << topology_name << stk::diag::dendl; + krinolog << " Adding phase part: conformal_part_name=" << conformal_io_part.name() + << ", nonconformal_part_name=" << nonconf_name + << ", original_mesh_part_name=" << io_part.name(); + krinolog << " " << ls_phase.tag(); + krinolog << stk::diag::dendl; + } + + + stk::mesh::Part & nonconf_part = my_aux_meta.get_part(nonconf_name); + phase_parts.insert(PhasePartTag(conformal_io_part.mesh_meta_data_ordinal(), nonconf_part.mesh_meta_data_ordinal(), io_part.mesh_meta_data_ordinal(), ls_phase.tag())); + + all_decomposed_blocks_selector |= conformal_io_part; + part_is_conformal_map[&conformal_io_part] = true; + part_to_nonconformal_part_map[&conformal_io_part] = &nonconf_part; + part_to_phase_map[&conformal_io_part] = ls_phase.tag(); + PhaseTagToPartMap & phase_to_conformal_map = nonconformal_to_phase_conformal_map[&nonconf_part]; + phase_to_conformal_map[ls_phase.tag()] = &conformal_io_part; +} + +void +Phase_Support::create_nonconformal_parts(const PartSet & decomposed_ioparts) +{ + const std::string nonconformal_part_suffix = "_nonconformal"; + for(PartSet::const_iterator it = decomposed_ioparts.begin(); it != decomposed_ioparts.end(); ++it) + { + const stk::mesh::Part & iopart = my_aux_meta.get_part((*it)->name()); + const std::string nonconformal_part_name = iopart.name() + nonconformal_part_suffix; + + if(!my_aux_meta.has_part(nonconformal_part_name)) + { + const bool restartOnlyIOPart = true; + stk::mesh::Part & nonconformal_part = + (iopart.topology() == stk::topology::INVALID_TOPOLOGY) ? + my_aux_meta.declare_io_part(nonconformal_part_name, iopart.primary_entity_rank(), restartOnlyIOPart) : + my_aux_meta.declare_io_part_with_topology(nonconformal_part_name, iopart.topology(), restartOnlyIOPart); + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Created nonconformal part " << nonconformal_part_name << stk::diag::dendl; + + all_decomposed_blocks_selector |= iopart; + all_decomposed_blocks_selector |= nonconformal_part; + part_to_nonconformal_part_map[&iopart] = &nonconformal_part; + part_is_nonconformal_map[&nonconformal_part] = true; + } + } +} + +stk::mesh::PartVector +Phase_Support::get_nonconformal_parts() const +{ + stk::mesh::PartVector result; + for(const auto & entry : part_is_nonconformal_map) + { + if(entry.second) result.push_back(const_cast(entry.first)); + } + return result; +} + +stk::mesh::PartVector +Phase_Support::get_conformal_parts() const +{ + stk::mesh::PartVector result; + for(const auto & entry : part_is_conformal_map) + { + if(entry.second) result.push_back(const_cast(entry.first)); + } + return result; +} + +std::vector +Phase_Support::get_level_set_phases(const PhaseVec & mesh_phases, const LevelSet & levelSet) +{ + // gather up the set of phases that depend on this levelSet + PhaseTag ls_neg_phase; + PhaseTag ls_pos_phase; + ls_neg_phase.add(levelSet.get_identifier(),-1); + ls_pos_phase.add(levelSet.get_identifier(),+1); + std::vector ls_phases; + for(unsigned phase_index=0; phase_index touching_surface_ordinals; + get_input_surfaces_touching_block(input_block_surface_info, block_ptr->mesh_meta_data_ordinal(), touching_surface_ordinals); + for (auto && surf_ordinal : touching_surface_ordinals) + { + stk::mesh::Part & surf_part = mesh_meta.get_part(surf_ordinal); + blocks_and_touching_sides.insert(&surf_part); + + // Add all subset parts to the set of parts + if (!(surf_part.subsets().empty())) + { + for (stk::mesh::PartVector::const_iterator subset = surf_part.subsets().begin(); subset != surf_part.subsets().end(); ++subset) + { + blocks_and_touching_sides.insert(*subset); + } + } + } + } + return blocks_and_touching_sides; +} + +void +Phase_Support::create_phase_parts(const PhaseVec& ls_phases, const PartSet& decomposed_ioparts) +{ + for (auto && ls_phase : ls_phases) + { + for (auto && io_part : decomposed_ioparts) + { + addPhasePart(*io_part, my_phase_parts, ls_phase); + } + } +} + +void +Phase_Support::subset_and_alias_surface_phase_parts(const PhaseVec& ls_phases, + const PartSet& decomposed_ioparts) +{ + std::set touching_block_ordinals; + + for (auto && io_part : decomposed_ioparts) + { + if (!(io_part->subsets().empty())) + { + for (auto && ls_phase_entry : ls_phases) + { + const PhaseTag & ls_phase = ls_phase_entry.tag(); + //FIXME: remove const_cast's + stk::mesh::Part * conformal_iopart = const_cast(find_conformal_io_part(*io_part, ls_phase)); + ThrowRequire(NULL != conformal_iopart); + + stk::mesh::Part * nonconformal_iopart = const_cast(find_nonconformal_part(*io_part)); + ThrowRequire(NULL != nonconformal_iopart); + + for (stk::mesh::PartVector::const_iterator subset = io_part->subsets().begin(); + subset != io_part->subsets().end(); ++subset) + { + stk::mesh::Part * io_part_subset = *subset; + ThrowRequire(NULL != io_part_subset); + + stk::mesh::Part * conformal_iopart_subset = const_cast(find_conformal_io_part(*io_part_subset, ls_phase)); + ThrowRequire(NULL != conformal_iopart_subset); + + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Adding " << conformal_iopart_subset->name() << " as subset of " << conformal_iopart->name() << stk::diag::dendl; + my_meta.declare_part_subset(*conformal_iopart, *conformal_iopart_subset); + + stk::mesh::Part * nonconformal_iopart_subset = const_cast(find_nonconformal_part(*io_part_subset)); + ThrowRequire(NULL != nonconformal_iopart_subset); + + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Adding " << nonconformal_iopart_subset->name() << " as subset of " << nonconformal_iopart->name() << stk::diag::dendl; + my_meta.declare_part_subset(*nonconformal_iopart, *nonconformal_iopart_subset); + + get_input_blocks_touching_surface(my_input_block_surface_connectivity, io_part_subset->mesh_meta_data_ordinal(), touching_block_ordinals); + for (auto && touching_block_ordinal : touching_block_ordinals) + { + const std::string conformal_part_alias = conformal_iopart->name() + "_" + my_meta.get_part(touching_block_ordinal).name(); + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Adding alias " << conformal_part_alias << " for conformal part " << conformal_iopart_subset->name() << stk::diag::dendl; + my_aux_meta.define_part_alias(*conformal_iopart_subset, conformal_part_alias); + } + } + } + } + } +} + +void +Phase_Support::build_decomposed_block_surface_connectivity() +{ + for (auto && part : my_meta.get_mesh_parts()) + { + if (part->primary_entity_rank() != my_meta.side_rank()) continue; + const PhasePartTag * phase_part = find_conformal_phase_part(*part); + if (nullptr == phase_part) continue; + stk::mesh::Part & orig_part = my_meta.get_part(phase_part->get_original_part_ordinal()); + if (orig_part == my_meta.universal_part()) continue; + + if (phase_part->is_interface()) + { + const stk::mesh::Part * conformal_touching_block = find_conformal_io_part(orig_part, phase_part->get_touching_phase()); + ThrowRequire(conformal_touching_block); + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Surface " << part->name() << " touches block " << conformal_touching_block->name() << "\n"; + std::vector touching_blocks = my_meta.get_blocks_touching_surface(part); + if (std::find(touching_blocks.begin(), touching_blocks.end(), conformal_touching_block) == touching_blocks.end()) + { + touching_blocks.push_back(conformal_touching_block); + } + my_meta.set_surface_to_block_mapping(part, touching_blocks); + } + else + { + std::set touching_block_ordinals; + get_input_blocks_touching_surface(my_input_block_surface_connectivity, orig_part.mesh_meta_data_ordinal(), touching_block_ordinals); + + for (auto && touching_block_ordinal : touching_block_ordinals) + { + stk::mesh::Part & touching_block = my_meta.get_part(touching_block_ordinal); + const stk::mesh::Part * conformal_touching_block = find_conformal_io_part(touching_block, phase_part->get_phase()); + ThrowRequire(conformal_touching_block); + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Surface " << part->name() << " touches block " << conformal_touching_block->name() << "\n"; + std::vector touching_blocks = my_meta.get_blocks_touching_surface(part); + if (std::find(touching_blocks.begin(), touching_blocks.end(), conformal_touching_block) == touching_blocks.end()) + { + touching_blocks.push_back(conformal_touching_block); + } + my_meta.set_surface_to_block_mapping(part, touching_blocks); + } + } + } +} + +void +Phase_Support::create_interface_phase_parts( + const PhaseVec& ls_phases, + const PartSet& decomposed_ioparts, + const Interface_Name_Generator& interface_name_gen) +{ + const int num_ls_phases = ls_phases.size(); + if (num_ls_phases > 1) + { + const int num_interfaces = num_ls_phases * (num_ls_phases - 1) / 2; + std::vector > interface_phases; + interface_phases.reserve(num_interfaces); + for (int i = 0; i < num_ls_phases; ++i) + { + for (int j = i+1; j < num_ls_phases; ++j) + { + std::pair phase_pair(i, j); + interface_phases.push_back(phase_pair); + } + } + ThrowRequire((int) interface_phases.size() == num_interfaces); + + for (int i = 0; i < num_interfaces; ++i) + { + const int name_compare = ls_phases[interface_phases[i].first].name().compare(ls_phases[interface_phases[i].second].name()); + ThrowRequire(name_compare != 0); + // form phase intersection + const auto & phase0 = (name_compare < 0) ? ls_phases[interface_phases[i].first] : ls_phases[interface_phases[i].second]; + const auto & phase1 = (name_compare < 0) ? ls_phases[interface_phases[i].second] : ls_phases[interface_phases[i].first]; + std::string superset_interface_phase_name = phase0.name() + "_" + phase1.name(); + const std::string superset_phase_part_name = interface_name_gen.interface_superset_name(superset_interface_phase_name); + + // assumes all sides have same topology + stk::mesh::Part &superset_phase_part = my_aux_meta.declare_io_part(superset_phase_part_name, my_meta.side_rank()); + + if(krinolog.shouldPrint(LOG_PARTS)) krinolog << "Adding interfacial phase part: conformal_part_name=" << superset_phase_part.name() << "\n"; + + for (auto && phase_pair : {std::make_pair(phase0,phase1), std::make_pair(phase1,phase0)}) + { + const auto & touching_phase = phase_pair.first.tag(); + const auto & opposite_phase = phase_pair.second.tag(); + + my_phase_parts.insert(PhasePartTag( + superset_phase_part.mesh_meta_data_ordinal(), my_meta.universal_part().mesh_meta_data_ordinal(), + my_meta.universal_part().mesh_meta_data_ordinal(), touching_phase, + opposite_phase)); + + for (auto * io_part : decomposed_ioparts) + { + ThrowRequire(NULL != io_part); + // only handle blocks for now -> creating interfacial surface "phases" + if (io_part->primary_entity_rank() == stk::topology::ELEMENT_RANK) + { + std::string subset_interface_phase_name = phase_pair.first.name() + "_" + phase_pair.second.name(); + const std::string subset_phase_part_name = interface_name_gen.interface_subset_name(io_part->name(), subset_interface_phase_name); + const bool restartOnlyIOPart = true; // Subset part is only output for restart + stk::mesh::Part &subset_phase_part = my_aux_meta.declare_io_part_with_topology(subset_phase_part_name, io_part->topology().side_topology(), restartOnlyIOPart); + my_meta.declare_part_subset(superset_phase_part, subset_phase_part); + + const stk::mesh::Part * const nonconf_part = find_nonconformal_part(*io_part); + ThrowRequire(NULL != nonconf_part); + + if(krinolog.shouldPrint(LOG_PARTS)) + { + krinolog << " Adding subset interfacial phase part: conformal_part_name=" << subset_phase_part.name() + << ", nonconformal_part_name=" << nonconf_part->name(); + krinolog << ", touching_phase=" << touching_phase + << ", opposite_phase=" << opposite_phase; + krinolog << "\n"; + } + + my_phase_parts.insert(PhasePartTag( + subset_phase_part.mesh_meta_data_ordinal(), nonconf_part->mesh_meta_data_ordinal(), + io_part->mesh_meta_data_ordinal(), touching_phase, + opposite_phase)); + + all_decomposed_blocks_selector |= subset_phase_part; + part_is_conformal_map[&subset_phase_part] = true; + part_to_nonconformal_part_map[&subset_phase_part] = nonconf_part; + auto & phase_to_conformal_map = nonconformal_to_phase_conformal_map[nonconf_part]; + auto & touching_phase_part = phase_to_conformal_map[touching_phase]; + auto & opposite_phase_part = phase_to_conformal_map[opposite_phase]; + auto key = std::make_pair(touching_phase_part, opposite_phase_part); + volume_to_interface_parts_map[key] = &subset_phase_part; + } + } + } + } + } +} + +void +Phase_Support::decompose_blocks( + const stk::mesh::PartVector& blocks_decomposed_by_ls, + const PhaseVec & ls_phases, + const Interface_Name_Generator & interface_name_gen) +{ + if(ls_phases.empty()) return; + + stk::topology topo; + for(auto && decompose_block : blocks_decomposed_by_ls) + { + topo = decompose_block->topology(); + if(topo != stk::topology::TET_4 && topo != stk::topology::TET_10 + && topo != stk::topology::TRI_3_2D && topo != stk::topology::TRI_6_2D) + { + stk::RuntimeDoomedAdHoc() << "Currently only Tetrahedron 4 or 10 (in 3D) and Triangle 3 or 6 (in 2D) element types are supported when using CDFEM.\n"; + return; + } + } + + PartSet decomposed_ioparts = get_blocks_and_touching_surfaces(my_meta, blocks_decomposed_by_ls, my_input_block_surface_connectivity); + + create_nonconformal_parts(decomposed_ioparts); + + create_phase_parts(ls_phases, decomposed_ioparts); + + subset_and_alias_surface_phase_parts(ls_phases, decomposed_ioparts); + + create_interface_phase_parts(ls_phases, decomposed_ioparts, interface_name_gen); +} + +//-------------------------------------------------------------------------------- + +void +Phase_Support::determine_block_phases(const std::set & FEmodel_block_names, const krino::PhaseVec & FEmodel_phases) +{ + if (FEmodel_phases.empty()) return; + + ThrowAssertMsg(my_mesh_block_phases.empty(), "determine_block_phases should only be called once per mesh"); + + for (auto && part : my_meta.get_parts()) + { + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK) + { + auto & block_phases = my_mesh_block_phases[part->mesh_meta_data_ordinal()]; + for(unsigned phase_index=0; phase_indexname() + "_" + phase_name; + std::transform(phase_part_name.begin(), phase_part_name.end(), phase_part_name.begin(), ::tolower); + if (FEmodel_block_names.find(phase_part_name) != FEmodel_block_names.end() ) + { + block_phases.insert(phase_index); + } + } + } + } +} + +//-------------------------------------------------------------------------------- + +void +Phase_Support::determine_block_phases(const PhaseVec & FEmodel_phases, const PartnamePhasenameMap & FEmodel_block_phase_names) +{ + if (FEmodel_phases.empty()) return; + + ThrowAssertMsg(my_mesh_block_phases.empty(), "determine_block_phases should only be called once per mesh"); + + if (FEmodel_block_phase_names.empty()) + { + stk::RuntimeDoomedAdHoc() << "Failure in determine_block_phases. Were the subdomains specified for the decomposed blocks in the finite element model specification?\n"; + return; + } + + std::map phase_name_to_index_map; + for(unsigned phase_index=0; phase_indexsecond); + } + } + } + else + { + stk::RuntimeDoomedAdHoc() << "The block " << map_entry.first << " is listed in the finite element model specification, but is not in the input mesh.\n"; + } + } +} + +//-------------------------------------------------------------------------------- + +std::vector +Phase_Support::get_blocks_decomposed_by_levelset(const std::vector ls_phases) const +{ + std::vector blocks_decomposed_by_ls; + for (auto && map_it : my_mesh_block_phases) + { + stk::mesh::Part & FEmodel_block = my_meta.get_part(map_it.first); + const auto & block_phases = map_it.second; + for(auto ls_phase : ls_phases) + { + if (block_phases.find(ls_phase) != block_phases.end()) + { + blocks_decomposed_by_ls.push_back(&FEmodel_block); + break; + } + } + } + + return blocks_decomposed_by_ls; +} + +//-------------------------------------------------------------------------------- + +void +Phase_Support::setup_phases(const krino::PhaseVec & FEmodel_phases) +{ + for (auto && map_it : my_mesh_block_phases) + { + stk::mesh::Part & FEmodel_block = my_meta.get_part(map_it.first); + const auto & block_phase_ordinals = map_it.second; + + PhaseVec block_phases; + for(auto && block_phase_ordinal : block_phase_ordinals) + { + block_phases.push_back(FEmodel_phases[block_phase_ordinal]); + } + + LS_Name_Generator interface_name_gen; + decompose_blocks({&FEmodel_block}, block_phases, interface_name_gen); + } + + build_decomposed_block_surface_connectivity(); +} + +//-------------------------------------------------------------------------------- + +void +Phase_Support::get_iopart_roots(const stk::mesh::Part & iopart, std::vector & subsets) +{ /* %TRACE% */ /* %TRACE% */ + if ( iopart.subsets().empty() ) + { + subsets.push_back(&iopart); + } + else + { + for (stk::mesh::PartVector::const_iterator subset = iopart.subsets().begin(); subset != iopart.subsets().end() ; ++subset ) + { + ThrowRequire(stk::io::is_part_io_part(**subset)); + get_iopart_roots(**subset, subsets); + } + } +} +//-------------------------------------------------------------------------------- +void +Phase_Support::get_blocks_touching_surface(const std::string & surface_name, std::vector & block_names) +{ /* %TRACE% */ /* %TRACE% */ + + std::set block_ordinal_set; + for (auto&& block_ordinal : block_ordinal_set) + { + block_names.push_back(my_meta.get_part(block_ordinal).name()); + } +} +//-------------------------------------------------------------------------------- +void +Phase_Support::get_input_surfaces_touching_block(const Block_Surface_Connectivity & input_block_surface_connectivity, + const stk::mesh::PartOrdinal block_ordinal, std::set & surface_ordinals) +{ + input_block_surface_connectivity.get_surfaces_touching_block(block_ordinal, surface_ordinals); +} + +//-------------------------------------------------------------------------------- +void +Phase_Support::get_input_blocks_touching_surface(const Block_Surface_Connectivity & input_block_surface_connectivity, + const stk::mesh::PartOrdinal surfaceOrdinal, std::set & blockOrdinals) +{ + input_block_surface_connectivity.get_blocks_touching_surface(surfaceOrdinal, blockOrdinals); +} +//-------------------------------------------------------------------------------- +const stk::mesh::Part * +Phase_Support::find_conformal_io_part(const stk::mesh::Part & io_part, const PhaseTag & phase) const +{ + const stk::mesh::Part * const nonconf_part = find_nonconformal_part(io_part); + auto entry = nonconformal_to_phase_conformal_map.find(nonconf_part); + if(entry == nonconformal_to_phase_conformal_map.end()) return &io_part; + PhaseTagToPartMap & tag_to_conformal_map = (*entry).second; + + const auto find_part = tag_to_conformal_map.find(phase); + if(find_part != tag_to_conformal_map.end()) + { + auto & tag_part_pair = *find_part; + return tag_part_pair.second; + } + + // This search is to handle the case where the phase passed in contains additional LS side tags that the + // conformal part phase tag doesn't care about. For example if the conformal phase is defined as "where LS1 is negative" + // it should match a phase tag that has (0,1) (1,-1) even though the tags are not == + // TODO: If we knew about all the LS's in the problem when decompose_blocks was called we could populate all the necessary entries + // then and wouldn't need this search. + for(auto && tag_part_pair : tag_to_conformal_map) + { + if(phase.contain(tag_part_pair.first)) + { + tag_to_conformal_map[phase] = tag_part_pair.second; + return tag_part_pair.second; + } + } + + return &io_part; +} + +//-------------------------------------------------------------------------------- + +bool +Phase_Support::is_conformal(const stk::mesh::Part * io_part) const +{ + PartToBoolMap::const_iterator entry = part_is_conformal_map.find(io_part); + if (entry != part_is_conformal_map.end()) return (entry->second); + return false; +} + +//-------------------------------------------------------------------------------- + +bool +Phase_Support::is_nonconformal(const stk::mesh::Part * io_part) const +{ + PartToBoolMap::const_iterator entry = part_is_nonconformal_map.find(io_part); + if (entry != part_is_nonconformal_map.end()) return (entry->second); + return false; +} + +//-------------------------------------------------------------------------------- + +bool +Phase_Support::is_interface(const stk::mesh::Part * io_part) const +{ + ThrowAssert(io_part); + auto phase_part = find_conformal_phase_part(*io_part); + return phase_part && phase_part->is_interface(); +} + +//-------------------------------------------------------------------------------- + +const stk::mesh::Part * +Phase_Support::find_nonconformal_part(const stk::mesh::Part & io_part) const +{ + PartToPartMap::const_iterator entry = part_to_nonconformal_part_map.find(&io_part); + if (entry != part_to_nonconformal_part_map.end()) return (entry->second); + return &io_part; +} + +//-------------------------------------------------------------------------------- + +const stk::mesh::Part * +Phase_Support::find_interface_part(const stk::mesh::Part & vol0, const stk::mesh::Part & vol1) const +{ + auto key = std::make_pair(&vol0, &vol1); + auto find_it = volume_to_interface_parts_map.find(key); + if(find_it != volume_to_interface_parts_map.end()) return find_it->second; + + return nullptr; +} + +//-------------------------------------------------------------------------------- + +const PhaseTag & +Phase_Support::get_iopart_phase(const stk::mesh::Part & io_part) const +{ + PartToPhaseTagMap::const_iterator entry = part_to_phase_map.find(&io_part); + if (entry != part_to_phase_map.end()) return (entry->second); + + static const PhaseTag empty_phase; + return empty_phase; +} + +//-------------------------------------------------------------------------------- + +void Phase_Support::register_blocks_for_level_set(LevelSet * levelSet, + const std::vector & blocks_decomposed_by_ls) +{ + nonconformalLsMapsAreFilled_ = false; + + // Loop over block names + for (auto && block_ptr : blocks_decomposed_by_ls) + { + // Add direct relationship between this block and level set + lsUsedByParts_[levelSet].insert(block_ptr); + + // Now get surfaces touching this block + std::set surfaceOrdinals; + get_input_surfaces_touching_block(my_input_block_surface_connectivity, block_ptr->mesh_meta_data_ordinal(), surfaceOrdinals); + for (auto && surfaceOrdinal : surfaceOrdinals) + { + // For each surface, add IO Part/Level Set pairing to maps + stk::mesh::Part & surfaceIOPart = my_meta.get_part(surfaceOrdinal); + lsUsedByParts_[levelSet].insert(&surfaceIOPart); + } + } +} + + +//-------------------------------------------------------------------------------- +bool Phase_Support::level_set_is_used_by_nonconformal_part(const LevelSet * levelSet, + const stk::mesh::Part * const ioPart) const +{ + if (!nonconformalLsMapsAreFilled_) + fill_nonconformal_level_set_maps(); + + IOPartSet & ioPartSet = lsUsedByNonconformalParts_[levelSet]; + bool contains = (ioPartSet.find(ioPart) != ioPartSet.end()); + return contains; +} + +//-------------------------------------------------------------------------------- +void Phase_Support::fill_nonconformal_level_set_maps() const +{ + if (nonconformalLsMapsAreFilled_ == true) return; + nonconformalLsMapsAreFilled_ = true; + + // In this method we duplicate the level-set-to-part maps, but use + // the nonconformal versions of each IOPart instead + + // lsUsedByNonconformalParts_ + lsUsedByNonconformalParts_.clear(); + std::map::const_iterator iterLSMap; + for (iterLSMap = lsUsedByParts_.begin(); iterLSMap != lsUsedByParts_.end(); ++iterLSMap) + { + const LevelSet * levelSet = iterLSMap->first; + const IOPartSet & ioPartSet = iterLSMap->second; + IOPartSet::const_iterator iterPart; + for (iterPart = ioPartSet.begin(); iterPart != ioPartSet.end(); ++iterPart) + { + const stk::mesh::Part * ioPart = *iterPart; + const stk::mesh::Part * nonconformalIOPart = find_nonconformal_part(*ioPart); + lsUsedByNonconformalParts_[levelSet].insert(nonconformalIOPart); + } + } +} + +const PhasePartTag * Phase_Support::find_conformal_phase_part(const stk::mesh::Part & conformal_part) const +{ + const PhasePartTag * result = NULL; + + const unsigned conformal_part_ordinal = conformal_part.mesh_meta_data_ordinal(); + + // Take advantage of the fact that PhasePartTags are uniquely identified by the conformal_part_ordinal + // and therefore the set of phase parts is sorted only based on that to use the binary search + // my_phase_parts.find(). + PhaseTag dummy_tag; + dummy_tag.add(LevelSet_Identifier(0), 1); + PhasePartTag search_tag(conformal_part_ordinal, 0, 0, dummy_tag); + + auto it = my_phase_parts.find(search_tag); + if(it != my_phase_parts.end()) result = &(*it); + + return result; +} + +//-------------------------------------------------------------------------------- +CDFEM_Irreversible_Phase_Support & +CDFEM_Irreversible_Phase_Support::get(stk::mesh::MetaData & meta) +{ + CDFEM_Irreversible_Phase_Support * support = const_cast(meta.get_attribute()); + if (NULL == support) + { + support = new CDFEM_Irreversible_Phase_Support(); + meta.declare_attribute_with_delete(support); + } + return *support; +} +//-------------------------------------------------------------------------- +CDFEM_Inequality_Spec * CDFEM_Irreversible_Phase_Support::add_death_spec(const std::string & death_name, bool is_death) +{ + // CDFEM death needs the decomposition to occur at the end of the time step, irreversible phase change + // needs it to occur at the start of the time step. For now throw if the user tries to do both in the same problem. + if(is_death) + { + has_death = true; + } + else + { + has_irreversible_phase_change = true; + } + ThrowInvalidArgMsgIf(has_death && has_irreversible_phase_change, + "Cannot have both CDFEM death and CDFEM irreversible phase change in the same problem."); + + for (auto&& death_spec : my_death_specs) + { + ThrowInvalidArgMsgIf(death_spec.name() == death_name, + "Only one CDFEM death specification with the same name is allowed per mesh (" << death_name << "). "); + } + my_death_specs.push_back(CDFEM_Inequality_Spec(death_name)); + return &my_death_specs.back(); +} + +//-------------------------------------------------------------------------- + +CDFEM_Inequality_Spec::CDFEM_Inequality_Spec(const std::string & name_) + : my_name(name_), + my_criterion_compare_type(INEQUALITY_CRITERION_TYPE_UNDEFINED), + my_ls(NULL) +{} + +CDFEM_Inequality_Spec::InequalityCriterionType +CDFEM_Inequality_Spec::int_to_inequality_criterion_type(const int inequality_criterion) +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::int_to_death_criterion_compare_type(const int death_criterion_compare)"); /* %TRACE% */ + + switch (inequality_criterion) + { + case int(INEQUALITY_CRITERION_TYPE_UNDEFINED): + return INEQUALITY_CRITERION_TYPE_UNDEFINED ; + case int(LESS_THAN ): + return LESS_THAN ; + case int(GREATER_THAN ): + return GREATER_THAN ; + default: + ThrowRuntimeError("Bad integer passed. Could not convert passed in integer " + << "death_criterion_compare = " << inequality_criterion + << " into a CDFEM_Death_Spec::DeathCriterionCompareType enum. " + << "The code and the Sierra XML database may be out of sync." << std::endl + << StackTrace); + } +} + +void CDFEM_Inequality_Spec::add_element_volume_name (const std::string & a_element_volume_name) +{ + /* %TRACE[NONE]% */ /* %TRACE% */ + + // Note: It is ok to add multiple volume names to vector, thus no return status given + my_element_volume_names.push_back(a_element_volume_name); +} + +bool CDFEM_Inequality_Spec::set_threshold_variable_name (const std::string & a_threshold_variable_name) +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::set_death_variable_name(const std::string & a_death_variable_name)"); /* %TRACE% */ + + // Set return status to false if value has already been set + bool return_status = (0 == my_threshold_variable_name.length()); + + if (return_status) + my_threshold_variable_name = a_threshold_variable_name; + + return return_status; +} + +bool CDFEM_Inequality_Spec::set_threshold_value (const double a_threshold_value) +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::set_threshold_value(const double a_threshold_value)"); /* %TRACE% */ + + // Set return status to false if value has already been set + bool return_status = (std::numeric_limits::max() != a_threshold_value); + + if (return_status) + my_threshold_value = a_threshold_value; + + return return_status; +} + +bool CDFEM_Inequality_Spec::set_criterion_compare_type + (const CDFEM_Inequality_Spec::InequalityCriterionType & a_criterion_compare_type) +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::set_criterion_compare_type(const CDFEM_Death_Spec::DeathCriterionCompareType & a_criterion_compare_type)"); /* %TRACE% */ + + // Set return status to false if value has already been set + bool return_status = (CDFEM_Inequality_Spec::INEQUALITY_CRITERION_TYPE_UNDEFINED == my_criterion_compare_type); + + if (return_status) + my_criterion_compare_type = a_criterion_compare_type; + + return return_status; +} + +void CDFEM_Inequality_Spec::sanity_check(const std::vector mesh_elem_blocks) const +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::sanity_check()"); /* %TRACE% */ + + ThrowErrorMsgIf(CDFEM_Inequality_Spec::INEQUALITY_CRITERION_TYPE_UNDEFINED == my_criterion_compare_type, + "CDFEM Death is not properly setup. Was the death criterion specified?"); + + const std::vector & volume_names = get_element_volume_names(); + + for (auto && block_name : volume_names) + { + ThrowErrorMsgIf( + std::find(mesh_elem_blocks.begin(), mesh_elem_blocks.end(), block_name) == mesh_elem_blocks.end(), + "Could not find an element volume named '" + << block_name << "' that was specified in the " + << "cdfem death command block for the cdfem death named '" + << name() << "'."); + } +} + +void CDFEM_Inequality_Spec::create_levelset(stk::mesh::MetaData & meta, stk::diag::Timer & parent_timer) +{ + /* %TRACE[ON]% */ Trace trace__("krino::CDFEM_Death_Spec::create_levelset()"); /* %TRACE% */ + + ThrowInvalidArgMsgIf( + LevelSetManager::get(meta).has_levelSet(my_name), + "Region already has a LevelSet named " << my_name); + + my_ls = &LevelSet::build(meta, my_name, parent_timer); + my_ls->set_isovar(get_threshold_variable_name(), get_threshold_value()); + + int deactivated_phase_sign = ( get_criterion_compare_type() == CDFEM_Inequality_Spec::LESS_THAN ) ? -1 : 1; + my_deactivated_phase.add(my_ls->get_identifier(), deactivated_phase_sign); + my_active_phase.add(my_ls->get_identifier(), -1 * deactivated_phase_sign); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Phase_Support.hpp b/packages/krino/krino/krino_lib/Akri_Phase_Support.hpp new file mode 100644 index 000000000000..05eb9443e4bf --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Phase_Support.hpp @@ -0,0 +1,212 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Phase_Support_h +#define Akri_Phase_Support_h +// +#include +#include + +#include +#include +#include + +#include + +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace diag { class Timer; } } + +namespace krino { + +class AuxMetaData; +class LevelSet; +struct LS_Field; + +typedef std::set< const stk::mesh::Part * > IOPartSet; +typedef std::set< LevelSet * > LevelSetSet; +typedef std::map> PartPhaseMap; +typedef std::map> PartnamePhasenameMap; + +class Phase_Support { +public: + typedef std::set PartSet; + + static bool exists_and_has_phases_defined(const stk::mesh::MetaData & meta); + static Phase_Support & get(stk::mesh::MetaData & meta); + static Phase_Support & get(const stk::mesh::MetaData & meta); + + void get_blocks_touching_surface(const std::string & surface_name, std::vector & block_names); + static void get_input_surfaces_touching_block(const Block_Surface_Connectivity & input_block_surface_info, + const stk::mesh::PartOrdinal block_ordinal, std::set & surface_ordinals); + void get_input_blocks_touching_surface(const Block_Surface_Connectivity & input_block_surface_info, + const stk::mesh::PartOrdinal surfaceOrdinal, std::set & blockOrdinals); + + void check_phase_parts() const; + + bool phases_defined() const { return !my_phase_parts.empty(); } + + void decompose_blocks(const stk::mesh::PartVector& blocks_decomposed_by_ls, + const PhaseVec & ls_phases, const Interface_Name_Generator & interface_name_gen); + std::vector get_blocks_decomposed_by_levelset(const std::vector ls_phases) const; + void setup_phases(const krino::PhaseVec & FEmodel_phases); + void set_input_block_surface_connectivity(const Block_Surface_Connectivity & input_block_surface_info) { my_input_block_surface_connectivity = input_block_surface_info; } + void build_decomposed_block_surface_connectivity(); + + bool is_nonconformal(const stk::mesh::Part * io_part) const; + bool is_conformal(const stk::mesh::Part * io_part) const; + bool is_interface(const stk::mesh::Part * io_part) const; + const stk::mesh::Part * find_conformal_io_part(const stk::mesh::Part & io_part, const PhaseTag & phase) const; + const stk::mesh::Part * find_nonconformal_part(const stk::mesh::Part & io_part) const; + const stk::mesh::Part * find_interface_part(const stk::mesh::Part & vol0, const stk::mesh::Part & vol1) const; + const PhaseTag & get_iopart_phase(const stk::mesh::Part & io_part) const; + + void add_decomposed_part(const stk::mesh::Part & part) { all_decomposed_blocks_selector |= part; } + const stk::mesh::Selector & get_all_decomposed_blocks_selector() const { return all_decomposed_blocks_selector; } + + stk::mesh::Selector get_interface_part_selector(const LS_Field & ls_field); + void register_blocks_for_level_set(LevelSet * levelSet, + const std::vector & blocks_decomposed_by_ls); + stk::mesh::Selector get_all_conformal_surfaces_selector() const; + + bool level_set_is_used_by_nonconformal_part(const LevelSet * levelSet, const stk::mesh::Part * const ioPart) const; + + static bool has_one_levelset_per_phase() { return oneLevelSetPerPhase; } + static void set_one_levelset_per_phase(const bool val) { oneLevelSetPerPhase = val; } + + stk::mesh::PartVector get_nonconformal_parts() const; + stk::mesh::PartVector get_conformal_parts() const; + + void determine_block_phases(const std::set & FEmodel_block_names, const PhaseVec & FEmodel_phases); + void determine_block_phases(const PhaseVec & FEmodel_phases, const PartnamePhasenameMap & FEmodel_block_phase_names); + static PartSet get_blocks_and_touching_surfaces(const stk::mesh::MetaData & mesh_meta, const stk::mesh::PartVector& input_blocks, const Block_Surface_Connectivity & input_block_surface_info); + + static bool has_phases(const std::string & mesh_name) {std::map::const_iterator pos=the_mesh_phases.find(mesh_name); return (pos != the_mesh_phases.end());} + static PhaseVec & get_phases(const std::string & mesh_name) {return the_mesh_phases[mesh_name];} + static std::vector get_level_set_phases(const PhaseVec & mesh_phases, const LevelSet & levelSet); + static PartnamePhasenameMap & get_block_phases_by_name(const std::string & mesh_name) {return the_mesh_block_phases_by_name[mesh_name];} + +private: + Phase_Support(stk::mesh::MetaData & meta); + + const PhasePartTag * find_conformal_phase_part(const stk::mesh::Part & conformal_part) const; + void create_nonconformal_parts(const PartSet & decomposed_ioparts); + void addPhasePart(stk::mesh::Part & io_part, PhasePartSet & phase_parts, const NamedPhase & ls_phase); + void create_phase_parts(const PhaseVec& ls_phases, const PartSet& decomposed_ioparts); + void subset_and_alias_surface_phase_parts(const PhaseVec& ls_phases, const PartSet& decomposed_ioparts); + void create_interface_phase_parts(const PhaseVec& ls_phases, const PartSet& decomposed_ioparts, const Interface_Name_Generator& interface_name_gen); + void get_iopart_roots(const stk::mesh::Part & iopart, std::vector & subsets); + void fill_nonconformal_level_set_maps() const; + +private: + stk::mesh::MetaData & my_meta; + AuxMetaData & my_aux_meta; + PhasePartSet my_phase_parts; + Block_Surface_Connectivity my_input_block_surface_connectivity; + PartPhaseMap my_mesh_block_phases; + std::map lsUsedByParts_; + mutable bool nonconformalLsMapsAreFilled_; + + mutable std::map lsUsedByNonconformalParts_; + static bool oneLevelSetPerPhase; + static std::map the_mesh_phases; + static std::map the_mesh_block_phases_by_name; + + typedef std::map< const stk::mesh::Part *, bool, stk::mesh::PartLess> PartToBoolMap; + typedef std::map< const stk::mesh::Part *, const stk::mesh::Part *, stk::mesh::PartLess > PartToPartMap; + typedef std::map PhaseTagToPartMap; + typedef std::map PartToPhaseTagToPartMap; + typedef std::map PartToPhaseTagMap; + typedef std::map, + const stk::mesh::Part *> VolumePartsToInterfacePartMap; + mutable PartToPhaseTagToPartMap nonconformal_to_phase_conformal_map; + VolumePartsToInterfacePartMap volume_to_interface_parts_map; + PartToBoolMap part_is_conformal_map; + PartToBoolMap part_is_nonconformal_map; + PartToPartMap part_to_nonconformal_part_map; + PartToPhaseTagMap part_to_phase_map; + + stk::mesh::Selector all_decomposed_blocks_selector; +}; + +class CDFEM_Inequality_Spec { +public: + + CDFEM_Inequality_Spec(const std::string & name_); + ~CDFEM_Inequality_Spec() {} + const std::string & name() const {return my_name;} + + enum InequalityCriterionType + { + INEQUALITY_CRITERION_TYPE_UNDEFINED = 0, + LESS_THAN , + GREATER_THAN + }; + + static InequalityCriterionType int_to_inequality_criterion_type(const int inequality_criterion); + + void add_element_volume_name(const std::string & a_element_volue_name); + bool set_threshold_variable_name(const std::string & a_threshold_variable_name); + bool set_threshold_value(const double a_threshold_value); + bool set_criterion_compare_type(const InequalityCriterionType & a_criterion_compare_type); + + void sanity_check(const std::vector mesh_elem_blocks) const; + const std::vector & get_element_volume_names() const { return my_element_volume_names; } + const std::string & get_threshold_variable_name () const { return my_threshold_variable_name; } + double get_threshold_value () const { return my_threshold_value; } + InequalityCriterionType get_criterion_compare_type() const { return my_criterion_compare_type; } + const PhaseTag & get_deactivated_phase() const { return my_deactivated_phase; } + const PhaseTag & get_active_phase() const { return my_active_phase; } + void create_levelset(stk::mesh::MetaData & meta, stk::diag::Timer & parent_timer); + const LevelSet & get_levelset() const { ThrowRequire(my_ls != NULL); return *my_ls; } + LevelSet & get_levelset() { ThrowRequire(my_ls != NULL); return *my_ls; } + + // for unit testing + void set_phases(const PhaseTag & active_phase, const PhaseTag & inactive_phase) + { + my_active_phase = active_phase; + my_deactivated_phase = inactive_phase; + } +protected: + std::string my_name; + std::vector my_element_volume_names; + std::string my_threshold_variable_name; + double my_threshold_value; + InequalityCriterionType my_criterion_compare_type; + LevelSet * my_ls; + PhaseTag my_deactivated_phase; + PhaseTag my_active_phase; +}; +typedef std::vector< CDFEM_Inequality_Spec > CDFEM_Inequality_Spec_Vec; + +class CDFEM_Irreversible_Phase_Support { +public: + ~CDFEM_Irreversible_Phase_Support() {} + + static CDFEM_Irreversible_Phase_Support & get(stk::mesh::MetaData & meta); + + CDFEM_Inequality_Spec * add_death_spec(const std::string & death_name, bool is_death); + + bool is_active() const {return has_death || has_irreversible_phase_change;} + + const CDFEM_Inequality_Spec_Vec & get_death_specs() const {return my_death_specs;} + + // For irreversible phase changes we decompose at the start of the time step, for death at the end. + bool decompose_at_start_of_time_step() { ThrowAssert(has_irreversible_phase_change == !has_death); return has_irreversible_phase_change; } + +private: + CDFEM_Irreversible_Phase_Support() : has_death(false), has_irreversible_phase_change(false) {} +private: + bool has_death; + bool has_irreversible_phase_change; + CDFEM_Inequality_Spec_Vec my_death_specs; +}; + +} // namespace krino + +#endif // Akri_Phase_Support_h diff --git a/packages/krino/krino/krino_lib/Akri_Plane.hpp b/packages/krino/krino/krino_lib/Akri_Plane.hpp new file mode 100644 index 000000000000..b2c7773a50f6 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Plane.hpp @@ -0,0 +1,20 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Plane3d_h +#define Akri_Plane3d_h + +#include + +namespace krino { + +typedef stk::math::Plane3 Plane3d; + +} // namespace krino + +#endif // Akri_Plane3d_h diff --git a/packages/krino/krino/krino_lib/Akri_Plane_Intersections.cpp b/packages/krino/krino/krino_lib/Akri_Plane_Intersections.cpp new file mode 100644 index 000000000000..ce4e72be2807 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Plane_Intersections.cpp @@ -0,0 +1,144 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +namespace krino +{ + +bool +find_intersection_of_three_planes(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2, Vector3d & point) +{ + const Vector3d & normal0 = plane0.normal(); + const Vector3d & normal1 = plane1.normal(); + const Vector3d & normal2 = plane2.normal(); + + const double a00 = normal0[0]; + const double a01 = normal0[1]; + const double a02 = normal0[2]; + const double a10 = normal1[0]; + const double a11 = normal1[1]; + const double a12 = normal1[2]; + const double a20 = normal2[0]; + const double a21 = normal2[1]; + const double a22 = normal2[2]; + const double b0 = plane0.constant(); + const double b1 = plane1.constant(); + const double b2 = plane2.constant(); + const double det = a00*(a22*a11-a21*a12)-a10*(a22*a01-a21*a02)+a20*(a12*a01-a11*a02); + + if (det == 0) + return false; + + const double x =( b0*(a22*a11-a21*a12)-b1*(a22*a01-a21*a02)+b2*(a12*a01-a11*a02))/det; + const double y =(-b0*(a22*a10-a20*a12)+b1*(a22*a00-a20*a02)-b2*(a12*a00-a10*a02))/det; + const double z =( b0*(a21*a10-a20*a11)-b1*(a21*a00-a20*a01)+b2*(a11*a00-a10*a01))/det; + + point = Vector3d{x,y,z}; + return true; +} + +Vector3d +triangle_parametric_coordinates_of_projected_point(const std::array & triCoords, const Vector3d & pt) +{ + const Vector3d v1 = triCoords[1] - triCoords[0]; + const Vector3d v2 = triCoords[2] - triCoords[0]; + const Vector3d normal = Cross(v1,v2); + const double invNormalMag2 = 1./normal.length_squared(); + const Vector3d diff = pt - triCoords[0]; + Vector3d paramPt; + paramPt[0] = Dot(Cross(diff,v2),normal) * invNormalMag2; + paramPt[1] = Dot(Cross(v1,diff),normal) * invNormalMag2; + paramPt[2] = 0.; + return paramPt; +} + +static bool within_tet_bounds(const Vector3d & pt) +{ + const double tol = 1.e-13; + return (pt[0] > -tol) && + (pt[1] > -tol) && + (pt[2] > -tol) && + ((1.-pt[0]-pt[1]-pt[2]) > -tol); +} + +bool find_intersection_of_three_planes_within_tet(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2, Vector3d & intersectionPoint) +{ + return find_intersection_of_three_planes(plane0, plane1, plane2, intersectionPoint) && within_tet_bounds(intersectionPoint); +} + +static bool +find_intersection_of_two_planes_and_coordinate_plane(const int coordinatePlane, const Plane3d & plane0, const Plane3d & plane1, Vector3d & point) +{ + const Vector3d & normal0 = plane0.normal(); + const Vector3d & normal1 = plane1.normal(); + + const std::array,3> activeCoordsByPlane = {{ {{1,2}}, {{0,2}}, {{0,1}} }}; + const int i0 = activeCoordsByPlane[coordinatePlane][0]; + const int i1 = activeCoordsByPlane[coordinatePlane][1]; + + const double a00 = normal0[i0]; + const double a01 = normal0[i1]; + const double a10 = normal1[i0]; + const double a11 = normal1[i1]; + const double b0 = plane0.constant(); + const double b1 = plane1.constant(); + const double det = a00*a11-a10*a01; + + if (det == 0) + return false; + + point[i0] = (b0*a11-b1*a01)/det; + point[i1] = (b1*a00-b0*a10)/det; + point[coordinatePlane] = 0.; + + return true; +} + +bool find_intersection_of_two_planes_and_side_of_tet(const int side, const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint) +{ + bool intersectsPlaneThatCoincidesWithSideOfTet = false; + if (side == 1) + { + const Plane3d side1Plane{Vector3d{1.,0.,0.},Vector3d{0.,0.,1.},Vector3d{0.,1.,0.}}; + intersectsPlaneThatCoincidesWithSideOfTet = find_intersection_of_three_planes(plane0, plane1, side1Plane, intersectionPoint); + } + else + { + const int coordinatePlane = (side == 0) ? 1 : ((side == 2) ? 0 : 2); + intersectsPlaneThatCoincidesWithSideOfTet = find_intersection_of_two_planes_and_coordinate_plane(coordinatePlane, plane0, plane1, intersectionPoint); + } + + return intersectsPlaneThatCoincidesWithSideOfTet && within_tet_bounds(intersectionPoint); + +} + +bool find_intersection_of_two_2D_planes(const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint) +{ + return find_intersection_of_two_planes_and_coordinate_plane(2, plane0, plane1, intersectionPoint); +} + +bool within_tri_bounds(const Vector3d & triangleParamCoords) +{ + const double tol = 1.e-13; + return (triangleParamCoords[0] > -tol) && + (triangleParamCoords[1] > -tol) && + ((1.-triangleParamCoords[0]-triangleParamCoords[1]) > -tol); +} + +bool find_intersection_of_two_2D_planes_within_tri(const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint) +{ + return find_intersection_of_two_planes_and_coordinate_plane(2, plane0, plane1, intersectionPoint) && within_tri_bounds(intersectionPoint); +} + +} // namespace krino + + + diff --git a/packages/krino/krino/krino_lib/Akri_Plane_Intersections.hpp b/packages/krino/krino/krino_lib/Akri_Plane_Intersections.hpp new file mode 100644 index 000000000000..b7a20f805b00 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Plane_Intersections.hpp @@ -0,0 +1,31 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_PLANE_INTERSECTIONS_H_ +#define KRINO_INCLUDE_AKRI_PLANE_INTERSECTIONS_H_ +#include +#include + +namespace krino { + +bool find_intersection_of_three_planes(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2, Vector3d & point); + +bool find_intersection_of_three_planes_within_tet(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2, Vector3d & point); + +bool find_intersection_of_two_planes_and_side_of_tet(const int side, const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint); + +bool find_intersection_of_two_2D_planes(const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint); + +bool find_intersection_of_two_2D_planes_within_tri(const Plane3d & plane0, const Plane3d & plane1, Vector3d & intersectionPoint); + +Vector3d triangle_parametric_coordinates_of_projected_point(const std::array & triCoords, const Vector3d & pt); + +bool within_tri_bounds(const Vector3d & triangleParamCoords); +} + +#endif /* KRINO_INCLUDE_AKRI_PLANE_INTERSECTIONS_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_ProlongationData.cpp b/packages/krino/krino/krino_lib/Akri_ProlongationData.cpp new file mode 100644 index 000000000000..84a59e23926a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ProlongationData.cpp @@ -0,0 +1,659 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +#include +#include + +#include + +namespace krino{ + +ProlongationElementData::ProlongationElementData(const stk::mesh::BulkData& stk_mesh, const std::vector & children_data, const std::vector< std::vector > & children_intg_wts) +{ + ThrowAssert(!children_data.empty() && children_data.size() == children_intg_wts.size()); + + const unsigned num_intg_pts = children_intg_wts[0].size(); + + // homogenize fields + const stk::mesh::FieldVector & all_fields = stk_mesh.mesh_meta_data().get_fields(); + my_field_indices.resize(all_fields.size(), -1); + for ( stk::mesh::FieldVector::const_iterator it = all_fields.begin(); it != all_fields.end() ; ++it ) + { + const FieldRef field = **it; + + if( field.entity_rank()!=stk::topology::ELEMENT_RANK || !field.type_is() ) continue; + + bool any_child_has_field = false; + for (auto && child_data : children_data) + { + if (NULL != child_data->get_field_data(field)) + { + any_child_has_field = true; + break; + } + } + + if (any_child_has_field) + { + const unsigned field_length = field.length(); + const unsigned field_data_index = my_field_data.size(); + my_field_indices[field.field().mesh_meta_data_ordinal()] = field_data_index; + my_field_data.resize(field_data_index+field_length, 0.0); + + // TODO: Add a method to distinguish between vector fields and gauss point fields. + const bool data_is_gauss_pt_field = (num_intg_pts == field_length); + + if (data_is_gauss_pt_field) + { + double tot_child_sum = 0.; + double tot_child_vol = 0.; + + for (unsigned n = 0; n < children_data.size(); ++n) + { + const double * subelem_field_data = children_data[n]->get_field_data(field); + if(NULL == subelem_field_data) + { + continue; + } + + const std::vector & child_intg_wts = children_intg_wts[n]; + ThrowAssertMsg(child_intg_wts.size() == num_intg_pts, "Children have different integration rules."); + + for (unsigned j=0; jget_field_data(field); + if(NULL == subelem_field_data) + { + continue; + } + + const std::vector & child_intg_wts = children_intg_wts[n]; + // We could relax this assertion if we had another way to distinguish gauss point fields from vector fields + ThrowAssertMsg(child_intg_wts.size() == num_intg_pts, "Children have different integration rules."); + + double child_vol = 0.; + for (unsigned j=0; j() ) continue; + + double * val = field_data(field, entity); + const bool has_field = (NULL != val); + + if (has_field) + { + const unsigned field_length = field.length(); + my_field_indices[field.field().mesh_meta_data_ordinal()] = my_field_data.size(); + for (unsigned i=0; i() ) continue; + const unsigned field_length = field.length(); + + double * val = field_data(field, entity); + const double * prolong_field = get_field_data(field); + + if (nullptr == val) continue; + if(nullptr == prolong_field) + { + std::stringstream err_msg; + err_msg << "Missing prolongation field data when restoring fields on entity:\n"; + err_msg << stk_mesh.identifier(entity) << " of rank " << stk_mesh.entity_rank(entity); + err_msg << " with parts:\n "; + for(auto && part : stk_mesh.bucket(entity).supersets()) + { + err_msg << part->name() << ", "; + } + err_msg << "\n"; + err_msg << "Missing field data for field " << field.name() << "\n"; + throw std::runtime_error(err_msg.str()); + } + + for (unsigned i=0; i +ProlongationNodeData::get_fields_on_node(const stk::mesh::BulkData& mesh, stk::mesh::Entity entity) +{ + const stk::mesh::FieldVector & all_fields = mesh.mesh_meta_data().get_fields(); + std::vector entity_fields; + entity_fields.reserve(all_fields.size()); + for ( auto && fieldPtr : all_fields ) + { + const FieldRef field = *fieldPtr; + if (field.field().entity_rank() == stk::topology::NODE_RANK && nullptr != field_data(field, entity)) + entity_fields.push_back(field.field().mesh_meta_data_ordinal()); + } + + std::sort(entity_fields.begin(), entity_fields.end()); + return entity_fields; +} + +Vector3d +ProlongationNodeData::get_node_coordinates(const CDMesh & mesh, stk::mesh::Entity node) +{ + const double * coordsPtr = field_data(mesh.get_coords_field(), node); + ThrowAssert(coordsPtr); + Vector3d coords(coordsPtr, mesh.spatial_dim()); + FieldRef cdfemSnapDispField = mesh.get_cdfem_support().get_cdfem_snap_displacements_field(); + if (cdfemSnapDispField.valid()) + { + FieldRef oldCdfemSnapDispField = cdfemSnapDispField.field_state(stk::mesh::StateOld); + double * cdfemSnapDispPtr = field_data(cdfemSnapDispField, node); + double * oldCdfemSnapDispPtr = field_data(oldCdfemSnapDispField, node); + if (nullptr != cdfemSnapDispPtr) + coords += Vector3d(oldCdfemSnapDispPtr, mesh.spatial_dim()) - Vector3d(cdfemSnapDispPtr, mesh.spatial_dim()); + } + return coords; +} + +std::vector +ProlongationNodeData::get_node_io_parts(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity entity) +{ + // This list of parts is used to determine if a node needs to be ALE prolonged + stk::mesh::PartVector node_parts = filter_non_io_parts(stk_mesh.bucket(entity).supersets()); + std::vector node_part_ids; + node_part_ids.reserve(node_parts.size()); + for (auto * node_part : node_parts) + node_part_ids.push_back(node_part->mesh_meta_data_ordinal()); + std::sort(node_part_ids.begin(), node_part_ids.end()); + return node_part_ids; +} + +ProlongationNodeData::ProlongationNodeData(const CDMesh & mesh, stk::mesh::Entity node, bool communicate_me_to_all_sharers) + : ProlongationPointData(get_node_coordinates(mesh, node)), + my_entityId(mesh.stk_bulk().identifier(node)), + myCommunicateMeToAllSharersFlag(communicate_me_to_all_sharers) +{ + const stk::mesh::BulkData& stk_mesh = mesh.stk_bulk(); + + my_fields = get_fields_on_node(stk_mesh, node); + my_ioparts = get_node_io_parts(stk_mesh, node); + + save_fields(stk_mesh, node); +} + +ProlongationPointData::ProlongationPointData(const CDMesh & mesh, const FacetDistanceQuery & facet_dist_query, + const std::vector & facet_nodes) + : my_coordinates(facet_dist_query.closest_point()) +{ + const Vector3d node_wts = facet_dist_query.closest_point_weights(); + + // interpolate fields + const stk::mesh::FieldVector & all_fields = mesh.stk_meta().get_fields(); + my_field_indices.resize(all_fields.size(), -1); + for ( stk::mesh::FieldVector::const_iterator it = all_fields.begin(); it != all_fields.end() ; ++it ) + { + const FieldRef field = **it; + + if( field.entity_rank()!=stk::topology::NODE_RANK || !field.type_is() ) continue; + + const unsigned field_length = field.length(); + + bool any_node_has_field = false; + for (auto && facet_node : facet_nodes) + { + if (NULL != facet_node->get_field_data(field)) + { + any_node_has_field = true; + break; + } + } + + if (any_node_has_field) + { + const unsigned field_data_index = my_field_data.size(); + my_field_indices[field.field().mesh_meta_data_ordinal()] = field_data_index; + my_field_data.resize(field_data_index+field_length, 0.0); + + double node_wt_sum = 0.0; + for (unsigned n = 0; n < facet_nodes.size(); ++n) + { + const double * node_field_data = facet_nodes[n]->get_field_data(field); + + if(node_field_data) + { + node_wt_sum += node_wts[n]; + for (unsigned i=0; i nodeSharedProcs; + stk::pack_and_communicate(commSparse,[&]() + { + for (auto entry : proc_prolong_nodes) + { + const ProlongationNodeData & prolongNode = *entry.second; + if (prolongNode.communicate_me_to_all_sharers()) + { + stk::mesh::Entity node = mesh.get_entity(stk::topology::NODE_RANK, prolongNode.entityId()); + mesh.comm_shared_procs(node, nodeSharedProcs); + for (int procId : nodeSharedProcs) + prolongNode.pack_into_buffer(commSparse.send_buffer(procId)); + } + } + }); +} + +static +void pack_facet_prolong_nodes(const stk::mesh::BulkData & mesh, const ProlongFacetVec & proc_prolong_facets, const std::vector & proc_target_bboxes, stk::CommSparse &commSparse) +{ + stk::pack_and_communicate(commSparse,[&]() + { + for ( int procId=0; procIdpack_into_buffer(buffer); + } + }); +} + +static +void receive_and_build_prolong_nodes(const CDMesh & mesh, EntityProlongationNodeMap & proc_prolong_nodes, stk::CommSparse &commSparse) +{ + stk::unpack_communications(commSparse, [&](int procId) + { + stk::CommBuffer & buffer = commSparse.recv_buffer(procId); + + while ( buffer.remaining() ) + { + ProlongationNodeData * node = ProlongationNodeData::unpack_from_buffer( buffer, mesh.stk_meta() ); // This calls new to create a new ProlongationNodeData + EntityProlongationNodeMap::iterator it = proc_prolong_nodes.find(node->entityId()); + if( it == proc_prolong_nodes.end() || it->second == nullptr ) + { + proc_prolong_nodes[node->entityId()] = node; + } + else + { + delete node; + } + } + }); +} + +void ProlongationFacet::communicate_shared_nodes( const CDMesh & mesh, EntityProlongationNodeMap & proc_prolong_nodes ) +{ + stk::CommSparse commSparse(mesh.stk_bulk().parallel()); + pack_nodes_that_need_to_be_communicated_to_sharers(mesh.stk_bulk(), proc_prolong_nodes, commSparse); + receive_and_build_prolong_nodes(mesh, proc_prolong_nodes, commSparse); +} + + +void +ProlongationFacet::communicate_facet_nodes( const CDMesh & mesh, const ProlongFacetVec & proc_prolong_facets, EntityProlongationNodeMap & proc_prolong_nodes, const std::vector & proc_target_bboxes ) +{ /* %TRACE[ON]% */ Trace trace__("krino:ProlongationFacet::communicate_facet_nodes()"); /* %TRACE% */ + const int num_procs = mesh.stk_bulk().parallel_size(); + if ( num_procs == 1 ) return; // Don't talk to yourself, it's embarrassing + + stk::CommSparse commSparse(mesh.stk_bulk().parallel()); + pack_facet_prolong_nodes(mesh.stk_bulk(), proc_prolong_facets, proc_target_bboxes, commSparse); + receive_and_build_prolong_nodes(mesh, proc_prolong_nodes, commSparse); +} + +void +ProlongationNodeData::pack_into_buffer(stk::CommBuffer & b) const +{ + b.pack(my_entityId); + + b.pack(my_coordinates.data(),3); + + const size_t num_fields = my_fields.size(); + b.pack(num_fields); + b.pack(my_fields.data(), my_fields.size()); + + const size_t num_parts = my_ioparts.size(); + b.pack(num_parts); + b.pack(my_ioparts.data(), my_ioparts.size()); + + b.pack(my_field_indices.data(),my_field_indices.size()); + + const size_t num_field_data = my_field_data.size(); + b.pack(num_field_data); + b.pack(my_field_data.data(),my_field_data.size()); +} + +ProlongationNodeData * +ProlongationNodeData::unpack_from_buffer( stk::CommBuffer & b, const stk::mesh::MetaData & stk_meta ) +{ + stk::mesh::EntityId global_id; + b.unpack(global_id); + + Vector3d coords; + b.unpack(coords.data(),3); + + size_t num_fields = 0; + b.unpack(num_fields); + std::vector node_fields(num_fields); + b.unpack(node_fields.data(), num_fields); + + size_t num_parts = 0; + b.unpack(num_parts); + std::vector node_ioparts(num_parts); + b.unpack(node_ioparts.data(), num_parts); + + ProlongationNodeData * node = new ProlongationNodeData(global_id, coords, node_fields, node_ioparts); + + const size_t len_field_indices = stk_meta.get_fields().size(); + std::vector & field_indices = node->get_field_indices(); + field_indices.resize(len_field_indices); + b.unpack(field_indices.data(), len_field_indices); + + size_t num_field_data = 0; + b.unpack(num_field_data); + std::vector & field_data = node->get_field_data(); + field_data.resize(num_field_data); + b.unpack(field_data.data(), num_field_data); + + return node; +} + +std::string +ProlongationData::missing_prolongation_fields_for_entity( const CDMesh & mesh, const stk::mesh::Entity dst ) const +{ + std::string missing_fields; + const FieldSet & ale_prolongation_fields = mesh.get_ale_prolongation_fields(); + for ( auto&& field : ale_prolongation_fields ) + { + if( !field.type_is() || field.entity_rank() != mesh.stk_bulk().entity_rank(dst) ) continue; + + double * val = field_data(field, dst); + if (NULL != val && NULL == get_field_data(field)) + { + missing_fields = missing_fields + " " + field.name(); + } + } + + return missing_fields; +} + +void ProlongationFacet::compute_common_fields() +{ + my_common_fields.clear(); + for (unsigned side_node_index=0; side_node_index & node_fields = my_prolong_nodes[side_node_index]->get_fields(); + if (0 == side_node_index) + { + my_common_fields = node_fields; + } + else + { + std::vector working_set; + working_set.swap(my_common_fields); + std::set_intersection(working_set.begin(),working_set.end(),node_fields.begin(),node_fields.end(),std::back_inserter(my_common_fields)); + } + } +} + +ProlongationFacet::ProlongationFacet(const CDMesh & mesh, stk::mesh::Entity side) +: my_mesh(mesh) +{ + const stk::mesh::BulkData & stk_mesh = my_mesh.stk_bulk(); + + ThrowAssert(stk_mesh.num_elements(side) > 0); + stk::mesh::Entity elem0 = stk_mesh.begin_elements(side)[0]; + const PhaseTag elem0_phase = mesh.determine_entity_phase(elem0); + + const unsigned num_side_nodes = stk_mesh.bucket(side).topology().base().num_nodes(); + const stk::mesh::Entity* side_nodes = stk_mesh.begin_nodes(side); + my_prolong_nodes.resize(num_side_nodes); + + for (unsigned side_node_index=0; side_node_index( my_prolong_nodes[0]->get_coordinates(), my_prolong_nodes[1]->get_coordinates()); + } + else + { + ThrowAssert(3 == my_prolong_nodes.size()); + my_facet = std::make_unique( my_prolong_nodes[0]->get_coordinates(), my_prolong_nodes[1]->get_coordinates(), my_prolong_nodes[2]->get_coordinates()); + } +} + +ProlongationFacet::ProlongationFacet(const CDMesh & mesh, const std::vector & prolong_nodes, const std::vector & common_fields) +: my_mesh (mesh), + my_prolong_nodes(prolong_nodes), + my_common_fields(common_fields) +{ + ThrowAssert((int)my_prolong_nodes.size() == my_mesh.spatial_dim()); + if (2 == my_prolong_nodes.size()) + { + my_facet = std::make_unique( my_prolong_nodes[0]->get_coordinates(), my_prolong_nodes[1]->get_coordinates()); + } + else + { + ThrowAssert(3 == my_prolong_nodes.size()); + my_facet = std::make_unique( my_prolong_nodes[0]->get_coordinates(), my_prolong_nodes[1]->get_coordinates(), my_prolong_nodes[2]->get_coordinates()); + } +} + +void ProlongationFacet::update_prolongation_point_data(const FacetDistanceQuery & dist_query) const +{ + ThrowAssert(&dist_query.facet() == my_facet.get()); + my_prolongation_point_data = std::make_unique(my_mesh, dist_query, my_prolong_nodes); +} + +bool ProlongationFacet::communicate_me(const BoundingBox & proc_target_bbox) const +{ + for(auto && prolong_node : my_prolong_nodes) + { + if (!proc_target_bbox.contains(prolong_node->get_coordinates())) + { + return false; + } + } + return true; +} + +std::set +ProlongationFacet::get_facet_nodes_to_communicate( const ProlongFacetVec & proc_prolong_facets, const BoundingBox & proc_target_bbox ) +{ + std::set procFacetNodes; + + for ( auto && facet : proc_prolong_facets ) + if (facet->communicate_me(proc_target_bbox)) + for (auto node : facet->my_prolong_nodes) + procFacetNodes.insert(node); + + return procFacetNodes; +} + +void +ProlongationFacet::communicate( const CDMesh & mesh, ProlongFacetVec & proc_prolong_facets, EntityProlongationNodeMap & proc_prolong_nodes, const std::vector & proc_target_bboxes ) +{ /* %TRACE[ON]% */ Trace trace__("krino:ProlongationFacet::communicate()"); /* %TRACE% */ + communicate_shared_nodes(mesh, proc_prolong_nodes); + communicate_facet_nodes(mesh, proc_prolong_facets, proc_prolong_nodes, proc_target_bboxes); + communicate_facets(mesh, proc_prolong_facets, proc_target_bboxes); +} + +static +void pack_facets_within_proc_bboxes(const stk::mesh::BulkData & mesh, const ProlongFacetVec & proc_prolong_facets, const std::vector & proc_target_bboxes, stk::CommSparse &commSparse) +{ + stk::pack_and_communicate(commSparse,[&]() + { + for ( int procId=0; procId & proc_target_bboxes ) +{ + stk::CommSparse commSparse(mesh.stk_bulk().parallel()); + pack_facets_within_proc_bboxes(mesh.stk_bulk(), proc_prolong_facets, proc_target_bboxes, commSparse); + receive_and_build_prolong_facets(mesh, proc_prolong_facets, commSparse); +} + +void +ProlongationFacet::pack_into_buffer(stk::CommBuffer & b) const +{ + const size_t num_prolong_nodes = my_prolong_nodes.size(); + b.pack(num_prolong_nodes); + for(auto && prolong_node : my_prolong_nodes) + { + b.pack(prolong_node->entityId()); + } + + b.pack(my_common_fields.size()); + for (unsigned field : my_common_fields) + b.pack(field); +} + +ProlongationFacet * +ProlongationFacet::unpack_from_buffer(const CDMesh & mesh, stk::CommBuffer & b ) +{ + size_t num_prolong_nodes = 0; + b.unpack(num_prolong_nodes); + std::vector prolong_nodes(num_prolong_nodes); + + for(auto && prolong_node : prolong_nodes) + { + stk::mesh::EntityId node_id; + b.unpack(node_id); + prolong_node = mesh.fetch_prolong_node(node_id); + ThrowRequireMsg(prolong_node, "Communication error, missing prolongation node " << node_id << " on processor " << mesh.stk_bulk().parallel_rank()); + } + + size_t num_common_fields = 0; + b.unpack(num_common_fields); + + std::vector common_fields(num_common_fields); + for (size_t ifield=0; ifield +#include +#include + +#include +#include +#include +#include + +namespace krino { + +class ProlongationData { +public: + ProlongationData() {} + ~ProlongationData() {} + + const double * get_field_data( const stk::mesh::FieldBase& state_field ) const { const int field_index = my_field_indices[state_field.mesh_meta_data_ordinal()]; return (field_index < 0) ? nullptr : &my_field_data[field_index]; } + std::string missing_prolongation_fields_for_entity( const CDMesh & mesh, const stk::mesh::Entity dst ) const; + void restore_fields(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity entity) const; + +protected: + void save_fields(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity entity); + const std::vector & get_field_data() const { return my_field_data; } + std::vector & get_field_data() { return my_field_data; } + const std::vector & get_field_indices() const { return my_field_indices; } + std::vector & get_field_indices() { return my_field_indices; } + +protected: + mutable std::vector my_field_indices; + mutable std::vector my_field_data; +}; + +class ProlongationPointData : public ProlongationData { +public: + ProlongationPointData(const Vector3d & coordinates) : my_coordinates(coordinates) {} + ProlongationPointData(const CDMesh & mesh, const FacetDistanceQuery & facet_dist_query, const std::vector & facet_nodes); + ~ProlongationPointData() {} + + const Vector3d & get_coordinates() const { return my_coordinates; } + Vector3d & get_coordinates() { return my_coordinates; } + +protected: + Vector3d my_coordinates; +}; + +class ProlongationElementData : public ProlongationData { +public: + ProlongationElementData(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity element) : ProlongationData() { save_fields(stk_mesh, element); } + ProlongationElementData(const stk::mesh::BulkData& stk_mesh, const std::vector & children_data, const std::vector< std::vector > & children_intg_wts); + ~ProlongationElementData() {} + +private: + //: copy constructor not allowed + ProlongationElementData(const ProlongationElementData & copy); +}; + +class ProlongationNodeData : public ProlongationPointData { +public: + ProlongationNodeData(const CDMesh & mesh, stk::mesh::Entity node, bool communicate_me_to_all_sharers); + ProlongationNodeData(const stk::mesh::EntityId in_entityId, const Vector3d & coordinates, const std::vector & fields, const std::vector & ioparts) + : ProlongationPointData(coordinates), my_entityId(in_entityId), myCommunicateMeToAllSharersFlag(false), my_fields(fields), my_ioparts(ioparts) {} + + ~ProlongationNodeData() {} + + static std::vector get_node_io_parts(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity entity); + static std::vector get_fields_on_node(const stk::mesh::BulkData& stk_mesh, stk::mesh::Entity entity); + static Vector3d get_node_coordinates(const CDMesh & mesh, stk::mesh::Entity node); + + static ProlongationNodeData * unpack_from_buffer( stk::CommBuffer & b, const stk::mesh::MetaData & stk_meta ); // static method that builds surface from data in buffer for off-processor communication + void pack_into_buffer(stk::CommBuffer & b) const; + bool communicate_me_to_all_sharers() const { return myCommunicateMeToAllSharersFlag; } + + const std::vector & get_fields() const { ThrowRequireMsg(!my_fields.empty(), "Fields not set for prolongation node."); return my_fields; } + const std::vector & get_io_parts() const { ThrowRequireMsg(!my_ioparts.empty(), "IO Parts not set for prolongation node."); return my_ioparts; } + stk::mesh::EntityId entityId() const { return my_entityId; } + +protected: + const stk::mesh::EntityId my_entityId; + const bool myCommunicateMeToAllSharersFlag; + mutable std::vector my_fields; + mutable std::vector my_ioparts; + +private: + //: copy constructor not allowed + ProlongationNodeData(const ProlongationNodeData & copy); +}; + +class ProlongationFacet { +public: + ProlongationFacet(const CDMesh & mesh, const std::vector & prolong_nodes, const std::vector & common_fields); + ProlongationFacet(const CDMesh & mesh, stk::mesh::Entity side); + + static void communicate( const CDMesh & mesh, ProlongFacetVec & proc_prolong_facets, EntityProlongationNodeMap & proc_prolong_nodes, const std::vector & proc_target_bboxes ); + static std::set get_facet_nodes_to_communicate( const ProlongFacetVec & proc_prolong_facets, const BoundingBox & proc_target_bbox ); + + void pack_into_buffer(stk::CommBuffer & b) const; + static ProlongationFacet * unpack_from_buffer( const CDMesh & mesh, stk::CommBuffer & b ); // static method that builds surface from data in buffer for off-processor communication + void compute_common_fields(); + + static const BoundingBox & get_bounding_box(const ProlongationFacet * prolong_facet) { return prolong_facet->get_facet()->bounding_box(); } + + Facet * get_facet() const { return my_facet.get(); } + const std::vector & get_common_fields() const { return my_common_fields; } + const ProlongationPointData * get_prolongation_point_data(const FacetDistanceQuery & dist_query) const { update_prolongation_point_data(dist_query); return my_prolongation_point_data.get(); } + const std::vector & get_prolongation_nodes() const { return my_prolong_nodes; } + bool communicate_me(const BoundingBox & proc_target_bbox) const; + +protected: + void update_prolongation_point_data(const FacetDistanceQuery & dist_query) const; + +protected: + const CDMesh & my_mesh; + std::unique_ptr my_facet; + mutable std::unique_ptr my_prolongation_point_data; + mutable std::vector my_prolong_nodes; + mutable std::vector my_common_fields; + +private: + //: copy constructor not allowed + ProlongationFacet(const ProlongationFacet & copy); + static void communicate_shared_nodes( const CDMesh & mesh, EntityProlongationNodeMap & proc_prolong_nodes ); + static void communicate_facets( const CDMesh & mesh, ProlongFacetVec & proc_prolong_facets, const std::vector & proc_target_bboxes ); + static void communicate_facet_nodes( const CDMesh & mesh, const ProlongFacetVec & proc_prolong_facets, EntityProlongationNodeMap & proc_prolong_nodes, const std::vector & proc_target_bboxes ); +}; + +} // namespace krino + +#endif // Akri_ProlongationData_h diff --git a/packages/krino/krino/krino_lib/Akri_QualityMetric.cpp b/packages/krino/krino/krino_lib/Akri_QualityMetric.cpp new file mode 100644 index 000000000000..fcc6a98472ce --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_QualityMetric.cpp @@ -0,0 +1,127 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino +{ + +double calculate_tet_volume_using_sides(const stk::math::Vector3d &side0, const stk::math::Vector3d &side2, const stk::math::Vector3d &side3) +{ + return Dot(side3, Cross(side2, side0))/6.0; +} + +double MeanRatioQualityMetric::tet_mean_ratio(const std::vector &nodeLocations) +{ + ThrowAssert(nodeLocations.size() == 4 || nodeLocations.size() == 10); + + const stk::math::Vector3d side0 = nodeLocations[1] - nodeLocations[0]; + const stk::math::Vector3d side2 = nodeLocations[0] - nodeLocations[2]; + const stk::math::Vector3d side3 = nodeLocations[3] - nodeLocations[0]; + + const double volumeMin = 1.0E-30; + const double tetVolume = calculate_tet_volume_using_sides(side0, side2, side3); + if( std::abs( tetVolume ) < volumeMin ) + return 0.0; + + const stk::math::Vector3d side1 = nodeLocations[2] - nodeLocations[1]; + const stk::math::Vector3d side4 = nodeLocations[3] - nodeLocations[1]; + const stk::math::Vector3d side5 = nodeLocations[3] - nodeLocations[2]; + + const double side0_length_squared = side0.length_squared(); + const double side1_length_squared = side1.length_squared(); + const double side2_length_squared = side2.length_squared(); + const double side3_length_squared = side3.length_squared(); + const double side4_length_squared = side4.length_squared(); + const double side5_length_squared = side5.length_squared(); + + const int sign = tetVolume < 0. ? -1 : 1; + return sign * 12. * std::pow(3.*std::abs(tetVolume), 2./3.) / (side0_length_squared + side1_length_squared + side2_length_squared + side3_length_squared + side4_length_squared + side5_length_squared); +} + +double ScaledJacobianQualityMetric::tet_scaled_jacobian(const std::vector &nodeLocations) +{ + ThrowAssert(nodeLocations.size() == 4 || nodeLocations.size() == 10); + + const stk::math::Vector3d side0 = nodeLocations[1] - nodeLocations[0]; + const stk::math::Vector3d side1 = nodeLocations[2] - nodeLocations[1]; + const stk::math::Vector3d side2 = nodeLocations[0] - nodeLocations[2]; + const stk::math::Vector3d side3 = nodeLocations[3] - nodeLocations[0]; + const stk::math::Vector3d side4 = nodeLocations[3] - nodeLocations[1]; + const stk::math::Vector3d side5 = nodeLocations[3] - nodeLocations[2]; + + const double jacobi = Dot(side3, Cross(side2, side0)); + + // products of lengths squared of each edge attached to a node. + const double side0_length_squared = side0.length_squared(); + const double side1_length_squared = side1.length_squared(); + const double side2_length_squared = side2.length_squared(); + const double side3_length_squared = side3.length_squared(); + const double side4_length_squared = side4.length_squared(); + const double side5_length_squared = side5.length_squared(); + + const double length_squared[4] = { + side0_length_squared * side2_length_squared * side3_length_squared, + side0_length_squared * side1_length_squared * side4_length_squared, + side1_length_squared * side2_length_squared * side5_length_squared, + side3_length_squared * side4_length_squared * side5_length_squared + }; + int which_node = 0; + if(length_squared[1] > length_squared[which_node]) + which_node = 1; + if(length_squared[2] > length_squared[which_node]) + which_node = 2; + if(length_squared[3] > length_squared[which_node]) + which_node = 3; + + double length_product = std::sqrt( length_squared[which_node] ); + if(length_product < std::abs(jacobi)) + length_product = std::abs(jacobi); + + const double lengthMin = 1.0E-30; + if( length_product < lengthMin ) + return 0.0; + + static const double root_of_2 = std::sqrt(2.0); + return root_of_2 * jacobi / length_product; +} + +double ScaledJacobianQualityMetric::tri2d_scaled_jacobian(const std::vector &nodeLocations) +{ + const double absScaledJacobian = tri3d_scaled_jacobian(nodeLocations); + const double normalZ = + (nodeLocations[1][0]-nodeLocations[0][0])*(nodeLocations[2][1]-nodeLocations[0][1]) - + (nodeLocations[1][1]-nodeLocations[0][1])*(nodeLocations[2][0]-nodeLocations[0][0]); + return (normalZ > 0.) ? absScaledJacobian : -absScaledJacobian; +} + +double ScaledJacobianQualityMetric::tri3d_scaled_jacobian(const std::vector &nodeLocations) +{ + ThrowAssert(nodeLocations.size() == 3 || nodeLocations.size() == 6); + + const stk::math::Vector3d edge0 = nodeLocations[1] - nodeLocations[0]; + const stk::math::Vector3d edge1 = nodeLocations[2] - nodeLocations[0]; + const stk::math::Vector3d edge2 = nodeLocations[2] - nodeLocations[1]; + + const double lenSqr0 = edge0.length_squared(); + const double lenSqr1 = edge1.length_squared(); + const double lenSqr2 = edge2.length_squared(); + + const double maxEdgeLengthProduct = std::sqrt( std::max(lenSqr0*lenSqr1, std::max(lenSqr1*lenSqr2, lenSqr0*lenSqr2)) ); + + const double lengthMin = 1.0E-30; + if( maxEdgeLengthProduct < lengthMin ) + return 0.0; + + static const double two_over_root_of_3 = 2./sqrt(3.0); + const double jacobian = Cross(edge0, edge1).length(); + return jacobian*two_over_root_of_3/maxEdgeLengthProduct; +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_QualityMetric.hpp b/packages/krino/krino/krino_lib/Akri_QualityMetric.hpp new file mode 100644 index 000000000000..02599303f86f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_QualityMetric.hpp @@ -0,0 +1,76 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_QUALITY_METRIC_H +#define AKRI_QUALITY_METRIC_H +#include +#include + +namespace krino +{ + +class QualityMetric +{ +public: + virtual ~QualityMetric() {} + + virtual bool is_first_quality_metric_better_than_second(const double firstValue, const double secondValue) const = 0; + virtual double get_element_quality_metric(const std::vector &nodeLocations) const = 0; + virtual double get_best_value_for_metric() const = 0; + virtual double get_acceptable_value_for_metric() const = 0; +}; + +class MeanRatioQualityMetric : public QualityMetric +{ +public: + virtual ~MeanRatioQualityMetric() {} + + virtual double get_best_value_for_metric() const override { return 1.0; } + virtual bool is_first_quality_metric_better_than_second(const double firstValue, const double secondValue) const override + { + return static_cast(firstValue) > static_cast(secondValue); + } + + double get_element_quality_metric(const std::vector &nodeLocations) const override + { + return tet_mean_ratio(nodeLocations); + } + + static double tet_mean_ratio(const std::vector &nodeLocations); + + virtual double get_acceptable_value_for_metric() const override { return 0.2; } +}; + +class ScaledJacobianQualityMetric : public QualityMetric +{ +public: + ScaledJacobianQualityMetric() = default; + virtual ~ScaledJacobianQualityMetric() {} + + virtual double get_best_value_for_metric() const override { return 1.0; } + virtual bool is_first_quality_metric_better_than_second( + const double firstValue, const double secondValue) const override + { + return static_cast(firstValue) > static_cast(secondValue); + } + + double get_element_quality_metric(const std::vector &nodeLocations) const override + { + return (nodeLocations.size() == 4 || nodeLocations.size() == 10) ? tet_scaled_jacobian(nodeLocations) : tri2d_scaled_jacobian(nodeLocations); + } + + static double tet_scaled_jacobian(const std::vector &nodeLocations); + static double tri2d_scaled_jacobian(const std::vector &nodeLocations); + static double tri3d_scaled_jacobian(const std::vector &nodeLocations); + + virtual double get_acceptable_value_for_metric() const override { return 0.1; } +}; + +} + +#endif diff --git a/packages/krino/krino/krino_lib/Akri_RegionInterface.cpp b/packages/krino/krino/krino_lib/Akri_RegionInterface.cpp new file mode 100644 index 000000000000..f04136783043 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_RegionInterface.cpp @@ -0,0 +1,15 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +namespace krino{ + +std::unique_ptr RegionInterface::the_currently_parsed_region; + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_RegionInterface.hpp b/packages/krino/krino/krino_lib/Akri_RegionInterface.hpp new file mode 100644 index 000000000000..09248bed11a0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_RegionInterface.hpp @@ -0,0 +1,65 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_RegionInterface_h +#define Akri_RegionInterface_h + +#include +#include + +namespace Ioss { class Region; } +namespace stk { namespace diag { class Timer; } } +namespace stk { namespace mesh { class MetaData; } } + +namespace krino { + +class RegionInterface { + + public: + static RegionInterface & set_currently_parsed_region(stk::mesh::MetaData & meta, + const std::string & region_name, + stk::diag::Timer & region_timer, + const std::string & name_of_input_mesh, + Ioss::Region * ioss_region) + { + the_currently_parsed_region = std::make_unique(meta, region_name, region_timer, name_of_input_mesh, ioss_region); + return *the_currently_parsed_region; + } + static void clear_currently_parsed_region() { the_currently_parsed_region.reset(); } + static RegionInterface & get_currently_parsed_region() { ThrowAssert(nullptr != the_currently_parsed_region); return *the_currently_parsed_region; } + + stk::mesh::MetaData & get_stk_mesh_meta_data() { return my_meta; } + const std::string & name() { return my_region_name; } + stk::diag::Timer & getRegionTimer() const { return my_region_timer; } + const std::string & name_of_input_mesh() const { return my_name_of_input_mesh; } + Ioss::Region * get_input_io_region() { return my_ioss_region; } + + // must be public to be used by make_unique + RegionInterface(stk::mesh::MetaData & meta, + const std::string & region_name, + stk::diag::Timer & region_timer, + const std::string & input_mesh, + Ioss::Region * ioss_region) + : my_meta(meta), + my_region_name(region_name), + my_region_timer(region_timer), + my_name_of_input_mesh(input_mesh), + my_ioss_region(ioss_region) {} + +private: + static std::unique_ptr the_currently_parsed_region; + stk::mesh::MetaData & my_meta; + const std::string my_region_name; + stk::diag::Timer & my_region_timer; + const std::string my_name_of_input_mesh; + Ioss::Region * my_ioss_region; +}; + +} // end krino namespace + +#endif /* Akri_RegionInterface_h */ diff --git a/packages/krino/krino/krino_lib/Akri_ReportHandler.hpp b/packages/krino/krino/krino_lib/Akri_ReportHandler.hpp new file mode 100644 index 000000000000..9c3c57c4f4d9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_ReportHandler.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_REPORTHANDLER_H_ +#define KRINO_INCLUDE_AKRI_REPORTHANDLER_H_ + +#include +#include + +#define ParallelThrowRequire(parallel,expr) ThrowRequire(stk::is_true_on_all_procs(parallel,expr)) +#define ParallelThrowRequireMsg(parallel,expr,message) ThrowRequireMsg(stk::is_true_on_all_procs(parallel,expr),message) +#define ParallelThrowAssert(parallel,expr) ThrowAssert(stk::is_true_on_all_procs(parallel,expr)) +#define ParallelThrowAssertMsg(parallel,expr,message) ThrowAssertMsg(stk::is_true_on_all_procs(parallel,expr),message) + + +#endif /* KRINO_INCLUDE_AKRI_REPORTHANDLER_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_SearchTree.cpp b/packages/krino/krino/krino_lib/Akri_SearchTree.cpp new file mode 100644 index 000000000000..ffd80f22bb40 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SearchTree.cpp @@ -0,0 +1,257 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include + +#include + +namespace krino{ + +template +SearchTree::SearchTree( std::vector & entities ) +{ /* %TRACE[ON]% */ Trace trace__("krino::SearchTree::SearchTree( std::vector & entities )"); /* %TRACE% */ + + if (!entities.empty()) + { + my_nodes.resize(2*entities.size() - 1); + const size_t tree_size = build( entities.begin(), entities.end() ); + ThrowRequire(tree_size == my_nodes.size()); + } +} + +template +SearchTree::SearchTree( const std::vector & entities, const std::function & get_bbox ) +{ /* %TRACE[ON]% */ Trace trace__("krino::SearchTree::SearchTree( EntityVec & entities, const std::function & get_bbox )"); /* %TRACE% */ + + if (!entities.empty()) + { + std::vector bbox_entities; + bbox_entities.reserve(entities.size()); + for (auto && entity : entities) + { + bbox_entities.emplace_back(get_bbox(entity), entity); + } + my_nodes.resize(2*entities.size() - 1); + const size_t tree_size = build( bbox_entities.begin(), bbox_entities.end() ); + ThrowRequire(tree_size == my_nodes.size()); + } +} + +template +void +SearchTree::find_closest_entities( const Vector3d & search_point, std::vector & return_vec, const Real max_search_radius ) +{ + return_vec.clear(); + + // Algorithm requires tol > std::numeric_limits::epsilon(), here just pick multiplier + const Real tol = 100.*std::numeric_limits::epsilon(); + + // if there are no entities at all return empty list + if ( empty() ) return; + + const VecType search_pt(search_point.data()); + + // first find upper bound for distance + // the very first estimate for this is the upper bound for the base of the tree + Real upperBnd2 = my_nodes[0].boxUpperBnd2( search_pt ); + Real max_search_radius2 = max_search_radius * max_search_radius; + + if ( upperBnd2 > max_search_radius2 && max_search_radius2 > 0.0 ) + { + upperBnd2 = max_search_radius2; + } + + // now descend relevant parts of tree updating the bounds as we go + Real lowerBnd2 = upperBnd2; + treeBounds(search_pt, lowerBnd2, upperBnd2); + + // exit now if no entities within narrow_band + if ( lowerBnd2 > max_search_radius2 && max_search_radius2 > 0.0 ) + { + return; + } + + // with the upper bound known, find all entities within the tolerance + find_closest_entities( search_pt, upperBnd2, tol, return_vec ); + + return; +} + +template +void +SearchTree::find_closest_entities( + const VecType & search_point, + const Real maxDist2, + const Real tol, + std::vector & nearest, + const size_t index) +{ /* %TRACE% */ /* %TRACE% */ + const SearchTreeNode & node = my_nodes[index]; + if ( node.have_children() ) + { + const size_t Lindex = index + 1; + const Real L_lowerBnd2 = my_nodes[Lindex].boxLowerBnd2( search_point ); + const Real L_eps = tol*(maxDist2+my_nodes[Lindex].boxSize2()); + if ( L_lowerBnd2 < maxDist2+L_eps ) + find_closest_entities( search_point, maxDist2, tol, nearest, Lindex ); + + const size_t Rindex = node.get_right_index(); + const Real R_lowerBnd2 = my_nodes[Rindex].boxLowerBnd2( search_point ); + const Real R_eps = tol*(maxDist2+my_nodes[Rindex].boxSize2()); + if ( R_lowerBnd2 < maxDist2+R_eps ) + find_closest_entities( search_point, maxDist2, tol, nearest, Rindex ); + } + else + { + EntityType entity = node.get_leaf_entity(); + nearest.push_back( entity ); + } +} + +template +void +SearchTree::treeBounds( const VecType & search_point, + Real & lowerBnd2, + Real & upperBnd2, + const size_t index) +{ /* %TRACE% */ /* %TRACE% */ + const SearchTreeNode & node = my_nodes[index]; + if (!node.have_children()) + { + if (0 == index) + { + // Special case of a single node. Otherwise, this node will already have been handled by parent. + compute_and_update_bounds(search_point, lowerBnd2, upperBnd2, index); + } + return; + } + + const size_t Lindex = index + 1; + const Real L_lowerBnd2 = compute_and_update_bounds(search_point, lowerBnd2, upperBnd2, Lindex); + + const size_t Rindex = node.get_right_index(); + const Real R_lowerBnd2 = compute_and_update_bounds(search_point, lowerBnd2, upperBnd2, Rindex); + + if ( L_lowerBnd2 < R_lowerBnd2 ) + { + if ( L_lowerBnd2 < upperBnd2 ) + treeBounds( search_point, lowerBnd2, upperBnd2, Lindex ); + if ( R_lowerBnd2 < upperBnd2 ) + treeBounds( search_point, lowerBnd2, upperBnd2, Rindex ); + } + else + { + if ( R_lowerBnd2 < upperBnd2 ) + treeBounds( search_point, lowerBnd2, upperBnd2, Rindex ); + if ( L_lowerBnd2 < upperBnd2 ) + treeBounds( search_point, lowerBnd2, upperBnd2, Lindex ); + } +} + +template +size_t +SearchTree::build( typename std::vector::iterator entity_begin, typename std::vector::iterator entity_end, const size_t index ) +{ + const size_t entity_size = std::distance(entity_begin, entity_end); + + // determine bounding box + BoundingBox & node_bbox = my_nodes[index].bounding_box(); + for ( auto entity_it = entity_begin; entity_it != entity_end; ++entity_it ) + { + const BoundingBox & entity_bbox = entity_it->first; + node_bbox.accommodate( entity_bbox ); + } + + if ( entity_size > 1 ) + { + // determine axis to split tree on + int max_spread_dim = node_bbox.max_span_direction(); + + auto compare = [max_spread_dim](const BoundingBoxEntity & lhs, const BoundingBoxEntity & rhs) { return lhs.first.center()[max_spread_dim] < rhs.first.center()[max_spread_dim]; }; + const size_t mid_pt = entity_size / 2; + + // This works around a bug in some versions of nth_element +#ifdef CRAY_LWK + std::partial_sort( entity_begin, entity_begin + mid_pt, entity_end, compare ); +#else + std::nth_element( entity_begin, entity_begin + mid_pt, entity_end, compare ); +#endif + + const size_t Lindex = index + 1; + const size_t Rindex = build( entity_begin, entity_begin + mid_pt, Lindex ); + my_nodes[index].set_right_index(Rindex); + const size_t next_index = build( entity_begin + mid_pt, entity_end, Rindex ); + return next_index; + } + else + { + ThrowAssert(1 == entity_size); + my_nodes[index].set_leaf_entity(entity_begin->second); + return index + 1; + } +} + +template +void +SearchTree::get_intersecting_entities( const BoundingBoxType& bbox, std::vector& return_vec, const size_t index ) +{ + const SearchTreeNode & node = my_nodes[index]; + if (!node.bounding_box().intersects(bbox)) return; + + if ( node.have_children() ) + { + if ( bbox.contains(node.bounding_box()) ) + { + add_descendants(return_vec, index); + } + else + { + const size_t Lindex = index + 1; + get_intersecting_entities( bbox, return_vec, Lindex ); + + const size_t Rindex = node.get_right_index(); + get_intersecting_entities( bbox, return_vec, Rindex ); + } + } + else + { + EntityType entity = node.get_leaf_entity(); + return_vec.push_back( entity ); + } +} + +template +void +SearchTree::add_descendants( std::vector& return_vec, const size_t index ) +{ + const SearchTreeNode & node = my_nodes[index]; + + if ( node.have_children() ) + { + const size_t Lindex = index + 1; + add_descendants( return_vec, Lindex ); + + const size_t Rindex = node.get_right_index(); + add_descendants( return_vec, Rindex ); + } + else + { + EntityType entity = node.get_leaf_entity(); + return_vec.push_back( entity ); + } +} + +// Explicit template instantiation +template class SearchTree; +template class SearchTree; + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_SearchTree.hpp b/packages/krino/krino/krino_lib/Akri_SearchTree.hpp new file mode 100644 index 000000000000..4e7b5cf3094f --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SearchTree.hpp @@ -0,0 +1,119 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_SearchTree_h +#define Akri_SearchTree_h + +#include + +#include +#include + +namespace krino { + +template +class SearchTreeNode { +public: + typedef ENTITY EntityType; + typedef BoundingBox BoundingBoxType; + typedef BoundingBoxType::Real Real; + typedef BoundingBoxType::VecType VecType; + + SearchTreeNode() : m_entity(0), m_right_index(0) {} + + const BoundingBoxType & bounding_box() const { return m_bbox; } + BoundingBoxType & bounding_box() { return m_bbox; } + Real boxLowerBnd2( const VecType & x ) const { return ( m_bbox.SqrDistLowerBnd(x) ); } + Real boxUpperBnd2( const VecType & x ) const { return ( m_bbox.SqrDistUpperBnd(x) ); } + Real boxSize2() const { return m_bbox.SqrSize(); } + + bool have_children() const { return (0 != m_right_index); } + void set_right_index(size_t right_index) { m_right_index = right_index; } + size_t get_right_index() const { return m_right_index; } + void set_leaf_entity(EntityType leaf_entity) { m_entity = leaf_entity; } + EntityType get_leaf_entity() const { return m_entity; } + +private: + BoundingBoxType m_bbox; + EntityType m_entity; + size_t m_right_index; +}; + +template +class SearchTree { +public: + typedef ENTITY EntityType; + typedef BoundingBox BoundingBoxType; + typedef std::pair BoundingBoxEntity; + typedef BoundingBoxType::Real Real; + typedef BoundingBoxType::VecType VecType; + + SearchTree( std::vector & entities ); // vector is modified by sorting + SearchTree( const std::vector & entities, const std::function & get_bbox ); + SearchTree() = delete; + + // All entities within the max_search_radius that may be the closest to the given point will be returned. + // If max_search_radius = 0, then all entities that may be the closest to the given point will be returned. + void find_closest_entities( const Vector3d& search_point, std::vector& return_vec, const Real max_search_radius = 0.0 ); + + void get_intersecting_entities( const BoundingBoxType& bbox, std::vector& return_vec) + { + return_vec.clear(); + if (!empty()) + { + get_intersecting_entities( bbox, return_vec, 0); + } + } + + bool empty() const { return my_nodes.empty(); } + size_t storage_size() const { return my_nodes.size() * sizeof(SearchTreeNode); } + +private: + size_t build( typename std::vector::iterator entity_begin, typename std::vector::iterator entity_end, const size_t index = 0 ); + double compute_and_update_bounds( const VecType & x, + Real & lowerBnd2, + Real & upperBnd2, + const size_t index = 0 ); + void treeBounds( const VecType & x, + Real & lowerBnd2, + Real & upperBnd2, + const size_t index = 0 ); + void find_closest_entities( const VecType & x, + const Real maxDist2, + const Real tol, + std::vector & nearest, + const size_t index = 0 ); + void get_intersecting_entities( const BoundingBoxType& bbox, std::vector& return_vec, const size_t index ); + void add_descendants( std::vector& return_vec, const size_t index ); +private: + std::vector> my_nodes; +}; + +template +inline double +SearchTree::compute_and_update_bounds( const VecType & search_point, + Real & lowerBnd2, + Real & upperBnd2, + const size_t index) +{ /* %TRACE% */ /* %TRACE% */ + const SearchTreeNode & node = my_nodes[index]; + const Real node_lowerBnd2 = node.boxLowerBnd2( search_point ); + if ( node_lowerBnd2 < upperBnd2 ) + { + const Real node_upperBnd2 = node.boxUpperBnd2( search_point ); + if ( node_upperBnd2 < upperBnd2 ) + upperBnd2 = node_upperBnd2; + if (!node.have_children() && node_lowerBnd2 < lowerBnd2) + lowerBnd2 = node_lowerBnd2; + } + return node_lowerBnd2; +} + +} // namespace krino + +#endif // Akri_SearchTree_h diff --git a/packages/krino/krino/krino_lib/Akri_Segment.hpp b/packages/krino/krino/krino_lib/Akri_Segment.hpp new file mode 100644 index 000000000000..df9a117e7c5d --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Segment.hpp @@ -0,0 +1,83 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Segment_h +#define Akri_Segment_h + +#include +#include +#include +#include + +namespace krino { + +template +class Segment3 { + public: + typedef REAL Real; + Segment3() : nodes{} {} ///< Default all coords zero + Segment3(const Vec& n0, const Vec& n1) : nodes{{n0, n1}} {} ///< Explicit set two end points + Segment3(MemberInit type) {/* type == NONE */} + + Real Length() const { return (nodes[1]-nodes[0]).length(); } + Real LengthSquared() const { return (nodes[1]-nodes[0]).length_squared(); } + + const Vec& GetNode(const int index) const { return nodes[index]; } + Vec& GetNode(const int index) { return nodes[index]; } + + const std::array,2>& GetNodes() const { return nodes; } + std::array,2>& GetNodes() { return nodes; } + + // + // Find the closest point projection between point and the face. + // + Real closest_projection(const Vec &point) const { + Vec edge_dir(nodes[1]-nodes[0]); + Real dotValA = Dot(edge_dir,(point-nodes[0])); + if(dotValA <= 0.0) { return 0.0; } + Real dotValB = Dot(edge_dir,(point-nodes[1])); + if(dotValB >= 0.0) { return 1.0; } + Real lenSquared = edge_dir.length_squared(); + if(lenSquared == 0.0) { return 0.0; } + return dotValA / lenSquared; + } + Real closest_projection(const Vec &point, Vec &proj_point) const { + const Real location = closest_projection(point); + proj_point = (1.0-location)*GetNode(0) + location*GetNode(1); + return location; + } + + Real DistanceSquared(const Vec& x, Real & parametric_coord) const { + Vector3d closest_pt(MemberInit::NONE); + parametric_coord = closest_projection(x, closest_pt); + return (x - closest_pt).length_squared(); + } + Real DistanceSquared(const Vec& x) const { + Vector3d closest_pt(MemberInit::NONE); + closest_projection(x, closest_pt); + return (x - closest_pt).length_squared(); + } + + friend std::ostream& operator<<( std::ostream& out, const Segment3& seg ) + { + out << "Segment3:" + << " Node0= " << seg.GetNode(0)[0] << ", " << seg.GetNode(0)[1] << ", " << seg.GetNode(0)[2] + << " Node1= " << seg.GetNode(1)[0] << ", " << seg.GetNode(1)[1] << ", " << seg.GetNode(1)[2] + << "\n"; + return out; + } + + private: + std::array,2> nodes; +}; + +typedef Segment3 Segment3d; + +} // namespace krino + +#endif // Akri_Segment_h diff --git a/packages/krino/krino/krino_lib/Akri_Snap.cpp b/packages/krino/krino/krino_lib/Akri_Snap.cpp new file mode 100644 index 000000000000..d182524bf69a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Snap.cpp @@ -0,0 +1,633 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino +{ + +static stk::math::Vector3d compute_snap_location(const std::vector & nodeLocations, const std::vector & weights) +{ + stk::math::Vector3d snapLocation{stk::math::Vector3d::ZERO}; + for (size_t i=0; i & nodes, std::vector & nodeLocations) +{ + nodeLocations.clear(); + for (auto node : nodes) + nodeLocations.emplace_back(field_data(coordsField, node), dim); +} + +static void fill_global_ids_of_elements_using_node(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + stk::mesh::Entity node, + std::vector & globalIdsOfSnapNodeElems) +{ + globalIdsOfSnapNodeElems.clear(); + for (auto elem : StkMeshEntities{mesh.begin_elements(node), mesh.end_elements(node)}) + if (elementSelector(mesh.bucket(elem))) + globalIdsOfSnapNodeElems.push_back(mesh.identifier(elem)); +} + +static double compute_quality_if_node_is_snapped_terminating_early_if_below_threshold(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const FieldRef coordsField, + stk::mesh::Entity node, + const stk::math::Vector3d & snapLocation, + const QualityMetric &qualityMetric, + const double qualityThreshold) +{ + const int dim = mesh.mesh_meta_data().spatial_dimension(); + + double qualityAfterSnap = qualityMetric.get_best_value_for_metric(); + std::vector nodeLocations; + + for (auto elem : StkMeshEntities{mesh.begin_elements(node), mesh.end_elements(node)}) + { + if (elementSelector(mesh.bucket(elem))) + { + nodeLocations.clear(); + for (auto elemNode : StkMeshEntities{mesh.begin_nodes(elem), mesh.end_nodes(elem)}) + { + if (elemNode == node) + nodeLocations.push_back(snapLocation); + else + nodeLocations.emplace_back(field_data(coordsField, elemNode), dim); + } + + const double elemQualityAfterSnap = qualityMetric.get_element_quality_metric(nodeLocations); + + if (qualityMetric.is_first_quality_metric_better_than_second(qualityAfterSnap, elemQualityAfterSnap)) + { + qualityAfterSnap = elemQualityAfterSnap; + if (qualityMetric.is_first_quality_metric_better_than_second(qualityThreshold, qualityAfterSnap)) + return qualityAfterSnap; + } + } + } + return qualityAfterSnap; +} + +static stk::math::Vector3d compute_intersection_point_location(const int dim, const FieldRef coordsField, const IntersectionPoint & intersectionPoint) +{ + std::vector intPtNodeLocations; + fill_node_locations(dim, coordsField, intersectionPoint.get_nodes(), intPtNodeLocations); + return compute_snap_location(intPtNodeLocations, intersectionPoint.get_weights()); +} + +static bool element_has_all_nodes(const std::vector & elemNodes, const std::vector & nodesToFind) +{ + for (auto && nodeToFind : nodesToFind) + if (std::find(elemNodes.begin(), elemNodes.end(), nodeToFind) == elemNodes.end()) + return false; + return true; +} + +static double estimate_quality_of_cutting_intersection_points(const stk::mesh::BulkData & mesh, + const FieldRef coordsField, + const std::vector & elemNodes, + const std::vector & elemNodeCoords, + const std::vector intersectionPointIndices, + const std::vector & intersectionPoints, + const QualityMetric &qualityMetric) +{ + if (intersectionPointIndices.empty()) + return std::max(0., qualityMetric.get_element_quality_metric(elemNodeCoords)); + + // apply the front intersection point to element and recursively call with remaining intersection points + const IntersectionPoint & intPtToApply = intersectionPoints[*intersectionPointIndices.begin()]; + const std::vector remainingIntersectionPointIndices(intersectionPointIndices.begin()+1, intersectionPointIndices.end()); + + const stk::math::Vector3d intPtLocation = compute_intersection_point_location(mesh.mesh_meta_data().spatial_dimension(), coordsField, intPtToApply); + + const auto & intPtNodes = intPtToApply.get_nodes(); + double qualityAfterCut = qualityMetric.get_best_value_for_metric(); + if (element_has_all_nodes(elemNodes, intPtNodes)) + { + std::vector cutElemNodes; + std::vector cutElemNodeCoords; + + for (auto intPtNode : intPtNodes) + { + cutElemNodes.clear(); + cutElemNodeCoords.clear(); + for (size_t nodeIndex=0; nodeIndex & interpNodes) +{ + for (auto && interpNode : interpNodes) + if (interpNode != node && !parts_are_compatible_for_snapping_when_ignoring_phase(mesh, auxMeta, phaseSupport, node, interpNode)) + return false; + return true; +} + +static double get_node_intersection_point_weight(const IntersectionPoint & intersectionPoint, stk::mesh::Entity node) +{ + const std::vector & nodes = intersectionPoint.get_nodes(); + const auto iter = std::find(nodes.begin(), nodes.end(), node); + ThrowRequire(iter != nodes.end()); + const auto index = std::distance(nodes.begin(), iter); + return intersectionPoint.get_weights()[index]; +} + +std::vector get_sorted_node_ids(const stk::mesh::BulkData & mesh, const std::vector & nodes) +{ + std::vector nodeIds; + nodeIds.reserve(nodes.size()); + for (auto && node : nodes) nodeIds.push_back(mesh.identifier(node)); + std::sort(nodeIds.begin(), nodeIds.end()); + return nodeIds; +} + +static void sort_intersection_points_for_cutting(const stk::mesh::BulkData & mesh, + const FieldRef coordsField, + const std::vector & intersectionPoints, + const stk::mesh::Entity node, + const bool globalIDsAreParallelConsistent, + std::vector & sortedIntersectionPointIndices) +{ + // This sorter is designed to match the priority used by the cutting algorithm with CUT_QUADS_BY_MINIMIZING_ANGLES, especially in 3D + auto sorter = [&intersectionPoints, &mesh, &coordsField, node, globalIDsAreParallelConsistent](const size_t intPtIndex0, const size_t intPtIndex1) + { + const IntersectionPoint & intPt0 = intersectionPoints[intPtIndex0]; + const IntersectionPoint & intPt1 = intersectionPoints[intPtIndex1]; + const size_t numDomains0 = intPt0.get_sorted_domains().size(); + const size_t numDomains1 = intPt1.get_sorted_domains().size(); + if (numDomains0 != numDomains1) + return numDomains0 > numDomains1; + // reduce precision to float to handle "ties" + const float wt0 = get_node_intersection_point_weight(intPt0, node); + const float wt1 = get_node_intersection_point_weight(intPt1, node); + if (wt0 != wt1) + return wt0 < wt1; + + if (globalIDsAreParallelConsistent) + { + const std::vector sortedNodes0 = get_sorted_node_ids(mesh, intPt0.get_nodes()); + const std::vector sortedNodes1 = get_sorted_node_ids(mesh, intPt1.get_nodes()); + return sortedNodes1 < sortedNodes0; + } + + const stk::math::Vector3d x0 = compute_intersection_point_location(mesh.mesh_meta_data().spatial_dimension(), coordsField, intPt0); + const stk::math::Vector3d x1 = compute_intersection_point_location(mesh.mesh_meta_data().spatial_dimension(), coordsField, intPt1); + return is_less_than_in_x_then_y_then_z(x0, x1); + }; + std::sort(sortedIntersectionPointIndices.begin(), sortedIntersectionPointIndices.end(), sorter); +} + +static void fill_sorted_intersection_point_indices_for_node_for_domains(const stk::mesh::BulkData & mesh, + const FieldRef coordsField, + const std::vector & intersectionPoints, + const std::vector & candidatesIntersectionPointIndices, + const stk::mesh::Entity node, + const std::vector & domains, + const bool globalIDsAreParallelConsistent, + std::vector & sortedIntersectionPointIndices) +{ + sortedIntersectionPointIndices.clear(); + for (auto && intPtIndex : candidatesIntersectionPointIndices) + { + if (first_sorted_vector_of_domains_contains_all_domains_in_second_vector(domains, intersectionPoints[intPtIndex].get_sorted_domains())) + sortedIntersectionPointIndices.push_back(intPtIndex); + } + + sort_intersection_points_for_cutting(mesh, coordsField, intersectionPoints, node, globalIDsAreParallelConsistent, sortedIntersectionPointIndices); +} + +static std::set get_intersected_elements(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const std::vector & intersectionPoints, + const std::vector & intersectionPointIndices) +{ + std::vector cutElems; + std::set intersectedElements; + for (size_t intPtIndex : intersectionPointIndices) + { + stk::mesh::get_entities_through_relations(mesh, intersectionPoints[intPtIndex].get_nodes(), stk::topology::ELEMENT_RANK, cutElems); + for (auto && cutElem : cutElems) + if (elementSelector(mesh.bucket(cutElem))) + intersectedElements.insert(cutElem); + } + return intersectedElements; +} + +static std::map> get_node_to_intersection_point_indices(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints) +{ + std::map> nodeToInsersectionPointIndices; + for (size_t intersectionPointIndex=0; intersectionPointIndex, std::map> determine_quality_per_node_per_domain(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const FieldRef coordsField, + const std::vector & intersectionPoints, + const QualityMetric &qualityMetric, + const bool globalIDsAreParallelConsistent) +{ + const int dim = mesh.mesh_meta_data().spatial_dimension(); + + const auto nodeToInsersectionPointIndices = get_node_to_intersection_point_indices(mesh, intersectionPoints); + + std::vector sortedIntersectionPointIndices; + std::vector elemNodes; + std::vector elemNodeCoords; + + std::map, std::map> domainsToNodesToQuality; + for (auto entry : nodeToInsersectionPointIndices) + { + stk::mesh::Entity node = entry.first; + const auto nodeIntersectionPointIndices = entry.second; + + std::set> nodeIntPtDomains; + for (auto && intPtIndex : nodeIntersectionPointIndices) + nodeIntPtDomains.insert(intersectionPoints[intPtIndex].get_sorted_domains()); + + for (auto && intPtDomains : nodeIntPtDomains) + { + fill_sorted_intersection_point_indices_for_node_for_domains(mesh, coordsField, intersectionPoints, nodeIntersectionPointIndices, node, intPtDomains, globalIDsAreParallelConsistent, sortedIntersectionPointIndices); + const std::set intersectedElements = get_intersected_elements(mesh, elementSelector, intersectionPoints, sortedIntersectionPointIndices); + + double qualityAfterCut = qualityMetric.get_best_value_for_metric(); + for (auto && elem : intersectedElements) + { + elemNodes.assign(mesh.begin_nodes(elem), mesh.end_nodes(elem)); + fill_node_locations(dim, coordsField, elemNodes, elemNodeCoords); + const double elemQualityAfterCuts = estimate_quality_of_cutting_intersection_points(mesh, coordsField, elemNodes, elemNodeCoords, sortedIntersectionPointIndices, intersectionPoints, qualityMetric); + + if (qualityMetric.is_first_quality_metric_better_than_second(qualityAfterCut, elemQualityAfterCuts)) + qualityAfterCut = elemQualityAfterCuts; + } + + domainsToNodesToQuality[intPtDomains][mesh.identifier(node)] = qualityAfterCut; + } + } + + return domainsToNodesToQuality; +} + +std::vector +build_snap_infos_from_intersection_points(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const NodeToCapturedDomainsMap & nodesToCapturedDomains, + const std::vector & intersectionPoints, + const QualityMetric &qualityMetric, + const bool globalIDsAreParallelConsistent) +{ + std::vector snapInfos; + + const AuxMetaData & auxMeta = AuxMetaData::get(mesh.mesh_meta_data()); + const Phase_Support phaseSupport = Phase_Support::get(mesh.mesh_meta_data()); + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + const int dim = mesh.mesh_meta_data().spatial_dimension(); + std::vector nodeLocations; + std::vector procsThatNeedToKnowAboutThisInfo; + std::vector globalIdsOfSnapNodeElems; + + int owner = mesh.parallel_rank(); + + const auto domainsToNodesToQuality = determine_quality_per_node_per_domain(mesh, elementSelector, coordsField, intersectionPoints, qualityMetric, globalIDsAreParallelConsistent); + + for (size_t intersectionPointIndex=0; intersectionPointIndexsecond; + const double cutQualityEstimate = nodesToQuality.at(mesh.identifier(node)); + + // For face and volume cuts, allow quality to go down to acceptable_value_for_metric because estimate is not that good + //const double minAcceptableQuality = (nodes.size() == 2) ? cutQualityEstimate : std::min(qualityMetric.get_acceptable_value_for_metric(), cutQualityEstimate); + const double minAcceptableQuality = cutQualityEstimate; + + const double postSnapQuality = compute_quality_if_node_is_snapped_terminating_early_if_below_threshold(mesh, elementSelector, coordsField, node, snapLocation, qualityMetric, minAcceptableQuality); + if (qualityMetric.is_first_quality_metric_better_than_second(postSnapQuality, minAcceptableQuality)) + { + const size_t nodeGlobalId = mesh.identifier(node); + + fill_global_ids_of_elements_using_node(mesh, elementSelector, node, globalIdsOfSnapNodeElems); + fill_procs_owning_or_sharing_or_ghosting_node(mesh, node, procsThatNeedToKnowAboutThisInfo); + + snapInfos.emplace_back(nodeGlobalId, intersectionPointIndex, nodeLocations[nodeIndex], owner, procsThatNeedToKnowAboutThisInfo, globalIdsOfSnapNodeElems, postSnapQuality, snapLocation, nodes.size()); + } + else if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Skipping snap of " << mesh.identifier(node) << " to " << snapLocation << " at " << debug_output(mesh, intersectionPoint) << " with snap quality at or below " << postSnapQuality << " and estimated cut quality " << cutQualityEstimate << stk::diag::dendl; + } + } + } + } + + return snapInfos; +} + +void interpolate_nodal_field(const stk::mesh::BulkData & mesh, + stk::mesh::Entity node, const FieldRef field, + const std::vector & interpNodes, + const std::vector & interpWeights, + std::vector & scratch) +{ + const unsigned fieldLength = field.length(); + + double * val = field_data(field, node); + if (nullptr == val) return; + + scratch.assign(fieldLength, 0.0); + + for (size_t iNode=0; iNode(field, interpNodes[iNode]); + if (nullptr == nodeVal) + { + krinolog << "When snapping node " << mesh.identifier(node) << ", the field " << field.name() << " is missing on interpolating node " << mesh.identifier(interpNodes[iNode]) << stk::diag::dendl; + krinolog << "Should the field " << field.name() << " be an interpolation field?" << stk::diag::dendl; + ThrowRequireMsg(false, "Interpolation field missing on interpolation node " << mesh.identifier(interpNodes[iNode])); + } + + for (unsigned i=0; i & intersectionPoints, + const std::vector & snapInfos, + NodeToCapturedDomainsMap & nodesToCapturedDomains ) +{ + ThrowRequire(mesh.parallel_size() == 1 || mesh.is_automatic_aura_on()); + + std::vector< const stk::mesh::FieldBase *> interpFieldVec; + for(auto && field : interpolationFieldSet) + interpFieldVec.push_back(&field.field()); + stk::mesh::communicate_field_data(mesh, interpFieldVec); + + std::vector scratch; + std::vector snapNodes; + snapNodes.reserve(snapInfos.size()); + + for (auto && snapInfo : snapInfos) + { + if (snapInfo.get_owner() == mesh.parallel_rank()) + { + const size_t intersectionPointIndex = snapInfo.get_intersection_point_index(); + stk::mesh::Entity snapNode = mesh.get_entity(stk::topology::NODE_RANK, snapInfo.get_node_global_id()); + snapNodes.push_back(snapNode); + const IntersectionPoint & intersectionPoint = intersectionPoints[intersectionPointIndex]; + + nodesToCapturedDomains[snapNode] = intersectionPoint.get_sorted_domains(); + + const auto & nodes = intersectionPoint.get_nodes(); + const auto & weights = intersectionPoint.get_weights(); + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Snapping node " << snapInfo.get_node_global_id() << " to " << debug_output(mesh, intersectionPoint) << stk::diag::dendl; + } + + for(auto && field : interpolationFieldSet) + interpolate_nodal_field(mesh, snapNode, field, nodes, weights, scratch); + } + } + + stk::mesh::communicate_field_data(mesh, interpFieldVec); + + communicate_node_captured_domains_for_given_nodes(mesh, snapNodes, nodesToCapturedDomains); +} + +template +size_t get_global_num_infos(const std::vector & infos, stk::ParallelMachine comm) +{ + size_t numInfos = 0; + int rank{stk::parallel_machine_rank(comm)}; + for (const auto &info : infos) + if (info.get_owner() == rank) + ++numInfos; + const size_t localNumInfos = numInfos; + stk::all_reduce_sum(comm, &localNumInfos, &numInfos, 1); + return numInfos; +} + +void pack_owned_snap_infos_that_other_procs_need_to_know_about(std::vector &snapInfos, stk::CommSparse &commSparse) +{ + stk::pack_and_communicate(commSparse,[&]() + { + for(const auto &snapInfo : snapInfos) + { + if ( snapInfo.get_owner() == commSparse.parallel_rank() ) + { + for ( const int procId : snapInfo.get_procs_that_need_to_know_about_this_info()) + { + if ( procId != commSparse.parallel_rank()) + { + commSparse.send_buffer(procId).pack(snapInfo.get_node_global_id()); + commSparse.send_buffer(procId).pack(snapInfo.get_intersection_point_index()); + stk::pack_vector_to_proc(commSparse, snapInfo.get_procs_that_need_to_know_about_this_info(), procId); + stk::pack_vector_to_proc(commSparse, snapInfo.get_conflicting_ids(), procId); + commSparse.send_buffer(procId).pack(snapInfo.get_post_worst_quality()); + commSparse.send_buffer(procId).pack(snapInfo.get_node_location()); + commSparse.send_buffer(procId).pack(snapInfo.get_snap_location()); + commSparse.send_buffer(procId).pack(snapInfo.get_snap_rank()); + } + } + } + } + }); +} + +void receive_snap_infos_that_this_proc_need_to_know_about_and_ghost(std::vector &snapInfos, stk::CommSparse &commSparse) +{ + stk::unpack_communications(commSparse, [&commSparse, &snapInfos](int procId) + { + size_t globalNodeId{0}; + commSparse.recv_buffer(procId).unpack(globalNodeId); + + size_t intersectionPointIndex{0}; + commSparse.recv_buffer(procId).unpack(intersectionPointIndex); + + std::vector procsThatNeedToKnowAboutThisInfo; + std::vector globalIdsOfSnapNodeElems; + stk::unpack_vector_from_proc(commSparse, procsThatNeedToKnowAboutThisInfo, procId); + stk::unpack_vector_from_proc(commSparse, globalIdsOfSnapNodeElems, procId); + + double postSnapQuality{0}; + commSparse.recv_buffer(procId).unpack(postSnapQuality); + + stk::math::Vector3d nodeLocation; + commSparse.recv_buffer(procId).unpack(nodeLocation); + + stk::math::Vector3d snapLocation; + commSparse.recv_buffer(procId).unpack(snapLocation); + + int snapRank; + commSparse.recv_buffer(procId).unpack(snapRank); + + snapInfos.emplace_back(globalNodeId, + intersectionPointIndex, + nodeLocation, + procId, + procsThatNeedToKnowAboutThisInfo, + globalIdsOfSnapNodeElems, + postSnapQuality, + snapLocation, + snapRank); + }); +} + +void communicate_snap_infos_that_other_procs_need_to_know_about(std::vector &snapInfos, stk::ParallelMachine comm) +{ + stk::CommSparse commSparse(comm); + + pack_owned_snap_infos_that_other_procs_need_to_know_about(snapInfos, commSparse); + receive_snap_infos_that_this_proc_need_to_know_about_and_ghost(snapInfos, commSparse); +} + +std::vector get_sorted_nodes_modified_in_current_snapping_iteration(const stk::mesh::BulkData & mesh, const std::vector & iterationSnapInfos) +{ + std::vector sortedSnappedNodes; + for (auto && snapInfo : iterationSnapInfos) + sortedSnappedNodes.push_back(mesh.get_entity(stk::topology::NODE_RANK, snapInfo.get_node_global_id())); + std::sort(sortedSnappedNodes.begin(), sortedSnappedNodes.end()); + return sortedSnappedNodes; +} + +double determine_quality(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const QualityMetric &qualityMetric) +{ + const FieldRef coordsField(mesh.mesh_meta_data().coordinate_field()); + std::vector nodeLocations; + + double quality = qualityMetric.get_best_value_for_metric(); + for (auto && bucket : mesh.get_buckets(stk::topology::ELEMENT_RANK, elementSelector)) + { + if (bucket->topology().base() == stk::topology::TETRAHEDRON_4 || bucket->topology().base() == stk::topology::TRIANGLE_3_2D) + { + for (auto && element : *bucket) + { + fill_element_node_coordinates(mesh, element, coordsField, nodeLocations); + const double elementQuality = qualityMetric.get_element_quality_metric(nodeLocations); + quality = std::min(quality, elementQuality); + } + } + } + + const double localQuality = quality; + stk::all_reduce_min(mesh.parallel(), &localQuality, &quality, 1); + + return quality; +} + +NodeToCapturedDomainsMap snap_as_much_as_possible_while_maintaining_quality(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const FieldSet & interpolationFields, + const InterfaceGeometry & geometry, + const bool globalIDsAreParallelConsistent) +{/* %TRACE[ON]% */ Trace trace__("krino::snap_as_much_as_possible_while_maintaining_quality()"); /* %TRACE% */ + + const ScaledJacobianQualityMetric qualityMetric; + size_t iteration{0}; + NodeToCapturedDomainsMap nodesToCapturedDomains; + stk::ParallelMachine comm = mesh.parallel(); + + std::vector intersectionPoints; + geometry.store_phase_for_uncut_elements(mesh); + intersectionPoints = build_all_intersection_points(mesh, geometry, nodesToCapturedDomains); + + while (true) + { + krinolog << "Snapping To Geometry Iteration " << std::to_string(++iteration) << stk::diag::dendl; + + std::vector snapInfos = build_snap_infos_from_intersection_points(mesh, elementSelector, nodesToCapturedDomains, intersectionPoints, qualityMetric, globalIDsAreParallelConsistent); + + bool done = stk::is_true_on_all_procs(comm, snapInfos.empty()); + if ( done ) + break; + + communicate_snap_infos_that_other_procs_need_to_know_about(snapInfos, comm); + + const std::vector independentSnapInfos = find_snap_info_independent_sets(snapInfos, qualityMetric, comm); + + krinolog << " Snapping " << get_global_num_infos(independentSnapInfos, comm) << " of " << get_global_num_infos(snapInfos, comm) << " snap candidates." << stk::diag::dendl; + + geometry.store_phase_for_elements_that_will_be_uncut_after_snapping(mesh, intersectionPoints, independentSnapInfos, nodesToCapturedDomains); + snap_nodes(mesh, interpolationFields, intersectionPoints, independentSnapInfos, nodesToCapturedDomains); + + const std::vector iterationSortedSnapNodes = get_sorted_nodes_modified_in_current_snapping_iteration(mesh, independentSnapInfos); + update_intersection_points_after_snap_iteration(mesh, geometry, iterationSortedSnapNodes, nodesToCapturedDomains, intersectionPoints); + } + + krinolog << "After snapping quality is " << determine_quality(mesh, elementSelector, qualityMetric) << stk::diag::dendl; + + return nodesToCapturedDomains; +} +} + + + diff --git a/packages/krino/krino/krino_lib/Akri_Snap.hpp b/packages/krino/krino/krino_lib/Akri_Snap.hpp new file mode 100644 index 000000000000..f56bc31ecd38 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Snap.hpp @@ -0,0 +1,35 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_SNAP_H_ +#define KRINO_INCLUDE_AKRI_SNAP_H_ +#include +#include +#include +#include + +namespace krino +{ +class InterfaceGeometry; +class QualityMetric; + +NodeToCapturedDomainsMap snap_as_much_as_possible_while_maintaining_quality(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const FieldSet & interpolationFields, + const InterfaceGeometry & geometry, + const bool globalIDsAreParallelConsistent); + +double determine_quality(const stk::mesh::BulkData & mesh, + const stk::mesh::Selector & elementSelector, + const QualityMetric &qualityMetric); + +} + + + +#endif /* KRINO_INCLUDE_AKRI_SNAP_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_SnapIndependentSetFinder.hpp b/packages/krino/krino/krino_lib/Akri_SnapIndependentSetFinder.hpp new file mode 100644 index 000000000000..4c2490eadee5 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SnapIndependentSetFinder.hpp @@ -0,0 +1,34 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_SNAPINDEPENDENTSETFINDER_H +#define AKRI_SNAPINDEPENDENTSETFINDER_H + +#include +#include +#include +#include + +namespace krino +{ + +typedef independent_set::IndependentSetFinder SnapInfoIndependentSetFinder; + +inline +std::vector find_snap_info_independent_sets(const std::vector &allSnapInfos, + const QualityMetric & qualityMetric, + stk::ParallelMachine comm) +{ + SnapInfo::Comparator comparator {qualityMetric}; + SnapInfo::ConflictFinder conflictFinder; + return SnapInfoIndependentSetFinder::find_independent_set(allSnapInfos, comparator, conflictFinder, false, comm); +} + +} + +#endif /* AKRI_SNAPINDEPENDENTSETFINDER_H */ diff --git a/packages/krino/krino/krino_lib/Akri_SnapInfo.cpp b/packages/krino/krino/krino_lib/Akri_SnapInfo.cpp new file mode 100644 index 000000000000..96d0abdefd56 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SnapInfo.cpp @@ -0,0 +1,71 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include + +namespace krino +{ + +template +std::string +to_string(const Container & container) +{ + std::ostringstream os; + os << " {"; + for(auto data : container) + os << " " << data; + os << " }"; + return os.str(); +} + +bool SnapInfo::Comparator::is_first_higher_priority_than_second(const SnapInfo& snapInfoA,const SnapInfo& snapInfoB) const +{ + if( snapInfoA.get_snap_rank() > snapInfoB.get_snap_rank() ) + return true; + else if ( snapInfoA.get_snap_rank() < snapInfoB.get_snap_rank() ) + return false; + + if(mQualityMetric.is_first_quality_metric_better_than_second(snapInfoA.get_post_worst_quality(),snapInfoB.get_post_worst_quality())) + return true; + else if(mQualityMetric.is_first_quality_metric_better_than_second(snapInfoB.get_post_worst_quality(),snapInfoA.get_post_worst_quality())) + return false; + + if (snapInfoA.get_node_global_id() != snapInfoB.get_node_global_id()) + { + if ( is_less_than_in_x_then_y_then_z(snapInfoA.get_node_location(), snapInfoB.get_node_location()) ) + return true; + else if ( is_less_than_in_x_then_y_then_z(snapInfoB.get_node_location(), snapInfoA.get_node_location()) ) + return false; + } + + if ( is_less_than_in_x_then_y_then_z(snapInfoA.get_snap_location(), snapInfoB.get_snap_location()) ) + return true; + else if ( is_less_than_in_x_then_y_then_z(snapInfoB.get_snap_location(), snapInfoA.get_snap_location()) ) + return false; + + return false; +} + +std::ostream & operator<<(std::ostream & os, const SnapInfo& snapInfo) +{ + os << " Owner: " << snapInfo.get_owner() << std::endl; + os << "Snap Node: " << snapInfo.get_node_global_id() << std::endl; + os << "ConflictingIds: " << to_string(snapInfo.get_conflicting_ids()) << std::endl; + os << "SnapLocation: " << snapInfo.get_snap_location().to_string(16) << std::endl; + os << "PostSnapWorstQuality: " << snapInfo.get_post_worst_quality() << std::endl; + os << "GetProcsThatNeedToKnow: " << to_string(snapInfo.get_procs_that_need_to_know_about_this_info()) << std::endl; + os << "Snap Rank: " << snapInfo.get_snap_rank() << std::endl; + return os; +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_SnapInfo.hpp b/packages/krino/krino/krino_lib/Akri_SnapInfo.hpp new file mode 100644 index 000000000000..889defbd38e9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SnapInfo.hpp @@ -0,0 +1,87 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_SNAPINFO_H +#define AKRI_SNAPINFO_H + +#include +#include +#include + +namespace krino +{ + +class SnapInfo +{ +public: + typedef size_t ExclusionIdentifierType; + typedef std::array GlobalId; + + SnapInfo(const size_t nodeGlobalId, + const size_t intersectionPointIndex, + const stk::math::Vector3d & nodeLocation, + const int owner, + const std::vector & procsThatNeedToKnowAboutThisInfo, + const std::vector & globalIdsOfSnapNodeElems, + const double& postSnapQuality, + const stk::math::Vector3d & snapLocation, + const int snapRank) + : mUniqueId(make_unique_id(nodeGlobalId, intersectionPointIndex)), + mOwner{owner}, + mProcsThatNeedToKnowAboutThisInfo{procsThatNeedToKnowAboutThisInfo}, + mGlobalIdsOfSnapNodeElems{globalIdsOfSnapNodeElems}, + mPostWorstQuality(postSnapQuality), // () for intel 17 + mNodeLocation(nodeLocation), + mSnapLocation(snapLocation), + mSnapRank{snapRank} + { + } + + static GlobalId make_unique_id(const size_t globalNodeId, const size_t intersectionPointIndex) { return GlobalId{globalNodeId, intersectionPointIndex}; } + const GlobalId &get_unique_id() const { return mUniqueId; } + size_t get_node_global_id() const { return mUniqueId[0]; } + size_t get_intersection_point_index() const { return mUniqueId[1]; } + int get_owner() const { return mOwner; } + const std::vector &get_procs_that_need_to_know_about_this_info() const { return mProcsThatNeedToKnowAboutThisInfo; } + double get_post_worst_quality() const { return mPostWorstQuality; } + const stk::math::Vector3d & get_snap_location() const { return mSnapLocation; }; + const stk::math::Vector3d & get_node_location() const { return mNodeLocation; }; + int get_snap_rank() const { return mSnapRank; } + const std::vector &get_conflicting_ids() const { return mGlobalIdsOfSnapNodeElems; } + + class ConflictFinder + { + public: + std::vector get_other_conflicting_infos(const SnapInfo& info) const {return {};} + }; + class Comparator + { + public: + Comparator(const QualityMetric &qualityMetric) : mQualityMetric{qualityMetric}{} + bool is_first_higher_priority_than_second(const SnapInfo& tetSnapInfoA,const SnapInfo& tetSnapInfoB) const; + + private: + const QualityMetric &mQualityMetric; + }; + +private: + const GlobalId mUniqueId; + const int mOwner{0u}; + const std::vector mProcsThatNeedToKnowAboutThisInfo; + const std::vector mGlobalIdsOfSnapNodeElems; + const double mPostWorstQuality{0.0}; + const stk::math::Vector3d mNodeLocation{}; + const stk::math::Vector3d mSnapLocation{}; + const int mSnapRank; +}; + +std::ostream & operator<<(std::ostream & os, const SnapInfo& snapInfo); + +} + +#endif /* AKRI_SNAPINFO_H */ diff --git a/packages/krino/krino/krino_lib/Akri_SnapToNode.cpp b/packages/krino/krino/krino_lib/Akri_SnapToNode.cpp new file mode 100644 index 000000000000..84b437bdd092 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SnapToNode.cpp @@ -0,0 +1,59 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include "../interface_geometry_interface/Akri_InterfaceGeometry.hpp" + +namespace krino { + +void determine_node_snapping_from_intersection_points(const stk::mesh::BulkData & mesh, + const std::vector & intersectionPoints, + const CDFEM_Snapper & snapper, + NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + const double snapTol = snapper.get_edge_tolerance(); + for (auto && intersectionPoint : intersectionPoints) + { + const auto & nodes = intersectionPoint.get_nodes(); + const auto & weights = intersectionPoint.get_weights(); + for (size_t nodeIndex=0; nodeIndex 1.-snapTol) + { + if (krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Snapping node " << debug_output(mesh, intersectionPoint) << " to " << mesh.identifier(nodes[nodeIndex]) << stk::diag::dendl; + } + + const auto & intersectionPointDomains = intersectionPoint.get_sorted_domains(); + auto & nodeCapturedDomains = nodesToCapturedDomains[nodes[nodeIndex]]; + nodeCapturedDomains.insert(nodeCapturedDomains.end(), intersectionPointDomains.begin(), intersectionPointDomains.end()); + } + } + } + + for (auto && nodeToCapturedDomains : nodesToCapturedDomains) + stk::util::sort_and_unique(nodeToCapturedDomains.second); +} + +void snap_to_node(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const CDFEM_Snapper & snapper, + NodeToCapturedDomainsMap & nodesToCapturedDomains) +{ + const std::vector intersectionPoints = build_uncaptured_intersection_points(mesh, interfaceGeometry, nodesToCapturedDomains); + + determine_node_snapping_from_intersection_points(mesh, intersectionPoints, snapper, nodesToCapturedDomains); + communicate_node_captured_domains_for_all_nodes(mesh, nodesToCapturedDomains); +} + +} + + diff --git a/packages/krino/krino/krino_lib/Akri_SnapToNode.hpp b/packages/krino/krino/krino_lib/Akri_SnapToNode.hpp new file mode 100644 index 000000000000..26fe17920793 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SnapToNode.hpp @@ -0,0 +1,26 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_INCLUDE_AKRI_SNAPTONODE_H_ +#define KRINO_INCLUDE_AKRI_SNAPTONODE_H_ + +#include +#include + +namespace krino { + +class CDFEM_Support; +class Phase_Support; + +void snap_to_node(const stk::mesh::BulkData & mesh, + const InterfaceGeometry & interfaceGeometry, + const CDFEM_Snapper & snapper, + NodeToCapturedDomainsMap & nodesToCapturedDomains); + +} +#endif /* KRINO_INCLUDE_AKRI_SNAPTONODE_H_ */ diff --git a/packages/krino/krino/krino_lib/Akri_SubElement.cpp b/packages/krino/krino/krino_lib/Akri_SubElement.cpp new file mode 100644 index 000000000000..6a531e1abab2 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElement.cpp @@ -0,0 +1,2833 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include + +#include +#include + +namespace krino{ + +bool +SubElementNode::on_common_edge(const SubElementNode * other) const +{ + NodeSet ancestors; + get_ancestors(ancestors); + if (ancestors.size() <= 2) + { + other->get_ancestors(ancestors); + } + if (ancestors.size() <= 2) + { + return true; + } + return false; +} + +SubElementMidSideNode::SubElementMidSideNode( const Mesh_Element * owner, + const SubElementNode *parent1, + const SubElementNode *parent2) + : SubElementNode(owner), + my_is_mesh_node(false), + my_parent1(parent1), + my_parent2(parent2) +{ + // fill base class data + my_cached_owner_coords = compute_owner_coords( owner ); + my_global_coords = 0.5*(my_parent1->coordinates()) + 0.5*(my_parent2->coordinates()); +} + +SubElementMidSideNode::SubElementMidSideNode( const Mesh_Element * owner, + const SubElementNode *parent1, + const SubElementNode *parent2, + stk::mesh::Entity meshNode, + stk::mesh::EntityId meshNodeId) + : SubElementMidSideNode(owner, parent1, parent2) +{ + my_is_mesh_node = true; + set_entity(meshNode, meshNodeId); +} + +SubElementChildNode::SubElementChildNode( const Mesh_Element * in_owner, + const NodeVec & parents, + const std::vector & weights ) + : SubElementNode(in_owner), + my_parents(parents), + my_weights(weights) +{ + // fill base class data + my_cached_owner_coords = compute_owner_coords( in_owner ); + my_global_coords = in_owner->coordinates( my_cached_owner_coords ); +} + +SubElementMeshNode::SubElementMeshNode( const Mesh_Element * in_owner, + stk::mesh::Entity nodeEntity, + stk::mesh::EntityId nodeEntityId, + const Vector3d & in_owner_coords, + const Vector3d & in_global_coords ) + : SubElementNode(in_owner) +{ + // fill base class data + set_entity(nodeEntity, nodeEntityId); + my_cached_owner_coords = in_owner_coords; + my_global_coords = in_global_coords; +} + +void +SubElementNode::get_parent_entities(std::vector & parent_entities) const +{ + NodeVec parents = get_parents(); + + const unsigned parent_size = parents.size(); + parent_entities.resize(parent_size); + + for (unsigned i=0; ientity(); + } +} + +static bool is_on_multiple_blocks(const stk::mesh::BulkData& mesh, stk::mesh::Entity node) +{ + bool foundVolumePart = false; + for (auto && part : mesh.bucket(node).supersets()) + { + if (part->primary_entity_rank() == stk::topology::ELEMENT_RANK && + !stk::mesh::is_auto_declared_part(*part) && + part->subsets().empty() && + part->name().compare(0,7,"refine_") != 0) + { + if (foundVolumePart) return true; + foundVolumePart = true; + } + } + return false; +} + +bool SubElementChildNode::needs_to_be_ale_prolonged(const CDMesh & mesh) const +{ + if (mesh.get_prolongation_model() == INTERPOLATION) + return false; + + const CDMesh* old_mesh = mesh.get_old_mesh(); + const bool is_initial_mesh = old_mesh->stash_step_count() < 0; + if (is_initial_mesh) + return false; + + if (is_on_multiple_blocks(mesh.stk_bulk(), entity())) + return true; + + // relatively unusual case of an edge node that is not on a block-block boundary. + // this is currently handled by using interpolation. This possibly needs further + // testing/development to treat these like mesh nodes where we see if they have + // changed phase. + return false; +} + +Vector3d SubElementChildNode::compute_owner_coords( const Mesh_Element * in_owner ) const +{ + Vector3d calcOwnerCoords{Vector3d::ZERO}; + ThrowAssert(my_parents.size() == my_weights.size()); + for (size_t i=0; iowner_coords(in_owner); + return calcOwnerCoords; +} + +void +SubElementChildNode::prolongate_fields(const CDMesh & mesh) const +{/* %TRACE[ON]% */ Trace trace__("SubElementEdgeNode::prolongate_fields() const"); /* %TRACE% */ + for (auto && parent : my_parents) + if (!parent->is_prolonged()) + parent->prolongate_fields(mesh); + + if (my_is_prolonged_flag) return; + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "SubElementEdgeNode::prolongate_fields for node#" << entityId() << "\n"; + my_is_prolonged_flag = true; + + const ProlongationPointData * prolong_node = needs_to_be_ale_prolonged(mesh) ? mesh.get_old_mesh()->find_prolongation_node(*this) : nullptr; + + prolong_cdfem_displacements(mesh, prolong_node); + + prolong_zeroed_fields(mesh, nullptr); + + prolong_ale_fields(mesh, prolong_node); + + prolong_interpolation_fields(mesh); +} + +bool SubElementMidSideNode::is_mesh_node_that_needs_to_be_prolonged(const CDMesh & mesh) const +{/* %TRACE[ON]% */ Trace trace__("SubElementMidSideNode::is_mesh_node_that_needs_to_be_prolonged() const"); /* %TRACE% */ + + ThrowRequire(my_is_mesh_node); + + const SubElementMeshNode * parent1 = dynamic_cast(my_parent1); + const SubElementMeshNode * parent2 = dynamic_cast(my_parent2); + const int num_ale_prolonged_parents = (parent1->needs_to_be_ale_prolonged(mesh) ? 1 : 0) + (parent2->needs_to_be_ale_prolonged(mesh) ? 1 : 0); + + if (num_ale_prolonged_parents == 0) return false; + if (num_ale_prolonged_parents == 2) return true; + + // 1 parent node needed to be ALE prolonged and this node is active (so the edge is not cut). + // This means the interface was cutting this edge, but now is not -> prolong OR + // the interface is passing through one of the parents of this uncut edge -> do not prolong. + + const bool have_or_did_have_interface = my_cached_owner->have_interface() || mesh.get_old_mesh()->find_mesh_element(my_cached_owner->entityId())->have_interface(); + + return have_or_did_have_interface && nullptr == mesh.get_old_mesh()->fetch_prolong_node(entityId()); +} + +void +SubElementMidSideNode::prolongate_fields(const CDMesh & mesh) const +{/* %TRACE[ON]% */ Trace trace__("SubElementMidSideNode::prolongate_fields() const"); /* %TRACE% */ + if (!my_parent1->is_prolonged()) + { + my_parent1->prolongate_fields(mesh); + } + if (!my_parent2->is_prolonged()) + { + my_parent2->prolongate_fields(mesh); + } + if (my_is_prolonged_flag) return; + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "SubElementMidSideNode::prolongate_fields for node#" << entityId() << "\n"; + my_is_prolonged_flag = true; + + const bool needs_to_be_prolonged = !my_is_mesh_node || is_mesh_node_that_needs_to_be_prolonged(mesh); + if (needs_to_be_prolonged) + { + // Note: CDFEM displacement is not present on midside nodes + prolong_zeroed_fields(mesh, nullptr); + + prolong_interpolation_fields(mesh); + + prolong_ale_fields(mesh); + } +} + +void +SubElementMidSideNode::prolong_interpolation_fields(const CDMesh & mesh) const +{ + const ElementObj * interp_elem = nullptr; + Vector3d interp_elem_p_coords; + const CDMesh* old_mesh = mesh.get_old_mesh(); + const Mesh_Element * old_owner = old_mesh->find_mesh_element(my_cached_owner->entityId()); + ThrowAssert(old_owner); + old_owner->find_child_coordinates_at_owner_coordinates(my_cached_owner_coords, interp_elem, interp_elem_p_coords); + + for(auto && field : mesh.get_interpolation_fields()) + { + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + interp_elem->evaluate_prolongation_field(*old_mesh, field, field_length, interp_elem_p_coords, val); + } +} + +void +SubElementMidSideNode::prolong_ale_fields(const CDMesh & mesh) const +{ + // simply average parent nodes + for(auto && field : mesh.get_ale_prolongation_fields()) + { + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (nullptr != val) + { + double * val1 = field_data(field, my_parent1->entity()); + double * val2 = field_data(field, my_parent2->entity()); + ThrowRequire(val1 && val2); + for (unsigned i=0; iis_prolonged()) + { + parent->prolongate_fields(mesh); + } + } + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "SubElementInternalNode::prolongate_fields for node#" << entityId() << "\n"; + my_is_prolonged_flag = true; + + const stk::mesh::BulkData& stk_mesh = mesh.stk_bulk(); + const stk::mesh::FieldVector & all_fields = stk_mesh.mesh_meta_data().get_fields(); + for ( stk::mesh::FieldVector::const_iterator it = all_fields.begin(); it != all_fields.end() ; ++it ) + { + const FieldRef field = (const FieldRef)(**it); + + // Do not try to prolong non-real variables + if( field.entity_rank()!=stk::topology::NODE_RANK || !field.type_is() ) continue; + + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + for (unsigned i=0; i(field, get_parents()[p]->entity()); + if (NULL == parent_val) + { + parent_error = true; + } + else + { + tot_wt += get_parent_weights()[p]; + for (unsigned i=0; ientity()) << stk::diag::dendl; + } + } + } +} + +bool on_interface_or_io_parts_have_changed(const stk::mesh::BulkData & mesh, const Phase_Support & phaseSupport, stk::mesh::Entity node, const ProlongationNodeData & oldProlongNode) +{ + const auto newParts = ProlongationNodeData::get_node_io_parts(mesh, node); + if (newParts != oldProlongNode.get_io_parts()) + return true; + for (auto && partOrdinal : newParts) + if (phaseSupport.is_interface(&mesh.mesh_meta_data().get_part(partOrdinal))) + return true; + return false; +} + +bool SubElementMeshNode::needs_to_be_ale_prolonged(const CDMesh & mesh) const +{/* %TRACE[ON]% */ Trace trace__("SubElementMeshNode::needs_to_be_ale_prolonged() const"); /* %TRACE% */ + const ProlongationNodeData * old_prolong_node = NULL; + const CDMesh* old_mesh = mesh.get_old_mesh(); + old_prolong_node = old_mesh->fetch_prolong_node(entityId()); + const bool is_initial_mesh = old_mesh->stash_step_count() < 0; + return !is_initial_mesh && nullptr != old_prolong_node && on_interface_or_io_parts_have_changed(mesh.stk_bulk(), mesh.get_phase_support(), entity(), *old_prolong_node); +} + +void +SubElementMeshNode::prolongate_fields(const CDMesh & mesh) const +{/* %TRACE[ON]% */ Trace trace__("SubElementMeshNode::prolongate_fields() const"); /* %TRACE% */ + + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "SubElementMeshNode::prolongate_fields for node#" << entityId() << "\n"; + my_is_prolonged_flag = true; + + const ProlongationPointData * prolong_data = NULL; + const ProlongationNodeData * old_prolong_node = NULL; + const CDMesh* old_mesh = mesh.get_old_mesh(); + old_prolong_node = old_mesh->fetch_prolong_node(entityId()); + + const bool needsToBeALEProlonged = needs_to_be_ale_prolonged(mesh); + if (mesh.get_prolongation_model() != INTERPOLATION && needsToBeALEProlonged) + { + prolong_data = old_mesh->find_prolongation_node(*this); + } + + if( !old_prolong_node && !prolong_data ) + { + return; + } + + prolong_cdfem_displacements(mesh, prolong_data, false); + + const ProlongationNodeData * nodeToExamineForPreExistingField = needsToBeALEProlonged ? nullptr : old_prolong_node; + prolong_zeroed_fields(mesh, nodeToExamineForPreExistingField); + + prolong_ale_fields(mesh, prolong_data, old_prolong_node); + + prolong_interpolation_fields(mesh, old_prolong_node); +} + +void +SubElementNode::prolong_zeroed_fields(const CDMesh & mesh, const ProlongationNodeData * nodeToExamineForPreExistingField) const +{ + const FieldSet & zeroed_fields = mesh.get_zeroed_fields(); + for(auto&& field : zeroed_fields) + { + if (!nodeToExamineForPreExistingField || !nodeToExamineForPreExistingField->get_field_data(field)) // If this node existed before and had this field, leave it alone + { + double * val = field_data(field, my_entity); + if (nullptr != val) std::fill(val, val+field.length(), 0.); + } + } +} + +void SubElementNode::prolong_cdfem_displacements(const CDMesh & mesh, + const ProlongationPointData * prolong_data, + const bool zero_if_no_prolong_data) const +{ + const FieldRef field = mesh.get_cdfem_displacements_field(); + if( !field.valid()) return; + + const unsigned field_length = field.length(); + for ( unsigned is = 0; is < field.number_of_states(); ++is ) + { + const stk::mesh::FieldState state = static_cast(is); + const FieldRef state_field = field.field_state(state); + + double * val = field_data(state_field, my_entity); + if(val == NULL) continue; + + if(!prolong_data) + { + if (zero_if_no_prolong_data) + { + std::fill(val, val+field_length, 0); + } + } + else + { + const double * prolong_field = prolong_data->get_field_data(state_field); + ThrowRequire(NULL != prolong_field); + std::copy(prolong_field, prolong_field+field_length, val); + + if (state == stk::mesh::StateNew) + { + const Vector3d & coords = coordinates(); + const Vector3d & old_coords = prolong_data->get_coordinates(); + for (unsigned i=0; i 0); + + for (auto && child : parents[0]->my_children) + { + if (child->get_num_parents() == numParents) + { + bool childOfAllParents = true; + for (size_t iParent=1; iParenthave_child(child)) + { + childOfAllParents = false; + break; + } + } + if (childOfAllParents) + return child; + } + } + return nullptr; +} + +bool SubElementNode::have_child() const +{ + return !my_children.empty(); +} + +bool SubElementNode::have_child(const SubElementNode* child) const +{ + return (std::find(my_children.begin(), my_children.end(), child) != my_children.end()); +} + +void +SubElementChildNode::prolong_ale_fields(const CDMesh & mesh, const ProlongationPointData * prolong_data) const +{ + const CDMesh* old_mesh = mesh.get_old_mesh(); + const ElementObj * interp_elem = nullptr; + Vector3d interp_elem_p_coords; + const FieldSet & ale_prolongation_fields = mesh.get_ale_prolongation_fields(); + for(FieldSet::const_iterator it = ale_prolongation_fields.begin(); it != ale_prolongation_fields.end(); ++it) + { + const FieldRef field = *it; + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + if(prolong_data) + { + // this node has changed phase + // prolong based on prolong_node + const double * prolong_field = prolong_data->get_field_data(field); + // We cannot yet handle the case where a prolongation field is not defined on the prolongation node that + // was found. Throw here to avoid the possibility of not prolonging a prolongation field that then + // has its time derivative screwed up because it has a mesh velocity associated with it. + // We think this should only occur in problems with multiple different level sets. + ThrowRequire(prolong_field); + std::copy(prolong_field, prolong_field+field_length, val); + } + else + { + if (nullptr == interp_elem) + { + const Mesh_Element * old_owner = old_mesh->find_mesh_element(my_cached_owner->entityId()); + ThrowAssert(old_owner); + old_owner->find_child_coordinates_at_owner_coordinates(my_cached_owner_coords, interp_elem, interp_elem_p_coords); + } + + interp_elem->evaluate_prolongation_field(*old_mesh, field, field_length, interp_elem_p_coords, val); + } + } +} + +void +SubElementMeshNode::prolong_ale_fields(const CDMesh & mesh, + const ProlongationPointData * prolong_data, + const ProlongationNodeData * old_node) const +{ + const FieldSet & ale_prolongation_fields = mesh.get_ale_prolongation_fields(); + for(FieldSet::const_iterator it = ale_prolongation_fields.begin(); it != ale_prolongation_fields.end(); ++it) + { + const FieldRef field = *it; + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + if(prolong_data) + { + // this node has changed phase + // prolong based on prolong_node + const double * prolong_field = prolong_data->get_field_data(field); + // We cannot yet handle the case where a prolongation field is not defined on the prolongation node that + // was found. Throw here to avoid the possibility of not prolonging a prolongation field that then + // has its time derivative screwed up because it has a mesh velocity associated with it. + // We think this should only occur in problems with multiple different level sets. + ThrowRequire(prolong_field); + std::copy(prolong_field, prolong_field+field_length, val); + } + else if(old_node) + { + const double * old_field = old_node->get_field_data(field); + if(!old_field) + { + const FieldRef initial_field = mesh.get_cdfem_support().get_initial_prolongation_field( field ); + if(initial_field.valid()) + { + const double * initial_data = old_node->get_field_data(initial_field); + std::copy(initial_data, initial_data+field_length, val); + } + else + { + std::fill(val, val+field_length, 0.); + } + } + } + } +} + +void +SubElementChildNode::prolong_interpolation_fields(const CDMesh & mesh) const +{ + const ElementObj * interp_elem = nullptr; + Vector3d interp_elem_p_coords; + const CDMesh* old_mesh = mesh.get_old_mesh(); + const Mesh_Element * old_owner = old_mesh->find_mesh_element(my_cached_owner->entityId()); + ThrowAssert(old_owner); + old_owner->find_child_coordinates_at_owner_coordinates(my_cached_owner_coords, interp_elem, interp_elem_p_coords); + + const FieldSet & interpolation_fields = mesh.get_interpolation_fields(); + for(FieldSet::const_iterator it = interpolation_fields.begin(); it != interpolation_fields.end(); ++it) + { + const FieldRef field = *it; + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + interp_elem->evaluate_prolongation_field(*old_mesh, field, field_length, interp_elem_p_coords, val); + } +} + +void +SubElementMeshNode::prolong_interpolation_fields(const CDMesh & mesh, const ProlongationNodeData * old_node) const +{ + const FieldSet & interpolation_fields = mesh.get_interpolation_fields(); + for(FieldSet::const_iterator it = interpolation_fields.begin(); it != interpolation_fields.end(); ++it) + { + const FieldRef field = *it; + const unsigned field_length = field.length(); + + double * val = field_data(field, my_entity); + if (NULL == val) continue; + + if(old_node) + { + const double * old_field = old_node->get_field_data(field); + if(!old_field) + { + const FieldRef initial_field = mesh.get_cdfem_support().get_initial_prolongation_field( field ); + if(initial_field.valid()) + { + const double * initial_data = old_node->get_field_data(initial_field); + std::copy(initial_data, initial_data+field_length, val); + } + else + { + std::fill(val, val+field_length, 0.); + } + } + } + } +} + +void removeParts(stk::mesh::PartVector & parts, const stk::mesh::PartVector & parts_to_remove) +{ + stk::mesh::PartVector::iterator parts_begin = parts.begin(); + stk::mesh::PartVector::iterator begin_parts_to_erase = parts.end(); + for(stk::mesh::PartVector::const_iterator it = parts_to_remove.begin(); it != parts_to_remove.end(); ++it) + { + begin_parts_to_erase = std::remove(parts_begin, begin_parts_to_erase, *it); + } + parts.erase(begin_parts_to_erase, parts.end()); +} + +std::vector SubElementNode::prolongation_node_fields(const CDMesh & mesh) const +{ + const FieldSet & ale_prolongation_fields = mesh.get_ale_prolongation_fields(); + + std::vector ale_prolongation_fields_on_node; + ale_prolongation_fields_on_node.reserve(ale_prolongation_fields.size()); + for(auto && field : ale_prolongation_fields) + if (nullptr != field_data(field, my_entity)) + ale_prolongation_fields_on_node.push_back(field.field().mesh_meta_data_ordinal()); + + std::sort(ale_prolongation_fields_on_node.begin(), ale_prolongation_fields_on_node.end()); + return ale_prolongation_fields_on_node; +} + +static bool float_less(double a, double b) +{ + return static_cast(a) < static_cast(b); +} + +bool SubElementNode::higher_priority_by_score_then_ancestry(const SubElementNode & a, const SubElementNode & b, const bool globalIDsAreParallelConsistent) +{ + // higher score wins + if (float_less(b.get_node_score(), a.get_node_score())) return true; + if (float_less(a.get_node_score(), b.get_node_score())) return false; + + if (globalIDsAreParallelConsistent) + return SubElementNodeAncestry::compare(a.get_ancestry(), b.get_ancestry(), SubElementNode::less_by_entity_id); + return SubElementNodeAncestry::compare(a.get_ancestry(), b.get_ancestry(), SubElementNode::less_by_coordinates_then_by_entity_id); +} + +bool SubElementNode::less_by_entity_id(const SubElementNode & a, const SubElementNode & b) +{ + // lower id wins (this can be an issue because it is sensitive to the global ids provided by percept, which are dependent on the number of procs) + return a.entityId() < b.entityId(); +} + +bool SubElementNode::less_by_coordinates_then_by_entity_id(const SubElementNode & a, const SubElementNode & b) +{ + const Vector3d & aCoord = a.coordinates(); + const Vector3d & bCoord = b.coordinates(); + if (float_less(aCoord[0], bCoord[0])) return true; + if (float_less(bCoord[0], aCoord[0])) return false; + if (float_less(aCoord[1], bCoord[1])) return true; + if (float_less(bCoord[1], aCoord[1])) return false; + if (float_less(aCoord[2], bCoord[2])) return true; + if (float_less(bCoord[2], aCoord[2])) return false; + + // as a last resort, lower id wins (this can be an issue because it is sensitive to the global ids provided by percept, which are dependent on the number of procs) + return a.entityId() < b.entityId(); +} + +bool SubElementNode::captures_intersection_point_domains(const std::vector & intersectionPointDomains) const +{ + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(my_sorted_node_domains, intersectionPointDomains); +} + +bool SubElementNode::captures_interface(const InterfaceID & interface) const +{ + if (interface.first_ls() == interface.second_ls()) + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(my_sorted_node_domains, {interface.first_ls()}); + return first_sorted_vector_of_domains_contains_all_domains_in_second_vector(my_sorted_node_domains, {interface.first_ls(),interface.second_ls()}); +} + +void SubElementNode::insert_node_domains(const std::vector & domainsToAdd) const +{ + my_sorted_node_domains.insert(my_sorted_node_domains.end(), domainsToAdd.begin(), domainsToAdd.end()); + stk::util::sort_and_unique(my_sorted_node_domains); +} + + +const SubElementNode * +SubElementNode::find_node_with_common_ancestry(const CDMesh & search_mesh) const +{ + // This only works with a lineage of edge nodes (not internal nodes). + if (is_mesh_node()) + { + return search_mesh.get_mesh_node(entityId()); + } + + const NodeVec parents = get_parents(); + const unsigned num_parents = parents.size(); + + if (num_parents == 2) + { + const SubElementNode * search_parent1 = search_mesh.find_node_with_common_ancestry(parents[0]); + const SubElementNode * search_parent2 = search_mesh.find_node_with_common_ancestry(parents[1]); + if (nullptr != search_parent1 && nullptr != search_parent2) + { + return SubElementNode::common_child({search_parent1, search_parent2}); + } + } + return nullptr; +} + +void +SubElementNode::get_ancestors(NodeSet & ancestors) const +{ + if (is_mesh_node()) + { + ancestors.insert(this); + return; + } + const NodeVec parents = get_parents(); + for(auto&& parent : parents) + { + parent->get_ancestors(ancestors); + } +} + +SubElementNodeAncestry +SubElementNode::get_ancestry() const +{ + return SubElementNodeAncestry(this); +} + +void +SubElementNode::build_stencil(std::map & stencil, const double self_weight) const +{ + if (is_mesh_node()) + { + stencil[this] += self_weight; + return; + } + const NodeVec parents = get_parents(); + const std::vector parent_weights = get_parent_weights(); + for(unsigned i=0; ibuild_stencil(stencil, self_weight * parent_weights[i]); + } +} + +void +SubElementNode::build_constraint_stencil(const FieldRef field, std::vector & entities, std::vector & weights) const +{ + ThrowRequire(!is_mesh_node()); + static const double wt_min = 1.e-9; + typedef std::tuple EntityAndWeight; + std::vector entitiesAndWeights; + + const MasterElement* master_elem = my_cached_owner->get_evaluation_master_element(field); + + const unsigned npe = master_elem->get_topology().num_nodes(); + std::vector shapefcn (npe,0.); + master_elem->shape_fcn(1, my_cached_owner_coords.data(), shapefcn.data()); + + const auto & nodes = my_cached_owner->get_nodes(); + for (unsigned n=0; n wt_min) + { + entitiesAndWeights.push_back(std::make_tuple(nodes[n]->entityId(), nodes[n]->entity(), shapefcn[n])); + } + } + + std::sort(entitiesAndWeights.begin(), entitiesAndWeights.end(), [](const EntityAndWeight & a, const EntityAndWeight & b) { return std::get<0>(a) > std::get<0>(b); }); + + entities.clear(); + weights.clear(); + + entities.push_back(entity()); + weights.push_back(-1.0); + + for (auto && entityAndWeight : entitiesAndWeights) + { + entities.push_back(std::get<1>(entityAndWeight)); + weights.push_back(std::get<2>(entityAndWeight)); + } +} + +// Notes on coordinate systems. +// (1) real coordinates +// This can be obtained using Element::coordinates( Vector3d of owner coordinates ). +// (2) owner coordinates +// This is the parametric coordinates of the finite element. +// This can be obtained using SubElement::owner_coordinates( Vector3d of subelement coordinates ). +// This is the type of coordinates stored in SubElement::my_coords, no matter what level of subelement. +// In places where both owner coordinates and subelement coordinates are used, this is kept in the var owner_coords. +// (3) subelement coordinates +// This is the parametric coordinates within the subelement. +// In places where both owner coordinates and subelement coordinates are used, this is kept in the var local_coords. + +SubElement::SubElement( const stk::topology topo, + const NodeVec & nodes, + const std::vector & side_ids, + const Mesh_Element * owner) + : ElementObj( topo, nodes), + my_parent_side_ids( side_ids ), + my_owner( owner ) +{ /* %TRACE% */ /* %TRACE% */ + ThrowAssert( nodes.size() == topology().num_nodes() ); + ThrowAssert( my_parent_side_ids.size() == topology().num_sides() ); + + set_permutation(); +} + +void +SubElement::set_permutation() +{ + // For true subelements (not just coincident with the owning mesh element), permute the element + // nodes and sides in a consistent way. This will produce consistent node and side ordering + // from decomposition to decomposition. In this way, repeated decompositions will produce identical results. + + bool coincident_with_owner = true; + for (size_t n=0; nget_nodes()[n]) + { + coincident_with_owner = false; + break; + } + } + if (coincident_with_owner) return; + + std::vector node_ancestries; + node_ancestries.reserve(my_nodes.size()); + for (auto&& node : my_nodes) + { + node_ancestries.emplace_back(node); + } + const unsigned permutation_index = topology().lexicographical_smallest_permutation(node_ancestries.data(), true); // only consider positive permutations (true means this) + + if (permutation_index == stk::mesh::DEFAULT_PERMUTATION) return; + + // permute nodes + NodeVec permuted_nodes(my_nodes.size()); + topology().permutation_nodes(my_nodes.data(), permutation_index, permuted_nodes.data()); + my_nodes = permuted_nodes; + + // permute sides + std::vector side_permutation = get_side_permutation(topology(), static_cast(permutation_index)); + + std::vector permuted_parent_side_ids(my_parent_side_ids.size()); + for (unsigned iside=0; isideentity()) return false; + } + return true; +} + +void +SubElement::get_owner_coord_transform(double * dOwnerdSub) const +{ +// const NodeVec & owner_nodes = my_owner->get_nodes(); +// for ( int n = 0; n < my_num_nodes; n++ ) +// { +// krinolog << "node " << n << ", owner node phys_coords = " << owner_nodes[n]->coordinates()[0] << "," << owner_nodes[n]->coordinates()[1] << stk::diag::dendl; +// } + + std::vector owner_coords; + fill_node_owner_coords(my_owner, owner_coords); + + // Hard coded for linear simplex elements with constant transformations + const unsigned nnodes = num_nodes(); + ThrowAssert(my_master_elem.num_intg_pts() == nnodes); + const double * d_shape = my_master_elem.shape_fcn_deriv(); + + const int dim = spatial_dim(); + for ( int i = 0; i < dim; i++ ) + { + for ( int j = 0; j < dim; j++ ) + { + double & dOwnerdSub_ij = dOwnerdSub[i*dim + j]; + + dOwnerdSub_ij = 0.0; + for ( unsigned n = 0; n < nnodes; n++ ) + { + dOwnerdSub_ij += owner_coords[n][i] * d_shape[n*dim + j]; + } + + //krinolog << "dOwnerdSub[" << i << "][" << j << "] = " << dOwnerdSub_ij << stk::diag::dendl; + } + } +} + +void +SubElement::determine_decomposed_elem_phase(const CDMesh & mesh) +{ + if(have_subelements()) + { + for(auto && subelem : my_subelements) + { + subelem->determine_decomposed_elem_phase(mesh); + } + // Phase for SubElement with subelements is left empty + return; + } + + if(!my_owner->have_interface()) + { + set_phase(my_owner->get_phase()); + } + else + { + const PhaseTag startPhase = my_phase.empty() ? my_owner->get_phase() : my_phase; + my_phase = update_phase(mesh, startPhase, my_owner->get_sorted_cutting_interfaces(), myInterfaceSigns); + } + + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "SubElement with nodes "; + for (auto && node : my_nodes) + krinolog << node->get_ancestry() << " "; + krinolog << "has phase " << my_phase << "\n"; + } +} + +std::vector SubElement::subelement_interface_signs(const InterfaceID interface, const int sign) const +{ + if (have_interface(interface) && sign != 0) + { + std::vector interfaceSigns = myInterfaceSigns; + interfaceSigns[my_owner->get_interface_index(interface)] = sign; + return interfaceSigns; + } + return myInterfaceSigns; +} + +void SubElement::initialize_interface_signs() +{ + myInterfaceSigns.assign(my_owner->get_num_interfaces(), 0); +} + +void SubElement::set_interface_signs(const std::vector & interfaceSigns) +{ + myInterfaceSigns = interfaceSigns; +} + +void SubElement::update_interface_signs(const InterfaceID interface, const int sign) +{ + set_interface_signs(subelement_interface_signs(interface, sign)); +} + +double +SubElement::relative_volume() const +{ /* %TRACE% */ /* %TRACE% */ + // This is a relative volume compared to the owner volume. + // Actually this is a relative volume if the "parametric" volume of the element is unity. + // Otherwise, it is off by a factor. + const int nelem = 1; + const int dim = spatial_dim(); + const int nint = my_master_elem.num_intg_pts(); + std::vector coords(my_nodes.size() * dim, 0.); + std::vector det_J(nint, 0.); + double error = 0.; + + // integration weights + const double * intg_weights = my_master_elem.intg_weights(); + + // load coords + int count = 0; + for ( auto && node : my_nodes ) + { + const Vector3d & owner_coords = node->owner_coords(my_owner); + for ( int j = 0; j < dim; j++ ) + { + coords[count++] = owner_coords[j]; + } + } + + // determinant at integration points + my_master_elem.determinant( dim, nelem, coords.data(), det_J.data(), &error ); + + double elem_volume = 0.; + for ( int ip = 0; ip < nint; ip++ ) + { + elem_volume += det_J[ip] * intg_weights[ip]; + } + + return elem_volume; +} + +double +SubElement::maximum_relative_angle() const +{ /* %TRACE% */ /* %TRACE% */ + // Find the maximum angle formed at the vertices in parametric coordinates. + // These are obviously differentt than that maximum angle in physical coordinates due to + // the shape of the owning element. + double max_angle = 0; + + const stk::topology topol = topology(); + const unsigned num_edges = topol.num_edges(); + for ( unsigned edge0 = 0; edge0 < num_edges; edge0++ ) + { + const unsigned * lnn0 = get_edge_node_ordinals(topol, edge0); + ThrowAssert( + 2 == topol.edge_topology(edge0).num_nodes() || 3 == topol.edge_topology(edge0).num_nodes()); + + for ( unsigned edge1 = edge0+1; edge1 < num_edges; edge1++ ) + { + const unsigned * lnn1 = get_edge_node_ordinals(topol, edge1); + ThrowAssert(2 == topol.edge_topology(edge1).num_nodes() || + 3 == topol.edge_topology(edge1).num_nodes()); + + int node0 = -1; + int node1 = -1; + if (lnn0[0] == lnn1[0]) + { + node0 = 0; node1 = 0; + } + else if (lnn0[0] == lnn1[1]) + { + node0 = 0; node1 = 1; + } + else if (lnn0[1] == lnn1[0]) + { + node0 = 1; node1 = 0; + } + else if (lnn0[1] == lnn1[1]) + { + node0 = 1; node1 = 1; + } + else + { + continue; + } + const Vector3d vec0 = my_nodes[lnn0[1-node0]]->owner_coords(my_owner) - my_nodes[lnn0[node0]]->owner_coords(my_owner); + const Vector3d vec1 = my_nodes[lnn1[1-node1]]->owner_coords(my_owner) - my_nodes[lnn1[node1]]->owner_coords(my_owner); + const double angle = std::acos( Dot(vec0.unit_vector(),vec1.unit_vector()) ); + + //if (angle > 2.4) + //{ + // krinolog << "DEBUG: bad angle = " << angle << " between edges=" << edge0 << "," << edge1 << " at node=" << lnn0[node0] << stk::diag::dendl; + //} + + if (angle > max_angle) + { + max_angle = angle; + } + } + } + + return max_angle; +} + +void +SubElement::decompose_edges(CDMesh & mesh, const InterfaceID interface_key) +{ /* %TRACE% */ /* %TRACE% */ + const std::string & owner_type = my_owner->topology().name(); + const std::string & sub_type = topology().name(); + ThrowRuntimeError("Subelement decomposition for subelement of type '" << sub_type + << "' which was generated from owning element of type '" << owner_type + << "' is missing the capability to generate conformal facets."); +} + +void +SubElement::find_refined_edges(std::vector & refined_edges) const +{ /* %TRACE% */ /* %TRACE% */ + + const stk::topology topol = topology(); + const unsigned num_edges = topol.num_edges(); + refined_edges.reserve(num_edges); + for ( unsigned edge = 0; edge < num_edges; edge++ ) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topol, edge); + + const int num_edge_nodes = topol.edge_topology(edge).num_nodes(); + ThrowRequire(2 == num_edge_nodes || 3 == num_edge_nodes); + + if ((2 == num_edge_nodes && + NULL != SubElementNode::common_child({my_nodes[edge_node_ordinals[0]], my_nodes[edge_node_ordinals[1]]})) || + (3 == num_edge_nodes && + (NULL != SubElementNode::common_child({my_nodes[edge_node_ordinals[0]], my_nodes[edge_node_ordinals[2]]}) || + NULL != SubElementNode::common_child({my_nodes[edge_node_ordinals[1]], my_nodes[edge_node_ordinals[2]]})))) + { + refined_edges.push_back(edge); + } + } +} + +int +SubElement::find_longest_bad_edge(std::vector & bad_edges) const +{ /* %TRACE% */ /* %TRACE% */ + + const stk::topology topol = topology(); + + const unsigned num_bad_edges = bad_edges.size(); + PointVec edge_midpt(num_bad_edges,Vector3d::ZERO); + + if (0 == num_bad_edges) return -1; + + double max_length = 0; + unsigned longest_bad_edge_index = 0; + for ( unsigned index = 0; index < num_bad_edges; index++ ) + { + const unsigned edge = bad_edges[index]; + + const unsigned * const lnn = get_edge_node_ordinals(topol, edge); + const int num_edge_nodes = topol.edge_topology(edge).num_nodes(); + + const SubElementNode * const node0 = my_nodes[lnn[0]]; + const SubElementNode * const node1 = my_nodes[lnn[1]]; + + const Vector3d & coord0 = node0->coordinates(); + const Vector3d & coord1 = node1->coordinates(); + + const double edge_straight_length = (coord0 - coord1).length(); + ThrowRequire(edge_straight_length > 0.0); + + if (2 == num_edge_nodes) + { + edge_midpt[index] = 0.5*(coord0 + coord1); + } + else + { + ThrowAssert (3 == num_edge_nodes); + edge_midpt[index] = my_nodes[lnn[0]]->coordinates(); + } + + // we need an absolute mechanism for selecting the edge to bisect so that all elements that share + // common edges will make the same decisions + if (utility::is_more(edge_straight_length,max_length)) + { + longest_bad_edge_index = index; + max_length = edge_straight_length; + } + else if (!utility::is_less(edge_straight_length,max_length)) // tie breaker + { + const Vector3d & edge_midside_coords = edge_midpt[index]; + // note that it is safe to assume that longest_bad_edge is already assigned if edge_length == max_length + const Vector3d longest_edge_midside_coords = edge_midpt[longest_bad_edge_index]; + + ThrowAssert((utility::is_not_equal(edge_midside_coords[0],longest_edge_midside_coords[0]) || + utility::is_not_equal(edge_midside_coords[1],longest_edge_midside_coords[1]))); + + if (utility::is_more(edge_midside_coords[0],longest_edge_midside_coords[0]) || + (!utility::is_less(edge_midside_coords[0],longest_edge_midside_coords[0]) && + (utility::is_more(edge_midside_coords[1],longest_edge_midside_coords[1])))) + { + longest_bad_edge_index = index; + max_length = edge_straight_length; + } + } + } + return bad_edges[longest_bad_edge_index]; +} + +int +SubElement::parent_side_id(const int iside) const +{ + return my_parent_side_ids[iside]; +} + +void +SubElement::debug_subelements(const NodeVec & lnodes, const InterfaceID & interface, const int case_id) const +{ /* %TRACE% */ /* %TRACE% */ + krinolog << "owner_id=" << my_owner->entityId() << ", after cutting with interface " << interface << ", case_id=" << case_id << stk::diag::dendl; + + for (unsigned n=0; nget_ancestry() << "]\n"; + } + } + krinolog << " interface signs = "; + const std::vector interfaces = my_owner->get_sorted_cutting_interfaces(); + ThrowRequire(interfaces.size() == myInterfaceSigns.size()); + for (unsigned i=0; idebug(); + } + krinolog << stk::diag::dendl; +} + +void +SubElement::debug() const +{ /* %TRACE% */ /* %TRACE% */ + const double sub_vol = relative_volume(); + krinolog << " owner_id=" << my_owner->entityId() << ", relative_volume=" << sub_vol << ", interface signs = "; + const std::vector interfaces = my_owner->get_sorted_cutting_interfaces(); + ThrowRequire(interfaces.size() == myInterfaceSigns.size()); + for (unsigned i=0; iget_ancestry() << "] with domains { "; + for (int domain : node->get_sorted_node_domains()) krinolog << domain << " "; + krinolog << "}\n"; + } + } + for (unsigned n=0; nhave_interface(interface) && (myInterfaceSigns[my_owner->get_interface_index(interface)] == 0); +} + +SubElement_Tri_6::SubElement_Tri_6( + const NodeVec & nodes, + const std::vector & parent_side_ids, + const Mesh_Element * owner) + : SubElement( stk::topology::TRIANGLE_6_2D, + nodes, + parent_side_ids, + owner) +{ /* %TRACE% */ /* %TRACE% */ +} + +SubElement_Tet_10::SubElement_Tet_10( + const NodeVec & nodes, + const std::vector & parent_side_ids, + const Mesh_Element * owner) + : SubElement( stk::topology::TETRAHEDRON_10, + nodes, + parent_side_ids, + owner) +{ /* %TRACE% */ /* %TRACE% */ +} + +SubElement_Tri_3::SubElement_Tri_3( + const NodeVec & nodes, + const std::vector & parent_side_ids, + const Mesh_Element * owner) + : SubElement( stk::topology::TRIANGLE_3_2D, + nodes, + parent_side_ids, + owner) +{ /* %TRACE% */ /* %TRACE% */ + +} + +void +SubElement_Tri_3::build_quadratic_subelements(CDMesh & mesh) +{ /* %TRACE% */ /* %TRACE% */ + + if ( my_subelements.size() > 0 ) + { + for ( auto && subelem : my_subelements ) + { + subelem->build_quadratic_subelements(mesh); + } + return; + } + + // create 1, 6-noded tri + NodeVec sub_nodes = my_nodes; + sub_nodes.resize(6,(SubElementNode *)NULL); + + sub_nodes[3] = mesh.create_midside_node(my_owner, my_nodes[0], my_nodes[1]); + sub_nodes[4] = mesh.create_midside_node(my_owner, my_nodes[1], my_nodes[2]); + sub_nodes[5] = mesh.create_midside_node(my_owner, my_nodes[2], my_nodes[0]); + + std::unique_ptr sub = std::make_unique( sub_nodes, my_parent_side_ids, my_owner ); + sub->set_interface_signs(get_interface_signs()); + add_subelement( std::move(sub) ); +} + +void SubElement_Tri_3::cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains) +{ + const std::vector weights{1.-pCoords[0]-pCoords[1], pCoords[0], pCoords[1]}; + + bool badCut = false; + for (auto && weight : weights) + { + if(weight < mesh.get_snapper().get_edge_tolerance()) + { + if (krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "Skipping cut of interior intersection point because of quality." << stk::diag::dendl; + badCut = true; + break; + } + } + + if (!badCut) + { + const SubElementNode * cutNode = mesh.create_child_internal_or_face_node( my_owner, my_nodes, weights ); + cutNode->set_node_domains(sortedDomains); + + NodeVec lnodes = my_nodes; + lnodes.push_back(cutNode); + + handle_tri(lnodes, get_interface_signs(), 0,1,3, 0,-1,-1, false,false,false); + handle_tri(lnodes, get_interface_signs(), 1,2,3, 1,-1,-1, false,false,false); + handle_tri(lnodes, get_interface_signs(), 2,0,3, 2,-1,-1, false,false,false); + } +} + +void +SubElement_Tri_3::determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) +{ + determine_node_signs_on_edge( mesh, interface_key, 0,1 ); + determine_node_signs_on_edge( mesh, interface_key, 1,2 ); + determine_node_signs_on_edge( mesh, interface_key, 2,0 ); +} + +void +SubElement_Tri_3::determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) +{ + // No-op, node scores are not used on tris +} + +void +SubElement_Tri_3::decompose_edges(CDMesh & mesh, const InterfaceID interface_key) +{ + process_edge( mesh, interface_key, 0,1 ); + process_edge( mesh, interface_key, 1,2 ); + process_edge( mesh, interface_key, 2,0 ); +} + +void +SubElement_Tri_3::fix_hanging_children(CDMesh & mesh, const InterfaceID & interface, const std::vector & edges_with_children) +{ + int edge_case_id = 0; + for (auto edge_with_children : edges_with_children) + { + edge_case_id += 1< node_signs = {{0, 0, 0}}; + + if (edge_case_id == 0) // uncut subelement + { + if (my_nodes[0]->node_sign_is_set()) node_signs[0] = my_nodes[0]->get_node_sign(); + if (my_nodes[1]->node_sign_is_set()) node_signs[1] = my_nodes[1]->get_node_sign(); + if (my_nodes[2]->node_sign_is_set()) node_signs[2] = my_nodes[2]->get_node_sign(); + + if (!(node_signs[0] >= 0 && node_signs[1] >= 0 && node_signs[2] >= 0) && + !(node_signs[0] <= 0 && node_signs[1] <= 0 && node_signs[2] <= 0)) + { + return; + } + } + else + { + for (auto && edge_with_child : edges_with_children) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topology(), edge_with_child); + const int i0 = edge_node_ordinals[0]; + const int i1 = edge_node_ordinals[1]; + node_signs[i0] = my_nodes[i0]->get_node_sign(); + node_signs[i1] = my_nodes[i1]->get_node_sign(); + } + } + + perform_decomposition(mesh, interface, node_signs); +} + +void +SubElement_Tri_3::perform_decomposition(CDMesh & mesh, const InterfaceID interface_key, const std::array & node_signs) +{ /* %TRACE% */ /* %TRACE% */ + + const int case_id = + (node_signs[0]+1) + + (node_signs[1]+1)*3 + + (node_signs[2]+1)*9; + + NodeVec lnodes = my_nodes; + lnodes.resize(6,(SubElementNode *)NULL); + + static const unsigned case_permutations[] = + { 0, 0, 0, 2, 0, 0, 2, 1, 1, 1, // 0-9 + 1, 2, 2, 0, 2, 2, 1, 1, 1, 1, // 10-19 + 2, 0, 0, 2, 0, 0, 0 }; // 20-26 + static const unsigned permute_case_ids[] = + { 0, 1, 2, 1, 4, 5, 2,21,24, 1, // 0-9 + 4,21, 4,13,22, 5,22,25, 2, 5, // 10-19 + 24,21,22,25,24,25,26 }; // 20-26 + + stk::topology topo = stk::topology::TRIANGLE_6_2D; + std::vector permute(6); + topo.permutation_node_ordinals(case_permutations[case_id], permute.begin()); + + const unsigned i0 = permute[0]; + const unsigned i1 = permute[1]; + const unsigned i2 = permute[2]; + const unsigned i3 = permute[3]; + const unsigned i5 = permute[5]; + + // nodes and sides permute the same way + const unsigned s0 = permute[0]; + const unsigned s1 = permute[1]; + const unsigned s2 = permute[2]; + + const int permute_case_id = permute_case_ids[case_id]; + + // FIXME: Remove this diagnostic + std::vector node_val(3); + node_val[2] = case_id/9; + node_val[1] = (case_id-9*node_val[2])/3; + node_val[0] = case_id-9*node_val[2]-3*node_val[1]; + ThrowRequire(permute_case_id == (node_val[i0] + node_val[i1]*3 + node_val[i2]*9)); + + const Simplex_Generation_Method simplexMethod = mesh.get_cdfem_support().get_simplex_generation_method(); + +// krinolog << "case_id, permute_case_id = " << case_id << ", " << permute_case_id << stk::diag::dendl; + + switch (permute_case_id) + { + case 0: // ls[0]<0 && ls[1]<0 && ls[2]<0 + case 1: // ls[0]=0 && ls[1]<0 && ls[2]<0 + { + update_interface_signs(interface_key, -1); + } + break; + + case 13: // ls[0]=0 && ls[1]=0 && ls[2]=0 + case 25: // ls[0]=0 && ls[1]>0 && ls[2]>0 + case 26: // ls[0]>0 && ls[1]>0 && ls[2]>0 + { + update_interface_signs(interface_key, +1); + } + break; + + case 2: // ls[0]>0 && ls[1]<0 && ls[2]<0 + case 24: // ls[0]<0 && ls[1]>0 && ls[2]>0 + { + lnodes[i3] = SubElementNode::common_child({lnodes[i0], lnodes[i1]}); + lnodes[i5] = SubElementNode::common_child({lnodes[i2], lnodes[i0]}); + ThrowRequire(nullptr != lnodes[i3] && nullptr != lnodes[i5]); + + const bool diag = determine_diagonal_for_cut_triangle(simplexMethod, lnodes, i0, i1, i2, i3, i5); + + const int sign = (permute_case_id==2) ? 1 : -1; + handle_tri(lnodes, subelement_interface_signs(interface_key, sign), i0,i3,i5, s0,-1,s2, false,true,false); + handle_quad(mesh, lnodes, subelement_interface_signs(interface_key, -sign), i3,i1,i2,i5, s0,s1,s2,-1, false,false,false,true, diag); + } + break; + + case 4: // ls[0]=0 && ls[1]=0 && ls[2]<0 + case 22: // ls[0]=0 && ls[1]=0 && ls[2]>0 + { + const int sign = (permute_case_id==4) ? -1 : 1; + update_interface_signs(interface_key, sign); + } + break; + + case 5: // ls[0]>0 && ls[1]=0 && ls[2]<0 + case 21: // ls[0]<0 && ls[1]=0 && ls[2]>0 + { + lnodes[i5] = SubElementNode::common_child({lnodes[i2], lnodes[i0]}); + ThrowRequire(nullptr != lnodes[i5]); + + const int sign = (permute_case_id==5) ? 1 : -1; + handle_tri(lnodes, subelement_interface_signs(interface_key, sign), i1,i5,i0, -1,s2,s0, true,false,false); + handle_tri(lnodes, subelement_interface_signs(interface_key, -sign), i5,i1,i2, -1,s1,s2, true,false,false); + } + break; + + default: ThrowRuntimeError("Subelement decomposition error. case_id,permute_case_id=" << case_id << "," << permute_case_id); + } + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + debug_subelements(lnodes, interface_key, case_id); + } +} + +bool +SubElement_Tri_3::determine_diagonal_for_cut_triangle(const Simplex_Generation_Method & simplexMethod, const NodeVec & lnodes, const int i0, const int i1, const int i2, const int i3, const int i5) +{ + /* + * 2 o + * / \ + * 5 o \ + * / \ \ + * o---o---o + * 0 3 1 + */ + + // true: connect nodes 3 and 2 + // false: connect nodes 5 and 1 + + if (simplexMethod == CUT_QUADS_BY_GLOBAL_IDENTIFIER) + { + SubElementNodeAncestry ancestry1 = lnodes[i1]->get_ancestry(); + SubElementNodeAncestry ancestry2 = lnodes[i2]->get_ancestry(); + + return ancestry2 < ancestry1; + } + else + { + ThrowRequire(simplexMethod == CUT_QUADS_BY_LARGEST_ANGLE); + + // Angle-based scheme + // Select diagonal that cuts largest angle in quad. Since there isn't an issue with + // conforming, this is always possible (unlike tet). + const int config = ElementObj::evaluate_quad(lnodes[i3],lnodes[i1],lnodes[i2],lnodes[i5]); + return (config == -1); + } +} + +void +SubElement_Tri_3::handle_tri( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, + const int s0, const int s1, const int s2, + const bool is_interface0, const bool is_interface1, const bool is_interface2) +{ + ThrowRequire(!is_degenerate(lnodes, i0,i1,i2)); + + NodeVec sub_nodes(3,(SubElementNode *)NULL); + std::vector sub_parent_ids(3); + + sub_nodes[0] = lnodes[i0]; + sub_nodes[1] = lnodes[i1]; + sub_nodes[2] = lnodes[i2]; + sub_parent_ids[0] = (s0>= 0) ? my_parent_side_ids[s0] : -1; + sub_parent_ids[1] = (s1>= 0) ? my_parent_side_ids[s1] : -1; + sub_parent_ids[2] = (s2>= 0) ? my_parent_side_ids[s2] : -1; + + std::unique_ptr sub = std::make_unique( sub_nodes, sub_parent_ids, my_owner); + sub->set_interface_signs(subInterfaceSigns); + add_subelement( std::move(sub) ); +} + +void +SubElement_Tri_3::handle_quad( CDMesh & mesh, + NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, + const int s0, const int s1, const int s2, const int s3, + const bool is_interface0, const bool is_interface1, const bool is_interface2, const bool is_interface3, + const bool face ) +{ +#if 1 + if (face) + { + handle_tri( lnodes, subInterfaceSigns, i0,i1,i2, s0,s1,-1, is_interface0,is_interface1,false ); + handle_tri( lnodes, subInterfaceSigns, i2,i3,i0, s2,s3,-1, is_interface2,is_interface3,false ); + } + else + { + handle_tri( lnodes, subInterfaceSigns, i0,i1,i3, s0,-1,s3, is_interface0,false,is_interface3 ); + handle_tri( lnodes, subInterfaceSigns, i2,i3,i1, s2,-1,s1, is_interface2,false,is_interface1 ); + } +#else + NodeVec quad_nodes; + std::vector weights; + const double x0 = 0; + const double y0 = 0; + + quad_nodes.push_back(lnodes[i0]); + weights.push_back(0.25*(1-x0)*(1-y0)); + quad_nodes.push_back(lnodes[i1]); + weights.push_back(0.25*(1+x0)*(1-y0)); + quad_nodes.push_back(lnodes[i2]); + weights.push_back(0.25*(1+x0)*(1+y0)); + quad_nodes.push_back(lnodes[i3]); + weights.push_back(0.25*(1-x0)*(1+y0)); + + lnodes[6] = mesh.create_internal_node( my_owner, quad_nodes, weights ); + + handle_tri(lnodes, ls_index, sign, i0,i1,6, s0,-1,-1); + handle_tri(lnodes, ls_index, sign, i1,i2,6, s1,-1,-1); + handle_tri(lnodes, ls_index, sign, i2,i3,6, s2,-1,-1); + handle_tri(lnodes, ls_index, sign, i3,i0,6, s3,-1,-1); +#endif +} + +bool +SubElement_Tri_3::is_degenerate( NodeVec & lnodes, + const int i0, const int i1, const int i2 ) +{ /* %TRACE% */ /* %TRACE% */ + + if ( lnodes[i0] == lnodes[i1] || + lnodes[i0] == lnodes[i2] || + lnodes[i1] == lnodes[i2] ) + { + // this tri is degenerate with two coincident nodes + return true; + } + + return false; +} + +SubElement_Tet_4::SubElement_Tet_4( + const NodeVec & nodes, + const std::vector & parent_side_ids, + const Mesh_Element * owner) + : SubElement( stk::topology::TETRAHEDRON_4, + nodes, + parent_side_ids, + owner) +{ /* %TRACE% */ /* %TRACE% */ +} + +void SubElement_Tet_4::cut_face_intersection_point_with_permutation(CDMesh & mesh, const std::array & permuteNodes, const std::array & permuteSides, const std::vector & faceNodeWeights, const std::vector & sortedDomains) +{ + const SubElementNode * cutNode = mesh.create_child_internal_or_face_node(my_owner, + {my_nodes[permuteNodes[0]], my_nodes[permuteNodes[1]], my_nodes[permuteNodes[2]]}, + {faceNodeWeights[0], faceNodeWeights[1], faceNodeWeights[2]}); + const auto & previousDomains = cutNode->get_sorted_node_domains(); + ThrowRequire(previousDomains.empty() || sortedDomains == previousDomains); + cutNode->set_node_domains(sortedDomains); + + NodeVec lnodes; + lnodes.reserve(5); + for (int i=0; i<4; ++i) + lnodes.push_back(my_nodes[permuteNodes[i]]); + lnodes.push_back(cutNode); + + handle_tet(lnodes, get_interface_signs(), 0,1,4,3, permuteSides[0],-1,-1,permuteSides[3]); + handle_tet(lnodes, get_interface_signs(), 1,2,4,3, permuteSides[1],-1,-1,permuteSides[3]); + handle_tet(lnodes, get_interface_signs(), 2,0,4,3, permuteSides[2],-1,-1,permuteSides[3]); +} + +void SubElement_Tet_4::cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains) +{ + const std::vector weights{1.-pCoords[0]-pCoords[1]-pCoords[2], pCoords[0], pCoords[1], pCoords[2]}; + + bool badCut = false; + for (auto && weight : weights) + { + if(weight < mesh.get_snapper().get_edge_tolerance()) + { + if (krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "Skipping cut of interior intersection point because of quality." << stk::diag::dendl; + badCut = true; + break; + } + } + + if (!badCut) + { + const SubElementNode * cutNode = mesh.create_child_internal_or_face_node( my_owner, my_nodes, weights ); + cutNode->set_node_domains(sortedDomains); + + NodeVec lnodes = my_nodes; + lnodes.push_back(cutNode); + + handle_tet(lnodes, get_interface_signs(), 0,3,1,4, -1,-1,-1,0); + handle_tet(lnodes, get_interface_signs(), 1,3,2,4, -1,-1,-1,1); + handle_tet(lnodes, get_interface_signs(), 0,2,3,4, -1,-1,-1,2); + handle_tet(lnodes, get_interface_signs(), 0,1,2,4, -1,-1,-1,3); + } +} + +void +SubElement_Tet_4::build_quadratic_subelements(CDMesh & mesh) +{ /* %TRACE% */ /* %TRACE% */ + + if ( my_subelements.size() > 0 ) + { + for ( auto && subelem : my_subelements ) + { + subelem->build_quadratic_subelements(mesh); + } + return; + } + + // create 1, 10-noded tet + NodeVec sub_nodes = my_nodes; + sub_nodes.resize(10,(SubElementNode *)NULL); + + const stk::topology tet10_topology = stk::topology::TETRAHEDRON_10; + + for (unsigned edge_i=0; edge_i sub = std::make_unique( sub_nodes, my_parent_side_ids, my_owner ); + sub->set_interface_signs(get_interface_signs()); + add_subelement( std::move(sub) ); +} + +struct FaceIntersection +{ + FaceIntersection(const int iFace, const Vector3d & coords, const std::vector & domains) + : face(iFace), + parametricCoords(coords), + sortedDomains(domains) {} + + int face; + Vector3d parametricCoords; + std::vector sortedDomains; +}; + +void +SubElement_Tet_4::cut_face_interior_intersection_points(CDMesh & mesh, const InterfaceID & interface1, const InterfaceID & interface2, int level) +{ /* %TRACE% */ /* %TRACE% */ + + if ( my_subelements.size() > 0 ) + { + for ( auto && subelem : my_subelements ) + { + subelem->cut_face_interior_intersection_points(mesh, interface1, interface2, level); + } + return; + } + + static constexpr std::array,4> permuteNodes{{ {{0,3,1,2}}, {{1,3,2,0}}, {{0,2,3,1}}, {{0,1,2,3}} }}; + static constexpr std::array,4> permuteSides{{ {{2,1,3,0}}, {{0,2,3,1}}, {{3,1,0,2}}, {{0,1,2,3}} }}; + + std::vector faceNodes(3); + // Note: this recursively cuts the first identified face interior intersection point + for (unsigned iFace=0; iFace faceIntersections; + my_owner->fill_face_interior_intersections(faceNodes, interface1, interface2, faceIntersections); + + for (auto && faceIntersection : faceIntersections) + { + const Vector3d & faceCoords = faceIntersection.parametricCoords; + const std::vector faceNodeWeights{1.-faceCoords[0]-faceCoords[1], faceCoords[0], faceCoords[1]}; + bool badCut = false; + for (auto && weight : faceNodeWeights) + { + if (weight < mesh.get_snapper().get_edge_tolerance()) + { + if (krinolog.shouldPrint(LOG_DEBUG)) + krinolog << "Skipping cut of interior face intersection point because of quality." << stk::diag::dendl; + badCut = true; + break; + } + } + if (!badCut) + { + ThrowRequireMsg(level < 8, "Face cut recursion level exceeded."); + cut_face_intersection_point_with_permutation(mesh, permuteNodes[iFace], permuteSides[iFace], faceNodeWeights, faceIntersection.sortedDomains); + cut_face_interior_intersection_points(mesh, interface1, interface2, ++level); + return; + } + } + } +} + +const unsigned ** +SubElement_Tet_4::get_permutation_side_ordinals() +{ + static const unsigned permutation_side_ordinals0[] = { 0, 1, 2, 3 }; + static const unsigned permutation_side_ordinals1[] = { 1, 2, 0, 3 }; + static const unsigned permutation_side_ordinals2[] = { 2, 0, 1, 3 }; + static const unsigned permutation_side_ordinals3[] = { 2, 1, 3, 0 }; + static const unsigned permutation_side_ordinals4[] = { 1, 3, 2, 0 }; + static const unsigned permutation_side_ordinals5[] = { 3, 2, 1, 0 }; + static const unsigned permutation_side_ordinals6[] = { 3, 1, 0, 2 }; + static const unsigned permutation_side_ordinals7[] = { 1, 0, 3, 2 }; + static const unsigned permutation_side_ordinals8[] = { 0, 3, 1, 2 }; + static const unsigned permutation_side_ordinals9[] = { 0, 2, 3, 1 }; + static const unsigned permutation_side_ordinals10[] = { 2, 3, 0, 1 }; + static const unsigned permutation_side_ordinals11[] = { 3, 0, 2, 1 }; + static const unsigned * permutation_side_ordinals[] = + { permutation_side_ordinals0 , permutation_side_ordinals1 , permutation_side_ordinals2, permutation_side_ordinals3 , permutation_side_ordinals4 , permutation_side_ordinals5 , + permutation_side_ordinals6 , permutation_side_ordinals7 , permutation_side_ordinals8, permutation_side_ordinals9, permutation_side_ordinals10, permutation_side_ordinals11 }; + return permutation_side_ordinals; +} + +double SubElement_Tet_4::tet_volume(const std::array & nodes) +{ + return Dot(nodes[3]-nodes[0],Cross(nodes[1]-nodes[0], nodes[2]-nodes[0]))/6.0; +} + +void +SubElement_Tet_4::fix_hanging_children(CDMesh & mesh, const InterfaceID & interface_key, const std::vector & edges_with_children) +{ + int edge_case_id = 0; + for (unsigned i=0; i node_signs = {{0, 0, 0, 0}}; + + if (edge_case_id == 0) // uncut subelement + { + if (my_nodes[0]->node_sign_is_set()) node_signs[0] = my_nodes[0]->get_node_sign(); + if (my_nodes[1]->node_sign_is_set()) node_signs[1] = my_nodes[1]->get_node_sign(); + if (my_nodes[2]->node_sign_is_set()) node_signs[2] = my_nodes[2]->get_node_sign(); + if (my_nodes[3]->node_sign_is_set()) node_signs[3] = my_nodes[3]->get_node_sign(); + + if (!(node_signs[0] >= 0 && node_signs[1] >= 0 && node_signs[2] >= 0 && node_signs[3] >= 0) && + !(node_signs[0] <= 0 && node_signs[1] <= 0 && node_signs[2] <= 0 && node_signs[3] <= 0)) + { + return; + } + } + else + { + for (auto && edge_with_child : edges_with_children) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(topology(), edge_with_child); + const int i0 = edge_node_ordinals[0]; + const int i1 = edge_node_ordinals[1]; + node_signs[i0] = my_nodes[i0]->get_node_sign(); + node_signs[i1] = my_nodes[i1]->get_node_sign(); + } + } + + perform_decomposition(mesh, interface_key, node_signs); + } + else + { + ThrowAssert(case_id == 2 || case_id == 3 || case_id == 4); + + static const int edge_case_permutations [] = + { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // 0-9 + 2, 6, -1, -1, 5, -1, -1, -1, -1, -1, // 10-19 + 0, 8, 5, -1, -1, -1, 0, -1, 0, -1, // 20-29 + -1, -1, -1, 1, -1, 4, -1, 3, -1, -1, // 30-39 + -1, 2, 2, -1, -1, -1, -1, -1, -1, 1, // 40-49 + -1, -1, 1, -1, -1, -1, -1, -1, -1, -1, // 50-59 + -1, -1, -1, -1 // 60-63 + }; + + const int permutation = edge_case_permutations[edge_case_id]; + ThrowRequire(permutation >= 0); + + stk::topology topo = stk::topology::TETRAHEDRON_10; + std::vector permute_nodes(10); + topo.permutation_node_ordinals(permutation, permute_nodes.begin()); + + const unsigned i0 = permute_nodes[0]; + const unsigned i1 = permute_nodes[1]; + const unsigned i2 = permute_nodes[2]; + const unsigned i3 = permute_nodes[3]; + const unsigned i5 = permute_nodes[5]; + const unsigned i6 = permute_nodes[6]; + const unsigned i7 = permute_nodes[7]; + const unsigned i8 = permute_nodes[8]; + + const unsigned ** permutation_side_ordinals = get_permutation_side_ordinals(); + const unsigned s0 = permutation_side_ordinals[permutation][0]; + const unsigned s1 = permutation_side_ordinals[permutation][1]; + const unsigned s2 = permutation_side_ordinals[permutation][2]; + const unsigned s3 = permutation_side_ordinals[permutation][3]; + + NodeVec lnodes = my_nodes; + lnodes.resize(10,(SubElementNode *)NULL); + + const int arbitrary_sign = 0; + const auto subInterfaceSigns = subelement_interface_signs(interface_key, arbitrary_sign); + const Simplex_Generation_Method simplexMethod = mesh.get_cdfem_support().get_simplex_generation_method(); + const bool globalIDsAreParallelConsistent = mesh.get_cdfem_support().get_global_ids_are_parallel_consistent(); + + if (case_id == 2) + { + lnodes[i6] = SubElementNode::common_child({lnodes[i0], lnodes[i2]}); + lnodes[i8] = SubElementNode::common_child({lnodes[i1], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i6] && nullptr != lnodes[i8]); + + + handle_tet( lnodes, subInterfaceSigns, i6,i2,i3,i8, -1,s1,-1,s2 ); + handle_tet( lnodes, subInterfaceSigns, i3,i0,i6,i8, s0,-1,-1,s2 ); + handle_tet( lnodes, subInterfaceSigns, i6,i0,i1,i8, -1,s0,-1,s3 ); + handle_tet( lnodes, subInterfaceSigns, i1,i2,i6,i8, s1,-1,-1,s3 ); + } + else if (case_id == 3) + { + lnodes[i6] = SubElementNode::common_child({lnodes[i0], lnodes[i2]}); + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + lnodes[i8] = SubElementNode::common_child({lnodes[i1], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i6] && nullptr != lnodes[i7] && nullptr != lnodes[i8]); + + const bool face0 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i3, i0, i1, i7, i8); + const bool face2 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i3, i2, i7, i6); + + // Connect 6-8 + handle_tet( lnodes, subInterfaceSigns, i1,i2,i6,i8, s1,-1,-1,s3 ); + handle_pyramid( lnodes, subInterfaceSigns, i1,i0,i7,i8,i6, s3,s2,-1,-1,s0, face0 ); + handle_pyramid( lnodes, subInterfaceSigns, i2,i3,i7,i6,i8, s1,s0,-1,-1,s2, face2 ); + } + else if (case_id == 4) + { + lnodes[i5] = SubElementNode::common_child({lnodes[i1], lnodes[i2]}); + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + lnodes[i8] = SubElementNode::common_child({lnodes[i1], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i5] && nullptr != lnodes[i7] && nullptr != lnodes[i8]); + + const bool face0 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i3, i0, i1, i7, i8); + const bool face1 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i1, i2, i3, i5, i8); + + // Connect 5-7 + handle_tet( lnodes, subInterfaceSigns, i0,i5,i2,i7, -1,-1,s2,s3 ); + handle_pyramid( lnodes, subInterfaceSigns, i1,i0,i7,i8,i5, s3,-1,-1,s1,s0, face0 ); + handle_pyramid( lnodes, subInterfaceSigns, i5,i8,i3,i2,i7, -1,s0,s2,-1,s1, face1 ); + } + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + debug_subelements(lnodes, interface_key, case_id); + } + } +} + +void +SubElement_Tet_4::determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) +{ + ThrowAssert(!have_subelements()); + determine_node_signs_on_edge( mesh, interface_key, 0,1 ); + determine_node_signs_on_edge( mesh, interface_key, 1,2 ); + determine_node_signs_on_edge( mesh, interface_key, 0,2 ); + determine_node_signs_on_edge( mesh, interface_key, 0,3 ); + determine_node_signs_on_edge( mesh, interface_key, 1,3 ); + determine_node_signs_on_edge( mesh, interface_key, 2,3 ); +} + +void +SubElement_Tet_4::determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) +{ + ThrowAssert(!have_subelements()); + + const Simplex_Generation_Method simplexMethod = mesh.get_cdfem_support().get_simplex_generation_method(); + if (simplexMethod == CUT_QUADS_BY_NEAREST_EDGE_CUT) + { + // nodal edge cut length based criterion + // Use globally consistent comparison at nodes based on the shortest relative edge length for the cut edges that use the node. + + // The general idea is to prefer edges that emanate away from nodes that have nearby cuts. This, for perfectly shaped elements, + // will cut the largest angles. + + determine_node_scores_on_edge( mesh, interface_key, 0,1 ); + determine_node_scores_on_edge( mesh, interface_key, 1,2 ); + determine_node_scores_on_edge( mesh, interface_key, 0,2 ); + determine_node_scores_on_edge( mesh, interface_key, 0,3 ); + determine_node_scores_on_edge( mesh, interface_key, 1,3 ); + determine_node_scores_on_edge( mesh, interface_key, 2,3 ); + } + else if (simplexMethod == CUT_QUADS_BY_LARGEST_ANGLE) + { + // nodal face angle criterion + // Use globally consistent comparison at nodes based on the largest angle for the cut faces that use the node. + // This does not rely on perfectly shaped elements to cut the larges angles. + + determine_node_scores_on_face( mesh, interface_key, 0,1,3 ); + determine_node_scores_on_face( mesh, interface_key, 1,2,3 ); + determine_node_scores_on_face( mesh, interface_key, 2,0,3 ); + determine_node_scores_on_face( mesh, interface_key, 2,0,3 ); + } +} + + +static std::pair get_quad_angle_measures(const Vector3d & x0, const Vector3d & x1, const Vector3d & x2, const Vector3d & x3) +{ + std::array sides{x1-x0, x2-x1, x3-x2, x0-x3}; + for (auto && side : sides) side.unitize(); + + // return measure02,measure13 where measureAB=std::max(-cos(A),-cos(B)) + return {std::max(Dot(sides[3],sides[0]), Dot(sides[1],sides[2])), std::max(Dot(sides[0],sides[1]), Dot(sides[2],sides[3]))}; +} + +static void determine_node_scores_on_triangle_face( const std::array & faceNodes ) +{ + /* + * 2 o + * / \ + * / o 4 + * / / \ + * o---o---o + * 0 3 1 + */ + + const std::pair measure23Andmeasure04 = get_quad_angle_measures(faceNodes[2]->coordinates(), faceNodes[0]->coordinates(), faceNodes[3]->coordinates(), faceNodes[4]->coordinates()); + faceNodes[2]->set_node_score(measure23Andmeasure04.first); + faceNodes[0]->set_node_score(measure23Andmeasure04.second); +} + +void +SubElement_Tet_4::determine_node_scores_on_face( const CDMesh & mesh, const InterfaceID interface, const int i0, const int i1, const int i2 ) +{ + + const SubElementNode * parent0 = my_nodes[i0]; + const SubElementNode * parent1 = my_nodes[i1]; + const SubElementNode * parent2 = my_nodes[i2]; + + if (parent0->get_node_on_interface() || parent1->get_node_on_interface() || parent2->get_node_on_interface()) return; + + const SubElementNode * child0 = SubElementNode::common_child({parent0, parent1}); + const SubElementNode * child1 = SubElementNode::common_child({parent1, parent2}); + const SubElementNode * child2 = SubElementNode::common_child({parent2, parent0}); + + const int caseId = + ((child0 == nullptr) ? 0 : 1) + + ((child1 == nullptr) ? 0 : 2) + + ((child2 == nullptr) ? 0 : 4); + + if (caseId == 3) + determine_node_scores_on_triangle_face({parent0, parent1, parent2, child0, child1}); + else if (caseId == 5) + determine_node_scores_on_triangle_face({parent2, parent0, parent1, child2, child0}); + else if (caseId == 6) + determine_node_scores_on_triangle_face({parent1, parent2, parent0, child1, child2}); +} + +void +SubElement_Tet_4::decompose_edges(CDMesh & mesh, const InterfaceID interface_key) +{ /* %TRACE% */ /* %TRACE% */ + + process_edge( mesh, interface_key, 0,1 ); + process_edge( mesh, interface_key, 1,2 ); + process_edge( mesh, interface_key, 0,2 ); + process_edge( mesh, interface_key, 0,3 ); + process_edge( mesh, interface_key, 1,3 ); + process_edge( mesh, interface_key, 2,3 ); +} + +void +SubElement_Tet_4::perform_decomposition(CDMesh & mesh, const InterfaceID interface_key, const std::array & node_signs) +{ /* %TRACE% */ /* %TRACE% */ + + // create between 4 to 6 conforming tetrahedral subelements + + const int case_id = + (node_signs[0]+1) + + (node_signs[1]+1)*3 + + (node_signs[2]+1)*9 + + (node_signs[3]+1)*27; + + NodeVec lnodes = my_nodes; + lnodes.resize(10,(SubElementNode *)NULL); + + static const unsigned case_permutations[] = + { 0, 0, 0, 1, 0, 0, 1, 5, 0, 2, // 0-9 + 2, 6, 1, 0, 0, 1, 1,10, 2, 2, // 10-19 + 2,11, 2, 4, 1, 8, 4, 4, 3, 3, // 20-29 + 4, 3, 3, 9, 5, 7, 7, 6, 6, 9, // 30-39 + 0, 9, 9, 6, 7, 7, 7, 9,11, 3, // 40-49 + 4, 3, 3, 4, 4, 8, 3, 4, 4,11, // 50-59 + 4, 2, 2,10, 8, 1,10, 0, 1, 6, // 60-69 + 2, 2, 7, 5, 1, 0, 0, 1, 0, 0, // 70-79 + 0 }; // 80 + + stk::topology topo = stk::topology::TETRAHEDRON_10; + std::vector permute_nodes(10); + topo.permutation_node_ordinals(case_permutations[case_id], permute_nodes.begin()); + + const unsigned i0 = permute_nodes[0]; + const unsigned i1 = permute_nodes[1]; + const unsigned i2 = permute_nodes[2]; + const unsigned i3 = permute_nodes[3]; + const unsigned i4 = permute_nodes[4]; + const unsigned i5 = permute_nodes[5]; + const unsigned i6 = permute_nodes[6]; + const unsigned i7 = permute_nodes[7]; + const unsigned i8 = permute_nodes[8]; + + const unsigned ** permutation_side_ordinals = get_permutation_side_ordinals(); + const unsigned s0 = permutation_side_ordinals[case_permutations[case_id]][0]; + const unsigned s1 = permutation_side_ordinals[case_permutations[case_id]][1]; + const unsigned s2 = permutation_side_ordinals[case_permutations[case_id]][2]; + const unsigned s3 = permutation_side_ordinals[case_permutations[case_id]][3]; + + static const unsigned permute_case_ids[] = + { 0, 1, 2, 1, 4, 5, 2, 5, 8, 1, // 0-9 + 4, 5, 4,13,14, 5,14,75, 2, 5, // 10-19 + 8, 5,14,75, 8,75,78, 1, 4, 5, // 20-29 + 4,13,14, 5,14,75, 4,13,14,13, // 30-39 + 40,67,14,67,76, 5,14,75,14,67, // 40-49 + 76,75,76,79, 2, 5, 8, 5,14,75, // 50-59 + 8,75,78, 5,14,75,14,67,76,75, // 60-69 + 76,79, 8,75,78,75,76,79,78,79, // 70-79 + 80 }; // 80 + + const int permute_case_id = permute_case_ids[case_id]; + + // FIXME: Remove this diagnostic + std::vector node_val(4); + node_val[3] = case_id/27; + node_val[2] = (case_id-27*node_val[3])/9; + node_val[1] = (case_id-27*node_val[3]-9*node_val[2])/3; + node_val[0] = case_id-27*node_val[3]-9*node_val[2]-3*node_val[1]; + ThrowRequire(permute_case_id == (node_val[i0] + node_val[i1]*3 + node_val[i2]*9 + node_val[i3]*27)); + + const Simplex_Generation_Method simplexMethod = mesh.get_cdfem_support().get_simplex_generation_method(); + const bool globalIDsAreParallelConsistent = mesh.get_cdfem_support().get_global_ids_are_parallel_consistent(); + + //krinolog << "permute_case_id " << permute_case_id << stk::diag::dendl; + + switch (permute_case_id) + { + case 0: // ls[0]<0 && ls[1]<0 && ls[2]<0 && ls[3]<0 + case 1: // ls[0]=0 && ls[1]<0 && ls[2]<0 && ls[3]<0 + case 4: // ls[0]=0 && ls[1]=0 && ls[2]<0 && ls[3]<0 + { + update_interface_signs(interface_key, -1); + } + break; + + case 40: // ls[0]=0 && ls[1]=0 && ls[2]=0 && ls[3]=0 + case 76: // ls[0]=0 && ls[1]=0 && ls[2]>0 && ls[3]>0 + case 79: // ls[0]=0 && ls[1]>0 && ls[2]>0 && ls[3]>0 + case 80: // ls[0]>0 && ls[1]>0 && ls[2]>0 && ls[3]>0 + { + update_interface_signs(interface_key, +1); + } + break; + + case 2: // ls[0]>0 && ls[1]<0 && ls[2]<0 && ls[3]<0 + case 78: // ls[0]<0 && ls[1]>0 && ls[2]>0 && ls[3]>0 + { + const int sign = (permute_case_id==2) ? -1 : 1; + + lnodes[i4] = SubElementNode::common_child({lnodes[i0], lnodes[i1]}); + lnodes[i6] = SubElementNode::common_child({lnodes[i0], lnodes[i2]}); + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i4] && nullptr != lnodes[i6] && nullptr != lnodes[i7]); + + // face0: true: connect 4 and 3, false: connect 7 and 1 + // face2: true: connect 7 and 2, false: connect 6 and 3 + // face3: true: connect 6 and 1, false: connect 4 and 2 + const bool face0 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i1, i3, i4, i7); + const bool face2 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i3, i2, i7, i6); + const bool face3 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i2, i1, i6, i4); + + handle_tet( lnodes, subelement_interface_signs(interface_key, -sign), i6,i4,i7,i0, s3,s0,s2,-1 ); + handle_wedge( mesh, lnodes, subelement_interface_signs(interface_key, sign), i4,i7,i6,i1,i3,i2, s0,s2,s3,-1,s1, face0,face2,!face3 ); + } + break; + + case 5: // ls[0]>0 && ls[1]=0 && ls[2]<0 && ls[3]<0 + case 75: // ls[0]<0 && ls[1]=0 && ls[2]>0 && ls[3]>0 + { + const int sign = (permute_case_id==5) ? -1 : 1; + + lnodes[i6] = SubElementNode::common_child({lnodes[i0], lnodes[i2]}); + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i6] && nullptr != lnodes[i7]); + + // face2: true: connect 7 and 2, false: connect 6 and 3 + const bool face2 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i3, i2, i7, i6); + + handle_tet( lnodes, subelement_interface_signs(interface_key, -sign), i6,i1,i7,i0, s3,s0,s2,-1 ); + handle_pyramid( lnodes, subelement_interface_signs(interface_key, sign), i7,i6,i2,i3,i1, -1,s3,s1,s0,s2, face2 ); + } + break; + + case 8: // ls[0]>0 && ls[1]>0 && ls[2]<0 && ls[3]<0 + { + lnodes[i5] = SubElementNode::common_child({lnodes[i1], lnodes[i2]}); + lnodes[i6] = SubElementNode::common_child({lnodes[i0], lnodes[i2]}); + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + lnodes[i8] = SubElementNode::common_child({lnodes[i1], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i5] && nullptr != lnodes[i6] && nullptr != lnodes[i7] && nullptr != lnodes[i8]); + + // face0: true: connect 7 and 1, false: connect 8 and 0 + // face1: true: connect 5 and 3, false: connect 8 and 2 + // face2: true: connect 7 and 2, false: connect 6 and 3 + // face3: true: connect 5 and 0, false: connect 6 and 1 + const bool face0 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i3, i0, i1, i7, i8); + const bool face1 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i1, i2, i3, i5, i8); + const bool face2 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i0, i3, i2, i7, i6); + const bool face3 = determine_diagonal_for_cut_triangular_face(simplexMethod, globalIDsAreParallelConsistent, lnodes, i2, i1, i0, i5, i6); + + // face 4: true: connect 6 and 8, false: connect 7 and 5 + const bool face4 = ElementObj::determine_diagonal_for_internal_quad_of_cut_tet_from_edge_nodes(simplexMethod, lnodes[i8], lnodes[i5], lnodes[i6], lnodes[i7], + face0, face1, face2, face3); + + ThrowAssert( mesh.num_ls_fields() > 1 || + simplexMethod != CUT_QUADS_BY_GLOBAL_IDENTIFIER || + face4 == ElementObj::determine_diagonal_for_internal_quad_of_cut_tet_from_owner_nodes(lnodes[i0], lnodes[i1], lnodes[i2], lnodes[i3]) ); + + handle_wedge( mesh, lnodes, subelement_interface_signs(interface_key, -1), i8,i3,i7,i5,i2,i6, s1,s2,-1,s0,s3, !face1,!face2,face4 ); + handle_wedge( mesh, lnodes, subelement_interface_signs(interface_key, 1), i8,i1,i5,i7,i0,i6, s0,s3,-1,s1,s2, !face0,!face3,face4 ); + } + break; + + case 13: // ls[0]=0 && ls[1]=0 && ls[2]=0 && ls[3]<0 + case 67: // ls[0]=0 && ls[1]=0 && ls[2]=0 && ls[3]>0 + { + const int sign = (permute_case_id==13) ? -1 : 1; + update_interface_signs(interface_key, sign); + } + break; + + case 14: // ls[0]>0 && ls[1]=0 && ls[2]=0 && ls[3]<0 + { + lnodes[i7] = SubElementNode::common_child({lnodes[i0], lnodes[i3]}); + ThrowRequire(nullptr != lnodes[i7]); + + handle_tet( lnodes, subelement_interface_signs(interface_key, 1), i1,i7,i2,i0, s0,s2,s3,-1 ); + handle_tet( lnodes, subelement_interface_signs(interface_key, -1), i2,i7,i1,i3, s2,s0,s1,-1 ); + } + break; + + default: ThrowRuntimeError("Subelement decomposition error."); + } + + if (krinolog.shouldPrint(LOG_DEBUG)) + { + debug_subelements(lnodes, interface_key, case_id); + } +} + +bool SubElement_Tet_4::determine_diagonal_for_cut_triangular_face(const Simplex_Generation_Method & simplexMethod, const bool globalIDsAreParallelConsistent, const NodeVec & lnodes, const int i0, const int i1, const int i2, const int i3, const int i5) +{ + /* + * 2 o + * / \ + * 5 o \ + * / \ \ + * o---o---o + * 0 3 1 + */ + + // true: connect nodes 3 and 2 + // false: connect nodes 5 and 1 + + if (simplexMethod == CUT_QUADS_BY_GLOBAL_IDENTIFIER) + { + return lnodes[i2]->get_ancestry() < lnodes[i1]->get_ancestry(); + } + else + { + ThrowRequire(simplexMethod == CUT_QUADS_BY_LARGEST_ANGLE || simplexMethod == CUT_QUADS_BY_NEAREST_EDGE_CUT); + return SubElementNode::higher_priority_by_score_then_ancestry(*lnodes[i2],*lnodes[i1], globalIDsAreParallelConsistent); + } +} + +void +SubElement::get_edge_position( + const SubElementNode * n0, + const SubElementNode * n1, + const SubElementNode * n2, + double & position ) +{ + const SubElementEdgeNode * edge_child = dynamic_cast( n2 ); + ThrowRequire(NULL != edge_child); + position = edge_child->get_position(n0,n1); +} + +void +SubElement_Tet_4::handle_pyramid( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, const int i4, + const int s0, const int s1, const int s2, const int s3, const int s4, + const bool face4 ) +{ + if (face4) + { + handle_tet( lnodes, subInterfaceSigns, i0,i1,i2,i4, s0,s1,-1,s4 ); + handle_tet( lnodes, subInterfaceSigns, i2,i3,i0,i4, s2,s3,-1,s4 ); + } + else + { + handle_tet( lnodes, subInterfaceSigns, i0,i1,i3,i4, s0,-1,s3,s4 ); + handle_tet( lnodes, subInterfaceSigns, i2,i3,i1,i4, s2,-1,s1,s4 ); + } +} + +void +SubElement_Tet_4::handle_tet( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, + const int s0, const int s1, const int s2, const int s3) +{ + ThrowRequire(!is_degenerate(lnodes, i0,i1,i2,i3)); + + NodeVec sub_nodes(4,(SubElementNode *)NULL); + std::vector sub_parent_ids(4); + + sub_nodes[0] = lnodes[i0]; + sub_nodes[1] = lnodes[i1]; + sub_nodes[2] = lnodes[i2]; + sub_nodes[3] = lnodes[i3]; + sub_parent_ids[0] = (s0>= 0) ? my_parent_side_ids[s0] : -1; + sub_parent_ids[1] = (s1>= 0) ? my_parent_side_ids[s1] : -1; + sub_parent_ids[2] = (s2>= 0) ? my_parent_side_ids[s2] : -1; + sub_parent_ids[3] = (s3>= 0) ? my_parent_side_ids[s3] : -1; + + std::unique_ptr sub = std::make_unique( sub_nodes, sub_parent_ids, my_owner); + sub->set_interface_signs(subInterfaceSigns); + add_subelement( std::move(sub) ); +} + +void +SubElement_Tet_4::handle_wedge( CDMesh & mesh, + NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, const int i4, const int i5, + const int s0, const int s1, const int s2, const int s3, const int s4, + const bool face0, const bool face1, const bool face2 ) +{ +/* + * PARENT Linear 6-Node Wedge Nodes + * 5 (SPACE_DIM=3!) + * . o + * . / \ + * . / \ Face_Quad_4_3D() 0-1-4-3 + * . / \ Face_Quad_4_3D() 1-2-5-4 + * . / \ Face_Quad_4_3D() 0-3-5-2 + * 2 . o---------o 4 Face_Tri_3_3D() 0-2-1 + * o . 3 . Face_Tri_3_3D() 3-4-5 + * /.\ . + * /. \ . + * /. \ . + * /. \ . + * o---------o + * 0 1 + * + */ + // face0: true: connect 0 and 4, false: connect 1 and 3 + // face1: true: connect 1 and 5, false: connect 2 and 4 + // face2: true: connect 0 and 5, false: connect 2 and 3 + + std::vector wedge_nodes(6); + wedge_nodes[0] = i0; + wedge_nodes[1] = i1; + wedge_nodes[2] = i2; + wedge_nodes[3] = i3; + wedge_nodes[4] = i4; + wedge_nodes[5] = i5; + + std::vector wedge_sides(5); + wedge_sides[0] = s0; + wedge_sides[1] = s1; + wedge_sides[2] = s2; + wedge_sides[3] = s3; + wedge_sides[4] = s4; + + // Each of the 3 quad faces can be subdivided in 2 ways, giving a total of 8 possible decompositions. + // 2 of these are illegal, however, since they don't result in tetrahedra. + + static const unsigned tet_nodes0[] = { 0,5,4,3, 0,2,1,5, 0,1,4,5 }; + static const unsigned tet_nodes1[] = { 1,3,5,4, 1,0,2,5, 1,0,5,3 }; + static const unsigned tet_nodes2[] = { 0,5,4,3, 0,2,1,4, 0,2,4,5 }; + static const unsigned tet_nodes3[] = { 0,0,0,0, 0,0,0,0, 0,0,0,0 }; // illegal + static const unsigned tet_nodes4[] = { 0,0,0,0, 0,0,0,0, 0,0,0,0 }; // illegal + static const unsigned tet_nodes5[] = { 1,3,5,4, 1,0,2,3, 1,2,5,3 }; + static const unsigned tet_nodes6[] = { 2,4,3,5, 2,1,0,4, 2,0,3,4 }; + static const unsigned tet_nodes7[] = { 2,4,3,5, 2,1,0,3, 2,1,3,4 }; + static const unsigned * tet_node_map[] = { tet_nodes0 , tet_nodes1 , tet_nodes2, tet_nodes3 , tet_nodes4 , tet_nodes5, tet_nodes6, tet_nodes7 }; + + static const int tet_sides0[] = { 2, 4, 0,-1, 2, 1,-1, 3, -1, 1,-1, 0 }; + static const int tet_sides1[] = { 0, 4, 1,-1, -1, 2, 1, 3, 0, 2,-1,-1 }; + static const int tet_sides2[] = { 2, 4, 0,-1, -1, 1, 0, 3, 2, 1,-1,-1 }; + static const int tet_sides3[] = {-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1 }; // illegal + static const int tet_sides4[] = {-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1 }; // illegal + static const int tet_sides5[] = { 0, 4, 1,-1, 0, 2,-1, 3, -1, 2,-1, 1 }; + static const int tet_sides6[] = { 1, 4, 2,-1, 1, 0,-1, 3, -1, 0,-1, 2 }; + static const int tet_sides7[] = { 1, 4, 2,-1, -1, 0, 2, 3, 1, 0,-1,-1 }; + static const int * tet_side_map[] = { tet_sides0 , tet_sides1 , tet_sides2 , tet_sides3 , tet_sides4 , tet_sides5, tet_sides6, tet_sides7 }; + + const unsigned case_id = + (face0 ? 0 : 1) + + (face1 ? 0 : 2) + + (face2 ? 0 : 4); + + //krinolog << "Wedge case_id = " << case_id << stk::diag::dendl; + + if (case_id < 3 || case_id > 4) + { + const unsigned * tet_nodes = tet_node_map[case_id]; + const int * tet_sides = tet_side_map[case_id]; + + unsigned lnn[12]; + int lsn[12]; + + for (int n=0; n<12; ++n) + { + lnn[n] = wedge_nodes[tet_nodes[n]]; + lsn[n] = (tet_sides[n]<0) ? -1 : wedge_sides[tet_sides[n]]; + } + + handle_tet(lnodes, subInterfaceSigns, lnn[0], lnn[1], lnn[2], lnn[3], lsn[0], lsn[1], lsn[2], lsn[3]); + handle_tet(lnodes, subInterfaceSigns, lnn[4], lnn[5], lnn[6], lnn[7], lsn[4], lsn[5], lsn[6], lsn[7]); + handle_tet(lnodes, subInterfaceSigns, lnn[8], lnn[9], lnn[10], lnn[11], lsn[8], lsn[9], lsn[10], lsn[11]); + } + else + { + ThrowRequire(case_id == 3 || case_id == 4); + if(krinolog.shouldPrint(LOG_DEBUG)) krinolog << "Schonhardt's polyhedron formed, Adding Steiner point." << "\n"; + + // Schonhardt's polyhedra should never be forced now that diagonals are cut using a globally consistent nodal criterion + ThrowRequireMsg(false, "Schonhardt polyhedron found. This should not happen."); + + NodeVec wedge_nodevec(6); + wedge_nodevec[0] = lnodes[i0]; + wedge_nodevec[1] = lnodes[i1]; + wedge_nodevec[2] = lnodes[i2]; + wedge_nodevec[3] = lnodes[i3]; + wedge_nodevec[4] = lnodes[i4]; + wedge_nodevec[5] = lnodes[i5]; + + const Vector3d & v0 = lnodes[i0]->owner_coords(my_owner); + const Vector3d & v1 = lnodes[i1]->owner_coords(my_owner); + const Vector3d & v2 = lnodes[i2]->owner_coords(my_owner); + const Vector3d & v3 = lnodes[i3]->owner_coords(my_owner); + const Vector3d & v4 = lnodes[i4]->owner_coords(my_owner); + const Vector3d & v5 = lnodes[i5]->owner_coords(my_owner); + + std::vector weights(6); + + // Use the centroid of 1 of the elements that will be within the volume of the wedge depending + // on which way that face2 is cut (which is on the internal quad, which may be non-planar). + // This is not guaranteed, however, to always produce tets that stay within the deformed wedge. + if (face2) + { + weights[0] = 1./4.; + weights[1] = 1./4.; + weights[4] = 1./4.; + weights[5] = 1./4.; + } + else + { + weights[1] = 1./4.; + weights[2] = 1./4.; + weights[3] = 1./4.; + weights[4] = 1./4.; + } + + const SubElementNode * centroid = mesh.create_steiner_node( my_owner, wedge_nodevec, weights ); + + const int i6 = lnodes.size(); + lnodes.push_back(centroid); + const Vector3d & v6 = lnodes[i6]->owner_coords(my_owner); + + // create 8 tets + handle_tet(lnodes, subInterfaceSigns, i0, i2, i1, i6, -1, -1, -1, s3); + handle_tet(lnodes, subInterfaceSigns, i3, i4, i5, i6, -1, -1, -1, s4); + + if (tet_volume({{v0, v2, v1, v6}}) < 0. || tet_volume({{v3, v4, v5, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + + if (face0) + { + handle_tet(lnodes, subInterfaceSigns, i0, i1, i4, i6, -1, -1, -1, s0); + handle_tet(lnodes, subInterfaceSigns, i0, i4, i3, i6, -1, -1, -1, s0); + + if (tet_volume({{v0, v1, v4, v6}}) < 0. || tet_volume({{v0, v4, v3, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + else + { + handle_tet(lnodes, subInterfaceSigns, i0, i1, i3, i6, -1, -1, -1, s0); + handle_tet(lnodes, subInterfaceSigns, i1, i4, i3, i6, -1, -1, -1, s0); + + if (tet_volume({{v0, v1, v3, v6}}) < 0. || tet_volume({{v1, v4, v3, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + + if (face1) + { + handle_tet(lnodes, subInterfaceSigns, i1, i2, i5, i6, -1, -1, -1, s1); + handle_tet(lnodes, subInterfaceSigns, i1, i5, i4, i6, -1, -1, -1, s1); + + if (tet_volume({{v1, v2, v5, v6}}) < 0. || tet_volume({{v1, v5, v4, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + else + { + handle_tet(lnodes, subInterfaceSigns, i1, i2, i4, i6, -1, -1, -1, s1); + handle_tet(lnodes, subInterfaceSigns, i2, i5, i4, i6, -1, -1, -1, s1); + + if (tet_volume({{v1, v2, v4, v6}}) < 0. || tet_volume({{v2, v5, v4, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + + if (face2) + { + handle_tet(lnodes, subInterfaceSigns, i0, i3, i5, i6, -1, -1, -1, s2); + handle_tet(lnodes, subInterfaceSigns, i0, i5, i2, i6, -1, -1, -1, s2); + + if (tet_volume({{v0, v3, v5, v6}}) < 0. || tet_volume({{v0, v5, v2, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + else + { + handle_tet(lnodes, subInterfaceSigns, i0, i3, i2, i6, -1, -1, -1, s2); + handle_tet(lnodes, subInterfaceSigns, i3, i5, i2, i6, -1, -1, -1, s2); + + if (tet_volume({{v0, v3, v2, v6}}) < 0. || tet_volume({{v3, v5, v2, v6}}) < 0.) + { + krinolog << "Error: Schonhard polyhedron decomposition includes inverted tets." << stk::diag::dendl; + } + } + } +} + +double +SubElement::parametric_distance( const SubElementNode * node0, const SubElementNode * node1 ) +{ + if (node0->is_mesh_node() && node1->is_mesh_node()) + return 1.0; + + std::map node0_stencil; + std::map node1_stencil; + node0->build_stencil(node0_stencil); + node1->build_stencil(node1_stencil); + + // parametric distance = sqrt(0.5*sum(dx_i^2)) + + double sum_sqr_dist = 0.; + for (auto && entry : node0_stencil) + { + const SubElementNode * parent = entry.first; + const double wt0 = entry.second; + + auto it = node1_stencil.find(parent); + const double wt1 = (it == node1_stencil.end()) ? 0.0 : (it->second); + + sum_sqr_dist += (wt0 - wt1)*(wt0 - wt1); + } + for (auto && entry : node1_stencil) + { + const SubElementNode * parent = entry.first; + const double wt1 = entry.second; + + auto it = node0_stencil.find(parent); + if (it == node0_stencil.end()) + { + sum_sqr_dist += wt1*wt1; + } + } + + return std::sqrt(0.5*sum_sqr_dist); +} + +void set_node_signs_for_edge(const InterfaceID interface, const SubElementNode * node1, const SubElementNode * node2, const int node1Sign, const int node2Sign, const double crossingLocation, const CDFEM_Snapper & snapper) +{ + if (node1Sign != node2Sign) + { + // determine tolerance for this edge that may have already been cut + const bool always_snap = snapper.always_snap(); + const double edge_tol = always_snap ? 0.0 : snapper.get_edge_tolerance()/SubElement::parametric_distance(node1, node2); + + if (always_snap || edge_tol > 0.5) + { + if (crossingLocation < 0.5) + { + node1->set_node_sign(0); + } + else + { + node2->set_node_sign(0); + } + } + else + { + if (crossingLocation < edge_tol) + { + node1->set_node_sign(0); + } + else if (crossingLocation > 1.-edge_tol) + { + node2->set_node_sign(0); + } + } + } + + node1->set_node_sign(node1Sign); + node2->set_node_sign(node2Sign); +} + +void +SubElement::determine_node_signs_on_edge( const CDMesh & mesh, const InterfaceID interface, const int i0, const int i1 ) +{ /* %TRACE% */ /* %TRACE% */ + + if (my_owner->have_interface(interface)) + { + const SubElementNode * parent1 = my_nodes[i0]; + const SubElementNode * parent2 = my_nodes[i1]; + + if (parent1->captures_interface(interface)) + parent1->set_node_sign(0); + if (parent2->captures_interface(interface)) + parent2->set_node_sign(0); + + const int sign = myInterfaceSigns[my_owner->get_interface_index(interface)]; + if (sign == 0) + { + const int sign1 = my_owner->interface_node_sign(interface, parent1); + const int sign2 = my_owner->interface_node_sign(interface, parent2); + + const double position = (sign1 == sign2) ? (-1.0) : my_owner->interface_crossing_position(interface, parent1, parent2); + set_node_signs_for_edge(interface, parent1, parent2, sign1, sign2, position, mesh.get_snapper()); + } + } +} + +void +SubElement::determine_node_scores_on_edge( const CDMesh & mesh, const InterfaceID interface, const int i0, const int i1 ) +{ /* %TRACE% */ /* %TRACE% */ + + const SubElementNode * parent1 = my_nodes[i0]; + const SubElementNode * parent2 = my_nodes[i1]; + + if (parent1->get_node_on_interface() || parent2->get_node_on_interface()) return; + + const SubElementNode * child = SubElementNode::common_child({parent1, parent2}); + + if (child) + { + const NodeVec & parents = child->get_parents(); + const std::vector parent_weights = child->get_parent_weights(); + for (size_t i=0; iset_node_score(1.-parent_weights[i]); + } +} + +void +SubElement::process_edge( CDMesh & mesh, const InterfaceID interface, const int i0, const int i1 ) +{ /* %TRACE% */ /* %TRACE% */ + const SubElementNode * parent1 = my_nodes[i0]; + const SubElementNode * parent2 = my_nodes[i1]; + + if (parent1->get_node_on_interface() || parent2->get_node_on_interface()) return; + + const SubElementNode * subnode = SubElementNode::common_child({parent1, parent2}); + + if (subnode == nullptr && + parent1->node_sign_is_set() && + parent2->node_sign_is_set() && + parent1->get_node_sign() == -parent2->get_node_sign() && + have_interface(interface)) + { + const double position = my_owner->interface_crossing_position(interface, parent1, parent2); + ThrowRequireMsg(position > 0. && position < 1., "Error process_edge " << position << " " << parent1->get_node_sign() << " " << parent2->get_node_sign()); + + std::unique_ptr newNode = std::make_unique(my_owner, position, parent1, parent2); + subnode = mesh.add_managed_node(std::move(newNode)); + + // add subnode as child to parents + parent1->add_child(subnode); + parent2->add_child(subnode); + } +} + +void +SubElement::determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) +{ + if(have_subelements()) + { + for ( auto && subelem : my_subelements ) + { + subelem->SubElement::determine_node_signs(mesh, interface_key); + } + return; + } + + determine_node_signs(mesh, interface_key); +} + +void +SubElement::determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) +{ + if(have_subelements()) + { + for ( auto && subelem : my_subelements ) + { + subelem->SubElement::determine_node_scores(mesh, interface_key); + } + return; + } + + determine_node_scores(mesh, interface_key); +} + +void +SubElement::decompose(CDMesh & mesh, const InterfaceID interface_key) +{ + if(have_subelements()) + { + for ( auto && subelem : my_subelements ) + { + subelem->decompose(mesh, interface_key); + } + return; + } + + decompose_edges(mesh, interface_key); +} + +std::vector +SubElement::get_edges_with_children(const InterfaceID & interface) const +{ + // Iterate edges looking for any common children of the edge nodes + const stk::topology Top = topology(); + const int num_edges = Top.num_edges(); + + std::vector edgesWithChildren; + for ( int edge = 0; edge < num_edges; ++edge ) + { + const unsigned * edge_node_ordinals = get_edge_node_ordinals(Top, edge); + + const SubElementNode * node0 = my_nodes[edge_node_ordinals[0]]; + const SubElementNode * node1 = my_nodes[edge_node_ordinals[1]]; + const SubElementNode * child = SubElementNode::common_child({node0, node1}); + if( child ) + { + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krinolog << "Found hanging node on edge " << edge << " of element id=" << entityId() << "\n"; + krinolog << " Ancestry: " << child->get_ancestry() << "\n"; + } + edgesWithChildren.push_back(edge); + } + } + return edgesWithChildren; +} + +void +SubElement::handle_hanging_children(CDMesh & mesh, const InterfaceID & interface) +{ + if(have_subelements()) + { + for ( auto && subelem : my_subelements ) + { + subelem->handle_hanging_children(mesh, interface); + } + return; + } + + const std::vector edgesWithChildren = get_edges_with_children(interface); + + fix_hanging_children(mesh, interface, edgesWithChildren); + + for ( auto && subelem : my_subelements ) + { + ThrowRequire(!subelem->have_edges_with_children()); + } +} + +void +SubElement::build_quadratic_subelements(CDMesh & mesh) +{ + ThrowRequireMsg(have_subelements(), "This subelement type does not support quadratic subelements."); + for ( auto && subelem : my_subelements ) + { + subelem->build_quadratic_subelements(mesh); + } +} + +void +SubElement::cut_face_interior_intersection_points(CDMesh & mesh, const InterfaceID & interface1, const InterfaceID & interface2, int level) +{ /* %TRACE% */ /* %TRACE% */ + + if (topology().num_faces() == 0) + return; + + ThrowRequireMsg(false, "This subelement type does not support cut_face_interior_intersection_points: " << topology()); +} + +bool +SubElement_Tet_4::is_degenerate( NodeVec & lnodes, + const int i0, const int i1, const int i2, const int i3 ) +{ /* %TRACE% */ /* %TRACE% */ + + if ( lnodes[i0] == lnodes[i1] || + lnodes[i0] == lnodes[i2] || + lnodes[i0] == lnodes[i3] || + lnodes[i1] == lnodes[i2] || + lnodes[i1] == lnodes[i3] || + lnodes[i2] == lnodes[i3] ) + { + // this tet is degenerate with two coincident nodes + return true; + } + + return false; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_SubElement.hpp b/packages/krino/krino/krino_lib/Akri_SubElement.hpp new file mode 100644 index 000000000000..cb6e086b947c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElement.hpp @@ -0,0 +1,431 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_SubElement_h +#define Akri_SubElement_h + +#include +#include +#include +#include + +#include +#include + +#include +#include +#include +#include +#include + +namespace krino { + +class ProlongationNodeData; +class ProlongationPointData; +class SubElementNodeAncestry; + +bool node_on_negative_side_of_interface(const SubElementNode * node, const InterfaceID key); + +class SubElement : public ElementObj { +public: + SubElement( const stk::topology topo, + const NodeVec & nodes, + const std::vector & side_ids, + const Mesh_Element * owner); + virtual ~SubElement() {} + + static double coordinate_relative_tol() { return 1.e-6; } + static double parametric_distance( const SubElementNode * node0, const SubElementNode * node1 ); + + void set_permutation(); + double relative_volume() const; + double maximum_relative_angle() const; + + void decompose(CDMesh & mesh, const InterfaceID interface_key); + virtual void decompose_edges(CDMesh & mesh, const InterfaceID interface_key); + virtual void determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key); + virtual void determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key); + + void handle_hanging_children(CDMesh & mesh, const InterfaceID & interface); + virtual void fix_hanging_children(CDMesh & mesh, const InterfaceID & interface, const std::vector & edges_with_children) {} + + virtual void build_quadratic_subelements(CDMesh & mesh); + virtual void cut_face_interior_intersection_points(CDMesh & mesh, const InterfaceID & interface1, const InterfaceID & interface2, int level = 0); + + static void get_edge_position(const SubElementNode * n0, const SubElementNode * n1, const SubElementNode * n2, double & position ); + + bool check_entity_nodes(const stk::mesh::BulkData & stkMesh) const; + void get_owner_coord_transform(double * dOwnerdSub) const; + const Mesh_Element & get_owner() const { return *my_owner; } + + int parent_side_id(const int iside) const; + virtual void determine_decomposed_elem_phase(const CDMesh & mesh) override final; + std::vector subelement_interface_signs(const InterfaceID interface, const int sign) const; + const std::vector & get_interface_signs() const { return myInterfaceSigns; } + void initialize_interface_signs(); + void set_interface_signs(const std::vector & interfaceSigns); + void update_interface_signs(const InterfaceID interface_key, const int sign); + unsigned num_sides() const { return my_parent_side_ids.size(); } + void debug_subelements(const NodeVec & lnodes, const InterfaceID & interface, const int case_id) const; + void debug() const; + bool have_interface(const InterfaceID& interface) const; + void determine_if_cut_by_interface(const InterfaceID & interface, bool & haveAnyCrossing, bool & haveRealCrossing) const; + +protected: + std::vector get_edges_with_children(const InterfaceID & interface) const; + void determine_node_signs_on_edge( const CDMesh & mesh, const InterfaceID interface_key, const int i0, const int i1 ); + void determine_node_scores_on_edge( const CDMesh & mesh, const InterfaceID interface_key, const int i0, const int i1 ); + void process_edge( CDMesh & mesh, const InterfaceID interface_key, const int i0, const int i1 ); + void find_refined_edges(std::vector & refined_edges) const; + int find_longest_bad_edge(std::vector & bad_edges) const; + +protected: + std::vector my_parent_side_ids; + const Mesh_Element * my_owner; + std::vector myInterfaceSigns; + +private: + //: Default constructor not allowed + SubElement(); +}; + +class SubElement_Tri_3 : public SubElement { +public: + SubElement_Tri_3( const NodeVec & nodes, + const std::vector & parent_side_ids, + const Mesh_Element * owner); + virtual ~SubElement_Tri_3() {} + + virtual void decompose_edges(CDMesh & mesh, const InterfaceID interface_key) override; + virtual void fix_hanging_children(CDMesh & mesh, const InterfaceID & interface, const std::vector & edges_with_children) override; + virtual void build_quadratic_subelements(CDMesh & mesh) override; + + virtual void determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) override; + virtual void determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) override; + virtual void cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains) override; + +protected: + void perform_decomposition(CDMesh & mesh, const InterfaceID interface_key, const std::array & node_signs); + bool determine_diagonal_for_cut_triangle(const Simplex_Generation_Method & simplexMethod, const NodeVec & lnodes, const int i0, const int i1, const int i2, const int i3, const int i5); + bool is_degenerate( NodeVec & lnodes, + const int i0, const int i1, const int i2 ); + void handle_tri( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, + const int s0, const int s1, const int s2, + const bool is_interface0, const bool is_interface1, const bool is_interface2); + void handle_quad( CDMesh & mesh, + NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, + const int s0, const int s1, const int s2, const int s3, + const bool is_interface0, const bool is_interface1, const bool is_interface2, const bool is_interface3, + const bool face ); +private: + //: Default constructor not allowed + SubElement_Tri_3(); + +}; + +class SubElement_Tri_6 : public SubElement { +public: + SubElement_Tri_6( const NodeVec & nodes, + const std::vector & side_ids, + const Mesh_Element * owner); + virtual ~SubElement_Tri_6() {} + +private: + //: Default constructor not allowed + SubElement_Tri_6(); + +}; + +class SubElement_Tet_4 : public SubElement { +public: + SubElement_Tet_4( const NodeVec & nodes, + const std::vector & side_ids, + const Mesh_Element * owner); + virtual ~SubElement_Tet_4() {} + + virtual void decompose_edges(CDMesh & mesh, const InterfaceID interface_key) override; + virtual void fix_hanging_children(CDMesh & mesh, const InterfaceID & interface, const std::vector & edges_with_children) override; + virtual void build_quadratic_subelements(CDMesh & mesh) override; + virtual void cut_face_interior_intersection_points(CDMesh & mesh, const InterfaceID & interface1, const InterfaceID & interface2, int level = 0) override; + + virtual void determine_node_signs(const CDMesh & mesh, const InterfaceID interface_key) override; + virtual void determine_node_scores(const CDMesh & mesh, const InterfaceID interface_key) override; + virtual void cut_interior_intersection_point(CDMesh & mesh, const Vector3d & pCoords, const std::vector & sortedDomains) override; + +protected: + void perform_decomposition(CDMesh & mesh, const InterfaceID interface_key, const std::array & node_signs); + void determine_node_scores_on_face( const CDMesh & mesh, const InterfaceID interface, const int i0, const int i1, const int i2 ); + static const unsigned ** get_permutation_side_ordinals(); + static double tet_volume(const std::array & nodes); + + bool is_degenerate( NodeVec & lnodes, + const int i0, const int i1, const int i2, const int i3 ); + void handle_tet( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, + const int s0, const int s1, const int s2, const int s3); + void handle_pyramid( NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, const int i4, + const int s0, const int s1, const int s2, const int s3, const int s4, + const bool face4 ); + void handle_wedge( CDMesh & mesh, + NodeVec & lnodes, + const std::vector & subInterfaceSigns, + const int i0, const int i1, const int i2, const int i3, const int i4, const int i5, + const int s0, const int s1, const int s2, const int s3, const int s4, + const bool face0, const bool face1, const bool face2 ); +private: + //: Default constructor not allowed + SubElement_Tet_4(); + + bool determine_diagonal_for_cut_triangular_face(const Simplex_Generation_Method & simplexMethod, const bool globalIDsAreParallelConsistent, const NodeVec & lnodes, const int i0, const int i1, const int i2, const int i3, const int i5); + void cut_face_intersection_point_with_permutation(CDMesh & mesh, const std::array & permuteNodes, const std::array & permuteSides, const std::vector & faceNodeWeights, const std::vector & sortedDomains); +}; + +class SubElement_Tet_10 : public SubElement { +public: + SubElement_Tet_10( const NodeVec & nodes, + const std::vector & side_ids, + const Mesh_Element * owner); + virtual ~SubElement_Tet_10() {} + +private: + //: Default constructor not allowed + SubElement_Tet_10(); + +}; + +class SubElementNode { +public: + SubElementNode(const Mesh_Element * in_owner) + : my_entity(), + my_entityId(0), + my_is_prolonged_flag(false), + my_cached_owner(in_owner) + {} + + virtual ~SubElementNode() {} + virtual bool is_mesh_node() const { return false; } + virtual NodeVec get_parents() const { throw std::runtime_error("Incorrect usage of SubElementNode. The type of node does not have parents."); } + virtual size_t get_num_parents() const { throw std::runtime_error("Incorrect usage of SubElementNode. The type of node does not have parents."); } + virtual std::vector get_parent_weights() const { throw std::runtime_error("Incorrect usage of SubElementNode. The type of node does not have parents."); } + virtual void prolongate_fields(const CDMesh & mesh) const = 0; + + void get_parent_entities(std::vector & parent_entities) const; + + void set_entity(const stk::mesh::BulkData & mesh, stk::mesh::Entity in_node_obj) const { my_entity = in_node_obj; my_entityId = mesh.identifier(my_entity); } + void set_entity(stk::mesh::Entity nodeEntity, stk::mesh::EntityId nodeEntityId) const { my_entity = nodeEntity; my_entityId = nodeEntityId; } + const Mesh_Element * get_active_element() const { return my_cached_owner; } + bool is_prolonged() const { return my_is_prolonged_flag; } + void set_prolonged_flag(const bool val) const { my_is_prolonged_flag = val; } // this is dangerous, know what you are doing + bool on_common_edge(const SubElementNode * other) const; + + bool entity_is_valid(const stk::mesh::BulkData & mesh) const { return mesh.is_valid(my_entity); } + bool check_entity(const stk::mesh::BulkData & mesh) const { return (my_entityId == 0) ? (my_entity == stk::mesh::Entity()) : (my_entityId == mesh.identifier(my_entity)); } + stk::mesh::Entity & entity() const { return my_entity; } + stk::mesh::EntityId entityId() const { return my_entityId; } + void set_entityId_from_entity(const stk::mesh::BulkData & mesh) const { ThrowAssert(mesh.is_valid(my_entity)); my_entityId = mesh.identifier(my_entity); } + + const Vector3d & owner_coords( const Mesh_Element * in_owner ) const { + if ( in_owner != my_cached_owner ) { + // call derived types function for recomputing owner_coords + my_cached_owner = in_owner; + my_cached_owner_coords = compute_owner_coords( in_owner ); + } + return my_cached_owner_coords; + } + bool get_node_on_interface() const { return my_node_sign == 0; } + + void set_node_domains(const std::vector & nodeDomains) const { my_sorted_node_domains = nodeDomains; } + const std::vector & get_sorted_node_domains() const { return my_sorted_node_domains; } + void insert_node_domains(const std::vector & domainsToAdd) const; + bool captures_intersection_point_domains(const std::vector & intersectionPointDomains) const; + bool captures_interface(const InterfaceID & interface) const; + bool captures_intersection_point_domains(const InterfaceID & interface) const; + static bool higher_priority_by_score_then_ancestry(const SubElementNode & a, const SubElementNode & b, const bool globalIDsAreParallelConsistent); + static bool less_by_entity_id(const SubElementNode & a, const SubElementNode & b); + static bool less_by_coordinates_then_by_entity_id(const SubElementNode & a, const SubElementNode & b); + bool node_sign_is_set() const { return my_node_sign != -2; } + void set_node_sign(const int sign) const { my_node_sign = (my_node_sign == 0 || my_node_sign == -sign) ? 0 : sign; } + int get_node_sign() const { ThrowRequire(node_sign_is_set()); return my_node_sign; } + void clear_node_sign() const { my_node_sign = -2; } + void clear_node_score() const { my_node_score = 1.; } + bool node_score_is_set() const { return my_node_score != 1.; } + void set_node_score(const double score) const { my_node_score = std::min(my_node_score, score); } + double get_node_score() const { ThrowRequire(node_sign_is_set()); return my_node_score; } + + // pure virtual function for recomputing local coordinates + virtual Vector3d compute_owner_coords( const Mesh_Element * in_owner ) const = 0; + + const Vector3d & coordinates() const { return my_global_coords; } + + void add_child(const SubElementNode* child) const { my_children.push_back(child); } + static const SubElementNode * common_child( const NodeVec & parents ); + bool have_child() const; + bool have_child(const SubElementNode* child) const; + + // This is called from Mesh::find_prolongation_node to determine the set of candidate prolongation nodes. + std::vector prolongation_node_fields(const CDMesh & mesh) const; + + const SubElementNode * find_node_with_common_ancestry(const CDMesh & search_mesh) const; + + void get_ancestors(NodeSet & ancestors) const; + SubElementNodeAncestry get_ancestry() const; + void build_stencil(std::map & stencil, const double self_weight = 1.0) const; + void build_constraint_stencil(const FieldRef field, std::vector & entities, std::vector & weights) const; + +protected: + void prolong_cdfem_displacements(const CDMesh & mesh, + const ProlongationPointData * prolong_data, + const bool zero_if_no_prolong_data = true) const; + void prolong_zeroed_fields(const CDMesh & mesh, const ProlongationNodeData * nodeToExamineForExistingField) const; + + mutable stk::mesh::Entity my_entity; + mutable stk::mesh::EntityId my_entityId; + mutable bool my_is_prolonged_flag; + Vector3d my_global_coords; + mutable signed char my_node_sign; + mutable double my_node_score; + + mutable const Mesh_Element * my_cached_owner; + mutable Vector3d my_cached_owner_coords; + + mutable std::vector my_children; + mutable std::vector my_sorted_node_domains; + +private: + //: copy constructor not allowed + SubElementNode(SubElementNode const & copy); +}; + +class SubElementChildNode : public SubElementNode { +public: + SubElementChildNode( const Mesh_Element * owner, + const NodeVec & parents, + const std::vector & weights ); + + virtual ~SubElementChildNode() {} + virtual void prolongate_fields(const CDMesh & mesh) const override; + virtual Vector3d compute_owner_coords( const Mesh_Element * in_owner ) const override; + + virtual NodeVec get_parents() const override { return my_parents; } + virtual size_t get_num_parents() const override { return my_parents.size(); } + virtual std::vector get_parent_weights() const override { return my_weights; } + bool needs_to_be_ale_prolonged(const CDMesh & mesh) const; + +private: + void prolong_ale_fields(const CDMesh & mesh, const ProlongationPointData * prolong_data) const; + void prolong_interpolation_fields(const CDMesh & mesh) const; + + NodeVec my_parents; + std::vector my_weights; +}; + +class SubElementSteinerNode : public SubElementChildNode { +public: + + SubElementSteinerNode( const Mesh_Element * in_owner, + const NodeVec & parents, + const std::vector & weights ) + : SubElementChildNode(in_owner, parents, weights) {} + + virtual ~SubElementSteinerNode() {} + virtual void prolongate_fields(const CDMesh & mesh) const override; + virtual Vector3d compute_owner_coords( const Mesh_Element * owner ) const override { + throw std::runtime_error("Incorrect usage of SubElementSteinerNode. The type of node only has one owner."); + } +}; + +class SubElementEdgeNode : public SubElementChildNode { +public: + SubElementEdgeNode( const Mesh_Element * owner, + const double & position, + const SubElementNode *parent1, + const SubElementNode *parent2) + : SubElementChildNode( owner, {parent1, parent2}, {1.-position, position}) {} + + virtual ~SubElementEdgeNode() {} + + double get_position() const { ThrowAssert(get_num_parents() == 2); return get_parent_weights()[1]; } + double get_position(const SubElementNode *parent1, const SubElementNode *parent2) const { ThrowAssert(check_parents(parent1,parent2)); return ((parent1==get_parents()[0]) ? get_parent_weights()[1] : get_parent_weights()[0]); } + +private: + bool check_parents(const SubElementNode *parent1, const SubElementNode *parent2) const { + return (get_num_parents() == 2 && ((parent1==get_parents()[0] && parent2==get_parents()[1]) || (parent2==get_parents()[0] && parent1==get_parents()[1]))); + } +}; + + class SubElementMidSideNode : public SubElementNode { +public: + SubElementMidSideNode() = delete; + SubElementMidSideNode( const Mesh_Element * owner, + const SubElementNode *parent1, + const SubElementNode *parent2); + SubElementMidSideNode( const Mesh_Element * owner, + const SubElementNode *parent1, + const SubElementNode *parent2, + stk::mesh::Entity meshNode, + stk::mesh::EntityId meshNodeId); + + virtual ~SubElementMidSideNode() {} + virtual void prolongate_fields(const CDMesh & mesh) const override; + virtual Vector3d compute_owner_coords( const Mesh_Element * in_owner ) const override { + return 0.5 * my_parent1->owner_coords(in_owner) + 0.5 * my_parent2->owner_coords(in_owner); + } + virtual bool is_mesh_node() const override { return my_is_mesh_node; } + + virtual NodeVec get_parents() const override { ThrowRequire(!my_is_mesh_node); return NodeVec{my_parent1,my_parent2}; } + virtual size_t get_num_parents() const override { return 2; } + virtual std::vector get_parent_weights() const override { ThrowRequire(!my_is_mesh_node); return std::vector{0.5,0.5}; } + +protected: + bool my_is_mesh_node; + const SubElementNode *my_parent1; + const SubElementNode *my_parent2; + +private: + void prolong_ale_fields(const CDMesh & mesh) const; + void prolong_interpolation_fields(const CDMesh & mesh) const; + bool is_mesh_node_that_needs_to_be_prolonged(const CDMesh & mesh) const; +}; + + +class SubElementMeshNode : public SubElementNode { +public: + + SubElementMeshNode( const Mesh_Element * owner, + stk::mesh::Entity nodeEntity, + stk::mesh::EntityId nodeEntityId, + const Vector3d & owner_coords, + const Vector3d & global_coords ); + + virtual ~SubElementMeshNode() {} + + virtual void prolongate_fields(const CDMesh & mesh) const override; + virtual Vector3d compute_owner_coords( const Mesh_Element * owner ) const override { return owner->get_node_parametric_coords(this); } + virtual bool is_mesh_node() const override { return true; } + bool needs_to_be_ale_prolonged(const CDMesh & mesh) const; +protected: + +private: + void prolong_ale_fields(const CDMesh & mesh, + const ProlongationPointData * prolong_data, + const ProlongationNodeData * old_node) const; + void prolong_interpolation_fields(const CDMesh & mesh, const ProlongationNodeData * old_node) const; + //: Default constructor not allowed + SubElementMeshNode(); +}; + +} // namespace krino + +#endif // Akri_SubElement_h diff --git a/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.cpp b/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.cpp new file mode 100644 index 000000000000..b592e297f5a9 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.cpp @@ -0,0 +1,246 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +namespace krino { + +SubElementChildNodeAncestry::SubElementChildNodeAncestry( stk::CommBuffer & b ) +{ + size_t ancestrySize = 0; + b.unpack(ancestrySize); + ThrowAssert(ancestrySize > 0); + + myAncestry.reserve(ancestrySize); + + size_t numParents = 0; + std::vector parentIDs; + std::vector parentWeights; + + for(unsigned index=0; indexis_mesh_node()) + { + myAncestry.emplace_back(std::vector{node->entityId()}, std::vector{0.}); + return; + } + + const NodeVec & parents = node->get_parents(); + const auto & parentWeights = node->get_parent_weights(); + std::vector parentIDs; + parentIDs.reserve(parents.size()); + + for (auto && parent : node->get_parents()) + { + if (parent->is_mesh_node()) + parentIDs.push_back(parent->entityId()); + else + parentIDs.push_back(0); + } + + myAncestry.emplace_back(parentIDs, parentWeights); + + for (auto && parent : node->get_parents()) + if (!parent->is_mesh_node()) + build_ancestry(parent); +} + +void +SubElementChildNodeAncestry::get_parent_node_keys(std::vector & parentNodeKeys) const +{ + parentNodeKeys.clear(); + for (auto&& cut : myAncestry) + for (auto && parentID : cut.myParentIDs) + if (parentID != 0) + parentNodeKeys.emplace_back(stk::topology::NODE_RANK, parentID); +} + +bool +SubElementChildNodeAncestry::is_shared(const stk::mesh::BulkData & mesh, const SubElementNode * node) +{ + if (node->is_mesh_node()) + { + return mesh.bucket(node->entity()).shared(); + } + for (auto && parent : node->get_parents()) + { + if (!is_shared(mesh, parent)) + { + return false; + } + } + return true; +} + +void +SubElementChildNodeAncestry::pack_into_buffer(stk::CommBuffer & b) const +{ + ThrowAssert(!myAncestry.empty()); + const size_t ancestrySize = myAncestry.size(); + b.pack(ancestrySize); + for (auto&& cut : myAncestry) + { + const size_t numParents = cut.myParentIDs.size(); + b.pack(numParents); + for (size_t i=0; i parents(numParents, nullptr); + + for (size_t i=0; i +SubElementChildNodeAncestry::get_constrained_node_ancestries(const std::unordered_map > & constrainedNodeMap) const +{ + std::set parentNodeIDs; + for (auto&& cut : myAncestry) + for (auto && parentID : cut.myParentIDs) + if (parentID != 0) + parentNodeIDs.insert(parentID); + + std::vector constrainedNodeAncestries; + constrainedNodeAncestries.push_back(*this); + for (auto&& parentNodeID : parentNodeIDs) + { + std::vector toBeConverted; + toBeConverted.swap(constrainedNodeAncestries); + auto it = constrainedNodeMap.find(parentNodeID); + if (it == constrainedNodeMap.end()) break; + constrainedNodeAncestries.reserve(it->second.size() * toBeConverted.size()); + for (auto&& constrainedParentNodeID : it->second) + { + for (auto&& unconverted : toBeConverted) + { + SubElementChildNodeAncestry converted = unconverted; + for (auto&& cut : converted.myAncestry) + { + for (auto && cutParentNodeID : cut.myParentIDs) + if (cutParentNodeID == parentNodeID) + cutParentNodeID = constrainedParentNodeID; + } + constrainedNodeAncestries.push_back(converted); + } + } + } + return constrainedNodeAncestries; +} + +const SubElementNode * +SubElementChildNodeAncestry::build_missing_child_nodes(CDMesh & mesh, unsigned & ancestryIndex) const +{ + ThrowAssert(ancestryIndex < myAncestry.size()); + const Cut & cut = myAncestry[ancestryIndex]; + const size_t numParents = cut.myParentIDs.size(); + std::vector parents(numParents, nullptr); + + for (size_t i=0; iget_ancestors(ancestors); + + std::vector ancestorNodes; + ancestorNodes.reserve(ancestors.size()); + for (auto&& ancestor : ancestors) + { + ThrowAssert(ancestor->entity_is_valid(mesh.stk_bulk())); + ancestorNodes.push_back(ancestor->entity()); + } + + std::vector elems; + stk::mesh::get_entities_through_relations(mesh.stk_bulk(), ancestorNodes, stk::topology::ELEMENT_RANK, elems); + + const Mesh_Element * owner = nullptr; + for(auto && elem : elems) + { + owner = mesh.find_mesh_element(mesh.stk_bulk().identifier(elem)); + if(owner != nullptr) break; + } + if(!owner) + { + // It is possible in parallel for both nodes of a parent edge to be shared with a processor, + // but that processor does not own any of the elements connected to that edge. In that case + // we do not need to build the missing edge node. + return nullptr; + } + + if (parents.size() == 2) + return mesh.create_edge_node(owner, parents[0], parents[1], cut.myParentWeights[1]); + + return mesh.create_child_internal_or_face_node(owner, parents, cut.myParentWeights); +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.hpp b/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.hpp new file mode 100644 index 000000000000..55c73d64a243 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElementChildNodeAncestry.hpp @@ -0,0 +1,49 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_SubElementChildNodeAncestry_h +#define Akri_SubElementChildNodeAncestry_h + +#include +#include +#include +#include + +namespace krino +{ +class CDMesh; +class SubElementNode; + +class SubElementChildNodeAncestry { +public: + SubElementChildNodeAncestry(const SubElementNode * node) { build_ancestry(node); } + SubElementChildNodeAncestry( stk::CommBuffer & b ); + + static bool is_shared(const stk::mesh::BulkData & mesh, const SubElementNode * node); + void pack_into_buffer(stk::CommBuffer & b) const; + const SubElementNode * find_subelement_node(CDMesh & mesh) const; + const SubElementNode * find_subelement_node(CDMesh & mesh, unsigned & ancestry_index) const; + void get_parent_node_keys(std::vector & parent_node_keys) const; + void build_missing_child_nodes(CDMesh & mesh) const; + std::vector get_constrained_node_ancestries(const std::unordered_map > & constrained_node_map) const; + +private: + struct Cut { + Cut(const std::vector & parentIDs, const std::vector & parentWeights) : myParentIDs(parentIDs), myParentWeights(parentWeights) {} + std::vector myParentIDs; + std::vector myParentWeights; + }; + void build_ancestry(const SubElementNode * in_node); + const SubElementNode * build_missing_child_nodes(CDMesh & mesh, unsigned & ancestry_index) const; + + std::vector myAncestry; +}; + +} + +#endif // Akri_SubElementChildNodeAncestry_h diff --git a/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.cpp b/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.cpp new file mode 100644 index 000000000000..9dad99d5cf55 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.cpp @@ -0,0 +1,32 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino { + +void SubElementNodeAncestry::print(std::ostream & os) const +{ + if (my_node->is_mesh_node()) + { + os << my_node->entityId(); + } + else + { + os << "{ "; + for (auto&& parent : get_parents()) + { + parent.print(os); + os << " "; + } + os << "}"; + } +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.hpp b/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.hpp new file mode 100644 index 000000000000..b36fc35423e0 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_SubElementNodeAncestry.hpp @@ -0,0 +1,65 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_SubElementNodeAncestry_h +#define Akri_SubElementNodeAncestry_h + +#include + +namespace krino { + +class SubElementNodeAncestry { +public: + SubElementNodeAncestry() = default; + SubElementNodeAncestry(const SubElementNodeAncestry & rhs) = default; + SubElementNodeAncestry(const SubElementNode * node) : my_node(node) {} + + template + static bool compare(const SubElementNodeAncestry & x, const SubElementNodeAncestry & y, const LESS & compare) + { + const std::vector xParents = x.get_parents(); + const std::vector yParents = y.get_parents(); + if (xParents.empty()) + { + if (yParents.empty()) return compare(*(x.my_node), *(y.my_node)); + else return true; + } + else if (yParents.empty()) return false; + else return xParents < yParents; + } + + void print(std::ostream & os) const; + +private: + std::vector get_parents() const + { + std::vector parents; + if (!my_node->is_mesh_node()) + { + const NodeVec nodeParents = my_node->get_parents(); + parents.reserve(nodeParents.size()); + for (auto && nodeParent : nodeParents) + parents.emplace_back(nodeParent); + std::sort(parents.begin(), parents.end()); + } + return parents; + } + + const SubElementNode * my_node = nullptr; +}; + +inline bool operator<(const SubElementNodeAncestry & x, const SubElementNodeAncestry & y) +{ + return SubElementNodeAncestry::compare(x,y,SubElementNode::less_by_entity_id); +} + +inline std::ostream & operator << (std::ostream & os, const SubElementNodeAncestry & ancestry) { ancestry.print(os); return os; } + +} + +#endif // Akri_SubElementNodeAncestry_h diff --git a/packages/krino/krino/krino_lib/Akri_Surface.cpp b/packages/krino/krino/krino_lib/Akri_Surface.cpp new file mode 100644 index 000000000000..6fc43d1f8dd7 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Surface.cpp @@ -0,0 +1,28 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino{ + +void +Surface::prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length) +{ + ThrowErrorMsgIf(NULL != my_transformation, + "This surface with type (" << type() + << ") has motion specified, but the prepare_to_compute() method has not been implemented yet to support motion."); +} + +BoundingBox +Surface::get_bounding_box() +{ + ThrowRuntimeError("This surface with type (" << type() << ") has not implemented get_bounding_box()."); +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Surface.hpp b/packages/krino/krino/krino_lib/Akri_Surface.hpp new file mode 100644 index 000000000000..78019bafe845 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Surface.hpp @@ -0,0 +1,98 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Surface_h +#define Akri_Surface_h + +#include +#include +#include +#include + +namespace krino { + +class Transformation; + +enum Surface_Type +{ + POINT=0, + SPHERE, + ELLIPSOID, + CYLINDER, + COMPOSITE_SURFACE, + PLANE, + RANDOM, + FACETED_SURFACE, + // Never, ever, ever add an entry after MAX_SURFACE_TYPE. Never. + MAX_SURFACE_TYPE +}; + +class Surface; +typedef std::vector SurfaceVec; +typedef std::vector< std::unique_ptr > SurfaceAutoVec; + +// abstract class used to define a surface. + +class Surface { + +public: + Surface() { Surface::set_transformation(nullptr); } + virtual ~Surface() {} + + virtual BoundingBox get_bounding_box(); + + // pre-calculations needed to compute distance + virtual void prepare_to_compute(const double time, const BoundingBox & point_bbox, const double truncation_length); + + // compute signed distance from specific point to surface + virtual double point_signed_distance(const Vector3d &x) const = 0; + + // compute signed distance from specific point to surface + // For distances larger than truncation_length (if truncation_length > 0.), the surface is allowed to return + // far_field_value instead of the actual signed distance. + virtual double truncated_point_signed_distance(const Vector3d &x, const double truncation_length, const double far_field_value) const = 0; + // If surface does return far_field_value instead of actual signed distance, the sign may be wrong. + virtual bool truncated_distance_may_have_wrong_sign() const = 0; + + // for debugging memory usage + virtual size_t storage_size() const = 0; + + // methods related to moving surfaces (transformations) + virtual void set_transformation(Transformation * trans) { my_transformation = trans; } + Transformation * get_transformation() { return my_transformation; } + const Transformation * get_transformation() const { return my_transformation; } + + // queries + virtual Surface_Type type() const = 0; + +protected: + Transformation * my_transformation; +}; + +class SurfaceThatTakesAdvantageOfNarrowBandAndThereforeMightHaveWrongSign : public Surface { +public: + virtual bool truncated_distance_may_have_wrong_sign() const override { return true; } + virtual double point_signed_distance(const Vector3d &x) const override + { + return truncated_point_signed_distance(x, 0., 0.); + } + virtual double truncated_point_signed_distance(const Vector3d &x, const double truncation_length, const double far_field_value) const override = 0; +}; + +class SurfaceThatDoesntTakeAdvantageOfNarrowBandAndThereforeHasCorrectSign : public Surface { +public: + virtual bool truncated_distance_may_have_wrong_sign() const override { return false; } + virtual double point_signed_distance(const Vector3d &x) const override = 0; + virtual double truncated_point_signed_distance(const Vector3d &x, const double truncation_length, const double far_field_value) const override + { + return point_signed_distance(x); + } +}; +} // namespace krino + +#endif // Akri_Surface_h diff --git a/packages/krino/krino/krino_lib/Akri_Transformation.cpp b/packages/krino/krino/krino_lib/Akri_Transformation.cpp new file mode 100644 index 000000000000..d7c563f2a588 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Transformation.cpp @@ -0,0 +1,112 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include + +namespace krino{ + +void +Quaternion::set_from_rotation_vector(const Vector3d & v) +{ + // the angle theta is the length of the rotation vector omega + const double theta = v.length(); + const double real_min = 10.0*std::numeric_limits::min(); + + double coef; + if ( theta > real_min ) { + coef = std::sin(0.5*theta)/theta; + } else { + coef = 0.5; + } + + q[0] = std::cos( 0.5*theta ); + q[1] = coef*v[0]; + q[2] = coef*v[1]; + q[3] = coef*v[2]; + + const double inv_length = 1.0/std::sqrt(q[0]*q[0] + q[1]*q[1] + q[2]*q[2] + q[3]*q[3]); + for (auto && val : q) val *= inv_length; +} + +Vector3d use_quaternion_to_rotate_3d_vector(const std::array & q, const Vector3d & v) +{ + return Vector3d( + ((2. * ( q[0] * q[0] + q[1] * q[1] ) - 1.) * v[0] + + (2. * ( q[1] * q[2] - q[0] * q[3] ) ) * v[1] + + (2. * ( q[1] * q[3] + q[0] * q[2] ) ) * v[2]), + ((2. * ( q[1] * q[2] + q[0] * q[3] ) ) * v[0] + + (2. * ( q[0] * q[0] + q[2] * q[2] ) - 1.) * v[1] + + (2. * ( q[2] * q[3] - q[0] * q[1] ) ) * v[2]), + ((2. * ( q[1] * q[3] - q[0] * q[2] ) ) * v[0] + + (2. * ( q[2] * q[3] + q[0] * q[1] ) ) * v[1] + + (2. * ( q[0] * q[0] + q[3] * q[3] ) - 1.) * v[2])); +} + + +Vector3d +Quaternion::rotate_3d_vector(const Vector3d & v) const +{ + return use_quaternion_to_rotate_3d_vector(q, v); +} + +Vector3d +Quaternion::reverse_rotate_3d_vector(const Vector3d & v) const +{ + return use_quaternion_to_rotate_3d_vector(std::array{q[0],-q[1],-q[2],-q[3]}, v); +} + +void +Transformation::initialize( const Vector3d & initial_displacement, const Vector3d & initial_rotation, const Vector3d & reference_point ) +{ + my_reference_point = reference_point; + my_update_orientation.set_from_rotation_vector(initial_rotation); + my_update_offset = initial_displacement - my_update_orientation.rotate_3d_vector(my_reference_point); + my_reference_point += initial_displacement; +} + +void +Transformation::initialize() +{ + // this form of initialization assumes that set_initial_displacement() and set_initial_rotation() have been called or are zero + const Vector3d initial_displacement = my_update_offset; + my_update_offset = initial_displacement - my_update_orientation.rotate_3d_vector(my_reference_point); + my_reference_point += initial_displacement; +} + +void +Transformation::update( const double time ) const +{ + if (time == my_last_update) + { + return; + } + if (my_last_update < 0.0) + { + my_last_update = time; + return; + } + + const double dt = time - my_last_update; + const Vector3d update_rotation_angle = dt*my_rotational_velocity; + my_update_orientation.set_from_rotation_vector(update_rotation_angle); + my_update_offset = my_reference_point - my_update_orientation.rotate_3d_vector(my_reference_point) + my_translational_velocity * dt; + my_reference_point += my_translational_velocity * dt; + + my_last_update = time; +} + +void +Transformation::apply( Vector3d & x0 ) const +{ + x0 = my_update_orientation.rotate_3d_vector(x0) + my_update_offset; +} + +} // namespace krino diff --git a/packages/krino/krino/krino_lib/Akri_Transformation.hpp b/packages/krino/krino/krino_lib/Akri_Transformation.hpp new file mode 100644 index 000000000000..602d3510af9a --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Transformation.hpp @@ -0,0 +1,65 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Transformation_h +#define Akri_Transformation_h + +#include +#include + +namespace krino { + +class Quaternion { + public: + Quaternion() : q{{ 1.0, 0.0, 0.0, 0.0 }} {} + + void set_from_rotation_vector(const Vector3d & v); + Vector3d rotate_3d_vector(const Vector3d & v) const; + Vector3d reverse_rotate_3d_vector(const Vector3d & v) const; + + private: + std::array q; ///< q[0] stores angle, (q[1],q[2],a[3]) stores axis. +}; + +class Transformation { +public: + Transformation() + : my_translational_velocity(Vector3d::ZERO), my_rotational_velocity(Vector3d::ZERO), + my_reference_point(Vector3d::ZERO), my_last_update(-1.0), my_update_orientation(), my_update_offset(Vector3d::ZERO) {} + virtual ~Transformation() {} + + void set_translational_velocity(const Vector3d & v) { my_translational_velocity = v; } + void set_rotational_velocity(const Vector3d & v) { my_rotational_velocity = v; } + void set_reference_point(const Vector3d & v) { my_reference_point = v; } + + // temporary storage until initialize() + void set_initial_displacement(const Vector3d & v) { my_update_offset = v; } + void set_initial_rotation(const Vector3d & v) { my_update_orientation.set_from_rotation_vector(v); } + + const Vector3d & get_translational_velocity() const { return my_translational_velocity; } + const Vector3d & get_rotational_velocity() const { return my_rotational_velocity; } + const Vector3d & get_reference_point() const { return my_reference_point; } + + void initialize( const Vector3d & initial_displacement, const Vector3d & initial_rotation, const Vector3d & reference_point ); + void initialize(); // this form assumes that set_initial_displacement() and set_initial_rotation() have been called or are zero + void update( const double time ) const; + void apply( Vector3d & x0 ) const; + +protected: + Vector3d my_translational_velocity; + Vector3d my_rotational_velocity; + mutable Vector3d my_reference_point; + mutable double my_last_update; + mutable Quaternion my_update_orientation; + mutable Vector3d my_update_offset; +}; + + +} // namespace krino + +#endif // Akri_Transformation_h diff --git a/packages/krino/krino/krino_lib/Akri_Triangle.hpp b/packages/krino/krino/krino_lib/Akri_Triangle.hpp new file mode 100644 index 000000000000..868fbe2b0a1e --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Triangle.hpp @@ -0,0 +1,169 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Triangle_h +#define Akri_Triangle_h + +#include +#include +#include +#include + +#include + +namespace krino { + +enum class ProjectionType{NODE, EDGE, FACE, NUM_PROJ_TYPE}; + +template +class Triangle3 { + public: + typedef REAL Real; + + + Triangle3() {} /// Default, all coords zero + Triangle3(const Vec &n0, const Vec &n1, const Vec &n2) : nodes{{n0, n1, n2}} {} /// Explicit set three coordinates + explicit Triangle3(const MemberInit) {/* MemberInit::NONE */} /// Special non-initialize constructor (for performance) + + Vec normal() const { return normal_dir().unit_vector(); } /// Unit vector + Vec normal_dir() const {return Cross(GetNode(1)-GetNode(0),GetNode(2)-GetNode(0)); } /// Non-unit normal (faster) + Real area() const { return 0.5*normal_dir().length(); } + + Vec ParametricToRealCoords(const Vec & Param) const { + // Avoids temporary constructions + return Vec( + GetNode(0)[0]*(1.0-Param[0]-Param[1]) + GetNode(1)[0]*Param[0] + GetNode(2)[0]*Param[1], + GetNode(0)[1]*(1.0-Param[0]-Param[1]) + GetNode(1)[1]*Param[0] + GetNode(2)[1]*Param[1], + GetNode(0)[2]*(1.0-Param[0]-Param[1]) + GetNode(1)[2]*Param[0] + GetNode(2)[2]*Param[1] + ); + } + + /// Compute the closest point on the triangle to an input point. Return the type of projection, i.e., + /// is the projected point on a node, edge, surface of the triangle. Optionally calculate parametric coordinates. + template ProjectionType ClosestPoint(const Vec& p, Vec& ClosestPt, T ParamPt = nullptr) const; + + Real DistanceSquared(const Vec& P, Vec& ParamPt) const; + Real DistanceSquared(const Vec& P) const; + + const Vec& GetNode(const int index) const { assert(index >= 0 && index < 3); return nodes[index]; } + Vec& GetNode(const int index) { assert(index >= 0 && index < 3); return nodes[index]; } + + void SetNodes(const Vec& n0, const Vec& n1, const Vec& n2) { nodes = {{n0, n1, n2}}; } // Change triangle coordinates +private: + std::array,3> nodes; +}; + +namespace detail { +template +struct assign_parametric_coords { + static void apply(const REAL & x, const REAL & y, T parametric_coords) + { + static_assert(std::is_pointer::value, "Expecting pointer"); + parametric_coords[0] = x; + parametric_coords[1] = y; + } +}; +template +struct assign_parametric_coords { + static void apply(const REAL, const REAL, std::nullptr_t) {} +}; +} + +template +inline REAL Triangle3::DistanceSquared(const Vec& P, Vec& ParamPt) const +{ + Vec ClosestPt(MemberInit::NONE); + ClosestPoint(P, ClosestPt, ParamPt.data()); + return (P-ClosestPt).length_squared(); +} + +template +inline REAL Triangle3::DistanceSquared(const Vec& P) const +{ + Vec ClosestPt(MemberInit::NONE); + ClosestPoint(P, ClosestPt); + return (P-ClosestPt).length_squared(); +} + +// Adapted from closest face projection from "Real time Collision Detection" text, highly optimized +template +template +ProjectionType Triangle3::ClosestPoint(const Vec& p, Vec& ClosestPt, T ParamPt) const +{ + const Vec& a = GetNode(0); + const Vec& b = GetNode(1); + const Vec& c = GetNode(2); + + Vec ab(b-a); + Vec ac(c-a); + Vec ap(p-a); + + Real d1(Dot(ab,ap)); + Real d2(Dot(ac,ap)); + + if(d1 <= 0.0 && d2 <= 0.0) { + ClosestPt = a; + detail::assign_parametric_coords::apply(0.0, 0.0, ParamPt); + return ProjectionType::NODE; + } + + Vec bp(p-b); + Real d3(Dot(ab,bp)); + Real d4(Dot(ac,bp)); + + if(d3 >= 0.0 && d4 <= d3) { + ClosestPt = b; + detail::assign_parametric_coords::apply(1.0, 0.0, ParamPt); + return ProjectionType::NODE; + } + + Real vc(d1*d4-d3*d2); + if(vc <= 0.0 && d1 >= 0.0 && d3 <= 0.0) { + Real v = d1/(d1-d3); + ClosestPt = a + v * ab; + detail::assign_parametric_coords::apply(v, 0.0, ParamPt); + return ProjectionType::EDGE; + } + + Vec cp(p-c); + Real d5(Dot(ab,cp)); + Real d6(Dot(ac,cp)); + if(d6 >= 0.0 && d5 <= d6) { + ClosestPt = c; + detail::assign_parametric_coords::apply(0.0, 1.0, ParamPt); + return ProjectionType::NODE; + } + + Real vb(d5*d2 - d1*d6); + if(vb <= 0.0 && d2 >= 0.0 && d6 <= 0.0) { + Real w(d2/(d2-d6)); + ClosestPt = a + w * ac; + detail::assign_parametric_coords::apply(0.0, w, ParamPt); + return ProjectionType::EDGE; + } + + Real va(d3*d6 - d5*d4); + if(va <= 0.0 && (d4-d3) >= 0.0 && (d5-d6) >= 0.0) { + Real w((d4-d3)/((d4-d3) + (d5-d6))); + ClosestPt = b + w * (c-b); + detail::assign_parametric_coords::apply(1.0-w, w, ParamPt); + return ProjectionType::EDGE; + } + + Real denom(1.0/(va+vb+vc)); + Real v(vb*denom); + Real w(vc*denom); + ClosestPt = a + ab*v + ac*w; + detail::assign_parametric_coords::apply(v, w, ParamPt); + return ProjectionType::FACE; +} + +typedef Triangle3 Triangle3d; + +} +#endif // Akri_Triangle_h diff --git a/packages/krino/krino/krino_lib/Akri_TypeDefs.hpp b/packages/krino/krino/krino_lib/Akri_TypeDefs.hpp new file mode 100644 index 000000000000..3a949159289b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_TypeDefs.hpp @@ -0,0 +1,27 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef SIERRA_Akri_TypeDefs_h +#define SIERRA_Akri_TypeDefs_h + +#include +#include +#include + +namespace krino { + + class NINT{}; + class NPE_VAR{}; + class NPE_COORD{}; + class DIM{}; + + typedef std::vector< Vector3d > PointVec; + +} + +#endif // SIERRA_Akri_TypeDefs_h diff --git a/packages/krino/krino/krino_lib/Akri_Utility.hpp b/packages/krino/krino/krino_lib/Akri_Utility.hpp new file mode 100644 index 000000000000..a8a7e7b69aa2 --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Utility.hpp @@ -0,0 +1,66 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef SIERRA_Akri_Utility_h +#define SIERRA_Akri_Utility_h + +#include +#include +#include +#include + +namespace krino { +namespace utility { + + inline bool sign_change( double f1, double f2 ) { + return ( (f1 < 0.) ? (f2 >= 0.) : (f2 < 0.) ); // GOMA sign convention + //return ( (f1 > 0.) ? (f2 <= 0.) : (f2 > 0.) ); // Marching cubes sign convention + } + + inline int sign( double f ) { + return ( (f < 0.) ? -1 : 1 ); // GOMA sign convention + //return ( (f > 0.) ? 1 : -1 ); // Marching cubes sign convention + } + + inline bool is_less(double f1, double f2, double tol) { return (f2-f1 > tol*(std::fabs(f1)+std::fabs(f2))); } + inline bool is_more(double f1, double f2, double tol) { return (is_less(f2,f1,tol)); } + inline bool is_not_equal(double f1, double f2, double tol) { return (is_less(f1,f2,tol) || is_less(f2,f1,tol)); } + inline bool is_equal(double f1, double f2, double tol) { return (!is_less(f1,f2,tol) && !is_less(f2,f1,tol)); } + + inline bool is_less(double f1, double f2) { return is_less(f1,f2,100.0*std::numeric_limits::epsilon()); } + inline bool is_more(double f1, double f2) { return is_more(f1,f2,100.0*std::numeric_limits::epsilon()); } + inline bool is_not_equal(double f1, double f2) { return is_not_equal(f1,f2,100.0*std::numeric_limits::epsilon()); } + inline bool is_equal(double f1, double f2) { return is_equal(f1,f2,100.0*std::numeric_limits::epsilon()); } + + inline bool is_less(double f1, int i1, double f2, int i2, double tol) { return is_less(f1,f2,tol) ? true : (is_more(f1,f2,tol) ? false : (i1::epsilon()); } + inline bool is_more(double f1, int i1, double f2, int i2) { return is_more(f1,i1,f2,i2,100.0*std::numeric_limits::epsilon()); } + + template + inline void + free_all(std::vector & vec) {std::vector empty_vec; vec.swap(empty_vec);} + + template + inline size_t + storage_size(const std::vector & vec) {return (sizeof(std::vector) + vec.size()*sizeof(T*)); } + + // linear cost, requires T::storage_size + template + inline size_t + storage_size(const std::vector> & autovec) + { + size_t store_size = sizeof(std::vector>) + autovec.size()*sizeof(std::unique_ptr); + for (auto && entry : autovec) store_size += entry->storage_size(); + return store_size; + } + +} // namespace utility +} // namespace krino + +#endif // SIERRA_Akri_Utility_h diff --git a/packages/krino/krino/krino_lib/Akri_Vec.cpp b/packages/krino/krino/krino_lib/Akri_Vec.cpp new file mode 100644 index 000000000000..fa4faa7d9e1c --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Vec.cpp @@ -0,0 +1,38 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +namespace krino { + +static bool float_less(double a, double b) +{ + return static_cast(a) < static_cast(b); +} + +bool is_less_than_in_x_then_y_then_z(const Vector3d& A, const Vector3d &B) +{ + if (float_less(A[0], B[0])) + return true; + else if (float_less(B[0], A[0])) + return false; + + if (float_less(A[1], B[1])) + return true; + else if (float_less(B[1], A[1])) + return false; + + if (float_less(A[2], B[2])) + return true; + else if (float_less(B[2], A[2])) + return false; + + return false; +} + +} diff --git a/packages/krino/krino/krino_lib/Akri_Vec.hpp b/packages/krino/krino/krino_lib/Akri_Vec.hpp new file mode 100644 index 000000000000..e1213d9bb77b --- /dev/null +++ b/packages/krino/krino/krino_lib/Akri_Vec.hpp @@ -0,0 +1,26 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Vec_h +#define Akri_Vec_h + +#include + +namespace krino { + +using stk::math::MemberInit; +using stk::math::Vec; +typedef stk::math::Vec Vector3d; +typedef stk::math::Vec Vector2d; +typedef stk::math::Vec Float3d; + +bool is_less_than_in_x_then_y_then_z(const Vector3d& A, const Vector3d &B); + +} // namespace krino + +#endif // Akri_Vec_h diff --git a/packages/krino/krino/krino_lib/CMakeLists.txt b/packages/krino/krino/krino_lib/CMakeLists.txt new file mode 100644 index 000000000000..ac224f4eba62 --- /dev/null +++ b/packages/krino/krino/krino_lib/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + DEPLIBS krino_master_element_lib) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_lib) + diff --git a/packages/krino/krino/master_element/Akri_MasterElement.hpp b/packages/krino/krino/master_element/Akri_MasterElement.hpp new file mode 100644 index 000000000000..5749c4a6ca5d --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElement.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElement_h +#define Akri_MasterElement_h + +#include + +namespace krino { + +// Set actual MasterElement type we will use +typedef MasterElementHybrid MasterElement; + +} // end namespace krino + +#endif // Akri_MasterElement_h diff --git a/packages/krino/krino/master_element/Akri_MasterElementBasis.hpp b/packages/krino/krino/master_element/Akri_MasterElementBasis.hpp new file mode 100644 index 000000000000..39cb2743a920 --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementBasis.hpp @@ -0,0 +1,701 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElementBasis_h +#define Akri_MasterElementBasis_h + +#define ATTR_RESTRICT __restrict__ + +namespace krino { + +class Basis +{ +public: + Basis(unsigned deg) : my_degree(deg) {} + + virtual ~Basis() {} + virtual void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const = 0; + virtual void shape_fcn(const int nint, const double* p_coords, double* result) const = 0; + virtual void shape_fcn_deriv(const int nint, const double* p_coords, double* result ) const = 0; + unsigned degree() const { return my_degree; } + +private: + unsigned my_degree; +}; + +class Basis_LINE_2 : public Basis +{ +public: + Basis_LINE_2() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[0] = -1.0; + p_coords[1] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[ip]; + result[ip*2 + 0] = ( 1.0 - x ) * 0.5; + result[ip*2 + 1] = ( 1.0 + x ) * 0.5; + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + result[ip*2 + 0] = -0.5; + result[ip*2 + 1] = 0.5; + } + } +}; + +class Basis_LINE_3 : public Basis +{ +public: + Basis_LINE_3() : Basis(2) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[0] = -1.0; + p_coords[1] = 1.0; + p_coords[2] = 0.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[ip]; + result[ip*3 + 0] = -x * ( 1.0 - x ) * 0.5; + result[ip*3 + 1] = x * ( 1.0 + x ) * 0.5; + result[ip*3 + 2] = ( 1.0 - x ) * ( 1.0 + x ); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[ip]; + result[ip*3 + 0] = x; + result[ip*3 + 1] = x; + result[ip*3 + 2] = -2.0*x; + } + } +}; + +class Basis_TRI_3 : public Basis +{ +public: + Basis_TRI_3() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[0] = 0.0; p_coords[1] = 0.0; + p_coords[2] = 1.0; p_coords[3] = 0.0; + p_coords[4] = 0.0; p_coords[5] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*3 + 0] = 1.0 - x - y; + result[ip*3 + 1] = x; + result[ip*3 + 2] = y; + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + result[ip*6 + 0] = -1.0; + result[ip*6 + 1] = -1.0; + result[ip*6 + 2] = 1.0; + result[ip*6 + 3] = 0.0; + result[ip*6 + 4] = 0.0; + result[ip*6 + 5] = 1.0; + } + } +}; + +class Basis_TRI_6 : public Basis +{ +public: + Basis_TRI_6() : Basis(2) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = 0.0; p_coords[ 1] = 0.0; + p_coords[ 2] = 1.0; p_coords[ 3] = 0.0; + p_coords[ 4] = 0.0; p_coords[ 5] = 1.0; + p_coords[ 6] = 0.5; p_coords[ 7] = 0.0; + p_coords[ 8] = 0.5; p_coords[ 9] = 0.5; + p_coords[10] = 0.0; p_coords[11] = 0.5; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*6 + 0] = (x + y - 1.0)*(2.0*x + 2.0*y - 1.0); + result[ip*6 + 1] = x*(2.0*x - 1.0); + result[ip*6 + 2] = y*(2.0*y - 1.0); + result[ip*6 + 3] = -4.0*x*(x + y - 1.0); + result[ip*6 + 4] = 4.0*x*y; + result[ip*6 + 5] = -4.0*y*(x + y - 1.0); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*12 + 0] = 4.0*x + 4.0*y - 3.0; + result[ip*12 + 1] = 4.0*x + 4.0*y - 3.0; + result[ip*12 + 2] = 4.0*x - 1.0; + result[ip*12 + 3] = 0.0; + result[ip*12 + 4] = 0.0; + result[ip*12 + 5] = 4.0*y - 1.0; + result[ip*12 + 6] = -4.0*(2.0*x + y - 1.0); + result[ip*12 + 7] = -4.0*x; + result[ip*12 + 8] = 4.0*y; + result[ip*12 + 9] = 4.0*x; + result[ip*12 + 10] = -4.0*y; + result[ip*12 + 11] = -4.0*(x + 2.0*y - 1.0); + } + } +}; + +class Basis_QUAD_4 : public Basis +{ +public: + Basis_QUAD_4() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = -1.0; p_coords[ 1] = -1.0; + p_coords[ 2] = 1.0; p_coords[ 3] = -1.0; + p_coords[ 4] = 1.0; p_coords[ 5] = 1.0; + p_coords[ 6] = -1.0; p_coords[ 7] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*4 + 0] = 0.25*(1.0 - x)*(1.0 - y); + result[ip*4 + 1] = 0.25*(1.0 + x)*(1.0 - y); + result[ip*4 + 2] = 0.25*(1.0 + x)*(1.0 + y); + result[ip*4 + 3] = 0.25*(1.0 - x)*(1.0 + y); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*8 + 0] = -0.25*(1.0 - y); + result[ip*8 + 1] = -0.25*(1.0 - x); + result[ip*8 + 2] = 0.25*(1.0 - y); + result[ip*8 + 3] = -0.25*(1.0 + x); + result[ip*8 + 4] = 0.25*(1.0 + y); + result[ip*8 + 5] = 0.25*(1.0 + x); + result[ip*8 + 6] = -0.25*(1.0 + y); + result[ip*8 + 7] = 0.25*(1.0 - x); + } + } +}; + +class Basis_QUAD_9 : public Basis +{ +public: + Basis_QUAD_9() : Basis(2) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = -1.0; p_coords[ 1] = -1.0; + p_coords[ 2] = 1.0; p_coords[ 3] = -1.0; + p_coords[ 4] = 1.0; p_coords[ 5] = 1.0; + p_coords[ 6] = -1.0; p_coords[ 7] = 1.0; + p_coords[ 8] = 0.0; p_coords[ 9] = -1.0; + p_coords[10] = 1.0; p_coords[11] = 0.0; + p_coords[12] = 0.0; p_coords[13] = 1.0; + p_coords[14] = -1.0; p_coords[15] = 0.0; + p_coords[16] = 0.0; p_coords[17] = 0.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*9 + 0] = 0.25*x*(x - 1.0)*y*(y - 1.0); + result[ip*9 + 1] = 0.25*x*(x + 1.0)*y*(y - 1.0); + result[ip*9 + 2] = 0.25*x*(x + 1.0)*y*(y + 1.0); + result[ip*9 + 3] = 0.25*x*(x - 1.0)*y*(y + 1.0); + result[ip*9 + 4] = 0.5*(1.0 - x)*(1.0 + x)*y*(y - 1.0); + result[ip*9 + 5] = 0.5*x*(x + 1.0)*(1.0 - y)*(1.0 + y); + result[ip*9 + 6] = 0.5*(1.0 - x)*(1.0 + x)*y*(y + 1.0); + result[ip*9 + 7] = 0.5*x*(x - 1.0)*(1.0 - y)*(1.0 + y); + result[ip*9 + 8] = (1.0 - x)*(1.0 + x)*(1.0 - y)*(1.0 + y); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[2*ip + 0]; + const double y = p_coords[2*ip + 1]; + result[ip*18 + 0] = (-0.25 + 0.5*x)*(-1. + y)*y; + result[ip*18 + 1] = (-1.0 + x)*x*(-0.25 + 0.5*y); + result[ip*18 + 2] = (0.25 + 0.5*x)*(-1. + y)*y; + result[ip*18 + 3] = x*(1. + x)*(-0.25 + 0.5*y); + result[ip*18 + 4] = (0.25 + 0.5*x)*y*(1. + y); + result[ip*18 + 5] = x*(1. + x)*(0.25 + 0.5*y); + result[ip*18 + 6] = (-0.25 + 0.5*x)*y*(1. + y); + result[ip*18 + 7] = (-1. + x)*x*(0.25 + 0.5*y); + result[ip*18 + 8] = x*(1.0 - y)*y; + result[ip*18 + 9] = 0.5*(1.0 - x)*(1.0 + x)*(-1.0 + 2.0*y); + result[ip*18 + 10] = 0.5*(1.0 - y)*(1.0 + y)*(1.0 + 2.0*x); + result[ip*18 + 11] = -x*(1.0 + x)*y; + result[ip*18 + 12] = -y*(1.0 + y)*x; + result[ip*18 + 13] = 0.5*(1.0 - x)*(1.0 + x)*(1.0 + 2.0*y); + result[ip*18 + 14] = 0.5*(1.0 - y)*(1.0+ y)*(-1.0 + 2.0*x); + result[ip*18 + 15] = (1.0 - x)*x*y; + result[ip*18 + 16] = -2.0*(1.0 - y)*(1.0 + y)*x; + result[ip*18 + 17] = -2.0*(1.0 - x)*(1.0 + x)*y; + } + } +}; + +class Basis_TET_4 : public Basis +{ +public: + Basis_TET_4() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = 0.0; p_coords[ 1] = 0.0; p_coords[ 2] = 0.0; + p_coords[ 3] = 1.0; p_coords[ 4] = 0.0; p_coords[ 5] = 0.0; + p_coords[ 6] = 0.0; p_coords[ 7] = 1.0; p_coords[ 8] = 0.0; + p_coords[ 9] = 0.0; p_coords[10] = 0.0; p_coords[11] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*4 + 0] = 1.0 - x - y - z; + result[ip*4 + 1] = x; + result[ip*4 + 2] = y; + result[ip*4 + 3] = z; + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + result[ip*12 + 0] = -1.0; + result[ip*12 + 1] = -1.0; + result[ip*12 + 2] = -1.0; + result[ip*12 + 3] = 1.0; + result[ip*12 + 4] = 0.0; + result[ip*12 + 5] = 0.0; + result[ip*12 + 6] = 0.0; + result[ip*12 + 7] = 1.0; + result[ip*12 + 8] = 0.0; + result[ip*12 + 9] = 0.0; + result[ip*12 + 10] = 0.0; + result[ip*12 + 11] = 1.0; + } + } +}; + +class Basis_TET_10 : public Basis +{ +public: + Basis_TET_10() : Basis(2) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = 0.0; p_coords[ 1] = 0.0; p_coords[ 2] = 0.0; + p_coords[ 3] = 1.0; p_coords[ 4] = 0.0; p_coords[ 5] = 0.0; + p_coords[ 6] = 0.0; p_coords[ 7] = 1.0; p_coords[ 8] = 0.0; + p_coords[ 9] = 0.0; p_coords[10] = 0.0; p_coords[11] = 1.0; + p_coords[12] = 0.5; p_coords[13] = 0.0; p_coords[14] = 0.0; + p_coords[15] = 0.5; p_coords[16] = 0.5; p_coords[17] = 0.0; + p_coords[18] = 0.0; p_coords[19] = 0.5; p_coords[20] = 0.0; + p_coords[21] = 0.0; p_coords[22] = 0.0; p_coords[23] = 0.5; + p_coords[24] = 0.5; p_coords[25] = 0.0; p_coords[26] = 0.5; + p_coords[27] = 0.0; p_coords[28] = 0.5; p_coords[29] = 0.5; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*10 + 0] = (-1. + x + y + z)*(-1. + 2.*x + 2.*y + 2.*z); + result[ip*10 + 1] = x*(-1. + 2.*x); + result[ip*10 + 2] = y*(-1. + 2.*y); + result[ip*10 + 3] = z*(-1. + 2.*z); + result[ip*10 + 4] = -4.*x*(-1. + x + y + z); + result[ip*10 + 5] = 4.*x*y; + result[ip*10 + 6] = -4.*y*(-1. + x + y + z); + result[ip*10 + 7] = -4.*z*(-1. + x + y + z); + result[ip*10 + 8] = 4.*x*z; + result[ip*10 + 9] = 4.*y*z; + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*30 + 0] = -3.+ 4.*x + 4.*y + 4.*z; + result[ip*30 + 1] = -3.+ 4.*x + 4.*y + 4.*z; + result[ip*30 + 2] = -3.+ 4.*x + 4.*y + 4.*z; + result[ip*30 + 3] = -1.+ 4.*x; + result[ip*30 + 4] = 0.; + result[ip*30 + 5] = 0.; + result[ip*30 + 6] = 0.; + result[ip*30 + 7] = -1.+ 4.*y; + result[ip*30 + 8] = 0.; + result[ip*30 + 9] = 0.; + result[ip*30 + 10] = 0.; + result[ip*30 + 11] = -1.+ 4.*z; + result[ip*30 + 12] = -4.*(-1.+ 2*x + y + z); + result[ip*30 + 13] = -4.*x; + result[ip*30 + 14] = -4.*x; + result[ip*30 + 15] = 4.*y; + result[ip*30 + 16] = 4.*x; + result[ip*30 + 17] = 0.; + result[ip*30 + 18] = -4.*y; + result[ip*30 + 19] = -4.*(-1.+ x + 2*y + z); + result[ip*30 + 20] = -4.*y; + result[ip*30 + 21] = -4.*z; + result[ip*30 + 22] = -4.*z; + result[ip*30 + 23] = -4.*(-1.+ x + y + 2*z); + result[ip*30 + 24] = 4.*z; + result[ip*30 + 25] = 0.; + result[ip*30 + 26] = 4.*x; + result[ip*30 + 27] = 0.; + result[ip*30 + 28] = 4.*z; + result[ip*30 + 29] = 4.*y; + } + } +}; + +class Basis_HEX_8 : public Basis +{ +public: + Basis_HEX_8() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = -1.0; p_coords[ 1] = -1.0; p_coords[ 2] = -1.0; + p_coords[ 3] = 1.0; p_coords[ 4] = -1.0; p_coords[ 5] = -1.0; + p_coords[ 6] = 1.0; p_coords[ 7] = 1.0; p_coords[ 8] = -1.0; + p_coords[ 9] = -1.0; p_coords[10] = 1.0; p_coords[11] = -1.0; + p_coords[12] = -1.0; p_coords[13] = -1.0; p_coords[14] = 1.0; + p_coords[15] = 1.0; p_coords[16] = -1.0; p_coords[17] = 1.0; + p_coords[18] = 1.0; p_coords[19] = 1.0; p_coords[20] = 1.0; + p_coords[21] = -1.0; p_coords[22] = 1.0; p_coords[23] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*8 + 0] = 0.125*(1.0 - x)*(1.0 - y)*(1.0 - z); + result[ip*8 + 1] = 0.125*(1.0 + x)*(1.0 - y)*(1.0 - z); + result[ip*8 + 2] = 0.125*(1.0 + x)*(1.0 + y)*(1.0 - z); + result[ip*8 + 3] = 0.125*(1.0 - x)*(1.0 + y)*(1.0 - z); + result[ip*8 + 4] = 0.125*(1.0 - x)*(1.0 - y)*(1.0 + z); + result[ip*8 + 5] = 0.125*(1.0 + x)*(1.0 - y)*(1.0 + z); + result[ip*8 + 6] = 0.125*(1.0 + x)*(1.0 + y)*(1.0 + z); + result[ip*8 + 7] = 0.125*(1.0 - x)*(1.0 + y)*(1.0 + z); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*24 + 0] = -(1.0 - y)*(1.0 - z)*0.125; + result[ip*24 + 1] = -(1.0 - x)*(1.0 - z)*0.125; + result[ip*24 + 2] = -(1.0 - x)*(1.0 - y)*0.125; + result[ip*24 + 3] = (1.0 - y)*(1.0 - z)*0.125; + result[ip*24 + 4] = -(1.0 + x)*(1.0 - z)*0.125; + result[ip*24 + 5] = -(1.0 + x)*(1.0 - y)*0.125; + result[ip*24 + 6] = (1.0 + y)*(1.0 - z)*0.125; + result[ip*24 + 7] = (1.0 + x)*(1.0 - z)*0.125; + result[ip*24 + 8] = -(1.0 + x)*(1.0 + y)*0.125; + result[ip*24 + 9] = -(1.0 + y)*(1.0 - z)*0.125; + result[ip*24 + 10] = (1.0 - x)*(1.0 - z)*0.125; + result[ip*24 + 11] = -(1.0 - x)*(1.0 + y)*0.125; + result[ip*24 + 12] = -(1.0 - y)*(1.0 + z)*0.125; + result[ip*24 + 13] = -(1.0 - x)*(1.0 + z)*0.125; + result[ip*24 + 14] = (1.0 - x)*(1.0 - y)*0.125; + result[ip*24 + 15] = (1.0 - y)*(1.0 + z)*0.125; + result[ip*24 + 16] = -(1.0 + x)*(1.0 + z)*0.125; + result[ip*24 + 17] = (1.0 + x)*(1.0 - y)*0.125; + result[ip*24 + 18] = (1.0 + y)*(1.0 + z)*0.125; + result[ip*24 + 19] = (1.0 + x)*(1.0 + z)*0.125; + result[ip*24 + 20] = (1.0 + x)*(1.0 + y)*0.125; + result[ip*24 + 21] = -(1.0 + y)*(1.0 + z)*0.125; + result[ip*24 + 22] = (1.0 - x)*(1.0 + z)*0.125; + result[ip*24 + 23] = (1.0 - x)*(1.0 + y)*0.125; + } + } +}; + +class Basis_HEX_27 : public Basis +{ +public: + Basis_HEX_27() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = -1.0; p_coords[ 1] = -1.0; p_coords[ 2] = -1.0; + p_coords[ 3] = 1.0; p_coords[ 4] = -1.0; p_coords[ 5] = -1.0; + p_coords[ 6] = 1.0; p_coords[ 7] = 1.0; p_coords[ 8] = -1.0; + p_coords[ 9] = -1.0; p_coords[10] = 1.0; p_coords[11] = -1.0; + p_coords[12] = -1.0; p_coords[13] = -1.0; p_coords[14] = 1.0; + p_coords[15] = 1.0; p_coords[16] = -1.0; p_coords[17] = 1.0; + p_coords[18] = 1.0; p_coords[19] = 1.0; p_coords[20] = 1.0; + p_coords[21] = -1.0; p_coords[22] = 1.0; p_coords[23] = 1.0; + p_coords[24] = 0.0; p_coords[25] = -1.0; p_coords[26] = -1.0; + p_coords[27] = 1.0; p_coords[28] = 0.0; p_coords[29] = -1.0; + p_coords[30] = 0.0; p_coords[31] = 1.0; p_coords[32] = -1.0; + p_coords[33] = -1.0; p_coords[34] = 0.0; p_coords[35] = -1.0; + p_coords[36] = -1.0; p_coords[37] = -1.0; p_coords[38] = 0.0; + p_coords[39] = 1.0; p_coords[40] = -1.0; p_coords[41] = 0.0; + p_coords[42] = 1.0; p_coords[43] = 1.0; p_coords[44] = 0.0; + p_coords[45] = -1.0; p_coords[46] = 1.0; p_coords[47] = 0.0; + p_coords[48] = 0.0; p_coords[49] = -1.0; p_coords[50] = 1.0; + p_coords[51] = 1.0; p_coords[52] = 0.0; p_coords[53] = 1.0; + p_coords[54] = 0.0; p_coords[55] = 1.0; p_coords[56] = 1.0; + p_coords[57] = -1.0; p_coords[58] = 0.0; p_coords[59] = 1.0; + p_coords[60] = 0.0; p_coords[61] = 0.0; p_coords[62] = 0.0; + p_coords[63] = 0.0; p_coords[64] = 0.0; p_coords[65] = -1.0; + p_coords[66] = 0.0; p_coords[67] = 0.0; p_coords[68] = 1.0; + p_coords[69] = -1.0; p_coords[70] = 0.0; p_coords[71] = 0.0; + p_coords[72] = 1.0; p_coords[73] = 0.0; p_coords[74] = 0.0; + p_coords[75] = 0.0; p_coords[76] = -1.0; p_coords[77] = 0.0; + p_coords[78] = 0.0; p_coords[79] = 1.0; p_coords[80] = 0.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*27 + 0] = 0.125*(-1. + x)*x*(-1. + y)*y*(-1. + z)*z; + result[ip*27 + 1] = 0.125*x*(1.+ x)*(-1. + y)*y*(-1. + z)*z; + result[ip*27 + 2] = 0.125*x*(1.+ x)*y*(1.+ y)*(-1. + z)*z; + result[ip*27 + 3] = 0.125*(-1. + x)*x*y*(1.+ y)*(-1. + z)*z; + result[ip*27 + 4] = 0.125*(-1. + x)*x*(-1. + y)*y*z*(1.+ z); + result[ip*27 + 5] = 0.125*x*(1.+ x)*(-1. + y)*y*z*(1.+ z); + result[ip*27 + 6] = 0.125*x*(1.+ x)*y*(1.+ y)*z*(1.+ z); + result[ip*27 + 7] = 0.125*(-1. + x)*x*y*(1.+ y)*z*(1.+ z); + result[ip*27 + 8] = 0.25*(1. - x)*(1. + x)*(-1. + y)*y*(-1. + z)*z; + result[ip*27 + 9] = 0.25*x*(1.+ x)*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*27 + 10] = 0.25*(1. - x)*(1. + x)*y*(1.+ y)*(-1. + z)*z; + result[ip*27 + 11] = 0.25*(-1. + x)*x*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*27 + 12] = 0.25*(-1. + x)*x*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*27 + 13] = 0.25*x*(1.+ x)*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*27 + 14] = 0.25*x*(1.+ x)*y*(1.+ y)*(1. - z)*(1. + z); + result[ip*27 + 15] = 0.25*(-1. + x)*x*y*(1.+ y)*(1. - z)*(1. + z); + result[ip*27 + 16] = 0.25*(1. - x)*(1. + x)*(-1. + y)*y*z*(1.+ z); + result[ip*27 + 17] = 0.25*x*(1.+ x)*(1. - y)*(1. + y)*z*(1.+ z); + result[ip*27 + 18] = 0.25*(1. - x)*(1. + x)*y*(1.+ y)*z*(1.+ z); + result[ip*27 + 19] = 0.25*(-1. + x)*x*(1. - y)*(1. + y)*z*(1.+ z); + result[ip*27 + 20] = (1. - x)*(1. + x)*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*27 + 21] = 0.5*(1. - x)*(1. + x)*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*27 + 22] = 0.5*(1. - x)*(1. + x)*(1. - y)*(1. + y)*z*(1.+ z); + result[ip*27 + 23] = 0.5*(-1. + x)*x*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*27 + 24] = 0.5*x*(1.+ x)*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*27 + 25] = 0.5*(1. - x)*(1. + x)*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*27 + 26] = 0.5*(1. - x)*(1. + x)*y*(1.+ y)*(1. - z)*(1. + z); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + result[ip*81 + 0] = (-0.125 + 0.25*x)*(-1. + y)*y*(-1. + z)*z; + result[ip*81 + 1] = (-1. + x)*x*(-0.125 + 0.25*y)*(-1. + z)*z; + result[ip*81 + 2] = (-1. + x)*x*(-1. + y)*y*(-0.125 + 0.25*z); + result[ip*81 + 3] = (0.125 + 0.25*x)*(-1. + y)*y*(-1. + z)*z; + result[ip*81 + 4] = x*(1. + x)*(-0.125 + 0.25*y)*(-1. + z)*z; + result[ip*81 + 5] = x*(1. + x)*(-1. + y)*y*(-0.125 + 0.25*z); + result[ip*81 + 6] = (0.125 + 0.25*x)*y*(1. + y)*(-1. + z)*z; + result[ip*81 + 7] = x*(1. + x)*(0.125 + 0.25*y)*(-1. + z)*z; + result[ip*81 + 8] = x*(1. + x)*y*(1. + y)*(-0.125 + 0.25*z); + result[ip*81 + 9] = (-0.125 + 0.25*x)*y*(1. + y)*(-1. + z)*z; + result[ip*81 + 10] = (-1. + x)*x*(0.125 + 0.25*y)*(-1. + z)*z; + result[ip*81 + 11] = (-1. + x)*x*y*(1. + y)*(-0.125 + 0.25*z); + result[ip*81 + 12] = (-0.125 + 0.25*x)*(-1. + y)*y*z*(1. + z); + result[ip*81 + 13] = (-1. + x)*x*(-0.125 + 0.25*y)*z*(1. + z); + result[ip*81 + 14] = (-1. + x)*x*(-1. + y)*y*(0.125 + 0.25*z); + result[ip*81 + 15] = (0.125 + 0.25*x)*(-1. + y)*y*z*(1. + z); + result[ip*81 + 16] = x*(1. + x)*(-0.125 + 0.25*y)*z*(1. + z); + result[ip*81 + 17] = x*(1. + x)*(-1. + y)*y*(0.125 + 0.25*z); + result[ip*81 + 18] = (0.125 + 0.25*x)*y*(1. + y)*z*(1. + z); + result[ip*81 + 19] = x*(1. + x)*(0.125 + 0.25*y)*z*(1. + z); + result[ip*81 + 20] = x*(1. + x)*y*(1. + y)*(0.125 + 0.25*z); + result[ip*81 + 21] = (-0.125 + 0.25*x)*y*(1. + y)*z*(1. + z); + result[ip*81 + 22] = (-1. + x)*x*(0.125 + 0.25*y)*z*(1. + z); + result[ip*81 + 23] = (-1. + x)*x*y*(1. + y)*(0.125 + 0.25*z); + result[ip*81 + 24] = -0.5*x*(-1. + y)*y*(-1. + z)*z; + result[ip*81 + 25] = (1. - x)*(1. + x)*(-0.25 + 0.5*y)*(-1. + z)*z; + result[ip*81 + 26] = (1. - x)*(1. + x)*(-1. + y)*y*(-0.25 + 0.5*z); + result[ip*81 + 27] = (0.25 + 0.5*x)*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*81 + 28] = x*(1. + x)*(-0.5*y)*(-1. + z)*z; + result[ip*81 + 29] = x*(1. + x)*(1. - y)*(1. + y)*(-0.25 + 0.5*z); + result[ip*81 + 30] = -0.5*x*y*(1. + y)*(-1. + z)*z; + result[ip*81 + 31] = (1. - x)*(1. + x)*(0.25 + 0.5*y)*(-1. + z)*z; + result[ip*81 + 32] = (1. - x)*(1. + x)*y*(1. + y)*(-0.25 + 0.5*z); + result[ip*81 + 33] = (-0.25 + 0.5*x)*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*81 + 34] = (-1. + x)*x*(-0.5*y)*(-1. + z)*z; + result[ip*81 + 35] = (-1. + x)*x*(1. - y)*(1. + y)*(-0.25 + 0.5*z); + result[ip*81 + 36] = (-0.25 + 0.5*x)*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*81 + 37] = (-1. + x)*x*(-0.25 + 0.5*y)*(1. - z)*(1. + z); + result[ip*81 + 38] = (-1. + x)*x*(-1. + y)*y*(-0.5*z); + result[ip*81 + 39] = (0.25 + 0.5*x)*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*81 + 40] = x*(1. + x)*(-0.25 + 0.5*y)*(1. - z)*(1. + z); + result[ip*81 + 41] = x*(1. + x)*(-1. + y)*y*(-0.5*z); + result[ip*81 + 42] = (0.25 + 0.5*x)*y*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 43] = x*(1. + x)*(0.25 + 0.5*y)*(1. - z)*(1. + z); + result[ip*81 + 44] = x*(1. + x)*y*(1. + y)*(-0.5*z); + result[ip*81 + 45] = (-0.25 + 0.5*x)*y*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 46] = (-1. + x)*x*(0.25 + 0.5*y)*(1. - z)*(1. + z); + result[ip*81 + 47] = (-1. + x)*x*y*(1. + y)*(-0.5*z); + result[ip*81 + 48] = -0.5*x*(-1. + y)*y*z*(1. + z); + result[ip*81 + 49] = (1. - x)*(1. + x)*(-0.25 + 0.5*y)*z*(1. + z); + result[ip*81 + 50] = (1. - x)*(1. + x)*(-1. + y)*y*(0.25 + 0.5*z); + result[ip*81 + 51] = (0.25 + 0.5*x)*(1. - y)*(1. + y)*z*(1. + z); + result[ip*81 + 52] = x*(1. + x)*(-0.5*y)*z*(1. + z); + result[ip*81 + 53] = x*(1. + x)*(1. - y)*(1. + y)*(0.25 + 0.5*z); + result[ip*81 + 54] = -0.5*x*y*(1. + y)*z*(1. + z); + result[ip*81 + 55] = (1. - x)*(1. + x)*(0.25 + 0.5*y)*z*(1. + z); + result[ip*81 + 56] = (1. - x)*(1. + x)*y*(1. + y)*(0.25 + 0.5*z); + result[ip*81 + 57] = (-0.25 + 0.5*x)*(1. - y)*(1. + y)*z*(1. + z); + result[ip*81 + 58] = (-1. + x)*x*(-0.5*y)*z*(1. + z); + result[ip*81 + 59] = (-1. + x)*x*(1. - y)*(1. + y)*(0.25 + 0.5*z); + result[ip*81 + 60] = -2.*x*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 61] = (1. - x)*(1. + x)*(-2.*y)*(1. - z)*(1. + z); + result[ip*81 + 62] = (1. - x)*(1. + x)*(1. - y)*(1. + y)*(-2.*z); + result[ip*81 + 63] = -x*(1. - y)*(1. + y)*(-1. + z)*z; + result[ip*81 + 64] = (1. - x)*(1. + x)*(-y)*(-1. + z)*z; + result[ip*81 + 65] = (1. - x)*(1. + x)*(1. - y)*(1. + y)*(-0.5 + z); + result[ip*81 + 66] = -x*(1. - y)*(1. + y)*z*(1. + z); + result[ip*81 + 67] = (1. - x)*(1. + x)*(-y)*z*(1. + z); + result[ip*81 + 68] = (1. - x)*(1. + x)*(1. - y)*(1. + y)*(0.5 + z); + result[ip*81 + 69] = (-0.5 + x)*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 70] = (-1. + x)*x*(-y)*(1. - z)*(1. + z); + result[ip*81 + 71] = (-1. + x)*x*(1. - y)*(1. + y)*(-z); + result[ip*81 + 72] = (0.5 + x)*(1. - y)*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 73] = x*(1. + x)*(-y)*(1. - z)*(1. + z); + result[ip*81 + 74] = x*(1. + x)*(1. - y)*(1. + y)*(-z); + result[ip*81 + 75] = -x*(-1. + y)*y*(1. - z)*(1. + z); + result[ip*81 + 76] = (1. - x)*(1. + x)*(-0.5 + y)*(1. - z)*(1. + z); + result[ip*81 + 77] = (1. - x)*(1. + x)*(-1. + y)*y*(-z); + result[ip*81 + 78] = -x*y*(1. + y)*(1. - z)*(1. + z); + result[ip*81 + 79] = (1. - x)*(1. + x)*(0.5 + y)*(1. - z)*(1. + z); + result[ip*81 + 80] = (1. - x)*(1. + x)*y*(1. + y)*(-z); + } + } +}; + +class Basis_WEDGE_6 : public Basis +{ +public: + Basis_WEDGE_6() : Basis(1) {} + + void nodal_parametric_coordinates(double* ATTR_RESTRICT p_coords) const + { + p_coords[ 0] = 0.0; p_coords[ 1] = 0.0; p_coords[ 2] = -1.0; + p_coords[ 3] = 1.0; p_coords[ 4] = 0.0; p_coords[ 5] = -1.0; + p_coords[ 6] = 0.0; p_coords[ 7] = 1.0; p_coords[ 8] = -1.0; + p_coords[ 9] = 0.0; p_coords[10] = 0.0; p_coords[11] = 1.0; + p_coords[12] = 1.0; p_coords[13] = 0.0; p_coords[14] = 1.0; + p_coords[15] = 0.0; p_coords[16] = 1.0; p_coords[17] = 1.0; + } + void shape_fcn(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for (int ip(0); ip < nint; ++ip) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + const double t = 1. - x - y; + + result[ip*6 + 0] = 0.5 * t * (1.0 - z); + result[ip*6 + 1] = 0.5 * x * (1.0 - z); + result[ip*6 + 2] = 0.5 * y * (1.0 - z); + result[ip*6 + 3] = 0.5 * t * (1.0 + z); + result[ip*6 + 4] = 0.5 * x * (1.0 + z); + result[ip*6 + 5] = 0.5 * y * (1.0 + z); + } + } + void shape_fcn_deriv(const int nint, const double* ATTR_RESTRICT p_coords, double* ATTR_RESTRICT result) const + { + for ( int ip(0); ip < nint; ++ip ) + { + const double x = p_coords[3*ip + 0]; + const double y = p_coords[3*ip + 1]; + const double z = p_coords[3*ip + 2]; + const double t = 1. - x - y; + + result[ip*18 + 0] = -0.5 * (1.0 - z); + result[ip*18 + 1] = -0.5 * (1.0 - z); + result[ip*18 + 2] = -0.5 * t; + result[ip*18 + 3] = 0.5 * (1.0 - z); + result[ip*18 + 4] = 0.; + result[ip*18 + 5] = -0.5 * x; + result[ip*18 + 6] = 0.; + result[ip*18 + 7] = 0.5 * (1.0 - z); + result[ip*18 + 8] = -0.5 * y; + result[ip*18 + 9] = -0.5 * (1.0 + z); + result[ip*18 + 10] = -0.5 * (1.0 + z); + result[ip*18 + 11] = 0.5 * t; + result[ip*18 + 12] = 0.5 * (1.0 + z); + result[ip*18 + 13] = 0.; + result[ip*18 + 14] = 0.5 * x; + result[ip*18 + 15] = 0.; + result[ip*18 + 16] = 0.5 * (1.0 + z); + result[ip*18 + 17] = 0.5 * y; + } + } +}; + +} // end namespace krino + +#endif // Akri_MasterElementBasis_h diff --git a/packages/krino/krino/master_element/Akri_MasterElementCalc.cpp b/packages/krino/krino/master_element/Akri_MasterElementCalc.cpp new file mode 100644 index 000000000000..fa29448343ac --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementCalc.cpp @@ -0,0 +1,456 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include + +namespace krino { + +void +MasterElementCalc::scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const int ndims, + const int nnodes, + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) //: (nvec,nelem,nint) +{ + for ( int ip(0); ip < nint; ++ip ) { + for ( int elem(0); elem < nelem; ++elem) { + for ( int dim(0); dim < ndims; ++dim ) { + double & val = vector[ip*ndims + dim]; + val = 0.0; + for ( int node(0); node < nnodes; ++node ) { + val += gradop[( (ip*nelem + elem)*nnodes + node)*ndims + dim] * sfield[ node ]; + } + } + } + } +} + +void +MasterElementCalc::determinant( + const int num_elem_dims, + const int num_coord_dims, + const int nint, + const int npe_g, + const double* deriv_g, // (num_elem_dims,npe_g,nint) + const int nelem, + const double* coords, // (num_coord_dims,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) // (nelem) +{ + if (num_elem_dims != num_coord_dims) + { + if (2 == num_elem_dims) + { + ThrowAssert(3 == num_coord_dims); + MasterElementCalc::determinant_element2d_in_3d(nint, npe_g, deriv_g, nelem, coords, det_J, error); + } + else + { + ThrowAssert(1 == num_elem_dims); + if (2 == num_coord_dims) + { + MasterElementCalc::determinant_element1d_in_2d(nint, npe_g, deriv_g, nelem, coords, det_J, error); + } + else + { + MasterElementCalc::determinant_element1d_in_3d(nint, npe_g, deriv_g, nelem, coords, det_J, error); + } + } + } + else + { + ThrowAssert(num_elem_dims >= 2 && num_elem_dims <= 3); + if (2 == num_elem_dims) MasterElementCalc::determinant_2d(nint, npe_g, deriv_g, nelem, coords, det_J, error); + else MasterElementCalc::determinant_3d(nint, npe_g, deriv_g, nelem, coords, det_J, error); + } +} + +void +MasterElementCalc::gradient_operator( + const int num_elem_dims, + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) +{ + ThrowAssert(num_elem_dims >= 2 && num_elem_dims <= 3); + if (2 == num_elem_dims) gradient_operator_2d(nint, npe_g, deriv_g, npe_f, deriv_f, nelem, coords, gradop, det_J, error); + else gradient_operator_3d(nint, npe_g, deriv_g, npe_f, deriv_f, nelem, coords, gradop, det_J, error); +} + +void +MasterElementCalc::determinant_2d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error) +{ + auto c2d = [coords,npe](int d, int i, int e) { return coords[d + 2*(i + npe*e)]; }; + auto d2d = [deriv,npe](int d, int n, int q) { return deriv[d + 2*(n + npe*q)]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds0 = 0.; + double dx_ds1 = 0.; + double dy_ds0 = 0.; + double dy_ds1 = 0.; + + for ( int kn(0); kn < npe; ++kn ) { + dx_ds0 += d2d(0,kn,ki)*c2d(0,kn,ke); + dx_ds1 += d2d(1,kn,ki)*c2d(0,kn,ke); + + dy_ds0 += d2d(0,kn,ki)*c2d(1,kn,ke); + dy_ds1 += d2d(1,kn,ki)*c2d(1,kn,ke); + } + + detj(ke,ki) = dx_ds0*dy_ds1 - dy_ds0*dx_ds1; + + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + } + } +} + +void +MasterElementCalc::determinant_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error) +{ + auto c3d = [coords,npe](int d, int i, int e) { return coords[d + 3*(i + npe*e)]; }; + auto d3d = [deriv,npe](int d, int n, int q) { return deriv[d + 3*(n + npe*q)]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds0 = 0.; + double dx_ds1 = 0.; + double dx_ds2 = 0.; + double dy_ds0 = 0.; + double dy_ds1 = 0.; + double dy_ds2 = 0.; + double dz_ds0 = 0.; + double dz_ds1 = 0.; + double dz_ds2 = 0.; + + for ( int kn(0); kn < npe; ++kn ) { + dx_ds0 += d3d(0,kn,ki)*c3d(0,kn,ke); + dx_ds1 += d3d(1,kn,ki)*c3d(0,kn,ke); + dx_ds2 += d3d(2,kn,ki)*c3d(0,kn,ke); + + dy_ds0 += d3d(0,kn,ki)*c3d(1,kn,ke); + dy_ds1 += d3d(1,kn,ki)*c3d(1,kn,ke); + dy_ds2 += d3d(2,kn,ki)*c3d(1,kn,ke); + + dz_ds0 += d3d(0,kn,ki)*c3d(2,kn,ke); + dz_ds1 += d3d(1,kn,ki)*c3d(2,kn,ke); + dz_ds2 += d3d(2,kn,ki)*c3d(2,kn,ke); + } + + detj(ke,ki) = dx_ds0*( dy_ds1*dz_ds2 - dz_ds1*dy_ds2 ) + + dy_ds0*( dz_ds1*dx_ds2 - dx_ds1*dz_ds2 ) + + dz_ds0*( dx_ds1*dy_ds2 - dy_ds1*dx_ds2 ); + + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + } + } +} + +void +MasterElementCalc::determinant_element2d_in_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error) +{ + auto c3d = [coords,npe](int d, int i, int e) { return coords[d + 3*(i + npe*e)]; }; + auto d2d = [deriv,npe](int d, int n, int q) { return deriv[d + 2*(n + npe*q)]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds0 = 0.; + double dx_ds1 = 0.; + double dy_ds0 = 0.; + double dy_ds1 = 0.; + double dz_ds0 = 0.; + double dz_ds1 = 0.; + + for ( int kn(0); kn < npe; ++kn ) { + dx_ds0 += d2d(0,kn,ki)*c3d(0,kn,ke); + dx_ds1 += d2d(1,kn,ki)*c3d(0,kn,ke); + + dy_ds0 += d2d(0,kn,ki)*c3d(1,kn,ke); + dy_ds1 += d2d(1,kn,ki)*c3d(1,kn,ke); + + dz_ds0 += d2d(0,kn,ki)*c3d(2,kn,ke); + dz_ds1 += d2d(1,kn,ki)*c3d(2,kn,ke); + } + + const double detXY = dx_ds0*dy_ds1 - dx_ds1*dy_ds0; + const double detYZ = dy_ds0*dz_ds1 - dy_ds1*dz_ds0; + const double detXZ =-dx_ds0*dz_ds1 + dx_ds1*dz_ds0; + + detj(ke,ki) = std::sqrt(detXY*detXY + detYZ*detYZ + detXZ*detXZ); + + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + } + } +} + +void +MasterElementCalc::determinant_element1d_in_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error) +{ + auto c3d = [coords,npe](int d, int i, int e) { return coords[d + 3*(i + npe*e)]; }; + auto d1d = [deriv,npe](int d, int n, int q) { return deriv[d + n + npe*q]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds = 0.; + double dy_ds = 0.; + double dz_ds = 0.; + + for ( int kn(0); kn < npe; ++kn ) { + dx_ds += d1d(0,kn,ki)*c3d(0,kn,ke); + dy_ds += d1d(0,kn,ki)*c3d(1,kn,ke); + dz_ds += d1d(0,kn,ki)*c3d(2,kn,ke); + } + + detj(ke,ki) = std::sqrt(dx_ds*dx_ds + dy_ds*dy_ds + dz_ds*dz_ds); + + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + } + } +} + +void +MasterElementCalc::determinant_element1d_in_2d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error) +{ + auto c2d = [coords,npe](int d, int i, int e) { return coords[d + 2*(i + npe*e)]; }; + auto d1d = [deriv,npe](int d, int n, int q) { return deriv[d + n + npe*q]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds = 0.; + double dy_ds = 0.; + + for ( int kn(0); kn < npe; ++kn ) { + dx_ds += d1d(0,kn,ki)*c2d(0,kn,ke); + dy_ds += d1d(0,kn,ki)*c2d(1,kn,ke); + } + + detj(ke,ki) = std::sqrt(dx_ds*dx_ds + dy_ds*dy_ds); + + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + } + } +} + +void +MasterElementCalc::gradient_operator_2d( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) +{ + auto c2d = [coords,npe_g](int d, int i, int e) { return coords[d + 2*(i + npe_g*e)]; }; + auto d2d = [deriv_g,npe_g](int d, int n, int q) { return deriv_g[d + 2*(n + npe_g*q)]; }; + auto d2df = [deriv_f,npe_f](int d, int n, int q) { return deriv_f[d + 2*(n + npe_f*q)]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + auto g2d = [gradop,npe_f,nelem](int d, int n, int e, int q) -> double& { return gradop[d + 2*(n + npe_f*(e+nelem*q))]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds0 = 0.; + double dx_ds1 = 0.; + double dy_ds0 = 0.; + double dy_ds1 = 0.; + + for ( int kn(0); kn < npe_g; ++kn ) { + dx_ds0 = dx_ds0+d2d(0,kn,ki)*c2d(0,kn,ke); + dx_ds1 = dx_ds1+d2d(1,kn,ki)*c2d(0,kn,ke); + + dy_ds0 = dy_ds0+d2d(0,kn,ki)*c2d(1,kn,ke); + dy_ds1 = dy_ds1+d2d(1,kn,ki)*c2d(1,kn,ke); + } + + detj(ke,ki) = dx_ds0*dy_ds1 - dy_ds0*dx_ds1; + + double denom = 0.0; + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + else + { + denom = 1./detj(ke,ki); + } + + // compute the gradient operators at the integration station - + for ( int kn(0); kn < npe_f; ++kn ) { + g2d(0,kn,ki,ke) = denom * ( d2df(0,kn,ki)*dy_ds1 - d2df(1,kn,ki)*dy_ds0 ); + g2d(1,kn,ki,ke) = denom * ( d2df(1,kn,ki)*dx_ds0 - d2df(0,kn,ki)*dx_ds1 ); + } + } + } +} + +void +MasterElementCalc::gradient_operator_3d( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) +{ + auto c3d = [coords,npe_g](int d, int i, int e) { return coords[d + 3*(i + npe_g*e)]; }; + auto d3d = [deriv_g,npe_g](int d, int n, int q) { return deriv_g[d + 3*(n + npe_g*q)]; }; + auto d3df = [deriv_f,npe_f](int d, int n, int q) { return deriv_f[d + 3*(n + npe_f*q)]; }; + auto detj = [det_J,nelem](int e, int q) -> double& { return det_J[e+nelem*q]; }; + auto g3d = [gradop,npe_f,nelem](int d, int n, int e, int q) -> double& { return gradop[d + 3*(n + npe_f*(e+nelem*q))]; }; + + for (int elem(0); elem < nelem; ++elem) error[elem] = 0.; + + for (int ke(0); ke < nelem; ++ke) { + for ( int ki(0); ki < nint; ++ki ) { + double dx_ds0 = 0.; + double dx_ds1 = 0.; + double dx_ds2 = 0.; + double dy_ds0 = 0.; + double dy_ds1 = 0.; + double dy_ds2 = 0.; + double dz_ds0 = 0.; + double dz_ds1 = 0.; + double dz_ds2 = 0.; + + for ( int kn(0); kn < npe_g; ++kn ) { + dx_ds0 = dx_ds0+d3d(0,kn,ki)*c3d(0,kn,ke); + dx_ds1 = dx_ds1+d3d(1,kn,ki)*c3d(0,kn,ke); + dx_ds2 = dx_ds2+d3d(2,kn,ki)*c3d(0,kn,ke); + + dy_ds0 = dy_ds0+d3d(0,kn,ki)*c3d(1,kn,ke); + dy_ds1 = dy_ds1+d3d(1,kn,ki)*c3d(1,kn,ke); + dy_ds2 = dy_ds2+d3d(2,kn,ki)*c3d(1,kn,ke); + + dz_ds0 = dz_ds0+d3d(0,kn,ki)*c3d(2,kn,ke); + dz_ds1 = dz_ds1+d3d(1,kn,ki)*c3d(2,kn,ke); + dz_ds2 = dz_ds2+d3d(2,kn,ki)*c3d(2,kn,ke); + } + + detj(ke,ki) = dx_ds0*( dy_ds1*dz_ds2 - dz_ds1*dy_ds2 ) + + dy_ds0*( dz_ds1*dx_ds2 - dx_ds1*dz_ds2 ) + + dz_ds0*( dx_ds1*dy_ds2 - dy_ds1*dx_ds2 ); + + double denom = 0.0; + if ( detj(ke,ki) <= 0. ) + { + error[ke] = 1.; + } + else + { + denom = 1./detj(ke,ki); + } + + // compute the gradient operators at the integration station - + for ( int kn(0); kn < npe_f; ++kn ) { + g3d(0,kn,ki,ke) = denom * + ( d3df(0,kn,ki)*(dy_ds1*dz_ds2 - dz_ds1*dy_ds2) + + d3df(1,kn,ki)*(dz_ds0*dy_ds2 - dy_ds0*dz_ds2) + + d3df(2,kn,ki)*(dy_ds0*dz_ds1 - dz_ds0*dy_ds1) ); + + g3d(1,kn,ki,ke) = denom * + ( d3df(0,kn,ki)*(dz_ds1*dx_ds2 - dx_ds1*dz_ds2) + + d3df(1,kn,ki)*(dx_ds0*dz_ds2 - dz_ds0*dx_ds2) + + d3df(2,kn,ki)*(dz_ds0*dx_ds1 - dx_ds0*dz_ds1) ); + + g3d(2,kn,ki,ke) = denom * + ( d3df(0,kn,ki)*(dx_ds1*dy_ds2 - dy_ds1*dx_ds2) + + d3df(1,kn,ki)*(dy_ds0*dx_ds2 - dx_ds0*dy_ds2) + + d3df(2,kn,ki)*(dx_ds0*dy_ds1 - dy_ds0*dx_ds1) ); + } + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/master_element/Akri_MasterElementCalc.hpp b/packages/krino/krino/master_element/Akri_MasterElementCalc.hpp new file mode 100644 index 000000000000..f5d99e687f9f --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementCalc.hpp @@ -0,0 +1,122 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElementCalc_h +#define Akri_MasterElementCalc_h + +namespace krino { + +class MasterElementCalc +{ +public: + static void scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const int ndims, + const int nnodes, + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ); //: (nvec,nelem,nint) + + static void determinant( + const int num_elem_dims, + const int num_coord_dims, + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error ); // (nelem) + + static void gradient_operator( + const int num_elem_dims, + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void determinant_2d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error); // (nelem) + static void determinant_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void determinant_element2d_in_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void determinant_element1d_in_3d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void determinant_element1d_in_2d( + const int nint, + const int npe, + const double* deriv, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void gradient_operator_2d( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error); // (nelem) + + static void gradient_operator_3d( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error); // (nelem) +}; + +} // end namespace krino + +#endif // Akri_MasterElementCalc_h diff --git a/packages/krino/krino/master_element/Akri_MasterElementHybrid.cpp b/packages/krino/krino/master_element/Akri_MasterElementHybrid.cpp new file mode 100644 index 000000000000..d8b7f86c13b7 --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementHybrid.cpp @@ -0,0 +1,181 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include // for get_cell_topology +#include + +#ifdef __INTEL_COMPILER +#include +#else +//FieldContainer has shadowed variables +//this disables the checking on GCC only +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#include +#pragma GCC diagnostic pop +#endif +#include +#include +#include +#include +#include +#include + +namespace krino { + +MasterElementHybrid::MasterElementHybrid( + stk::topology topology, + std::unique_ptr basis) +: m_topology(topology), + m_Basis(std::move(basis)) +{ + // set the cubature + Intrepid::DefaultCubatureFactory cubatureFactory; + Teuchos::RCP> intrepidCubature = cubatureFactory.create(stk::mesh::get_cell_topology(topology), 2*m_Basis->degree()); + m_numIntgPts = intrepidCubature->getNumPoints(); + + m_numNodes = topology.num_nodes(); + m_numElemDims = intrepidCubature->getDimension(); + + // Allocate reference data + m_shapeFuncs.resize(m_numIntgPts*m_numNodes); + m_pointGrads.resize(m_numIntgPts*m_numNodes*m_numElemDims ); + m_refPoints.resize(m_numIntgPts*m_numElemDims); + m_refWeights.resize(m_numIntgPts); + m_refCoords.resize(m_numNodes*m_numElemDims); + + // retrieve the cubature points and weights + std::vector refPointsDims = {m_numIntgPts, m_numElemDims}; + Intrepid::FieldContainer refPointsFC( refPointsDims, m_refPoints.data() ); + std::vector refWeightsDims = {m_numIntgPts}; + Intrepid::FieldContainer refWeightsFC( refWeightsDims, m_refWeights.data() ); + intrepidCubature->getCubature(refPointsFC, refWeightsFC); + + // compute the reference values and gradients at the integration points + m_Basis->shape_fcn(m_numIntgPts, m_refPoints.data(), m_shapeFuncs.data()); + m_Basis->shape_fcn_deriv(m_numIntgPts, m_refPoints.data(), m_pointGrads.data()); + m_Basis->nodal_parametric_coordinates(m_refCoords.data()); + + m_centroidParCoords.resize(m_numElemDims, 0.); + for(int n=0; n < m_numNodes; ++n) + { + for(int d=0; d < m_numElemDims; ++d) + { + m_centroidParCoords[d] += m_refCoords[n*m_numElemDims + d]; + } + } +} + +void +MasterElementHybrid::determinant( + const int numCoordDims, + const int nelem, + const double* coords, // (numCoordDims,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const // (nelem) +{ + MasterElementCalc::determinant(m_numElemDims, numCoordDims, m_numIntgPts, m_numNodes, m_pointGrads.data(), nelem, coords, det_J, error); +} + +void +MasterElementHybrid::shape_fcn( + const int nint, // returns array(npe,nint) + const double* p_coords, + double* result) const +{ + m_Basis->shape_fcn(nint, p_coords, result); +} + +void +MasterElementHybrid::shape_fcn_deriv( + const int nint, + const double* p_coords, + double* result ) const +{ + m_Basis->shape_fcn_deriv(nint, p_coords, result); +} + + +void +MasterElementHybrid::interpolate_point( + const int npar_coord, + const double * par_coord, // (npar_coord) + const int ncomp_field, + const double * field, // (ncomp_field,num_nodes) + double * result ) const // (ncomp_field) +{ + std::vector shape(m_numNodes); + shape_fcn(1, par_coord, shape.data()); + for ( int comp(0); comp < ncomp_field; ++comp ) { + result[ comp ] = 0.0; + for ( int node(0); node < m_numNodes; ++node ) { + result[ comp ] += shape[node] * field[ ncomp_field * node + comp ]; + } + } +} + +void +MasterElementHybrid::scalar_gradient( + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const //: (nvec,nelem,nint) +{ + MasterElementCalc::scalar_gradient(m_numIntgPts, nelem, m_numElemDims, m_numNodes, gradop, det_J, sfield, vector); +} + +void +MasterElementHybrid::scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const //: (nvec,nelem,nint) +{ + MasterElementCalc::scalar_gradient(nint, nelem, m_numElemDims, m_numNodes, gradop, det_J, sfield, vector); +} + +void +MasterElementHybrid::determinant( + const int numCoordDims, + const int nint, + const int npe_g, + const double* deriv_g, // (m_numElemDims,npe_g,nint) + const int nelem, + const double* coords, // (numCoordDims,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const // (nelem) +{ + MasterElementCalc::determinant(m_numElemDims, numCoordDims, nint, npe_g, deriv_g, nelem, coords, det_J, error); +} + +void +MasterElementHybrid::gradient_operator( + const int numCoordDims, + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) const +{ + ThrowRequireMsg(m_numElemDims == numCoordDims, "MasterElementHybrid::gradient_operator does not support lower rank elements in higher dimensions (e.g. BAR,QUAD,TRI in 3D)."); + MasterElementCalc::gradient_operator(m_numElemDims, nint, npe_g, deriv_g, npe_f, deriv_f, nelem, coords, gradop, det_J, error); +} + +} // namespace krino diff --git a/packages/krino/krino/master_element/Akri_MasterElementHybrid.hpp b/packages/krino/krino/master_element/Akri_MasterElementHybrid.hpp new file mode 100644 index 000000000000..e0bac17fb04b --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementHybrid.hpp @@ -0,0 +1,137 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElementHybrid_h +#define Akri_MasterElementHybrid_h + +#include +#include +#include + +namespace krino { class Basis; } + +namespace krino { + +class MasterElementHybrid +{ +public: + static const MasterElementHybrid & getMasterElement(stk::topology t); + + MasterElementHybrid( + stk::topology topology, + std::unique_ptr basis); + + // Copy and assignment are not allowed + MasterElementHybrid( const MasterElementHybrid & ) = delete; + MasterElementHybrid & operator=( const MasterElementHybrid & ) = delete; + + stk::topology get_topology() const { return m_topology; } + unsigned topology_dimension() const { return m_topology.dimension(); } + + // returns the number of integration points + unsigned num_intg_pts() const { return m_numIntgPts; } + + // returns the number of nodes + unsigned num_nodes() const { return m_numNodes; } + + //: Query the integration weights + const double* intg_weights() const { return m_refWeights.data(); } + + //: Query the integration points/stations + const double* intg_pt_locations() const { return m_refPoints.data(); } + + const double * nodal_parametric_coordinates() const { return m_refCoords.data(); } + const double * centroid_parametric_coordinates() const { return m_centroidParCoords.data(); } + + void determinant( + const int numCoordDims, + const int nelem, + const double* coords, // (numCoordDims,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const; // (nelem) + void determinant( + const int numCoordDims, + const int nint, + const int npe_g, + const double* deriv_g, // (m_numElemDims,npe_g,nint) + const int nelem, + const double* coords, // (numCoordDims,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const ; // (nelem) + + //: Returns the values of the nodal interpolation shape functions + //: at the integration stations. + const double* shape_fcn() const { return m_shapeFuncs.data(); } + void shape_fcn( + const int nint, // returns array(npe,nint) + const double* p_coords, + double* result) const; + + //: Returns the derivatives of the nodal interpolation shape functions + //: with respect to the local parametric coordinates at the integration + //: stations. + const double* shape_fcn_deriv() const { return m_pointGrads.data(); } + void shape_fcn_deriv( + const int nint, + const double* p_coords, + double* result ) const; + + void interpolate_point( + const int npar_coord, + const double * par_coord, // (npar_coord) + const int ncomp_field, + const double * field, // (ncomp_field,num_nodes) + double * result ) const; // (ncomp_field) + + void gradient_operator( + const int numCoordDims, + const int nint, + const int npe_g, + const double* deriv_g, // (numElemDims,npe_g,nint) + const int npe_f, + const double* deriv_f, // (numElemDims,npe_f,nint) + const int nelem, + const double* coords, // (numElemDims,npe,nelem) + double* gradop, // (numElemDims,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) const ; + + void scalar_gradient( + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const ; //: (nvec,nelem,nint) + void scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const ; //: (nvec,nelem,nint) + +private: + stk::topology m_topology; + int m_numNodes; + int m_numElemDims; + int m_numIntgPts; + + std::unique_ptr m_Basis; + + // Local FieldContainers + std::vector m_shapeFuncs; + std::vector m_pointGrads; + std::vector m_refPoints; + std::vector m_refWeights; + std::vector m_refCoords; + std::vector m_centroidParCoords; +}; + +} // end namespace krino + +#endif // Akri_MasterElementHybrid_h diff --git a/packages/krino/krino/master_element/Akri_MasterElementIntrepid.cpp b/packages/krino/krino/master_element/Akri_MasterElementIntrepid.cpp new file mode 100644 index 000000000000..3b026bb7189c --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementIntrepid.cpp @@ -0,0 +1,287 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include "Akri_MasterElementCalc.hpp" + +#ifdef __INTEL_COMPILER +#include +#else +//FieldContainer has shadowed variables +//this disables the checking on GCC only +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#include +#pragma GCC diagnostic pop +#endif + +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include // for get_cell_topology + +namespace krino { + +const MasterElementIntrepid & +MasterElementIntrepid::getMasterElement(stk::topology t, const unsigned spatial_dimension) +{ + static std::vector> all_master_elems(stk::topology::BEGIN_TOPOLOGY + stk::topology::NUM_TOPOLOGIES); + std::unique_ptr & master_elem = all_master_elems[t()]; + if (nullptr == master_elem.get()) + { + std::unique_ptr>> basis; + switch(t()) + { + case stk::topology::LINE_2: + basis = std::make_unique>>(); + break; + case stk::topology::LINE_3: + basis = std::make_unique>>(2, Intrepid::POINTTYPE_SPECTRAL); + break; + case stk::topology::TRI_3: + basis = std::make_unique>>(); + break; + case stk::topology::TRI_6: + basis = std::make_unique>>(); + break; + case stk::topology::QUAD_4: + basis = std::make_unique>>(); + break; + case stk::topology::QUAD_9: + basis = std::make_unique>>(); + break; + case stk::topology::TRI_3_2D: + basis = std::make_unique>>(); + break; + case stk::topology::TRI_6_2D: + basis = std::make_unique>>(); + break; + case stk::topology::QUAD_4_2D: + basis = std::make_unique>>(); + break; + case stk::topology::QUAD_9_2D: + basis = std::make_unique>>(); + break; + case stk::topology::TET_4: + basis = std::make_unique>>(); + break; + case stk::topology::TET_10: + basis = std::make_unique>>(); + break; + case stk::topology::HEX_8: + basis = std::make_unique>>(); + break; + case stk::topology::HEX_27: + basis = std::make_unique>>(); + break; + default: + throw std::runtime_error("Element topology not found in MasterElementIntrepid::build: " + t.name()); + break; + } + master_elem = std::make_unique(t, std::move(basis), spatial_dimension); + } + return *master_elem; +} + +MasterElementIntrepid::MasterElementIntrepid( + stk::topology topology, + std::unique_ptr > > basis, + unsigned spatial_dimension) +: m_topology(topology), + m_numCoordDims(spatial_dimension), + m_intrepidBasis(std::move(basis)) +{ + shards::CellTopology cellType = stk::mesh::get_cell_topology(topology); + + // set the cubature + Intrepid::DefaultCubatureFactory cubatureFactory; + Teuchos::RCP> intrepidCubature = cubatureFactory.create(cellType, 2*m_intrepidBasis->getDegree()); + m_numIntgPts = intrepidCubature->getNumPoints(); + + m_numNodes = topology.num_nodes(); + m_numElemDims = intrepidCubature->getDimension(); + + // Allocate reference data + m_shapeFuncs.resize(m_numIntgPts*m_numNodes); + m_pointGrads.resize(m_numIntgPts*m_numNodes*m_numElemDims ); + m_refPoints.resize(m_numIntgPts*m_numElemDims); + m_refWeights.resize(m_numIntgPts); + m_refCoords.resize(m_numNodes*m_numElemDims); + + // retrieve the cubature points and weights + std::vector refPointsDims = {m_numIntgPts, m_numElemDims}; + Intrepid::FieldContainer refPointsFC( refPointsDims, m_refPoints.data() ); + std::vector refWeightsDims = {m_numIntgPts}; + Intrepid::FieldContainer refWeightsFC( refWeightsDims, m_refWeights.data() ); + intrepidCubature->getCubature(refPointsFC, refWeightsFC); + + // compute the refernce values and gradients at the integration points + Intrepid::FieldContainer pointVals(m_numNodes, m_numIntgPts); + Intrepid::FieldContainer pointGrads(m_numNodes, m_numIntgPts, m_numElemDims); + m_intrepidBasis->getValues(pointVals, refPointsFC, Intrepid::OPERATOR_VALUE); + m_intrepidBasis->getValues(pointGrads, refPointsFC, Intrepid::OPERATOR_GRAD); + + // re-order shape functions for consistency with other master elements + for ( int ip(0); ip < m_numIntgPts; ++ip ) { + for ( int node(0); node < m_numNodes; ++node ) { + m_shapeFuncs[ip*m_numNodes + node] = pointVals(node, ip); + } + } + for ( int ip(0); ip < m_numIntgPts; ++ip ) { + for ( int node(0); node < m_numNodes; ++node ) { + for ( int dim(0); dim < m_numElemDims; ++dim ) { + m_pointGrads[(ip*m_numNodes + node)*m_numElemDims + dim] = pointGrads(node, ip, dim); + } + } + } + + for ( int node(0); node < m_numNodes; ++node ) { + const double * node_coords = Intrepid::CellTools::getReferenceNode( cellType, node ); + for ( int dim(0); dim < m_numElemDims; ++dim ) { + m_refCoords[node*m_numElemDims + dim] = node_coords[dim]; + } + } +} + +void +MasterElementIntrepid::determinant( + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const // (nelem) +{ + determinant(m_numIntgPts, m_numNodes, m_pointGrads.data(), nelem, coords, det_J, error); +} + +void +MasterElementIntrepid::shape_fcn( + const int nint, // returns array(npe,nint) + const double* p_coords, + double* result) const +{ + Intrepid::FieldContainer pointVals(m_numNodes, nint); + + // create the pcoordVec FC from the p_coords ptr and it's dimensions + std::vector pcoordDims = { nint, m_numElemDims }; + Intrepid::FieldContainer pcoordVec( pcoordDims, const_cast< double * >(p_coords) ); + + // compute the shape function values at the integration points + m_intrepidBasis->getValues(pointVals, pcoordVec, Intrepid::OPERATOR_VALUE); + + // re-order shape functions for consistency with other master elements + for ( int ip(0); ip < nint; ++ip ) { + for ( int node(0); node < m_numNodes; ++node ) { + result[ip*m_numNodes + node] = pointVals(node,ip); + } + } +} + +void +MasterElementIntrepid::shape_fcn_deriv( + const int nint, + const double* p_coords, + double* result ) const +{ + Intrepid::FieldContainer resultVec(m_numNodes, nint, m_numElemDims); + + // create the pcoordVec FC from the p_coords ptr and it's dimensions + std::vector pcoordDims = { nint, m_numElemDims }; + Intrepid::FieldContainer pcoordVec( pcoordDims, const_cast< double * >(p_coords) ); + + m_intrepidBasis->getValues(resultVec, pcoordVec, Intrepid::OPERATOR_GRAD); + + // re-order shape functions for consistency with other master elements + for ( int ip(0); ip < nint; ++ip ) { + for ( int node(0); node < m_numNodes; ++node ) { + for ( int dim(0); dim < m_numElemDims; ++dim ) { + result[(ip*m_numNodes + node)*m_numElemDims + dim] = resultVec(node,ip,dim); + } + } + } +} + +void +MasterElementIntrepid::interpolate_point( + const int npar_coord, + const double * par_coord, // (npar_coord) + const int ncomp_field, + const double * field, // (num_nodes,ncomp_field) + double * result ) const // (ncomp_field) +{ + std::vector shape(m_numNodes); + shape_fcn(1, par_coord, shape.data()); + for ( int comp(0); comp < ncomp_field; ++comp ) { + result[ comp ] = 0.0; + for ( int node(0); node < m_numNodes; ++node ) { + result[ comp ] += shape[node] * field[ m_numNodes * comp + node ]; + } + } +} + +void +MasterElementIntrepid::scalar_gradient( + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const //: (nvec,nelem,nint) +{ + MasterElementCalc::scalar_gradient(m_numIntgPts, nelem, m_numElemDims, m_numNodes, gradop, det_J, sfield, vector); +} + +void +MasterElementIntrepid::scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const //: (nvec,nelem,nint) +{ + MasterElementCalc::scalar_gradient(nint, nelem, m_numElemDims, m_numNodes, gradop, det_J, sfield, vector); +} + +void +MasterElementIntrepid::determinant( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const // (nelem) +{ + MasterElementCalc::determinant(m_numElemDims, m_numCoordDims, nint, npe_g, deriv_g, nelem, coords, det_J, error); +} + +void +MasterElementIntrepid::gradient_operator( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) const +{ + ThrowRequireMsg(m_numElemDims == m_numCoordDims, "MasterElementHybrid::gradient_operator does not support lower rank elements in higher dimensions (e.g. BAR,QUAD,TRI in 3D)."); + MasterElementCalc::gradient_operator(m_numElemDims, nint, npe_g, deriv_g, npe_f, deriv_f, nelem, coords, gradop, det_J, error); +} + +} // namespace krino diff --git a/packages/krino/krino/master_element/Akri_MasterElementIntrepid.hpp b/packages/krino/krino/master_element/Akri_MasterElementIntrepid.hpp new file mode 100644 index 000000000000..c35933b1d337 --- /dev/null +++ b/packages/krino/krino/master_element/Akri_MasterElementIntrepid.hpp @@ -0,0 +1,135 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MasterElementIntrepid_h +#define Akri_MasterElementIntrepid_h + +#include +#include + +namespace Intrepid { template class FieldContainer; } +namespace Intrepid { template class Basis; } + +namespace krino { + +class MasterElementIntrepid +{ +public: + MasterElementIntrepid( + stk::topology topology, + std::unique_ptr > > basis, + unsigned spatial_dimension); + + // Copy and assignment are not allowed + MasterElementIntrepid( const MasterElementIntrepid & ) = delete; + MasterElementIntrepid & operator=( const MasterElementIntrepid & ) = delete; + + static const MasterElementIntrepid & getMasterElement(stk::topology t, const unsigned spatial_dimension); + + stk::topology get_topology() const { return m_topology; } + unsigned dimension() const { return m_topology.dimension(); } + + // returns the number of integration points + unsigned num_intg_pts() const { return m_numIntgPts; } + + // returns the number of nodes + unsigned num_nodes() const { return m_numNodes; } + + //: Query the integration weights + const double* intg_weights() const { return m_refWeights.data(); } + + //: Query the integration points/stations + const double* intg_pt_locations() const { return m_refPoints.data(); } + + const double * nodal_parametric_coordinates() const { return m_refCoords.data(); } + + void determinant( + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const; // (nelem) + void determinant( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* det_J, // (nelem,nint) + double* error ) const ; // (nelem) + + //: Returns the values of the nodal interpolation shape functions + //: at the integration stations. + const double* shape_fcn() const { return m_shapeFuncs.data(); } + void shape_fcn( + const int nint, // returns array(npe,nint) + const double* p_coords, + double* result) const; + + //: Returns the derivatives of the nodal interpolation shape functions + //: with respect to the local parametric coordinates at the integration + //: stations. + const double* shape_fcn_deriv() const { return m_pointGrads.data(); } + void shape_fcn_deriv( + const int nint, + const double* p_coords, + double* result ) const; + + void interpolate_point( + const int npar_coord, + const double * par_coord, // (npar_coord) + const int ncomp_field, + const double * field, // (num_nodes,ncomp_field) + double * result ) const; // (ncomp_field) + + void gradient_operator( + const int nint, + const int npe_g, + const double* deriv_g, // (nvec,npe_g,nint) + const int npe_f, + const double* deriv_f, // (nvec,npe_f,nint) + const int nelem, + const double* coords, // (nvec,npe,nelem) + double* gradop, // (nvec,npe,nelem,nint) + double* det_J, // (nelem,nint) + double* error) const ; + + void scalar_gradient( + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const ; //: (nvec,nelem,nint) + void scalar_gradient( + const int nint, //: number of intg points + const int nelem, //: number of elements to process + const double* gradop, //: (nvec,npe,nelem,nint) + const double* det_J, //: (nelem,nint) + const double* sfield, //: (npe,nelem) + double* vector ) const ; //: (nvec,nelem,nint) + +private: + stk::topology m_topology; + int m_numNodes; + int m_numElemDims; + int m_numCoordDims; + int m_numIntgPts; + + // the Intrepid Basis + std::unique_ptr>> m_intrepidBasis; + + // Local FieldContainers + std::vector m_shapeFuncs; + std::vector m_pointGrads; + std::vector m_refPoints; + std::vector m_refWeights; + std::vector m_refCoords; +}; + +} // end namespace krino + +#endif // Akri_MasterElementIntrepid_h diff --git a/packages/krino/krino/master_element/CMakeLists.txt b/packages/krino/krino/master_element/CMakeLists.txt new file mode 100644 index 000000000000..da7d6357181c --- /dev/null +++ b/packages/krino/krino/master_element/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_master_element_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + ) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_master_element_lib) + diff --git a/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.cpp b/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.cpp new file mode 100644 index 000000000000..f1eb515d80bf --- /dev/null +++ b/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.cpp @@ -0,0 +1,139 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include + +namespace krino { + +void +CDFEM_Options_Parser::parse(const YAML::Node & region_node, RegionInterface & region) +{ + const YAML::Node cdfem_node = YAML_Parser::get_map_if_present(region_node, "cdfem_options"); + if ( cdfem_node ) + { + CDFEM_Support & cdfem_support = CDFEM_Support::get(region.get_stk_mesh_meta_data()); + + std::string cdfem_edge_degeneracy_handling_string; + if (YAML_Parser::get_if_present(cdfem_node, "cdfem_edge_degeneracy_handling", cdfem_edge_degeneracy_handling_string)) + { + std::transform(cdfem_edge_degeneracy_handling_string.begin(), cdfem_edge_degeneracy_handling_string.end(), cdfem_edge_degeneracy_handling_string.begin(), ::toupper); + static std::map valid_entries = + { {"SNAP_TO_NODE", SNAP_TO_NODE}, {"SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS", SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE} }; + auto it = valid_entries.find(cdfem_edge_degeneracy_handling_string); + if (it == valid_entries.end()) + { + stk::RuntimeDoomedAdHoc() << "Invalid cdfem_edge_degeneracy_handling type: " << YAML_Parser::info(cdfem_node); + } + else + { + cdfem_support.set_cdfem_edge_degeneracy_handling( it->second ); + } + } + + double cdfem_edge_tol = 0.0; + if (YAML_Parser::get_if_present(cdfem_node, "cdfem_edge_tolerance", cdfem_edge_tol)) + { + const double minimum_edge_tol = 1.e-12; + if (cdfem_edge_tol < minimum_edge_tol) + { + krinolog << "Using minimum edge tolerance of " << minimum_edge_tol << " instead of specified tolerance of " << cdfem_edge_tol << stk::diag::dendl; + cdfem_edge_tol = minimum_edge_tol; + } + cdfem_support.set_cdfem_edge_tol( cdfem_edge_tol ); + } + + std::string cdfem_simplex_generation_method_string; + if (YAML_Parser::get_if_present(cdfem_node, "cdfem_simplex_generation_method", cdfem_simplex_generation_method_string)) + { + std::transform(cdfem_simplex_generation_method_string.begin(), cdfem_simplex_generation_method_string.end(), cdfem_simplex_generation_method_string.begin(), ::toupper); + static std::map valid_entries = { + {"CUT_QUADS_BY_GLOBAL_IDENTIFIER", CUT_QUADS_BY_GLOBAL_IDENTIFIER}, + {"CUT_QUADS_BY_LARGEST_ANGLE", CUT_QUADS_BY_LARGEST_ANGLE}, + {"CUT_QUADS_BY_NEAREST_EDGE_CUT", CUT_QUADS_BY_NEAREST_EDGE_CUT} + }; + auto it = valid_entries.find(cdfem_simplex_generation_method_string); + if (it == valid_entries.end()) + { + stk::RuntimeDoomedAdHoc() << "Invalid cdfem_simplex_generation_method type: " << YAML_Parser::info(cdfem_node); + } + else + { + cdfem_support.set_simplex_generation_method( it->second ); + } + } + + int num_init_decomp_cycles = 0; + if (YAML_Parser::get_if_present(cdfem_node, "number_of_initial_decomposition_cycles", num_init_decomp_cycles)) + { + cdfem_support.set_num_initial_decomposition_cycles( num_init_decomp_cycles ); + } + + bool interface_refinement_specified = false; + int interface_minimum_refinement_level = 0; + if(YAML_Parser::get_if_present(cdfem_node, "cdfem_interface_minimum_refinement_level", interface_minimum_refinement_level)) + { + interface_refinement_specified = true; + } + + int interface_maximum_refinement_level = 0; + if(YAML_Parser::get_if_present(cdfem_node, "cdfem_interface_maximum_refinement_level", interface_maximum_refinement_level)) + { + interface_refinement_specified = true; + } + + if (interface_refinement_specified) + { + cdfem_support.activate_interface_refinement( interface_minimum_refinement_level, interface_maximum_refinement_level ); + } + + int nonconformal_adapt_levels = 0; + if (YAML_Parser::get_if_present(cdfem_node, "cdfem_nonconformal_adaptivity_levels", nonconformal_adapt_levels)) + { + cdfem_support.activate_nonconformal_adaptivity( nonconformal_adapt_levels ); + } + + int post_adapt_refine_levels = 0; + if (YAML_Parser::get_if_present(cdfem_node, "post_adaptivity_uniform_refinement_levels", post_adapt_refine_levels)) + { + cdfem_support.set_post_adapt_refinement_levels( post_adapt_refine_levels ); + } + + uint64_t nonconformal_adapt_target_element_count = 0; + if (YAML_Parser::get_if_present(cdfem_node, "nonconformal_adaptivity_target_element_count", nonconformal_adapt_target_element_count)) + { + cdfem_support.activate_nonconformal_adapt_target_count( nonconformal_adapt_target_element_count ); + } + + int post_cdfem_refinement_levels = 0; + if (YAML_Parser::get_if_present(cdfem_node, "post_cdfem_refinement_levels", post_cdfem_refinement_levels)) + { + cdfem_support.set_post_cdfem_refinement_levels( post_cdfem_refinement_levels ); + } + + const YAML::Node post_cdfem_refinement_blocks_seq = YAML_Parser::get_sequence_if_present(cdfem_node, "post_cdfem_refinement_blocks"); + if (post_cdfem_refinement_blocks_seq) + { + std::vector post_cdfem_refinement_blocks; + for ( auto && post_cdfem_refinement_block_node : post_cdfem_refinement_blocks_seq ) + { + const std::string post_cdfem_refinement_block = post_cdfem_refinement_block_node.as(); + post_cdfem_refinement_blocks.push_back(post_cdfem_refinement_block); + } + cdfem_support.set_post_cdfem_refinement_blocks( post_cdfem_refinement_blocks ); + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.hpp b/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.hpp new file mode 100644 index 000000000000..dfdf2a05e559 --- /dev/null +++ b/packages/krino/krino/parser/Akri_CDFEM_Options_Parser.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_CDFEM_Options_Parser_h +#define Akri_CDFEM_Options_Parser_h + +namespace YAML { class Node; } +namespace krino { class RegionInterface; } + +namespace krino { +namespace CDFEM_Options_Parser { + void parse(const YAML::Node & node, RegionInterface & region); +} +} + +#endif // Akri_CDFEM_Options_Parser_h diff --git a/packages/krino/krino/parser/Akri_IC_Parser.cpp b/packages/krino/krino/parser/Akri_IC_Parser.cpp new file mode 100644 index 000000000000..f8199ab14a45 --- /dev/null +++ b/packages/krino/krino/parser/Akri_IC_Parser.cpp @@ -0,0 +1,457 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +namespace krino { + +namespace { + +Sphere * +parse_sphere(const YAML::Node & ic_node) +{ + std::string name; + YAML_Parser::get_if_present(ic_node, "name", name); + + std::vector center; + if (YAML_Parser::get_if_present(ic_node, "center", center)) + { + if (center.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for center for IC sphere.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing center for IC sphere.\n"; + } + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for sphere must be -1 or 1.\n"; + } + } + + double radius = 0.0; + if (!YAML_Parser::get_if_present(ic_node, "radius", radius)) + { + stk::RuntimeDoomedAdHoc() << "Missing radius for IC sphere.\n"; + } + + return new Sphere(name, Vector3d(center.data()), radius, sign); +} + +Ellipsoid * +parse_ellipsoid(const YAML::Node & ic_node) +{ + std::string name; + YAML_Parser::get_if_present(ic_node, "name", name); + + std::vector center; + if (YAML_Parser::get_if_present(ic_node, "center", center)) + { + if (center.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for center for IC sphere.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing center for IC sphere.\n"; + } + + std::vector semiaxes; + if (YAML_Parser::get_if_present(ic_node, "semiaxes", semiaxes)) + { + if (semiaxes.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for semiaxes for IC ellipsoid.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing semiaxes for IC ellipsoid.\n"; + } + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for ellipsoid must be -1 or 1.\n"; + } + } + + std::vector rotationVec; + if (YAML_Parser::get_if_present(ic_node, "rotation", rotationVec)) + { + if (semiaxes.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for rotation for IC ellipsoid.\n"; + } + } + + return new Ellipsoid(name, center, semiaxes, rotationVec, sign); +} + +Plane * +parse_plane(const YAML::Node & ic_node) +{ + std::string name; + YAML_Parser::get_if_present(ic_node, "name", name); + + std::vector normal; + if (YAML_Parser::get_if_present(ic_node, "normal", normal)) + { + if (normal.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for center for IC plane.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing normal for IC plane.\n"; + } + + double multiplier = 1.0; + YAML_Parser::get_if_present(ic_node, "multiplier", multiplier); + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for IC plane must be -1 or 1.\n"; + } + } + multiplier *= sign; + + double offset = 0.0; + if (!YAML_Parser::get_if_present(ic_node, "offset", offset)) + { + stk::RuntimeDoomedAdHoc() << "Missing offset for IC plane.\n"; + } + + return new Plane(name, normal.data(), offset, multiplier); +} + +Cylinder * +parse_cylinder(const YAML::Node & ic_node) +{ + std::string name; + YAML_Parser::get_if_present(ic_node, "name", name); + + std::vector p1; + if (YAML_Parser::get_if_present(ic_node, "p1", p1)) + { + if (p1.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for p1 for IC cylinder.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing normal for IC cylinder.\n"; + } + + std::vector p2; + if (YAML_Parser::get_if_present(ic_node, "p2", p2)) + { + if (p2.size() != 3) + { + stk::RuntimeDoomedAdHoc() << "Expecting 3 real values for center for IC cylinder.\n"; + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing p2 for IC cylinder.\n"; + } + + double radius = 0.0; + if (!YAML_Parser::get_if_present(ic_node, "radius", radius)) + { + stk::RuntimeDoomedAdHoc() << "Missing radius for IC cylinder.\n"; + } + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for IC cylinder must be -1 or 1.\n"; + } + } + + return new Cylinder(name, p1.data(), p2.data(), radius, sign); +} + +std::unique_ptr +parse_binder(const YAML::Node & ic_node) +{ + std::string binder_type; + if (!YAML_Parser::get_if_present(ic_node, "type", binder_type)) + { + stk::RuntimeDoomedAdHoc() << "Missing type for Binder IC.\n"; + } + + double interface_size = 0.0; + double smooth_bridge_size = 0.0; + double smooth_bridge_offset = 0.0; + double other_ls_scale_factor = 0.0; + int ibinder_type = 0; + bool root_smooth_bridge = false; + + if (binder_type == "interface") + { + ibinder_type = 0; + if (!YAML_Parser::get_if_present(ic_node, "interface_size", interface_size)) + { + stk::RuntimeDoomedAdHoc() << "Missing interface_size for IC binder.\n"; + } + } + else if (binder_type == "smooth_bridge") + { + ibinder_type = 1; + YAML_Parser::get_if_present(ic_node, "smooth_bridge_size", smooth_bridge_size); + YAML_Parser::get_if_present(ic_node, "smooth_bridge_offset", smooth_bridge_offset); + YAML_Parser::get_if_present(ic_node, "other_ls_scale_factor", other_ls_scale_factor); + YAML_Parser::get_if_present(ic_node, "root_smooth_bridge", root_smooth_bridge); + + if (smooth_bridge_size < 0.0) + { + stk::RuntimeDoomedAdHoc() << "IC binder: Smooth bridge size should not be negative.\n"; + } + + if (smooth_bridge_size != 0.0) + { + if (smooth_bridge_offset <= 0.0) + { + stk::RuntimeDoomedAdHoc() << "IC binder: Smooth bridge offset should be greater than zero when a bridge size is specified.\n"; + } + if (other_ls_scale_factor <= 0.0) + { + stk::RuntimeDoomedAdHoc() << "IC binder: Scaling of other level sets should be greater than zero when a bridge size is specified. Typical values are O(1e2).\n"; + } + } + } + else + { + stk::RuntimeDoomedAdHoc() << "Binder IC type should be either interface or smooth_bridge. \n"; + } + + return std::make_unique(interface_size, smooth_bridge_size, smooth_bridge_offset, other_ls_scale_factor, ibinder_type, root_smooth_bridge); +} + +Faceted_Surface * +parse_facets(const YAML::Node & ic_node, const stk::diag::Timer &parent_timer) +{ + std::string surface_name; + YAML_Parser::get_if_present(ic_node, "name", surface_name); + + std::string facet_filename; + if (!YAML_Parser::get_if_present(ic_node, "filename", facet_filename)) + { + stk::RuntimeDoomedAdHoc() << "Missing filename for IC facets.\n"; + } + + std::string facet_format; + if (!YAML_Parser::get_if_present(ic_node, "format", facet_format)) + { + stk::RuntimeDoomedAdHoc() << "Missing format for IC facets.\n"; + } + + bool scaleSpecified = false; + double scale = 1.0; + if (YAML_Parser::get_if_present(ic_node, "scale", scale)) + { + scaleSpecified = true; + if (scale <= 0.0) + { + stk::RuntimeDoomedAdHoc() << "Scale for IC facets must be >= 0.\n"; + } + } + + Vector3d scaleVec{scale, scale, scale}; + std::vector scaleComponents = {"scaleX","scaleY","scaleZ"}; + for (int i=0; i<3; i++) + { + if (YAML_Parser::get_if_present(ic_node, scaleComponents[i], scaleVec[i])) + { + if (scaleSpecified) + stk::RuntimeDoomedAdHoc() << "Cannot specify both scale and " << scaleComponents[i] << "\n"; + if (scaleVec[i] <= 0.0) + stk::RuntimeDoomedAdHoc() << scaleComponents[i] << " for IC facets must be >= 0.\n"; + } + } + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for IC facets must be -1 or 1.\n"; + } + } + + std::transform(facet_format.begin(), facet_format.end(), facet_format.begin(), ::toupper); + Faceted_Surface_From_File * surface = nullptr; + + if (facet_format == "STL") + surface = new STLSurface(surface_name, parent_timer, facet_filename, sign, scaleVec); + else if (facet_format == "FAC") + surface = new FACSurface(surface_name, parent_timer, facet_filename, sign, scaleVec); + else if (facet_format == "PLY") + surface = new PLYSurface(surface_name, parent_timer, facet_filename, sign, scaleVec); + else if (facet_format == "EXO") + surface = new EXOSurface(surface_name, parent_timer, facet_filename, sign, scaleVec); + else + stk::RuntimeDoomedAdHoc() << "Unrecognized facet format: " << facet_format; + + return surface; +} + +MeshSurface * +parse_mesh_surface(const YAML::Node & ic_node, LevelSet & ls) +{ + std::string surface_name; + ThrowRequire(YAML_Parser::get_if_present(ic_node, "mesh", surface_name)); + + double sign = 1.0; + if (YAML_Parser::get_if_present(ic_node, "sign", sign)) + { + if (sign != -1.0 && sign == 1.0) + { + stk::RuntimeDoomedAdHoc() << "Sign for IC facets must be -1 or 1.\n"; + } + } + + ThrowErrorMsgIf(!ls.aux_meta().has_part(surface_name), "Could not locate a surface named " << surface_name); + const stk::mesh::Part & io_part = ls.aux_meta().get_part(surface_name); + + const stk::mesh::Field* coords = reinterpret_cast*>(&LevelSet::get_current_coordinates(ls.meta()).field()); + ThrowRequire(nullptr != coords); + + const stk::mesh::Selector surface_selector = stk::mesh::Selector(io_part); + return new MeshSurface(ls.meta(), *coords, surface_selector, sign); +} + +void +parse_composition_method(const YAML::Node & ic_node, IC_Alg& ic_alg) +{ + // This is a little strange because composition looks like an IC, but really sets a flag + std::string composition_method; + ThrowRequire(YAML_Parser::get_if_present(ic_node, "composition_method", composition_method)); + + std::transform(composition_method.begin(), composition_method.end(), composition_method.begin(), ::toupper); + + if (composition_method == "MINIMUM_SIGNED_DISTANCE") + ic_alg.set_composition_method(Composite_Surface::MINIMUM_SIGNED_DISTANCE); + else if (composition_method == "MAXIMUM_SIGNED_DISTANCE") + ic_alg.set_composition_method(Composite_Surface::MAXIMUM_SIGNED_DISTANCE); + else + stk::RuntimeDoomedAdHoc() << "Unrecognized composition_method: " << composition_method; +} + +void +parse_IC(const YAML::Node & ic_node, LevelSet &ls) +{ + if (ic_node.Type() == YAML::NodeType::Scalar) + { + // support random specified as Scalar (no :) + std::string ic_type = ic_node.as(); + if (ic_type == "random") + { + Random * random = new Random(0); + ls.get_IC_alg().addSurface(random); + } + else if (ic_type == "analytic_isosurface") + { + Analytic_Isosurface * surf = new Analytic_Isosurface(); + ls.get_IC_alg().addSurface(surf); + } + else + { + stk::RuntimeDoomedAdHoc() << "Unrecognized Levelset IC type: " << YAML_Parser::info(ic_node); + } + return; + } + + if ( YAML_Parser::get_null_if_present(ic_node, "sphere") ) + { + ls.get_IC_alg().addSurface(parse_sphere(ic_node)); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "ellipsoid") ) + { + ls.get_IC_alg().addSurface(parse_ellipsoid(ic_node)); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "plane") ) + { + ls.get_IC_alg().addSurface(parse_plane(ic_node)); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "cylinder") ) + { + ls.get_IC_alg().addSurface(parse_cylinder(ic_node)); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "facets") ) + { + ls.get_IC_alg().addSurface(parse_facets(ic_node, ls.get_timer())); + } + else if ( YAML_Parser::get_scalar_if_present(ic_node, "mesh") ) + { + ls.get_IC_alg().addSurface(parse_mesh_surface(ic_node, ls)); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "random") ) + { + int seed = 0; + YAML_Parser::get_if_present(ic_node, "seed", seed); + Random * random = new Random(seed); + ls.get_IC_alg().addSurface(random); + } + else if ( YAML_Parser::get_null_if_present(ic_node, "binder") ) + { + ls.get_IC_alg().addCalculator(parse_binder(ic_node)); + } + else if ( YAML_Parser::get_scalar_if_present(ic_node, "composition_method") ) + { + parse_composition_method(ic_node, ls.get_IC_alg()); + } + else + { + stk::RuntimeDoomedAdHoc() << "Unrecognized Levelset IC type: " << YAML_Parser::info(ic_node); + } +} + +} + +void +IC_Parser::parse(const YAML::Node & node, LevelSet & ls) +{ + const YAML::Node ic_nodes = YAML_Parser::get_sequence_if_present(node, "initial_conditions"); + if ( ic_nodes ) + { + for ( auto && ic_node : ic_nodes ) + { + parse_IC(ic_node, ls); + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_IC_Parser.hpp b/packages/krino/krino/parser/Akri_IC_Parser.hpp new file mode 100644 index 000000000000..833d49664d92 --- /dev/null +++ b/packages/krino/krino/parser/Akri_IC_Parser.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_IC_Parser_h +#define Akri_IC_Parser_h + +namespace YAML { class Node; } +namespace krino { class LevelSet; } + +namespace krino { +namespace IC_Parser { + void parse(const YAML::Node & node, LevelSet & ls); +} +} + +#endif // Akri_IC_Parser_h diff --git a/packages/krino/krino/parser/Akri_LevelSet_Parser.cpp b/packages/krino/krino/parser/Akri_LevelSet_Parser.cpp new file mode 100644 index 000000000000..8196db1a77e1 --- /dev/null +++ b/packages/krino/krino/parser/Akri_LevelSet_Parser.cpp @@ -0,0 +1,167 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +namespace krino { + +namespace { + +void +register_blocks_for_level_set(RegionInterface & reg, LevelSet & ls) +{ + const std::string composite_name = ls.get_composite_name(); + if (!composite_name.empty()) + { + LS_SideTag::declare_composite(ls.get_identifier(), LevelSet::get_identifier(composite_name)); + } + + Phase_Support & phase_support = Phase_Support::get(reg.get_stk_mesh_meta_data()); + const PhaseVec & mesh_phases = Phase_Support::get_phases(reg.name_of_input_mesh()); + const std::vector ls_phases = Phase_Support::get_level_set_phases(mesh_phases, ls); + const std::vector decomposed_blocks = phase_support.get_blocks_decomposed_by_levelset(ls_phases); + phase_support.register_blocks_for_level_set(&ls, decomposed_blocks); +} + +} + +void +LevelSet_Parser::parse(const YAML::Node & region_node, RegionInterface & region) +{ + const YAML::Node ls_nodes = YAML_Parser::get_sequence_if_present(region_node, "level_set_interfaces"); + if ( ls_nodes ) + { + for ( auto && ls_node : ls_nodes ) + { + std::string ls_name; + YAML_Parser::get_if_present(ls_node, "name", ls_name); + if (ls_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Blank or missing levelset name.\n"; + } + LevelSet & ls = LevelSet::build(region.get_stk_mesh_meta_data(), ls_name, region.getRegionTimer()); + + std::string distance_name; + if (krino::YAML_Parser::get_if_present(ls_node, "distance_variable", distance_name)) + { + ls.set_distance_name(distance_name); + } + + std::vector extension_velocity; + if (krino::YAML_Parser::get_if_present(ls_node, "extension_velocity", extension_velocity)) + { + if (extension_velocity.size() != ls.spatial_dimension) + { + stk::RuntimeDoomedAdHoc() << "Expecting " << ls.spatial_dimension << " real values for extension_velocity for level set " << ls_name << ".\n"; + } + ls.set_extension_velocity(Vector3d(extension_velocity.data(), extension_velocity.size())); + } + + double narrow_band_multiplier = 0.0; + if (YAML_Parser::get_if_present(ls_node, "narrow_band_element_size_multiplier", narrow_band_multiplier)) + { + if( narrow_band_multiplier < 0. ) + { + stk::RuntimeDoomedAdHoc() << "Error: Narrow band element size multiplier must be >= 0.\n"; + } + else if ( narrow_band_multiplier < 1. ) + { + stk::RuntimeWarningAdHoc() << "Narrow band element size multiplier is less than 1. " + << "Except in certain cases of adaptive refinement around the interface, this will produce errors in the distance field." + << std::endl; + } + ls.narrow_band_multiplier(narrow_band_multiplier); + } + + std::string redistance_method_name; + if (YAML_Parser::get_if_present(ls_node, "redistance_method", redistance_method_name)) + { + std::transform(redistance_method_name.begin(), redistance_method_name.end(), redistance_method_name.begin(), ::toupper); + Redistance_Method redistance_method = CLOSEST_POINT; + if (redistance_method_name == "CLOSEST_POINT") + redistance_method = CLOSEST_POINT; + else if (redistance_method_name == "FAST_MARCHING") + redistance_method = FAST_MARCHING; + else + stk::RuntimeWarningAdHoc() << "Unrecognized redistance method: " << redistance_method_name << std::endl; + + ls.set_redistance_method(redistance_method); + } + + bool perform_initial_redistance; + if (YAML_Parser::get_if_present(ls_node, "perform_initial_redistance", perform_initial_redistance)) + { + ls.perform_initial_redistance(perform_initial_redistance); + } + + double initial_offset_distance = 0.0; + if (YAML_Parser::get_if_present(ls_node, "initial_offset_distance", initial_offset_distance)) + { + ls.set_ic_offset(initial_offset_distance); + } + + double initial_scale_factor = 1.0; + if (YAML_Parser::get_if_present(ls_node, "initial_scale_factor", initial_scale_factor)) + { + ls.set_ic_scale(initial_scale_factor); + } + + double narrow_band_size = 0.0; + if (YAML_Parser::get_if_present(ls_node, "narrow_band_size", narrow_band_size)) + { + if( narrow_band_size < 0. ) + { + stk::RuntimeDoomedAdHoc() << "Error: Narrow band size must be >= 0.\n"; + } + ls.narrow_band_size(narrow_band_size); + } + + const YAML::Node comp_dist_surfs = YAML_Parser::get_sequence_if_present(ls_node, "compute_surface_distance"); + if ( comp_dist_surfs ) + { + std::vector compute_distance_surfaces; + for ( auto && comp_dist_surf : comp_dist_surfs ) + { + const std::string surface_name = comp_dist_surf.as(); + + ThrowErrorMsgIf( !ls.aux_meta().has_part(surface_name), + "Could not locate a surface named " << surface_name); + + stk::mesh::Part & io_part = ls.aux_meta().get_part(surface_name); + ThrowErrorMsgIf( ls.meta().side_rank() != io_part.primary_entity_rank(), + "Part " << surface_name << " is not a side-rank part."); + + ls.get_compute_surface_distance_parts().push_back(&io_part); + compute_distance_surfaces.push_back(surface_name); + } + ThrowErrorMsgIf( ls.get_compute_surface_distance_parts().empty(), + "Please specify surfaces for compute surface distance."); + } + + IC_Parser::parse(ls_node, ls); + + register_blocks_for_level_set(region, ls); + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_LevelSet_Parser.hpp b/packages/krino/krino/parser/Akri_LevelSet_Parser.hpp new file mode 100644 index 000000000000..8016393f28f7 --- /dev/null +++ b/packages/krino/krino/parser/Akri_LevelSet_Parser.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_LevelSet_Parser_h +#define Akri_LevelSet_Parser_h + +namespace YAML { class Node; } +namespace krino { class RegionInterface; } + +namespace krino { +namespace LevelSet_Parser { + void parse(const YAML::Node & node, RegionInterface & region); +} +} + +#endif // Akri_LevelSet_Parser_h diff --git a/packages/krino/krino/parser/Akri_MeshInput_Parser.cpp b/packages/krino/krino/parser/Akri_MeshInput_Parser.cpp new file mode 100644 index 000000000000..d455924ffa11 --- /dev/null +++ b/packages/krino/krino/parser/Akri_MeshInput_Parser.cpp @@ -0,0 +1,181 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +#include +#include +#include +#include + +#include + +namespace krino { + +void +MeshInput_Parser::parse(const YAML::Node & base_node) +{ + const YAML::Node fem_nodes = YAML_Parser::get_sequence_if_present(base_node, "finite_element_models"); + if (!fem_nodes) return; + + for ( auto && fem_node : fem_nodes ) + { + std::string model_name; + YAML_Parser::get_if_present(fem_node, "name", model_name); + if (model_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Missing finite element model name.\n"; + } + std::shared_ptr options = MeshInputOptions::get_or_create(model_name); + + const bool has_generated_mesh = parse_generated_mesh(fem_node, *options); + + std::string mesh_name; + YAML_Parser::get_if_present(fem_node, "mesh", mesh_name); + if (!mesh_name.empty() && !has_generated_mesh) + { + options->set_filename(mesh_name); + } + else if (!has_generated_mesh) + { + stk::RuntimeDoomedAdHoc() << "Must specify input mesh name or generated mesh options.\n"; + } + + std::string decomposition_method; + if (YAML_Parser::get_if_present(fem_node, "decomposition_method", decomposition_method)) + { + // no checking here for validity + std::transform(decomposition_method.begin(), decomposition_method.end(), decomposition_method.begin(), ::toupper); + options->set_decomposition_method(decomposition_method); + } + + Phase_Parser::parse(fem_node, model_name); + } +} + +bool +MeshInput_Parser::parse_generated_mesh(const YAML::Node & fem_node, MeshInputOptions & options) +{ + const YAML::Node generated_mesh_node = YAML_Parser::get_map_if_present(fem_node, "generated_mesh"); + if (!generated_mesh_node) return false; + + double mesh_size = 0.0; + if (!YAML_Parser::get_if_present(generated_mesh_node, "mesh_size", mesh_size) || mesh_size < 0.0) + { + stk::RuntimeDoomedAdHoc() << "Missing or invalid mesh_size for generated_mesh.\n"; + } + options.set_generated_mesh_size(mesh_size); + + std::vector domain; + if (YAML_Parser::get_if_present(generated_mesh_node, "domain", domain)) + { + if (options.get_generated_mesh_domain_type() != MeshInputOptions::NO_GENERATED_MESH) + { + stk::RuntimeDoomedAdHoc() << "Must only specify domain or interface_bounding_box_with_dimension options.\n"; + } + options.set_generated_mesh_domain_type(MeshInputOptions::GENERATED_MESH_FOR_SPECIFIED_DOMAIN); + if (domain.size() != 4 && domain.size() != 6) + { + stk::RuntimeDoomedAdHoc() << "Domain must be a vector of length 4 for 2D or 6 for 3D (xmin,ymin,zmin, xmax,ymax,zmax).\n"; + } + options.set_generated_mesh_domain(domain); + } + + int interface_spatial_dim = 0; + if (YAML_Parser::get_if_present(generated_mesh_node, "interface_bounding_box_with_dimension", interface_spatial_dim)) + { + if (options.get_generated_mesh_domain_type() != MeshInputOptions::NO_GENERATED_MESH) + { + stk::RuntimeDoomedAdHoc() << "Must only specify domain or interface_bounding_box options.\n"; + } + if (interface_spatial_dim != 2 && interface_spatial_dim != 3) + { + stk::RuntimeDoomedAdHoc() << "interface_bounding_box_with_dimension only support 2 or 3 dimensions.\n"; + } + const MeshInputOptions::GeneratedMeshDomainType mesh_type = + interface_spatial_dim == 2 ? + MeshInputOptions::GENERATED_2D_MESH_FOR_INTERFACE_BOUNDING_BOX : + MeshInputOptions::GENERATED_3D_MESH_FOR_INTERFACE_BOUNDING_BOX; + options.set_generated_mesh_domain_type(mesh_type); + } + + std::string generated_mesh_element_type_string; + if (YAML_Parser::get_if_present(generated_mesh_node, "element_type", generated_mesh_element_type_string)) + { + std::transform(generated_mesh_element_type_string.begin(), generated_mesh_element_type_string.end(), generated_mesh_element_type_string.begin(), ::toupper); + static std::map valid_entries = + { {"TRIANGLE", stk::topology::TRIANGLE_3_2D}, + {"TRI", stk::topology::TRIANGLE_3_2D}, + {"QUADRILATERAL", stk::topology::QUADRILATERAL_4_2D}, + {"QUAD", stk::topology::QUADRILATERAL_4_2D}, + {"HEXAHEDRON", stk::topology::HEXAHEDRON_8}, + {"HEX", stk::topology::HEXAHEDRON_8}, + {"TETRAHEDRON", stk::topology::TETRAHEDRON_4}, + {"TET", stk::topology::TETRAHEDRON_4} }; + auto it = valid_entries.find(generated_mesh_element_type_string); + if (it == valid_entries.end()) + { + stk::RuntimeDoomedAdHoc() << "Invalid cdfem_simplex_generation_method type: " << YAML_Parser::info(generated_mesh_node); + } + else + { + options.set_generated_mesh_element_type( it->second ); + if (options.get_generated_mesh_spatial_dimension() != (int)options.get_generated_mesh_element_type().dimension()) + { + stk::RuntimeDoomedAdHoc() << "Mismatch in spatial dimension for generated mesh element type and domain specification. "; + } + } + } + else + { + stk::topology default_topology = + (options.get_generated_mesh_spatial_dimension() == 2) ? + stk::topology::TRIANGLE_3_2D : + stk::topology::TETRAHEDRON_4; + options.set_generated_mesh_element_type( default_topology ); + } + + std::string generated_mesh_type_string; + if (YAML_Parser::get_if_present(generated_mesh_node, "mesh_type", generated_mesh_type_string)) + { + std::transform(generated_mesh_type_string.begin(), generated_mesh_type_string.end(), generated_mesh_type_string.begin(), ::toupper); + static std::map valid_entries = + { {"CUBIC", BoundingBoxMeshStructureType::CUBIC_BOUNDING_BOX_MESH}, + {"BCC", BoundingBoxMeshStructureType::BCC_BOUNDING_BOX_MESH}, + {"FLAT_WALLED_BCC", BoundingBoxMeshStructureType::FLAT_WALLED_BCC_BOUNDING_BOX_MESH}, + {"TRIANGULAR_LATTICE", BoundingBoxMeshStructureType::TRIANGULAR_LATTICE_BOUNDING_BOX_MESH}, + {"FLAT_WALLED_TRIANGULAR_LATTICE", BoundingBoxMeshStructureType::FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH}}; + auto it = valid_entries.find(generated_mesh_type_string); + if (it == valid_entries.end()) + { + stk::RuntimeDoomedAdHoc() << "Invalid mesh_type: " << YAML_Parser::info(generated_mesh_node); + } + else + { + options.set_generated_mesh_structure_type(it->second); + if ((BoundingBoxMeshStructureType::BCC_BOUNDING_BOX_MESH == it->second || BoundingBoxMeshStructureType::FLAT_WALLED_BCC_BOUNDING_BOX_MESH == it->second) && options.get_generated_mesh_spatial_dimension() != 3) + { + stk::RuntimeDoomedAdHoc() << "BCC meshes only supported in 3D"; + } + if ((BoundingBoxMeshStructureType::TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == it->second || BoundingBoxMeshStructureType::FLAT_WALLED_TRIANGULAR_LATTICE_BOUNDING_BOX_MESH == it->second) && options.get_generated_mesh_spatial_dimension() != 2) + { + stk::RuntimeDoomedAdHoc() << "BCC meshes only supported in 2D"; + } + } + } + + if (options.get_generated_mesh_domain_type() == MeshInputOptions::NO_GENERATED_MESH) + { + stk::RuntimeDoomedAdHoc() << "Must specify domain or interface_bounding_box_with_dimension for generated_mesh.\n"; + } + return true; +} + + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_MeshInput_Parser.hpp b/packages/krino/krino/parser/Akri_MeshInput_Parser.hpp new file mode 100644 index 000000000000..1dcd2342aa5d --- /dev/null +++ b/packages/krino/krino/parser/Akri_MeshInput_Parser.hpp @@ -0,0 +1,22 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_MeshInput_Parser_h +#define Akri_MeshInput_Parser_h + +namespace YAML { class Node; } +namespace krino { class MeshInputOptions; } + +namespace krino { +namespace MeshInput_Parser { + void parse(const YAML::Node & node); + bool parse_generated_mesh(const YAML::Node & fem_node, MeshInputOptions & options); +} +} + +#endif // Akri_MeshInput_Parser_h diff --git a/packages/krino/krino/parser/Akri_Phase_Parser.cpp b/packages/krino/krino/parser/Akri_Phase_Parser.cpp new file mode 100644 index 000000000000..64f74ac76a99 --- /dev/null +++ b/packages/krino/krino/parser/Akri_Phase_Parser.cpp @@ -0,0 +1,101 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include + +namespace krino { + +void +Phase_Parser::parse(const YAML::Node & fem_node, const std::string & fem_model_name) +{ + PhaseVec & mesh_phases = Phase_Support::get_phases(fem_model_name); + + const YAML::Node subdom_nodes = YAML_Parser::get_sequence_if_present(fem_node, "subdomains"); + + if (subdom_nodes) + { + for ( auto && subdom_node : subdom_nodes ) + { + std::string subdom_name; + YAML_Parser::get_if_present(subdom_node, "name", subdom_name); + if (subdom_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Missing subdomain name in finite element model " << fem_model_name; + } + mesh_phases.push_back(NamedPhase(subdom_name)); + + const YAML::Node where_nodes = YAML_Parser::get_sequence_if_present(subdom_node, "level_set_regions"); + + if (where_nodes) + { + for ( auto && where_node : where_nodes ) + { + std::string negative_ls_name; + if (YAML_Parser::get_if_present(where_node, "negative_level_set", negative_ls_name)) + { + mesh_phases.back().tag().add(LevelSet::get_identifier(negative_ls_name),-1); + } + + std::string positive_ls_name; + if (YAML_Parser::get_if_present(where_node, "positive_level_set", positive_ls_name)) + { + mesh_phases.back().tag().add(LevelSet::get_identifier(positive_ls_name),+1); + } + } + } + + std::string smallest_ls_name; + if (YAML_Parser::get_if_present(subdom_node, "smallest_level_set", smallest_ls_name)) + { + if ( where_nodes ) + { + stk::RuntimeDoomedAdHoc() << "Cannot combine \"negative_level_set|positive_level_set\" syntax with \"smallest_level_set\" syntax."; + } + Phase_Support::set_one_levelset_per_phase(true); + mesh_phases.back().tag().add(LevelSet::get_identifier(smallest_ls_name),-1); + } + } + } + + const YAML::Node part_nodes = YAML_Parser::get_sequence_if_present(fem_node, "parts"); + + if (part_nodes) + { + std::map> & FEmodel_block_phase_names = Phase_Support::get_block_phases_by_name(fem_model_name); + + for ( auto && part_node : part_nodes ) + { + std::string part_name; + YAML_Parser::get_if_present(part_node, "name", part_name); + if (part_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Missing part name in finite element model " << fem_model_name; + } + + const YAML::Node part_subdom_nodes = YAML_Parser::get_sequence_if_present(part_node, "subdomains"); + if (part_subdom_nodes) + { + std::vector & block_phase_names = FEmodel_block_phase_names[part_name]; + for ( auto && subdom_node : part_subdom_nodes ) + { + const std::string subdom_name = subdom_node.as(); + block_phase_names.push_back(subdom_name); + } + } + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_Phase_Parser.hpp b/packages/krino/krino/parser/Akri_Phase_Parser.hpp new file mode 100644 index 000000000000..53c0f08b7c0f --- /dev/null +++ b/packages/krino/krino/parser/Akri_Phase_Parser.hpp @@ -0,0 +1,22 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Phase_Parser_h +#define Akri_Phase_Parser_h + +#include + +namespace YAML { class Node; } + +namespace krino { +namespace Phase_Parser { + void parse(const YAML::Node & fem_node, const std::string & fem_model_name); +} +} + +#endif // Akri_Phase_Parser_h diff --git a/packages/krino/krino/parser/Akri_Region_Parser.cpp b/packages/krino/krino/parser/Akri_Region_Parser.cpp new file mode 100644 index 000000000000..56310b64bade --- /dev/null +++ b/packages/krino/krino/parser/Akri_Region_Parser.cpp @@ -0,0 +1,84 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include + +namespace krino { + +void +Region_Parser::parse(const YAML::Node & simulation_node, Simulation & simulation) +{ + const YAML::Node region_nodes = YAML_Parser::get_sequence_if_present(simulation_node, "regions"); + if ( !region_nodes ) return; + + for ( auto && region_node : region_nodes ) + { + std::string region_name; + YAML_Parser::get_if_present(region_node, "name", region_name); + if (region_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Blank or missing region name.\n"; + } + Region * region = new Region(simulation, region_name ); + + int initial_refinement_levels = 0; + if (YAML_Parser::get_if_present(region_node, "initial_uniform_refinement_levels", initial_refinement_levels)) + { + region->set_initial_refinement_levels(initial_refinement_levels); + } + + bool use_32bit_ids = false; + YAML_Parser::get_if_present(region_node, "use_32bit_ids", use_32bit_ids); + + bool force_64bit_ids = !use_32bit_ids; + YAML_Parser::get_if_present(region_node, "force_64bit_ids", force_64bit_ids); + + if (use_32bit_ids && force_64bit_ids) + { + stk::RuntimeDoomedAdHoc() << "Can't specify options use_32bit_ids=true and force_64bit_ids=true together in region " << region_name << "\n"; + } + + std::string fem_model_name; + YAML_Parser::get_if_present(region_node, "finite_element_model", fem_model_name); + if (fem_model_name.empty()) + { + stk::RuntimeDoomedAdHoc() << "Blank or missing finite element model for region " << region_name << "\n"; + } + region->associate_input_mesh(fem_model_name, use_32bit_ids, force_64bit_ids); + + RegionInterface::set_currently_parsed_region(region->get_stk_mesh_meta_data(), region->name(), region->getRegionTimer(), region->name_of_input_mesh(), region->get_input_io_region()); + + Phase_Support & phase_support = krino::Phase_Support::get(region->get_stk_mesh_meta_data()); + const PhaseVec & mesh_phases = Phase_Support::get_phases(region->name_of_input_mesh()); + const PartnamePhasenameMap & mesh_block_phase_names = Phase_Support::get_block_phases_by_name(region->name_of_input_mesh()); + phase_support.determine_block_phases(mesh_phases, mesh_block_phase_names); + + + const Block_Surface_Connectivity block_surf_info(region->get_stk_mesh_meta_data()); + phase_support.set_input_block_surface_connectivity(block_surf_info); + phase_support.setup_phases(mesh_phases); + + LevelSet_Parser::parse(region_node, RegionInterface::get_currently_parsed_region()); + CDFEM_Options_Parser::parse(region_node, RegionInterface::get_currently_parsed_region()); + ResultsOutput_Parser::parse(region_node, *region); + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_Region_Parser.hpp b/packages/krino/krino/parser/Akri_Region_Parser.hpp new file mode 100644 index 000000000000..a860592c7b53 --- /dev/null +++ b/packages/krino/krino/parser/Akri_Region_Parser.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Region_Parser_h +#define Akri_Region_Parser_h + +namespace YAML { class Node; } +namespace krino { class Simulation; } + +namespace krino { +namespace Region_Parser { + void parse(const YAML::Node & node, Simulation & simulation); +} +} + +#endif // Akri_Region_Parser_h diff --git a/packages/krino/krino/parser/Akri_ResultsOutput_Parser.cpp b/packages/krino/krino/parser/Akri_ResultsOutput_Parser.cpp new file mode 100644 index 000000000000..a94751ac5e60 --- /dev/null +++ b/packages/krino/krino/parser/Akri_ResultsOutput_Parser.cpp @@ -0,0 +1,72 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include + +namespace krino { + +void +ResultsOutput_Parser::parse(const YAML::Node & region_node, Region & region) +{ + const YAML::Node results_node = YAML_Parser::get_map_if_present(region_node, "output"); + if ( results_node ) + { + ResultsOutputOptions * options = region.get_results_options(); + + std::string results_database_name; + if (YAML_Parser::get_if_present(results_node, "database_name", results_database_name)) + { + options->set_filename(results_database_name); + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing results database_name for region " << region.name() << ".\n"; + } + + std::string results_title; + if (YAML_Parser::get_if_present(results_node, "title", results_title)) + { + options->set_title(results_title); + } + + bool compose_results; + if (YAML_Parser::get_if_present(results_node, "compose_results", compose_results)) + { + if (compose_results) options->add_property(Ioss::Property("COMPOSE_RESULTS", 1)); + } + + int output_frequency = 1; + if (YAML_Parser::get_if_present(results_node, "output_frequency", output_frequency)) + { + options->add_step_increment(0, output_frequency); + } + + const YAML::Node nodal_variable_nodes = YAML_Parser::get_sequence_if_present(results_node, "nodal_variables"); + for ( auto && variable_node : nodal_variable_nodes ) + { + const std::string field_name = variable_node.as(); + options->add_nodal_field(field_name, field_name); + } + + const YAML::Node element_variable_nodes = YAML_Parser::get_sequence_if_present(results_node, "element_variables"); + for ( auto && variable_node : element_variable_nodes ) + { + const std::string field_name = variable_node.as(); + options->add_element_field(field_name, field_name); + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_ResultsOutput_Parser.hpp b/packages/krino/krino/parser/Akri_ResultsOutput_Parser.hpp new file mode 100644 index 000000000000..352a0947d673 --- /dev/null +++ b/packages/krino/krino/parser/Akri_ResultsOutput_Parser.hpp @@ -0,0 +1,21 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_ResultsOutput_Parser_h +#define Akri_ResultsOutput_Parser_h + +namespace YAML { class Node; } +namespace krino { class Region; } + +namespace krino { +namespace ResultsOutput_Parser { + void parse(const YAML::Node & node, Region & region); +} +} + +#endif // Akri_ResultsOutput_Parser_h diff --git a/packages/krino/krino/parser/Akri_Simulation_Parser.cpp b/packages/krino/krino/parser/Akri_Simulation_Parser.cpp new file mode 100644 index 000000000000..be02d91cbf15 --- /dev/null +++ b/packages/krino/krino/parser/Akri_Simulation_Parser.cpp @@ -0,0 +1,54 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include + +#include + +namespace krino { + +void +Simulation_Parser::parse(const YAML::Node & node) +{ + const YAML::Node sim_node = YAML_Parser::get_map_if_present(node, "simulation"); + if ( sim_node ) + { + Simulation & simulation = Simulation::build("krino simulation"); + + double start_time = 0.0; + if (YAML_Parser::get_if_present(sim_node, "start_time", start_time)) + { + simulation.set_current_time(start_time); + } + + double stop_time = 0.0; + if (YAML_Parser::get_if_present(sim_node, "stop_time", stop_time)) + { + simulation.set_stop_time(stop_time); + } + + double time_step = 0.0; + if (YAML_Parser::get_if_present(sim_node, "time_step", time_step)) + { + simulation.set_time_step(time_step); + } + + Region_Parser::parse(sim_node, simulation); + } + else + { + stk::RuntimeDoomedAdHoc() << "Missing simulation.\n"; + } +} + +} // namespace krino diff --git a/packages/krino/krino/parser/Akri_Simulation_Parser.hpp b/packages/krino/krino/parser/Akri_Simulation_Parser.hpp new file mode 100644 index 000000000000..45c02b36ca47 --- /dev/null +++ b/packages/krino/krino/parser/Akri_Simulation_Parser.hpp @@ -0,0 +1,20 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Simulation_Parser_h +#define Akri_Simulation_Parser_h + +namespace YAML { class Node; } + +namespace krino { +namespace Simulation_Parser { + void parse(const YAML::Node & node); +} +} + +#endif // Akri_Simulation_Parser_h diff --git a/packages/krino/krino/parser/Akri_YAML.hpp b/packages/krino/krino/parser/Akri_YAML.hpp new file mode 100644 index 000000000000..1a5de9994874 --- /dev/null +++ b/packages/krino/krino/parser/Akri_YAML.hpp @@ -0,0 +1,48 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_KRINO_PARSER_AKRI_YAML_HPP_ +#define KRINO_KRINO_PARSER_AKRI_YAML_HPP_ +#include + +#ifdef KRINO_HAVE_YAML + +#ifdef __INTEL_COMPILER +#include +#else +//YAML has shadowed variables +//this disables the checking on GCC only +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#include +#pragma GCC diagnostic pop +#endif + +#else +// Fake struct to mimic YAML Node if we don't have YAML +namespace YAML { + struct NodeType { + enum value { Undefined, Null, Scalar, Sequence, Map }; + }; + + struct Node { + NodeType::value Type() const { return NodeType::Null; } + + template const T as() const { return T(); } + + explicit operator bool() const { return false; } + + Node * begin() const { return nullptr; } + Node * end() const { return nullptr; } + + Node operator[](std::string) const { return Node(); } + }; +} +#endif + +#endif /* KRINO_KRINO_PARSER_AKRI_YAML_HPP_ */ diff --git a/packages/krino/krino/parser/Akri_YAML_Parser.cpp b/packages/krino/krino/parser/Akri_YAML_Parser.cpp new file mode 100644 index 000000000000..9f1e4df98276 --- /dev/null +++ b/packages/krino/krino/parser/Akri_YAML_Parser.cpp @@ -0,0 +1,235 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include + +#ifdef KRINO_HAVE_YAML + +static void emit(YAML::Emitter& emout, const YAML::Node & node) { + // recursive depth first + YAML::NodeType::value type = node.Type(); + std::string out; + switch (type) + { + case YAML::NodeType::Scalar: + out = node.as(); + emout << out; + break; + case YAML::NodeType::Sequence: + emout << YAML::BeginSeq; + for (unsigned int i = 0; i < node.size(); ++i) { + const YAML::Node & subnode = node[i]; + emit(emout, subnode); + } + emout << YAML::EndSeq; + break; + case YAML::NodeType::Map: + emout << YAML::BeginMap ; + for (auto && entry : node) { + const YAML::Node & key = entry.first; + const YAML::Node & value = entry.second; + out = key.as(); + emout << YAML::Key << out; + emout << YAML::Value; + emit(emout, value); + } + emout << YAML::EndMap ; + break; + case YAML::NodeType::Null: + emout << " (empty) "; + break; + default: + std::cerr << "Warning: emit: unknown/unsupported node type" << std::endl; + break; + } +} + +/// uses Emitter to print node to stream +static void emit(std::ostream& sout, const YAML::Node & node) { + YAML::Emitter out; + emit(out,node); + sout << out.c_str() << std::endl; +} + +static YAML::Node parse_yaml(std::istream & input_stream) +{ + return YAML::Load(input_stream); + YAML::Node doc; + + try { + doc = YAML::Load(input_stream); + } + catch (YAML::ParserException &e) { + throw std::runtime_error(e.what()); + } + + return doc; +} + +static std::string line_info(const YAML::Node & node) { + std::ostringstream sout; + sout << "(line,column) = (" + << node.Mark().line+1 << ", " + << node.Mark().column+1 << ")"; + return sout.str(); +} + +#else + +static YAML::Node parse_yaml(std::istream & input_stream) { throw std::runtime_error("YAML parser not enabled in krino build."); } +static void emit(std::ostream& sout, const YAML::Node & node) {} +static std::string line_info(const YAML::Node & node) { return std::string(); } + +#endif + +namespace krino{ +namespace YAML_Parser { + +std::string info(const YAML::Node & node) { + std::ostringstream sout; + sout << "Node at " << line_info(node) << " => \n" ; + emit(sout, node); + return sout.str(); +} + +const YAML::Node +get_if_present(const YAML::Node& node, const std::string& key) +{ + static std::string types[] = {"Null", "Scalar", "Sequence", "Map"}; + std::ostringstream err_msg; + + if (node.Type() == YAML::NodeType::Null || node.Type() == YAML::NodeType::Scalar) + { + emit(err_msg, node); + err_msg << "Check structure of input file."; + stk::RuntimeDoomedAdHoc() + << "parsing within non-searchable node of type = " << types[node.Type()] + << " for key= " << key + << " at " << line_info(node) + << " node= " << err_msg.str() << std::endl; + YAML::Node empty; + return empty; + } + return node[key]; +} + +const YAML::Node +get_type_if_present(const YAML::Node& node, const std::string& key, YAML::NodeType::value type) +{ + static std::string types[] = {"Null", "Scalar", "Sequence", "Map"}; + std::ostringstream err_msg; + + const YAML::Node value = get_if_present(node, key); + if (value && (value.Type() != type)) + { + emit(err_msg, node); + err_msg << "Check indentation of input file."; + stk::RuntimeDoomedAdHoc() + << "parsing expected type " << types[type] << " got type = " << types[value.Type()] + << " for key= " << key + << " at " << line_info(node) + << " node= " << err_msg.str() << std::endl; + } + return value; +} + +// template specialization +template<> +bool get_if_present(const YAML::Node & node, const std::string& key, bool& result) +{ + std::string resultString; + const bool haveNode = get_if_present(node, key, resultString); + + if (haveNode) + { + result = false; + std::transform(resultString.begin(), resultString.end(), resultString.begin(), ::toupper); + if (resultString == "TRUE" || resultString == "YES" || resultString == "1") + result = true; + else if (resultString == "FALSE" || resultString == "NO" || resultString == "0") + result = false; + else + { + std::ostringstream err_msg; + emit(err_msg, node); + stk::RuntimeDoomedAdHoc() << "Failed to parse boolean " + << " for key= " << key + << " at " << line_info(node) + << " node= " << err_msg.str() << std::endl; + } + return true; + } + return false; +} + + +void parse() +{/* %TRACE% */ Trace trace__("krino::YAML_Parser::parse()"); /* %TRACE% */ + const std::string inputFileName = stk::EnvData::getInputFileName(); + const std::string &aprepro = sierra::Env::get_param("aprepro"); + const bool use_aprepro = aprepro.empty() || aprepro != "off"; + const std::string &aprepro_defines = sierra::Env::get_param("define"); + + // parallel version of input file + mpi_filebuf input_parallel_file(use_aprepro, aprepro_defines); + if (!input_parallel_file.open(stk::EnvData::parallel_comm(), 0, std::ios::in, inputFileName.c_str())) { + throw std::runtime_error("failed to open input file"); + } + if(use_aprepro) { + sierra::Env::outputP0()< +#include +#include + +namespace krino{ +namespace YAML_Parser { + +void parse(); +std::string info(const YAML::Node & node); + +const YAML::Node +get_if_present(const YAML::Node& node, const std::string& key); + +/// these can be used to check and ensure a type of yaml node is as expected +const YAML::Node +get_type_if_present(const YAML::Node& node, const std::string& key, YAML::NodeType::value type); + +inline const YAML::Node +get_null_if_present(const YAML::Node& node, const std::string& key) {return get_type_if_present(node, key, YAML::NodeType::Null); } + +inline const YAML::Node +get_scalar_if_present(const YAML::Node& node, const std::string& key) {return get_type_if_present(node, key, YAML::NodeType::Scalar); } + +inline const YAML::Node +get_sequence_if_present(const YAML::Node& node, const std::string& key) {return get_type_if_present(node, key, YAML::NodeType::Sequence); } + +inline const YAML::Node +get_map_if_present(const YAML::Node& node, const std::string& key) {return get_type_if_present(node, key, YAML::NodeType::Map); } + +/// Doesn't change @param result unless the @param key is present in the @param node +template +bool get_if_present(const YAML::Node & node, const std::string& key, T& result) +{ + const YAML::Node value = get_if_present(node, key); + if (value) + { + result = value.as(); + return true; + } + return false; +} + +template<> +bool get_if_present(const YAML::Node & node, const std::string& key, bool& result); + +} // namespace parser +} // namespace krino + +#endif // Akri_YAML_Parser_h diff --git a/packages/krino/krino/parser/CMakeLists.txt b/packages/krino/krino/parser/CMakeLists.txt new file mode 100644 index 000000000000..66cbc42a19c1 --- /dev/null +++ b/packages/krino/krino/parser/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_parser_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + DEPLIBS krino_lib krino_region_lib) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_parser_lib) + diff --git a/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.cpp b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.cpp new file mode 100644 index 000000000000..432c925d4a24 --- /dev/null +++ b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.cpp @@ -0,0 +1,230 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include + +namespace krino { +namespace rebalance_utils { + +namespace { + +class MultipleCriteriaSettings : public stk::balance::GraphCreationSettings +{ +public: + MultipleCriteriaSettings(stk::mesh::BulkData & stkMeshBulkData, + const std::vector *> critFields, + const double default_weight = 0.0) + : m_stkMeshBulkData(stkMeshBulkData), + m_critFields(critFields), + m_defaultWeight(default_weight) + { + method = "rcb"; + setUseNodeBalancer(true); + setNodeBalancerTargetLoadBalance(getImbalanceTolerance()); + setNodeBalancerMaxIterations(10); + } + virtual ~MultipleCriteriaSettings() = default; + + virtual double + getGraphEdgeWeight(stk::topology element1Topology, stk::topology element2Topology) const override + { + return 1.0; + } + virtual bool areVertexWeightsProvidedViaFields() const override { return true; } + virtual bool includeSearchResultsInGraph() const override { return false; } + virtual int getGraphVertexWeight(stk::topology type) const override { return 1; } + virtual double getImbalanceTolerance() const override { return 1.05; } + virtual void setDecompMethod(const std::string & input_method) override { method = input_method; } + virtual std::string getDecompMethod() const override { return method; } + virtual int getNumCriteria() const override { return m_critFields.size(); } + virtual bool isMultiCriteriaRebalance() const override { return true; } + virtual bool shouldFixMechanisms() const override { return false; } + + virtual double getGraphVertexWeight(stk::mesh::Entity entity, int criteria_index) const override + { + ThrowRequireWithSierraHelpMsg( + criteria_index >= 0 && static_cast(criteria_index) < m_critFields.size()); + const double * weight = stk::mesh::field_data(*m_critFields[criteria_index], entity); + if (weight != nullptr) + { + ThrowRequireWithSierraHelpMsg(*weight >= 0); + return *weight; + } + else + { + return m_defaultWeight; + } + } + +protected: + MultipleCriteriaSettings() = delete; + MultipleCriteriaSettings(const MultipleCriteriaSettings &) = delete; + MultipleCriteriaSettings & operator=(const MultipleCriteriaSettings &) = delete; + + const stk::mesh::BulkData & m_stkMeshBulkData; + const std::vector *> m_critFields; + const double m_defaultWeight; +}; + +class CDFEMRebalance final : public MultipleCriteriaSettings +{ +public: + CDFEMRebalance(stk::mesh::BulkData & bulk_data, + CDMesh * cdmesh, + const std::string & coordinates_field_name, + const std::vector *> & weights_fields, + const double imbalance_threshold, + const double default_weight = 0.) + : MultipleCriteriaSettings(bulk_data, weights_fields, default_weight), + my_cdmesh(cdmesh), + my_bulk_data(bulk_data), + my_coordinates_field_name(coordinates_field_name), + my_imbalance_threshold(imbalance_threshold) + {} + + ~CDFEMRebalance() = default; + + double getImbalanceTolerance() const override { return my_imbalance_threshold; } + std::string getCoordinateFieldName() const override { return my_coordinates_field_name; } + + void modifyDecomposition(stk::balance::DecompositionChangeList & decomp_changes) const override; + bool shouldPrintMetrics() const override { return true; } + bool isIncrementalRebalance() const override { return true; } + + virtual double getGraphVertexWeight(stk::mesh::Entity entity, int criteria_index) const override + { + double scaleVertexWeightForTestingDueToSmallMesh = 12; + return scaleVertexWeightForTestingDueToSmallMesh*MultipleCriteriaSettings::getGraphVertexWeight(entity, criteria_index); + } + +private: + CDMesh * my_cdmesh; + stk::mesh::BulkData & my_bulk_data; + std::string my_coordinates_field_name; + double my_imbalance_threshold; +}; + +void CDFEMRebalance::modifyDecomposition(stk::balance::DecompositionChangeList & decomp_changes) const +{ + /* Algorithm: + * 1) Go through change list and update destinations of all adaptivity children to match their + * root parent. Also move family trees with the parent+child entities. + * 2) Go through change list and remove any CDFEM child elements whose parents aren't being moved, + * as well as update the destination of all CDFEM children with parents that are being moved to + * the parent destination. + */ + + impl::update_rebalance_for_adaptivity(decomp_changes, my_bulk_data); + + if(my_cdmesh) + { + impl::update_rebalance_for_cdfem(decomp_changes, my_bulk_data, *my_cdmesh); + } +} + +} // anonymous namespace + +void +update_parent_child_rebalance_weights(const stk::mesh::BulkData & bulk_data, + stk::mesh::Field & element_weights_field, + const CDMesh * cdmesh) +{ + // First sum CDFEM child weights to their CDFEM parents, then adaptivity children to + // their parents. Adaptivity intermediate parents should not have their weights + // summed, they should be 0. + if(cdmesh) + { + impl::accumulate_cdfem_child_weights_to_parents(bulk_data, element_weights_field, *cdmesh); + } + + impl::accumulate_adaptivity_child_weights_to_parents(bulk_data, element_weights_field); +} + +bool rebalance_mesh(stk::mesh::BulkData & bulk_data, + CDMesh * cdmesh, + const std::string & element_weights_field_name, + const std::string & coordinates_field_name, + const std::vector & selections_to_rebalance_separately, + const std::string & decomp_method, + const double imbalance_threshold) +{ + const auto & meta = bulk_data.mesh_meta_data(); + auto weights_base = meta.get_field(stk::topology::ELEMENT_RANK, element_weights_field_name); + ThrowRequireMsg(weights_base, + "Failed to find element rank field " << element_weights_field_name + << " to use for rebalance weights."); + const auto element_weights_field = static_cast *>(weights_base); + + update_parent_child_rebalance_weights(bulk_data, *element_weights_field, cdmesh); + + ThrowAssert(impl::check_family_tree_element_and_side_ownership(bulk_data)); + + CDFEMRebalance balancer( + bulk_data, cdmesh, coordinates_field_name, {element_weights_field}, imbalance_threshold); + balancer.setDecompMethod(decomp_method); + const bool rebalanced = + stk::balance::balanceStkMesh(balancer, bulk_data, selections_to_rebalance_separately); + + ThrowAssert(impl::check_family_tree_element_and_side_ownership(bulk_data)); + + if(cdmesh) + { + cdmesh->rebuild_after_rebalance(); + } + + return rebalanced; +} + +bool rebalance_mesh(stk::mesh::BulkData & bulk_data, + CDMesh * cdmesh, + const std::vector & element_weights_field_names, + const std::string & coordinates_field_name, + const std::string & decomp_method, + const double imbalance_threshold) +{ + const auto & meta = bulk_data.mesh_meta_data(); + + std::vector *> weights_fields; + for (auto && field_name : element_weights_field_names) + { + auto weights_base = meta.get_field(stk::topology::ELEMENT_RANK, field_name); + ThrowRequireMsg(weights_base, + "Failed to find element rank field " << field_name << " to use for rebalance weights."); + const auto element_weights_field = static_cast *>(weights_base); + + update_parent_child_rebalance_weights(bulk_data, *element_weights_field, cdmesh); + weights_fields.push_back(element_weights_field); + } + + ThrowAssert(impl::check_family_tree_element_and_side_ownership(bulk_data)); + + CDFEMRebalance balancer( + bulk_data, cdmesh, coordinates_field_name, weights_fields, imbalance_threshold); + balancer.setDecompMethod(decomp_method); + const bool rebalanced = stk::balance::balanceStkMesh(balancer, bulk_data); + if (rebalanced) + stk::balance::balanceStkMeshNodes(balancer, bulk_data); + + ThrowAssert(impl::check_family_tree_element_and_side_ownership(bulk_data)); + + if (cdmesh) + { + cdmesh->rebuild_after_rebalance(); + } + + return rebalanced; +} +} +} + diff --git a/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.hpp b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.hpp new file mode 100644 index 000000000000..dc77cc83328f --- /dev/null +++ b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils.hpp @@ -0,0 +1,46 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_H_ +#define KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_H_ + +#include +#include +#include + +namespace krino { class CDMesh; } + +namespace krino { +namespace rebalance_utils { + +// This function will call STK rebalance to rebalance the specified selections of the +// mesh based on the ELEMENT_RANK field element_weights_field. If cdmesh != nullptr the +// rebalance operation will ensure that all CDFEM child elements are moved to the same +// processor as their parent elements. The weights field will be adjusted +// such that the parent elements are weighted with the sum of their child +// weights, and the child weights are 0 for both CDFEM and adaptivity parents/children. +bool rebalance_mesh(stk::mesh::BulkData & bulk_data, + CDMesh * cdmesh, + const std::string & element_weights_field_name, + const std::string & coordinates_field_name, + const std::vector & selections_to_rebalance_separately, + const std::string & decomp_method = "parmetis", + const double imbalance_threshold = 1.05); + +// This version handles multiple criteria rebalancing with different weights for each +// criterion. +bool rebalance_mesh(stk::mesh::BulkData & bulk_data, + CDMesh * cdmesh, + const std::vector & element_weights_field_names, + const std::string & coordinates_field_name, + const std::string & decomp_method = "parmetis", + const double imbalance_threshold = 1.05); +} +} + +#endif /* KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_H_ */ diff --git a/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.cpp b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.cpp new file mode 100644 index 000000000000..2b6f450d3546 --- /dev/null +++ b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.cpp @@ -0,0 +1,348 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { +namespace rebalance_utils { +namespace impl { + +void set_family_tree_destinations(stk::balance::DecompositionChangeList & decomp_changes, const stk::mesh::BulkData & bulk_data) +{ + // At this point decomp_changes has all adaptivity parent + child elements that are moving + // and their dest procs match. + // First iterate the element family trees and set their destinations. + auto changes = decomp_changes.get_all_partition_changes(); + for (auto && change : changes) + { + const auto elem = change.first; + const auto dest_proc = change.second; + + const auto * fts = bulk_data.begin(elem, stk::topology::CONSTRAINT_RANK); + const int num_fts = bulk_data.num_connectivity(elem, stk::topology::CONSTRAINT_RANK); + for (int i = 0; i < num_fts; ++i) + { + if (bulk_data.bucket(elem).owned()) + { + ThrowRequire(!decomp_changes.has_entity(fts[i]) || + decomp_changes.get_entity_destination(fts[i]) == dest_proc); + decomp_changes.set_entity_destination(fts[i], dest_proc); + } + } + } + + std::vector child_sides; + const auto side_rank = bulk_data.mesh_meta_data().side_rank(); + changes = decomp_changes.get_all_partition_changes(); + for (auto && change : changes) + { + const auto elem = change.first; + const auto dest_proc = change.second; + + if (bulk_data.entity_rank(elem) != stk::topology::ELEMENT_RANK || + is_refinement_child(bulk_data, elem) || !has_refinement_children(bulk_data, elem)) + continue; + + const auto * root_sides = bulk_data.begin(elem, side_rank); + const int num_root_sides = bulk_data.num_connectivity(elem, side_rank); + for (int i = 0; i < num_root_sides; ++i) + { + if (!bulk_data.bucket(root_sides[i]).owned()) continue; + + get_refinement_all_children(bulk_data, root_sides[i], child_sides); + child_sides.push_back(root_sides[i]); + + for (auto && child_side : child_sides) + { + ThrowRequire(bulk_data.bucket(child_side).owned()); + const auto * fts = bulk_data.begin(child_side, stk::topology::CONSTRAINT_RANK); + const int num_fts = bulk_data.num_connectivity(child_side, stk::topology::CONSTRAINT_RANK); + for (int j = 0; j < num_fts; ++j) + { + const auto ft = fts[j]; + if (!decomp_changes.has_entity(ft) || + decomp_changes.get_entity_destination(ft) > dest_proc) + { + decomp_changes.set_entity_destination(ft, dest_proc); + } + } + } + } + } +} + +void +update_rebalance_for_adaptivity(stk::balance::DecompositionChangeList & decomp_changes, + const stk::mesh::BulkData & bulk_data) +{ + auto all_changes = decomp_changes.get_all_partition_changes(); + + // First pass remove all refinement children from the list of changes. + // Second pass will set their destinations all to the destination of their root parent + // if it is moving. + for(auto && change : all_changes) + { + stk::mesh::Entity entity = change.first; + if(is_refinement_child(bulk_data, entity)) + { + decomp_changes.delete_entity(entity); + } + } + + all_changes = decomp_changes.get_all_partition_changes(); + stk::mesh::EntityVector adapt_children; + for(auto && change : all_changes) + { + stk::mesh::Entity entity = change.first; + const auto dest = change.second; + + get_refinement_all_children(bulk_data, entity, adapt_children); + for(auto && child : adapt_children) + { + decomp_changes.set_entity_destination(child, dest); + } + } + + set_family_tree_destinations(decomp_changes, bulk_data); + + all_changes = decomp_changes.get_all_partition_changes(); + for(auto && change : all_changes) + { + stk::mesh::Entity entity = change.first; + const auto dest = change.second; + + if (bulk_data.entity_rank(entity) == stk::topology::CONSTRAINT_RANK) + { + auto side_rank = bulk_data.mesh_meta_data().side_rank(); + const auto * conn_sides = bulk_data.begin(entity, side_rank); + const int num_sides = bulk_data.num_connectivity(entity, side_rank); + for (int i = 0; i < num_sides; ++i) + { + ThrowRequire(!decomp_changes.has_entity(conn_sides[i])); + const auto * conn_fts = bulk_data.begin(conn_sides[i], stk::topology::CONSTRAINT_RANK); + const int num_fts = + bulk_data.num_connectivity(conn_sides[i], stk::topology::CONSTRAINT_RANK); + for (int j = 0; j < num_fts; ++j) + { + ThrowErrorMsgIf(decomp_changes.get_entity_destination(conn_fts[j]) != dest, + "Family Tree:\n" << debug_entity(bulk_data, conn_fts[j]) + << "\nHas destination proc = " + << decomp_changes.get_entity_destination(conn_fts[j]) + << ", which is different than " << dest + << " the destination for family tree:\n" + << debug_entity(bulk_data, entity) << "\n\n"); + } + } + } + } +} + +void +update_rebalance_for_cdfem(stk::balance::DecompositionChangeList & decomp_changes, + const stk::mesh::BulkData & bulk_data, + const CDMesh & cdmesh) +{ + auto all_changes = decomp_changes.get_all_partition_changes(); + std::vector subelements; + const auto & cdfem_parent_part = cdmesh.get_parent_part(); + const auto & cdfem_child_part = cdmesh.get_child_part(); + for(auto && change : all_changes) + { + stk::mesh::Entity entity = change.first; + const auto dest = change.second; + + if(bulk_data.bucket(entity).member(cdfem_parent_part)) + { + const auto * mesh_elem = cdmesh.find_mesh_element(bulk_data.identifier(entity)); + ThrowRequire(mesh_elem); + + subelements.clear(); + mesh_elem->get_subelements(subelements); + + for(auto && subelem : subelements) + { + auto subelem_entity = subelem->entity(); + ThrowRequire(bulk_data.is_valid(subelem_entity)); + + decomp_changes.set_entity_destination(subelem_entity, dest); + } + } + else if(bulk_data.bucket(entity).member(cdfem_child_part)) + { + const auto parent_elem = cdmesh.get_parent_element(entity); + if(!decomp_changes.has_entity(parent_elem)) decomp_changes.delete_entity(entity); + } + } +} + +void +accumulate_cdfem_child_weights_to_parents(const stk::mesh::BulkData & bulk_data, + stk::mesh::Field & element_weights_field, + const CDMesh & cdmesh) +{ + auto selector = + stk::mesh::selectField(element_weights_field) & cdmesh.get_child_part() & + bulk_data.mesh_meta_data().locally_owned_part(); + const auto & buckets = bulk_data.get_buckets(stk::topology::ELEMENT_RANK, selector); + for(auto && b_ptr : buckets) + { + double * weight_data = stk::mesh::field_data(element_weights_field, *b_ptr); + const int b_size = b_ptr->size(); + for(int i=0; i < b_size; ++i) + { + const auto child_elem = (*b_ptr)[i]; + const auto parent = cdmesh.get_parent_element(child_elem); + double * parent_weight_data = stk::mesh::field_data(element_weights_field, parent); + ThrowRequire(parent_weight_data); + *parent_weight_data += weight_data[i]; + weight_data[i] = 0.; + } + } +} + +void accumulate_adaptivity_child_weights_to_parents( + const stk::mesh::BulkData & bulk_data, stk::mesh::Field & element_weights_field) +{ + auto selector = stk::mesh::selectField(element_weights_field) & + bulk_data.mesh_meta_data().locally_owned_part(); + std::vector all_children; + const auto & buckets = bulk_data.get_buckets(stk::topology::ELEMENT_RANK, selector); + for (auto && b_ptr : buckets) + { + for (auto && elem : *b_ptr) + { + if (is_refinement_child(bulk_data, elem)) continue; + + all_children.clear(); + get_refinement_all_children(bulk_data, elem, all_children); + + double child_weights_sum = 0.; + for (auto && child : all_children) + { + double & child_weight = *stk::mesh::field_data(element_weights_field, child); + child_weights_sum += child_weight; + child_weight = 0.; + } + double & parent_weight = *stk::mesh::field_data(element_weights_field, elem); + parent_weight += child_weights_sum; + } + } +} + +namespace +{ +bool is_owned(const stk::mesh::BulkData & mesh, const stk::mesh::Entity entity) +{ + const bool owned_part = mesh.bucket(entity).member(mesh.mesh_meta_data().locally_owned_part()); + const bool owner_rank = mesh.parallel_rank() == mesh.parallel_owner_rank(entity); + ThrowErrorMsgIf(owned_part != owner_rank, + "Mismatch between parallel_owner_rank and locally_owned_part membership for:\n" + << debug_entity(mesh, entity) << "\n"); + return owner_rank; +} +} + +bool check_family_tree_element_and_side_ownership(const stk::mesh::BulkData & bulk_data) +{ + const auto & meta = bulk_data.mesh_meta_data(); + bool passed = true; + + const auto & locally_owned_part = meta.locally_owned_part(); + const auto & elem_buckets = bulk_data.get_buckets(stk::topology::ELEMENT_RANK, locally_owned_part); + for(auto && b_ptr : elem_buckets) + { + for(auto && elem : *b_ptr) + { + const auto * fts = bulk_data.begin(elem, stk::topology::CONSTRAINT_RANK); + const int num_fts = bulk_data.num_connectivity(elem, stk::topology::CONSTRAINT_RANK); + for(int i=0; i < num_fts; ++i) + { + if(!is_owned(bulk_data, fts[i])) + { + krinolog << "Found non-owned family tree connected to owned element.\n"; + krinolog << "Family tree:\n" << debug_entity(bulk_data, fts[i]) << "\n"; + passed = false; + } + } + } + } + const auto side_rank = meta.side_rank(); + const auto & side_buckets = bulk_data.get_buckets(side_rank, locally_owned_part); + for(auto && b_ptr : side_buckets) + { + for(auto && side : *b_ptr) + { + const auto * fts = bulk_data.begin(side, stk::topology::CONSTRAINT_RANK); + const int num_fts = bulk_data.num_connectivity(side, stk::topology::CONSTRAINT_RANK); + for(int i=0; i < num_fts; ++i) + { + if(!is_owned(bulk_data, fts[i])) + { + krinolog << "Found non-owned family tree connected to owned side.\n"; + krinolog << "Family tree:\n" << debug_entity(bulk_data, fts[i]) << "\n"; + passed = false; + } + } + } + } + + const auto & ft_buckets = bulk_data.get_buckets(stk::topology::CONSTRAINT_RANK, locally_owned_part); + for(auto && b_ptr : ft_buckets) + { + for(auto && ft : *b_ptr) + { + const auto * elems = bulk_data.begin(ft, stk::topology::ELEMENT_RANK); + const int num_elems = bulk_data.num_connectivity(ft, stk::topology::ELEMENT_RANK); + for(int i=0; i < num_elems; ++i) + { + if(!is_owned(bulk_data, elems[i])) + { + krinolog << "Found non-owned element connected to owned family tree.\n"; + krinolog << "Element ID:\n" << bulk_data.identifier(elems[i]) << "\n"; + krinolog << "Family tree:\n" << debug_entity(bulk_data, ft) << "\n"; + passed = false; + } + } + const auto * sides = bulk_data.begin(ft, side_rank); + const int num_sides = bulk_data.num_connectivity(ft, side_rank); + for(int i=0; i < num_sides; ++i) + { + if(!is_owned(bulk_data, sides[i])) + { + krinolog << "Found non-owned side connected to owned family tree.\n"; + krinolog << "Element ID:\n" << bulk_data.identifier(sides[i]) << "\n"; + krinolog << "Family tree:\n" << debug_entity(bulk_data, ft) << "\n"; + passed = false; + } + } + } + } + + return passed; +} + +} +} +} diff --git a/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.hpp b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.hpp new file mode 100644 index 000000000000..85865baa15a4 --- /dev/null +++ b/packages/krino/krino/rebalance_utils/Akri_RebalanceUtils_Impl.hpp @@ -0,0 +1,44 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_IMPL_H_ +#define KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_IMPL_H_ + +#include + +namespace stk { namespace balance { class DecompositionChangeList; } } +namespace stk { namespace mesh { class BulkData; } } +namespace krino { class CDMesh; } + +namespace krino { +namespace rebalance_utils { +namespace impl { + +void +update_rebalance_for_adaptivity(stk::balance::DecompositionChangeList & decomp, + const stk::mesh::BulkData & bulk_data); + +void +update_rebalance_for_cdfem(stk::balance::DecompositionChangeList & decomp, + const stk::mesh::BulkData & bulk_data, + const CDMesh & cdmesh); + +void +accumulate_cdfem_child_weights_to_parents(const stk::mesh::BulkData & bulk_data, + stk::mesh::Field & element_weights_field, + const CDMesh & cdmesh); + +void accumulate_adaptivity_child_weights_to_parents( + const stk::mesh::BulkData & bulk_data, stk::mesh::Field & element_weights_field); + +bool check_family_tree_element_and_side_ownership(const stk::mesh::BulkData & bulk_data); +} +} +} + +#endif /* KRINO_REBALANCE_UTILS_INCLUDE_AKRI_REBALANCEUTILS_IMPL_H_ */ diff --git a/packages/krino/krino/rebalance_utils/CMakeLists.txt b/packages/krino/krino/rebalance_utils/CMakeLists.txt new file mode 100644 index 000000000000..b2820a96ae3b --- /dev/null +++ b/packages/krino/krino/rebalance_utils/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_rebalance_utils_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + DEPLIBS krino_lib) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_rebalance_utils_lib) + diff --git a/packages/krino/krino/region/Akri_Region.cpp b/packages/krino/krino/region/Akri_Region.cpp new file mode 100644 index 000000000000..ebf7ac13eade --- /dev/null +++ b/packages/krino/krino/region/Akri_Region.cpp @@ -0,0 +1,664 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino{ + +//-------------------------------------------------------------------------------- + +Region::Region(Simulation & owning_simulation, const std::string & regionName) +: my_simulation(owning_simulation), + my_meta(nullptr), + my_bulk(nullptr), + my_name(regionName), + my_timerRegion(std::string("Region ") + regionName, sierra::Diag::TIMER_REGION, my_simulation.get_timer()), + my_timerInitialize("Initialize", my_timerRegion), + my_timerExecute("Execute", my_timerRegion), + my_timerMeshInput("Mesh input", my_timerRegion), + my_timerMeshOutput("Mesh output", my_timerRegion), + my_output_file_index(0), + my_output_file_created(false), + my_initial_refinement_levels(0) +{ /* %TRACE[ON]% */ Trace trace__("krino::Region::Region()"); /* %TRACE% */ + my_simulation.add_region(this); + myIOBroker = std::make_unique(stk::EnvData::parallel_comm()); + + std::vector entity_rank_names = stk::mesh::entity_rank_names(); + entity_rank_names.push_back("FAMILY_TREE"); + stk_IO().set_rank_name_vector(entity_rank_names); + + my_results_options = std::make_unique(); +} +//-------------------------------------------------------------------------------- +Region::~Region() +{ +} + +static bool locally_has_64bit_ids_in_use_for_nodes_or_elements(const stk::mesh::BulkData & mesh) +{ + const uint64_t max32bitId = ~0U; + for (auto entityRank : {stk::topology::NODE_RANK, stk::topology::ELEMENT_RANK}) + for (auto && bucketPtr : mesh.buckets(entityRank)) + for (auto && entity : *bucketPtr) + if (mesh.identifier(entity) > max32bitId) + return true; + + return false; +} + +static bool cdfem_mesh_displacements_requested_in_results_fields(const std::string & cdfemMeshDisplacementsFieldName, const std::set & resultsFields) +{ + for (auto && resultsField : resultsFields) + if (stk::equal_case(resultsField.first, cdfemMeshDisplacementsFieldName)) + return true; + return false; +} + +//-------------------------------------------------------------------------------- +void Region::commit() +{ /* %TRACE[ON]% */ Trace trace__("krino::Region::commit()"); /* %TRACE% */ + + auto & meta = get_stk_mesh_meta_data(); + LevelSet::setup(meta); + krino::CDFEM_Support & cdfem_support = krino::CDFEM_Support::get(meta); + + if (krino::CDFEM_Support::is_active(meta)) + { + if (cdfem_mesh_displacements_requested_in_results_fields(CDFEM_Support::cdfem_mesh_displacements_field_name(), my_results_options->get_nodal_fields())) + cdfem_support.register_cdfem_mesh_displacements_field(); + + if (cdfem_support.get_num_initial_decomposition_cycles() > 1) + cdfem_support.register_parent_node_ids_field(); // Needed to use piecewise linear location on previously cut edges + + cdfem_support.setup_fields(); + } + + auto & active_part = AuxMetaData::get(meta).active_part(); + stk::mesh::BulkData::AutomaticAuraOption auto_aura_option = stk::mesh::BulkData::NO_AUTO_AURA; + + if (my_initial_refinement_levels > 0 || (krino::CDFEM_Support::is_active(meta) && cdfem_support.get_interface_maximum_refinement_level() > 0) || + (krino::CDFEM_Support::is_active(meta) && cdfem_support.get_post_cdfem_refinement_levels() > 0)) + { + auto_aura_option = stk::mesh::BulkData::AUTO_AURA; + HAdapt::setup(meta, active_part, my_timerExecute); + } + + if (cdfem_support.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + { + auto_aura_option = stk::mesh::BulkData::AUTO_AURA; + } + + if (krino::CDFEM_Support::is_active(meta)) + { + cdfem_support.add_interpolation_field(cdfem_support.get_coords_field()); + const LevelSetManager & region_ls = LevelSetManager::get(meta); + for(auto&& ls : region_ls) + { + cdfem_support.add_interpolation_field(ls->get_distance_field()); + } + cdfem_support.finalize_fields(); + + if(cdfem_support.get_interface_maximum_refinement_level() > 0 || + cdfem_support.get_post_cdfem_refinement_levels() > 0) + { + cdfem_support.set_nonconformal_hadapt( + [&meta](const std::string & marker_field, int debug_level) + { + HAdapt::do_adaptive_refinement(meta, marker_field); + }); + } + } + + if (nullptr != my_generated_mesh.get()) + { + set_generated_mesh_domain(); + my_generated_mesh->populate_mesh(stk::EnvData::parallel_comm(), auto_aura_option); + my_bulk = &my_generated_mesh->bulk_data(); + stk_IO().set_bulk_data( Teuchos::rcpFromRef( *my_bulk ) ); + if (my_generated_mesh->has_flat_boundaries()) + my_generated_mesh->create_domain_sides(); + } + else + { + my_bulk = new stk::mesh::BulkData(meta,stk::EnvData::parallel_comm(),auto_aura_option); + stk_IO().set_bulk_data( Teuchos::rcp( my_bulk ) ); + stk_IO().populate_bulk_data(); + } + + if (AuxMetaData::get(get_stk_mesh_meta_data()).get_assert_32bit_flag()) + { + const bool has_64bit_ids_in_use = stk::is_true_on_any_proc(my_bulk->parallel(), locally_has_64bit_ids_in_use_for_nodes_or_elements(*my_bulk)); + ThrowErrorMsgIf(has_64bit_ids_in_use, "Option use_32_bit ids is active, but input file uses 64 bit ids."); + } + else + { + my_bulk->set_large_ids_flag(true); + } + + if (my_bulk->is_automatic_aura_on() || my_bulk->parallel_size() == 1) + { + // Used for element side connectivty checks + stk::mesh::create_exposed_block_boundary_sides(*my_bulk, meta.universal_part(), {&AuxMetaData::get(meta).exposed_boundary_part()}); + } + + + + activate_all_entities(*my_bulk, active_part); + + LevelSet::post_commit_setup(meta); +} + +namespace { + +void zero_error_indicator(const LevelSetManager & region_ls, stk::mesh::BulkData & mesh) +{ + auto & meta = mesh.mesh_meta_data(); + const auto & cdfem_support = CDFEM_Support::get(meta); + const auto & aux_meta = AuxMetaData::get(meta); + auto indicator_field = + aux_meta.get_field(stk::topology::ELEMENT_RANK, + cdfem_support.get_nonconformal_adapt_indicator_name()); + + const auto & buckets = mesh.get_buckets(stk::topology::ELEMENT_RANK, + meta.locally_owned_part()); + for(auto && b_ptr : buckets) + { + auto * data = field_data(indicator_field, *b_ptr); + auto length = b_ptr->size(); + std::fill(data, data + length, 0.); + } +} + +void mark_selected_elements(const std::string & marker_field_name, const int current_refinement_level, const AuxMetaData & auxMeta, const int max_refinement_levels, const stk::mesh::Selector & selector) +{ + FieldRef marker_field = auxMeta.get_field(stk::topology::ELEMENT_RANK, marker_field_name); + const bool do_adapt = current_refinement_level < max_refinement_levels; + if (do_adapt) + { + stk::mesh::field_fill(1, marker_field, selector); + } +} + +void do_adaptive_refinement(const krino::CDFEM_Support & cdfemSupport, const LevelSetManager & region_ls, stk::mesh::BulkData & mesh) +{ + const auto target_count = cdfemSupport.get_nonconformal_adapt_target_count(); + if(target_count > 0) zero_error_indicator(region_ls, mesh); + { + stk::diag::TimeBlock adapt_timer__(cdfemSupport.get_timer_adapt()); + + const std::string & marker_name = "refine_field"; //cdfemSupport.get_nonconformal_adapt_marker_name(); + auto & h_adapt = cdfemSupport.get_nonconformal_hadapt(); + + const int num_refinement_levels = cdfemSupport.get_interface_maximum_refinement_level(); + const int num_refinement_steps = (target_count > 0) ? num_refinement_levels : 2*num_refinement_levels; + + const auto & indicator_field_name = cdfemSupport.get_nonconformal_adapt_indicator_name(); + + const bool do_post_adapt_refinement = cdfemSupport.get_post_adapt_refinement_levels() > 0; + std::function marker_function = + [&mesh, ®ion_ls, num_refinement_steps, do_post_adapt_refinement, target_count, indicator_field_name] + (const std::string & marker_field_name, int num_refinements) + { + const bool do_adapt = num_refinements < num_refinement_steps; + const bool more_to_do = do_adapt || do_post_adapt_refinement; + if(target_count > 0) zero_error_indicator(region_ls, mesh); + LevelSet::initialize(mesh.mesh_meta_data(), more_to_do); + if(!do_adapt) return; + + if(target_count == 0) + { + const LevelSetInterfaceGeometry interfaceGeometry(mesh.mesh_meta_data()); + CDMesh::mark_interface_elements_for_adaptivity(mesh, interfaceGeometry, marker_field_name, num_refinements); + } + else + { + HAdapt::mark_based_on_indicator_field(mesh, + marker_field_name, + indicator_field_name, + num_refinement_steps, + num_refinements, + target_count); + } + }; + + perform_multilevel_adaptivity(mesh, marker_name, marker_function, h_adapt, cdfem_do_not_refine_or_unrefine_selector(cdfemSupport)); + } +} + +void do_post_adapt_uniform_refinement(const Simulation & simulation, const krino::CDFEM_Support & cdfemSupport, const AuxMetaData & auxMeta, stk::mesh::BulkData & mesh) +{ + if ( cdfemSupport.get_post_adapt_refinement_levels() > 0 ) + { + if ( simulation.is_transient() ) + { + krinolog << "Can not do post-adaptivity uniform mesh refinement for transient problems..."; + } + else + { + krinolog << "Performing " << cdfemSupport.get_post_adapt_refinement_levels() << " levels of post-adaptivity uniform mesh refinement..." << std::endl; + + // Doing adaptive refinement with a uniform marker is better than doing uniform refinement here because of how + // the transition elements are handled. + const std::string & marker_name = "refine_field"; + auto & h_adapt = cdfemSupport.get_nonconformal_hadapt(); + const int num_levels = cdfemSupport.get_post_adapt_refinement_levels(); + FieldRef marker_field = auxMeta.get_field(stk::topology::ELEMENT_RANK, marker_name); + + std::function marker_function = + [&mesh, marker_field, num_levels] + (const std::string & marker_field_name, int num_refinements) + { + const bool do_adapt = num_refinements < num_levels; + LevelSet::initialize(mesh.mesh_meta_data(), do_adapt); + if (do_adapt) + { + stk::mesh::field_fill(1, marker_field); + } + }; + + perform_multilevel_adaptivity(mesh, marker_name, marker_function, h_adapt, cdfem_do_not_refine_or_unrefine_selector(cdfemSupport)); + } + } +} + +void do_post_cdfem_uniform_refinement(const Simulation & simulation, const krino::CDFEM_Support & cdfemSupport, const AuxMetaData & auxMeta, stk::mesh::BulkData & mesh) +{ + if ( cdfemSupport.get_post_cdfem_refinement_levels() > 0 ) + { + const int num_levels = cdfemSupport.get_post_cdfem_refinement_levels(); + if ( simulation.is_transient() ) + { + krinolog << "Can not do post-cdfem mesh refinement for transient problems..."; + } + else + { + krinolog << "Performing " << num_levels << " levels of post-cdfem mesh refinement..." << std::endl; + + // Doing adaptive refinement with a uniform marker is better than doing uniform refinement here because of how + // the transition elements are handled. + const std::string & marker_name = "refine_field"; + auto & h_adapt = cdfemSupport.get_nonconformal_hadapt(); + const stk::mesh::Selector & refinement_selector = cdfemSupport.get_post_cdfem_refinement_selector(); + std::function marker_function = + [&auxMeta, num_levels, &refinement_selector] + (const std::string & marker_field_name, int num_refinements) + { + mark_selected_elements(marker_field_name, num_refinements, auxMeta, num_levels, refinement_selector); + }; + + CDMesh::get_new_mesh()->delete_cdfem_parent_elements(); // Extreme work-around for the way percept messes up the active part on cdfem parents. + perform_multilevel_adaptivity(mesh, marker_name, marker_function, h_adapt); + } + } +} + +} + +//-------------------------------------------------------------------------------- +void Region::initialize() +{ /* %TRACE[ON]% */ Trace trace__("krino::Region::initialize()"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timerInitialize); + + const bool cdfem_is_active = krino::CDFEM_Support::is_active(get_stk_mesh_meta_data()); + krino::CDFEM_Support & cdfem_support = krino::CDFEM_Support::get(get_stk_mesh_meta_data()); + const bool adapt_is_active = cdfem_support.get_interface_maximum_refinement_level() > 0 || + cdfem_support.get_post_cdfem_refinement_levels() > 0; + + const LevelSetManager & region_ls = LevelSetManager::get(get_stk_mesh_meta_data()); + + if (my_initial_refinement_levels > 0) + { + cdfem_support.set_global_ids_are_NOT_parallel_consistent(); + HAdapt::do_uniform_refinement(get_stk_mesh_meta_data(), my_initial_refinement_levels); + } + + if (cdfem_is_active) + { + auto & bulk = get_stk_mesh_bulk_data(); + if(adapt_is_active) + { + do_adaptive_refinement(cdfem_support, region_ls, bulk); + + const auto & auxMeta = AuxMetaData::get(get_stk_mesh_meta_data()); + do_post_adapt_uniform_refinement(my_simulation, cdfem_support, auxMeta, bulk); + + const LevelSetInterfaceGeometry interfaceGeometry(get_stk_mesh_meta_data()); + krino::CDMesh::decompose_mesh(bulk, interfaceGeometry, my_simulation.get_time_step_count(), {}); + + do_post_cdfem_uniform_refinement(my_simulation, cdfem_support, auxMeta, bulk); + } + else + { + if ( cdfem_support.get_post_adapt_refinement_levels() > 0 ) + { + krinolog << "Post-adaptivity uniform refinement levels selected without any adaptivity levels. Not performing additional uniform refinement." << std::endl; + } + + const int num_init_decomp_cycles = cdfem_support.get_num_initial_decomposition_cycles(); + for (int icycle=0; icycleinitialize(0.); + + if (my_simulation.is_transient()) + { + // initialize does not end with the facets constructed so manually construct them now + ls->build_facets_locally(get_stk_mesh_meta_data().universal_part()); + + // debugging + if (krinolog.shouldPrint(LOG_FACETS)) + { + ls->facets_exoii(); + } + } + } + } + + // Skip output of empty parts + for (auto && part : get_stk_mesh_meta_data().get_parts()) + { + if (stk::io::is_part_io_part(*part)) + { + uint64_t local_num_entities = stk::mesh::count_selected_entities( + *part, get_stk_mesh_bulk_data().buckets(part->primary_entity_rank())); + uint64_t global_num_entities = 0; + stk::all_reduce_sum( + get_stk_mesh_bulk_data().parallel(), &local_num_entities, &global_num_entities, 1); + if(global_num_entities == 0) + { + stk::io::remove_io_part_attribute(*part); + } + } + } +} +//-------------------------------------------------------------------------------- + +void Region::execute() +{ /* %TRACE[ON]% */ Trace trace__("krino::Region::execute()"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timerExecute); + + // This is a hack for now to exit immediately when CDFEM is active + if (krino::CDFEM_Support::is_active(get_stk_mesh_meta_data())) + { + return; + } + + double deltaTime = time_step(); + + const LevelSetManager & region_ls = LevelSetManager::get(get_stk_mesh_meta_data()); + for(auto&& ls : region_ls) + { + ls->advance_semilagrangian(deltaTime); + } +} + +unsigned Region::spatial_dimension() const { return my_meta->spatial_dimension(); } +const stk::mesh::BulkData& Region::get_stk_mesh_bulk_data() const { ThrowRequire(my_bulk); return *my_bulk; } +stk::mesh::BulkData& Region::get_stk_mesh_bulk_data() { ThrowRequire(my_bulk); return *my_bulk; } +const stk::mesh::MetaData& Region::get_stk_mesh_meta_data() const { ThrowRequire(my_meta); return *my_meta; } +stk::mesh::MetaData& Region::get_stk_mesh_meta_data() { ThrowRequire(my_meta); return *my_meta; } +double Region::time_step() const { return my_simulation.get_time_step(); } + +stk::io::StkMeshIoBroker & Region::stk_IO() +{ + ThrowRequire(myIOBroker); + return *myIOBroker; +} + +Ioss::Region * Region::get_input_io_region() +{ + return stk_IO().get_input_io_region().get(); +} + +std::string Region::name_of_input_mesh() const +{ + return my_input_model_name; +} + +void Region::create_output_mesh() +{ + bool output_mesh = my_results_options->get_num_step_increments() != 0; + + if(!output_mesh) return; + + my_results_options->get_scheduler().set_termination_time(my_simulation.get_stop_time()); + + my_output_file_index = stk_IO().create_output_mesh(my_results_options->get_filename(), stk::io::WRITE_RESULTS, my_results_options->get_properties()); + + Teuchos::RCP active_selector = Teuchos::rcp(new stk::mesh::Selector(AuxMetaData::get(get_stk_mesh_meta_data()).active_part())); + stk_IO().set_subset_selector(my_output_file_index, active_selector); + + stk_IO().write_output_mesh(my_output_file_index); + + declare_output_variables(my_output_file_index); + + my_output_file_created = true; +} + +void +Region::declare_output_variables(size_t result_output_index) +{ + for (auto && outField : my_results_options->get_nodal_fields()) + { + const std::string & varName = outField.first; + const std::string & newName = outField.second; + stk::mesh::FieldBase *theField = get_stk_mesh_meta_data().get_field(stk::topology::NODE_RANK, varName); + if ( nullptr == theField ) + { + krinolog << "Sorry, no nodal field by the name " << varName << std::endl; + krinolog << "Available fields: " << std::endl; + for (auto && field : get_stk_mesh_meta_data().get_fields(stk::topology::NODE_RANK)) + { + krinolog << " " << field->name() << std::endl; + } + } + else + { + stk_IO().add_field(result_output_index, *theField, newName); + } + } + + for (auto && outField : my_results_options->get_element_fields()) + { + const std::string & varName = outField.first; + const std::string & newName = outField.second; + stk::mesh::FieldBase *theField = get_stk_mesh_meta_data().get_field(stk::topology::ELEMENT_RANK, varName); + if ( nullptr == theField ) + { + krinolog << "Sorry, no element field by the name " << varName << std::endl; + krinolog << "Available fields: " << std::endl; + for (auto && field : get_stk_mesh_meta_data().get_fields(stk::topology::ELEMENT_RANK)) + { + krinolog << " " << field->name() << std::endl; + } + } + else + { + stk_IO().add_field(result_output_index, *theField, newName); + } + } +} + +void Region::process_output(bool forceOutput) +{ + stk::diag::TimeBlock mesh_output_timeblock(my_timerMeshOutput); + + if(my_results_options->get_num_step_increments() == 0) return; + + stk::util::Scheduler & scheduler = my_results_options->get_scheduler(); + + if(forceOutput) scheduler.set_force_schedule(); + + const int stepCounter = my_simulation.get_time_step_count(); + const double currentTime = my_simulation.get_current_time(); + + const bool doOutput = scheduler.is_it_time(currentTime, stepCounter); + + if(!doOutput) return; + + // A couple of krino tests that just compute surface distances never call Region::initialize() + // where we normally create the output mesh. + if(!my_output_file_created) create_output_mesh(); + + stk_IO().begin_output_step(my_output_file_index, currentTime); + stk_IO().write_defined_output_fields(my_output_file_index); + stk_IO().end_output_step(my_output_file_index); +} + +void +Region::associate_input_mesh(const std::string & model_name, bool assert_32bit_ids, bool force_64bit_ids) +{ + stk::diag::TimeBlock mesh_input_timeblock(my_timerMeshInput); + + MeshInputOptions * db_options = MeshInputOptions::get(model_name); + ThrowRequireMsg(db_options != nullptr, "No finite element model found with name " << model_name); + my_input_model_name = model_name; + + ThrowRequire(db_options->is_valid()); + if (db_options->use_generated_mesh()) + { + stk::topology generated_mesh_element_type = db_options->get_generated_mesh_element_type(); + std::vector entity_rank_names = stk::mesh::entity_rank_names(); + entity_rank_names.push_back("FAMILY_TREE"); + my_generated_mesh = std::make_unique(generated_mesh_element_type,entity_rank_names); + my_meta = &my_generated_mesh->meta_data(); + stk::mesh::Field & coords_field = my_meta->declare_field>(stk::topology::NODE_RANK, "coordinates", 1); + stk::mesh::put_field_on_mesh(coords_field, my_meta->universal_part(), generated_mesh_element_type.dimension(), nullptr); + } + else + { + const std::string directory = sierra::Env::working_directory().c_str(); + const std::string filename(Ioss::Utils::local_filename(db_options->get_filename(), db_options->get_filetype(), directory)); + + stk::io::StkMeshIoBroker & stk_io = stk_IO(); + + stk_io.property_add(Ioss::Property("MAXIMUM_NAME_LENGTH", 180)); + + if (!db_options->get_decomposition_method().empty()) + { + stk_io.property_add(Ioss::Property("DECOMPOSITION_METHOD", Ioss::Utils::uppercase(db_options->get_decomposition_method()))); + } + + stk_io.add_mesh_database(db_options->get_filename(), stk::io::READ_MESH); + stk_io.create_input_mesh(); + my_meta = &stk_io.meta_data(); + AuxMetaData::create(*my_meta); + auto & active_part = AuxMetaData::get(*my_meta).active_part(); + stk::mesh::Selector activeSelector = active_part; + stk_io.set_active_selector(activeSelector); + } + + if (assert_32bit_ids) + { + AuxMetaData::get(*my_meta).set_assert_32bit_flag(); + } + if (!force_64bit_ids) + { + AuxMetaData::get(*my_meta).clear_force_64bit_flag(); + } +} + +void +Region::set_generated_mesh_domain() +{ + MeshInputOptions * db_options = MeshInputOptions::get(my_input_model_name); + ThrowRequire(db_options != nullptr); + my_generated_mesh->set_mesh_structure_type(db_options->get_generated_mesh_structure_type()); + const double mesh_size = db_options->get_generated_mesh_size(); + if (db_options->get_generated_mesh_domain_type() == MeshInputOptions::GENERATED_MESH_FOR_SPECIFIED_DOMAIN) + { + typename BoundingBoxMesh::BoundingBoxType bbox; + const std::vector & domain = db_options->get_generated_mesh_domain(); + if (db_options->get_generated_mesh_spatial_dimension() == 2) + { + ThrowRequire(domain.size() == 4); + const Vector3d min(domain[0], domain[1], 0.); + const Vector3d max(domain[2], domain[3], 0.); + ThrowRequireMsg(max[0]>min[0] && max[1]>min[1], "Invalid domain specified."); + bbox = BoundingBoxMesh::BoundingBoxType(min, max); + } + else + { + ThrowRequire(domain.size() == 6); + const Vector3d min(domain[0], domain[1], domain[2]); + const Vector3d max(domain[3], domain[4], domain[5]); + ThrowRequireMsg(max[0]>min[0] && max[1]>min[1] && max[2]>min[2], "Invalid domain specified."); + bbox = BoundingBoxMesh::BoundingBoxType(min, max); + } + my_generated_mesh->set_domain(bbox, mesh_size); + } + else + { + typename BoundingBoxMesh::BoundingBoxType domain_bbox; + const LevelSetManager & region_ls = LevelSetManager::get(get_stk_mesh_meta_data()); + for(auto&& ls : region_ls) + { + if (ls->has_IC_surfaces()) + { + BoundingBox ls_IC_surf_bbox = ls->get_IC_surface_bounding_box(); + domain_bbox.accommodate(ls_IC_surf_bbox); + } + } + + if (db_options->get_generated_mesh_spatial_dimension() == 2) + { + Vector3d min = domain_bbox.get_min(); + Vector3d max = domain_bbox.get_max(); + min[2] = 0.; + max[2] = 0.; + domain_bbox = typename BoundingBoxMesh::BoundingBoxType(min, max); + } + my_generated_mesh->set_domain(domain_bbox, mesh_size, 1); + } +} + +} // namespace krino + diff --git a/packages/krino/krino/region/Akri_Region.hpp b/packages/krino/krino/region/Akri_Region.hpp new file mode 100644 index 000000000000..7b175775ae6b --- /dev/null +++ b/packages/krino/krino/region/Akri_Region.hpp @@ -0,0 +1,81 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Region_h +#define Akri_Region_h + +#include +#include +#include + +namespace stk { namespace mesh { class MetaData; } } +namespace stk { namespace mesh { class BulkData; } } +namespace stk { namespace mesh { class Part; } } +namespace stk { namespace io { class StkMeshIoBroker; } } +namespace krino { class BoundingBoxMesh; } +namespace krino { class RegionForwarder; } +namespace krino { class ResultsOutputOptions; } +namespace krino { class Simulation; } +namespace Ioss { class Region; } + +namespace krino{ + +class Region { +public: + Region(Simulation & owning_simulation, const std::string & regionName); + virtual ~Region(); + + virtual void commit(); + virtual void initialize(); + virtual void execute(); + + double time_step() const; + const std::string & name() const { return my_name; } + unsigned spatial_dimension() const; + const stk::mesh::BulkData& get_stk_mesh_bulk_data() const; + stk::mesh::BulkData& get_stk_mesh_bulk_data(); + const stk::mesh::MetaData& get_stk_mesh_meta_data() const; + stk::mesh::MetaData& get_stk_mesh_meta_data(); + stk::diag::Timer & getRegionTimer() const { return my_timerRegion; } + stk::diag::Timer & getMeshInputTimer() const { return my_timerMeshInput; } + stk::diag::Timer & getMeshOutputTimer() const { return my_timerMeshOutput; } + + stk::io::StkMeshIoBroker & stk_IO(); + std::string name_of_input_mesh() const; + Ioss::Region * get_input_io_region(); + void associate_input_mesh(const std::string & model_name, bool assert_32bit_ids, bool force_64bit_ids); + void set_generated_mesh_domain(); + void create_output_mesh(); + void declare_output_variables(size_t result_output_index); + void process_output(bool forceOutput); + ResultsOutputOptions * get_results_options() { return my_results_options.get(); } + void set_initial_refinement_levels(int levels) { my_initial_refinement_levels = levels; } + +private: + Simulation & my_simulation; + stk::mesh::MetaData * my_meta; + stk::mesh::BulkData * my_bulk; + std::unique_ptr myIOBroker; + std::unique_ptr my_generated_mesh; + std::unique_ptr my_results_options; + std::string my_name; + std::string my_input_model_name; + + mutable stk::diag::Timer my_timerRegion; ///< Region's root timer + mutable stk::diag::Timer my_timerInitialize; ///< Initialize timer + mutable stk::diag::Timer my_timerExecute; ///< Execute timer + mutable stk::diag::Timer my_timerMeshInput; ///< Mesh input timer + mutable stk::diag::Timer my_timerMeshOutput; ///< Mesh output timer + size_t my_output_file_index; + bool my_output_file_created; + int my_initial_refinement_levels; +}; + +} // namespace krino + +#endif // Akri_Region_h diff --git a/packages/krino/krino/region/Akri_RegisterProduct.cpp b/packages/krino/krino/region/Akri_RegisterProduct.cpp new file mode 100644 index 000000000000..891ad313cb77 --- /dev/null +++ b/packages/krino/krino/region/Akri_RegisterProduct.cpp @@ -0,0 +1,30 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include + +namespace krino { + +const char * +get_product_name() +{ /* %TRACE% */ /* %TRACE% */ + return "Krino"; +} + + +void +register_product() +{ /* %TRACE% */ /* %TRACE% */ + // Register krino + stk::ProductRegistry::instance().addRegion(get_product_name()); +} + +} // namespace krino + diff --git a/packages/krino/krino/region/Akri_RegisterProduct.hpp b/packages/krino/krino/region/Akri_RegisterProduct.hpp new file mode 100644 index 000000000000..ab4d53824791 --- /dev/null +++ b/packages/krino/krino/region/Akri_RegisterProduct.hpp @@ -0,0 +1,20 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_RegisterProduct_h +#define Akri_RegisterProduct_h + +namespace krino { + +const char *get_product_name(); + +void register_product(); + +} // namespace krino + +#endif // Akri_RegisterProduct_h diff --git a/packages/krino/krino/region/Akri_ResultsOutputOptions.hpp b/packages/krino/krino/region/Akri_ResultsOutputOptions.hpp new file mode 100644 index 000000000000..2a0b1796bd2c --- /dev/null +++ b/packages/krino/krino/region/Akri_ResultsOutputOptions.hpp @@ -0,0 +1,88 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_ResultsOutputOptions_h +#define Akri_ResultsOutputOptions_h + +#include +#include +#include +#include +#include // for String +#include "stk_topology/topology.hpp" // for topology, etc +#include + +namespace stk { namespace mesh { class Part; } } +namespace stk { namespace mesh { class MetaData; } } + +namespace krino { + + typedef std::pair StepIncrement; + typedef std::pair FieldName_OutputName_Pair; + + class ResultsOutputOptions { + + public: + + ResultsOutputOptions() : + my_scheduler(), + my_numStepIncrements(0) + { + my_scheduler.set_lookahead(1); + my_filename = "default_filename"; + } + + stk::util::Scheduler & get_scheduler() { return my_scheduler; } + + void set_title(std::string title) { my_title = title; } + const std::string & get_title() const { return my_title; } + + void set_name(std::string theName) { my_name = theName; } + const std::string & get_name() const { return my_name; } + + void set_filename(std::string filename) { my_filename = filename; } + const std::string & get_filename() const { return my_filename; } + + void add_step_increment(int start, int increment) { + StepIncrement aStep(start, increment); + my_scheduler.add_interval(start, increment); + my_numStepIncrements++; + } + unsigned get_num_step_increments() const { return my_numStepIncrements; } + + void add_nodal_field(const std::string & internalName, const std::string & newName) + { + FieldName_OutputName_Pair aPair(internalName, newName); + my_nodal_fields.insert(aPair); + } + const std::set & get_nodal_fields() const { return my_nodal_fields; } + + void add_element_field(const std::string & internalName, const std::string & newName) + { + FieldName_OutputName_Pair aPair(internalName, newName); + my_element_fields.insert(aPair); + } + const std::set & get_element_fields() const { return my_element_fields; } + + void add_property(const Ioss::Property & property) { my_properties.add(property); } + Ioss::PropertyManager & get_properties() { return my_properties; } + + private: + stk::util::Scheduler my_scheduler; + unsigned my_numStepIncrements; + std::string my_name; + std::string my_title; + std::string my_filename; + std::set my_nodal_fields; + std::set my_element_fields; + Ioss::PropertyManager my_properties; + }; + +} // namespace krino + +#endif /* Akri_ResultsOutputOptions_h */ diff --git a/packages/krino/krino/region/Akri_Simulation.cpp b/packages/krino/krino/region/Akri_Simulation.cpp new file mode 100644 index 000000000000..313f6c1e4842 --- /dev/null +++ b/packages/krino/krino/region/Akri_Simulation.cpp @@ -0,0 +1,179 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +namespace krino{ + +std::unique_ptr Simulation::the_simulation; + +Simulation & Simulation::build(const std::string & in_name) +{ + ThrowRequireMsg(!the_simulation, "Simulation already set."); + the_simulation = std::make_unique(in_name); + return *the_simulation; +} + +Simulation & Simulation::get() +{ + ThrowRequireMsg(the_simulation, "Simulation should already be set."); + return *the_simulation; +} + +Simulation::Simulation(const std::string & in_name) + : my_name(in_name), + my_timer("krino", sierra::Diag::sierraTimer()), + my_is_transient(false), + my_stop_time(0.0), + my_step_count(0), + my_current_time(0.0), + my_time_step_size(0.0) +{ + stk::diag::setEnabledTimerMetricsMask(stk::diag::METRICS_CPU_TIME | stk::diag::METRICS_WALL_TIME); +} + +Simulation::~Simulation() {} + +void Simulation::add_region(Region * region) +{ + my_regions.emplace_back(region); +} + +void Simulation::commit() +{/* %TRACE% */ Trace trace__("krino::Simulation::commit()"); /* %TRACE% */ + for (auto && region : my_regions) + { + region->commit(); + } +} + +void Simulation::execute() +{/* %TRACE% */ Trace trace__("krino::Simulation::execute()"); /* %TRACE% */ + stk::diag::TimeBlock timer__(my_timer); + + //===================================== + // start-up procedure + //===================================== + + // initial conditions + for (auto && region : my_regions) + { + region->initialize(); + } + + for (auto && region : my_regions) + { + region->process_output(false); + } + + //===================================== + // time integration + //===================================== + + while ( my_current_time < my_stop_time ) + { + static const double sqrt_epsilon = std::sqrt(std::numeric_limits::epsilon()); + if (my_current_time+my_time_step_size > my_stop_time*(1.-sqrt_epsilon)) + { + my_time_step_size = my_stop_time - my_current_time; + my_current_time = my_stop_time; + } + else + { + my_current_time += my_time_step_size; + } + ++my_step_count; + + const double percentComplete = 100.0*my_current_time/my_stop_time; + + krinolog << "Krino Simulation " << my_name + << ", step " << my_step_count + << ", time " << my_current_time + << ", time step " << my_time_step_size + << ", " << percentComplete << "% complete" + << stk::diag::dendl; + + for (auto && region : my_regions) + { + region->execute(); + } + + for (auto && region : my_regions) + { + region->process_output(false); + } + + for (auto && region : my_regions) + { + region->get_stk_mesh_bulk_data().update_field_data_states(); + } + } + + timer__.stop(); + print_performance_info(); +} + +void +Simulation::print_performance_info() const +{ + /* %TRACE% */ Trace trace__("krino::Simulation::print_timer_information()"); /* %TRACE% */ + + sierra::Env::outputP0() << sierra::Env::section_separator() << std::endl + << "Timing summary running on " << sierra::Env::parallel_size() << " processor" << (sierra::Env::parallel_size() == 1 ? "" : "s") << std::endl; + stk::diag::printTimersTable(sierra::Env::outputP0(), sierra::Diag::sierraTimer(), stk::diag::METRICS_CPU_TIME | stk::diag::METRICS_WALL_TIME, false, sierra::Env::parallel_comm()); + sierra::Env::outputP0() << std::endl << std::endl; + + { + size_t now, hwm; + stk::get_memory_usage(now, hwm); + // min, max, sum + size_t global_now[3] = {now,now,now}; + size_t global_hwm[3] = {hwm,hwm,hwm}; + + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceSum<1>( &global_now[2] ) ); + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceMin<1>( &global_now[0] ) ); + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceMax<1>( &global_now[1] ) ); + + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceSum<1>( &global_hwm[2] ) ); + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceMin<1>( &global_hwm[0] ) ); + stk::all_reduce(sierra::Env::parallel_comm(), stk::ReduceMax<1>( &global_hwm[1] ) ); + + sierra::Env::outputP0() << "Memory Overview: " << std::endl; + + sierra::Env::outputP0() << " total (over all cores) current/high-water mark = " + << std::setw(15) << stk::human_bytes(global_now[2]) + << std::setw(15) << stk::human_bytes(global_hwm[2]) + << std::endl; + + sierra::Env::outputP0() << " min (over all cores) current/high-water mark = " + << std::setw(15) << stk::human_bytes(global_now[0]) + << std::setw(15) << stk::human_bytes(global_hwm[0]) + << std::endl; + + sierra::Env::outputP0() << " max (over all cores) current/high-water mark = " + << std::setw(15) << stk::human_bytes(global_now[1]) + << std::setw(15) << stk::human_bytes(global_hwm[1]) + << std::endl; + } +} + +} // namespace krino diff --git a/packages/krino/krino/region/Akri_Simulation.hpp b/packages/krino/krino/region/Akri_Simulation.hpp new file mode 100644 index 000000000000..62a0c300e12b --- /dev/null +++ b/packages/krino/krino/region/Akri_Simulation.hpp @@ -0,0 +1,68 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef Akri_Simulation_h +#define Akri_Simulation_h + +#include +#include +#include +#include +#include + +namespace krino{ + +class Region; + +class Simulation { +public: + static Simulation & build(const std::string & in_name); + Simulation(const std::string & in_name); // public to allow make_unique, but should be created using build() + ~Simulation(); + + void commit(); + void initialize() {} + void execute(); + + void add_region(Region * region); + + const std::string & get_name() const { return my_name; } + bool is_transient() const { return my_is_transient; } + double get_time_step() const { return my_time_step_size; } + double get_current_time() const { return my_current_time; } + double get_stop_time() const { return my_stop_time; } + int get_time_step_count() const { return my_step_count; } + + void set_time_step(const double in_time_step) { my_time_step_size = in_time_step; } + void set_current_time(const double in_time) { my_current_time = in_time; } + void set_stop_time(const double in_time) { my_is_transient = true; my_stop_time = in_time; } + + stk::diag::Timer & get_timer() const { return my_timer; } + void print_performance_info() const; + + static Simulation & get(); + static void reset() { the_simulation.reset(); } + +private: + static std::unique_ptr the_simulation; + +private: + std::string my_name; + mutable stk::diag::Timer my_timer; + bool my_is_transient; + double my_stop_time; + unsigned my_step_count; + double my_current_time; + double my_time_step_size; + std::vector> my_regions; +}; + +} // namespace krino + +#endif // Akri_Simulation_h + diff --git a/packages/krino/krino/region/Akri_Startup.cpp b/packages/krino/krino/region/Akri_Startup.cpp new file mode 100644 index 000000000000..2496ae35d651 --- /dev/null +++ b/packages/krino/krino/region/Akri_Startup.cpp @@ -0,0 +1,306 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino{ + +namespace { + +std::string +get_program_path(const char *program) +{ + // If we already have the full path, just return it + if (program[0] == '/') + return program; + + char full_path[PATH_MAX]; + if (strchr(program, '/') != nullptr) { + realpath(program, full_path); + return full_path; + } + + char *PATH = getenv("PATH"); + while (PATH && *PATH) { + // Get the character past the end of the next directory in PATH, i.e. + // either the '/' or the '\0' + char *end = strchr(PATH, ':'); + if (!end) { + end = PATH+strlen(PATH); + } + + // Set current = directory + '/' + program + strncpy(full_path, PATH, end-PATH); + full_path[end-PATH] = '/'; + strcpy(&full_path[end-PATH+1], program); + + // Check whether possible exists + if (access(full_path, X_OK) == 0) + return full_path; + + // Advance to the next directory + PATH = *end ? end+1 : end; + } + + // Not found; this shouldn't happen, but maybe the executable got deleted + // after it was invoked before we got here -- or we have some crazy + // parallel machine where the executable is inaccessible on the compute + // nodes despite it somehow having been loaded. No big deal, just return + // the non-absolute path. + return program; +} + +} // namespace + +Startup::Startup(int argc, char ** argv) + : my_flag_exit_early(false) +{ + if ( MPI_SUCCESS != MPI_Init( &argc , &argv ) ) { + throw std::runtime_error("MPI_Init failed"); + } + + stk::EnvData::instance().m_parallelComm = MPI_COMM_WORLD; + MPI_Comm_size(stk::EnvData::parallel_comm(), &stk::EnvData::instance().m_parallelSize); + MPI_Comm_rank(stk::EnvData::parallel_comm(), &stk::EnvData::instance().m_parallelRank); + + stk::register_message_type(stk::MSG_WARNING, 10000000, "Warning"); + stk::register_message_type(stk::MSG_DOOMED, 10000000, "Parser error"); + stk::register_message_type(stk::MSG_EXCEPTION, 1000000, "Exception"); + sierra::Diag::registerWriter("krinolog", krinolog, theDiagWriterParser()); + + // Register this so that -version will know this region is used. + register_product(); + + stk::set_report_handler(report_handler); + + setup_commandline_options(); + + // parse command line options + const stk::OptionsSpecification &desc = stk::get_options_specification(); + stk::ParsedOptions &parsedOptions = stk::get_parsed_options(); + stk::parse_command_line_args(argc, const_cast(argv), desc, parsedOptions); + + for (auto && writer : sierra::Diag::getWriterRegistry()) + { + if (parsedOptions.count(writer.first)) + { + writer.second.first->setPrintMask(writer.second.second->parse(parsedOptions[writer.first].as().c_str())); + } + } + + if ( parsedOptions.count("help") ) { + if (0 == stk::EnvData::parallel_rank()) + { + std::cerr << desc << std::endl; + } + my_flag_exit_early = true; + } + + if (parsedOptions.count("version")) { + if (0 == stk::EnvData::parallel_rank()) + { + std::cerr << "Version: Krino1.0" << std::endl; + } + my_flag_exit_early = true; + } + + int local_flag_exit_early = my_flag_exit_early; + MPI_Allreduce(&local_flag_exit_early, &my_flag_exit_early, 1, MPI_INT, MPI_MAX, stk::EnvData::parallel_comm()); + if (my_flag_exit_early) return; + + const std::string inputFileName = sierra::Env::get_param("input-deck"); + if (stk::EnvData::instance().m_inputFileRequired) + { + if(inputFileName == "") + { + throw std::runtime_error("No input file specified. An input file must be specified with the '-i' option"); + } + + stk::EnvData::setInputFileName(inputFileName); + } + + // setup logfile as inputFileName.log + std::string logFileName = parsedOptions["output-log"].as(); + if (logFileName == "") + { + int dotPos = inputFileName.rfind("."); + if ( -1 == dotPos ) { + // lacking extension + logFileName = inputFileName + ".log"; + } + else { + // with extension; swap with .log + logFileName = inputFileName.substr(0, dotPos) + ".log"; + } + } + + // set up output streams + const std::string output_description = + (0 == stk::EnvData::parallel_rank()) ? + "outfile=" + logFileName + " out>outfile+pout dout>out" : + "out>pout dout>out"; + std::string parallel_output_description = " pout>null"; + if (parsedOptions.count("pout")) + { + std::ostringstream s; + s << " poutfile=" << logFileName << "." << stk::EnvData::parallel_size() << "." << stk::EnvData::parallel_rank() << " pout>poutfile"; + parallel_output_description = s.str(); + } + stk::bind_output_streams(output_description+parallel_output_description); + stk::EnvData::instance().m_outputP0 = &sierra::out(); + + // output run info + const std::string program_path = get_program_path(argv[0]); + const char * build_date_time = __DATE__ " " __TIME__; + stk::EnvData::instance().m_executablePath = program_path; + + stk::EnvData::instance().m_productName = krino::get_product_name(); + stk::ProductRegistry::AttributeMap &product_attributes = stk::ProductRegistry::instance().getProductAttributeMap(sierra::Env::product_name()); + product_attributes[stk::ProductRegistry::BUILD_TIME] = build_date_time; + product_attributes[stk::ProductRegistry::EXECUTABLE] = program_path; + + sierra::Env::outputP0() + << sierra::Env::subsection_separator() + << std::endl + << "Executable Name = " << sierra::Env::product_name() << std::endl + << "Executable Version= " << stk::ProductRegistry::version() << std::endl + << "Executable Date = " << stk::ProductRegistry::instance().getProductAttribute(sierra::Env::product_name(), stk::ProductRegistry::BUILD_TIME) << std::endl + << "Executable File = " << sierra::Env::executable_file() << std::endl + << "Run Start Date = " << sierra::Env::startup_date() << std::endl << std::endl + << "Working Directory = " << sierra::Env::working_directory() << std::endl + << "Parsed Input File = " << sierra::Env::getInputFileName() << std::endl + << sierra::Env::subsection_separator() + << std::endl << std::endl ; +} + +void Startup::setup_commandline_options() +{ + stk::OptionsSpecification desc("Allowed options"); + desc.add_options() + ("help,h", "produce help message") + ("input-deck,i", "Analysis input file", stk::DefaultValue("")) + ("output-log,o", "Output log file path, one of : 'cout', 'cerr', or a file path", stk::DefaultValue("")) + ("aprepro,a", "Process (on) or don't process (off) input with aprepro. Default=on.", stk::ImplicitValue("on")) + ("define,D", "Define symbols for use in aprepro processing of input file", stk::ValueType()) + ("pout", "use separate output log file for each MPI process"); + + for (auto && writer : sierra::Diag::getWriterRegistry()) + { + std::ostringstream str; + str << "Diagnostic writer " << writer.first << std::endl; + writer.second.second->describe(str); + desc.add_options()(writer.first.c_str(), str.str().c_str(), stk::ValueType()); + } + + stk::get_options_specification().add(desc); +} + +Startup::~Startup() +{ + MPI_Finalize(); +} + +void Startup::handle_exception(const char * what, const bool is_parsing) +{ + krinolog << stk::diag::dendl; + krinolog << "Exception: " << what << stk::diag::dendl; + krinolog << stk::diag::Traceback::printTraceback(stk::diag::Traceback::snapshot()) << stk::diag::dendl; + if (is_parsing) + { + if (0 == stk::EnvData::parallel_rank()) + { + std::cerr << "*** Parser Error ***\n*** check log file for more information ***" << std::endl; + } + std::cout << std::flush; + std::cerr << std::flush; + + ::sleep(1); // Give the other processors a chance at + // catching up, seems to help hanging problems. + + MPI_Finalize(); + std::exit(1); + } + + if (0 == stk::EnvData::parallel_rank()) + { + std::cerr << "*** ABORT on P0 ***\n*** check log file for more information ***" << std::endl; + } + else + { + // give root proc chance to die first + ::sleep(2); + std::cerr << "*** ABORT on P" < +#include + +namespace krino{ + +class Startup +{ + public: + + Startup(int argc, char ** argv); + ~Startup(); + + bool exit_early() const { return my_flag_exit_early; } + void handle_exception(const char * what, const bool is_parsing); + + static void setup_commandline_options(); + static void report_handler(const char *message, int type); + +private: + int my_flag_exit_early; +}; + +} // namespace krino + +#endif // Akri_Startup_h diff --git a/packages/krino/krino/region/CMakeLists.txt b/packages/krino/krino/region/CMakeLists.txt new file mode 100644 index 000000000000..35b1a27d73b2 --- /dev/null +++ b/packages/krino/krino/region/CMakeLists.txt @@ -0,0 +1,19 @@ +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + krino_region_lib + HEADERS ${HEADERS} + SOURCES ${SOURCES} + DEPLIBS krino_lib krino_adaptivity_interface_lib) + +INSTALL(FILES ${HEADERS} DESTINATION + ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/krino_region_lib) + diff --git a/packages/krino/krino/unit_tests/Akri_UnitMathUtils.cpp b/packages/krino/krino/unit_tests/Akri_UnitMathUtils.cpp new file mode 100644 index 000000000000..8df8c1a1f209 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_UnitMathUtils.cpp @@ -0,0 +1,64 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino { + +void expect_root(const double goldRoot, const double xTol, const std::function & f) +{ + const unsigned maxIters = 100; + const auto result = find_root(f, 0., 1., f(0.), f(1.), maxIters, xTol); + ASSERT_TRUE(result.first); + EXPECT_NEAR(goldRoot, result.second, xTol); +} + +void expect_root_newton_raphson(const double goldRoot, const double guess, const double fTol, const std::function(const double)> & f) +{ + const unsigned maxIters = 100; + const auto result = find_root_newton_raphson(f, guess, maxIters, fTol); + ASSERT_TRUE(result.first); + const auto valueAndDeriv = f(result.second); + const double xTol = fTol / std::abs(valueAndDeriv.second); + EXPECT_NEAR(0., valueAndDeriv.first, fTol); + EXPECT_NEAR(goldRoot, result.second, xTol); +} + +TEST(find_root, givenPolynomialFunction_findRootWithinTolerance) +{ + const double tol = 1.e-5; + expect_root(0.25, tol, [](const double x){ return x-0.25; }); + expect_root(0.25, tol, [](const double x){ return x*x-0.25*0.25; }); + expect_root(0.25, tol, [](const double x){ return x*x*x-0.25*0.25*0.25; }); +} + + +TEST(find_root_newton_raphson, givenPolynomialFunctionWithCorrectJacobian_findRootWithinTolerance) +{ + const double tol = 1.e-5; + const double guess = 1.; + expect_root_newton_raphson(0.25, guess, tol, [](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x-0.25, 1.); }); + expect_root_newton_raphson(0.25, guess, tol, [](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x*x-0.25*0.25, 2.*x); }); + expect_root_newton_raphson(0.25, guess, tol, [](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x*x*x-0.25*0.25*0.25, 3.*x*x); }); +} + +TEST(find_root_newton_raphson, givenPolynomialFunctionWithWRONGJacobian_findRootWithinTolerance) +{ + const double tol = 1.e-5; + const double guess = 1.; + const double error = 0.1; // Less than 1 to make function overshoot + expect_root_newton_raphson(0.25, guess, tol, [error](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x-0.25, 1.*error); }); + expect_root_newton_raphson(0.25, guess, tol, [error](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x*x-0.25*0.25, 2.*x*error); }); + expect_root_newton_raphson(0.25, guess, tol, [error](const double x){ std::cout << "Eval at " << x << std::endl; return std::make_pair(x*x*x-0.25*0.25*0.25, 3.*x*x*error); }); +} + +} + diff --git a/packages/krino/krino/unit_tests/Akri_UnitTestUtils.cpp b/packages/krino/krino/unit_tests/Akri_UnitTestUtils.cpp new file mode 100644 index 000000000000..fbb85740d585 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_UnitTestUtils.cpp @@ -0,0 +1,23 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +namespace krino { + +void expect_eq(const Vector3d & gold, const Vector3d & result, const double relativeTol=1.e-6) +{ + const double absoluteTol = relativeTol * (gold.length() + result.length()); + for (int i=0; i<3; ++i) + EXPECT_NEAR(gold[i], result[i], absoluteTol) <<"gold: " << gold << " actual:" << result; +} + +} + + diff --git a/packages/krino/krino/unit_tests/Akri_UnitTestUtils.hpp b/packages/krino/krino/unit_tests/Akri_UnitTestUtils.hpp new file mode 100644 index 000000000000..ebb0e3b7dbe0 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_UnitTestUtils.hpp @@ -0,0 +1,19 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_UNIT_TESTS_INCLUDE_AKRI_UNITTESTUTILS_H_ +#define KRINO_UNIT_TESTS_INCLUDE_AKRI_UNITTESTUTILS_H_ +#include + +namespace krino { + +void expect_eq(const Vector3d & gold, const Vector3d & result, const double relativeTol=1.e-6); + +} + +#endif /* KRINO_UNIT_TESTS_INCLUDE_AKRI_UNITTESTUTILS_H_ */ diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Analytic_CDMesh.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Analytic_CDMesh.cpp new file mode 100644 index 000000000000..59ac23793422 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Analytic_CDMesh.cpp @@ -0,0 +1,276 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +static void expect_good_mesh(const stk::mesh::BulkData & mesh, const CDMesh & cdmesh) +{ + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(cdmesh.check_element_side_parts()); +} + +template +class AnalyticDecompositionFixture : public ::testing::Test +{ +public: + AnalyticDecompositionFixture() + : fixture(), cdfemSupport(CDFEM_Support::get(fixture.meta_data())) + { + AuxMetaData & aux_meta = AuxMetaData::get(fixture.meta_data()); + auto & vec_type = fixture.meta_data().spatial_dimension() == 2 ? FieldType::VECTOR_2D : FieldType::VECTOR_3D; + coord_field = aux_meta.register_field("coordinates", vec_type, stk::topology::NODE_RANK, 1u, 1u, fixture.meta_data().universal_part()); + cdfemSupport.set_coords_field(coord_field); + cdfemSupport.add_interpolation_field(coord_field); + + cdfemSupport.set_prolongation_model(INTERPOLATION); + } + + void setup_phase_support(const stk::mesh::PartVector & blocks) + { + PhaseTag p, n; + const LevelSet_Identifier id0(0); + p.add(id0, 1); + n.add(id0, -1); + PhaseVec named_phases{{"A", p}, {"B", n}}; + + Phase_Support & phase_support = Phase_Support::get(fixture.meta_data()); + Block_Surface_Connectivity block_surface_info; + phase_support.set_input_block_surface_connectivity(block_surface_info); + LevelSet * ls_ptr = nullptr; + phase_support.register_blocks_for_level_set(ls_ptr, blocks); + phase_support.decompose_blocks(blocks, named_phases, LS_Name_Generator()); + LS_Field lsField("LS", id0); + cdfemSupport.add_ls_field(lsField, nullptr); + } + + stk::mesh::Part & declare_input_block(const std::string & name, const stk::topology topo) + { + auto & block_part = fixture.meta_data().declare_part_with_topology(name, topo); + stk::io::put_io_part_attribute(block_part); + return block_part; + } + + void decompose_mesh(const InterfaceGeometry & interfaceGeometry) + { + NodeToCapturedDomainsMap nodesToCapturedDomains; + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + nodesToCapturedDomains = snap_as_much_as_possible_while_maintaining_quality(krino_mesh->stk_bulk(), krino_mesh->get_active_part(), cdfemSupport.get_interpolation_fields(), interfaceGeometry, cdfemSupport.get_global_ids_are_parallel_consistent()); + interfaceGeometry.prepare_to_process_elements(krino_mesh->stk_bulk(), nodesToCapturedDomains); + + if(!krino_mesh->my_old_mesh) + { + krino_mesh->my_old_mesh = std::make_shared(fixture.bulk_data(), std::shared_ptr()); + krino_mesh->my_old_mesh->generate_nonconformal_elements(); + } + + krino_mesh->generate_nonconformal_elements(); + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + krino_mesh->snap_nearby_intersections_to_nodes(interfaceGeometry, nodesToCapturedDomains); + krino_mesh->set_phase_of_uncut_elements(interfaceGeometry); + krino_mesh->triangulate(interfaceGeometry); + krino_mesh->my_old_mesh->stash_field_data(-1, *krino_mesh); + + + krino_mesh->decompose(); + krino_mesh->modify_mesh(); + krino_mesh->prolongation(); + } + + void commit() + { + krino_mesh = std::make_shared(fixture.bulk_data(), std::shared_ptr()); + } + + void write_results(const std::string & filename) + { + stk::io::write_mesh(filename, fixture.bulk_data()); + } + + void test_build_good_mesh(const bool doSnapping, + const InterfaceGeometry & interfaceGeometry, + const typename BoundingBoxMesh::BoundingBoxType & domain, + const double meshSize, + const std::string & filename = "") + { + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size > 2) return; + + if (doSnapping) + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + else + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_NODE); + + auto & block1_part = aux_meta.get_part("block_1"); + setup_phase_support({&block1_part}); + + fixture.set_domain(domain, meshSize); + fixture.populate_mesh(); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part(),&aux_meta.active_part()}); + + commit(); + + try + { + decompose_mesh(interfaceGeometry); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + expect_good_mesh(mesh, *krino_mesh); + + std::cout << log.get_log() << std::endl; + if (!filename.empty()) + write_results(filename); + } + + MESH_FIXTURE fixture; + FieldRef coord_field; + CDFEM_Support & cdfemSupport; + std::shared_ptr krino_mesh; + LogRedirecter log; +}; + +template +class SphereDecompositionFixture : public AnalyticDecompositionFixture +{ +public: + SphereDecompositionFixture() + { + mySphereGeometry.reset(new AnalyticSurfaceInterfaceGeometry(mySphere, AuxMetaData::get(this->fixture.meta_data()).active_part(), this->cdfemSupport, Phase_Support::get(this->fixture.meta_data()))); + } +protected: + const InterfaceGeometry & get_interface_geometry() const { return *mySphereGeometry; } + typename BoundingBoxMesh::BoundingBoxType get_domain() const + { + const Vector3d extents = (2 == this->fixture.meta_data().spatial_dimension()) ? Vector3d(1.,1.,0.) : Vector3d(1.,1.,1.); + typename BoundingBoxMesh::BoundingBoxType domain(-0.5*extents, 0.5*extents); + return domain; + } + double get_mesh_size() const { return 1./6.; } + Sphere mySphere{"test sphere", Vector3d::ZERO, 0.35}; + std::unique_ptr mySphereGeometry; +}; + +typedef SphereDecompositionFixture CDMeshSphereTestsBboxMesh2D; +TEST_F(CDMeshSphereTestsBboxMesh2D, Sphere_SnapMesh) +{ + const bool doSnap = true; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "2DSnapSphere.e"); +} + +TEST_F(CDMeshSphereTestsBboxMesh2D, Sphere_CutMesh) +{ + const bool doSnap = false; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "2DCutSphere.e"); +} + +typedef SphereDecompositionFixture CDMeshSphereTestsBboxMesh3D; +TEST_F(CDMeshSphereTestsBboxMesh3D, Sphere_SnapMesh) +{ + const bool doSnap = true; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "3DSnapSphere.e"); +} + +TEST_F(CDMeshSphereTestsBboxMesh3D, Sphere_CutMesh) +{ + const bool doSnap = false; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "3DCutSphere.e"); +} + +template +class CubeDecompositionFixture : public AnalyticDecompositionFixture +{ +public: + CubeDecompositionFixture() + { + const double x = 0.25; + const std::array cubeVerts = + {{ + {-x,-x,-x}, {+x,-x,-x}, {+x,+x,-x}, {-x,+x,-x}, + {-x,-x,+x}, {+x,-x,+x}, {+x,+x,+x}, {-x,+x,+x} + }}; + + const std::array,12> facetsVerts + {{ + {{0,4,7}}, {{0,7,3}}, + {{1,2,6}}, {{1,6,5}}, + {{0,1,5}}, {{0,5,4}}, + {{2,3,7}}, {{2,7,6}}, + {{0,3,2}}, {{0,2,1}}, + {{4,5,6}}, {{4,6,7}} + }}; + for (auto && facetVerts : facetsVerts) + { + std::unique_ptr facet = std::make_unique( cubeVerts[facetVerts[0]], cubeVerts[facetVerts[1]], cubeVerts[facetVerts[2]] ); + myCube.add( std::move(facet) ); + } + + myCubeGeometry.reset(new AnalyticSurfaceInterfaceGeometry(myCube, AuxMetaData::get(this->fixture.meta_data()).active_part(), this->cdfemSupport, Phase_Support::get(this->fixture.meta_data()))); + } +protected: + const InterfaceGeometry & get_interface_geometry() const { return *myCubeGeometry; } + typename BoundingBoxMesh::BoundingBoxType get_domain() const + { + const Vector3d extents = (2 == this->fixture.meta_data().spatial_dimension()) ? Vector3d(1.,1.,0.) : Vector3d(1.,1.,1.); + typename BoundingBoxMesh::BoundingBoxType domain(-0.5*extents, 0.5*extents); + return domain; + } + double get_mesh_size() const { return 1./6.; } + Faceted_Surface myCube{"test cube"}; + std::unique_ptr myCubeGeometry; +}; + +typedef CubeDecompositionFixture CDMeshCubeTestsBboxMesh2D; +TEST_F(CDMeshCubeTestsBboxMesh2D, Cube_SnapMesh) +{ + const bool doSnap = true; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "2DSnapCube.e"); +} + +typedef CubeDecompositionFixture CDMeshCubeTestsBboxMesh3D; +TEST_F(CDMeshCubeTestsBboxMesh3D, Sphere_SnapMesh) +{ + const bool doSnap = true; + test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size()); //test_build_good_mesh(doSnap, get_interface_geometry(), get_domain(), get_mesh_size(), "3DSnapCube.e"); +} + +} // namespace krino + diff --git a/packages/krino/krino/unit_tests/Akri_Unit_CDFEM_Parent_Edge.cpp b/packages/krino/krino/unit_tests/Akri_Unit_CDFEM_Parent_Edge.cpp new file mode 100644 index 000000000000..5b912bda3b65 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_CDFEM_Parent_Edge.cpp @@ -0,0 +1,782 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include + +namespace krino +{ + +TEST(CDFEM_Parent_Edge_One_LS, Two_Nodes_No_Snapping) +{ + const InterfaceID iface(0,0); + std::vector > nodes_isovar(2); + nodes_isovar[0].resize(1); + nodes_isovar[1].resize(1); + nodes_isovar[0][0] = 1; + nodes_isovar[1][0] = 1; + + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = -1; + edge.find_crossings(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = 2; + edge.find_crossings(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_DOUBLE_EQ(1./3., edge.get_crossing_position(iface)); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); +} + +TEST(CDFEM_Parent_Edge_One_LS, Three_Nodes_No_Snapping) +{ + std::vector > nodes_isovar(3); + nodes_isovar[0].resize(1); + nodes_isovar[1].resize(1); + nodes_isovar[2].resize(1); + nodes_isovar[0][0] = 1; + nodes_isovar[1][0] = 1; + nodes_isovar[2][0] = 1; + const InterfaceID iface(0,0); + + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = -1; + nodes_isovar[2][0] = -1; + edge.find_crossings(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = 1; + nodes_isovar[2][0] = -1; + edge.find_crossings(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = 1; + nodes_isovar[1][0] = -1; + nodes_isovar[2][0] = 1; + edge.find_crossings(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = 2; + nodes_isovar[2][0] = 4; + edge.find_crossings(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + const InterfaceID interface_id(0,0); + EXPECT_TRUE(edge.have_crossing(interface_id)); + EXPECT_DOUBLE_EQ(1./6., edge.get_crossing_position(interface_id)); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + + nodes_isovar[0][0] = -1; + nodes_isovar[1][0] = -1; + nodes_isovar[2][0] = 1; + edge.find_crossings(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(interface_id)); + EXPECT_DOUBLE_EQ(3./4., edge.get_crossing_position(interface_id)); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); +} + +TEST(CDFEM_Parent_Edge_Two_LS, Two_Nodes_No_Snapping) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const InterfaceID iface(0,1); + + std::vector > nodes_isovar(2); + nodes_isovar[0].resize(2); + nodes_isovar[1].resize(2); + + // crossing_sign convention, iface.first phase corresponds to (-) for one LS=one interface case + // iface.first lower everywhere + { + nodes_isovar[0][0] = 0; + nodes_isovar[0][1] = 1; + nodes_isovar[1][0] = 0; + nodes_isovar[1][1] = 1; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(0, edge.get_uncrossed_phase()); + } + + // iface.second lower everywhere + { + nodes_isovar[0][0] = 2; + nodes_isovar[0][1] = 1; + nodes_isovar[1][0] = 2; + nodes_isovar[1][1] = 1; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_EQ(1, edge.get_uncrossed_phase()); + } + + // first lower at node 0, second lower at node 1 + { + nodes_isovar[0][0] = 0.5; + nodes_isovar[0][1] = 1; + nodes_isovar[1][0] = 1.5; + nodes_isovar[1][1] = 1; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_DOUBLE_EQ(0.5, edge.get_crossing_position(iface)); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + } + + // second lower at node 0, first lower at node 1 + { + nodes_isovar[0][0] = 1.5; + nodes_isovar[0][1] = 1; + nodes_isovar[1][0] = 0.5; + nodes_isovar[1][1] = 1; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_DOUBLE_EQ(0.5, edge.get_crossing_position(iface)); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + } + + // Equal at node 0, first lower at node 1 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = 0.; + nodes_isovar[1][0] = 0; + nodes_isovar[1][1] = 1.; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_DOUBLE_EQ(0., edge.get_crossing_position(iface)); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + } + + // Equal at node 0, second lower at node 1 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = 0.; + nodes_isovar[1][0] = 0; + nodes_isovar[1][1] = -1.; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface)); + } + // Equal at node 0, first lower at node 1 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = 1.; + nodes_isovar[1][0] = 0; + nodes_isovar[1][1] = 0.; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_DOUBLE_EQ(1., edge.get_crossing_position(iface)); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + } + + // Equal at node 1, second lower at node 0 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = -1.; + nodes_isovar[1][0] = 0.; + nodes_isovar[1][1] = 0.; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface)); + } + + // (0, +delta) at node 0, (0, -) at node 1 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = 1.e-16; + nodes_isovar[1][0] = 0.; + nodes_isovar[1][1] = -1.; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_NEAR(0., edge.get_crossing_position(iface), 1.e-15); + EXPECT_EQ(1, edge.get_crossing_sign(iface)); + } + + // (0, -) at node 0, (0, +delta) at node 1 + { + nodes_isovar[0][0] = 0.; + nodes_isovar[0][1] = -1.; + nodes_isovar[1][0] = 0.; + nodes_isovar[1][1] = 1.e-16; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_NEAR(1., edge.get_crossing_position(iface), 1.e-15); + EXPECT_EQ(-1, edge.get_crossing_sign(iface)); + } +} + +TEST(CDFEM_Parent_Edge_Three_LS, Two_Nodes_No_Snapping) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + + std::vector > nodes_isovar(2); + nodes_isovar[0].resize(3); + nodes_isovar[1].resize(3); + + { + nodes_isovar[0][0] = -0.01288; + nodes_isovar[0][1] = 0.021996; + nodes_isovar[0][2] = 0.01; + nodes_isovar[1][0] = 0.038335; + nodes_isovar[1][1] = 0.037250; + nodes_isovar[1][2] = 0.01; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + EXPECT_FALSE(edge.have_crossing(iface12)); + EXPECT_TRUE(edge.have_crossing(iface02)); + const double crossing_pos = (nodes_isovar[0][0] - nodes_isovar[0][2]) / + (nodes_isovar[0][0] - nodes_isovar[1][0] + nodes_isovar[1][2] - nodes_isovar[0][2]); + EXPECT_DOUBLE_EQ(crossing_pos, edge.get_crossing_position(iface02)); + EXPECT_EQ(1, edge.get_crossing_sign(iface02)); + } + + { + nodes_isovar[0][0] = 0.038335; + nodes_isovar[0][1] = 0.037250; + nodes_isovar[0][2] = 0.01; + nodes_isovar[1][0] = -0.01288; + nodes_isovar[1][1] = 0.021996; + nodes_isovar[1][2] = 0.01; + CDFEM_Parent_Edge edge(nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + EXPECT_FALSE(edge.have_crossing(iface12)); + EXPECT_TRUE(edge.have_crossing(iface02)); + const double crossing_pos = (nodes_isovar[0][0] - nodes_isovar[0][2]) / + (nodes_isovar[0][0] - nodes_isovar[1][0] + nodes_isovar[1][2] - nodes_isovar[0][2]); + EXPECT_DOUBLE_EQ(crossing_pos, edge.get_crossing_position(iface02)); + EXPECT_EQ(-1, edge.get_crossing_sign(iface02)); + } +} + +TEST(CDFEM_Parent_Edge_Three_LS, Three_Nodes_No_Snapping) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + + std::vector > nodes_isovar(3); + nodes_isovar[0].resize(3); + nodes_isovar[1].resize(3); + nodes_isovar[2].resize(3); + + { + nodes_isovar[0][0] = 0.2; + nodes_isovar[0][1] = 0.0025391738062501383; + nodes_isovar[0][2] = 0.01; + nodes_isovar[1][0] = 0.19; + nodes_isovar[1][1] = -0.00048874386459929649; + nodes_isovar[1][2] = 0.01; + nodes_isovar[2][0] = 0.17; + nodes_isovar[2][1] = -0.0052539980592431739; + nodes_isovar[2][2] = 0.01; + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + EXPECT_FALSE(edge.have_crossing(iface12)); + EXPECT_FALSE(edge.have_crossing(iface02)); + } + + // Check that uncrossed phase is correct for 3 node problem with 2 crossings on the edge. + { + nodes_isovar[0][0] = 0.015; + nodes_isovar[0][1] = 1.; + nodes_isovar[0][2] = 0.01; + nodes_isovar[1][0] = 0.0095; + nodes_isovar[1][1] = 1.; + nodes_isovar[1][2] = 0.01; + nodes_isovar[2][0] = 0.015; + nodes_isovar[2][1] = 1.; + nodes_isovar[2][2] = 0.01; + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + EXPECT_FALSE(edge.have_crossing(iface12)); + EXPECT_FALSE(edge.have_crossing(iface02)); + EXPECT_EQ(2, edge.get_uncrossed_phase()); + } + + // Test edge that goes from phase 1-0-2 in the piecewise approximation, but there is no 0-2 in the linear version, + // so result is just 1-2. + { + nodes_isovar[0][0] = 0.72535; + nodes_isovar[0][1] = -0.844886; + nodes_isovar[0][2] = 0.10576; + nodes_isovar[1][0] = -0.58386; + nodes_isovar[1][1] = -0.931365; + nodes_isovar[1][2] = 0.7754522; + nodes_isovar[2][0] = -0.28731; + nodes_isovar[2][1] = 0.711750; + nodes_isovar[2][2] = -0.5794; + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + EXPECT_TRUE(edge.have_crossing(iface12)); + EXPECT_FALSE(edge.have_crossing(iface02)); + } + + // Test edge that goes from phase 1-0-2 in the piecewise approximation, with different locations than those + // given by a simple linear approximation. + { + nodes_isovar[0][0] = 0.25; + nodes_isovar[0][1] = 1.0; + nodes_isovar[0][2] = 0.0; + nodes_isovar[1][0] = 0.25; + nodes_isovar[1][1] = 1.0; + nodes_isovar[1][2] = 0.0; + nodes_isovar[2][0] = 0.25; + nodes_isovar[2][1] = 0.0; + nodes_isovar[2][2] = 1.0; + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_TRUE(edge.have_any_crossings()); + EXPECT_TRUE(edge.have_crossing(iface01)); + EXPECT_FALSE(edge.have_crossing(iface12)); + EXPECT_TRUE(edge.have_crossing(iface02)); + EXPECT_DOUBLE_EQ(0.625, edge.get_crossing_position(iface02)); + EXPECT_DOUBLE_EQ(0.875, edge.get_crossing_position(iface01)); + } + +} + +TEST(CDFEM_Parent_Edge_Two_LS, Two_Crossings_Same_Edge) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const InterfaceID iface01(0,1); + + std::vector > nodes_isovar(3); + nodes_isovar[0].resize(2); + nodes_isovar[1].resize(2); + nodes_isovar[2].resize(2); + + // Interface (0,1) has 2 crossings, one between each parent and the mid node. + // We will treat this as an uncrossed edge regardless of snapping. + nodes_isovar[0][0] = 0.02; + nodes_isovar[0][1] = 0.01; + nodes_isovar[1][0] = 0.; + nodes_isovar[1][1] = 0.01; + nodes_isovar[2][0] = 0.02; + nodes_isovar[2][1] = 0.01; + + // No snapping + { + CDFEM_Parent_Edge edge({0.0,0.5,1.0}, nodes_isovar); + EXPECT_FALSE(edge.have_any_crossings()); + EXPECT_FALSE(edge.have_crossing(iface01)); + } +} + +void expect_all_edge_segments_have_finite_or_zero_length(const CDFEM_Parent_Edge & edge, const double snapTol) +{ + std::vector crossingLocations; + for (auto && crossing : edge.get_crossings()) + { + crossingLocations.push_back(crossing.second); + } + std::sort(crossingLocations.begin(), crossingLocations.end()); + double previousCrossingLocation = 0.0; + for (auto && crossingLocation : crossingLocations) + { + const double intervalSize = crossingLocation- previousCrossingLocation; + EXPECT_TRUE(intervalSize == 0.0 || intervalSize >= snapTol) << "Found infinitesmal interval " << intervalSize << " on edge " << edge; + previousCrossingLocation = crossingLocation; + } + const double lastIntervalSize = 1.0 - previousCrossingLocation; + EXPECT_TRUE(lastIntervalSize == 0.0 || lastIntervalSize >= snapTol) << "Found infinitesmal interval " << lastIntervalSize << " on edge " << edge; +} + +TEST(CDFEM_Parent_Edge_Two_LS, LSPerPhaseInfinitesimalSnapTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{-CDFEM_Parent_Edge::MinSize(),0.0},{1.0,0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + EXPECT_TRUE(edge.have_any_crossings()); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); +} + +TEST(CDFEM_Parent_Edge_Two_LS, LSPerPhaseInfinitesimalSnapTo1) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{1.0,0.0},{-CDFEM_Parent_Edge::MinSize(),0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + EXPECT_TRUE(edge.have_any_crossings()); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); +} + +void expect_all_fake_crossings_are_really_fake(const CDFEM_Parent_Edge & edge) +{ + EXPECT_TRUE(edge.all_fake_crossings_are_really_fake()); +} + +TEST(CDFEM_Parent_Edge_Three_LS, LSPerPhaseInfinitesimalSnapInMiddle) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{-1.0,1.+CDFEM_Parent_Edge::MinSize(),0.0},{1.+CDFEM_Parent_Edge::MinSize(),-1.0,0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + EXPECT_EQ(1u,edge.get_crossings().size()); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); + expect_all_fake_crossings_are_really_fake(edge); +} + +TEST(CDFEM_Parent_Edge_Three_LS, LSPerPhaseTieInMiddle) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{0.,-1.,1.},{0.,1.,-1.}}; + CDFEM_Parent_Edge edge(nodesIsovar); + EXPECT_EQ(1u,edge.get_crossings().size()); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); + expect_all_fake_crossings_are_really_fake(edge); +} + +TEST(CDFEM_Parent_Edge_Three_LS, UnderflowAtEndStillResultsInCorrectFakeCrossing) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{ -0.6, -0.6, 0.6 },{ -6e-16, -5.9e-16, -7e-16 }}; + CDFEM_Parent_Edge edge(nodesIsovar); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); + expect_all_fake_crossings_are_really_fake(edge); +} + +TEST(CDFEM_Parent_Edge_Three_LS, WithScaling_UnderflowAtEndStillResultsInCorrectFakeCrossing) +{ + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{ -0.6e8, -0.6e8, 0.6e8 },{ -6e-8, -5.9e-8, -7e-8 }}; + CDFEM_Parent_Edge edge(nodesIsovar); + + expect_all_edge_segments_have_finite_or_zero_length(edge, CDFEM_Parent_Edge::MinSize()); + expect_all_fake_crossings_are_really_fake(edge); +} + +/////////////////////////////////////////////////////////////////////////////////////////////////// + +TEST(CDFEM_Parent_Edge_Two_LS, SnapTo0) +{ + const double snapTol = 0.1; + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{-0.01,0.0},{1.0,0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + EXPECT_TRUE(edge.have_any_crossings()); + + edge.collapse_small_segments_while_preserving_topology(snapTol); + expect_all_edge_segments_have_finite_or_zero_length(edge, snapTol); +} + +TEST(CDFEM_Parent_Edge_Two_LS, SnapTo1) +{ + const double snapTol = 0.1; + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{1.0,0.0},{-0.01,0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.collapse_small_segments_while_preserving_topology(snapTol); + expect_all_edge_segments_have_finite_or_zero_length(edge, snapTol); +} + +TEST(CDFEM_Parent_Edge_Three_LS, SnapInMiddle) +{ + const double snapTol = 0.1; + Phase_Support::set_one_levelset_per_phase(true); + + const std::vector > nodesIsovar = {{-1.0,1.1,0.0},{1.1,-1.0,0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.collapse_small_segments_while_preserving_topology(snapTol); + expect_all_edge_segments_have_finite_or_zero_length(edge, snapTol); +} + +TEST(CDFEM_Parent_Edge_Three_LS, OneSnapInMiddleMakesOtherSnapUnnecessary) +{ + const double snapTol = 0.1; + Phase_Support::set_one_levelset_per_phase(true); + std::vector locs = {0.4,0.44,0.53}; + const double phi0At0 = -1.0; + const double phi0At1 = (0.-(1.-locs[0])*phi0At0)/locs[0]; + const double phi1At1 = -0.1; + const double phi1At0 = (0.-locs[1]*phi1At1)/(1.-locs[1]); + const double phi1AtLocs2 = (1.-locs[2])*phi1At0 + locs[2]*phi1At1; + const double phi2At1 = -1.0; + const double phi2At0 = (phi1AtLocs2-locs[2]*phi2At1)/(1.-locs[2]); + + const std::vector > nodesIsovar = {{phi0At0, phi1At0, phi2At0, 0.0}, {phi0At1, phi1At1, phi2At1, 0.0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.collapse_small_segments_while_preserving_topology(snapTol); + expect_all_edge_segments_have_finite_or_zero_length(edge, snapTol); + + const std::vector > oppositeNodesIsovar = {{phi0At1, phi1At1, phi2At1, 0.0}, {phi0At0, phi1At0, phi2At0, 0.0}}; + CDFEM_Parent_Edge oppositeEdge(oppositeNodesIsovar); + + oppositeEdge.collapse_small_segments_while_preserving_topology(snapTol); + expect_all_edge_segments_have_finite_or_zero_length(oppositeEdge, snapTol); + + for (auto && crossing : edge.get_crossings()) + EXPECT_DOUBLE_EQ(crossing.second, 1.-oppositeEdge.get_crossing_position(crossing.first)) << "Snapping opposite edges give different results " << edge << " compared to " << oppositeEdge; +} + +void expect_crossing_at_position_with_sign(const CDFEM_Parent_Edge & edge, const InterfaceID & iface, const double pos, const int sign) +{ + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_EQ(pos, edge.get_crossing_position(iface)); + EXPECT_EQ(sign, edge.get_crossing_sign(iface)); +} + +void expect_crossing_at_position_with_sign(const CDFEM_Parent_Edge & edge, const int ls, const double pos, const int sign) +{ + const InterfaceID iface(ls,ls); + EXPECT_TRUE(edge.have_crossing(iface)); + EXPECT_EQ(pos, edge.get_crossing_position(iface)); + EXPECT_EQ(sign, edge.get_crossing_sign(iface)); +} + +void expect_fake_crossing_at_position_with_sign(const CDFEM_Parent_Edge & edge, const InterfaceID & iface, const double pos, const int sign) +{ + const auto result = edge.get_crossing_position_and_sign(iface); + EXPECT_LE(0, std::get<0>(result)) << "Did not find expected fake crossing " << iface << " on edge " << edge; + EXPECT_EQ(pos, std::get<0>(result)); + EXPECT_EQ(sign, std::get<1>(result)); + EXPECT_TRUE(std::get<2>(result)) << "Found real crossing when fake one was expected for " << iface << " on edge " << edge; +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAt0MovesNegCrossingTo0) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{1}, {-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0}, {}); + + expect_crossing_at_position_with_sign(edge, 0, 0., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAt0MovesPosCrossingTo0) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{-1}, {1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0}, {}); + + expect_crossing_at_position_with_sign(edge, 0, 0., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAt1MovesNegCrossingTo1) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{1}, {-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({}, {0}); + + expect_crossing_at_position_with_sign(edge, 0, 1., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAt1MovesPosCrossingTo1) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{-1}, {1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({}, {0}); + + expect_crossing_at_position_with_sign(edge, 0, 1., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAtBothEndsMovesNegCrossingToClosestAt0) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{0.9}, {-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0}, {0}); + + expect_crossing_at_position_with_sign(edge, 0, 0., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAtBothEndsMovesNegCrossingToClosestAt1) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{1}, {-0.9}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0}, {0}); + + expect_crossing_at_position_with_sign(edge, 0, 1., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_One_LS, nodeDomainsAtBothEndsMovesPosCrossingToClosestAt0) +{ + Phase_Support::set_one_levelset_per_phase(false); + const std::vector > nodesIsovar = {{-0.9}, {1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0}, {0}); + + expect_crossing_at_position_with_sign(edge, 0, 0., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAt0MovesNegCrossingTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{1,-1}, {-1,1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1}, {}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAt0MovesPosCrossingTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-1,1}, {1,-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1}, {}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAt1MovesNegCrossingTo1) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{1,-1}, {-1,1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({}, {0,1}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 1., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAt1MovesPosCrossingTo1) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-1,1}, {1,-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({}, {0,1}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 1., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAtBothEndsMovesNegCrossingToClosestAt0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{0.9,-0.9}, {-1,1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1}, {0,1}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAtBothEndsMovesNegCrossingToClosestAt1) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{1,-1}, {-0.9,0.9}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1}, {0,1}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 1., -1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Two_LS_Per_Phase, nodeDomainsAtBothEndsMovesPosCrossingToClosestAt0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-0.9,0.9}, {1,-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1}, {0,1}); + + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Three_LS_Per_Phase, nodeDomainsMoveAllCrossingsTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-1,0,2}, {2,0,-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1,2}, {}); + + expect_fake_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., 1); + expect_fake_crossing_at_position_with_sign(edge, InterfaceID(1,2), 0., 1); + expect_crossing_at_position_with_sign(edge, InterfaceID(0,2), 0., 1); +} + +TEST(CDFEM_Parent_Edge_Snapping_Three_LS_Per_Phase, nodeDomainsWithMiddlePhase2MoveAllCrossingsTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-1,2,0}, {2,-1,0}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,1,2}, {}); + + expect_fake_crossing_at_position_with_sign(edge, InterfaceID(0,2), 0., 1); + expect_fake_crossing_at_position_with_sign(edge, InterfaceID(1,2), 0., -1); + expect_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., 1); +} + + +TEST(CDFEM_Parent_Edge_Snapping_Three_LS_Per_Phase, nodeDomainsCenterPhaseMoveAllCrossingsTo0) +{ + Phase_Support::set_one_levelset_per_phase(true); + const std::vector > nodesIsovar = {{-1,0,2}, {2,0,-1}}; + CDFEM_Parent_Edge edge(nodesIsovar); + + edge.adjust_crossing_locations_based_on_node_captured_domains({0,2}, {}); + + expect_fake_crossing_at_position_with_sign(edge, InterfaceID(0,1), 0., 1); + expect_crossing_at_position_with_sign(edge, InterfaceID(0,2), 0., 1); +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_CDMesh.cpp b/packages/krino/krino/unit_tests/Akri_Unit_CDMesh.cpp new file mode 100644 index 000000000000..efff1945a32a --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_CDMesh.cpp @@ -0,0 +1,3092 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +namespace krino { + +class LevelSet; + +namespace { + template +void build_one_tet4_mesh(DECOMP_FIXTURE & fixture, + stk::mesh::Part & elem_part, + const int parallel_rank, const int parallel_size) +{ + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + ASSERT_TRUE(parallel_size == 1 || parallel_size == 2); + ThrowRequire(elem_part.topology() == stk::topology::TETRAHEDRON_4); + ASSERT_EQ(stk::topology::ELEMENT_RANK, elem_part.primary_entity_rank()); + + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts(2); + elem_parts[1] = &aux_meta.active_part(); + + std::vector elem_nodes = {1, 2, 3, 4}; + + stk::mesh::Entity element; + if(parallel_rank == 0) + { + elem_parts[0] = &elem_part; + element = fixture.create_element(elem_parts, 1, elem_nodes); + } + } + mesh.modification_end(); + + if(parallel_rank == 0) + { + EXPECT_EQ(1u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::ELEMENT_RANK))); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + ASSERT_TRUE(mesh.is_valid(node1)); + ASSERT_TRUE(mesh.is_valid(node2)); + ASSERT_TRUE(mesh.is_valid(node3)); + ASSERT_TRUE(mesh.is_valid(node4)); + + double * node1_coords = field_data(fixture.coord_field, node1); + double * node2_coords = field_data(fixture.coord_field, node2); + double * node3_coords = field_data(fixture.coord_field, node3); + double * node4_coords = field_data(fixture.coord_field, node4); + + node1_coords[0] = 1.; + node1_coords[1] = 1.; + node1_coords[2] = 1.; + + node2_coords[0] = -1.; + node2_coords[1] = 1.; + node2_coords[2] = -1.; + + node3_coords[0] = 1.; + node3_coords[1] = -1.; + node3_coords[2] = -1.; + + node4_coords[0] = -1.; + node4_coords[1] = -1.; + node4_coords[2] = 1.; + } +} + +template +void build_two_tet4_mesh_np2(DECOMP_FIXTURE & fixture, + stk::mesh::Part & elem1_part, stk::mesh::Part & elem2_part, stk::mesh::Part & surface_part, + const int parallel_rank, const int parallel_size, const bool add_side = true, + const bool build_all_on_P0 = false) +{ + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + ASSERT_TRUE(parallel_size == 1 || parallel_size == 2); + ThrowRequire(elem1_part.topology() == stk::topology::TETRAHEDRON_4); + ASSERT_EQ(meta.side_rank(), surface_part.primary_entity_rank()); + ASSERT_EQ(stk::topology::ELEMENT_RANK, elem1_part.primary_entity_rank()); + ASSERT_EQ(stk::topology::ELEMENT_RANK, elem2_part.primary_entity_rank()); + + stk::mesh::Entity sideEntity; + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts(2); + elem_parts[1] = &aux_meta.active_part(); + + std::vector elem1_nodes = {1, 3, 2, 4}; + std::vector elem2_nodes = {1, 2, 3, 5}; + + stk::mesh::Entity element; + if(parallel_rank == 0) + { + elem_parts[0] = &elem1_part; + element = fixture.create_element(elem_parts, 1, elem1_nodes); + } + if((parallel_rank == 1 && !build_all_on_P0) || (parallel_rank == 0 && build_all_on_P0) || + parallel_size == 1) + { + elem_parts[0] = &elem2_part; + element = fixture.create_element(elem_parts, 2, elem2_nodes); + } + + if(parallel_size > 1 && !build_all_on_P0) + { + const int opp_rank = parallel_rank == 0 ? 1 : 0; + for(auto i=1; i <= 3; ++i) + { + const auto node = mesh.get_entity(stk::topology::NODE_RANK, i); + mesh.add_node_sharing(node, opp_rank); + } + } + + if(add_side && (parallel_rank == 0 || !build_all_on_P0)) + { + sideEntity = mesh.declare_solo_side(7, {&surface_part}); + for(auto i=1; i <= 3; ++i) + { + auto side_node = mesh.get_entity(stk::topology::NODE_RANK, i); + mesh.declare_relation(sideEntity, side_node, i-1); + } + attach_entity_to_elements(mesh, sideEntity); + } + } + mesh.modification_end(); + + if(parallel_rank == 0 || !build_all_on_P0) + { + EXPECT_EQ(2u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::ELEMENT_RANK))); + if(add_side) + { + EXPECT_EQ(1u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(meta.side_rank()))); + EXPECT_EQ(1u, stk::mesh::count_selected_entities(surface_part, mesh.buckets(meta.side_rank()))); + + EXPECT_EQ(2u, mesh.num_connectivity(sideEntity, stk::topology::ELEMENT_RANK)); + } + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + const auto node5 = mesh.get_entity(stk::topology::NODE_RANK, 5); + + ASSERT_TRUE(mesh.is_valid(node1)); + ASSERT_TRUE(mesh.is_valid(node2)); + ASSERT_TRUE(mesh.is_valid(node3)); + ASSERT_TRUE(mesh.is_valid(node4)); + ASSERT_TRUE(mesh.is_valid(node5)); + + double * node1_coords = field_data(fixture.coord_field, node1); + double * node2_coords = field_data(fixture.coord_field, node2); + double * node3_coords = field_data(fixture.coord_field, node3); + double * node4_coords = field_data(fixture.coord_field, node4); + double * node5_coords = field_data(fixture.coord_field, node5); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + node1_coords[2] = 0.; + + node2_coords[0] = 0.; + node2_coords[1] = 0.; + node2_coords[2] = 1.; + + node3_coords[0] = 0.; + node3_coords[1] = 1.; + node3_coords[2] = 0.; + + node4_coords[0] = -1.; + node4_coords[1] = 0.; + node4_coords[2] = 0.; + + node5_coords[0] = 1.; + node5_coords[1] = 0.; + node5_coords[2] = 0.; + } +} + +template +void build_two_tri3_mesh_np2(DECOMP_FIXTURE & fixture, + stk::mesh::Part & elem1_part, stk::mesh::Part & elem2_part, stk::mesh::Part & surface_part, + const int parallel_rank, const int parallel_size, const bool add_side = true, + const bool build_all_on_P0 = false) +{ + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + ASSERT_TRUE(parallel_size == 1 || parallel_size == 2); + ThrowRequire(elem1_part.topology() == stk::topology::TRIANGLE_3_2D); + ASSERT_EQ(meta.side_rank(), surface_part.primary_entity_rank()); + ASSERT_EQ(stk::topology::ELEMENT_RANK, elem1_part.primary_entity_rank()); + ASSERT_EQ(stk::topology::ELEMENT_RANK, elem2_part.primary_entity_rank()); + + stk::mesh::Entity sideEntity; + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts(2); + elem_parts[1] = &aux_meta.active_part(); + + std::vector elem1_nodes = {2, 1, 3}; + std::vector elem2_nodes = {1, 2, 4}; + + stk::mesh::Entity element; + if(parallel_rank == 0) + { + elem_parts[0] = &elem1_part; + element = fixture.create_element(elem_parts, 1, elem1_nodes); + } + if((parallel_rank == 1 && !build_all_on_P0) || (parallel_rank == 0 && build_all_on_P0) || + parallel_size == 1) + { + elem_parts[0] = &elem2_part; + element = fixture.create_element(elem_parts, 2, elem2_nodes); + } + + if(parallel_size > 1 && !build_all_on_P0) + { + const int opp_rank = parallel_rank == 0 ? 1 : 0; + for(auto i=1; i <= 2; ++i) + { + const auto node = mesh.get_entity(stk::topology::NODE_RANK, i); + mesh.add_node_sharing(node, opp_rank); + } + } + + if(add_side && (parallel_rank == 0 || !build_all_on_P0)) + { + sideEntity = mesh.declare_solo_side(7, {&surface_part}); + for(auto i=1; i <= 2; ++i) + { + auto side_node = mesh.get_entity(stk::topology::NODE_RANK, i); + mesh.declare_relation(sideEntity, side_node, i-1); + } + attach_entity_to_elements(mesh, sideEntity); + } + } + mesh.modification_end(); + + if(parallel_rank == 0 || !build_all_on_P0) + { + EXPECT_EQ(2u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::ELEMENT_RANK))); + if(add_side) + { + EXPECT_EQ(1u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(meta.side_rank()))); + EXPECT_EQ(1u, stk::mesh::count_selected_entities(surface_part, mesh.buckets(meta.side_rank()))); + + EXPECT_EQ(2u, mesh.num_connectivity(sideEntity, stk::topology::ELEMENT_RANK)); + } + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + ASSERT_TRUE(mesh.is_valid(node1)); + ASSERT_TRUE(mesh.is_valid(node2)); + ASSERT_TRUE(mesh.is_valid(node3)); + ASSERT_TRUE(mesh.is_valid(node4)); + + double * node1_coords = field_data(fixture.coord_field, node1); + double * node2_coords = field_data(fixture.coord_field, node2); + double * node3_coords = field_data(fixture.coord_field, node3); + double * node4_coords = field_data(fixture.coord_field, node4); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + + node2_coords[0] = 0.; + node2_coords[1] = 1.; + + node3_coords[0] = 1.; + node3_coords[1] = 0.; + + node4_coords[0] = -1.; + node4_coords[1] = 0.; + } +} +} + +struct SingleLSPolicy +{ + void setup_ls_field(const bool is_death, stk::mesh::MetaData & meta, CDFEM_Support & cdfem_support) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + Phase_Support::set_one_levelset_per_phase(false); + ls_isovar = aux_meta.declare_field("LS", FieldType::REAL, stk::topology::NODE_RANK, 1u); + cdfem_support.add_interpolation_field(ls_isovar); + + LevelSet * ls_ptr = nullptr; + ls_field = std::make_shared("LS", LevelSet_Identifier(0), ls_isovar, 0., ls_ptr); + if(is_death) + { + death_spec = std::unique_ptr(new CDFEM_Inequality_Spec("death_spec")); + } + cdfem_support.add_ls_field(*ls_field, death_spec.get()); + } + + void register_ls_on_blocks(const stk::mesh::PartVector & blocks, stk::mesh::MetaData & meta, + Block_Surface_Connectivity & block_surface_info, const bool register_fields) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + PhaseTag p, n; + const LevelSet_Identifier id0(0); + p.add(id0, 1); + n.add(id0, -1); + PhaseVec named_phases{{"A", p}, {"B", n}}; + + if(death_spec) + { + death_spec->set_phases(p, n); + } + + Phase_Support & phase_support = Phase_Support::get(meta); + phase_support.set_input_block_surface_connectivity(block_surface_info); + LevelSet * ls_ptr = nullptr; + phase_support.register_blocks_for_level_set(ls_ptr, blocks); + phase_support.decompose_blocks(blocks, named_phases, LS_Name_Generator()); + + for(auto && b : blocks) + { + auto conformal_A = phase_support.find_conformal_io_part(*b, p); + auto conformal_B = phase_support.find_conformal_io_part(*b, n); + ThrowRequire(conformal_A != nullptr); + ThrowRequire(conformal_B != nullptr); + if(register_fields) + { + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *b); + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *conformal_A); + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *conformal_B); + } + } + } + + FieldRef ls_isovar; + std::shared_ptr ls_field; + std::unique_ptr death_spec; +}; + +template +struct LSPerPhasePolicy +{ + void setup_ls_field(const bool is_death, stk::mesh::MetaData & meta, CDFEM_Support & cdfem_support) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + Phase_Support::set_one_levelset_per_phase(true); + ThrowRequire(!is_death); + for(unsigned i=0; i < NUM_LS; ++i) + { + const std::string isovar_name = "LS" + std::to_string(i); + FieldRef ls_isovar = aux_meta.declare_field(isovar_name, FieldType::REAL, stk::topology::NODE_RANK, 1u); + ls_isovars.push_back(ls_isovar); + cdfem_support.add_interpolation_field(ls_isovar); + + LevelSet * ls_ptr = nullptr; + auto ls_field = std::make_shared(isovar_name, LevelSet_Identifier(i), ls_isovar, 0., ls_ptr); + ls_fields.push_back(ls_field); + cdfem_support.add_ls_field(*ls_field, nullptr); + } + } + + void register_ls_on_blocks(const stk::mesh::PartVector & blocks, stk::mesh::MetaData & meta, + Block_Surface_Connectivity & block_surface_info, const bool register_fields) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + PhaseVec named_phases; + for(unsigned ls=0; ls < NUM_LS; ++ls) + { + PhaseTag tag; + tag.add(LevelSet_Identifier(ls), -1); + named_phases.push_back(NamedPhase("P" + std::to_string(ls), tag)); + } + + Phase_Support & phase_support = Phase_Support::get(meta); + phase_support.set_input_block_surface_connectivity(block_surface_info); + LevelSet * ls_ptr = nullptr; + phase_support.register_blocks_for_level_set(ls_ptr, blocks); + phase_support.decompose_blocks(blocks, named_phases, LS_Name_Generator()); + + for(auto && b : blocks) + { + for( unsigned ls=0; ls < NUM_LS; ++ls ) + { + auto conformal_part = phase_support.find_conformal_io_part(*b, named_phases[ls].tag()); + ThrowRequire(conformal_part != nullptr); + if(register_fields) + { + // Need to register every LS on every conformal part + for( unsigned ls2=0; ls2 < NUM_LS; ++ls2 ) + { + aux_meta.register_field(ls_isovars[ls2].name(), FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *conformal_part); + } + aux_meta.register_field(ls_isovars[ls].name(), FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *b); + } + } + } + } + + std::vector ls_isovars; + std::vector > ls_fields; +}; + +template +struct LSPerInterfacePolicy +{ + void setup_ls_field(const bool is_death, stk::mesh::MetaData & meta, CDFEM_Support & cdfem_support) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + Phase_Support::set_one_levelset_per_phase(false); + ThrowRequire(!is_death); + for(unsigned i=0; i < NUM_LS; ++i) + { + const std::string isovar_name = "LS" + std::to_string(i); + FieldRef ls_isovar = aux_meta.declare_field(isovar_name, FieldType::REAL, stk::topology::NODE_RANK, 1u); + ls_isovars.push_back(ls_isovar); + cdfem_support.add_interpolation_field(ls_isovar); + + LevelSet * ls_ptr = nullptr; + auto ls_field = std::make_shared(isovar_name, LevelSet_Identifier(i), ls_isovar, 0., ls_ptr); + ls_fields.push_back(ls_field); + cdfem_support.add_ls_field(*ls_field, nullptr); + } + } + + void register_ls_on_blocks(const stk::mesh::PartVector & blocks, stk::mesh::MetaData & meta, + Block_Surface_Connectivity & block_surface_info, const bool register_fields) + { + AuxMetaData & aux_meta = AuxMetaData::get(meta); + PhaseVec named_phases; + const unsigned numPhases = 1<>ls)%2 == 0; + const int lsSign = lsIsNeg ? -1 : 1; + tag.add(LevelSet_Identifier(ls), lsSign); + phaseName += (lsIsNeg ? "-" : "+"); + } + named_phases.push_back(NamedPhase(phaseName, tag)); + } + + Phase_Support & phase_support = Phase_Support::get(meta); + phase_support.set_input_block_surface_connectivity(block_surface_info); + LevelSet * ls_ptr = nullptr; + phase_support.register_blocks_for_level_set(ls_ptr, blocks); + phase_support.decompose_blocks(blocks, named_phases, LS_Name_Generator()); + + if(register_fields) + { + for(auto && b : blocks) + { + for( unsigned ls=0; ls < NUM_LS; ++ls ) + { + aux_meta.register_field(ls_isovars[ls].name(), FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *b); + + for (unsigned phase=0; phase ls_isovars; + std::vector > ls_fields; +}; + +template +class CompleteDecompositionFixture : public ::testing::Test +{ +public: + CompleteDecompositionFixture() + : fixture(), cdfemSupport(CDFEM_Support::get(fixture.meta_data())) + { + AuxMetaData & aux_meta = AuxMetaData::get(fixture.meta_data()); + auto & vec_type = fixture.meta_data().spatial_dimension() == 2 ? FieldType::VECTOR_2D : FieldType::VECTOR_3D; + coord_field = aux_meta.register_field("coordinates", vec_type, stk::topology::NODE_RANK, 1u, 1u, fixture.meta_data().universal_part()); + cdfemSupport.set_coords_field(coord_field); + cdfemSupport.add_interpolation_field(coord_field); + cdfemSupport.register_parent_node_ids_field(); + + cdfemSupport.set_prolongation_model(INTERPOLATION); + } + + void setup_ls_field(const bool is_death = false) + { + ls_policy.setup_ls_field(is_death, fixture.meta_data(), cdfemSupport); + } + + void register_ls_on_blocks(const stk::mesh::PartVector & blocks, const bool register_fields = true) + { + ls_policy.register_ls_on_blocks(blocks, fixture.meta_data(), block_surface_info, register_fields); + } + + stk::mesh::Part & declare_input_block(const std::string & name, const stk::topology topo) + { + auto & block_part = fixture.meta_data().declare_part_with_topology(name, topo); + stk::io::put_io_part_attribute(block_part); + return block_part; + } + + stk::mesh::Part & declare_input_surface(const std::string & name, const stk::topology topo, const std::set & touching_blocks) + { + auto & surface_part = fixture.meta_data().declare_part_with_topology(name, topo); + stk::io::put_io_part_attribute(surface_part); + + block_surface_info.add_surface(surface_part.mesh_meta_data_ordinal(), touching_blocks); + return surface_part; + } + + stk::mesh::PartVector declare_input_surfaces_touching_block(const unsigned numSurfaces, const stk::mesh::Part & touchingBlock) + { + const stk::topology topo = touchingBlock.topology().side_topology(); + stk::mesh::PartVector surfaces; + for (unsigned i=0; iget_active_part(), cdfemSupport, Phase_Support::get(fixture.meta_data())); + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + nodesToSnappedDomains = snap_as_much_as_possible_while_maintaining_quality(krino_mesh->stk_bulk(), krino_mesh->get_active_part(), cdfemSupport.get_interpolation_fields(), interfaceGeometry, cdfemSupport.get_global_ids_are_parallel_consistent()); + interfaceGeometry.prepare_to_process_elements(krino_mesh->stk_bulk(), nodesToSnappedDomains); + + if(!krino_mesh->my_old_mesh) + { + krino_mesh->my_old_mesh = std::make_shared(fixture.bulk_data(), std::shared_ptr()); + krino_mesh->my_old_mesh->generate_nonconformal_elements(); + } + + krino_mesh->generate_nonconformal_elements(); + if (cdfemSupport.get_cdfem_edge_degeneracy_handling() == SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE) + krino_mesh->snap_nearby_intersections_to_nodes(interfaceGeometry, nodesToSnappedDomains); + krino_mesh->set_phase_of_uncut_elements(interfaceGeometry); + krino_mesh->triangulate(interfaceGeometry); + krino_mesh->my_old_mesh->stash_field_data(-1, *krino_mesh); + + + krino_mesh->decompose(); + krino_mesh->modify_mesh(); + krino_mesh->prolongation(); + + if(krinolog.shouldPrint(LOG_DEBUG)) + { + krino_mesh->debug_output(); + } + } + + void debug_output() + { + krino_mesh->debug_output(); + } + + void commit() + { + krino_mesh = std::make_shared(fixture.bulk_data(), std::shared_ptr()); + } + + stk::mesh::Entity create_element(stk::mesh::PartVector & elem_parts, stk::mesh::EntityId elem_id, + std::vector elem_nodes) + { + auto elem = stk::mesh::declare_element( fixture.bulk_data(), elem_parts, elem_id, elem_nodes ); + { + const stk::mesh::Entity * const nodes = fixture.bulk_data().begin_nodes(elem); + for(unsigned i=0; i < elem_nodes.size(); ++i) + { + EXPECT_EQ(elem_nodes[i], fixture.bulk_data().identifier(nodes[i])); + if (!fixture.bulk_data().bucket(nodes[i]).member(cdfemSupport.get_active_part())) + fixture.bulk_data().change_entity_parts(nodes[i], stk::mesh::ConstPartVector{&cdfemSupport.get_active_part()}, {}); + } + } + return elem; + } + + void run_rebalance_with(const std::string& decomp_method) + { + /* This is a 2 processor test to confirm that we can rebalance a mesh with CDFEM cut elements, + * and then successfully cut the mesh again. We create an initial mesh with 2 tets both owned + * by P0, do a decomposition, rebalance so that 1 parent element should end up on each of P0 and + * P1, and then do a second decomposition. + */ + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size != 2) return; + + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + FieldRef elem_weight_field = + aux_meta.register_field("element_weight", FieldType::REAL, stk::topology::ELEMENT_RANK, + 1u, 1, fixture.meta_data().universal_part()); + + commit(); + + const bool build_all_on_P0 = true; + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, + parallel_size, true, build_all_on_P0); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + if(parallel_rank == 0) + { + auto & node_buckets = mesh.buckets(stk::topology::NODE_RANK); + for(auto && b_ptr : node_buckets) + { + for(auto && node : *b_ptr) + { + const double * coords = field_data(coord_field, node); + double * ls_data = field_data(ls_policy.ls_isovar, node); + if(ls_data) *ls_data = coords[1]-0.5; + } + } + } + stk::mesh::communicate_field_data(mesh, {&ls_policy.ls_isovar.field(), &coord_field.field()}); + + ASSERT_NO_THROW(decompose_mesh()); + + if(parallel_rank == 1) + { + EXPECT_EQ(0u, stk::mesh::get_num_entities(mesh)); + } + + const stk::mesh::Selector parent_selector = krino_mesh->get_parent_part(); + if(parallel_rank == 0) + { + auto & elem_buckets = mesh.buckets(stk::topology::ELEMENT_RANK); + for(auto && b_ptr : elem_buckets) + { + const bool is_parent = parent_selector(*b_ptr); + for(auto && elem : *b_ptr) + { + double * weight = field_data(elem_weight_field, elem); + *weight = is_parent ? 1. : 0.; + } + } + } + + rebalance_utils::rebalance_mesh(mesh, + krino_mesh.get(), + elem_weight_field.name(), + coord_field.name(), + {fixture.meta_data().universal_part()}, + decomp_method); + + // Both procs should now own 1 parent element and 4 children + EXPECT_EQ(1u, stk::mesh::count_selected_entities( + fixture.meta_data().locally_owned_part() & parent_selector, + mesh.buckets(stk::topology::ELEMENT_RANK))); + EXPECT_EQ(4u, stk::mesh::count_selected_entities( + fixture.meta_data().locally_owned_part() & krino_mesh->get_child_part(), + mesh.buckets(stk::topology::ELEMENT_RANK))); + + krino_mesh = std::make_shared(mesh, krino_mesh); + + auto & node_buckets = mesh.buckets(stk::topology::NODE_RANK); + for(auto && b_ptr : node_buckets) + { + for(auto && node : *b_ptr) + { + const double * coords = field_data(coord_field, node); + double * ls_data = field_data(ls_policy.ls_isovar, node); + if(ls_data) *ls_data = coords[2]-0.5; + } + } + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + } + + MESH_FIXTURE fixture; + FieldRef coord_field; + CDFEM_Support & cdfemSupport; + std::shared_ptr krino_mesh; + Block_Surface_Connectivity block_surface_info; + LS_FIELD_POLICY ls_policy; + LogRedirecter log; +}; + +namespace { +template +void build_two_tri3_mesh_on_one_or_two_procs(CompleteDecompositionFixture & fixture, + stk::mesh::Part & block_part, const int parallel_rank) +{ + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.fixture.meta_data(); + const int parallel_size = mesh.parallel_size(); + mesh.modification_begin(); + { + /* + * 4---3 + * |\ 2| + * | \ | + * |1 \| + * 1---2 + */ + stk::mesh::PartVector elem_parts; + elem_parts.push_back(&block_part); + elem_parts.push_back(&fixture.cdfemSupport.get_active_part()); + + std::vector elem1_nodes = {1, 2, 4}; + std::vector elem2_nodes = {2, 3, 4}; + + if(parallel_rank == 0) fixture.create_element(elem_parts, 1, elem1_nodes); + if(parallel_rank == 1 || parallel_size == 1) fixture.create_element(elem_parts, 2, elem2_nodes); + + if(parallel_size > 1) + { + const int opp_rank = parallel_rank == 0 ? 1 : 0; + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + mesh.add_node_sharing(node2, opp_rank); + mesh.add_node_sharing(node4, opp_rank); + } + } + mesh.modification_end(); + + EXPECT_EQ(2u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::ELEMENT_RANK))); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + ASSERT_TRUE(mesh.is_valid(node1)); + ASSERT_TRUE(mesh.is_valid(node2)); + ASSERT_TRUE(mesh.is_valid(node3)); + ASSERT_TRUE(mesh.is_valid(node4)); + + double * node1_coords = field_data(fixture.coord_field, node1); + double * node2_coords = field_data(fixture.coord_field, node2); + double * node3_coords = field_data(fixture.coord_field, node3); + double * node4_coords = field_data(fixture.coord_field, node4); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + + node2_coords[0] = 1.; + node2_coords[1] = 0.; + + node3_coords[0] = 1.; + node3_coords[1] = 1.; + + node4_coords[0] = 0.; + node4_coords[1] = 1.; +} + +template +void build_two_tri3_mesh_on_one_or_two_procs_with_sides(CompleteDecompositionFixture & fixture, + stk::mesh::Part & blockPart, const stk::mesh::PartVector & sideParts, const int parallel_rank) +{ + build_two_tri3_mesh_on_one_or_two_procs(fixture, blockPart, parallel_rank); + + ThrowRequire(sideParts.size() == 4); + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + const int parallel_size = mesh.parallel_size(); + + mesh.modification_begin(); + if(parallel_rank == 0) + { + const auto element1 = mesh.get_entity(stk::topology::ELEMENT_RANK,1); + mesh.declare_element_side(element1, 0, stk::mesh::PartVector{sideParts[0]}); + mesh.declare_element_side(element1, 2, stk::mesh::PartVector{sideParts[3]}); + } + if(parallel_rank == 1 || parallel_size == 1) + { + const auto element2 = mesh.get_entity(stk::topology::ELEMENT_RANK,2); + mesh.declare_element_side(element2, 0, stk::mesh::PartVector{sideParts[1]}); + mesh.declare_element_side(element2, 1, stk::mesh::PartVector{sideParts[2]}); + } + mesh.modification_end(); +} + +void check_two_tri3_snapped_mesh_np2(CompleteDecompositionFixture & fixture, const int parallel_rank) +{ + stk::mesh::BulkData & mesh = fixture.fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + std::vector entities; + + // Should be no new nodes because of snapped interface, 3 nodes owned by P0, 1 by P1 + mesh.get_entities(stk::topology::NODE_RANK, meta.universal_part(), entities); + EXPECT_EQ(4u, entities.size()); + mesh.get_entities(stk::topology::NODE_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(4u, entities.size()); + mesh.get_entities(stk::topology::NODE_RANK, aux_meta.active_part() & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_EQ(3u, entities.size()); + } + else + { + EXPECT_EQ(1u, entities.size()); + } + + // Should be 1 interface edge + mesh.get_entities(stk::topology::EDGE_RANK, aux_meta.active_part() & + aux_meta.get_part("surface_block_1_A_B") & aux_meta.get_part("surface_block_1_B_A"), entities); + EXPECT_EQ(1u, entities.size()); + + // Should be 2 coincident subelements, no parents + mesh.get_entities(stk::topology::ELEMENT_RANK, meta.universal_part(), entities); + EXPECT_EQ(2u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(2u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, !aux_meta.active_part(), entities); + EXPECT_EQ(0u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B"), entities); + EXPECT_EQ(1u, entities.size()); +} + +} + +typedef CompleteDecompositionFixture CDMeshTests2D; +TEST_F(CDMeshTests2D, IsovariableNotDefinedOnDecomposedBlock) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}, false); + + commit(); + + EXPECT_ANY_THROW(krino_mesh->check_isovariable_field_existence_on_decomposed_blocks(true)); +} + +TEST_F(CDMeshTests2D, IsovariableNotDefinedOnBlock1) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}, false); + + auto & meta = fixture.meta_data(); + auto & aux_meta = AuxMetaData::get(meta); + + auto * A_part = meta.get_part("block_1_A"); + ASSERT_TRUE(A_part != nullptr); + auto * B_part = meta.get_part("block_1_B"); + ASSERT_TRUE(B_part != nullptr); + + // Catch the case where the field exists on both conformal parts, but not + // the initial un-decomposed part so we can't do the initial decomposition. + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, + 1u, 1u, *A_part); + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, + 1u, 1u, *B_part); + + commit(); + + EXPECT_ANY_THROW(krino_mesh->check_isovariable_field_existence_on_decomposed_blocks(true)); +} + +TEST_F(CDMeshTests2D, IsovariableOnlyOnBlock1SteadyState) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}, false); + + auto & meta = fixture.meta_data(); + auto & aux_meta = AuxMetaData::get(meta); + + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, + 1u, 1u, block_part); + + commit(); + + EXPECT_NO_THROW(krino_mesh->check_isovariable_field_existence_on_decomposed_blocks(false)); +} + +TEST_F(CDMeshTests2D, DeathIsovariableNotDefinedOnDecomposedBlock) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + const bool is_death = true; + setup_ls_field(is_death); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}, false); + + commit(); + + EXPECT_ANY_THROW(krino_mesh->check_isovariable_field_existence_on_decomposed_blocks(true)); +} + +TEST_F(CDMeshTests2D, DeathIsovariableNotDefinedOnDeadBlock) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + const bool is_death = true; + setup_ls_field(is_death); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}, false); + + auto & meta = fixture.meta_data(); + auto & aux_meta = AuxMetaData::get(meta); + auto * alive_part = meta.get_part("block_1_A"); + ASSERT_TRUE(alive_part != nullptr); + + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, + 1u, 1u, block_part); + aux_meta.register_field("LS", FieldType::REAL, stk::topology::NODE_RANK, + 1u, 1u, *alive_part); + + commit(); + + EXPECT_NO_THROW(krino_mesh->check_isovariable_field_existence_on_decomposed_blocks(true)); +} + +typedef CompleteDecompositionFixture CDMeshTests2D; +TEST_F(CDMeshTests2D, Single_Tri3_Decomposition) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts; + elem_parts.push_back(&block_part); + elem_parts.push_back(&aux_meta.active_part()); + std::vector node_ids = {1, 2, 3}; + + create_element(elem_parts, 1, node_ids); + } + mesh.modification_end(); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + + double * node1_coords = field_data(coord_field, node1); + double * node2_coords = field_data(coord_field, node2); + double * node3_coords = field_data(coord_field, node3); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + + node2_coords[0] = 1.; + node2_coords[1] = 0.; + + node3_coords[0] = 0.; + node3_coords[1] = 1.; + + *field_data(ls_policy.ls_isovar, node1) = -1; + *field_data(ls_policy.ls_isovar, node2) = 1; + *field_data(ls_policy.ls_isovar, node3) = -1; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + std::vector entities; + + // Should have added 2 nodes at the cutting locations + mesh.get_entities(stk::topology::NODE_RANK, meta.universal_part(), entities); + EXPECT_EQ(5u, entities.size()); + mesh.get_entities(stk::topology::NODE_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(5u, entities.size()); + + // Should be 1 interface edge + mesh.get_entities(stk::topology::EDGE_RANK, aux_meta.active_part() & + aux_meta.get_part("surface_block_1_A_B") & aux_meta.get_part("surface_block_1_B_A"), entities); + EXPECT_EQ(1u, entities.size()); + + // Should be 3 conformal elements plus the parent element + mesh.get_entities(stk::topology::ELEMENT_RANK, meta.universal_part(), entities); + EXPECT_EQ(4u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(3u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, !aux_meta.active_part(), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B"), entities); + EXPECT_EQ(2u, entities.size()); +} + +TEST_F(CDMeshTests2D, Two_Tri3_Snapped_Interface_Decomposition_NP2) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size != 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs(*this, block_part, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + { + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + *field_data(ls_policy.ls_isovar, node1) = -1; + *field_data(ls_policy.ls_isovar, node2) = 0; + *field_data(ls_policy.ls_isovar, node3) = 1; + *field_data(ls_policy.ls_isovar, node4) = 0; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + check_two_tri3_snapped_mesh_np2(*this, parallel_rank); + + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_TRUE(entities.empty()); + } + else + { + EXPECT_EQ(1u, entities.size()); + } + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_EQ(1u, entities.size()); + } + else + { + EXPECT_TRUE(entities.empty()); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } + + // Swap the A and B elements + { + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + *field_data(ls_policy.ls_isovar, node1) = 1; + *field_data(ls_policy.ls_isovar, node2) = 0; + *field_data(ls_policy.ls_isovar, node3) = -1; + *field_data(ls_policy.ls_isovar, node4) = 0; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + check_two_tri3_snapped_mesh_np2(*this, parallel_rank); + + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_EQ(1u, entities.size()); + } + else + { + EXPECT_TRUE(entities.empty()); + } + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_TRUE(entities.empty()); + } + else + { + EXPECT_EQ(1u, entities.size()); + } + } +} + +TEST_F(CDMeshTests2D, Two_Tri3_Death_Snapped_Interface_Decomposition_NP2) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size != 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + setup_ls_field(true); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs(*this, block_part, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + { + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + *field_data(ls_policy.ls_isovar, node1) = -1; + *field_data(ls_policy.ls_isovar, node2) = 0; + *field_data(ls_policy.ls_isovar, node3) = 1; + *field_data(ls_policy.ls_isovar, node4) = 0; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + check_two_tri3_snapped_mesh_np2(*this, parallel_rank); + + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_TRUE(entities.empty()); + } + else + { + EXPECT_EQ(1u, entities.size()); + } + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_EQ(1u, entities.size()); + } + else + { + EXPECT_TRUE(entities.empty()); + } + } +} + +TEST_F(CDMeshTests2D, Two_Tri3_Death_Snapped_Interface_Decomposition_NP2_Opposite_Ownership) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size != 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + setup_ls_field(true); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs(*this, block_part, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + { + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + *field_data(ls_policy.ls_isovar, node1) = 1; + *field_data(ls_policy.ls_isovar, node2) = 0; + *field_data(ls_policy.ls_isovar, node3) = -1; + *field_data(ls_policy.ls_isovar, node4) = 0; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + check_two_tri3_snapped_mesh_np2(*this, parallel_rank); + + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_EQ(1u, entities.size()); + } + else + { + EXPECT_TRUE(entities.empty()); + } + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B") & meta.locally_owned_part(), entities); + if(parallel_rank == 0) + { + EXPECT_TRUE(entities.empty()); + } + else + { + EXPECT_EQ(1u, entities.size()); + } + } +} + +TEST_F(CDMeshTests2D, Two_Tri3_Periodic) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_tol(0.1); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + AuxMetaData & aux_meta = AuxMetaData::get(fixture.meta_data()); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs(*this, block_part, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, fixture.meta_data().universal_part(), {&aux_meta.exposed_boundary_part()}); + + { + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + const auto node4 = mesh.get_entity(stk::topology::NODE_RANK, 4); + + *field_data(ls_policy.ls_isovar, node1) = -0.99; + *field_data(ls_policy.ls_isovar, node2) = -0.8; + *field_data(ls_policy.ls_isovar, node3) = 0.2; + *field_data(ls_policy.ls_isovar, node4) = 0.01; + + krino_mesh->add_periodic_node_pair(node3, node4); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + // Periodic constraint should cause interface to snap to both 3 and 4 so no elements + // get cut. + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A"), entities); + EXPECT_EQ(0u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B"), entities); + EXPECT_EQ(2u, entities.size()); + } +} + +TEST_F(CDMeshTests2D, Two_Tri3_PeriodicParallelNonSharedNode) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size == 1 || (parallel_size % 2) != 0) return; + + cdfemSupport.set_cdfem_edge_tol(0.1); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + const stk::mesh::EntityId starting_id = 1 + 3*parallel_rank; + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts; + elem_parts.push_back(&block_part); + elem_parts.push_back(&cdfemSupport.get_active_part()); + + std::vector elem_nodes = {starting_id, starting_id + 1, starting_id + 2}; + + create_element(elem_parts, parallel_rank + 1, elem_nodes); + } + mesh.modification_end(); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + EXPECT_EQ(1u, stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::ELEMENT_RANK))); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, starting_id); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, starting_id + 1); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, starting_id + 2); + + ASSERT_TRUE(mesh.is_valid(node1)); + ASSERT_TRUE(mesh.is_valid(node2)); + ASSERT_TRUE(mesh.is_valid(node3)); + + double * node1_coords = field_data(coord_field, node1); + double * node2_coords = field_data(coord_field, node2); + double * node3_coords = field_data(coord_field, node3); + + const double x0 = 1.1 * parallel_rank; + node1_coords[0] = x0; + node1_coords[1] = 0.; + + node2_coords[0] = x0 + 1.; + node2_coords[1] = 0.; + + node3_coords[0] = x0 + 1.; + node3_coords[1] = 1.; + + // Going to add "periodic" constraint between node1 on P0 and P1, so ghost those nodes appropriately + mesh.modification_begin(); + auto & ghosting = mesh.create_ghosting("test_ghosting"); + mesh.modification_end(); + stk::mesh::EntityProcVec add_send; + const int mod = parallel_rank % 2; + if(mod == 0) + { + add_send.push_back(std::make_pair(node1, parallel_rank + 1)); + } + else + { + add_send.push_back(std::make_pair(node1, parallel_rank - 1)); + } + mesh.modification_begin(); + mesh.change_ghosting(ghosting, add_send); + mesh.modification_end(); + + ASSERT_EQ(4u, + stk::mesh::count_selected_entities(meta.universal_part(), mesh.buckets(stk::topology::NODE_RANK))); + { + // Procs with mod == 0 will setup isovars so that the 1-2 edge has a crossing within the snap tolerance + // of node 1. Procs with mod == 1 will have the crossing outside the snap tolerance + *field_data(ls_policy.ls_isovar, node1) = (mod == 0) ? -0.01 : -1.; + *field_data(ls_policy.ls_isovar, node2) = 1.; + *field_data(ls_policy.ls_isovar, node3) = 1.; + + auto other_node1 = mesh.get_entity(stk::topology::NODE_RANK, + (mod == 0) ? starting_id + 3 : starting_id - 3); + krino_mesh->add_periodic_node_pair(node1, other_node1); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + // Periodic constraint should cause interface to snap to node1 so the element is entirely in the + // A phase. + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B"), entities); + EXPECT_EQ(0u, entities.size()); + } +} + +void set_level_set(const stk::mesh::BulkData & mesh, FieldRef lsField, const std::vector & nodeIds, const std::vector & nodeLS) +{ + ThrowRequire(nodeIds.size() == nodeLS.size()); + for (size_t i=0; i(lsField, node) = nodeLS[i]; + } +} + +TEST_F(CDMeshTests2D, Two_Tri3_Check_Compatibility_When_Snapping) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + AuxMetaData & aux_meta = AuxMetaData::get(fixture.meta_data()); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs(*this, block_part, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, fixture.meta_data().universal_part(), {&aux_meta.exposed_boundary_part()}); + + set_level_set(mesh, ls_policy.ls_isovar, {1,2,3,4} , {-1., -1., 1.e20, 1.}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + std::vector entities; + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_A"), entities); + EXPECT_EQ(2u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_B"), entities); + EXPECT_EQ(1u, entities.size()); + + //fixture.write_results("Two_Tri3_Check_Compatibility_When_Snapping.e"); +} + +void set_level_sets(const stk::mesh::BulkData & mesh, std::vector & lsFields, const std::vector & nodeIds, const std::vector> & nodeLS) +{ + ThrowRequire(nodeIds.size() == nodeLS.size()); + const size_t numFields = lsFields.size(); + for (size_t i=0; i(lsFields[j], node) = nodeLS[i][j]; + } +} + +typedef CompleteDecompositionFixture > CDMeshTests2DLSPerPhase; +TEST_F(CDMeshTests2DLSPerPhase, Two_Tri3_Check_Compatibility_When_Snapping) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + AuxMetaData & aux_meta = AuxMetaData::get(fixture.meta_data()); + + aux_meta.set_assert_32bit_flag(); + aux_meta.clear_force_64bit_flag(); + + setup_ls_field(); + + auto & blockPart = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&blockPart}); + const auto & sideParts = declare_input_surfaces_touching_block(4, blockPart); + + commit(); + + build_two_tri3_mesh_on_one_or_two_procs_with_sides(*this, blockPart, sideParts, parallel_rank); + + stk::mesh::create_exposed_block_boundary_sides(mesh, fixture.meta_data().universal_part(), {&aux_meta.exposed_boundary_part()}); + + const double eps = 1.e-13; + set_level_sets(mesh, ls_policy.ls_isovars, {1,2,3,4} , {{-1.,1.,1.+eps}, {-1.,1.,1.+eps}, {1.e2,1.,-1.}, {1.,-1.,-1.+eps}}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + //std::cout << log.get_log() << std::endl; + + std::vector entities; + mesh.get_entities(stk::topology::NODE_RANK, fixture.meta_data().universal_part(), entities); + EXPECT_EQ(7u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P0"), entities); + EXPECT_EQ(3u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P1"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P2"), entities); + EXPECT_EQ(2u, entities.size()); + + //fixture.write_results("Two_Tri3_Check_Compatibility_When_Snapping_LSPerPhase.e"); +} + +typedef CompleteDecompositionFixture CDMeshTests3D; +TEST_F(CDMeshTests3D, Write_Results_No_Side) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size, false); + + fixture.write_results("Write_Results_No_Side.e"); +} + +TEST_F(CDMeshTests3D, Write_Results_With_Side) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + fixture.write_results("Write_Results_With_Side.e"); +} + +namespace +{ +void randomize_ls_field(const stk::mesh::BulkData & mesh, + const FieldRef & field, + std::mt19937 & mt, + std::uniform_real_distribution & dist) +{ + auto & node_buckets = mesh.buckets(stk::topology::NODE_RANK); + for(auto && b_ptr : node_buckets) + { + for(auto && node : *b_ptr) + { + double * ls_data = field_data(field, node); + if(ls_data) *ls_data = dist(mt); + } + } +} +void set_ls_field_on_part(const stk::mesh::BulkData & mesh, + const stk::mesh::Part & part, + const FieldRef & ls_field, + const double ls_value) +{ + auto & node_buckets = mesh.get_buckets(stk::topology::NODE_RANK, part); + for(auto && b_ptr : node_buckets) + { + for(auto && node : *b_ptr) + { + double * ls_data = field_data(ls_field, node); + if(ls_data) *ls_data = ls_value; + } + } +} + +} + +TEST_F(CDMeshTests3D, Random_TwoTet4_InternalSideset) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + + if (parallel_size > 2) return; + + // Use a large snap tolerance to make snapping more common since it is a frequent source + // of parallel bugs + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + randomize_ls_field(mesh, ls_policy.ls_isovar, mt, dist); + stk::mesh::communicate_field_data(mesh, {&ls_policy.ls_isovar.field(), &coord_field.field()}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + if(HasNonfatalFailure()) + { + std::cout << "Failure on iteration " << i << std::endl; + krino_mesh->debug_output(); + std::cout << log.get_log() << std::endl; + std::ostringstream fname; + fname << "Random_TwoTet4_InternalSideset_iter_" << i << ".e"; + fixture.write_results(fname.str()); + ASSERT_TRUE(false); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +typedef CompleteDecompositionFixture CDMeshTestsBboxMesh2D; +TEST_F(CDMeshTestsBboxMesh2D, Random_SnapMesh) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + const double approxMinRelativeSize = 0.25; + + setup_ls_field(); + + auto & block1_part = aux_meta.get_part("block_1"); + + register_ls_on_blocks({&block1_part}); + + typename BoundingBoxMesh::BoundingBoxType domain(Vector3d::ZERO, Vector3d(1.,1.,0.)); + const double mesh_size = 1./3.; + fixture.set_domain(domain, mesh_size); + fixture.populate_mesh(); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part(),&aux_meta.active_part()}); + + double overallMinEdgeLength = std::numeric_limits::max(); + double overallMaxEdgeLength = -std::numeric_limits::max(); + double overallMinVolume = std::numeric_limits::max(); + double overallMaxVolume = -std::numeric_limits::max(); + const double expectedMinLength = mesh_size*approxMinRelativeSize; + const double expectedMinVol = std::pow(mesh_size*approxMinRelativeSize, 2.) / 2.; + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + randomize_ls_field(mesh, ls_policy.ls_isovar, mt, dist); + set_ls_field_on_part(mesh, aux_meta.exposed_boundary_part(), ls_policy.ls_isovar, 1.); + stk::mesh::communicate_field_data(mesh, {&ls_policy.ls_isovar.field(), &coord_field.field()}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + double minEdgeLength, maxEdgeLength, minVolume, maxVolume; + compute_element_quality(mesh, minEdgeLength, maxEdgeLength, minVolume, maxVolume); + overallMinEdgeLength = std::min(overallMinEdgeLength, minEdgeLength); + overallMaxEdgeLength = std::max(overallMaxEdgeLength, maxEdgeLength); + overallMinVolume = std::min(overallMinVolume, minVolume); + overallMaxVolume = std::max(overallMaxVolume, maxVolume); + + bool failedQuality = false; + if (minVolume < 0.5*expectedMinVol) + { + failedQuality = true; + std::cout << "Failed quality requirements: minEdgeLength=" << minEdgeLength + << ", maxEdgeLength=" << maxEdgeLength + << ", minVolume=" << minVolume + << ", maxVolume=" << maxVolume << std::endl; + } + + if(HasNonfatalFailure() || failedQuality) + { + std::cout << "Failure on iteration " << i << std::endl; + krino_mesh->debug_output(); + std::cout << log.get_log() << std::endl; + std::ostringstream fname; + fname << "Random_SnapTri3_iter_" << i << ".e"; + SimpleStkFixture::write_results(fname.str(), mesh); + ASSERT_TRUE(false); + } + } + std::cout << "Expected quality: minEdgeLength~=" << expectedMinLength << ", minVolume~=" << expectedMinVol << std::endl; + std::cout << "Quality results: minEdgeLength=" << overallMinEdgeLength + << ", maxEdgeLength=" << overallMaxEdgeLength + << ", minVolume=" << overallMinVolume + << ", maxVolume=" << overallMaxVolume << std::endl; +} + +typedef CompleteDecompositionFixture> CDMeshTestsBboxMesh2DLSPerPhase; +TEST_F(CDMeshTestsBboxMesh2DLSPerPhase, Random_SnapMesh) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + const double approxMinRelativeSize = 0.25; + + setup_ls_field(); + + auto & block1_part = aux_meta.get_part("block_1"); + + register_ls_on_blocks({&block1_part}); + + typename BoundingBoxMesh::BoundingBoxType domain(Vector3d::ZERO, Vector3d(1.,1.,0.)); + const double mesh_size = 1./3.; + fixture.set_domain(domain, mesh_size); + fixture.populate_mesh(); + fixture.create_domain_sides(); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part(),&aux_meta.active_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for(auto && isovar : ls_isovars) sync_fields.push_back(&isovar.field()); + + double overallMinEdgeLength = std::numeric_limits::max(); + double overallMaxEdgeLength = -std::numeric_limits::max(); + double overallMinVolume = std::numeric_limits::max(); + double overallMaxVolume = -std::numeric_limits::max(); + const double expectedMinLength = mesh_size*approxMinRelativeSize; + const double expectedMinVol = std::pow(mesh_size*approxMinRelativeSize, 2.) / 2.; + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + for(auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + double minEdgeLength, maxEdgeLength, minVolume, maxVolume; + compute_element_quality(mesh, minEdgeLength, maxEdgeLength, minVolume, maxVolume); + overallMinEdgeLength = std::min(overallMinEdgeLength, minEdgeLength); + overallMaxEdgeLength = std::max(overallMaxEdgeLength, maxEdgeLength); + overallMinVolume = std::min(overallMinVolume, minVolume); + overallMaxVolume = std::max(overallMaxVolume, maxVolume); + + if(HasNonfatalFailure()) + { + std::cout << "Failure on iteration " << i << std::endl; + krino_mesh->debug_output(); + std::cout << log.get_log() << std::endl; + std::ostringstream fname; + fname << "Random_SnapTri3_iter_" << i << ".e"; + SimpleStkFixture::write_results(fname.str(), mesh); + ASSERT_TRUE(false); + } + } + std::cout << "Expected quality: minEdgeLength~=" << expectedMinLength << ", minVolume~=" << expectedMinVol << std::endl; + std::cout << "Quality results: minEdgeLength=" << overallMinEdgeLength + << ", maxEdgeLength=" << overallMaxEdgeLength + << ", minVolume=" << overallMinVolume + << ", maxVolume=" << overallMaxVolume << std::endl; +} + +typedef CompleteDecompositionFixture CDMeshTestsBboxMesh3D; +TEST_F(CDMeshTestsBboxMesh3D, Random_SnapMesh) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + const double approxMinRelativeSize = 0.25; + + setup_ls_field(); + + auto & block1_part = aux_meta.get_part("block_1"); + + register_ls_on_blocks({&block1_part}); + + typename BoundingBoxMesh::BoundingBoxType domain(Vector3d::ZERO, Vector3d(1.,1.,1.)); + const double mesh_size = 1./3.; + fixture.set_domain(domain, mesh_size); + fixture.populate_mesh(); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part(),&aux_meta.active_part()}); + + double overallMinEdgeLength = std::numeric_limits::max(); + double overallMaxEdgeLength = -std::numeric_limits::max(); + double overallMinVolume = std::numeric_limits::max(); + double overallMaxVolume = -std::numeric_limits::max(); + const double expectedMinLength = mesh_size*approxMinRelativeSize; + const double expectedMinVol = std::pow(mesh_size*approxMinRelativeSize, 3.) / 6.; + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 1000; +#else + const int num_cases = 250; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%250 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + randomize_ls_field(mesh, ls_policy.ls_isovar, mt, dist); + set_ls_field_on_part(mesh, aux_meta.exposed_boundary_part(), ls_policy.ls_isovar, 1.); + stk::mesh::communicate_field_data(mesh, {&ls_policy.ls_isovar.field(), &coord_field.field()}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + double minEdgeLength, maxEdgeLength, minVolume, maxVolume; + compute_element_quality(mesh, minEdgeLength, maxEdgeLength, minVolume, maxVolume); + overallMinEdgeLength = std::min(overallMinEdgeLength, minEdgeLength); + overallMaxEdgeLength = std::max(overallMaxEdgeLength, maxEdgeLength); + overallMinVolume = std::min(overallMinVolume, minVolume); + overallMaxVolume = std::max(overallMaxVolume, maxVolume); + + bool failedQuality = false; + if (minVolume < 0.5*expectedMinVol) + { + failedQuality = true; + std::cout << "Failed quality requirements: minEdgeLength=" << minEdgeLength + << ", maxEdgeLength=" << maxEdgeLength + << ", minVolume=" << minVolume + << ", maxVolume=" << maxVolume << std::endl; + } + + if(HasNonfatalFailure() || failedQuality) + { + std::cout << "Failure on iteration " << i << std::endl; + krino_mesh->debug_output(); + std::cout << log.get_log() << std::endl; + std::ostringstream fname; + fname << "Random_SnapTet4_iter_" << i << ".e"; + SimpleStkFixture::write_results(fname.str(), mesh); + ASSERT_TRUE(false); + } + } + std::cout << "Expected quality: minEdgeLength~=" << expectedMinLength << ", minVolume~=" << expectedMinVol << std::endl; + std::cout << "Actual quality results: minEdgeLength=" << overallMinEdgeLength + << ", maxEdgeLength=" << overallMaxEdgeLength + << ", minVolume=" << overallMinVolume + << ", maxVolume=" << overallMaxVolume << std::endl; +} + +typedef CompleteDecompositionFixture CDMeshTestsBboxMesh3DBCC; +TEST_F(CDMeshTestsBboxMesh3DBCC, Random_SnapMesh) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + const double approxMinRelativeSize = 0.25; + + setup_ls_field(); + + auto & block1_part = aux_meta.get_part("block_1"); + + register_ls_on_blocks({&block1_part}); + + typename BoundingBoxMesh::BoundingBoxType domain(Vector3d::ZERO, Vector3d(1.,1.,1.)); + const double mesh_size = 1./3.; + fixture.set_domain(domain, mesh_size); + fixture.set_mesh_structure_type(BCC_BOUNDING_BOX_MESH); + fixture.populate_mesh(); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part(),&aux_meta.active_part()}); + + const double BCCsize = std::sqrt(3.)/2.*mesh_size; + double overallMinEdgeLength = std::numeric_limits::max(); + double overallMaxEdgeLength = -std::numeric_limits::max(); + double overallMinVolume = std::numeric_limits::max(); + double overallMaxVolume = -std::numeric_limits::max(); + const double expectedMinLength = BCCsize*approxMinRelativeSize; + const double expectedMinVol = std::pow(BCCsize*approxMinRelativeSize, 3.) / (6.*std::sqrt(2.)); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 1000; +#else + const int num_cases = 250; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%250 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + randomize_ls_field(mesh, ls_policy.ls_isovar, mt, dist); + set_ls_field_on_part(mesh, aux_meta.exposed_boundary_part(), ls_policy.ls_isovar, 1.); + stk::mesh::communicate_field_data(mesh, {&ls_policy.ls_isovar.field(), &coord_field.field()}); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + double minEdgeLength, maxEdgeLength, minVolume, maxVolume; + compute_element_quality(mesh, minEdgeLength, maxEdgeLength, minVolume, maxVolume); + overallMinEdgeLength = std::min(overallMinEdgeLength, minEdgeLength); + overallMaxEdgeLength = std::max(overallMaxEdgeLength, maxEdgeLength); + overallMinVolume = std::min(overallMinVolume, minVolume); + overallMaxVolume = std::max(overallMaxVolume, maxVolume); + + bool failedQuality = false; + if (minVolume < 0.5*expectedMinVol) + { + failedQuality = true; + std::cout << "Failed quality requirements: minEdgeLength=" << minEdgeLength + << ", maxEdgeLength=" << maxEdgeLength + << ", minVolume=" << minVolume + << ", maxVolume=" << maxVolume << std::endl; + } + + if(HasNonfatalFailure() || failedQuality) + { + std::cout << "Failure on iteration " << i << std::endl; + krino_mesh->debug_output(); + std::cout << log.get_log() << std::endl; + std::ostringstream fname; + fname << "Random_SnapTet4_iter_" << i << ".e"; + SimpleStkFixture::write_results(fname.str(), mesh); + ASSERT_TRUE(false); + } + } + std::cout << "Expected quality: minEdgeLength~=" << expectedMinLength << ", minVolume~=" << expectedMinVol << std::endl; + std::cout << "Actual quality results: minEdgeLength=" << overallMinEdgeLength + << ", maxEdgeLength=" << overallMaxEdgeLength + << ", minVolume=" << overallMinVolume + << ", maxVolume=" << overallMaxVolume << std::endl; +} + +TEST_F(CDMeshTests2DLSPerPhase, Tri3_3LS_SnappedTriplePoint) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + cdfemSupport.set_cdfem_edge_tol(0.15); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts; + elem_parts.push_back(&block_part); + elem_parts.push_back(&aux_meta.active_part()); + std::vector node_ids = {1, 2, 3}; + + create_element(elem_parts, 1, node_ids); + } + mesh.modification_end(); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + + double * node1_coords = field_data(coord_field, node1); + double * node2_coords = field_data(coord_field, node2); + double * node3_coords = field_data(coord_field, node3); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + + node2_coords[0] = 1.; + node2_coords[1] = 0.; + + node3_coords[0] = 0.; + node3_coords[1] = 1.; + + const auto & ls_isovars = ls_policy.ls_isovars; + *field_data(ls_isovars[0], node1) = 0.; + *field_data(ls_isovars[0], node2) = 0.; + *field_data(ls_isovars[0], node3) = 0.; + + *field_data(ls_isovars[1], node1) = 0.1; + *field_data(ls_isovars[1], node2) = -0.2; + *field_data(ls_isovars[1], node3) = -0.01; + + *field_data(ls_isovars[2], node1) = 0.2; + *field_data(ls_isovars[2], node2) = -0.25; + *field_data(ls_isovars[2], node3) = -0.005; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + std::vector entities; + + // This assumes that the element is cut first by the (0,1) interface, + // then the (0, 2) virtual interface, and then the (1, 2) interface. + // THere are other valid decompositions if the element is cut in a different order. + // Should have added 3 nodes at the cutting locations + mesh.get_entities(stk::topology::NODE_RANK, meta.universal_part(), entities); + EXPECT_EQ(5u, entities.size()); + mesh.get_entities(stk::topology::NODE_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(5u, entities.size()); + + mesh.get_entities(stk::topology::EDGE_RANK, aux_meta.active_part() & + aux_meta.get_part("surface_block_1_P0_P1") & aux_meta.get_part("surface_block_1_P1_P0"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::EDGE_RANK, aux_meta.active_part() & + aux_meta.get_part("surface_block_1_P1_P2") & aux_meta.get_part("surface_block_1_P2_P1"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::EDGE_RANK, aux_meta.active_part() & + aux_meta.get_part("surface_block_1_P0_P2") & aux_meta.get_part("surface_block_1_P2_P0"), entities); + EXPECT_EQ(0u, entities.size()); + + // Should be 3 conformal elements plus the parent element + mesh.get_entities(stk::topology::ELEMENT_RANK, meta.universal_part(), entities); + EXPECT_EQ(4u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.active_part(), entities); + EXPECT_EQ(3u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, !aux_meta.active_part(), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P0"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P1"), entities); + EXPECT_EQ(1u, entities.size()); + mesh.get_entities(stk::topology::ELEMENT_RANK, aux_meta.get_part("block_1_P2"), entities); + EXPECT_EQ(1u, entities.size()); +} + +TEST_F(CDMeshTests2DLSPerPhase, Tri3_3LS_TriplePointDebug) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + + if (parallel_size > 1) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + cdfemSupport.set_cdfem_edge_tol(0.01); + + setup_ls_field(); + + auto & block_part = declare_input_block("block_1", stk::topology::TRIANGLE_3_2D); + register_ls_on_blocks({&block_part}); + + commit(); + + mesh.modification_begin(); + { + stk::mesh::PartVector elem_parts; + elem_parts.push_back(&block_part); + elem_parts.push_back(&aux_meta.active_part()); + std::vector node_ids = {1, 2, 3}; + + create_element(elem_parts, 1, node_ids); + } + mesh.modification_end(); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto node1 = mesh.get_entity(stk::topology::NODE_RANK, 1); + const auto node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + const auto node3 = mesh.get_entity(stk::topology::NODE_RANK, 3); + + double * node1_coords = field_data(coord_field, node1); + double * node2_coords = field_data(coord_field, node2); + double * node3_coords = field_data(coord_field, node3); + + node1_coords[0] = 0.; + node1_coords[1] = 0.; + + node2_coords[0] = 1.; + node2_coords[1] = 0.; + + node3_coords[0] = 0.; + node3_coords[1] = 1.; + + const auto & ls_isovars = ls_policy.ls_isovars; + *field_data(ls_isovars[0], node1) = -0.2; + *field_data(ls_isovars[1], node1) = 0.1; + *field_data(ls_isovars[2], node1) = 0.6; + + *field_data(ls_isovars[0], node2) = 0.7; + *field_data(ls_isovars[1], node2) = -0.5; + *field_data(ls_isovars[2], node2) = 0.4; + + *field_data(ls_isovars[0], node3) = 0.1; + *field_data(ls_isovars[1], node3) = 0.3; + *field_data(ls_isovars[2], node3) = -0.5; + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + // Test output, but remove output unless actually debugging. + fixture.write_results("debug_2d.e"); + std::remove("debug_2d.e"); +} + +typedef CompleteDecompositionFixture > CDMeshTests2DLSPerPhase; +TEST_F(CDMeshTests2DLSPerPhase, Random_TwoTri3_InternalSideset_Snap) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + + setup_ls_field(); + + const stk::topology tri3 = stk::topology::TRIANGLE_3_2D; + auto & block1_part = declare_input_block("block_1", tri3); + auto & block2_part = declare_input_block("block_2", tri3); + auto & surface_part = declare_input_surface("surface_1", tri3.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + commit(); + + build_two_tri3_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for(auto && isovar : ls_isovars) sync_fields.push_back(&isovar.field()); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + for(auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + if (false) + { + std::ostringstream fname; + fname << "Random_TwoTri3_InternalSideset_Snap_iter_" << i << ".e"; + fixture.write_results(fname.str()); + } + + if(HasNonfatalFailure()) + { + std::cout << "Failure on iteration " << i << std::endl; + std::ostringstream fname; + fname << "Random_TwoTri3_InternalSideset_Snap_iter_" << i << ".e"; + fixture.write_results(fname.str()); + ASSERT_TRUE(false); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +typedef CompleteDecompositionFixture > CDMeshTests3DLSPerInterface; +TEST_F(CDMeshTests3DLSPerInterface, Random_OneTet4) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + aux_meta.set_assert_32bit_flag(); + aux_meta.clear_force_64bit_flag(); + + // Use a large snap tolerance to make snapping more common since it is a frequent source + // of parallel bugs + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + + register_ls_on_blocks({&block1_part}); + + commit(); + + build_one_tet4_mesh(*this, block1_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for(auto && isovar : ls_isovars) sync_fields.push_back(&isovar.field()); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + for(auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + if(HasNonfatalFailure()) + { + std::cout << log.get_log() << std::endl; + std::cout << "Failure on iteration " << i << std::endl; + std::ostringstream fname; + fname << "Random_TwoTet4_InternalSideset_iter_" << i << ".e"; + fixture.write_results(fname.str()); + ASSERT_TRUE(false); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +typedef CompleteDecompositionFixture > CDMeshTests3DLSPerInterface; +TEST_F(CDMeshTests3DLSPerInterface, OneTet4_CutBasedOnNearestEdgeCut) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 1) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + aux_meta.set_assert_32bit_flag(); + aux_meta.clear_force_64bit_flag(); + + // Use a large snap tolerance to make snapping more common since it is a frequent source + // of parallel bugs + cdfemSupport.set_cdfem_edge_tol(0.001); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_NEAREST_EDGE_CUT); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + + register_ls_on_blocks({&block1_part}); + + commit(); + + build_one_tet4_mesh(*this, block1_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const std::array nodes = {{ mesh.get_entity(stk::topology::NODE_RANK, 1), mesh.get_entity(stk::topology::NODE_RANK, 2), mesh.get_entity(stk::topology::NODE_RANK, 3), mesh.get_entity(stk::topology::NODE_RANK, 4) }}; + const auto & ls_isovars = ls_policy.ls_isovars; + *field_data(ls_isovars[0], nodes[0]) = -1; + *field_data(ls_isovars[0], nodes[1]) = 1.; + *field_data(ls_isovars[0], nodes[2]) = 2.; + *field_data(ls_isovars[0], nodes[3]) = 3.; + + commit(); + decompose_mesh(); + + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + EXPECT_EQ(1u+1u, mesh.num_elements(nodes[0])); + EXPECT_EQ(1u+1u, mesh.num_elements(nodes[1])); + EXPECT_EQ(2u+1u, mesh.num_elements(nodes[2])); + EXPECT_EQ(3u+1u, mesh.num_elements(nodes[3])); + + // regression test + const ScaledJacobianQualityMetric qualityMetric; + const double quality = determine_quality(mesh, krino_mesh->get_active_part(), qualityMetric); + const double goldQuality = 0.21; + EXPECT_GT(quality, goldQuality); +} + +typedef CompleteDecompositionFixture > CDMeshTests3DLSPerPhase; +TEST_F(CDMeshTests3DLSPerPhase, Random_TwoTet4_InternalSideset) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + // Use a large snap tolerance to make snapping more common since it is a frequent source + // of parallel bugs + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for(auto && isovar : ls_isovars) sync_fields.push_back(&isovar.field()); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + for(auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + if(HasNonfatalFailure()) + { + std::cout << "Failure on iteration " << i << std::endl; + std::ostringstream fname; + fname << "Random_TwoTet4_InternalSideset_iter_" << i << ".e"; + fixture.write_results(fname.str()); + ASSERT_TRUE(false); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +TEST_F(CDMeshTests3DLSPerPhase, Random_TwoTet4_InternalSideset_Snap) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + cdfemSupport.set_cdfem_edge_degeneracy_handling(SNAP_TO_INTERFACE_WHEN_QUALITY_ALLOWS_THEN_SNAP_TO_NODE); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides(mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for(auto && isovar : ls_isovars) sync_fields.push_back(&isovar.field()); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); +#ifdef NDEBUG + const int num_cases = 5000; +#else + const int num_cases = 1000; +#endif + for(int i=0; i < num_cases; ++i) + { + if (i%1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + MeshClone::stash_or_restore_mesh(mesh, 0); // restore original uncut mesh + commit(); // new krino_mesh each time + + for(auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + EXPECT_TRUE(check_induced_parts(mesh)); + EXPECT_TRUE(check_face_and_edge_ownership(mesh)); + EXPECT_TRUE(check_face_and_edge_relations(mesh)); + EXPECT_TRUE(check_shared_entity_nodes(mesh)); + EXPECT_TRUE(krino_mesh->check_element_side_parts()); + + if(HasNonfatalFailure()) + { + std::cout << "Failure on iteration " << i << std::endl; + std::ostringstream fname; + fname << "Random_TwoTet4_InternalSideset_iter_" << i << ".e"; + fixture.write_results(fname.str()); + ASSERT_TRUE(false); + } + + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +TEST_F(CDMeshTests3DLSPerPhase, RestoreAfterFailedStep) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + + if (parallel_size > 2) return; + + stk::mesh::BulkData & mesh = fixture.bulk_data(); + stk::mesh::MetaData & meta = fixture.meta_data(); + AuxMetaData & aux_meta = AuxMetaData::get(meta); + + // Use a large snap tolerance to make snapping more common since it is a frequent source + // of parallel bugs + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", + tet4.side_topology(), + {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + commit(); + + build_two_tet4_mesh_np2( + *this, block1_part, block2_part, surface_part, parallel_rank, parallel_size); + + stk::mesh::create_exposed_block_boundary_sides( + mesh, meta.universal_part(), {&aux_meta.exposed_boundary_part()}); + + const auto & ls_isovars = ls_policy.ls_isovars; + std::vector sync_fields = {&coord_field.field()}; + for (auto && isovar : ls_isovars) + sync_fields.push_back(&isovar.field()); + + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution dist(-1., 1.); + for (int i = 0; i < 100; ++i) + { + if (i % 1000 == 0) std::cout << "Testing random configuration " << i << std::endl; + + // We want to test restoring the mesh after failed time steps for a variety of + // random decompositions: + // 1) Do a random decomposition and stash the mesh to act like a successful time + // step. + // 2) Do a second random decomposition to simulate the changes of a time step that + // will fail. + // 3) Restore the mesh to the stashed mesh, and rebuild the CDMesh, confirm that + // does not fail. + + auto randomize_all_fields = [&]() + { + for (auto && isovar : ls_isovars) + { + randomize_ls_field(mesh, isovar, mt, dist); + } + stk::mesh::communicate_field_data(mesh, sync_fields); + }; + + auto run_decomp = [&]() + { + try + { + decompose_mesh(); + } + catch (const std::exception & exception) + { + std::cout << log.get_log() << std::endl; + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + }; + // Step 1. + randomize_all_fields(); + run_decomp(); + krino::MeshClone::stash_or_restore_mesh(mesh, i); + krino_mesh = std::make_shared(mesh, krino_mesh); + + // Step 2. + randomize_all_fields(); + run_decomp(); + krino::MeshClone::stash_or_restore_mesh(mesh, i); + + // Step 3. + ASSERT_NO_THROW(krino_mesh->rebuild_after_rebalance()); + krino_mesh = std::make_shared(mesh, krino_mesh); + } +} + +TEST_F(CDMeshTests3D, Rebalance_with_rcb) +{ + run_rebalance_with("rcb"); +} + +TEST_F(CDMeshTests3D, Rebalance_with_parmetis) +{ + run_rebalance_with("parmetis"); +} + +typedef CompleteDecompositionFixture NonconformalAdaptivityTest; +TEST_F(NonconformalAdaptivityTest, InternalSidePositivePermutationNonOwnedElement) +{ + /* This tests that percept can correctly handle an internal side where the element + * with the same owning proc as the side has a negative permutation and the second + * connected element (with a different owning processor) has a positive permutation. + * In serial it just tests use of the adaptivity interface. + */ + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + + if (parallel_size > 2) return; + + cdfemSupport.set_cdfem_edge_tol(0.1); + cdfemSupport.set_simplex_generation_method(CUT_QUADS_BY_GLOBAL_IDENTIFIER); + + setup_ls_field(); + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + register_ls_on_blocks({&block1_part, &block2_part}); + + auto & aux_meta = AuxMetaData::get(fixture.meta_data()); + FieldRef marker_field = + aux_meta.register_field("refine_marker", FieldType::INTEGER, stk::topology::ELEMENT_RANK, + 1u, 1, fixture.meta_data().universal_part()); + + auto & meta = fixture.meta_data(); + auto & active_part = aux_meta.active_part(); + stk::diag::TimerSet enabledTimerSet(0); + stk::diag::Timer root_timer = createRootTimer("test", enabledTimerSet); + HAdapt::setup(meta, active_part, root_timer); + + commit(); + + const bool build_all_on_P0 = false; + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_part, parallel_rank, + parallel_size, true, build_all_on_P0); + + auto elem_1 = mesh.get_entity(stk::topology::ELEMENT_RANK, 1u); + int & elem_1_marker = *field_data(marker_field, elem_1); + elem_1_marker = 1; + + if(parallel_size == 2) + { + stk::mesh::EntityProcVec changes; + if(parallel_rank == 0) + { + changes.push_back(std::make_pair(mesh.get_entity(stk::topology::FACE_RANK, 7), 1)); + } + mesh.change_entity_owner(changes); + } + + EXPECT_NO_THROW(HAdapt::do_adaptive_refinement(meta, marker_field.name())); +} + +typedef CompleteDecompositionFixture MeshCloneTest; +TEST_F(MeshCloneTest, FaceOwnershipAndPartChangeBetweenClones) +{ + /* + * This test regression tests a bug where a shared face both changed parts and + * parallel owners between calls to MeshClone::stash_or_restore_mesh(), leading to a + * throw when copying field data to the clone mesh because the parts of the face were not + * updated on the clone. + */ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + const int parallel_rank = stk::parallel_machine_rank(pm); + stk::mesh::BulkData & mesh = fixture.bulk_data(); + + if (parallel_size != 2) return; + + const stk::topology tet4 = stk::topology::TETRAHEDRON_4; + auto & block1_part = declare_input_block("block_1", tet4); + auto & block2_part = declare_input_block("block_2", tet4); + auto & surface_1_part = declare_input_surface("surface_1", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + auto & surface_2_part = declare_input_surface("surface_2", tet4.side_topology(), {block1_part.mesh_meta_data_ordinal(), block2_part.mesh_meta_data_ordinal()}); + + auto & aux_meta = AuxMetaData::get(fixture.meta_data()); + aux_meta.register_field("side_field", FieldType::REAL, stk::topology::FACE_RANK, + 1u, 1u, surface_1_part); + + commit(); + + build_two_tet4_mesh_np2(*this, block1_part, block2_part, surface_1_part, parallel_rank, parallel_size); + + // Stash the initial mesh. + ASSERT_NO_THROW(MeshClone::stash_or_restore_mesh(mesh, 0)); + + // Change the parallel owner of the shared face, then change its surface part from surface_1 to + // surface_2. + const auto side_1 = mesh.get_entity(stk::topology::FACE_RANK, 7); + const auto current_owner = mesh.parallel_owner_rank(side_1); + stk::mesh::EntityProcVec owner_changes; + if(parallel_rank == current_owner) + { + owner_changes.emplace_back(side_1, (current_owner + 1) % 2); + } + mesh.change_entity_owner(owner_changes); + ASSERT_TRUE(mesh.is_valid(side_1)); + const auto new_owner = mesh.parallel_owner_rank(side_1); + ASSERT_NE(new_owner, current_owner); + + mesh.modification_begin(); + if(new_owner == parallel_rank) + { + mesh.change_entity_parts(side_1, stk::mesh::ConstPartVector{&surface_2_part}, stk::mesh::ConstPartVector{&surface_1_part}); + } + mesh.modification_end(); + + // Confirm that updating the stash mesh succeeds + try + { + MeshClone::stash_or_restore_mesh(mesh, 1); + } + catch (const std::exception & exception) + { + std::cout << "Decomposing mesh failed with exception:\n"; + std::cout << exception.what() << "\n"; + ASSERT_TRUE(false); + } + + // Change the shared face part back to surface_1, then restore from the stash and + // confirm that the parts of the face are correct. + mesh.modification_begin(); + if(new_owner == parallel_rank) + { + mesh.change_entity_parts(side_1, stk::mesh::ConstPartVector{&surface_1_part}, stk::mesh::ConstPartVector{&surface_2_part}); + } + mesh.modification_end(); + ASSERT_TRUE(mesh.bucket(side_1).member(surface_1_part)); + MeshClone::stash_or_restore_mesh(mesh, 1); + const auto side_1_new = mesh.get_entity(stk::topology::FACE_RANK, 7); + EXPECT_TRUE(mesh.bucket(side_1_new).member(surface_2_part)); + EXPECT_FALSE(mesh.bucket(side_1_new).member(surface_1_part)); +} + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_ContourElement.cpp b/packages/krino/krino/unit_tests/Akri_Unit_ContourElement.cpp new file mode 100644 index 000000000000..372f6cdbb820 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_ContourElement.cpp @@ -0,0 +1,83 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + +#include + +namespace krino { + +TEST(SingleElementFixture, LS_Element_Tet4) +{ + stk::topology tet4 = stk::topology::TETRAHEDRON_4; + SingleElementFixture test_fixture(tet4); + + test_fixture.generate_mesh(); + stk::mesh::MetaData & meta = test_fixture.stk_fixture.meta_data(); + stk::mesh::BulkData & bulk = test_fixture.stk_fixture.bulk_data(); + + const unsigned ndim = meta.spatial_dimension(); + const stk::mesh::FieldBase & coords_field = test_fixture.coord_field.field(); + const stk::mesh::FieldBase & scalar_field = test_fixture.scalar_field.field(); + + stk::mesh::Entity elem = test_fixture.my_elem; + const stk::mesh::Entity* elem_nodes = bulk.begin_nodes(elem); + const unsigned npe = bulk.num_nodes(elem); + + // Set coordinates + const double coords[4][3] = {{0.,0.,0.},{1.,0.,0.},{0.,1.,0.},{0.,0.,4.}}; + for (unsigned node=0; node(stk::mesh::field_data(coords_field, elem_nodes[node])); + for (unsigned dim=0; dim(stk::mesh::field_data(scalar_field, elem_nodes[node])); + *scalar_data = isovar[node]; + } + + // + // Create facets on 0 isosurface + // + + const double isoval = 0.0; + krino::ContourElement ls_elem( bulk, elem, coords_field, scalar_field, isoval ); + const double length_scale = 1.0; // Used for snapping facets to vertices of element when distance is small compared to length_scale + ls_elem.compute_subelement_decomposition(length_scale); + + Faceted_Surface faceted_surface("tmp"); + ls_elem.build_subelement_facets(faceted_surface); + const auto & facets = faceted_surface.get_facets(); + + ASSERT_EQ(1u, facets.size()); + + Facet & facet = *facets[0]; + + EXPECT_EQ(2.0, facet.facet_vertex(0)[2]); + EXPECT_EQ(2.0, facet.facet_vertex(1)[2]); + EXPECT_EQ(2.0, facet.facet_vertex(2)[2]); + + const Vector3d normal = facet.facet_normal(); + const double area = facet.facet_area(); + + EXPECT_EQ(0.0, normal[0]); + EXPECT_EQ(0.0, normal[1]); + EXPECT_EQ(1.0, normal[2]); + + EXPECT_EQ(0.125, area); +} + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Element.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Element.cpp new file mode 100644 index 000000000000..d799a4402563 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Element.cpp @@ -0,0 +1,718 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +template +class Mesh_Element_Fixture : public ::testing::Test +{ +public: + Mesh_Element_Fixture() : + elem_fixture(static_cast(TOPO)), + krino_mesh(elem_fixture.stk_fixture.bulk_data(), std::shared_ptr()), + interfaceGeometry(krino_mesh.get_active_part(),krino_mesh.get_cdfem_support(), krino_mesh.get_phase_support()) + { + elem_fixture.generate_mesh(); + check_entity_counts(); + Phase_Support::get(stk_meta()).add_decomposed_part(stk_meta().universal_part()); + Phase_Support::set_one_levelset_per_phase(false); + const NodeToCapturedDomainsMap nodesToCapturedDomains; + interfaceGeometry.prepare_to_process_elements(krino_mesh.stk_bulk(), nodesToCapturedDomains); + } + virtual ~Mesh_Element_Fixture() {}; + void check_entity_counts() + { + std::vector entities; + stk::mesh::get_entities(stk_bulk(), stk::topology::ELEMENT_RANK, entities); + ASSERT_EQ(1u, entities.size()); + stk::mesh::get_entities(stk_bulk(), stk::topology::NODE_RANK, entities); + ASSERT_EQ(elem_fixture.my_topology.num_nodes(), entities.size()); + } + stk::mesh::BulkData & stk_bulk() { return elem_fixture.stk_fixture.bulk_data(); } + stk::mesh::MetaData & stk_meta() { return elem_fixture.stk_fixture.meta_data(); } + stk::mesh::Entity elem() { return elem_fixture.my_elem; } + + unsigned node_ordinal(const stk::mesh::Entity node) + { + const stk::mesh::Entity * const elem_nodes = stk_bulk().begin_nodes(elem()); + const unsigned num_nodes = stk_bulk().num_nodes(elem()); + const stk::mesh::Entity * found = std::find(elem_nodes, elem_nodes+num_nodes, node); + return found - elem_nodes; + } + + void generate_nonconformal_elements() { + krino_mesh.generate_nonconformal_elements(); + } + void triangulate() + { + Mesh_Element & meshElem = get_mesh_element(); + meshElem.create_cutter(krino_mesh, interfaceGeometry); // update cutter with for edges that now have crossings found + get_mesh_element().create_cutter(krino_mesh, interfaceGeometry); + krino_mesh.triangulate(interfaceGeometry); + } + + LevelSetElementCutter & get_cutter() + { + Mesh_Element & meshElem = get_mesh_element(); + meshElem.create_cutter(krino_mesh, interfaceGeometry); + LevelSetElementCutter * cutter = dynamic_cast(meshElem.get_cutter()); + ThrowRequire(cutter); + return *cutter; + } + + void find_edge_crossings(const std::vector & node_LS_values) + { + std::vector > nodesIsovar(2); + LevelSetElementCutter & cutter = get_cutter(); + for (unsigned iEdge=0; iEdge > & node_LS_values) + { + std::vector > nodesIsovar(2); + LevelSetElementCutter & cutter = get_cutter(); + for (unsigned iEdge=0; iEdge & node_LS_values) + { + generate_nonconformal_elements(); + find_edge_crossings(node_LS_values); + triangulate(); + } + + void generate_mesh_element_and_cutter(const std::vector > & node_LS_values) + { + generate_nonconformal_elements(); + find_edge_crossings(node_LS_values); + triangulate(); + } + + Mesh_Element & get_mesh_element() { + return *krino_mesh.elements.front(); + } + + std::array get_edge_nodes(const unsigned edgeOrdinal) + { + const auto & nodes = get_mesh_element().get_nodes(); + const unsigned * edge_node_ordinals = get_edge_node_ordinals(elem_fixture.my_topology, edgeOrdinal); + return {{nodes[edge_node_ordinals[0]], nodes[edge_node_ordinals[1]]}}; + } + + Segment3d get_edge_segment(const unsigned edge_ord) + { + const auto & edgeNodes = get_edge_nodes(edge_ord); + return Segment3d(get_mesh_element().get_node_parametric_coords(edgeNodes[0]), + get_mesh_element().get_node_parametric_coords(edgeNodes[1])); + } + + SingleElementFixture elem_fixture; + CDMesh krino_mesh; + LevelSetInterfaceGeometry interfaceGeometry; +}; + +typedef Mesh_Element_Fixture Mesh_Element_Tri3; +TEST_F(Mesh_Element_Tri3, generate) +{ + generate_nonconformal_elements(); + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_EQ(elem(), mesh_elem.entity()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + ASSERT_EQ(3u, mesh_nodes.size()); + const stk::mesh::Entity * const elem_nodes = stk_bulk().begin_nodes(elem()); + for(unsigned i=0; i < mesh_nodes.size(); ++i) + { + EXPECT_EQ(mesh_nodes[i]->entity(), elem_nodes[i]); + } +} + +typedef Mesh_Element_Tri3 Mesh_Element_Tri3_One_LS; +TEST_F(Mesh_Element_Tri3_One_LS, All_Nodes_Positive) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + const std::vector node_LS_values(3, 1.); + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); + + for(unsigned i=0; i < mesh_elem.topology().num_edges(); ++i) + { + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(InterfaceID(0,0), get_edge_segment(i))); + } +} + +TEST_F(Mesh_Element_Tri3_One_LS, All_Nodes_Negative) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + const std::vector node_LS_values(3, -1.); + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); + + for(unsigned i=0; i < mesh_elem.topology().num_edges(); ++i) + { + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(InterfaceID(0,0), get_edge_segment(i))); + } +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_Pos_Node1_2_Neg) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 1.; + node_LS_values[1] = -0.5; + node_LS_values[2] = -0.5; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + EXPECT_DOUBLE_EQ(2./3., mesh_elem.interface_crossing_position(iface, get_edge_segment(0))); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(1))); + EXPECT_DOUBLE_EQ(1./3., mesh_elem.interface_crossing_position(iface, get_edge_segment(2))); +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_Snapped_Node1_2_Pos) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 0; + node_LS_values[1] = 1.; + node_LS_values[2] = 1.; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(0))); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(1))); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(2))); +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_Snapped_Node1_2_Neg) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 0; + node_LS_values[1] = -1.; + node_LS_values[2] = -1.; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + EXPECT_EQ( 0, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + // NOTE: Because we snap-away from nodes, crossing will be epsilon away from nodes. + EXPECT_NEAR(0., mesh_elem.interface_crossing_position(iface, get_edge_segment(0)), std::numeric_limits::epsilon()); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(1))); + EXPECT_NEAR(1., mesh_elem.interface_crossing_position(iface, get_edge_segment(2)), std::numeric_limits::epsilon()); +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_Snapped_Node1_Pos_Node_2_Neg) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 0; + // Crossing position 0.608351703529745 for edge 1 + // gives a test case that fails to intersect exactly with node 0 + node_LS_values[1] = 1.; + node_LS_values[2] = -(1/0.60835170352974499152765019971412 - 1.); + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + EXPECT_EQ( 0, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + // NOTE: Because we snap-away from nodes, crossing will be epsilon away from nodes. + EXPECT_DOUBLE_EQ(node_LS_values[1]/(node_LS_values[1] - node_LS_values[2]), mesh_elem.interface_crossing_position(iface, get_edge_segment(1))); + EXPECT_NEAR(1., mesh_elem.interface_crossing_position(iface, get_edge_segment(2)), std::numeric_limits::epsilon()); +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_1_Snapped_Node2_Pos) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 0; + node_LS_values[1] = 0; + node_LS_values[2] = 1.; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(0))); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(1))); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface, get_edge_segment(2))); +} + +TEST_F(Mesh_Element_Tri3_One_LS, Node0_1_Snapped_Node2_Neg) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + + std::vector node_LS_values(3); + node_LS_values[0] = 0; + node_LS_values[1] = 0; + node_LS_values[2] = -1.; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + EXPECT_EQ( 0, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ( 0, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + + // NOTE: Edge 0 is from nodes 0->1, Edge 1 is 1->2, Edge 2 is 2->0 + // TODO: What should intersections be for snapped edge? + // I don't think we should ever be looking for the interface crossing position of it + // NOTE: Because we snap-away from nodes, crossing will be epsilon away from nodes. + EXPECT_NEAR(0., mesh_elem.interface_crossing_position(iface, get_edge_segment(1)), std::numeric_limits::epsilon()); + EXPECT_NEAR(1., mesh_elem.interface_crossing_position(iface, get_edge_segment(2)), std::numeric_limits::epsilon()); +} + +typedef Mesh_Element_Tri3 Mesh_Element_Tri3_Three_LS; +TEST_F(Mesh_Element_Tri3_Three_LS, All_Phase2_Unsnapped) +{ + const LS_Field ls1("LS1", LevelSet_Identifier(1)); + const LS_Field ls2("LS2", LevelSet_Identifier(2)); + const LS_Field ls3("LS3", LevelSet_Identifier(3)); + CDFEM_Support & cdfem_supp = CDFEM_Support::get(elem_fixture.stk_fixture.meta_data()); + cdfem_supp.add_ls_field(ls1); + cdfem_supp.add_ls_field(ls2); + cdfem_supp.add_ls_field(ls3); + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + krino_mesh.add_interface_id(iface01); + krino_mesh.add_interface_id(iface02); + krino_mesh.add_interface_id(iface12); + Phase_Support::set_one_levelset_per_phase(true); + + std::vector > node_LS_values(3); + node_LS_values[0].resize(3); + node_LS_values[1].resize(3); + node_LS_values[2].resize(3); + // LS 0 + node_LS_values[0][0] = 1; + node_LS_values[1][0] = 1; + node_LS_values[2][0] = 1; + // LS 1 + node_LS_values[0][1] = 1; + node_LS_values[1][1] = 1; + node_LS_values[2][1] = 1; + // LS 2 + node_LS_values[0][2] = -1; + node_LS_values[1][2] = -1; + node_LS_values[2][2] = -1; + + generate_mesh_element_and_cutter(node_LS_values); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); +} + +TEST_F(Mesh_Element_Tri3_Three_LS, One_Interface) +{ + const LS_Field ls1("LS1", LevelSet_Identifier(1)); + const LS_Field ls2("LS2", LevelSet_Identifier(2)); + const LS_Field ls3("LS3", LevelSet_Identifier(3)); + CDFEM_Support & cdfem_supp = CDFEM_Support::get(elem_fixture.stk_fixture.meta_data()); + cdfem_supp.add_ls_field(ls1); + cdfem_supp.add_ls_field(ls2); + cdfem_supp.add_ls_field(ls3); + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + krino_mesh.add_interface_id(iface01); + krino_mesh.add_interface_id(iface02); + krino_mesh.add_interface_id(iface12); + Phase_Support::set_one_levelset_per_phase(true); + + std::vector > node_LS_values(3); + node_LS_values[0].resize(3); + node_LS_values[1].resize(3); + node_LS_values[2].resize(3); + // LS 0 + node_LS_values[0][0] = 0.038335; + node_LS_values[1][0] = 0.014437; + node_LS_values[2][0] = -0.01288; + // LS 1 + node_LS_values[0][1] = 0.037250; + node_LS_values[1][1] = 0.070753; + node_LS_values[2][1] = 0.021996; + // LS 2 + node_LS_values[0][2] = 0.01; + node_LS_values[1][2] = 0.01; + node_LS_values[2][2] = 0.01; + + generate_mesh_element_and_cutter(node_LS_values); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + + const Vector3d node0_coords = mesh_nodes[0]->owner_coords(&mesh_elem); + const Vector3d node1_coords = mesh_nodes[1]->owner_coords(&mesh_elem); + const Vector3d node2_coords = mesh_nodes[2]->owner_coords(&mesh_elem); + const Segment3d edge0(node0_coords, node1_coords); + const Segment3d edge1(node1_coords, node2_coords); + const Segment3d edge2(node2_coords, node0_coords); + + krino_mesh.determine_node_signs(iface01); + + if (mesh_elem.have_interface(iface01)) + { + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[2]->get_node_sign()); + } + + krino_mesh.determine_node_signs(iface02); + + EXPECT_TRUE(mesh_elem.have_interface(iface02)); + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + + krino_mesh.determine_node_signs(iface12); + + if (mesh_elem.have_interface(iface12)) + { + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[2]->get_node_sign()); + } + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge2)); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge2)); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge0)); +} + +TEST_F(Mesh_Element_Tri3_Three_LS, Handle_Hanging_Child) +{ + const LS_Field ls1("LS1", LevelSet_Identifier(1)); + const LS_Field ls2("LS2", LevelSet_Identifier(2)); + const LS_Field ls3("LS3", LevelSet_Identifier(3)); + CDFEM_Support & cdfem_supp = CDFEM_Support::get(elem_fixture.stk_fixture.meta_data()); + cdfem_supp.add_ls_field(ls1); + cdfem_supp.add_ls_field(ls2); + cdfem_supp.add_ls_field(ls3); + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + krino_mesh.add_interface_id(iface01); + krino_mesh.add_interface_id(iface02); + krino_mesh.add_interface_id(iface12); + Phase_Support::set_one_levelset_per_phase(true); + + std::vector > node_LS_values(3); + node_LS_values[0].resize(3); + node_LS_values[1].resize(3); + node_LS_values[2].resize(3); + // LS 0 + node_LS_values[0][0] = 0.04; + node_LS_values[1][0] = 0.015; + node_LS_values[2][0] = 0.025; + // LS 1 + node_LS_values[0][1] = 0.; + node_LS_values[1][1] = 0.02; + node_LS_values[2][1] = 0.02; + // LS 2 + node_LS_values[0][2] = 0.01; + node_LS_values[1][2] = 0.01; + node_LS_values[2][2] = 0.01; + + generate_mesh_element_and_cutter(node_LS_values); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + + const Vector3d node0_coords = mesh_nodes[0]->owner_coords(&mesh_elem); + const Vector3d node1_coords = mesh_nodes[1]->owner_coords(&mesh_elem); + const Vector3d node2_coords = mesh_nodes[2]->owner_coords(&mesh_elem); + const Segment3d edge0(node0_coords, node1_coords); + const Segment3d edge1(node1_coords, node2_coords); + const Segment3d edge2(node2_coords, node0_coords); + + krino_mesh.determine_node_signs(iface01); + + if (mesh_elem.have_interface(iface01)) + { + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[2]->get_node_sign()); + } + + krino_mesh.determine_node_signs(iface02); + + if (mesh_elem.have_interface(iface02)) + { + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[2]->get_node_sign()); + }; + + krino_mesh.determine_node_signs(iface12); + + EXPECT_TRUE(mesh_elem.have_interface(iface12)); + EXPECT_EQ(-1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[2]->get_node_sign()); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge2)); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge2)); + + EXPECT_DOUBLE_EQ(0.5, mesh_elem.interface_crossing_position(iface12, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge1)); + EXPECT_DOUBLE_EQ(0.5, mesh_elem.interface_crossing_position(iface12, edge2)); +} + +TEST_F(Mesh_Element_Tri3_Three_LS, Zero_Crossings_For_Phases_Present_Bug) +{ + const LS_Field ls1("LS1", LevelSet_Identifier(1)); + const LS_Field ls2("LS2", LevelSet_Identifier(2)); + const LS_Field ls3("LS3", LevelSet_Identifier(3)); + CDFEM_Support & cdfem_supp = CDFEM_Support::get(elem_fixture.stk_fixture.meta_data()); + cdfem_supp.add_ls_field(ls1); + cdfem_supp.add_ls_field(ls2); + cdfem_supp.add_ls_field(ls3); + const InterfaceID iface01(0,1); + const InterfaceID iface02(0,2); + const InterfaceID iface12(1,2); + krino_mesh.add_interface_id(iface01); + krino_mesh.add_interface_id(iface02); + krino_mesh.add_interface_id(iface12); + Phase_Support::set_one_levelset_per_phase(true); + + std::vector > node_LS_values(4); + node_LS_values[0].resize(3); + node_LS_values[1].resize(3); + node_LS_values[2].resize(3); + node_LS_values[3].resize(3); + // Node 0 + node_LS_values[0][0] = -0.00765969; + node_LS_values[0][1] = 0.532721; + node_LS_values[0][2] = 0.; + // Node 1 + node_LS_values[1][0] = -0.000100754; + node_LS_values[1][1] = 0.; + node_LS_values[1][2] = 0.; + // Node 2 + node_LS_values[2][0] = -0.00666939; + node_LS_values[2][1] = 0.337202; + node_LS_values[2][2] = 0.; + // Node 3 (Mid-node for edge 1) + node_LS_values[3][0] = -2.76e-6; + node_LS_values[3][1] = -0.00614775; + node_LS_values[3][2] = 0.; + + generate_mesh_element_and_cutter(node_LS_values); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_FALSE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + EXPECT_EQ(3u, mesh_nodes.size()); + + const Vector3d node0_coords = mesh_nodes[0]->owner_coords(&mesh_elem); + const Vector3d node1_coords = mesh_nodes[1]->owner_coords(&mesh_elem); + const Vector3d node2_coords = mesh_nodes[2]->owner_coords(&mesh_elem); + const Segment3d edge0(node0_coords, node1_coords); + const Segment3d edge1(node1_coords, node2_coords); + const Segment3d edge2(node2_coords, node0_coords); + + krino_mesh.determine_node_signs(iface01); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface01, edge2)); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface02, edge2)); + + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge0)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge1)); + EXPECT_ANY_THROW(mesh_elem.interface_crossing_position(iface12, edge2)); +} + +typedef Mesh_Element_Fixture Mesh_Element_Tet4; +TEST_F(Mesh_Element_Tet4, generate) +{ + generate_nonconformal_elements(); + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_EQ(elem(), mesh_elem.entity()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + ASSERT_EQ(4u, mesh_nodes.size()); + const stk::mesh::Entity * const elem_nodes = stk_bulk().begin_nodes(elem()); + for(unsigned i=0; i < mesh_nodes.size(); ++i) + { + EXPECT_EQ(mesh_nodes[i]->entity(), elem_nodes[i]); + } +} + +TEST_F(Mesh_Element_Tet4, OneInterfaceCheckNodeScore) +{ + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + Phase_Support::set_one_levelset_per_phase(false); + + std::vector node_LS_values(4); + node_LS_values[0] = 1.; + node_LS_values[1] = -0.2; + node_LS_values[2] = -0.5; + node_LS_values[3] = -0.8; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + ASSERT_EQ(4u, mesh_nodes.size()); + EXPECT_EQ(+1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[3]->get_node_sign()); + + krino_mesh.decompose_edges(iface); + krino_mesh.determine_node_scores(iface); + + EXPECT_GT(mesh_nodes[0]->get_node_score(), mesh_nodes[3]->get_node_score()); + EXPECT_GT(mesh_nodes[3]->get_node_score(), mesh_nodes[2]->get_node_score()); + EXPECT_GT(mesh_nodes[2]->get_node_score(), mesh_nodes[1]->get_node_score()); +} + +TEST_F(Mesh_Element_Tet4, OneInterfaceCheckNodeScore_ScoreBasedOnAngleNotPosition) +{ + krino_mesh.get_cdfem_support().set_simplex_generation_method(CUT_QUADS_BY_LARGEST_ANGLE); + + const InterfaceID iface(0,0); + krino_mesh.add_interface_id(iface); + Phase_Support::set_one_levelset_per_phase(false); + + std::vector node_LS_values(4); + node_LS_values[0] = -1.0; + node_LS_values[1] = -1.01; + node_LS_values[2] = -1.02; + node_LS_values[3] = 1.0; + + generate_mesh_element_and_cutter(node_LS_values); + krino_mesh.determine_node_signs(iface); + + Mesh_Element & mesh_elem = get_mesh_element(); + EXPECT_TRUE(mesh_elem.have_interface()); + const NodeVec & mesh_nodes = mesh_elem.get_nodes(); + ASSERT_EQ(4u, mesh_nodes.size()); + EXPECT_EQ(-1, mesh_nodes[0]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[1]->get_node_sign()); + EXPECT_EQ(-1, mesh_nodes[2]->get_node_sign()); + EXPECT_EQ(+1, mesh_nodes[3]->get_node_sign()); + + krino_mesh.decompose_edges(iface); + krino_mesh.determine_node_scores(iface); + + EXPECT_GT(mesh_nodes[0]->get_node_score(), mesh_nodes[1]->get_node_score()); + EXPECT_GT(mesh_nodes[0]->get_node_score(), mesh_nodes[2]->get_node_score()); + EXPECT_GT(mesh_nodes[2]->get_node_score(), mesh_nodes[1]->get_node_score()); +} + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Element_Cutter.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Element_Cutter.cpp new file mode 100644 index 000000000000..b44c1914a3c8 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Element_Cutter.cpp @@ -0,0 +1,188 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace krino +{ + +static std::function &)> +build_always_false_diagonal_picker() +{ + auto diagonalPicker = + [](const std::array & faceNodes) + { + return false; + }; + return diagonalPicker; +} + +static void build_simple_parent_edges(const stk::topology topology, + const std::vector & nodeIds, + const std::vector> & nodalIsovars, + ParentEdgeMap & parentEdges, + std::vector & elementParentEdges, + std::vector & areParentEdgesAreOrientedSameAsElementEdges) +{ + const unsigned numEdges = topology.num_edges(); + + elementParentEdges.clear(); + for(unsigned i=0; i < numEdges; ++i) + { + const unsigned * edgeLNN = get_edge_node_ordinals(topology, i); + const unsigned i0 = edgeLNN[0]; + const unsigned i1 = edgeLNN[1]; + const ParentEdgeKey edge_key(nodeIds[i0], nodeIds[i1]); + CDFEM_Parent_Edge & parentEdge = parentEdges[edge_key]; + + if(!parentEdge.valid()) + parentEdge = CDFEM_Parent_Edge({nodalIsovars[i0], nodalIsovars[i1]}); + + elementParentEdges.push_back(&parentEdge); + } + + areParentEdgesAreOrientedSameAsElementEdges.clear(); + areParentEdgesAreOrientedSameAsElementEdges.resize(numEdges, true); +} + +struct ElementWithCutter : public ::testing::Test +{ + ElementWithCutter() {} + + void build_parent_edges_and_cutter(const stk::topology topology, + const std::vector & nodeIds, + const std::vector > & nodalIsovars) + { + Phase_Support::set_one_levelset_per_phase(true); + const auto diagonalPicker = build_always_false_diagonal_picker(); + + const MasterElement & masterElem = MasterElementDeterminer::getMasterElement(topology); + + std::vector elementParentEdges; + std::vector areParentEdgesAreOrientedSameAsElementEdges; + + build_simple_parent_edges(topology, nodeIds, nodalIsovars, parentEdges, elementParentEdges, areParentEdgesAreOrientedSameAsElementEdges); + + cutter.reset( new One_LS_Per_Phase_Cutter(masterElem, elementParentEdges, areParentEdgesAreOrientedSameAsElementEdges, diagonalPicker) ); + } + + ParentEdgeMap parentEdges; + CDFEM_Snapper snapper; + std::unique_ptr cutter; +}; + +struct TriangleWithTriplePoint : public ElementWithCutter +{ + const stk::topology topology{stk::topology::TRIANGLE_3_2D}; + const std::vector > nodalIsovars{ {-1., 0., 0.}, {0., -1., 0.}, {1.,1.,0.} }; + const std::vector nodeIds{1,2,3}; + + const InterfaceID iface01{0,1}; + const InterfaceID iface02{0,2}; + const InterfaceID iface12{1,2}; +}; + +struct TriangleWithFakeTriplePoint : public ElementWithCutter +{ + const stk::topology topology{stk::topology::TRIANGLE_3_2D}; + const std::vector > nodalIsovars{ {2., 2.,-1., 0.}, {-1.,0.5, 2., 0.}, {0.5, -1., 2., 0.} }; + const std::vector nodeIds{1,2,3}; +}; + +TEST_F(TriangleWithTriplePoint, givenCutter_haveExpectedInterfaces) +{ + build_parent_edges_and_cutter(topology, nodeIds, nodalIsovars); + + std::vector interfacesWithCuttingSurface; + cutter->fill_interfaces_with_cutting_surface(interfacesWithCuttingSurface); + EXPECT_EQ(3u, interfacesWithCuttingSurface.size()); + + EXPECT_TRUE(cutter->have_cutting_surface(iface01)); + EXPECT_TRUE(cutter->have_cutting_surface(iface02)); + EXPECT_TRUE(cutter->have_cutting_surface(iface12)); +} + +static bool is_nearly_eq(const Vector3d & v0, const Vector3d & v1, const double relativeTol=1.e-6) +{ + const double absoluteTol = relativeTol * (v0.length() + v1.length()); + for (int i=0; i<3; ++i) + if (std::abs(v0[i]-v1[i]) > absoluteTol) return false; + return true; +} + +void expect_to_find_all_first_in_second(const std::vector & vec0, const std::vector & vec1, const std::string & errorMsg) +{ + for (auto && val0 : vec0) + { + bool found = false; + for (auto && val1 : vec1) + { + if (is_nearly_eq(val0.parametricCoords, val1.parametricCoords) && val0.sortedDomains == val1.sortedDomains) + { + found = true; + break; + } + } + EXPECT_TRUE(found) << errorMsg << val0; + } +} + +void expect_num_interfaces_with_cutting_surface(size_t goldNumInterfacesWithCuttingSurfaces, const Element_Cutter & cutter) +{ + std::vector interfacesWithCuttingSurface; + cutter.fill_interfaces_with_cutting_surface(interfacesWithCuttingSurface); + EXPECT_EQ(goldNumInterfacesWithCuttingSurfaces, interfacesWithCuttingSurface.size()); +} + +void expect_intersections(const std::vector & goldIntersections, const std::vector & actualIntersections) +{ + EXPECT_EQ(goldIntersections.empty(), actualIntersections.empty()); + expect_to_find_all_first_in_second(actualIntersections, goldIntersections, "Actual intersection not found in gold intersections: "); + expect_to_find_all_first_in_second(goldIntersections, actualIntersections, "Gold intersection not found in actual intersections: "); +} + +TEST_F(TriangleWithTriplePoint, whenFindingIntersectionPoints_findPointAtCentroid) +{ + build_parent_edges_and_cutter(topology, nodeIds, nodalIsovars); + + std::vector triangleIntersections; + cutter->fill_interior_intersections(triangleIntersections); + + const std::vector goldIntersections{ {Vector3d{1./3.,1./3.,0.}, std::vector{0,1,2}} }; + expect_intersections(goldIntersections, triangleIntersections); +} + +TEST_F(TriangleWithFakeTriplePoint, whenFindingIntersectionPoints_findCorrectPoints) +{ + build_parent_edges_and_cutter(topology, nodeIds, nodalIsovars); + + std::vector triangleIntersections; + cutter->fill_interior_intersections(triangleIntersections); + + expect_num_interfaces_with_cutting_surface(4u, *cutter); + + const std::vector goldIntersections{ {Vector3d{4./9., 4./9., 0.}, std::vector{0,1,3}} }; + expect_intersections(goldIntersections, triangleIntersections); +} + + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Explicit_Hamilton_Jacobi.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Explicit_Hamilton_Jacobi.cpp new file mode 100644 index 000000000000..33e73c71a2e4 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Explicit_Hamilton_Jacobi.cpp @@ -0,0 +1,903 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +namespace krino { + +struct ProblemFields +{ + stk::mesh::Field * levelSetField = nullptr; + stk::mesh::Field * coordsField = nullptr; + stk::mesh::Field * RHS = nullptr; + stk::mesh::Field * RHSNorm = nullptr; + stk::mesh::Field * speedField = nullptr; +}; + +void associate_input_mesh(stk::io::StkMeshIoBroker & stkIo, const std::string & meshName) +{ + stkIo.property_add(Ioss::Property("DECOMPOSITION_METHOD", "RIB")); + stkIo.add_mesh_database(meshName, stk::io::READ_MESH); + stkIo.create_input_mesh(); +} + +stk::mesh::BulkData & read_mesh(stk::io::StkMeshIoBroker & stkIo) +{ + stkIo.populate_bulk_data(); + return stkIo.bulk_data(); +} + +void declare_fields(stk::mesh::MetaData & meta, ProblemFields & fields) +{ + fields.levelSetField = &meta.declare_field>(stk::topology::NODE_RANK, "LevelSet", 2); + stk::mesh::put_field_on_mesh(*fields.levelSetField, meta.universal_part(), nullptr); + fields.RHS = &meta.declare_field>(stk::topology::NODE_RANK, "RHS", 1); + stk::mesh::put_field_on_mesh(*fields.RHS, meta.universal_part(), nullptr); + fields.RHSNorm = &meta.declare_field>(stk::topology::NODE_RANK, "RHSNorm", 1); + stk::mesh::put_field_on_mesh(*fields.RHSNorm, meta.universal_part(), nullptr); + auto constCoordsField = static_cast*>(meta.coordinate_field()); + fields.coordsField = const_cast*>(constCoordsField); + + if (true) + { + fields.speedField = &meta.declare_field>(stk::topology::ELEMENT_RANK, "Speed", 1); + stk::mesh::put_field_on_mesh(*fields.speedField, meta.universal_part(), nullptr); + } +} + +const int TetFaceTable[4][3] = { {0, 1, 2}, + {1, 2, 3}, + {0, 2, 3}, + {0, 1, 3} }; + +const int TetEdgeNodeOrder[6][2] = // [edge][edge_node] + { {0,1}, {1,2}, {2,0}, {0,3}, {1,3}, {2,3} }; + +void initialize_level_set(const stk::mesh::BulkData & mesh, const ProblemFields & fields, std::function initial_level_set, const double multiplier = 1.0) +{ + for (auto & bptr : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto & node : *bptr) + { + const double * x = stk::mesh::field_data(*fields.coordsField, node); + double* LS = stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateNP1), node); + *LS = initial_level_set(x) * multiplier; + } + } +} + +double initialize_constant_speed(const stk::mesh::BulkData & mesh, const ProblemFields & fields, const double speed) +{ + stk::mesh::field_fill(speed, *fields.speedField); + return speed; +} + +double compute_tet_vol(const stk::mesh::Entity * elemNodes, const stk::mesh::Field & coordsField) +{ + std::array xNode; + for (int n=0; n<4; ++n) xNode[n] = Vector3d(stk::mesh::field_data(coordsField, elemNodes[n])); + + return Dot(xNode[1]-xNode[0],Cross(xNode[2]-xNode[0],xNode[3]-xNode[0]))/6.; +} + +double compute_tri_vol(const stk::mesh::Entity * elemNodes, const stk::mesh::Field & coordsField) +{ + std::array xNode; + for (int n=0; n<3; ++n) xNode[n] = Vector3d(stk::mesh::field_data(coordsField, elemNodes[n]),2); + + return 0.5*Cross(xNode[1]-xNode[0],xNode[2]-xNode[0]).length(); +} + +double compute_vol(const stk::mesh::Entity * elemNodes, const unsigned numElemNodes, const stk::mesh::Field & coordsField) +{ + if (numElemNodes == 3) + return compute_tri_vol(elemNodes, coordsField); + else + return compute_tet_vol(elemNodes, coordsField); +} + +void compute_tet_gradOP_and_vol(const stk::mesh::Entity * elemNodes, const stk::mesh::Field & coordsField, std::vector & gradOP, double & vol) +{ + std::array xNode; + for (int n=0; n<4; ++n) xNode[n] = Vector3d(stk::mesh::field_data(coordsField, elemNodes[n])); + + std::array xFace; + for (int f=0; f<4; ++f) xFace[f] = (xNode[TetFaceTable[f][0]]+xNode[TetFaceTable[f][1]]+xNode[TetFaceTable[f][2]])/3.; + + std::array xEdge; + for (int e=0; e<6; ++e) xEdge[e] = 0.5*(xNode[TetEdgeNodeOrder[e][0]]+xNode[TetEdgeNodeOrder[e][1]]); + + vol = Dot(xNode[1]-xNode[0],Cross(xNode[2]-xNode[0],xNode[3]-xNode[0]))/6.; + const double norm = 0.5/vol; + + gradOP[0] = (Cross(xEdge[3]-xEdge[0],xNode[0]-xFace[3])+ + Cross(xEdge[2]-xEdge[3],xNode[0]-xFace[2])+ + Cross(xEdge[0]-xEdge[2],xNode[0]-xFace[0]))*norm; + gradOP[1] = (Cross(xEdge[0]-xEdge[4],xNode[1]-xFace[3])+ + Cross(xEdge[1]-xEdge[0],xNode[1]-xFace[0])+ + Cross(xEdge[4]-xEdge[1],xNode[1]-xFace[1]))*norm; + gradOP[2] = (Cross(xEdge[2]-xEdge[1],xNode[2]-xFace[0])+ + Cross(xEdge[5]-xEdge[2],xNode[2]-xFace[2])+ + Cross(xEdge[1]-xEdge[5],xNode[2]-xFace[1]))*norm; + gradOP[3] = (Cross(xEdge[5]-xEdge[4],xNode[3]-xFace[1])+ + Cross(xEdge[3]-xEdge[5],xNode[3]-xFace[2])+ + Cross(xEdge[4]-xEdge[3],xNode[3]-xFace[3]))*norm; +} + +void compute_tri_gradOP_and_vol(const stk::mesh::Entity * elemNodes, const stk::mesh::Field & coordsField, std::vector & gradOP, double & vol) +{ + std::array xNode; + for (int n=0; n<3; ++n) xNode[n] = Vector3d(stk::mesh::field_data(coordsField, elemNodes[n]),2); + + vol = 0.5*Cross(xNode[1]-xNode[0],xNode[2]-xNode[0]).length(); + const double norm = 0.5/vol; + + gradOP[0] = (crossZ(xNode[0]-xNode[2])+crossZ(xNode[1]-xNode[0]))*norm; + gradOP[1] = (crossZ(xNode[1]-xNode[0])+crossZ(xNode[2]-xNode[1]))*norm; + gradOP[2] = (crossZ(xNode[2]-xNode[1])+crossZ(xNode[0]-xNode[2]))*norm; +} + +void compute_gradOP_and_vol(const stk::mesh::Entity * elemNodes, const stk::mesh::Field & coordsField, std::vector & gradOP, double &vol) +{ + if (gradOP.size() == 3) + compute_tri_gradOP_and_vol(elemNodes, coordsField, gradOP, vol); + else + compute_tet_gradOP_and_vol(elemNodes, coordsField, gradOP, vol); +} + +Vector3d compute_scalar_gradient(const std::vector & nodalAreaVectors, const stk::mesh::Entity * elemNodes, const stk::mesh::Field & levelSetField) +{ + Vector3d grad(Vector3d::ZERO); + for (unsigned i=0; i & coordsField) +{ + const unsigned nodesPerElem = mesh.mesh_meta_data().spatial_dimension() + 1; + + double minVol = std::numeric_limits::max(); + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + minVol = std::min(minVol, compute_vol(elemNodes, nodesPerElem, coordsField)); + } + } + + return std::pow(minVol, 1./mesh.mesh_meta_data().spatial_dimension()); +} + +double mesh_minimum_length_scale(const stk::mesh::BulkData & mesh, const stk::mesh::Field & coordsField) +{ + const unsigned dim = mesh.mesh_meta_data().spatial_dimension(); + std::vector gradOP(dim+1); + + double vol = 0.; + double maxGradLength = 0.; + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + compute_gradOP_and_vol(elemNodes, coordsField, gradOP, vol); + for (unsigned n=0; n gradOP(dim+1); + + stk::mesh::field_fill(0.0, *fields.RHS); + stk::mesh::field_fill(0.0, *fields.RHSNorm); + + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const unsigned numElemNodes = mesh.num_nodes(elem); + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + double vol = 0.; + compute_gradOP_and_vol(elemNodes, *fields.coordsField, gradOP, vol); + const Vector3d normalDir = compute_scalar_gradient(gradOP, elemNodes, fields.levelSetField->field_of_state(stk::mesh::StateN)).unit_vector(); + + const double elementSpeed = *stk::mesh::field_data(*fields.speedField, elem); + + std::vector volHamiltonianCoeffs(dim+1); // K_i in Barth-Sethian + double sumNegCoeffs = 0.; + double sumPosCoeffs = 0.; + double sumNegContrib = 0.; + double volHamiltonian = 0.; + for (unsigned n=0; nfield_of_state(stk::mesh::StateN), node); + volHamiltonianCoeffs[n] = elementSpeed*vol*Dot(normalDir, gradOP[n]); + volHamiltonian += volHamiltonianCoeffs[n] * LSOld; + + if (volHamiltonianCoeffs[n] < 0.) + { + sumNegCoeffs += volHamiltonianCoeffs[n]; + sumNegContrib += volHamiltonianCoeffs[n] * LSOld; + } + else + { + sumPosCoeffs += volHamiltonianCoeffs[n]; + } + } + + std::vector alpha(dim+1, 0.); // delta phi_i in Barth-Sethian + double sumPosAlpha = 0.; + for (unsigned n=0; nfield_of_state(stk::mesh::StateN), node); + if (volHamiltonianCoeffs[n] > 0.) + { + alpha[n] = volHamiltonianCoeffs[n]/sumPosCoeffs*(sumNegContrib-sumNegCoeffs*LSOld)/volHamiltonian; + if (alpha[n] > 0.) sumPosAlpha += alpha[n]; + } + } + + for (unsigned n=0; n 0.) + { + const double wt = alpha[n]/sumPosAlpha; + residual += wt * volHamiltonian; + residualNorm += wt*vol; + } + } + } + } +} + +void assemble_residual_for_nodal_speed(const stk::mesh::BulkData & mesh, const ProblemFields & fields, const double eps) +{ + // Not extensively tested. This is an adaptation of Barth-Sethian positive coefficient scheme for nodal speed fields + + const unsigned dim = mesh.mesh_meta_data().spatial_dimension(); + std::vector gradOP(dim+1); + + stk::mesh::field_fill(0.0, *fields.RHS); + stk::mesh::field_fill(0.0, *fields.RHSNorm); + + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const unsigned numElemNodes = mesh.num_nodes(elem); + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + double vol = 0.; + compute_gradOP_and_vol(elemNodes, *fields.coordsField, gradOP, vol); + const Vector3d normalDir = compute_scalar_gradient(gradOP, elemNodes, fields.levelSetField->field_of_state(stk::mesh::StateN)).unit_vector(); + + for (unsigned n=0; nfield_of_state(stk::mesh::StateN), elemNodes[n]); + + //const double nodalSpeed = *stk::mesh::field_data(fields.speed, node); + const double nodalSpeed = 1.0; + + const double volHamiltonianCoeffs_n = vol*nodalSpeed*Dot(normalDir, gradOP[n]); // K_n in Barth-Sethian, probably should use nodal volume not elem volume + + if (volHamiltonianCoeffs_n > 0.) + { + double sumNegCoeffs = 0.; + double sumPosCoeffs = 0.; + double sumNegContrib = 0.; + double volHamiltonian = 0.; + for (unsigned j=0; jfield_of_state(stk::mesh::StateN), elemNodes[j]); + const double volHamiltonianCoeffs_j = vol*nodalSpeed*Dot(normalDir, gradOP[j]); + volHamiltonian += volHamiltonianCoeffs_j * LSOldj; + + if (volHamiltonianCoeffs_j < 0.) + { + sumNegCoeffs += volHamiltonianCoeffs_j; + sumNegContrib += volHamiltonianCoeffs_j * LSOldj; + } + else + { + sumPosCoeffs += volHamiltonianCoeffs_j; + } + } + + const double wt = volHamiltonianCoeffs_n/sumPosCoeffs*(sumNegContrib-sumNegCoeffs*LSOld)/volHamiltonian; + if (wt > 0.) + { + double & residual = *stk::mesh::field_data(*fields.RHS, node); + double & residualNorm = *stk::mesh::field_data(*fields.RHSNorm, node); + residual += wt * volHamiltonian; + residualNorm += wt*vol; + } + } + } + } + } +} + +double assemble_and_update_Eikonal(const stk::mesh::BulkData & mesh, const ProblemFields & fields, const double eps, const double dt, const bool computeArrivalTime) +{ + // This is a hybrid between the Barth-Sethian positive coefficient scheme and the Morgan-Waltz scheme for reinitialization. + // Uses element based speed and nodal sign function to assemble nodal contributions for Hamiltonian. + // The assembled nodal Hamiltonian is then used with nodal source term to explicitly update signed distance + // (or arrival time for non-unit speed). + // Unlike the elemental algorithm developed by Barth-Sethian, this algorithm converges to the exact solution + // for the "Distance Function Test" described in Morgan-Waltz. Unlike the Morgan-Waltz algorithm, this + // form converges much faster and is tolerant of meshes with obtuse angles because it uses the positive coefficient + // form in Barth-Sethian. + assert(!computeArrivalTime || nullptr != fields.speedField); + + const unsigned dim = mesh.mesh_meta_data().spatial_dimension(); + std::vector gradOP(dim+1); + + stk::mesh::field_fill(0.0, *fields.RHS); + stk::mesh::field_fill(0.0, *fields.RHSNorm); + + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const unsigned numElemNodes = mesh.num_nodes(elem); + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + double vol = 0.; + compute_gradOP_and_vol(elemNodes, *fields.coordsField, gradOP, vol); + const Vector3d normalDir = compute_scalar_gradient(gradOP, elemNodes, fields.levelSetField->field_of_state(stk::mesh::StateN)).unit_vector(); + + double elementSpeed = 1.0; + if (computeArrivalTime) + { + elementSpeed = *stk::mesh::field_data(*fields.speedField, elem); + } + + for (unsigned n=0; nfield_of_state(stk::mesh::StateN), elemNodes[n]); + + double nodalSpeed = 0.; + + const double sign = LSOld/sqrt(LSOld*LSOld + eps*eps); + nodalSpeed = sign*elementSpeed; + + const double volHamiltonianCoeffs_n = vol*nodalSpeed*Dot(normalDir, gradOP[n]); // K_n in Barth-Sethian, probably should use nodal volume not elem volume + + if (volHamiltonianCoeffs_n > 0.) + { + double sumNegCoeffs = 0.; + double sumPosCoeffs = 0.; + double sumNegContrib = 0.; + double volHamiltonian = 0.; + for (unsigned j=0; jfield_of_state(stk::mesh::StateN), elemNodes[j]); + const double volHamiltonianCoeffs_j = vol*nodalSpeed*Dot(normalDir, gradOP[j]); + volHamiltonian += volHamiltonianCoeffs_j * LSOldj; + + if (volHamiltonianCoeffs_j < 0.) + { + sumNegCoeffs += volHamiltonianCoeffs_j; + sumNegContrib += volHamiltonianCoeffs_j * LSOldj; + } + else + { + sumPosCoeffs += volHamiltonianCoeffs_j; + } + } + + const double wt = volHamiltonianCoeffs_n/sumPosCoeffs*(sumNegContrib-sumNegCoeffs*LSOld)/volHamiltonian; + if (wt > 0.) + { + double & residual = *stk::mesh::field_data(*fields.RHS, node); + double & residualNorm = *stk::mesh::field_data(*fields.RHSNorm, node); + residual += wt * volHamiltonian; + residualNorm += wt*vol; + } + } + } + } + } + + double sumSqrResid = 0.; + size_t sumCount = 0; + + for (auto & bptr : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto & node : *bptr) + { + const double residField = *stk::mesh::field_data(*fields.RHS, node); + const double residNormField = *stk::mesh::field_data(*fields.RHSNorm, node); + + const double Hamiltonian = (residNormField > 0.) ? (residField/residNormField) : 0.; + + const double LSOld = *stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateN), node); + double & LS = *stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateNP1), node); + const double sign = LSOld/sqrt(LSOld*LSOld + eps*eps); + + LS = LSOld - dt * (Hamiltonian - sign); + + if (computeArrivalTime || std::abs(LSOld) < eps) + { + sumSqrResid += (Hamiltonian - sign)*(Hamiltonian - sign); + sumCount++; + } + } + } + return std::sqrt(sumSqrResid/sumCount); +} + + +double apply_level_set_update(const stk::mesh::BulkData & mesh, const ProblemFields & fields, const double eps, const double dt) +{ + double sumResid = 0.; + size_t sumCount = 0; + + for (auto & bptr : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto & node : *bptr) + { + const double residField = *stk::mesh::field_data(*fields.RHS, node); + const double residNormField = *stk::mesh::field_data(*fields.RHSNorm, node); + + const double resid = (residNormField > 0.) ? (residField/residNormField) : 0.; + + const double LSOld = *stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateN), node); + double & LS = *stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateNP1), node); + + LS = LSOld - dt * resid; + + if (std::abs(LSOld) < eps) + { + sumResid += std::abs(resid); + sumCount++; + } + } + } + return sumResid/sumCount; +} + +bool domain_contains_interface(const stk::mesh::BulkData & mesh, const stk::mesh::Field & levelSetField) +{ + bool hasNeg = false; + bool hasPos = false; + + for (auto & bptr : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto & node : *bptr) + { + const double LS = *stk::mesh::field_data(levelSetField, node); + + if (LS < 0.) hasNeg = true; + if (LS > 0.) hasPos = true; + + if (hasNeg && hasPos) return true; + } + } + return false; +} + +void evolve_level_set(const stk::mesh::BulkData & mesh, const ProblemFields & fields, const double eps, const double dt) +{ + assemble_residual_for_element_speed(mesh, fields, eps); + apply_level_set_update(mesh, fields, eps, dt); +} + +void reinitialize_level_set( + stk::mesh::BulkData & mesh, + const ProblemFields & fields, + const double eps, + const double dtau, + stk::io::StkMeshIoBroker * stkIo = nullptr, + const double outputStartTime = 0., + const double outputStopTime = 0., + const size_t outputFileIndex = 0) +{ + if (!domain_contains_interface(mesh, fields.levelSetField->field_of_state(stk::mesh::StateNP1))) + { + return; + } + + const double convergedTol = 0.01; + bool converged = false; + const int maxIters = 1000; + const int printFreq = 50; + const double dOutputTime = (outputStopTime-outputStartTime)/(maxIters+1); + for (int iter = 0; iterfield_of_state(stk::mesh::StateNP1))) + { + std::cout << "Error, input level set field does not contain zero level set for initializing arrival time calculation." << std::endl; + return; + } + + bool converged = false; + const int maxIters = 5000; + const int printFreq = 50; + for (int iter = 0; iter eps) return 1.; + + static const double pi = std::atan(1)*4; + return 0.5*(1+ signedDist/eps + std::sin(pi*signedDist/eps)/pi); +} + +double delta(const double signedDist, const double eps) +{ + if (signedDist < -eps || signedDist > eps) return 0.; + + static const double pi = std::atan(1)*4; + return 0.5/eps * (1. + std::cos(pi*signedDist/eps)); +} + +double compute_level_set_volume(stk::mesh::BulkData & mesh, const ProblemFields & fields, const double eps) +{ + double vol = 0.; + for (auto & bptr : mesh.buckets(stk::topology::ELEMENT_RANK)) + { + for (auto & elem : *bptr) + { + const unsigned numElemNodes = mesh.num_nodes(elem); + const stk::mesh::Entity * elemNodes = mesh.begin_nodes(elem); + + double avgLS = 0.; + for (unsigned n=0; nfield_of_state(stk::mesh::StateNP1), elemNodes[n]); + avgLS += LS/numElemNodes; + } + + vol += Heaviside(avgLS, eps) * compute_vol(elemNodes, numElemNodes, *fields.coordsField); + } + } + return vol; +} + +double compute_unit_radius_error_norm(stk::mesh::BulkData & mesh, const ProblemFields & fields) +{ + double norm = 0.; + unsigned normCount = 0; + for (auto & bptr : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto & node : *bptr) + { + double & LS = *stk::mesh::field_data(fields.levelSetField->field_of_state(stk::mesh::StateNP1), node); + const Vector3d x(stk::mesh::field_data(*fields.coordsField, node), mesh.mesh_meta_data().spatial_dimension()); + + const double error = LS - (x.length() - 1.0); + norm += std::abs(error); + ++normCount; + } + } + return norm/normCount; +} + +double poor_initial_condition_for_unit_circle(const double * x) +{ + return ((x[0]-1.)*(x[0]-1.)+(x[1]-1.)*(x[1]-1.)+0.1)*(std::sqrt(x[0]*x[0]+x[1]*x[1])-1.); +} + +double poor_initial_condition_for_unit_sphere(const double * x) +{ + return ((x[0]-1.)*(x[0]-1.)+(x[1]-1.)*(x[1]-1.)+(x[2]-1.)*(x[2]-1.)+0.1)*(std::sqrt(x[0]*x[0]+x[1]*x[1]+x[2]*x[2])-1.); +} + +double flower_2D(const double * x) +{ + const int Nlobes = 3; + const double r = std::sqrt(x[0]*x[0]+x[1]*x[1]); + const double theta = std::atan2(x[1],x[0]); + const double rSurf = 0.2 + 0.1*std::sin(Nlobes*theta); + return r-rSurf; +} + +TEST(HamiltonJacobi, 2DPoorInitialCondition_ComputingArrivalTimeProducesLowErrorEverywhere) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 1) return; + + stk::io::StkMeshIoBroker stkIo(pm); + ProblemFields fields; + + associate_input_mesh(stkIo, "square.g"); + declare_fields(stkIo.meta_data(),fields); + stk::mesh::BulkData & mesh = read_mesh(stkIo); + + initialize_level_set(mesh, fields, poor_initial_condition_for_unit_circle); + initialize_constant_speed(mesh, fields, 1.0); + + const double dx = mesh_minimum_length_scale(mesh, *fields.coordsField); + const double eps = 1.5*dx; // Should have same units as level set + const double dtau = 0.2*dx; // Reinitialization time step, based on unit advection speed used in reinitialization + + compute_arrival_time(mesh, fields, eps, dtau); + + const double errorNorm = compute_unit_radius_error_norm(mesh, fields); + std::cout << "Error norm " << errorNorm << std::endl; + EXPECT_LT(errorNorm, 0.001); +} + +TEST(HamiltonJacobi, 3DPoorInitialCondition_ComputingArrivalTimeProducesLowErrorEverywhere) +{ +#ifdef NDEBUG +#else + return; // Optimized only due to length +#endif + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 1) return; + + stk::io::StkMeshIoBroker stkIo(pm); + ProblemFields fields; + + associate_input_mesh(stkIo, "cube_coarse.g"); + declare_fields(stkIo.meta_data(),fields); + stk::mesh::BulkData & mesh = read_mesh(stkIo); + + initialize_level_set(mesh, fields, poor_initial_condition_for_unit_sphere); + initialize_constant_speed(mesh, fields, 1.0); + + const double dx = mesh_minimum_length_scale(mesh, *fields.coordsField); + const double eps = 1.5*dx; // Should have same units as level set + const double dtau = 0.2*dx; // Reinitialization time step, based on unit advection speed used in reinitialization + + compute_arrival_time(mesh, fields, eps, dtau); + + const double errorNorm = compute_unit_radius_error_norm(mesh, fields); + std::cout << "Error norm " << errorNorm << std::endl; + EXPECT_LT(errorNorm, 0.01); +} + +void test_circle_with_flower(const double speed) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 1) return; + + stk::io::StkMeshIoBroker stkIo(pm); + ProblemFields fields; + + associate_input_mesh(stkIo, "circle.g"); + declare_fields(stkIo.meta_data(),fields); + stk::mesh::BulkData & mesh = read_mesh(stkIo); + + const double maxSpeed = initialize_constant_speed(mesh, fields, speed); + initialize_level_set(mesh, fields, flower_2D, 1./maxSpeed); + + const double dx = mesh_minimum_length_scale(mesh, *fields.coordsField); + const double eps = 1.5*dx / maxSpeed; // Should have same units as level set + const double dtau = 0.2*dx / maxSpeed; // Units of time + + compute_arrival_time(mesh, fields, eps, dtau); +} + +TEST(HamiltonJacobi, CircleWithFlowerIC_ArrivalTimeConvergesForAnySpeed) +{ + // Probably would be better to test that these converge in exactly the same number of steps + test_circle_with_flower(1.0); + test_circle_with_flower(10.0); +} + +TEST(HamiltonJacobi, CircleWithFlowerIC_ReinitializationThenEvolveRuns) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 1) return; + + stk::io::StkMeshIoBroker stkIo(pm); + ProblemFields fields; + + associate_input_mesh(stkIo, "circle.g"); + declare_fields(stkIo.meta_data(), fields); + stk::mesh::BulkData & mesh = read_mesh(stkIo); + + std::string outputFileName = "circle_flower.e"; + auto outputFileIndex = create_mesh(outputFileName, stkIo); + + const double maxSpeed = initialize_constant_speed(mesh, fields, 5.0); + initialize_level_set(mesh, fields, flower_2D); + + const double Courant = 0.25; + const double Ttotal = 0.1; + const double dx = mesh_minimum_length_scale(mesh, *fields.coordsField); + const unsigned Nt = (Ttotal+0.5*(Courant*dx/maxSpeed))/(Courant*dx/maxSpeed); + const double dt = Ttotal/Nt; + const double eps = 1.5*dx; + const double dtau = 0.2*dx; // Reinitialization time step, based on unit advection speed used in reinitialization + + write_fields(stkIo, outputFileIndex, 0.0); + reinitialize_level_set(mesh, fields, eps, dtau, &stkIo, 0.0, dt, outputFileIndex); + + std::cout << "Evolving to time " << Ttotal << " with " << Nt << " steps with Courant number " << Courant << std::endl; + + double time = 0.0; + for (unsigned n=0; n 1) return; + + stk::io::StkMeshIoBroker stkIo(pm); + ProblemFields fields; + + associate_input_mesh(stkIo, "cylinder_coarse.g"); + declare_fields(stkIo.meta_data(), fields); + stk::mesh::BulkData & mesh = read_mesh(stkIo); + + std::string outputFileName = "cylinder_flower.e"; + auto outputFileIndex = create_mesh(outputFileName, stkIo); + + const double maxSpeed = initialize_constant_speed(mesh, fields, 5.0); + initialize_level_set(mesh, fields, flower_2D); + + const double Courant = 0.25; + const double Ttotal = 0.01; + const double dx = mesh_minimum_length_scale(mesh, *fields.coordsField); + const unsigned Nt = (Ttotal+0.5*(Courant*dx/maxSpeed))/(Courant*dx/maxSpeed); + const double dt = Ttotal/Nt; + const double eps = 1.5*dx; + const double dtau = 0.2*dx; // Reinitialization time step, based on unit advection speed used in reinitialization + + write_fields(stkIo, outputFileIndex, 0.0); + reinitialize_level_set(mesh, fields, eps, dtau, &stkIo, 0.0, dt, outputFileIndex); + + std::cout << "Evolving to time " << Ttotal << " with " << Nt << " steps with Courant number " << Courant << std::endl; + + double time = 0.0; + for (unsigned n=0; n + +#include + +#include +#include +#include +#include +#include + +#include +#include + +namespace krino +{ + +namespace { + int num_random_cases() { return 10000; } + double clip(const double in) { return std::floor(1000*in)/1000.; } +} // namespace + +TEST(Plane_Cutting_Surface, random_edge_cuts) +{ + const bool debug_output = false; + const Vector3d plane_pt0(0., 0., 0.); + const Vector3d plane_pt1(1., 0., 0.); + const Vector3d plane_pt2(0., 1., 0.); + Plane_Cutting_Surface surf(plane_pt0, plane_pt1, plane_pt2); + + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_rank = stk::parallel_machine_rank(pm); + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution coord(-1., 1.); + + const int num_cases = num_random_cases(); + for (int icase=0; icase::epsilon()); + } + else + { + EXPECT_ANY_THROW(surf.interface_crossing_position(segment)); + } + } +} + +TEST(Intersecting_Planes_Cutting_Surface, planar_with_random_edge_cuts) +{ + const Vector3d plane_pt0(0., 0., 0.); + const Vector3d plane_pt1(1., 0., 0.); + const Vector3d plane_pt2(1., 1., 0.); + const Vector3d plane_pt3(0., 1., 0.); + Intersecting_Planes_Cutting_Surface surf(plane_pt0, plane_pt1, plane_pt2, plane_pt3); + + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_rank = stk::parallel_machine_rank(pm); + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution coord(-1., 1.); + + const int num_cases = num_random_cases(); + for (int icase=0; icase::epsilon()); + } + else + { + EXPECT_ANY_THROW(surf.interface_crossing_position(segment)); + } + } +} + +TEST(Intersecting_Planes_Cutting_Surface, positive_dihedral_with_random_edge_cuts) +{ + const bool debug_output = false; + const Vector3d plane_pt0(0., 0., 0.); + const Vector3d plane_pt1(0., 1., 1.); + const Vector3d plane_pt2(1., 0., 0.); + const Vector3d plane_pt3(0., 1., 0.); + Intersecting_Planes_Cutting_Surface surf(plane_pt0, plane_pt1, plane_pt2, plane_pt3); + + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_rank = stk::parallel_machine_rank(pm); + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution coord(-1., 1.); + + const int num_cases = num_random_cases(); + for (int icase=0; icase 0.5*pt0[1]) ? 1 : 0) + ((pt1[2] > 0.5*pt1[1]) ? 2 : 0); + switch (case_id) + { + case 0: EXPECT_NEAR(position, pos1, std::numeric_limits::epsilon()); break; + case 3: EXPECT_NEAR(position, pos0, std::numeric_limits::epsilon()); break; + } + } + else + { + EXPECT_ANY_THROW(surf.interface_crossing_position(segment)); + } + } +} + +TEST(Intersecting_Planes_Cutting_Surface, negative_dihedral_with_random_edge_cuts) +{ + const bool debug_output = false; + const Vector3d plane_pt0(0., 0., 0.); + const Vector3d plane_pt1(0., 1., 0.); + const Vector3d plane_pt2(1., 0., 0.); + const Vector3d plane_pt3(0., 1., 1.); + Intersecting_Planes_Cutting_Surface surf(plane_pt0, plane_pt1, plane_pt2, plane_pt3); + + + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_rank = stk::parallel_machine_rank(pm); + std::mt19937 mt(std::mt19937::default_seed + parallel_rank); + std::uniform_real_distribution coord(-1., 1.); + + const int num_cases = num_random_cases(); + for (int icase=0; icase 0.5*pt0[1]) ? 1 : 0) + ((pt1[2] > 0.5*pt1[1]) ? 2 : 0); + switch (case_id) + { + case 0: EXPECT_NEAR(position, pos1, std::numeric_limits::epsilon()); break; + case 3: EXPECT_NEAR(position, pos0, std::numeric_limits::epsilon()); break; + } + } + else + { + EXPECT_ANY_THROW(surf.interface_crossing_position(segment)); + } + } +} + +TEST(Intersecting_Planes_Cutting_Surface, infinitesimal_triangle_that_requires_robust_dihedral_angle) +{ + const double goldPosition = 0.5181038869168293; + const double otherCrossing = 0.4818961330726974; + const Vector3d plane_pt0(otherCrossing, 0., 1.-otherCrossing); + const Vector3d plane_pt1(0., 0., goldPosition); + const Vector3d plane_pt2(0., (1.-1.e-10), 0.); + const Vector3d plane_pt3(1.e-10, (1.-1.e-10), 0.); + Intersecting_Planes_Cutting_Surface surf(plane_pt0, plane_pt1, plane_pt2, plane_pt3); + + const Vector3d node0(0., 0., 0.); + const Vector3d node3(0., 0., 1.); + const double position = surf.interface_crossing_position(Segment3d(node0,node3)); + EXPECT_DOUBLE_EQ(position, goldPosition); +} + +void expect_intersection(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2, const Vector3d & goldIntersection) +{ + Vector3d intersectionPoint; + EXPECT_TRUE(find_intersection_of_three_planes(plane0, plane1, plane2, intersectionPoint)); + expect_eq(goldIntersection, intersectionPoint); +} + +void expect_intersection_with_side_of_tet(const int side, const Plane3d & plane0, const Plane3d & plane1, const Vector3d & goldIntersection) +{ + Vector3d intersectionPoint; + EXPECT_TRUE(find_intersection_of_two_planes_and_side_of_tet(side, plane0, plane1, intersectionPoint)); + expect_eq(goldIntersection, intersectionPoint); +} + +void expect_no_intersection(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2) +{ + Vector3d intersectionPoint; + EXPECT_FALSE(find_intersection_of_three_planes(plane0, plane1, plane2, intersectionPoint)); +} + +void expect_no_intersection_within_tet(const Plane3d & plane0, const Plane3d & plane1, const Plane3d & plane2) +{ + Vector3d intersectionPoint; + EXPECT_FALSE(find_intersection_of_three_planes_within_tet(plane0, plane1, plane2, intersectionPoint)); +} + +void expect_no_intersection_with_side_of_tet(const int side, const Plane3d & plane0, const Plane3d & plane1) +{ + Vector3d intersectionPoint; + EXPECT_FALSE(find_intersection_of_two_planes_and_side_of_tet(side, plane0, plane1, intersectionPoint)); +} + +struct IntersectPlanes : public ::testing::Test +{ + const Vector3d pt0{0., 0., 0.}; + const Vector3d pt1{1., 0., 0.}; + const Vector3d pt2{0., 1., 0.}; + const Vector3d pt3{0., 0., 1.}; + const Plane3d plane0{pt0, pt1, pt3}; + const Plane3d plane1{pt1, pt2, pt3}; + const Plane3d plane2{pt2, pt0, pt3}; + const Plane3d plane3{pt0, pt2, pt1}; + + const Vector3d offsetPt0{-0.1, -0.1, -0.1}; + const Vector3d offsetPt1{1.1, -0.1, -0.1}; + const Vector3d offsetPt2{-0.1, 1.1, -0.1}; + const Vector3d offsetPt3{-0.1, -0.1, 1.1}; + const Plane3d offsetPlane0{offsetPt0, offsetPt1, offsetPt3}; + const Plane3d offsetPlane1{offsetPt1, offsetPt2, offsetPt3}; + const Plane3d offsetPlane2{offsetPt2, offsetPt0, offsetPt3}; + const Plane3d offsetPlane3{offsetPt0, offsetPt2, offsetPt1}; + +}; + +TEST_F(IntersectPlanes, given3Planes_FindCorrectIntersection) +{ + expect_intersection(plane0, plane1, plane2, Vector3d{0., 0., 1.}); + expect_intersection(plane0, plane1, plane3, Vector3d{1., 0., 0.}); + expect_intersection(plane1, plane2, plane3, Vector3d{0., 1., 0.}); + expect_intersection(plane0, plane2, plane3, Vector3d{0., 0., 0.}); + + expect_no_intersection(plane0, plane0, plane1); +} + +TEST_F(IntersectPlanes, given3PlanesThatDoNotIntersectWithinTetBounds_FindNoIntersection) +{ + expect_no_intersection_within_tet(offsetPlane0, offsetPlane1, offsetPlane2); + expect_no_intersection_within_tet(offsetPlane0, offsetPlane1, offsetPlane3); + expect_no_intersection_within_tet(offsetPlane1, offsetPlane2, offsetPlane3); + expect_no_intersection_within_tet(offsetPlane0, offsetPlane2, offsetPlane3); +} + +TEST_F(IntersectPlanes, given2PlanesThatIntersectSideOfTet_FindCorrectIntersection) +{ + expect_intersection_with_side_of_tet(0, plane1, plane2, Vector3d{0., 0., 1.}); + expect_intersection_with_side_of_tet(0, plane1, plane3, Vector3d{1., 0., 0.}); + expect_intersection_with_side_of_tet(0, plane2, plane3, Vector3d{0., 0., 0.}); + + expect_intersection_with_side_of_tet(1, plane2, plane3, Vector3d{0., 1., 0.}); + expect_intersection_with_side_of_tet(1, plane0, plane2, Vector3d{0., 0., 1.}); + expect_intersection_with_side_of_tet(1, plane0, plane3, Vector3d{1., 0., 0.}); + + expect_intersection_with_side_of_tet(2, plane0, plane1, Vector3d{0., 0., 1.}); + expect_intersection_with_side_of_tet(2, plane0, plane3, Vector3d{0., 0., 0.}); + expect_intersection_with_side_of_tet(2, plane1, plane3, Vector3d{0., 1., 0.}); + + expect_intersection_with_side_of_tet(3, plane0, plane1, Vector3d{1., 0., 0.}); + expect_intersection_with_side_of_tet(3, plane0, plane2, Vector3d{0., 0., 0.}); + expect_intersection_with_side_of_tet(3, plane1, plane2, Vector3d{0., 1., 0.}); +} + +TEST_F(IntersectPlanes, given2PlanesThatDoNotIntersectSideOfTetAtAll_FindNoIntersection) +{ + expect_no_intersection_with_side_of_tet(0, plane0, plane2); + expect_no_intersection_with_side_of_tet(1, plane1, plane2); + expect_no_intersection_with_side_of_tet(2, plane2, plane1); + expect_no_intersection_with_side_of_tet(3, plane3, plane2); +} + +TEST_F(IntersectPlanes, given2PlanesThatDoNotIntersectSideOfTetWithinTetBounds_FindNoIntersection) +{ + expect_no_intersection_with_side_of_tet(0, offsetPlane1, offsetPlane2); + expect_no_intersection_with_side_of_tet(0, offsetPlane1, offsetPlane3); + expect_no_intersection_with_side_of_tet(0, offsetPlane2, offsetPlane3); + + expect_no_intersection_with_side_of_tet(1, offsetPlane2, offsetPlane3); + expect_no_intersection_with_side_of_tet(1, offsetPlane0, offsetPlane2); + expect_no_intersection_with_side_of_tet(1, offsetPlane0, offsetPlane3); + + expect_no_intersection_with_side_of_tet(2, offsetPlane0, offsetPlane1); + expect_no_intersection_with_side_of_tet(2, offsetPlane0, offsetPlane3); + expect_no_intersection_with_side_of_tet(2, offsetPlane1, offsetPlane3); + + expect_no_intersection_with_side_of_tet(3, offsetPlane0, offsetPlane1); + expect_no_intersection_with_side_of_tet(3, offsetPlane0, offsetPlane2); + expect_no_intersection_with_side_of_tet(3, offsetPlane1, offsetPlane2); +} + +static Vector3d compute_2d_plane_direction(const Vector3d & pt0, const Vector3d & pt1) +{ + return Vector3d(pt1[1]-pt0[1],pt0[0]-pt1[0],0.); +} + +static Plane3d build_2d_plane(const Vector3d & pt0, const Vector3d & pt1) +{ + return Plane3d(compute_2d_plane_direction(pt0,pt1),pt0); +} + +struct Intersect2DPlanes : public ::testing::Test +{ + Intersect2DPlanes() + : plane0{build_2d_plane(pt0, pt1)}, + plane1{build_2d_plane(pt1, pt2)}, + plane2{build_2d_plane(pt0, pt2)}, + offsetPlane0{build_2d_plane(offsetPt0, offsetPt1)}, + offsetPlane1{build_2d_plane(offsetPt1, offsetPt2)}, + offsetPlane2{build_2d_plane(offsetPt0, offsetPt2)} + { + } + + const Vector3d pt0{0., 0., 0.}; + const Vector3d pt1{1., 0., 0.}; + const Vector3d pt2{0., 1., 0.}; + + const Vector3d offsetPt0{-0.1, -0.1, 0.}; + const Vector3d offsetPt1{1.1, -0.1, 0.}; + const Vector3d offsetPt2{-0.1, 1.1, 0.}; + + Plane3d plane0; + Plane3d plane1; + Plane3d plane2; + + Plane3d offsetPlane0; + Plane3d offsetPlane1; + Plane3d offsetPlane2; +}; + +void expect_2d_intersection(const Plane3d & plane0, const Plane3d & plane1, const Vector3d & goldIntersection) +{ + Vector3d intersectionPoint; + EXPECT_TRUE(find_intersection_of_two_2D_planes(plane0, plane1, intersectionPoint)); + expect_eq(goldIntersection, intersectionPoint); +} + +void expect_no_2d_intersection_within_tri(const Plane3d & plane0, const Plane3d & plane1) +{ + Vector3d intersectionPoint; + EXPECT_FALSE(find_intersection_of_two_2D_planes_within_tri(plane0, plane1, intersectionPoint)); +} + +void expect_no_2d_intersection(const Plane3d & plane0, const Plane3d & plane1) +{ + Vector3d intersectionPoint; + EXPECT_FALSE(find_intersection_of_two_2D_planes(plane0, plane1, intersectionPoint)); +} + +TEST_F(Intersect2DPlanes, given2Plane2Ds_FindCorrectIntersection) +{ + expect_2d_intersection(plane0, plane1, Vector3d{1., 0., 0.}); + expect_2d_intersection(plane1, plane2, Vector3d{0., 1., 0.}); + expect_2d_intersection(plane0, plane2, Vector3d{0., 0., 0.}); + + expect_no_2d_intersection(plane0, plane0); +} + +TEST_F(Intersect2DPlanes, given2Plane2DsThatDoNotIntersectWithinTriBounds_FindNoIntersection) +{ + expect_no_2d_intersection_within_tri(offsetPlane0, offsetPlane1); + expect_no_2d_intersection_within_tri(offsetPlane1, offsetPlane2); + expect_no_2d_intersection_within_tri(offsetPlane0, offsetPlane2); +} + +TEST(ProjectionOf3DPointsIntoTriangle, givenTriangleCheckProjectionOfPointOnAndOffPlane) +{ + const Vector3d pt0{0., 0., 0.}; + const Vector3d pt1{1., 0., 0.}; + const Vector3d pt2{0., 1., 1.}; + const std::array triCoords{{ pt0, pt1, pt2 }}; + + expect_eq(Vector3d{0.,0.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt0)); + expect_eq(Vector3d{1.,0.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt1)); + expect_eq(Vector3d{0.,1.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt2)); + + const Vector3d normal = Cross(pt1-pt0, pt2-pt0).unit_vector(); + expect_eq(Vector3d{0.,0.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt0+normal)); + expect_eq(Vector3d{1.,0.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt1+normal)); + expect_eq(Vector3d{0.,1.,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, pt2+normal)); + + const double oneThird = 1./3.; + const Vector3d midPt = oneThird*(pt0+pt1+pt2); + expect_eq(Vector3d{oneThird,oneThird,0.}, triangle_parametric_coordinates_of_projected_point(triCoords, midPt+normal)); +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.cpp b/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.cpp new file mode 100644 index 000000000000..bf1aa985a09b --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.cpp @@ -0,0 +1,27 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include + +namespace krino { + +LogRedirecter::LogRedirecter() +: myOriginalBuffer(krinolog.getStream().rdbuf()) +{ + krinolog.getStream().rdbuf(&myBuffer); +} + +LogRedirecter::~LogRedirecter() +{ + krinolog.getStream().rdbuf(myOriginalBuffer); +} + +} + diff --git a/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.hpp b/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.hpp new file mode 100644 index 000000000000..9b26c01006fc --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_LogRedirecter.hpp @@ -0,0 +1,32 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_UNIT_LOGREDIRECTER_H_ +#define AKRI_UNIT_LOGREDIRECTER_H_ + +#include + +namespace krino { + +class LogRedirecter +{ +public: + LogRedirecter(); + ~LogRedirecter(); + + void clear() { myBuffer.str(""); } + std::string get_log() const { return myBuffer.str(); } +private: + std::stringbuf myBuffer; + std::streambuf * myOriginalBuffer; +}; + +} + + +#endif diff --git a/packages/krino/krino/unit_tests/Akri_Unit_LowerEnvelope.cpp b/packages/krino/krino/unit_tests/Akri_Unit_LowerEnvelope.cpp new file mode 100644 index 000000000000..de5b17ccc7d5 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_LowerEnvelope.cpp @@ -0,0 +1,260 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include + + +namespace krino +{ + +TEST(Lower_Envelope, Find_Crossing_Segment) +{ + double s = 0.0; + + ASSERT_TRUE(find_lower_envelope_crossing_point({{{0., 1.}, {0., 0.}}}, s)); + EXPECT_DOUBLE_EQ(1.0, s); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{{0., 1.}, {1., 0.}}}, s)); + EXPECT_DOUBLE_EQ(0.5, s); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{{0., 1.}, {0.5, 0.}}}, s)); + EXPECT_DOUBLE_EQ(2./3., s); +} + +TEST(Lower_Envelope, Find_Crossing_Triangle) +{ + std::array pt = {{0., 0.}}; + + const std::vector phi000 = {0., 0., 0.}; + const std::vector phi011 = {0., 1., 1.}; + const std::vector phi101 = {1., 0., 1.}; + const std::vector phi110 = {1., 1., 0.}; + + EXPECT_FALSE(find_lower_envelope_crossing_point({{phi110, phi110, phi101}}, pt)); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi110, phi011, phi101}}, pt)); + std::array goldPt = {{1./3., 1./3.}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{{1., 1., 0.75}, {0., 1., 0.75}, {1., 0., 0.75}}}, pt)); + goldPt = {{0.25, 0.25}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi000, phi011, phi101}}, pt)); + goldPt = {{0., 0.}}; + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi011, phi000, phi101}}, pt)); + goldPt = {{1., 0.}}; + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi011, phi101, phi000}}, pt)); + goldPt = {{0., 1.}}; + EXPECT_EQ(goldPt, pt); +} + +TEST(Lower_Envelope, Find_Crossing_Tetrahedron) +{ + std::array pt = {{0., 0., 0.}}; + + const std::vector phi0000 = {0., 0., 0., 0.}; + const std::vector phi1110 = {1., 1., 1., 0.}; + const std::vector phi1101 = {1., 1., 0., 1.}; + const std::vector phi1011 = {1., 0., 1., 1.}; + const std::vector phi0111 = {0., 1., 1., 1.}; + + EXPECT_FALSE(find_lower_envelope_crossing_point({{phi1110, phi1110, phi1011, phi0111}}, pt)); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi1110, phi1101, phi1011, phi0111}}, pt)); + std::array goldPt = {{0.25, 0.25, 0.25}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi0000, phi0111, phi1011, phi1101}}, pt)); + goldPt = {{0., 0., 0.}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi0111, phi0000, phi1011, phi1101}}, pt)); + goldPt = {{1., 0., 0.}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi0111, phi1011, phi0000, phi1101}}, pt)); + goldPt = {{0., 1., 0.}}; + EXPECT_EQ(goldPt, pt); + + ASSERT_TRUE(find_lower_envelope_crossing_point({{phi0111, phi1011, phi1101, phi0000}}, pt)); + goldPt = {{0., 0., 1.}}; + EXPECT_EQ(goldPt, pt); +} + + +TEST(Lower_Envelope, Two_LS_Bug) +{ + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope({0., 0.}, {1., 0.}); + ASSERT_EQ(1u, envelope.size()); + EXPECT_EQ(1, envelope[0].ls_index()); + EXPECT_DOUBLE_EQ(0.0, envelope[0].left_endpoint()); + EXPECT_DOUBLE_EQ(1., envelope[0].right_endpoint()); +} + +TEST(Lower_Envelope, Two_LS_Lower_Envelope) +{ + { + // 2 level sets, infinitesimal crossing on left by convention that highest level set index wins + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope({0., 0.}, {0.25, 1.}); + ASSERT_EQ(2u, envelope.size()); + const LS_Segment & env1 = envelope[0]; + const LS_Segment & env2 = envelope[1]; + EXPECT_EQ(1, env1.ls_index()); + EXPECT_EQ(0, env2.ls_index()); + EXPECT_DOUBLE_EQ(0.0, env1.left_endpoint()); + EXPECT_DOUBLE_EQ(0.0, env1.right_endpoint()); + EXPECT_DOUBLE_EQ(0.0, env2.left_endpoint()); + EXPECT_DOUBLE_EQ(1.0, env2.right_endpoint()); + } + + { + // 2 level sets, infinitesimal crossing on right by convention that highest level set index wins + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope({0.3, 0.6}, {0., 0.}); + ASSERT_EQ(2u, envelope.size()); + const LS_Segment & env1 = envelope[0]; + const LS_Segment & env2 = envelope[1]; + EXPECT_EQ(0, env1.ls_index()); + EXPECT_EQ(1, env2.ls_index()); + EXPECT_DOUBLE_EQ(0.0, env1.left_endpoint()); + EXPECT_DOUBLE_EQ(1.0, env1.right_endpoint()); + EXPECT_DOUBLE_EQ(1.0, env2.left_endpoint()); + EXPECT_DOUBLE_EQ(1.0, env2.right_endpoint()); + } +} + +void expect_good_edge(const Segment_Vector & envelope) +{ + for (size_t i=0; i= SegmentLowerEnvelope::MinSize()) << "Unexpected infinitesimal, non-zero segment at end of edge " << envelope; + } + else + { + EXPECT_GE(envelope[i].length(), SegmentLowerEnvelope::MinSize()) << "Unexpected internal infinitesimal internal segment on edge " << envelope; + } + + if (i & phi0, const std::vector & phi1) +{ + ASSERT_FALSE(envelope.empty()); + EXPECT_EQ(get_min(phi0), envelope.front().ls_index()) << "Front segment of edge does not match phase at node on edge " << envelope; + EXPECT_EQ(get_min(phi1), envelope.back().ls_index()) << "Back segment of edge does not match phase at node on edge " << envelope; +} + +TEST(Lower_Envelope, Three_LS_Lower_Envelope) +{ + { + // 3 level sets, edge is B from 0 to 0.5, C from 0.5 to 1.0 and + // 1st level set intersects both others at 0.5 but is never the lowest + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope({0.5, 0., 1.}, {0.5, 1., 0.}); + ASSERT_EQ(2u, envelope.size()); + const LS_Segment & env1 = envelope[0]; + const LS_Segment & env2 = envelope[1]; + EXPECT_EQ(1, env1.ls_index()); + EXPECT_EQ(2, env2.ls_index()); + EXPECT_DOUBLE_EQ(0.0, env1.left_endpoint()); + EXPECT_DOUBLE_EQ(0.5, env1.right_endpoint()); + EXPECT_DOUBLE_EQ(0.5, env2.left_endpoint()); + EXPECT_DOUBLE_EQ(1., env2.right_endpoint()); + + expect_good_edge(envelope); + } + + { + // 3 level sets, left is A, middle C, right B + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope({0., 1., 0.25}, {1., 0., 0.25}); + ASSERT_EQ(3u, envelope.size()); + const LS_Segment & env1 = envelope[0]; + const LS_Segment & env2 = envelope[1]; + const LS_Segment & env3 = envelope[2]; + EXPECT_EQ(0, env1.ls_index()); + EXPECT_EQ(2, env2.ls_index()); + EXPECT_EQ(1, env3.ls_index()); + EXPECT_DOUBLE_EQ(0.0, env1.left_endpoint()); + EXPECT_DOUBLE_EQ(0.25, env1.right_endpoint()); + EXPECT_DOUBLE_EQ(0.25, env2.left_endpoint()); + EXPECT_DOUBLE_EQ(0.75, env2.right_endpoint()); + EXPECT_DOUBLE_EQ(0.75, env3.left_endpoint()); + EXPECT_DOUBLE_EQ(1.0, env3.right_endpoint()); + + expect_good_edge(envelope); + } + + { + // 3 level sets with infinitesmal transitions near ends + const std::vector phi0 = {1.56125e-17, -4.77049e-18, 0.}; + const std::vector phi1 = {-0.0417425, 0.0477226, 0.}; + + { + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope(phi0, phi1); + + expect_good_edge(envelope); + expect_end_segments_to_match_end_phases(envelope, phi0, phi1); + } + { + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope(phi1, phi0); + + expect_good_edge(envelope); + expect_end_segments_to_match_end_phases(envelope, phi1, phi0); + } + } + + { + // 3 level sets with infinitesmal transitions near middle + const std::vector phi0 = {-1., (1.+1.e-12), 0.}; + const std::vector phi1 = {(1.+1.e-12), -1., 0.}; + + { + Segment_Vector envelope01 = SegmentLowerEnvelope::find_lower_envelope(phi0, phi1); + expect_good_edge(envelope01); + expect_end_segments_to_match_end_phases(envelope01, phi0, phi1); + EXPECT_EQ(2u, envelope01.size()); + + Segment_Vector envelope10 = SegmentLowerEnvelope::find_lower_envelope(phi1, phi0); + expect_good_edge(envelope10); + expect_end_segments_to_match_end_phases(envelope10, phi1, phi0); + EXPECT_EQ(2u, envelope10.size()); + + EXPECT_DOUBLE_EQ(envelope01[0].right_endpoint(), envelope10[0].right_endpoint()); + } + } +} + +void expect_segments_lengths(const Segment_Vector & segments, const std::vector goldSegmentLengthsByLS) +{ + for (auto && segment : segments) + { + ASSERT_TRUE(segment.ls_index() < (int)goldSegmentLengthsByLS.size()); + EXPECT_DOUBLE_EQ(goldSegmentLengthsByLS[segment.ls_index()], segment.length()); + } +} + +TEST(Lower_Envelope,Sensitive_LS) +{ + std::array,2> phi = {{ {-1.e-17,-2.e-17,1.0,0}, {2.e-17,1.0,-2.e-17,0} }}; + const double goldSegmentLengthForPhi0 = phi[0][0]/(phi[0][0]-phi[1][0]); + const std::vector goldSegmentLengthsByLS = { goldSegmentLengthForPhi0, 0., 0., 1.-goldSegmentLengthForPhi0 }; + + Segment_Vector envelope = SegmentLowerEnvelope::find_lower_envelope(phi[0], phi[1]); + expect_segments_lengths(envelope, goldSegmentLengthsByLS); +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.cpp b/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.cpp new file mode 100644 index 000000000000..a7a04758b117 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.cpp @@ -0,0 +1,278 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include +#include // for declare_element +#include + +#include + +namespace krino { + +void build_mesh(stk::mesh::BulkData & mesh, const std::vector & elem_nodes, const std::vector & elem_procs, std::vector & elem_parts) +{ + if (elem_nodes.empty()) return; + + const size_t numElem = elem_nodes.size(); + EXPECT_TRUE(elem_procs.size() == numElem); + EXPECT_TRUE(elem_parts.size() == numElem); + const size_t nodesPerElem = elem_nodes[0].size(); + const int parallel_size = mesh.parallel_size(); + const int parallel_rank = mesh.parallel_rank(); + + mesh.modification_begin(); + + // Create nodes and elements + std::set nodes_I_declared; + for (size_t e=0; e 1) + { + for (size_t e=0; e sides; + stk::mesh::get_entities( mesh, mesh.mesh_meta_data().side_rank(), sides ); + + EXPECT_TRUE(1 == sides.size()); + + for (auto && side : sides) + { + EXPECT_TRUE(mesh.bucket(side).member(block_1)); + EXPECT_TRUE(mesh.bucket(side).member(block_2)); + } + + // cleanup + mesh.modification_begin(); + for (auto && side : sides) + { + EXPECT_TRUE(disconnect_and_destroy_entity(mesh, side)); + } + mesh.modification_end(); +} +} + +TEST(MeshHelpers, DeclareElementSide) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 2) return; + + // This test will create a two element mesh (quad4 elements) on 1 or 2 processors. + + /* Mesh + * 4---5---6 P0 owns nodes 1,2,4,5; P, elem 1 + * | 1 | 2 | P1 : 3,6, elem 2 + * 1---2---3 + */ + + unsigned spatialDim = 2; + stk::mesh::MetaData meta(spatialDim); + stk::mesh::BulkData mesh(meta, pm); + + stk::mesh::Part& block_1 = meta.declare_part_with_topology("block_1", stk::topology::QUAD_4_2D); + stk::mesh::Part& block_2 = meta.declare_part_with_topology("block_2", stk::topology::QUAD_4_2D); + stk::mesh::Part& surface_1 = meta.declare_part_with_topology("surface_1", stk::topology::LINE_2); + + meta.commit(); + + const std::vector elem_nodes{ {1, 2, 5, 4}, {2, 3, 6, 5} }; + const std::vector elem_procs{0, 1}; + std::vector elem_parts{{&block_1}, {&block_2}}; + + build_mesh(mesh, elem_nodes, elem_procs, elem_parts); + + // All elements and nodes appear everywhere via aura + stk::mesh::Entity element1 = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + stk::mesh::Entity element2 = mesh.get_entity(stk::topology::ELEMENT_RANK, 2); + stk::mesh::Entity node2 = mesh.get_entity(stk::topology::NODE_RANK, 2); + stk::mesh::Entity node5 = mesh.get_entity(stk::topology::NODE_RANK, 5); + + std::vector side_nodes; + side_nodes.push_back(node2); + side_nodes.push_back(node5); + + mesh.initialize_face_adjacent_element_graph(); + + { + // Case 1: Declare side on owning processor for both elements + mesh.modification_begin(); + + if (mesh.bucket(element1).owned()) + { + const unsigned elem1_local_side_id = stk::mesh::get_entity_subcell_id(mesh, element1, meta.side_rank(), surface_1.topology(), side_nodes); + mesh.declare_element_side(element1, elem1_local_side_id, stk::mesh::ConstPartVector{&surface_1}); + } + if (mesh.bucket(element2).owned()) + { + const unsigned elem2_local_side_id = stk::mesh::get_entity_subcell_id(mesh, element2, meta.side_rank(), surface_1.topology(), side_nodes); + mesh.declare_element_side(element2, elem2_local_side_id, stk::mesh::ConstPartVector{&surface_1}); + } + + mesh.modification_end(); + + test_and_cleanup_internal_side(mesh, block_1, block_2); + } + + { + // Case 2: Declare side of element1 on processor that owns element1 + mesh.modification_begin(); + + if (mesh.bucket(element1).owned()) + { + const unsigned elem1_local_side_id = stk::mesh::get_entity_subcell_id(mesh, element1, meta.side_rank(), surface_1.topology(), side_nodes); + mesh.declare_element_side(element1, elem1_local_side_id, stk::mesh::ConstPartVector{&surface_1}); + } + + mesh.modification_end(); + + test_and_cleanup_internal_side(mesh, block_1, block_2); + } + + { + // Case 3: Declare side of element2 on processor that owns element2 + mesh.modification_begin(); + + if (mesh.bucket(element2).owned()) + { + const unsigned elem2_local_side_id = stk::mesh::get_entity_subcell_id(mesh, element2, meta.side_rank(), surface_1.topology(), side_nodes); + mesh.declare_element_side(element2, elem2_local_side_id, stk::mesh::ConstPartVector{&surface_1}); + } + + mesh.modification_end(); + + test_and_cleanup_internal_side(mesh, block_1, block_2); + } +} + +TEST(MeshHelpers, FullyCoincidentVolumeElements) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + + // This test will create a two element mesh (quad4 elements), on more than 2 processors only + // ranks 0 and 1 will have any elements. We test larger number of processors to ensure that + // we get a parallel-consistent result to avoid potential parallel hangs in the full app. + + unsigned spatialDim = 2; + stk::mesh::MetaData meta(spatialDim); + stk::mesh::BulkData mesh(meta, pm); + + stk::mesh::Part& block_1 = meta.declare_part_with_topology("block_1", stk::topology::QUAD_4_2D); + stk::mesh::Part& active_part = meta.declare_part("active"); + meta.commit(); + + const std::vector elem_nodes{ {1, 2, 3, 4}, {2, 3, 4, 1} }; + const std::vector elem_procs{0, 1}; + std::vector elem_parts{{&block_1}, {&block_1}}; + + build_mesh(mesh, elem_nodes, elem_procs, elem_parts); + + const bool ok = check_coincident_elements(mesh, active_part); + EXPECT_FALSE(ok); +} + +TEST(MeshHelpers, PartiallyCoincidentActiveVolumeElements) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 2) return; + + // This test will create a two element mesh (quad4 elements) on 1 or 2 processors. + + unsigned spatialDim = 2; + stk::mesh::MetaData meta(spatialDim); + stk::mesh::BulkData mesh(meta, pm); + + stk::mesh::Part& block_1 = meta.declare_part_with_topology("block_1", stk::topology::QUAD_4_2D); + stk::mesh::Part& active_part = meta.declare_part("active"); + meta.commit(); + + const std::vector elem_nodes{ {1, 2, 3, 4}, {1, 2, 5, 6} }; + const std::vector elem_procs{0, 1}; + std::vector elem_parts{{&block_1, &active_part}, {&block_1, &active_part}}; + + build_mesh(mesh, elem_nodes, elem_procs, elem_parts); + + const bool ok = check_coincident_elements(mesh, active_part); + EXPECT_FALSE(ok); +} + +TEST(MeshHelpers, NotCoincidentActiveDegenerateVolumeElements) +{ + stk::ParallelMachine pm = MPI_COMM_WORLD; + const int parallel_size = stk::parallel_machine_size(pm); + if (parallel_size > 2) return; + + // This test will create a two element mesh (quad4 elements) on 1 or 2 processors. + + unsigned spatialDim = 2; + stk::mesh::MetaData meta(spatialDim); + stk::mesh::BulkData mesh(meta, pm); + + stk::mesh::Part& block_1 = meta.declare_part_with_topology("block_1", stk::topology::QUAD_4_2D); + stk::mesh::Part& active_part = meta.declare_part("active"); + meta.commit(); + + const std::vector elem_nodes{ {1, 2, 2, 3}, {3, 2, 2, 4} }; + const std::vector elem_procs{0, 1}; + std::vector elem_parts{{&block_1, &active_part}, {&block_1, &active_part}}; + + build_mesh(mesh, elem_nodes, elem_procs, elem_parts); + + const bool ok = check_coincident_elements(mesh, active_part); + EXPECT_TRUE(ok); +} + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.hpp b/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.hpp new file mode 100644 index 000000000000..976a24bacbcd --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_MeshHelpers.hpp @@ -0,0 +1,24 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef KRINO_UNIT_TESTS_INCLUDE_AKRI_UNIT_MESHHELPERS_H_ +#define KRINO_UNIT_TESTS_INCLUDE_AKRI_UNIT_MESHHELPERS_H_ + +#include +#include + +namespace krino +{ + +void build_mesh(stk::mesh::BulkData & mesh, + const std::vector & elem_nodes, + const std::vector & elem_procs, + std::vector & elem_parts); +} + +#endif /* KRINO_UNIT_TESTS_INCLUDE_AKRI_UNIT_MESHHELPERS_H_ */ diff --git a/packages/krino/krino/unit_tests/Akri_Unit_MortonIndex.cpp b/packages/krino/krino/unit_tests/Akri_Unit_MortonIndex.cpp new file mode 100644 index 000000000000..805731063269 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_MortonIndex.cpp @@ -0,0 +1,52 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include +#include +#include + +namespace krino +{ + +TEST(MortonIndex, specified_index) +{ + const std::vector valid_indices {0, 1, 2, 4, 3434, 23, 1414415, 76285, MAX_VALID_MORTON3D_INDEX}; + for (int valid_index : valid_indices) + { + EXPECT_EQ(valid_index, morton3d_decode_index(morton3d_encode_index(valid_index))); + } +#ifndef NDEBUG + const std::vector invalid_indices {MAX_VALID_MORTON3D_INDEX+1, 3000000, 2147483647}; + for (int invalid_index : invalid_indices) + { + EXPECT_ANY_THROW(morton3d_encode_index(invalid_index)); + } +#endif +} + +TEST(MortonIndex, specified_indices) +{ + const std::vector valid_indices {0, 1, 2, 4, 3434, 23, 1414415, 76285, MAX_VALID_MORTON3D_INDEX}; + for (int ix : valid_indices) + { + for (int iy : valid_indices) + { + for (int iz : valid_indices) + { + std::array out_indices = morton3d_decode_indices(morton3d_encode_indices({{ix,iy,iz}})); + EXPECT_EQ(ix, out_indices[0]); + EXPECT_EQ(iy, out_indices[1]); + EXPECT_EQ(iz, out_indices[2]); + } + } + } +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_ParallelErrorMessage.cpp b/packages/krino/krino/unit_tests/Akri_Unit_ParallelErrorMessage.cpp new file mode 100644 index 000000000000..99d3c4f1a609 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_ParallelErrorMessage.cpp @@ -0,0 +1,42 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino +{ + +template void write_rank_message(T & os, const int rank) +{ + os << "Rank " << rank << " message.\n"; +} + +TEST(ParallelErrorMessage, ConcatenateErrors) +{ + stk::Parallel world_comm(MPI_COMM_WORLD); + ParallelErrorMessage err(world_comm); + + write_rank_message(err, world_comm.parallel_rank()); + auto global_message = err.gather_message(); + EXPECT_TRUE(global_message.first); + + if (world_comm.parallel_rank() == 0) + { + std::ostringstream expected; + for (int i = 0; i < world_comm.parallel_size(); ++i) + { + write_rank_message(expected, i); + expected << std::endl; + } + EXPECT_EQ(expected.str(), global_message.second); + } +} +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.cpp new file mode 100644 index 000000000000..4d56eb46bd9f --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.cpp @@ -0,0 +1,197 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +namespace krino +{ + +Part_Decomposition_Fixture::Part_Decomposition_Fixture() +: fixture(3) +{ + AuxMetaData & aux_meta = AuxMetaData::get(get_meta_data()); + aux_meta.declare_io_part_with_topology("block_1", stk::topology::TETRAHEDRON_4); + aux_meta.declare_io_part_with_topology("block_2", stk::topology::TETRAHEDRON_4); + aux_meta.declare_io_part_with_topology("surface_1", stk::topology::TRIANGLE_3); +} + +Part_Decomposition_Fixture::~Part_Decomposition_Fixture() +{ +} + +Block_Surface_Connectivity Part_Decomposition_Fixture::addOneSidedSideset() +{ + Block_Surface_Connectivity block_surface_info; + stk::mesh::PartOrdinal surface_1_ordinal = get_meta_data().get_part("surface_1")->mesh_meta_data_ordinal(); + stk::mesh::PartOrdinal block_1_ordinal = get_meta_data().get_part("block_1")->mesh_meta_data_ordinal(); + block_surface_info.add_surface(surface_1_ordinal, {block_1_ordinal}); + return block_surface_info; +} + +Block_Surface_Connectivity Part_Decomposition_Fixture::addTwoSidedSideset() +{ + Block_Surface_Connectivity block_surface_info; + stk::mesh::PartOrdinal block_1_ordinal = get_meta_data().get_part("block_1")->mesh_meta_data_ordinal(); + stk::mesh::PartOrdinal block_2_ordinal = get_meta_data().get_part("block_2")->mesh_meta_data_ordinal(); + + stk::mesh::Part & surface_1 = *get_meta_data().get_part("surface_1"); + stk::mesh::Part & surface_1_block_1 = get_meta_data().declare_part_with_topology("surface_block_1_tri3_1", stk::topology::TRIANGLE_3); + stk::mesh::Part & surface_1_block_2 = get_meta_data().declare_part_with_topology("surface_block_2_tri3_1", stk::topology::TRIANGLE_3); + get_meta_data().declare_part_subset(surface_1, surface_1_block_1); + get_meta_data().declare_part_subset(surface_1, surface_1_block_2); + block_surface_info.add_surface(surface_1.mesh_meta_data_ordinal(), {block_1_ordinal, block_2_ordinal}); + block_surface_info.add_surface(surface_1_block_1.mesh_meta_data_ordinal(), {block_1_ordinal}); + block_surface_info.add_surface(surface_1_block_2.mesh_meta_data_ordinal(), {block_2_ordinal}); + return block_surface_info; +} + +stk::mesh::MetaData & Part_Decomposition_Fixture::get_meta_data() +{ + return fixture.meta_data(); +} + +stk::mesh::Part * Part_Decomposition_Fixture::findPart(const std::string & part_name) +{ + stk::mesh::Part * result = nullptr; + const stk::mesh::PartVector & mesh_parts = fixture.meta_data().get_parts(); + stk::mesh::PartVector::const_iterator found; + found = std::find_if(mesh_parts.begin(), mesh_parts.end(), PartNameIs(part_name)); + if( found != mesh_parts.end() ) + { + result = *found; + } + return result; +} + +stk::mesh::Part * Part_Decomposition_Fixture::findSuperset(const std::string & superset_name, const stk::mesh::Part * const part) +{ + stk::mesh::Part * result = nullptr; + stk::mesh::PartVector::const_iterator found; + found = std::find_if(part->supersets().begin(), part->supersets().end(), PartNameIs(superset_name)); + if( found != part->supersets().end() ) + { + result = *found; + } + return result; +} + +PhaseVec Part_Decomposition_Fixture::ls_phases(int num_ls, bool one_phase_per_ls) +{ + static bool init = false; + static std::vector phase_tags; + static std::vector named_phases; + if(!init) + { + const LevelSet_Identifier id0(0); + const LevelSet_Identifier id1(1); + const LevelSet_Identifier id2(2); + const LevelSet_Identifier id3(3); + PhaseTag pp, nn, pn, np; + pp.add(id0,1); pp.add(id1,1); + nn.add(id0,-1); nn.add(id1,-1); + pn.add(id0,1); pn.add(id1,-1); + np.add(id0,-1); np.add(id1,1); + + phase_tags.push_back(pp); + phase_tags.push_back(nn); + phase_tags.push_back(pn); + phase_tags.push_back(np); + + named_phases.push_back(NamedPhase("A", pp)); + named_phases.push_back(NamedPhase("B", nn)); + named_phases.push_back(NamedPhase("C", pn)); + named_phases.push_back(NamedPhase("D", np)); + + PhaseTag ls1, ls2, ls3, ls4; + ls1.add(id0,-1); + ls2.add(id1,-1); + ls3.add(id2,-1); + ls4.add(id3,-1); + named_phases.push_back(NamedPhase("LS1", ls1)); + named_phases.push_back(NamedPhase("LS2", ls2)); + named_phases.push_back(NamedPhase("LS3", ls3)); + named_phases.push_back(NamedPhase("LS4", ls4)); + + init = true; + } + + PhaseVec result; + if(!one_phase_per_ls) + { + result.push_back(named_phases[0]); + result.push_back(named_phases[1]); + if(num_ls == 2) + { + result.push_back(named_phases[2]); + result.push_back(named_phases[3]); + } + } + else + { + for(int i=0; i < num_ls; ++i) + { + result.push_back(named_phases[4+i]); + } + } + return result; +} + +PhaseVec Part_Decomposition_Fixture::death_phases() +{ + static bool init = false; + const LevelSet_Identifier id0(0); + static PhaseTag pos, neg; + pos.add(id0,1); neg.add(id0,-1); + static NamedPhase dead("dead", pos), alive("", neg); + static PhaseVec named_phases; + if(!init) + { + named_phases.push_back(alive); + named_phases.push_back(dead); + init = true; + } + + return named_phases; +} + +const Interface_Name_Generator & Part_Decomposition_Fixture::ls_name_generator() +{ + static LS_Name_Generator name_gen; + return name_gen; +} + +const Interface_Name_Generator & Part_Decomposition_Fixture::death_name_generator() +{ + static Death_Name_Generator name_gen("test"); + return name_gen; +} + +void Part_Decomposition_Fixture::performDecomposition(const stk::mesh::PartVector & used_blocks, + const Block_Surface_Connectivity & input_block_surface_info, + bool cdfem_death, int num_ls, bool one_ls_per_phase) +{ + Phase_Support & phase_support = Phase_Support::get(get_meta_data()); + phase_support.set_input_block_surface_connectivity(input_block_surface_info); + if(cdfem_death) + { + phase_support.decompose_blocks(used_blocks, + Part_Decomposition_Fixture::death_phases(), Part_Decomposition_Fixture::death_name_generator()); + phase_support.build_decomposed_block_surface_connectivity(); + } + else + { + phase_support.decompose_blocks(used_blocks, + Part_Decomposition_Fixture::ls_phases(num_ls, one_ls_per_phase), Part_Decomposition_Fixture::ls_name_generator()); + phase_support.build_decomposed_block_surface_connectivity(); + } +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.hpp b/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.hpp new file mode 100644 index 000000000000..5239d8f69a28 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Part_Decomposition_Fixture.hpp @@ -0,0 +1,75 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_UNIT_PHASE_SUPPORT_H_ +#define AKRI_UNIT_PHASE_SUPPORT_H_ + +#include + +#include +#include +#include +#include + +namespace stk { namespace mesh { class Part; } } +namespace stk { namespace mesh { class MetaData; } } +namespace krino { class Block_Surface_Connectivity; } +namespace krino { class Interface_Name_Generator; } +namespace krino { class NamedPhase; } + +namespace krino +{ + +struct PartNameIs +{ + PartNameIs(const std::string & name) : match_name(name) {} + bool operator()(const stk::mesh::Part * part) { + return part->name() == match_name; + } + std::string match_name; +}; + +class Part_Decomposition_Fixture : public ::testing::Test +{ +public: + Part_Decomposition_Fixture(); + virtual ~Part_Decomposition_Fixture(); + + void performDecomposition(const std::vector & used_blocks, const Block_Surface_Connectivity & input_block_surface_info, bool cdfem_death, int num_ls = 1, bool one_ls_per_phase=false); + + stk::mesh::MetaData & get_meta_data(); + + Block_Surface_Connectivity addOneSidedSideset(); + Block_Surface_Connectivity addTwoSidedSideset(); + +protected: + stk::mesh::Part * findPart(const std::string & part_name); + stk::mesh::Part * findSuperset(const std::string & superset_name, const stk::mesh::Part * const part); + void assert_conformal_part_exists(const std::string & conformal_part_name, const std::string & nonconformal_part_name) + { + const stk::mesh::Part * conformal_part = findPart(conformal_part_name); + Phase_Support & phase_support = Phase_Support::get(get_meta_data()); + ASSERT_TRUE( conformal_part != NULL ); + EXPECT_TRUE( phase_support.is_conformal(conformal_part) ); + EXPECT_EQ(nonconformal_part_name, phase_support.find_nonconformal_part(*conformal_part)->name() ); + } + +private: + static PhaseVec ls_phases(int num_ls, bool one_ls_per_phase=false); + static PhaseVec death_phases(); + + static const Interface_Name_Generator & ls_name_generator(); + static const Interface_Name_Generator & death_name_generator(); + + SimpleStkFixture fixture; + LogRedirecter log; +}; + +} // namespace krino + +#endif /* AKRI_UNIT_PHASE_SUPPORT_H_ */ diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Phase_Support.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Phase_Support.cpp new file mode 100644 index 000000000000..f6b66c10a291 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Phase_Support.cpp @@ -0,0 +1,231 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include + +#include + +namespace krino +{ + +TEST_F(Part_Decomposition_Fixture, One_Block_LS) +{ + Block_Surface_Connectivity block_surface_info; + performDecomposition({findPart("block_1")}, block_surface_info, false); + + assert_conformal_part_exists("block_1_A", "block_1_nonconformal"); + assert_conformal_part_exists("block_1_B", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_A_B", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_B_A", "block_1_nonconformal"); +} + +TEST_F(Part_Decomposition_Fixture, One_Block_Death) +{ + Block_Surface_Connectivity block_surface_info; + performDecomposition({findPart("block_1")}, block_surface_info, true); + + assert_conformal_part_exists("block_1", "block_1_nonconformal"); + assert_conformal_part_exists("block_1_dead", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_test", "block_1_nonconformal"); +} + +TEST_F(Part_Decomposition_Fixture, OneSidedSideset_LS) +{ + Block_Surface_Connectivity block_surface_info = addOneSidedSideset(); + performDecomposition({findPart("block_1")}, block_surface_info, false); + + assert_conformal_part_exists("surface_1_A", "surface_1_nonconformal"); + assert_conformal_part_exists("surface_1_B", "surface_1_nonconformal"); +} + +TEST_F(Part_Decomposition_Fixture, OneSidedSideset_Death) +{ + Block_Surface_Connectivity block_surface_info = addOneSidedSideset(); + performDecomposition({findPart("block_1")}, block_surface_info, true); + + assert_conformal_part_exists("surface_1", "surface_1_nonconformal"); + assert_conformal_part_exists("surface_1_dead", "surface_1_nonconformal"); +} + +TEST_F(Part_Decomposition_Fixture, TwoSidedSideset_LS) +{ + Block_Surface_Connectivity block_surface_info = addTwoSidedSideset(); + performDecomposition({findPart("block_1")}, block_surface_info, false); + + //const stk::mesh::Part * surf_1_A_block_1 = findPart("surface_1_A_block_1"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_A_block_1 = findPart("surface_block_1_tri3_1_A"); + ASSERT_TRUE( surf_1_A_block_1 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_A", surf_1_A_block_1) != NULL ); + + //const stk::mesh::Part * surf_1_B_block_1 = findPart("surface_1_B_block_1"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_B_block_1 = findPart("surface_block_1_tri3_1_B"); + ASSERT_TRUE( surf_1_B_block_1 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_B", surf_1_B_block_1) != NULL ); + + //const stk::mesh::Part * surf_1_A_block_2 = findPart("surface_1_A_block_2"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_A_block_2 = findPart("surface_block_2_tri3_1_A"); + ASSERT_TRUE( surf_1_A_block_2 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_A", surf_1_A_block_2) != NULL ); + + //const stk::mesh::Part * surf_1_B_block_2 = findPart("surface_1_B_block_2"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_B_block_2 = findPart("surface_block_2_tri3_1_B"); + ASSERT_TRUE( surf_1_B_block_2 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_B", surf_1_B_block_2) != NULL ); +} + +TEST_F(Part_Decomposition_Fixture, TwoSidedSideset_Death) +{ + Block_Surface_Connectivity block_surface_info = addTwoSidedSideset(); + performDecomposition({findPart("block_1")}, block_surface_info, true); + + //const stk::mesh::Part * surf_1_block_1 = findPart("surface_1_block_1"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_block_1 = findPart("surface_block_1_tri3_1"); + ASSERT_TRUE( surf_1_block_1 != NULL ); + EXPECT_TRUE( findSuperset("surface_1", surf_1_block_1) != NULL ); + + //const stk::mesh::Part * surf_1_dead_block_1 = findPart("surface_1_dead_block_1"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_dead_block_1 = findPart("surface_block_1_tri3_1_dead"); + ASSERT_TRUE( surf_1_dead_block_1 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_dead", surf_1_dead_block_1) != NULL ); + + //const stk::mesh::Part * surf_1_block_2 = findPart("surface_1_block_2"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_block_2 = findPart("surface_block_2_tri3_1"); + ASSERT_TRUE( surf_1_block_2 != NULL ); + EXPECT_TRUE( findSuperset("surface_1", surf_1_block_2) != NULL ); + + //const stk::mesh::Part * surf_1_dead_block_2 = findPart("surface_1_dead_block_2"); // No support for aliases in stk yet + const stk::mesh::Part * surf_1_dead_block_2 = findPart("surface_block_2_tri3_1_dead"); + ASSERT_TRUE( surf_1_dead_block_2 != NULL ); + EXPECT_TRUE( findSuperset("surface_1_dead", surf_1_dead_block_2) != NULL ); +} + +TEST_F(Part_Decomposition_Fixture, Multiple_LS_Decomposition) +{ + Block_Surface_Connectivity block_surface_info; + performDecomposition({findPart("block_1")}, block_surface_info, false, 2); + + assert_conformal_part_exists("block_1_A", "block_1_nonconformal"); + assert_conformal_part_exists("block_1_B", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_A_B", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_B_A", "block_1_nonconformal"); + + assert_conformal_part_exists("block_1_C", "block_1_nonconformal"); + assert_conformal_part_exists("block_1_D", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_C_D", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_D_C", "block_1_nonconformal"); + + assert_conformal_part_exists("surface_block_1_A_C", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_C_A", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_A_D", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_D_A", "block_1_nonconformal"); + + assert_conformal_part_exists("surface_block_1_B_C", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_C_B", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_B_D", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_D_B", "block_1_nonconformal"); +} + +TEST_F(Part_Decomposition_Fixture, find_conformal_io_part) +{ + std::vector decomposed_blocks; + decomposed_blocks.push_back("block_1"); + Block_Surface_Connectivity block_surface_info; + + stk::mesh::Part * block_1 = findPart("block_1"); + performDecomposition({block_1}, block_surface_info, false, 2); + const LevelSet_Identifier id0(0); + const LevelSet_Identifier id1(1); + LS_SideTag p0(id0,1); + LS_SideTag p1(id1,1); + LS_SideTag n0(id0,-1); + LS_SideTag n1(id1,-1); + PhaseTag pp, nn, pn, np; + pp.add(p0); pp.add(p1); // "A" + nn.add(n0); nn.add(n1); // "B" + pn.add(p0); pn.add(n1); // "C" + np.add(n0); np.add(p1); // "D" + + // Test volume conformal io part lookup + Phase_Support & phase_support = Phase_Support::get(get_meta_data()); + const stk::mesh::Part * block_1_A = phase_support.find_conformal_io_part(*block_1, pp); + ASSERT_TRUE( block_1_A != NULL ); + EXPECT_EQ( "block_1_A", block_1_A->name() ); + + const stk::mesh::Part * block_1_B = phase_support.find_conformal_io_part(*block_1, nn); + ASSERT_TRUE( block_1_B != NULL ); + EXPECT_EQ( "block_1_B", block_1_B->name() ); + + const stk::mesh::Part * block_1_C = phase_support.find_conformal_io_part(*block_1, pn); + ASSERT_TRUE( block_1_C != NULL ); + EXPECT_EQ( "block_1_C", block_1_C->name() ); + + const stk::mesh::Part * block_1_D = phase_support.find_conformal_io_part(*block_1, np); + ASSERT_TRUE( block_1_D != NULL ); + EXPECT_EQ( "block_1_D", block_1_D->name() ); + + const stk::mesh::Part * surface_block_1_A_B = phase_support.find_interface_part(*block_1_A, *block_1_B); + ASSERT_TRUE( surface_block_1_A_B != NULL ); + EXPECT_EQ( "surface_block_1_A_B", surface_block_1_A_B->name() ); + + const stk::mesh::Part * surface_block_1_A_C = phase_support.find_interface_part(*block_1_A, *block_1_C); + ASSERT_TRUE( surface_block_1_A_C != NULL ); + EXPECT_EQ( "surface_block_1_A_C", surface_block_1_A_C->name() ); + + const stk::mesh::Part * surface_block_1_A_D = phase_support.find_interface_part(*block_1_A, *block_1_D); + ASSERT_TRUE( surface_block_1_A_D != NULL ); + EXPECT_EQ( "surface_block_1_A_D", surface_block_1_A_D->name() ); + + const stk::mesh::Part * surface_block_1_C_D = phase_support.find_interface_part(*block_1_C, *block_1_D); + ASSERT_TRUE( surface_block_1_C_D != NULL ); + EXPECT_EQ( "surface_block_1_C_D", surface_block_1_C_D->name() ); +} + +TEST_F(Part_Decomposition_Fixture, get_blocks_touching_surface) +{ + Block_Surface_Connectivity block_surface_info = addTwoSidedSideset(); + performDecomposition({findPart("block_1")}, block_surface_info, false); + + std::vector blocks; + + blocks = get_meta_data().get_blocks_touching_surface(get_meta_data().get_part("surface_1_A")); + EXPECT_EQ( 2u, blocks.size() ); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_1_A"))); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_2"))); + + blocks = get_meta_data().get_blocks_touching_surface(get_meta_data().get_part("surface_block_1_tri3_1_A")); + EXPECT_EQ( 1u, blocks.size() ); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_1_A"))); + + blocks = get_meta_data().get_blocks_touching_surface(get_meta_data().get_part("surface_block_2_tri3_1_A")); + EXPECT_EQ( 1u, blocks.size() ); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_2"))); + + blocks = get_meta_data().get_blocks_touching_surface(get_meta_data().get_part("surface_block_1_A_B")); + EXPECT_EQ( 1u, blocks.size() ); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_1_A"))); + + blocks = get_meta_data().get_blocks_touching_surface(get_meta_data().get_part("surface_block_1_B_A")); + EXPECT_EQ( 1u, blocks.size() ); + EXPECT_TRUE( blocks.end() != std::find(blocks.begin(), blocks.end(), get_meta_data().get_part("block_1_B"))); + +} + +TEST_F(Part_Decomposition_Fixture, One_Block_Two_LS_One_LS_Per_Phase) +{ + Block_Surface_Connectivity block_surface_info; + performDecomposition({findPart("block_1")}, block_surface_info, false, 2, true); + + assert_conformal_part_exists("block_1_LS1", "block_1_nonconformal"); + assert_conformal_part_exists("block_1_LS2", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_LS1_LS2", "block_1_nonconformal"); + assert_conformal_part_exists("surface_block_1_LS2_LS1", "block_1_nonconformal"); +} + +} // namespace krino diff --git a/packages/krino/krino/unit_tests/Akri_Unit_RebalanceUtils.cpp b/packages/krino/krino/unit_tests/Akri_Unit_RebalanceUtils.cpp new file mode 100644 index 000000000000..388ddd4a5c9b --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_RebalanceUtils.cpp @@ -0,0 +1,446 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +namespace krino { +namespace rebalance_utils { + +namespace { + +/* + * Builds a single tri mesh with 1 level of adaptivity. Parent element is ID 1, + * Child elem and node IDs are in the ascii art below + * + * 3 + * / \ + * / 5 \ + * 6 /_____\ 5 + * /\ /\ + * / \ 3 / \ + * / 2 \ / 4 \ + * /______\/_____\ + * 1 4 2 + */ + +void create_block_and_register_fields(SimpleStkFixture & fixture) +{ + auto & meta = fixture.meta_data(); + meta.declare_part_with_topology("block_1", stk::topology::TRIANGLE_3_2D); + + meta.declare_field > + (stk::topology::NODE_RANK, "coordinates"); + auto & load_field = + meta.declare_field>(stk::topology::ELEMENT_RANK, "element_weights"); + stk::mesh::put_field_on_mesh(load_field, meta.universal_part(), nullptr); + + fixture.commit(); +} + +void build_unadapted_single_tri_mesh(SimpleStkFixture & fixture) +{ + auto & bulk_data = fixture.bulk_data(); + auto & block_1 = *fixture.meta_data().get_part("block_1"); + + bulk_data.modification_begin(); + if(bulk_data.parallel_rank() == 0) + { + stk::mesh::declare_element(bulk_data, block_1, 1, {1, 2, 3}); + } + bulk_data.modification_end(); +} + +void build_one_level_adapted_single_tri_mesh(SimpleStkFixture & fixture) +{ + auto & bulk_data = fixture.bulk_data(); + auto & block_1 = *fixture.meta_data().get_part("block_1"); + + bulk_data.modification_begin(); + if(bulk_data.parallel_rank() == 0) + { + auto parent_elem = stk::mesh::declare_element(bulk_data, block_1, 1, {1, 2, 3}); + auto child1 = stk::mesh::declare_element(bulk_data, block_1, 2, {1, 4, 6}); + auto child2 = stk::mesh::declare_element(bulk_data, block_1, 3, {4, 5, 6}); + auto child3 = stk::mesh::declare_element(bulk_data, block_1, 4, {4, 2, 5}); + auto child4 = stk::mesh::declare_element(bulk_data, block_1, 5, {6, 5, 3}); + auto family_tree = bulk_data.declare_constraint(1); + bulk_data.declare_relation(family_tree, parent_elem, 0); + bulk_data.declare_relation(family_tree, child1, 1); + bulk_data.declare_relation(family_tree, child2, 2); + bulk_data.declare_relation(family_tree, child3, 3); + bulk_data.declare_relation(family_tree, child4, 4); + } + bulk_data.modification_end(); +} + +void build_two_level_adapted_single_tri_mesh(SimpleStkFixture & fixture) +{ + build_one_level_adapted_single_tri_mesh(fixture); + + auto & bulk_data = fixture.bulk_data(); + auto & block_1 = *fixture.meta_data().get_part("block_1"); + + // Refine child elem 3 an additional time and make others into transition elements + bulk_data.modification_begin(); + if(bulk_data.parallel_rank() == 0) + { + { + auto parent = bulk_data.get_entity(stk::topology::ELEMENT_RANK, 3); + auto child1 = stk::mesh::declare_element(bulk_data, block_1, 6, {4, 8, 7}); + auto child2 = stk::mesh::declare_element(bulk_data, block_1, 7, {7, 8, 9}); + auto child3 = stk::mesh::declare_element(bulk_data, block_1, 8, {8, 5, 9}); + auto child4 = stk::mesh::declare_element(bulk_data, block_1, 9, {9, 6, 7}); + + auto family_tree = bulk_data.declare_constraint(2); + bulk_data.declare_relation(family_tree, parent, 0); + bulk_data.declare_relation(family_tree, child1, 1); + bulk_data.declare_relation(family_tree, child2, 2); + bulk_data.declare_relation(family_tree, child3, 3); + bulk_data.declare_relation(family_tree, child4, 4); + } + + { + auto parent = bulk_data.get_entity(stk::topology::ELEMENT_RANK, 2); + auto child1 = stk::mesh::declare_element(bulk_data, block_1, 10, {1, 4, 7}); + auto child2 = stk::mesh::declare_element(bulk_data, block_1, 11, {1, 7, 6}); + + auto family_tree = bulk_data.declare_constraint(3); + bulk_data.declare_relation(family_tree, parent, 0); + bulk_data.declare_relation(family_tree, child1, 1); + bulk_data.declare_relation(family_tree, child2, 2); + } + { + auto parent = bulk_data.get_entity(stk::topology::ELEMENT_RANK, 4); + auto child1 = stk::mesh::declare_element(bulk_data, block_1, 12, {4, 2, 8}); + auto child2 = stk::mesh::declare_element(bulk_data, block_1, 13, {2, 5, 8}); + + auto family_tree = bulk_data.declare_constraint(4); + bulk_data.declare_relation(family_tree, parent, 0); + bulk_data.declare_relation(family_tree, child1, 1); + bulk_data.declare_relation(family_tree, child2, 2); + } + { + auto parent = bulk_data.get_entity(stk::topology::ELEMENT_RANK, 4); + auto child1 = stk::mesh::declare_element(bulk_data, block_1, 14, {9, 5, 3}); + auto child2 = stk::mesh::declare_element(bulk_data, block_1, 15, {9, 3, 6}); + + auto family_tree = bulk_data.declare_constraint(5); + bulk_data.declare_relation(family_tree, parent, 0); + bulk_data.declare_relation(family_tree, child1, 1); + bulk_data.declare_relation(family_tree, child2, 2); + } + } + bulk_data.modification_end(); +} + +} + +TEST(UpdateRebalanceForAdaptivity, OneLevel) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_one_level_adapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::balance::DecompositionChangeList change_list(fixture.bulk_data(), {}); + auto parent_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + + stk::mesh::EntityVector child_elems; + for(int child_id=2; child_id < 6; ++child_id) + { + auto child_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, child_id); + ASSERT_TRUE(mesh.is_valid(child_elem)); + child_elems.push_back(child_elem); + } + + const int dest_proc = 2; + change_list.set_entity_destination(parent_elem, dest_proc); + + for(auto && child_elem : child_elems) + { + ASSERT_FALSE(change_list.has_entity(child_elem)); + } + + impl::update_rebalance_for_adaptivity(change_list, mesh); + + for(auto && child_elem : child_elems) + { + EXPECT_TRUE(change_list.has_entity(child_elem)); + EXPECT_EQ(dest_proc, change_list.get_entity_destination(child_elem)); + } +} + +TEST(UpdateRebalanceForAdaptivity, OneLevelChildMovedWithoutParent) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_one_level_adapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::balance::DecompositionChangeList change_list(fixture.bulk_data(), {}); + + stk::mesh::EntityVector child_elems; + for(int child_id=2; child_id < 6; ++child_id) + { + auto child_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, child_id); + ASSERT_TRUE(mesh.is_valid(child_elem)); + child_elems.push_back(child_elem); + change_list.set_entity_destination(child_elem, child_id); + } + + impl::update_rebalance_for_adaptivity(change_list, mesh); + + for(auto && child_elem : child_elems) + { + EXPECT_FALSE(change_list.has_entity(child_elem)); + } +} + +TEST(UpdateRebalanceForAdaptivity, TwoLevels) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_two_level_adapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::balance::DecompositionChangeList change_list(fixture.bulk_data(), {}); + auto parent_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + + stk::mesh::EntityVector child_elems; + for(int child_id=2; child_id < 15; ++child_id) + { + auto child_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, child_id); + ASSERT_TRUE(mesh.is_valid(child_elem)); + child_elems.push_back(child_elem); + } + + const int dest_proc = 2; + change_list.set_entity_destination(parent_elem, dest_proc); + + impl::update_rebalance_for_adaptivity(change_list, mesh); + + for(auto && child_elem : child_elems) + { + EXPECT_TRUE(change_list.has_entity(child_elem)); + EXPECT_EQ(dest_proc, change_list.get_entity_destination(child_elem)); + } + + stk::mesh::EntityVector family_trees; + mesh.get_entities( + stk::topology::CONSTRAINT_RANK, mesh.mesh_meta_data().locally_owned_part(), family_trees); + for(auto && ft : family_trees) + { + EXPECT_TRUE(change_list.has_entity(ft)); + EXPECT_EQ(dest_proc, change_list.get_entity_destination(ft)); + } +} + +TEST(UpdateRebalanceForAdaptivity, TwoLevelsFirstLevelChildInitialDifferentProc) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_two_level_adapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::balance::DecompositionChangeList change_list(fixture.bulk_data(), {}); + auto parent_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + + stk::mesh::EntityVector child_elems; + for(int child_id=2; child_id < 15; ++child_id) + { + auto child_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, child_id); + ASSERT_TRUE(mesh.is_valid(child_elem)); + child_elems.push_back(child_elem); + } + + const int dest_proc = 2; + change_list.set_entity_destination(parent_elem, dest_proc); + change_list.set_entity_destination(mesh.get_entity(stk::topology::ELEMENT_RANK, 3), 5); + + impl::update_rebalance_for_adaptivity(change_list, mesh); + + for(auto && child_elem : child_elems) + { + EXPECT_TRUE(change_list.has_entity(child_elem)); + EXPECT_EQ(dest_proc, change_list.get_entity_destination(child_elem)); + } +} + +TEST(AccumulateAdaptivityChildWeights, TwoLevelAdaptedTri) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_two_level_adapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::mesh::Field & weights_field = static_cast &>( + *fixture.meta_data().get_field(stk::topology::ELEMENT_RANK, "element_weights")); + + auto parent_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + double & parent_weight = *stk::mesh::field_data(weights_field, parent_elem); + parent_weight = 10.; + stk::mesh::EntityVector child_elems; + for (int child_id = 2; child_id < 15; ++child_id) + { + auto child_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, child_id); + ASSERT_TRUE(mesh.is_valid(child_elem)); + child_elems.push_back(child_elem); + + double & weight = *stk::mesh::field_data(weights_field, child_elem); + weight = 1.; + } + + impl::accumulate_adaptivity_child_weights_to_parents(mesh, weights_field); + + for (auto && child_elem : child_elems) + { + const double & weight = *stk::mesh::field_data(weights_field, child_elem); + EXPECT_DOUBLE_EQ(0., weight); + } + EXPECT_DOUBLE_EQ(23., parent_weight); +} + +TEST(AccumulateAdaptivityChildWeights, UnadaptedElement) +{ + SimpleStkFixture fixture(2, MPI_COMM_SELF); + create_block_and_register_fields(fixture); + build_unadapted_single_tri_mesh(fixture); + + const auto & mesh = fixture.bulk_data(); + + stk::mesh::Field & weights_field = static_cast &>( + *fixture.meta_data().get_field(stk::topology::ELEMENT_RANK, "element_weights")); + + auto parent_elem = mesh.get_entity(stk::topology::ELEMENT_RANK, 1); + double & parent_weight = *stk::mesh::field_data(weights_field, parent_elem); + parent_weight = 10.; + + impl::accumulate_adaptivity_child_weights_to_parents(mesh, weights_field); + + EXPECT_DOUBLE_EQ(10., parent_weight); +} + +TEST(Rebalance, MultipleWeightFields) +{ + SimpleStkFixture fixture(2, MPI_COMM_WORLD); + + auto & mesh = fixture.bulk_data(); + auto & meta = fixture.meta_data(); + + if (mesh.parallel_size() != 2) return; + + stk::mesh::Part & block_1 = meta.declare_part_with_topology("block_1", stk::topology::QUAD_4_2D); + stk::mesh::Part & block_2 = meta.declare_part_with_topology("block_2", stk::topology::QUAD_4_2D); + + auto & coords_field = meta.declare_field>( + stk::topology::NODE_RANK, "coordinates"); + stk::mesh::put_field_on_mesh(coords_field, meta.universal_part(), nullptr); + + auto & weights_field_1 = meta.declare_field>( + stk::topology::ELEMENT_RANK, "element_weights_1"); + stk::mesh::put_field_on_mesh(weights_field_1, block_1, nullptr); + + auto & weights_field_2 = meta.declare_field>( + stk::topology::ELEMENT_RANK, "element_weights_2"); + stk::mesh::put_field_on_mesh(weights_field_2, block_2, nullptr); + + meta.commit(); + + // Create mesh with two disconnected blocks each containing two elements. Initially block_1 will + // be + // all owned by P0 and block_2 all by P1. Each element gets a weight of 1 in the weight field for + // its + // block, rebalance should put one element from each block on each proc. + const std::vector elem_nodes{ + {1, 2, 5, 4}, {2, 3, 6, 5}, {7, 8, 11, 12}, {8, 9, 10, 11}}; + const std::vector elem_procs{0, 0, 1, 1}; + std::vector elem_parts{{&block_1}, {&block_1}, {&block_2}, {&block_2}}; + std::vector> node_coords{{0, 0}, + {1, 0}, + {2, 0}, + {2, 1}, + {1, 1}, + {0, 1}, + {3, 0}, + {4, 0}, + {5, 0}, + {3, 1}, + {4, 1}, + {5, 1}}; + + build_mesh(mesh, elem_nodes, elem_procs, elem_parts); + + for (auto && b : mesh.buckets(stk::topology::NODE_RANK)) + { + for (auto && node : *b) + { + double * coords = stk::mesh::field_data(coords_field, node); + coords[0] = node_coords[mesh.identifier(node) - 1][0]; + coords[1] = node_coords[mesh.identifier(node) - 1][1]; + } + } + + stk::mesh::field_fill(1., weights_field_1); + stk::mesh::field_fill(1., weights_field_2); + + const auto parallel_rank = mesh.parallel_rank(); + const auto & owned_part = meta.locally_owned_part(); + if (parallel_rank == 0) + { + EXPECT_EQ(2u, + stk::mesh::count_selected_entities( + owned_part & block_1, mesh.buckets(stk::topology::ELEMENT_RANK))); + EXPECT_EQ(0u, + stk::mesh::count_selected_entities( + owned_part & block_2, mesh.buckets(stk::topology::ELEMENT_RANK))); + } + if (parallel_rank == 1) + { + EXPECT_EQ(0u, + stk::mesh::count_selected_entities( + owned_part & block_1, mesh.buckets(stk::topology::ELEMENT_RANK))); + EXPECT_EQ(2u, + stk::mesh::count_selected_entities( + owned_part & block_2, mesh.buckets(stk::topology::ELEMENT_RANK))); + } + + rebalance_utils::rebalance_mesh( + mesh, nullptr, {weights_field_1.name(), weights_field_2.name()}, "coordinates", "parmetis"); + + EXPECT_EQ(1u, + stk::mesh::count_selected_entities( + owned_part & block_1, mesh.buckets(stk::topology::ELEMENT_RANK))); + EXPECT_EQ(1u, + stk::mesh::count_selected_entities( + owned_part & block_2, mesh.buckets(stk::topology::ELEMENT_RANK))); +} +} +} + diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.cpp b/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.cpp new file mode 100644 index 000000000000..6db2f2adce90 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.cpp @@ -0,0 +1,136 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include + +#include + +#include +#include +#include +#include +#include + +#include +#include + +namespace krino { + +void SimpleStkFixture::write_results(const std::string & filename, stk::mesh::BulkData & mesh, const bool use64bitIds) +{ + stk::io::StkMeshIoBroker io(mesh.parallel()); + io.set_bulk_data(mesh); + + Ioss::PropertyManager properties; + if (use64bitIds) + { + properties.add(Ioss::Property("INTEGER_SIZE_API", 8)); + properties.add(Ioss::Property("INTEGER_SIZE_DB", 8)); + } + + auto index = io.create_output_mesh(filename, stk::io::WRITE_RESULTS, properties); + io.write_output_mesh(index); + + for(auto && field : mesh.mesh_meta_data().get_fields()) + { + io.add_field(index, *field); + } + + io.begin_output_step(index, 0.); + io.write_defined_output_fields(index); + io.end_output_step(index); +} + +SingleElementFixture::SingleElementFixture(const stk::topology & topology) + : my_topology(topology), + stk_fixture(my_topology.dimension()) +{ + AuxMetaData & aux_meta = AuxMetaData::get(stk_fixture.meta_data()); + block_part = &stk_fixture.meta_data().declare_part_with_topology("block_1", my_topology); + const FieldType & vec_type = (my_topology.dimension() == 3) ? FieldType::VECTOR_3D : FieldType::VECTOR_2D; + coord_field = aux_meta.register_field("coordinates", vec_type, stk::topology::NODE_RANK, 1u, 1u, *block_part); + CDFEM_Support::get(stk_fixture.meta_data()).set_coords_field( coord_field ); + scalar_field = aux_meta.register_field("scalar_field", FieldType::REAL, stk::topology::NODE_RANK, 1u, 1u, *block_part); + stk_fixture.commit(); +} + +void +SingleElementFixture::generate_mesh() +{ + const AuxMetaData & aux_meta = AuxMetaData::get(stk_fixture.meta_data()); + stk_fixture.bulk_data().modification_begin(); + { + stk::mesh::PartVector elem_parts; + elem_parts.push_back(block_part); + elem_parts.push_back(&aux_meta.active_part()); + elem_parts.push_back(&stk_fixture.meta_data().locally_owned_part()); + stk::mesh::EntityIdVector node_ids(my_topology.num_nodes()); + for(unsigned i=0; i < node_ids.size(); ++i) + { + node_ids[i] = i+1; + } + const stk::mesh::EntityId elem_id = 1; + my_elem = stk::mesh::declare_element( stk_fixture.bulk_data(), elem_parts, elem_id, node_ids ); + const stk::mesh::Entity * const nodes = stk_fixture.bulk_data().begin_nodes(my_elem); + for(unsigned i=0; i < node_ids.size(); ++i) + { + EXPECT_EQ(node_ids[i], stk_fixture.bulk_data().identifier(nodes[i])); + } + } + stk_fixture.bulk_data().modification_end(); + + // set node coordinates + stk::mesh::field_fill(0., coord_field); + const stk::mesh::Entity * const nodes = stk_fixture.bulk_data().begin_nodes(my_elem); + for(unsigned i=0; i < my_topology.num_nodes(); ++i) + { + if (i > 0) + { + double * node_coords = field_data(coord_field, nodes[i]); + node_coords[i-1] = 1.0; + } + } +} + +TEST(SingleElementFixture, tri3) +{ + stk::topology tri3 = stk::topology::TRIANGLE_3_2D; + SingleElementFixture test_fixture(tri3); + + test_fixture.generate_mesh(); + + EXPECT_EQ(2u, test_fixture.stk_fixture.meta_data().spatial_dimension()); + + const stk::mesh::BucketVector & elem_buckets = test_fixture.stk_fixture.bulk_data().buckets(stk::topology::ELEMENT_RANK); + ASSERT_EQ(1u, elem_buckets.size()); + EXPECT_EQ(1u, (*elem_buckets.begin())->size()); + EXPECT_EQ(3u, test_fixture.stk_fixture.bulk_data().num_nodes((*elem_buckets[0])[0])); + const stk::mesh::BucketVector & node_buckets = test_fixture.stk_fixture.bulk_data().buckets(stk::topology::NODE_RANK); + ASSERT_EQ(1u, node_buckets.size()); + EXPECT_EQ(3u, (*node_buckets.begin())->size()); +} + +TEST(SingleElementFixture, tet4) +{ + stk::topology tet4 = stk::topology::TETRAHEDRON_4; + SingleElementFixture test_fixture(tet4); + + test_fixture.generate_mesh(); + + EXPECT_EQ(3u, test_fixture.stk_fixture.meta_data().spatial_dimension()); + + const stk::mesh::BucketVector & elem_buckets = test_fixture.stk_fixture.bulk_data().buckets(stk::topology::ELEMENT_RANK); + ASSERT_EQ(1u, elem_buckets.size()); + EXPECT_EQ(1u, (*elem_buckets.begin())->size()); + EXPECT_EQ(4u, test_fixture.stk_fixture.bulk_data().num_nodes((*elem_buckets[0])[0])); + const stk::mesh::BucketVector & node_buckets = test_fixture.stk_fixture.bulk_data().buckets(stk::topology::NODE_RANK); + ASSERT_EQ(1u, node_buckets.size()); + EXPECT_EQ(4u, (*node_buckets.begin())->size()); +} + +} diff --git a/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.hpp b/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.hpp new file mode 100644 index 000000000000..f3d969b484ba --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_Single_Element_Fixtures.hpp @@ -0,0 +1,79 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#ifndef AKRI_UNIT_SINGLE_ELEMENT_FIXTURES_H_ +#define AKRI_UNIT_SINGLE_ELEMENT_FIXTURES_H_ + +#include // for BulkData +#include // for MetaData + +#include "Akri_AuxMetaData.hpp" +#include "Akri_FieldRef.hpp" + +namespace krino { + +inline std::vector entity_rank_names_with_ft() +{ + auto entity_rank_names = stk::mesh::entity_rank_names(); + entity_rank_names.push_back("FAMILY_TREE"); + return entity_rank_names; +} + +class SimpleStkFixture +{ +public: + SimpleStkFixture(unsigned dimension, MPI_Comm comm = MPI_COMM_WORLD) + : meta(dimension, entity_rank_names_with_ft()), + bulk(meta, comm) + { + meta.set_mesh_bulk_data(&bulk); + AuxMetaData::create(meta); + } + void commit() { meta.commit(); } + void write_results(const std::string & filename) { write_results(filename, bulk); } + static void write_results(const std::string & filename, stk::mesh::BulkData & mesh, const bool use64bitIds = true); + stk::mesh::MetaData & meta_data() { return meta; } + stk::mesh::BulkData & bulk_data() { return bulk; } + +private: + stk::mesh::MetaData meta; + stk::mesh::BulkData bulk; +}; + +class SimpleStkFixture2d : public SimpleStkFixture +{ +public: + SimpleStkFixture2d(MPI_Comm comm = MPI_COMM_WORLD) : SimpleStkFixture(2) {} +}; + +class SimpleStkFixture3d : public SimpleStkFixture +{ +public: + SimpleStkFixture3d(MPI_Comm comm = MPI_COMM_WORLD) : SimpleStkFixture(3) {} +}; + +// Fixture to create a single element stk mesh of the given topology. +class SingleElementFixture +{ +public: + SingleElementFixture(const stk::topology & topology); + + void generate_mesh(); + + stk::topology my_topology; + SimpleStkFixture stk_fixture; + stk::mesh::Part * block_part; + FieldRef coord_field; + FieldRef scalar_field; + stk::mesh::Entity my_elem; +}; + + +} + +#endif /* AKRI_UNIT_SINGLE_ELEMENT_FIXTURES_H_ */ diff --git a/packages/krino/krino/unit_tests/Akri_Unit_main.cpp b/packages/krino/krino/unit_tests/Akri_Unit_main.cpp new file mode 100644 index 000000000000..d079d13ad299 --- /dev/null +++ b/packages/krino/krino/unit_tests/Akri_Unit_main.cpp @@ -0,0 +1,32 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Use of this source code is governed by a BSD-style +// license that can be found in the LICENSE file. + +#include +#include +#include +#include + +#include +#include +#include + +#include + +int main(int argc, char **argv) { + Kokkos::ScopeGuard guard(argc, argv); + + sierra::Env::set_input_file_required(false); + + testing::InitGoogleTest(&argc, argv); + + krino::Startup startup__(argc, argv); + + stk::unit_test_util::create_parallel_output(sierra::Env::parallel_rank()); + + return RUN_ALL_TESTS(); +} diff --git a/packages/krino/krino/unit_tests/CMakeLists.txt b/packages/krino/krino/unit_tests/CMakeLists.txt new file mode 100644 index 000000000000..3d92207e1423 --- /dev/null +++ b/packages/krino/krino/unit_tests/CMakeLists.txt @@ -0,0 +1,14 @@ + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_EXECUTABLE_AND_TEST( + krino_unit + SOURCES ${SOURCES} + COMM serial mpi + NUM_MPI_PROCS 1-4 + NOEXEPREFIX NOEXESUFFIX + ) diff --git a/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt b/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt index 65456ef38091..961a9218c3b9 100644 --- a/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt +++ b/packages/stk/stk_emend/stk_emend/independent_set/CMakeLists.txt @@ -46,8 +46,18 @@ # SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${${PACKAGE_NAME}_SOURCE_DIR}) FILE(GLOB HEADERS *.hpp) +FILE(GLOB SOURCES *.cpp) + +TRIBITS_ADD_LIBRARY( + stk_emend + HEADERS ${HEADERS} + SOURCES ${SOURCES} + ) INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_emend/independent_set) diff --git a/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp b/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp new file mode 100644 index 000000000000..b2ef6c6c65a0 --- /dev/null +++ b/packages/stk/stk_emend/stk_emend/independent_set/IndependentSetDummy.cpp @@ -0,0 +1,3 @@ +namespace independent_set { +void IndependentSetDummy() {} +} From 7723a6a81a50b66f2a3b660427a8c08356721648 Mon Sep 17 00:00:00 2001 From: rstumin Date: Wed, 20 Oct 2021 13:37:58 -0600 Subject: [PATCH 52/98] fixed some scalar traits type compile errors --- .../Smoothed-Aggregation/MueLu_SaPFactory_def.hpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp index 9a6bc42eb819..7abe736f3ce6 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp @@ -546,8 +546,8 @@ namespace MueLu { notFlippedLeftBound = leftBound; notFlippedRghtBound = rghtBound; - if ((Teuchos::ScalarTraits::real(rsumTarget) >= Teuchos::ScalarTraits::real(leftBound*nEntries)) && - (Teuchos::ScalarTraits::real(rsumTarget) <= Teuchos::ScalarTraits::real(rghtBound*nEntries))) + if ((Teuchos::ScalarTraits::real(rsumTarget) >= Teuchos::ScalarTraits::real(leftBound*as(nEntries))) && + (Teuchos::ScalarTraits::real(rsumTarget) <= Teuchos::ScalarTraits::real(rghtBound*as(nEntries)))) hasFeasibleSol = true; else { hasFeasibleSol=false; @@ -558,7 +558,7 @@ namespace MueLu { // something large so that an if statement will be false aBigNumber = Teuchos::ScalarTraits::zero(); for (LocalOrdinal i = 0; i < nEntries; i++) { - if ( Teuchos::ScalarTraits::magnitude(orig[i]) > aBigNumber) + if ( Teuchos::ScalarTraits::magnitude(orig[i]) > Teuchos::ScalarTraits::magnitude(aBigNumber)) aBigNumber = Teuchos::ScalarTraits::magnitude(orig[i]); } aBigNumber = aBigNumber+ (Teuchos::ScalarTraits::magnitude(leftBound) + Teuchos::ScalarTraits::magnitude(rghtBound))*as(100.0); @@ -594,13 +594,13 @@ namespace MueLu { // compute how far the rowSum is off from the target row sum taking into account // numbers that have been shifted to satisfy bound constraint - rowSumDeviation = leftBound*closestToLeftBound + (nEntries-closestToRghtBound)*rghtBound - rsumTarget; + rowSumDeviation = leftBound*as(closestToLeftBound) + as((nEntries-closestToRghtBound))*rghtBound - rsumTarget; for (LocalOrdinal i=closestToLeftBound; i < closestToRghtBound; i++) rowSumDeviation += origSorted[i]; // the code that follow after this if statement assumes that rowSumDeviation is positive. If this // is not the case, flip the signs of everything so that rowSumDeviation is now positive. // Later we will flip the data back to its original form. - if (rowSumDeviation < Teuchos::ScalarTraits::zero()) { + if (Teuchos::ScalarTraits::real(rowSumDeviation) < Teuchos::ScalarTraits::zero()) { flipped = true; temp = leftBound; leftBound = -rghtBound; rghtBound = temp; From 01871501b3ac49bd4cf48c324bc7af0c39bccc64 Mon Sep 17 00:00:00 2001 From: Evan Harvey Date: Wed, 20 Oct 2021 16:47:24 -0600 Subject: [PATCH 53/98] packages/framework: Point to top-level ini files --- packages/framework/pr_tools/trilinos_pr.ini | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/framework/pr_tools/trilinos_pr.ini b/packages/framework/pr_tools/trilinos_pr.ini index cd4e817353a5..570296de3400 100644 --- a/packages/framework/pr_tools/trilinos_pr.ini +++ b/packages/framework/pr_tools/trilinos_pr.ini @@ -76,7 +76,7 @@ # ===================================================================================================================== [load-env] -supported-systems : ../../../../GenConfig/LoadEnv/examples/trilinos/supported-systems.ini -supported-envs : ../../../../GenConfig/LoadEnv/examples/trilinos/supported-envs.ini -environment-specs : ../../../../GenConfig/LoadEnv/examples/trilinos/environment-specs.ini +supported-systems : ../../../../GenConfig/LoadEnv/examples/supported-systems.ini +supported-envs : ../../../../GenConfig/LoadEnv/examples/supported-envs.ini +environment-specs : ../../../../GenConfig/LoadEnv/examples/environment-specs.ini pullrequest-specs : ./pullrequest-specs.ini From 6870a3e9862c2b4ecd7ba9b3ab3ced074e0079eb Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Wed, 20 Oct 2021 21:00:50 -0600 Subject: [PATCH 54/98] Tpetra: Fixing stride bug --- packages/tpetra/core/src/Tpetra_MultiVector_def.hpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/packages/tpetra/core/src/Tpetra_MultiVector_def.hpp b/packages/tpetra/core/src/Tpetra_MultiVector_def.hpp index deb9a3d2617b..f13ca22e662d 100644 --- a/packages/tpetra/core/src/Tpetra_MultiVector_def.hpp +++ b/packages/tpetra/core/src/Tpetra_MultiVector_def.hpp @@ -322,7 +322,9 @@ namespace { // (anonymous) { // FIXME (mfh 15 Mar 2019) DualView doesn't have a stride // method yet, but its Views do. - size_t strides[WrappedOrNotDualViewType::t_dev::Rank]; + // NOTE: dv.stride() returns a vector of length one + // more than its rank + size_t strides[WrappedOrNotDualViewType::t_dev::Rank+1]; dv.stride(strides); const size_t LDA = strides[1]; const size_t numRows = dv.extent (0); From 3d18a538f99523c61475b6475428eade9452b86f Mon Sep 17 00:00:00 2001 From: rstumin Date: Thu, 21 Oct 2021 08:51:45 -0600 Subject: [PATCH 55/98] fixed one more comparison that needed a teuchos scalar traits cast to a real. --- .../Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp index 7abe736f3ce6..264e165d9983 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp @@ -400,7 +400,7 @@ namespace MueLu { if (nnz != 0) { vals = ArrayView(const_cast(vals1.getRawPtr()), nnz); - Scalar rsumTarget = Teuchos::ScalarTraits::zero(); + Scalar rsumTarget = zero; for (size_t j = 0; j < nnz; j++) rsumTarget += vals[j]; if (nnz > as(maxEntriesPerRow)) { @@ -600,7 +600,7 @@ namespace MueLu { // the code that follow after this if statement assumes that rowSumDeviation is positive. If this // is not the case, flip the signs of everything so that rowSumDeviation is now positive. // Later we will flip the data back to its original form. - if (Teuchos::ScalarTraits::real(rowSumDeviation) < Teuchos::ScalarTraits::zero()) { + if (Teuchos::ScalarTraits::real(rowSumDeviation) < Teuchos::ScalarTraits::real(Teuchos::ScalarTraits::zero())) { flipped = true; temp = leftBound; leftBound = -rghtBound; rghtBound = temp; From c96aeed141bdfa1cf59d8bcbe5e16cc6c7cd59b4 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Thu, 21 Oct 2021 11:21:25 -0600 Subject: [PATCH 56/98] STK: Updated snapshot 10-21-21 11:21 --- packages/stk/.clang-format | 12 ++ .../stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp | 28 ++- .../stk_mesh/stk_mesh/base/SideSetHelper.cpp | 2 +- .../stk_mesh/stk_mesh/base/SideSetUtil.cpp | 2 +- .../stk_mesh/stk_mesh/base/SkinMeshUtil.cpp | 2 +- .../baseImpl/elementGraph/ElemElemGraph.cpp | 201 +++++++++++------- .../baseImpl/elementGraph/ElemElemGraph.hpp | 21 +- .../elementGraph/ElemElemGraphImpl.cpp | 3 - .../elementGraph/ElemElemGraphImpl.hpp | 42 +++- .../ElemGraphShellConnections.cpp | 8 +- .../baseImpl/elementGraph/GraphEdgeData.cpp | 109 +++++++--- .../baseImpl/elementGraph/GraphEdgeData.hpp | 67 +----- .../stk_mesh/UnitTestConnectivity.cpp | 1 - .../UnitTestGraphWithShellConnections.cpp | 4 +- .../element_graph/UnitTestElemElemGraph.cpp | 12 +- .../ngp/UnitTestNgpVirtualFunction.cpp | 3 + .../stk_util/registry/ProductRegistry.cpp | 2 +- 17 files changed, 305 insertions(+), 214 deletions(-) create mode 100644 packages/stk/.clang-format diff --git a/packages/stk/.clang-format b/packages/stk/.clang-format new file mode 100644 index 000000000000..737390ac5373 --- /dev/null +++ b/packages/stk/.clang-format @@ -0,0 +1,12 @@ +BasedOnStyle: Google +AlignAfterOpenBracket: DontAlign +AlignConsecutiveAssignments: 'false' +AlignConsecutiveDeclarations: 'false' +AllowShortFunctionsOnASingleLine: 'Inline' +BreakBeforeBraces: Linux +ColumnLimit: '120' +IndentWidth: '2' +ReflowComments: 'true' +SpaceAfterCStyleCast: 'true' +BinPackParameters: false +ConstructorInitializerAllOnOneLineOrOnePerLine: true diff --git a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp index 6481f55e257c..55fe6152a797 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp @@ -330,25 +330,31 @@ void DeviceMesh::fill_sparse_connectivities(const stk::mesh::BulkData& bulk_in) for(stk::mesh::EntityRank connectedRank=stk::topology::EDGE_RANK; connectedRank 0; for(unsigned iEntity=0; iEntity 0) { + const stk::mesh::Entity* connectedEntities = stkBucket.begin(iEntity, connectedRank); + const stk::mesh::ConnectivityOrdinal* connectedOrdinals = stkBucket.begin_ordinals(iEntity, connectedRank); + const stk::mesh::Permutation* permutations = hasPermutation ? stkBucket.begin_permutations(iEntity, connectedRank) : nullptr; + for(unsigned i=0; i areAllConnectedElemsAir(eeGraph.get_mesh().bucket(element).topology().num_sides(), true); - const GraphEdgesForElement& graphEdges = eeGraph.get_edges_for_element(local_id); + GraphEdgesForElement graphEdges = eeGraph.get_edges_for_element(local_id); for(const GraphEdge & graphEdge : graphEdges) { if(is_connected_element_air(graphEdge)) diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraph.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraph.cpp index 8ecc85a202eb..6d899c2ed603 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraph.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraph.cpp @@ -136,9 +136,24 @@ void ElemElemGraph::fill_from_mesh() SideNodeToReceivedElementDataMap elementSidesReceived = communicate_shared_sides(elementSideIdsToSend); fill_parallel_graph(elementSideIdsToSend, elementSidesReceived); + stk::util::sort_and_unique(m_edgesToAdd, GraphEdgeLessByElem1()); + m_graph.add_sorted_edges(m_edgesToAdd); + + { + std::vector emptyAdd; + m_edgesToAdd.swap(emptyAdd); + } + GraphInfo graphInfo(m_graph, m_parallelInfoForGraphEdges, m_element_topologies); remove_graph_edges_blocked_by_shell(graphInfo); + m_graph.delete_sorted_edges(m_edgesToDelete); + + { + std::vector emptyDelete; + m_edgesToDelete.swap(emptyDelete); + } + m_modCycleWhenGraphModified = m_bulk_data.synchronized_count(); } @@ -146,7 +161,7 @@ size_t ElemElemGraph::num_parallel_edges() const { size_t numParallelEdges = 0; for (size_t i = 0; i < m_graph.get_num_elements_in_graph(); ++i) { - const GraphEdgesForElement& graphEdges = m_graph.get_edges_for_element(i); + const GraphEdgesForElement graphEdges = m_graph.get_edges_for_element(i); for (const GraphEdge& graphEdge : graphEdges) { if (!graphEdge.is_elem2_local()) { ++numParallelEdges; @@ -251,6 +266,8 @@ int ElemElemGraph::size_data_members() void ElemElemGraph::clear_data_members() { m_graph.clear(); + m_edgesToAdd.clear(); + m_edgesToDelete.clear(); m_idMapper.clear(); m_element_topologies.clear(); m_any_shell_elements_exist = false; @@ -264,21 +281,19 @@ void ElemElemGraph::clear_data_members() void ElemElemGraph::fill_elements_attached_to_local_nodes(const stk::mesh::EntityVector& sideNodesOfReceivedElement, stk::mesh::EntityId elementId, stk::topology elementTopology, - stk::mesh::EntityVector& scratchEntityVector, impl::SerialElementDataVector& connectedElementDataVector) const { connectedElementDataVector.clear(); impl::get_elements_with_larger_ids_connected_via_sidenodes(m_bulk_data, elementId, elementTopology, m_idMapper, sideNodesOfReceivedElement, - scratchEntityVector, connectedElementDataVector); + m_scratchEntityVector, connectedElementDataVector); } void ElemElemGraph::get_elements_attached_to_remote_nodes(const stk::mesh::EntityVector& sideNodesOfReceivedElement, stk::mesh::EntityId elementId, stk::topology elementTopology, - stk::mesh::EntityVector& scratchEntityVector, impl::ParallelElementDataVector& connectedElementDataVector) const { connectedElementDataVector.clear(); impl::get_elements_connected_via_sidenodes(m_bulk_data, elementId, elementTopology, m_idMapper, - sideNodesOfReceivedElement, scratchEntityVector, connectedElementDataVector); + sideNodesOfReceivedElement, m_scratchEntityVector, connectedElementDataVector); } bool is_coincident(const stk::mesh::impl::TopologyChecker& topoChecker, @@ -310,7 +325,6 @@ void ElemElemGraph::add_local_graph_edges_for_elem(const stk::mesh::MeshIndex &m impl::LocalId local_elem_id, std::vector &graphEdges, std::vector &coincidentGraphEdges, - stk::mesh::EntityVector& scratchEntityVector, stk::mesh::EntityVector& side_nodes, impl::SerialElementDataVector& connectedElementDataVector, bool only_consider_upper_symmetry) const @@ -325,7 +339,7 @@ void ElemElemGraph::add_local_graph_edges_for_elem(const stk::mesh::MeshIndex &m for(int side_index=0; side_index(0); for (const impl::SerialElementData & otherElem: connectedElementDataVector) { @@ -345,38 +359,39 @@ void ElemElemGraph::add_local_graph_edges_for_elem(const stk::mesh::MeshIndex &m stk::util::sort_and_unique(graphEdges, GraphEdgeLessByElem2()); } -template -void add_edges_to_graph(const std::vector &newGraphEdges, GraphType &graph) +class GraphEdgeAdder { - if (!newGraphEdges.empty()) - { - for(const stk::mesh::GraphEdge &graphEdge : newGraphEdges) - { - graph.add_edge(graphEdge); - graph.add_edge(create_symmetric_edge(graphEdge)); - } - } -} +public: + GraphEdgeAdder(std::vector& edges) : m_edges(edges) {} + void add_edge(const GraphEdge& edge) { m_edges.emplace_back(edge); } +private: + std::vector& m_edges; +}; void ElemElemGraph::fill_graph() { + m_edgesToAdd.clear(); + const stk::mesh::BucketVector& elemBuckets = m_bulk_data.get_buckets(stk::topology::ELEM_RANK, m_bulk_data.mesh_meta_data().locally_owned_part()); - std::vector newGraphEdges; - std::vector coincidentGraphEdges; - stk::mesh::EntityVector scratchEntityVector; stk::mesh::EntityVector side_nodes; impl::SerialElementDataVector connectedElementDataVector; + const bool only_consider_upper_symmetry = true; for(size_t i=0; i newlySharedEdges; - stk::mesh::EntityVector scratchEntityVector; impl::ParallelElementDataVector localElementsAttachedToReceivedNodes; for (SideNodeToReceivedElementDataMap::value_type & receivedElementDataForNodes: elementSidesReceived) { for(const stk::mesh::impl::ParallelElementData &remoteElementData : receivedElementDataForNodes.second) { get_elements_attached_to_remote_nodes(remoteElementData.get_side_nodes(), remoteElementData.get_element_identifier(), - remoteElementData.get_element_topology(), scratchEntityVector, localElementsAttachedToReceivedNodes); + remoteElementData.get_element_topology(), localElementsAttachedToReceivedNodes); for(const impl::ParallelElementData &localElemAttachedToNodes : localElementsAttachedToReceivedNodes) create_parallel_graph_edge(localElemAttachedToNodes, remoteElementData, elementSidesToSend, newlySharedEdges); } @@ -603,7 +617,7 @@ void ElemElemGraph::connect_remote_element_to_existing_graph( const impl::Shared impl::LocalId negSgnRemoteElemId = -1 * static_cast(receivedSharedEdge.get_remote_element_global_id()); GraphEdge graphEdge(local_elem_id, side_index, negSgnRemoteElemId, receivedSharedEdge.get_remote_element_side_index()); - m_graph.add_edge(graphEdge); + m_edgesToAdd.push_back(graphEdge); impl::ParallelInfo parInfo(receivedSharedEdge.get_remote_processor_rank(), permutationIfConnected.permutation_number, @@ -1052,9 +1066,16 @@ void ElemElemGraph::collect_local_shell_connectivity_data(const stk::mesh::impl: } } -void ElemElemGraph::communicate_shell_connectivity(std::vector& shellConnectivityList, +bool ElemElemGraph::communicate_if_shell_connectivity(std::vector& shellConnectivityList, const std::vector &deletedShells) { + unsigned localNumShells = shellConnectivityList.size(); + unsigned globalMaxShells = 0; + stk::all_reduce_max(m_bulk_data.parallel(), &localNumShells, &globalMaxShells, 1); + if (globalMaxShells == 0) { + return false; + } + stk::CommSparse shellComm(m_bulk_data.parallel()); pack_shell_connectivity(shellComm, shellConnectivityList, deletedShells); shellComm.allocate_buffers(); @@ -1075,6 +1096,8 @@ void ElemElemGraph::communicate_shell_connectivity(std::vector 0; } void ElemElemGraph::delete_local_connections_and_collect_remote(const stk::mesh::impl::DeletedElementInfoVector &elements_to_delete, @@ -1091,7 +1114,7 @@ void ElemElemGraph::delete_local_connections_and_collect_remote(const stk::mesh: bool local_connection = connected_elem_id >= 0; if (local_connection) { - m_graph.delete_edge(create_symmetric_edge(graphEdge)); + m_edgesToDelete.push_back(create_symmetric_edge(graphEdge)); } else { impl::ParallelInfo& parallelInfo = m_parallelInfoForGraphEdges.get_parallel_info_for_graph_edge(graphEdge); int remote_proc = parallelInfo.get_proc_rank_of_neighbor(); @@ -1109,9 +1132,12 @@ void ElemElemGraph::delete_local_connections_and_collect_remote(const stk::mesh: { m_coincidentGraph.delete_edge(create_symmetric_edge(graphEdge)); } - - m_graph.delete_all_edges(elem_to_delete_id); m_coincidentGraph.delete_all_edges(elem_to_delete_id); + + GraphEdgesForElement graphEdgesForElement = m_graph.get_edges_for_element(elem_to_delete_id); + for(const GraphEdge& edge : graphEdgesForElement) { + m_edgesToDelete.push_back(edge); + } } } @@ -1156,7 +1182,7 @@ void ElemElemGraph::delete_remote_connection(stk::mesh::Entity connected_elem, s const GraphEdge & graphEdge = m_graph.get_edge_for_element(connected_elem_id, conn_elem_index); if (graphEdge.elem2() == static_cast(-deleted_elem_global_id)) { m_parallelInfoForGraphEdges.erase_parallel_info_for_graph_edge(graphEdge); - m_graph.delete_edge_from_graph(connected_elem_id, conn_elem_index); + m_edgesToDelete.push_back(graphEdge); found_deleted_elem = true; break; } @@ -1213,7 +1239,7 @@ void ElemElemGraph::reconnect_volume_elements_across_deleted_shells(std::vector< stk::mesh::Entity remoteElement = m_bulk_data.get_entity(stk::topology::ELEM_RANK, data.m_farElementId); if (m_bulk_data.is_valid(remoteElement)) { impl::LocalId remoteElementId = get_local_element_id(remoteElement); - m_graph.add_edge(stk::mesh::GraphEdge(localElementId, data.m_nearElementSide, remoteElementId, data.m_farElementSide)); + m_edgesToAdd.push_back(stk::mesh::GraphEdge(localElementId, data.m_nearElementSide, remoteElementId, data.m_farElementSide)); } } else { @@ -1244,13 +1270,15 @@ stk::mesh::impl::DeletedElementInfoVector ElemElemGraph::filter_delete_elements_ void ElemElemGraph::delete_elements(const stk::mesh::impl::DeletedElementInfoVector &elements_to_delete_argument) { + m_edgesToAdd.clear(); + m_edgesToDelete.clear(); stk::mesh::impl::DeletedElementInfoVector elements_to_delete = filter_delete_elements_argument(elements_to_delete_argument); std::vector shellConnectivityList; std::vector deletedNonCoincidentShells; collect_local_shell_connectivity_data(elements_to_delete, shellConnectivityList, deletedNonCoincidentShells); - communicate_shell_connectivity(shellConnectivityList, deletedNonCoincidentShells); + const bool shellsExist = communicate_if_shell_connectivity(shellConnectivityList, deletedNonCoincidentShells); std::vector local_elem_and_remote_connected_elem; delete_local_connections_and_collect_remote(elements_to_delete, local_elem_and_remote_connected_elem); @@ -1262,21 +1290,25 @@ void ElemElemGraph::delete_elements(const stk::mesh::impl::DeletedElementInfoVec delete_remote_connections(remote_edges); - unsigned localNumShells = shellConnectivityList.size(); - unsigned globalMaxShells = 0; - stk::all_reduce_max(m_bulk_data.parallel(), &localNumShells, &globalMaxShells, 1); - if (globalMaxShells > 0) { + stk::util::sort_and_unique(m_edgesToDelete, GraphEdgeLessByElem1()); + m_graph.delete_sorted_edges(m_edgesToDelete); + { + std::vector emptyDelete; + m_edgesToDelete.swap(emptyDelete); + } + + if (shellsExist) { reconnect_volume_elements_across_deleted_shells(shellConnectivityList); } - m_modCycleWhenGraphModified = m_bulk_data.synchronized_count(); -} + stk::util::sort_and_unique(m_edgesToAdd, GraphEdgeLessByElem1()); + m_graph.add_sorted_edges(m_edgesToAdd); + { + std::vector emptyAdd; + m_edgesToAdd.swap(emptyAdd); + } -template -void add_both_edges_between_local_elements(const GraphEdge& graphEdge, GraphType &graph) -{ - graph.add_edge(graphEdge); - graph.add_edge(create_symmetric_edge(graphEdge)); + m_modCycleWhenGraphModified = m_bulk_data.synchronized_count(); } template @@ -1285,24 +1317,13 @@ void ElemElemGraph::add_new_local_edges_to_graph(GraphType &graph, const std::ve for (const stk::mesh::GraphEdge& graphEdge : newGraphEdges) { stk::mesh::Entity neighbor = m_idMapper.local_to_entity(graphEdge.elem2()); - if (is_valid_graph_element(neighbor)) - add_both_edges_between_local_elements(graphEdge, graph); + if (is_valid_graph_element(neighbor)) { + graph.add_edge(graphEdge); + graph.add_edge(create_symmetric_edge(graphEdge)); + } } } -void ElemElemGraph::add_local_edges(stk::mesh::Entity elem_to_add, impl::LocalId new_elem_id, - stk::mesh::EntityVector& scratchEntityVector, - stk::mesh::EntityVector& side_nodes, - impl::SerialElementDataVector& connectedElementDataVector) -{ - std::vector newGraphEdges; - std::vector coincidentGraphEdges; - bool only_consider_upper_symmetry = false; - add_local_graph_edges_for_elem(m_bulk_data.mesh_index(elem_to_add), new_elem_id, newGraphEdges, coincidentGraphEdges, scratchEntityVector, side_nodes, connectedElementDataVector, only_consider_upper_symmetry); - add_new_local_edges_to_graph(m_graph, newGraphEdges); - add_new_local_edges_to_graph(m_coincidentGraph, coincidentGraphEdges); -} - void ElemElemGraph::add_vertex(impl::LocalId newElemLocalId, stk::mesh::Entity elem) { m_idMapper.add_new_entity_with_local_id(elem, newElemLocalId); @@ -1332,14 +1353,17 @@ stk::mesh::EntityVector ElemElemGraph::filter_add_elements_arguments(const stk:: void ElemElemGraph::add_elements_locally(const stk::mesh::EntityVector& allElementsNotAlreadyInGraph) { m_idMapper.make_space_for_new_elements(allElementsNotAlreadyInGraph); - stk::mesh::EntityVector scratchEntityVector; stk::mesh::EntityVector side_nodes; impl::SerialElementDataVector connectedElementDataVector; + const bool only_consider_upper_symmetry = false; for(stk::mesh::Entity newElem : allElementsNotAlreadyInGraph) { impl::LocalId newElemLocalId = get_new_local_element_id_from_pool(); add_vertex(newElemLocalId, newElem); - add_local_edges(newElem, newElemLocalId, scratchEntityVector, side_nodes, connectedElementDataVector); + add_local_graph_edges_for_elem(m_bulk_data.mesh_index(newElem), newElemLocalId, m_newGraphEdges, m_coincidentGraphEdges, side_nodes, connectedElementDataVector, only_consider_upper_symmetry); + GraphEdgeAdder graphEdgeAdder(m_edgesToAdd); + add_new_local_edges_to_graph(graphEdgeAdder, m_newGraphEdges); + add_new_local_edges_to_graph(m_coincidentGraph, m_coincidentGraphEdges); } } @@ -1372,7 +1396,7 @@ void ElemElemGraph::add_elements(const stk::mesh::EntityVector &allUnfilteredEle { addedShells.insert(element); } - } else { + } else if (m_any_shell_elements_exist) { stk::mesh::EntityVector connectedShells = impl::gather_shells_connected_to_solid_element_on_given_side(m_bulk_data, element, side); bool shouldAddThisElementSide = false; @@ -1394,12 +1418,21 @@ void ElemElemGraph::add_elements(const stk::mesh::EntityVector &allUnfilteredEle SideNodeToReceivedElementDataMap elementSidesReceived = communicate_shared_sides(only_added_elements); fill_parallel_graph(only_added_elements, elementSidesReceived); + stk::util::sort_and_unique(m_edgesToAdd, GraphEdgeLessByElem1()); + m_graph.add_sorted_edges(m_edgesToAdd); + + { + std::vector emptyAdd; + m_edgesToAdd.swap(emptyAdd); + } + bool anyShellsExist = m_any_shell_elements_exist; if (m_bulk_data.parallel_size() > 1) { anyShellsExist = stk::is_true_on_any_proc(m_bulk_data.parallel(), m_any_shell_elements_exist); } if (anyShellsExist) { + ThrowRequire(m_edgesToDelete.empty()); stk::mesh::EntityVector addedShellsVector; GraphInfo graphInfo(m_graph, m_parallelInfoForGraphEdges, m_element_topologies); remove_graph_edges_blocked_by_shell(graphInfo); @@ -1426,6 +1459,14 @@ void ElemElemGraph::add_elements(const stk::mesh::EntityVector &allUnfilteredEle unpack_remote_edge_across_shell(comm); } + stk::util::sort_and_unique(m_edgesToDelete, GraphEdgeLessByElem1()); + m_graph.delete_sorted_edges(m_edgesToDelete); + + { + std::vector emptyDelete; + m_edgesToDelete.swap(emptyDelete); + } + m_modCycleWhenGraphModified = m_bulk_data.synchronized_count(); } @@ -1442,7 +1483,7 @@ void ElemElemGraph::break_remote_shell_connectivity_and_pack(stk::CommSparse &co int sharingProc = get_owning_proc_id_of_remote_element(localElem, index); if (phase == 1) { - m_graph.delete_edge_from_graph(leftId, index); + m_edgesToDelete.push_back(graphEdge); } else { @@ -1500,12 +1541,13 @@ void ElemElemGraph::pack_remote_edge_across_shell(stk::CommSparse &comm, stk::me for(size_t i=0; i(remoteElemId))) { - delete_graph_edge(graphEdge); + m_edgesToDelete.push_back(graphEdge); break; } else @@ -1675,13 +1717,6 @@ bool ElemElemGraph::is_valid_graph_edge(const GraphEdge &graphEdge) const return true; } -void ElemElemGraph::delete_graph_edge(const GraphEdge &graphEdge) -{ - m_parallelInfoForGraphEdges.erase_parallel_info_for_graph_edge(graphEdge); - m_coincidentGraph.delete_edge(graphEdge); - m_graph.delete_edge(graphEdge); -} - namespace impl { impl::ElemSideToProcAndFaceId gather_element_side_ids_to_send(const stk::mesh::BulkData& bulkData) @@ -1699,11 +1734,11 @@ impl::ElemSideToProcAndFaceId gather_element_side_ids_to_send(const stk::mesh::B const unsigned num_elements = bulkData.num_elements(node); for(unsigned elemIdx=0; elemIdx &graphEdges, std::vector &coincidentGraphEdges, - stk::mesh::EntityVector& scratchEntityVector, stk::mesh::EntityVector& side_nodes, impl::SerialElementDataVector& connectedElementDataVector, bool only_consider_upper_symmetry = true) const; @@ -245,12 +244,10 @@ class ElemElemGraph void fill_elements_attached_to_local_nodes(const stk::mesh::EntityVector& sideNodesOfReceivedElement, stk::mesh::EntityId elementId, stk::topology elementTopology, - stk::mesh::EntityVector& scratchNodeVector, impl::SerialElementDataVector& connectedElementDataVector) const; void get_elements_attached_to_remote_nodes(const stk::mesh::EntityVector& sideNodesOfReceivedElement, stk::mesh::EntityId elementId, stk::topology elementTopology, - stk::mesh::EntityVector& scratchEntityVector, impl::ParallelElementDataVector& connectedElementDataVector) const; impl::LocalId get_new_local_element_id_from_pool(); @@ -273,8 +270,8 @@ class ElemElemGraph std::vector& shellConnectivityList, std::vector &deletedShells); - void communicate_shell_connectivity(std::vector& shellConnectivityList, - const std::vector &deletedShells); + bool communicate_if_shell_connectivity(std::vector& shellConnectivityList, + const std::vector &deletedShells); void delete_local_connections_and_collect_remote(const stk::mesh::impl::DeletedElementInfoVector &elements_to_delete, std::vector& local_elem_and_remote_connected_elem); @@ -300,16 +297,19 @@ class ElemElemGraph bool is_valid_graph_edge(const GraphEdge &graphEdge) const; - void delete_graph_edge(const GraphEdge &graphEdge); - stk::mesh::BulkData &m_bulk_data; Graph m_graph; + std::vector m_edgesToAdd; + std::vector m_edgesToDelete; + std::vector m_newGraphEdges; + std::vector m_coincidentGraphEdges; ParallelInfoForGraphEdges m_parallelInfoForGraphEdges; unsigned m_modCycleWhenGraphModified; std::vector m_deleted_element_local_id_pool; std::vector m_element_topologies; bool m_any_shell_elements_exist; std::vector m_deleted_elem_pool; + mutable stk::mesh::EntityVector m_scratchEntityVector; impl::SparseGraph m_coincidentGraph; impl::ElementLocalIdMapper m_idMapper; SideConnector m_sideConnector; @@ -321,11 +321,6 @@ class ElemElemGraph const stk::mesh::PartVector& skin_parts, std::vector &shared_modified); - void add_local_edges(stk::mesh::Entity elem_to_add, impl::LocalId new_elem_id, - stk::mesh::EntityVector& scratchEntityVector, - stk::mesh::EntityVector& side_nodes, - impl::SerialElementDataVector& connectedElementDataVector); - template void add_new_local_edges_to_graph(GraphType &graph, const std::vector &newGraphEdges); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.cpp index 38dccc89a949..cd95704217c7 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.cpp @@ -37,7 +37,6 @@ bool fill_topologies(stk::mesh::ElemElemGraph& eeGraph, std::vector& element_topologies) { const stk::mesh::BulkData& bulkData = eeGraph.get_mesh(); - stk::mesh::Graph& graph = eeGraph.get_graph(); bool areAnyElementsShells = false; const stk::mesh::BucketVector & elemBuckets = bulkData.get_buckets(stk::topology::ELEM_RANK, bulkData.mesh_meta_data().locally_owned_part()); @@ -45,11 +44,9 @@ bool fill_topologies(stk::mesh::ElemElemGraph& eeGraph, areAnyElementsShells |= bucket->topology().is_shell(); stk::topology elemTopology = bucket->topology(); - unsigned numSides = elemTopology.num_sides(); for(stk::mesh::Entity element : *bucket) { impl::LocalId elemLocalId = localMapper.entity_to_local(element); element_topologies[elemLocalId] = elemTopology; - graph.reserve_edges(elemLocalId, numSides); } } return areAnyElementsShells; diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.hpp index 9f6f9fb86e78..a0ec6ec7f9f4 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemElemGraphImpl.hpp @@ -297,7 +297,7 @@ struct GraphEdge {} GraphEdge(const GraphEdge&& rhs) - : vertex1(std::move(rhs.vertex1)), vertex2(std::move(rhs.vertex2)) + : vertex1(rhs.vertex1), vertex2(rhs.vertex2) {} GraphEdge& operator=(const GraphEdge&) = default; @@ -350,7 +350,45 @@ struct GraphEdge impl::LocalId vertex2; }; -typedef GraphEdge CoincidentElementConnection; +using CoincidentElementConnection = GraphEdge; + +struct GraphEdgeLessByElem1 { + bool operator()(const GraphEdge& a, const GraphEdge& b) const + { + impl::LocalId a_elem1 = a.elem1(); + impl::LocalId b_elem1 = b.elem1(); + + if (a_elem1 != b_elem1) + { + return a_elem1 < b_elem1; + } + + impl::LocalId a_elem2 = std::abs(a.elem2()); + impl::LocalId b_elem2 = std::abs(b.elem2()); + if (a_elem2 != b_elem2) + { + return a_elem2 < b_elem2; + } + + int a_side2 = a.side2(); + int b_side2 = b.side2(); + if (a_side2 != b_side2) + { + return a_side2 < b_side2; + } + else + { + return a.side1() < b.side1(); + } + } +}; + +inline +bool operator<(const GraphEdge& a, const GraphEdge& b) +{ + GraphEdgeLessByElem1 lessByElem1; + return lessByElem1(a, b); +} struct GraphEdgeLessByElem2 { bool operator()(const GraphEdge& a, const GraphEdge& b) const diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemGraphShellConnections.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemGraphShellConnections.cpp index 66f636901104..e8578433b975 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemGraphShellConnections.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/ElemGraphShellConnections.cpp @@ -96,7 +96,7 @@ bool SideConnections::does_side_have_both_connection_to_shell_and_to_nonshell(in } -void delete_non_shell_graph_edges(GraphInfo &graphInfo, const stk::mesh::impl::ElementSidePair &elementSidePair) +void fill_non_shell_graph_edges_to_delete(GraphInfo &graphInfo, const stk::mesh::impl::ElementSidePair &elementSidePair, std::vector& edgesToDelete) { for(const stk::mesh::GraphEdge& graphEdge : graphInfo.graph.get_edges_for_element_side(elementSidePair.first, elementSidePair.second)) { @@ -107,19 +107,21 @@ void delete_non_shell_graph_edges(GraphInfo &graphInfo, const stk::mesh::impl::E { if(!impl::is_local_element(graphEdge.elem2())) graphInfo.parGraphInfo.erase_parallel_info_for_graph_edge(graphEdge); - graphInfo.graph.delete_edge(graphEdge); + edgesToDelete.push_back(graphEdge); } } } void remove_graph_edges_blocked_by_shell(GraphInfo &graphInfo) { + std::vector edgesToDelete; for(size_t localId = 0; localId < graphInfo.graph.get_num_elements_in_graph(); localId++) { SideConnections sideConnectionsForElement(graphInfo.elementTopologies[localId].num_sides()); for(int side : sideConnectionsForElement.get_sides_connected_to_shell_and_nonshell(graphInfo, localId)) - delete_non_shell_graph_edges(graphInfo, stk::mesh::impl::ElementSidePair(localId, side)); + fill_non_shell_graph_edges_to_delete(graphInfo, stk::mesh::impl::ElementSidePair(localId, side), edgesToDelete); } + graphInfo.graph.delete_sorted_edges(edgesToDelete); } } diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.cpp index 2de58d56c3ee..aa3ea37716bb 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.cpp @@ -1,5 +1,6 @@ #include "GraphEdgeData.hpp" #include "ElemElemGraphImpl.hpp" +#include #include namespace stk @@ -9,43 +10,44 @@ namespace mesh void Graph::set_num_local_elements(size_t n) { - m_graphEdges.resize(n); + m_elemOffsets.resize(n+1); } void Graph::add_new_element() { - m_graphEdges.push_back(GraphEdgesForElement()); - constexpr unsigned maxNumSides = 6; - m_graphEdges.back().reserve(maxNumSides); + if (m_elemOffsets.empty()) { + m_elemOffsets.assign(1, 0); + } + m_elemOffsets.push_back(m_graphEdges.size()); } size_t Graph::get_num_elements_in_graph() const { - return m_graphEdges.size(); + return m_elemOffsets.size() - 1; } size_t Graph::get_num_edges() const { - return m_numEdges; + return m_graphEdges.size(); } size_t Graph::get_num_edges_for_element(impl::LocalId elem) const { - return m_graphEdges[elem].size(); + return m_elemOffsets[elem+1] - m_elemOffsets[elem]; } const GraphEdge & Graph::get_edge_for_element(impl::LocalId elem1, size_t index) const { - return m_graphEdges[elem1].get_edge_at_index(index); + return m_graphEdges[m_elemOffsets[elem1]+index]; } void fill_graph_edges_for_elem_side(const GraphEdgesForElement &graphEdgesForElement, int side, std::vector& edges) { for(size_t i = 0; i < graphEdgesForElement.size(); ++i) { - if(graphEdgesForElement.get_edge_at_index(i).side1() == side) + if(graphEdgesForElement[i].side1() == side) { - edges.push_back(graphEdgesForElement.get_edge_at_index(i)); + edges.push_back(graphEdgesForElement[i]); } } } @@ -53,50 +55,93 @@ void fill_graph_edges_for_elem_side(const GraphEdgesForElement &graphEdgesForEle std::vector Graph::get_edges_for_element_side(impl::LocalId elem, int side) const { std::vector edges; - fill_graph_edges_for_elem_side(m_graphEdges[elem], side, edges); + fill_graph_edges_for_elem_side(get_edges_for_element(elem), side, edges); return edges; } -const GraphEdgesForElement& Graph::get_edges_for_element(impl::LocalId elem) const +GraphEdgesForElement Graph::get_edges_for_element(impl::LocalId elem) const { - return m_graphEdges[elem]; + const unsigned begin = m_elemOffsets[elem]; + const unsigned end = m_elemOffsets[elem+1]; + return GraphEdgesForElement(&m_graphEdges[begin], &m_graphEdges[end]); } -void Graph::reserve_edges(impl::LocalId localElemId, size_t numEdges) +void Graph::set_offsets() { - m_graphEdges[localElemId].reserve(numEdges); -} + const unsigned numOffsets = m_elemOffsets.size(); + m_elemOffsets.assign(std::max(1u, numOffsets), 0); -void Graph::add_edge(const GraphEdge &graphEdge) -{ - m_graphEdges[graphEdge.elem1()].emplace_back(graphEdge); - ++m_numEdges; + impl::LocalId prevElem = impl::INVALID_LOCAL_ID; + unsigned edgeCounter = 0; + for(const GraphEdge& edge : m_graphEdges) { + impl::LocalId elem1 = edge.elem1(); + if (elem1 != prevElem) { + if (prevElem != impl::INVALID_LOCAL_ID) { + m_elemOffsets[prevElem] = edgeCounter; + } + edgeCounter = 0; + prevElem = elem1; + } + ++edgeCounter; + } + + if (prevElem != impl::INVALID_LOCAL_ID) { + m_elemOffsets[prevElem] = edgeCounter; + } + + unsigned edgeOffset = 0; + size_t numElems = m_elemOffsets.size()-1; + for(size_t i=0; i::iterator; + +void Graph::add_sorted_edges(const std::vector& graphEdges) { - m_graphEdges[elem].erase_at_index(offset); - --m_numEdges; + ThrowAssertMsg(stk::util::is_sorted_and_unique(graphEdges, GraphEdgeLessByElem1()),"Input vector 'graphEdges' is expected to be sorted-and-unique"); + if (!graphEdges.empty()) { + stk::util::insert_keep_sorted(graphEdges, m_graphEdges, GraphEdgeLessByElem1()); + set_offsets(); + } } -void Graph::delete_edge(const GraphEdge &graphEdge) +void Graph::replace_sorted_edges(std::vector& graphEdges) { - const size_t numConnected = m_graphEdges[graphEdge.elem1()].size(); - for(size_t i=0; i& edgesToDelete) { - m_numEdges -= m_graphEdges[elem].size(); - m_graphEdges[elem].clear(); + for(const GraphEdge& edgeToDelete : edgesToDelete) { + impl::LocalId elem1 = edgeToDelete.elem1(); + for(unsigned offset = m_elemOffsets[elem1]; offset < m_elemOffsets[elem1+1]; ++offset) { + GraphEdge& thisEdge = m_graphEdges[offset]; + if (thisEdge == edgeToDelete) { + thisEdge.vertex1 = impl::INVALID_LOCAL_ID; + } + } + } + + if (!edgesToDelete.empty()) { + const unsigned offset = m_elemOffsets[edgesToDelete[0].elem1()]; + m_graphEdges.erase(std::remove_if(m_graphEdges.begin()+offset, m_graphEdges.end(), + [](const GraphEdge& edge) + { return edge.vertex1 == impl::INVALID_LOCAL_ID; }), + m_graphEdges.end()); + set_offsets(); + } } void Graph::clear() { - m_numEdges = 0; m_graphEdges.clear(); + m_elemOffsets.clear(); } impl::ParallelInfo& ParallelInfoForGraphEdges::get_parallel_info_for_graph_edge(const GraphEdge& graphEdge) diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.hpp index eb3a0a4b0661..c6640523b300 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/elementGraph/GraphEdgeData.hpp @@ -35,6 +35,8 @@ #define GRAPHEDGEDATA_HPP_ #include "ElemElemGraphImpl.hpp" +#include +#include namespace stk { @@ -43,51 +45,7 @@ namespace mesh struct GraphEdge; -class GraphEdgesForElement -{ -public: - typedef std::vector::const_iterator const_iterator; - - const_iterator begin() const - { - return graphEdges.begin(); - } - const_iterator end() const - { - return graphEdges.end(); - } - - size_t size() const - { - return graphEdges.size(); - } - size_t capacity() const - { - return graphEdges.capacity(); - } - void reserve(size_t size) - { - graphEdges.reserve(size); - } - const GraphEdge & get_edge_at_index(impl::LocalId elem) const - { - return graphEdges[elem]; - } - void emplace_back(const GraphEdge &graphEdge) - { - graphEdges.push_back(graphEdge); - } - void erase_at_index(impl::LocalId elem) - { - graphEdges.erase(graphEdges.begin() + elem); - } - void clear() - { - graphEdges.clear(); - } -private: - std::vector graphEdges; -}; +using GraphEdgesForElement = PairIter; class Graph { @@ -98,23 +56,18 @@ class Graph size_t get_num_edges() const; size_t get_num_edges_for_element(impl::LocalId elem) const; const GraphEdge & get_edge_for_element(impl::LocalId elem1, size_t index) const; - const GraphEdgesForElement& get_edges_for_element(impl::LocalId elem) const; + GraphEdgesForElement get_edges_for_element(impl::LocalId elem) const; std::vector get_edges_for_element_side(impl::LocalId elem, int side) const; - void reserve_edges(impl::LocalId localElemId, size_t numEdges); - void add_edge(const GraphEdge &graphEdge); - void delete_edge_from_graph(impl::LocalId local_elem_id, int offset); - void delete_edge(const GraphEdge &graphEdge); - void delete_all_edges(impl::LocalId elem); + void add_sorted_edges(const std::vector& graphEdge); + void replace_sorted_edges(std::vector& graphEdge); + void delete_sorted_edges(const std::vector& graphEdge); void clear(); - void delete_vertex(stk::mesh::impl::LocalId id) - { - m_graphEdges.erase(m_graphEdges.begin()+id); - } private: - std::vector m_graphEdges; - size_t m_numEdges = 0; + void set_offsets(); + std::vector m_graphEdges; + std::vector m_elemOffsets; }; class ParallelInfoForGraphEdges diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp index 2939e67a3119..30bc3a86673d 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp @@ -40,7 +40,6 @@ namespace { const stk::mesh::EntityRank nodeRank = stk::topology::NODE_RANK; -const stk::mesh::EntityRank edgeRank = stk::topology::EDGE_RANK; const stk::mesh::EntityRank faceRank = stk::topology::FACE_RANK; const stk::mesh::EntityRank elemRank = stk::topology::ELEM_RANK; const stk::mesh::EntityRank constraintRank = stk::topology::CONSTRAINT_RANK; diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestGraphWithShellConnections.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestGraphWithShellConnections.cpp index 9b44890d0ab4..72901b331b4c 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestGraphWithShellConnections.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestGraphWithShellConnections.cpp @@ -59,8 +59,8 @@ class GraphWithShells : public ::testing::Test void add_two_edges(const stk::mesh::GraphEdge& graphEdge1, const stk::mesh::GraphEdge& graphEdge2) { graph.add_new_element(); - graph.add_edge(graphEdge1); - graph.add_edge(graphEdge2); + std::vector edges = {graphEdge1, graphEdge2}; + graph.add_sorted_edges(edges); } void expect_graph_has_edges_for_element(ProcAndId procAndId, const std::vector &expectedEdges) { diff --git a/packages/stk/stk_unit_tests/stk_mesh/face_creation/element_graph/UnitTestElemElemGraph.cpp b/packages/stk/stk_unit_tests/stk_mesh/face_creation/element_graph/UnitTestElemElemGraph.cpp index d978c36d0b52..2c90eb94812f 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/face_creation/element_graph/UnitTestElemElemGraph.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/face_creation/element_graph/UnitTestElemElemGraph.cpp @@ -1020,10 +1020,12 @@ TEST(ElementGraph, test_parallel_graph_info_data_structure) stk::mesh::Graph graph; graph.set_num_local_elements(2); - graph.add_edge(stk::mesh::GraphEdge(0, 4, 1, 1)); - graph.add_edge(stk::mesh::GraphEdge(1, 1, 0, 4)); stk::mesh::GraphEdge graphEdge(1, 5, -3, other_side_ord); - graph.add_edge(graphEdge); + std::vector edges = + { stk::mesh::GraphEdge(0, 4, 1, 1), + stk::mesh::GraphEdge(1, 1, 0, 4), + graphEdge }; + graph.add_sorted_edges(edges); stk::mesh::ParallelInfoForGraphEdges parallel_graph(stk::parallel_machine_rank(MPI_COMM_WORLD)); int other_proc = 1; @@ -3973,8 +3975,8 @@ TEST( ElementGraph, Hex0AddShell1Hex0Parallel ) } else if (p_rank == 1) { // Connectivity for Shell Element 3 - unsigned hex1Index = 1; - unsigned hex2Index = 0; + unsigned hex1Index = 0; + unsigned hex2Index = 1; EXPECT_EQ(2u, elemElemGraph.get_num_connected_elems(shell3)); EXPECT_EQ(1, elemElemGraph.get_connected_remote_id_and_via_side(shell3, hex1Index).side); EXPECT_EQ(0, elemElemGraph.get_connected_remote_id_and_via_side(shell3, hex2Index).side); diff --git a/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp b/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp index 62e284586ce3..f0f771ba7ece 100644 --- a/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp +++ b/packages/stk/stk_unit_tests/stk_util/ngp/UnitTestNgpVirtualFunction.cpp @@ -34,6 +34,7 @@ #include "gtest/gtest.h" #include +#include #include namespace ngp { @@ -78,6 +79,8 @@ void test_device_class() TEST(NgpDevice, virtualFunction) { + if (stk::parallel_machine_size(MPI_COMM_WORLD) > 1) GTEST_SKIP(); + test_device_class(); } diff --git a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp index 6f3012616b9b..ff1fe46cbdfb 100644 --- a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp +++ b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp @@ -42,7 +42,7 @@ //In Sierra, STK_VERSION_STRING is provided on the compile line by bake. //For Trilinos stk snapshots, the following macro definition gets populated with //the real version string by the trilinos_snapshot.sh script. -#define STK_VERSION_STRING "5.3.1-48-ga8ff7841" +#define STK_VERSION_STRING "stk_version_not_set" #endif namespace stk { From b690724b1c2fb3694fa968af40e37c792b00c43c Mon Sep 17 00:00:00 2001 From: rstumin Date: Thu, 21 Oct 2021 12:44:58 -0600 Subject: [PATCH 57/98] introduced new variable with LocalOrdinal type to remove a casting error. --- .../Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp index 264e165d9983..4d2d1d67fb9d 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp @@ -615,9 +615,9 @@ namespace MueLu { /* reverse bounds */ - temp = closestToLeftBound; + LocalOrdinal itemp = closestToLeftBound; closestToLeftBound = nEntries-closestToRghtBound; - closestToRghtBound = nEntries-temp; + closestToRghtBound = nEntries-itemp; closestToLeftBoundDist = origSorted[closestToLeftBound] - leftBound; if (closestToRghtBound==nEntries) closestToRghtBoundDist= aBigNumber; else closestToRghtBoundDist= origSorted[closestToRghtBound] - rghtBound; From aacae8b0aedeec0b8f01bb97ed5a62d66f532322 Mon Sep 17 00:00:00 2001 From: Christian Glusa Date: Thu, 21 Oct 2021 14:37:12 -0600 Subject: [PATCH 58/98] MueLu: Add test driver for hierarchical matrices --- packages/muelu/research/CMakeLists.txt | 3 +- packages/muelu/research/caglusa/Anear.mtx | 48580 ++++++++++++++++ .../muelu/research/caglusa/CMakeLists.txt | 29 + packages/muelu/research/caglusa/RHS.mtx | 1026 + packages/muelu/research/caglusa/X_ex.mtx | 1026 + packages/muelu/research/caglusa/aux.mtx | 3070 + packages/muelu/research/caglusa/aux.xml | 53 + .../muelu/research/caglusa/basismatrix.mtx | 9210 +++ packages/muelu/research/caglusa/coeffmap.mtx | 4539 ++ packages/muelu/research/caglusa/coords.mtx | 1026 + .../research/caglusa/ghosted_coeffmap.mtx | 5511 ++ .../muelu/research/caglusa/hierarchical.xml | 24 + .../research/caglusa/kernelApproximations.mtx | 27705 +++++++++ packages/muelu/research/caglusa/main.cpp | 438 + packages/muelu/research/caglusa/rowmap.mtx | 2049 + packages/muelu/research/caglusa/transfer0.mtx | 651 + packages/muelu/research/caglusa/transfer1.mtx | 1299 + packages/muelu/research/caglusa/transfer2.mtx | 2595 + packages/muelu/research/caglusa/transfer3.mtx | 5187 ++ packages/muelu/research/caglusa/transfer4.mtx | 10371 ++++ 20 files changed, 124390 insertions(+), 2 deletions(-) create mode 100644 packages/muelu/research/caglusa/Anear.mtx create mode 100644 packages/muelu/research/caglusa/CMakeLists.txt create mode 100644 packages/muelu/research/caglusa/RHS.mtx create mode 100644 packages/muelu/research/caglusa/X_ex.mtx create mode 100644 packages/muelu/research/caglusa/aux.mtx create mode 100644 packages/muelu/research/caglusa/aux.xml create mode 100644 packages/muelu/research/caglusa/basismatrix.mtx create mode 100644 packages/muelu/research/caglusa/coeffmap.mtx create mode 100644 packages/muelu/research/caglusa/coords.mtx create mode 100644 packages/muelu/research/caglusa/ghosted_coeffmap.mtx create mode 100644 packages/muelu/research/caglusa/hierarchical.xml create mode 100644 packages/muelu/research/caglusa/kernelApproximations.mtx create mode 100644 packages/muelu/research/caglusa/main.cpp create mode 100644 packages/muelu/research/caglusa/rowmap.mtx create mode 100644 packages/muelu/research/caglusa/transfer0.mtx create mode 100644 packages/muelu/research/caglusa/transfer1.mtx create mode 100644 packages/muelu/research/caglusa/transfer2.mtx create mode 100644 packages/muelu/research/caglusa/transfer3.mtx create mode 100644 packages/muelu/research/caglusa/transfer4.mtx diff --git a/packages/muelu/research/CMakeLists.txt b/packages/muelu/research/CMakeLists.txt index 92767a1dbbbd..8174bf4c973b 100644 --- a/packages/muelu/research/CMakeLists.txt +++ b/packages/muelu/research/CMakeLists.txt @@ -14,6 +14,5 @@ IF (${PACKAGE_NAME}_ENABLE_Experimental) TRIBITS_ADD_EXAMPLE_DIRECTORIES(semicoarsening) TRIBITS_ADD_EXAMPLE_DIRECTORIES(tawiesn/crada) TRIBITS_ADD_EXAMPLE_DIRECTORIES(tawiesn/aria) + TRIBITS_ADD_EXAMPLE_DIRECTORIES(caglusa) ENDIF() - - diff --git 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${PACKAGE_NAME}_ENABLE_Belos AND ${PACKAGE_NAME}_ENABLE_Ifpack2 AND ${PACKAGE_NAME}_ENABLE_Amesos2) + + TRIBITS_ADD_EXECUTABLE( + HierarchicalDriver + SOURCES main.cpp + COMM mpi + ) + + TRIBITS_ADD_TEST( + HierarchicalDriver + NAME "HierarchicalDriver-fractionalLaplacian1D" + COMM mpi + NUM_MPI_PROCS 4 + ) + + TRIBITS_COPY_FILES_TO_BINARY_DIR(caglusa_cp + SOURCE_FILES + hierarchical.xml aux.xml + rowmap.mtx coeffmap.mtx ghosted_coeffmap.mtx + Anear.mtx basismatrix.mtx kernelApproximations.mtx + transfer0.mtx transfer1.mtx transfer2.mtx transfer3.mtx transfer4.mtx + X_ex.mtx RHS.mtx + aux.mtx coords.mtx + ) + +ENDIF() diff --git a/packages/muelu/research/caglusa/RHS.mtx b/packages/muelu/research/caglusa/RHS.mtx new file mode 100644 index 000000000000..ea7f84b0567b --- /dev/null +++ b/packages/muelu/research/caglusa/RHS.mtx @@ -0,0 +1,1026 @@ +%%MatrixMarket matrix array real general +% +1023 1 +9.7656250000000000e-04 +9.7656250000000000e-04 +9.7656250000000000e-04 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Tpetra::Operator::node_type> + class HierarchicalOperator : public Tpetra::Operator { + + public: + using matrix_type = Tpetra::CrsMatrix; + using vec_type = Tpetra::MultiVector; + using map_type = Tpetra::Map; + + //! @name Constructor/Destructor + //@{ + + //! Constructor + HierarchicalOperator(const RCP >& nearField, + const RCP >& kernelApproximations, + const RCP >& basisMatrix, + std::vector > >& transferMatrices) + : + nearField_(nearField), + kernelApproximations_(kernelApproximations), + basisMatrix_(basisMatrix), + transferMatrices_(transferMatrices) + { + auto map = nearField_->getDomainMap(); + clusterCoeffMap_ = basisMatrix_->getDomainMap(); + TEUCHOS_ASSERT(map->isSameAs(*nearField_->getRangeMap())); + TEUCHOS_ASSERT(map->isSameAs(*basisMatrix->getRangeMap())); + // TEUCHOS_ASSERT(clusterCoeffMap_->isSameAs(*basisMatrix->getDomainMap())); + TEUCHOS_ASSERT(clusterCoeffMap_->isSameAs(*kernelApproximations_->getDomainMap())); + TEUCHOS_ASSERT(clusterCoeffMap_->isSameAs(*kernelApproximations_->getRangeMap())); + TEUCHOS_ASSERT(clusterCoeffMap_->isSameAs(*kernelApproximations_->getRowMap())); + + for (size_t i = 0; iisSameAs(*transferMatrices_[i]->getDomainMap())); + TEUCHOS_ASSERT(clusterCoeffMap_->isSameAs(*transferMatrices_[i]->getRangeMap())); + } + + allocateMemory(1); + } + + //! Returns the Tpetra::Map object associated with the domain of this operator. + Teuchos::RCP > getDomainMap() const { + return nearField_->getDomainMap(); + } + + //! Returns the Tpetra::Map object associated with the range of this operator. + Teuchos::RCP > getRangeMap() const { + return nearField_->getRangeMap(); + } + + //! Returns in Y the result of a Tpetra::Operator applied to a Tpetra::MultiVector X. + /*! + \param[in] X - Tpetra::MultiVector of dimension NumVectors to multiply with matrix. + \param[out] Y -Tpetra::MultiVector of dimension NumVectors containing result. + */ + void apply(const Tpetra::MultiVector& X, + Tpetra::MultiVector& Y, + Teuchos::ETransp mode = Teuchos::NO_TRANS, + Scalar alpha = Teuchos::ScalarTraits::one(), + Scalar beta = Teuchos::ScalarTraits::zero()) const { + const Scalar one = Teuchos::ScalarTraits::one(); + + allocateMemory(X.getNumVectors()); + + // near field + nearField_->apply(X, Y, mode, alpha, beta); + + // auto out = Teuchos::getFancyOStream (Teuchos::rcpFromRef (std::cerr)); + // Y.describe(*out, Teuchos::VERB_EXTREME); + + // upward pass + basisMatrix_->apply(X, *coefficients_, Teuchos::TRANS); + + bool flip = true; + for (int i = Teuchos::as(transferMatrices_.size())-1; i>=0; i--) + if (flip) { + coefficients2_->assign(*coefficients_); + transferMatrices_[i]->apply(*coefficients_, *coefficients2_, Teuchos::NO_TRANS, one, one); + flip = false; + } else { + coefficients_->assign(*coefficients2_); + transferMatrices_[i]->apply(*coefficients2_, *coefficients_, Teuchos::NO_TRANS, one, one); + flip = true; + } + + if (flip) + kernelApproximations_->apply(*coefficients_, *coefficients2_, mode, alpha); + else + kernelApproximations_->apply(*coefficients2_, *coefficients_, mode, alpha); + // coefficients2_->describe(*out, Teuchos::VERB_EXTREME); + + // downward pass + for (size_t i = 0; iassign(*coefficients2_); + transferMatrices_[i]->apply(*coefficients2_, *coefficients_, Teuchos::TRANS, one, one); + flip = false; + } else { + coefficients2_->assign(*coefficients_); + transferMatrices_[i]->apply(*coefficients_, *coefficients2_, Teuchos::TRANS, one, one); + flip = true; + } + if (flip) + basisMatrix_->apply(*coefficients2_, Y, Teuchos::NO_TRANS, one, one); + else + basisMatrix_->apply(*coefficients_, Y, Teuchos::NO_TRANS, one, one); + } + + + RCP > restrict(const RCP& P) { + + RCP temp = rcp(new matrix_type(nearField_->getRowMap(), 0)); + MatrixMatrix::Multiply(*nearField_, false, *P, false, *temp); + RCP newNearField = rcp(new matrix_type(P->getDomainMap(), 0)); + MatrixMatrix::Multiply(*P, true, *temp, false, *newNearField); + + RCP newBasisMatrix = rcp(new matrix_type(P->getDomainMap(), clusterCoeffMap_, 0)); + MatrixMatrix::Multiply(*P, true, *basisMatrix_, false, *newBasisMatrix); + + // auto out = Teuchos::getFancyOStream (Teuchos::rcpFromRef (std::cerr)); + // clusterCoeffMap_->describe(*out, Teuchos::VERB_EXTREME); + // clusterCoeffMap_->getComm()->barrier(); + // newBasisMatrix->getColMap()->describe(*out, Teuchos::VERB_EXTREME); + + return rcp(new HierarchicalOperator(newNearField, kernelApproximations_, newBasisMatrix, transferMatrices_)); + } + + double getCompression() { + size_t nnz = (nearField_->getGlobalNumEntries() + + kernelApproximations_->getGlobalNumEntries() + + basisMatrix_->getGlobalNumEntries()); + for (size_t i = 0; i < transferMatrices_.size(); i++) + nnz += transferMatrices_[i]->getGlobalNumEntries(); + return Teuchos::as(nnz) / (getDomainMap()->getGlobalNumElements()*getDomainMap()->getGlobalNumElements()); + } + + private: + + void allocateMemory(size_t numVectors) const { + if (coefficients_.is_null() || coefficients_->getNumVectors() != numVectors) { + coefficients_ = rcp(new vec_type(clusterCoeffMap_, numVectors)); + coefficients2_ = rcp(new vec_type(clusterCoeffMap_, numVectors)); + } + } + + RCP nearField_; + RCP kernelApproximations_; + RCP basisMatrix_; + std::vector > transferMatrices_; + RCP clusterCoeffMap_; + mutable RCP coefficients_, coefficients2_; + }; + +} + +namespace Xpetra { + + template + class HierarchicalOperator : public Xpetra::Operator { + + public: + using tHOp = Tpetra::HierarchicalOperator; + using map_type = Map; + using vec_type = MultiVector; + using matrix_type = Matrix; + + //! @name Constructor/Destructor + //@{ + + //! Constructor + HierarchicalOperator(const RCP& op) : op_(op) { } + + HierarchicalOperator(const RCP& nearField, + const RCP& kernelApproximations, + const RCP& basisMatrix, + std::vector >& transferMatrices) { + #include "MueLu_UseShortNames.hpp" + + std::vector > tTransferMatrices; + for (size_t i = 0; i(rcp_dynamic_cast(transferMatrices[i])->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(); + tTransferMatrices.push_back(transferT); + } + + op_ = rcp(new tHOp(rcp_dynamic_cast(rcp_dynamic_cast(nearField)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + rcp_dynamic_cast(rcp_dynamic_cast(kernelApproximations)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + rcp_dynamic_cast(rcp_dynamic_cast(basisMatrix)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + tTransferMatrices)); + } + + //! Returns the Tpetra::Map object associated with the domain of this operator. + Teuchos::RCP getDomainMap() const { + return toXpetra(op_->getDomainMap()); + } + + //! Returns the Tpetra::Map object associated with the range of this operator. + Teuchos::RCP getRangeMap() const { + return toXpetra(op_->getRangeMap()); + } + + //! \brief Computes the operator-multivector application. + /*! Loosely, performs \f$Y = \alpha \cdot A^{\textrm{mode}} \cdot X + \beta \cdot Y\f$. However, the details of operation + vary according to the values of \c alpha and \c beta. Specifically + - if beta == 0, apply() must overwrite \c Y, so that any values in \c Y (including NaNs) are ignored. + - if alpha == 0, apply() may short-circuit the operator, so that any values in \c X (including NaNs) are ignored. + */ + void apply (const vec_type& X, vec_type& Y, + Teuchos::ETransp mode = Teuchos::NO_TRANS, + Scalar alpha = Teuchos::ScalarTraits::one(), + Scalar beta = Teuchos::ScalarTraits::zero()) const { + op_->apply(Xpetra::toTpetra(X), Xpetra::toTpetra(Y), mode, alpha, beta); + } + + //! Compute a residual R = B - (*this) * X + void residual(const vec_type & X, + const vec_type & B, + vec_type& R) const { + Tpetra::Details::residual(*op_, toTpetra(X), toTpetra(B), toTpetra(R)); + } + + RCP > restrict(const RCP& P) { + #include "MueLu_UseShortNames.hpp" + return rcp(new HierarchicalOperator(op_->restrict(rcp_dynamic_cast(rcp_dynamic_cast(P)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst()))); + } + + double getCompression() { + return op_->getCompression(); + } + + private: + RCP op_; + }; +} + + +template +int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib lib, int argc, char *argv[]) { + #include "MueLu_UseShortNames.hpp" + + std::string xmlHierachical = "hierarchical.xml"; + std::string xmlAuxHierarchy = "aux.xml"; + + switch (clp.parse(argc, argv)) { + case Teuchos::CommandLineProcessor::PARSE_HELP_PRINTED: return EXIT_SUCCESS; break; + case Teuchos::CommandLineProcessor::PARSE_ERROR: + case Teuchos::CommandLineProcessor::PARSE_UNRECOGNIZED_OPTION: return EXIT_FAILURE; break; + case Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL: break; + } + + using HOp = Xpetra::HierarchicalOperator; + + RCP fancy = Teuchos::fancyOStream(Teuchos::rcpFromRef(std::cout)); + Teuchos::FancyOStream& out = *fancy; + out.setOutputToRootOnly(0); + bool success = true; + const Scalar one = Teuchos::ScalarTraits::one(); + + RCP< const Teuchos::Comm > comm = Teuchos::DefaultComm::getComm(); + + Teuchos::ParameterList hierachicalParams; + Teuchos::updateParametersFromXmlFileAndBroadcast(xmlHierachical, Teuchos::Ptr(&hierachicalParams), *comm); + + // row, domain and range map of the operator + auto map = Xpetra::IO::ReadMap(hierachicalParams.get("map"), lib, comm); + // 1-to-1 map for the cluster coefficients + auto clusterCoeffMap = Xpetra::IO::ReadMap(hierachicalParams.get("coefficient map"), lib, comm); + // overlapping map for the cluster coefficients + auto ghosted_clusterCoeffMap = Xpetra::IO::ReadMap(hierachicalParams.get("ghosted coefficient map"), lib, comm); + + // near field interactions + auto nearField = Xpetra::IO::Read(hierachicalParams.get("near field matrix"), map); + + // far field basis expansion coefficients + auto basisMatrix = Xpetra::IO::Read(hierachicalParams.get("basis expansion coefficient matrix"), map, clusterCoeffMap, clusterCoeffMap, map); + // far field interactions + auto kernelApproximations = Xpetra::IO::Read(hierachicalParams.get("far field interaction matrix"), clusterCoeffMap, ghosted_clusterCoeffMap, clusterCoeffMap, clusterCoeffMap); + + auto transfersList = hierachicalParams.sublist("shift coefficient matrices"); + std::vector > transferMatrices; + for (int i = 0; i < transfersList.numParams(); i++) { + std::string filename = transfersList.get(std::to_string(i)); + auto transfer = Xpetra::IO::Read(filename, clusterCoeffMap, clusterCoeffMap, clusterCoeffMap, clusterCoeffMap); + transferMatrices.push_back(transfer); + } + + auto op = rcp(new HOp(nearField, kernelApproximations, basisMatrix, transferMatrices)); + + out << "Compression: " << op->getCompression() << " of dense matrix."<< std::endl; + + auto X_ex = Xpetra::IO::ReadMultiVector(hierachicalParams.get("exact solution"), map); + auto RHS = Xpetra::IO::ReadMultiVector(hierachicalParams.get("right-hand side"), map); + auto X = MultiVectorFactory::Build(map, 1); + + { + op->apply(*X_ex, *X); + + // Xpetra::IO::Write("X.mtx", *X); + X->update(one, *RHS, -one); + out << "|op*X_ex - RHS| = " << X->getVector(0)->norm2() << std::endl; + // Xpetra::IO::Write("diff.mtx", *X); + } + + { + op->apply(*X_ex, *X, Teuchos::NO_TRANS, -one); + + // Xpetra::IO::Write("X2.mtx", *X); + X->update(one, *RHS, one); + out << "|(-op)*X_ex + RHS| = " << X->getVector(0)->norm2() << std::endl; + // Xpetra::IO::Write("diff2.mtx", *X); + } + + { + op->apply(*X_ex, *X, Teuchos::TRANS, -one); + + // Xpetra::IO::Write("X2.mtx", *X); + X->update(one, *RHS, one); + out << "|(-op^T)*X_ex + RHS| = " << X->getVector(0)->norm2() << std::endl; + // Xpetra::IO::Write("diff2.mtx", *X); + } + + { + // Solve linear system using unpreconditioned Krylov method + + using MV = typename HOp::vec_type; + using OP = Belos::OperatorT; + + RCP belosOp = rcp(new Belos::XpetraOp(op)); + RCP > belosProblem = rcp(new Belos::LinearProblem(belosOp, X, RHS)); + + std::string belosType = "Pseudoblock CG"; + RCP belosList = Teuchos::parameterList(); + belosList->set("Maximum Iterations", 1000); // Maximum number of iterations allowed + belosList->set("Convergence Tolerance", 1e-5); // Relative convergence tolerance requested + belosList->set("Verbosity", Belos::Errors + Belos::Warnings + Belos::StatusTestDetails); + belosList->set("Output Frequency", 1); + belosList->set("Output Style", Belos::Brief); + + bool set = belosProblem->setProblem(); + if (set == false) { + throw MueLu::Exceptions::RuntimeError("ERROR: Belos::LinearProblem failed to set up correctly!"); + } + + // Create an iterative solver manager + Belos::SolverFactory solverFactory; + RCP< Belos::SolverManager > solver = solverFactory.create(belosType, belosList); + solver->setProblem(belosProblem); + + // Perform solve + Belos::ReturnType ret = solver->solve(); + int numIts = solver->getNumIters(); + + // Get the number of iterations for this solve. + out << "Number of iterations performed for this solve: " << numIts << std::endl; + + // Xpetra::IO::Write("X.mtx", *X); + X->update(one, *X_ex, -one); + out << "|X-X_ex| = " << X->getVector(0)->norm2() << std::endl; + + success &= (ret == Belos::Converged); + + } + + // { + // // Solve linear system using a AMG preconditioned Krylov method + + // auto auxOp = Xpetra::IO::Read(hierachicalParams.get("auxiliary operator"), map); + // auto coords = Xpetra::IO::coordinateType,LocalOrdinal,GlobalOrdinal,Node>::ReadMultiVector(hierachicalParams.get("coordinates"), map); + + // Teuchos::ParameterList auxParams; + // Teuchos::updateParametersFromXmlFileAndBroadcast(xmlAuxHierarchy, Teuchos::Ptr(&auxParams), *comm); + // auxParams.sublist("user data").set("Coordinates", coords); + + // auto auxH = MueLu::CreateXpetraPreconditioner(auxOp, auxParams); + + // auto H = rcp(new Hierarchy()); + // RCP lvl = H->GetLevel(0); + // lvl->Set("A", rcp_dynamic_cast(op)); + // for(int lvlNo = 1; lvlNoGetNumLevels(); lvlNo++) { + // H->AddNewLevel(); + // RCP auxLvl = auxH->GetLevel(lvlNo); + // RCP fineLvl = H->GetLevel(lvlNo-1); + // RCP lvl = H->GetLevel(lvlNo); + // auto P = auxLvl->Get >("P"); + // lvl->Set("P", P); + + // auto fineA = rcp_dynamic_cast(fineLvl->Get >("A")); + // auto coarseA = fineA->restrict(P); + // lvl->Set("A", rcp_dynamic_cast(coarseA)); + // } + + // RCP mueLuFactory = rcp(new ParameterListInterpreter(auxParams,op->getDomainMap()->getComm())); + // H->setlib(op->getDomainMap()->lib()); + // H->SetProcRankVerbose(op->getDomainMap()->getComm()->getRank()); + // mueLuFactory->SetupHierarchy(*H); + + // } + + return ( success ? EXIT_SUCCESS : EXIT_FAILURE ); +} //main + +//- -- -------------------------------------------------------- +#define MUELU_AUTOMATIC_TEST_ETI_NAME main_ +#include "MueLu_Test_ETI.hpp" + +int main(int argc, char *argv[]) { + return Automatic_Test_ETI(argc,argv); +} diff --git a/packages/muelu/research/caglusa/rowmap.mtx b/packages/muelu/research/caglusa/rowmap.mtx new file mode 100644 index 000000000000..a89e8c64e66b --- /dev/null +++ b/packages/muelu/research/caglusa/rowmap.mtx @@ -0,0 +1,2049 @@ +%%MatrixMarket matrix array integer general +% +2046 1 +0 +0 +1 +0 +2 +0 +3 +0 +4 +0 +5 +0 +6 +0 +7 +0 +8 +0 +9 +0 +10 +0 +11 +0 +12 +0 +13 +0 +14 +0 +15 +0 +16 +0 +17 +0 +18 +0 +19 +0 +20 +0 +21 +0 +22 +0 +23 +0 +24 +0 +25 +0 +26 +0 +27 +0 +28 +0 +29 +0 +30 +0 +31 +0 +32 +0 +33 +0 +34 +0 +35 +0 +36 +0 +37 +0 +38 +0 +39 +0 +40 +0 +41 +0 +42 +0 +43 +0 +44 +0 +45 +0 +46 +0 +47 +0 +48 +0 +49 +0 +50 +0 +51 +0 +52 +0 +53 +0 +54 +0 +55 +0 +56 +0 +57 +0 +58 +0 +59 +0 +60 +0 +61 +0 +62 +0 +63 +0 +64 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+2247 2255 1.226433507083489e-01 +2247 2256 -7.898266143120435e-02 +2247 2257 -2.040533508482650e-01 +2247 2258 -3.205658723744574e-02 +2247 2259 1.582637096187322e-01 +2247 2260 -1.173436103509271e-01 +2247 2261 3.440881837090131e-02 +2247 2262 4.551820017945861e-01 +2247 2263 9.500818362211275e-01 +2247 2264 7.751613393474791e-01 +2247 2265 -3.524913251505098e-02 +2247 2266 -1.763260094650470e-01 +2247 2267 1.714825278878462e-01 +2247 2268 -6.675829549002529e-02 +2248 2251 2.163688115667714e-02 +2248 2252 -5.220965998265751e-02 +2248 2253 4.636253866511447e-02 +2248 2254 6.873636058250207e-03 +2248 2255 -7.297122858953514e-02 +2248 2256 4.361555150731784e-02 +2248 2257 1.016285359894895e-01 +2248 2258 1.413095968572884e-02 +2248 2259 -6.347065826161916e-02 +2248 2260 5.417647031984923e-02 +2248 2261 -1.467336790749558e-02 +2248 2262 -1.533011412395509e-01 +2248 2263 -1.151051233747923e-01 +2248 2264 4.718042883535921e-01 +2248 2265 1.003092729754152e+00 +2248 2266 4.009285655348384e-01 +2248 2267 -2.866596804778884e-01 +2248 2268 1.012997478615632e-01 +2249 2251 -1.242564713429316e-02 +2249 2252 2.983957599313233e-02 +2249 2253 -2.623252505678690e-02 +2249 2254 -3.826530502172932e-03 +2249 2255 3.967378200088001e-02 +2249 2256 -2.296833469170512e-02 +2249 2257 -5.147043285304104e-02 +2249 2258 -6.878577509575953e-03 +2249 2259 3.008346487896668e-02 +2249 2260 -2.675090448249389e-02 +2249 2261 7.073583005506205e-03 +2249 2262 6.969985820549054e-02 +2249 2263 4.603749937464054e-02 +2249 2264 -1.341009959651868e-01 +2249 2265 2.709112098464875e-02 +2249 2266 7.978124774257940e-01 +2249 2267 8.496052943251796e-01 +2249 2268 -1.833267155555124e-01 +2250 2251 4.056073820312835e-03 +2250 2252 -9.719999626669617e-03 +2250 2253 8.507818082536710e-03 +2250 2254 1.232479383922180e-03 +2250 2255 -1.265402077883358e-02 +2250 2256 7.233284760851675e-03 +2250 2257 1.597136003720089e-02 +2250 2258 2.104266184682774e-03 +2250 2259 -9.119197464263174e-03 +2250 2260 8.224868937523154e-03 +2250 2261 -2.156636620475577e-03 +2250 2262 -2.084168245043927e-02 +2250 2263 -1.325717275337946e-02 +2250 2264 3.581468700212909e-02 +2250 2265 -6.054059071083845e-03 +2250 2266 -8.784171983802572e-02 +2250 2267 3.337714682644796e-01 +2250 2268 1.121496109519649e+00 From 77a45dd9856da83f343186974e351e279e608328 Mon Sep 17 00:00:00 2001 From: rstumin Date: Fri, 22 Oct 2021 00:23:18 -0600 Subject: [PATCH 59/98] one more casting fix --- .../src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp index 4d2d1d67fb9d..84ff4905b2d4 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_SaPFactory_def.hpp @@ -633,7 +633,7 @@ namespace MueLu { while ((Teuchos::ScalarTraits::magnitude(rowSumDeviation) > Teuchos::ScalarTraits::magnitude(as(1.e-10)*rsumTarget))){ // && ( (closestToLeftBound < nEntries ) || (closestToRghtBound < nEntries))) { if (closestToRghtBound != closestToLeftBound) - delta = rowSumDeviation/ (closestToRghtBound - closestToLeftBound); + delta = rowSumDeviation/ as(closestToRghtBound - closestToLeftBound); else delta = aBigNumber; if (Teuchos::ScalarTraits::magnitude(closestToLeftBoundDist) <= Teuchos::ScalarTraits::magnitude(closestToRghtBoundDist)) { From 511cf50efc9320939f0725713ef20bb305ad3f00 Mon Sep 17 00:00:00 2001 From: Steve Skutnik Date: Fri, 22 Oct 2021 16:45:27 -0400 Subject: [PATCH 60/98] ML: Fix socket references for Windows builds --- packages/ml/src/CMakeLists.txt | 4 ++++ packages/ml/src/MLAPI/MLAPI_Workspace.cpp | 4 ++++ packages/ml/src/Utils/ml_epetra_utils.cpp | 5 ++++- 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/packages/ml/src/CMakeLists.txt b/packages/ml/src/CMakeLists.txt index 122c357215dd..4201ff7553ce 100644 --- a/packages/ml/src/CMakeLists.txt +++ b/packages/ml/src/CMakeLists.txt @@ -329,3 +329,7 @@ TRIBITS_ADD_LIBRARY( HEADERS ${HEADERS} SOURCES ${SOURCES} ) + +if (WIN32) + target_link_libraries (ml PUBLIC ws2_32) +endif () diff --git a/packages/ml/src/MLAPI/MLAPI_Workspace.cpp b/packages/ml/src/MLAPI/MLAPI_Workspace.cpp index adea81e4e75d..f58e7dda54da 100644 --- a/packages/ml/src/MLAPI/MLAPI_Workspace.cpp +++ b/packages/ml/src/MLAPI/MLAPI_Workspace.cpp @@ -16,6 +16,10 @@ #ifdef _MSC_VER #include "winprocess.h" #endif +#include +#ifdef _WIN32 +#include +#endif namespace MLAPI { diff --git a/packages/ml/src/Utils/ml_epetra_utils.cpp b/packages/ml/src/Utils/ml_epetra_utils.cpp index 34fab14d69da..70f81f7ef76f 100644 --- a/packages/ml/src/Utils/ml_epetra_utils.cpp +++ b/packages/ml/src/Utils/ml_epetra_utils.cpp @@ -43,6 +43,10 @@ #ifdef _MSC_VER # include "winprocess.h" #endif +#include +#ifdef _WIN32 +#include +#endif #ifdef HAVE_ML_TEUCHOS using namespace Teuchos; @@ -52,7 +56,6 @@ using namespace Teuchos; #include "EpetraExt_MatrixMatrix.h" #endif - // ====================================================================== typedef struct { From 71a927685106eaa07e3f68d49c4e46e2ad10e56e Mon Sep 17 00:00:00 2001 From: Steve Skutnik Date: Fri, 22 Oct 2021 12:08:33 -0400 Subject: [PATCH 61/98] Fix TeuchosParameterlist Windows build configuration Corrects an error in the target_link_libraries macro for TeuchosParameterlist such that it can correctly target the Windows socket library (ws2_w32.a) --- packages/teuchos/parameterlist/src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/teuchos/parameterlist/src/CMakeLists.txt b/packages/teuchos/parameterlist/src/CMakeLists.txt index 2374fe597f79..e5db66fa4013 100644 --- a/packages/teuchos/parameterlist/src/CMakeLists.txt +++ b/packages/teuchos/parameterlist/src/CMakeLists.txt @@ -25,5 +25,5 @@ TRIBITS_ADD_LIBRARY( ) if (WIN32) - target_link_libraries (teuchosparameterlist ws2_32) + target_link_libraries (teuchosparameterlist PUBLIC ws2_32) endif () From d3a9411ad1ccdaa4a87de7ddd042f9d0025fcbed Mon Sep 17 00:00:00 2001 From: Steve Skutnik Date: Fri, 22 Oct 2021 16:53:44 -0400 Subject: [PATCH 62/98] Fix invalid enum reference for Thyra SpmdVectorDefaultBase --- .../adapter_support/Thyra_SpmdVectorDefaultBase_def.hpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/thyra/core/src/support/operator_vector/adapter_support/Thyra_SpmdVectorDefaultBase_def.hpp b/packages/thyra/core/src/support/operator_vector/adapter_support/Thyra_SpmdVectorDefaultBase_def.hpp index 3213c3a961ec..560f819c4228 100644 --- a/packages/thyra/core/src/support/operator_vector/adapter_support/Thyra_SpmdVectorDefaultBase_def.hpp +++ b/packages/thyra/core/src/support/operator_vector/adapter_support/Thyra_SpmdVectorDefaultBase_def.hpp @@ -57,7 +57,7 @@ #include "Teuchos_Assert.hpp" #include "Teuchos_dyn_cast.hpp" #include "Teuchos_Assert.hpp" - +#include "Teuchos_Range1D.hpp" namespace Thyra { @@ -200,7 +200,7 @@ void SpmdVectorDefaultBase::acquireDetachedVectorViewImpl( #ifdef THYRA_DEBUG TEUCHOS_ASSERT(sub_vec); #endif - if( rng_in == Range1D::Invalid ) { + if( rng_in == Range1D::INVALID ) { // Just return an null view *sub_vec = RTOpPack::ConstSubVectorView(); return; @@ -270,7 +270,7 @@ void SpmdVectorDefaultBase::acquireNonconstDetachedVectorViewImpl( #ifdef THYRA_DEBUG TEUCHOS_ASSERT(sub_vec); #endif - if( rng_in == Range1D::Invalid ) { + if( rng_in == Range1D::INVALID ) { // Just return an null view *sub_vec = RTOpPack::SubVectorView(); return; From d02666c64de6819d0e0faa049db907fe82494852 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Fri, 22 Oct 2021 16:29:53 -0600 Subject: [PATCH 63/98] shylubasker: remove deprecated code --- packages/shylu/shylu_node/basker/src/shylubasker_def.hpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp b/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp index b5f973fb1248..8a2da3fd7c5a 100644 --- a/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp +++ b/packages/shylu/shylu_node/basker/src/shylubasker_def.hpp @@ -2202,11 +2202,7 @@ namespace BaskerNS //Next test if Kokkos has that many threads! //This is a common mistake in mpi-based apps #ifdef KOKKOS_ENABLE_OPENMP - #ifdef KOKKOS_ENABLE_DEPRECATED_CODE - int check_value = Kokkos::OpenMP::max_hardware_threads(); - #else int check_value = Kokkos::OpenMP::impl_max_hardware_threads(); - #endif if(nthreads > check_value) { BASKER_ASSERT(0==1, "Basker SetThreads Assert: Number of thread not available"); From 06d8083a598f714c7cab35bb02203b0a1dfbddfc Mon Sep 17 00:00:00 2001 From: Jennifer Loe Date: Mon, 25 Oct 2021 08:43:33 -0600 Subject: [PATCH 64/98] Belos: Kokkos solvers adapter (#9827) * Added Belos-Kokkos Adapter and tests. --- packages/belos/CMakeLists.txt | 4 + packages/belos/cmake/Belos_config.h.in | 3 + packages/belos/cmake/Dependencies.cmake | 2 +- packages/belos/kokkos/CMakeLists.txt | 4 + .../kokkos/example/BlockCGKokkosExFile.cpp | 215 + .../kokkos/example/BlockGmresKokkosExFile.cpp | 223 + packages/belos/kokkos/example/CMakeLists.txt | 23 + packages/belos/kokkos/example/bcsstk12.mtx | 17874 ++++++++++++++++ .../belos/kokkos/src/BelosKokkosAdapter.hpp | 686 + packages/belos/kokkos/src/CMakeLists.txt | 39 + .../kokkos/test/BelosKokkosMVOPTester.hpp | 1610 ++ packages/belos/kokkos/test/CMakeLists.txt | 8 + packages/belos/kokkos/test/KokkosMVOPTest.cpp | 553 + 13 files changed, 21243 insertions(+), 1 deletion(-) create mode 100644 packages/belos/kokkos/CMakeLists.txt create mode 100644 packages/belos/kokkos/example/BlockCGKokkosExFile.cpp create mode 100644 packages/belos/kokkos/example/BlockGmresKokkosExFile.cpp create mode 100644 packages/belos/kokkos/example/CMakeLists.txt create mode 100644 packages/belos/kokkos/example/bcsstk12.mtx create mode 100644 packages/belos/kokkos/src/BelosKokkosAdapter.hpp create mode 100644 packages/belos/kokkos/src/CMakeLists.txt create mode 100644 packages/belos/kokkos/test/BelosKokkosMVOPTester.hpp create mode 100644 packages/belos/kokkos/test/CMakeLists.txt create mode 100644 packages/belos/kokkos/test/KokkosMVOPTest.cpp diff --git a/packages/belos/CMakeLists.txt b/packages/belos/CMakeLists.txt index 3f82f7e5de80..1e6b02c137dc 100644 --- a/packages/belos/CMakeLists.txt +++ b/packages/belos/CMakeLists.txt @@ -112,6 +112,10 @@ IF (Belos_ENABLE_Tpetra) ADD_SUBDIRECTORY(tpetra) ENDIF() +IF (Belos_ENABLE_KokkosKernels) + ADD_SUBDIRECTORY(kokkos) +ENDIF() + IF (Belos_ENABLE_Xpetra) ADD_SUBDIRECTORY(xpetra) ENDIF() diff --git a/packages/belos/cmake/Belos_config.h.in b/packages/belos/cmake/Belos_config.h.in index 58033a25f870..a0e404b5ff0c 100644 --- a/packages/belos/cmake/Belos_config.h.in +++ b/packages/belos/cmake/Belos_config.h.in @@ -13,6 +13,9 @@ /* Define if want to build with EpetraExt enabled */ #cmakedefine HAVE_BELOS_EPETRAEXT +/* Define if want to build with KokkosKernels enabled */ +#cmakedefine HAVE_BELOS_KOKKOSKERNELS + /* Define if want to build with ML enabled */ #cmakedefine HAVE_BELOS_ML diff --git a/packages/belos/cmake/Dependencies.cmake b/packages/belos/cmake/Dependencies.cmake index 532176ceebff..ea5f6a8a3df6 100644 --- a/packages/belos/cmake/Dependencies.cmake +++ b/packages/belos/cmake/Dependencies.cmake @@ -1,5 +1,5 @@ SET(LIB_REQUIRED_DEP_PACKAGES Teuchos) -SET(LIB_OPTIONAL_DEP_PACKAGES Epetra Tpetra Xpetra Thyra AztecOO Triutils) +SET(LIB_OPTIONAL_DEP_PACKAGES Epetra Tpetra Xpetra Thyra AztecOO Triutils KokkosKernels) SET(TEST_REQUIRED_DEP_PACKAGES) SET(TEST_OPTIONAL_DEP_PACKAGES Galeri Triutils EpetraExt Ifpack ML AztecOO) SET(LIB_REQUIRED_DEP_TPLS) diff --git a/packages/belos/kokkos/CMakeLists.txt b/packages/belos/kokkos/CMakeLists.txt new file mode 100644 index 000000000000..635ad11fded6 --- /dev/null +++ b/packages/belos/kokkos/CMakeLists.txt @@ -0,0 +1,4 @@ +ADD_SUBDIRECTORY(src) + +TRIBITS_ADD_TEST_DIRECTORIES(test) +TRIBITS_ADD_EXAMPLE_DIRECTORIES(example) diff --git a/packages/belos/kokkos/example/BlockCGKokkosExFile.cpp b/packages/belos/kokkos/example/BlockCGKokkosExFile.cpp new file mode 100644 index 000000000000..47f7887ee3b4 --- /dev/null +++ b/packages/belos/kokkos/example/BlockCGKokkosExFile.cpp @@ -0,0 +1,215 @@ +//@HEADER +// ************************************************************************ +// +// Belos: Block Linear Solvers Package +// Copyright 2004 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +//@HEADER +// +// This driver reads a problem from a file, which must be in Matrix Market (*.mtx). +// The problem right-hand side will be generated randomly. +// +// NOTE: No preconditioner is used in this example. +// +#include "BelosConfigDefs.hpp" +#include "BelosLinearProblem.hpp" +#include "BelosBlockCGSolMgr.hpp" +#include "BelosOutputManager.hpp" + +#include "Teuchos_CommandLineProcessor.hpp" +#include "Teuchos_ParameterList.hpp" +#include "Teuchos_StandardCatchMacros.hpp" + +#include "BelosKokkosAdapter.hpp" +#include "KokkosKernels_IOUtils.hpp" +#ifdef HAVE_MPI + #include +#endif + +int main(int argc, char *argv[]) { + +#ifdef HAVE_MPI + MPI_Init(&argc,&argv); +#endif + +bool success = true; + Kokkos::initialize(); + { + + typedef double ST; + typedef int OT; + typedef Kokkos::DefaultExecutionSpace EXSP; + typedef Teuchos::ScalarTraits SCT; + typedef SCT::magnitudeType MT; + typedef Belos::KokkosMultiVec MV; + typedef Belos::KokkosCrsOperator OP; + typedef Belos::MultiVec KMV; + typedef Belos::Operator KOP; + typedef Belos::MultiVecTraits MVT; + typedef Belos::OperatorTraits OPT; + + using Teuchos::ParameterList; + using Teuchos::RCP; + using Teuchos::rcp; + using Teuchos::rcpFromRef; + +bool verbose = true; +try { + int frequency = 25; // frequency of status test output. + int numrhs = 1; // number of right-hand sides to solve for + int maxiters = -1; // maximum number of iterations allowed per linear system + bool expresidual = false; // use explicit residual + std::string filename("bcsstk12.mtx"); // example matrix + MT tol = 1.0e-5; // relative residual tolerance + + Teuchos::CommandLineProcessor cmdp(false,true); + cmdp.setOption("verbose","quiet",&verbose,"Print messages and results."); + cmdp.setOption("expres","impres",&expresidual,"Use explicit residual throughout."); + cmdp.setOption("frequency",&frequency,"Solvers frequency for printing residuals (#iters)."); + cmdp.setOption("filename",&filename,"Filename for test matrix. Acceptable file extensions: *.hb,*.mtx,*.triU,*.triS"); + cmdp.setOption("tol",&tol,"Relative residual tolerance used by Gmres solver."); + cmdp.setOption("num-rhs",&numrhs,"Number of right-hand sides to be solved for."); + cmdp.setOption("max-iters",&maxiters,"Maximum number of iterations per linear system (-1 = adapted to problem/block size)."); + + if (cmdp.parse(argc,argv) != Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL) { + return -1; + } + if (!verbose) + frequency = -1; // reset frequency if test is not verbose + + // Read in a matrix Market file and use it to test the Kokkos Operator. + KokkosSparse::CrsMatrix crsMat = + KokkosKernels::Impl::read_kokkos_crst_matrix>(filename.c_str()); + RCP> A = + rcp(new Belos::KokkosCrsOperator(crsMat)); + OT numRows = crsMat.numRows(); + + Teuchos::RCP X = Teuchos::rcp( new MV(numRows, numrhs) ); + X->MvRandom(); + Teuchos::RCP B = Teuchos::rcp( new MV(numRows, numrhs) ); + OPT::Apply(*A,*X,*B); + X->MvInit(0.0); + + // + // ********Other information used by block solver*********** + // *****************(can be user specified)****************** + // + const int NumGlobalElements = B->GetGlobalLength(); + if (maxiters == -1) + maxiters = NumGlobalElements - 1; // maximum number of iterations to run + + ParameterList belosList; + belosList.set( "Maximum Iterations", maxiters ); // Maximum number of iterations allowed + belosList.set( "Convergence Tolerance", tol ); // Relative convergence tolerance requested + belosList.set( "Explicit Residual Test", expresidual); // use explicit residual + + if (verbose) { + belosList.set( "Verbosity", Belos::Errors + Belos::Warnings + + Belos::StatusTestDetails + Belos::FinalSummary + Belos::TimingDetails); + if (frequency > 0) + belosList.set( "Output Frequency", frequency ); + } + else + belosList.set( "Verbosity", Belos::Errors + Belos::Warnings ); + + // + // Construct an unpreconditioned linear problem instance. + // + Belos::LinearProblem problem( A, X, B ); + bool set = problem.setProblem(); + if (set == false) { + std::cout << std::endl << "ERROR: Belos::LinearProblem failed to set up correctly!" << std::endl; + return -1; + } + // + // ******************************************************************* + // **************Start the block CG iteration************************* + // ******************************************************************* + // + // Create an iterative solver manager. + RCP< Belos::SolverManager > newSolver + = rcp( new Belos::BlockCGSolMgr(rcpFromRef(problem), rcpFromRef(belosList)) ); + + // + // **********Print out information about problem******************* + // + std::cout << std::endl << std::endl; + std::cout << "Dimension of matrix: " << NumGlobalElements << std::endl; + std::cout << "Number of right-hand sides: " << numrhs << std::endl; + std::cout << "Max number of Gmres iterations: " << maxiters << std::endl; + std::cout << "Relative residual tolerance: " << tol << std::endl; + std::cout << std::endl; + // + // Perform solve + // + Belos::ReturnType ret; + ret = newSolver->solve(); + + // + // Compute actual residuals. + // + bool badRes = false; + std::vector actual_resids( numrhs ); + std::vector rhs_norm( numrhs ); + MV resid(numRows, numrhs); + OPT::Apply( *A, *X, resid ); + MVT::MvAddMv( -1.0, resid, 1.0, *B, resid ); + MVT::MvNorm( resid, actual_resids ); + MVT::MvNorm( *B, rhs_norm ); + std::cout<< "---------- Actual Residuals (normalized) ----------"< tol) badRes = true; + } + + if (ret!=Belos::Converged || badRes) { + success = false; + std::cout << std::endl << "ERROR: Belos did not converge!" << std::endl; + } else { + success = true; + std::cout << std::endl << "SUCCESS: Belos converged!" << std::endl; + } + + } + TEUCHOS_STANDARD_CATCH_STATEMENTS(verbose, std::cerr, success); + } + Kokkos::finalize(); +#ifdef HAVE_MPI + MPI_Finalize(); +#endif + return success ? EXIT_SUCCESS : EXIT_FAILURE; +} diff --git a/packages/belos/kokkos/example/BlockGmresKokkosExFile.cpp b/packages/belos/kokkos/example/BlockGmresKokkosExFile.cpp new file mode 100644 index 000000000000..0b7a969128a5 --- /dev/null +++ b/packages/belos/kokkos/example/BlockGmresKokkosExFile.cpp @@ -0,0 +1,223 @@ +//@HEADER +// ************************************************************************ +// +// Belos: Block Linear Solvers Package +// Copyright 2004 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +//@HEADER +// +// This driver reads a problem from a file, which must be in Matrix Market (*.mtx). +// The problem right-hand side will be generated randomly. +// +// NOTE: No preconditioner is used in this example. +// +#include "BelosConfigDefs.hpp" +#include "BelosLinearProblem.hpp" +#include "BelosBlockGmresSolMgr.hpp" +#include "BelosOutputManager.hpp" + +#include "Teuchos_CommandLineProcessor.hpp" +#include "Teuchos_ParameterList.hpp" +#include "Teuchos_StandardCatchMacros.hpp" + +#include "BelosKokkosAdapter.hpp" +#include "KokkosKernels_IOUtils.hpp" +#ifdef HAVE_MPI + #include +#endif + +int main(int argc, char *argv[]) { + +#ifdef HAVE_MPI + MPI_Init(&argc,&argv); +#endif + +bool success = true; + Kokkos::initialize(); + { + + typedef double ST; + typedef int OT; + typedef Kokkos::DefaultExecutionSpace EXSP; + typedef Teuchos::ScalarTraits SCT; + typedef SCT::magnitudeType MT; + typedef Belos::KokkosMultiVec MV; + typedef Belos::KokkosCrsOperator OP; + typedef Belos::MultiVec KMV; + typedef Belos::Operator KOP; + typedef Belos::MultiVecTraits MVT; + typedef Belos::OperatorTraits OPT; + + using Teuchos::ParameterList; + using Teuchos::RCP; + using Teuchos::rcp; + using Teuchos::rcpFromRef; + +bool verbose = true; +try { + int frequency = 25; // frequency of status test output. + int numrhs = 1; // number of right-hand sides to solve for + int maxiters = -1; // maximum number of iterations allowed per linear system + int maxsubspace = 50; // maximum number of blocks the solver can use for the subspace + int maxrestarts = 35; // number of restarts allowed + bool expresidual = false; // use explicit residual + std::string filename("bcsstk12.mtx"); // example matrix + std::string rhsfile(""); + MT tol = 1.0e-5; // relative residual tolerance + + Teuchos::CommandLineProcessor cmdp(false,true); + cmdp.setOption("verbose","quiet",&verbose,"Print messages and results."); + cmdp.setOption("expres","impres",&expresidual,"Use explicit residual throughout."); + cmdp.setOption("frequency",&frequency,"Solvers frequency for printing residuals (#iters)."); + cmdp.setOption("filename",&filename,"Filename for test matrix. Acceptable file extensions: *.hb,*.mtx,*.triU,*.triS"); + cmdp.setOption("rhsfile",&rhsfile,"Filename for right-hand side. (*.mtx file) "); + cmdp.setOption("tol",&tol,"Relative residual tolerance used by Gmres solver."); + cmdp.setOption("num-rhs",&numrhs,"Number of right-hand sides to be solved for."); + cmdp.setOption("max-iters",&maxiters,"Maximum number of iterations per linear system (-1 = adapted to problem/block size)."); + cmdp.setOption("max-subspace",&maxsubspace,"Maximum number of blocks the solver can use for the subspace."); + cmdp.setOption("max-restarts",&maxrestarts,"Maximum number of restarts allowed for GMRES solver."); + + if (cmdp.parse(argc,argv) != Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL) { + return -1; + } + if (!verbose) + frequency = -1; // reset frequency if test is not verbose + + // Read in a matrix Market file and use it to test the Kokkos Operator. + KokkosSparse::CrsMatrix crsMat = + KokkosKernels::Impl::read_kokkos_crst_matrix>(filename.c_str()); + RCP> A = + rcp(new Belos::KokkosCrsOperator(crsMat)); + OT numRows = crsMat.numRows(); + + Teuchos::RCP X = Teuchos::rcp( new MV(numRows, numrhs) ); + X->MvRandom(); + Teuchos::RCP B = Teuchos::rcp( new MV(numRows, numrhs) ); + OPT::Apply(*A,*X,*B); + X->MvInit(0.0); + + // + // ********Other information used by block solver*********** + // *****************(can be user specified)****************** + // + const int NumGlobalElements = B->GetGlobalLength(); + if (maxiters == -1) + maxiters = NumGlobalElements - 1; // maximum number of iterations to run + + ParameterList belosList; + belosList.set( "Maximum Iterations", maxiters ); // Maximum number of iterations allowed + belosList.set( "Convergence Tolerance", tol ); // Relative convergence tolerance requested + belosList.set( "Num Blocks", maxsubspace); // Maximum number of blocks in Krylov factorization + belosList.set( "Maximum Restarts", maxrestarts ); // Maximum number of restarts allowed + belosList.set( "Explicit Residual Test", expresidual); // use explicit residual + + if (verbose) { + belosList.set( "Verbosity", Belos::Errors + Belos::Warnings + + Belos::StatusTestDetails + Belos::FinalSummary + Belos::TimingDetails); + if (frequency > 0) + belosList.set( "Output Frequency", frequency ); + } + else + belosList.set( "Verbosity", Belos::Errors + Belos::Warnings ); + + // + // Construct an unpreconditioned linear problem instance. + // + Belos::LinearProblem problem( A, X, B ); + bool set = problem.setProblem(); + if (set == false) { + std::cout << std::endl << "ERROR: Belos::LinearProblem failed to set up correctly!" << std::endl; + return -1; + } + // + // ******************************************************************* + // **************Start the block Gmres iteration************************* + // ******************************************************************* + // + // Create an iterative solver manager. + RCP< Belos::SolverManager > newSolver + = rcp( new Belos::BlockGmresSolMgr(rcpFromRef(problem), rcpFromRef(belosList)) ); + + // + // **********Print out information about problem******************* + // + std::cout << std::endl << std::endl; + std::cout << "Dimension of matrix: " << NumGlobalElements << std::endl; + std::cout << "Number of right-hand sides: " << numrhs << std::endl; + std::cout << "Max number of Gmres iterations: " << maxiters << std::endl; + std::cout << "Relative residual tolerance: " << tol << std::endl; + std::cout << std::endl; + // + // Perform solve + // + Belos::ReturnType ret; + ret = newSolver->solve(); + + // + // Compute actual residuals. + // + bool badRes = false; + std::vector actual_resids( numrhs ); + std::vector rhs_norm( numrhs ); + MV resid(numRows, numrhs); + OPT::Apply( *A, *X, resid ); + MVT::MvAddMv( -1.0, resid, 1.0, *B, resid ); + MVT::MvNorm( resid, actual_resids ); + MVT::MvNorm( *B, rhs_norm ); + std::cout<< "---------- Actual Residuals (normalized) ----------"< tol) badRes = true; + } + + if (ret!=Belos::Converged || badRes) { + success = false; + std::cout << std::endl << "ERROR: Belos did not converge!" << std::endl; + } else { + success = true; + std::cout << std::endl << "SUCCESS: Belos converged!" << std::endl; + } + + } + TEUCHOS_STANDARD_CATCH_STATEMENTS(verbose, std::cerr, success); + } + Kokkos::finalize(); +#ifdef HAVE_MPI + MPI_Finalize(); +#endif + return success ? EXIT_SUCCESS : EXIT_FAILURE; +} diff --git a/packages/belos/kokkos/example/CMakeLists.txt b/packages/belos/kokkos/example/CMakeLists.txt new file mode 100644 index 000000000000..b493959ea9af --- /dev/null +++ b/packages/belos/kokkos/example/CMakeLists.txt @@ -0,0 +1,23 @@ +INCLUDE_DIRECTORIES(${Belos_SOURCE_DIR}/kokkos/src) + +TRIBITS_ADD_EXECUTABLE_AND_TEST( + Kokkos_BlockGmresEx + SOURCES BlockGmresKokkosExFile.cpp + ARGS "--verbose" + "--verbose --num-rhs=4" + COMM serial mpi + ) + +TRIBITS_ADD_EXECUTABLE_AND_TEST( + Kokkos_BlockCGEx + SOURCES BlockCGKokkosExFile.cpp + ARGS "--verbose" + "--verbose --num-rhs=4" + COMM serial mpi + ) + +TRIBITS_COPY_FILES_TO_BINARY_DIR(CopyExampleMtxFiles + SOURCE_DIR ${Belos_SOURCE_DIR}/kokkos/example + SOURCE_FILES bcsstk12.mtx + EXEDEPS Kokkos_BlockCGEx Kokkos_BlockGmresEx + ) diff --git a/packages/belos/kokkos/example/bcsstk12.mtx b/packages/belos/kokkos/example/bcsstk12.mtx new file mode 100644 index 000000000000..d734671ce1d3 --- /dev/null +++ b/packages/belos/kokkos/example/bcsstk12.mtx @@ -0,0 +1,17874 @@ +%%MatrixMarket matrix coordinate real symmetric +%------------------------------------------------------------------------------- +% UF Sparse Matrix Collection, Tim Davis +% http://www.cise.ufl.edu/research/sparse/matrices/HB/bcsstk12 +% name: HB/bcsstk12 +% [SYMMETRIC STIFFNESS MATRIX, ORE CAR (CONSISTENT MASSES)] +% id: 34 +% date: 1982 +% author: J. Lewis +% ed: I. Duff, R. Grimes, J. Lewis +% fields: title A name id kind notes date author ed +% kind: duplicate structural problem +%------------------------------------------------------------------------------- +% notes: +% duplicate of HB/bcsstk11 +%------------------------------------------------------------------------------- +1473 1473 17857 +1 1 1011851.60912 +2 1 4110093.43272 +3 1 -4.47034835815e-8 +4 1 -311975.890718 +5 1 -1184718.57235 +6 1 9.31322574615e-9 +52 1 22134.9913963 +53 1 90320.9940529 +54 1 -18909.0650259 +55 1 -144050.092155 +56 1 -547025.666412 +57 1 358351.461509 +2 2 16788621.6609 +3 2 -1.9371509552e-7 +4 2 -1184718.57235 +5 2 -4498931.28739 +6 2 2.98023223877e-8 +52 2 90320.9940529 +53 2 370626.696215 +54 2 4631.25243447 +55 2 -547025.666412 +56 2 -2077312.65726 +57 2 1360828.33484 +3 3 18240145.4814 +4 3 1.02445483208e-8 +5 3 3.35276126862e-8 +6 3 758227.34113 +52 3 18909.0650259 +53 3 -4631.25243457 +54 3 -5293544.01962 +55 3 358351.461509 +56 3 1360828.33484 +57 3 -2284273.33935 +4 4 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Belos: Block Linear Solvers Package +// Copyright 2004 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Jennifer A. Loe (jloe@sandia.gov) +// +// ************************************************************************ +//@HEADER + +/*! \file BelosKokkosAdapter.hpp + \brief Implementation of the interface between Belos virtual classes and Kokkos concrete classes. + Allows the user to use a Kokkos::view as a Belos::MultiVector in the Belos solvers. + \warning Note: This class does not currently allow the user to run Belos solvers which + require accessing non-contiguous columns of data in memory. +*/ + +#include +#include +#include +#include + +#include +#include +#include + +#include + + +#ifndef BELOS_KOKKOS_ADAPTER_HPP +#define BELOS_KOKKOS_ADAPTER_HPP +namespace Belos { + +//Forward class declaration of KokkosCrsOperator: +template +class KokkosCrsOperator; + +/// \class KokkosMultiVec +/// \brief Implementation of Belos::MultiVec using Kokkos::View. +/// \author Jennifer Loe +/// +/// \tparam ScalarType The type of entries of the multivector. +/// \tparam Device The Kokkos::ExecutionSpace where the multivector +/// should reside. +/// +/// Belos::MultiVec offers a simple abstract interface for +/// multivector operations in Belos solver algorithms. This class +/// implements Belos::MultiVec using Kokkos::View. +template +class KokkosMultiVec : public MultiVec { + +public: + + using ViewVectorType = Kokkos::View; + using ConstViewVectorType = Kokkos::View; + using ViewMatrixType = Kokkos::View; + using ConstViewMatrixType = Kokkos::View; + + //Unmanaged view types: + using UMHostViewVectorType = + Kokkos::View>; + using UMHostConstViewVectorType = + Kokkos::View>; + using UMHostViewMatrixType = + Kokkos::View>; + using UMHostConstViewMatrixType = + Kokkos::View>; + +protected: + ViewMatrixType myView; + +public: + //! @name Constructors/Destructor + //@{ + + /// \brief Returns a multivector with `numrows` rows and `numvecs` columns. + /// + /// The `label` string indicates the label for the internal `Kokkos::view`. + /// If `zeroOut` is set to `true`, the multivector will be initialized to zeros. + KokkosMultiVec (const std::string label, const int numrows, const int numvecs, const bool zeroOut = true) : + myView (Kokkos::view_alloc(Kokkos::WithoutInitializing,label),numrows,numvecs) + { if (zeroOut) { Kokkos::deep_copy(myView,0); } } + + /// \brief Returns a multivector with `numrows` rows and `numvecs` columns. + /// + /// If `zeroOut` is set to `true`, the multivector will be initialized to zeros. + KokkosMultiVec (const int numrows, const int numvecs, const bool zeroOut = true) : + myView (Kokkos::view_alloc(Kokkos::WithoutInitializing,"MV"),numrows,numvecs) + { if (zeroOut) { Kokkos::deep_copy(myView,0); } } + + /// \brief Returns a single column multivector with `numrows` rows. + /// + /// If `zeroOut` is set to `true`, the multivector will be initialized to zeros. + KokkosMultiVec (const int numrows, const bool zeroOut = true) : + myView(Kokkos::view_alloc(Kokkos::WithoutInitializing,"MV"),numrows,1) + { if (zeroOut) { Kokkos::deep_copy(myView,0); } } + + //! Copy constructor (performs deep copy). + + /// This copy constructor returns a new KokksMultiVec containing a + /// deep copy of the multivector given by the user. + KokkosMultiVec (const KokkosMultiVec &sourceVec) : + myView(Kokkos::view_alloc(Kokkos::WithoutInitializing,"MV"),(int)sourceVec.GetGlobalLength(),sourceVec.GetNumberVecs()) + { Kokkos::deep_copy(myView,sourceVec.GetInternalViewConst()); } + + //! Copy constructor for type conversion. (Performs deep copy.) + + /// This copy constructor returns a new KokksMultiVec containing a + /// deep copy of the multivector given by the user. + /// The internal data of the multivector is converted from + /// `ScalarType` to `ScalarType2`. + template < class ScalarType2 > + KokkosMultiVec (const KokkosMultiVec &sourceVec) : + myView(Kokkos::view_alloc(Kokkos::WithoutInitializing, "MV"),(int)sourceVec.GetGlobalLength(),sourceVec.GetNumberVecs()) + { Kokkos::deep_copy(myView,sourceVec.GetInternalViewConst()); } + + //! Assignment operator (performs deep copy). + + /// This `=` operator performs a deep copy of + /// the right-hand side KokkosMultiVec to the + /// left-hand side KokkosMultiVec. The left-hand + /// side MultiVec will be resized if necessary. + KokkosMultiVec & operator=(const KokkosMultiVec & sourceVec) { + int len = sourceVec.GetGlobalLength(); + int cols = sourceVec.GetNumberVecs(); + if( len != (int)myView.extent(0) || cols != (int)myView.extent(1) ){ + Kokkos::resize(myView, len, cols); + } + Kokkos::deep_copy(myView,sourceVec.GetInternalViewConst()); + return *this; + } + + //! Assignment operator for type conversion. (Performs deep copy.) + + /// This `=` operator performs a deep copy of + /// the right-hand side KokkosMultiVec to the + /// left-hand side KokkosMultiVec. The left-hand + /// side MultiVec will be resized if necessary. + /// The internal data of the right-hand side multivec + /// is converted from `ScalarType` to `ScalarType2`. + template < class ScalarType2 > + KokkosMultiVec & operator=(const KokkosMultiVec & sourceVec) { + int len = sourceVec.GetGlobalLength(); + int cols = sourceVec.GetNumberVecs(); + if( len != (int)myView.extent(0) || cols != (int)myView.extent(1) ){ + Kokkos::resize(myView, len, cols); + } + Kokkos::deep_copy(myView,sourceVec.GetInternalViewConst()); + return *this; + } + + //! Create a KokkosMultiVec from a given `Kokkos::view`. + + /// Returns a KokkosMultiVec that internally stores the + /// data given in `sourceView`. If `makeCopy` has value + /// `true`, then this function makes a deep copy of the + /// `Kokkos::view`. If `false`, then the KokkosMultiVec stores a + /// shallow copy of the given `Kokkos::view`. (This option assumes that + /// the user will make no changes to that view outside of + /// the KokkosMultiVec interface.) + KokkosMultiVec (const ViewMatrixType & sourceView, bool makeCopy = true) { + if( makeCopy ){ + if( sourceView.extent(0) != myView.extent(0) || sourceView.extent(1) != myView.extent(1) ){ + Kokkos::resize(myView, sourceView.extent(0), sourceView.extent(1)); + } + Kokkos::deep_copy(myView, sourceView); + } + else{ + myView = sourceView; + } + } + + //! Create a KokkosMultiVec with ScalarType2 from a given `Kokkos::view` with ScalarType1. + + /// Returns a KokkosMultiVec that internally stores the + /// data given in `sourceView`. This function always makes + /// a deep copy of the sourceView in order to change scalar + /// types. + template < class ScalarType2 > //TODO: Fix this so that passing in a view without device specified actually compiles... + KokkosMultiVec (const Kokkos::View & sourceView) : + myView(Kokkos::view_alloc(Kokkos::WithoutInitializing, "MV"),sourceView.extent(0),sourceView.extent(1)) + { Kokkos::deep_copy(myView,sourceView); } + + //! Destructor (default) + ~KokkosMultiVec(){} + + //@} + + //! @name Data Access Methods + //@{ + + //! Reader (const) method for internal view. + + /// Returns the (const) view that stores internal data + /// for the KokkosMultiVec. + ConstViewMatrixType GetInternalViewConst() const { + return myView; + } + + //! Reader/Writer method for internal view. + + /// Returns the view that stores internal data + /// for the KokkosMultiVec. + /// \warning ** Be careful!! ** The KokkosMultiVec does + /// NOT expect users to use this function to + /// make changes to its internal data. Most + /// necessary changes can be made via other functions. + /// Make sure you know what you are doing! + ViewMatrixType GetInternalViewNonConst(){ + return myView; + } + //@} + + //! @name Copy/View functions inherited from Belos::MultiVec + //@{ + + //! Creates a MultiVec with same data distribution as `this`. + + /// A virtual "copy constructor" that returns a pointer to a new + /// Belos::MultiVec. (Underneath, the vector is a KokkosMultiVec, + /// and its properties can be accessed via `dynamic_cast`.) + /// This vector's entries are + /// not copied; instead, a new MultiVec is created with the same + /// data distribution, but with numvecs columns (numvecs > 0). + /// Multivector entries are not initialized. + /// + /// \param numvecs [in] The number of columns in the output + /// multivector. Must be positive. + MultiVec * Clone ( const int numvecs ) const{ + KokkosMultiVec * ptr = new KokkosMultiVec(myView.extent(0),numvecs, false); + return ptr; + } + + //! \brief Creates a MultiVec which is a (deep) copy of `this`. + /// + /// A virtual "copy constructor" returning a pointer to a new + /// object of Belos::MultiVec. (KokkosMultiVec underneath.) + /// All of this vector's entries are + /// copied and a new stand-alone multivector is created. (deep + /// copy). + MultiVec * CloneCopy () const{ + KokkosMultiVec * ptr = new KokkosMultiVec(myView.extent(0),myView.extent(1), false); + Kokkos::deep_copy(ptr->GetInternalViewNonConst(),myView); + return ptr; + } + + //! \brief Creates a MultiVec which is a (deep) copy of selected columns of `this`. + /// + /// A virtual "copy constructor" returning a pointer to a new Belos::MultiVec. + /// This vector's entries are copied and a new + /// stand-alone MultiVector is created where only selected columns + /// are chosen. (deep copy). + /// Indexing is zero-based, so an `std::vector index` with values 0, 3, 5 would + /// indicate copying the first, 4th, and 6th columns of the original multivector. + /// Indices need not be contiguous or ordered. + /// Result is `output[:,i] = (*this)[:,index[i]]`. + MultiVec * CloneCopy ( const std::vector& index ) const{ + // JAL- If debug options needed, could add validity checks of index. + // See debug code in belos/src/tpetra/BelosMultiVecTraits_Tpetra.hpp. + int numvecs = index.size(); + KokkosMultiVec * B = new KokkosMultiVec("B",myView.extent(0),numvecs, false); + bool isContigAscending = true; + + //Check whether the given indices are contiguous and ascending. + for(unsigned int i=0; i< (index.size()-1); i++){ + if( index[i+1] != index[i]+1 ){ + isContigAscending = false; + } + } + + //Copy the vectors: (Case depends on indices.) + if(isContigAscending && index.size()==(unsigned)this->GetNumberVecs()){ //Copy entire multivec. + Kokkos::deep_copy(B->GetInternalViewNonConst(),myView); + } + else if (isContigAscending){ //Copy contiguous subset + ViewMatrixType ThisSub = Kokkos::subview(myView, Kokkos::ALL, std::make_pair(index.front(), index.back()+1)); + Kokkos::deep_copy(B->GetInternalViewNonConst(),ThisSub); + } + else{ //Copy columns one by one + for(unsigned int i=0; iGetInternalViewNonConst(), Kokkos::ALL, i); + auto ThisSub = Kokkos::subview(myView, Kokkos::ALL, index[i]); + Kokkos::deep_copy(Bsub, ThisSub); + } + } + return B; + } + + //! \brief Creates a (read-only) MultiVec which is a shallow copy of selected columns of `this`. + /// + /// A virtual view constructor returning a pointer to a new Belos::MultiVec with + /// selected columns. (Column indexing is zero-based.) The view is read-only. + /// This vector's entries are shared and hence no + /// memory is allocated for the columns. (Internally, we create + /// a `Kokkos::subview`.) + /// \warning At this time, the Kokkos-Belos adapter only supports + /// viewing column indices that form a contiguous subset in memory. + /// Thus, the values in `index` must be contiguous and ascending (e.g. 0,1,2,3). + const MultiVec * CloneView ( const std::vector& index ) const { //TODO This isn't const!! + bool isContigAscending = true; + //Check whether the given indices are contiguous and ascending. + for(unsigned int i=0; i< (index.size()-1); i++){ + if( index[i+1] != index[i]+1 ){ + isContigAscending = false; + } + } + if(isContigAscending ){ + const KokkosMultiVec * B = + new KokkosMultiVec(Kokkos::subview(myView, Kokkos::ALL, std::make_pair(index.front(), index.back()+1)),false); + return B; + } + else{ + throw std::runtime_error("CloneView asked for non-contiguous subset. \n This feature is not yet supported in Belos for Kokkos."); + } + } + + + //! \brief Creates a nonconst MultiVec which is a shallow copy of selected columns of `this`. + /// + /// A virtual view constructor returning a pointer to a new Belos::MultiVec with + /// selected columns. (Column indexing is zero-based.) + /// This vector's entries are shared and hence no + /// memory is allocated for the columns. (Internally, we create + /// a `Kokkos::subview`.) Writing to this view will change the + /// entries of the original multivector. + /// \warning At this time, the Kokkos-Belos adapter only supports + /// viewing column indices that form a contiguous subset in memory. + /// Thus, the values in `index` must be contiguous and ascending (e.g. 0,1,2,3). + MultiVec * CloneViewNonConst ( const std::vector& index ){ + bool isContigAscending = true; + //Check whether the given indices are contiguous and ascending. + for(unsigned int i=0; i< (index.size()-1); i++){ + if( index[i+1] != index[i]+1 ){ + isContigAscending = false; + } + } + if(isContigAscending ){ + KokkosMultiVec * B = + new KokkosMultiVec(Kokkos::subview(myView, Kokkos::ALL, std::make_pair(index.front(), index.back()+1)),false); + return B; + } + else{ + throw std::runtime_error("CloneViewNonConst asked for non-contiguous subset. \n This feature is not yet supported in Belos for Kokkos."); + } + } + + //! Copy the vectors in A to the vectors in (*this) specified by index. (Deep copy.) + + /// Copies vectors of A to a sub-block of vectors of this multivector. (Deep copy.) + /// The sub-block to be overwritten is given by the indices and need not be contiguous. + /// Result is (*this)[:,index[i]] = A[:,i]. + /// Column indexing is zero-based. + /// + void SetBlock ( const MultiVec& A, const std::vector& index ){ + KokkosMultiVec *A_vec = dynamic_cast(&const_cast &>(A)); + + if( index.size() > myView.extent(1) ){ + throw std::runtime_error("Error in KokkosMultiVec::SetBlock. A cannot have more vectors than (*this)."); + } + bool isContigAscending = true; + //Check whether the given indices are contiguous and ascending. + for(unsigned int i=0; i< (index.size()-1); i++){ + if( index[i+1] != index[i]+1 ){ + isContigAscending = false; + } + } + + //Perform deep copy of sub block: + if(isContigAscending && index.size()==(unsigned)this->GetNumberVecs()){ //Copy entire multivec. + Kokkos::deep_copy(myView,A_vec->GetInternalViewConst()); + } + else if (isContigAscending){ //Copy contiguous subset + ConstViewMatrixType Asub = Kokkos::subview(A_vec->GetInternalViewConst(), Kokkos::ALL, std::make_pair(0,(int)index.size())); + ViewMatrixType ThisSub = Kokkos::subview(myView, Kokkos::ALL, std::make_pair(index.front(), index.back()+1)); + Kokkos::deep_copy(ThisSub, Asub); + } + else{ //Copy columns one by one + for(unsigned int i=0; iGetInternalViewConst(), Kokkos::ALL, i); + ViewVectorType ThisSub = Kokkos::subview(myView, Kokkos::ALL, index[i]); + Kokkos::deep_copy(ThisSub, Asub); + } + } + } + //@} + + //! @name Attribue functions inherited from Belos::MultiVec + //@{ + //! Returns the number of rows in the multivector. + ptrdiff_t GetGlobalLength () const { + return static_cast(myView.extent(0)); + } + + //! Returns the number of columns in the multivector. + int GetNumberVecs () const { return myView.extent(1); } + //@} + + //! @name Mathematical functions inherited from Belos::MultiVec + //@{ + //! \brief `*this <- alpha * A * B + beta * (*this)` + /// + /// where alpha and beta are scalars and the dimensions of `A*B` match + /// the dimensions of `(*this)`. + void MvTimesMatAddMv ( const ScalarType alpha, const MultiVec& A, + const Teuchos::SerialDenseMatrix& B, const ScalarType beta ){ + KokkosMultiVec *A_vec = dynamic_cast(&const_cast &>(A)); + if( myView.extent(1) == 1 && A_vec->GetInternalViewConst().extent(1) == 1){ //B is a scalar. + ScalarType scal1 = alpha*B(0,0); + ViewVectorType mysub = Kokkos::subview(myView, Kokkos::ALL, 0); + ConstViewVectorType Asub = Kokkos::subview(A_vec->GetInternalViewConst(), Kokkos::ALL, 0); + KokkosBlas::axpby(scal1, Asub, beta, mysub); + } + else{ + UMHostConstViewMatrixType mat_h(B.values(), A_vec->GetInternalViewConst().extent(1), myView.extent(1)); + ViewMatrixType mat_d(Kokkos::view_alloc(Kokkos::WithoutInitializing,"mat"), A_vec->GetInternalViewConst().extent(1), myView.extent(1)); + Kokkos::deep_copy(mat_d, mat_h); + if( myView.extent(1) == 1 ){ // B has only 1 col + ConstViewVectorType Bsub = Kokkos::subview(mat_d, Kokkos::ALL, 0); + ViewVectorType mysub = Kokkos::subview(myView, Kokkos::ALL, 0); + KokkosBlas::gemv("N", alpha, A_vec->GetInternalViewConst(), Bsub, beta, mysub); + } + else{ + KokkosBlas::gemm("N", "N", alpha, A_vec->GetInternalViewConst(), mat_d, beta, myView); + } + } + } + + //! `*this <- alpha * A + beta * B` + /// + /// Scale and add two vectors. Store the result in `*this`. + void MvAddMv ( const ScalarType alpha, const MultiVec& A, const ScalarType beta, + const MultiVec& B){ + KokkosMultiVec *A_vec = dynamic_cast(&const_cast &>(A)); + KokkosMultiVec *B_vec = dynamic_cast(&const_cast &>(B)); + + KokkosBlas::update(alpha, A_vec->GetInternalViewConst(), beta, B_vec->GetInternalViewConst(), (ScalarType) 0.0, myView); + } + + /// `*this <- alpha * this` + /// + //! Scale (multiply) each element of the vectors in \c *this with \c alpha. + void MvScale ( const ScalarType alpha ) { + KokkosBlas::scal(myView, alpha, myView); + } + + /// `*this[:,i] <- alpha[i] * this[:,i]` + /// + //! Scale (multiply) each element of the \c i-th vector in \c *this with \c alpha[i]. + void MvScale ( const std::vector& alpha ){ + + //Move scalar values to a Kokkos View: + UMHostConstViewVectorType scalars_h(alpha.data(), alpha.size()); + ViewVectorType scalars_d(Kokkos::view_alloc(Kokkos::WithoutInitializing,"scalars_d"), alpha.size()); + Kokkos::deep_copy(scalars_d, scalars_h); + + KokkosBlas::scal(myView, scalars_d, myView); + } + + //! B <- alpha * A^T * (*this) + /// + /// Computes matrix product with transpose. Result is a dense matrix. + /// Conjugate transpose is used as appropriate. + void MvTransMv ( const ScalarType alpha, const MultiVec& A, Teuchos::SerialDenseMatrix& B ) const{ + KokkosMultiVec *A_vec = dynamic_cast(&const_cast &>(A)); + if(A_vec->myView.extent(1) == 1 && myView.extent(1) == 1){ + ConstViewVectorType Asub = Kokkos::subview(A_vec->GetInternalViewConst(), Kokkos::ALL, 0); + ViewVectorType mysub = Kokkos::subview(myView, Kokkos::ALL, 0); + ScalarType soln = KokkosBlas::dot(Asub, mysub); + soln = alpha*soln; + B(0,0) = soln; + } + // *** + // For MvTransMv, this option runs slower than GEMM on NVIDIA V100. + // Do not enable for now. + // **** + // else if( myView.extent(1) == 1 ){ // Only 1 col in soln vec + // ViewVectorType soln(Kokkos::view_alloc(Kokkos::WithoutInitializing,"soln"), A_vec->GetInternalViewConst().extent(1)); + // ViewVectorType mysub = Kokkos::subview(myView, Kokkos::ALL, 0); + // KokkosBlas::gemv("C", alpha, A_vec->GetInternalViewConst(), mysub, ScalarType(0.0), soln); + // for( unsigned int i = 0; i < soln.extent(0); i++){ + // B(i,0) = soln(i); + // } + // } + else{ + UMHostViewMatrixType soln_h(B.values(), A_vec->GetInternalViewConst().extent(1), myView.extent(1)); + ViewMatrixType soln_d(Kokkos::view_alloc(Kokkos::WithoutInitializing,"mat"), A_vec->GetInternalViewConst().extent(1), myView.extent(1)); + KokkosBlas::gemm("C", "N", alpha, A_vec->GetInternalViewConst(), myView, ScalarType(0.0), soln_d); + Kokkos::deep_copy(soln_h, soln_d); + } + } + + + //! b[i] = A[i]^T * this[i] + + /// Performs a dot product between A and (*this). + /// Uses conjugate transpose when appropriate. + /// Output is a vector. + void MvDot ( const MultiVec& A, std::vector& b ) const{ + //Put output vector in unmanaged Kokkos view: + UMHostViewVectorType dotView_h(b.data(),myView.extent(1)); + ViewVectorType dotView_d(Kokkos::view_alloc(Kokkos::WithoutInitializing,"Dot"),myView.extent(1)); + + KokkosMultiVec *A_vec = dynamic_cast(&const_cast &>(A)); + + KokkosBlas::dot(dotView_d, A_vec->GetInternalViewConst(), myView); + Kokkos::deep_copy(dotView_h, dotView_d); + } + + //! alpha[i] = norm of i-th column of (*this) + + /// Valid norm types are Belos::TwoNorm, Belos::OneNorm, + /// and Belos::InfNorm. + void MvNorm ( std::vector& normvec, NormType norm_type = TwoNorm ) const{ + + //Put output vector in unmanaged Kokkos view: + UMHostViewVectorType normView_h(normvec.data(),myView.extent(1)); + ViewVectorType normView_d(Kokkos::view_alloc(Kokkos::WithoutInitializing,"Norm"),myView.extent(1)); + + switch( norm_type ) { + case ( OneNorm ) : + KokkosBlas::nrm1(normView_d, myView); + break; + case ( TwoNorm ) : + KokkosBlas::nrm2(normView_d, myView); + break; + case ( InfNorm ) : + KokkosBlas::nrminf(normView_d, myView); + break; + default: + TEUCHOS_TEST_FOR_EXCEPTION(true, std::invalid_argument, + "Belos::KokkosMultiVec::MvNorm: Invalid norm_type " + << norm_type << ". The current list of valid norm " + "types is {OneNorm, TwoNorm, InfNorm}."); + } + Kokkos::deep_copy(normView_h, normView_d); + } + //@} + + //! @name Initialization functions inherited from Belos::MultiVec + //@{ + //! Fill all columns of *this with random values. + void MvRandom() { + int rand_seed = std::rand(); + Kokkos::Random_XorShift64_Pool<> pool(rand_seed); + Kokkos::fill_random(myView, pool, -1,1); + } + + //! Initialize each element of (*this) to the scalar value alpha. + void MvInit ( const ScalarType alpha ) { + Kokkos::deep_copy(myView,alpha); + } + //@} + + //! @name Print function inherited from Belos::MultiVec + //@{ + //! Print (*this) to the given output stream. + + /// (This function will first copy the multivector to host space + /// if needed.) + void MvPrint( std::ostream& os ) const { + typename ViewMatrixType::HostMirror hostView("myViewMirror", myView.extent(0), myView.extent(1)); + Kokkos::deep_copy(hostView, myView); + for(unsigned int i = 0; i < (hostView.extent(0)); i++){ + for (unsigned int j = 0; j < (hostView.extent(1)); j++){ + os << hostView(i , j) << " "; + } + os << std::endl; + } + os << std::endl; + } + //@} + +}; + +/// \class KokkosCrsOperator +/// \brief Implementation of Belos::Operator using KokkosSparse::CrsMatrix. +template +class KokkosCrsOperator : public Operator { + +private: + // Shallow copy of the CrsMatrix used for SpMV. + KokkosSparse::CrsMatrix myMatrix; + +public: + //! @name Constructor/Destructor + //@{ + //! Constructor obtains a shallow copy of the given CrsMatrix. + KokkosCrsOperator (const KokkosSparse::CrsMatrix mat) + : myMatrix(mat) {} + + //! Destructor. + ~KokkosCrsOperator(){} + //@} + + //! @name Methods relating to applying the operator + //@{ + + /// \brief Apply the operator to x, putting the result in y. + /// + /// Take the KokkosMultiVec \c x and apply the operator (or its + /// transpose or Hermitian transpose) to it, writing the result + /// into the KokkosMultiVec \c y. (This performs a sparse matrix- + /// vector product.) + /// + /// \param x [in] The input multivector. + /// + /// \param y [out] The output multivector. x and y may not alias + /// (i.e., be views of) one another. + /// + /// \param trans [in] Whether to apply the operator (Belos::NOTRANS), its + /// transpose (Belos::TRANS), or its Hermitian transpose (Belos::CONJTRANS). + /// The default is Belos::NOTRANS. (Defined in BelosTypes.hpp.) + /// + void Apply (const MultiVec& x, MultiVec& y, ETrans trans=NOTRANS) const{ + + // Determine transpose mode: + char mode[] = "X"; + switch(trans){ + case NOTRANS: + mode[0]='N'; + break; + case TRANS: + mode[0]='T'; + break; + case CONJTRANS: + mode[0]='C'; + break; + default: + TEUCHOS_TEST_FOR_EXCEPTION(true, std::invalid_argument, + "Belos::KokkosCrsOperator::Apply: Invalid ETrans type "); + } + + //Use dynamic_cast to tell the compiler these are Kokkos Multivecs. + KokkosMultiVec *x_vec = + dynamic_cast *>(&const_cast &>(x)); + KokkosMultiVec *y_vec = dynamic_cast *>(&y); + + //KokkosSparse::spmv computes y = beta*y + alpha*Op(A)*x + ScalarType alpha = 1.0; + ScalarType beta = 0; + KokkosSparse::spmv(mode, alpha, myMatrix, x_vec->GetInternalViewConst(), beta, y_vec->GetInternalViewNonConst()); + } + + /// \brief Whether this operator implements applying the transpose. + /// + /// This function returns true since we can always apply the transpose + /// of a Kokkos::CrsMatrix. + /// + bool HasApplyTranspose () const { + return true; + } + //@} +}; +}// end namespace Belos +#endif diff --git a/packages/belos/kokkos/src/CMakeLists.txt b/packages/belos/kokkos/src/CMakeLists.txt new file mode 100644 index 000000000000..4d8c6851c1f1 --- /dev/null +++ b/packages/belos/kokkos/src/CMakeLists.txt @@ -0,0 +1,39 @@ + + +# +# A) Package-specific configuration options +# + +# +# B) Define the header and source files (and directories) +# + +# +# src +# + +SET(HEADERS "") +SET(SOURCES "") + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) + +# +# Core Files +# + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +APPEND_SET(HEADERS + BelosKokkosAdapter.hpp + ) + +# +# C) Define the targets for package's library(s) +# +#TRIBITS_ADD_LIBRARY( +# beloskokkos +# HEADERS ${HEADERS} +# SOURCES ${SOURCES} +# DEPLIBS belos +# ) + diff --git a/packages/belos/kokkos/test/BelosKokkosMVOPTester.hpp b/packages/belos/kokkos/test/BelosKokkosMVOPTester.hpp new file mode 100644 index 000000000000..51a4be03b13e --- /dev/null +++ b/packages/belos/kokkos/test/BelosKokkosMVOPTester.hpp @@ -0,0 +1,1610 @@ +//@HEADER +// ************************************************************************ +// +// Belos: Block Linear Solvers Package +// Copyright 2004 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +//@HEADER +// +#ifndef BELOS_KOKKOS_MVOPTESTER_HPP +#define BELOS_KOKKOS_MVOPTESTER_HPP + +// Assumptions that I have made: +// * I assume/verify that a multivector must have at least one std::vector. This seems +// to be consistent with Epetra_MultiVec. +// * I do not assume that an operator is deterministic; I do assume that the +// operator, applied to 0, will return 0. + +/*! \file BelosKokkosMVOPTester.hpp + \brief Test routines for Kokkos MultiVecTraits and OperatorTraits conformity. + Note: This tester file is a direct copy of the BelosMVOPTester.hpp, + except that the tests for accessing non-contiguous columns of data have + been removed for the testing of the Kokkos adapter. +*/ + +#include "BelosConfigDefs.hpp" +#include "BelosTypes.hpp" + +#include "BelosMultiVecTraits.hpp" +#include "BelosOperatorTraits.hpp" +#include "BelosOutputManager.hpp" + +#include "Teuchos_RCP.hpp" +#include "Teuchos_SetScientific.hpp" +#include "Teuchos_SerialDenseHelpers.hpp" + +namespace Belos { + + /// \brief Test correctness of a MultiVecTraits specialization and + /// multivector implementation. + /// + /// \tparam ScalarType The type of the entries in the multivectors; + /// the first template parameter of MultiVecTraits. + /// \tparam MV The multivector type; the second template parameter + /// of MultiVecTraits. + /// + /// \param om [in/out] A valid OutputManager, for displaying test results. + /// + /// \param A [in] An initial multivector, to use for making new + /// multivectors. (Belos doesn't currently have a "vector space" + /// abstraction; making a new multivector requires a valid input + /// multivector to clone.) + /// + /// \return Test result: true if all tests passed, else false. + template< class ScalarType, class MV > + bool + TestKokkosMultiVecTraits (const Teuchos::RCP > &om, + const Teuchos::RCP &A) + { + using Teuchos::SetScientific; + using std::endl; + typedef MultiVecTraits MVT; + typedef Teuchos::ScalarTraits STS; + typedef typename STS::magnitudeType MagType; + + // Make sure that all floating-point numbers are printed with the + // right precision. + SetScientific sci (om->stream (Warnings)); + + // FIXME (mfh 09 Jan 2013) Added an arbitrary tolerance in case + // norms are not computed deterministically (which is possible + // even with MPI only, and more likely with threads). + const MagType tol = Teuchos::as (100) * STS::eps (); + + /* MVT Contract: + + Clone(MV,int) + CloneCopy(MV) + CloneCopy(MV,vector) + USER: will request positive number of vectors + MV: will return a multivector with exactly the number of + requested vectors. + vectors are the same dimension as the cloned MV + + + CloneView(MV,vector) [const and non-const] + USER: There is no assumed communication between creation and + destruction of a view. I.e., after a view is created, changes to the + source multivector are not reflected in the view. Likewise, until + destruction of the view, changes in the view are not reflected in the + source multivector. + + GetGlobalLength + MV: will always be positive (MV cannot have zero vectors) + + GetNumberVecs + MV: will always be positive (MV cannot have zero vectors) + + MvAddMv + USER: multivecs will be of the same dimension and same number of vecs + MV: input vectors will not be modified + performing C=0*A+1*B will assign B to C exactly + + MvTimesMatAddMv + USER: multivecs and serialdensematrix will be of the proper shape + MV: input arguments will not be modified + following arithmetic relations hold exactly: + A*I = A + 0*B = B + 1*B = B + + MvTransMv + USER: SerialDenseMatrix will be large enough to hold results. + MV: SerialDenseMatrix will not be resized. + Inner products will satisfy |a'*b| <= |a|*|b| + alpha == 0 => SerialDenseMatrix == 0 + + MvDot + USER: Results vector will be large enough for results. + Both multivectors will have the same number of vectors. + (Epetra crashes, otherwise.) + MV: Inner products will satisfy |a'*b| <= |a|*|b| + Results vector will not be resized. + + MvNorm + MV: vector norm is always non-negative, and zero + only for zero vectors. + results vector should not be resized + + SetBlock + USER: indices will be distinct + MV: assigns copies of the vectors to the specified + locations, leaving the other vectors untouched. + + MvRandom + MV: Generate zero vector with "zero" probability + Don't gen the same vectors twice. + + MvInit + MV: Init(alpha) sets all elements to alpha + + MvScale (two versions) + MV: scales multivector values + + MvPrint + MV: routine does not modify vectors (not tested here) + *********************************************************************/ + + const ScalarType one = STS::one(); + const ScalarType zero = STS::zero(); + const MagType zero_mag = Teuchos::ScalarTraits::zero(); + + // Don't change these two without checking the initialization of ind below + const int numvecs = 10; + const int numvecs_2 = 5; + + std::vector ind(numvecs_2); + std::vector indContig(numvecs_2); + + /* Initialize indices for selected copies/views + The MVT specialization should not assume that + these are ordered or even distinct. + Also retrieve the edges. + + However, to spice things up, grab the first std::vector, + last std::vector, and choose the others randomly. + */ + TEUCHOS_TEST_FOR_EXCEPT(numvecs_2 != 5); + ind[0] = 0; + ind[1] = 5; + ind[2] = 2; + ind[3] = 2; + ind[4] = 9; + + indContig[0] = 2; + indContig[1] = 3; + indContig[2] = 4; + indContig[3] = 5; + indContig[4] = 6; + + /*********** GetNumberVecs() ***************************************** + Verify: + 1) This number should be strictly positive + *********************************************************************/ + if ( MVT::GetNumberVecs(*A) <= 0 ) { + om->stream(Warnings) + << "*** ERROR *** MultiVectorTraits::GetNumberVecs()." << endl + << "Returned <= 0." << endl; + return false; + } + + + /*********** GetGlobalLength() *************************************** + Verify: + 1) This number should be strictly positive + *********************************************************************/ + if ( MVT::GetGlobalLength(*A) <= 0 ) { + om->stream(Warnings) + << "*** ERROR *** MultiVectorTraitsExt::GetGlobalLength()" << endl + << "Returned <= 0." << endl; + return false; + } + + + /*********** Clone() and MvNorm() ************************************ + Verify: + 1) Clone() allows us to specify the number of vectors + 2) Clone() returns a multivector of the same dimension + 3) Vector norms shouldn't be negative + 4) MvNorm result std::vector should not be resized + *********************************************************************/ + { + Teuchos::RCP B = MVT::Clone(*A,numvecs); + std::vector norms(2*numvecs); + bool ResizeWarning = false; + if ( MVT::GetNumberVecs(*B) != numvecs ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::Clone()." << endl + << "Did not allocate requested number of vectors." << endl; + return false; + } + if ( MVT::GetGlobalLength(*B) != MVT::GetGlobalLength(*A) ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::Clone()." << endl + << "Did not allocate requested number of vectors." << endl; + return false; + } + MVT::MvNorm(*B, norms); + if ( norms.size() != 2*numvecs && ResizeWarning==false ) { + om->stream(Warnings) + << "*** WARNING *** MultiVecTraits::MvNorm()." << endl + << "Method resized the output vector." << endl; + ResizeWarning = true; + } + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::Clone()." << endl + << "Vector had negative norm." << endl; + return false; + } + } + } + + + /*********** MvRandom() and MvNorm() and MvInit() ******************** + Verify: + 1) Set vectors to zero + 2) Check that norm is zero + 3) Perform MvRandom. + 4) Verify that vectors aren't zero anymore + 5) Perform MvRandom again. + 6) Verify that std::vector norms are different than before + + Without knowing something about the random distribution, + this is about the best that we can do, to make sure that MvRandom + did at least *something*. + + Also, make sure std::vector norms aren't negative. + *********************************************************************/ + { + Teuchos::RCP B = MVT::Clone(*A,numvecs); + std::vector norms(numvecs), norms2(numvecs); + + MVT::MvInit(*B); + MVT::MvNorm(*B, norms); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvInit() " + << "and MultiVecTraits::MvNorm()" << endl + << "Supposedly zero vector has non-zero norm." << endl; + return false; + } + } + MVT::MvRandom(*B); + MVT::MvNorm(*B, norms); + MVT::MvRandom(*B); + MVT::MvNorm(*B, norms2); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvRandom()." << endl + << "Random vector was empty (very unlikely)." << endl; + return false; + } + else if ( norms[i] < zero_mag || norms2[i] < zero_mag ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvRandom()." << endl + << "Vector had negative norm." << endl; + return false; + } + else if ( norms[i] == norms2[i] ) { + om->stream(Warnings) + << "*** ERROR *** MutliVecTraits::MvRandom()." << endl + << "Vectors not random enough." << endl; + return false; + } + } + } + + + /*********** MvRandom() and MvNorm() and MvScale() ******************* + Verify: + 1) Perform MvRandom. + 2) Verify that vectors aren't zero + 3) Set vectors to zero via MvScale + 4) Check that norm is zero + *********************************************************************/ + { + Teuchos::RCP B = MVT::Clone(*A,numvecs); + std::vector norms(numvecs); + + MVT::MvRandom(*B); + MVT::MvScale(*B,STS::zero()); + MVT::MvNorm(*B, norms); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvScale(alpha) " + << "Supposedly zero vector has non-zero norm." << endl; + return false; + } + } + + MVT::MvRandom(*B); + std::vector zeros(numvecs,STS::zero()); + MVT::MvScale(*B,zeros); + MVT::MvNorm(*B, norms); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvScale(alphas) " + << "Supposedly zero vector has non-zero norm." << endl; + return false; + } + } + } + + + /*********** MvInit() and MvNorm() *********************************** + A std::vector of ones of dimension n should have norm std::sqrt(n) + 1) Init vectors to all ones + 2) Verify that norm is std::sqrt(n) + 3) Verify that norms aren't negative + + Note: I'm not sure that we can expect this to hold in practice. + Maybe something like std::abs(norm-std::sqrt(n)) < STS::eps() ??? + The sum of 1^2==1 should be n, but what about std::sqrt(n)? + They may be using a different square root than ScalartTraits + On my iBook G4 and on jeter, this test works. + Right now, this has been demoted to a warning. + *********************************************************************/ + { + Teuchos::RCP B = MVT::Clone(*A,numvecs); + std::vector norms(numvecs); + + MVT::MvInit(*B,one); + MVT::MvNorm(*B, norms); + bool BadNormWarning = false; + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvRandom()." << endl + << "Vector had negative norm." << endl; + return false; + } + else if ( norms[i] != STS::squareroot(MVT::GetGlobalLength(*B)) && !BadNormWarning ) { + om->stream(Warnings) + << endl + << "Warning testing MultiVecTraits::MvInit()." << endl + << "Ones std::vector should have norm std::sqrt(dim)." << endl + << "norms[i]: " << norms[i] << "\tdim: " << MVT::GetGlobalLength(*B) << endl << endl; + BadNormWarning = true; + } + } + } + + + /*********** MvInit() and MvNorm() *********************************** + A std::vector of zeros of dimension n should have norm 0 + 1) Verify that norms aren't negative + 2) Verify that norms are zero + + We must know this works before the next tests. + *********************************************************************/ + { + Teuchos::RCP B = MVT::Clone(*A,numvecs); + std::vector norms(numvecs); + MVT::MvInit(*B, zero_mag); + MVT::MvNorm(*B, norms); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvInit()." << endl + << "Vector had negative norm." << endl; + return false; + } + else if ( norms[i] != zero_mag ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvInit()." << endl + << "Zero std::vector should have norm zero." << endl; + return false; + } + } + } + + + /*********** CloneCopy(MV,std::vector) and MvNorm ******************** + 1) Check quantity/length of vectors + 2) Check std::vector norms for agreement + 3) Zero out B and make sure that C norms are not affected + *********************************************************************/ + { + Teuchos::RCP B, C; + std::vector norms(numvecs), norms2(numvecs); + + B = MVT::Clone(*A,numvecs); + MVT::MvRandom(*B); + MVT::MvNorm(*B, norms); + C = MVT::CloneCopy(*B,ind); + MVT::MvNorm(*C, norms2); + if ( MVT::GetNumberVecs(*C) != numvecs_2 ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy(ind)." << endl + << "Wrong number of vectors." << endl; + return false; + } + if ( MVT::GetGlobalLength(*C) != MVT::GetGlobalLength(*B) ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy(ind)." << endl + << "Vector lengths don't match." << endl; + return false; + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy(ind)." << endl + << "Copied vectors do not agree: " + << norms2[i] << " != " << norms[ind[i]] << endl + << "Difference " << STS::magnitude (norms2[i] - norms[ind[i]]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + MVT::MvInit(*B,zero); + MVT::MvNorm(*C, norms); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy(ind)." << endl + << "Copied vectors were not independent." << endl + << norms2[i] << " != " << norms[i] << endl + << "Difference " << STS::magnitude (norms2[i] - norms[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + } + + /*********** CloneCopy(MV) and MvNorm ******************************** + 1) Check quantity + 2) Check value of norms + 3) Zero out B and make sure that C is still okay + *********************************************************************/ + { + Teuchos::RCP B, C; + std::vector norms(numvecs), norms2(numvecs); + + B = MVT::Clone(*A,numvecs); + MVT::MvRandom(*B); + MVT::MvNorm(*B, norms); + C = MVT::CloneCopy(*B); + MVT::MvNorm(*C, norms2); + if ( MVT::GetNumberVecs(*C) != numvecs ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy()." << endl + << "Wrong number of vectors." << endl; + return false; + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy()." << endl + << "Copied vectors do not agree: " + << norms2[i] << " != " << norms[i] << endl + << "Difference " << STS::magnitude (norms2[i] - norms[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + MVT::MvInit(*B,zero); + MVT::MvNorm(*C, norms); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneCopy()." << endl + << "Copied vectors were not independent." << endl + << norms2[i] << " != " << norms[i] << endl + << "Difference " << STS::magnitude (norms2[i] - norms[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + } + + + /*********** CloneView(MV,std::vector) and MvNorm ******************** + Check that we have a view of the selected vectors + 1) Check quantity + 2) Check value of norms + 3) Zero out B and make sure that C is zero as well + *********************************************************************/ + { + Teuchos::RCP B, C; + std::vector norms(numvecs), norms2(numvecs); + + B = MVT::Clone(*A,numvecs); + MVT::MvRandom(*B); + MVT::MvNorm(*B, norms); + C = MVT::CloneViewNonConst(*B,indContig); + MVT::MvNorm(*C, norms2); + if ( MVT::GetNumberVecs(*C) != numvecs_2 ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneView(indContig)." << endl + << "Wrong number of vectors." << endl; + return false; + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::CloneView(indContig)." << endl + << "Viewed vectors do not agree." << endl; + return false; + } + } + } + + + /*********** CloneView(const MV,std::vector) and MvNorm() ************ + Check that we have a view of the selected vectors. + 1) Check quantity + 2) Check value of norms for agreement + 3) Zero out B and make sure that C is zerod as well + *********************************************************************/ + { + Teuchos::RCP B; + Teuchos::RCP C; + std::vector normsB(numvecs), normsC(numvecs_2); + std::vector allind(numvecs); + for (int i=0; istream(Warnings) + << "*** ERROR *** const MultiVecTraits::CloneView(indContig)." << endl + << "Wrong number of vectors." << endl; + return false; + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** const MultiVecTraits::CloneView(indContig)." << endl + << "Viewed vectors do not agree." << endl; + return false; + } + } + } + + /*********** SetBlock() and MvNorm() ********************************* + SetBlock() will copy the vectors from C into B + 1) Verify that the specified vectors were copied + 2) Verify that the other vectors were not modified + 3) Verify that C was not modified + 4) Change C and then check B to make sure it was not modified + + Use a different index set than has been used so far (distinct entries). + This is because duplicate entries will cause the std::vector to be + overwritten, making it more difficult to test. + *********************************************************************/ + { + Teuchos::RCP B, C; //numvecs = 10, numvecs_2 = 5 + std::vector normsB1(numvecs), normsB2(numvecs), + normsC1(numvecs_2), normsC2(numvecs_2); + + B = MVT::Clone(*A,numvecs); + C = MVT::Clone(*A,numvecs_2); + // Just do every other one, interleaving the vectors of C into B + ind.resize(numvecs_2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Operation modified source vectors." << endl; + return false; + } + } + // check that the correct vectors of B were modified + // and the others were not + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Copied vectors do not agree: " << endl + << normsB2[i] << " != " << normsC1[i/2] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsC1[i/2]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + else { + // should be an original vector + if (STS::magnitude (normsB1[i] - normsB2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Incorrect vectors were modified." << endl + << normsB1[i] << " != " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsB2[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + } + MVT::MvInit(*C,zero); + MVT::MvNorm(*B,normsB1); + // verify that we copied and didn't reference + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Copied vectors were not independent." << endl + << normsB1[i] << " != " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB1[i] - normsB2[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + } + + + /*********** SetBlock() and MvNorm() ********************************* + SetBlock() will copy the vectors from C into B + 1) Verify that the specified vectors were copied + 2) Verify that the other vectors were not modified + 3) Verify that C was not modified + 4) Change C and then check B to make sure it was not modified + + Use a different index set than has been used so far (distinct entries). + This is because duplicate entries will cause the std::vector to be + overwritten, making it more difficult to test. + + These tests are the same as the ones above, except that the + number of indices (to be copied into B) is less than the number + of vectors in C, so that not all of C is put into B. + *********************************************************************/ + { + Teuchos::RCP B, C; + // set these: we assume below that setSize*2=BSize + const int CSize = 6, + setSize = 5, + BSize = 2*setSize; + std::vector normsB1(BSize), normsB2(BSize), + normsC1(CSize), normsC2(CSize); + + B = MVT::Clone(*A,BSize); + C = MVT::Clone(*A,CSize); + // Just do every other one, interleaving the vectors of C into B + ind.resize(setSize); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Operation modified source vectors." << endl; + return false; + } + } + // check that the correct vectors of B were modified + // and the others were not + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Copied vectors do not agree: " << endl + << normsB2[i] << " != " << normsC1[i/2] << endl + << "Difference " << diff << " exceeds the tolerance 100*eps = " + << tol << endl; + return false; + } + } + else { + // should be an original vector + const MagType diff = STS::magnitude (normsB1[i] - normsB2[i]); + //if ( normsB1[i] != normsB2[i] ) { + if (diff > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Incorrect vectors were modified." << endl + << normsB1[i] << " != " << normsB2[i] << endl + << "Difference " << diff << " exceeds the tolerance 100*eps = " + << tol << endl; + return false; + } + } + } + MVT::MvInit(*C,zero); + MVT::MvNorm(*B,normsB1); + // verify that we copied and didn't reference + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::SetBlock()." << endl + << "Copied vectors were not independent." << endl + << normsB1[i] << " != " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB1[i] - normsB2[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + } + + + /*********** MvTransMv() ********************************************* + Performs C = alpha * A^H * B, where + alpha is type ScalarType + A,B are type MV with p and q vectors, respectively + C is a SerialDenseMatrix ALREADY sized to p by q + + Verify: + 1) C is not resized by the routine + 3) Check that zero*(A^H B) == zero + 3) Check inner product inequality: + [ |a1|*|b1| ... |ap|*|b1| ] + [a1 ... ap]^H [b1 ... bq] <= [ ... |ai|*|bj| ... ] + [ |ap|*|b1| ... |ap|*|bq| ] + 4) Zero B and check that C is zero + 5) Zero A and check that C is zero + + Note: Should we really require that C is correctly sized already? + Epetra does (and crashes if it isn't.) + *********************************************************************/ + { + const int p = 7; + const int q = 9; + Teuchos::RCP B, C; + std::vector normsB(p), normsC(q); + Teuchos::SerialDenseMatrix SDM(p,q); + + B = MVT::Clone(*A,p); + C = MVT::Clone(*A,q); + + // randomize the multivectors + MVT::MvRandom(*B); + MVT::MvNorm(*B,normsB); + MVT::MvRandom(*C); + MVT::MvNorm(*C,normsC); + + // perform SDM = zero() * B^H * C + MVT::MvTransMv( zero, *B, *C, SDM ); + + // check the sizes: not allowed to have shrunk + if ( SDM.numRows() != p || SDM.numCols() != q ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTransMv()." << endl + << "Routine resized SerialDenseMatrix." << endl; + return false; + } + + // check that zero**A^H*B == zero + if ( SDM.normOne() != zero ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTransMv()." << endl + << "Scalar argument processed incorrectly." << endl; + return false; + } + + // perform SDM = one * B^H * C + MVT::MvTransMv( one, *B, *C, SDM ); + + // check the norms: a^H b = |a| |b| cos(theta) <= |a| |b| + // with equality only when a and b are colinear + for (int i=0; i STS::magnitude(normsB[i]*normsC[j]) ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTransMv()." << endl + << "Triangle inequality did not hold: " + << STS::magnitude(SDM(i,j)) + << " > " + << STS::magnitude(normsB[i]*normsC[j]) + << endl; + return false; + } + } + } + MVT::MvInit(*C); + MVT::MvRandom(*B); + MVT::MvTransMv( one, *B, *C, SDM ); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTransMv()." << endl + << "Inner products not zero for C==0." << endl; + return false; + } + } + } + MVT::MvInit(*B); + MVT::MvRandom(*C); + MVT::MvTransMv( one, *B, *C, SDM ); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTransMv()." << endl + << "Inner products not zero for B==0." << endl; + return false; + } + } + } + } + + + /*********** MvDot() ************************************************* + Verify: + 1) Results std::vector not resized + 2) Inner product inequalities are satisfied + 3) Zero vectors give zero inner products + *********************************************************************/ + { + const int p = 7; + const int q = 9; + Teuchos::RCP B, C; + std::vector iprods(p+q); + std::vector normsB(numvecs), normsC(numvecs); + + B = MVT::Clone(*A,p); + C = MVT::Clone(*A,p); + + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB); + MVT::MvNorm(*C,normsC); + MVT::MvDot( *B, *C, iprods ); + if ( iprods.size() != p+q ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvDot." << endl + << "Routine resized results std::vector." << endl; + return false; + } + for (int i=0; i STS::magnitude(normsB[i]*normsC[i]) ) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvDot()." << endl + << "Inner products not valid." << endl; + return false; + } + } + MVT::MvInit(*B); + MVT::MvRandom(*C); + MVT::MvDot( *B, *C, iprods ); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvDot()." << endl + << "Inner products not zero for B==0." << endl; + return false; + } + } + MVT::MvInit(*C); + MVT::MvRandom(*B); + MVT::MvDot( *B, *C, iprods ); + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvDot()." << endl + << "Inner products not zero for C==0." << endl; + return false; + } + } + } + + + /*********** MvAddMv() *********************************************** + D = alpha*B + beta*C + 1) Use alpha==0,beta==1 and check that D == C + 2) Use alpha==1,beta==0 and check that D == B + 3) Use D==0 and D!=0 and check that result is the same + 4) Check that input arguments are not modified + *********************************************************************/ + { + const int p = 7; + Teuchos::RCP B, C, D; + std::vector normsB1(p), normsB2(p), + normsC1(p), normsC2(p), + normsD1(p), normsD2(p); + + Teuchos::SerialDenseMatrix Alpha(1,1), Beta(1,1); + Teuchos::randomSyncedMatrix( Alpha ); + Teuchos::randomSyncedMatrix( Beta ); + ScalarType alpha = Alpha(0,0), + beta = Beta(0,0); + + B = MVT::Clone(*A,p); + C = MVT::Clone(*A,p); + D = MVT::Clone(*A,p); + + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + + // check that 0*B+1*C == C + MVT::MvAddMv(zero,*B,one,*C,*D); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + MVT::MvNorm(*D,normsD1); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsC1[i] - normsC2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsC1[i] - normsD1[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Assignment did not work." << endl; + return false; + } + } + + // check that 1*B+0*C == B + MVT::MvAddMv(one,*B,zero,*C,*D); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + MVT::MvNorm(*D,normsD1); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsC1[i] - normsC2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsB1[i] - normsD1[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Assignment did not work." << endl; + return false; + } + } + + // check that alpha*B+beta*C -> D is invariant under initial D + // first, try random D + MVT::MvRandom(*D); + MVT::MvAddMv(alpha,*B,beta,*C,*D); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + MVT::MvNorm(*D,normsD1); + // check that input args are not modified + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsC1[i] - normsC2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + } + // next, try zero D + MVT::MvInit(*D); + MVT::MvAddMv(alpha,*B,beta,*C,*D); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + MVT::MvNorm(*D,normsD2); + // check that input args are not modified and that D is the same + // as the above test + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsC1[i] - normsC2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Input arguments were modified." << endl; + return false; + } + else if (STS::magnitude (normsD1[i] - normsD2[i]) > tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv()." << endl + << "Results varies depending on initial state of dest vectors." << endl; + return false; + } + } + } + + /*********** MvAddMv() *********************************************** + Similar to above, but where B or C are potentially the same + object as D. This case is commonly used, for example, to affect + A <- alpha*A + via + MvAddMv(alpha,A,zero,A,A) + ** OR ** + MvAddMv(zero,A,alpha,A,A) + + The result is that the operation has to be "atomic". That is, + B and C are no longer reliable after D is modified, so that + the assignment to D must be the last thing to occur. + + D = alpha*B + beta*C + + 1) Use alpha==0,beta==1 and check that D == C + 2) Use alpha==1,beta==0 and check that D == B + *********************************************************************/ + { + const int p = 7; + Teuchos::RCP B, D; + Teuchos::RCP C; + std::vector normsB(p), + normsD(p); + std::vector lclindex(p); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv() #2" << endl + << "Assignment did not work." << endl; + return false; + } + } + + // check that 1*B+0*C == B + MVT::MvAddMv(one,*B,zero,*C,*D); + MVT::MvNorm(*D,normsD); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvAddMv() #2" << endl + << "Assignment did not work." << endl; + return false; + } + } + + } + + /*********** MvTimesMatAddMv() 7 by 5 ******************************** + C = alpha*B*SDM + beta*C + 1) Use alpha==0, SDM!=0, beta==1 and check that C is unchanged + 2) Use alpha==0, SDM!=0, beta==0 and check that C is set to zero + 3) Use alpha==1, SDM==I, beta==0 and check that C is set to B + 4) Use alpha==1, SDM==0, beta==1 and check that C is unchanged + 5) Test with non-square matrices + 6) Always check that input arguments are not modified + *********************************************************************/ + { + const int p = 7, q = 5; + Teuchos::RCP B, C; + Teuchos::SerialDenseMatrix SDM(p,q); + std::vector normsC1(q), normsC2(q), + normsB1(p), normsB2(p); + + B = MVT::Clone(*A,p); + C = MVT::Clone(*A,q); + + // Test 1: alpha==0, SDM!=0, beta==1 and check that C is unchanged + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + Teuchos::randomSyncedMatrix(SDM); + MVT::MvTimesMatAddMv(zero,*B,SDM,one,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 1 failed." << endl; + return false; + } + } + + // Test 2: alpha==0, SDM!=0, beta==0 and check that C is set to zero + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + Teuchos::randomSyncedMatrix(SDM); + MVT::MvTimesMatAddMv(zero,*B,SDM,zero,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 2 failed: " + << normsC2[i] + << " != " + << zero + << endl; + return false; + } + } + + // Test 3: alpha==1, SDM==|I|, beta==0 and check that C is set to B + // |0| + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + SDM.scale(zero); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 3 failed: " + << normsB1[i] + << " != " + << normsC2[i] + << endl; + return false; + } + } + + // Test 4: alpha==1, SDM==0, beta==1 and check that C is unchanged + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + SDM.scale(zero); + MVT::MvTimesMatAddMv(one,*B,SDM,one,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 4 failed." << endl; + return false; + } + } + } + + /*********** MvTimesMatAddMv() 5 by 7 ******************************** + C = alpha*B*SDM + beta*C + 1) Use alpha==0, SDM!=0, beta==1 and check that C is unchanged + 2) Use alpha==0, SDM!=0, beta==0 and check that C is set to zero + 3) Use alpha==1, SDM==I, beta==0 and check that C is set to B + 4) Use alpha==1, SDM==0, beta==1 and check that C is unchanged + 5) Test with non-square matrices + 6) Always check that input arguments are not modified + *********************************************************************/ + { + const int p = 5, q = 7; + Teuchos::RCP B, C; + Teuchos::SerialDenseMatrix SDM(p,q); + std::vector normsC1(q), normsC2(q), + normsB1(p), normsB2(p); + + B = MVT::Clone(*A,p); + C = MVT::Clone(*A,q); + + // Test 5: alpha==0, SDM!=0, beta==1 and check that C is unchanged + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + Teuchos::randomSyncedMatrix(SDM); + MVT::MvTimesMatAddMv(zero,*B,SDM,one,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 5 failed." << endl; + return false; + } + } + + // Test 6: alpha==0, SDM!=0, beta==0 and check that C is set to zero + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + Teuchos::randomSyncedMatrix(SDM); + MVT::MvTimesMatAddMv(zero,*B,SDM,zero,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 6 failed: " + << normsC2[i] + << " != " + << zero + << endl; + return false; + } + } + + // Test 7: alpha==1, SDM==[I 0], beta==0 and check that C is set to B + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + SDM.scale(zero); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 7 failed." << endl; + return false; + } + } + for (int i=p; istream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 7 failed." << endl; + return false; + } + } + + // Test 8: alpha==1, SDM==0, beta==1 and check that C is unchanged + MVT::MvRandom(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + MVT::MvNorm(*C,normsC1); + SDM.scale(zero); + MVT::MvTimesMatAddMv(one,*B,SDM,one,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Input vectors were modified." << endl; + return false; + } + } + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** MultiVecTraits::MvTimesMatAddMv()." << endl + << "Arithmetic test 8 failed." << endl; + return false; + } + } + } + + return true; + + } + + + + /// \brief Test correctness of OperatorTraits specialization and its + /// operator implementation. + /// + /// \tparam ScalarType The type of the entries in the multivectors; + /// the first template parameter of MultiVecTraits and + /// OperatorTraits. + /// \tparam MV The multivector type; the second template parameter + /// of MultiVecTraits and OperatorTraits. + /// \tparam OP The operator type; the third template parameter + /// of OperatorTraits. + /// + /// \param om [in/out] A valid OutputManager, for displaying test results. + /// + /// \param A [in] An initial multivector, to use for making new + /// multivectors. (Belos doesn't currently have a "vector space" + /// abstraction; making a new multivector requires a valid input + /// multivector to clone.) + /// + /// \param M [in] The operator to test. + /// + /// \return Test result: true if all tests passed, else false. + template< class ScalarType, class MV, class OP> + bool + TestKokkosOperatorTraits (const Teuchos::RCP > &om, + const Teuchos::RCP &A, + const Teuchos::RCP &M) + { + using Teuchos::SetScientific; + using std::endl; + typedef MultiVecTraits MVT; + typedef Teuchos::ScalarTraits STS; + typedef typename STS::magnitudeType MagType; + + // Make sure that all floating-point numbers are printed with the + // right precision. + SetScientific sci (om->stream (Warnings)); + + // FIXME (mfh 09 Jan 2013) Added an arbitrary tolerance in case + // norms are not computed deterministically (which is possible + // even with MPI only, and more likely with threads). + const MagType tol = Teuchos::as (100) * STS::eps (); + + /* OPT Contract: + Apply() + MV: OP*zero == zero + Warn if OP is not deterministic (OP*A != OP*A) + Does not modify input arguments + *********************************************************************/ + + typedef MultiVecTraits MVT; + typedef Teuchos::ScalarTraits STS; + typedef OperatorTraits OPT; + typedef typename STS::magnitudeType MagType; + + const int numvecs = 10; + + Teuchos::RCP B = MVT::Clone(*A,numvecs), + C = MVT::Clone(*A,numvecs); + + std::vector normsB1(numvecs), normsB2(numvecs), + normsC1(numvecs), normsC2(numvecs); + bool NonDeterministicWarning; + + /*********** Apply() ************************************************* + Verify: + 1) OP*B == OP*B; OP is deterministic (just warn on this) + 2) OP*zero == 0 + 3) OP*B doesn't modify B + 4) OP*B is invariant under initial state of destination vectors + *********************************************************************/ + MVT::MvInit(*B); + MVT::MvRandom(*C); + MVT::MvNorm(*B,normsB1); + OPT::Apply(*M,*B,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [1]" << endl + << "Apply() modified the input vectors." << endl + << "Original: " << normsB1[i] << "; After: " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsB1[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + if (normsC2[i] != STS::zero()) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [1]" << endl + << "Operator applied to zero did not return zero." << endl; + return false; + } + } + + // If we send in a random matrix, we should not get a zero return + MVT::MvRandom(*B); + MVT::MvNorm(*B,normsB1); + OPT::Apply(*M,*B,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + bool ZeroWarning = false; + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [2]" << endl + << "Apply() modified the input vectors." << endl + << "Original: " << normsB1[i] << "; After: " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsB1[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + if (normsC2[i] == STS::zero() && ZeroWarning==false ) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [2]" << endl + << "Operator applied to random vectors returned zero." << endl; + ZeroWarning = true; + } + } + + // Apply operator with C init'd to zero + MVT::MvRandom(*B); + MVT::MvNorm(*B,normsB1); + MVT::MvInit(*C); + OPT::Apply(*M,*B,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC1); + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [3]" << endl + << "Apply() modified the input vectors." << endl + << "Original: " << normsB1[i] << "; After: " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsB1[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + } + + // Apply operator with C init'd to random + // Check that result is the same as before; warn if not. + // This could be a result of a bug, or a stochastic + // operator. We do not want to prejudice against a + // stochastic operator. + MVT::MvRandom(*C); + OPT::Apply(*M,*B,*C); + MVT::MvNorm(*B,normsB2); + MVT::MvNorm(*C,normsC2); + NonDeterministicWarning = false; + for (int i=0; i tol) { + om->stream(Warnings) + << "*** ERROR *** OperatorTraits::Apply() [4]" << endl + << "Apply() modified the input vectors." << endl + << "Original: " << normsB1[i] << "; After: " << normsB2[i] << endl + << "Difference " << STS::magnitude (normsB2[i] - normsB1[i]) + << " exceeds the tolerance 100*eps = " << tol << endl; + return false; + } + if (normsC1[i] != normsC2[i] && !NonDeterministicWarning) { + om->stream(Warnings) + << endl + << "*** WARNING *** OperatorTraits::Apply() [4]" << endl + << "Apply() returned two different results." << endl << endl; + NonDeterministicWarning = true; + } + } + + return true; + + } + +} + +#endif diff --git a/packages/belos/kokkos/test/CMakeLists.txt b/packages/belos/kokkos/test/CMakeLists.txt new file mode 100644 index 000000000000..2a37af1bd697 --- /dev/null +++ b/packages/belos/kokkos/test/CMakeLists.txt @@ -0,0 +1,8 @@ +INCLUDE_DIRECTORIES(${Belos_SOURCE_DIR}/kokkos/src) + +TRIBITS_ADD_EXECUTABLE_AND_TEST( + KokkosMVOPTest + SOURCES KokkosMVOPTest.cpp + COMM serial mpi + ) + diff --git a/packages/belos/kokkos/test/KokkosMVOPTest.cpp b/packages/belos/kokkos/test/KokkosMVOPTest.cpp new file mode 100644 index 000000000000..1f64b64354f4 --- /dev/null +++ b/packages/belos/kokkos/test/KokkosMVOPTest.cpp @@ -0,0 +1,553 @@ +//@HEADER +// ************************************************************************ +// +// Belos: Block Linear Solvers Package +// Copyright 2004 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Michael A. Heroux (maherou@sandia.gov) +// +// ************************************************************************ +//@HEADER +// +// This test uses the MVOPTester.hpp functions to test the Belos adapters +// to Kokkos. +// + + +#include "BelosConfigDefs.hpp" +#include "BelosKokkosMVOPTester.hpp" +#include "BelosOutputManager.hpp" +#include "BelosKokkosAdapter.hpp" + +#include "Teuchos_StandardCatchMacros.hpp" +#ifdef HAVE_MPI + #include +#endif + +using std::cout; +using std::endl; +using Teuchos::RCP; +using Belos::Warnings; +using Belos::OutputManager; + +template +bool TestKokkosMultiVecOneScalar(const Teuchos::RCP >& ); + +template +bool TestKokkosMultiVecTwoScalar(const Teuchos::RCP > & outputMgr); + +int main(int argc, char *argv[]) +{ +#ifdef HAVE_MPI + MPI_Init(&argc,&argv); +#endif + bool isPassed; + bool success = true; + Kokkos::initialize(); + { + bool verbose = false; + if (argc>1) { + if (argv[1][0]=='-' && argv[1][1]=='v') { + verbose = true; + } + } + typedef double ScalarType; + typedef float ScalarType2; + typedef Belos::MultiVec KMV; + typedef Belos::Operator KOP; + typedef Belos::MultiVec KMV2; + typedef Belos::Operator KOP2; + typedef Kokkos::DefaultExecutionSpace EXSP; + + // Create an output manager to handle the I/O from the solver (defaults to std::cout). + Teuchos::RCP > myOutputMgr = Teuchos::rcp( new Belos::OutputManager() ); + Teuchos::RCP > myOutputMgr2 = Teuchos::rcp( new Belos::OutputManager() ); + if (verbose) { + myOutputMgr->setVerbosity( Warnings ); + myOutputMgr2->setVerbosity( Warnings ); + } +try { + // number of global elements + int dim = 10; + int blockSize = 5; + std::vector norms(blockSize); + + + //***************************************************************************************************************************** + //***************************************************************************************************************************** + // Run native Kokkos::Multivec test (double). + isPassed = TestKokkosMultiVecOneScalar(myOutputMgr); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestKokkosMultiVecOneScalar() double. \n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestKokkosMultiVecOneScalar() double. ***\n\n"); + } + + // Run native Kokkos::Multivec test (single). + isPassed = TestKokkosMultiVecOneScalar(myOutputMgr2); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestKokkosMultiVecOneScalar() single. \n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestKokkosMultiVecOneScalar() single. ***\n\n"); + } + + //***************************************************************************************************************************** + //***************************************************************************************************************************** + // Run native Kokkos::Multivec tests with mixed single-double precisions: + isPassed = TestKokkosMultiVecTwoScalar(myOutputMgr); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestKokkosMultiVecTwoScalar() \n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestKokkosMultiVecTwoScalar() ***\n\n"); + } + + //***************************************************************************************************************************** + //***************************************************************************************************************************** + // Run Belos tests on Kokkos MultiVec (double precision): + Teuchos::RCP> ivec = Teuchos::rcp( new Belos::KokkosMultiVec(dim, blockSize) ); + ivec->MvRandom(); + isPassed = Belos::TestKokkosMultiVecTraits(myOutputMgr,ivec); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestMultiVecTraits() double.\n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestMultiVecTraits() double. ***\n\n"); + } + + // Run Belos tests on Kokkos MultiVec (single precision): + Teuchos::RCP> ivec_2 = Teuchos::rcp( new Belos::KokkosMultiVec(dim, blockSize) ); + ivec_2->MvRandom(); + isPassed = Belos::TestKokkosMultiVecTraits(myOutputMgr2,ivec_2); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestMultiVecTraits() single. \n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestMultiVecTraits() single. ***\n\n"); + } + //***************************************************************************************************************************** + //***************************************************************************************************************************** + // Read in a matrix Market file and use it to test the Kokkos Operator (double precision). + KokkosSparse::CrsMatrix crsMat = + KokkosKernels::Impl::read_kokkos_crst_matrix>("bcsstk13.mtx"); + Teuchos::RCP> myOp = + Teuchos::rcp(new Belos::KokkosCrsOperator(crsMat)); + + Teuchos::RCP> ivec3 = Teuchos::rcp( new Belos::KokkosMultiVec(2003, 2) ); + + isPassed = Belos::TestKokkosOperatorTraits(myOutputMgr,ivec3,myOp); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestOperatorTraits() double. \n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestOperatorTraits() double ***\n\n"); + } + // Read in a matrix Market file and use it to test the Kokkos Operator (single precision). + KokkosSparse::CrsMatrix crsMat2 = + KokkosKernels::Impl::read_kokkos_crst_matrix>("bcsstk13.mtx"); + Teuchos::RCP> myOp2 = + Teuchos::rcp(new Belos::KokkosCrsOperator(crsMat2)); + + Teuchos::RCP> ivec3_2 = Teuchos::rcp( new Belos::KokkosMultiVec(2003, 2) ); + + isPassed = Belos::TestKokkosOperatorTraits(myOutputMgr2,ivec3_2,myOp2); + success = isPassed && success; + if (isPassed) { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter PASSED TestOperatorTraits() single\n"); + } + else { + myOutputMgr->print(Belos::Warnings,"*** KokkosAdapter FAILED TestOperatorTraits() single ***\n\n"); + } + //***************************************************************************************************************************** + //***************************************************************************************************************************** + + if (!success) { + myOutputMgr->print(Belos::Warnings,"End Result: TEST FAILED\n"); + } else { + myOutputMgr->print(Belos::Warnings,"End Result: TEST PASSED\n"); + } + }//end try block + + + TEUCHOS_STANDARD_CATCH_STATEMENTS(verbose,std::cerr,success); + } + Kokkos::finalize(); +#ifdef HAVE_MPI + MPI_Finalize(); +#endif + return success ? EXIT_SUCCESS : EXIT_FAILURE; +} + +template +bool TestKokkosMultiVecOneScalar(const Teuchos::RCP > & outputMgr){ + int dim = 10; + int blockSize = 5; + std::vector norms(blockSize); + + /// Test KokkosMultiVec constructors: + // Test constructor #1: + Belos::KokkosMultiVec myVec1("myLabel", dim, blockSize); + if ( myVec1.GetNumberVecs() != blockSize ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 1 returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVec1.GetGlobalLength() != dim ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 1 returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVec1.MvNorm(norms); + for(int i = 0; i < blockSize; i++){ + if( norms[i] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 1 returned wrong nrm2 value. " + << "Vector was not initialized to zeros." << endl; + return false; + } + } + // Test constructor #2: + Belos::KokkosMultiVec myVec2(dim, blockSize); + if ( myVec2.GetNumberVecs() != blockSize ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 2 returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVec2.GetGlobalLength() != dim ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 2 returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVec2.MvNorm(norms); + for(int i = 0; i < blockSize; i++){ + if( norms[i] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 2 returned wrong nrm2 value. " + << "Vector was not initialized to zeros." << endl; + return false; + } + } + // Test constructor #3: + Belos::KokkosMultiVec myVec3(2*dim); + if ( myVec3.GetNumberVecs() != 1 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 3 returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVec3.GetGlobalLength() != 2*dim ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 3 returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVec3.MvNorm(norms); + if( norms[0] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec constructor 3 returned wrong nrm2 value. " + << "Vector was not initialized to zeros." << endl; + return false; + } + // Test copy constructor (should deep copy). + Belos::KokkosMultiVec myVecCopy(myVec3); + if ( myVecCopy.GetNumberVecs() != 1 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec copy constructor returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecCopy.GetGlobalLength() != 2*dim ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec copy constructor returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVecCopy.MvRandom(); + myVecCopy.MvNorm(norms); + if( norms[0] == 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec MvRandom did not fill with random values. " << endl; + return false; + } + myVec3.MvNorm(norms); + if( norms[0] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec copy constructor did not deep copy. " << endl; + return false; + } + // Test assignment operator (should also deep copy). + myVecCopy = myVec2; + if ( myVecCopy.GetNumberVecs() != blockSize ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec assignment = returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecCopy.GetGlobalLength() != dim ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec assignment = returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVec2.MvInit(3.0); + myVecCopy.MvNorm(norms); + for(int i = 0; i < blockSize; i++){ + if( norms[i] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec assignment = returned wrong nrm2 value. " + << "Vector was not deep copied." << endl; + return false; + } + } + // Test view to multivec: + int numCols2 = 4; + int numRows2 = 60; + Kokkos::View myView("View2MV", numRows2, numCols2); + typename Kokkos::View::HostMirror myView_h("View2MV_host", numRows2, numCols2); + Kokkos::deep_copy(myView, 42); + Belos::KokkosMultiVec myVec4( myView ); + if ( myVec4.GetNumberVecs() != (int)myView.extent(1) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVec4.GetGlobalLength() != (int)myView.extent(0) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + Kokkos::deep_copy(myView, 55); + Kokkos::deep_copy(myView_h, myVec4.GetInternalViewConst()); + if ( myView_h(5,1) != 42 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec view to multivec did not make a deep copy!" << endl; + return false; + } + // Tesst view to multivec with shallow copy: + Kokkos::deep_copy(myView, 100); + Belos::KokkosMultiVec myVec5( myView, false ); + if ( myVec5.GetNumberVecs() != (int)myView.extent(1) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec shallow returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVec5.GetGlobalLength() != (int)myView.extent(0) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec shallow returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + Kokkos::deep_copy(myView, 500); + Kokkos::deep_copy(myView_h, myVec5.GetInternalViewConst()); + if ( myView_h(5,1) != 500 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec view to multivec shallow made a deep copy!" << endl; + return false; + } + // Test GetInternalViewNonConst: + auto myView2 = myVec5.GetInternalViewNonConst(); + Kokkos::deep_copy(myView2, 0); + std::vector norms2(4); + myVec5.MvNorm(norms2); + for(int i = 0; i < (int)myView2.extent(1); i++){ + if( norms[i] != 0 ){ + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec GetInternalViewNonConst returned wrong nrm2 value. " + << "Vector was not editable." << endl; + return false; + } + } + + return true; +} + + +template +bool TestKokkosMultiVecTwoScalar(const Teuchos::RCP > & outputMgr){ + // Test view to multivec ST1 to ST2: + int numCols = 4; + int numRows = 60; + Kokkos::View myViewST1("View2MV1", numRows, numCols); + typename Kokkos::View::HostMirror myViewST2_h("View2MV1_host", numRows, numCols); + Kokkos::deep_copy(myViewST1, 42); + Belos::KokkosMultiVec myVecST2A( myViewST1 ); + if ( myVecST2A.GetNumberVecs() != (int)myViewST1.extent(1) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec 2 scalar returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST2A.GetGlobalLength() != (int)myViewST1.extent(0) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec 2 scalar returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + Kokkos::deep_copy(myViewST1, 55); + std::cout << "At line 424. " << std::endl; + Kokkos::deep_copy(myViewST2_h, myVecST2A.GetInternalViewConst()); + if ( myViewST2_h(5,1) != 42 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec view to multivec 2 scalar did not make a deep copy!" << endl; + return false; + } + // Test view to multivec ST2 to ST1: + Kokkos::View myViewST2("View2MV2", numRows, numCols); + typename Kokkos::View::HostMirror myViewST1_h("View2MV2_host", numRows, numCols); + Kokkos::deep_copy(myViewST2, 56); + Belos::KokkosMultiVec myVecST1A( myViewST2 ); + if ( myVecST1A.GetNumberVecs() != (int)myViewST2.extent(1) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec 2 scalar returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST1A.GetGlobalLength() != (int)myViewST2.extent(0) ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec view to multivec 2 scalar returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + Kokkos::deep_copy(myViewST2, 22); + std::cout << "At line 449. " << std::endl; + Kokkos::deep_copy(myViewST1_h, myVecST1A.GetInternalViewConst()); + if ( myViewST1_h(5,1) != 56 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec view to multivec 2 scalar did not make a deep copy!" << endl; + return false; + } + //Test multivec copy constructor ST1 to ST2: + Belos::KokkosMultiVec myVecST2B( myVecST1A ); + if ( myVecST1A.GetNumberVecs() != myVecST2B.GetNumberVecs() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated copy constructor returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST1A.GetGlobalLength() != myVecST2B.GetGlobalLength() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated copy constructor returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVecST1A.MvInit(3.0); + std::cout << "At line 471. " << std::endl; + Kokkos::deep_copy(myViewST2_h, myVecST2B.GetInternalViewConst()); + if ( myViewST2_h(5,1) != 56 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec templated copy constructor did not make a deep copy!" << endl; + return false; + } + //Test multivec copy constructor ST2 to ST1: + Belos::KokkosMultiVec myVecST1B( myVecST2A ); + if ( myVecST1B.GetNumberVecs() != myVecST2A.GetNumberVecs() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated copy constructor returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST1B.GetGlobalLength() != myVecST2A.GetGlobalLength() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated copy constructor returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVecST2A.MvInit(3.0); + Kokkos::deep_copy(myViewST1_h, myVecST1B.GetInternalViewConst()); + if ( myViewST1_h(5,1) != 42 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec templated copy constructor did not make a deep copy!" << endl; + return false; + } + //Test assignment operator ST1 to ST2: + Belos::KokkosMultiVec myVecST2C = myVecST1A; + if ( myVecST1A.GetNumberVecs() != myVecST2C.GetNumberVecs() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated assignment operator returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST1A.GetGlobalLength() != myVecST2C.GetGlobalLength() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated copy constructor returned wrong value " + << "*** ERROR *** KokkosMultiVec templated assignment operator returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVecST1A.MvInit(1.0); + std::cout << "At line 515. " << std::endl; + Kokkos::deep_copy(myViewST2_h, myVecST2C.GetInternalViewConst()); + if ( myViewST2_h(5,1) != 3 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec templated assign op did not make a deep copy!" << endl; + return false; + } + //Test assignement operator ST2 to ST1: + Belos::KokkosMultiVec myVecST1C = myVecST2A; + if ( myVecST1C.GetNumberVecs() != myVecST2A.GetNumberVecs() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated assignment operator returned wrong value " + << "for GetNumberVecs()." << endl; + return false; + } + if ( myVecST1C.GetGlobalLength() != myVecST2A.GetGlobalLength() ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultiVec templated assignment operator returned wrong value " + << "for GetGlobalLength()." << endl; + return false; + } + myVecST2A.MvInit(2.0); + Kokkos::deep_copy(myViewST1_h, myVecST1C.GetInternalViewConst()); + if ( myViewST1_h(5,1) != 3 ) { + outputMgr->stream(Warnings) + << "*** ERROR *** KokkosMultivec templated assign op did not make a deep copy!" << endl; + return false; + } + + return true; +} From 6e0ee32c24250a0de26a2c79d85076e23dcb7e77 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 25 Oct 2021 10:56:45 -0600 Subject: [PATCH 65/98] Tpetra: clean up includes/typedefs/setup functions for AsyncTransfer tests --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 195 ++++-------------- 1 file changed, 36 insertions(+), 159 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index e80c4f8ddd6b..55ef0433bf0c 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -42,164 +42,41 @@ #include #include +#include #include #include -#include -#include #include -#include "Tpetra_CrsGraph.hpp" -#include "Tpetra_CrsMatrix.hpp" -#include "Tpetra_MultiVector.hpp" + #include "Tpetra_Core.hpp" -#include "Tpetra_Distributor.hpp" -#include "Tpetra_Map.hpp" -#include "Tpetra_Util.hpp" -#include "Tpetra_Import.hpp" -#include "Tpetra_Import_Util.hpp" -#include "Tpetra_Import_Util2.hpp" -#include "Tpetra_Details_packCrsMatrix.hpp" -#include "Tpetra_Details_unpackCrsMatrixAndCombine.hpp" +#include "Tpetra_CrsMatrix.hpp" #include "Tpetra_Export.hpp" -#include "Tpetra_RowMatrixTransposer.hpp" -#include "TpetraExt_MatrixMatrix.hpp" -#include "Tpetra_Details_Behavior.hpp" -#include "Tpetra_Details_gathervPrint.hpp" -#include -#include +#include "Tpetra_Import.hpp" +#include "Tpetra_Map.hpp" +#include "Tpetra_MultiVector.hpp" namespace { + using std::endl; + using Teuchos::as; using Teuchos::Array; - using Teuchos::ArrayRCP; - using Teuchos::ArrayView; - using Teuchos::arrayViewFromVector; using Teuchos::Comm; using Teuchos::FancyOStream; - using Teuchos::getFancyOStream; - using Teuchos::includesVerbLevel; - using Teuchos::OrdinalTraits; - using Teuchos::OSTab; - using Teuchos::outArg; - using Teuchos::ParameterList; - using Teuchos::parameterList; using Teuchos::RCP; using Teuchos::rcp; - using Teuchos::rcpFromRef; - using Teuchos::REDUCE_MAX; - using Teuchos::reduceAll; + using Teuchos::OrdinalTraits; using Teuchos::ScalarTraits; using Teuchos::tuple; - using Tpetra::ADD; using Tpetra::DistObject; - using Tpetra::createContigMap; - using Tpetra::CrsGraph; using Tpetra::CrsMatrix; - using Tpetra::MultiVector; using Tpetra::Export; + using Tpetra::getDefaultComm; + using Tpetra::global_size_t; using Tpetra::Import; using Tpetra::INSERT; using Tpetra::Map; - using Tpetra::REPLACE; - using Tpetra::StaticProfile; - - using std::cerr; - using std::cout; - using std::ostream_iterator; - using std::endl; - - using Node = Tpetra::Map<>::node_type; - - // Command-line argument values (initially set to defaults). - bool testMpi = true; - double errorTolSlack = 1e+1; - std::string distributorSendType ("Send"); - bool barrierBetween = true; - bool verbose = false; - - TEUCHOS_STATIC_SETUP() - { - Teuchos::CommandLineProcessor &clp = Teuchos::UnitTestRepository::getCLP(); - clp.addOutputSetupOptions(true); - clp.setOption( - "test-mpi", "test-serial", &testMpi, - "Test MPI (if available) or force test of serial. In a serial build," - " this option is ignored and a serial comm is always used." ); - clp.setOption( - "error-tol-slack", &errorTolSlack, - "Slack off of machine epsilon used to check test results" ); - // FIXME (mfh 02 Apr 2012) It would be better to ask Distributor - // for the list of valid send types, but setOption() needs a const - // char[], not an std::string. - clp.setOption ("distributor-send-type", &distributorSendType, - "In MPI tests, the type of send operation that the Tpetra::" - "Distributor will use. Valid values include \"Isend\", " - "\"Rsend\", \"Send\", and \"Ssend\"."); - clp.setOption ("barrier-between", "no-barrier-between", &barrierBetween, - "In MPI tests, whether Tpetra::Distributor will execute a " - "barrier between posting receives and posting sends."); - clp.setOption ("verbose", "quiet", &verbose, "Whether to print verbose " - "output."); - } - - RCP > - getDefaultComm() - { - if (testMpi) { - return Tpetra::getDefaultComm (); - } - else { - return rcp (new Teuchos::SerialComm ()); - } - } - - RCP - getDistributorParameterList () - { - static RCP plist; // NOT THREAD SAFE, but that's OK here. - if (plist.is_null ()) { - plist = parameterList ("Tpetra::Distributor"); - plist->set ("Send type", distributorSendType); - plist->set ("Barrier between receives and sends", barrierBetween); - - if (verbose && getDefaultComm()->getRank() == 0) { - cout << "ParameterList for Distributor: " << *plist << endl; - } - - if (verbose) { - // Tell Distributor to print verbose output. - Teuchos::VerboseObject::setDefaultVerbLevel (Teuchos::VERB_EXTREME); - } - } - return plist; - } - - RCP getImportParameterList () { - return getDistributorParameterList (); // For now. - } - - RCP getExportParameterList () { - return parameterList (* (getDistributorParameterList ())); // For now. - } - - RCP getCrsGraphParameterList () { - static RCP plist; // NOT THREAD SAFE, but that's OK here. - if (plist.is_null ()) { - plist = parameterList ("Tpetra::CrsGraph"); - plist->set ("Import", * (getImportParameterList ())); - plist->set ("Export", * (getExportParameterList ())); - - if (verbose && getDefaultComm()->getRank() == 0) { - cout << "ParameterList for CrsGraph: " << *plist << endl; - } - } - return plist; - } - - RCP getCrsMatrixParameterList () { - return parameterList (* (getCrsGraphParameterList ())); // For now. - } + using Tpetra::MultiVector; // @@ -214,7 +91,7 @@ namespace { using mv_type = MultiVector; public: - MultiVectorTransferFixture(Teuchos::FancyOStream& o, bool& s) + MultiVectorTransferFixture(FancyOStream& o, bool& s) : out(o), success(s), comm(getDefaultComm()), @@ -252,7 +129,7 @@ namespace { private: void setupMaps(int collectRank) { const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + const global_size_t INVALID = OrdinalTraits::invalid(); const size_t sourceNumLocalElements = 3; const size_t totalElements = numProcs*sourceNumLocalElements; @@ -267,7 +144,7 @@ namespace { sourceMV->randomize(); targetMV = rcp(new mv_type(targetMap, 1)); - targetMV->putScalar(Teuchos::ScalarTraits::zero()); + targetMV->putScalar(ScalarTraits::zero()); } void compareMultiVectors(RCP resultMV, RCP referenceMV) { @@ -280,7 +157,7 @@ namespace { } } - Teuchos::FancyOStream& out; + FancyOStream& out; bool& success; RCP> comm; @@ -303,12 +180,12 @@ namespace { public: RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { RCP sourceMap = sourceMV->getMap(); - Import importer(sourceMap, targetMap, getImportParameterList()); + Import importer(sourceMap, targetMap); expertSetRemoteLIDsContiguous(importer, false); TEUCHOS_ASSERT(!importer.areRemoteLIDsContiguous()); RCP referenceMV = rcp(new mv_type(targetMap, 1)); - referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->putScalar(ScalarTraits::zero()); referenceMV->doImport(*sourceMV, importer, INSERT); TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); @@ -325,12 +202,12 @@ namespace { public: RCP generateWithClassicalCodePath(RCP sourceMV, RCP targetMap) const { RCP sourceMap = sourceMV->getMap(); - Export exporter(sourceMap, targetMap, getExportParameterList()); + Export exporter(sourceMap, targetMap); expertSetRemoteLIDsContiguous(exporter, false); TEUCHOS_ASSERT(!exporter.areRemoteLIDsContiguous()); RCP referenceMV = rcp(new mv_type(targetMap, 1)); - referenceMV->putScalar(Teuchos::ScalarTraits::zero()); + referenceMV->putScalar(ScalarTraits::zero()); referenceMV->doExport(*sourceMV, exporter, INSERT); TEUCHOS_ASSERT(!referenceMV->importsAreAliased()); @@ -346,7 +223,7 @@ namespace { using crs_type = CrsMatrix; public: - DiagonalCrsMatrixTransferFixture(Teuchos::FancyOStream& o, bool& s) + DiagonalCrsMatrixTransferFixture(FancyOStream& o, bool& s) : out(o), success(s), comm(getDefaultComm()), @@ -387,7 +264,7 @@ namespace { private: void setupMaps() { const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + const global_size_t INVALID = OrdinalTraits::invalid(); const size_t targetNumLocalElements = 3; const size_t totalElements = numProcs*targetNumLocalElements; @@ -398,8 +275,8 @@ namespace { } void setupMatrices() { - sourceMat = rcp(new crs_type(sourceMap, 1, StaticProfile, getCrsMatrixParameterList())); - targetMat = rcp(new crs_type(targetMap, 1, StaticProfile, getCrsMatrixParameterList())); + sourceMat = rcp(new crs_type(sourceMap, 1)); + targetMat = rcp(new crs_type(targetMap, 1)); for (GO row = sourceMap->getMinGlobalIndex(); row <= sourceMap->getMaxGlobalIndex(); row++) { sourceMat->insertGlobalValues(row, tuple(row), tuple(row)); @@ -468,7 +345,7 @@ namespace { } } - Teuchos::FancyOStream& out; + FancyOStream& out; bool& success; RCP> comm; @@ -491,7 +368,7 @@ namespace { public: RCP generateUsingAllInOne(RCP sourceMat, RCP targetMap) const { RCP sourceMap = sourceMat->getMap(); - Import importer(sourceMap, targetMap, getImportParameterList()); + Import importer(sourceMap, targetMap); Teuchos::ParameterList dummy; RCP referenceMat = Tpetra::importAndFillCompleteCrsMatrix( @@ -509,7 +386,7 @@ namespace { public: RCP generateUsingAllInOne(RCP sourceMat, RCP targetMap) const { RCP sourceMap = sourceMat->getMap(); - Export exporter(sourceMap, targetMap, getExportParameterList()); + Export exporter(sourceMap, targetMap); Teuchos::ParameterList dummy; RCP referenceMat = Tpetra::exportAndFillCompleteCrsMatrix( @@ -526,7 +403,7 @@ namespace { using crs_type = CrsMatrix; public: - LowerTriangularCrsMatrixTransferFixture(Teuchos::FancyOStream& o, bool& s) + LowerTriangularCrsMatrixTransferFixture(FancyOStream& o, bool& s) : out(o), success(s), comm(getDefaultComm()), @@ -589,7 +466,7 @@ namespace { private: void setupMaps() { const GO indexBase = 0; - const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + const global_size_t INVALID = OrdinalTraits::invalid(); const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; const size_t targetNumLocalElements = 4; @@ -599,8 +476,8 @@ namespace { } void setupMatrices() { - sourceMat = rcp(new crs_type(sourceMap, 24, StaticProfile, getCrsMatrixParameterList())); - targetMat = rcp(new crs_type(targetMap, 24, StaticProfile, getCrsMatrixParameterList())); + sourceMat = rcp(new crs_type(sourceMap, 24)); + targetMat = rcp(new crs_type(targetMap, 24)); Array cols(1); Array vals(1); @@ -618,7 +495,7 @@ namespace { sourceMat->fillComplete(); } - Teuchos::FancyOStream& out; + FancyOStream& out; bool& success; RCP> comm; @@ -645,7 +522,7 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { - Import importer(source->getMap(), target->getMap(), getImportParameterList()); + Import importer(source->getMap(), target->getMap()); target->beginImport(*source, importer, INSERT); target->endImport(*source, importer, INSERT); } @@ -711,7 +588,7 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { - Export exporter(target->getMap(), source->getMap(), getExportParameterList()); + Export exporter(target->getMap(), source->getMap()); target->beginImport(*source, exporter, INSERT); target->endImport(*source, exporter, INSERT); } @@ -777,7 +654,7 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { - Export exporter(source->getMap(), target->getMap(), getExportParameterList()); + Export exporter(source->getMap(), target->getMap()); target->beginExport(*source, exporter, INSERT); target->endExport(*source, exporter, INSERT); } @@ -843,7 +720,7 @@ namespace { public: void operator()(DistObjectRCP source, DistObjectRCP target) const { - Import importer(target->getMap(), source->getMap(), getImportParameterList()); + Import importer(target->getMap(), source->getMap()); target->beginExport(*source, importer, INSERT); target->endExport(*source, importer, INSERT); } From 1da9e1404b518765dbcbde9f6dde85b3e7e60327 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 25 Oct 2021 10:58:37 -0600 Subject: [PATCH 66/98] Tpetra: fix template parameter ordering in AsyncTransfer for consistency --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 55ef0433bf0c..008a89978ed4 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -528,7 +528,7 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank0, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -541,7 +541,7 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank1, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -554,7 +554,7 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, DiagonalCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -567,7 +567,7 @@ namespace { fixture.checkResults(ReferenceImportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -594,7 +594,7 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank0, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -607,7 +607,7 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank1, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -620,7 +620,7 @@ namespace { fixture.checkResults(ReferenceImportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, DiagonalCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -633,7 +633,7 @@ namespace { fixture.checkResults(ReferenceImportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -660,7 +660,7 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank0, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -673,7 +673,7 @@ namespace { fixture.checkResults(ReferenceExportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank1, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -686,7 +686,7 @@ namespace { fixture.checkResults(ReferenceExportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, DiagonalCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -699,7 +699,7 @@ namespace { fixture.checkResults(ReferenceExportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -726,7 +726,7 @@ namespace { } }; - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank0, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -739,7 +739,7 @@ namespace { fixture.checkResults(ReferenceExportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank1, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -752,7 +752,7 @@ namespace { fixture.checkResults(ReferenceExportMultiVector()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, DiagonalCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -765,7 +765,7 @@ namespace { fixture.checkResults(ReferenceExportMatrix()); } - TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, LowerTriangularCrsMatrix, LO, GO, Scalar ) + TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); if (fixture.shouldSkipTest()) { @@ -784,22 +784,22 @@ namespace { // #define UNIT_TEST_GROUP_SC_LO_GO( SC, LO, GO ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank0, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank1, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, DiagonalCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank0, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank1, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, DiagonalCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, LowerTriangularCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank0, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank1, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, DiagonalCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, LowerTriangularCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank0, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank1, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, DiagonalCrsMatrix, LO, GO, SC ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, LowerTriangularCrsMatrix, LO, GO, SC ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank0, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, MultiVector_rank1, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, DiagonalCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardImport, LowerTriangularCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank0, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, MultiVector_rank1, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, DiagonalCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseImport, LowerTriangularCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank0, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, MultiVector_rank1, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, DiagonalCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncForwardExport, LowerTriangularCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank0, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, MultiVector_rank1, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, DiagonalCrsMatrix, SC, LO, GO ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( AsyncReverseExport, LowerTriangularCrsMatrix, SC, LO, GO ) \ TPETRA_ETI_MANGLING_TYPEDEFS() From ac8f397feb25d61a31c79b95d7a6ca47fc497de1 Mon Sep 17 00:00:00 2001 From: "Timothy A. Smith" Date: Mon, 25 Oct 2021 11:25:55 -0600 Subject: [PATCH 67/98] Tpetra: AsyncTransfer test cleanup: remove shouldSkipTest, fix maps, simplify MultiVector result check --- .../ImportExport2/AsyncTransfer_UnitTests.cpp | 104 ++---------------- 1 file changed, 9 insertions(+), 95 deletions(-) diff --git a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp index 008a89978ed4..d2f4459433cf 100644 --- a/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/AsyncTransfer_UnitTests.cpp @@ -101,15 +101,6 @@ namespace { ~MultiVectorTransferFixture() { } - bool shouldSkipTest() { - return numProcs < 2; - } - - void printSkippedTestMessage() { - out << "This test is only meaningful if running with multiple MPI " - "processes, but you ran it with only 1 process." << endl; - } - void setup(int collectRank) { setupMaps(collectRank); setupMultiVectors(); @@ -151,8 +142,8 @@ namespace { auto data = resultMV->getLocalViewHost(Tpetra::Access::ReadOnly); auto referenceData = referenceMV->getLocalViewHost(Tpetra::Access::ReadOnly); - for (GO globalRow = targetMap->getMinGlobalIndex(); globalRow <= targetMap->getMaxGlobalIndex(); ++globalRow) { - const LO localRow = targetMap->getLocalElement(globalRow); + TEST_EQUALITY(data.size(), referenceData.size()); + for (LO localRow = 0; localRow < as(data.size()); localRow++) { TEST_EQUALITY(data(localRow, 0), referenceData(localRow, 0)); } } @@ -233,15 +224,6 @@ namespace { ~DiagonalCrsMatrixTransferFixture() { } - bool shouldSkipTest() { - return numProcs < 2; - } - - void printSkippedTestMessage() { - out << "This test is only meaningful if running with multiple MPI " - "processes, but you ran it with only 1 process." << endl; - } - void setup() { setupMaps(); setupMatrices(); @@ -413,14 +395,6 @@ namespace { ~LowerTriangularCrsMatrixTransferFixture() { } - bool shouldSkipTest() { - return numProcs%2 != 0; - } - - void printSkippedTestMessage() { - out << "This test is only meaningful if running with an even number of MPI processes." << endl; - } - void setup() { setupMaps(); setupMatrices(); @@ -468,16 +442,20 @@ namespace { const GO indexBase = 0; const global_size_t INVALID = OrdinalTraits::invalid(); - const size_t sourceNumLocalElements = (myRank%2 == 0) ? 3 : 5; + const size_t sourceNumLocalElements = isExtraRank() ? 4 : (myRank%2 == 0 ? 3 : 5); const size_t targetNumLocalElements = 4; sourceMap = rcp(new map_type(INVALID, sourceNumLocalElements, indexBase, comm)); targetMap = rcp(new map_type(INVALID, targetNumLocalElements, indexBase, comm)); } + bool isExtraRank() { + return numProcs%2 == 1 && myRank == numProcs-1; + } + void setupMatrices() { - sourceMat = rcp(new crs_type(sourceMap, 24)); - targetMat = rcp(new crs_type(targetMap, 24)); + sourceMat = rcp(new crs_type(sourceMap, sourceMap->getGlobalNumElements())); + targetMat = rcp(new crs_type(targetMap, targetMap->getGlobalNumElements())); Array cols(1); Array vals(1); @@ -531,10 +509,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(0); fixture.performTransfer(ForwardImport()); @@ -544,10 +518,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(1); fixture.performTransfer(ForwardImport()); @@ -557,10 +527,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ForwardImport()); @@ -570,10 +536,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardImport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ForwardImport()); @@ -597,10 +559,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(0); fixture.performTransfer(ReverseImport()); @@ -610,10 +568,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(1); fixture.performTransfer(ReverseImport()); @@ -623,10 +577,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ReverseImport()); @@ -636,10 +586,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseImport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ReverseImport()); @@ -663,10 +609,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(0); fixture.performTransfer(ForwardExport()); @@ -676,10 +618,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(1); fixture.performTransfer(ForwardExport()); @@ -689,10 +627,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ForwardExport()); @@ -702,10 +636,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncForwardExport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ForwardExport()); @@ -729,10 +659,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank0, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(0); fixture.performTransfer(ReverseExport()); @@ -742,10 +668,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, MultiVector_rank1, Scalar, LO, GO ) { MultiVectorTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(1); fixture.performTransfer(ReverseExport()); @@ -755,10 +677,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, DiagonalCrsMatrix, Scalar, LO, GO ) { DiagonalCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ReverseExport()); @@ -768,10 +686,6 @@ namespace { TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( AsyncReverseExport, LowerTriangularCrsMatrix, Scalar, LO, GO ) { LowerTriangularCrsMatrixTransferFixture fixture(out, success); - if (fixture.shouldSkipTest()) { - fixture.printSkippedTestMessage(); - return; - } fixture.setup(); fixture.performTransfer(ReverseExport()); From d84e340173f3f72474d138bb7a64b123ab6d15b6 Mon Sep 17 00:00:00 2001 From: Brian Kelley Date: Mon, 25 Oct 2021 13:11:18 -0600 Subject: [PATCH 68/98] MueLu: remove dependence on Tpetra deprecated in MMKernelDriver. Remaining TODO: retest this with ViennaCL and MKL just in case --- .../muelu/test/scaling/MMKernelDriver.cpp | 47 +++++++++---------- 1 file changed, 22 insertions(+), 25 deletions(-) diff --git a/packages/muelu/test/scaling/MMKernelDriver.cpp b/packages/muelu/test/scaling/MMKernelDriver.cpp index e8823986ec37..dfeb9d37f68b 100644 --- a/packages/muelu/test/scaling/MMKernelDriver.cpp +++ b/packages/muelu/test/scaling/MMKernelDriver.cpp @@ -275,18 +275,17 @@ void Multiply_ViennaCL(const Xpetra::Matrix Cu = Utilities::Op2TpetraCrs(rcp(&C,false)); RCP Cnc = Teuchos::rcp_const_cast(Cu); - const KCRS & Amat = Au->getLocalMatrix(); - const KCRS & Bmat = Bu->getLocalMatrix(); - KCRS Cmat = Cu->getLocalMatrix(); + const KCRS & Amat = Au->getLocalMatrixDevice(); + const KCRS & Bmat = Bu->getLocalMatrixDevice(); using no_init_view=Kokkos::ViewAllocateWithoutInitializing; c_lno_view_t Arowptr = Amat.graph.row_map, Browptr = Bmat.graph.row_map; lno_view_t Crowptr(no_init_view("Crowptr"),C.getNodeNumRows()+1); c_lno_nnz_view_t Acolind = Amat.graph.entries, Bcolind = Bmat.graph.entries; - lno_nnz_view_t Ccolind = Cmat.graph.entries; + lno_nnz_view_t Ccolind; const scalar_view_t Avals = Amat.values, Bvals = Bmat.values; - scalar_view_t Cvals = Cmat.values; + scalar_view_t Cvals; // ********************************** // Copy in the data for ViennaCL @@ -335,8 +334,8 @@ void Multiply_ViennaCL(const Xpetra::Matrix(CVCL.handle1()); const unsigned int * CcolindVCL = viennacl::cuda_arg(CVCL.handle2()); @@ -446,17 +445,14 @@ void Multiply_MKL_SPMM(const Xpetra::Matrix Cu = Utilities::Op2TpetraCrs(rcp(&C,false)); RCP Cnc = Teuchos::rcp_const_cast(Cu); - const KCRS & Amat = Au->getLocalMatrix(); - const KCRS & Bmat = Bu->getLocalMatrix(); - KCRS Cmat = Cu->getLocalMatrix(); + const KCRS & Amat = Au->getLocalMatrixDevice(); + const KCRS & Bmat = Bu->getLocalMatrixDevice(); if(A.getNodeNumRows()!=C.getNodeNumRows()) throw std::runtime_error("C is not sized correctly"); c_lno_view_t Arowptr = Amat.graph.row_map, Browptr = Bmat.graph.row_map; lno_view_t Crowptr(no_init_view("Crowptr"),C.getNodeNumRows()+1); c_lno_nnz_view_t Acolind = Amat.graph.entries, Bcolind = Bmat.graph.entries; - lno_nnz_view_t Ccolind = Cmat.graph.entries; const scalar_view_t Avals = Amat.values, Bvals = Bmat.values; - scalar_view_t Cvals = Cmat.values; sparse_matrix_t AMKL; sparse_matrix_t BMKL; @@ -536,6 +532,8 @@ void Multiply_MKL_SPMM(const Xpetra::Matrix crs_matrix_type; - typedef typename crs_matrix_type::local_matrix_type KCRS; - typedef typename KCRS::StaticCrsGraphType graph_t; - typedef typename graph_t::row_map_type::non_const_type lno_view_t; - typedef typename graph_t::row_map_type::const_type c_lno_view_t; - typedef typename graph_t::entries_type::non_const_type lno_nnz_view_t; - typedef typename graph_t::entries_type::const_type c_lno_nnz_view_t; - typedef typename KCRS::values_type::non_const_type scalar_view_t; - typedef typename KCRS::device_type device_t; + typedef typename crs_matrix_type::local_matrix_device_type KCRS; + typedef typename KCRS::StaticCrsGraphType graph_t; + typedef typename graph_t::row_map_type::non_const_type lno_view_t; + typedef typename graph_t::row_map_type::const_type c_lno_view_t; + typedef typename graph_t::entries_type::non_const_type lno_nnz_view_t; + typedef typename graph_t::entries_type::const_type c_lno_nnz_view_t; + typedef typename KCRS::values_type::non_const_type scalar_view_t; + typedef typename KCRS::device_type device_t; RCP Au = Utilities::Op2TpetraCrs(rcp(&A,false)); RCP Bu = Utilities::Op2TpetraCrs(rcp(&B,false)); RCP Cu = Utilities::Op2TpetraCrs(rcp(&C,false)); RCP Cnc = Teuchos::rcp_const_cast(Cu); - const KCRS & Amat = Au->getLocalMatrix(); - const KCRS & Bmat = Bu->getLocalMatrix(); - KCRS Cmat = Cu->getLocalMatrix(); + const KCRS & Amat = Au->getLocalMatrixDevice(); + const KCRS & Bmat = Bu->getLocalMatrixDevice(); c_lno_view_t Arowptr = Amat.graph.row_map, Browptr = Bmat.graph.row_map; lno_view_t Crowptr("Crowptr",A.getNodeNumRows()+1); c_lno_nnz_view_t Acolind = Amat.graph.entries, Bcolind = Bmat.graph.entries; - lno_nnz_view_t Ccolind = Cmat.graph.entries; const scalar_view_t Avals = Amat.values, Bvals = Bmat.values; - scalar_view_t Cvals = Cmat.values; + lno_nnz_view_t Ccolind; + scalar_view_t Cvals; // KokkosKernelsHandle typedef KokkosKernels::Experimental::KokkosKernelsHandle< From fd4b703bbb70cdae854863cb03d27555d25ffe39 Mon Sep 17 00:00:00 2001 From: Jacob Domagala Date: Wed, 20 Oct 2021 14:43:51 +0200 Subject: [PATCH 69/98] Sacado: Make Sacado_FadKokkosTests_Cuda UVM free --- .../UnitTests/Fad_Fad_KokkosTests_Cuda.cpp | 4 -- .../sacado/test/UnitTests/Fad_KokkosTests.hpp | 50 ++++++++++++------- .../test/UnitTests/Fad_KokkosTests_Cuda.cpp | 4 -- 3 files changed, 31 insertions(+), 27 deletions(-) diff --git a/packages/sacado/test/UnitTests/Fad_Fad_KokkosTests_Cuda.cpp b/packages/sacado/test/UnitTests/Fad_Fad_KokkosTests_Cuda.cpp index 4cc7eb8d0866..40ee81bc9c77 100644 --- a/packages/sacado/test/UnitTests/Fad_Fad_KokkosTests_Cuda.cpp +++ b/packages/sacado/test/UnitTests/Fad_Fad_KokkosTests_Cuda.cpp @@ -35,11 +35,7 @@ #include "Kokkos_Core.hpp" // Instantiate tests for Cuda device -#if defined(KOKKOS_ENABLE_CUDA_UVM) #define SACADO_TEST_DFAD 1 -#else -#define SACADO_TEST_DFAD 0 -#endif using Kokkos::Cuda; VIEW_FAD_TESTS_D( Cuda ) diff --git a/packages/sacado/test/UnitTests/Fad_KokkosTests.hpp b/packages/sacado/test/UnitTests/Fad_KokkosTests.hpp index 6303a13a9d69..ca379dc1bc64 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosTests.hpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosTests.hpp @@ -250,16 +250,16 @@ struct ValueAssignKernel { typedef typename Kokkos::ThreadLocalScalarType::type local_scalar_type; static const size_type stride = Kokkos::ViewScalarStride::stride; - const ViewType m_v; - const ValueType m_s; + const ViewType m_v; + const ViewType m_s; - ValueAssignKernel(const ViewType& v, const ValueType& s) : + ValueAssignKernel(const ViewType& v, const ViewType& s) : m_v(v), m_s(s) {}; // Multiply entries for row 'i' with a value KOKKOS_INLINE_FUNCTION void operator() (const size_type i) const { - local_scalar_type s = Sacado::partition_scalar(m_s); + local_scalar_type s = Sacado::partition_scalar(m_s(0)); m_v(i) = s; } @@ -272,7 +272,7 @@ struct ValueAssignKernel { } // Kernel launch - static void apply(const ViewType& v, const ValueType& s) { + static void apply(const ViewType& v, const ViewType& s) { const size_type nrow = v.extent(0); #if defined (KOKKOS_ENABLE_CUDA) && defined (SACADO_VIEW_CUDA_HIERARCHICAL) @@ -654,11 +654,10 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FadType a(fad_size, 2.3456); for (size_type i=0; i(0, fad_size), KOKKOS_LAMBDA(const int i) { + a(0).fastAccessDx(i) = 7.89 + i; + }); + ValueAssignKernel::apply( v, a ); // Copy to host host_view_type hv = Kokkos::create_mirror_view(v); Kokkos::deep_copy(hv, v); + host_view_type ha = Kokkos::create_mirror_view(a); + Kokkos::deep_copy(ha, a); + // Check success = true; for (size_type i=0; i(0, num_rows), KOKKOS_LAMBDA(const size_type i) { + for (size_type j = 0; j < fad_size; ++j) + v(i).fastAccessDx(j) = 7.89 + j; + }); // Create scalar view ScalarViewType s; @@ -1028,9 +1038,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( #else s = ScalarViewType ("scalar view", fad_size+1); #endif - Kokkos::deep_copy( s, FadType(fad_size,0.0) ); - // Call atomic_add kernel, which adds up entries in v + // Call atomic_add kernel, which adds up entries in v AtomicAddKernel::apply( v, s ); // Copy to host @@ -1038,7 +1047,10 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( Kokkos::deep_copy(hs, s); // Check - FadType b = num_rows*a; + auto hv = Kokkos::create_mirror_view(v); + Kokkos::deep_copy(hv, v); + + FadType b = num_rows*hv(0); success = checkFads(b, hs(), out); } @@ -2232,9 +2244,9 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, MultiplyUpdate, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, MultiplyConst, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, MultiplyMixed, F, L, D ) \ - TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, AtomicAdd, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, Rank8, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, Roger, F, L, D ) \ + TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, AtomicAdd, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, AssignDifferentStrides, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, DynRankDimensionScalar, F, L, D ) \ TEUCHOS_UNIT_TEST_TEMPLATE_3_INSTANT( Kokkos_View_Fad, DynRankAssignStatic0, F, L, D ) \ diff --git a/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda.cpp b/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda.cpp index 354d205c6fa5..870392225039 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda.cpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda.cpp @@ -32,11 +32,7 @@ #include "Kokkos_Macros.hpp" -#if defined(KOKKOS_ENABLE_CUDA_UVM) #define SACADO_TEST_DFAD 1 -#else -#define SACADO_TEST_DFAD 0 -#endif #include "Fad_KokkosTests.hpp" // Instantiate tests for Cuda device. We can only test DFad is UVM is enabled. From 14c1e5272f2276f549deef9b6776f77ed8c37d8f Mon Sep 17 00:00:00 2001 From: Jacob Domagala Date: Mon, 25 Oct 2021 22:01:24 +0200 Subject: [PATCH 70/98] Sacado: Re-enable Sacado unit tests for UVM-Off PR tester --- .../std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake | 1 - 1 file changed, 1 deletion(-) diff --git a/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake b/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake index cf2af6363165..22b58523bac6 100644 --- a/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake +++ b/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake @@ -146,7 +146,6 @@ set (Domi_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (Kokkos_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (KokkosKernels_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (ROL_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") -set (Sacado_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (SEACAS_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (ShyLU_DD_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") set (STK_ENABLE_TESTS OFF CACHE BOOL "Turn off tests for non-UVM build") From 4d9a4f03663a93b886ced839a8b6b78ecdee04e5 Mon Sep 17 00:00:00 2001 From: Brian Kelley Date: Mon, 25 Oct 2021 14:48:21 -0600 Subject: [PATCH 71/98] MueLu: remove Tpetra deprecated from Region --- .../muelu/test/unit_tests/RegionMatrix.cpp | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/packages/muelu/test/unit_tests/RegionMatrix.cpp b/packages/muelu/test/unit_tests/RegionMatrix.cpp index 580c104b7732..96d175bb6be8 100644 --- a/packages/muelu/test/unit_tests/RegionMatrix.cpp +++ b/packages/muelu/test/unit_tests/RegionMatrix.cpp @@ -328,18 +328,18 @@ void test_matrix(RCP > using entries_type = typename local_graph_type::entries_type; using values_type = typename local_matrix_type::values_type; - local_matrix_type orignalA = A->getLocalMatrix(); // Local matrix - entries_type refEntries = orignalA.graph.entries; // view of local column indices - values_type refValues = orignalA.values; // view of local values + local_matrix_type orignalA = A->getLocalMatrixDevice(); // Local matrix + entries_type refEntries = orignalA.graph.entries; // view of local column indices + values_type refValues = orignalA.values; // view of local values typename entries_type::HostMirror refEntries_h = Kokkos::create_mirror_view(refEntries); Kokkos::deep_copy(refEntries_h, refEntries); typename values_type::HostMirror refValues_h = Kokkos::create_mirror_view(refValues); Kokkos::deep_copy(refValues_h, refValues); - local_matrix_type compositeA = compositeMatrix->getLocalMatrix(); // Local matrix - entries_type compositeEntries = compositeA.graph.entries; // view of local column indices - values_type compositeValues = compositeA.values; // view of local values + local_matrix_type compositeA = compositeMatrix->getLocalMatrixDevice(); // Local matrix + entries_type compositeEntries = compositeA.graph.entries; // view of local column indices + values_type compositeValues = compositeA.values; // view of local values typename entries_type::HostMirror compositeEntries_h = Kokkos::create_mirror_view(compositeEntries); Kokkos::deep_copy(compositeEntries_h, compositeEntries); @@ -429,9 +429,9 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, CompositeToRegionMatrix, Scalar, using entries_type = typename local_graph_type::entries_type; using values_type = typename local_matrix_type::values_type; - local_matrix_type myLocalA = regionMats->getLocalMatrix(); // Local matrix - entries_type myEntries = myLocalA.graph.entries; // view of local column indices - values_type myValues = myLocalA.values; // view of local values + local_matrix_type myLocalA = regionMats->getLocalMatrixDevice(); // Local matrix + entries_type myEntries = myLocalA.graph.entries; // view of local column indices + values_type myValues = myLocalA.values; // view of local values typename entries_type::HostMirror myEntries_h = Kokkos::create_mirror_view(myEntries); Kokkos::deep_copy(myEntries_h, myEntries); @@ -447,8 +447,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, CompositeToRegionMatrix, Scalar, TEST_EQUALITY(regionMats->getNodeNumEntries(), 105); // In the serial case we can just compare to the values in A - entries_type refEntries = A->getLocalMatrix().graph.entries; - values_type refValues = A->getLocalMatrix().values; + entries_type refEntries = A->getLocalMatrixDevice().graph.entries; + values_type refValues = A->getLocalMatrixDevice().values; typename entries_type::HostMirror refEntries_h = Kokkos::create_mirror_view(refEntries); Kokkos::deep_copy(refEntries_h, refEntries); typename values_type::HostMirror refValues_h = Kokkos::create_mirror_view(refValues); @@ -619,18 +619,18 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, RegionToCompositeMatrix, Scalar, using entries_type = typename local_graph_type::entries_type; using values_type = typename local_matrix_type::values_type; - local_matrix_type orignalA = A->getLocalMatrix(); // Local matrix - entries_type refEntries = orignalA.graph.entries; // view of local column indices - values_type refValues = orignalA.values; // view of local values + local_matrix_type orignalA = A->getLocalMatrixDevice(); // Local matrix + entries_type refEntries = orignalA.graph.entries; // view of local column indices + values_type refValues = orignalA.values; // view of local values typename entries_type::HostMirror refEntries_h = Kokkos::create_mirror_view(refEntries); Kokkos::deep_copy(refEntries_h, refEntries); typename values_type::HostMirror refValues_h = Kokkos::create_mirror_view(refValues); Kokkos::deep_copy(refValues_h, refValues); - local_matrix_type compositeA = compositeMatrix->getLocalMatrix(); // Local matrix - entries_type compositeEntries = compositeA.graph.entries; // view of local column indices - values_type compositeValues = compositeA.values; // view of local values + local_matrix_type compositeA = compositeMatrix->getLocalMatrixDevice(); // Local matrix + entries_type compositeEntries = compositeA.graph.entries; // view of local column indices + values_type compositeValues = compositeA.values; // view of local values typename entries_type::HostMirror compositeEntries_h = Kokkos::create_mirror_view(compositeEntries); Kokkos::deep_copy(compositeEntries_h, compositeEntries); @@ -1120,9 +1120,9 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, Laplace2D, Scalar, LocalOrdinal, using entries_type = typename local_graph_type::entries_type; using values_type = typename local_matrix_type::values_type; - local_matrix_type myLocalA = regionMats->getLocalMatrix(); // Local matrix - entries_type myEntries = myLocalA.graph.entries; // view of local column indices - values_type myValues = myLocalA.values; // view of local values + local_matrix_type myLocalA = regionMats->getLocalMatrixDevice(); // Local matrix + entries_type myEntries = myLocalA.graph.entries; // view of local column indices + values_type myValues = myLocalA.values; // view of local values typename entries_type::HostMirror myEntries_h = Kokkos::create_mirror_view(myEntries); Kokkos::deep_copy(myEntries_h, myEntries); @@ -1139,8 +1139,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, Laplace2D, Scalar, LocalOrdinal, TEST_EQUALITY(regionMats->getNodeNumEntries(), 128); // In the serial case we can just compare to the values in A - entries_type refEntries = A->getLocalMatrix().graph.entries; - values_type refValues = A->getLocalMatrix().values; + entries_type refEntries = A->getLocalMatrixDevice().graph.entries; + values_type refValues = A->getLocalMatrixDevice().values; typename entries_type::HostMirror refEntries_h = Kokkos::create_mirror_view(refEntries); Kokkos::deep_copy(refEntries_h, refEntries); typename values_type::HostMirror refValues_h = Kokkos::create_mirror_view(refValues); @@ -1298,9 +1298,9 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, Laplace3D, Scalar, LocalOrdinal, using entries_type = typename local_graph_type::entries_type; using values_type = typename local_matrix_type::values_type; - local_matrix_type myLocalA = regionMats->getLocalMatrix(); // Local matrix - entries_type myEntries = myLocalA.graph.entries; // view of local column indices - values_type myValues = myLocalA.values; // view of local values + local_matrix_type myLocalA = regionMats->getLocalMatrixDevice(); // Local matrix + entries_type myEntries = myLocalA.graph.entries; // view of local column indices + values_type myValues = myLocalA.values; // view of local values typename entries_type::HostMirror myEntries_h = Kokkos::create_mirror_view(myEntries); Kokkos::deep_copy(myEntries_h, myEntries); @@ -1317,8 +1317,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(RegionMatrix, Laplace3D, Scalar, LocalOrdinal, TEST_EQUALITY(regionMats->getNodeNumEntries(), 692); // In the serial case we can just compare to the values in A - entries_type refEntries = A->getLocalMatrix().graph.entries; - values_type refValues = A->getLocalMatrix().values; + entries_type refEntries = A->getLocalMatrixDevice().graph.entries; + values_type refValues = A->getLocalMatrixDevice().values; typename entries_type::HostMirror refEntries_h = Kokkos::create_mirror_view(refEntries); Kokkos::deep_copy(refEntries_h, refEntries); typename values_type::HostMirror refValues_h = Kokkos::create_mirror_view(refValues); From dddef5c6c29abf0bf90609ff3e894c4656d71dd8 Mon Sep 17 00:00:00 2001 From: Jacob Domagala Date: Mon, 25 Oct 2021 23:45:04 +0200 Subject: [PATCH 72/98] Sacado: Fad_KokkosAtomicTests_Cuda_Hierarchical UVM free --- .../test/UnitTests/Fad_KokkosAtomicTests.hpp | 20 ++++++++++++------- ...ad_KokkosAtomicTests_Cuda_Hierarchical.cpp | 5 +---- 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp index 8e0be8ed1560..aa8360bcaf83 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp @@ -261,10 +261,13 @@ bool testAtomic(const TagType& tag, Teuchos::FancyOStream& out) // Create and fill view ViewType v; + ViewType s0; #if defined (SACADO_DISABLE_FAD_VIEW_SPEC) - v = ViewType ("view", num_rows); + v = ViewType ("view", num_rows); + s0 = ViewType ("", 1); #else - v = ViewType ("view", num_rows, fad_size+1); + v = ViewType ("view", num_rows, fad_size+1); + s0 = ViewType ("", 1, fad_size+1); #endif host_view_type h_v = Kokkos::create_mirror_view(v); for (size_type i=0; i(num_rows, size_type(1), fad_size, i, size_type(0)); Kokkos::deep_copy(v, h_v); + Kokkos::deep_copy(s0, tag.init()); + // Create scalar view ScalarViewType s; - FadType s0 = FadType(fad_size,tag.init()); #if defined (SACADO_DISABLE_FAD_VIEW_SPEC) s = ScalarViewType ("scalar view"); #else s = ScalarViewType ("scalar view", fad_size+1); #endif - Kokkos::deep_copy( s, s0 ); + Kokkos::deep_copy( s, tag.init() ); // Call atomic_add kernel, which adds up entries in v AtomicKernel::apply( tag, v, s ); @@ -290,12 +294,14 @@ bool testAtomic(const TagType& tag, Teuchos::FancyOStream& out) Kokkos::deep_copy(hs, s); // Compute correct result - FadType b = s0; + auto b = Kokkos::create_mirror_view(s0); + Kokkos::deep_copy(b, s0); + for (size_type i=0; i LeftContiguous32; From 029e7838f6e8d7424a32ed899d6a5ea131787eb5 Mon Sep 17 00:00:00 2001 From: Jacob Domagala Date: Tue, 26 Oct 2021 00:09:15 +0200 Subject: [PATCH 73/98] Sacado: Run DFad tests for remaining Sacado tests --- .../sacado/test/UnitTests/Fad_KokkosAtomicTests_Cuda.cpp | 5 +---- .../test/UnitTests/Fad_KokkosTests_Cuda_Hierarchical.cpp | 5 +---- .../test/UnitTests/Fad_KokkosTests_NoViewSpec_Cuda.cpp | 5 +---- 3 files changed, 3 insertions(+), 12 deletions(-) diff --git a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests_Cuda.cpp b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests_Cuda.cpp index 22b8b1a4cf53..7fb6b28e303c 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests_Cuda.cpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests_Cuda.cpp @@ -32,11 +32,8 @@ #include "Kokkos_Macros.hpp" -#if defined(KOKKOS_ENABLE_CUDA_UVM) #define SACADO_TEST_DFAD 1 -#else -#define SACADO_TEST_DFAD 0 -#endif + #include "Fad_KokkosAtomicTests.hpp" // Instantiate tests for Cuda device. We can only test DFad is UVM is enabled. diff --git a/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda_Hierarchical.cpp b/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda_Hierarchical.cpp index 442b093266e3..c693231fef59 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda_Hierarchical.cpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosTests_Cuda_Hierarchical.cpp @@ -37,11 +37,8 @@ #include "Kokkos_Macros.hpp" -#if defined(KOKKOS_ENABLE_CUDA_UVM) #define SACADO_TEST_DFAD 1 -#else -#define SACADO_TEST_DFAD 0 -#endif + #include "Fad_KokkosTests.hpp" typedef Kokkos::LayoutContiguous LeftContiguous32; diff --git a/packages/sacado/test/UnitTests/Fad_KokkosTests_NoViewSpec_Cuda.cpp b/packages/sacado/test/UnitTests/Fad_KokkosTests_NoViewSpec_Cuda.cpp index 7135f5deee40..40c49dab3569 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosTests_NoViewSpec_Cuda.cpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosTests_NoViewSpec_Cuda.cpp @@ -35,11 +35,8 @@ #include "Kokkos_Macros.hpp" -#if defined(KOKKOS_ENABLE_CUDA_UVM) #define SACADO_TEST_DFAD 1 -#else -#define SACADO_TEST_DFAD 0 -#endif + #include "Fad_KokkosTests.hpp" // Instantiate tests for Cuda device From 448daebe9f0105556673fd3a075a6081040b6786 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Fri, 22 Oct 2021 16:03:05 -0600 Subject: [PATCH 74/98] intrepid2: remove deprecation warnings remove Rank and MDRangePolicy from Experimental namespace --- packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp | 4 ++-- .../perf-test/ComputeBasis/test_hgrad_vector.hpp | 4 ++-- .../intrepid2/src/Cell/Intrepid2_CellToolsDefJacobian.hpp | 4 ++-- .../Intrepid2_FunctionSpaceToolsDef.hpp | 4 ++-- .../src/Shared/Intrepid2_ArrayToolsDefTensor.hpp | 8 ++++---- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp index fbc85c747cef..16186f06bbb0 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp +++ b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp @@ -210,8 +210,8 @@ namespace Intrepid2 { typedef F_hgrad_eval FunctorType; - using range_policy_type = Kokkos::Experimental::MDRangePolicy - < DeviceSpaceType, Kokkos::Experimental::Rank<2>, Kokkos::IndexType >; + using range_policy_type = Kokkos::MDRangePolicy + < DeviceSpaceType, Kokkos::Rank<2>, Kokkos::IndexType >; range_policy_type policy( { 0, 0 }, { numCells, numPoints } ); diff --git a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp index b2166912709a..f24dc63375ab 100644 --- a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp +++ b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad_vector.hpp @@ -173,8 +173,8 @@ namespace Intrepid2 { typedef F_hgrad_eval FunctorType; - using range_policy_type = Kokkos::Experimental::MDRangePolicy - < DeviceSpaceType, Kokkos::Experimental::Rank<2>, Kokkos::IndexType >; + using range_policy_type = Kokkos::MDRangePolicy + < DeviceSpaceType, Kokkos::Rank<2>, Kokkos::IndexType >; range_policy_type policy( { 0, 0 }, { numCellsAdjusted, numPoints } ); diff --git a/packages/intrepid2/src/Cell/Intrepid2_CellToolsDefJacobian.hpp b/packages/intrepid2/src/Cell/Intrepid2_CellToolsDefJacobian.hpp index b5371ac9ce59..9f0c32423b5b 100644 --- a/packages/intrepid2/src/Cell/Intrepid2_CellToolsDefJacobian.hpp +++ b/packages/intrepid2/src/Cell/Intrepid2_CellToolsDefJacobian.hpp @@ -805,8 +805,8 @@ namespace Intrepid2 { // resolve the -1 default argument for endCell into the true end cell index int endCellResolved = (endCell == -1) ? worksetCell.extent_int(0) : endCell; - using range_policy_type = Kokkos::Experimental::MDRangePolicy - < ExecSpaceType, Kokkos::Experimental::Rank<2>, Kokkos::IndexType >; + using range_policy_type = Kokkos::MDRangePolicy + < ExecSpaceType, Kokkos::Rank<2>, Kokkos::IndexType >; range_policy_type policy( { 0, 0 }, { jacobian.extent(0), jacobian.extent(1) } ); Kokkos::parallel_for( policy, FunctorType(jacobian, worksetCell, gradients, startCell, endCellResolved) ); diff --git a/packages/intrepid2/src/Discretization/FunctionSpaceTools/Intrepid2_FunctionSpaceToolsDef.hpp b/packages/intrepid2/src/Discretization/FunctionSpaceTools/Intrepid2_FunctionSpaceToolsDef.hpp index 56ec1249785d..465225c464cd 100644 --- a/packages/intrepid2/src/Discretization/FunctionSpaceTools/Intrepid2_FunctionSpaceToolsDef.hpp +++ b/packages/intrepid2/src/Discretization/FunctionSpaceTools/Intrepid2_FunctionSpaceToolsDef.hpp @@ -142,8 +142,8 @@ namespace Intrepid2 { // F = outputVals.extent(1), // P = outputVals.extent(2); - // using range_policy_type = Kokkos::Experimental::MDRangePolicy - // < DeviceType, Kokkos::Experimental::Rank<3>, Kokkos::IndexType >; + // using range_policy_type = Kokkos::MDRangePolicy + // < DeviceType, Kokkos::Rank<3>, Kokkos::IndexType >; // range_policy_type policy( { 0, 0, 0 }, // { C, F, P } ); diff --git a/packages/intrepid2/src/Shared/Intrepid2_ArrayToolsDefTensor.hpp b/packages/intrepid2/src/Shared/Intrepid2_ArrayToolsDefTensor.hpp index 571b752fbecb..922aa506aba7 100644 --- a/packages/intrepid2/src/Shared/Intrepid2_ArrayToolsDefTensor.hpp +++ b/packages/intrepid2/src/Shared/Intrepid2_ArrayToolsDefTensor.hpp @@ -793,14 +793,14 @@ namespace Intrepid2 { typedef FunctorArrayTools::F_matvecProduct FunctorType; if (hasField) { - using range_policy_type = Kokkos::Experimental::MDRangePolicy - < ExecSpaceType, Kokkos::Experimental::Rank<3>, Kokkos::IndexType >; + using range_policy_type = Kokkos::MDRangePolicy + < ExecSpaceType, Kokkos::Rank<3>, Kokkos::IndexType >; range_policy_type policy( { 0, 0, 0 }, { output.extent(0), output.extent(1), output.extent(2) } ); Kokkos::parallel_for( policy, FunctorType(output, leftInput, rightInput, isTranspose) ); } else { - using range_policy_type = Kokkos::Experimental::MDRangePolicy - < ExecSpaceType, Kokkos::Experimental::Rank<2>, Kokkos::IndexType >; + using range_policy_type = Kokkos::MDRangePolicy + < ExecSpaceType, Kokkos::Rank<2>, Kokkos::IndexType >; range_policy_type policy( { 0, 0 }, { output.extent(0), output.extent(1) } ); Kokkos::parallel_for( policy, FunctorType(output, leftInput, rightInput, isTranspose) ); From eb03da39cc1b39f518b7cf5d0a4e4eb4aa3ce26f Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Fri, 22 Oct 2021 16:06:09 -0600 Subject: [PATCH 75/98] amesos2: resolve unused warning in superlu interface --- packages/amesos2/src/Amesos2_Superlu_def.hpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/amesos2/src/Amesos2_Superlu_def.hpp b/packages/amesos2/src/Amesos2_Superlu_def.hpp index 5af71193dffa..14b58f1e71a5 100644 --- a/packages/amesos2/src/Amesos2_Superlu_def.hpp +++ b/packages/amesos2/src/Amesos2_Superlu_def.hpp @@ -1060,7 +1060,6 @@ Superlu::triangular_solve_factor() if (data_.options.ConditionNumber == SLU::YES) { using STM = Teuchos::ScalarTraits; const magnitude_type eps = STM::eps (); - int n = data_.perm_r.extent(0); SCformat *Lstore = (SCformat*)(data_.L.Store); int nsuper = 1 + Lstore->nsuper; @@ -1077,6 +1076,7 @@ Superlu::triangular_solve_factor() condition_flag = (((double)max_cols * nsuper) * eps * multiply_fact >= data_.rcond); #ifdef HAVE_AMESOS2_VERBOSE_DEBUG + int n = data_.perm_r.extent(0); std::cout << this->getComm()->getRank() << " : anorm = " << data_.anorm << ", rcond = " << data_.rcond << ", n = " << n << ", num super cols = " << nsuper << ", max super cols = " << max_cols From 98bc0c8eca7212c57c9ec874b440c86117896bcf Mon Sep 17 00:00:00 2001 From: iyamazaki Date: Tue, 26 Oct 2021 00:33:41 -0600 Subject: [PATCH 76/98] Amesos2::SuperLU_dist: shift the local row and col scaling by offset --- packages/amesos2/src/Amesos2_Superludist_def.hpp | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/packages/amesos2/src/Amesos2_Superludist_def.hpp b/packages/amesos2/src/Amesos2_Superludist_def.hpp index 4cd1fea25c5d..ef0ed950d7ef 100644 --- a/packages/amesos2/src/Amesos2_Superludist_def.hpp +++ b/packages/amesos2/src/Amesos2_Superludist_def.hpp @@ -572,7 +572,9 @@ namespace Amesos2 { if (data_.options.Equil == SLUD::YES && data_.rowequ) { SLUD::int_t ld = as(local_len_rhs); for(global_size_type j = 0; j < nrhs; ++j) { - for(size_t i = 0; i < local_len_rhs; ++i) bvals_[i + j*ld] *= data_.R[i]; + for(size_t i = 0; i < local_len_rhs; ++i) { + bvals_[i + j*ld] *= data_.R[first_global_row_b + i]; + } } } @@ -624,7 +626,9 @@ namespace Amesos2 { if (data_.options.Equil == SLUD::YES && data_.colequ) { SLUD::int_t ld = as(local_len_rhs); for(global_size_type j = 0; j < nrhs; ++j) { - for(size_t i = 0; i < local_len_rhs; ++i) xvals_[i + j*ld] *= data_.C[i]; + for(size_t i = 0; i < local_len_rhs; ++i) { + xvals_[i + j*ld] *= data_.C[first_global_row_b + i]; + } } } } From 0e6d9712163480d788b5127003f3841e0426fd66 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Mon, 25 Oct 2021 20:41:14 -0600 Subject: [PATCH 77/98] Disable override of Sacado_NEW_FAD_DESIGN_IS_DEFAULT with PR tester --- cmake/std/PullRequestLinuxCuda10.1.105TestingSettings.cmake | 4 +++- .../PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake | 4 +++- cmake/std/PullRequestLinuxCuda10.1.243TestingSettings.cmake | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/cmake/std/PullRequestLinuxCuda10.1.105TestingSettings.cmake b/cmake/std/PullRequestLinuxCuda10.1.105TestingSettings.cmake index d684fc7c97be..9fc5038fdfdd 100644 --- a/cmake/std/PullRequestLinuxCuda10.1.105TestingSettings.cmake +++ b/cmake/std/PullRequestLinuxCuda10.1.105TestingSettings.cmake @@ -78,7 +78,9 @@ set (TPL_DLlib_LIBRARIES "-ldl" CACHE FILEPATH "Set by default for CUDA PR testi # The compile times for two Panzer files went up to over 6 hours. This # turns off one feature that allows these in about 24 minutes. Please remove # when issue #7532 is resolved. -set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) +# Compile time issues addressed by #8377. Commenting out the override of +# Sacado_NEW_FAD_DESIGN_IS_DEFAULT to return to default settings. +#set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) # Disable some packages that can't be tested with this PR build set (Trilinos_ENABLE_ShyLU_NodeTacho OFF CACHE BOOL diff --git a/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake b/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake index cf2af6363165..4af04bc73ee4 100644 --- a/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake +++ b/cmake/std/PullRequestLinuxCuda10.1.105uvmOffTestingSettings.cmake @@ -77,7 +77,9 @@ set (TPL_DLlib_LIBRARIES "-ldl" CACHE FILEPATH "Set by default for CUDA PR testi # The compile times for two Panzer files went up to over 6 hours. This # turns off one feature that allows these in about 24 minutes. Please remove # when issue #7532 is resolved. -set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) +# Compile time issues addressed by #8377. Commenting out the override of +# Sacado_NEW_FAD_DESIGN_IS_DEFAULT to return to default settings. +#set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) # Disable some packages that can't be tested with this PR build set (Trilinos_ENABLE_ShyLU_NodeTacho OFF CACHE BOOL diff --git a/cmake/std/PullRequestLinuxCuda10.1.243TestingSettings.cmake b/cmake/std/PullRequestLinuxCuda10.1.243TestingSettings.cmake index 07a87bbab985..c65b54ffffa5 100644 --- a/cmake/std/PullRequestLinuxCuda10.1.243TestingSettings.cmake +++ b/cmake/std/PullRequestLinuxCuda10.1.243TestingSettings.cmake @@ -84,7 +84,9 @@ set (TPL_DLlib_LIBRARIES "-ldl" CACHE FILEPATH "Set by default for CUDA PR testi # The compile times for two Panzer files went up to over 6 hours. This # turns off one feature that allows these in about 24 minutes. Please remove # when issue #7532 is resolved. -set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) +# Compile time issues addressed by #8377. Commenting out the override of +# Sacado_NEW_FAD_DESIGN_IS_DEFAULT to return to default settings. +#set (Sacado_NEW_FAD_DESIGN_IS_DEFAULT OFF CACHE BOOL "Temporary fix for issue #7532" ) # Disable some packages that can't be tested with this PR build set (Trilinos_ENABLE_ShyLU_NodeTacho OFF CACHE BOOL From 15c606f4c774b5a39fb9b90ce5b3aeeb3792d30e Mon Sep 17 00:00:00 2001 From: Christian Glusa Date: Tue, 19 Oct 2021 13:14:21 -0600 Subject: [PATCH 78/98] MueLu: Simplify passing precomputed objects --- .../MueLu_CreateXpetraPreconditioner.hpp | 6 +- .../MueCentral/MueLu_HierarchyUtils_def.hpp | 84 +++++++++++++++++-- packages/muelu/src/MueCentral/MueLu_Level.hpp | 2 +- packages/muelu/test/scaling/Driver.cpp | 5 ++ 4 files changed, 87 insertions(+), 10 deletions(-) diff --git a/packages/muelu/adapters/xpetra/MueLu_CreateXpetraPreconditioner.hpp b/packages/muelu/adapters/xpetra/MueLu_CreateXpetraPreconditioner.hpp index 69c7ebe30c59..a3c8fcd6f7a1 100644 --- a/packages/muelu/adapters/xpetra/MueLu_CreateXpetraPreconditioner.hpp +++ b/packages/muelu/adapters/xpetra/MueLu_CreateXpetraPreconditioner.hpp @@ -126,13 +126,13 @@ namespace MueLu { RCP H = mueLuFactory->CreateHierarchy(label); H->setlib(op->getDomainMap()->lib()); - // Stick the non-serializible data on the hierarchy. - HierarchyUtils::AddNonSerializableDataToHierarchy(*mueLuFactory,*H, nonSerialList); - // Set fine level operator H->GetLevel(0)->Set("A", op); H->SetProcRankVerbose(op->getDomainMap()->getComm()->getRank()); + // Stick the non-serializible data on the hierarchy. + HierarchyUtils::AddNonSerializableDataToHierarchy(*mueLuFactory,*H, nonSerialList); + mueLuFactory->SetupHierarchy(*H); tm->stop(); diff --git a/packages/muelu/src/MueCentral/MueLu_HierarchyUtils_def.hpp b/packages/muelu/src/MueCentral/MueLu_HierarchyUtils_def.hpp index 1c91ef188a51..cb2b805a156f 100644 --- a/packages/muelu/src/MueCentral/MueLu_HierarchyUtils_def.hpp +++ b/packages/muelu/src/MueCentral/MueLu_HierarchyUtils_def.hpp @@ -98,15 +98,52 @@ namespace MueLu { !IsParamMuemexVariable(name), Exceptions::InvalidArgument, std::string("MueLu::Utils::AddNonSerializableDataToHierarchy: parameter list contains unknown data type(") + name + ")"); + // Get a valid communicator and lib + RCP > comm; + if (!level->GetComm().is_null()) + comm = level->GetComm(); + else if (level->IsAvailable("A")) { + RCP mat; + level->Get("A", mat); + comm = mat->getMap()->getComm(); + } else { + RCP level0 = H.GetLevel(0); + if (!level0->GetComm().is_null()) + comm = level0->GetComm(); + else { + RCP mat; + level0->Get("A", mat); + comm = mat->getMap()->getComm(); + } + } + Xpetra::UnderlyingLib lib = level->lib(); + if (name == "A") { - level->Set(name, Teuchos::getValue > (levelListEntry->second),NoFactory::get()); + RCP mat; + if (levelListEntry->second.isType()) + // We might also want to read maps here. + mat = Xpetra::IO::Read(Teuchos::getValue(levelListEntry->second), lib, comm); + else + mat = Teuchos::getValue > (levelListEntry->second); + level->Set(name, mat, NoFactory::get()); M->SetFactory(name, NoFactory::getRCP()); // TAW: not sure about this: be aware that this affects all levels // However, A is accessible through NoFactory anyway, so it should // be fine here. } else if(name == "P" || name == "R" || name == "K" || name == "M") { + RCP mat; + if (levelListEntry->second.isType()) + // We might also want to read maps here. + mat = Xpetra::IO::Read(Teuchos::getValue(levelListEntry->second), lib, comm); + else + mat = Teuchos::getValue > (levelListEntry->second); + + RCP fact = M->GetFactory(name); + level->AddKeepFlag(name,fact.get(),MueLu::UserData); + level->Set(name, mat, fact.get()); + level->AddKeepFlag(name,NoFactory::get(),MueLu::UserData); - level->Set(name, Teuchos::getValue > (levelListEntry->second), NoFactory::get()); + level->Set(name, mat, NoFactory::get()); } else if (name == "Mdiag") { @@ -115,15 +152,50 @@ namespace MueLu { } else if (name == "Nullspace") { - level->AddKeepFlag(name,NoFactory::get(),MueLu::UserData); - level->Set(name, Teuchos::getValue >(levelListEntry->second), NoFactory::get()); + RCP vec; + if (levelListEntry->second.isType()) { + TEUCHOS_ASSERT(level->IsAvailable("A")); + RCP mat; + level->Get("A", mat); + auto map = mat->getMap(); + vec = Xpetra::IO::ReadMultiVector(Teuchos::getValue(levelListEntry->second), map); + } else + vec = Teuchos::getValue > (levelListEntry->second); + level->AddKeepFlag(name, NoFactory::get(), MueLu::UserData); + level->Set(name, vec, NoFactory::get()); //M->SetFactory(name, NoFactory::getRCP()); // TAW: generally it is a bad idea to overwrite the factory manager data here // One should do this only in very special cases } else if(name == "Coordinates") //Scalar of Coordinates MV is always double { + RCP vec; + if (levelListEntry->second.isType()) { + TEUCHOS_ASSERT(level->IsAvailable("A")); + RCP mat; + level->Get("A", mat); + size_t blkSize = mat->GetFixedBlockSize(); + RCP nodeMap = mat->getRowMap(); + if (blkSize > 1) { + // Create a nodal map, as coordinates have not been expanded to a DOF map yet. + RCP dofMap = mat->getRowMap(); + GO indexBase = dofMap->getIndexBase(); + size_t numLocalDOFs = dofMap->getNodeNumElements(); + TEUCHOS_TEST_FOR_EXCEPTION(numLocalDOFs % blkSize, Exceptions::RuntimeError, + "HierarchyUtils: block size (" << blkSize << ") is incompatible with the number of local dofs in a row map (" << numLocalDOFs); + ArrayView GIDs = dofMap->getNodeElementList(); + + Array nodeGIDs(numLocalDOFs/blkSize); + for (size_t i = 0; i < numLocalDOFs; i += blkSize) + nodeGIDs[i/blkSize] = (GIDs[i] - indexBase)/blkSize + indexBase; + + Xpetra::global_size_t INVALID = Teuchos::OrdinalTraits::invalid(); + nodeMap = MapFactory::Build(dofMap->lib(), INVALID, nodeGIDs(), indexBase, dofMap->getComm()); + } + vec = Xpetra::IO::coordinateType,LocalOrdinal,GlobalOrdinal,Node>::ReadMultiVector(Teuchos::getValue(levelListEntry->second), nodeMap); + } else + vec = Teuchos::getValue > (levelListEntry->second); level->AddKeepFlag(name,NoFactory::get(),MueLu::UserData); - level->Set(name, Teuchos::getValue >(levelListEntry->second), NoFactory::get()); + level->Set(name, vec, NoFactory::get()); //M->SetFactory(name, NoFactory::getRCP()); // TAW: generally it is a bad idea to overwrite the factory manager data here } else if(name == "Node Comm") @@ -214,7 +286,6 @@ namespace MueLu { } else if(name == "Coordinates") {//Scalar of Coordinates MV is always double level->AddKeepFlag(name,NoFactory::get(),MueLu::UserData); level->Set(name, Teuchos::getValue >(userListEntry->second), NoFactory::get()); - level->print(std::cout, MueLu::VERB_EXTREME); } else if(name == "Node Comm") { level->AddKeepFlag(name,NoFactory::get(),MueLu::UserData); @@ -282,6 +353,7 @@ namespace MueLu { throw std::runtime_error("Invalid non-serializable data on list"); } } + // level->print(std::cout, MueLu::Debug); } } } diff --git a/packages/muelu/src/MueCentral/MueLu_Level.hpp b/packages/muelu/src/MueCentral/MueLu_Level.hpp index f189fdc8f3f6..be33b4ed2d74 100644 --- a/packages/muelu/src/MueCentral/MueLu_Level.hpp +++ b/packages/muelu/src/MueCentral/MueLu_Level.hpp @@ -194,7 +194,7 @@ namespace MueLu { /* printf("(l=%d) getting \"%20s\" generated by %10p [actually, generated by %p (%43s)]\n", levelID_, ename.c_str(), factory, fac, fac->description().c_str());*/ - TEUCHOS_TEST_FOR_EXCEPTION(!IsKey(fac, ename), Exceptions::RuntimeError, "\"" + ename + "\" not found on level " + toString(GetLevelID()) + "."); + TEUCHOS_TEST_FOR_EXCEPTION(!IsKey(fac, ename), Exceptions::RuntimeError, "\"" + ename + "\" generated by factory \"" + fac->description() + "\" not found on level " + toString(GetLevelID()) + "."); if (!IsAvailable(ename, fac)) { TEUCHOS_TEST_FOR_EXCEPTION(NumRequests(fac, ename) < 1 && GetKeepFlag(ename, fac) == 0, Exceptions::RuntimeError, diff --git a/packages/muelu/test/scaling/Driver.cpp b/packages/muelu/test/scaling/Driver.cpp index e84784bd11fb..4f9bb5c03fa8 100644 --- a/packages/muelu/test/scaling/Driver.cpp +++ b/packages/muelu/test/scaling/Driver.cpp @@ -230,6 +230,7 @@ int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib& lib, int ar std::string rangeMapFile; clp.setOption("rangemap", &rangeMapFile, "rangemap data file"); std::string matrixFile; clp.setOption("matrix", &matrixFile, "matrix data file"); std::string rhsFile; clp.setOption("rhs", &rhsFile, "rhs data file"); + std::string solFile; clp.setOption("sol", &solFile, "write the solution to this file"); std::string coordFile; clp.setOption("coords", &coordFile, "coordinates data file"); std::string coordMapFile; clp.setOption("coordsmap", &coordMapFile, "coordinates map data file"); std::string nullFile; clp.setOption("nullspace", &nullFile, "nullspace data file"); @@ -563,6 +564,10 @@ MueLu::MueLu_AMGX_initialize_plugins(); }//end reruns + if (solFile != "") + Xpetra::IO::Write(solFile, *X); + + #ifdef HAVE_MUELU_AMGX // Finalize AMGX MueLu::MueLu_AMGX_finalize_plugins(); From 78fac347f6e5b7f155ba4d53378523dae5e63c66 Mon Sep 17 00:00:00 2001 From: Christian Glusa Date: Wed, 20 Oct 2021 13:54:14 -0600 Subject: [PATCH 79/98] MueLu: Rebase gold files --- .../Output/operator_solve_5_np1_epetra.gold | 25 ------------------- .../Output/operator_solve_5_np1_tpetra.gold | 25 ------------------- .../Output/operator_solve_5_np4_epetra.gold | 25 ------------------- .../Output/operator_solve_5_np4_tpetra.gold | 25 ------------------- .../Output/operator_solve_6_np1_epetra.gold | 22 ---------------- .../Output/operator_solve_6_np1_tpetra.gold | 22 ---------------- .../Output/operator_solve_6_np4_epetra.gold | 22 ---------------- .../Output/operator_solve_6_np4_tpetra.gold | 22 ---------------- .../Output/operator_solve_7_np1_epetra.gold | 22 ---------------- .../Output/operator_solve_7_np1_tpetra.gold | 22 ---------------- .../Output/operator_solve_7_np4_epetra.gold | 22 ---------------- .../Output/operator_solve_7_np4_tpetra.gold | 22 ---------------- .../Output/operator_solve_5_np1_tpetra.gold | 25 ------------------- .../Output/operator_solve_5_np4_tpetra.gold | 25 ------------------- .../Output/operator_solve_6_np1_tpetra.gold | 22 ---------------- .../Output/operator_solve_6_np4_tpetra.gold | 22 ---------------- .../Output/operator_solve_7_np1_tpetra.gold | 22 ---------------- .../Output/operator_solve_7_np4_tpetra.gold | 22 ---------------- 18 files changed, 414 deletions(-) diff --git a/packages/muelu/test/interface/default/Output/operator_solve_5_np1_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_5_np1_epetra.gold index 5df79af4ee13..cfd6b4cb2877 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_5_np1_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_5_np1_epetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_5_np1_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_5_np1_tpetra.gold index 56db68d6a235..a47f7f59617f 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_5_np1_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_5_np1_tpetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_5_np4_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_5_np4_epetra.gold index 97116a5e3822..e7b0bdd1e23d 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_5_np4_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_5_np4_epetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_5_np4_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_5_np4_tpetra.gold index 4f8366aa67da..7f67123c53fc 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_5_np4_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_5_np4_tpetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_6_np1_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_6_np1_epetra.gold index fd00a4b79e67..fc7703a6b858 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_6_np1_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_6_np1_epetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_6_np1_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_6_np1_tpetra.gold index eb86e150b9a8..4f7220c773d6 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_6_np1_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_6_np1_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_6_np4_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_6_np4_epetra.gold index 3c07213c30d1..7f2e4df41b0c 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_6_np4_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_6_np4_epetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_6_np4_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_6_np4_tpetra.gold index c14179bbd366..a32e937c5a07 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_6_np4_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_6_np4_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/default/Output/operator_solve_7_np1_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_7_np1_epetra.gold index 553c57aac0f5..9136ab9e667d 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_7_np1_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_7_np1_epetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> diff --git a/packages/muelu/test/interface/default/Output/operator_solve_7_np1_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_7_np1_tpetra.gold index 565507f9a78c..26b1dc8ef187 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_7_np1_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_7_np1_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> diff --git a/packages/muelu/test/interface/default/Output/operator_solve_7_np4_epetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_7_np4_epetra.gold index 9ffca77409c7..996f2f1c60d5 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_7_np4_epetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_7_np4_epetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 [unused] relaxation: damping factor = 1 [unused] Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> diff --git a/packages/muelu/test/interface/default/Output/operator_solve_7_np4_tpetra.gold b/packages/muelu/test/interface/default/Output/operator_solve_7_np4_tpetra.gold index c2cc052d8f54..7f07fca1fa52 100644 --- a/packages/muelu/test/interface/default/Output/operator_solve_7_np4_tpetra.gold +++ b/packages/muelu/test/interface/default/Output/operator_solve_7_np4_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory) -Matrix filtering (MueLu::FilteredAFactory) -Build (MueLu::CoalesceDropFactory) -Build (MueLu::AmalgamationFactory) -[empty list] -algorithm = "classical" classical algorithm = "default": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Filtered matrix is not being constructed as no filtering is being done -Build (MueLu::TentativePFactory) -Build (MueLu::UncoupledAggregationFactory) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregates (Phase 1 (main)) -BuildAggregates (Phase 2a (secondary)) -BuildAggregates (Phase 2b (expansion)) -BuildAggregates (Phase 3 (cleanup)) -Nullspace factory (MueLu::NullspaceFactory) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory) -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np1_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np1_tpetra.gold index d2369aa0b0b8..282e22593f7b 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np1_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np1_tpetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np4_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np4_tpetra.gold index 9401a0fbba43..ed3796b9fc90 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np4_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_5_np4_tpetra.gold @@ -6,31 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] -Transpose P (MueLu::TransPFactory) -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np1_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np1_tpetra.gold index dbe8eb0eebd0..600b17ed42f7 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np1_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np1_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np4_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np4_tpetra.gold index 3b8329245db7..14ac90e59970 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np4_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_6_np4_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Transpose P (MueLu::TransPFactory) matrixmatrix: kernel params -> [empty list] diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np1_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np1_tpetra.gold index d4fd71378201..26b1dc8ef187 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np1_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np1_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> diff --git a/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np4_tpetra.gold b/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np4_tpetra.gold index 15c4d606eda0..7f07fca1fa52 100644 --- a/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np4_tpetra.gold +++ b/packages/muelu/test/interface/kokkos/Output/operator_solve_7_np4_tpetra.gold @@ -6,28 +6,6 @@ smoother -> relaxation: sweeps = 1 relaxation: damping factor = 1 Level 1 -Prolongator smoothing (MueLu::SaPFactory_kokkos) -Build (MueLu::CoalesceDropFactory_kokkos) -Build (MueLu::AmalgamationFactory_kokkos) -[empty list] -algorithm = "classical": threshold = 0, blocksize = 1 -lightweight wrap = 1 -Build (MueLu::TentativePFactory_kokkos) -Build (MueLu::UncoupledAggregationFactory_kokkos) -BuildAggregates (Phase - (Dirichlet)) -BuildAggregatesDeterministic (Phase 1 (main)) -BuildAggregatesDeterministic (Phase 2a (secondary)) -BuildAggregatesDeterministic (Phase 2b (expansion)) -BuildAggregatesDeterministic (Phase 3 (cleanup)) -aggregation: deterministic = 1 [unused] -Nullspace factory (MueLu::NullspaceFactory_kokkos) -Fine level nullspace = Nullspace -Build (MueLu::CoarseMapFactory_kokkos) -[empty list] -matrixmatrix: kernel params -> - [empty list] -matrixmatrix: kernel params -> - [empty list] Computing Ac (MueLu::RAPFactory) transpose: use implicit = 1 matrixmatrix: kernel params -> From b155965ec39d77c095ca9286e70889ac5f450d18 Mon Sep 17 00:00:00 2001 From: Brian Kelley Date: Tue, 26 Oct 2021 16:04:47 -0600 Subject: [PATCH 80/98] MueLu: fix ReitzingerPFactory for non-UVM --- .../MueLu_ReitzingerPFactory_def.hpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_ReitzingerPFactory_def.hpp b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_ReitzingerPFactory_def.hpp index 883edffc743b..a5c69c6fcd6b 100644 --- a/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_ReitzingerPFactory_def.hpp +++ b/packages/muelu/src/Transfers/Smoothed-Aggregation/MueLu_ReitzingerPFactory_def.hpp @@ -388,13 +388,13 @@ namespace MueLu { ArrayView columns; ArrayView values; Pe->getLocalRowView(i,columns,values); - // FIXME: This won't work on fancy nodes - ArrayView values_nc = Teuchos::av_const_cast(values); + Teuchos::Array newValues(values.size()); for (LO j=0; j<(LO)values.size(); j++) - if ((values_nc[j] == one || values_nc[j] == neg_one)) - values_nc[j] = zero; + if ((values[j] == one || values[j] == neg_one)) + newValues[j] = zero; else - values_nc[j] /= two; + newValues[j] = values[j] / two; + Pe->replaceLocalValues(i,columns,newValues()); }//end for i < Ne Pe->fillComplete(Pe->getDomainMap(),Pe->getRangeMap()); } From 69402959951d12ae4de8aeaa18271fcc2efc3db5 Mon Sep 17 00:00:00 2001 From: Jacob Domagala Date: Wed, 27 Oct 2021 14:42:17 +0200 Subject: [PATCH 81/98] Sacado: Use Kokkos::View instead of Kokkos::View for singular Fad variables in Fad_KokkosTests and Fad_KokkosAtomicTests --- .../test/UnitTests/Fad_KokkosAtomicTests.hpp | 10 +++---- .../sacado/test/UnitTests/Fad_KokkosTests.hpp | 26 ++++++++++--------- 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp index aa8360bcaf83..472513c9b896 100644 --- a/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp +++ b/packages/sacado/test/UnitTests/Fad_KokkosAtomicTests.hpp @@ -261,13 +261,13 @@ bool testAtomic(const TagType& tag, Teuchos::FancyOStream& out) // Create and fill view ViewType v; - ViewType s0; + ScalarViewType s0; #if defined (SACADO_DISABLE_FAD_VIEW_SPEC) v = ViewType ("view", num_rows); - s0 = ViewType ("", 1); + s0 = ScalarViewType (""); #else v = ViewType ("view", num_rows, fad_size+1); - s0 = ViewType ("", 1, fad_size+1); + s0 = ScalarViewType ("", fad_size+1); #endif host_view_type h_v = Kokkos::create_mirror_view(v); for (size_type i=0; i +template struct ValueAssignKernel { typedef typename ViewType::execution_space execution_space; typedef typename ViewType::size_type size_type; @@ -251,15 +251,15 @@ struct ValueAssignKernel { static const size_type stride = Kokkos::ViewScalarStride::stride; const ViewType m_v; - const ViewType m_s; + const ScalarViewType m_s; - ValueAssignKernel(const ViewType& v, const ViewType& s) : + ValueAssignKernel(const ViewType& v, const ScalarViewType& s) : m_v(v), m_s(s) {}; // Multiply entries for row 'i' with a value KOKKOS_INLINE_FUNCTION void operator() (const size_type i) const { - local_scalar_type s = Sacado::partition_scalar(m_s(0)); + local_scalar_type s = Sacado::partition_scalar(m_s()); m_v(i) = s; } @@ -272,7 +272,7 @@ struct ValueAssignKernel { } // Kernel launch - static void apply(const ViewType& v, const ViewType& s) { + static void apply(const ViewType& v, const ScalarViewType& s) { const size_type nrow = v.extent(0); #if defined (KOKKOS_ENABLE_CUDA) && defined (SACADO_VIEW_CUDA_HIERARCHICAL) @@ -713,21 +713,23 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( Kokkos_View_Fad, ValueAssign, FadType, Layout, Device ) { typedef Kokkos::View ViewType; + typedef Kokkos::View ScalarViewType; typedef typename ViewType::size_type size_type; typedef typename ViewType::HostMirror host_view_type; + typedef typename ScalarViewType::HostMirror host_scalar_view_type; const size_type num_rows = global_num_rows; const size_type fad_size = global_fad_size; // Create and fill view ViewType v; - ViewType a; + ScalarViewType a; #if defined (SACADO_DISABLE_FAD_VIEW_SPEC) v = ViewType ("view", num_rows); - a = ViewType ("fad", 1); + a = ScalarViewType ("fad"); #else v = ViewType ("view", num_rows, fad_size+1); - a = ViewType ("fad", 1, fad_size+1); + a = ScalarViewType ("fad", fad_size+1); #endif typename ViewType::array_type va = v; Kokkos::deep_copy( va, 1.0 ); @@ -736,22 +738,22 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( Kokkos::deep_copy(a, 2.3456); Kokkos::parallel_for(Kokkos::RangePolicy< Device>(0, fad_size), KOKKOS_LAMBDA(const int i) { - a(0).fastAccessDx(i) = 7.89 + i; + a().fastAccessDx(i) = 7.89 + i; }); - ValueAssignKernel::apply( v, a ); + ValueAssignKernel::apply( v, a ); // Copy to host host_view_type hv = Kokkos::create_mirror_view(v); Kokkos::deep_copy(hv, v); - host_view_type ha = Kokkos::create_mirror_view(a); + host_scalar_view_type ha = Kokkos::create_mirror_view(a); Kokkos::deep_copy(ha, a); // Check success = true; for (size_type i=0; i Date: Tue, 26 Oct 2021 09:28:05 -0600 Subject: [PATCH 82/98] MueLu: Construct Ifpack2Smoother using Operator instead of Matrix --- .../muelu/research/caglusa/CMakeLists.txt | 2 +- .../Smoothers/MueLu_Ifpack2Smoother_decl.hpp | 2 +- .../Smoothers/MueLu_Ifpack2Smoother_def.hpp | 93 ++++++++++++------- .../muelu/src/Utils/MueLu_Utilities_decl.hpp | 90 +++++++++++------- .../muelu/src/Utils/MueLu_Utilities_def.hpp | 81 +++++++++------- .../src/Operator/Xpetra_TpetraOperator.hpp | 7 +- 6 files changed, 172 insertions(+), 103 deletions(-) diff --git a/packages/muelu/research/caglusa/CMakeLists.txt b/packages/muelu/research/caglusa/CMakeLists.txt index 0e96e0382f05..ee89be39796e 100644 --- a/packages/muelu/research/caglusa/CMakeLists.txt +++ b/packages/muelu/research/caglusa/CMakeLists.txt @@ -18,7 +18,7 @@ IF (${PACKAGE_NAME}_ENABLE_Tpetra AND ${PACKAGE_NAME}_ENABLE_Belos AND ${PACKAGE TRIBITS_COPY_FILES_TO_BINARY_DIR(caglusa_cp SOURCE_FILES - hierarchical.xml aux.xml + hierarchical.xml muelu.xml aux.xml rowmap.mtx coeffmap.mtx ghosted_coeffmap.mtx Anear.mtx basismatrix.mtx kernelApproximations.mtx transfer0.mtx transfer1.mtx transfer2.mtx transfer3.mtx transfer4.mtx diff --git a/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_decl.hpp b/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_decl.hpp index 2d6c7c141580..87b0c0a0d622 100644 --- a/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_decl.hpp +++ b/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_decl.hpp @@ -234,7 +234,7 @@ namespace MueLu { RCP > prec_; //! matrix, used in apply if solving residual equation - RCP A_; + RCP A_; }; // class Ifpack2Smoother diff --git a/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_def.hpp b/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_def.hpp index dcca37279288..e054c31dc2e5 100644 --- a/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_def.hpp +++ b/packages/muelu/src/Smoothers/MueLu_Ifpack2Smoother_def.hpp @@ -137,7 +137,14 @@ namespace MueLu { if(!precList.is_null() && precList->isParameter("partitioner: type") && precList->get("partitioner: type") == "linear" && !precList->isParameter("partitioner: local parts")) { - precList->set("partitioner: local parts", (int)A_->getNodeNumRows() / A_->GetFixedBlockSize()); + LO matrixBlockSize = 1; + int lclSize = A_->getRangeMap()->getNodeNumElements(); + RCP matA = rcp_dynamic_cast(A_); + if (!matA.is_null()) { + lclSize = matA->getNodeNumRows(); + matrixBlockSize = matA->GetFixedBlockSize(); + } + precList->set("partitioner: local parts", lclSize / matrixBlockSize); } prec_->setParameters(*precList); @@ -207,31 +214,38 @@ namespace MueLu { template void Ifpack2Smoother::Setup(Level& currentLevel) { FactoryMonitor m(*this, "Setup Smoother", currentLevel); - A_ = Factory::Get< RCP >(currentLevel, "A"); + A_ = Factory::Get< RCP >(currentLevel, "A"); ParameterList& paramList = const_cast(this->GetParameterList()); // If the user asked us to convert the matrix into BlockCrsMatrix form, we do that now - if(paramList.isParameter("smoother: use blockcrsmatrix storage") && paramList.get("smoother: use blockcrsmatrix storage") && A_->GetFixedBlockSize()) { - // NOTE: Don't think you can move this out of the if block. You can't. The test MueLu_MeshTyingBlocked_SimpleSmoother_2dof_medium_MPI_1 will fail - int blocksize = A_->GetFixedBlockSize(); - using TpetraBlockCrsMatrix = Xpetra::TpetraBlockCrsMatrix; - RCP AcrsWrap = rcp_dynamic_cast(A_); - if(AcrsWrap.is_null()) - throw std::runtime_error("Ifpack2Smoother: Cannot convert matrix A to CrsMatrixWrap object."); - RCP Acrs = AcrsWrap->getCrsMatrix(); - if(Acrs.is_null()) - throw std::runtime_error("Ifpack2Smoother: Cannot extract CrsMatrix from matrix A."); - RCP At = rcp_dynamic_cast(Acrs); - if(At.is_null()) - throw std::runtime_error("Ifpack2Smoother: Cannot extract TpetraCrsMatrix from matrix A."); - - RCP > blockCrs = Tpetra::convertToBlockCrsMatrix(*At->getTpetra_CrsMatrix(),blocksize); - RCP blockCrs_as_crs = rcp(new TpetraBlockCrsMatrix(blockCrs)); - RCP blockWrap = rcp(new CrsMatrixWrap(blockCrs_as_crs)); - A_ = blockWrap; - this->GetOStream(Statistics0) << "Ifpack2Smoother: Using BlockCrsMatrix storage with blocksize "<("smoother: use blockcrsmatrix storage")) { + int blocksize = 1; + RCP matA = rcp_dynamic_cast(A_); + if (!matA.is_null()) + blocksize = matA->GetFixedBlockSize(); + if (blocksize) { + // NOTE: Don't think you can move this out of the if block. You can't. The test MueLu_MeshTyingBlocked_SimpleSmoother_2dof_medium_MPI_1 will fail + + using TpetraBlockCrsMatrix = Xpetra::TpetraBlockCrsMatrix; + RCP AcrsWrap = rcp_dynamic_cast(A_); + if(AcrsWrap.is_null()) + throw std::runtime_error("Ifpack2Smoother: Cannot convert matrix A to CrsMatrixWrap object."); + RCP Acrs = AcrsWrap->getCrsMatrix(); + if(Acrs.is_null()) + throw std::runtime_error("Ifpack2Smoother: Cannot extract CrsMatrix from matrix A."); + RCP At = rcp_dynamic_cast(Acrs); + if(At.is_null()) + throw std::runtime_error("Ifpack2Smoother: Cannot extract TpetraCrsMatrix from matrix A."); + + RCP > blockCrs = Tpetra::convertToBlockCrsMatrix(*At->getTpetra_CrsMatrix(),blocksize); + RCP blockCrs_as_crs = rcp(new TpetraBlockCrsMatrix(blockCrs)); + RCP blockWrap = rcp(new CrsMatrixWrap(blockCrs_as_crs)); + A_ = blockWrap; + this->GetOStream(Statistics0) << "Ifpack2Smoother: Using BlockCrsMatrix storage with blocksize "<getMatrix(0,0)->getNodeNumRows(); size_t numPres = bA->getMatrix(1,0)->getNodeNumRows(); - size_t numRows = A_->getNodeNumRows(); + size_t numRows = rcp_dynamic_cast(A_, true)->getNodeNumRows(); ArrayRCP blockSeeds(numRows, Teuchos::OrdinalTraits::invalid()); @@ -423,8 +437,11 @@ namespace MueLu { ArrayRCP dof_ids; // We need to unamalgamate, if the FixedBlockSize > 1 - if(A_->GetFixedBlockSize() > 1) { - LO blocksize = (LO) A_->GetFixedBlockSize(); + LO blocksize = 1; + RCP matA = rcp_dynamic_cast(A_); + if (!matA.is_null()) + blocksize = matA->GetFixedBlockSize(); + if(blocksize > 1) { dof_ids.resize(aggregate_ids.size() * blocksize); for(LO i=0; i<(LO)aggregate_ids.size(); i++) { for(LO j=0; j<(LO)blocksize; j++) @@ -498,12 +515,13 @@ namespace MueLu { dimension = basis->getBaseCellTopology().getDimension(); else TEUCHOS_TEST_FOR_EXCEPTION(true,std::invalid_argument,"Unrecognized smoother neighborhood type. Supported types are node, edge, face."); + RCP matA = rcp_dynamic_cast(A_, true); vector> seeds; - MueLuIntrepid::FindGeometricSeedOrdinals(basis, *elemToNode, seeds, *A_->getRowMap(), *A_->getColMap()); + MueLuIntrepid::FindGeometricSeedOrdinals(basis, *elemToNode, seeds, *matA->getRowMap(), *matA->getColMap()); // Ifpack2 wants the seeds in an array of the same length as the number of local elements, // with local partition #s marked for the ones that are seeds, and invalid for the rest - int myNodeCount = A_->getRowMap()->getNodeNumElements(); + int myNodeCount = matA->getRowMap()->getNodeNumElements(); ArrayRCP nodeSeeds(myNodeCount,lo_invalid); int localPartitionNumber = 0; for (LocalOrdinal seed : seeds[dimension]) @@ -547,7 +565,8 @@ namespace MueLu { for(size_t k = 0; k < Teuchos::as(TVertLineIdSmoo.size()); k++) { if(maxPart < TVertLineIdSmoo[k]) maxPart = TVertLineIdSmoo[k]; } - size_t numLocalRows = A_->getNodeNumRows(); + RCP matA = rcp_dynamic_cast(A_, true); + size_t numLocalRows = matA->getNodeNumRows(); TEUCHOS_TEST_FOR_EXCEPTION(numLocalRows % TVertLineIdSmoo.size() != 0, Exceptions::RuntimeError, "MueLu::Ifpack2Smoother::Setup(): the number of local nodes is incompatible with the TVertLineIdsSmoo."); @@ -556,15 +575,15 @@ namespace MueLu { //It is encoded in either the MueLu Level, or in the Xpetra matrix block size. //This value is needed by Ifpack2 to do decoupled block relaxation. int actualDofsPerNode = numLocalRows / TVertLineIdSmoo.size(); - LO matrixBlockSize = A_->GetFixedBlockSize(); + LO matrixBlockSize = matA->GetFixedBlockSize(); if(matrixBlockSize > 1 && actualDofsPerNode > 1) { - TEUCHOS_TEST_FOR_EXCEPTION(actualDofsPerNode != A_->GetFixedBlockSize(), Exceptions::RuntimeError, + TEUCHOS_TEST_FOR_EXCEPTION(actualDofsPerNode != matrixBlockSize, Exceptions::RuntimeError, "MueLu::Ifpack2Smoother::Setup(): A is a block matrix but its block size and DOFs/node from partitioner disagree"); } else if(matrixBlockSize > 1) { - actualDofsPerNode = A_->GetFixedBlockSize(); + actualDofsPerNode = matrixBlockSize; } myparamList.set("partitioner: PDE equations", actualDofsPerNode); @@ -650,7 +669,11 @@ namespace MueLu { Factory::Get::magnitudeType,LO,GO,NO> > >(currentLevel, "Coordinates"); Teuchos::RCP::magnitudeType,LO,GO,NO> > coordinates = Teuchos::rcpFromRef(Xpetra::toTpetra::magnitudeType,LO,GO,NO>(*xCoordinates)); - size_t numDofsPerNode = A_->getNodeNumRows() / xCoordinates->getMap()->getNodeNumElements(); + RCP matA = rcp_dynamic_cast(A_); + size_t lclSize = A_->getRangeMap()->getNodeNumElements(); + if (!matA.is_null()) + lclSize = matA->getNodeNumRows(); + size_t numDofsPerNode = lclSize / xCoordinates->getMap()->getNodeNumElements(); myparamList.set("partitioner: coordinates", coordinates); myparamList.set("partitioner: PDE equations", (int) numDofsPerNode); } @@ -716,7 +739,9 @@ namespace MueLu { Teuchos::RCP > chebyPrec = rcp_dynamic_cast >(prec_); if (chebyPrec != Teuchos::null) { lambdaMax = chebyPrec->getLambdaMaxForApply(); - A_->SetMaxEigenvalueEstimate(lambdaMax); + RCP matA = rcp_dynamic_cast(A_); + if (!matA.is_null()) + matA->SetMaxEigenvalueEstimate(lambdaMax); this->GetOStream(Statistics1) << "chebyshev: max eigenvalue (calculated by Ifpack2)" << " = " << lambdaMax << std::endl; } TEUCHOS_TEST_FOR_EXCEPTION(lambdaMax == negone, Exceptions::RuntimeError, "MueLu::Ifpack2Smoother::Setup(): no maximum eigenvalue estimate"); diff --git a/packages/muelu/src/Utils/MueLu_Utilities_decl.hpp b/packages/muelu/src/Utils/MueLu_Utilities_decl.hpp index a1625473badb..7b06e46a8761 100644 --- a/packages/muelu/src/Utils/MueLu_Utilities_decl.hpp +++ b/packages/muelu/src/Utils/MueLu_Utilities_decl.hpp @@ -56,6 +56,7 @@ #ifdef HAVE_MUELU_TPETRA #include +#include #endif #include #include @@ -198,8 +199,8 @@ namespace MueLu { static const Tpetra::CrsMatrix& Op2TpetraCrs(const Xpetra::Matrix& Op); static Tpetra::CrsMatrix& Op2NonConstTpetraCrs(Xpetra::Matrix& Op); - static RCP > Op2TpetraRow(RCP > Op); - static RCP< Tpetra::RowMatrix > Op2NonConstTpetraRow(RCP > Op); + static RCP > Op2TpetraRow(RCP > Op); + static RCP< Tpetra::RowMatrix > Op2NonConstTpetraRow(RCP > Op); static const RCP > Map2TpetraMap(const Xpetra::Map& map); @@ -316,9 +317,13 @@ namespace MueLu { typedef Xpetra::CrsMatrixWrap CrsMatrixWrap; typedef Xpetra::CrsMatrix CrsMatrix; typedef Xpetra::Matrix Matrix; + typedef Xpetra::Operator Operator; typedef Xpetra::Vector Vector; typedef Xpetra::MultiVector MultiVector; typedef Xpetra::Map Map; +#ifdef HAVE_MUELU_TPETRA + typedef Xpetra::TpetraOperator TpetraOperator; +#endif #ifdef HAVE_MUELU_EPETRA typedef Xpetra::EpetraMapT EpetraMap; typedef Xpetra::EpetraMultiVectorT EpetraMultiVector; @@ -527,49 +532,66 @@ namespace MueLu { #endif } - static RCP > Op2TpetraRow(RCP Op) { + static RCP > Op2TpetraRow(RCP Op) { #if ((defined(EPETRA_HAVE_OMP) && (!defined(HAVE_TPETRA_INST_OPENMP) || !defined(HAVE_TPETRA_INST_INT_INT))) || \ (!defined(EPETRA_HAVE_OMP) && (!defined(HAVE_TPETRA_INST_SERIAL) || !defined(HAVE_TPETRA_INST_INT_INT)))) throw Exceptions::RuntimeError("Op2TpetraRow: Tpetra has not been compiled with support for LO=GO=int."); #else - RCP crsOp = rcp_dynamic_cast(Op); - if (crsOp == Teuchos::null) - throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); - - RCP crsMat = crsOp->getCrsMatrix(); - const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); - RCP > tmp_BlockCrs; - if(!tmp_Crs.is_null()) { - return tmp_Crs->getTpetra_CrsMatrixNonConst(); - } - else { - tmp_BlockCrs= rcp_dynamic_cast >(crsMat); - if (tmp_BlockCrs.is_null()) - throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); - return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + RCP mat = rcp_dynamic_cast(Op); + if (!mat.is_null()) { + RCP crsOp = rcp_dynamic_cast(mat); + if (crsOp == Teuchos::null) + throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); + + RCP crsMat = crsOp->getCrsMatrix(); + const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); + RCP > tmp_BlockCrs; + if(!tmp_Crs.is_null()) { + return tmp_Crs->getTpetra_CrsMatrixNonConst(); + } + else { + tmp_BlockCrs= rcp_dynamic_cast >(crsMat); + if (tmp_BlockCrs.is_null()) + throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); + return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + } + } else { + RCP tpOp = rcp_dynamic_cast(Op, true); + RCP> tOp = tpOp->getOperatorConst(); + RCP > tRow = rcp_dynamic_cast >(tOp, true); + return tRow; } #endif } - static RCP< Tpetra::RowMatrix > Op2NonConstTpetraRow(RCP Op) { + + static RCP< Tpetra::RowMatrix > Op2NonConstTpetraRow(RCP Op) { #if ((defined(EPETRA_HAVE_OMP) && (!defined(HAVE_TPETRA_INST_OPENMP) || !defined(HAVE_TPETRA_INST_INT_INT))) || \ (!defined(EPETRA_HAVE_OMP) && (!defined(HAVE_TPETRA_INST_SERIAL) || !defined(HAVE_TPETRA_INST_INT_INT)))) throw Exceptions::RuntimeError("Op2NonConstTpetraRow: Tpetra has not been compiled with support for LO=GO=int."); #else - RCP crsOp = rcp_dynamic_cast(Op); - if (crsOp == Teuchos::null) - throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); - - RCP crsMat = crsOp->getCrsMatrix(); - const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); - RCP > tmp_BlockCrs; - if(!tmp_Crs.is_null()) { - return tmp_Crs->getTpetra_CrsMatrixNonConst(); - } - else { - tmp_BlockCrs= rcp_dynamic_cast >(crsMat); - if (tmp_BlockCrs.is_null()) - throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); - return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + RCP mat = rcp_dynamic_cast(Op); + if (!mat.is_null()) { + RCP crsOp = rcp_dynamic_cast(mat); + if (crsOp == Teuchos::null) + throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); + + RCP crsMat = crsOp->getCrsMatrix(); + const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); + RCP > tmp_BlockCrs; + if(!tmp_Crs.is_null()) { + return tmp_Crs->getTpetra_CrsMatrixNonConst(); + } + else { + tmp_BlockCrs= rcp_dynamic_cast >(crsMat); + if (tmp_BlockCrs.is_null()) + throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); + return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + } + } else { + RCP tpOp = rcp_dynamic_cast(Op, true); + RCP> tOp = tpOp->getOperator(); + RCP > tRow = rcp_dynamic_cast >(tOp, true); + return tRow; } #endif }; diff --git a/packages/muelu/src/Utils/MueLu_Utilities_def.hpp b/packages/muelu/src/Utils/MueLu_Utilities_def.hpp index 85f1112797dc..d8b14fcba193 100644 --- a/packages/muelu/src/Utils/MueLu_Utilities_def.hpp +++ b/packages/muelu/src/Utils/MueLu_Utilities_def.hpp @@ -74,6 +74,7 @@ #include #include #include +#include #include #include #endif @@ -300,42 +301,58 @@ namespace MueLu { } template - RCP > Utilities::Op2TpetraRow(RCP > Op) { - RCP > crsOp = rcp_dynamic_cast >(Op); - if (crsOp == Teuchos::null) - throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); - - RCP > crsMat = crsOp->getCrsMatrix(); - const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); - RCP > tmp_BlockCrs; - if(!tmp_Crs.is_null()) { - return tmp_Crs->getTpetra_CrsMatrixNonConst(); - } - else { - tmp_BlockCrs= rcp_dynamic_cast >(crsMat); - if (tmp_BlockCrs.is_null()) - throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); - return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + RCP > Utilities::Op2TpetraRow(RCP > Op) { + RCP > mat = rcp_dynamic_cast >(Op); + if (!mat.is_null()) { + RCP > crsOp = rcp_dynamic_cast >(mat); + if (crsOp == Teuchos::null) + throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); + + RCP > crsMat = crsOp->getCrsMatrix(); + const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); + RCP > tmp_BlockCrs; + if(!tmp_Crs.is_null()) { + return tmp_Crs->getTpetra_CrsMatrixNonConst(); + } + else { + tmp_BlockCrs= rcp_dynamic_cast >(crsMat); + if (tmp_BlockCrs.is_null()) + throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); + return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + } + } else { + RCP > tpOp = rcp_dynamic_cast >(Op, true); + RCP> tOp = tpOp->getOperatorConst(); + RCP > tRow = rcp_dynamic_cast >(tOp, true); + return tRow; } } template - RCP > Utilities::Op2NonConstTpetraRow(RCP > Op) { - RCP > crsOp = rcp_dynamic_cast >(Op); - if (crsOp == Teuchos::null) - throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); - - RCP > crsMat = crsOp->getCrsMatrix(); - const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); - RCP > tmp_BlockCrs; - if(!tmp_Crs.is_null()) { - return tmp_Crs->getTpetra_CrsMatrixNonConst(); - } - else { - tmp_BlockCrs= rcp_dynamic_cast >(crsMat); - if (tmp_BlockCrs.is_null()) - throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); - return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + RCP > Utilities::Op2NonConstTpetraRow(RCP > Op) { + RCP > mat = rcp_dynamic_cast >(Op); + if (!mat.is_null()) { + RCP > crsOp = rcp_dynamic_cast >(mat); + if (crsOp == Teuchos::null) + throw Exceptions::BadCast("Cast from Xpetra::Matrix to Xpetra::CrsMatrixWrap failed"); + + RCP > crsMat = crsOp->getCrsMatrix(); + const RCP > tmp_Crs = rcp_dynamic_cast >(crsMat); + RCP > tmp_BlockCrs; + if(!tmp_Crs.is_null()) { + return tmp_Crs->getTpetra_CrsMatrixNonConst(); + } + else { + tmp_BlockCrs= rcp_dynamic_cast >(crsMat); + if (tmp_BlockCrs.is_null()) + throw Exceptions::BadCast("Cast from Xpetra::CrsMatrix to Xpetra::TpetraCrsMatrix and Xpetra::TpetraBlockCrsMatrix failed"); + return tmp_BlockCrs->getTpetra_BlockCrsMatrixNonConst(); + } + } else { + RCP > tpOp = rcp_dynamic_cast >(Op, true); + RCP> tOp = tpOp->getOperator(); + RCP > tRow = rcp_dynamic_cast >(tOp, true); + return tRow; } } diff --git a/packages/xpetra/src/Operator/Xpetra_TpetraOperator.hpp b/packages/xpetra/src/Operator/Xpetra_TpetraOperator.hpp index bf547e389234..99434ef46206 100644 --- a/packages/xpetra/src/Operator/Xpetra_TpetraOperator.hpp +++ b/packages/xpetra/src/Operator/Xpetra_TpetraOperator.hpp @@ -119,11 +119,16 @@ namespace Xpetra { //! @name Xpetra specific //@{ + TpetraOperator() { } + //! TpetraOperator constructor to wrap a Tpetra::Operator object TpetraOperator(const Teuchos::RCP > &op) : op_(op) { } //TODO removed const //! Gets the operator out - RCP > getOperator(){return op_;} + virtual RCP > getOperator(){return op_;} + + //! Gets the operator out + virtual RCP > getOperatorConst() const {return op_;} //! Compute a residual R = B - (*this) * X void residual(const Xpetra::MultiVector< Scalar, LocalOrdinal, GlobalOrdinal, Node > & X, From e35f02fec058f450264c3db03728d8e4591896f5 Mon Sep 17 00:00:00 2001 From: Christian Glusa Date: Tue, 26 Oct 2021 09:29:26 -0600 Subject: [PATCH 83/98] MueLu: Derive HierarchicalOperator from RowMatrix --- packages/muelu/research/caglusa/main.cpp | 453 +++++++++++++++++++--- packages/muelu/research/caglusa/muelu.xml | 18 + 2 files changed, 422 insertions(+), 49 deletions(-) create mode 100644 packages/muelu/research/caglusa/muelu.xml diff --git a/packages/muelu/research/caglusa/main.cpp b/packages/muelu/research/caglusa/main.cpp index 8e70c329f5be..ad37e30af93e 100644 --- a/packages/muelu/research/caglusa/main.cpp +++ b/packages/muelu/research/caglusa/main.cpp @@ -1,19 +1,61 @@ -// Teuchos +// @HEADER +// +// *********************************************************************** +// +// MueLu: A package for multigrid based preconditioning +// Copyright 2012 Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact +// Jonathan Hu (jhu@sandia.gov) +// Ray Tuminaro (rstumin@sandia.gov) +// +// *********************************************************************** +// +// @HEADER #include #include -#include -#include +#include -#include +#include +#include +#include "MueLu_Exceptions.hpp" #include #ifdef HAVE_MUELU_BELOS #include #include -#include -#include #include // => This header defines Belos::XpetraOp #include // => This header defines Belos::MueLuOp #endif @@ -28,13 +70,40 @@ namespace Tpetra { class LocalOrdinal = typename Tpetra::Operator::local_ordinal_type, class GlobalOrdinal = typename Tpetra::Operator::global_ordinal_type, class Node = typename Tpetra::Operator::node_type> - class HierarchicalOperator : public Tpetra::Operator { + class HierarchicalOperator : public Tpetra::RowMatrix { public: using matrix_type = Tpetra::CrsMatrix; using vec_type = Tpetra::MultiVector; using map_type = Tpetra::Map; + //! The RowMatrix representing the base class of CrsMatrix + using row_matrix_type = RowMatrix; + + using impl_scalar_type = typename row_matrix_type::impl_scalar_type; + using mag_type = typename Kokkos::ArithTraits::mag_type; + + using local_inds_device_view_type = + typename row_matrix_type::local_inds_device_view_type; + using local_inds_host_view_type = + typename row_matrix_type::local_inds_host_view_type; + using nonconst_local_inds_host_view_type = + typename row_matrix_type::nonconst_local_inds_host_view_type; + + using global_inds_device_view_type = + typename row_matrix_type::global_inds_device_view_type; + using global_inds_host_view_type = + typename row_matrix_type::global_inds_host_view_type; + using nonconst_global_inds_host_view_type = + typename row_matrix_type::nonconst_global_inds_host_view_type; + + using values_device_view_type = + typename row_matrix_type::values_device_view_type; + using values_host_view_type = + typename row_matrix_type::values_host_view_type; + using nonconst_values_host_view_type = + typename row_matrix_type::nonconst_values_host_view_type; + //! @name Constructor/Destructor //@{ @@ -145,14 +214,42 @@ namespace Tpetra { RCP newBasisMatrix = rcp(new matrix_type(P->getDomainMap(), clusterCoeffMap_, 0)); MatrixMatrix::Multiply(*P, true, *basisMatrix_, false, *newBasisMatrix); - // auto out = Teuchos::getFancyOStream (Teuchos::rcpFromRef (std::cerr)); - // clusterCoeffMap_->describe(*out, Teuchos::VERB_EXTREME); - // clusterCoeffMap_->getComm()->barrier(); - // newBasisMatrix->getColMap()->describe(*out, Teuchos::VERB_EXTREME); - return rcp(new HierarchicalOperator(newNearField, kernelApproximations_, newBasisMatrix, transferMatrices_)); } + RCP toMatrix() { + const Scalar one = Teuchos::ScalarTraits::one(); + + // construct identity on clusterCoeffMap_ + RCP identity = rcp(new matrix_type(clusterCoeffMap_, 1)); + Teuchos::ArrayView gblRows = clusterCoeffMap_->getNodeElementList (); + for (auto it = gblRows.begin (); it != gblRows.end (); ++it) { + Teuchos::Array col (1, *it); + Teuchos::Array val (1, one); + identity->insertGlobalValues (*it, col (), val ()); + } + identity->fillComplete (); + + // transfer = basisMatrix_ * (identity + transferMatrices_[0]) * ... * (identity + transferMatrices_[n-1]) + RCP transfer = rcp(new matrix_type(*basisMatrix_)); + for (size_t i = 0; i temp = MatrixMatrix::add(one, false, *identity, one, false, *transferMatrices_[i]); + RCP temp2 = rcp(new matrix_type(basisMatrix_->getRowMap(), 0)); + MatrixMatrix::Multiply(*transfer, false, *temp, true, *temp2); + transfer = temp2; + } + + // farField = transfer * kernelApproximations_ * transfer^T + RCP temp = rcp(new matrix_type(basisMatrix_->getRowMap(), 0)); + MatrixMatrix::Multiply(*transfer, false, *kernelApproximations_, false, *temp); + RCP farField = rcp(new matrix_type(basisMatrix_->getRowMap(), 0)); + MatrixMatrix::Multiply(*temp, false, *transfer, true, *farField); + + // nearField_ + farField + return MatrixMatrix::add(one, false, *nearField_, one, false, *farField); + + } + double getCompression() { size_t nnz = (nearField_->getGlobalNumEntries() + kernelApproximations_->getGlobalNumEntries() + @@ -162,6 +259,171 @@ namespace Tpetra { return Teuchos::as(nnz) / (getDomainMap()->getGlobalNumElements()*getDomainMap()->getGlobalNumElements()); } + // Fake RowMatrix interface + Teuchos::RCP > getRowMap() const { + return nearField_->getRowMap(); + } + + Teuchos::RCP > getColMap() const { + return nearField_->getColMap(); + } + + Teuchos::RCP > getComm() const { + return nearField_->getDomainMap()->getComm(); + } + + Teuchos::RCP > getGraph() const { + return nearField_->getCrsGraph(); + } + + global_size_t getGlobalNumRows() const { + return nearField_->getGlobalNumRows(); + } + + global_size_t getGlobalNumCols() const { + return nearField_->getGlobalNumCols(); + } + + size_t getNodeNumRows() const { + return nearField_->getNodeNumRows(); + } + + size_t getNodeNumCols() const { + return nearField_->getNodeNumCols(); + } + + GlobalOrdinal getIndexBase() const { + return nearField_->getIndexBase(); + } + + global_size_t getGlobalNumEntries() const { + return nearField_->getGlobalNumEntries(); + } + + size_t getNodeNumEntries() const { + return nearField_->getNodeNumEntries(); + } + + size_t getNumEntriesInGlobalRow (GlobalOrdinal globalRow) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + size_t getNumEntriesInLocalRow (LocalOrdinal localRow) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + size_t getGlobalMaxNumRowEntries () const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + size_t getNodeMaxNumRowEntries () const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + bool hasColMap () const { + return false; + } + + bool isLocallyIndexed() const { + return true; + } + + bool isGloballyIndexed() const { + return true; + } + + bool isFillComplete() const { + return true; + } + + bool supportsRowViews() const { + return false; + } + + void + getGlobalRowCopy (GlobalOrdinal GlobalRow, + nonconst_global_inds_host_view_type &Indices, + nonconst_values_host_view_type &Values, + size_t& NumEntries) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + void + getGlobalRowCopy (GlobalOrdinal GlobalRow, + const Teuchos::ArrayView &Indices, + const Teuchos::ArrayView &Values, + size_t &NumEntries) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } +#endif + + void + getLocalRowCopy (LocalOrdinal LocalRow, + nonconst_local_inds_host_view_type &Indices, + nonconst_values_host_view_type &Values, + size_t& NumEntries) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + void + getLocalRowCopy (LocalOrdinal LocalRow, + const Teuchos::ArrayView &Indices, + const Teuchos::ArrayView &Values, + size_t &NumEntries) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } +#endif + + void + getGlobalRowView (GlobalOrdinal GlobalRow, + global_inds_host_view_type &indices, + values_host_view_type &values) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + void + getGlobalRowView (GlobalOrdinal GlobalRow, + Teuchos::ArrayView &indices, + Teuchos::ArrayView &values) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } +#endif + + void + getLocalRowView (LocalOrdinal LocalRow, + local_inds_host_view_type & indices, + values_host_view_type & values) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + void + getLocalRowView (LocalOrdinal LocalRow, + Teuchos::ArrayView& indices, + Teuchos::ArrayView& values) const { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } +#endif + + void getLocalDiagCopy (Vector &diag) const { + nearField_->getLocalDiagCopy(diag); + } + + void leftScale (const Vector& x) { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + void rightScale (const Vector& x) { + throw MueLu::Exceptions::RuntimeError("Not implemented."); + } + + mag_type getFrobeniusNorm() const { + return 0.; + } + private: void allocateMemory(size_t numVectors) const { @@ -187,7 +449,7 @@ namespace Xpetra { class LocalOrdinal, class GlobalOrdinal, class Node = KokkosClassic::DefaultNode::DefaultNodeType> - class HierarchicalOperator : public Xpetra::Operator { + class HierarchicalOperator : public TpetraOperator { public: using tHOp = Tpetra::HierarchicalOperator; @@ -205,17 +467,18 @@ namespace Xpetra { const RCP& kernelApproximations, const RCP& basisMatrix, std::vector >& transferMatrices) { - #include "MueLu_UseShortNames.hpp" + using TpCrs = TpetraCrsMatrix; + using CrsWrap = CrsMatrixWrap; std::vector > tTransferMatrices; for (size_t i = 0; i(rcp_dynamic_cast(transferMatrices[i])->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(); + auto transferT = rcp_dynamic_cast(rcp_dynamic_cast(transferMatrices[i])->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(); tTransferMatrices.push_back(transferT); } - op_ = rcp(new tHOp(rcp_dynamic_cast(rcp_dynamic_cast(nearField)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), - rcp_dynamic_cast(rcp_dynamic_cast(kernelApproximations)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), - rcp_dynamic_cast(rcp_dynamic_cast(basisMatrix)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + op_ = rcp(new tHOp(rcp_dynamic_cast(rcp_dynamic_cast(nearField)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + rcp_dynamic_cast(rcp_dynamic_cast(kernelApproximations)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), + rcp_dynamic_cast(rcp_dynamic_cast(basisMatrix)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst(), tTransferMatrices)); } @@ -250,14 +513,23 @@ namespace Xpetra { } RCP > restrict(const RCP& P) { - #include "MueLu_UseShortNames.hpp" - return rcp(new HierarchicalOperator(op_->restrict(rcp_dynamic_cast(rcp_dynamic_cast(P)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst()))); + return rcp(new HierarchicalOperator(op_->restrict(rcp_dynamic_cast >(rcp_dynamic_cast >(P)->getCrsMatrix(), true)->getTpetra_CrsMatrixNonConst()))); + } + + RCP toMatrix() { + auto tpMat = rcp(new TpetraCrsMatrix(op_->toMatrix())); + return rcp(new CrsMatrixWrap(rcp_dynamic_cast >(tpMat))); } double getCompression() { return op_->getCompression(); } + //! Gets the operator out + RCP > getOperator() { return op_; } + + RCP > getOperatorConst() const { return op_; } + private: RCP op_; }; @@ -268,8 +540,12 @@ template int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib lib, int argc, char *argv[]) { #include "MueLu_UseShortNames.hpp" - std::string xmlHierachical = "hierarchical.xml"; + std::string xmlHierachical = "hierarchical.xml"; + std::string xmlMueLu = "muelu.xml"; std::string xmlAuxHierarchy = "aux.xml"; + clp.setOption("xml", &xmlHierachical); + clp.setOption("xmlMueLu", &xmlMueLu); + clp.setOption("xmlAux", &xmlAuxHierarchy); switch (clp.parse(argc, argv)) { case Teuchos::CommandLineProcessor::PARSE_HELP_PRINTED: return EXIT_SUCCESS; break; @@ -285,6 +561,7 @@ int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib lib, int arg out.setOutputToRootOnly(0); bool success = true; const Scalar one = Teuchos::ScalarTraits::one(); + const Scalar zero = Teuchos::ScalarTraits::zero(); RCP< const Teuchos::Comm > comm = Teuchos::DefaultComm::getComm(); @@ -349,12 +626,17 @@ int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib lib, int arg // Xpetra::IO::Write("diff2.mtx", *X); } +#ifdef HAVE_MUELU_BELOS { // Solve linear system using unpreconditioned Krylov method + out << "\n*********************************************************\n"; + out << "Unpreconditioned Krylov method\n"; + out << "*********************************************************\n\n"; using MV = typename HOp::vec_type; using OP = Belos::OperatorT; + X->putScalar(zero); RCP belosOp = rcp(new Belos::XpetraOp(op)); RCP > belosProblem = rcp(new Belos::LinearProblem(belosOp, X, RHS)); @@ -385,46 +667,119 @@ int main_(Teuchos::CommandLineProcessor &clp, Xpetra::UnderlyingLib lib, int arg // Xpetra::IO::Write("X.mtx", *X); X->update(one, *X_ex, -one); - out << "|X-X_ex| = " << X->getVector(0)->norm2() << std::endl; + out << "|X-X_ex| = " << X->getVector(0)->norm2() << std::endl << std::endl; success &= (ret == Belos::Converged); } +#endif // HAVE_MUELU_BELOS + + { + // Solve linear system using a AMG preconditioned Krylov method + + //////////////////////////////////////////////////////////////// + // Build the auxiliary hierachy + out << "\n*********************************************************\n"; + out << "Building the auxiliary hierachy\n"; + out << "*********************************************************\n\n"; + + auto auxOp = Xpetra::IO::Read(hierachicalParams.get("auxiliary operator"), map); + auto coords = Xpetra::IO::coordinateType,LocalOrdinal,GlobalOrdinal,Node>::ReadMultiVector(hierachicalParams.get("coordinates"), map); + + Teuchos::ParameterList auxParams; + Teuchos::updateParametersFromXmlFileAndBroadcast(xmlAuxHierarchy, Teuchos::Ptr(&auxParams), *comm); + auxParams.sublist("user data").set("Coordinates", coords); + + auto auxH = MueLu::CreateXpetraPreconditioner(auxOp, auxParams); + + //////////////////////////////////////////////////////////////// + // Construct the main hierarchy + out << "\n*********************************************************\n"; + out << "Building the main hierachy\n"; + out << "*********************************************************\n\n"; + + Teuchos::ParameterList params; + Teuchos::updateParametersFromXmlFileAndBroadcast(xmlMueLu, Teuchos::Ptr(¶ms), *comm); + params.set("coarse: max size", 1); + params.set("max levels", auxH->GetNumLevels()); + + auto H = rcp(new Hierarchy()); + RCP lvl = H->GetLevel(0); + lvl->Set("A", rcp_dynamic_cast(op)); + lvl->Set("Coordinates", coords); + for(int lvlNo = 1; lvlNoGetNumLevels(); lvlNo++) { + H->AddNewLevel(); + RCP auxLvl = auxH->GetLevel(lvlNo); + // auto mgr = auxLvl->GetFactoryManager(); + // auxLvl->print(std::cout, MueLu::Debug); + RCP fineLvl = H->GetLevel(lvlNo-1); + lvl = H->GetLevel(lvlNo); + auto P = auxLvl->Get >("P"); + lvl->Set("P", P); + params.sublist("level "+std::to_string(lvlNo)).set("P", P); + + auto fineA = rcp_dynamic_cast(fineLvl->Get >("A")); + auto coarseA = fineA->restrict(P); + if (lvlNo+1 == auxH->GetNumLevels()) + lvl->Set("A", coarseA->toMatrix()); + else + lvl->Set("A", rcp_dynamic_cast(coarseA)); + } + + RCP mueLuFactory = rcp(new ParameterListInterpreter(params,op->getDomainMap()->getComm())); + H->setlib(op->getDomainMap()->lib()); + H->SetProcRankVerbose(op->getDomainMap()->getComm()->getRank()); + mueLuFactory->SetupHierarchy(*H); + H->IsPreconditioner(true); + + +#ifdef HAVE_MUELU_BELOS + //////////////////////////////////////////////////////////////// + // Set up the Krylov solver - // { - // // Solve linear system using a AMG preconditioned Krylov method + using MV = typename HOp::vec_type; + using OP = Belos::OperatorT; - // auto auxOp = Xpetra::IO::Read(hierachicalParams.get("auxiliary operator"), map); - // auto coords = Xpetra::IO::coordinateType,LocalOrdinal,GlobalOrdinal,Node>::ReadMultiVector(hierachicalParams.get("coordinates"), map); + X->putScalar(zero); + RCP belosOp = rcp(new Belos::XpetraOp(op)); + RCP belosPrec = rcp(new Belos::MueLuOp (H)); + RCP > belosProblem = rcp(new Belos::LinearProblem(belosOp, X, RHS)); - // Teuchos::ParameterList auxParams; - // Teuchos::updateParametersFromXmlFileAndBroadcast(xmlAuxHierarchy, Teuchos::Ptr(&auxParams), *comm); - // auxParams.sublist("user data").set("Coordinates", coords); + std::string belosType = "Pseudoblock CG"; + RCP belosList = Teuchos::parameterList(); + belosList->set("Maximum Iterations", 1000); // Maximum number of iterations allowed + belosList->set("Convergence Tolerance", 1e-5); // Relative convergence tolerance requested + belosList->set("Verbosity", Belos::Errors + Belos::Warnings + Belos::StatusTestDetails); + belosList->set("Output Frequency", 1); + belosList->set("Output Style", Belos::Brief); - // auto auxH = MueLu::CreateXpetraPreconditioner(auxOp, auxParams); + belosProblem->setRightPrec(belosPrec); - // auto H = rcp(new Hierarchy()); - // RCP lvl = H->GetLevel(0); - // lvl->Set("A", rcp_dynamic_cast(op)); - // for(int lvlNo = 1; lvlNoGetNumLevels(); lvlNo++) { - // H->AddNewLevel(); - // RCP auxLvl = auxH->GetLevel(lvlNo); - // RCP fineLvl = H->GetLevel(lvlNo-1); - // RCP lvl = H->GetLevel(lvlNo); - // auto P = auxLvl->Get >("P"); - // lvl->Set("P", P); + bool set = belosProblem->setProblem(); + if (set == false) { + throw MueLu::Exceptions::RuntimeError("ERROR: Belos::LinearProblem failed to set up correctly!"); + } - // auto fineA = rcp_dynamic_cast(fineLvl->Get >("A")); - // auto coarseA = fineA->restrict(P); - // lvl->Set("A", rcp_dynamic_cast(coarseA)); - // } + // Create an iterative solver manager + Belos::SolverFactory solverFactory; + RCP< Belos::SolverManager > solver = solverFactory.create(belosType, belosList); + solver->setProblem(belosProblem); + + // Perform solve + Belos::ReturnType ret = solver->solve(); + int numIts = solver->getNumIters(); + + // Get the number of iterations for this solve. + out << "Number of iterations performed for this solve: " << numIts << std::endl; + + // Xpetra::IO::Write("X.mtx", *X); + X->update(one, *X_ex, -one); + out << "|X-X_ex| = " << X->getVector(0)->norm2() << std::endl; - // RCP mueLuFactory = rcp(new ParameterListInterpreter(auxParams,op->getDomainMap()->getComm())); - // H->setlib(op->getDomainMap()->lib()); - // H->SetProcRankVerbose(op->getDomainMap()->getComm()->getRank()); - // mueLuFactory->SetupHierarchy(*H); + success &= (ret == Belos::Converged); - // } +#endif // HAVE_MUELU_BELOS + } return ( success ? EXIT_SUCCESS : EXIT_FAILURE ); } //main diff --git a/packages/muelu/research/caglusa/muelu.xml b/packages/muelu/research/caglusa/muelu.xml new file mode 100644 index 000000000000..1fa2cbd50020 --- /dev/null +++ b/packages/muelu/research/caglusa/muelu.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + > + + + + + From b34b94d5fc0c8373e5b6412210f25f96c794d593 Mon Sep 17 00:00:00 2001 From: kokkos-devops-admin <64657714+kokkos-devops-admin@users.noreply.github.com> Date: Wed, 27 Oct 2021 09:49:42 -0600 Subject: [PATCH 84/98] cmake/std/atdm: Fix typo --- cmake/std/atdm/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/std/atdm/README.md b/cmake/std/atdm/README.md index fcb864ae26dc..ea0081dbe2bb 100644 --- a/cmake/std/atdm/README.md +++ b/cmake/std/atdm/README.md @@ -1572,7 +1572,7 @@ each system. These contributed configurations are used just like any other custom configuration as described in Custom systems and -configurations.. For example, to load the contributed custom 'weaver' +configurations. For example, to load the contributed custom 'weaver' configuration to do a CUDA optimized build, do: ``` From 8606fb3b8042a4ca67c42d8c8404d349128fe6ad Mon Sep 17 00:00:00 2001 From: Evan Harvey <57234914+e10harvey@users.noreply.github.com> Date: Wed, 27 Oct 2021 10:23:18 -0600 Subject: [PATCH 85/98] packages/framework: Fix typo --- .../pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py b/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py index 493d3d4d5c14..47565ba6ff0d 100644 --- a/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py +++ b/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py @@ -347,7 +347,7 @@ def config_script(self): """ Returns the configuration script name - This arbitrary name will be used for all runs until an override is established + This arbitrary name will be used for all runs until an override is established Returns: String containing the job-specific configuration script to load. From 46303e5ea28c69722b87c7577c307c32652e6d57 Mon Sep 17 00:00:00 2001 From: K Devine Date: Wed, 27 Oct 2021 12:02:04 -0600 Subject: [PATCH 86/98] Tpetra: deprecate and remove use of StaticProfile (#9865) * tpetra: #9799 deprecating constructors that take StaticProfile as argument; everything is static profile. Removed StaticProfile and pftype from library * tpetra: #9799 removing use of StaticProfile from Tpetra tests * tpetra: #9799 Fixed one test that was edited incorrectly. * tpetra: #9799 removed use of deprecated Tpetra::StaticProfile * ifpack2: #9799 corrected use of deprecated getLocalRowCopy --- .../Tpetra_CrsMatrix_Adapter_UnitTests.cpp | 4 +- .../amesos2/test/solvers/SolverFactory.cpp | 2 +- .../test/BlockDavidson/cxx_main_lap.cpp | 2 +- .../test/BlockKrylovSchur/cxx_main_lap.cpp | 2 +- .../anasazi/tpetra/test/IRTR/cxx_main_lap.cpp | 2 +- .../tpetra/test/MVOPTester/cxx_main.cpp | 2 +- .../tpetra/test/FixedPoint/test_fp_hb.cpp | 2 +- .../LinearSolverFactory.cpp | 2 +- .../LinearSolverFactory/SolverFactory.cpp | 2 +- .../test/MVOPTester/cxx_main_complex.cpp | 2 +- .../tpetra/test/Native/nonsymm_matrix.cpp | 2 +- .../example/RelaxationWithEquilibration.cpp | 16 +- packages/ifpack2/src/Ifpack2_ILUT_def.hpp | 4 +- .../src/Ifpack2_SparseContainer_def.hpp | 4 +- packages/ifpack2/src/Ifpack2_Utilities.hpp | 2 +- .../supportgraph/Ifpack2_SupportGraph_def.hpp | 2 +- .../test/unit_tests/Ifpack2_SolverFactory.cpp | 2 +- .../test/unit_tests/Ifpack2_UnitTest234.cpp | 3 +- .../unit_tests/Ifpack2_UnitTestChebyshev2.cpp | 2 +- .../Ifpack2_UnitTestContainerFactory.cpp | 2 +- .../unit_tests/Ifpack2_UnitTestHelpers.hpp | 25 ++- ...k2_UnitTestLocalSparseTriangularSolver.cpp | 3 +- .../unit_tests/Ifpack2_UnitTestRelaxation.cpp | 2 +- .../disc-fe/src/Panzer_L2Projection.cpp | 2 +- .../src/Panzer_LocalPartitioningUtilities.cpp | 3 +- ...zer_BlockedTpetraLinearObjFactory_impl.hpp | 3 +- .../Panzer_TpetraLinearObjFactory_impl.hpp | 3 +- .../src/solvers/MiniEM_DiscreteCurl.hpp | 2 +- .../src/solvers/MiniEM_DiscreteGradient.hpp | 2 +- .../shylu_dd/bddc/src/shylu_UtilBDDC.hpp | 4 +- ...tokhos_TpetraCrsMatrixMPVectorUnitTest.hpp | 22 +-- .../Stokhos_TpetraCrsMatrixUQPCEUnitTest.hpp | 16 +- .../stokhos/test/UnitTest/tpetra_mat_vec.cpp | 4 +- .../test/TpetraThyraWrappers_UnitTests.cpp | 2 +- .../AdditiveSchwarzHalo.cpp | 2 +- .../fem_assembly_TotalElementLoop.hpp | 4 +- .../advanced/Benchmarks/CrsMatrixMatVec.cpp | 3 +- .../CrsMatrix_sumIntoLocalValues.cpp | 6 +- .../Benchmarks/blockCrsMatrixMatVec.cpp | 3 +- .../example/advanced/Benchmarks/localView.cpp | 3 +- .../tpetra/core/inout/MatrixMarket_Tpetra.hpp | 18 +- .../tpetra/core/inout/Tpetra_MatrixIO_def.hpp | 2 +- .../src/Tpetra_BlockCrsMatrix_Helpers_def.hpp | 2 +- .../tpetra/core/src/Tpetra_ConfigDefs.hpp | 3 + .../tpetra/core/src/Tpetra_CrsGraph_decl.hpp | 62 ++++++- .../tpetra/core/src/Tpetra_CrsGraph_def.hpp | 94 ++++++++++- .../tpetra/core/src/Tpetra_CrsMatrix_decl.hpp | 58 +++++-- .../tpetra/core/src/Tpetra_CrsMatrix_def.hpp | 158 ++++++++++-------- .../tpetra/core/src/Tpetra_FECrsGraph_def.hpp | 8 +- .../tpetra/core/src/Tpetra_RowMatrix_def.hpp | 5 +- .../tpetra/core/test/Block/BlockCrsMatrix.cpp | 16 +- .../core/test/CrsGraph/CrsGraph_Issue601.cpp | 8 +- .../test/CrsGraph/CrsGraph_ReindexColumns.cpp | 4 +- .../CrsGraph/CrsGraph_StaticImportExport.cpp | 10 +- .../test/CrsGraph/CrsGraph_UnitTests0.cpp | 44 ++--- .../test/CrsGraph/CrsGraph_UnitTests1.cpp | 16 +- .../test/CrsGraph/CrsGraph_UnitTests_Swap.cpp | 3 +- .../CrsGraph_UnpackIntoStaticGraph.cpp | 4 +- .../test/CrsGraph/CrsGraph_getNumDiags.cpp | 6 +- .../CrsGraph_insertGlobalIndicesFiltered.cpp | 13 +- .../test/CrsMatrix/CrsMatrix_GetRowCopy.cpp | 6 +- .../CrsMatrix/CrsMatrix_LeftRightScale.cpp | 2 - .../CrsMatrix_MultipleFillCompletes.cpp | 2 +- .../CrsMatrix/CrsMatrix_NodeConversion.cpp | 2 - .../CrsMatrix_NonlocalAfterResume.cpp | 3 +- .../CrsMatrix/CrsMatrix_NonlocalSumInto.cpp | 2 +- .../CrsMatrix_NonlocalSumInto_Ignore.cpp | 2 +- .../CrsMatrix/CrsMatrix_ReindexColumns.cpp | 2 +- .../CrsMatrix_ReplaceDomainMapAndImporter.cpp | 2 - .../CrsMatrix_ReplaceRangeMapAndExporter.cpp | 2 - .../CrsMatrix_StaticImportExport.cpp | 10 +- .../CrsMatrix/CrsMatrix_TransformValues.cpp | 4 +- .../test/CrsMatrix/CrsMatrix_UnitTests.cpp | 6 +- .../test/CrsMatrix/CrsMatrix_UnitTests2.cpp | 3 +- .../test/CrsMatrix/CrsMatrix_UnitTests3.cpp | 11 +- .../test/CrsMatrix/CrsMatrix_UnitTests4.cpp | 9 +- .../CrsMatrix/CrsMatrix_UnitTests_Swap.cpp | 2 +- .../core/test/CrsMatrix/Equilibration.cpp | 8 +- .../test/CrsMatrix/Regression/Albany182.cpp | 7 +- .../Tpetra_Test_CrsMatrix_WithGraph.hpp | 24 ++- .../sumIntoStaticProfileExtraSpace.cpp | 5 +- .../core/test/Distributor/Issue1752.cpp | 6 +- .../Distributor/createfromsendsandrecvs.cpp | 3 +- .../test/FECrsGraph/FECrsGraph_UnitTests.cpp | 21 ++- .../FEMultiVector/FEMultiVector_UnitTests.cpp | 2 +- .../ImportExport_ImportConstructExpert.cpp | 3 +- .../core/test/ImportExport/UnpackLongRows.cpp | 4 +- .../ImportExport2/ImportExport2_UnitTests.cpp | 17 +- .../FECrs_MatrixMatrix_UnitTests.cpp | 6 +- .../MatrixMatrix/MatrixMatrix_UnitTests.cpp | 2 +- .../core/test/RowMatrixTransposer/main.cpp | 4 +- .../core/test/TpetraUtils_MatrixGenerator.hpp | 9 +- .../CrsGraph/Xpetra_TpetraCrsGraph_def.hpp | 8 +- .../CrsMatrix/Xpetra_TpetraCrsMatrix_def.hpp | 8 +- .../xpetra/sup/Utils/Xpetra_MatrixMatrix.hpp | 2 +- .../input/Zoltan2_TpetraRowGraphAdapter.hpp | 2 +- .../input/Zoltan2_TpetraRowMatrixAdapter.hpp | 2 +- .../core/src/input/Zoltan2_XpetraTraits.hpp | 2 +- .../zoltan2/sphynx/src/Zoltan2_Sphynx.hpp | 2 +- .../test/core/helpers/UserInputForTests.hpp | 4 +- 100 files changed, 523 insertions(+), 407 deletions(-) diff --git a/packages/amesos2/test/adapters/Tpetra_CrsMatrix_Adapter_UnitTests.cpp b/packages/amesos2/test/adapters/Tpetra_CrsMatrix_Adapter_UnitTests.cpp index 065775085f0b..c5f76bac01fd 100644 --- a/packages/amesos2/test/adapters/Tpetra_CrsMatrix_Adapter_UnitTests.cpp +++ b/packages/amesos2/test/adapters/Tpetra_CrsMatrix_Adapter_UnitTests.cpp @@ -197,7 +197,7 @@ namespace { // create a Map const size_t numLocal = 10; RCP > map = rcp( new Map(INVALID,numLocal,0,comm) ); - RCP eye = rcp( new MAT(map,1,Tpetra::StaticProfile) ); + RCP eye = rcp( new MAT(map,1) ); GO base = numLocal*rank; for( size_t i = 0; i < numLocal; ++i ){ eye->insertGlobalValues(base+i,tuple(base+i),tuple(ST::one())); @@ -230,7 +230,7 @@ namespace { // create a Map const size_t numLocal = 10; RCP > map = rcp( new Map(INVALID,numLocal,0,comm) ); - RCP eye = rcp( new MAT(map,1,Tpetra::StaticProfile) ); + RCP eye = rcp( new MAT(map,1) ); GO base = numLocal*rank; for( size_t i = 0; i < numLocal; ++i ){ eye->insertGlobalValues(base+i,tuple(base+i),tuple(ST::one())); diff --git a/packages/amesos2/test/solvers/SolverFactory.cpp b/packages/amesos2/test/solvers/SolverFactory.cpp index 39da8cff961e..6b51e67f0ab5 100644 --- a/packages/amesos2/test/solvers/SolverFactory.cpp +++ b/packages/amesos2/test/solvers/SolverFactory.cpp @@ -124,7 +124,7 @@ namespace { const size_t maxNumEntPerRow = 3; const SC two = static_cast (2.0); const SC minusOne = static_cast (-1.0); - RCP A (new MAT (rowMap, maxNumEntPerRow, Tpetra::StaticProfile)); + RCP A (new MAT (rowMap, maxNumEntPerRow)); if (rowMap->getNodeNumElements () != 0) { for (LO lclRow = rowMap->getMinLocalIndex (); diff --git a/packages/anasazi/tpetra/test/BlockDavidson/cxx_main_lap.cpp b/packages/anasazi/tpetra/test/BlockDavidson/cxx_main_lap.cpp index 7a9030691d1d..d104d911bbf3 100644 --- a/packages/anasazi/tpetra/test/BlockDavidson/cxx_main_lap.cpp +++ b/packages/anasazi/tpetra/test/BlockDavidson/cxx_main_lap.cpp @@ -117,7 +117,7 @@ int main(int argc, char *argv[]) // create map RCP > map = rcp (new Map<> (dim,0,comm)); - RCP > K = rcp (new CrsMatrix (map, 4, Tpetra::StaticProfile)); + RCP > K = rcp (new CrsMatrix (map, 4)); int base = MyPID*ROWS_PER_PROC; if (MyPID != NumImages-1) { for (int i=0; i > map = rcp (new Map<> (dim,0,comm)); - RCP > K = rcp (new CrsMatrix (map, 4, Tpetra::StaticProfile)); + RCP > K = rcp (new CrsMatrix (map, 4)); int base = MyPID*ROWS_PER_PROC; if (MyPID != NumImages-1) { for (int i=0; i > map = rcp (new Map<> (dim, 0, comm)); - RCP > K = rcp(new CrsMatrix(map,4,Tpetra::StaticProfile)); + RCP > K = rcp(new CrsMatrix(map,4)); int base = MyPID*ROWS_PER_PROC; if (MyPID != NumImages-1) { for (int i=0; i RCP > constructDiagMatrix(const RCP > &map) { - RCP > op = rcp( new CrsMatrix(map,1,Tpetra::StaticProfile) ); + RCP > op = rcp( new CrsMatrix(map,1) ); for (size_t i=0; igetNodeNumElements(); ++i) { op->insertGlobalValues(map->getGlobalElement(i),tuple(map->getGlobalElement(i)), tuple(ScalarTraits::one())); } diff --git a/packages/belos/tpetra/test/FixedPoint/test_fp_hb.cpp b/packages/belos/tpetra/test/FixedPoint/test_fp_hb.cpp index 6859d7173f1b..ab630b103d60 100644 --- a/packages/belos/tpetra/test/FixedPoint/test_fp_hb.cpp +++ b/packages/belos/tpetra/test/FixedPoint/test_fp_hb.cpp @@ -217,7 +217,7 @@ int main(int argc, char *argv[]) { int NumMyElements = diagonal.getMap()->getNodeNumElements(); auto MyGlobalElements = diagonal.getMap()->getNodeElementList(); Teuchos::ArrayRCP dd=diagonal.getDataNonConst(); - RCP > invDiagMatrix = Teuchos::rcp(new CrsMatrix(A->getRowMap(), 1, Tpetra::StaticProfile)); + RCP > invDiagMatrix = Teuchos::rcp(new CrsMatrix(A->getRowMap(), 1)); for (Teuchos_Ordinal i=0; iinsertGlobalValues(MyGlobalElements[i], diff --git a/packages/belos/tpetra/test/LinearSolverFactory/LinearSolverFactory.cpp b/packages/belos/tpetra/test/LinearSolverFactory/LinearSolverFactory.cpp index 160f3ab7f126..286349fa3c94 100644 --- a/packages/belos/tpetra/test/LinearSolverFactory/LinearSolverFactory.cpp +++ b/packages/belos/tpetra/test/LinearSolverFactory/LinearSolverFactory.cpp @@ -112,7 +112,7 @@ createTestMatrix (Teuchos::FancyOStream& out, // lets us use local indices. RCP colMap = rowMap; const size_t maxNumEntPerRow = 1; - RCP A (new MAT (rowMap, colMap, maxNumEntPerRow, Tpetra::StaticProfile)); + RCP A (new MAT (rowMap, colMap, maxNumEntPerRow)); if (rowMap->getNodeNumElements () != 0) { Teuchos::Array vals (1); diff --git a/packages/belos/tpetra/test/LinearSolverFactory/SolverFactory.cpp b/packages/belos/tpetra/test/LinearSolverFactory/SolverFactory.cpp index f7483a2c084b..b242507de441 100644 --- a/packages/belos/tpetra/test/LinearSolverFactory/SolverFactory.cpp +++ b/packages/belos/tpetra/test/LinearSolverFactory/SolverFactory.cpp @@ -86,7 +86,7 @@ createTestMatrix (Teuchos::FancyOStream& out, // lets us use local indices. RCP colMap = rowMap; const size_t maxNumEntPerRow = 1; - RCP A (new MAT (rowMap, colMap, maxNumEntPerRow, Tpetra::StaticProfile)); + RCP A (new MAT (rowMap, colMap, maxNumEntPerRow)); if (rowMap->getNodeNumElements () != 0) { Teuchos::Array vals (1); diff --git a/packages/belos/tpetra/test/MVOPTester/cxx_main_complex.cpp b/packages/belos/tpetra/test/MVOPTester/cxx_main_complex.cpp index f3348ad13b5f..a05eee75cc82 100644 --- a/packages/belos/tpetra/test/MVOPTester/cxx_main_complex.cpp +++ b/packages/belos/tpetra/test/MVOPTester/cxx_main_complex.cpp @@ -105,7 +105,7 @@ namespace { template RCP > constructDiagMatrix(const RCP > &map) { - RCP > op = rcp( new CrsMatrix(map,1,Tpetra::StaticProfile) ); + RCP > op = rcp( new CrsMatrix(map,1) ); for (size_t i=0; igetNodeNumElements(); ++i) { op->insertGlobalValues(map->getGlobalElement(i),tuple(map->getGlobalElement(i)), tuple(ScalarTraits::one())); } diff --git a/packages/belos/tpetra/test/Native/nonsymm_matrix.cpp b/packages/belos/tpetra/test/Native/nonsymm_matrix.cpp index e01e1ca73174..be9cb296283a 100644 --- a/packages/belos/tpetra/test/Native/nonsymm_matrix.cpp +++ b/packages/belos/tpetra/test/Native/nonsymm_matrix.cpp @@ -97,7 +97,7 @@ createNonsymmTridiagMatrix (const Teuchos::RCP >& rowMap, LO (rowMap->getNodeNumElements ()); const GO gblMinGblInd = rowMap->getMinAllGlobalIndex (); const GO gblMaxGblInd = rowMap->getMaxAllGlobalIndex (); - auto A = rcp (new crs_matrix_type (rowMap, 3, Tpetra::StaticProfile)); + auto A = rcp (new crs_matrix_type (rowMap, 3)); const SC ONE = STS::one (); const SC TWO = ONE + ONE; diff --git a/packages/ifpack2/example/RelaxationWithEquilibration.cpp b/packages/ifpack2/example/RelaxationWithEquilibration.cpp index 4eb218d7664b..307bdb956b79 100644 --- a/packages/ifpack2/example/RelaxationWithEquilibration.cpp +++ b/packages/ifpack2/example/RelaxationWithEquilibration.cpp @@ -380,17 +380,20 @@ tpetraToEpetraCrsMatrix (const Tpetra::CrsMatrix& A_t, // We can use static profile, since we know the structure in advance. Epetra_CrsMatrix A_e (Copy, rowMap, colMap, numEntPerRow.data (), true); - Teuchos::Array lclColIndsBuf (A_t.getNodeMaxNumRowEntries ()); - Teuchos::Array valsBuf (A_t.getNodeMaxNumRowEntries ()); + using tmatrix_t = Tpetra::CrsMatrix; + + typename tmatrix_t::nonconst_local_inds_host_view_type + lclColInds ("ifpack2::lclColInds", A_t.getNodeMaxNumRowEntries()); + typename tmatrix_t::nonconst_values_host_view_type + vals ("ifpack2::vals", A_t.getNodeMaxNumRowEntries()); + int lclErrCode = 0; for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { size_t numEnt = A_t.getNumEntriesInLocalRow (lclRow); - Teuchos::ArrayView lclColInds = lclColIndsBuf (0, numEnt); - Teuchos::ArrayView vals = valsBuf (0, numEnt); A_t.getLocalRowCopy (static_cast (lclRow), lclColInds, vals, numEnt); lclErrCode = A_e.InsertMyValues (lclRow, static_cast (numEnt), - vals.getRawPtr (), lclColInds.getRawPtr ()); + vals.data(), lclColInds.data()); if (lclErrCode != 0) { break; } @@ -880,8 +883,7 @@ gatherCrsMatrixAndMultiVector (LO& errCode, export_type exp (A.getRowMap (), rowMap_gathered); auto A_gathered = Teuchos::rcp (new crs_matrix_type (rowMap_gathered, - A.getGlobalMaxNumRowEntries (), - Tpetra::StaticProfile)); + A.getGlobalMaxNumRowEntries ())); A_gathered->doExport (A, exp, Tpetra::INSERT); auto domainMap_gathered = computeGatherMap (A.getDomainMap (), Teuchos::null); auto rangeMap_gathered = computeGatherMap (A.getRangeMap (), Teuchos::null); diff --git a/packages/ifpack2/src/Ifpack2_ILUT_def.hpp b/packages/ifpack2/src/Ifpack2_ILUT_def.hpp index 63d962a5b822..8295eeef7dbc 100644 --- a/packages/ifpack2/src/Ifpack2_ILUT_def.hpp +++ b/packages/ifpack2/src/Ifpack2_ILUT_def.hpp @@ -716,7 +716,7 @@ void ILUT::compute () } L_ = rcp (new crs_matrix_type (A_local_->getRowMap(), A_local_->getColMap(), - nnzPerRow(), Tpetra::StaticProfile)); + nnzPerRow())); for (local_ordinal_type row_i = 0 ; row_i < myNumRows ; ++row_i) { L_->insertLocalValues (row_i, L_tmp_idx[row_i](), L_tmpv[row_i]()); @@ -729,7 +729,7 @@ void ILUT::compute () } U_ = rcp (new crs_matrix_type (A_local_->getRowMap(), A_local_->getColMap(), - nnzPerRow(), Tpetra::StaticProfile)); + nnzPerRow())); for (local_ordinal_type row_i = 0 ; row_i < myNumRows ; ++row_i) { U_->insertLocalValues (row_i, U_tmp_idx[row_i](), U_tmpv[row_i]()); diff --git a/packages/ifpack2/src/Ifpack2_SparseContainer_def.hpp b/packages/ifpack2/src/Ifpack2_SparseContainer_def.hpp index 75c3d81e9090..fd5d282957c1 100644 --- a/packages/ifpack2/src/Ifpack2_SparseContainer_def.hpp +++ b/packages/ifpack2/src/Ifpack2_SparseContainer_def.hpp @@ -553,7 +553,7 @@ extract () } //now that row sizes are known, can allocate the diagonal matrix RCP tempMap(new InverseMap(blockPointSize, 0, this->localComm_)); - diagBlocks_[i] = rcp(new InverseCrs(tempMap, rowEntryCounts, Tpetra::StaticProfile)); + diagBlocks_[i] = rcp(new InverseCrs(tempMap, rowEntryCounts)); Inverses_[i] = rcp(new InverseType(diagBlocks_[i])); //insert the actual entries, one row at a time for(LO blockRow = 0; blockRow < blockSize; blockRow++) @@ -617,7 +617,7 @@ extract () rowEntryCounts[j] = this->getInputRowView(this->blockRows_[blockStart + j]).size(); } RCP tempMap(new InverseMap(blockSize, 0, this->localComm_)); - diagBlocks_[i] = rcp(new InverseCrs(tempMap, rowEntryCounts, Tpetra::StaticProfile)); + diagBlocks_[i] = rcp(new InverseCrs(tempMap, rowEntryCounts)); Inverses_[i] = rcp(new InverseType(diagBlocks_[i])); for(LO blockRow = 0; blockRow < blockSize; blockRow++) { diff --git a/packages/ifpack2/src/Ifpack2_Utilities.hpp b/packages/ifpack2/src/Ifpack2_Utilities.hpp index 274e8aea4640..69ad73cefc60 100644 --- a/packages/ifpack2/src/Ifpack2_Utilities.hpp +++ b/packages/ifpack2/src/Ifpack2_Utilities.hpp @@ -79,7 +79,7 @@ namespace Details { // make sure that we are using the correct diagonal column // indices, so it probably wouldn't help much. Teuchos::RCP diagonalGraph; - diagonalGraph = Teuchos::rcp(new crs_graph_type(graph.getRowMap(), maxDiagEntPerRow, Tpetra::StaticProfile)); + diagonalGraph = Teuchos::rcp(new crs_graph_type(graph.getRowMap(), maxDiagEntPerRow)); const map_type& meshRowMap = *(graph.getRowMap()); Teuchos::Array diagGblColInds(maxDiagEntPerRow); diff --git a/packages/ifpack2/src/supportgraph/Ifpack2_SupportGraph_def.hpp b/packages/ifpack2/src/supportgraph/Ifpack2_SupportGraph_def.hpp index 8f39d7b117ef..102f6076e9c0 100644 --- a/packages/ifpack2/src/supportgraph/Ifpack2_SupportGraph_def.hpp +++ b/packages/ifpack2/src/supportgraph/Ifpack2_SupportGraph_def.hpp @@ -473,7 +473,7 @@ SupportGraph::findSupport () // Create the CrsMatrix for the support graph Support_ = rcp (new crs_matrix_type (A_local_->getRowMap(), A_local_->getColMap(), - localnumnz, Tpetra::StaticProfile)); + localnumnz)); // Fill in the matrix with the stl vectors for each row for (size_t row = 0; row < num_verts; ++row) { diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_SolverFactory.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_SolverFactory.cpp index 6f5c32b197ea..0e4fd0068201 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_SolverFactory.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_SolverFactory.cpp @@ -73,7 +73,7 @@ namespace { // lets us use local indices. RCP colMap = rowMap; const size_t maxNumEntPerRow = 1; - RCP A (new MAT (rowMap, colMap, maxNumEntPerRow, Tpetra::StaticProfile)); + RCP A (new MAT (rowMap, colMap, maxNumEntPerRow)); if (rowMap->getNodeNumElements () != 0) { Teuchos::Array vals (1); diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTest234.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTest234.cpp index bf0ffbfe7212..43c860fd98fe 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTest234.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTest234.cpp @@ -119,8 +119,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_1_DECL(Chebyshev, Issue234, SC) // For a diagonal matrix, we can use the row Map as the column Map. const size_t maxNumEntPerRow = 1; RCP A = - rcp (new crs_matrix_type (rowMap, colMap, maxNumEntPerRow, - Tpetra::StaticProfile)); + rcp (new crs_matrix_type (rowMap, colMap, maxNumEntPerRow)); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { A->insertLocalValues (lclRow, tuple (lclRow), tuple (ONE)); } diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestChebyshev2.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestChebyshev2.cpp index 83665ca935d7..4b8bbcee0bb1 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestChebyshev2.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestChebyshev2.cpp @@ -379,7 +379,7 @@ TEUCHOS_UNIT_TEST(Ifpack2Chebyshev, Convergence) RCP domainMap = rowMap; // Create the matrix, with static profile. - RCP A (new crs_matrix_type (rowMap, 3, Tpetra::StaticProfile)); + RCP A (new crs_matrix_type (rowMap, 3)); // Fill the matrix. Array cols (3); diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestContainerFactory.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestContainerFactory.cpp index 7a632a03b6c4..e3620888601d 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestContainerFactory.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestContainerFactory.cpp @@ -105,7 +105,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(ContainerFactory, TestTypesAndInput, SC, LO, G // For a diagonal matrix, we can use the row Map as the column Map. const size_t maxNumEntPerRow = 1; - RCP A = rcp (new crs_matrix_type (rowMap, colMap, maxNumEntPerRow, Tpetra::StaticProfile)); + RCP A = rcp (new crs_matrix_type (rowMap, colMap, maxNumEntPerRow)); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { A->insertLocalValues (lclRow, tuple (lclRow), tuple (ONE)); } diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestHelpers.hpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestHelpers.hpp index b11516eaf06c..2380213f3d97 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestHelpers.hpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestHelpers.hpp @@ -100,7 +100,7 @@ create_tridiag_graph (const LocalOrdinal num_rows_per_proc) rcp (new map_type (INVALID, num_rows_per_proc, indexBase, comm)); RCP > crsgraph = - rcp (new Tpetra::CrsGraph (rowmap, 3, Tpetra::StaticProfile)); + rcp (new Tpetra::CrsGraph (rowmap, 3)); Teuchos::Array cols; const LocalOrdinal lclNumRows = @@ -143,7 +143,7 @@ create_test_graph (const LocalOrdinal num_rows_per_proc) Teuchos::RCP > rowmap = Teuchos::rcp(new Tpetra::Map(INVALID, num_rows_per_proc, indexBase, comm)); size_t global_size = rowmap->getGlobalNumElements(); - Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, global_size, Tpetra::StaticProfile)); + Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, global_size)); Teuchos::Array cols; for(LocalOrdinal l_row = 0; (size_t) l_rowgetNodeNumElements(); l_row++) { @@ -180,7 +180,7 @@ Teuchos::RCP > create_banded_g Teuchos::RCP > rowmap = Teuchos::rcp(new Tpetra::Map(INVALID, num_rows_per_proc, indexBase, comm)); const size_t maxNumEntPerRow = 5; - Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow, Tpetra::StaticProfile)); + Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow)); // Fill the graph with only diagonal entries Teuchos::Array gblColInds (maxNumEntPerRow); @@ -219,7 +219,7 @@ template Teuchos::RCP > create_diagonal_graph(Teuchos::RCP > rowmap) { const size_t maxNumEntPerRow = 1; - Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow, Tpetra::StaticProfile)); + Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow)); // Fill the graph with only diagonal entries Teuchos::Array gblColInds (maxNumEntPerRow); @@ -325,7 +325,7 @@ Teuchos::RCP > create_dense_lo Teuchos::RCP > rowmap = Teuchos::rcp(new Tpetra::Map(INVALID, num_rows_per_proc, indexBase, comm)); const size_t maxNumEntPerRow = num_rows_per_proc; - Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow, Tpetra::StaticProfile)); + Teuchos::RCP > crsgraph = Teuchos::rcp(new Tpetra::CrsGraph(rowmap, maxNumEntPerRow)); // Fill the graph with only diagonal entries Teuchos::Array gblColInds (maxNumEntPerRow); @@ -353,8 +353,7 @@ Teuchos::RCP > c { Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, - 3/*tri-diagonal matrix*/, - Tpetra::StaticProfile)); + 3/*tri-diagonal matrix*/)); Teuchos::Array col(3); Teuchos::Array coef(3); @@ -403,7 +402,7 @@ Teuchos::RCP > c template Teuchos::RCP > create_test_matrix2(const Teuchos::RCP >& rowmap) { - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 3/*tri-diagonal matrix*/, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 3/*tri-diagonal matrix*/)); Teuchos::Array col(1); Teuchos::Array coef(1); @@ -458,7 +457,7 @@ Teuchos::RCP > c template Teuchos::RCP > create_test_matrix3(const Teuchos::RCP >& rowmap) { - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 3/*tri-diagonal matrix*/, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 3/*tri-diagonal matrix*/)); /* NOTE: this utility creates a matrix whose column map is equal to its row map. At processor boundaries, @@ -520,7 +519,7 @@ Teuchos::RCP > c template Teuchos::RCP > create_banded_matrix(const Teuchos::RCP >& rowmap, const GlobalOrdinal bw) { - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5)); Teuchos::Array col(1); Teuchos::Array coef(1); @@ -794,7 +793,7 @@ Teuchos::RCP > c // // Beyond this the matrix is diagonal. We also explicitly stick in some hard zeros for the line partitioning test - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 4, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 4)); Teuchos::Array indices(4); Teuchos::Array values(4); @@ -850,7 +849,7 @@ Teuchos::RCP > c // // Beyond this the matrix is diagonal. - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5)); Teuchos::Array indices(5); Teuchos::Array values(5); @@ -906,7 +905,7 @@ Teuchos::RCP > c // // Beyond this the matrix is diagonal. We also explicitly stick in some hard zeros for the line partitioning test - Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5, Tpetra::StaticProfile)); + Teuchos::RCP > crsmatrix = Teuchos::rcp(new Tpetra::CrsMatrix(rowmap, 5)); Teuchos::Array indices(5); Teuchos::Array values(5); diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestLocalSparseTriangularSolver.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestLocalSparseTriangularSolver.cpp index 4c4e6d0945c9..f15c6d2f0d09 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestLocalSparseTriangularSolver.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestLocalSparseTriangularSolver.cpp @@ -264,8 +264,7 @@ void testCompareToLocalSolve (bool& success, Teuchos::FancyOStream& out, out << "Construct the test matrix A" << endl; RCP A = rcp (new crs_matrix_type (rowMap, colMap, - static_cast (maxNumEntPerRow), - Tpetra::StaticProfile)); + static_cast (maxNumEntPerRow))); out << "Fill the test matrix A" << endl; // Pick the entries of the matrix so that triangular solves are diff --git a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestRelaxation.cpp b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestRelaxation.cpp index ba0840e058ad..0d5cf4be3cae 100644 --- a/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestRelaxation.cpp +++ b/packages/ifpack2/test/unit_tests/Ifpack2_UnitTestRelaxation.cpp @@ -504,7 +504,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(Ifpack2Relaxation, SGS_mult_sweeps, Scalar, Lo RCP domainMap = rowMap; RCP rangeMap = rowMap; RCP A = - rcp (new crs_matrix_type (rowMap, 6, Tpetra::StaticProfile)); + rcp (new crs_matrix_type (rowMap, 6)); { const size_t lclNumRows = rowMap->getNodeNumElements (); diff --git a/packages/panzer/disc-fe/src/Panzer_L2Projection.cpp b/packages/panzer/disc-fe/src/Panzer_L2Projection.cpp index 76c51845bc80..047a37c1c69e 100644 --- a/packages/panzer/disc-fe/src/Panzer_L2Projection.cpp +++ b/packages/panzer/disc-fe/src/Panzer_L2Projection.cpp @@ -363,7 +363,7 @@ namespace panzer { } Teuchos::ArrayView nEntriesPerRowView(nEntriesPerRow); - RCP ghostedGraph = rcp(new GraphType(ghostedTargetMap,ghostedSourceMap,nEntriesPerRowView,Tpetra::StaticProfile)); + RCP ghostedGraph = rcp(new GraphType(ghostedTargetMap,ghostedSourceMap,nEntriesPerRowView)); for (blockItr=elementBlockIds.begin();blockItr!=elementBlockIds.end();++blockItr) { std::string blockId = *blockItr; diff --git a/packages/panzer/disc-fe/src/Panzer_LocalPartitioningUtilities.cpp b/packages/panzer/disc-fe/src/Panzer_LocalPartitioningUtilities.cpp index 0cc4ce01f54d..9ece49dac0e1 100644 --- a/packages/panzer/disc-fe/src/Panzer_LocalPartitioningUtilities.cpp +++ b/packages/panzer/disc-fe/src/Panzer_LocalPartitioningUtilities.cpp @@ -264,8 +264,7 @@ buildNodeToCellMatrix(const Teuchos::RCP > & comm, const unsigned int num_nodes_per_cell = owned_cells_to_nodes.extent(1); // The matrix is indexed by (global cell, global node) = local node - cell_to_node = rcp(new crs_type(cell_map,num_nodes_per_cell, - Tpetra::StaticProfile)); + cell_to_node = rcp(new crs_type(cell_map,num_nodes_per_cell)); std::vector local_node_indexes(num_nodes_per_cell); std::vector global_node_indexes(num_nodes_per_cell); diff --git a/packages/panzer/disc-fe/src/lof/Panzer_BlockedTpetraLinearObjFactory_impl.hpp b/packages/panzer/disc-fe/src/lof/Panzer_BlockedTpetraLinearObjFactory_impl.hpp index e35c070206a3..c0b0fa544945 100644 --- a/packages/panzer/disc-fe/src/lof/Panzer_BlockedTpetraLinearObjFactory_impl.hpp +++ b/packages/panzer/disc-fe/src/lof/Panzer_BlockedTpetraLinearObjFactory_impl.hpp @@ -1036,8 +1036,7 @@ buildTpetraGhostedGraph(int i,int j) const } } Teuchos::ArrayView nEntriesPerRowView(nEntriesPerRow); - RCP graph = rcp(new CrsGraphType(map_i,map_j, nEntriesPerRowView, - Tpetra::StaticProfile)); + RCP graph = rcp(new CrsGraphType(map_i,map_j, nEntriesPerRowView)); diff --git a/packages/panzer/disc-fe/src/lof/Panzer_TpetraLinearObjFactory_impl.hpp b/packages/panzer/disc-fe/src/lof/Panzer_TpetraLinearObjFactory_impl.hpp index 03b4b1502bc9..763ee9e34af5 100644 --- a/packages/panzer/disc-fe/src/lof/Panzer_TpetraLinearObjFactory_impl.hpp +++ b/packages/panzer/disc-fe/src/lof/Panzer_TpetraLinearObjFactory_impl.hpp @@ -712,8 +712,7 @@ buildGhostedGraph() const Teuchos::ArrayView nEntriesPerRowView(nEntriesPerRow); Teuchos::RCP graph = Teuchos::rcp(new CrsGraphType(rMap,cMap, - nEntriesPerRowView, - Tpetra::StaticProfile)); + nEntriesPerRowView)); // Now insert entries into the graph for(blockItr=elementBlockIds.begin();blockItr!=elementBlockIds.end();++blockItr) { diff --git a/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteCurl.hpp b/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteCurl.hpp index 3713995d4541..54aed44dc9b2 100644 --- a/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteCurl.hpp +++ b/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteCurl.hpp @@ -176,7 +176,7 @@ void addDiscreteCurlToRequestHandler( edge_basis->getValues(Kokkos::subview(curlAtDofCoordsNonOriented, 0, Kokkos::ALL(), Kokkos::ALL(), Kokkos::ALL()), Kokkos::subview(dofCoords, 0, Kokkos::ALL(), Kokkos::ALL()), Intrepid2::OPERATOR_CURL); // create the global curl matrix - RCP curl_matrix = rcp(new matrix(rowmap,colmap,basisCoeffsLI.extent(1),Tpetra::StaticProfile)); + RCP curl_matrix = rcp(new matrix(rowmap,colmap,basisCoeffsLI.extent(1))); // loop over element blocks std::vector elementBlockIds; diff --git a/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteGradient.hpp b/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteGradient.hpp index c2055bcad0c0..48d736e05955 100644 --- a/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteGradient.hpp +++ b/packages/panzer/mini-em/src/solvers/MiniEM_DiscreteGradient.hpp @@ -96,7 +96,7 @@ void addDiscreteGradientToRequestHandler( RCP domainmap = global_tloc->getMapForBlock(nBlockIndex); RCP rowmap = global_tloc->getMapForBlock(eBlockIndex); RCP colmap = ghosted_tloc->getMapForBlock(nBlockIndex); - RCP grad_matrix = rcp(new matrix(rowmap, colmap, 2, Tpetra::StaticProfile)); + RCP grad_matrix = rcp(new matrix(rowmap, colmap, 2)); RCP field_pattern = blockedDOFMngr->getGeometricFieldPattern(); shards::CellTopology cell_topology = field_pattern->getCellTopology(); diff --git a/packages/shylu/shylu_dd/bddc/src/shylu_UtilBDDC.hpp b/packages/shylu/shylu_dd/bddc/src/shylu_UtilBDDC.hpp index 1d4864683f52..37b650b0c580 100644 --- a/packages/shylu/shylu_dd/bddc/src/shylu_UtilBDDC.hpp +++ b/packages/shylu/shylu_dd/bddc/src/shylu_UtilBDDC.hpp @@ -262,7 +262,7 @@ namespace bddc { 0, Comm)); RCP colMap = rcp(new Map(IGO, Teuchos::ArrayView(proc), 0, Comm) ); - CrsGraph nodeProcs(nodeMap, colMap, 1, Tpetra::StaticProfile); + CrsGraph nodeProcs(nodeMap, colMap, 1); std::vector zero(1, 0); for (LO i=0; i(zero)); @@ -315,7 +315,7 @@ namespace bddc { 0, Comm)); RCP colMap = rcp(new Map(IGO, Teuchos::ArrayView(proc), 0, Comm) ); - CrsGraph nodeProcs(nodeMap, colMap, 1, Tpetra::StaticProfile); + CrsGraph nodeProcs(nodeMap, colMap, 1); std::vector zero(1, 0); for (LO i=0; i(zero)); diff --git a/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp b/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp index b3f44635b715..0bf286dc6bd6 100644 --- a/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp +++ b/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp @@ -657,7 +657,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -778,7 +778,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -915,7 +915,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1076,7 +1076,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1221,7 +1221,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1376,7 +1376,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1518,7 +1518,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(1), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(1))); Array columnIndices(1); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1672,7 +1672,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(1), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(1))); Array columnIndices(1); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1826,7 +1826,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(1), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(1))); Array columnIndices(1); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -2002,7 +2002,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -2164,7 +2164,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); diff --git a/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixUQPCEUnitTest.hpp b/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixUQPCEUnitTest.hpp index e35620acfab8..dd62e5e8c954 100644 --- a/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixUQPCEUnitTest.hpp +++ b/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixUQPCEUnitTest.hpp @@ -697,7 +697,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -843,7 +843,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1000,7 +1000,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1155,7 +1155,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1329,7 +1329,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1528,7 +1528,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1701,7 +1701,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -1885,7 +1885,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(3), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(3))); Array columnIndices(3); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); diff --git a/packages/stokhos/test/UnitTest/tpetra_mat_vec.cpp b/packages/stokhos/test/UnitTest/tpetra_mat_vec.cpp index 7aee742ec0f9..50c271213d28 100644 --- a/packages/stokhos/test/UnitTest/tpetra_mat_vec.cpp +++ b/packages/stokhos/test/UnitTest/tpetra_mat_vec.cpp @@ -43,7 +43,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); @@ -139,7 +139,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_2_DECL( Tpetra::createUniformContigMapWithNode( nrow, comm); RCP graph = - rcp(new Tpetra_CrsGraph(map, size_t(2), Tpetra::StaticProfile)); + rcp(new Tpetra_CrsGraph(map, size_t(2))); Array columnIndices(2); ArrayView myGIDs = map->getNodeElementList(); const size_t num_my_row = myGIDs.size(); diff --git a/packages/thyra/adapters/tpetra/test/TpetraThyraWrappers_UnitTests.cpp b/packages/thyra/adapters/tpetra/test/TpetraThyraWrappers_UnitTests.cpp index e6972f732d11..33b5c234a70c 100644 --- a/packages/thyra/adapters/tpetra/test/TpetraThyraWrappers_UnitTests.cpp +++ b/packages/thyra/adapters/tpetra/test/TpetraThyraWrappers_UnitTests.cpp @@ -140,7 +140,7 @@ createTriDiagonalTpetraOperator(const int numLocalRows) // Create a Tpetra::Matrix using the Map, with a static allocation dictated by numNz RCP< Tpetra::CrsMatrix > A = - Teuchos::rcp( new Tpetra::CrsMatrix(map, numNz (), Tpetra::StaticProfile) ); + Teuchos::rcp( new Tpetra::CrsMatrix(map, numNz ()) ); // We are done with NumNZ { diff --git a/packages/tpetra/core/example/Additive-Schwarz-Halo/AdditiveSchwarzHalo.cpp b/packages/tpetra/core/example/Additive-Schwarz-Halo/AdditiveSchwarzHalo.cpp index c00de918e429..da07c6bb5291 100644 --- a/packages/tpetra/core/example/Additive-Schwarz-Halo/AdditiveSchwarzHalo.cpp +++ b/packages/tpetra/core/example/Additive-Schwarz-Halo/AdditiveSchwarzHalo.cpp @@ -117,7 +117,7 @@ int main (int argc, char *argv[]) [ 1 2] this matrix has an eigenvalue lambda=3, with eigenvector v = [1 ... 1] */ - A = rcp (new MAT(map, 3, Tpetra::StaticProfile)); + A = rcp (new MAT(map, 3)); if (myImageID == 0) { Array vals(tuple(static_cast(2)*ST::one(), ST::one())); Array cols(tuple(myImageID, myImageID+1)); diff --git a/packages/tpetra/core/example/Finite-Element-Assembly/fem_assembly_TotalElementLoop.hpp b/packages/tpetra/core/example/Finite-Element-Assembly/fem_assembly_TotalElementLoop.hpp index 1a7ee2df3f0d..c58335c20f40 100644 --- a/packages/tpetra/core/example/Finite-Element-Assembly/fem_assembly_TotalElementLoop.hpp +++ b/packages/tpetra/core/example/Finite-Element-Assembly/fem_assembly_TotalElementLoop.hpp @@ -155,7 +155,7 @@ int executeTotalElementLoopSP_(const Teuchos::RCP >& co Teuchos::TimeMonitor::getStackedTimer()->startBaseTimer(); RCP timerElementLoopGraph = rcp(new TimeMonitor(*TimeMonitor::getNewTimer("1) ElementLoop (Graph)"))); - RCP crs_graph = rcp(new crs_graph_type(row_map, maxEntriesPerRow, Tpetra::StaticProfile)); + RCP crs_graph = rcp(new crs_graph_type(row_map, maxEntriesPerRow)); // Using 4 because we're using quads for this example, so there will be 4 nodes associated with each element. Teuchos::Array global_ids_in_row(4); @@ -435,7 +435,7 @@ executeTotalElementLoopSPKokkos_ Teuchos::TimeMonitor::getStackedTimer()->startBaseTimer(); RCP timerElementLoopGraph = rcp(new TimeMonitor(*TimeMonitor::getNewTimer("1) ElementLoop (Graph)"))); - RCP crs_graph = rcp(new crs_graph_type(row_map, maxEntriesPerRow, Tpetra::StaticProfile)); + RCP crs_graph = rcp(new crs_graph_type(row_map, maxEntriesPerRow)); // Using 4 because we're using quads for this example, so there will be 4 nodes associated with each element. Teuchos::Array global_ids_in_row(4); diff --git a/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrixMatVec.cpp b/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrixMatVec.cpp index f6cebb6dad65..a5d2f1620ca8 100644 --- a/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrixMatVec.cpp +++ b/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrixMatVec.cpp @@ -219,8 +219,7 @@ getTpetraGraph (const Teuchos::RCP >& comm, const GO gblNumCols = static_cast (rowMap->getGlobalNumElements ()); // Create the graph structure of the sparse matrix. RCP G = - rcp (new graph_type (rowMap, opts.numEntPerRow, - Tpetra::StaticProfile)); + rcp (new graph_type (rowMap, opts.numEntPerRow)); // Fill in the sparse graph. Teuchos::Array gblColInds (opts.numEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { // for each of my rows diff --git a/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrix_sumIntoLocalValues.cpp b/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrix_sumIntoLocalValues.cpp index e6bb4b53726d..6252bbd9c266 100644 --- a/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrix_sumIntoLocalValues.cpp +++ b/packages/tpetra/core/example/advanced/Benchmarks/CrsMatrix_sumIntoLocalValues.cpp @@ -88,8 +88,7 @@ createCrsMatrix (RCP rowAndColMap, //TM mon (*TM::getNewCounter ("CrsMatrix constructor")); return rcp (new crs_matrix_type (rowAndColMap, rowAndColMap, - maxNumEntPerRow, - Tpetra::StaticProfile)); + maxNumEntPerRow)); } RCP @@ -99,8 +98,7 @@ createCrsGraph (RCP rowAndColMap, //TM mon (*TM::getNewCounter ("CrsGraph constructor")); return rcp (new crs_graph_type (rowAndColMap, rowAndColMap, - maxNumEntPerRow, - Tpetra::StaticProfile)); + maxNumEntPerRow)); } void diff --git a/packages/tpetra/core/example/advanced/Benchmarks/blockCrsMatrixMatVec.cpp b/packages/tpetra/core/example/advanced/Benchmarks/blockCrsMatrixMatVec.cpp index b0e3beb5996b..e3c1b087e177 100644 --- a/packages/tpetra/core/example/advanced/Benchmarks/blockCrsMatrixMatVec.cpp +++ b/packages/tpetra/core/example/advanced/Benchmarks/blockCrsMatrixMatVec.cpp @@ -460,8 +460,7 @@ getTpetraGraph (const Teuchos::RCP >& comm, const GO gblNumCols = static_cast (rowMap->getGlobalNumElements ()); // Create the graph structure of the sparse matrix. RCP G = - rcp (new graph_type (rowMap, opts.numEntPerRow, - Tpetra::StaticProfile)); + rcp (new graph_type (rowMap, opts.numEntPerRow)); // Fill in the sparse graph. Teuchos::Array gblColInds (opts.numEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { // for each of my rows diff --git a/packages/tpetra/core/example/advanced/Benchmarks/localView.cpp b/packages/tpetra/core/example/advanced/Benchmarks/localView.cpp index 51b0d744342e..7d7342239851 100644 --- a/packages/tpetra/core/example/advanced/Benchmarks/localView.cpp +++ b/packages/tpetra/core/example/advanced/Benchmarks/localView.cpp @@ -275,8 +275,7 @@ namespace { // (anonymous) const GO gblNumCols = static_cast (rowMap->getGlobalNumElements ()); // Create the graph structure of the sparse matrix. RCP G = - rcp (new graph_type (rowMap, opts.numEntPerRow, - Tpetra::StaticProfile)); + rcp (new graph_type (rowMap, opts.numEntPerRow)); // Fill in the graph structure of the sparse matrix. Teuchos::Array gblColInds (opts.numEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { // for each of my rows diff --git a/packages/tpetra/core/inout/MatrixMarket_Tpetra.hpp b/packages/tpetra/core/inout/MatrixMarket_Tpetra.hpp index 7c0896c4300d..811ee6623167 100644 --- a/packages/tpetra/core/inout/MatrixMarket_Tpetra.hpp +++ b/packages/tpetra/core/inout/MatrixMarket_Tpetra.hpp @@ -803,8 +803,7 @@ namespace Tpetra { // Construct the CrsMatrix, using the row map, with the // constructor specifying the number of nonzeros for each row. RCP A = - rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow (), - StaticProfile)); + rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow ())); // List of the global indices of my rows. // They may or may not be contiguous. @@ -894,7 +893,7 @@ namespace Tpetra { // constructor specifying the number of nonzeros for each row. RCP A = rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow(), - StaticProfile, constructorParams)); + constructorParams)); // List of the global indices of my rows. // They may or may not be contiguous. @@ -956,9 +955,9 @@ namespace Tpetra { RCP A; // the matrix to return. if (colMap.is_null ()) { // the user didn't provide a column Map - A = rcp (new sparse_matrix_type (rowMap, myNumEntriesPerRow, StaticProfile)); + A = rcp (new sparse_matrix_type (rowMap, myNumEntriesPerRow)); } else { // the user provided a column Map - A = rcp (new sparse_matrix_type (rowMap, colMap, myNumEntriesPerRow, StaticProfile)); + A = rcp (new sparse_matrix_type (rowMap, colMap, myNumEntriesPerRow)); } // List of the global indices of my rows. @@ -1571,7 +1570,7 @@ namespace Tpetra { RCP proc0Graph = rcp(new sparse_graph_type(proc0Map,numEntriesPerRow (), - StaticProfile,constructorParams)); + constructorParams)); if(myRank == rootRank) { typedef Teuchos::MatrixMarket::Raw::GraphElement element_type; @@ -1598,7 +1597,7 @@ namespace Tpetra { rcp(new map_type(dims[0],0,pComm,GloballyDistributed)); // Create the graph with that distribution too - distGraph = rcp(new sparse_graph_type(distMap,colMap,0,StaticProfile,constructorParams)); + distGraph = rcp(new sparse_graph_type(distMap,colMap,0,constructorParams)); // Create an importer/exporter/vandelay to redistribute the graph typedef Import import_type; @@ -1608,7 +1607,7 @@ namespace Tpetra { distGraph->doImport(*proc0Graph,importer,INSERT); } else { - distGraph = rcp(new sparse_graph_type(rowMap,colMap,0,StaticProfile,constructorParams)); + distGraph = rcp(new sparse_graph_type(rowMap,colMap,0,constructorParams)); // Create an importer/exporter/vandelay to redistribute the graph typedef Import import_type; @@ -3799,8 +3798,7 @@ namespace Tpetra { // know how many entries there are in each row, so we can use // static profile. RCP A_proc0 = - rcp (new sparse_matrix_type (gatherRowMap, gatherNumEntriesPerRow (), - Tpetra::StaticProfile)); + rcp (new sparse_matrix_type (gatherRowMap, gatherNumEntriesPerRow())); if (myRank == rootRank) { if (debug) { cerr << "-- Proc 0: Filling gather matrix" << endl; diff --git a/packages/tpetra/core/inout/Tpetra_MatrixIO_def.hpp b/packages/tpetra/core/inout/Tpetra_MatrixIO_def.hpp index fceedf05f7cb..63138d4fa4ad 100644 --- a/packages/tpetra/core/inout/Tpetra_MatrixIO_def.hpp +++ b/packages/tpetra/core/inout/Tpetra_MatrixIO_def.hpp @@ -203,7 +203,7 @@ readHBMatrix (const std::string &filename, else { domMap = createUniformContigMapWithNode(numCols,comm); } - A = rcp(new Tpetra::CrsMatrix(rowMap, myNNZ (), Tpetra::StaticProfile)); + A = rcp(new Tpetra::CrsMatrix(rowMap, myNNZ ())); // free this locally, A will keep it allocated as long as it is needed by A (up until allocation of nonzeros) { // Classic idiom for freeing an std::vector; resize doesn't diff --git a/packages/tpetra/core/src/Tpetra_BlockCrsMatrix_Helpers_def.hpp b/packages/tpetra/core/src/Tpetra_BlockCrsMatrix_Helpers_def.hpp index 5eb8b0dc1a90..cb636b540c10 100644 --- a/packages/tpetra/core/src/Tpetra_BlockCrsMatrix_Helpers_def.hpp +++ b/packages/tpetra/core/src/Tpetra_BlockCrsMatrix_Helpers_def.hpp @@ -329,7 +329,7 @@ namespace Tpetra { // We can use static profile because the point graph should have at least as many entries per // row as the mesh graph. RCP meshCrsGraph = rcp(new crs_graph_type(meshRowMap, meshColMap, - pointMatrix.getGlobalMaxNumRowEntries(), Tpetra::StaticProfile)); + pointMatrix.getGlobalMaxNumRowEntries())); // Fill the graph by walking through the matrix. For each mesh row, we query the collection of point // rows associated with it. The point column ids are converted to mesh column ids and put into an array. // As each point row collection is finished, the mesh column ids are sorted, made unique, and inserted diff --git a/packages/tpetra/core/src/Tpetra_ConfigDefs.hpp b/packages/tpetra/core/src/Tpetra_ConfigDefs.hpp index 66f40c403ba0..3e68282a3e7d 100644 --- a/packages/tpetra/core/src/Tpetra_ConfigDefs.hpp +++ b/packages/tpetra/core/src/Tpetra_ConfigDefs.hpp @@ -124,12 +124,15 @@ namespace Tpetra { IDNotPresent /*!< At least one of the specified indices was not present in the Map */ }; +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /*! Allocation profile for matrix/graph entries */ enum ProfileType { StaticProfile }; #define TPETRA_DEFAULT_PROFILE_TYPE Tpetra::StaticProfile +#endif + /*! Optimize storage option */ enum OptimizeOption { DoOptimizeStorage, /*!< Indicates that storage should be optimized */ diff --git a/packages/tpetra/core/src/Tpetra_CrsGraph_decl.hpp b/packages/tpetra/core/src/Tpetra_CrsGraph_decl.hpp index 989e4a55c041..13de58644f8f 100644 --- a/packages/tpetra/core/src/Tpetra_CrsGraph_decl.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsGraph_decl.hpp @@ -332,15 +332,22 @@ namespace Tpetra { /// \param maxNumEntriesPerRow [in] Maximum number of graph /// entries per row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const size_t maxNumEntriesPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const size_t maxNumEntriesPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying a (possibly different) upper @@ -351,15 +358,22 @@ namespace Tpetra { /// \param numEntPerRow [in] Maximum number of graph entries to /// allocate for each row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const Kokkos::DualView& numEntPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const Kokkos::DualView& numEntPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying a (possibly different) upper @@ -371,15 +385,22 @@ namespace Tpetra { /// \param numEntPerRow [in] Maximum number of graph entries to /// allocate for each row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::ArrayView& numEntPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::ArrayView& numEntPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); @@ -395,16 +416,24 @@ namespace Tpetra { /// \param maxNumEntriesPerRow [in] Maximum number of graph /// entries per row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const size_t maxNumEntriesPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const size_t maxNumEntriesPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying column Map and number of entries in each row. @@ -417,16 +446,24 @@ namespace Tpetra { /// \param numEntPerRow [in] Maximum number of graph entries to /// allocate for each row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Kokkos::DualView& numEntPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Kokkos::DualView& numEntPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying column Map and number of entries @@ -440,16 +477,24 @@ namespace Tpetra { /// \param numEntPerRow [in] Maximum number of graph entries to /// allocate for each row. This is a strict upper bound. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Teuchos::ArrayView& numEntPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Teuchos::ArrayView& numEntPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); @@ -1102,8 +1147,10 @@ namespace Tpetra { */ bool isStorageOptimized () const; +#ifdef TPETRA_ENABLE_DEPRECATED_CODE //! Returns \c true if the graph was allocated with static data structures. ProfileType getProfileType () const; +#endif /// \brief Get a copy of the given row, using global indices. /// @@ -2561,9 +2608,8 @@ namespace Tpetra { { using Teuchos::rcp; using graph_type = CrsGraph; - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; return rcp(new graph_type(map, maxNumEntriesPerRow, - pftype, params)); + params)); } /// \brief Nonmember CrsGraph constructor that fuses Import and diff --git a/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp b/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp index ba011df0095d..8e5df80becf9 100644 --- a/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp @@ -288,18 +288,30 @@ namespace Tpetra { return Details::Behavior::verbose("CrsGraph"); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const size_t maxNumEntriesPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, maxNumEntriesPerRow, params) + {} +#endif + + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const size_t maxNumEntriesPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , numAllocForAllRows_ (maxNumEntriesPerRow) { const char tfecfFuncName[] = - "CrsGraph(rowMap,maxNumEntriesPerRow,pftype,params): "; + "CrsGraph(rowMap,maxNumEntriesPerRow,params): "; staticAssertions (); TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (maxNumEntriesPerRow == Teuchos::OrdinalTraits::invalid (), @@ -310,20 +322,33 @@ namespace Tpetra { checkInternalState (); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const size_t maxNumEntriesPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, colMap, maxNumEntriesPerRow, params) + {} +#endif + + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const size_t maxNumEntriesPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , colMap_ (colMap) , numAllocForAllRows_ (maxNumEntriesPerRow) { const char tfecfFuncName[] = - "CrsGraph(rowMap,colMap,maxNumEntriesPerRow,pftype,params): "; + "CrsGraph(rowMap,colMap,maxNumEntriesPerRow,params): "; staticAssertions (); TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC( maxNumEntriesPerRow == Teuchos::OrdinalTraits::invalid (), @@ -334,18 +359,30 @@ namespace Tpetra { checkInternalState (); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::ArrayView& numEntPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, numEntPerRow, params) + {} +#endif + + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::ArrayView& numEntPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , numAllocForAllRows_ (0) { const char tfecfFuncName[] = - "CrsGraph(rowMap,numEntPerRow,pftype,params): "; + "CrsGraph(rowMap,numEntPerRow,params): "; staticAssertions (); const size_t lclNumRows = rowMap.is_null () ? @@ -388,19 +425,30 @@ namespace Tpetra { +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const Kokkos::DualView& numEntPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, numEntPerRow, params) + {} +#endif + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const Kokkos::DualView& numEntPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , k_numAllocPerRow_ (numEntPerRow.h_view) , numAllocForAllRows_ (0) { const char tfecfFuncName[] = - "CrsGraph(rowMap,numEntPerRow,pftype,params): "; + "CrsGraph(rowMap,numEntPerRow,params): "; staticAssertions (); const size_t lclNumRows = rowMap.is_null () ? @@ -427,13 +475,26 @@ namespace Tpetra { } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Kokkos::DualView& numEntPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, colMap, numEntPerRow, params) + {} +#endif + + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Kokkos::DualView& numEntPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , colMap_ (colMap) @@ -441,7 +502,7 @@ namespace Tpetra { , numAllocForAllRows_ (0) { const char tfecfFuncName[] = - "CrsGraph(rowMap,colMap,numEntPerRow,pftype,params): "; + "CrsGraph(rowMap,colMap,numEntPerRow,params): "; staticAssertions (); const size_t lclNumRows = rowMap.is_null () ? @@ -468,20 +529,33 @@ namespace Tpetra { } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsGraph:: CrsGraph (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Teuchos::ArrayView& numEntPerRow, const ProfileType /* pftype */, const Teuchos::RCP& params) : + CrsGraph ( + rowMap, colMap, numEntPerRow, params) + {} +#endif + + template + CrsGraph:: + CrsGraph (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Teuchos::ArrayView& numEntPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) , rowMap_ (rowMap) , colMap_ (colMap) , numAllocForAllRows_ (0) { const char tfecfFuncName[] = - "CrsGraph(rowMap,colMap,numEntPerRow,pftype,params): "; + "CrsGraph(rowMap,colMap,numEntPerRow,params): "; staticAssertions (); const size_t lclNumRows = rowMap.is_null () ? @@ -921,13 +995,16 @@ namespace Tpetra { return isOpt; } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED ProfileType CrsGraph:: getProfileType () const { return StaticProfile; } +#endif template global_size_t @@ -3318,8 +3395,7 @@ namespace Tpetra { // number of entries in each nonlocal row. RCP nonlocalGraph = - rcp(new crs_graph_type(nonlocalRowMap, numEntPerNonlocalRow(), - StaticProfile)); + rcp(new crs_graph_type(nonlocalRowMap, numEntPerNonlocalRow())); { size_type curPos = 0; for (auto mapIter = this->nonlocals_.begin (); @@ -7174,7 +7250,7 @@ namespace Tpetra { // If the user gave us a null destGraph, then construct the new // destination graph. We will replace its column Map later. if (destGraph.is_null()) { - destGraph = rcp(new this_type(MyRowMap, 0, StaticProfile, graphparams)); + destGraph = rcp(new this_type(MyRowMap, 0, graphparams)); } /***************************************************/ diff --git a/packages/tpetra/core/src/Tpetra_CrsMatrix_decl.hpp b/packages/tpetra/core/src/Tpetra_CrsMatrix_decl.hpp index 2fc74c0ee4e3..6feec1b68d92 100644 --- a/packages/tpetra/core/src/Tpetra_CrsMatrix_decl.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsMatrix_decl.hpp @@ -538,15 +538,23 @@ namespace Tpetra { /// entries per row. This is a strict upper bound. It may /// differ on different processes. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + TPETRA_DEPRECATED + CrsMatrix (const Teuchos::RCP& rowMap, + const size_t maxNumEntriesPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsMatrix (const Teuchos::RCP& rowMap, const size_t maxNumEntriesPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying (possibly different) number of entries in each row. @@ -557,15 +565,23 @@ namespace Tpetra { /// entries to allocate for each row. This is a strict upper /// bound. It may differ on different processes. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + TPETRA_DEPRECATED + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::ArrayView& numEntPerRowToAlloc, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::ArrayView& numEntPerRowToAlloc, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); @@ -583,16 +599,25 @@ namespace Tpetra { /// per row. This is a strict upper bound. It may differ on /// different processes. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + TPETRA_DEPRECATED + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const size_t maxNumEntPerRow, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const size_t maxNumEntPerRow, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); /// \brief Constructor specifying column Map and number of entries in each row. @@ -609,18 +634,26 @@ namespace Tpetra { /// entries to allocate for each row. This is a strict upper /// bound. It may differ on different processes. /// +#ifdef TPETRA_ENABLE_DEPRECATED_CODE /// \param pftype [in] If you specify this, then this must always /// be StaticProfile. No other values exist or are permitted. +#endif /// /// \param params [in/out] Optional list of parameters. If not /// null, any missing parameters will be filled in with their /// default values. +#ifdef TPETRA_ENABLE_DEPRECATED_CODE + TPETRA_DEPRECATED + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Teuchos::ArrayView& numEntPerRowToAlloc, + const ProfileType pftype, + const Teuchos::RCP& params = Teuchos::null); +#endif CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Teuchos::ArrayView& numEntPerRowToAlloc, - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE, const Teuchos::RCP& params = Teuchos::null); - /// \brief Constructor specifying a matrix and a previously /// constructed graph, presumably a subset of the matrix's graph. @@ -953,10 +986,6 @@ namespace Tpetra { /// possible upper bounds on the number of entries in each row /// of the matrix. This will avoid expensive reallocation if /// your bound was not large enough. - ///
  • If your upper bound on the number of entries in each row - /// will always be correct, create the matrix with - /// StaticProfile. This uses a faster and more compact data - /// structure to store the matrix.
    • ///
  • If you plan to reuse a matrix's graph structure, but /// change its values, in repeated fillComplete() / resumeFill() /// cycles, you can get the best performance by creating the @@ -1018,10 +1047,6 @@ namespace Tpetra { /// possible upper bounds on the number of entries in each row /// of the matrix. This will avoid expensive reallocation if /// your bound was not large enough.
    • - ///
  • If your upper bound on the number of entries in each row - /// will always be correct, create the matrix with - /// StaticProfile. This uses a faster and more compact data - /// structure to store the matrix.
    • ///
  • If you plan to reuse a matrix's graph structure, but /// change its values, in repeated fillComplete() / resumeFill() /// cycles, you can get the best performance by creating the @@ -2471,8 +2496,10 @@ namespace Tpetra { */ bool isStorageOptimized () const; +#ifdef TPETRA_ENABLE_DEPRECATED_CODE //! Returns \c true if the matrix was allocated with static data structures. - ProfileType getProfileType () const; + TPETRA_DEPRECATED ProfileType getProfileType () const; +#endif //! Indicates that the graph is static, so that new entries cannot be added to this matrix. bool isStaticGraph () const; @@ -4152,9 +4179,8 @@ namespace Tpetra { { using matrix_type = CrsMatrix; - const ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; return Teuchos::rcp(new matrix_type(map, maxNumEntriesPerRow, - pftype, params)); + params)); } template diff --git a/packages/tpetra/core/src/Tpetra_CrsMatrix_def.hpp b/packages/tpetra/core/src/Tpetra_CrsMatrix_def.hpp index bef5d73e27da..64589eee83b1 100644 --- a/packages/tpetra/core/src/Tpetra_CrsMatrix_def.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsMatrix_def.hpp @@ -140,25 +140,37 @@ struct AbsMax { namespace Tpetra { +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsMatrix:: CrsMatrix (const Teuchos::RCP& rowMap, size_t maxNumEntriesPerRow, const ProfileType pftype, const Teuchos::RCP& params) : + CrsMatrix ( + rowMap, maxNumEntriesPerRow, params) + {} +#endif + + template + CrsMatrix:: + CrsMatrix (const Teuchos::RCP& rowMap, + size_t maxNumEntriesPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) { - const char tfecfFuncName[] = "CrsMatrix(RCP, size_t, " - "ProfileType[, RCP]): "; + const char tfecfFuncName[] = "CrsMatrix(RCP, size_t " + "[, RCP]): "; Teuchos::RCP graph; try { graph = Teuchos::rcp (new crs_graph_type (rowMap, maxNumEntriesPerRow, - pftype, params)); + params)); } catch (std::exception& e) { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (true, std::runtime_error, "CrsGraph constructor (RCP, " - "size_t, ProfileType[, RCP]) threw an exception: " + "size_t [, RCP]) threw an exception: " << e.what ()); } // myGraph_ not null means that the matrix owns the graph. That's @@ -170,27 +182,39 @@ namespace Tpetra { checkInternalState (); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsMatrix:: CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::ArrayView& numEntPerRowToAlloc, const ProfileType pftype, const Teuchos::RCP& params) : + CrsMatrix ( + rowMap, numEntPerRowToAlloc, params) + {} +#endif + + template + CrsMatrix:: + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::ArrayView& numEntPerRowToAlloc, + const Teuchos::RCP& params) : dist_object_type (rowMap) { const char tfecfFuncName[] = "CrsMatrix(RCP, " - "ArrayView, ProfileType[, RCP]): "; + "ArrayView[, RCP]): "; Teuchos::RCP graph; try { using Teuchos::rcp; graph = rcp(new crs_graph_type(rowMap, numEntPerRowToAlloc, - pftype, params)); + params)); } catch (std::exception& e) { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (true, std::runtime_error, "CrsGraph constructor " - "(RCP, ArrayView, " - "ProfileType[, RCP]) threw an exception: " + "(RCP, ArrayView" + "[, RCP]) threw an exception: " << e.what ()); } // myGraph_ not null means that the matrix owns the graph. That's @@ -202,18 +226,30 @@ namespace Tpetra { checkInternalState (); } - +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsMatrix:: CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const size_t maxNumEntPerRow, const ProfileType pftype, const Teuchos::RCP& params) : + CrsMatrix ( + rowMap, colMap, maxNumEntPerRow, params) + {} +#endif + + template + CrsMatrix:: + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const size_t maxNumEntPerRow, + const Teuchos::RCP& params) : dist_object_type (rowMap) { const char tfecfFuncName[] = "CrsMatrix(RCP, " - "RCP, size_t, ProfileType[, RCP]): "; + "RCP, size_t[, RCP]): "; const char suffix[] = " Please report this bug to the Tpetra developers."; @@ -230,12 +266,12 @@ namespace Tpetra { try { graph = Teuchos::rcp (new crs_graph_type (rowMap, colMap, maxNumEntPerRow, - pftype, params)); + params)); } catch (std::exception& e) { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (true, std::runtime_error, "CrsGraph constructor (RCP, " - "RCP, size_t, ProfileType[, RCP]) threw an " + "RCP, size_t[, RCP]) threw an " "exception: " << e.what ()); } // myGraph_ not null means that the matrix owns the graph. That's @@ -247,28 +283,41 @@ namespace Tpetra { checkInternalState (); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED CrsMatrix:: CrsMatrix (const Teuchos::RCP& rowMap, const Teuchos::RCP& colMap, const Teuchos::ArrayView& numEntPerRowToAlloc, const ProfileType pftype, const Teuchos::RCP& params) : + CrsMatrix ( + rowMap, colMap, numEntPerRowToAlloc, params) + {} +#endif + + template + CrsMatrix:: + CrsMatrix (const Teuchos::RCP& rowMap, + const Teuchos::RCP& colMap, + const Teuchos::ArrayView& numEntPerRowToAlloc, + const Teuchos::RCP& params) : dist_object_type (rowMap) { const char tfecfFuncName[] = "CrsMatrix(RCP, RCP, " - "ArrayView, ProfileType[, RCP]): "; + "ArrayView[, RCP]): "; Teuchos::RCP graph; try { graph = Teuchos::rcp (new crs_graph_type (rowMap, colMap, numEntPerRowToAlloc, - pftype, params)); + params)); } catch (std::exception& e) { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (true, std::runtime_error, "CrsGraph constructor (RCP, " - "RCP, ArrayView, ProfileType[, " + "RCP, ArrayView[, " "RCP]) threw an exception: " << e.what ()); } // myGraph_ not null means that the matrix owns the graph. That's @@ -819,12 +868,15 @@ namespace Tpetra { return getCrsGraphRef ().getComm (); } +#ifdef TPETRA_ENABLE_DEPRECATED_CODE template + TPETRA_DEPRECATED ProfileType CrsMatrix:: getProfileType () const { return this->getCrsGraphRef ().getProfileType (); } +#endif template bool @@ -1198,27 +1250,9 @@ namespace Tpetra { } // Allocate matrix values. - // "Static profile" means that the number of matrix entries in - // each row was fixed at the time the CrsMatrix constructor was - // called. This lets us use 1-D storage for the matrix's - // values. ("1-D storage" means the same as that used by the - // three arrays in the compressed sparse row storage format.) - - if (debug) { - TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC - (this->staticGraph_.is_null (), std::logic_error, - "this->getProfileType() == StaticProfile, but staticGraph_ " - "is null." << suffix); - } - const size_t lclNumRows = this->staticGraph_->getNodeNumRows (); typename Graph::local_graph_device_type::row_map_type k_ptrs = this->staticGraph_->rowPtrsUnpacked_dev_; - TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC - (k_ptrs.extent (0) != lclNumRows+1, std::logic_error, - "With StaticProfile, row offsets array has length " - << k_ptrs.extent (0) << " != (lclNumRows+1) = " - << (lclNumRows+1) << "."); const size_t lclTotalNumEntries = this->staticGraph_->rowPtrsUnpacked_host_(lclNumRows); @@ -1353,22 +1387,16 @@ namespace Tpetra { typedef decltype (myGraph_->k_numRowEntries_) row_entries_type; - // StaticProfile means that the matrix's column indices and - // values are currently stored in a 1-D format, with row offsets - // in rowPtrsUnpacked_ and local column indices in lclIndsUnpacked_wdv. - - // StaticProfile also means that the graph's array of row - // offsets must already be allocated. typename Graph::local_graph_device_type::row_map_type curRowOffsets = myGraph_->rowPtrsUnpacked_dev_; if (debug) { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (curRowOffsets.extent (0) == 0, std::logic_error, - "(StaticProfile branch) curRowOffsets.extent(0) == 0."); + "curRowOffsets.extent(0) == 0."); TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (curRowOffsets.extent (0) != lclNumRows + 1, std::logic_error, - "(StaticProfile branch) curRowOffsets.extent(0) = " + "curRowOffsets.extent(0) = " << curRowOffsets.extent (0) << " != lclNumRows + 1 = " << (lclNumRows + 1) << "."); const size_t numOffsets = curRowOffsets.extent (0); @@ -1376,7 +1404,7 @@ namespace Tpetra { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (numOffsets != 0 && myGraph_->lclIndsUnpacked_wdv.extent (0) != valToCheck, - std::logic_error, "(StaticProfile branch) numOffsets = " << + std::logic_error, "numOffsets = " << numOffsets << " != 0 and myGraph_->lclIndsUnpacked_wdv.extent(0) = " << myGraph_->lclIndsUnpacked_wdv.extent (0) << " != curRowOffsets(" << numOffsets << ") = " << valToCheck << "."); @@ -1403,7 +1431,7 @@ namespace Tpetra { // The matrix's current 1-D storage is "unpacked." This means // the row offsets may differ from what the final row offsets // should be. This could happen, for example, if the user - // specified StaticProfile in the constructor and set an upper + // set an upper // bound on the number of entries per row, but didn't fill all // those entries. if (debug && curRowOffsets.extent (0) != 0) { @@ -1413,14 +1441,14 @@ namespace Tpetra { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (static_cast (valToCheck) != static_cast (valuesUnpacked_wdv.extent (0)), - std::logic_error, "(StaticProfile unpacked branch) Before " + std::logic_error, "(unpacked branch) Before " "allocating or packing, curRowOffsets(" << (numOffsets-1) << ") = " << valToCheck << " != valuesUnpacked_wdv.extent(0)" " = " << valuesUnpacked_wdv.extent (0) << "."); TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (static_cast (valToCheck) != static_cast (myGraph_->lclIndsUnpacked_wdv.extent (0)), - std::logic_error, "(StaticProfile unpacked branch) Before " + std::logic_error, "(unpacked branch) Before " "allocating or packing, curRowOffsets(" << (numOffsets-1) << ") = " << valToCheck << " != myGraph_->lclIndsUnpacked_wdv.extent(0) = " @@ -1461,13 +1489,13 @@ namespace Tpetra { TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (static_cast (k_ptrs.extent (0)) != lclNumRows + 1, std::logic_error, - "(StaticProfile unpacked branch) After packing k_ptrs, " + "(unpacked branch) After packing k_ptrs, " "k_ptrs.extent(0) = " << k_ptrs.extent (0) << " != " "lclNumRows+1 = " << (lclNumRows+1) << "."); const auto valToCheck = getEntryOnHost (k_ptrs, lclNumRows); TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (valToCheck != lclTotalNumEntries, std::logic_error, - "(StaticProfile unpacked branch) After filling k_ptrs, " + "(unpacked branch) After filling k_ptrs, " "k_ptrs(lclNumRows=" << lclNumRows << ") = " << valToCheck << " != total number of entries on the calling process = " << lclTotalNumEntries << "."); @@ -1529,7 +1557,7 @@ namespace Tpetra { range_type (0, lclNumRows), valsPacker); if (debug) { - const char myPrefix[] = "(StaticProfile \"Optimize Storage\"" + const char myPrefix[] = "(\"Optimize Storage\"" "=true branch) After packing, "; TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (k_ptrs.extent (0) == 0, std::logic_error, myPrefix @@ -1574,7 +1602,7 @@ namespace Tpetra { if (debug) { const char myPrefix[] = - "(StaticProfile \"Optimize Storage\"=false branch) "; + "(\"Optimize Storage\"=false branch) "; TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC (myGraph_->rowPtrsUnpacked_dev_.extent (0) == 0, std::logic_error, myPrefix << "myGraph->rowPtrsUnpacked_dev_.extent(0) = 0. This probably means " @@ -1636,13 +1664,9 @@ namespace Tpetra { // The graph has optimized storage when indices are allocated, // myGraph_->k_numRowEntries_ is empty, and there are more than - // zero rows on this process. It's impossible for the graph to - // have dynamic profile (getProfileType() == DynamicProfile) and - // be optimized (isStorageOptimized()). + // zero rows on this process. if (requestOptimizedStorage) { // Free the old, unpacked, unoptimized allocations. - // Change the graph from dynamic to static allocation profile - // Free graph data structures that are only needed for // unpacked 1-D storage. if (verbose) { @@ -1745,12 +1769,12 @@ namespace Tpetra { using row_entries_type = decltype (staticGraph_->k_numRowEntries_); - // StaticProfile means that the matrix's values are currently + // The matrix's values are currently // stored in a 1-D format. However, this format is "unpacked"; // it doesn't necessarily have the same row offsets as indicated // by the ptrs array returned by allocRowPtrs. This could - // happen, for example, if the user specified StaticProfile in - // the constructor and fixed the number of matrix entries in + // happen, for example, if the user + // fixed the number of matrix entries in // each row, but didn't fill all those entries. // // As above, we don't need to keep the "packed" row offsets @@ -2264,8 +2288,8 @@ namespace Tpetra { if (!graph.colMap_.is_null() && graph.isLocallyIndexed()) { // This branch is similar in function to the following branch, but for - // the special case that the target graph is locally indexed (and the - // profile type is StaticProfile). In this case, we cannot simply filter + // the special case that the target graph is locally indexed. + // In this case, we cannot simply filter // out global indices that don't exist on the receiving process and // insert the remaining (global) indices, but we must convert them (the // remaining global indices) to local and call `insertLocalValues`. @@ -4496,7 +4520,6 @@ CrsMatrix:: // return exclude that case. RCP nonlocalRowMap; - // Keep this for CrsGraph's constructor, so we can use StaticProfile. Teuchos::Array numEntPerNonlocalRow (myNumNonlocalRows); { Teuchos::Array myNonlocalGblRows (myNumNonlocalRows); @@ -4551,7 +4574,7 @@ CrsMatrix:: // 3. Use the values and column indices for each nonlocal row, as // stored in nonlocals_, to construct a CrsMatrix corresponding - // to nonlocal rows. We may use StaticProfile, since we have + // to nonlocal rows. We have // exact counts of the number of entries in each nonlocal row. if (verbose) { @@ -4560,8 +4583,7 @@ CrsMatrix:: std::cerr << os.str(); } RCP nonlocalMatrix = - rcp (new crs_matrix_type (nonlocalRowMap, numEntPerNonlocalRow (), - StaticProfile)); + rcp (new crs_matrix_type (nonlocalRowMap, numEntPerNonlocalRow ())); { size_type curPos = 0; for (auto mapIter = nonlocals_.begin (); mapIter != nonlocals_.end (); @@ -7927,8 +7949,7 @@ CrsMatrix:: // If A and B's row Maps are the same, we can compute an upper // bound on the number of entries in each row of C, before // actually computing the sum. A reasonable upper bound is the - // sum of the two entry counts in each row. If we choose this as - // the actual per-row upper bound, we can use static profile. + // sum of the two entry counts in each row. if (A_rowMap->isSameAs (*B_rowMap)) { const LO localNumRows = static_cast (A_rowMap->getNodeNumElements ()); Array C_maxNumEntriesPerRow (localNumRows, 0); @@ -7949,11 +7970,10 @@ CrsMatrix:: } // Construct the result matrix C. if (constructorSublist.is_null ()) { - C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow (), - StaticProfile)); + C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow ())); } else { C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow (), - StaticProfile, constructorSublist)); + constructorSublist)); } // Since A and B have the same row Maps, we could add them // together all at once and merge values before we call @@ -8332,7 +8352,7 @@ CrsMatrix:: // If the user gave us a null destMat, then construct the new // destination matrix. We will replace its column Map later. if (destMat.is_null ()) { - destMat = rcp (new this_type (MyRowMap, 0, StaticProfile, matrixparams)); + destMat = rcp (new this_type (MyRowMap, 0, matrixparams)); } /***************************************************/ diff --git a/packages/tpetra/core/src/Tpetra_FECrsGraph_def.hpp b/packages/tpetra/core/src/Tpetra_FECrsGraph_def.hpp index fce1ddc2cbfd..4869ead9cb68 100644 --- a/packages/tpetra/core/src/Tpetra_FECrsGraph_def.hpp +++ b/packages/tpetra/core/src/Tpetra_FECrsGraph_def.hpp @@ -78,7 +78,7 @@ FECrsGraph(const Teuchos::RCP & ownedRowMap, const Teuchos::RCP & ownedDomainMap, const Teuchos::RCP & ownedRangeMap, const Teuchos::RCP& params): - crs_graph_type(ownedPlusSharedRowMap, maxNumEntriesPerRow, StaticProfile, params), + crs_graph_type(ownedPlusSharedRowMap, maxNumEntriesPerRow, params), ownedRowsImporter_(ownedPlusSharedToOwnedimporter), ownedDomainMap_(ownedDomainMap.is_null() ? ownedRowMap : ownedDomainMap), ownedRangeMap_(ownedRangeMap.is_null() ? ownedRowMap : ownedRangeMap) @@ -114,7 +114,7 @@ FECrsGraph (const Teuchos::RCP & ownedRowMap, const Teuchos::RCP & ownedDomainMap, const Teuchos::RCP & ownedRangeMap, const Teuchos::RCP& params): - crs_graph_type( ownedPlusSharedRowMap, numEntPerRow, StaticProfile, params), + crs_graph_type( ownedPlusSharedRowMap, numEntPerRow, params), ownedRowsImporter_(ownedPlusSharedToOwnedimporter), ownedDomainMap_(ownedDomainMap.is_null() ? ownedRowMap : ownedDomainMap), ownedRangeMap_(ownedRangeMap.is_null() ? ownedRowMap : ownedRangeMap) @@ -152,7 +152,7 @@ FECrsGraph(const Teuchos::RCP & ownedRowMap, const Teuchos::RCP & ownedDomainMap, const Teuchos::RCP & ownedRangeMap, const Teuchos::RCP& params): - crs_graph_type(ownedPlusSharedRowMap, ownedPlusSharedColMap,maxNumEntriesPerRow, StaticProfile, params), + crs_graph_type(ownedPlusSharedRowMap, ownedPlusSharedColMap,maxNumEntriesPerRow, params), ownedRowsImporter_(ownedPlusSharedToOwnedimporter), ownedDomainMap_(ownedDomainMap.is_null() ? ownedRowMap : ownedDomainMap), ownedRangeMap_(ownedRangeMap.is_null() ? ownedRowMap : ownedRangeMap) @@ -189,7 +189,7 @@ FECrsGraph (const Teuchos::RCP & ownedRowMap, const Teuchos::RCP & ownedDomainMap, const Teuchos::RCP & ownedRangeMap, const Teuchos::RCP& params): - crs_graph_type(ownedPlusSharedRowMap, ownedPlusSharedColMap, numEntPerRow, StaticProfile, params), + crs_graph_type(ownedPlusSharedRowMap, ownedPlusSharedColMap, numEntPerRow, params), ownedRowsImporter_(ownedPlusSharedToOwnedimporter), ownedDomainMap_(ownedDomainMap.is_null() ? ownedRowMap : ownedDomainMap), ownedRangeMap_(ownedRangeMap.is_null() ? ownedRowMap : ownedRangeMap) diff --git a/packages/tpetra/core/src/Tpetra_RowMatrix_def.hpp b/packages/tpetra/core/src/Tpetra_RowMatrix_def.hpp index ad4f52c71ed1..40a7e0eec4e6 100644 --- a/packages/tpetra/core/src/Tpetra_RowMatrix_def.hpp +++ b/packages/tpetra/core/src/Tpetra_RowMatrix_def.hpp @@ -201,11 +201,10 @@ namespace Tpetra { } // Construct the result matrix C. if (constructorSublist.is_null ()) { - C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow (), - StaticProfile)); + C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow ())); } else { C = rcp (new crs_matrix_type (C_rowMap, C_maxNumEntriesPerRow (), - StaticProfile, constructorSublist)); + constructorSublist)); } // Since A and B have the same row Maps, we could add them // together all at once and merge values before we call diff --git a/packages/tpetra/core/test/Block/BlockCrsMatrix.cpp b/packages/tpetra/core/test/Block/BlockCrsMatrix.cpp index 3f2857822cce..e33f75f88ef5 100644 --- a/packages/tpetra/core/test/Block/BlockCrsMatrix.cpp +++ b/packages/tpetra/core/test/Block/BlockCrsMatrix.cpp @@ -99,7 +99,7 @@ namespace { // We just want to check that the constructors of BlockCrsMatrix // work. out << "Creating mesh graph" << endl; - graph_type graph (meshRowMapPtr, 0, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, 0); graph.fillComplete (); // Test the default constructor. We can't wrap this in a @@ -205,7 +205,7 @@ namespace { out << "Creating mesh graph" << endl; const size_t maxNumEntPerRow = 2; - graph_type graph (meshRowMapPtr, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, maxNumEntPerRow); // Fill the graph. gids_type gblColInds ("gblColIds",maxNumEntPerRow); @@ -911,7 +911,7 @@ namespace { out << "Creating mesh graph" << endl; const size_t maxNumEntPerRow = 2; - graph_type graph (meshRowMapPtr, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, maxNumEntPerRow); // Fill the graph. Teuchos::Array gblColInds (maxNumEntPerRow); @@ -1043,7 +1043,7 @@ namespace { out << "Creating mesh graph" << endl; const size_t maxNumEntPerRow = 2; - graph_type graph (meshRowMapPtr, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, maxNumEntPerRow); // Fill the graph. Teuchos::Array gblColInds (maxNumEntPerRow); @@ -1276,7 +1276,7 @@ namespace { // Make a graph. It happens to have two entries per row. out << "Creating mesh graph" << endl; - graph_type graph (meshRowMapPtr, 2, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, 2); if (meshRowMapPtr->getNodeNumElements () > 0) { const GO myMinGblRow = meshRowMapPtr->getMinGlobalIndex (); @@ -1401,7 +1401,7 @@ namespace { // Make a graph. It happens to have two entries per row. out << "Creating mesh graph" << endl; - graph_type graph (meshRowMapPtr, 2, Tpetra::StaticProfile); + graph_type graph (meshRowMapPtr, 2); if (meshRowMapPtr->getNodeNumElements () > 0) { const GO myMinGblRow = meshRowMapPtr->getMinGlobalIndex (); @@ -1584,7 +1584,7 @@ namespace { out << "Create graph with overlapping mesh row Map" << endl; // Make a graph. It happens to have two entries per row. - graph_type overlapGraph (overlapMeshRowMapPtr, 2, Tpetra::StaticProfile); + graph_type overlapGraph (overlapMeshRowMapPtr, 2); if (overlapMeshRowMapPtr->getNodeNumElements () > 0) { const GO myMinGblRow = overlapMeshRowMapPtr->getMinGlobalIndex (); const GO myMaxGblRow = overlapMeshRowMapPtr->getMaxGlobalIndex (); @@ -1618,7 +1618,7 @@ namespace { RCP graph; try { out << "Create empty graph with nonoverlapping mesh row Map" << endl; - graph = rcp (new graph_type (meshRowMapPtr, 0, Tpetra::StaticProfile)); + graph = rcp (new graph_type (meshRowMapPtr, 0)); out << "Create Export from overlap to nonoverlap mesh row Map" << endl; theExport = rcp (new export_type (overlapMeshRowMapPtr, meshRowMapPtr)); diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_Issue601.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_Issue601.cpp index b640b3b65f38..99a4654670b0 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_Issue601.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_Issue601.cpp @@ -97,11 +97,9 @@ namespace { // (anonymous) RCP rowMap = rcp (new map_type (INV, myGblRowInds (), indexBase, comm)); - const Tpetra::ProfileType profileTypes[1] = {Tpetra::StaticProfile}; bool insertLocalEntryValues[] = { true, false }; - // Test both dynamic and static profile. - for (Tpetra::ProfileType profileType : profileTypes) { + { Teuchos::OSTab tab2 (out); @@ -116,7 +114,7 @@ namespace { // (anonymous) Teuchos::OSTab tab3 (out); const size_t maxNumEntPerRow = static_cast (insertLocalEntry ? 2 : 1); - crs_graph_type G (rowMap, maxNumEntPerRow, profileType); + crs_graph_type G (rowMap, maxNumEntPerRow); const GO gblRow0 = static_cast (myRank); const GO gblRow1 = static_cast ((myRank + 1) % numProcs); @@ -211,7 +209,7 @@ namespace { // (anonymous) return; } } // insertLocalEntry - } // profileType + } } // diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_ReindexColumns.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_ReindexColumns.cpp index a678a86ef8cf..21c24c927816 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_ReindexColumns.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_ReindexColumns.cpp @@ -102,7 +102,7 @@ namespace { "to be contiguous, but is not."); const size_t maxNumEntPerRow = 3; - graph_type graph (rowMap, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (rowMap, maxNumEntPerRow); // Make the usual tridiagonal graph. Let the graph create its own // column Map. We'll use that column Map to create a new column @@ -561,7 +561,7 @@ namespace { "to be contiguous, but is not."); const size_t maxNumEntPerRow = 3; - graph_type graph (rowMap, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (rowMap, maxNumEntPerRow); // Make the usual tridiagonal graph. Let the graph create its own // column Map. We'll use that column Map to create a new column diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_StaticImportExport.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_StaticImportExport.cpp index 6591bf3fc383..496a84561aa1 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_StaticImportExport.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_StaticImportExport.cpp @@ -81,7 +81,7 @@ generate_crs_graph(const RCP>& map) using graph_type = Tpetra::CrsGraph; // Create a Tpetra::Matrix using the Map, with dynamic allocation. - auto A = rcp(new graph_type(map, 3, Tpetra::StaticProfile)); + auto A = rcp(new graph_type(map, 3)); // const size_t numMyElements = map->getNodeNumElements (); // The list of global elements owned by this MPI process. @@ -157,7 +157,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(CrsGraph, ImportToStaticGraph, LO, GO, NT) Tpetra::Details::Behavior::enable_verbose_behavior(); // Make a new sparse graph whose row map is the global Map. out << prefix << "Creating empty graph from global map.\n"; - B = rcp(new graph_type(global_map, 0, Tpetra::StaticProfile)); + B = rcp(new graph_type(global_map, 0)); out << prefix << "Empty graph from global map created.\n"; // Redistribute the data, NOT in place, from graph A (which lives @@ -259,7 +259,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(CrsGraph, ImportToStaticGraphLocal, LO, GO, NT Tpetra::Details::Behavior::enable_verbose_behavior(); // Make a new sparse graph whose row map is the global Map. out << prefix << "Creating empty graph from proc 0 map.\n"; - auto B = graph_type(proc_zero_map, 0, Tpetra::StaticProfile); + auto B = graph_type(proc_zero_map, 0); out << prefix << "Empty graph from proc 0 map created.\n"; // Redistribute the data, NOT in place, from graph A (which lives @@ -276,12 +276,12 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(CrsGraph, ImportToStaticGraphLocal, LO, GO, NT using export_type = Tpetra::Export; export_type exporter1(proc_zero_map, global_map); comm->barrier(); - auto B = graph_type(global_map, 0, Tpetra::StaticProfile); + auto B = graph_type(global_map, 0); B.doExport(*A, exporter1, Tpetra::INSERT); B.fillComplete(); export_type exporter2(global_map, global_map); - auto C = graph_type(global_map, 0, Tpetra::StaticProfile); + auto C = graph_type(global_map, 0); C.doExport(B, exporter2, Tpetra::INSERT); C.fillComplete(); } diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests0.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests0.cpp index f769d3387e06..303e27bc4188 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests0.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests0.cpp @@ -45,8 +45,6 @@ namespace { // (anonymous) - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Tpetra::TestingUtilities::arcp_from_view; using Teuchos::arcp; using Teuchos::arcpClone; @@ -237,7 +235,7 @@ namespace { // (anonymous) // send in a parameterlist, check the defaults RCP params = parameterList(); // create static-profile graph, fill-complete without inserting (and therefore, without allocating) - GRPH graph (map, 3, StaticProfile); + GRPH graph (map, 3); for (GO i = map->getMinGlobalIndex(); i <= map->getMaxGlobalIndex(); ++i) { graph.insertGlobalIndices (i, tuple (i)); } @@ -252,7 +250,6 @@ namespace { // (anonymous) graph.fillComplete(params); TEST_EQUALITY_CONST(params->get("Optimize Storage"), true); TEST_EQUALITY(graph.getNodeNumEntries(), 0); - TEST_EQUALITY_CONST(graph.getProfileType(), StaticProfile); TEST_EQUALITY_CONST(graph.isStorageOptimized(), true); int lclSuccess = success ? 1 : 0; @@ -358,9 +355,8 @@ namespace { // (anonymous) RCP params = parameterList(); for (int T=0; T<4; ++T) { if ( (T & 1) != 1 ) continue; - ProfileType pftype = StaticProfile; params->set("Optimize Storage",((T & 2) == 2)); - GRAPH trigraph(rmap,cmap, ginds.size(),pftype); // only allocate as much room as necessary + GRAPH trigraph(rmap,cmap, ginds.size()); // only allocate as much room as necessary size_t numindices; { @@ -380,12 +376,10 @@ namespace { // (anonymous) trigraph.insertGlobalIndices(myrowind,ginds(j,1)); } TEST_EQUALITY( trigraph.getNumEntriesInLocalRow(0), trigraph.getNumAllocatedEntriesInLocalRow(0) ); // test that we only allocated as much room as necessary - // If StaticProfile, then attempt to insert one additional entry + // Attempt to insert one additional entry // in my row that is not already in the row, and verify that it // throws an exception. - if (pftype == StaticProfile) { - TEST_THROW( trigraph.insertGlobalIndices(myrowind,tuple(myrowind+2)), std::runtime_error ); - } + TEST_THROW( trigraph.insertGlobalIndices(myrowind,tuple(myrowind+2)), std::runtime_error ); trigraph.fillComplete(params); // check that inserting global entries throws (inserting local entries is still allowed) { @@ -433,7 +427,7 @@ namespace { // (anonymous) // add too many entries to a static graph // let node i contribute to row i+1, where node the last node contributes to row 0 - GRAPH diaggraph(map,1,StaticProfile); + GRAPH diaggraph(map,1); GO grow = myRank; Array colinds(1); colinds[0] = grow; @@ -625,13 +619,12 @@ namespace { // (anonymous) for (int T=0; T<4; ++T) { if ( (T & 1) != 1 ) continue; - ProfileType pftype = StaticProfile; RCP params = parameterList (); params->set("Optimize Storage",((T & 2) == 2)); // create a diagonal graph, but where only my middle row has an entry ArrayRCP toalloc = arcpClone( tuple(0,1,0) ); - GRAPH ddgraph(map, toalloc (), pftype); + GRAPH ddgraph(map, toalloc ()); ddgraph.insertGlobalIndices(mymiddle, tuple(mymiddle)); { // before globalAssemble(), there should be one local entry on middle, none on the others @@ -640,11 +633,9 @@ namespace { // (anonymous) ddgraph.getGlobalRowView(mymiddle ,myrow_gbl); TEST_COMPARE_ARRAYS( myrow_gbl, tuple(mymiddle) ); ddgraph.getGlobalRowView(mymiddle+1,myrow_gbl); TEST_EQUALITY( myrow_gbl.size(), 0 ); } - if (pftype == StaticProfile) { // no room for more, on any row - TEST_THROW( ddgraph.insertGlobalIndices(mymiddle-1,tuple(mymiddle+1)), std::runtime_error ); - TEST_THROW( ddgraph.insertGlobalIndices(mymiddle ,tuple(mymiddle+1)), std::runtime_error ); - TEST_THROW( ddgraph.insertGlobalIndices(mymiddle+1,tuple(mymiddle+1)), std::runtime_error ); - } + TEST_THROW( ddgraph.insertGlobalIndices(mymiddle-1,tuple(mymiddle+1)), std::runtime_error ); + TEST_THROW( ddgraph.insertGlobalIndices(mymiddle ,tuple(mymiddle+1)), std::runtime_error ); + TEST_THROW( ddgraph.insertGlobalIndices(mymiddle+1,tuple(mymiddle+1)), std::runtime_error ); ddgraph.fillComplete(params); // after fillComplete(), there should be a single entry on my middle, corresponding to the diagonal, none on the others { @@ -693,8 +684,7 @@ namespace { // (anonymous) Teuchos::OSTab tab1 (out); - const Tpetra::ProfileType profileTypes[1] = {Tpetra::StaticProfile}; - for (ProfileType pftype : profileTypes) { + { Teuchos::OSTab tab2 (out); for (bool optimizeStorage : {false, true}) { out << "Optimize Storage: " << (optimizeStorage ? "true" : "false") @@ -713,7 +703,7 @@ namespace { // (anonymous) // contributed by a single off-node contribution, no // filtering. let node i contribute to row i+1, where node // the last node contributes to row 0 - GRAPH diaggraph (map, 1, pftype); + GRAPH diaggraph (map, 1); GO grow = myRank+1; if (as (grow) == numProcs) { grow = 0; @@ -735,11 +725,11 @@ namespace { // (anonymous) TEST_COMPARE_ARRAYS( myrow_gbl, tuple (myrowind) ); } - if (pftype == StaticProfile) { // no room for more + { // no room for more out << "Attempt to insert global column index " << (myrowind+1) << " into global row " << myrowind << "; it should throw, because the graph" - << " is StaticProfile, has an upper bound of one entry " + << " has an upper bound of one entry " << "per row, and already has a different column index " << grow << " in this row." << endl; @@ -780,7 +770,7 @@ namespace { // (anonymous) // contributions for column i of the graph: (i-1,i), (i,i), // (i+1,i). allocate only as much space as we need. some // hacking here to support this test when numProcs == 1 or 2 - GRAPH ngraph(map,3,pftype); + GRAPH ngraph(map,3); Array grows(3); grows[0] = (numProcs+myRank-1) % numProcs; // my left neighbor grows[1] = (numProcs+myRank ) % numProcs; // myself @@ -795,8 +785,8 @@ namespace { // (anonymous) out << "Calling globalAssemble()" << endl; ngraph.globalAssemble(); TEST_EQUALITY( ngraph.getNumEntriesInLocalRow(0), - ( numProcs == 1 && pftype == StaticProfile ? 1 : - ngraph.getNumAllocatedEntriesInLocalRow(0) )); + (numProcs == 1 ? 1 + : ngraph.getNumAllocatedEntriesInLocalRow(0) )); out << "Calling fillComplete(params)" << endl; ngraph.fillComplete (params); @@ -843,7 +833,7 @@ namespace { // (anonymous) STD_TESTS(ngraph); } } // optimizeStorage - } // pftype + } // All procs fail if any node fails int globalSuccess_int = -1; diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests1.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests1.cpp index 34ff87cfdcac..a898894b59ba 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests1.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests1.cpp @@ -46,8 +46,6 @@ namespace { // (anonymous) using Tpetra::TestingUtilities::getDefaultComm; - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Teuchos::arcp; using Teuchos::arcpClone; using Teuchos::Array; @@ -131,7 +129,7 @@ namespace { // (anonymous) { // create static-profile graph, fill-complete without inserting // (and therefore, without allocating) - GRAPH graph(map,1,StaticProfile); + GRAPH graph(map,1); graph.fillComplete(); } @@ -342,7 +340,7 @@ namespace { // (anonymous) RCP cmap = rcp (new map_type (INVALID, numLocal, 0, comm)); // must allocate enough for all submitted indices. - RCP G = rcp(new GRAPH(rmap,cmap,2,StaticProfile) ); + RCP G = rcp(new GRAPH(rmap,cmap,2) ); TEST_EQUALITY_CONST( G->hasColMap(), true ); const GO myrowind = rmap->getGlobalElement(0); @@ -389,7 +387,7 @@ namespace { // (anonymous) // create Map RCP map = rcp (new map_type (INVALID, 3, 0, comm)); { - GRAPH graph(map,1,StaticProfile); + GRAPH graph(map,1); // test labeling const std::string lbl("graphA"); std::string desc1 = graph.description(); @@ -400,7 +398,7 @@ namespace { // (anonymous) TEST_EQUALITY( graph.getObjectLabel(), lbl ); } { - GRAPH graph(map,1,StaticProfile); + GRAPH graph(map,1); // test describing at different verbosity levels if (myRank==0) out << "Describing with verbosity VERB_DEFAULT..." << endl; graph.describe(out); @@ -546,7 +544,7 @@ namespace { // (anonymous) colind[0] = Teuchos::as(0); colind[1] = Teuchos::as(1); - RCP G = rcp(new GRAPH(rmap,rmap,0,StaticProfile) ); + RCP G = rcp(new GRAPH(rmap,rmap,0) ); TEST_NOTHROW( G->setAllIndices(rowptr,colind) ); TEST_EQUALITY_CONST( G->hasColMap(), true ); @@ -571,7 +569,7 @@ namespace { // (anonymous) const size_t num_local = 1; RCP row_map = rcp(new map_type(Invalid, num_local, 0, comm)); - RCP G = rcp(new graph_type(row_map, 1, StaticProfile)); + RCP G = rcp(new graph_type(row_map, 1)); auto row = row_map->getGlobalElement(0); G->insertGlobalIndices(row, tuple(row, row, row, row)); G->insertGlobalIndices(row, tuple(row, row, row, row)); @@ -609,7 +607,7 @@ namespace { // (anonymous) colind[0] = Teuchos::as(0); colind[1] = Teuchos::as(1); - RCP G = rcp(new GRAPH(rmap,cmap,0,StaticProfile) ); + RCP G = rcp(new GRAPH(rmap,cmap,0) ); TEST_NOTHROW( G->setAllIndices(rowptr,colind) ); TEST_EQUALITY_CONST( G->hasColMap(), true ); diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests_Swap.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests_Swap.cpp index 80670e054fd5..26967669045a 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests_Swap.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnitTests_Swap.cpp @@ -341,7 +341,7 @@ class crsGraph_Swap_Tester } } - RCP output_graph(new graph_type(row_map, num_ent_per_row (), Tpetra::StaticProfile)); + RCP output_graph(new graph_type(row_map, num_ent_per_row ())); for(auto& r: gbl_rows) { @@ -412,7 +412,6 @@ using Teuchos::VERB_HIGH; using Teuchos::VERB_LOW; using Teuchos::VERB_MEDIUM; using Teuchos::VERB_NONE; -using Tpetra::StaticProfile; using Tpetra::TestingUtilities::getDefaultComm; typedef Tpetra::global_size_t GST; diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnpackIntoStaticGraph.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnpackIntoStaticGraph.cpp index c45620c22e2e..714d659b5902 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_UnpackIntoStaticGraph.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_UnpackIntoStaticGraph.cpp @@ -97,7 +97,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(CrsGraph, PackThenUnpackAndCombine, LO, GO, NT auto num_loc_rows = static_cast(4); const auto num_gbl_rows = Tpetra::global_size_t(num_loc_rows*comm->getSize()); auto map1 = rcp(new map_type(num_gbl_rows, 0, comm)); - auto A = rcp(new graph_type(map1, 1, Tpetra::StaticProfile)); + auto A = rcp(new graph_type(map1, 1)); for (LO loc_row=0; loc_rowgetGlobalElement(loc_row); A->insertGlobalIndices(gbl_row, tuple(gbl_row)); @@ -105,7 +105,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL(CrsGraph, PackThenUnpackAndCombine, LO, GO, NT // Off diagonal graph with half-bandwidth=1 and no diagonal entries out << "Building second graph" << endl; - auto B = rcp(new graph_type(map1, 2)); // could use StaticProfile + auto B = rcp(new graph_type(map1, 2)); for (LO loc_row=0; loc_rowgetGlobalElement(loc_row); // B[0,0:1] = [-, 1] diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_getNumDiags.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_getNumDiags.cpp index 65d92b9de9a4..49dbd6df8267 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_getNumDiags.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_getNumDiags.cpp @@ -90,7 +90,7 @@ namespace { // (anonymous) const GO actualLocalNumDiags = lclNumRows; const GO actualGlobalNumDiags = gblNumRows; - crs_graph_type graph (rowMap, 1, Tpetra::StaticProfile); + crs_graph_type graph (rowMap, 1); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { const GO gblRow = rowMap->getGlobalElement (lclRow); const GO gblCol = gblRow; @@ -131,7 +131,7 @@ namespace { // (anonymous) const GO actualGlobalNumDiags = gblNumRows; RCP colMap = rowMap; - crs_graph_type graph (rowMap, colMap, 1, Tpetra::StaticProfile); + crs_graph_type graph (rowMap, colMap, 1); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { const LO lclCol = lclRow; graph.insertLocalIndices (lclRow, 1, &lclCol); @@ -187,7 +187,7 @@ namespace { // (anonymous) gblColInds.size (), indexBase, comm)); } - crs_graph_type graph (rowMap, colMap, 1, Tpetra::StaticProfile); + crs_graph_type graph (rowMap, colMap, 1); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { // Not actually a diagonal entry, since the global indices differ. const LO lclCol = lclRow; diff --git a/packages/tpetra/core/test/CrsGraph/CrsGraph_insertGlobalIndicesFiltered.cpp b/packages/tpetra/core/test/CrsGraph/CrsGraph_insertGlobalIndicesFiltered.cpp index f569d81bb624..502b8f14e525 100644 --- a/packages/tpetra/core/test/CrsGraph/CrsGraph_insertGlobalIndicesFiltered.cpp +++ b/packages/tpetra/core/test/CrsGraph/CrsGraph_insertGlobalIndicesFiltered.cpp @@ -134,9 +134,8 @@ namespace { // (anonymous) // Buffer for storing output of getGlobalRowCopy. gids_type gblColIndsBuf("gcids",maxNumEntPerRow); - const Tpetra::ProfileType profileTypes[1] = {Tpetra::StaticProfile}; - for (auto profileType_src : profileTypes) { - crs_graph_type graph_src (rowMap_src, maxNumEntPerRow, profileType_src); + { + crs_graph_type graph_src (rowMap_src, maxNumEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { const GO gblRow = rowMap_src->getGlobalElement (lclRow); // Every row of the source graph gets the same column indices. @@ -144,10 +143,10 @@ namespace { // (anonymous) } graph_src.fillComplete (domMap, ranMap); - for (auto profileType_tgt : profileTypes) { + { // Filtering only happens if the target graph has a column // Map, so we must give it a column Map. - crs_graph_type graph_tgt (rowMap_tgt, colMap_tgt, maxNumEntPerRow, profileType_tgt); + crs_graph_type graph_tgt (rowMap_tgt, colMap_tgt, maxNumEntPerRow); // mfh 20 Jul 2017: If we clone this test in order to test // CrsMatrix column index filtering, then we should include @@ -167,8 +166,8 @@ namespace { // (anonymous) } } } - } // for each target graph profile type - } // for each source graph profile type + } + } // Make sure that the test succeeded on all processes. lclSuccess = success ? 1 : 0; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_GetRowCopy.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_GetRowCopy.cpp index 1bd18d60947e..9a8eadb71634 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_GetRowCopy.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_GetRowCopy.cpp @@ -42,7 +42,7 @@ */ // Test Tpetra::CrsMatrix::get{Global,Local}RowCopy for the case where -// the matrix has StaticProfile, but has never yet been made fill +// the matrix has never yet been made fill // complete. #include "Tpetra_TestingUtilities.hpp" @@ -91,7 +91,7 @@ namespace { indexBase, comm)); // Leave room for three locally owned entries per row. // We will only fill in two entries per row. - crs_matrix_type A (rowMap, 3, Tpetra::StaticProfile); + crs_matrix_type A (rowMap, 3); const GO gblNumCols = gblNumRows; out << "Fill the matrix" << endl; @@ -197,7 +197,7 @@ namespace { // Leave room for three locally owned entries per row. // We will only fill in two entries per row. - crs_matrix_type A (rowMap, colMap, 3, Tpetra::StaticProfile); + crs_matrix_type A (rowMap, colMap, 3); out << "Fill the matrix" << endl; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_LeftRightScale.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_LeftRightScale.cpp index a15a944cfb26..602151163ca8 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_LeftRightScale.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_LeftRightScale.cpp @@ -93,8 +93,6 @@ namespace { using Tpetra::createUniformContigMapWithNode; using Tpetra::createVector; using Tpetra::createCrsMatrix; - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Tpetra::OptimizeOption; using Tpetra::GloballyDistributed; using Tpetra::INSERT; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_MultipleFillCompletes.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_MultipleFillCompletes.cpp index 9cfd55d8118f..85a29b48892f 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_MultipleFillCompletes.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_MultipleFillCompletes.cpp @@ -93,7 +93,7 @@ namespace { if (myRank == 0) { cerr << " Create a matrix with room for 2 entries in each row" << endl; } - MAT matrix (map, 2, Tpetra::StaticProfile); // room for two on each row + MAT matrix (map, 2); // room for two on each row if (myRank == 0) { cerr << " Test insertGlobalValues does not throw " diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NodeConversion.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NodeConversion.cpp index 1d2cfb11e317..0cfd5cc8d3c3 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NodeConversion.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NodeConversion.cpp @@ -77,8 +77,6 @@ namespace { using Tpetra::createUniformContigMapWithNode; using Tpetra::createVector; using Tpetra::createCrsMatrix; - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Tpetra::OptimizeOption; using Tpetra::DoOptimizeStorage; using Tpetra::DoNotOptimizeStorage; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalAfterResume.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalAfterResume.cpp index f4c11f8aaec2..19033e3b2b84 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalAfterResume.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalAfterResume.cpp @@ -160,8 +160,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( CrsMatrix, NonlocalAfterResume, LO, GO, Scala //---------------------------------------------------------------------- // put in diagonal, locally //---------------------------------------------------------------------- - Tpetra::ProfileType pftype = Tpetra::StaticProfile; - Tpetra::CrsMatrix matrix(rmap,cmap,3,pftype); + Tpetra::CrsMatrix matrix(rmap,cmap,3); for (GO r=rmap->getMinGlobalIndex(); r <= rmap->getMaxGlobalIndex(); ++r) { matrix.insertGlobalValues(r,tuple(r),tuple(ST::one())); } diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto.cpp index 8e6674b7025b..929510230330 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto.cpp @@ -195,7 +195,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( CrsMatrix, NonlocalSumInto, LocalOrdinalType, RCP graph; { // We have a good upper bound for the number of entries per row, so use static profile. - RCP nonconstGraph (new crs_graph_type (rowMap, 2, Tpetra::StaticProfile)); + RCP nonconstGraph (new crs_graph_type (rowMap, 2)); TEUCHOS_TEST_FOR_EXCEPTION(globalMinRow >= globalMaxRow, std::logic_error, "This test only works if globalMinRow < globalMaxRow."); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto_Ignore.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto_Ignore.cpp index c96d0db780fd..1a6efb01d03b 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto_Ignore.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_NonlocalSumInto_Ignore.cpp @@ -210,7 +210,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL( CrsMatrix, NonlocalSumInto_Ignore, LocalOrdin // is in the CrsMatrix_NonlocalSumInto.cpp test) so that there // would actually be room for the incoming entries from remote // calls to sumIntoGlobalValues(). - RCP nonconstGraph (new crs_graph_type (rowMap, 2, Tpetra::StaticProfile)); + RCP nonconstGraph (new crs_graph_type (rowMap, 2)); TEUCHOS_TEST_FOR_EXCEPTION(globalMinRow >= globalMaxRow, std::logic_error, "This test only works if globalMinRow < globalMaxRow."); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReindexColumns.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReindexColumns.cpp index cd82eea8fbfe..64c1aa4da47c 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReindexColumns.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReindexColumns.cpp @@ -102,7 +102,7 @@ namespace { "to be contiguous, but is not."); const size_t maxNumEntPerRow = 3; - graph_type graph (rowMap, maxNumEntPerRow, Tpetra::StaticProfile); + graph_type graph (rowMap, maxNumEntPerRow); // Make the usual tridiagonal graph. Let the graph create its own // column Map. We'll use that column Map to create a new column diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceDomainMapAndImporter.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceDomainMapAndImporter.cpp index 735e41e50c08..eec31e830020 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceDomainMapAndImporter.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceDomainMapAndImporter.cpp @@ -80,8 +80,6 @@ namespace { using Tpetra::global_size_t; using Tpetra::createContigMapWithNode; using Tpetra::createVector; - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Tpetra::OptimizeOption; using Tpetra::DoOptimizeStorage; using Tpetra::DoNotOptimizeStorage; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceRangeMapAndExporter.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceRangeMapAndExporter.cpp index 1496d0deae2c..015a0f65b25b 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceRangeMapAndExporter.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_ReplaceRangeMapAndExporter.cpp @@ -80,8 +80,6 @@ namespace { using Tpetra::global_size_t; using Tpetra::createContigMapWithNode; using Tpetra::createVector; - using Tpetra::ProfileType; - using Tpetra::StaticProfile; using Tpetra::OptimizeOption; using Tpetra::DoOptimizeStorage; using Tpetra::DoNotOptimizeStorage; diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_StaticImportExport.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_StaticImportExport.cpp index fa9639fa2b34..ee7afdc9347f 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_StaticImportExport.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_StaticImportExport.cpp @@ -85,7 +85,7 @@ generate_crs_matrix(const RCP>& map) const SC neg_one = static_cast(-1.0); // Create a Tpetra::Matrix using the Map, with dynamic allocation. - auto A = rcp(new matrix_type(map, 3, Tpetra::StaticProfile)); + auto A = rcp(new matrix_type(map, 3)); // const size_t numMyElements = map->getNodeNumElements (); // The list of global elements owned by this MPI process. @@ -161,7 +161,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(CrsMatrix, ImportToStaticMatrix, SC, LO, GO, N Tpetra::Details::Behavior::enable_verbose_behavior(); // Make a new sparse matrix whose row map is the global Map. out << prefix << "Creating empty matrix from global map.\n"; - B = rcp(new matrix_type(global_map, 0, Tpetra::StaticProfile)); + B = rcp(new matrix_type(global_map, 0)); out << prefix << "Empty matrix from global map created.\n"; // Redistribute the data, NOT in place, from matrix A (which lives @@ -263,7 +263,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(CrsMatrix, ImportToStaticMatrixLocal, SC, LO, Tpetra::Details::Behavior::enable_verbose_behavior(); // Make a new sparse matrix whose row map is the global Map. out << prefix << "Creating empty matrix from proc 0 map.\n"; - auto B = matrix_type(proc_zero_map, 0, Tpetra::StaticProfile); + auto B = matrix_type(proc_zero_map, 0); out << prefix << "Empty matrix from proc 0 map created.\n"; // Redistribute the data from matrix A (which lives @@ -280,7 +280,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(CrsMatrix, ImportToStaticMatrixLocal, SC, LO, export_type exporter1(proc_zero_map, global_map); comm->barrier(); out << prefix << "Creating empty matrix from global map.\n"; - auto B = matrix_type(global_map, 0, Tpetra::StaticProfile); + auto B = matrix_type(global_map, 0); B.doExport(*A, exporter1, Tpetra::INSERT); B.fillComplete(); @@ -288,7 +288,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(CrsMatrix, ImportToStaticMatrixLocal, SC, LO, export_type exporter2(global_map, global_map); comm->barrier(); out << prefix << "Creating another empty matrix from global map.\n"; - auto C = matrix_type(global_map, 0, Tpetra::StaticProfile); + auto C = matrix_type(global_map, 0); out << prefix << "Exporting between global map matrices\n"; C.doExport(B, exporter2, Tpetra::INSERT); C.fillComplete(); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_TransformValues.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_TransformValues.cpp index 53fbac871f5e..5ee1919ce884 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_TransformValues.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_TransformValues.cpp @@ -80,7 +80,7 @@ namespace { // (anonymous) RCP rowMap = rcp (new map_type (gblNumRows, lclNumRows, indexBase, comm)); - crs_matrix_type matrix (rowMap, 1, Tpetra::StaticProfile); + crs_matrix_type matrix (rowMap, 1); out << "Fill matrix by calling insertGlobalValues" << endl; if (rowMap->getNodeNumElements () != 0) { @@ -232,7 +232,7 @@ namespace { // (anonymous) RCP rowMap = rcp (new map_type (gblNumRows, lclNumRows, indexBase, comm)); - crs_matrix_type matrix (rowMap, 1, Tpetra::StaticProfile); + crs_matrix_type matrix (rowMap, 1); out << "Fill matrix by calling insertGlobalValues" << endl; if (rowMap->getNodeNumElements () != 0) { diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests.cpp index 3e3f4119591b..f3146663534a 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests.cpp @@ -114,13 +114,12 @@ namespace { // (anonymous) { RCPMap map = createContigMapWithNode(INVALID,numLocal,comm); MV mv(map,1); - zero = rcp( new MAT(map,0,TPETRA_DEFAULT_PROFILE_TYPE) ); + zero = rcp( new MAT(map,0) ); TEST_THROW(zero->apply(mv,mv), std::runtime_error); # if defined(HAVE_TPETRA_THROW_EFFICIENCY_WARNINGS) // throw exception because we required increased allocation TEST_THROW(zero->insertGlobalValues(map->getMinGlobalIndex(),tuple(0),tuple(ST::one())), std::runtime_error); # endif - TEST_ASSERT( zero->getProfileType() == TPETRA_DEFAULT_PROFILE_TYPE ); zero->fillComplete(); } STD_TESTS((*zero)); @@ -184,11 +183,10 @@ namespace { // (anonymous) GO base = numLocal*myImageID; RCP > eye; { - RCP eye_crs = rcp(new MAT(map,numLocal,TPETRA_DEFAULT_PROFILE_TYPE)); + RCP eye_crs = rcp(new MAT(map,numLocal)); for (size_t i=0; iinsertGlobalValues(base+i,tuple(base+i),tuple(ST::one())); } - TEST_ASSERT( eye_crs->getProfileType() == TPETRA_DEFAULT_PROFILE_TYPE ); eye_crs->fillComplete(); eye = eye_crs; } diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests2.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests2.cpp index ffddcfc6574a..c7357c878a0f 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests2.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests2.cpp @@ -257,14 +257,13 @@ inline void tupleToArray(Array &arr, const tuple &tup) RCP lclmap = createLocalMapWithNode (P, comm); // create the matrix - MAT A(rowmap,P,TPETRA_DEFAULT_PROFILE_TYPE); + MAT A(rowmap,P); for (GO i=0; i(M); ++i) { for (GO j=0; j(P); ++j) { A.insertGlobalValues( M*myImageID+i, tuple(j), tuple(M*myImageID+i + j*M*N) ); } } // call fillComplete() - TEST_EQUALITY_CONST( A.getProfileType() == TPETRA_DEFAULT_PROFILE_TYPE, true ); A.fillComplete(lclmap,rowmap); // build the input multivector X MV X(lclmap,numVecs); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests3.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests3.cpp index e798fbc6da9d..46df4bd9c225 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests3.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests3.cpp @@ -213,7 +213,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) // send in a parameterlist, check the defaults RCP defparams = parameterList(); // create static-profile matrix, fill-complete without inserting (and therefore, without allocating) - MAT matrix(map,1,Tpetra::StaticProfile); + MAT matrix(map,1); matrix.fillComplete(defparams); TEST_EQUALITY_CONST(defparams->get("Optimize Storage"), true); } @@ -222,7 +222,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) // send in a parameterlist, check the defaults RCP defparams = parameterList(); // create static-profile graph, fill-complete without inserting (and therefore, without allocating) - GRPH graph(map,1,Tpetra::StaticProfile); + GRPH graph(map,1); graph.fillComplete(defparams); TEST_EQUALITY_CONST(defparams->get("Optimize Storage"), true); } @@ -265,9 +265,8 @@ inline void tupleToArray(Array &arr, const tuple &tup) RCP params = parameterList(); for (int T=0; T<4; ++T) { if ( (T & 1) != 1 ) continue; - Tpetra::ProfileType pftype = Tpetra::StaticProfile; params->set("Optimize Storage",((T & 2) == 2)); - MAT matrix(rmap,cmap, ginds.size(), pftype); // only allocate as much room as necessary + MAT matrix(rmap,cmap, ginds.size()); // only allocate as much room as necessary RowMatrix &rowmatrix = matrix; typename MAT::nonconst_global_inds_host_view_type GCopy("gids",4); @@ -303,9 +302,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) // checks if an index exists the graph and only inserts if it doesn't. Thus, the // following test needs to be modified to insert another *unique* index and not a // repeat. - if (pftype == Tpetra::StaticProfile) { - TEST_THROW( matrix.insertGlobalValues(myrowind, tuple(myrowind+5), tuple(ST::one())), std::runtime_error ); - } + TEST_THROW( matrix.insertGlobalValues(myrowind, tuple(myrowind+5), tuple(ST::one())), std::runtime_error ); matrix.fillComplete(params); // check for throws and no-throws/values TEST_THROW( matrix.getGlobalRowView(myrowind,CGView,CSView), std::runtime_error ); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests4.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests4.cpp index 900d1f45c782..7052a750ef00 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests4.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests4.cpp @@ -361,8 +361,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) RCP > map = createContigMapWithNode(INVALID,1,comm); const Scalar SZERO = ScalarTraits::zero(); { - Tpetra::ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; - MAT matrix(map,map,1,pftype); + MAT matrix(map,map,1); TEST_EQUALITY_CONST( matrix.isFillActive(), true ); TEST_EQUALITY_CONST( matrix.isFillComplete(), false ); matrix.insertLocalValues( 0, tuple(0), tuple(0) ); @@ -395,8 +394,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) TEST_THROW( matrix.fillComplete(), std::runtime_error ); } { - Tpetra::ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; - MAT matrix(map,map,1,pftype); + MAT matrix(map,map,1); TEST_EQUALITY_CONST( matrix.isFillActive(), true ); TEST_EQUALITY_CONST( matrix.isFillComplete(), false ); matrix.insertLocalValues( 0, tuple(0), tuple(0) ); @@ -605,8 +603,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) auto map = createContigMapWithNode (INVALID, 1, comm); // construct matrix - Tpetra::ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; - CrsMatrix A (map, map, 1, pftype); + CrsMatrix A (map, map, 1); A.insertLocalValues (0, tuple (0), tuple (STS::zero ())); A.fillComplete (map, map); diff --git a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests_Swap.cpp b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests_Swap.cpp index f961cb8d1ffc..2b1294a95686 100644 --- a/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests_Swap.cpp +++ b/packages/tpetra/core/test/CrsMatrix/CrsMatrix_UnitTests_Swap.cpp @@ -410,7 +410,7 @@ class crsMatrix_Swap_Tester } } - RCP output_graph(new graph_type(row_map, num_ent_per_row (), Tpetra::StaticProfile)); + RCP output_graph(new graph_type(row_map, num_ent_per_row ())); for(auto& r: gbl_rows) { diff --git a/packages/tpetra/core/test/CrsMatrix/Equilibration.cpp b/packages/tpetra/core/test/CrsMatrix/Equilibration.cpp index cdcba5905354..3769504a1def 100644 --- a/packages/tpetra/core/test/CrsMatrix/Equilibration.cpp +++ b/packages/tpetra/core/test/CrsMatrix/Equilibration.cpp @@ -978,7 +978,7 @@ makeSymmetricPositiveDefiniteTridiagonalMatrixTest (Teuchos::FancyOStream& out, out << "Create CrsGraph" << endl; const size_t maxNumEntPerRow = 3; RCP G = - rcp (new crs_graph_type (rowMap, maxNumEntPerRow, Tpetra::StaticProfile)); + rcp (new crs_graph_type (rowMap, maxNumEntPerRow)); std::vector globalIndices (maxNumEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { @@ -1333,7 +1333,7 @@ makeMatrixTestWithExplicitZeroDiag (Teuchos::FancyOStream& out, out << "Create CrsGraph" << endl; const size_t maxNumEntPerRow = 1; RCP G = - rcp (new crs_graph_type (rowMap, maxNumEntPerRow, Tpetra::StaticProfile)); + rcp (new crs_graph_type (rowMap, maxNumEntPerRow)); std::vector globalIndices (maxNumEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { @@ -1571,7 +1571,7 @@ makeMatrixTestWithImplicitZeroDiag (Teuchos::FancyOStream& out, out << "Create CrsGraph" << endl; const size_t maxNumEntPerRow = 1; RCP G = - rcp (new crs_graph_type (rowMap, maxNumEntPerRow, Tpetra::StaticProfile)); + rcp (new crs_graph_type (rowMap, maxNumEntPerRow)); // Process 1 gets an implicit zero diagonal entry. std::vector globalIndices (maxNumEntPerRow); @@ -1809,7 +1809,7 @@ makeMatrixTestWithExplicitInfAndNan (Teuchos::FancyOStream& out, out << "Create CrsGraph" << endl; const size_t maxNumEntPerRow = 1; RCP G = - rcp (new crs_graph_type (rowMap, maxNumEntPerRow, Tpetra::StaticProfile)); + rcp (new crs_graph_type (rowMap, maxNumEntPerRow)); std::vector globalIndices (maxNumEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { diff --git a/packages/tpetra/core/test/CrsMatrix/Regression/Albany182.cpp b/packages/tpetra/core/test/CrsMatrix/Regression/Albany182.cpp index a1f52e31a5c8..ef9f17eeae7a 100644 --- a/packages/tpetra/core/test/CrsMatrix/Regression/Albany182.cpp +++ b/packages/tpetra/core/test/CrsMatrix/Regression/Albany182.cpp @@ -1003,15 +1003,14 @@ namespace { // (anonymous) out << "Target matrix is correct!" << endl; } - const Tpetra::ProfileType pftypes[1] = {Tpetra::StaticProfile}; - for (Tpetra::ProfileType profileType : pftypes) { - out << ">>> Target matrix is {StaticProfile, locally indexed}" << endl; + { + out << ">>> Target matrix is locally indexed" << endl; Teuchos::OSTab tab2 (out); const size_t maxNumEntPerRow = 10; // needs to be an upper bound RCP A_nonoverlapping = rcp (new CrsMatrixType (rowMap_nonoverlapping, colMap_expected, - maxNumEntPerRow, profileType)); + maxNumEntPerRow)); export_type exp (A_overlapping.getRowMap (), rowMap_nonoverlapping); A_nonoverlapping->doExport (A_overlapping, exp, Tpetra::ADD); A_nonoverlapping->fillComplete (domMap, ranMap); diff --git a/packages/tpetra/core/test/CrsMatrix/Tpetra_Test_CrsMatrix_WithGraph.hpp b/packages/tpetra/core/test/CrsMatrix/Tpetra_Test_CrsMatrix_WithGraph.hpp index 91aac2dfa621..1a077e9588f2 100644 --- a/packages/tpetra/core/test/CrsMatrix/Tpetra_Test_CrsMatrix_WithGraph.hpp +++ b/packages/tpetra/core/test/CrsMatrix/Tpetra_Test_CrsMatrix_WithGraph.hpp @@ -181,13 +181,13 @@ inline void tupleToArray(Array &arr, const tuple &tup) const size_t numLocal = 10; RCP > map = createContigMapWithNode(INVALID,numLocal,comm); { - Tpetra::CrsGraph diaggraph (map, 1, Tpetra::StaticProfile); + Tpetra::CrsGraph diaggraph (map, 1); // A pre-constructed graph must be fill complete before being used to construct a CrsMatrix TEST_THROW( MAT matrix(rcpFromRef(diaggraph)), std::runtime_error ); } { // create a simple diagonal graph - Tpetra::CrsGraph diaggraph (map, 1, Tpetra::StaticProfile); + Tpetra::CrsGraph diaggraph (map, 1); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { diaggraph.insertGlobalIndices(r,tuple(r)); } @@ -252,7 +252,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { out << "Create tridiagonal CrsGraph with StaticProfile" << endl; - GRPH trigraph (map, 3, Tpetra::StaticProfile); + GRPH trigraph (map, 3); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { if (r == map->getMinAllGlobalIndex()) { trigraph.insertGlobalIndices(r,tuple(r,r+1)); @@ -272,7 +272,6 @@ inline void tupleToArray(Array &arr, const tuple &tup) "and test allowed functionality" << endl; MAT matrix(rcpFromRef(trigraph)); - TEST_EQUALITY_CONST( matrix.getProfileType() == Tpetra::StaticProfile, true ); // insert throws exception: not allowed with static graph TEST_THROW( matrix.insertGlobalValues(map->getMinGlobalIndex(),tuple(map->getMinGlobalIndex()),tuple(ST::one())), std::runtime_error ); // suminto and replace are allowed @@ -321,7 +320,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { out << "Create a diagonal CrsGraph" << endl; - GRPH diaggraph (map, 1, Tpetra::StaticProfile); + GRPH diaggraph (map, 1); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { diaggraph.insertGlobalIndices(r,tuple(r)); } @@ -351,7 +350,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { out << "Create a diagonal CrsGraph" << endl; - GRPH diaggraph (map, 1, Tpetra::StaticProfile); + GRPH diaggraph (map, 1); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { diaggraph.insertGlobalIndices(r,tuple(r)); } @@ -376,7 +375,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { out << "Create a diagonal CrsGraph" << endl; - GRPH diaggraph (map, 1, Tpetra::StaticProfile); + GRPH diaggraph (map, 1); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { diaggraph.insertGlobalIndices(r,tuple(r)); } @@ -432,7 +431,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { out << "Create a diagonal CrsGraph" << endl; - RCP diaggraph = rcp( new GRPH (map, 1, Tpetra::StaticProfile) ); + RCP diaggraph = rcp( new GRPH (map, 1) ); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { diaggraph->insertGlobalIndices(r,tuple(r)); } @@ -489,7 +488,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) // First test: use a constant upper bound (3) on the number of // entries in each row, and insert using global indices. { - MAT bdmat (rmap, cmap, 3, Tpetra::StaticProfile); + MAT bdmat (rmap, cmap, 3); TEST_EQUALITY(bdmat.getRowMap(), rmap); TEST_EQUALITY_CONST(bdmat.hasColMap(), true); TEST_EQUALITY(bdmat.getColMap(), cmap); @@ -534,7 +533,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) { Teuchos::Array nnzperrow (numLocal); std::fill(nnzperrow.begin(), nnzperrow.end(), 3); - MAT bdmat (rmap, cmap, nnzperrow (), Tpetra::StaticProfile); + MAT bdmat (rmap, cmap, nnzperrow ()); TEST_EQUALITY(bdmat.getRowMap(), rmap); TEST_EQUALITY_CONST(bdmat.hasColMap(), true); TEST_EQUALITY(bdmat.getColMap(), cmap); @@ -604,7 +603,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) RCP > map = createContigMapWithNode(INVALID,numLocal,comm); out << "Create a tridiagonal CrsGraph" << endl; - Tpetra::CrsGraph graph (map, 3, Tpetra::StaticProfile); + Tpetra::CrsGraph graph (map, 3); for (GO r=map->getMinGlobalIndex(); r <= map->getMaxGlobalIndex(); ++r) { if (r == map->getMinAllGlobalIndex()) { graph.insertGlobalIndices(r,tuple(r,r+1)); @@ -623,7 +622,6 @@ inline void tupleToArray(Array &arr, const tuple &tup) out << "Create a CrsMatrix using the tridiagonal CrsGraph" << endl; MAT matrix(rcpFromRef(graph)); - TEST_ASSERT( matrix.getProfileType () == Tpetra::StaticProfile ); TEST_ASSERT( matrix.isStaticGraph () ); // Make sure that all processes finished and were successful. @@ -832,7 +830,7 @@ inline void tupleToArray(Array &arr, const tuple &tup) const size_t numLocal = 10; RCP > map = createContigMapWithNode(INVALID,numLocal,comm); { - MAT matrix(map, 1, Tpetra::StaticProfile); + MAT matrix(map, 1); // room for one on each row for (GO r=map->getMinGlobalIndex(); r<=map->getMaxGlobalIndex(); ++r) { diff --git a/packages/tpetra/core/test/CrsMatrix/sumIntoStaticProfileExtraSpace.cpp b/packages/tpetra/core/test/CrsMatrix/sumIntoStaticProfileExtraSpace.cpp index 4ffe85c8a1c7..a202399d2984 100644 --- a/packages/tpetra/core/test/CrsMatrix/sumIntoStaticProfileExtraSpace.cpp +++ b/packages/tpetra/core/test/CrsMatrix/sumIntoStaticProfileExtraSpace.cpp @@ -65,7 +65,7 @@ TEUCHOS_UNIT_TEST( CrsMatrix, sumIntoStaticProfileExtraSpace ) int lclSuccess = 1; int gblSuccess = 0; - out << "CrsMatrix: Test sumIntoLocalValues, StaticProfile, " + out << "CrsMatrix: Test sumIntoLocalValues, " "not yet fill complete, extra space in each row" << endl; Teuchos::OSTab tab1 (out); @@ -83,8 +83,7 @@ TEUCHOS_UNIT_TEST( CrsMatrix, sumIntoStaticProfileExtraSpace ) (new map_type (gblNumInds, lclNumInds, indexBase, comm)); constexpr size_t maxNumEntPerRow = 5; - crs_matrix_type A (rowAndColMap, rowAndColMap, maxNumEntPerRow, - Tpetra::StaticProfile); + crs_matrix_type A (rowAndColMap, rowAndColMap, maxNumEntPerRow); for (LO lclRow = 0; lclRow < lclNumInds; ++lclRow) { const size_t numEnt = A.getNumEntriesInLocalRow (lclRow); diff --git a/packages/tpetra/core/test/Distributor/Issue1752.cpp b/packages/tpetra/core/test/Distributor/Issue1752.cpp index d721a7444656..5c7830e58f57 100644 --- a/packages/tpetra/core/test/Distributor/Issue1752.cpp +++ b/packages/tpetra/core/test/Distributor/Issue1752.cpp @@ -236,7 +236,7 @@ TEUCHOS_UNIT_TEST(Distributor, ReverseDistributeToNonuniformMap) // Create matrix using the unique map out << std::right << std::setfill('*') << std::setw(80) << "Proc " << my_rank << ": Creating matrix with unique map" << endl; - matrix_type unique_mtx(unique_map, 3, Tpetra::StaticProfile); + matrix_type unique_mtx(unique_map, 3); fill_and_complete(unique_mtx); // Sanity check the unique matrix @@ -258,7 +258,7 @@ TEUCHOS_UNIT_TEST(Distributor, ReverseDistributeToNonuniformMap) import_type importer(unique_map, default_map); // Matrix built with default map - matrix_type default_mtx_fwd(default_map, 3, Tpetra::StaticProfile); + matrix_type default_mtx_fwd(default_map, 3); // Do a forward import (an import operation using an Import plan) from the // unique matrix to the default matrix. i.e., communicate entries @@ -285,7 +285,7 @@ TEUCHOS_UNIT_TEST(Distributor, ReverseDistributeToNonuniformMap) } // Matrix built with default map - matrix_type default_mtx_rev(default_map, 3, Tpetra::StaticProfile); + matrix_type default_mtx_rev(default_map, 3); // Do a reverse mode import (an import operation using an Export plan) from the // unique matrix to the default matrix. i.e., communicate entries diff --git a/packages/tpetra/core/test/Distributor/createfromsendsandrecvs.cpp b/packages/tpetra/core/test/Distributor/createfromsendsandrecvs.cpp index cc8da7481de2..944fb53e4153 100644 --- a/packages/tpetra/core/test/Distributor/createfromsendsandrecvs.cpp +++ b/packages/tpetra/core/test/Distributor/createfromsendsandrecvs.cpp @@ -84,8 +84,7 @@ namespace { // (anonymous) const GO gblNumCols = static_cast (rowMap->getGlobalNumElements ()); // Create the graph structure of the sparse matrix. RCP G = - rcp (new graph_type (rowMap, numEntPerRow, - Tpetra::StaticProfile)); + rcp (new graph_type (rowMap, numEntPerRow)); // Fill in the sparse graph. Teuchos::Array gblColInds (numEntPerRow); for (LO lclRow = 0; lclRow < lclNumRows; ++lclRow) { // for each of my rows diff --git a/packages/tpetra/core/test/FECrsGraph/FECrsGraph_UnitTests.cpp b/packages/tpetra/core/test/FECrsGraph/FECrsGraph_UnitTests.cpp index 026ba6db23a0..25afabe022ac 100644 --- a/packages/tpetra/core/test/FECrsGraph/FECrsGraph_UnitTests.cpp +++ b/packages/tpetra/core/test/FECrsGraph/FECrsGraph_UnitTests.cpp @@ -55,7 +55,6 @@ namespace { // (anonymous) using Tpetra::TestingUtilities::getDefaultComm; using Tpetra::createContigMapWithNode; using Tpetra::createNonContigMapWithNode; -using Tpetra::StaticProfile; using Teuchos::RCP; using Teuchos::ArrayRCP; using Teuchos::rcp; @@ -398,7 +397,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Diagonal, LO, GO, Node ) // Trivial test that makes sure a diagonal graph can be built - CG g1(map,1,StaticProfile); + CG g1(map,1); FEG g2(map,map,1); Tpetra::beginAssembly(g2); @@ -430,7 +429,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Diagonal_LocalIndex, LO, GO, Node // Trivial test that makes sure a diagonal graph can be built - CG g1(map,1,StaticProfile); + CG g1(map,1); FEG g2(map,map,map,1); Tpetra::beginAssembly(g2); @@ -466,9 +465,9 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Assemble1D, LO, GO, Node ) //pack.print(comm->getRank(),std::cout); // Comparative assembly - // FIXME: We should be able to get away with 3 for StaticProfile here, but we need 4 since duplicates are + // FIXME: We should be able to get away with 3 here, but we need 4 since duplicates are // not being handled correctly. - CG g1(pack.uniqueMap,4,StaticProfile); + CG g1(pack.uniqueMap,4); FEG g2(pack.uniqueMap,pack.overlapMap,4); g2.beginAssembly(); @@ -509,10 +508,10 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Assemble1D_LocalIndex, LO, GO, No // pack.print(comm->getRank(),std::cout);fflush(stdout); // Comparative assembly - // FIXME: We should be able to get away with 3 for StaticProfile here, but we need 4 since duplicates are + // FIXME: We should be able to get away with 3 here, but we need 4 since duplicates are // not being handled correctly. - CG g1(pack.uniqueMap,4,StaticProfile); + CG g1(pack.uniqueMap,4); FEG g2(pack.uniqueMap,pack.overlapMap,pack.overlapMap,4); g2.beginAssembly(); @@ -552,8 +551,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Assemble2D_OPSDomain, LO, GO, Nod // Comparative assembly - CG g0(pack.overlapMap,9,StaticProfile); - CG g1(pack.uniqueMap,9,StaticProfile); + CG g0(pack.overlapMap,9); + CG g1(pack.uniqueMap,9); FEG g2(pack.uniqueMap,pack.overlapMap,9); FEG g3(pack.uniqueMap,pack.overlapMap,9,pack.overlapMap); @@ -576,7 +575,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Assemble2D_OPSDomain, LO, GO, Nod Tpetra::Import import(pack.uniqueMap,pack.overlapMap); Teuchos::FancyOStream myout(Teuchos::rcpFromRef(std::cout)); - CG g11(pack.uniqueMap,9,StaticProfile); + CG g11(pack.uniqueMap,9); g11.doExport(g0,import,Tpetra::INSERT); g11.fillComplete(pack.uniqueMap,pack.uniqueMap); success = compare_final_graph_structure(out,g11,g1); @@ -595,7 +594,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_3_DECL( FECrsGraph, Assemble2D_OPSDomain, LO, GO, Nod // a) use overlapMap as domainMap during fillComplete (this will generate the // correct colMap), and b) reset domainMap to be the unique map (so that the // checks in compare_final_graph_structure do not fail b/c of the domain map). - CG g12(pack.uniqueMap,9,StaticProfile); + CG g12(pack.uniqueMap,9); g12.doExport(g0,import,Tpetra::INSERT); g12.fillComplete(pack.overlapMap,pack.uniqueMap); auto importer = g12.getImporter(); diff --git a/packages/tpetra/core/test/FEMultiVector/FEMultiVector_UnitTests.cpp b/packages/tpetra/core/test/FEMultiVector/FEMultiVector_UnitTests.cpp index f1e6ead3d6b8..231b484ea0e6 100644 --- a/packages/tpetra/core/test/FEMultiVector/FEMultiVector_UnitTests.cpp +++ b/packages/tpetra/core/test/FEMultiVector/FEMultiVector_UnitTests.cpp @@ -120,7 +120,7 @@ namespace { // create CrsGraph object RCP > graph = - rcp (new Tpetra::CrsGraph (map, 3, Tpetra::StaticProfile)); + rcp (new Tpetra::CrsGraph (map, 3)); // Create a simple tridiagonal source graph. Array entry(1); diff --git a/packages/tpetra/core/test/ImportExport/ImportExport_ImportConstructExpert.cpp b/packages/tpetra/core/test/ImportExport/ImportExport_ImportConstructExpert.cpp index ea09dc501bf5..94e90a7d8cb7 100644 --- a/packages/tpetra/core/test/ImportExport/ImportExport_ImportConstructExpert.cpp +++ b/packages/tpetra/core/test/ImportExport/ImportExport_ImportConstructExpert.cpp @@ -103,8 +103,7 @@ namespace { const GO gblNumCols = static_cast (rowMap->getGlobalNumElements ()); RCP G = - rcp (new graph_type (rowMap, numEntPerRow, - Tpetra::StaticProfile)); + rcp (new graph_type (rowMap, numEntPerRow)); Teuchos::Array gblColInds (numEntPerRow); for (LO lclRow = 0; lclRow < NumRows; ++lclRow) { diff --git a/packages/tpetra/core/test/ImportExport/UnpackLongRows.cpp b/packages/tpetra/core/test/ImportExport/UnpackLongRows.cpp index 423184a872f2..02fe30109aef 100644 --- a/packages/tpetra/core/test/ImportExport/UnpackLongRows.cpp +++ b/packages/tpetra/core/test/ImportExport/UnpackLongRows.cpp @@ -154,8 +154,8 @@ generate_graphs( shared_map = rcp(new map_type(invalid, indices(), 0, comm)); } - owned = rcp(new graph_type(owned_map, rows_per_rank + dense_rows, Tpetra::StaticProfile)); - shared = rcp(new graph_type(shared_map, rows_per_rank + dense_rows, Tpetra::StaticProfile)); + owned = rcp(new graph_type(owned_map, rows_per_rank + dense_rows)); + shared = rcp(new graph_type(shared_map, rows_per_rank + dense_rows)); { using Teuchos::tuple; diff --git a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp index 7e405fd2609f..4da14baaba68 100644 --- a/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp +++ b/packages/tpetra/core/test/ImportExport2/ImportExport2_UnitTests.cpp @@ -101,7 +101,6 @@ namespace { using Tpetra::INSERT; using Tpetra::Map; using Tpetra::REPLACE; - using Tpetra::StaticProfile; using std::cerr; using std::cout; @@ -255,10 +254,10 @@ namespace { out << "Creating source and target CrsGraphs" << endl; } RCP > src_graph = - rcp (new CrsGraph (src_map, 1, StaticProfile, + rcp (new CrsGraph (src_map, 1, getCrsGraphParameterList ())); RCP > tgt_graph = - rcp (new CrsGraph (tgt_map, 1, StaticProfile, + rcp (new CrsGraph (tgt_map, 1, getCrsGraphParameterList ())); // Create a simple diagonal source graph. @@ -327,10 +326,10 @@ namespace { createContigMap (INVALID, tgt_num_local, comm); RCP > src_graph = - rcp (new CrsGraph (src_map, 24, StaticProfile, + rcp (new CrsGraph (src_map, 24, getCrsGraphParameterList ())); RCP > tgt_graph = - rcp (new CrsGraph (tgt_map, 24, StaticProfile, + rcp (new CrsGraph (tgt_map, 24, getCrsGraphParameterList ())); // This time make src_graph be a full lower-triangular graph. @@ -447,10 +446,10 @@ namespace { // Create CrsMatrix objects. RCP > src_mat = - rcp (new CrsMatrix (src_map, 1, StaticProfile, + rcp (new CrsMatrix (src_map, 1, crsMatPlist)); RCP > tgt_mat = - rcp (new CrsMatrix (tgt_map, 1, StaticProfile, + rcp (new CrsMatrix (tgt_map, 1, crsMatPlist)); // Create a simple diagonal source graph. @@ -604,9 +603,9 @@ namespace { createContigMap (INVALID, tgt_num_local, comm); RCP > src_mat = - rcp (new CrsMatrix (src_map, 24, StaticProfile, crsMatPlist)); + rcp (new CrsMatrix (src_map, 24, crsMatPlist)); RCP > tgt_mat = - rcp (new CrsMatrix (tgt_map, 24, StaticProfile, crsMatPlist)); + rcp (new CrsMatrix (tgt_map, 24, crsMatPlist)); // This time make src_mat a full lower-triangular matrix. Each // row of column-indices will have length 'globalrow', and diff --git a/packages/tpetra/core/test/MatrixMatrix/FECrs_MatrixMatrix_UnitTests.cpp b/packages/tpetra/core/test/MatrixMatrix/FECrs_MatrixMatrix_UnitTests.cpp index f6a9ebf874d7..c1f1268c85c6 100644 --- a/packages/tpetra/core/test/MatrixMatrix/FECrs_MatrixMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/MatrixMatrix/FECrs_MatrixMatrix_UnitTests.cpp @@ -166,7 +166,7 @@ generate_crs_graph (const MeshInfo<4,LO,GO,NT>& mesh) { using CG = Tpetra::CrsGraph; - Teuchos::RCP g(new CG(mesh.uniqueMap,9,Tpetra::StaticProfile)); + Teuchos::RCP g(new CG(mesh.uniqueMap,9)); for (const auto& elem_dofs : mesh.element2node) { for (const GO gid_i : elem_dofs) { for (const GO gid_j : elem_dofs) { @@ -366,8 +366,8 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL (Tpetra_MatMat, FECrsMatrix, SC, LO, GO, NT) auto C_row_map = transA ? feA.getDomainMap() : feA.getRangeMap(); // For the test, use a ridicolously large upper bound for the nnz per row - MAT feC(C_row_map,feA.getGraph()->getGlobalNumEntries(),Tpetra::StaticProfile); - MAT C(C_row_map, A.getGraph()->getGlobalNumEntries(),Tpetra::StaticProfile); + MAT feC(C_row_map,feA.getGraph()->getGlobalNumEntries()); + MAT C(C_row_map, A.getGraph()->getGlobalNumEntries()); Tpetra::MatrixMatrix::Multiply(feA, transA, feB, transB, feC, true, "", params); Tpetra::MatrixMatrix::Multiply( A, transA, B, transB, C, true, "", params); diff --git a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp index 63b13fd6a208..810ca4e1fda2 100644 --- a/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp +++ b/packages/tpetra/core/test/MatrixMatrix/MatrixMatrix_UnitTests.cpp @@ -1137,7 +1137,7 @@ TEUCHOS_UNIT_TEST_TEMPLATE_4_DECL(Tpetra_MatMat, operations_test,SC,LO, GO, NT) n += A->getNodeMaxNumRowEntries(); RCP rm = B->getRowMap(); - RCP E = rcp (new Matrix_t(rm, n, Tpetra::StaticProfile)); + RCP E = rcp (new Matrix_t(rm, n)); auto one = Teuchos::ScalarTraits::one(); Tpetra::MatrixMatrix::Add(*B, BT, one, *E, one); diff --git a/packages/tpetra/core/test/RowMatrixTransposer/main.cpp b/packages/tpetra/core/test/RowMatrixTransposer/main.cpp index 63c2cfa6830c..98fab5cf549b 100644 --- a/packages/tpetra/core/test/RowMatrixTransposer/main.cpp +++ b/packages/tpetra/core/test/RowMatrixTransposer/main.cpp @@ -132,8 +132,8 @@ main (int argc, char* argv[]) } // Create a Tpetra::CrsMatrix using the Map, with a static allocation dictated by NumNz - crs_matrix_type A (map, NumNz (), Tpetra::StaticProfile); - crs_matrix_type AT(map, NumNz (), Tpetra::StaticProfile); + crs_matrix_type A (map, NumNz ()); + crs_matrix_type AT(map, NumNz ()); RCP< crs_matrix_type > TestMatrix = Teuchos::null; // We are done with NumNZ diff --git a/packages/tpetra/core/test/TpetraUtils_MatrixGenerator.hpp b/packages/tpetra/core/test/TpetraUtils_MatrixGenerator.hpp index d7117f946d71..df95f274688c 100644 --- a/packages/tpetra/core/test/TpetraUtils_MatrixGenerator.hpp +++ b/packages/tpetra/core/test/TpetraUtils_MatrixGenerator.hpp @@ -265,9 +265,8 @@ namespace Tpetra { // Construct the CrsMatrix, using the row map, with the // constructor specifying the number of nonzeros for each row. - Tpetra::ProfileType pftype = TPETRA_DEFAULT_PROFILE_TYPE; RCP A = - rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow (), pftype)); + rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow ())); // List of the global indices of my rows. // They may or may not be contiguous. @@ -357,7 +356,7 @@ namespace Tpetra { // constructor specifying the number of nonzeros for each row. RCP A = rcp (new sparse_matrix_type (pRowMap, myNumEntriesPerRow, - StaticProfile, constructorParams)); + constructorParams)); // List of the global indices of my rows. // They may or may not be contiguous. @@ -419,9 +418,9 @@ namespace Tpetra { // RCP A; // the matrix to return. if (colMap.is_null ()) { // the user didn't provide a column Map - A = rcp (new sparse_matrix_type (rowMap, myNumEntriesPerRow, StaticProfile)); + A = rcp (new sparse_matrix_type (rowMap, myNumEntriesPerRow)); } else { // the user provided a column Map - A = rcp (new sparse_matrix_type (rowMap, colMap, myNumEntriesPerRow, StaticProfile)); + A = rcp (new sparse_matrix_type (rowMap, colMap, myNumEntriesPerRow)); } // List of the global indices of my rows. diff --git a/packages/xpetra/src/CrsGraph/Xpetra_TpetraCrsGraph_def.hpp b/packages/xpetra/src/CrsGraph/Xpetra_TpetraCrsGraph_def.hpp index 6ca14f192d1d..daaede863359 100644 --- a/packages/xpetra/src/CrsGraph/Xpetra_TpetraCrsGraph_def.hpp +++ b/packages/xpetra/src/CrsGraph/Xpetra_TpetraCrsGraph_def.hpp @@ -63,19 +63,19 @@ namespace Xpetra { template TpetraCrsGraph::TpetraCrsGraph(const RCP< const map_type > &rowMap, size_t maxNumEntriesPerRow, const RCP< ParameterList > ¶ms) -: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), maxNumEntriesPerRow, Tpetra::StaticProfile, params))) { } +: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), maxNumEntriesPerRow, params))) { } template TpetraCrsGraph::TpetraCrsGraph(const RCP< const Map > &rowMap, const ArrayRCP< const size_t > &NumEntriesPerRowToAlloc, const RCP< ParameterList > ¶ms) -: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), NumEntriesPerRowToAlloc(), Tpetra::StaticProfile, params))) { } +: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), NumEntriesPerRowToAlloc(), params))) { } template TpetraCrsGraph::TpetraCrsGraph(const RCP< const Map>&rowMap, const RCP< const Map > &colMap, size_t maxNumEntriesPerRow, const RCP< ParameterList > ¶ms) -: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), maxNumEntriesPerRow, Tpetra::StaticProfile, params))) { } +: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), maxNumEntriesPerRow, params))) { } template TpetraCrsGraph::TpetraCrsGraph(const RCP< const Map > &rowMap, const RCP< const Map > &colMap, const ArrayRCP< const size_t > &NumEntriesPerRowToAlloc, const RCP< ParameterList > ¶ms) -: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), NumEntriesPerRowToAlloc(), Tpetra::StaticProfile, params))) { } +: graph_(Teuchos::rcp(new Tpetra::CrsGraph< LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), NumEntriesPerRowToAlloc(), params))) { } template diff --git a/packages/xpetra/src/CrsMatrix/Xpetra_TpetraCrsMatrix_def.hpp b/packages/xpetra/src/CrsMatrix/Xpetra_TpetraCrsMatrix_def.hpp index 7f47477ca38b..d6353d4f8a57 100644 --- a/packages/xpetra/src/CrsMatrix/Xpetra_TpetraCrsMatrix_def.hpp +++ b/packages/xpetra/src/CrsMatrix/Xpetra_TpetraCrsMatrix_def.hpp @@ -54,19 +54,19 @@ namespace Xpetra { template TpetraCrsMatrix::TpetraCrsMatrix(const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &rowMap, size_t maxNumEntriesPerRow, const Teuchos::RCP< Teuchos::ParameterList > ¶ms) - : mtx_ (Teuchos::rcp (new Tpetra::CrsMatrix (toTpetra(rowMap), maxNumEntriesPerRow, Tpetra::StaticProfile, params))) { } + : mtx_ (Teuchos::rcp (new Tpetra::CrsMatrix (toTpetra(rowMap), maxNumEntriesPerRow, params))) { } template TpetraCrsMatrix::TpetraCrsMatrix(const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &rowMap, const ArrayRCP< const size_t > &NumEntriesPerRowToAlloc, const Teuchos::RCP< Teuchos::ParameterList > ¶ms) - : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix (toTpetra(rowMap), NumEntriesPerRowToAlloc(), Tpetra::StaticProfile, params))) { } + : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix (toTpetra(rowMap), NumEntriesPerRowToAlloc(), params))) { } template TpetraCrsMatrix::TpetraCrsMatrix(const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &rowMap, const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &colMap, size_t maxNumEntriesPerRow, const Teuchos::RCP< Teuchos::ParameterList > ¶ms) - : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix(toTpetra(rowMap), toTpetra(colMap), maxNumEntriesPerRow, Tpetra::StaticProfile, params))) { } + : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix(toTpetra(rowMap), toTpetra(colMap), maxNumEntriesPerRow, params))) { } template TpetraCrsMatrix::TpetraCrsMatrix(const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &rowMap, const Teuchos::RCP< const Map< LocalOrdinal, GlobalOrdinal, Node > > &colMap, const ArrayRCP< const size_t > &NumEntriesPerRowToAlloc, const Teuchos::RCP< Teuchos::ParameterList > ¶ms) - : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix< Scalar, LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), NumEntriesPerRowToAlloc(), Tpetra::StaticProfile, params))) { } + : mtx_(Teuchos::rcp(new Tpetra::CrsMatrix< Scalar, LocalOrdinal, GlobalOrdinal, Node >(toTpetra(rowMap), toTpetra(colMap), NumEntriesPerRowToAlloc(), params))) { } template TpetraCrsMatrix::TpetraCrsMatrix(const Teuchos::RCP< const CrsGraph< LocalOrdinal, GlobalOrdinal, Node > > &graph, const Teuchos::RCP< Teuchos::ParameterList > ¶ms) diff --git a/packages/xpetra/sup/Utils/Xpetra_MatrixMatrix.hpp b/packages/xpetra/sup/Utils/Xpetra_MatrixMatrix.hpp index 355c34d6138e..f17cad4ecd70 100644 --- a/packages/xpetra/sup/Utils/Xpetra_MatrixMatrix.hpp +++ b/packages/xpetra/sup/Utils/Xpetra_MatrixMatrix.hpp @@ -266,7 +266,7 @@ Note: this class is not in the Xpetra_UseShortNames.hpp allocPerRow[i] = Aprime->getNumEntriesInLocalRow(i) + Bprime->getNumEntriesInLocalRow(i); } //Construct C - RCP C = rcp(new tcrs_matrix_type(Aprime->getRowMap(), allocPerRow(), Tpetra::StaticProfile)); + RCP C = rcp(new tcrs_matrix_type(Aprime->getRowMap(), allocPerRow())); //Compute the sum in C (already took care of transposes) Tpetra::MatrixMatrix::Add( *Aprime, false, alpha, diff --git a/packages/zoltan2/core/src/input/Zoltan2_TpetraRowGraphAdapter.hpp b/packages/zoltan2/core/src/input/Zoltan2_TpetraRowGraphAdapter.hpp index 041fea92b6f6..65f5701bd88a 100644 --- a/packages/zoltan2/core/src/input/Zoltan2_TpetraRowGraphAdapter.hpp +++ b/packages/zoltan2/core/src/input/Zoltan2_TpetraRowGraphAdapter.hpp @@ -545,7 +545,7 @@ RCP TpetraRowGraphAdapter::doMigration( // target graph RCP G = - rcp(new tcrsgraph_t(tmap, nnz_size_t(), Tpetra::StaticProfile)); + rcp(new tcrsgraph_t(tmap, nnz_size_t())); G->doImport(*pCrsGraphSrc, importer, Tpetra::INSERT); G->fillComplete(); diff --git a/packages/zoltan2/core/src/input/Zoltan2_TpetraRowMatrixAdapter.hpp b/packages/zoltan2/core/src/input/Zoltan2_TpetraRowMatrixAdapter.hpp index 177a0f7a02f3..181f3b4e5c8f 100644 --- a/packages/zoltan2/core/src/input/Zoltan2_TpetraRowMatrixAdapter.hpp +++ b/packages/zoltan2/core/src/input/Zoltan2_TpetraRowMatrixAdapter.hpp @@ -480,7 +480,7 @@ RCP TpetraRowMatrixAdapter::doMigration( } RCP M = - rcp(new tcrsmatrix_t(tmap, nnz(), Tpetra::StaticProfile)); + rcp(new tcrsmatrix_t(tmap, nnz())); M->doImport(from, importer, Tpetra::INSERT); M->fillComplete(); diff --git a/packages/zoltan2/core/src/input/Zoltan2_XpetraTraits.hpp b/packages/zoltan2/core/src/input/Zoltan2_XpetraTraits.hpp index d907444990ac..cfb4be490aa6 100644 --- a/packages/zoltan2/core/src/input/Zoltan2_XpetraTraits.hpp +++ b/packages/zoltan2/core/src/input/Zoltan2_XpetraTraits.hpp @@ -463,7 +463,7 @@ struct XpetraTraits > } // target graph - RCP G = rcp(new tgraph_t(tmap, nnz_size_t(), Tpetra::StaticProfile)); + RCP G = rcp(new tgraph_t(tmap, nnz_size_t())); G->doImport(from, importer, Tpetra::INSERT); G->fillComplete(); diff --git a/packages/zoltan2/sphynx/src/Zoltan2_Sphynx.hpp b/packages/zoltan2/sphynx/src/Zoltan2_Sphynx.hpp index fb116672e0f9..df93757aa5fb 100644 --- a/packages/zoltan2/sphynx/src/Zoltan2_Sphynx.hpp +++ b/packages/zoltan2/sphynx/src/Zoltan2_Sphynx.hpp @@ -373,7 +373,7 @@ namespace Zoltan2 { // Create the degree matrix with max row size set to 1 Teuchos::RCP degMat(new matrix_t (graph_->getRowMap(), graph_->getRowMap(), - 1, Tpetra::StaticProfile)); + 1)); scalar_t *val = new scalar_t[1]; lno_t *ind = new lno_t[1]; diff --git a/packages/zoltan2/test/core/helpers/UserInputForTests.hpp b/packages/zoltan2/test/core/helpers/UserInputForTests.hpp index c45165a9eb9f..0b52bd5f5805 100644 --- a/packages/zoltan2/test/core/helpers/UserInputForTests.hpp +++ b/packages/zoltan2/test/core/helpers/UserInputForTests.hpp @@ -1688,7 +1688,7 @@ void UserInputForTests::getUIChacoGraph(FILE *fptr, bool haveAssign, fromMap = rcp(new map_t(nvtxs, nvtxs, base, tcomm_)); fromMatrix = - rcp(new tcrsMatrix_t(fromMap, rowSizes(), Tpetra::StaticProfile)); + rcp(new tcrsMatrix_t(fromMap, rowSizes())); if (haveEdges){ @@ -1736,7 +1736,7 @@ void UserInputForTests::getUIChacoGraph(FILE *fptr, bool haveAssign, fromMap = rcp(new map_t(nvtxs, 0, base, tcomm_)); fromMatrix = - rcp(new tcrsMatrix_t(fromMap, rowSizes(), Tpetra::StaticProfile)); + rcp(new tcrsMatrix_t(fromMap, rowSizes())); fromMatrix->fillComplete(); } From 2ac5617d676a7afb4330fd7a01e2c65b147c1af9 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Fri, 22 Oct 2021 16:11:03 -0600 Subject: [PATCH 87/98] stokhos: resolve -Werror error: calling a __device__ from a __host__ __device__ function Co-author credit @masterleinad --- .../src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp index e01a3d15320e..5e1a5773c1f5 100644 --- a/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp +++ b/packages/stokhos/src/kokkos/Cuda/Stokhos_Cuda_WarpShuffle.hpp @@ -72,19 +72,35 @@ template KOKKOS_INLINE_FUNCTION Scalar shfl_down(const Scalar &val, const int& delta, const int& width, const int& mask){ +#ifdef __CUDA_ARCH__ return __shfl_down_sync(mask, val, delta, width); +#else + (void) delta; + (void) width; + (void) mask; + return val; +#endif } template KOKKOS_INLINE_FUNCTION Scalar shfl_up(const Scalar &val, const int& delta, const int& width, const int& mask){ +#ifdef __CUDA_ARCH__ return __shfl_up_sync(mask, val, delta, width); +#else + (void) delta; + (void) width; + (void) mask; + return val; +#endif } KOKKOS_INLINE_FUNCTION void sync_warp(const int& mask) { +#ifdef __CUDA_ARCH__ __syncwarp(mask); +#endif } } // namespace Stokhos From 8bf37eef5695ed69f74bc3243e4d89ab4b0abf33 Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Wed, 27 Oct 2021 16:06:50 -0600 Subject: [PATCH 88/98] MueLu: Adding support for driving Galeri options via ParameterList in Driver --- packages/muelu/test/scaling/CMakeLists.txt | 12 +++++++++++- packages/muelu/test/scaling/Driver.cpp | 13 ++++++++++++- 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/packages/muelu/test/scaling/CMakeLists.txt b/packages/muelu/test/scaling/CMakeLists.txt index 1e089dc43537..5794d7e76b10 100644 --- a/packages/muelu/test/scaling/CMakeLists.txt +++ b/packages/muelu/test/scaling/CMakeLists.txt @@ -63,7 +63,7 @@ IF (${PACKAGE_NAME}_HAVE_TPETRA_SOLVER_STACK OR ${PACKAGE_NAME}_HAVE_EPETRA_SOLV ) TRIBITS_COPY_FILES_TO_BINARY_DIR(Driver_cp - SOURCE_FILES scaling.xml scaling.yaml scaling-complex.xml scaling-withglobalconstants.xml scaling-complex-withglobalconstants.xml circ_nsp_dependency.xml isorropia.xml iso_poisson.xml conchas_milestone_zoltan.xml conchas_milestone_zoltan2.xml conchas_milestone_zoltan2_complex.xml sa_with_ilu.xml sa_with_Ifpack2_line_detection.xml rap.xml smoother.xml smoother_complex.xml tripleMatrixProduct.xml scaling-ml.xml elasticity3D.xml amgx.json amgx.xml scaling-with-rerun.xml scaling_distance2_agg.xml smooVec.mm smooVecCoalesce.xml pairwise.xml sa_enforce_constraints.xml recurMG.xml + SOURCE_FILES scaling.xml scaling.yaml scaling-complex.xml scaling-withglobalconstants.xml scaling-complex-withglobalconstants.xml circ_nsp_dependency.xml isorropia.xml iso_poisson.xml conchas_milestone_zoltan.xml conchas_milestone_zoltan2.xml conchas_milestone_zoltan2_complex.xml sa_with_ilu.xml sa_with_Ifpack2_line_detection.xml rap.xml smoother.xml smoother_complex.xml tripleMatrixProduct.xml scaling-ml.xml elasticity3D.xml amgx.json amgx.xml scaling-with-rerun.xml scaling_distance2_agg.xml smooVec.mm smooVecCoalesce.xml pairwise.xml sa_enforce_constraints.xml recurMG.xml anisotropic.xml CATEGORIES BASIC PERFORMANCE ) @@ -114,6 +114,15 @@ TRIBITS_ADD_TEST( CATEGORIES PERFORMANCE ) + +TRIBITS_ADD_TEST( + Driver + NAME Driver_anisotropic + ARGS "xml=anisotropic.xml --tol=1e-8" + NUM_MPI_PROCS 4 + COMM mpi # HAVE_MPI required + ) + # not very elegant. The best would probably to make Reuse.cpp work for both Epetra and Tpetra IF (${PACKAGE_NAME}_HAVE_TPETRA_SOLVER_STACK) TRIBITS_ADD_EXECUTABLE( @@ -188,6 +197,7 @@ IF (${PACKAGE_NAME}_HAVE_EPETRA_SOLVER_STACK AND (NOT Xpetra_INT_LONG_LONG)) NUM_MPI_PROCS 4 COMM mpi # HAVE_MPI required ) + TRIBITS_ADD_TEST( Driver diff --git a/packages/muelu/test/scaling/Driver.cpp b/packages/muelu/test/scaling/Driver.cpp index 678c414148c6..4bf53b7019fc 100644 --- a/packages/muelu/test/scaling/Driver.cpp +++ b/packages/muelu/test/scaling/Driver.cpp @@ -307,8 +307,19 @@ MueLu::MueLu_AMGX_initialize_plugins(); if (paramList.isParameter(name)) realParams.setEntry(name, paramList.getEntry(name)); } - } + // Galeri updates (only works with Run1) + if(paramList.sublist("Run1").isSublist("Galeri")) { + ParameterList& moreParams = paramList.sublist("Run1").sublist("Galeri"); + std::cout<<"*** moreParams ***"< > nodeComm; From c47b1dcfb72c628b5ccd4b966031ad1ca9fb727b Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Wed, 27 Oct 2021 16:17:05 -0600 Subject: [PATCH 89/98] MueLu: Adding support for driving Galeri options via ParameterList in Driver --- packages/muelu/test/scaling/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/muelu/test/scaling/CMakeLists.txt b/packages/muelu/test/scaling/CMakeLists.txt index 5794d7e76b10..eb82d3baff79 100644 --- a/packages/muelu/test/scaling/CMakeLists.txt +++ b/packages/muelu/test/scaling/CMakeLists.txt @@ -118,7 +118,7 @@ TRIBITS_ADD_TEST( TRIBITS_ADD_TEST( Driver NAME Driver_anisotropic - ARGS "xml=anisotropic.xml --tol=1e-8" + ARGS "--xml=anisotropic.xml --tol=1e-6" NUM_MPI_PROCS 4 COMM mpi # HAVE_MPI required ) From e442df732449fa4baad5ec6eebb3b75e2345244f Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Wed, 27 Oct 2021 16:21:23 -0600 Subject: [PATCH 90/98] MueLu: Adding support for driving Galeri options via ParameterList in Driver --- packages/muelu/test/scaling/anisotropic.xml | 73 +++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 packages/muelu/test/scaling/anisotropic.xml diff --git a/packages/muelu/test/scaling/anisotropic.xml b/packages/muelu/test/scaling/anisotropic.xml new file mode 100644 index 000000000000..780315391b9e --- /dev/null +++ b/packages/muelu/test/scaling/anisotropic.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 3ea77b0a259a0475f223096dc908090a085b637e Mon Sep 17 00:00:00 2001 From: Chris Siefert Date: Wed, 27 Oct 2021 21:19:35 -0600 Subject: [PATCH 91/98] MueLu: Removing superfluous cout --- packages/muelu/test/scaling/Driver.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/packages/muelu/test/scaling/Driver.cpp b/packages/muelu/test/scaling/Driver.cpp index c7fd5f8c06b4..b2b4751eb6e5 100644 --- a/packages/muelu/test/scaling/Driver.cpp +++ b/packages/muelu/test/scaling/Driver.cpp @@ -312,7 +312,6 @@ MueLu::MueLu_AMGX_initialize_plugins(); // Galeri updates (only works with Run1) if(paramList.sublist("Run1").isSublist("Galeri")) { ParameterList& moreParams = paramList.sublist("Run1").sublist("Galeri"); - std::cout<<"*** moreParams ***"< Date: Thu, 28 Oct 2021 09:03:27 -0600 Subject: [PATCH 92/98] STK: Snapshot 10-28-21 09:02 --- packages/stk/CMakeLists.txt | 2 +- .../stk_expreval/stk_expreval/Evaluator.hpp | 2 +- .../cmake_install_test/build_stk_using_cmake | 2 +- .../stk/stk_mesh/stk_mesh/base/Bucket.cpp | 532 ++++++-- .../stk/stk_mesh/stk_mesh/base/Bucket.hpp | 315 ++++- .../stk_mesh/base/BucketConnectivity.hpp | 1170 +++++++++++++++++ .../stk/stk_mesh/stk_mesh/base/BulkData.cpp | 62 +- .../stk/stk_mesh/stk_mesh/base/BulkData.hpp | 219 +-- .../stk_mesh/base/ConnectedSparseNodes.hpp | 115 -- .../stk_mesh/base/ConnectedTopologyNodes.hpp | 101 -- .../stk_mesh/stk_mesh/base/Connectivity.cpp | 250 ---- .../stk_mesh/stk_mesh/base/Connectivity.hpp | 249 ---- .../stk_mesh/stk_mesh/base/DeviceField.hpp | 95 +- .../stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp | 28 +- .../stk/stk_mesh/stk_mesh/base/DeviceMesh.hpp | 2 +- .../stk/stk_mesh/stk_mesh/base/FieldBase.hpp | 20 +- .../stk_mesh/base/FieldDataManager.hpp | 1 + .../stk_mesh/stk_mesh/base/GetNgpField.hpp | 24 +- .../stk/stk_mesh/stk_mesh/base/HostField.hpp | 51 +- .../stk_mesh/stk_mesh/base/NgpFieldBase.hpp | 12 +- .../stk_mesh/base/SparseConnectivity.cpp | 193 --- .../stk_mesh/base/SparseConnectivity.hpp | 151 --- packages/stk/stk_mesh/stk_mesh/base/Types.hpp | 3 - .../stk_mesh/baseImpl/BucketRepository.cpp | 47 + .../stk_mesh/baseImpl/BucketRepository.hpp | 3 + .../stk_mesh/baseImpl/MeshImplUtils.cpp | 53 +- .../stk_mesh/baseImpl/MeshImplUtils.hpp | 15 +- .../stk_mesh/baseImpl/MeshModification.cpp | 1 - .../stk_mesh/baseImpl/MeshPrintUtils.cpp | 14 - .../stk_mesh/baseImpl/MeshPrintUtils.hpp | 3 - .../stk_mesh/baseImpl/NgpFieldAux.hpp | 35 - .../stk_unit_test_utils/BucketTester.hpp | 2 +- .../stk_unit_test_utils/CMakeLists.txt | 5 + .../stk_unit_test_utils/TextMesh.cpp | 512 +------- .../stk_unit_test_utils/TextMeshFixture.cpp | 168 +++ .../stk_unit_test_utils/TextMeshFixture.hpp | 81 ++ .../stk_unit_test_utils/TextMeshUtils.cpp | 557 ++++++++ .../stk_unit_test_utils/TextMeshUtils.hpp | 228 ++++ .../stk_mesh/UnitTestBucket.cpp | 91 +- .../stk_mesh/UnitTestBucketConnectivity.cpp | 345 +++++ .../stk_mesh/UnitTestConnectivity.cpp | 385 ------ .../stk_mesh/UnitTestSparseConnectivity.cpp | 256 ---- .../stk_mesh/UnitTestTextMesh.cpp | 202 +-- .../stk_util/environment/Scheduler.cpp | 15 +- .../stk_util/registry/ProductRegistry.cpp | 2 +- 45 files changed, 3723 insertions(+), 2896 deletions(-) create mode 100644 packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/ConnectedTopologyNodes.hpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/Connectivity.hpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp delete mode 100644 packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp create mode 100644 packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.cpp create mode 100644 packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.hpp create mode 100644 packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.cpp create mode 100644 packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.hpp create mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp delete mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp delete mode 100644 packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp diff --git a/packages/stk/CMakeLists.txt b/packages/stk/CMakeLists.txt index 22e87d5cb36f..9df9f3455c2a 100644 --- a/packages/stk/CMakeLists.txt +++ b/packages/stk/CMakeLists.txt @@ -72,7 +72,7 @@ IF ( ${PACKAGE_NAME}_DISABLE_MPI_NEIGHBOR_COMM ) SET(STK_DISABLE_MPI_NEIGHBOR_COMM TRUE) ENDIF() -IF (NOT ${PACAKGE_NAME}_ENABLE_SEACASAprepro_lib) +IF (NOT ${PACKAGE_NAME}_ENABLE_SEACASAprepro_lib) SET(NOT_HAVE_STK_SEACASAPREPRO_LIB TRUE) ENDIF() diff --git a/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp b/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp index 420e0cef16c9..0e78f9e1347f 100644 --- a/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp +++ b/packages/stk/stk_expreval/stk_expreval/Evaluator.hpp @@ -487,6 +487,7 @@ class ParsedEval using NodeView = Kokkos::View; public: + ParsedEval() = default; ParsedEval(Eval& eval); KOKKOS_DEFAULTED_FUNCTION ParsedEval(const ParsedEval&) = default; @@ -529,7 +530,6 @@ class DeviceVariableMap using VariableMapView = Kokkos::View; public: - KOKKOS_DEFAULTED_FUNCTION ~DeviceVariableMap() = default; KOKKOS_INLINE_FUNCTION diff --git a/packages/stk/stk_integration_tests/cmake_install_test/build_stk_using_cmake b/packages/stk/stk_integration_tests/cmake_install_test/build_stk_using_cmake index 67a4e05d8a41..bf41a0226134 100755 --- a/packages/stk/stk_integration_tests/cmake_install_test/build_stk_using_cmake +++ b/packages/stk/stk_integration_tests/cmake_install_test/build_stk_using_cmake @@ -77,7 +77,7 @@ exe "TRILINOS_DIR=${trilinos_dir} \ TRILINOS_INSTALL_DIR=${trilinos_install_dir} \ CMAKE_BUILD_TYPE=${build_type} \ CUDA=${cuda_on_or_off} \ - ./run_cmake_stk ${stk_build_dir}/tpl_paths >& ${stk_config_log}" + ./run_cmake_stk >& ${stk_config_log}" printf "Now building trilinos/stk using make...\n"; exe "make VERBOSE=1 -j8 >& ${stk_make_log}"; diff --git a/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp b/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp index 18696c21f07f..e18d12a7653f 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Bucket.cpp @@ -38,9 +38,8 @@ #include // for operator<<, basic_ostream, etc #include // for BulkData, field_data, etc #include // for Entity -#include -#include #include // for MetaData, get_cell_topology, etc +#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity #include "stk_mesh/base/FieldBase.hpp" // for FieldBase #include #include "stk_mesh/base/Part.hpp" // for Part @@ -51,20 +50,127 @@ namespace stk { namespace mesh { namespace impl { template class BucketConnectivity; } } } + //---------------------------------------------------------------------- namespace stk { namespace mesh { namespace { +#ifndef NDEBUG +struct CheckSizeFunctor +{ + template + void operator()(const Bucket& bucket, const Connectivity& connectivity, const Bucket*) const + { ThrowAssert(bucket.size() == static_cast(connectivity.size())); } + + bool is_modifying() const { return false; } +}; +#endif + +struct AddEntityFunctor +{ + template + void operator()(Bucket&, Connectivity& connectivity, Bucket*) + { connectivity.add_entity(); } + + bool is_modifying() const { return true; } +}; + +struct RemoveEntityFunctor +{ + template + void operator()(Bucket&, Connectivity& connectivity, Bucket*) + { connectivity.remove_entity(); } + + bool is_modifying() const { return true; } +}; + +struct DeclareRelationFunctor +{ + DeclareRelationFunctor(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, + Permutation permutation) + : m_bucket_ordinal(bucket_ordinal), + m_to(to), + m_ordinal(ordinal), + m_permutation(permutation), + m_modified(false) + {} + + template + void operator()(Bucket& bucket, Connectivity& connectivity) + { + ThrowAssert( (Connectivity::target_rank == static_cast(stk::topology::INVALID_RANK) && + bucket.mesh().entity_rank(m_to) > static_cast(stk::topology::ELEMENT_RANK)) || + bucket.mesh().entity_rank(m_to) == Connectivity::target_rank ); + ThrowAssert(!m_modified); + m_modified = connectivity.add_connectivity(m_bucket_ordinal, m_to, m_ordinal, m_permutation); + } + + unsigned m_bucket_ordinal; + Entity m_to; + ConnectivityOrdinal m_ordinal; + Permutation m_permutation; + bool m_modified; +}; + +struct DestroyRelationFunctor +{ + DestroyRelationFunctor(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) + : m_bucket_ordinal(bucket_ordinal), + m_to(to), + m_ordinal(ordinal), + m_modified(false) + {} + + template + void operator()(Bucket& bucket, Connectivity& connectivity) + { + ThrowAssert( (Connectivity::target_rank == static_cast(stk::topology::INVALID_RANK) && + bucket.mesh().entity_rank(m_to) > static_cast(stk::topology::ELEMENT_RANK)) || + bucket.mesh().entity_rank(m_to) == Connectivity::target_rank); + ThrowAssert(!m_modified); + m_modified = connectivity.remove_connectivity(m_bucket_ordinal, m_to, m_ordinal); + } + + unsigned m_bucket_ordinal; + Entity m_to; + ConnectivityOrdinal m_ordinal; + bool m_modified; +}; + +struct DebugPrintFunctor +{ + DebugPrintFunctor(std::ostream& out, unsigned ordinal = -1u) : m_out(out), m_ordinal(ordinal) {} + + template + void operator()(const Bucket&, const Connectivity& connectivity, const Bucket*) const + { + if (m_ordinal == -1u) { + connectivity.debug_dump(m_out); + } + else { + connectivity.debug_dump(m_out, m_ordinal); + } + } + + bool is_modifying() const { return false; } + + std::ostream& m_out; + unsigned m_ordinal; +}; + +template void setup_connectivity(stk::topology bucket_topology, EntityRank from_rank, EntityRank to_rank, - ConnectivityType& conn_type) + ConnectivityType& conn_type, + FixedConnectivity& fixed_conn) { if (bucket_topology != stk::topology::END_TOPOLOGY && bucket_topology.num_sub_topology(to_rank) > 0 && to_rank == stk::topology::NODE_RANK) { + fixed_conn.set_num_connectivity(bucket_topology.num_sub_topology(to_rank)); conn_type = FIXED_CONNECTIVITY; } else if (from_rank > stk::topology::ELEMENT_RANK || @@ -76,6 +182,31 @@ void setup_connectivity(stk::topology bucket_topology, } //namespace anonymous +namespace impl { + +struct OverwriteEntityFunctor +{ + OverwriteEntityFunctor(unsigned old_ordinal, unsigned new_ordinal) : m_old_ordinal(old_ordinal), m_new_ordinal(new_ordinal) {} + + template + void operator()(Bucket& bucket, Connectivity& connectivity, Bucket* otherBucket) + { + impl::BucketConnectivity & otherConnectivity = get_other_connectivity(otherBucket); + otherConnectivity.copy_entity(m_old_ordinal, connectivity, m_new_ordinal); + } + + bool is_modifying() const { return true; } + + template + static + impl::BucketConnectivity& get_other_connectivity(Bucket* other_bucket); + + unsigned m_old_ordinal; + unsigned m_new_ordinal; +}; + +} + //---------------------------------------------------------------------- bool raw_part_equal( const unsigned * lhs , const unsigned * rhs ) @@ -108,17 +239,18 @@ bool BucketLess::operator()( const unsigned * lhs , const Bucket * rhs_bucket ) const { return bucket_key_less( lhs , rhs_bucket->key() ); } +//---------------------------------------------------------------------- + Bucket::Bucket(BulkData & arg_mesh, EntityRank arg_entity_rank, const std::vector & arg_key, size_t arg_capacity, unsigned bucket_id) : m_mesh(arg_mesh), - m_sparse_connectivity(arg_mesh.get_sparse_connectivity()), m_entity_rank(arg_entity_rank), + m_topology(), m_key(arg_key), m_partOrdsBeginEnd(m_key.data()+1,m_key.data()+m_key[0]), - m_topology(get_topology(m_mesh.mesh_meta_data(), arg_entity_rank, superset_part_ordinals())), m_capacity(arg_capacity), m_size(0), m_bucket_id(bucket_id), @@ -129,16 +261,28 @@ Bucket::Bucket(BulkData & arg_mesh, m_node_kind(INVALID_CONNECTIVITY_TYPE), m_edge_kind(INVALID_CONNECTIVITY_TYPE), m_face_kind(INVALID_CONNECTIVITY_TYPE), - m_topoNodes(m_topology, m_entities), - m_sparseNodes(m_sparse_connectivity, m_entity_rank, m_entities), + m_element_kind(INVALID_CONNECTIVITY_TYPE), + m_fixed_node_connectivity(), + m_fixed_edge_connectivity(), + m_fixed_face_connectivity(), + m_fixed_element_connectivity(), + m_dynamic_node_connectivity(arg_entity_rank, &m_mesh), + m_dynamic_edge_connectivity(arg_entity_rank, &m_mesh), + m_dynamic_face_connectivity(arg_entity_rank, &m_mesh), + m_dynamic_element_connectivity(arg_entity_rank, &m_mesh), + m_dynamic_other_connectivity(arg_entity_rank, &m_mesh), m_owned(has_superset(*this, m_mesh.mesh_meta_data().locally_owned_part())), m_shared(has_superset(*this, m_mesh.mesh_meta_data().globally_shared_part())), m_aura(has_superset(*this, m_mesh.mesh_meta_data().aura_part())) { ThrowAssertMsg(arg_capacity != 0, "Buckets should never have zero capacity"); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::NODE_RANK, m_node_kind); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::EDGE_RANK, m_edge_kind); - setup_connectivity(m_topology, arg_entity_rank, stk::topology::FACE_RANK, m_face_kind); + + m_topology = get_topology(m_mesh.mesh_meta_data(), arg_entity_rank, superset_part_ordinals()); + + setup_connectivity(m_topology, arg_entity_rank, stk::topology::NODE_RANK, m_node_kind, m_fixed_node_connectivity); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::EDGE_RANK, m_edge_kind, m_fixed_edge_connectivity); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::FACE_RANK, m_face_kind, m_fixed_face_connectivity); + setup_connectivity(m_topology, arg_entity_rank, stk::topology::ELEMENT_RANK, m_element_kind, m_fixed_element_connectivity); m_parts.reserve(m_key.size()); supersets(m_parts); @@ -152,36 +296,93 @@ Bucket::~Bucket() m_mesh.destroy_bucket_callback(m_entity_rank, *this, m_capacity); } -void Bucket::change_connected_nodes(unsigned bucket_ordinal, stk::mesh::Entity* new_nodes) +size_t Bucket::memory_size_in_bytes() const { - const unsigned numNodes = m_topology.num_nodes(); - for (unsigned i=0; inum_nodes(bucket_ordinal); + Entity *nodes=0; + if (m_node_kind == FIXED_CONNECTIVITY) + { + nodes = m_fixed_node_connectivity.begin(bucket_ordinal); + } + else + { + nodes = m_dynamic_node_connectivity.begin(bucket_ordinal); + } + + for (unsigned i=0;i stk::topology::NODE_RANK && - entity_rank() <= stk::topology::ELEM_RANK) { - const unsigned numNodes = m_topology.num_nodes(); - ThrowRequireMsg(m_node_kind == FIXED_CONNECTIVITY, "Bucket topo="< 0 && fromNumNodes == numNodes) { - const Entity* entityNodes = from_bucket.begin_nodes(from_ordinal); - if (m_topology == stk::topology::INVALID_TOPOLOGY || from_bucket.topology() == stk::topology::INVALID_TOPOLOGY) { - const ConnectivityOrdinal* ords = from_bucket.begin_node_ordinals(from_ordinal); - for(unsigned i=0; imesh().add_entity_callback(entity_rank(), bucket_id(), m_size); ++m_size; + + AddEntityFunctor functor; + process_all_connectivity(functor); } bool Bucket::destroy_relation(Entity e_from, Entity e_to, const RelationIdentifier local_id ) { - EntityRank toRank = mesh().entity_rank(e_to); - if (toRank != stk::topology::NODE_RANK) { - EntityRank fromRank = mesh().entity_rank(e_from); - return m_sparse_connectivity.remove_connectivity(fromRank, e_from, toRank, e_to, local_id); - } - - Bucket& fromBucket = mesh().bucket(e_from); - if (fromBucket.bucket_id() != bucket_id()) { - return fromBucket.destroy_relation(e_from, e_to, local_id); - } - const unsigned from_bucket_ordinal = mesh().bucket_ordinal(e_from); - - CONN_TYPE(m_node_kind, m_topoNodes.set_connected_node(from_bucket_ordinal, Entity(), local_id), m_sparseNodes.set_connected_node(from_bucket_ordinal, Entity(), local_id)); - return true; + DestroyRelationFunctor functor(from_bucket_ordinal, e_to, static_cast(local_id)); + modify_connectivity(functor, m_mesh.entity_rank(e_to)); + + return functor.m_modified; } bool Bucket::declare_relation(unsigned bucket_ordinal, Entity e_to, const ConnectivityOrdinal ordinal, Permutation permutation ) { - EntityRank toRank = mesh().entity_rank(e_to); - if (toRank == stk::topology::NODE_RANK) { - return (m_node_kind==FIXED_CONNECTIVITY ? m_topoNodes.set_connected_node(bucket_ordinal, e_to, ordinal) : m_sparseNodes.reset_connected_node(bucket_ordinal, e_to, ordinal)); - } + DeclareRelationFunctor functor(bucket_ordinal, e_to, ordinal, permutation); + modify_connectivity(functor, m_mesh.entity_rank(e_to)); - return m_sparse_connectivity.add_connectivity(entity_rank(), m_entities[bucket_ordinal], - toRank, e_to, ordinal, permutation); + return functor.m_modified; } void Bucket::remove_entity() @@ -522,6 +722,9 @@ void Bucket::remove_entity() --m_size; initialize_slot(m_size, Entity()); + + RemoveEntityFunctor functor; + process_all_connectivity(functor); } void Bucket::copy_entity(Entity entity) @@ -534,11 +737,73 @@ void Bucket::copy_entity(Entity entity) ThrowAssert(mesh().entity_rank(entity) == m_entity_rank); mark_for_modification(); + Bucket* old_bucket = mesh().bucket_ptr(entity); + const unsigned old_ordinal = mesh().bucket_ordinal(entity); this->mesh().add_entity_callback(this->entity_rank(), this->bucket_id(), m_size); reset_entity_location(entity, m_size); ++m_size; + + // Unfortunately, we had to copy/paste modify_connectivity to allow dynamic->fixed moves. The + // modify_connectivity framework couldn't elegantly handle this case. + switch(m_node_kind) { + case FIXED_CONNECTIVITY: + if (old_bucket->m_node_kind == FIXED_CONNECTIVITY) { + old_bucket->m_fixed_node_connectivity.copy_entity(old_ordinal, m_fixed_node_connectivity); + } + else { + ThrowAssert(old_bucket->m_node_kind != INVALID_CONNECTIVITY_TYPE); + old_bucket->m_dynamic_node_connectivity.copy_to_fixed(old_ordinal, m_fixed_node_connectivity); + } + break; + case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_node_connectivity.copy_entity(old_ordinal, m_dynamic_node_connectivity); break; + default: break; + } + + switch(m_edge_kind) { + case FIXED_CONNECTIVITY: + if (old_bucket->m_edge_kind == FIXED_CONNECTIVITY) { + old_bucket->m_fixed_edge_connectivity.copy_entity(old_ordinal, m_fixed_edge_connectivity); + } + else { + ThrowAssert(old_bucket->m_edge_kind != INVALID_CONNECTIVITY_TYPE); + old_bucket->m_dynamic_edge_connectivity.copy_to_fixed(old_ordinal, m_fixed_edge_connectivity); + } + break; + case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_edge_connectivity.copy_entity(old_ordinal, m_dynamic_edge_connectivity); break; + default: break; + } + + switch(m_face_kind) { + case FIXED_CONNECTIVITY: + if (old_bucket->m_face_kind == FIXED_CONNECTIVITY) { + old_bucket->m_fixed_face_connectivity.copy_entity(old_ordinal, m_fixed_face_connectivity); + } + else { + ThrowAssert(old_bucket->m_face_kind != INVALID_CONNECTIVITY_TYPE); + old_bucket->m_dynamic_face_connectivity.copy_to_fixed(old_ordinal, m_fixed_face_connectivity); + } + break; + case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_face_connectivity.copy_entity(old_ordinal, m_dynamic_face_connectivity); break; + default: break; + } + + switch(m_element_kind) { + case FIXED_CONNECTIVITY: + if (old_bucket->m_element_kind == FIXED_CONNECTIVITY) { + old_bucket->m_fixed_element_connectivity.copy_entity(old_ordinal, m_fixed_element_connectivity); + } + else { + ThrowAssert(old_bucket->m_element_kind != INVALID_CONNECTIVITY_TYPE); + old_bucket->m_dynamic_element_connectivity.copy_to_fixed(old_ordinal, m_fixed_element_connectivity); + } + break; + case DYNAMIC_CONNECTIVITY: old_bucket->m_dynamic_element_connectivity.copy_entity(old_ordinal, m_dynamic_element_connectivity); break; + default: break; + } + + old_bucket->m_dynamic_other_connectivity.copy_entity(old_ordinal, m_dynamic_other_connectivity); } void Bucket::overwrite_entity(unsigned to_ordinal, Entity entity, const FieldVector* fields) @@ -548,7 +813,11 @@ void Bucket::overwrite_entity(unsigned to_ordinal, Entity entity, const FieldVec ThrowAssert(mesh().bucket_ptr(entity) != nullptr); ThrowAssert(mesh().entity_rank(entity) == m_entity_rank); + const MeshIndex from_index = m_mesh.mesh_index(entity); reset_entity_location(entity, to_ordinal, fields); + + impl::OverwriteEntityFunctor functor(from_index.bucket_ordinal, to_ordinal); + process_all_connectivity(functor, from_index.bucket); } @@ -569,5 +838,96 @@ void Bucket::parent_topology( EntityRank parent_rank, std::vector stk::util::sort_and_unique(parent_topologies); } +void Bucket::check_size_invariant() const +{ +#ifndef NDEBUG +// for (size_t i = 0; i < m_entities.size(); ++i) { +// if (i < m_size) { +// ThrowAssert(mesh().is_valid(m_entities[i])); +// } +// else { +// ThrowAssert(!mesh().is_valid(m_entities[i])); +// } +// } + + CheckSizeFunctor functor; + const_cast(this)->process_all_connectivity(functor); +#endif +} + +void Bucket::debug_dump(std::ostream& out, unsigned ordinal) const +{ + DebugPrintFunctor functor(out, ordinal); + const_cast(this)->process_all_connectivity(functor); +} + +void Bucket::debug_check_for_invalid_connectivity_request(ConnectivityType const* type) const +{ +#ifndef NDEBUG + EntityRank rank = stk::topology::END_RANK; + if (type == &m_node_kind) { + rank = stk::topology::NODE_RANK; + } + else if (type == &m_edge_kind) { + rank = stk::topology::EDGE_RANK; + } + else if (type == &m_face_kind) { + rank = stk::topology::FACE_RANK; + } + else if (type == &m_element_kind) { + rank = stk::topology::ELEMENT_RANK; + } + else { + ThrowAssert(false); + } + // Asking for connectivity between entities of equal rank is always invalid and ok to ask for + // Asking for connectivity between for FACE_RANK in 2d is always invalid and ok to ask for + bool isThisEntityAskingForConnectivityToItsOwnRank = entity_rank() == rank; + bool isThisEntityAskingForFaceConnectivityOnTwoDimensionalMesh = rank == stk::topology::FACE_RANK && mesh().mesh_meta_data().spatial_dimension() == 2; + ThrowAssert( isThisEntityAskingForConnectivityToItsOwnRank || isThisEntityAskingForFaceConnectivityOnTwoDimensionalMesh); +#endif +} + +namespace impl { + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_fixed_node_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_fixed_edge_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_fixed_face_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_fixed_element_connectivity; } + + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_dynamic_node_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_dynamic_edge_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_dynamic_face_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_dynamic_element_connectivity; } + +template <> +impl::BucketConnectivity& OverwriteEntityFunctor::get_other_connectivity(Bucket* other_bucket) +{ return other_bucket->m_dynamic_other_connectivity; } + +} + } // namespace mesh } // namespace stk diff --git a/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp b/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp index 5a4b3966bd6f..f1b6ac4da84a 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Bucket.hpp @@ -38,12 +38,10 @@ #include // for size_t, NULL #include // for lower_bound #include // for ostream +#include // for BucketConnectivity #include // for Entity #include // for contains_ordinal, Part #include -#include -#include -#include #include // for topology, etc #include // for ThrowAssert, etc #include @@ -56,6 +54,7 @@ namespace stk { namespace mesh { class FieldBase; } } namespace stk { namespace mesh { class DeviceMesh; } } namespace stk { namespace mesh { namespace impl { class BucketRepository; } } } namespace stk { namespace mesh { namespace impl { class Partition; } } } +namespace stk { namespace mesh { namespace impl { struct OverwriteEntityFunctor; } } } namespace stk { namespace mesh { @@ -76,28 +75,36 @@ print( std::ostream & , const std::string & indent , const Bucket & ); // The part count and parts are equal bool raw_part_equal( const unsigned * lhs , const unsigned * rhs ); -#define CONN_TYPE(conn_type, fixed_conn, sparse_conn) \ - ((conn_type == FIXED_CONNECTIVITY) ? fixed_conn : sparse_conn) +#define CONNECTIVITY_TYPE_SWITCH(entity_kind, fixed_func_sig, dynamic_func_sig, check_invalid) \ + switch(entity_kind) { \ + case FIXED_CONNECTIVITY: \ + return fixed_func_sig; \ + case DYNAMIC_CONNECTIVITY: \ + return dynamic_func_sig; \ + default: \ + if (check_invalid) { \ + check_for_invalid_connectivity_request(&entity_kind); \ + } \ + return 0; \ + } -#define RANK_SWITCH(rank, begin_or_end, item_type, bucket_ordinal) \ +#define RANK_SWITCH(rank, begin_or_end, postfix, bucket_ordinal) \ \ - switch(rank) { \ - case stk::topology::NODE_RANK: \ - switch(m_node_kind) { \ - case FIXED_CONNECTIVITY: return m_topoNodes.begin_or_end##item_type(bucket_ordinal); \ - case DYNAMIC_CONNECTIVITY: return m_sparseNodes.begin_or_end##item_type(bucket_ordinal); \ - default: return nullptr; \ - } \ - default: \ - return m_sparse_connectivity.begin_or_end##item_type(m_entities[bucket_ordinal], rank); \ + switch(rank) { \ + case stk::topology::NODE_RANK: return begin_or_end##_node##postfix(bucket_ordinal); \ + case stk::topology::EDGE_RANK: return begin_or_end##_edge##postfix(bucket_ordinal); \ + case stk::topology::FACE_RANK: return begin_or_end##_face##postfix(bucket_ordinal); \ + case stk::topology::ELEMENT_RANK: return begin_or_end##_element##postfix(bucket_ordinal); \ + default: \ + return begin_other##postfix(bucket_ordinal) + get_others_##begin_or_end##_index(bucket_ordinal, rank); \ } //---------------------------------------------------------------------- -/** \brief A container for a homogeneous collection of +/** \brief A container for the connectivity for a homogeneous collection of * \ref stk::mesh::Entity "entities". * - * The entities are homogeneous in that they are of the same rank and topology - * and are members of the same parts. + * The entities are homogeneous in that they are of the same entity type + * and are members of the same of parts. */ class Bucket { @@ -127,6 +134,8 @@ class Bucket /** \brief Number of entities associated with this bucket */ size_type size() const { return m_size ; } + size_t memory_size_in_bytes() const; + /** \brief Capacity of this bucket */ size_t capacity() const { return m_capacity ; } @@ -203,83 +212,87 @@ class Bucket int parallel_owner_rank(unsigned ordinal) const; + void check_size_invariant() const; + //generic rank connectivity calls Entity const* begin(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, begin, _connectivity, bucket_ordinal) } + { RANK_SWITCH(rank, begin, s, bucket_ordinal) } ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal, EntityRank rank) const { RANK_SWITCH(rank, begin, _ordinals, bucket_ordinal) } Permutation const* begin_permutations(unsigned bucket_ordinal, EntityRank rank) const - { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], rank); } + { RANK_SWITCH(rank, begin, _permutations, bucket_ordinal) } Entity const* end(unsigned bucket_ordinal, EntityRank rank) const - { RANK_SWITCH(rank, end, _connectivity, bucket_ordinal) } + { RANK_SWITCH(rank, end, s, bucket_ordinal) } ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal, EntityRank rank) const { RANK_SWITCH(rank, end, _ordinals, bucket_ordinal) } Permutation const* end_permutations(unsigned bucket_ordinal, EntityRank rank) const - { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], rank); } + { RANK_SWITCH(rank, end, _permutations, bucket_ordinal) } unsigned num_connectivity(unsigned bucket_ordinal, EntityRank rank) const; Entity const* begin_nodes(unsigned bucket_ordinal) const - { return CONN_TYPE(m_node_kind, m_topoNodes.begin_connectivity(bucket_ordinal), m_sparseNodes.begin_connectivity(bucket_ordinal)); } + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin(bucket_ordinal), m_dynamic_node_connectivity.begin(bucket_ordinal), true) } Entity const* begin_edges(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin(bucket_ordinal), m_dynamic_edge_connectivity.begin(bucket_ordinal), true) } Entity const* begin_faces(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin(bucket_ordinal), m_dynamic_face_connectivity.begin(bucket_ordinal), true) } Entity const* begin_elements(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin(bucket_ordinal), m_dynamic_element_connectivity.begin(bucket_ordinal), true) } ConnectivityOrdinal const* begin_node_ordinals(unsigned bucket_ordinal) const - { return CONN_TYPE(m_node_kind, m_topoNodes.begin_ordinals(bucket_ordinal), m_sparseNodes.begin_ordinals(bucket_ordinal)); } + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_node_connectivity.begin_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* begin_edge_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_edge_connectivity.begin_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* begin_face_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_face_connectivity.begin_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* begin_element_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_ordinals(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin_ordinals(bucket_ordinal), m_dynamic_element_connectivity.begin_ordinals(bucket_ordinal), true) } - Permutation const* begin_node_permutations(unsigned bucket_ordinal) const { return nullptr; } + Permutation const* begin_node_permutations(unsigned bucket_ordinal) const + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.begin_permutations(bucket_ordinal), m_dynamic_node_connectivity.begin_permutations(bucket_ordinal), true) } Permutation const* begin_edge_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.begin_permutations(bucket_ordinal), m_dynamic_edge_connectivity.begin_permutations(bucket_ordinal), true) } Permutation const* begin_face_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.begin_permutations(bucket_ordinal), m_dynamic_face_connectivity.begin_permutations(bucket_ordinal), true) } Permutation const* begin_element_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.begin_permutations(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.begin_permutations(bucket_ordinal), m_dynamic_element_connectivity.begin_permutations(bucket_ordinal), true) } unsigned num_nodes(unsigned bucket_ordinal) const - { return CONN_TYPE(m_node_kind, m_topoNodes.num_nodes_per_entity(bucket_ordinal), m_sparseNodes.num_nodes_per_entity(bucket_ordinal)); } + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.num_connectivity(bucket_ordinal), m_dynamic_node_connectivity.num_connectivity(bucket_ordinal), false) } unsigned num_edges(unsigned bucket_ordinal) const - { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.num_connectivity(bucket_ordinal), m_dynamic_edge_connectivity.num_connectivity(bucket_ordinal), false) } unsigned num_faces(unsigned bucket_ordinal) const - { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.num_connectivity(bucket_ordinal), m_dynamic_face_connectivity.num_connectivity(bucket_ordinal), false) } unsigned num_elements(unsigned bucket_ordinal) const - { return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.num_connectivity(bucket_ordinal), m_dynamic_element_connectivity.num_connectivity(bucket_ordinal), false) } Entity const* end_nodes(unsigned bucket_ordinal) const - { return CONN_TYPE(m_node_kind, m_topoNodes.end_connectivity(bucket_ordinal), m_sparseNodes.end_connectivity(bucket_ordinal)); } + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end(bucket_ordinal), m_dynamic_node_connectivity.end(bucket_ordinal), true) } Entity const* end_edges(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end(bucket_ordinal), m_dynamic_edge_connectivity.end(bucket_ordinal), true) } Entity const* end_faces(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end(bucket_ordinal), m_dynamic_face_connectivity.end(bucket_ordinal), true) } Entity const* end_elements(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_connectivity(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end(bucket_ordinal), m_dynamic_element_connectivity.end(bucket_ordinal), true) } ConnectivityOrdinal const* end_node_ordinals(unsigned bucket_ordinal) const - { return CONN_TYPE(m_node_kind, m_topoNodes.end_ordinals(bucket_ordinal), m_sparseNodes.end_ordinals(bucket_ordinal)); } + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end_ordinals(bucket_ordinal), m_dynamic_node_connectivity.end_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* end_edge_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end_ordinals(bucket_ordinal), m_dynamic_edge_connectivity.end_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* end_face_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end_ordinals(bucket_ordinal), m_dynamic_face_connectivity.end_ordinals(bucket_ordinal), true) } ConnectivityOrdinal const* end_element_ordinals(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_ordinals(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end_ordinals(bucket_ordinal), m_dynamic_element_connectivity.end_ordinals(bucket_ordinal), true) } - Permutation const* end_node_permutations(unsigned bucket_ordinal) const { return nullptr; } + Permutation const* end_node_permutations(unsigned bucket_ordinal) const + { CONNECTIVITY_TYPE_SWITCH(m_node_kind, m_fixed_node_connectivity.end_permutations(bucket_ordinal), m_dynamic_node_connectivity.end_permutations(bucket_ordinal), true) } Permutation const* end_edge_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::EDGE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_edge_kind, m_fixed_edge_connectivity.end_permutations(bucket_ordinal), m_dynamic_edge_connectivity.end_permutations(bucket_ordinal), true) } Permutation const* end_face_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::FACE_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_face_kind, m_fixed_face_connectivity.end_permutations(bucket_ordinal), m_dynamic_face_connectivity.end_permutations(bucket_ordinal), true) } Permutation const* end_element_permutations(unsigned bucket_ordinal) const - { return m_sparse_connectivity.end_permutations(m_entities[bucket_ordinal], stk::topology::ELEM_RANK); } + { CONNECTIVITY_TYPE_SWITCH(m_element_kind, m_fixed_element_connectivity.end_permutations(bucket_ordinal), m_dynamic_element_connectivity.end_permutations(bucket_ordinal), true) } bool has_permutation(EntityRank rank) const; @@ -291,7 +304,7 @@ class Bucket using ConnectedOrdinals = util::StridedArray; using Permutations = util::StridedArray; -#ifndef STK_HIDE_DEPRECATED_CODE // Delete after November 2021 +#ifndef STK_HIDE_DEPRECATED_CODE // Delete after September 2021 STK_DEPRECATED unsigned get_num_nodes_per_entity() const { return topology().num_nodes(); } #endif @@ -336,17 +349,44 @@ class Bucket void reset_bucket_parts(const OrdinalVector& newPartOrdinals); protected: - void change_connected_nodes(unsigned bucket_ordinal, Entity* new_nodes); - void change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, ConnectivityOrdinal elem_connectivity_ordinal, Permutation permut); - void change_existing_permutation_for_connected_edge(unsigned bucket_ordinal_of_higher_ranked_entity, ConnectivityOrdinal edge_connectivity_ordinal, Permutation permut); - void change_existing_permutation_for_connected_face(unsigned bucket_ordinal_of_higher_ranked_entity, ConnectivityOrdinal face_connectivity_ordinal, Permutation permut); + void change_existing_connectivity(unsigned bucket_ordinal, stk::mesh::Entity* new_nodes); + void change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, unsigned elem_connectivity_ordinal, stk::mesh::Permutation permut); + void change_existing_permutation_for_connected_edge(unsigned bucket_ordinal_of_higher_ranked_entity, unsigned edge_connectivity_ordinal, stk::mesh::Permutation permut); + void change_existing_permutation_for_connected_face(unsigned bucket_ordinal_of_higher_ranked_entity, unsigned face_connectivity_ordinal, stk::mesh::Permutation permut); virtual ~Bucket(); -protected: +private: + bool destroy_relation(Entity e_from, Entity e_to, const RelationIdentifier local_id ); bool declare_relation(unsigned bucket_ordinal, Entity e_to, const ConnectivityOrdinal ordinal, Permutation permutation); + // The following *_other* functions should not be made available externally, in + // order to avoid external confusion with "constraint" and "other" connectivities. + // They are currently used within this class to provide connectivities + // externally through another interface. + Entity const* begin_others(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.begin(bucket_ordinal); + } + ConnectivityOrdinal const* begin_other_ordinals(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.begin_ordinals(bucket_ordinal); + } + Permutation const* begin_other_permutations(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.begin_permutations(bucket_ordinal); + } + unsigned num_other(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.num_connectivity(bucket_ordinal); + } + Entity const* end_others(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.end(bucket_ordinal); + } + ConnectivityOrdinal const* end_other_ordinals(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.end_ordinals(bucket_ordinal); + } + Permutation const* end_other_permutations(unsigned bucket_ordinal) const { + return m_dynamic_other_connectivity.end_permutations(bucket_ordinal); + } + void supersets( PartVector & ) const ; /** \brief The \ref stk::mesh::BulkData "bulk data manager" @@ -403,34 +443,65 @@ class Bucket // Optional fields argument, only copy listed fields void reset_entity_location(Entity entity, unsigned to_ordinal, const std::vector* fields = nullptr); - friend class BulkData; - friend class impl::Partition; + unsigned get_others_begin_index(unsigned bucket_ordinal, EntityRank rank) const; + unsigned get_others_end_index(unsigned bucket_ordinal, EntityRank rank) const; + unsigned get_others_index_count(unsigned bucket_ordinal, EntityRank rank) const; + + template + void modify_connectivity(T& callable, EntityRank rank); + + template + void process_all_connectivity(T& callable, Bucket* other_bucket = nullptr); + + void check_for_invalid_connectivity_request(ConnectivityType const* type) const + { +#ifndef NDEBUG + debug_check_for_invalid_connectivity_request(type); +#endif + } + + void debug_check_for_invalid_connectivity_request(ConnectivityType const* type) const; + friend class impl::BucketRepository; + friend class impl::Partition; + friend struct impl::OverwriteEntityFunctor; + friend class BulkData; // Replacement friend. + friend struct Entity; friend class DeviceMesh; BulkData & m_mesh ; // Where this bucket resides - SparseConnectivity & m_sparse_connectivity; const EntityRank m_entity_rank ; // Type of entities for this bucket + stk::topology m_topology ; // The topology of this bucket std::vector m_key ; // REFACTOR std::pair m_partOrdsBeginEnd; - stk::topology m_topology ; // The topology of this bucket const size_t m_capacity ; // Capacity for entities size_type m_size ; // Number of entities - unsigned m_bucket_id; + unsigned m_bucket_id; // Index into its BucketRepository's m_bucket[entity_rank()], these are NOT unique unsigned m_ngp_bucket_id; bool m_is_modified; PartVector m_parts; // Entity data - std::vector m_entities; + std::vector m_entities; // Array of entity handles; will be removed soon impl::Partition *m_partition; ConnectivityType m_node_kind; ConnectivityType m_edge_kind; ConnectivityType m_face_kind; - ConnectedTopologyNodes m_topoNodes; - ConnectedSparseNodes m_sparseNodes; + ConnectivityType m_element_kind; + + impl::BucketConnectivity m_fixed_node_connectivity; // fixed connectivity to nodes + impl::BucketConnectivity m_fixed_edge_connectivity; // fixed connectivity to edges + impl::BucketConnectivity m_fixed_face_connectivity; // fixed connectivity to faces + impl::BucketConnectivity m_fixed_element_connectivity; // fixed connectivity to elements + + impl::BucketConnectivity m_dynamic_node_connectivity; // dynamic connectivity to nodes + impl::BucketConnectivity m_dynamic_edge_connectivity; // dynamic connectivity to edges + impl::BucketConnectivity m_dynamic_face_connectivity; // dynamic connectivity to faces + impl::BucketConnectivity m_dynamic_element_connectivity; // dynamic connectivity to elements + + impl::BucketConnectivity m_dynamic_other_connectivity; // dynamic connectivity to everything else bool m_owned; bool m_shared; @@ -439,6 +510,8 @@ class Bucket std::vector m_ngp_field_bucket_id; std::vector m_ngp_field_is_modified; }; +#undef CONNECTIVITY_TYPE_SWITCH +#undef RANK_SWITCH /** \brief Is this bucket a subset of the given * \ref stk::mesh::Part "part" by partID @@ -519,16 +592,31 @@ inline unsigned Bucket::num_connectivity(unsigned bucket_ordinal, EntityRank rank) const { switch(rank) { - case stk::topology::NODE_RANK: return num_nodes(bucket_ordinal); + case stk::topology::NODE_RANK: return num_nodes(bucket_ordinal); + case stk::topology::EDGE_RANK: return num_edges(bucket_ordinal); + case stk::topology::FACE_RANK: return num_faces(bucket_ordinal); + case stk::topology::ELEMENT_RANK: return num_elements(bucket_ordinal); default: - return m_sparse_connectivity.num_connectivity(m_entities[bucket_ordinal], rank); + return get_others_index_count(bucket_ordinal, rank); } } inline bool Bucket::has_permutation(EntityRank rank) const { - return SparseConnectivity::has_permutation(entity_rank(), rank); + switch(rank) { + case stk::topology::NODE_RANK: + return m_node_kind == FIXED_CONNECTIVITY ? m_fixed_node_connectivity.has_permutation() : m_dynamic_node_connectivity.has_permutation(); + case stk::topology::EDGE_RANK: + return m_edge_kind == FIXED_CONNECTIVITY ? m_fixed_edge_connectivity.has_permutation() : m_dynamic_edge_connectivity.has_permutation(); + case stk::topology::FACE_RANK: + return m_face_kind == FIXED_CONNECTIVITY ? m_fixed_face_connectivity.has_permutation() : m_dynamic_face_connectivity.has_permutation(); + case stk::topology::ELEMENT_RANK: + return m_element_kind == FIXED_CONNECTIVITY ? m_fixed_element_connectivity.has_permutation() : m_dynamic_element_connectivity.has_permutation(); + case stk::topology::CONSTRAINT_RANK: + default: + return false; + } } inline @@ -541,15 +629,106 @@ ConnectivityType Bucket::connectivity_type(EntityRank rank) const return m_edge_kind; case stk::topology::FACE_RANK: return m_face_kind; + case stk::topology::ELEMENT_RANK: + return m_element_kind; default: return DYNAMIC_CONNECTIVITY; } } +template +inline +void Bucket::process_all_connectivity(T& callable, Bucket* other_bucket) +{ + if (callable.is_modifying()) { + mark_for_modification(); + } + + switch(m_node_kind) { + case FIXED_CONNECTIVITY: + callable.template operator()(*this, m_fixed_node_connectivity, other_bucket); break; + case DYNAMIC_CONNECTIVITY: + callable.template operator()(*this, m_dynamic_node_connectivity, other_bucket); break; + default: break; + } + + switch(m_edge_kind) { + case FIXED_CONNECTIVITY: + callable.template operator()(*this, m_fixed_edge_connectivity, other_bucket); break; + case DYNAMIC_CONNECTIVITY: + callable.template operator()(*this, m_dynamic_edge_connectivity, other_bucket); break; + default: break; + } + + switch(m_face_kind) { + case FIXED_CONNECTIVITY: + callable.template operator()(*this, m_fixed_face_connectivity, other_bucket); break; + case DYNAMIC_CONNECTIVITY: + callable.template operator()(*this, m_dynamic_face_connectivity, other_bucket); break; + default: break; + } + + switch(m_element_kind) { + case FIXED_CONNECTIVITY: + callable.template operator()(*this, m_fixed_element_connectivity, other_bucket); break; + case DYNAMIC_CONNECTIVITY: + callable.template operator()(*this, m_dynamic_element_connectivity, other_bucket); break; + default: break; + } + + callable.template operator()(*this, m_dynamic_other_connectivity, other_bucket); +} + +template +inline +void Bucket::modify_connectivity(T& callable, EntityRank rank) +{ + switch(rank) { + case stk::topology::NODE_RANK: + ThrowAssert(m_node_kind != INVALID_CONNECTIVITY_TYPE); + mark_for_modification(); + + switch(m_node_kind) { + case FIXED_CONNECTIVITY: callable(*this, m_fixed_node_connectivity); break; + case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_node_connectivity); break; + default: break; + } + break; + case stk::topology::EDGE_RANK: + ThrowAssert(m_edge_kind != INVALID_CONNECTIVITY_TYPE); + switch(m_edge_kind) { + case FIXED_CONNECTIVITY: callable(*this, m_fixed_edge_connectivity); break; + case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_edge_connectivity); break; + default: break; + } + break; + case stk::topology::FACE_RANK: + ThrowAssert(m_face_kind != INVALID_CONNECTIVITY_TYPE); + switch(m_face_kind) { + case FIXED_CONNECTIVITY: callable(*this, m_fixed_face_connectivity); break; + case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_face_connectivity); break; + default: break; + } + break; + case stk::topology::ELEMENT_RANK: + ThrowAssert(m_element_kind != INVALID_CONNECTIVITY_TYPE); + switch(m_element_kind) { + case FIXED_CONNECTIVITY: callable(*this, m_fixed_element_connectivity); break; + case DYNAMIC_CONNECTIVITY: callable(*this, m_dynamic_element_connectivity); break; + default: break; + } + break; + default: + callable(*this, m_dynamic_other_connectivity); + break; + } +} + typedef Bucket::iterator BucketIterator; } // namespace mesh } // namespace stk -#endif + +#endif diff --git a/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp b/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp new file mode 100644 index 000000000000..c5d6391af751 --- /dev/null +++ b/packages/stk/stk_mesh/stk_mesh/base/BucketConnectivity.hpp @@ -0,0 +1,1170 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#ifndef STK_MESH_BUCKET_CONNECTIVITY_HPP +#define STK_MESH_BUCKET_CONNECTIVITY_HPP + +#include "stk_mesh/base/Types.hpp" // for ConnectivityOrdinal, etc +#include // for Entity +#include "stk_util/util/ReportHandler.hpp" + +namespace stk { +namespace mesh { + +class BulkData; + +namespace impl { + +struct LowerConnectivityCompare +{ + bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const + { + // only compare ordinals + return first_ordinal < second_ordinal; + } +}; + +template +struct LowerConnectivitityRankSensitiveCompare +{ + LowerConnectivitityRankSensitiveCompare(const BULKDATA &bulk_data) : m_mesh(bulk_data) { } + + const BULKDATA &m_mesh; + + bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, + Entity second_entity, ConnectivityOrdinal second_ordinal) const; +}; + +struct HigherConnectivityCompare +{ + bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const + { + // Needs to match LessRelation in BulkData.hpp + return std::make_pair(first_ordinal, first_entity.is_local_offset_valid() ? first_entity.local_offset() : Entity::MaxEntity) < + std::make_pair(second_ordinal, second_entity.is_local_offset_valid() ? second_entity.local_offset() : Entity::MaxEntity); + } +}; + +template +struct HigherConnectivityRankSensitiveCompare +{ + HigherConnectivityRankSensitiveCompare(const BULKDATA &bulk_data) : m_mesh(bulk_data) { } + + const BULKDATA &m_mesh; + + bool operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, + ConnectivityOrdinal second_ordinal) const; +}; + +template +inline void check_bucket_ordinal(unsigned bucket_ordinal, Connectivity const* connectivity) +{ + ThrowAssertMsg(bucket_ordinal < connectivity->size(), + "bucket_ordinal " << bucket_ordinal << " is out of range, bucket size is " << connectivity->size()); +} + +template +class BucketConnectivity; + +template +size_t capacity_in_bytes(const VecType& v) +{ + return sizeof(typename VecType::value_type)*v.capacity(); +} + +template +class BucketConnectivity +{ + public: + typedef BucketConnectivity SelfType; + typedef BucketConnectivity OtherType; + + static const EntityRank target_rank = TargetRank; + static const ConnectivityType connectivity_type = FIXED_CONNECTIVITY; + + typedef std::vector EntityVector; + typedef std::vector ConnectivityOrdinalVector; + typedef std::vector PermutationVector; + + BucketConnectivity() //default constructed BucketConnectivity implies connectivity is not used + : m_num_connectivity(0u) + , m_targets() + , m_ordinals() + , m_permutations() + {} + + BucketConnectivity(unsigned arg_num_connectivity) + : m_num_connectivity(0) + , m_targets() + , m_ordinals() + , m_permutations() + { + set_num_connectivity(arg_num_connectivity); + } + + void set_num_connectivity(unsigned arg_num_connectivity) + { + ThrowAssertMsg(m_num_connectivity == 0, "Cannot reset num_connectivity"); + ThrowAssertMsg(arg_num_connectivity != 0, "Cannot set num connectivity to 0 for fixed connectivity"); + + m_num_connectivity = arg_num_connectivity; + + // Ordinal is the same for all fixed, just counts up + m_ordinals.resize(m_num_connectivity); + for (ConnectivityOrdinal ord=static_cast(0); ord < static_cast(m_num_connectivity); ++ord) { + m_ordinals[ord] = ord; + } + } + + // Entity iterator + + Entity const* begin(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[bucket_ordinal * m_num_connectivity]; } + + Entity * begin(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[bucket_ordinal * m_num_connectivity]; } + + Entity const* end(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[(bucket_ordinal + 1) * m_num_connectivity]; } + + Entity * end(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[(bucket_ordinal + 1) * m_num_connectivity]; } + + // Ordinal iterator + + ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return m_ordinals.data(); } + + ConnectivityOrdinal * begin_ordinals(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return m_ordinals.data(); } + + ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return m_ordinals.data() + m_num_connectivity; } + + ConnectivityOrdinal * end_ordinals(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return m_ordinals.data() + m_num_connectivity; } + + // Permutation iterator + + Permutation const* begin_permutations(unsigned bucket_ordinal) const + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[bucket_ordinal * m_num_connectivity]; + } + + Permutation * begin_permutations(unsigned bucket_ordinal) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[bucket_ordinal * m_num_connectivity]; + } + + Permutation const* end_permutations(unsigned bucket_ordinal) const + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[(bucket_ordinal + 1) * m_num_connectivity]; + } + + Permutation * end_permutations(unsigned bucket_ordinal) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[(bucket_ordinal + 1) * m_num_connectivity]; + } + + // Queries + + unsigned num_connectivity(unsigned /*bucket_ordinal*/) const + { return m_num_connectivity; } + + // return number of entities + unsigned size() const + { return m_targets.size() / m_num_connectivity; } + + // Modification API + + bool add_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation = INVALID_PERMUTATION) + { + ThrowAssertMsg(ordinal < m_num_connectivity, + "Ordinal " << (uint32_t)ordinal << " exceeds topological limit: " << m_num_connectivity); + impl::check_bucket_ordinal(bucket_ordinal, this); +#ifndef NDEBUG + // TODO - Add topology invariant; target entity should match a sub topology +#endif + + unsigned index = m_num_connectivity*bucket_ordinal + ordinal; + + if (m_targets[index] == to) { + ThrowAssert(!has_permutation() || m_permutations[index] == permutation); + // Already exists + return false; + } + + m_targets[index] = to; + + if (has_permutation()) { + m_permutations[index] = permutation; + } + + return true; + } + + bool remove_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) + { + ThrowAssertMsg(ordinal < m_num_connectivity, + "Ordinal " << (uint32_t)ordinal << " exceeds topological limit: " << m_num_connectivity); + impl::check_bucket_ordinal(bucket_ordinal, this); + + unsigned index = m_num_connectivity*bucket_ordinal + ordinal; + if (m_targets[index] != to) { + return false; + } + + // Clear + m_targets[index] = Entity(); + if (has_permutation()) { + m_permutations[index] = INVALID_PERMUTATION; + } + + return true; + } + + void begin_modification() + {} + + template // hack to get around dependency + void end_modification(BULKDATA* mesh = NULL); + + void add_entity() + { + const unsigned new_conn_size = m_targets.size() + m_num_connectivity; + Entity invalid; + m_targets.resize(new_conn_size, invalid); // Not a perf issue: vectors are smart when resizing + if (has_permutation()) { + m_permutations.resize(new_conn_size, INVALID_PERMUTATION); + } + } + + // Always removes last entity + void remove_entity() + { + ThrowAssertMsg(size() > 0, "Cannot remove, connectivity is already empty"); + + const unsigned new_conn_size = m_targets.size() - m_num_connectivity; + m_targets.resize(new_conn_size); + if (has_permutation()) { + m_permutations.resize(new_conn_size); + } + } + + void copy_entity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal=-1u) + { + ThrowAssertMsg(size() > 0, "Cannot move, connectivity is empty"); + + if (to_ordinal == -1u) { // check if we should just append + to_ordinal = to.size(); + to.add_entity(); // make room for new entity + } + + // Copy connectivity to other BucketConnectivity + copy_connectivity(from_ordinal, to, to_ordinal); + } + + void copy_to_fixed(unsigned from_ordinal, SelfType& to) + { ThrowAssert(false); } + + void copy_to_fixed(unsigned from_ordinal, OtherType& to) + { ThrowAssert(false); } + + bool has_permutation() const + { + const static bool rv = TargetRank != stk::topology::NODE_RANK; + return rv; + } + + size_t heap_memory_in_bytes() const + { + return capacity_in_bytes(m_targets) + + capacity_in_bytes(m_ordinals) + + capacity_in_bytes(m_permutations); + } + + void debug_dump(std::ostream& out) const + { + out << "For fixed connectivity to rank: " << TargetRank << "\n"; + out << " size is: " << size() << "\n"; + for (int i = 0, ie = size(); i < ie; ++i) { + out << " At ordinal " << i << "\n"; + debug_dump(out, i); + } + out << std::endl; + } + + void debug_dump(std::ostream& out, unsigned ordinal) const + { + for (int j = m_num_connectivity * ordinal, je = m_num_connectivity*(ordinal+1); j < je; ++j) { + out << " target:" << m_targets[j].local_offset() << "\n"; + } + } + +private: + + void copy_connectivity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal) + { + unsigned to_offset = to_ordinal * m_num_connectivity; + unsigned from_offset = from_ordinal * m_num_connectivity; + + std::copy(m_targets.begin() + from_offset, + m_targets.begin() + from_offset + m_num_connectivity, + to.m_targets.begin() + to_offset); + + if (has_permutation()) { + std::copy(m_permutations.begin() + from_offset, + m_permutations.begin() + from_offset + m_num_connectivity, + to.m_permutations.begin() + to_offset); + } + } + + // Illegal + BucketConnectivity(const SelfType&); + SelfType& operator=(const SelfType&); + + // MEMBERS + + unsigned m_num_connectivity; + + // connectivity data + EntityVector m_targets; + ConnectivityOrdinalVector m_ordinals; // shared for all entities + PermutationVector m_permutations; + + // friend OtherType; // 1337! Will have to wait for c++11 + friend class BucketConnectivity; +}; + +// Want a way for all dynamic connectivity instantiations to share the same id space +struct Counter +{ + static int counter; +}; + +// Profiling data for an individual dynamic connectivity object +struct DynConnData +{ + // from-rank for the associated dynamic connectivity + EntityRank m_from_rank; + + // to-rank for the associated dynamic connectivity + EntityRank m_to_rank; + + // the maximum capacity ever achieved by connectivity vectors + size_t m_max_capacity; + + // at the point at which maximum capacity (member above) was achieved, how much memory + // was lost due to "abandoned space". + // "abandoned space" - When an entity overflows its current chunks, it gets additional + // chunks but must be copied to the end. The space left behind is abandoned and will + // not be reused until the next compress (resize_and_order_by_index). + size_t m_abandoned_space; + + // at the point at which maximum capacity (member above) was achieved, how much memory + // was lost due to unused chunk capacity. If chunk size is > 1, it's possible that an + // entity is not using all the space available in it's chunk. For example, if chunk size + // is 8 and an entity has 5 connectivities, then unused chunk capacity is 3 for that + // entity. This member stores the sum over all entities. + size_t m_unused_chunk_capacity; + + // The number of times this dynamic connectivity had to be grown + size_t m_num_growths; + + // The number of times any entity overflowed it's chunk allocation and had to be + // copied to the end + size_t m_num_entity_relocations; + + // at the point at which maximum capacity (member above) was achieved, what is the + // total amount of wasted memory + size_t m_total_unused_memory; + + // at the point at which maximum capacity (member above) was achieved, what is the + // amount of memory that is wasted due to vector capacity growth over-provisioning. + size_t m_unused_capacity; + + // at the point at which maximum capacity (member above) was achieved, what is the + // number of connectivity being stored. + size_t m_total_num_conn; + + DynConnData(EntityRank from_rank, EntityRank to_rank) : + m_from_rank(from_rank), + m_to_rank(to_rank), + m_max_capacity(0), + m_abandoned_space(0), + m_unused_chunk_capacity(0), + m_num_growths(0), + m_num_entity_relocations(0), + m_total_unused_memory(0), + m_unused_capacity(0), + m_total_num_conn(0) + {} +}; + +template +class BucketConnectivity +{ + enum connectivity_direction { Lower=0,Higher=1,Adjacent=2 }; + +public: + typedef BucketConnectivity SelfType; + typedef BucketConnectivity OtherType; + + static const EntityRank target_rank = TargetRank; + static const ConnectivityType connectivity_type = DYNAMIC_CONNECTIVITY; + + typedef std::vector EntityVector; + typedef std::vector ConnectivityOrdinalVector; + typedef std::vector PermutationVector; + typedef std::vector UInt32Vector; + typedef std::vector UInt16Vector; + + static const unsigned chunk_size = 1u; + + BucketConnectivity(EntityRank from_rank, BulkData *bulk_data) + : m_from_rank(from_rank) + , m_direction( (m_from_rank > TargetRank) ? Lower : ((m_from_rank == TargetRank) ? Adjacent : Higher)) + , m_active(false) + , m_needs_shrink_to_fit(false) + , m_num_inactive(0) + , m_indices() + , m_num_connectivities() + , m_total_connectivities(0) + , m_targets() + , m_ordinals() + , m_permutations() + , m_bulk_data(bulk_data) + , m_id(Counter::counter++) + , m_rank_sensitive_higher_connectivity_cmp(*m_bulk_data) + , m_rank_sensitive_lower_connectivity_cmp(*m_bulk_data) + , m_last_capacity(0) + { + } + + // Entity iterator + + Entity const* begin(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[m_active ? m_indices[bucket_ordinal] : 0]; } + + Entity * begin(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_targets[m_active ? m_indices[bucket_ordinal] : 0]; } + + Entity const* end(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return begin(bucket_ordinal) + num_connectivity(bucket_ordinal); } + + Entity * end(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return begin(bucket_ordinal) + num_connectivity(bucket_ordinal); } + + // Ordinal iterator + + ConnectivityOrdinal const* begin_ordinals(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_ordinals[m_active ? m_indices[bucket_ordinal] : 0]; } + + ConnectivityOrdinal * begin_ordinals(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return &m_ordinals[m_active ? m_indices[bucket_ordinal] : 0]; } + + ConnectivityOrdinal const* end_ordinals(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return begin_ordinals(bucket_ordinal) + num_connectivity(bucket_ordinal); } + + ConnectivityOrdinal * end_ordinals(unsigned bucket_ordinal) + { impl::check_bucket_ordinal(bucket_ordinal, this); + return begin_ordinals(bucket_ordinal) + num_connectivity(bucket_ordinal); } + + // Permutation iterator + + Permutation const* begin_permutations(unsigned bucket_ordinal) const + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[m_active ? m_indices[bucket_ordinal] : 0]; + } + + Permutation * begin_permutations(unsigned bucket_ordinal) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return &m_permutations[m_active ? m_indices[bucket_ordinal] : 0]; + } + + Permutation const* end_permutations(unsigned bucket_ordinal) const + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return begin_permutations(bucket_ordinal) + num_connectivity(bucket_ordinal); + } + + Permutation * end_permutations(unsigned bucket_ordinal) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + if (!has_permutation()) return NULL; + return begin_permutations(bucket_ordinal) + num_connectivity(bucket_ordinal); + } + + // Queries + + unsigned num_connectivity(unsigned bucket_ordinal) const + { impl::check_bucket_ordinal(bucket_ordinal, this); + return m_active ? m_num_connectivities[bucket_ordinal] : 0; } + + // return number of entities + unsigned size() const + { return m_active ? m_indices.size() : m_num_inactive; } + + // Modification API + + bool add_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation = INVALID_PERMUTATION) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + + m_needs_shrink_to_fit = true; + + if (!m_active) { + activate(); + } + + if (target_rank <= stk::topology::ELEMENT_RANK) { + switch(m_direction) + { + case Lower: return add_helper(bucket_ordinal, to, ordinal, permutation, LowerConnectivityCompare()); + case Higher: return add_helper(bucket_ordinal, to, ordinal, permutation, HigherConnectivityCompare()); + case Adjacent: return add_helper(bucket_ordinal, to, ordinal, permutation, LowerConnectivityCompare()); // same comparing as lower + default: + ThrowAssertMsg(false, "What type of connectivity are you trying to add? " << m_direction); + return false; + } + } + else { + switch(m_direction) + { + case Lower: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_lower_connectivity_cmp); + case Higher: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_higher_connectivity_cmp); + case Adjacent: return add_helper(bucket_ordinal, to, ordinal, permutation, m_rank_sensitive_lower_connectivity_cmp); + default: + ThrowAssertMsg(false, "What type of connectivity are you trying to add? " << m_direction); + return false; + } + } + } + + bool remove_connectivity(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal) + { + impl::check_bucket_ordinal(bucket_ordinal, this); + + if (!m_active) return false; + + uint32_t found_idx = ~0u; + const uint32_t end_i = m_indices[bucket_ordinal]+m_num_connectivities[bucket_ordinal]; + for (uint32_t i = m_indices[bucket_ordinal]; i < end_i; ++i) + { + //remove connectivity + if ( m_targets[i] == to && m_ordinals[i] == ordinal ) { + found_idx = i; + --m_num_connectivities[bucket_ordinal]; + --m_total_connectivities; + break; + } + } + + //slide memory down + if (found_idx != ~0u) { + m_needs_shrink_to_fit = true; + for (uint32_t i = found_idx; i < end_i - 1; ++i) { + m_targets[i] = m_targets[i+1]; + m_ordinals[i] = m_ordinals[i+1]; + if (has_permutation()) { + m_permutations[i] = m_permutations[i+1]; + } + } + } + + return found_idx != ~0u; + } + + void begin_modification() + {} + + template + void end_modification(BULKDATA* mesh = NULL); + + void add_entity() + { + if (m_active) { + m_indices.push_back(m_targets.size()); + m_num_connectivities.push_back(0); + m_needs_shrink_to_fit = true; + } + else { + ++m_num_inactive; + } + } + + void remove_entity() + { + ThrowAssertMsg(size() > 0, "Cannot remove, connectivity is already empty"); + + if (m_active) { + m_indices.pop_back(); + m_total_connectivities -= m_num_connectivities.back(); + m_num_connectivities.pop_back(); + m_needs_shrink_to_fit = true; + } + else { + --m_num_inactive; + } + } + + void copy_entity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal=-1u) + { + ThrowAssert(m_from_rank == to.m_from_rank); + impl::check_bucket_ordinal(from_ordinal, this); + + if (to_ordinal == -1u) { + to_ordinal = to.size(); + to.add_entity(); + } + impl::check_bucket_ordinal(to_ordinal, &to); + + // Manage activation state + if (!m_active) { + if (to.m_active) { + to.m_total_connectivities -= to.m_num_connectivities[to_ordinal]; + to.m_num_connectivities[to_ordinal] = 0; + to.m_needs_shrink_to_fit = true; + } + return; + } + if (m_active && !to.m_active) { + to.activate(); + } + + // Copy data + if (&to == this) { + // easy + // note this implements swap semantics instead of copy, but this is necessary + // to avoid aliasing in certain situations when sorting Partitions + std::swap(m_indices[to_ordinal], m_indices[from_ordinal]); + std::swap(m_num_connectivities[to_ordinal], m_num_connectivities[from_ordinal]); + + m_needs_shrink_to_fit = true; + to.m_needs_shrink_to_fit = true; + } + else { + // much harder + const unsigned from_num = m_num_connectivities[from_ordinal]; + const unsigned to_num = to.m_num_connectivities[to_ordinal]; + const int delta_num = from_num - to_num; + if (delta_num > 0) { + // If adding additional connectivity, need to reserve space + to.add_connectivity_helper(to_ordinal, delta_num); + } + else { + to.m_num_connectivities[to_ordinal] = from_num; + to.m_total_connectivities += delta_num; + } + if (delta_num != 0) { + to.m_needs_shrink_to_fit = true; + } + copy_connectivity(from_ordinal, to, to_ordinal); + } + } + + void copy_to_fixed(unsigned from_ordinal, OtherType& to) + { + const unsigned num_conn_to_move = m_active ? m_num_connectivities[from_ordinal] : 0; + + ThrowAssert(OtherType::connectivity_type == FIXED_CONNECTIVITY); + ThrowAssertMsg(size() > 0, "Cannot move, connectivity is empty"); + ThrowAssertMsg(num_conn_to_move <= to.num_connectivity(666 /*any unsigned, doesn't matter*/), "Incompatible"); + + const unsigned to_offset = to.m_targets.size(); + to.add_entity(); // make room for new entity + + const unsigned from_offset = m_active ? m_indices[from_ordinal] : 0; + +#ifndef NDEBUG + // Check the ordinals are compatible with fixed connectivity + ConnectivityOrdinal const* ordinals = m_ordinals.data() + from_offset; + for (unsigned i = 0; i < num_conn_to_move; ++i) { + ThrowAssert(ordinals[i] == i); + } +#endif + + std::copy(m_targets.begin() + from_offset, + m_targets.begin() + from_offset + num_conn_to_move, + to.m_targets.begin() + to_offset); + + if (has_permutation()) { + std::copy(m_permutations.begin() + from_offset, + m_permutations.begin() + from_offset + num_conn_to_move, + to.m_permutations.begin() + to_offset); + } + } + + void copy_to_fixed(unsigned from_ordinal, SelfType& to) + { ThrowAssert(false); } + + bool has_permutation() const + { return does_rank_have_valid_permutations(TargetRank) && does_rank_have_valid_permutations(m_from_rank); } + + size_t heap_memory_in_bytes() const + { + return capacity_in_bytes(m_targets) + + capacity_in_bytes(m_ordinals) + + capacity_in_bytes(m_permutations); + } + + void debug_dump(std::ostream& out) const + { + out << "For dynamic connectivity to rank: " << TargetRank << ", with id: " << m_id << "\n"; + if (m_active) { + out << " size is: " << m_indices.size() << "\n"; + for (int i = 0, ie = m_indices.size(); i < ie; ++i) { + out << " At ordinal " << i << "\n"; + debug_dump(out, i, false); + } + out << std::endl; + } + else { + out << " size is: " << m_num_inactive << ", but inactive" << std::endl; + } + } + + void debug_dump(std::ostream& out, unsigned ordinal, bool add_context=true) const + { + if (m_active) { + int idx = m_indices[ordinal]; + int num = m_num_connectivities[ordinal]; + if (add_context) { + out << "For dynamic connectivity to rank: " << TargetRank << ", with id: " << m_id << "\n"; + } + out << " Index is: " << idx << ", Num is: " << num << "\n"; + for (int j = idx, je = idx + num; j < je; ++j) { + out << " (target:" << m_targets[j].local_offset() << ", ordinal:" << (uint32_t)m_ordinals[j] << ")\n"; + } + } + else { + out << " Index is: 0, Num is: 0\n"; + } + } + +private: + + bool does_rank_have_valid_permutations(stk::mesh::EntityRank rank) const + { + return rank > stk::topology::NODE_RANK && rank < stk::topology::CONSTRAINT_RANK; + } + + void copy_connectivity(unsigned from_ordinal, SelfType& to, unsigned to_ordinal) + { + unsigned num_conn = m_num_connectivities[from_ordinal]; + unsigned to_offset = to.m_indices[to_ordinal]; + unsigned from_offset = m_indices[from_ordinal]; + ThrowAssert(to.m_num_connectivities[to_ordinal] == num_conn); + + std::copy(m_targets.begin() + from_offset, + m_targets.begin() + from_offset + num_conn, + to.m_targets.begin() + to_offset); + + std::copy(m_ordinals.begin() + from_offset, + m_ordinals.begin() + from_offset + num_conn, + to.m_ordinals.begin() + to_offset); + + if (has_permutation()) { + std::copy(m_permutations.begin() + from_offset, + m_permutations.begin() + from_offset + num_conn, + to.m_permutations.begin() + to_offset); + } + } + + static unsigned num_chunks(unsigned num) + { return (num + chunk_size -1)/chunk_size; } + + void activate() + { + ThrowAssert(!m_active); + + m_indices.resize(m_num_inactive, 0); + m_num_connectivities.resize(m_num_inactive, 0); + + m_active = true; + m_num_inactive = 0; + } + + template + void resize_and_order_by_index_helper(Vector & data, unsigned capacity, bool update_index = false) + { + Vector temp; + temp.reserve(capacity); + + uint32_t current_index=0; + for(size_t i=0, e=m_indices.size(); i 0 ? 2 * old_capacity : 8*chunk_size; + while (new_capacity < minimum_size) { + new_capacity *= 2; + } + return new_capacity; + } + + // The old capacity is at or above the threshold for being careful about growing + // the connectivity representation(and memory footprint). Only grow the capacity + // if compressing the representation will not yield sufficient unused capacity. + if (capacity_ratio * m_total_connectivities > old_capacity) + { + return 2 * old_capacity; + } + else + { + return old_capacity; + } + } + + void add_connectivity_helper(unsigned bucket_ordinal, unsigned num_to_add=1) + { + const unsigned chunks_needed_by_entity = num_chunks(m_num_connectivities[bucket_ordinal]+num_to_add); + const unsigned chunks_used_by_entity = num_chunks(m_num_connectivities[bucket_ordinal]); + + if (chunks_needed_by_entity == chunks_used_by_entity) + { + m_total_connectivities += num_to_add; + m_num_connectivities[bucket_ordinal] += num_to_add; + return; + } + + const unsigned chunks_available = num_chunks(m_targets.capacity() - m_targets.size()); + + if (chunks_available < chunks_needed_by_entity) + { + const unsigned new_capacity = compute_new_connectivity_capacity(m_targets.size() + chunks_needed_by_entity * chunk_size); + resize_and_order_by_index(new_capacity); + } + + const bool last_entity_by_index = (chunks_used_by_entity > 0) && + (m_indices[bucket_ordinal] + chunks_used_by_entity*chunk_size == m_targets.size()); + Entity invalid; + + //copy to end + if (!last_entity_by_index) + { + uint32_t new_index = static_cast(m_targets.size()); + + m_targets.insert(m_targets.end(), chunks_needed_by_entity*chunk_size, invalid); + std::copy(begin(bucket_ordinal), end(bucket_ordinal), m_targets.begin() + new_index); + + m_ordinals.insert(m_ordinals.end(), chunks_needed_by_entity*chunk_size, INVALID_CONNECTIVITY_ORDINAL); + std::copy(begin_ordinals(bucket_ordinal), end_ordinals(bucket_ordinal), m_ordinals.begin() + new_index); + + if (has_permutation()) { + m_permutations.insert(m_permutations.end(), chunks_needed_by_entity*chunk_size, INVALID_PERMUTATION); + std::copy(begin_permutations(bucket_ordinal), end_permutations(bucket_ordinal), m_permutations.begin() + new_index); + } + + m_indices[bucket_ordinal] = new_index; + } + //add new chunk to end + else { + const unsigned extra_chunks_needed = chunks_needed_by_entity - chunks_used_by_entity; + m_targets.insert(m_targets.end(), extra_chunks_needed*chunk_size, invalid); + m_ordinals.insert(m_ordinals.end(), extra_chunks_needed*chunk_size, INVALID_CONNECTIVITY_ORDINAL); + if (has_permutation()) { + m_permutations.insert(m_permutations.end(), extra_chunks_needed*chunk_size, INVALID_PERMUTATION); + } + } + + m_total_connectivities += num_to_add; + m_num_connectivities[bucket_ordinal] += num_to_add; + } + + template + bool add_helper(unsigned bucket_ordinal, Entity to, ConnectivityOrdinal ordinal, Permutation permutation, + const ConnectivityComparator &compare) + { +#ifndef NDEBUG + // TODO - If downward conn, check to's rank and topology +#endif + bool rv = true; + + add_connectivity_helper(bucket_ordinal); + + const uint32_t begin_index = m_indices[bucket_ordinal] + m_num_connectivities[bucket_ordinal] - 1; + + if (m_num_connectivities[bucket_ordinal] == 1) { + m_targets[begin_index] = to; + m_ordinals[begin_index] = ordinal; + if (has_permutation()) { + m_permutations[begin_index] = permutation; + } + return true; + } + + for (uint32_t i = begin_index, e = m_indices[bucket_ordinal]; i > e; --i) + { + //slide up + if ( compare(to, ordinal, m_targets[i-1], m_ordinals[i-1u]) ) { + m_targets[i] = m_targets[i-1u]; + m_ordinals[i] = m_ordinals[i-1u]; + if (has_permutation()) { + m_permutations[i] = m_permutations[i-1u]; + } + //insert if on last iteration + if ((i-1)==e) { + m_targets[i-1u] = to; + m_ordinals[i-1u] = ordinal; + if (has_permutation()) { + m_permutations[i-1u] = permutation; + } + } + } + //insert + else if ( compare(m_targets[i-1], m_ordinals[i-1u], to, ordinal) ) { + m_targets[i] = to; + m_ordinals[i] = ordinal; + if (has_permutation()) { + m_permutations[i] = permutation; + } + break; + } + //duplicate -- insert new and remove the original + else + { + m_targets[i] = to; + m_ordinals[i] = ordinal; + if (has_permutation()) { + m_permutations[i] = permutation; + } + remove_connectivity(bucket_ordinal, to, ordinal); + rv = false; + break; + } + } + + return rv; + } + + // Illegal + BucketConnectivity(const SelfType&); + SelfType& operator=(const SelfType&); + + // MEMBERS + + EntityRank m_from_rank; + connectivity_direction m_direction; + + bool m_active; // In many cases, uses will not make use of dynamic connectivity, so don't even waste the memory unless it looks like they want it + bool m_needs_shrink_to_fit; // True if this object potentially has partially full vectors or out-of-order entities + unsigned m_num_inactive; + + // meta data + UInt32Vector m_indices; // Common index into vectors below that stores where connectivity starts for a partition_offset (entity). + UInt32Vector m_num_connectivities; + unsigned m_total_connectivities; + + // connectivity data + EntityVector m_targets; + ConnectivityOrdinalVector m_ordinals; + PermutationVector m_permutations; + + BulkData * m_bulk_data; + int m_id; + + impl::HigherConnectivityRankSensitiveCompare m_rank_sensitive_higher_connectivity_cmp; + impl::LowerConnectivitityRankSensitiveCompare m_rank_sensitive_lower_connectivity_cmp; + + size_t m_last_capacity; + + size_t m_data_idx; +}; + +} + +// +// BucketConnectivity +// + +template +template // hack to get around dependency +inline +void impl::BucketConnectivity::end_modification(BULKDATA* mesh) +{ + //TODO: If bucket is blocked, no longer need to shrink to fit! + + if (m_targets.size() < m_targets.capacity()) { + + { + EntityVector temp(m_targets.begin(), m_targets.end()); + m_targets.swap(temp); + } + + { + PermutationVector temp(m_permutations.begin(), m_permutations.end()); + m_permutations.swap(temp); + } + } + +} + +template +template +inline +void impl::BucketConnectivity::end_modification(BULKDATA* mesh) +{ + if (m_active && m_needs_shrink_to_fit) { + resize_and_order_by_index(); + + { + UInt32Vector temp(m_indices.begin(), m_indices.end()); + m_indices.swap(temp); + } + + { + UInt32Vector temp(m_num_connectivities.begin(), m_num_connectivities.end()); + m_num_connectivities.swap(temp); + } + + m_needs_shrink_to_fit = false; + } +} + +template +inline +bool impl::LowerConnectivitityRankSensitiveCompare::operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, + Entity second_entity, ConnectivityOrdinal second_ordinal) const +{ + const EntityRank first_rank = m_mesh.entity_rank(first_entity); + const EntityRank second_rank = m_mesh.entity_rank(second_entity); + + return (first_rank < second_rank) + || ((first_rank == second_rank) && (first_ordinal < second_ordinal)); +} + +template +inline +bool impl::HigherConnectivityRankSensitiveCompare::operator()(Entity first_entity, ConnectivityOrdinal first_ordinal, Entity second_entity, ConnectivityOrdinal second_ordinal) const +{ + const EntityRank first_rank = m_mesh.entity_rank(first_entity); + const EntityRank second_rank = m_mesh.entity_rank(second_entity); + + if (first_rank < second_rank) { + return true; + } + if (first_rank > second_rank) { + return false; + } + // Needs to match LessRelation in BulkData.hpp + return std::make_pair(first_ordinal, first_entity.is_local_offset_valid() ? first_entity.local_offset() : Entity::MaxEntity) < + std::make_pair(second_ordinal, second_entity.is_local_offset_valid() ? second_entity.local_offset() : Entity::MaxEntity); +} + + + + + +}} //namespace stk::mesh::impl + +#endif diff --git a/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp b/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp index 94a407d97780..fe61ee565acc 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/BulkData.cpp @@ -100,6 +100,10 @@ namespace stk { namespace mesh { +namespace impl { +int Counter::counter = 0; +} + // Static constant on BulkData: const uint16_t BulkData::orphaned_node_marking = 25000; @@ -372,7 +376,6 @@ BulkData::BulkData(MetaData & mesh_meta_data, *this, mesh_meta_data.entity_rank_count(), bucket_capacity), - m_sparse_connectivity(mesh_meta_data.entity_rank_count()), m_use_identifiers_for_resolving_sharing(false), m_modSummary(*this), m_meshDiagnosticObserver(std::make_shared(*this)), @@ -549,11 +552,13 @@ void BulkData::mark_entity_and_upward_related_entities_as_modified(Entity entity size_t BulkData::count_relations(Entity entity) const { + const MeshIndex &mesh_idx = mesh_index(entity); + const EntityRank end_rank = static_cast(m_mesh_meta_data.entity_rank_count()); size_t count = 0; for (EntityRank irank = stk::topology::BEGIN_RANK; irank < end_rank; ++irank) { - count += num_connectivity(entity, irank); + count += mesh_idx.bucket->num_connectivity(mesh_idx.bucket_ordinal, irank); } return count; } @@ -606,7 +611,6 @@ Entity BulkData::generate_new_entity(unsigned preferred_offset) } else if (!m_deleted_entities.empty()) { new_local_offset = m_deleted_entities.front(); - m_sparse_connectivity.get_connectivity(Entity(new_local_offset)).clear(); m_deleted_entities.pop_front(); } @@ -622,7 +626,6 @@ Entity BulkData::generate_new_entity(unsigned preferred_offset) m_mark_entity.push_back(NOT_MARKED); m_closure_count.push_back(static_cast(0)); m_local_ids.push_back(stk::mesh::GetInvalidLocalId()); - m_sparse_connectivity.update_size_of_entity_index_space(m_mesh_indexes.size()); #ifdef SIERRA_MIGRATION if (m_add_fmwk_data) { @@ -796,7 +799,6 @@ PARTVECTOR add_root_topology_part(const PARTVECTOR &parts, stk::mesh::Part &root PARTVECTOR initialParts(parts.size() + 1); initialParts = parts; initialParts.push_back(&rootTopoPart); - stk::util::sort_and_unique(initialParts, PartLess()); return initialParts; } @@ -1632,12 +1634,10 @@ void BulkData::comm_procs( EntityKey key, std::vector & procs ) const void BulkData::comm_procs(Entity entity, std::vector & procs ) const { - procs.clear(); ThrowAssertMsg(is_valid(entity), "BulkData::comm_procs ERROR, input entity "<comm_map), procs); - } + + impl::fill_sorted_procs(internal_entity_comm_map(entity), procs); } void BulkData::comm_shared_procs(EntityKey key, std::vector & procs ) const @@ -2299,7 +2299,7 @@ void BulkData::internal_declare_relation( Entity entity , { require_ok_to_modify(); - stk::mesh::EntityRank entityRank = entity_rank(entity); + stk::mesh::EntityRank erank = entity_rank(entity); OrdinalVector scratch2, scratch3; @@ -2308,15 +2308,14 @@ void BulkData::internal_declare_relation( Entity entity , Entity e = i->entity(); const unsigned n = i->relation_ordinal(); const Permutation permut = i->getPermutation(); - const EntityRank eRank = entity_rank(e); - if ( eRank < entityRank ) { + if ( entity_rank(e) < erank ) { internal_declare_relation( entity , e , n, permut, ordinal_scratch, scratch2, scratch3); } - else if ( entityRank < eRank ) { + else if ( erank < entity_rank(e) ) { internal_declare_relation( e , entity , n, permut, ordinal_scratch, scratch2, scratch3); } else { - ThrowErrorMsg("declare_relation given entities of the same entity rank ("< " < ghostStatus(get_size_of_entity_index_space(), false); - m_entity_repo->clear_all_cache(); - stk::mesh::impl::comm_sync_aura_send_recv(*this, add_send, entityProcMapping, ghostStatus ); @@ -3667,22 +3664,25 @@ void BulkData::fill_list_of_entities_to_send_for_aura_ghosting(EntityProcMapping // Iterate over all shared entities, ensure that upwardly related // entities to each shared entity will be ghosted to the sharing proc. Selector shared = mesh_meta_data().globally_shared_part(); - const SparseConnectivity& sparseConnectivity = m_sparse_connectivity; std::vector sharingProcs; impl::for_each_selected_entity_run_no_threads(*this, stk::topology::NODE_RANK, shared, - [&sendAuraEntityProcs, &sparseConnectivity, &entitySharing, &sharingProcs, &end_rank] + [&sendAuraEntityProcs, &entitySharing, &sharingProcs, &end_rank] (const BulkData& bulk, const MeshIndex& meshIndex) { const Bucket& bucket = *meshIndex.bucket; const unsigned bucketOrd = meshIndex.bucket_ordinal; - const Connectivity& connObject = sparseConnectivity.get_connectivity(bucket[bucketOrd]); + const EntityRank nextHigherRank = stk::topology::EDGE_RANK; bulk.comm_shared_procs(bucket[bucketOrd], sharingProcs); - PairIterEntity conn = connObject.get_connectivity(stk::topology::EDGE_RANK, end_rank); - for (Entity relEntity : conn) { - const Connectivity& relConnectivity = sparseConnectivity.get_connectivity(relEntity); - for (const int sharingProc : sharingProcs) { - stk::mesh::impl::insert_upward_relations(bulk, relConnectivity, entitySharing, relEntity, sharingProc, sendAuraEntityProcs); + for (const int sharingProc : sharingProcs) { + + for (EntityRank higherRank = nextHigherRank; higherRank < end_rank; ++higherRank) { + const unsigned num_rels = bucket.num_connectivity(bucketOrd, higherRank); + const Entity* rels = bucket.begin(bucketOrd, higherRank); + + for (unsigned r = 0; r < num_rels; ++r) { + stk::mesh::impl::insert_upward_relations(bulk, entitySharing, rels[r], stk::topology::NODE_RANK, sharingProc, sendAuraEntityProcs); + } } } } @@ -3881,7 +3881,7 @@ void BulkData::change_connectivity_for_edge_or_face(stk::mesh::Entity side, cons if(bucket(elements[i]).owned()) { stk::mesh::Bucket& bucket_edge = bucket(side); - bucket_edge.change_connected_nodes(bucket_ordinal(side), nodes.data()); + bucket_edge.change_existing_connectivity(bucket_ordinal(side), nodes.data()); stk::mesh::Permutation new_permutation = get_permutation(*this, elements[i], nodes); ThrowRequireWithSierraHelpMsg(new_permutation!=stk::mesh::INVALID_PERMUTATION); @@ -4685,7 +4685,7 @@ void BulkData::internal_finish_modification_end(ModEndOptimizationFlag opt) m_bucket_repository.internal_default_sort_bucket_entities(should_sort_faces_by_node_ids()); } - m_bucket_repository.sync_from_partitions(); + m_bucket_repository.internal_modification_end(); m_meshModification.set_sync_state_synchronized(); m_add_node_sharing_called = false; @@ -5083,8 +5083,12 @@ void BulkData::internal_update_all_sharing_procs() const EntityCommListInfoVector& all_comm = m_entity_comm_list; for (const EntityCommListInfo& info : all_comm) { - if (info.entity_comm != nullptr && info.entity_comm->isShared) { - const EntityRank rank = info.key.rank(); + const Entity entity = info.entity; + const Bucket& bkt = bucket(entity); + + if (bkt.shared() && info.entity_comm != nullptr) { + const EntityRank rank = bkt.entity_rank(); + const EntityCommInfoVector& commInfo = info.entity_comm->comm_map; const unsigned len = commInfo.size(); unsigned i = 0; @@ -6355,7 +6359,7 @@ void BulkData::sort_entities(const stk::mesh::EntitySorterBase& sorter) ThrowRequireMsg(in_synchronized_state(), "Error, sort_entities cannot be called from inside a modification cycle."); m_bucket_repository.internal_custom_sort_bucket_entities(sorter); - m_bucket_repository.sync_from_partitions(); + m_bucket_repository.internal_modification_end(); if(parallel_size() > 1) check_mesh_consistency(); diff --git a/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp b/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp index bd73f2e42267..4976764cea06 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/BulkData.hpp @@ -62,7 +62,6 @@ #include "stk_mesh/base/Bucket.hpp" // for Bucket #include "stk_mesh/base/EntityKey.hpp" // for EntityKey, hash_value #include "stk_mesh/base/FieldDataManager.hpp" -#include "stk_mesh/base/SparseConnectivity.hpp" #include "stk_mesh/base/Relation.hpp" // for Relation, etc #include "stk_topology/topology.hpp" // for topology, etc #include "stk_util/util/ReportHandler.hpp" // for ThrowAssert, etc @@ -870,9 +869,6 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu void set_large_ids_flag(bool largeIds) { m_supportsLargeIds = largeIds; } protected: //functions - SparseConnectivity& get_sparse_connectivity() { return m_sparse_connectivity; } - const SparseConnectivity& get_sparse_connectivity() const { return m_sparse_connectivity; } - Entity declare_entity( EntityRank ent_rank , EntityId ent_id);// Mod Mark @@ -1585,7 +1581,6 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu FieldDataManager *m_field_data_manager; mutable std::vector m_selector_to_buckets_maps; impl::BucketRepository m_bucket_repository; // needs to be destructed first! - SparseConnectivity m_sparse_connectivity; bool m_use_identifiers_for_resolving_sharing; std::string m_lastModificationDescription; stk::EmptyModificationSummary m_modSummary; @@ -1609,11 +1604,9 @@ void get_entities(EntityRank rank, Selector const& selector, EntityVector& outpu inline unsigned BulkData::num_connectivity(Entity entity, EntityRank rank) const { - if (rank == stk::topology::NODE_RANK) { - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket==nullptr ? 0 : mesh_idx.bucket->num_nodes(mesh_idx.bucket_ordinal); - } - return m_sparse_connectivity.num_connectivity(entity, rank); + ThrowAssert(bucket_ptr(entity)); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->num_connectivity(mesh_idx.bucket_ordinal, rank); } inline unsigned @@ -1638,11 +1631,8 @@ inline Entity const* BulkData::begin(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - if (rank == stk::topology::NODE_RANK) { - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->begin_nodes(mesh_idx.bucket_ordinal); - } - return m_sparse_connectivity.begin_connectivity(entity, rank); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin(mesh_idx.bucket_ordinal, rank); } inline Entity const* @@ -1653,25 +1643,28 @@ BulkData::begin_nodes(Entity entity) const return mesh_idx.bucket->begin_nodes(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::begin_edges(Entity entity) const +inline Entity const* +BulkData::begin_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.begin_connectivity(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_edges(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::begin_faces(Entity entity) const +inline Entity const* +BulkData::begin_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.begin_connectivity(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_faces(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::begin_elements(Entity entity) const +inline Entity const* +BulkData::begin_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.begin_connectivity(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_elements(mesh_idx.bucket_ordinal); } inline ConnectivityOrdinal const* @@ -1690,60 +1683,68 @@ BulkData::begin_node_ordinals(Entity entity) const return mesh_idx.bucket->begin_node_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::begin_edge_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::begin_edge_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.begin_ordinals(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_edge_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::begin_face_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::begin_face_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.begin_ordinals(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_face_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::begin_element_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::begin_element_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.begin_ordinals(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_element_ordinals(mesh_idx.bucket_ordinal); } inline Permutation const* BulkData::begin_permutations(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - return m_sparse_connectivity.begin_permutations(entity, rank); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_permutations(mesh_idx.bucket_ordinal, rank); } -inline -Permutation const* BulkData::begin_node_permutations(Entity entity) const +inline Permutation const* +BulkData::begin_node_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::NODE_RANK)); - return m_sparse_connectivity.begin_permutations(entity, stk::topology::NODE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_node_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::begin_edge_permutations(Entity entity) const +inline Permutation const* +BulkData::begin_edge_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.begin_permutations(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_edge_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::begin_face_permutations(Entity entity) const +inline Permutation const* +BulkData::begin_face_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.begin_permutations(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_face_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::begin_element_permutations(Entity entity) const +inline Permutation const* +BulkData::begin_element_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.begin_permutations(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->begin_element_permutations(mesh_idx.bucket_ordinal); } inline unsigned @@ -1754,36 +1755,36 @@ BulkData::num_nodes(Entity entity) const return mesh_idx.bucket->num_nodes(mesh_idx.bucket_ordinal); } -inline -unsigned BulkData::num_edges(Entity entity) const +inline unsigned +BulkData::num_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.num_connectivity(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->num_edges(mesh_idx.bucket_ordinal); } -inline -unsigned BulkData::num_faces(Entity entity) const +inline unsigned +BulkData::num_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.num_connectivity(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->num_faces(mesh_idx.bucket_ordinal); } -inline -unsigned BulkData::num_elements(Entity entity) const +inline unsigned +BulkData::num_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.num_connectivity(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->num_elements(mesh_idx.bucket_ordinal); } inline Entity const* BulkData::end(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - if (rank == stk::topology::NODE_RANK) { - const MeshIndex &mesh_idx = mesh_index(entity); - return mesh_idx.bucket->end_nodes(mesh_idx.bucket_ordinal); - } - return m_sparse_connectivity.end_connectivity(entity, rank); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end(mesh_idx.bucket_ordinal, rank); } inline Entity const* @@ -1794,25 +1795,28 @@ BulkData::end_nodes(Entity entity) const return mesh_idx.bucket->end_nodes(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::end_edges(Entity entity) const +inline Entity const* +BulkData::end_edges(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.end_connectivity(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_edges(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::end_faces(Entity entity) const +inline Entity const* +BulkData::end_faces(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.end_connectivity(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_faces(mesh_idx.bucket_ordinal); } -inline -Entity const* BulkData::end_elements(Entity entity) const +inline Entity const* +BulkData::end_elements(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.end_connectivity(entity, stk::topology::ELEMENT_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_elements(mesh_idx.bucket_ordinal); } inline ConnectivityOrdinal const* @@ -1831,67 +1835,75 @@ BulkData::end_node_ordinals(Entity entity) const return mesh_idx.bucket->end_node_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::end_edge_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::end_edge_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.end_ordinals(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_edge_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::end_face_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::end_face_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.end_ordinals(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_face_ordinals(mesh_idx.bucket_ordinal); } -inline -ConnectivityOrdinal const* BulkData::end_element_ordinals(Entity entity) const +inline ConnectivityOrdinal const* +BulkData::end_element_ordinals(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.end_ordinals(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_element_ordinals(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::end_permutations(Entity entity, EntityRank rank) const +inline Permutation const* +BulkData::end_permutations(Entity entity, EntityRank rank) const { ThrowAssert(is_valid_connectivity(entity, rank)); - return m_sparse_connectivity.end_permutations(entity, rank); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_permutations(mesh_idx.bucket_ordinal, rank); } -inline -Permutation const* BulkData::end_node_permutations(Entity entity) const +inline Permutation const* +BulkData::end_node_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::NODE_RANK)); - return m_sparse_connectivity.end_permutations(entity, stk::topology::NODE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_node_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::end_edge_permutations(Entity entity) const +inline Permutation const* +BulkData::end_edge_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::EDGE_RANK)); - return m_sparse_connectivity.end_permutations(entity, stk::topology::EDGE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_edge_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::end_face_permutations(Entity entity) const +inline Permutation const* +BulkData::end_face_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::FACE_RANK)); - return m_sparse_connectivity.end_permutations(entity, stk::topology::FACE_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_face_permutations(mesh_idx.bucket_ordinal); } -inline -Permutation const* BulkData::end_element_permutations(Entity entity) const +inline Permutation const* +BulkData::end_element_permutations(Entity entity) const { ThrowAssert(is_valid_connectivity(entity, stk::topology::ELEMENT_RANK)); - return m_sparse_connectivity.end_permutations(entity, stk::topology::ELEM_RANK); + const MeshIndex &mesh_idx = mesh_index(entity); + return mesh_idx.bucket->end_element_permutations(mesh_idx.bucket_ordinal); } -inline -bool BulkData::has_permutation(Entity entity, EntityRank rank) const +inline bool +BulkData::has_permutation(Entity entity, EntityRank rank) const { ThrowAssert(bucket_ptr(entity)); - return m_sparse_connectivity.has_permutation(entity_rank(entity), rank); + return bucket(entity).has_permutation(rank); } inline bool @@ -1918,16 +1930,13 @@ BulkData::in_receive_ghost( EntityKey key ) const inline bool BulkData::in_receive_ghost( Entity entity ) const { - if (m_entitycomm[entity.local_offset()] == nullptr) { - return false; - } - - const int owner_rank = parallel_owner_rank(entity); - if (owner_rank == parallel_rank()) { - return false; + const std::vector & ghosts= ghostings(); + for (size_t i=ghosts.size()-1;i>=AURA;--i) + { + if ( in_receive_ghost(*ghosts[i], entity) ) + return true; } - - return m_entitycomm[entity.local_offset()]->isGhost; + return false; } inline bool diff --git a/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp b/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp deleted file mode 100644 index 2f7fb3dd4c58..000000000000 --- a/packages/stk/stk_mesh/stk_mesh/base/ConnectedSparseNodes.hpp +++ /dev/null @@ -1,115 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#ifndef STK_MESH_CONNECTED_SPARSE_NODES_HPP -#define STK_MESH_CONNECTED_SPARSE_NODES_HPP - -#include -#include -#include -#include -#include - -namespace stk { -namespace mesh { - -class ConnectedSparseNodes { -public: - ConnectedSparseNodes(SparseConnectivity& sparseConnectivity, - EntityRank fromRank, - const EntityVector& fromEntities) - : m_sparseConnectivity(sparseConnectivity), - m_fromEntities(fromEntities), - m_fromRank(fromRank) - {} - - ~ConnectedSparseNodes(){} - - unsigned num_nodes_per_entity(unsigned fromEntity) const - { return m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } - - const Entity* begin_connectivity(unsigned fromEntity) const - { return m_sparseConnectivity.begin_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } - - const Entity* end_connectivity(unsigned fromEntity) const - { return m_sparseConnectivity.end_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } - - const ConnectivityOrdinal* begin_ordinals(unsigned fromEntity) const - { return m_sparseConnectivity.begin_ordinals(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } - - const ConnectivityOrdinal* end_ordinals(unsigned fromEntity) const - { return m_sparseConnectivity.end_ordinals(m_fromEntities[fromEntity], stk::topology::NODE_RANK); } - - bool set_connected_node(unsigned fromEntity, Entity connectedNode, ConnectivityOrdinal ordinal) - { - if (connectedNode.local_offset() > 0) { - return m_sparseConnectivity.add_connectivity(m_fromRank, m_fromEntities[fromEntity], - stk::topology::NODE_RANK, connectedNode, ordinal, - INVALID_PERMUTATION); - } - else { - const unsigned numBefore = m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); - bool returnVal = m_sparseConnectivity.remove_connectivity(m_fromRank, m_fromEntities[fromEntity], - stk::topology::NODE_RANK, connectedNode, ordinal); - const unsigned numAfter = m_sparseConnectivity.num_connectivity(m_fromEntities[fromEntity], stk::topology::NODE_RANK); - ThrowRequireMsg((numBefore==0 && numAfter==0) || (numBefore>0 && numAfter==numBefore-1),"remove didn't work"); - return returnVal; - } - } - - bool reset_connected_node(unsigned fromEntity, Entity connectedNode, ConnectivityOrdinal ordinal) - { - return m_sparseConnectivity.replace_or_add_connectivity(m_fromRank, m_fromEntities[fromEntity], - stk::topology::NODE_RANK, connectedNode, ordinal); - } - - void reset_connected_nodes(unsigned fromEntity, unsigned numNodes, const Entity* connectedNodes) - { - for(unsigned i=0; i -#include // for EntityRank, ConnectivityOrdinal, EntityVector -#include -#include - -namespace stk { -namespace mesh { - -class ConnectedTopologyNodes { -public: - ConnectedTopologyNodes(stk::topology fromTopology, const EntityVector& fromEntities) - : m_connectedNodes(fromTopology.num_nodes()*fromEntities.size(), Entity()), - m_ordinals(fromTopology.num_nodes()), - m_numNodesPerEntity(fromTopology.num_nodes()) - { - for (unsigned n=0; n m_ordinals; - unsigned m_numNodesPerEntity; -}; - -} // namespace mesh -} // namespace stk - -#endif //STK_MESH_CONNECTED_TOPOLOGY_NODES_HPP - diff --git a/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp b/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp deleted file mode 100644 index 790ebf1bcb12..000000000000 --- a/packages/stk/stk_mesh/stk_mesh/base/Connectivity.cpp +++ /dev/null @@ -1,250 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include -#include -#include - -namespace stk { -namespace mesh { - -Connectivity::Connectivity() - : m_connectivity(nullptr), - m_offsetsAndOrdinals(nullptr) -{ - m_offsetsAndOrdinals = new ConnectivityOrdinal[m_capacityIndex + 1]; - for(unsigned i=0; i -#include // for EntityRank -#include -#include -#include - -namespace stk { -namespace mesh { - -class Connectivity { -public: - Connectivity(); - - static constexpr uint16_t MAX_NUM_RANKS = stk::topology::NUM_RANKS+1; - - Connectivity(const Connectivity& rhs) - : m_connectivity(nullptr), - m_offsetsAndOrdinals(nullptr) - { - *this = rhs; - } - - Connectivity(Connectivity && rhs) noexcept - : m_connectivity(nullptr), - m_offsetsAndOrdinals(nullptr) - { - *this = std::move(rhs); - } - - Connectivity& operator=(const Connectivity& rhs) - { - delete [] m_connectivity; - delete [] m_offsetsAndOrdinals; - - unsigned capacity = rhs.get_capacity(); - if (capacity > 0) { - m_connectivity = new Entity[capacity]; - } - - m_offsetsAndOrdinals = new ConnectivityOrdinal[m_firstOrdinalIndex + capacity]; - for(unsigned i=0; itemplate make_field_sync_debugger(); @@ -146,11 +122,6 @@ class DeviceField : public NgpFieldBase } } - void set_execution_space(const stk::ngp::ExecSpace& execSpace) override - { - asyncCopyState.set_execution_space(execSpace); - } - void update_field() override { ThrowRequireMsg(hostBulk->synchronized_count() >= synchronizedCount, "Invalid sync state detected for NgpField: " << hostField->name()); @@ -201,8 +172,8 @@ class DeviceField : public NgpFieldBase size_t num_syncs_to_device() const override { return hostField->num_syncs_to_device(); } void fence() override { - asyncCopyState.execSpace.fence(); - asyncCopyState.reset_state(); + get_execution_space().fence(); + reset_execution_space(); } void modify_on_host() override @@ -257,29 +228,41 @@ class DeviceField : public NgpFieldBase void sync_to_host() override { - asyncCopyState.set_state(Kokkos::DefaultExecutionSpace(), impl::DEVICE_TO_HOST); + reset_execution_space(); internal_sync_to_host(); Kokkos::fence(); - asyncCopyState.reset_state(); + reset_execution_space(); } void sync_to_host(const stk::ngp::ExecSpace& newExecSpace) override { - asyncCopyState.set_state(newExecSpace, impl::DEVICE_TO_HOST_ASYNC); + set_execution_space(newExecSpace); + internal_sync_to_host(); + } + + void sync_to_host(stk::ngp::ExecSpace&& newExecSpace) override + { + set_execution_space(std::forward(newExecSpace)); internal_sync_to_host(); } void sync_to_device() override { - asyncCopyState.set_state(Kokkos::DefaultExecutionSpace(), impl::HOST_TO_DEVICE); + reset_execution_space(); internal_sync_to_device(); Kokkos::fence(); - asyncCopyState.reset_state(); + reset_execution_space(); } void sync_to_device(const stk::ngp::ExecSpace& newExecSpace) override { - asyncCopyState.set_state(newExecSpace, impl::HOST_TO_DEVICE_ASYNC); + set_execution_space(newExecSpace); + internal_sync_to_device(); + } + + void sync_to_device(stk::ngp::ExecSpace&& newExecSpace) override + { + set_execution_space(std::forward(newExecSpace)); internal_sync_to_device(); } @@ -407,6 +390,22 @@ class DeviceField : public NgpFieldBase return hostField->need_sync_to_device(); } + stk::ngp::ExecSpace& get_execution_space() const override { + return hostField->get_execution_space(); + } + + void set_execution_space(const stk::ngp::ExecSpace& executionSpace) override { + hostField->set_execution_space(executionSpace); + } + + void set_execution_space(stk::ngp::ExecSpace&& executionSpace) override { + hostField->set_execution_space(std::forward(executionSpace)); + } + + void reset_execution_space() override { + hostField->reset_execution_space(); + } + protected: void debug_modification_begin() override @@ -473,7 +472,7 @@ class DeviceField : public NgpFieldBase } } - Kokkos::deep_copy(asyncCopyState.execSpace, newDeviceSelectedBucketOffset, newHostSelectedBucketOffset); + Kokkos::deep_copy(get_execution_space(), newDeviceSelectedBucketOffset, newHostSelectedBucketOffset); } void construct_bool_bucket_views(const BucketVector & buckets, const std::string& suffix, @@ -502,7 +501,7 @@ class DeviceField : public NgpFieldBase hostAllFieldsBucketsNumComponentsPerEntity[bucket->bucket_id()] = field_scalars_per_entity(*hostField, *bucket); } - Kokkos::deep_copy(asyncCopyState.execSpace, deviceAllFieldsBucketsNumComponentsPerEntity, hostAllFieldsBucketsNumComponentsPerEntity); + Kokkos::deep_copy(get_execution_space(), deviceAllFieldsBucketsNumComponentsPerEntity, hostAllFieldsBucketsNumComponentsPerEntity); } void construct_field_buckets_num_components_per_entity_view(const BucketVector & buckets) @@ -513,7 +512,7 @@ class DeviceField : public NgpFieldBase hostFieldBucketsNumComponentsPerEntity[i] = field_scalars_per_entity(*hostField, *buckets[i]); } - Kokkos::deep_copy(asyncCopyState.execSpace, deviceFieldBucketsNumComponentsPerEntity, hostFieldBucketsNumComponentsPerEntity); + Kokkos::deep_copy(get_execution_space(), deviceFieldBucketsNumComponentsPerEntity, hostFieldBucketsNumComponentsPerEntity); } void construct_field_buckets_pointer_view(const BucketVector& buckets) @@ -532,7 +531,7 @@ class DeviceField : public NgpFieldBase hostBucketSizes[i] = buckets[i]->size(); } - Kokkos::deep_copy(asyncCopyState.execSpace, deviceBucketSizes, hostBucketSizes); + Kokkos::deep_copy(get_execution_space(), deviceBucketSizes, hostBucketSizes); } void set_field_buckets_pointer_view(const BucketVector& buckets) @@ -551,7 +550,7 @@ class DeviceField : public NgpFieldBase hostBucketPtrData(i) = reinterpret_cast(deviceBucketPtr); } - Kokkos::deep_copy(asyncCopyState.execSpace, deviceBucketPtrData, hostBucketPtrData); + Kokkos::deep_copy(get_execution_space(), deviceBucketPtrData, hostBucketPtrData); } void copy_unmodified_buckets(const BucketVector& buckets, FieldDataDeviceViewType destDevView, unsigned numPerEntity) @@ -578,7 +577,7 @@ class DeviceField : public NgpFieldBase UnmanagedView unInnerSrcView(srcPtr, ORDER_INDICES(bucketCapacity, numPerEntity)); UnmanagedView unInnerDestView(destPtr, ORDER_INDICES(bucketCapacity, numPerEntity)); - Kokkos::deep_copy(asyncCopyState.execSpace, unInnerDestView, unInnerSrcView); + Kokkos::deep_copy(get_execution_space(), unInnerDestView, unInnerSrcView); } void move_unmodified_buckets(const BucketVector& buckets, unsigned numPerEntity) @@ -648,16 +647,16 @@ class DeviceField : public NgpFieldBase hostFieldBucketsMarkedModified(bucketIdx) = isModified; } - Kokkos::deep_copy(asyncCopyState.execSpace, deviceFieldBucketsMarkedModified, hostFieldBucketsMarkedModified); + Kokkos::deep_copy(get_execution_space(), deviceFieldBucketsMarkedModified, hostFieldBucketsMarkedModified); - impl::transpose_new_and_modified_buckets_to_device(asyncCopyState.execSpace, *hostField, deviceBucketPtrData, deviceData, + impl::transpose_new_and_modified_buckets_to_device(get_execution_space(), *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity, deviceFieldBucketsMarkedModified); } void copy_device_to_host() { if (hostField) { - impl::transpose_to_pinned_and_mapped_memory(asyncCopyState.execSpace, *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); + impl::transpose_to_pinned_and_mapped_memory(get_execution_space(), *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); clear_device_sync_state(); hostField->increment_num_syncs_to_host(); } @@ -675,7 +674,7 @@ class DeviceField : public NgpFieldBase void copy_host_to_device() { if (hostField) { - impl::transpose_from_pinned_and_mapped_memory(asyncCopyState.execSpace, *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); + impl::transpose_from_pinned_and_mapped_memory(get_execution_space(), *hostField, deviceBucketPtrData, deviceData, deviceBucketSizes, deviceFieldBucketsNumComponentsPerEntity); clear_host_sync_state(); hostField->increment_num_syncs_to_device(); } @@ -744,8 +743,6 @@ class DeviceField : public NgpFieldBase typename BoolViewType::HostMirror hostFieldBucketsMarkedModified; BoolViewType deviceFieldBucketsMarkedModified; - impl::AsyncCopyState asyncCopyState; - NgpDebugger fieldSyncDebugger; }; diff --git a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp index 55fe6152a797..6481f55e257c 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp +++ b/packages/stk/stk_mesh/stk_mesh/base/DeviceMesh.cpp @@ -330,31 +330,25 @@ void DeviceMesh::fill_sparse_connectivities(const stk::mesh::BulkData& bulk_in) for(stk::mesh::EntityRank connectedRank=stk::topology::EDGE_RANK; connectedRank 0; for(unsigned iEntity=0; iEntity 0) { - const stk::mesh::Entity* connectedEntities = stkBucket.begin(iEntity, connectedRank); - const stk::mesh::ConnectivityOrdinal* connectedOrdinals = stkBucket.begin_ordinals(iEntity, connectedRank); - const stk::mesh::Permutation* permutations = hasPermutation ? stkBucket.begin_permutations(iEntity, connectedRank) : nullptr; - for(unsigned i=0; i const A * declare_attribute_no_delete(const A * a) { @@ -348,7 +364,8 @@ class FieldBase m_numSyncsToHost(0), m_numSyncsToDevice(0), m_modifiedOnHost(false), - m_modifiedOnDevice(false) + m_modifiedOnDevice(false), + m_execSpace(Kokkos::DefaultExecutionSpace()) { FieldBase * const pzero = nullptr ; const shards::ArrayDimTag * const dzero = nullptr ; @@ -383,6 +400,7 @@ class FieldBase mutable size_t m_numSyncsToDevice; mutable bool m_modifiedOnHost; mutable bool m_modifiedOnDevice; + mutable stk::ngp::ExecSpace m_execSpace; mutable Teuchos::any m_stkFieldSyncDebugger; }; diff --git a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp index 0a02b25b0c84..c117cd39be7c 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/FieldDataManager.hpp @@ -70,6 +70,7 @@ class AllocatorAdaptor : public AllocatorAdaptorInterface { } }; + class FieldDataManager { public: diff --git a/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp b/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp index 358d24d4b571..aeac5705a84a 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/GetNgpField.hpp @@ -47,7 +47,8 @@ NgpField & get_updated_ngp_field_async(const FieldBase & stkFiel NgpFieldBase * ngpField = impl::get_ngp_field(stkField); if (ngpField == nullptr) { - ngpField = new NgpField(stkField.get_mesh(), stkField, execSpace, true); + ngpField = new NgpField(stkField.get_mesh(), stkField, true); + ngpField->set_execution_space(execSpace); impl::set_ngp_field(stkField, ngpField); ngpField->clear_host_sync_state(); } @@ -61,6 +62,27 @@ NgpField & get_updated_ngp_field_async(const FieldBase & stkFiel return dynamic_cast< NgpField& >(*ngpField); } +template class NgpDebugger = DefaultNgpFieldSyncDebugger> +NgpField & get_updated_ngp_field_async(const FieldBase & stkField, stk::ngp::ExecSpace&& execSpace) +{ + NgpFieldBase * ngpField = impl::get_ngp_field(stkField); + + if (ngpField == nullptr) { + ngpField = new NgpField(stkField.get_mesh(), stkField, true); + ngpField->set_execution_space(std::forward(execSpace)); + impl::set_ngp_field(stkField, ngpField); + ngpField->clear_host_sync_state(); + } + else { + if (stkField.get_mesh().synchronized_count() != ngpField->synchronized_count()) { + ngpField->set_execution_space(std::forward(execSpace)); + ngpField->update_field(); + } + } + + return dynamic_cast< NgpField& >(*ngpField); +} + template class NgpDebugger = DefaultNgpFieldSyncDebugger> NgpField & get_updated_ngp_field(const FieldBase & stkField) { diff --git a/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp b/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp index 5cfc1794dcc7..d900b8ba46b8 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/HostField.hpp @@ -65,8 +65,7 @@ class HostField : public NgpFieldBase : NgpFieldBase(), hostBulk(nullptr), field(nullptr), - synchronizedCount(0), - asyncCopyState(impl::AsyncCopyState()) + synchronizedCount(0) { } @@ -74,18 +73,11 @@ class HostField : public NgpFieldBase : NgpFieldBase(), hostBulk(&b), field(&f), - synchronizedCount(0), - asyncCopyState(impl::AsyncCopyState()) + synchronizedCount(0) { field->template make_field_sync_debugger(); update_field(); - } - - HostField(const stk::mesh::BulkData& b, const stk::mesh::FieldBase& f, - const stk::ngp::ExecSpace& execSpace, bool isFromGetUpdatedNgpField = false) - : HostField(b, f, isFromGetUpdatedNgpField) - { - asyncCopyState.set_state(execSpace, impl::INVALID); + reset_execution_space(); } HostField(const HostField&) = default; @@ -101,8 +93,6 @@ class HostField : public NgpFieldBase void set_field_states(HostField* fields[]) {} - void set_execution_space(const stk::ngp::ExecSpace& execSpace) override { asyncCopyState.set_execution_space(execSpace); } - size_t num_syncs_to_host() const override { return field->num_syncs_to_host(); } size_t num_syncs_to_device() const override { return field->num_syncs_to_device(); } void fence() override {} @@ -214,6 +204,14 @@ class HostField : public NgpFieldBase } } + void sync_to_host(stk::ngp::ExecSpace&& execSpace) override + { + if (need_sync_to_host()) { + copy_device_to_host(); + clear_device_sync_state(); + } + } + void sync_to_device() override { sync_to_device(Kokkos::DefaultExecutionSpace()); @@ -231,6 +229,17 @@ class HostField : public NgpFieldBase } } + void sync_to_device(stk::ngp::ExecSpace&& execSpace) override + { + if (need_sync_to_device()) { + if (hostBulk->synchronized_count() != synchronizedCount) { + update_field(); + } + copy_host_to_device(); + clear_host_sync_state(); + } + } + size_t synchronized_count() const override { return field->mesh_meta_data().mesh_bulk_data().synchronized_count(); } FieldState state() const { return field->state(); } @@ -257,6 +266,21 @@ class HostField : public NgpFieldBase void notify_sync_debugger_clear_host_sync_state() override {} void notify_sync_debugger_clear_device_sync_state() override {} + stk::ngp::ExecSpace& get_execution_space() const override { + return field->get_execution_space(); + } + + void set_execution_space(const stk::ngp::ExecSpace& executionSpace) override { + field->set_execution_space(executionSpace); + } + + void set_execution_space(stk::ngp::ExecSpace&& executionSpace) override { + field->set_execution_space(std::forward(executionSpace)); + } + + void reset_execution_space() override { + field->reset_execution_space(); + } private: void set_modify_on_device() { @@ -277,7 +301,6 @@ class HostField : public NgpFieldBase const stk::mesh::FieldBase * field; size_t synchronizedCount; - impl::AsyncCopyState asyncCopyState; }; } diff --git a/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp b/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp index 3cdbcc52481a..492e62d79832 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/NgpFieldBase.hpp @@ -32,13 +32,19 @@ class NgpFieldBase virtual void clear_host_sync_state() = 0; virtual void clear_device_sync_state() = 0; virtual void sync_to_host() = 0; - virtual void sync_to_host(const stk::ngp::ExecSpace& execSpace) = 0; + virtual void sync_to_host(const stk::ngp::ExecSpace& newExecSpace) = 0; + virtual void sync_to_host(stk::ngp::ExecSpace&& newExecSpace) = 0; virtual void sync_to_device() = 0; - virtual void sync_to_device(const stk::ngp::ExecSpace& execSpace) = 0; + virtual void sync_to_device(const stk::ngp::ExecSpace& newExecSpace) = 0; + virtual void sync_to_device(stk::ngp::ExecSpace&& newExecSpace) = 0; virtual size_t synchronized_count() const = 0; virtual size_t num_syncs_to_host() const = 0; virtual size_t num_syncs_to_device() const = 0; - virtual void set_execution_space(const stk::ngp::ExecSpace& execSpace) = 0; + virtual stk::ngp::ExecSpace& get_execution_space() const = 0; + virtual void set_execution_space(const stk::ngp::ExecSpace& executionSpace) = 0; + virtual void set_execution_space(stk::ngp::ExecSpace&& executionSpace) = 0; + virtual void reset_execution_space() = 0; + virtual void fence() = 0; virtual void debug_modification_begin() = 0; diff --git a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp deleted file mode 100644 index b0b351e3d407..000000000000 --- a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.cpp +++ /dev/null @@ -1,193 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include -#include -#include - -namespace stk { -namespace mesh { - -SparseConnectivity::SparseConnectivity(unsigned numRanks) - : m_numRanks(numRanks) -{ - update_num_ranks(numRanks); -} - -void SparseConnectivity::update_num_ranks(unsigned numRanks) -{ - const unsigned minNumRanks = stk::topology::NUM_RANKS; - m_numRanks = std::max(numRanks, minNumRanks); - - m_entityPermutationOffset.resize(m_numRanks); - m_permutations.resize(m_numRanks); - for(unsigned rank=0; rank()); - } -} - -void SparseConnectivity::update_size_of_entity_index_space(unsigned numEntities) -{ - m_meshConnectivity.resize(numEntities); -} - -bool SparseConnectivity::has_permutation(EntityRank fromRank, EntityRank toRank) -{ - return (fromRank > stk::topology::NODE_RANK && fromRank < stk::topology::CONSTRAINT_RANK) - && (toRank > stk::topology::NODE_RANK && toRank < stk::topology::CONSTRAINT_RANK); -} - -const Permutation* SparseConnectivity::begin_permutations(Entity fromEntity, - EntityRank connectedRank) const -{ - if (static_cast(connectedRank) < m_entityPermutationOffset.size() && - fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { - const int entityOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; - return m_permutations[connectedRank][entityOffset].data(); - } - return nullptr; -} - -const Permutation* SparseConnectivity::end_permutations(Entity fromEntity, - EntityRank connectedRank) const -{ - if (static_cast(connectedRank) < m_entityPermutationOffset.size() && - fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { - const int entityOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; - const std::vector& perms = m_permutations[connectedRank][entityOffset]; - return (perms.data()+perms.size()); - } - return nullptr; -} - -bool SparseConnectivity::add_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal, - Permutation permutation) -{ - Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; - int insertLocation = conn.add_connectivity(connectedRank, - connectedEntity, ordinal, (connectedRank > fromRank)); - - if (insertLocation >= 0 && has_permutation(fromRank, connectedRank)) { - if (fromEntity.local_offset() >= m_entityPermutationOffset[connectedRank].size()) { - m_entityPermutationOffset[connectedRank].resize(fromEntity.local_offset()+1); - m_entityPermutationOffset[connectedRank][fromEntity.local_offset()] = 0; - } - unsigned& permOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; - if (permOffset == 0) { - permOffset = m_permutations[connectedRank].size(); - m_permutations[connectedRank].push_back(std::vector(1, permutation)); - return true; - } - std::vector& permutations = m_permutations[connectedRank][permOffset]; - permutations.insert(permutations.begin()+insertLocation, permutation); - } - - return insertLocation >= 0; -} - -bool SparseConnectivity::replace_or_add_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal) -{ - Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; - int insertLocation = conn.replace_or_add_connectivity(connectedRank, - connectedEntity, ordinal); - - return insertLocation >= 0; -} - -bool SparseConnectivity::remove_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal) -{ - Connectivity& conn = m_meshConnectivity[fromEntity.local_offset()]; - int location = conn.remove_connectivity(connectedRank, connectedEntity, ordinal); - - if (location >= 0) { - if (has_permutation(fromRank, connectedRank)) { - const unsigned permOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; - std::vector& permutations = m_permutations[connectedRank][permOffset]; - permutations.erase(permutations.begin()+location); - } - return true; - } - return false; -} - -bool SparseConnectivity::replace_permutation(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - ConnectivityOrdinal ordinal, - Permutation newPermutation) -{ - if (fromEntity.local_offset() < m_entityPermutationOffset[connectedRank].size()) { - const ConnectivityOrdinal* ordsBegin = begin_ordinals(fromEntity, connectedRank); - const ConnectivityOrdinal* ordsEnd = end_ordinals(fromEntity, connectedRank); - - bool foundIt = false; - const bool downward = fromRank > connectedRank; - unsigned idx = ordsEnd - ordsBegin; - if (downward) { - const ConnectivityOrdinal* iter = std::lower_bound(ordsBegin, ordsEnd, ordinal); - idx = iter - ordsBegin; - foundIt = (iter != ordsEnd && *iter == ordinal); - } - else { - const ConnectivityOrdinal* iter = std::find(ordsBegin, ordsEnd, ordinal); - idx = iter - ordsBegin; - foundIt = (iter != ordsEnd); - } - if (foundIt) { - const int entityPermOffset = m_entityPermutationOffset[connectedRank][fromEntity.local_offset()]; - std::vector& perms = m_permutations[connectedRank][entityPermOffset]; - perms[idx] = newPermutation; - return true; - } - } - return false; -} - -} // namespace mesh -} // namespace stk - diff --git a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp b/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp deleted file mode 100644 index a05f87d84a73..000000000000 --- a/packages/stk/stk_mesh/stk_mesh/base/SparseConnectivity.hpp +++ /dev/null @@ -1,151 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#ifndef STK_MESH_SPARSECONNECTIVITY_HPP -#define STK_MESH_SPARSECONNECTIVITY_HPP - -#include -#include // for EntityRank -#include -#include -#include - -namespace stk { -namespace mesh { - -class SparseConnectivity { -public: - SparseConnectivity(unsigned numRanks = stk::topology::NUM_RANKS); - virtual ~SparseConnectivity(){} - - void update_num_ranks(unsigned numRanks); - void update_size_of_entity_index_space(unsigned numEntities); - - static bool has_permutation(EntityRank fromRank, EntityRank toRank); - - unsigned num_connectivity(Entity fromEntity, EntityRank connectedRank) const; - - const Entity* begin_connectivity(Entity fromEntity, EntityRank connectedRank) const; - const Entity* end_connectivity(Entity fromEntity, EntityRank connectedRank) const; - - const ConnectivityOrdinal* begin_ordinals(Entity fromEntity, EntityRank connectedRank) const; - const ConnectivityOrdinal* end_ordinals(Entity fromEntity, EntityRank connectedRank) const; - - const Permutation* begin_permutations(Entity fromEntity, EntityRank connectedRank) const; - const Permutation* end_permutations(Entity fromEntity, EntityRank connectedRank) const; - - bool add_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal, - Permutation permutation); - - bool replace_or_add_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal); - - bool remove_connectivity(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - Entity connectedEntity, - ConnectivityOrdinal ordinal); - - bool replace_permutation(EntityRank fromRank, - Entity fromEntity, - EntityRank connectedRank, - ConnectivityOrdinal ordinal, - Permutation newPermutation); - - PairIterEntity get_connectivity(Entity fromEntity, EntityRank connectedRank) const; - - const Connectivity& get_connectivity(Entity entity) const { return m_meshConnectivity[entity.local_offset()]; } - Connectivity& get_connectivity(Entity entity) { return m_meshConnectivity[entity.local_offset()]; } - -private: - - std::vector m_meshConnectivity; - std::vector> m_entityPermutationOffset; - std::vector>> m_permutations; - unsigned m_numRanks; -}; - -inline -unsigned SparseConnectivity::num_connectivity(Entity fromEntity, - EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].num_connectivity(connectedRank); -} - -inline -const Entity* SparseConnectivity::begin_connectivity(Entity fromEntity, - EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].begin_connectivity(connectedRank); -} - -inline -const Entity* SparseConnectivity::end_connectivity(Entity fromEntity, - EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].end_connectivity(connectedRank); -} - -inline -PairIterEntity SparseConnectivity::get_connectivity(Entity fromEntity, EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].get_connectivity(connectedRank); -} - -inline -const ConnectivityOrdinal* SparseConnectivity::begin_ordinals(Entity fromEntity, - EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].begin_ordinals(connectedRank); -} - -inline -const ConnectivityOrdinal* SparseConnectivity::end_ordinals(Entity fromEntity, - EntityRank connectedRank) const -{ - return m_meshConnectivity[fromEntity.local_offset()].end_ordinals(connectedRank); -} - -} // namespace mesh -} // namespace stk - -#endif //STK_MESH_SPARSECONNECTIVITY_HPP - diff --git a/packages/stk/stk_mesh/stk_mesh/base/Types.hpp b/packages/stk/stk_mesh/stk_mesh/base/Types.hpp index 13729f625b3c..083a6e1018ba 100644 --- a/packages/stk/stk_mesh/stk_mesh/base/Types.hpp +++ b/packages/stk/stk_mesh/stk_mesh/base/Types.hpp @@ -236,9 +236,6 @@ typedef std::vector EntityCommInfoVector; typedef PairIter< EntityCommInfoVector::const_iterator > PairIterEntityComm ; #endif - -using PairIterEntity = PairIter; - /** \} */ //---------------------------------------------------------------------- diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp index 575e12b98169..2143cdaf75f2 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.cpp @@ -42,6 +42,7 @@ #include // for Partition, lower_bound #include #include +#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity #include "stk_mesh/base/FieldBase.hpp" // for FieldBase #include "stk_mesh/base/MetaData.hpp" // for MetaData #include "stk_mesh/base/Types.hpp" // for BucketVector, EntityRank, etc @@ -277,6 +278,52 @@ Partition* BucketRepository::create_partition( return partition; } +void BucketRepository::internal_modification_end() +{ + sync_from_partitions(); + + for(EntityRank from_rank = stk::topology::NODE_RANK; from_rank < stk::topology::NUM_RANKS; ++from_rank) + { + const BucketVector &buckets = this->buckets(from_rank); + unsigned num_buckets = buckets.size(); + for(unsigned j = 0; j < num_buckets; ++j) + { + ThrowAssert(buckets[j] != NULL); + Bucket &bucket = *buckets[j]; + + // Update the hop-saving connectivity data on this bucket. + // + for(EntityRank to_rank = stk::topology::NODE_RANK; to_rank < stk::topology::NUM_RANKS; ++to_rank) + { + if (from_rank == to_rank) { + continue; + } + + switch(to_rank) + { + case stk::topology::NODE_RANK: + bucket.m_fixed_node_connectivity.end_modification(&bucket.m_mesh); + break; + case stk::topology::EDGE_RANK: + bucket.m_dynamic_edge_connectivity.end_modification(&bucket.m_mesh); + break; + case stk::topology::FACE_RANK: + bucket.m_dynamic_face_connectivity.end_modification(&bucket.m_mesh); + break; + case stk::topology::ELEMENT_RANK: + bucket.m_dynamic_element_connectivity.end_modification(&bucket.m_mesh); + break; + case stk::topology::INVALID_RANK: + break; + default: + bucket.m_dynamic_other_connectivity.end_modification(&bucket.m_mesh); + break; + } + } + } + } +} + void BucketRepository::sync_from_partitions() { for (EntityRank rank = stk::topology::NODE_RANK; rank < static_cast(m_partitions.size()); ++rank) diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp index db99005a0d88..11398d136ee8 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/BucketRepository.hpp @@ -132,6 +132,9 @@ class BucketRepository PartOrdinal* keyPtr, PartOrdinal* keyEnd); + // For use by BulkData::internal_modification_end(). + void internal_modification_end(); + // Update m_buckets from the partitions. void sync_from_partitions(); void sync_from_partitions(EntityRank rank); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp index 7d66af99bfbd..3b5dc54a2c99 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.cpp @@ -1264,10 +1264,52 @@ void comm_sync_aura_send_recv( } } +void insert_upward_relations(const BulkData& bulk_data, Entity rel_entity, + const EntityRank rank_of_orig_entity, + const int share_proc, + std::vector& send) +{ + EntityRank rel_entity_rank = bulk_data.entity_rank(rel_entity); + ThrowAssert(rel_entity_rank > rank_of_orig_entity); + + // If related entity is higher rank, I own it, and it is not + // already shared by proc, ghost it to the sharing processor. + if ( bulk_data.bucket(rel_entity).owned() && ! bulk_data.in_shared(rel_entity, share_proc) ) { + + send.emplace_back(rel_entity,share_proc); + + // There may be even higher-ranking entities that need to be ghosted, so we must recurse + const EntityRank end_rank = static_cast(bulk_data.mesh_meta_data().entity_rank_count()); + for (EntityRank irank = static_cast(rel_entity_rank + 1); irank < end_rank; ++irank) + { + const int num_rels = bulk_data.num_connectivity(rel_entity, irank); + Entity const* rels = bulk_data.begin(rel_entity, irank); + + for (int r = 0; r < num_rels; ++r) + { + Entity const rel_of_rel_entity = rels[r]; + if (bulk_data.is_valid(rel_of_rel_entity)) { + insert_upward_relations(bulk_data, rel_of_rel_entity, rel_entity_rank, share_proc, send); + } + } + } + } +} + +EntityRank get_highest_upward_connected_rank(const BulkData& mesh, Entity entity) +{ + const EntityRank entityRank = mesh.entity_rank(entity); + EntityRank highestRank = static_cast(mesh.mesh_meta_data().entity_rank_count()-1); + while(highestRank > entityRank && mesh.num_connectivity(entity, highestRank) == 0) { + highestRank = static_cast(highestRank-1); + } + return highestRank; +} + void insert_upward_relations(const BulkData& bulk_data, - const Connectivity& entityConnectivity, const EntityProcMapping& entitySharing, Entity rel_entity, + const EntityRank rank_of_orig_entity, const int share_proc, EntityProcMapping& send) { @@ -1279,8 +1321,13 @@ void insert_upward_relations(const BulkData& bulk_data, send.addEntityProc(rel_entity,share_proc); - PairIterEntity conn = entityConnectivity.get_highest_rank_connectivity(bulk_data.entity_rank(rel_entity)); - for( Entity upwardEntity : conn) { + const unsigned bucketOrd = idx.bucket_ordinal; + const EntityRank upwardRank = get_highest_upward_connected_rank(bulk_data, rel_entity); + const int numRels = bucket.num_connectivity(bucketOrd, upwardRank); + Entity const* rels = bucket.begin(bucketOrd, upwardRank); + + for (int r = 0; r < numRels; ++r) { + Entity const upwardEntity = rels[r]; if (bulk_data.is_valid(upwardEntity) && bulk_data.bucket(upwardEntity).owned()) { if (!entitySharing.find(upwardEntity, share_proc)) { send.addEntityProc(upwardEntity, share_proc); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp index 8403ea4f2a17..e493ac58311a 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshImplUtils.hpp @@ -59,12 +59,14 @@ struct EntityGhostData; //stk-mesh capabilities. //---------------------------------------------------------------------- +void find_entities_these_nodes_have_in_common(const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); + +void find_entities_with_larger_ids_these_nodes_have_in_common_and_locally_owned(stk::mesh::EntityId id, const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); + void remove_entities_not_connected_to_other_nodes(const BulkData& mesh, EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& elementsInCommon); -void find_entities_these_nodes_have_in_common(const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); - template void find_entities_these_nodes_have_in_common_and(const BulkData& mesh, EntityRank rank, unsigned numNodes, const Entity* nodes, @@ -87,8 +89,6 @@ void find_entities_these_nodes_have_in_common_and(const BulkData& mesh, EntityRa } } -void find_entities_with_larger_ids_these_nodes_have_in_common_and_locally_owned(stk::mesh::EntityId id, const BulkData& mesh, stk::mesh::EntityRank rank, unsigned numNodes, const Entity* nodes, std::vector& entity_vector); - bool do_these_nodes_have_any_shell_elements_in_common(BulkData& mesh, unsigned numNodes, const Entity* nodes); void find_locally_owned_elements_these_nodes_have_in_common(const BulkData& mesh, unsigned numNodes, const Entity* nodes, std::vector& elems); @@ -244,10 +244,15 @@ void comm_sync_aura_send_recv( EntityProcMapping& entityProcMapping, std::vector& ghostStatus ); +void insert_upward_relations(const BulkData& bulk_data, Entity rel_entity, + const EntityRank rank_of_orig_entity, + const int share_proc, + std::vector& send); + void insert_upward_relations(const BulkData& bulk_data, - const Connectivity& entityConnectivity, const EntityProcMapping& entitySharing, Entity rel_entity, + const EntityRank rank_of_orig_entity, const int share_proc, EntityProcMapping& send); diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp index c301ada91b24..b7bb82c7bb7a 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshModification.cpp @@ -21,7 +21,6 @@ bool MeshModification::modification_begin(const std::string description) if (numRanks > m_bulkData.m_selector_to_buckets_maps.size()) { m_bulkData.m_selector_to_buckets_maps.resize(numRanks); } - m_bulkData.m_sparse_connectivity.update_num_ranks(m_bulkData.mesh_meta_data().entity_rank_count()); } if ( this->in_modifiable_state() ) return false ; diff --git a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp index 8945a5620fe3..c4c8fba02cdd 100644 --- a/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp +++ b/packages/stk/stk_mesh/stk_mesh/baseImpl/MeshPrintUtils.cpp @@ -187,20 +187,6 @@ void print_connectivity_of_rank(const BulkData& M, Entity entity, } } -void print_upward_connectivity(const BulkData& bulk, Entity entity, std::ostream& out) -{ - EntityRank nextRank = static_cast(bulk.entity_rank(entity)+1); - EntityRank endRank = static_cast(bulk.mesh_meta_data().entity_rank_count()); - - for(EntityRank rank = nextRank; rank < endRank; ++rank) { - const unsigned num = bulk.num_connectivity(entity, rank); - const Entity* conn = bulk.begin(entity, rank); - for(unsigned i=0; i void transpose_from_pinned_and_mapped_memory(ExecSpaceType & execSpace, const FieldBase & stkField, diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp index 58d544df65f0..3a7d0423dd7a 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/BucketTester.hpp @@ -49,7 +49,7 @@ class BucketTester : public stk::mesh::Bucket void my_change_connected_nodes(unsigned bucket_ordinal, Entity* new_nodes) { - this->change_connected_nodes(bucket_ordinal, new_nodes); + this->change_existing_connectivity(bucket_ordinal, new_nodes); } void my_change_existing_permutation_for_connected_element(unsigned bucket_ordinal_of_lower_ranked_entity, diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/CMakeLists.txt b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/CMakeLists.txt index 8d8e9959e3bd..e74727fc5431 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/CMakeLists.txt +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/CMakeLists.txt @@ -12,7 +12,10 @@ SET(HEADERS_NEED_IO GeneratedMeshToFile.hpp ReadWriteSidesetTester.hpp StkMeshFromGeneratedMesh.hpp + TextMeshFixture.hpp TextMeshToFile.hpp + TextMeshUtils.hpp + TextMesh.hpp ioUtils.hpp ) SET(SOURCES_NEED_IO @@ -22,7 +25,9 @@ SET(SOURCES_NEED_IO GenerateALefRAMesh.cpp GeneratedMeshToFile.cpp ReadWriteSidesetTester.cpp + TextMeshFixture.cpp TextMeshToFile.cpp + TextMeshUtils.cpp TextMesh.cpp ioUtils.cpp meshCreationHelpers.cpp diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp index 94884859a0d0..ff3ea1df74e0 100644 --- a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMesh.cpp @@ -1,6 +1,7 @@ // ####################### Start Clang Header Tool Managed Headers ######################## // clang-format off #include "TextMesh.hpp" +#include "TextMeshUtils.hpp" #include // for toupper #include // for size_t #include // for remove, etc @@ -34,480 +35,6 @@ namespace stk { namespace unit_test_util { - -using EntityIdSet = std::set; - -class TopologyMapping -{ -public: - stk::topology::topology_t topology(const std::string& name) - { - auto it = m_nameToTopology.find(name); - return (it != m_nameToTopology.end() ? it->second : stk::topology::INVALID_TOPOLOGY); - } - -private: - std::unordered_map m_nameToTopology = - { - { "NODE" , stk::topology::NODE }, - { "LINE_2" , stk::topology::LINE_2 }, - { "LINE_3" , stk::topology::LINE_3 }, - { "TRI_3" , stk::topology::TRI_3 }, - { "TRI_4" , stk::topology::TRI_4 }, - { "TRI_6" , stk::topology::TRI_6 }, - { "QUAD_4" , stk::topology::QUAD_4 }, - { "QUAD_6" , stk::topology::QUAD_6 }, - { "QUAD_8" , stk::topology::QUAD_8 }, - { "QUAD_9" , stk::topology::QUAD_9 }, - { "PARTICLE" , stk::topology::PARTICLE }, - { "LINE_2_1D" , stk::topology::LINE_2_1D }, - { "LINE_3_1D" , stk::topology::LINE_3_1D }, - { "BEAM_2" , stk::topology::BEAM_2 }, - { "BEAM_3" , stk::topology::BEAM_3 }, - { "SHELL_LINE_2" , stk::topology::SHELL_LINE_2 }, - { "SHELL_LINE_3" , stk::topology::SHELL_LINE_3 }, - { "SPRING_2" , stk::topology::SPRING_2 }, - { "SPRING_3" , stk::topology::SPRING_3 }, - { "TRI_3_2D" , stk::topology::TRI_3_2D }, - { "TRI_4_2D" , stk::topology::TRI_4_2D }, - { "TRI_6_2D" , stk::topology::TRI_6_2D }, - { "QUAD_4_2D" , stk::topology::QUAD_4_2D }, - { "QUAD_8_2D" , stk::topology::QUAD_8_2D }, - { "QUAD_9_2D" , stk::topology::QUAD_9_2D }, - { "SHELL_TRI_3" , stk::topology::SHELL_TRI_3 }, - { "SHELL_TRI_4" , stk::topology::SHELL_TRI_4 }, - { "SHELL_TRI_6" , stk::topology::SHELL_TRI_6 }, - { "SHELL_QUAD_4" , stk::topology::SHELL_QUAD_4 }, - { "SHELL_QUAD_8" , stk::topology::SHELL_QUAD_8 }, - { "SHELL_QUAD_9" , stk::topology::SHELL_QUAD_9 }, - { "TET_4" , stk::topology::TET_4 }, - { "TET_8" , stk::topology::TET_8 }, - { "TET_10" , stk::topology::TET_10 }, - { "TET_11" , stk::topology::TET_11 }, - { "PYRAMID_5" , stk::topology::PYRAMID_5 }, - { "PYRAMID_13" , stk::topology::PYRAMID_13 }, - { "PYRAMID_14" , stk::topology::PYRAMID_14 }, - { "WEDGE_6" , stk::topology::WEDGE_6 }, - { "WEDGE_12" , stk::topology::WEDGE_12 }, - { "WEDGE_15" , stk::topology::WEDGE_15 }, - { "WEDGE_18" , stk::topology::WEDGE_18 }, - { "HEX_8" , stk::topology::HEX_8 }, - { "HEX_20" , stk::topology::HEX_20 }, - { "HEX_27" , stk::topology::HEX_27 }, - }; -}; - -class PartIdMapping -{ -public: - PartIdMapping() - : m_idsAssigned(false) - { } - - void register_part_name(const std::string& name) - { - m_partNames.push_back(name); - handle_block_part(name); - } - - void register_part_name_with_id(const std::string& name, unsigned id) - { - register_part_name(name); - assign(name, id); - } - - unsigned get(const std::string& name) - { - if (!m_idsAssigned) assign_ids(); - - auto it = m_ids.find(name); - ThrowRequireMsg(it != m_ids.end(), "PartIdMapping has no ID for invalid part name " << name); - return it->second; - } - -private: - void handle_block_part(const std::string& name) - { - const std::string blockPrefix = "BLOCK_"; - const unsigned prefixLength = blockPrefix.length(); - - if (name.length() < prefixLength+1) return; - - const std::string namePrefix = name.substr(0, prefixLength); - const std::string nameSuffix = name.substr(prefixLength); - - if (namePrefix != blockPrefix) return; - - unsigned id; - std::istringstream nameSuffixStream(nameSuffix); - nameSuffixStream >> id; - if (nameSuffixStream.fail()) { - return; - } - assign(name, id); - } - - void assign_ids() - { - unsigned nextPartId = 1; - for (const std::string& name : m_partNames) { - if (m_ids.find(name) == m_ids.end()) { - while (is_assigned(nextPartId)) nextPartId++; - - assign(name, nextPartId); - } - } - - m_idsAssigned = true; - } - - void assign(const std::string& name, unsigned id) - { - validate_name_and_id(name, id); - m_ids[name] = id; - m_assignedIds.insert(id); - } - - void validate_name_and_id(const std::string& name, unsigned id) - { - if (is_registered(name)) { - ThrowRequireMsg(m_ids[name] == id, - "Cannot assign part '" << name << "' two different ids: " << m_ids[name] << " and " << id); - } - else { - ThrowRequireMsg(!is_assigned(id), - "Part id " << id << " has already been assigned, cannot assign it to part '" << name << "'"); - } - } - - bool is_registered(const std::string& name) - { - return m_ids.count(name) > 0; - } - - bool is_assigned(unsigned id) const - { - return m_assignedIds.count(id) > 0; - } - - std::vector m_partNames; - std::set m_assignedIds; - std::unordered_map m_ids; - bool m_idsAssigned; -}; - -struct ElementData -{ - int proc; - stk::mesh::EntityId identifier; - stk::topology topology; - stk::mesh::EntityIdVector nodeIds; - std::string partName = ""; - unsigned partId; -}; - -struct TextMeshData -{ - unsigned spatialDim; - std::vector elementDataVec; - EntityIdSet nodeIds; - - void add_element(const ElementData& elem) - { - elementDataVec.push_back(elem); - for (const stk::mesh::EntityId& nodeId : elem.nodeIds) { - nodeIds.insert(nodeId); - associate_node_with_proc(nodeId, elem.proc); - } - } - - const EntityIdSet nodes_on_proc(int proc) const - { - auto it = m_nodesOnProc.find(proc); - return it != m_nodesOnProc.end() ? it->second : EntityIdSet(); - } - - const std::set procs_for_node(const stk::mesh::EntityId& nodeId) const - { - auto it = m_procsForNode.find(nodeId); - return it != m_procsForNode.end() ? it->second : std::set(); - } - -private: - void associate_node_with_proc(const stk::mesh::EntityId& nodeId, int proc) - { - m_procsForNode[nodeId].insert(proc); - m_nodesOnProc[proc].insert(nodeId); - } - - std::unordered_map> m_procsForNode; - std::unordered_map m_nodesOnProc; -}; - -class Lexer -{ -public: - Lexer() - : m_token(""), - m_isNumber(false) - { } - - void set_input_string(const std::string& input) - { - m_input = input; - m_currentIndex = 0; - read_next_token(); - } - - int get_int() - { - read_next_token(); - return std::stoi(m_oldToken); - } - - unsigned get_unsigned() - { - read_next_token(); - return std::stoul(m_oldToken); - } - - std::string get_string() - { - read_next_token(); - return make_upper_case(m_oldToken); - } - - void get_newline() - { - read_next_token(); - } - - bool has_token() const { return m_token != ""; } - bool has_newline() const { return m_token == "\n"; } - bool has_number() const { return has_token() && m_isNumber; } - bool has_string() const { return has_token() && !has_number() && !has_newline(); } - -private: - void read_next_token() - { - m_oldToken = m_token; - - if (char_is_newline()) { - m_isNumber = false; - m_token = "\n"; - m_currentIndex++; - return; - } - - m_token = ""; - m_isNumber = true; - - while (has_more_input()) { - if (char_is_whitespace()) { - m_currentIndex++; - continue; - } - - if (char_is_comma()) { - m_currentIndex++; - break; - } - - if (char_is_newline()) { - break; - } - - m_isNumber &= char_is_digit(); - m_token += current_char(); - m_currentIndex++; - } - } - - bool has_more_input() - { - return m_currentIndex < m_input.size(); - } - - bool char_is_whitespace() { return current_char() == ' '; } - bool char_is_comma() { return current_char() == ','; } - bool char_is_newline() { return current_char() == '\n'; } - bool char_is_digit() { return std::isdigit(static_cast(current_char())); } - - char current_char() { return m_input[m_currentIndex]; } - - std::string make_upper_case(std::string str) - { - std::transform(str.begin(), str.end(), str.begin(), ::toupper); - return str; - } - - std::string m_input; - unsigned m_currentIndex; - - std::string m_oldToken; - std::string m_token; - - bool m_isNumber; -}; - -class TextMeshParser -{ -public: - TextMeshParser(unsigned dim) - { - m_data.spatialDim = dim; - } - - TextMeshData parse(const std::string& meshDescription) - { - initialize_parse(meshDescription); - parse_description(); - set_part_ids(); - return m_data; - } - -private: - void initialize_parse(const std::string& meshDescription) - { - m_lexer.set_input_string(meshDescription); - m_lineNumber = 1; - validate_required_field(m_lexer.has_token()); - } - - void parse_description() - { - while (m_lexer.has_token()) { - ElementData elemData = parse_element(); - m_data.add_element(elemData); - - validate_no_extra_fields(); - parse_newline(); - } - } - - ElementData parse_element() - { - ElementData elem; - elem.proc = parse_proc_id(); - elem.identifier = parse_elem_id(); - elem.topology = parse_topology(); - elem.nodeIds = parse_node_ids(elem.topology); - elem.partName = parse_part(elem.topology); - return elem; - } - - int parse_proc_id() - { - validate_required_field(m_lexer.has_number()); - return parse_int(); - } - - stk::mesh::EntityId parse_elem_id() - { - validate_required_field(m_lexer.has_number()); - return parse_unsigned(); - } - - stk::topology parse_topology() - { - validate_required_field(m_lexer.has_string()); - std::string topologyName = parse_string(); - - stk::topology topology = m_topologyMapping.topology(topologyName); - validate_topology(topology, topologyName); - - return topology; - } - - stk::mesh::EntityIdVector parse_node_ids(const stk::topology& topology) - { - stk::mesh::EntityIdVector nodeIds; - while (m_lexer.has_number()) { - nodeIds.push_back(parse_unsigned()); - } - validate_node_count(topology, nodeIds.size()); - return nodeIds; - } - - std::string parse_part(const stk::topology& topology) - { - std::string partName; - - if (m_lexer.has_string()) { - partName = parse_string(); - } - else { - partName = "block_" + topology.name(); - } - - if (m_lexer.has_number()) { - unsigned partId = parse_unsigned(); - m_partIds.register_part_name_with_id(partName, partId); - } - else { - m_partIds.register_part_name(partName); - } - - return partName; - } - - int parse_int() { return m_lexer.get_int(); } - unsigned parse_unsigned() { return m_lexer.get_unsigned(); } - std::string parse_string() { return m_lexer.get_string(); } - - void parse_newline() - { - m_lexer.get_newline(); - m_lineNumber++; - } - - void validate_required_field(bool hasNextRequiredField) - { - ThrowRequireMsg(hasNextRequiredField, - "Error! Each line must contain the following fields (with at least one node): " - "Processor, GlobalId, Element Topology, NodeIds. Error on line " << m_lineNumber << "."); - } - - void validate_no_extra_fields() - { - ThrowRequireMsg(!m_lexer.has_token() || m_lexer.has_newline(), - "Error! Each line should not contain more than the following fields (with at least one node): " - "Processor, GlobalId, Element Topology, NodeIds, Part Name, PartId. " - "Error on line " << m_lineNumber << "."); - } - - void validate_topology(const stk::topology& topology, const std::string& providedName) - { - ThrowRequireMsg(topology != stk::topology::INVALID_TOPOLOGY, - "Error! Topology = >>" << providedName << "<< is invalid from line " << m_lineNumber << "."); - ThrowRequireMsg(topology.defined_on_spatial_dimension(m_data.spatialDim), - "Error on input line " << m_lineNumber << ". Topology = " << topology - << " is not defined on spatial dimension = " << m_data.spatialDim - << " set in MetaData."); - } - - void validate_node_count(const stk::topology& topology, size_t numNodes) - { - size_t numTopologyNodes = topology.num_nodes(); - ThrowRequireMsg(numNodes == numTopologyNodes, - "Error! The input line appears to contain " << numNodes << " nodes, but the topology " - << topology << " needs " << numTopologyNodes << " nodes on line " << m_lineNumber << "."); - } - - void set_part_ids() - { - for (ElementData& elem : m_data.elementDataVec) { - elem.partId = m_partIds.get(elem.partName); - } - } - - unsigned m_lineNumber; - TextMeshData m_data; - Lexer m_lexer; - TopologyMapping m_topologyMapping; - PartIdMapping m_partIds; -}; - class MetaDataInitializer { public: @@ -529,7 +56,7 @@ class MetaDataInitializer stk::mesh::Part& part = m_meta.declare_part_with_topology(elementData.partName, elementData.topology); stk::io::put_io_part_attribute(part); - m_meta.set_part_id(part, elementData.partId); + m_meta.set_part_id(part, m_data.partIds.get(elementData.partName)); } } } @@ -608,41 +135,6 @@ class BulkDataInitializer stk::mesh::MetaData& m_meta; }; -class Coordinates -{ -public: - Coordinates(const TextMeshData& data, const std::vector coordinates) - { - validate_num_coordinates(data, coordinates); - fill_coordinate_map(data, coordinates); - } - - const std::vector& operator[](const stk::mesh::EntityId& nodeId) const - { - auto it(m_nodalCoords.find(nodeId)); - return it->second; - } - -private: - void validate_num_coordinates(const TextMeshData& data, const std::vector& coordinates) - { - ThrowRequireMsg(coordinates.size() == data.nodeIds.size()*data.spatialDim, - "Number of coordinates: " << coordinates.size() - << ", Number of nodes: " << data.nodeIds.size() - << ", Spatial dimension: " << data.spatialDim); - } - - void fill_coordinate_map(const TextMeshData& data, const std::vector& coordinates) - { - std::vector::const_iterator coordIter = coordinates.begin(); - for (const stk::mesh::EntityId& nodeId : data.nodeIds) { - m_nodalCoords[nodeId] = std::vector(coordIter, coordIter+data.spatialDim); - coordIter += data.spatialDim; - } - } - - std::unordered_map> m_nodalCoords; -}; class CoordinateInitializer { diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.cpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.cpp new file mode 100644 index 000000000000..a6b52ed16c90 --- /dev/null +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.cpp @@ -0,0 +1,168 @@ +#include +#include +#include // for Field +#include +#include // for MetaData, put_field, etc +#include +#include +#include +#include +#include +#include + +#include "gtest/gtest.h" +#include "mpi.h" + +namespace stk +{ +namespace unit_test_util +{ +TextMeshFixture::TextMeshFixture(unsigned spatialDim) : stk::unit_test_util::MeshFixture(spatialDim) {} + +void TextMeshFixture::verify_shared_nodes(const stk::mesh::EntityIdVector& nodeIds, int sharingProc) +{ + std::vector counts; + stk::mesh::count_entities(get_meta().globally_shared_part(), get_bulk(), counts); + EXPECT_EQ(nodeIds.size(), counts[stk::topology::NODE_RANK]); + + for (stk::mesh::EntityId nodeId : nodeIds) { + EXPECT_TRUE(get_bulk().in_shared(stk::mesh::EntityKey(stk::topology::NODE_RANK, nodeId), sharingProc)); + } +} + +void TextMeshFixture::verify_num_elements(size_t goldCount) +{ + std::vector counts; + stk::mesh::count_entities(get_meta().universal_part(), get_bulk(), counts); + EXPECT_EQ(goldCount, counts[stk::topology::ELEM_RANK]); +} + +void TextMeshFixture::verify_single_element( + stk::mesh::EntityId elemId, stk::topology topology, const stk::mesh::EntityIdVector& nodeIds) +{ + stk::mesh::Entity element = get_bulk().get_entity(stk::topology::ELEM_RANK, elemId); + EXPECT_TRUE(get_bulk().is_valid(element)); + EXPECT_EQ(topology, get_bulk().bucket(element).topology()); + verify_nodes_on_element(element, nodeIds); +} + +void TextMeshFixture::verify_part_membership(const std::vector golds) +{ + for (const PartInfo& gold : golds) { + stk::mesh::Part* blockPart = get_meta().get_part(gold.blockName); + + verify_part(blockPart); + verify_elements_on_part(blockPart, gold.ids); + } +} + +void TextMeshFixture::verify_part_ids(const std::vector& golds) +{ + for (const PartNameId& gold : golds) { + stk::mesh::Part* blockPart = get_meta().get_part(gold.first); + + verify_part(blockPart); + EXPECT_EQ(blockPart->id(), gold.second); + } +} + +void TextMeshFixture::verify_coordinates( + const stk::mesh::EntityIdVector& goldNodeIds, const std::vector& goldCoordinates) +{ + CoordinateVerifier cv(get_bulk(), goldNodeIds, goldCoordinates); + cv.verify(); +} + +void TextMeshFixture::verify_nodes_on_element(stk::mesh::Entity element, const stk::mesh::EntityIdVector& goldNodeIds) +{ + stk::mesh::EntityVector nodes(get_bulk().begin_nodes(element), get_bulk().end_nodes(element)); + EXPECT_EQ(goldNodeIds, get_node_ids(nodes)); +} + +stk::mesh::EntityIdVector TextMeshFixture::get_node_ids(const stk::mesh::EntityVector& nodes) +{ + stk::mesh::EntityIdVector nodeIds; + for (const stk::mesh::Entity& node : nodes) { + nodeIds.emplace_back(get_bulk().identifier(node)); + } + return nodeIds; +} + +void TextMeshFixture::verify_part(stk::mesh::Part* blockPart) +{ + ASSERT_TRUE(blockPart != nullptr); + EXPECT_TRUE(stk::io::is_part_io_part(*blockPart)); +} + +void TextMeshFixture::verify_elements_on_part(stk::mesh::Part* blockPart, const std::set& goldIds) +{ + stk::mesh::EntityVector elems; + stk::mesh::get_selected_entities(*blockPart, get_bulk().buckets(stk::topology::ELEM_RANK), elems); + + ASSERT_EQ(goldIds.size(), elems.size()); + for (const stk::mesh::Entity& elem : elems) { + stk::mesh::EntityId elemId = get_bulk().identifier(elem); + EXPECT_EQ(1u, goldIds.count(elemId)); + } +} + +TextMeshFixture::CoordinateVerifier::CoordinateVerifier( + const stk::mesh::BulkData& b, const stk::mesh::EntityIdVector& ids, const std::vector& coords) + : bulk(b), + meta(bulk.mesh_meta_data()), + spatialDim(meta.spatial_dimension()), + goldNodeIds(ids), + goldCoordinates(coords) +{ +} + +void TextMeshFixture::CoordinateVerifier::verify() +{ + verify_num_nodes(); + + for (size_t nodeIndex = 0; nodeIndex < goldNodeIds.size(); nodeIndex++) { + stk::mesh::EntityId nodeId = goldNodeIds[nodeIndex]; + EXPECT_TRUE(bulk.is_valid(get_node(nodeId))); + + const double* nodalCoords = get_nodal_coordinates(nodeId); + const double* goldCoords = &goldCoordinates[nodeIndex * spatialDim]; + + verify_nodal_coordinates(nodeId, goldCoords, nodalCoords); + } +} + +void TextMeshFixture::CoordinateVerifier::verify_num_nodes() +{ + stk::mesh::EntityVector nodes; + stk::mesh::get_entities(bulk, stk::topology::NODE_RANK, nodes); + EXPECT_EQ(goldNodeIds.size(), nodes.size()); +} + +const double* TextMeshFixture::CoordinateVerifier::get_nodal_coordinates(const stk::mesh::EntityId& nodeId) +{ + const stk::mesh::CoordinatesField& coordsField = + static_cast(*meta.coordinate_field()); + return stk::mesh::field_data(coordsField, get_node(nodeId)); +} + +const stk::mesh::Entity TextMeshFixture::CoordinateVerifier::get_node(const stk::mesh::EntityId& nodeId) +{ + return bulk.get_entity(stk::topology::NODE_RANK, nodeId); +} + +void TextMeshFixture::CoordinateVerifier::verify_nodal_coordinates( + const stk::mesh::EntityId& nodeId, const double* goldCoords, const double* nodalCoords) +{ + for (unsigned i = 0; i < spatialDim; i++) { + EXPECT_NEAR(goldCoords[i], nodalCoords[i], 1.0e-9) << error_message(nodeId, i); + } +} + +std::string TextMeshFixture::CoordinateVerifier::error_message(const stk::mesh::EntityId& nodeId, unsigned coordIndex) +{ + std::stringstream message; + message << "Proc " << bulk.parallel_rank() << ", Node ID " << nodeId << ", coord index " << coordIndex; + return message.str(); +} +} // namespace unit_test_util +} // namespace stk diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.hpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.hpp new file mode 100644 index 000000000000..98211091058b --- /dev/null +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshFixture.hpp @@ -0,0 +1,81 @@ +#ifndef STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_UNITTESTTEXTMESH_HPP_ +#define STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_UNITTESTTEXTMESH_HPP_ + +#include +#include // for MetaData, put_field, etc +#include +#include +#include + +namespace stk +{ +namespace unit_test_util +{ +class TextMeshFixture : public stk::unit_test_util::MeshFixture +{ + protected: + TextMeshFixture(unsigned spatialDim); + + void verify_shared_nodes(const stk::mesh::EntityIdVector& nodeIds, int sharingProc); + + void verify_num_elements(size_t goldCount); + + void verify_single_element( + stk::mesh::EntityId elemId, stk::topology topology, const stk::mesh::EntityIdVector& nodeIds); + + struct PartInfo { + std::string blockName; + std::set ids; + }; + + void verify_part_membership(const std::vector golds); + + using PartNameId = std::pair; + + void verify_part_ids(const std::vector& golds); + + void verify_coordinates(const stk::mesh::EntityIdVector& goldNodeIds, const std::vector& goldCoordinates); + + private: + void verify_nodes_on_element(stk::mesh::Entity element, const stk::mesh::EntityIdVector& goldNodeIds); + + stk::mesh::EntityIdVector get_node_ids(const stk::mesh::EntityVector& nodes); + + void verify_part(stk::mesh::Part* blockPart); + + void verify_elements_on_part(stk::mesh::Part* blockPart, const std::set& goldIds); + + class CoordinateVerifier + { + public: + CoordinateVerifier( + const stk::mesh::BulkData& b, const stk::mesh::EntityIdVector& ids, const std::vector& coords); + + void verify(); + + private: + void verify_num_nodes(); + + const double* get_nodal_coordinates(const stk::mesh::EntityId& nodeId); + + const stk::mesh::Entity get_node(const stk::mesh::EntityId& nodeId); + + void verify_nodal_coordinates( + const stk::mesh::EntityId& nodeId, const double* goldCoords, const double* nodalCoords); + + std::string error_message(const stk::mesh::EntityId& nodeId, unsigned coordIndex); + + const stk::mesh::BulkData& bulk; + const stk::mesh::MetaData& meta; + + const unsigned spatialDim; + + const stk::mesh::EntityIdVector& goldNodeIds; + const std::vector& goldCoordinates; + }; +}; + +} // namespace unit_test_util +} // namespace stk + +#endif /* STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_UNITTESTTEXTMESH_HPP_ */ diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.cpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.cpp new file mode 100644 index 000000000000..60534a17e282 --- /dev/null +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.cpp @@ -0,0 +1,557 @@ +// ####################### Start Clang Header Tool Managed Headers ######################## +// clang-format off +#include "TextMeshUtils.hpp" +#include // for toupper +#include // for size_t +#include // for remove, etc +#include // for insert_iterator +#include +#include // for set +#include // for operator<<, etc +#include // for is_part_io_part, etc +#include // for BulkData +#include // for declare_element +#include // for Field +#include // for get_entities +#include // for MetaData, etc +#include // for basic_string, etc +#include // for pair +#include // for vector + +#include "stk_mesh/base/FieldParallel.hpp" +#include "stk_mesh/base/CoordinateSystems.hpp" // for Cartesian +#include "stk_mesh/base/Entity.hpp" // for Entity +#include "stk_mesh/base/FieldBase.hpp" // for field_data +#include "stk_mesh/base/Types.hpp" // for EntityId, etc +#include "stk_topology/topology.hpp" // for topology, etc +#include "stk_util/util/ReportHandler.hpp" // for ThrowRequireMsg + +namespace stk { namespace mesh { class Part; } } +// clang-format on +// ####################### End Clang Header Tool Managed Headers ######################## + +namespace stk +{ +namespace unit_test_util +{ +TopologyMapping::TopologyMapping() +{ + initialize_topology_map(); +} + +void TopologyMapping::initialize_topology_map() +{ + m_nameToTopology = { + {"NODE", stk::topology::NODE}, + {"LINE_2", stk::topology::LINE_2}, + {"LINE_3", stk::topology::LINE_3}, + {"TRI_3", stk::topology::TRI_3}, + {"TRI_4", stk::topology::TRI_4}, + {"TRI_6", stk::topology::TRI_6}, + {"QUAD_4", stk::topology::QUAD_4}, + {"QUAD_6", stk::topology::QUAD_6}, + {"QUAD_8", stk::topology::QUAD_8}, + {"QUAD_9", stk::topology::QUAD_9}, + {"PARTICLE", stk::topology::PARTICLE}, + {"LINE_2_1D", stk::topology::LINE_2_1D}, + {"LINE_3_1D", stk::topology::LINE_3_1D}, + {"BEAM_2", stk::topology::BEAM_2}, + {"BEAM_3", stk::topology::BEAM_3}, + {"SHELL_LINE_2", stk::topology::SHELL_LINE_2}, + {"SHELL_LINE_3", stk::topology::SHELL_LINE_3}, + {"SPRING_2", stk::topology::SPRING_2}, + {"SPRING_3", stk::topology::SPRING_3}, + {"TRI_3_2D", stk::topology::TRI_3_2D}, + {"TRI_4_2D", stk::topology::TRI_4_2D}, + {"TRI_6_2D", stk::topology::TRI_6_2D}, + {"QUAD_4_2D", stk::topology::QUAD_4_2D}, + {"QUAD_8_2D", stk::topology::QUAD_8_2D}, + {"QUAD_9_2D", stk::topology::QUAD_9_2D}, + {"SHELL_TRI_3", stk::topology::SHELL_TRI_3}, + {"SHELL_TRI_4", stk::topology::SHELL_TRI_4}, + {"SHELL_TRI_6", stk::topology::SHELL_TRI_6}, + {"SHELL_QUAD_4", stk::topology::SHELL_QUAD_4}, + {"SHELL_QUAD_8", stk::topology::SHELL_QUAD_8}, + {"SHELL_QUAD_9", stk::topology::SHELL_QUAD_9}, + {"TET_4", stk::topology::TET_4}, + {"TET_8", stk::topology::TET_8}, + {"TET_10", stk::topology::TET_10}, + {"TET_11", stk::topology::TET_11}, + {"PYRAMID_5", stk::topology::PYRAMID_5}, + {"PYRAMID_13", stk::topology::PYRAMID_13}, + {"PYRAMID_14", stk::topology::PYRAMID_14}, + {"WEDGE_6", stk::topology::WEDGE_6}, + {"WEDGE_12", stk::topology::WEDGE_12}, + {"WEDGE_15", stk::topology::WEDGE_15}, + {"WEDGE_18", stk::topology::WEDGE_18}, + {"HEX_8", stk::topology::HEX_8}, + {"HEX_20", stk::topology::HEX_20}, + {"HEX_27", stk::topology::HEX_27}, + }; +} + +stk::topology::topology_t TopologyMapping::topology(const std::string& name) const +{ + auto it = m_nameToTopology.find(name); + return (it != m_nameToTopology.end() ? it->second : stk::topology::INVALID_TOPOLOGY); +} + +PartIdMapping::PartIdMapping() : m_idsAssigned(false) {} + +void PartIdMapping::register_part_name(const std::string& name) +{ + m_partNames.push_back(name); + handle_block_part(name); +} + +void PartIdMapping::register_part_name_with_id(const std::string& name, unsigned id) +{ + register_part_name(name); + assign(name, id); +} + +unsigned PartIdMapping::get_part_id(const std::string& name) const +{ + auto it = m_ids.find(name); + ThrowRequireMsg(it != m_ids.end(), "PartIdMapping has no ID for invalid part name " << name); + return it->second; +} + +unsigned PartIdMapping::get(const std::string& name) const +{ + if (!m_idsAssigned) assign_ids(); + return get_part_id(name); +} + +std::string PartIdMapping::get_part_name(unsigned id) const +{ + auto it = m_parts.find(id); + ThrowRequireMsg(it != m_parts.end(), "PartIdMapping has no part name for invalid id " << id); + return it->second; +} + +std::string PartIdMapping::get(unsigned id) const +{ + if (!m_idsAssigned) assign_ids(); + return get_part_name(id); +} + +unsigned PartIdMapping::size() const +{ + if (!m_idsAssigned) assign_ids(); + return m_ids.size(); +} + +std::vector PartIdMapping::get_part_names_sorted_by_id() const +{ + if (!m_idsAssigned) assign_ids(); + + std::vector names; + names.reserve(m_parts.size()); + + for (auto iter : m_parts) { + names.push_back(iter.second); + } + + return names; +} + +void PartIdMapping::handle_block_part(const std::string& name) +{ + const std::string blockPrefix = "BLOCK_"; + const unsigned prefixLength = blockPrefix.length(); + + if (name.length() < prefixLength + 1) return; + + const std::string namePrefix = name.substr(0, prefixLength); + const std::string nameSuffix = name.substr(prefixLength); + + if (namePrefix != blockPrefix) return; + + unsigned id; + std::istringstream nameSuffixStream(nameSuffix); + nameSuffixStream >> id; + if (nameSuffixStream.fail()) { + return; + } + assign(name, id); +} + +void PartIdMapping::assign_ids() const +{ + unsigned nextPartId = 1; + for (const std::string& name : m_partNames) { + if (m_ids.find(name) == m_ids.end()) { + while (is_assigned(nextPartId)) nextPartId++; + + assign(name, nextPartId); + } + } + + m_idsAssigned = true; +} + +void PartIdMapping::assign(const std::string& name, unsigned id) const +{ + validate_name_and_id(name, id); + m_ids[name] = id; + m_parts[id] = name; +} + +void PartIdMapping::validate_name_and_id(const std::string& name, unsigned id) const +{ + if (is_registered(name)) { + ThrowRequireMsg( + m_ids[name] == id, "Cannot assign part '" << name << "' two different ids: " << m_ids[name] << " and " << id); + } else { + ThrowRequireMsg( + !is_assigned(id), "Part id " << id << " has already been assigned, cannot assign it to part '" << name << "'"); + } +} + +bool PartIdMapping::is_registered(const std::string& name) const +{ + return m_ids.count(name) > 0; +} + +bool PartIdMapping::is_assigned(unsigned id) const +{ + return m_parts.count(id) > 0; +} + +void TextMeshData::add_element(const ElementData& elem) +{ + elementDataVec.push_back(elem); + for (const stk::mesh::EntityId& nodeId : elem.nodeIds) { + nodeIds.insert(nodeId); + associate_node_with_proc(nodeId, elem.proc); + } +} + +const EntityIdSet TextMeshData::nodes_on_proc(int proc) const +{ + auto it = m_nodesOnProc.find(proc); + return it != m_nodesOnProc.end() ? it->second : EntityIdSet(); +} + +unsigned TextMeshData::num_nodes_on_proc(int proc) const +{ + auto it = m_nodesOnProc.find(proc); + return it != m_nodesOnProc.end() ? it->second.size() : 0; +} + +const std::set TextMeshData::procs_for_node(const stk::mesh::EntityId& nodeId) const +{ + auto it = m_procsForNode.find(nodeId); + return it != m_procsForNode.end() ? it->second : std::set(); +} + +void TextMeshData::associate_node_with_proc(const stk::mesh::EntityId& nodeId, int proc) +{ + m_procsForNode[nodeId].insert(proc); + m_nodesOnProc[proc].insert(nodeId); +} + +TextMeshLexer::TextMeshLexer() : m_currentIndex(0), m_token(""), m_isNumber(false) {} + +void TextMeshLexer::set_input_string(const std::string& input) +{ + m_input = input; + m_currentIndex = 0; + read_next_token(); +} + +int TextMeshLexer::get_int() +{ + read_next_token(); + return std::stoi(m_oldToken); +} + +unsigned TextMeshLexer::get_unsigned() +{ + read_next_token(); + return std::stoul(m_oldToken); +} + +std::string TextMeshLexer::get_string() +{ + read_next_token(); + return make_upper_case(m_oldToken); +} + +void TextMeshLexer::get_newline() +{ + read_next_token(); +} + +bool TextMeshLexer::has_token() const +{ + return m_token != ""; +} +bool TextMeshLexer::has_newline() const +{ + return m_token == "\n"; +} +bool TextMeshLexer::has_number() const +{ + return has_token() && m_isNumber; +} +bool TextMeshLexer::has_string() const +{ + return has_token() && !has_number() && !has_newline(); +} + +void TextMeshLexer::read_next_token() +{ + m_oldToken = m_token; + + if (char_is_newline()) { + m_isNumber = false; + m_token = "\n"; + m_currentIndex++; + return; + } + + m_token = ""; + m_isNumber = true; + + while (has_more_input()) { + if (char_is_whitespace()) { + m_currentIndex++; + continue; + } + + if (char_is_comma()) { + m_currentIndex++; + break; + } + + if (char_is_newline()) { + break; + } + + m_isNumber &= char_is_digit(); + m_token += current_char(); + m_currentIndex++; + } +} + +bool TextMeshLexer::has_more_input() +{ + return m_currentIndex < m_input.size(); +} + +bool TextMeshLexer::char_is_whitespace() +{ + return current_char() == ' '; +} +bool TextMeshLexer::char_is_comma() +{ + return current_char() == ','; +} +bool TextMeshLexer::char_is_newline() +{ + return current_char() == '\n'; +} +bool TextMeshLexer::char_is_digit() +{ + return std::isdigit(static_cast(current_char())); +} + +char TextMeshLexer::current_char() +{ + return m_input[m_currentIndex]; +} + +std::string TextMeshLexer::make_upper_case(std::string str) +{ + std::transform(str.begin(), str.end(), str.begin(), ::toupper); + return str; +} + +TextMeshParser::TextMeshParser(unsigned dim) : m_lineNumber(0) +{ + m_data.spatialDim = dim; +} + +TextMeshData TextMeshParser::parse(const std::string& meshDescription) +{ + initialize_parse(meshDescription); + parse_description(); + return m_data; +} + +void TextMeshParser::initialize_parse(const std::string& meshDescription) +{ + m_lexer.set_input_string(meshDescription); + m_lineNumber = 1; + validate_required_field(m_lexer.has_token()); +} + +void TextMeshParser::parse_description() +{ + while (m_lexer.has_token()) { + ElementData elemData = parse_element(); + m_data.add_element(elemData); + + validate_no_extra_fields(); + parse_newline(); + } +} + +ElementData TextMeshParser::parse_element() +{ + ElementData elem; + elem.proc = parse_proc_id(); + elem.identifier = parse_elem_id(); + elem.topology = parse_topology(); + elem.nodeIds = parse_node_ids(elem.topology); + elem.partName = parse_part(elem.topology); + return elem; +} + +int TextMeshParser::parse_proc_id() +{ + validate_required_field(m_lexer.has_number()); + return parse_int(); +} + +stk::mesh::EntityId TextMeshParser::parse_elem_id() +{ + validate_required_field(m_lexer.has_number()); + return parse_unsigned(); +} + +stk::topology TextMeshParser::parse_topology() +{ + validate_required_field(m_lexer.has_string()); + std::string topologyName = parse_string(); + + stk::topology topology = m_topologyMapping.topology(topologyName); + validate_topology(topology, topologyName); + + return topology; +} + +stk::mesh::EntityIdVector TextMeshParser::parse_node_ids(const stk::topology& topology) +{ + stk::mesh::EntityIdVector nodeIds; + while (m_lexer.has_number()) { + nodeIds.push_back(parse_unsigned()); + } + validate_node_count(topology, nodeIds.size()); + return nodeIds; +} + +std::string TextMeshParser::parse_part(const stk::topology& topology) +{ + std::string partName; + + if (m_lexer.has_string()) { + partName = parse_string(); + } else { + partName = "block_" + topology.name(); + } + + if (m_lexer.has_number()) { + unsigned partId = parse_unsigned(); + m_data.partIds.register_part_name_with_id(partName, partId); + } else { + m_data.partIds.register_part_name(partName); + } + + return partName; +} + +int TextMeshParser::parse_int() +{ + return m_lexer.get_int(); +} +unsigned TextMeshParser::parse_unsigned() +{ + return m_lexer.get_unsigned(); +} +std::string TextMeshParser::parse_string() +{ + return m_lexer.get_string(); +} + +void TextMeshParser::parse_newline() +{ + m_lexer.get_newline(); + m_lineNumber++; +} + +void TextMeshParser::validate_required_field(bool hasNextRequiredField) +{ + ThrowRequireMsg(hasNextRequiredField, + "Error! Each line must contain the following fields (with at least one node): " + "Processor, GlobalId, Element Topology, NodeIds. Error on line " + << m_lineNumber << "."); +} + +void TextMeshParser::validate_no_extra_fields() +{ + ThrowRequireMsg(!m_lexer.has_token() || m_lexer.has_newline(), + "Error! Each line should not contain more than the following fields (with at least one node): " + "Processor, GlobalId, Element Topology, NodeIds, Part Name, PartId. " + "Error on line " + << m_lineNumber << "."); +} + +void TextMeshParser::validate_topology(const stk::topology& topology, const std::string& providedName) +{ + ThrowRequireMsg(topology != stk::topology::INVALID_TOPOLOGY, + "Error! Topology = >>" << providedName << "<< is invalid from line " << m_lineNumber << "."); + ThrowRequireMsg(topology.defined_on_spatial_dimension(m_data.spatialDim), + "Error on input line " << m_lineNumber << ". Topology = " << topology + << " is not defined on spatial dimension = " << m_data.spatialDim << " set in MetaData."); +} + +void TextMeshParser::validate_node_count(const stk::topology& topology, size_t numNodes) +{ + size_t numTopologyNodes = topology.num_nodes(); + ThrowRequireMsg(numNodes == numTopologyNodes, "Error! The input line appears to contain " + << numNodes << " nodes, but the topology " << topology << " needs " + << numTopologyNodes << " nodes on line " << m_lineNumber << "."); +} + +Coordinates::Coordinates() {} + +Coordinates::Coordinates(const TextMeshData& data, const std::vector& coordinates) +{ + set_coordinate_data(data, coordinates); +} + +void Coordinates::set_coordinate_data(const TextMeshData& data, const std::vector& coordinates) +{ + if (!coordinates.empty()) { + validate_num_coordinates(data, coordinates); + fill_coordinate_map(data, coordinates); + } +} + +const std::vector& Coordinates::operator[](const stk::mesh::EntityId& nodeId) const +{ + auto it(m_nodalCoords.find(nodeId)); + return it->second; +} + +void Coordinates::validate_num_coordinates(const TextMeshData& data, const std::vector& coordinates) +{ + ThrowRequireMsg(coordinates.size() == data.nodeIds.size() * data.spatialDim, + "Number of coordinates: " << coordinates.size() << ", Number of nodes: " << data.nodeIds.size() + << ", Spatial dimension: " << data.spatialDim); +} + +void Coordinates::fill_coordinate_map(const TextMeshData& data, const std::vector& coordinates) +{ + std::vector::const_iterator coordIter = coordinates.begin(); + for (const stk::mesh::EntityId& nodeId : data.nodeIds) { + m_nodalCoords[nodeId] = std::vector(coordIter, coordIter + data.spatialDim); + coordIter += data.spatialDim; + } +} + +} // namespace unit_test_util +} // namespace stk diff --git a/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.hpp b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.hpp new file mode 100644 index 000000000000..92566803d61a --- /dev/null +++ b/packages/stk/stk_unit_test_utils/stk_unit_test_utils/TextMeshUtils.hpp @@ -0,0 +1,228 @@ +#ifndef STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_TEXTMESHUTILS_HPP_ +#define STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_TEXTMESHUTILS_HPP_ + +// ####################### Start Clang Header Tool Managed Headers ######################## +// clang-format off +#include "TextMesh.hpp" +#include // for toupper +#include // for size_t +#include // for remove, etc +#include // for insert_iterator +#include +#include // for set +#include // for operator<<, etc +#include // for is_part_io_part, etc +#include // for BulkData +#include // for declare_element +#include // for Field +#include // for get_entities +#include // for MetaData, etc +#include // for basic_string, etc +#include // for pair +#include // for vector + +#include "stk_mesh/base/FieldParallel.hpp" +#include "stk_mesh/base/CoordinateSystems.hpp" // for Cartesian +#include "stk_mesh/base/Entity.hpp" // for Entity +#include "stk_mesh/base/FieldBase.hpp" // for field_data +#include "stk_mesh/base/Types.hpp" // for EntityId, etc +#include "stk_topology/topology.hpp" // for topology, etc +#include "stk_util/util/ReportHandler.hpp" // for ThrowRequireMsg + +namespace stk { namespace mesh { class Part; } } +// clang-format on +// ####################### End Clang Header Tool Managed Headers ######################## + +namespace stk +{ +namespace unit_test_util +{ +using EntityIdSet = std::set; + +class TopologyMapping +{ + public: + TopologyMapping(); + stk::topology::topology_t topology(const std::string& name) const; + + private: + void initialize_topology_map(); + std::unordered_map m_nameToTopology; +}; + +class PartIdMapping +{ + public: + PartIdMapping(); + + void register_part_name(const std::string& name); + + void register_part_name_with_id(const std::string& name, unsigned id); + + unsigned get(const std::string& name) const; + + std::string get(unsigned id) const; + + unsigned size() const; + + std::vector get_part_names_sorted_by_id() const; + + private: + void handle_block_part(const std::string& name); + + void assign_ids() const; + + void assign(const std::string& name, unsigned id) const; + + void validate_name_and_id(const std::string& name, unsigned id) const; + + bool is_registered(const std::string& name) const; + + bool is_assigned(unsigned id) const; + + unsigned get_part_id(const std::string& name) const; + std::string get_part_name(unsigned id) const; + + std::vector m_partNames; + mutable std::unordered_map m_ids; + mutable std::map m_parts; + mutable bool m_idsAssigned; +}; + +struct ElementData { + int proc; + stk::mesh::EntityId identifier; + stk::topology topology; + stk::mesh::EntityIdVector nodeIds; + std::string partName = ""; +}; + +struct TextMeshData { + unsigned spatialDim; + std::vector elementDataVec; + PartIdMapping partIds; + EntityIdSet nodeIds; + + void add_element(const ElementData& elem); + + const EntityIdSet nodes_on_proc(int proc) const; + + unsigned num_nodes_on_proc(int proc) const; + + const std::set procs_for_node(const stk::mesh::EntityId& nodeId) const; + + private: + void associate_node_with_proc(const stk::mesh::EntityId& nodeId, int proc); + + std::unordered_map> m_procsForNode; + std::unordered_map m_nodesOnProc; +}; + +class TextMeshLexer +{ + public: + TextMeshLexer(); + + void set_input_string(const std::string& input); + + int get_int(); + + unsigned get_unsigned(); + + std::string get_string(); + + void get_newline(); + + bool has_token() const; + bool has_newline() const; + bool has_number() const; + bool has_string() const; + + private: + void read_next_token(); + + bool has_more_input(); + bool char_is_whitespace(); + bool char_is_comma(); + bool char_is_newline(); + bool char_is_digit(); + + char current_char(); + + std::string make_upper_case(std::string str); + + std::string m_input; + unsigned m_currentIndex; + + std::string m_oldToken; + std::string m_token; + + bool m_isNumber; +}; + +class TextMeshParser +{ + public: + TextMeshParser(unsigned dim); + + TextMeshData parse(const std::string& meshDescription); + + private: + void initialize_parse(const std::string& meshDescription); + + void parse_description(); + + ElementData parse_element(); + + int parse_proc_id(); + + stk::mesh::EntityId parse_elem_id(); + + stk::topology parse_topology(); + + stk::mesh::EntityIdVector parse_node_ids(const stk::topology& topology); + + std::string parse_part(const stk::topology& topology); + + int parse_int(); + unsigned parse_unsigned(); + std::string parse_string(); + + void parse_newline(); + + void validate_required_field(bool hasNextRequiredField); + + void validate_no_extra_fields(); + + void validate_topology(const stk::topology& topology, const std::string& providedName); + + void validate_node_count(const stk::topology& topology, size_t numNodes); + + unsigned m_lineNumber; + TextMeshData m_data; + TextMeshLexer m_lexer; + TopologyMapping m_topologyMapping; +}; + +class Coordinates +{ + public: + Coordinates(); + Coordinates(const TextMeshData& data, const std::vector& coordinates); + + const std::vector& operator[](const stk::mesh::EntityId& nodeId) const; + + void set_coordinate_data(const TextMeshData& data, const std::vector& coordinates); + + private: + void validate_num_coordinates(const TextMeshData& data, const std::vector& coordinates); + + void fill_coordinate_map(const TextMeshData& data, const std::vector& coordinates); + + std::unordered_map> m_nodalCoords; +}; + +} // namespace unit_test_util +} // namespace stk + +#endif /* STK_STK_UNIT_TEST_UTILS_STK_UNIT_TEST_UTILS_TEXTMESHUTILS_HPP_ */ diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp index 232600e5ed98..59838cf9313d 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucket.cpp @@ -194,7 +194,7 @@ TEST(UnitTestingOfBucket, bucketSortChangeEntityId) void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity elem, stk::mesh::Entity side, stk::mesh::EntityVector& nodes) { - stk::mesh::EntityRank sideRank = bulk.entity_rank(side); + stk::mesh::EntityRank rank = bulk.entity_rank(side); Entity const *rels_itr = bulk.begin_nodes(side); unsigned num_nodes = bulk.num_nodes(side); @@ -205,7 +205,7 @@ void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity ele stk::mesh::Permutation const *perms = bulk.begin_permutations(side, stk::topology::ELEM_RANK); std::pair ordinalAndPermutation = - stk::mesh::get_ordinal_and_permutation(bulk, elem, sideRank, nodes); + stk::mesh::get_ordinal_and_permutation(bulk, elem, rank, nodes); stk::mesh::Permutation gold_permutation = ordinalAndPermutation.second; ASSERT_TRUE(gold_permutation!=stk::mesh::INVALID_PERMUTATION); @@ -226,8 +226,8 @@ void test_nodes_and_permutation(stk::mesh::BulkData& bulk, stk::mesh::Entity ele stk::mesh::ConnectivityOrdinal elements_side_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; - unsigned num_sides = bulk.num_connectivity(elem, sideRank); - const stk::mesh::Entity *sides = bulk.begin(elem, sideRank); + unsigned num_sides = bulk.num_connectivity(elem, rank); + const stk::mesh::Entity *sides = bulk.begin(elem, rank); for (unsigned i=0;i 1) { GTEST_SKIP(); } - - setup_mesh(1, 1, 1); - - stk::mesh::Entity elem1 = get_bulk().get_entity(stk::topology::ELEM_RANK, 1); - stk::mesh::Bucket& bucket = get_bulk().bucket(elem1); - unsigned bucket_ordinal = get_bulk().bucket_ordinal(elem1); - EXPECT_EQ(0u, bucket_ordinal); - - const stk::mesh::Entity* nodes = bucket.begin_nodes(bucket_ordinal); - stk::mesh::ConnectivityOrdinal ord = 0; - stk::mesh::Permutation perm = stk::mesh::INVALID_PERMUTATION; - - BucketTester& bktTester = static_cast(bucket); - EXPECT_FALSE(bktTester.my_declare_relation(bucket_ordinal, nodes[0], ord, perm)); -} - TEST_F(BucketHex, changing_conn_on_bucket_for_face_to_element) { if (stk::parallel_machine_size(MPI_COMM_WORLD) == 1) @@ -386,31 +356,41 @@ TEST_F(BucketHex, changing_conn_on_bucket_for_face_to_element) std::pair ordinalAndPermutation = stk::mesh::get_ordinal_and_permutation(bulk, elem, stk::topology::FACE_RANK, new_nodes); - stk::mesh::ConnectivityOrdinal faceElemOrdinal = ordinalAndPermutation.first; stk::mesh::Permutation new_permutation = ordinalAndPermutation.second; - stk::mesh::ConnectivityOrdinal elemFaceOrdinal = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + unsigned faces_element_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + unsigned num_elems = bulk.num_elements(side); + const stk::mesh::Entity *elements = bulk.begin_elements(side); + for (unsigned i=0;i(i); + break; + } + } + + unsigned elements_face_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; unsigned num_faces = bulk.num_faces(elem); const stk::mesh::Entity *faces = bulk.begin_faces(elem); - const stk::mesh::ConnectivityOrdinal *faceOrds = bulk.begin_ordinals(elem, stk::topology::FACE_RANK); for (unsigned i=0;i(i); break; } } - ASSERT_TRUE(elemFaceOrdinal!=stk::mesh::INVALID_CONNECTIVITY_ORDINAL); + ASSERT_TRUE(elements_face_offset!=stk::mesh::INVALID_CONNECTIVITY_ORDINAL); stk::mesh::unit_test::BucketTester& bucket_side = static_cast(bulk.bucket(side)); bucket_side.my_change_connected_nodes(bulk.bucket_ordinal(side), &new_nodes[0]); - bucket_side.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(side), faceElemOrdinal, new_permutation); + bucket_side.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(side), faces_element_offset, new_permutation); stk::mesh::unit_test::BucketTester& bucket_elem = static_cast(bulk.bucket(elem)); - bucket_elem.my_change_existing_permutation_for_connected_face(bulk.bucket_ordinal(elem), elemFaceOrdinal, new_permutation); + bucket_elem.my_change_existing_permutation_for_connected_face(bulk.bucket_ordinal(elem), elements_face_offset, new_permutation); test_nodes_and_permutation(bulk, elem, side, new_nodes); } @@ -444,33 +424,42 @@ TEST_F(BucketHex, changing_conn_on_bucket_for_edge_to_element) std::pair ordinalAndPermutation = stk::mesh::get_ordinal_and_permutation(bulk, elem, stk::topology::EDGE_RANK, new_nodes); - stk::mesh::ConnectivityOrdinal edgeElemOrdinal = ordinalAndPermutation.first; stk::mesh::Permutation new_permutation = ordinalAndPermutation.second; - stk::mesh::ConnectivityOrdinal elemEdgeOrdinal = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + unsigned edges_element_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; + unsigned num_elems = bulk.num_elements(edge); + const stk::mesh::Entity *elements = bulk.begin_elements(edge); + for (unsigned i=0;i(i); + break; + } + } + + unsigned elements_edge_offset = stk::mesh::INVALID_CONNECTIVITY_ORDINAL; unsigned num_edges = bulk.num_edges(elem); const stk::mesh::Entity *edges = bulk.begin_edges(elem); - const stk::mesh::ConnectivityOrdinal *edgeOrds = bulk.begin_ordinals(elem, stk::topology::EDGE_RANK); for (unsigned i=0;i(i); break; } } - ASSERT_TRUE(elemEdgeOrdinal != stk::mesh::INVALID_CONNECTIVITY_ORDINAL); + ASSERT_TRUE(elements_edge_offset != stk::mesh::INVALID_CONNECTIVITY_ORDINAL); stk::mesh::unit_test::BucketTester& bucket_edge = static_cast(bulk.bucket(edge)); bucket_edge.my_change_connected_nodes(bulk.bucket_ordinal(edge), &new_nodes[0]); - - bucket_edge.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(edge), edgeElemOrdinal, new_permutation); + bucket_edge.my_change_existing_permutation_for_connected_element(bulk.bucket_ordinal(edge), edges_element_offset, new_permutation); stk::mesh::unit_test::BucketTester& bucket_elem = static_cast(bulk.bucket(elem)); - bucket_elem.my_change_existing_permutation_for_connected_edge(bulk.bucket_ordinal(elem), elemEdgeOrdinal, new_permutation); + bucket_elem.my_change_existing_permutation_for_connected_edge(bulk.bucket_ordinal(elem), elements_edge_offset, new_permutation); test_nodes_and_permutation(bulk, elem, edge, new_nodes); } @@ -482,6 +471,8 @@ void do_nonmodifying_debug_check(const stk::mesh::BulkData & bulk, const stk::me const stk::mesh::BucketVector & buckets = bulk.buckets(stk::topology::NODE_RANK); ASSERT_EQ(buckets.size(), 1u); + buckets[0]->check_size_invariant(); + EXPECT_FALSE(buckets[0]->get_ngp_field_bucket_is_modified(coordsField.mesh_meta_data_ordinal())); } diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp new file mode 100644 index 000000000000..81e4d791a248 --- /dev/null +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestBucketConnectivity.cpp @@ -0,0 +1,345 @@ +// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering +// Solutions of Sandia, LLC (NTESS). Under the terms of Contract +// DE-NA0003525 with NTESS, the U.S. Government retains certain rights +// in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above +// copyright notice, this list of conditions and the following +// disclaimer in the documentation and/or other materials provided +// with the distribution. +// +// * Neither the name of NTESS nor the names of its contributors +// may be used to endorse or promote products derived from this +// software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// + +#include // for NULL +#include // for uint64_t +#include // for copy +#include +#include // for vector +#include "gtest/gtest.h" // for AssertHelper, TEST + +// CRW: this should be in BucketConnectivity.hpp, but circular dependency for now +#include "stk_mesh/base/BulkData.hpp" + +#include "stk_mesh/base/BucketConnectivity.hpp" // for BucketConnectivity +#include "stk_mesh/base/Entity.hpp" // for Entity, operator<< +#include "stk_mesh/base/Types.hpp" // for ConnectivityOrdinal, etc +#include "stk_topology/topology.hpp" // for topology, etc +namespace stk { namespace mesh { class BulkData; } } + +using namespace stk::mesh; + +namespace { + +typedef impl::BucketConnectivity fixed_conn; +typedef impl::BucketConnectivity dynamic_conn; + +void check_uninit_conn_size(fixed_conn& conn, unsigned num_conn, unsigned ordinal) +{ + EXPECT_EQ(conn.num_connectivity(ordinal), num_conn); +} + +void check_uninit_conn_size(dynamic_conn& conn, unsigned num_conn, unsigned ordinal) +{ + EXPECT_EQ(conn.num_connectivity(ordinal), 0u); +} + +void check_even_conn_removed(fixed_conn& conn, unsigned num_conn, unsigned ordinal) +{ + EXPECT_EQ(conn.num_connectivity(ordinal), num_conn); + + Entity const* targets = conn.begin(ordinal); + for (unsigned i = 0; i < num_conn; ++i) { + Entity e_to(ordinal * num_conn + i + 1); + if ( (i % 2) == 0 ) { + EXPECT_EQ(targets[i], Entity()); + } + else { + EXPECT_EQ(targets[i], e_to); + } + } +} + +void check_even_conn_removed(dynamic_conn& conn, unsigned num_conn, unsigned ordinal) +{ + EXPECT_EQ(conn.num_connectivity(ordinal), num_conn / 2); + + Entity const* targets = conn.begin(ordinal); + ConnectivityOrdinal const* ordinals = conn.begin_ordinals(ordinal); + for (unsigned i = 0; i < num_conn / 2; ++i) { + Entity e_to(ordinal * num_conn + ((2*i) + 1) + 1); + EXPECT_EQ(targets[i], e_to); + EXPECT_EQ(ordinals[i], static_cast((2*i) + 1)); + } +} + +template +void test_simple_add(Connectivity& connectivity, unsigned num_entities_to_add, unsigned num_to_add) +{ + // Populate connectivity all at once for each entity + + EXPECT_EQ(connectivity.size(), 0u); + + for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { + connectivity.add_entity(); + + EXPECT_EQ(connectivity.size(), ord + 1); + check_uninit_conn_size(connectivity, num_to_add, ord); + + for (uint64_t i = 0; i < num_to_add; ++i) { + Entity e_to(ord * num_to_add + i + 1); + connectivity.add_connectivity(ord, e_to, static_cast(i)); + } + + EXPECT_EQ(connectivity.num_connectivity(ord), num_to_add); + + Entity const* begin = connectivity.begin(ord); + Entity const* end = connectivity.end(ord); + ConnectivityOrdinal const* begin_ord = connectivity.begin_ordinals(ord); + ConnectivityOrdinal const* end_ord = connectivity.end_ordinals(ord); + + EXPECT_EQ(end - begin, num_to_add); + EXPECT_EQ(end_ord - begin_ord, num_to_add); + + for (uint64_t i = 0; i < num_to_add; ++i) { + Entity expected_to(ord * num_to_add + i + 1); + EXPECT_EQ(expected_to, begin[i]); + EXPECT_EQ(static_cast(i), begin_ord[i]); + } + } +} + +template +void test_complex_add(Connectivity& connectivity, unsigned num_entities_to_add, unsigned num_to_add) +{ + // Populate connectivity one at a time for each entity + + EXPECT_EQ(connectivity.size(), 0u); + + for (uint64_t i = 0; i < num_to_add; ++i) { + for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { + if (i == 0) { + connectivity.add_entity(); + } + + if (i == 0) { + EXPECT_EQ(connectivity.size(), ord + 1); + } + else { + EXPECT_EQ(connectivity.size(), num_entities_to_add); + } + + Entity e_to(ord * num_to_add + i + 1); + connectivity.add_connectivity(ord, e_to, static_cast(i)); + } + } + + for (unsigned ord = 0; ord < num_entities_to_add; ++ord) { + EXPECT_EQ(connectivity.num_connectivity(ord), num_to_add); + + Entity const* begin = connectivity.begin(ord); + Entity const* end = connectivity.end(ord); + ConnectivityOrdinal const* begin_ord = connectivity.begin_ordinals(ord); + ConnectivityOrdinal const* end_ord = connectivity.end_ordinals(ord); + + EXPECT_EQ(end - begin, num_to_add); + EXPECT_EQ(end_ord - begin_ord, num_to_add); + + for (uint64_t i = 0; i < num_to_add; ++i) { + Entity expected_to(ord * num_to_add + i + 1); + EXPECT_EQ(expected_to, begin[i]); + EXPECT_EQ(static_cast(i), begin_ord[i]); + } + } +} + +template +void test_remove(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) +{ + test_simple_add(connectivity, num_entities, num_to_add); + + unsigned ord_to_remove_from = num_entities / 2; + + for (uint64_t i = 0; i < num_to_add; ++i) { + Entity e_to(ord_to_remove_from * num_to_add + i + 1); + if ( (i % 2) == 0 ) { + bool rv = connectivity.remove_connectivity(ord_to_remove_from, e_to, static_cast(i)); + EXPECT_TRUE(rv); + } + } + + check_even_conn_removed(connectivity, num_to_add, ord_to_remove_from); +} + +template +void test_inter_conn_copy(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) +{ + // TODO +} + +template +void test_intra_conn_copy(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) +{ + // TODO +} + +template +void test_mod_end(Connectivity& connectivity, unsigned num_entities, unsigned num_to_add) +{ + // TODO +} + +} + +TEST(BucketConnectivity, fixed_simple_add) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_simple_add(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_simple_add) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_simple_add(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, fixed_complex_add) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_complex_add(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_complex_add) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_complex_add(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, fixed_remove) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_remove(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_remove) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_remove(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, fixed_intra_conn_copy) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_intra_conn_copy(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_intra_conn_copy) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_intra_conn_copy(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, fixed_inter_conn_copy) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_inter_conn_copy(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_inter_conn_copy) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_inter_conn_copy(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, fixed_mod_end) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + fixed_conn conn(num_to_add); + + test_mod_end(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} + +TEST(BucketConnectivity, dynamic_mod_end) +{ + const unsigned num_to_add = 8; + const unsigned num_entities = 100; + BulkData * bulk = NULL; + dynamic_conn conn(stk::topology::ELEMENT_RANK, bulk); + + test_mod_end(conn, num_entities, num_to_add); + conn.end_modification(bulk); +} diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp deleted file mode 100644 index 30bc3a86673d..000000000000 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestConnectivity.cpp +++ /dev/null @@ -1,385 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include -#include -#include -#include - -namespace { - -const stk::mesh::EntityRank nodeRank = stk::topology::NODE_RANK; -const stk::mesh::EntityRank faceRank = stk::topology::FACE_RANK; -const stk::mesh::EntityRank elemRank = stk::topology::ELEM_RANK; -const stk::mesh::EntityRank constraintRank = stk::topology::CONSTRAINT_RANK; - -class ConnectivityTester : public stk::mesh::Connectivity { -public: - void expect_null_ptrs() - { - EXPECT_EQ(nullptr, m_connectivity); - EXPECT_EQ(nullptr, m_offsetsAndOrdinals); - } - - void expect_zeros_and_empty() - { - const unsigned numOffsets = stk::mesh::Connectivity::MAX_NUM_RANKS+1; - for(unsigned r=0; r& numPerRank) - { - EXPECT_TRUE(stk::mesh::Connectivity::MAX_NUM_RANKS == numPerRank.size()); - for(unsigned r=0; r(r))); - } - } - - void expect_connectivity(const std::vector& conn) - { - EXPECT_EQ(conn.size(), m_offsetsAndOrdinals[stk::mesh::Connectivity::MAX_NUM_RANKS]); - for(unsigned i=0; i& ords) - { - EXPECT_EQ(ords.size(), m_offsetsAndOrdinals[stk::mesh::Connectivity::MAX_NUM_RANKS]); - for(unsigned i=0; i& numPerRank) - { - ConnectivityTester& connTester = static_cast(connObject); - connTester.expect_num_per_rank(numPerRank); - } - - void expect_num_per_rank(const std::vector& numPerRank) - { - expect_num_per_rank(connectivity, numPerRank); - } - - void expect_connectivity(stk::mesh::Connectivity& connObject, const std::vector& conn) - { - ConnectivityTester& connTester = static_cast(connObject); - connTester.expect_connectivity(conn); - } - - void expect_connectivity(const std::vector& conn) - { - expect_connectivity(connectivity, conn); - } - - void expect_ordinals(const std::vector& ords) - { - ConnectivityTester& connTester = static_cast(connectivity); - connTester.expect_ordinals(ords); - } - - void add_2nodes_2elems() - { - const bool allowDuplicateOrdinals = true; - - EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - } - -protected: - stk::mesh::Connectivity connectivity; - stk::mesh::Entity node1, node2, node3; - stk::mesh::Entity face1, face2, face3; - stk::mesh::Entity elem1, elem2, elem3; - stk::mesh::Entity constraint1; - stk::mesh::Entity highest1; - stk::mesh::ConnectivityOrdinal ordinal1, ordinal2, ordinal3; -}; - -TEST_F(TestConnectivity, defaultConstruct_zerosAndEmpty) -{ - ConnectivityTester& connTester = static_cast(connectivity); - connTester.expect_zeros_and_empty(); -} - -TEST_F(TestConnectivity, addConnectivity) -{ - add_2nodes_2elems(); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - expect_connectivity({node1, node2, elem1, elem2}); - expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); -} - -TEST_F(TestConnectivity, addConnectivity_then_clear) -{ - add_2nodes_2elems(); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - connectivity.clear(); - expect_num_per_rank({0, 0, 0, 0, 0, 0}); -} - -TEST_F(TestConnectivity, assignment) -{ - add_2nodes_2elems(); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - - stk::mesh::Connectivity connCopy = connectivity; - expect_num_per_rank(connCopy, {2, 0, 0, 2, 0, 0}); - expect_num_per_rank(connectivity, {2, 0, 0, 2, 0, 0}); - - connCopy = std::move(connectivity); - expect_num_per_rank(connCopy, {2, 0, 0, 2, 0, 0}); - ConnectivityTester& connTester = static_cast(connectivity); - connTester.expect_null_ptrs(); -} - -TEST_F(TestConnectivity, replaceOrAddConnectivity_not_pre_existing) -{ - EXPECT_EQ(0, connectivity.replace_or_add_connectivity(nodeRank, node1, ordinal1)); - EXPECT_EQ(1, connectivity.replace_or_add_connectivity(nodeRank, node2, ordinal2)); - EXPECT_EQ(0, connectivity.replace_or_add_connectivity(elemRank, elem1, ordinal1)); - EXPECT_EQ(1, connectivity.replace_or_add_connectivity(elemRank, elem2, ordinal2)); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - expect_connectivity({node1, node2, elem1, elem2}); - expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); -} - -TEST_F(TestConnectivity, replaceOrAddConnectivity_pre_existing) -{ - const bool allowDuplicateOrdinals = true; - EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(nodeRank, node1, ordinal1)); - EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(nodeRank, node2, ordinal2)); - EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(elemRank, elem1, ordinal1)); - EXPECT_EQ(-1, connectivity.replace_or_add_connectivity(elemRank, elem2, ordinal2)); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - expect_connectivity({node1, node2, elem1, elem2}); - expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); -} - -TEST_F(TestConnectivity, addAndRemoveConnectivity) -{ - const bool allowDuplicateOrdinals = true; - - EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(nodeRank, node2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - expect_num_per_rank({2, 0, 0, 2, 0, 0}); - expect_connectivity({node1, node2, elem1, elem2}); - expect_ordinals({ordinal1, ordinal2, ordinal1, ordinal2}); - - EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); - expect_num_per_rank({2, 0, 0, 1, 0, 0}); - expect_connectivity({node1, node2, elem2}); - expect_ordinals({ordinal1, ordinal2, ordinal2}); - - stk::mesh::PairIterEntity conn = connectivity.get_connectivity(elemRank); - const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); - const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); - EXPECT_EQ(elem2, elems[0]); - EXPECT_EQ(1u, conn.size()); - EXPECT_EQ(conn.begin(), elems); - EXPECT_EQ(conn.end(), elems+1); - EXPECT_EQ(ordinal2, ords[0]); - - EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); - expect_num_per_rank({2, 0, 0, 0, 0, 0}); - expect_connectivity({node1, node2}); - expect_ordinals({ordinal1, ordinal2}); - conn = connectivity.get_connectivity(elemRank); - EXPECT_EQ(connectivity.begin_connectivity(elemRank), connectivity.end_connectivity(elemRank)); - EXPECT_TRUE(conn.empty()); - EXPECT_EQ(conn.begin(), conn.end()); - EXPECT_EQ(connectivity.begin_ordinals(elemRank), connectivity.end_ordinals(elemRank)); -} - -TEST_F(TestConnectivity, addAndRemoveMultipleRanks) -{ - const bool allowDuplicateOrdinals = true; - - EXPECT_EQ(0, connectivity.add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(faceRank, face1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(0, connectivity.add_connectivity(constraintRank, constraint1, ordinal1, allowDuplicateOrdinals)); - expect_num_per_rank({1, 0, 1, 2, 1, 0}); - - EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); - expect_num_per_rank({1, 0, 1, 1, 1, 0}); - - const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); - const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); - EXPECT_EQ(elem2, elems[0]); - EXPECT_EQ(ordinal2, ords[0]); - - EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); - expect_num_per_rank({1, 0, 1, 0, 1, 0}); - - EXPECT_EQ(connectivity.begin_connectivity(elemRank), connectivity.end_connectivity(elemRank)); - EXPECT_EQ(connectivity.begin_ordinals(elemRank), connectivity.end_ordinals(elemRank)); - EXPECT_NE(connectivity.begin_connectivity(faceRank), connectivity.end_connectivity(faceRank)); - EXPECT_NE(connectivity.begin_ordinals(faceRank), connectivity.end_ordinals(faceRank)); -} - -TEST_F(TestConnectivity, addRemoveAddAddRemoveAdd) -{ - const bool allowDuplicateOrdinals = true; - - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - expect_num_per_rank({0, 0, 0, 1, 0, 0}); - - EXPECT_EQ(0, connectivity.remove_connectivity(elemRank, elem1, ordinal1)); - expect_num_per_rank({0, 0, 0, 0, 0, 0}); - - EXPECT_EQ(0, connectivity.add_connectivity(elemRank, elem1, ordinal1, allowDuplicateOrdinals)); - expect_num_per_rank({0, 0, 0, 1, 0, 0}); - - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - expect_num_per_rank({0, 0, 0, 2, 0, 0}); - - EXPECT_EQ(1, connectivity.remove_connectivity(elemRank, elem2, ordinal2)); - expect_num_per_rank({0, 0, 0, 1, 0, 0}); - - EXPECT_EQ(1, connectivity.add_connectivity(elemRank, elem2, ordinal2, allowDuplicateOrdinals)); - expect_num_per_rank({0, 0, 0, 2, 0, 0}); - - const stk::mesh::Entity* elems = connectivity.begin_connectivity(elemRank); - const stk::mesh::ConnectivityOrdinal* ords = connectivity.begin_ordinals(elemRank); - EXPECT_EQ(elem1, elems[0]); - EXPECT_EQ(elem2, elems[1]); - EXPECT_EQ(ordinal1, ords[0]); - EXPECT_EQ(ordinal2, ords[1]); -} - -TEST_F(TestConnectivity, addAndRemoveMultipleConnectivity) -{ - const bool allowDuplicateOrdinals = true; - - EXPECT_EQ(0, connectivity.add_connectivity(faceRank, face1, ordinal1, allowDuplicateOrdinals)); - EXPECT_EQ(1, connectivity.add_connectivity(faceRank, face2, ordinal2, allowDuplicateOrdinals)); - EXPECT_EQ(2, connectivity.add_connectivity(faceRank, face3, ordinal3, allowDuplicateOrdinals)); - expect_num_per_rank({0, 0, 3, 0, 0, 0}); - - { - const stk::mesh::Entity* faces = connectivity.begin_connectivity(faceRank); - const stk::mesh::ConnectivityOrdinal* ordinals = connectivity.begin_ordinals(faceRank); - - EXPECT_EQ(face1, faces[0]); - EXPECT_EQ(face2, faces[1]); - EXPECT_EQ(face3, faces[2]); - EXPECT_EQ(ordinal1, ordinals[0]); - EXPECT_EQ(ordinal2, ordinals[1]); - EXPECT_EQ(ordinal3, ordinals[2]); - } - - EXPECT_EQ(1, connectivity.remove_connectivity(faceRank, face2, ordinal2)); - expect_num_per_rank({0, 0, 2, 0, 0, 0}); - - int indexOfRemovedEntity = connectivity.remove_connectivity(faceRank, face2, ordinal2); - bool duplicateRemoveCausedNoChange = (indexOfRemovedEntity == -1); - EXPECT_TRUE(duplicateRemoveCausedNoChange); - - expect_num_per_rank({0, 0, 2, 0, 0, 0}); - expect_connectivity({face1, face3}); - expect_ordinals({ordinal1, ordinal3}); - - EXPECT_EQ(1, connectivity.remove_connectivity(faceRank, face3, ordinal3)); - expect_num_per_rank({0, 0, 1, 0, 0, 0}); - expect_connectivity({face1}); - expect_ordinals({ordinal1}); - - EXPECT_EQ(0, connectivity.remove_connectivity(faceRank, face1, ordinal1)); - expect_num_per_rank({0, 0, 0, 0, 0, 0}); - - EXPECT_EQ(connectivity.begin_connectivity(faceRank), connectivity.end_connectivity(faceRank)); - EXPECT_EQ(connectivity.begin_ordinals(faceRank), connectivity.end_ordinals(faceRank)); -} - -TEST_F(TestConnectivity, moveInVector) -{ - const bool allowDuplicateOrdinals = true; - std::vector connectivities(1); - connectivities[0].add_connectivity(nodeRank, node1, ordinal1, allowDuplicateOrdinals); - { - ConnectivityTester& connTester = static_cast(connectivities[0]); - connTester.expect_num_per_rank({1, 0, 0, 0, 0, 0}); - connTester.expect_connectivity({node1}); - connTester.expect_ordinals({ordinal1}); - } - - connectivities.resize(2); - { - ConnectivityTester& connTester = static_cast(connectivities[0]); - connTester.expect_num_per_rank({1, 0, 0, 0, 0, 0}); - connTester.expect_connectivity({node1}); - connTester.expect_ordinals({ordinal1}); - } -} - -class MyClass { -public: - stk::mesh::Entity* entityPtr; - stk::mesh::ConnectivityOrdinal* ordPtr; -}; - -TEST_F(TestConnectivity, simpleStructSize) -{ - EXPECT_EQ(16u, sizeof(MyClass)); - EXPECT_EQ(sizeof(MyClass), sizeof(stk::mesh::Connectivity)); -} - -} - diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp deleted file mode 100644 index 6692f677c238..000000000000 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestSparseConnectivity.cpp +++ /dev/null @@ -1,256 +0,0 @@ -// Copyright 2002 - 2008, 2010, 2011 National Technology Engineering -// Solutions of Sandia, LLC (NTESS). Under the terms of Contract -// DE-NA0003525 with NTESS, the U.S. Government retains certain rights -// in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following -// disclaimer in the documentation and/or other materials provided -// with the distribution. -// -// * Neither the name of NTESS nor the names of its contributors -// may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// - -#include -#include -#include -#include - -namespace { - -const stk::mesh::EntityRank nodeRank = stk::topology::NODE_RANK; -const stk::mesh::EntityRank edgeRank = stk::topology::EDGE_RANK; -const stk::mesh::EntityRank faceRank = stk::topology::FACE_RANK; -const stk::mesh::EntityRank elemRank = stk::topology::ELEM_RANK; -const stk::mesh::EntityRank constraintRank = stk::topology::CONSTRAINT_RANK; - -TEST(SparseConnectivity, hasPermutation) -{ - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, elemRank)); - EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(edgeRank, elemRank)); - EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(faceRank, elemRank)); - EXPECT_TRUE (stk::mesh::SparseConnectivity::has_permutation(edgeRank, faceRank)); - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, edgeRank)); - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, faceRank)); - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(nodeRank, constraintRank)); - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(faceRank, constraintRank)); - EXPECT_FALSE(stk::mesh::SparseConnectivity::has_permutation(elemRank, constraintRank)); -} - -TEST(SparseConnectivity, addAndRemoveConnectivity) -{ - stk::mesh::SparseConnectivity sparseConnectivity; - - unsigned nodeEntityOffset = 1; - unsigned elemEntityOffset = 9; - sparseConnectivity.update_size_of_entity_index_space(10); - - stk::mesh::Entity node(nodeEntityOffset); - stk::mesh::Entity elem(elemEntityOffset); - stk::mesh::ConnectivityOrdinal ordinal = 0; - stk::mesh::Permutation perm = stk::mesh::Permutation::INVALID_PERMUTATION; - - EXPECT_TRUE(sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm)); - bool addAlreadyExistingShouldBeFalse = sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm); - EXPECT_FALSE(addAlreadyExistingShouldBeFalse); - - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); - - stk::mesh::Entity elem2(elemEntityOffset+1); - sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1, perm); - - EXPECT_EQ(2u, sparseConnectivity.num_connectivity(node, elemRank)); - - sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, ordinal); - - stk::mesh::PairIterEntity conn = sparseConnectivity.get_connectivity(node, elemRank); - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); - EXPECT_EQ(1u, conn.size()); - - const stk::mesh::Entity* elems = sparseConnectivity.begin_connectivity(node, elemRank); - EXPECT_EQ(elem2, elems[0]); - EXPECT_EQ(elems, conn.begin()); - - sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); - - EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); - conn = sparseConnectivity.get_connectivity(node, elemRank); - EXPECT_TRUE(conn.empty()); -} - -TEST(SparseConnectivity, replaceOrAddAndRemoveConnectivity) -{ - stk::mesh::SparseConnectivity sparseConnectivity; - - unsigned nodeEntityOffset = 1; - unsigned elemEntityOffset = 9; - sparseConnectivity.update_size_of_entity_index_space(10); - - stk::mesh::Entity node(nodeEntityOffset); - stk::mesh::Entity elem(elemEntityOffset); - stk::mesh::Entity elem2(elemEntityOffset+1); - stk::mesh::ConnectivityOrdinal ordinal = 0; - - EXPECT_TRUE(sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal)); - bool replaceAlreadyExistingShouldBeFalse = sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal); - EXPECT_FALSE(replaceAlreadyExistingShouldBeFalse); - - bool replaceWithDifferentElemShouldBeTrue = sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem, ordinal); - EXPECT_TRUE(replaceWithDifferentElemShouldBeTrue); - - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); - - sparseConnectivity.replace_or_add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); - - EXPECT_EQ(2u, sparseConnectivity.num_connectivity(node, elemRank)); - - sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, ordinal); - - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); - - const stk::mesh::Entity* elems = sparseConnectivity.begin_connectivity(node, elemRank); - EXPECT_EQ(elem2, elems[0]); - - sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem2, ordinal+1); - - EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); -} - -TEST(SparseConnectivity, beginEnd) -{ - stk::mesh::SparseConnectivity sparseConnectivity; - - unsigned nodeEntityOffset = 1; - unsigned elemEntityOffset = 9; - sparseConnectivity.update_size_of_entity_index_space(10); - stk::mesh::Entity node(nodeEntityOffset); - stk::mesh::Entity elem(elemEntityOffset); - stk::mesh::ConnectivityOrdinal ordinal = 0; - stk::mesh::Permutation perm = stk::mesh::Permutation::INVALID_PERMUTATION; - - sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, ordinal, perm); - - stk::mesh::Entity elem2(elemEntityOffset+1); - sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem2, ordinal+1, perm); - - const stk::mesh::Entity* beginElems = sparseConnectivity.begin_connectivity(node, elemRank); - const stk::mesh::Entity* endElems = sparseConnectivity.end_connectivity(node, elemRank); - - EXPECT_EQ(2u, std::distance(beginElems, endElems)); - - EXPECT_EQ(elem, beginElems[0]); - EXPECT_EQ(elem2, beginElems[1]); - - const stk::mesh::ConnectivityOrdinal* beginElemOrds = sparseConnectivity.begin_ordinals(node, elemRank); - const stk::mesh::ConnectivityOrdinal* endElemOrds = sparseConnectivity.end_ordinals(node, elemRank); - - EXPECT_EQ(2u, std::distance(beginElemOrds, endElemOrds)); - - EXPECT_EQ(ordinal, beginElemOrds[0]); - EXPECT_EQ(ordinal+1, beginElemOrds[1]); - - EXPECT_EQ(nullptr, sparseConnectivity.begin_permutations(node, elemRank)); - EXPECT_EQ(nullptr, sparseConnectivity.end_permutations(node, elemRank)); -} - -TEST(SparseConnectivity, permutations) -{ - stk::mesh::SparseConnectivity sparseConnectivity; - - unsigned faceEntityOffset = 1; - unsigned elemEntityOffset = 9; - sparseConnectivity.update_size_of_entity_index_space(10); - stk::mesh::Entity face(faceEntityOffset); - stk::mesh::Entity elem(elemEntityOffset); - stk::mesh::ConnectivityOrdinal ordinal = 0; - stk::mesh::Permutation perm = static_cast(1); - stk::mesh::Permutation perm2 = static_cast(-1); - - sparseConnectivity.add_connectivity(faceRank, face, elemRank, elem, ordinal, perm); - - stk::mesh::Entity elem2(elemEntityOffset+1); - sparseConnectivity.add_connectivity(faceRank, face, elemRank, elem2, ordinal+1, perm2); - - const stk::mesh::Permutation* beginElemPerms = sparseConnectivity.begin_permutations(face, elemRank); - const stk::mesh::Permutation* endElemPerms = sparseConnectivity.end_permutations(face, elemRank); - - EXPECT_EQ(2u, std::distance(beginElemPerms, endElemPerms)); - - EXPECT_EQ(perm, beginElemPerms[0]); - EXPECT_EQ(perm2, beginElemPerms[1]); -} - -TEST(SparseConnectivity, addConnMultiple) -{ - stk::mesh::SparseConnectivity sparseConnectivity; - - unsigned nodeEntityOffset = 1; - unsigned node2EntityOffset = 2; - unsigned elemEntityOffset = 3; - unsigned faceEntityOffset = 10; - sparseConnectivity.update_size_of_entity_index_space(4); - - stk::mesh::Entity node(nodeEntityOffset); - stk::mesh::Entity node2(node2EntityOffset); - stk::mesh::Entity face(faceEntityOffset); - stk::mesh::Entity elem(elemEntityOffset); - stk::mesh::ConnectivityOrdinal nodeElemOrd = 5; - stk::mesh::ConnectivityOrdinal node2ElemOrd = 6; - stk::mesh::ConnectivityOrdinal nodeFaceOrd = 2; - stk::mesh::ConnectivityOrdinal elemFaceOrd = 3; - stk::mesh::Permutation invalidPerm = stk::mesh::Permutation::INVALID_PERMUTATION; - stk::mesh::Permutation perm = static_cast(0); - - sparseConnectivity.add_connectivity(nodeRank, node, elemRank, elem, nodeElemOrd, invalidPerm); - const stk::mesh::Connectivity& nodeConn = sparseConnectivity.get_connectivity(node); - (void)nodeConn; - - sparseConnectivity.add_connectivity(nodeRank, node, faceRank, face, nodeFaceOrd, invalidPerm); - sparseConnectivity.add_connectivity(elemRank, elem, faceRank, face, elemFaceOrd, perm); - - sparseConnectivity.update_size_of_entity_index_space(11); - - sparseConnectivity.add_connectivity(nodeRank, node2, elemRank, elem, node2ElemOrd, invalidPerm); - - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, elemRank)); - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node, faceRank)); - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(elem, faceRank)); - EXPECT_EQ(1u, sparseConnectivity.num_connectivity(node2, elemRank)); - - const stk::mesh::Permutation* perms = sparseConnectivity.begin_permutations(elem, faceRank); - const stk::mesh::Permutation* endPerms = sparseConnectivity.end_permutations(elem, faceRank); - EXPECT_TRUE(perms != nullptr); - EXPECT_TRUE(endPerms != nullptr); - EXPECT_EQ(1u, std::distance(perms, endPerms)); - EXPECT_EQ(perm, perms[0]); - - EXPECT_TRUE(sparseConnectivity.remove_connectivity(nodeRank, node, elemRank, elem, nodeElemOrd)); - EXPECT_TRUE(sparseConnectivity.remove_connectivity(nodeRank, node2, elemRank, elem, node2ElemOrd)); - - EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node, elemRank)); - EXPECT_EQ(0u, sparseConnectivity.num_connectivity(node2, elemRank)); -} - -} - diff --git a/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp b/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp index 87bb2ea7f49a..4916f05f327f 100644 --- a/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp +++ b/packages/stk/stk_unit_tests/stk_mesh/UnitTestTextMesh.cpp @@ -1,193 +1,21 @@ -#include "gtest/gtest.h" -#include "mpi.h" -#include -#include -#include // for Field -#include // for MetaData, put_field, etc +#include #include +#include // for Field #include -#include +#include // for MetaData, put_field, etc +#include #include #include -#include +#include +#include +#include -namespace { +#include "gtest/gtest.h" +#include "mpi.h" -class TextMeshFixture : public stk::unit_test_util::MeshFixture +namespace { -protected: - TextMeshFixture(unsigned spatialDim) : stk::unit_test_util::MeshFixture(spatialDim) - { } - - void verify_shared_nodes(const stk::mesh::EntityIdVector& nodeIds, int sharingProc) - { - std::vector counts; - stk::mesh::count_entities(get_meta().globally_shared_part(), get_bulk(), counts); - EXPECT_EQ(nodeIds.size(), counts[stk::topology::NODE_RANK]); - - for (stk::mesh::EntityId nodeId : nodeIds) { - EXPECT_TRUE(get_bulk().in_shared(stk::mesh::EntityKey(stk::topology::NODE_RANK, nodeId), sharingProc)); - } - } - - void verify_num_elements(size_t goldCount) - { - std::vector counts; - stk::mesh::count_entities(get_meta().universal_part(), get_bulk(), counts); - EXPECT_EQ(goldCount, counts[stk::topology::ELEM_RANK]); - } - - void verify_single_element(stk::mesh::EntityId elemId, - stk::topology topology, - const stk::mesh::EntityIdVector& nodeIds) - { - stk::mesh::Entity element = get_bulk().get_entity(stk::topology::ELEM_RANK, elemId); - EXPECT_TRUE(get_bulk().is_valid(element)); - EXPECT_EQ(topology, get_bulk().bucket(element).topology()); - verify_nodes_on_element(element, nodeIds); - } - - struct PartInfo - { - std::string blockName; - std::set ids; - }; - - void verify_part_membership(const std::vector golds) - { - for (const PartInfo& gold : golds) { - stk::mesh::Part* blockPart = get_meta().get_part(gold.blockName); - - verify_part(blockPart); - verify_elements_on_part(blockPart, gold.ids); - } - } - - using PartNameId = std::pair; - - void verify_part_ids(const std::vector& golds) - { - for (const PartNameId& gold : golds) { - stk::mesh::Part* blockPart = get_meta().get_part(gold.first); - - verify_part(blockPart); - EXPECT_EQ(blockPart->id(), gold.second); - } - } - - void verify_coordinates(const stk::mesh::EntityIdVector& goldNodeIds, const std::vector& goldCoordinates) - { - CoordinateVerifier cv(get_bulk(), goldNodeIds, goldCoordinates); - cv.verify(); - } - -private: - void verify_nodes_on_element(stk::mesh::Entity element, const stk::mesh::EntityIdVector& goldNodeIds) - { - stk::mesh::EntityVector nodes(get_bulk().begin_nodes(element), get_bulk().end_nodes(element)); - EXPECT_EQ(goldNodeIds, get_node_ids(nodes)); - } - - stk::mesh::EntityIdVector get_node_ids(const stk::mesh::EntityVector& nodes) - { - stk::mesh::EntityIdVector nodeIds; - for(const stk::mesh::Entity& node : nodes) { - nodeIds.emplace_back(get_bulk().identifier(node)); - } - return nodeIds; - } - - void verify_part(stk::mesh::Part* blockPart) - { - ASSERT_TRUE(blockPart != nullptr); - EXPECT_TRUE(stk::io::is_part_io_part(*blockPart)); - } - - void verify_elements_on_part(stk::mesh::Part* blockPart, const std::set& goldIds) - { - stk::mesh::EntityVector elems; - stk::mesh::get_selected_entities(*blockPart, get_bulk().buckets(stk::topology::ELEM_RANK), elems); - - ASSERT_EQ(goldIds.size(), elems.size()); - for (const stk::mesh::Entity& elem : elems) { - stk::mesh::EntityId elemId = get_bulk().identifier(elem); - EXPECT_EQ(1u, goldIds.count(elemId)); - } - } - - class CoordinateVerifier - { - public: - CoordinateVerifier(const stk::mesh::BulkData& b, - const stk::mesh::EntityIdVector& ids, - const std::vector& coords) - : bulk(b), meta(bulk.mesh_meta_data()), - spatialDim(meta.spatial_dimension()), - goldNodeIds(ids), goldCoordinates(coords) - { } - - void verify() - { - verify_num_nodes(); - - for(size_t nodeIndex=0; nodeIndex(*meta.coordinate_field()); - return stk::mesh::field_data(coordsField, get_node(nodeId)); - } - - const stk::mesh::Entity get_node(const stk::mesh::EntityId& nodeId) - { - return bulk.get_entity(stk::topology::NODE_RANK, nodeId); - } - - void verify_nodal_coordinates(const stk::mesh::EntityId& nodeId, - const double* goldCoords, - const double* nodalCoords) - { - for (unsigned i=0; i& goldCoordinates; - }; -}; - -class TestTextMesh : public TextMeshFixture +class TestTextMesh : public stk::unit_test_util::TextMeshFixture { protected: TestTextMesh() : TextMeshFixture(3) @@ -891,7 +719,7 @@ TEST_F(TestTextMesh, particleHexWithCoordinates) verify_coordinates(stk::mesh::EntityIdVector{1,2,3,4,5,6,7,8,9}, coordinates); } -class TestTextMeshAura : public TextMeshFixture +class TestTextMeshAura : public stk::unit_test_util::TextMeshFixture { protected: TestTextMeshAura() : TextMeshFixture(3) @@ -929,7 +757,7 @@ TEST_F(TestTextMeshAura, twoQuadShellWithCoordinates) if (rank == 1) verify_shared_nodes(stk::mesh::EntityIdVector{2,5}, 0); } -class TestTextMesh2d : public TextMeshFixture +class TestTextMesh2d : public stk::unit_test_util::TextMeshFixture { protected: TestTextMesh2d() : TextMeshFixture(2) @@ -1044,7 +872,7 @@ TEST_F(TestTextMesh2d, twoQuadOneShellParallel) } } -class TestTextMesh1d : public TextMeshFixture +class TestTextMesh1d : public stk::unit_test_util::TextMeshFixture { protected: TestTextMesh1d() : TextMeshFixture(1) @@ -1089,4 +917,4 @@ TEST(GetMeshSpecTest, TestGetMeshSpecWithMultiProc) test_get_mesh_spec(blockCountToDist, numProcs, expectedDist); } -} // namespace +} // namespace diff --git a/packages/stk/stk_util/stk_util/environment/Scheduler.cpp b/packages/stk/stk_util/stk_util/environment/Scheduler.cpp index 0b44907f8891..0b41401a1b75 100644 --- a/packages/stk/stk_util/stk_util/environment/Scheduler.cpp +++ b/packages/stk/stk_util/stk_util/environment/Scheduler.cpp @@ -377,19 +377,22 @@ bool Scheduler::is_it_time(double t, Step step) // it is called again, it will compare time with lastTime_ and if // they match, return true again. - // If called multiple times, return same response... - if (time == lastTime_) - { - return true; - } - // force_write always causes a write even if the time is outside // the bounds set by startTime and terminationTime... + // Needs to happen before the "time == lastime" check to make + // sure force flag is unset if (force_schedule()) { lastTime_ = time; return true; } + // If called multiple times, return same response... + if (time == lastTime_) + { + return true; + } + + // If user specified a start time; that overrides // everything except for the force_write setting. // If user did not specify the start time, then startTime_ = -TIME_MAX diff --git a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp index ff1fe46cbdfb..0a3d948c7fd6 100644 --- a/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp +++ b/packages/stk/stk_util/stk_util/registry/ProductRegistry.cpp @@ -42,7 +42,7 @@ //In Sierra, STK_VERSION_STRING is provided on the compile line by bake. //For Trilinos stk snapshots, the following macro definition gets populated with //the real version string by the trilinos_snapshot.sh script. -#define STK_VERSION_STRING "stk_version_not_set" +#define STK_VERSION_STRING "5.3.1-215-gc8a71448" #endif namespace stk { From 44fdc4594106f2633d7c09d5d3e7736b4929a972 Mon Sep 17 00:00:00 2001 From: K Devine Date: Thu, 28 Oct 2021 09:31:58 -0600 Subject: [PATCH 93/98] tpetra: fixed indexing error in describe() #9870 (#9874) --- packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp b/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp index 8e5df80becf9..4d0910a3fc77 100644 --- a/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp +++ b/packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp @@ -5125,14 +5125,14 @@ namespace Tpetra { if (isGloballyIndexed()) { auto rowview = gblInds_wdv.getHostView(Access::ReadOnly); for (size_t j=0; j < rowinfo.numEntries; ++j){ - GlobalOrdinal colgid = rowview[j] + rowinfo.offset1D; + GlobalOrdinal colgid = rowview[j + rowinfo.offset1D]; out << colgid << " "; } } else if (isLocallyIndexed()) { auto rowview = lclIndsUnpacked_wdv.getHostView(Access::ReadOnly); for (size_t j=0; j < rowinfo.numEntries; ++j) { - LocalOrdinal collid = rowview[j] + rowinfo.offset1D; + LocalOrdinal collid = rowview[j + rowinfo.offset1D]; out << colMap_->getGlobalElement(collid) << " "; } } From 4275f6b0e0994d1c9fdfe39d90654e9bfae11624 Mon Sep 17 00:00:00 2001 From: Nathan Ellingwood Date: Thu, 28 Oct 2021 10:39:30 -0600 Subject: [PATCH 94/98] Snapshot of kokkos.git from commit 8dc4a906d43ae8eacc951cc5d7e95ad2dfa617dc From repository at git@github.com:kokkos/kokkos.git At commit: commit 8dc4a906d43ae8eacc951cc5d7e95ad2dfa617dc Author: Nathan Ellingwood Date: Thu Oct 28 09:53:19 2021 -0600 Update master_history for Kokkos 3.5.0 --- packages/kokkos/.clang-format-ignore | 1 + packages/kokkos/.clang-tidy | 2 +- packages/kokkos/.jenkins | 133 +- packages/kokkos/.travis.yml | 15 +- packages/kokkos/CHANGELOG.md | 160 ++ packages/kokkos/CMakeLists.txt | 4 +- packages/kokkos/Makefile.kokkos | 241 ++- packages/kokkos/Makefile.targets | 11 + packages/kokkos/README.md | 154 +- packages/kokkos/algorithms/CMakeLists.txt | 4 +- .../kokkos/algorithms/src/Kokkos_Random.hpp | 114 +- .../kokkos/algorithms/src/Kokkos_Sort.hpp | 5 +- .../algorithms/unit_tests/TestRandom.hpp | 114 +- packages/kokkos/appveyor.yml | 6 +- packages/kokkos/benchmarks/atomic/main.cpp | 6 +- .../benchmarks/bytes_and_flops/bench.hpp | 2 +- .../benchmarks/bytes_and_flops/main.cpp | 2 +- packages/kokkos/benchmarks/gather/main.cpp | 2 +- .../benchmarks/stream/stream-kokkos.cpp | 77 +- packages/kokkos/bin/hpcbind | 8 +- packages/kokkos/bin/nvcc_wrapper | 16 +- packages/kokkos/cmake/CTestConfig.cmake.in | 91 - packages/kokkos/cmake/KokkosCI.cmake | 350 --- packages/kokkos/cmake/KokkosCTest.cmake.in | 261 --- packages/kokkos/cmake/KokkosCore_config.h.in | 16 +- .../kokkos/cmake/Modules/FindTPLCUDA.cmake | 7 +- .../cmake/Modules/FindTPLLIBQUADMATH.cmake | 1 + packages/kokkos/cmake/deps/quadmath.cmake | 46 + packages/kokkos/cmake/kokkos_arch.cmake | 151 +- .../kokkos/cmake/kokkos_compiler_id.cmake | 14 +- .../kokkos/cmake/kokkos_enable_devices.cmake | 6 +- .../kokkos/cmake/kokkos_enable_options.cmake | 10 + packages/kokkos/cmake/kokkos_functions.cmake | 2 +- .../kokkos/cmake/kokkos_test_cxx_std.cmake | 2 +- packages/kokkos/cmake/kokkos_tpls.cmake | 7 + .../kokkos/cmake/tpls/FindTPLquadmath.cmake | 46 + .../performance_tests/TestDynRankView.hpp | 2 +- .../performance_tests/TestGlobal2LocalIds.hpp | 2 +- .../performance_tests/TestScatterView.hpp | 2 +- .../TestUnorderedMapPerformance.hpp | 2 +- .../kokkos/containers/src/Kokkos_Bitset.hpp | 34 +- .../kokkos/containers/src/Kokkos_DualView.hpp | 91 +- .../containers/src/Kokkos_DynRankView.hpp | 75 +- .../containers/src/Kokkos_DynamicView.hpp | 393 ++-- .../containers/src/Kokkos_ErrorReporter.hpp | 3 +- .../containers/src/Kokkos_OffsetView.hpp | 9 +- .../containers/src/Kokkos_ScatterView.hpp | 6 +- .../containers/src/Kokkos_StaticCrsGraph.hpp | 4 +- .../containers/src/Kokkos_UnorderedMap.hpp | 21 +- .../kokkos/containers/src/Kokkos_Vector.hpp | 6 +- .../src/impl/Kokkos_Bitset_impl.hpp | 12 - .../src/impl/Kokkos_Functional_impl.hpp | 2 +- .../containers/unit_tests/TestDualView.hpp | 2 +- .../containers/unit_tests/TestDynViewAPI.hpp | 105 +- .../containers/unit_tests/TestDynamicView.hpp | 2 +- .../containers/unit_tests/TestOffsetView.hpp | 2 +- .../containers/unit_tests/TestScatterView.hpp | 40 + .../unit_tests/TestStaticCrsGraph.hpp | 6 - .../unit_tests/TestUnorderedMap.hpp | 21 +- .../kokkos/core/cmake/KokkosCore_config.h.in | 104 - packages/kokkos/core/perf_test/CMakeLists.txt | 4 +- .../core/perf_test/PerfTestGramSchmidt.cpp | 2 +- .../kokkos/core/perf_test/PerfTestHexGrad.cpp | 2 +- .../PerfTest_ExecSpacePartitioning.cpp | 18 +- .../core/perf_test/PerfTest_ViewAllocate.cpp | 3 +- .../core/perf_test/PerfTest_ViewResize_8.cpp | 8 + .../kokkos/core/perf_test/test_atomic.cpp | 4 +- .../perf_test/test_atomic_minmax_simple.cpp | 4 +- .../kokkos/core/perf_test/test_mempool.cpp | 12 +- .../kokkos/core/perf_test/test_taskdag.cpp | 4 +- packages/kokkos/core/src/CMakeLists.txt | 23 + .../kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp | 99 +- .../Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp | 7 +- .../core/src/Cuda/Kokkos_Cuda_Error.hpp | 27 +- .../core/src/Cuda/Kokkos_Cuda_Graph_Impl.hpp | 33 +- .../kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp | 211 +- .../core/src/Cuda/Kokkos_Cuda_Instance.cpp | 243 ++- .../core/src/Cuda/Kokkos_Cuda_Instance.hpp | 73 +- .../src/Cuda/Kokkos_Cuda_KernelLaunch.hpp | 35 +- .../core/src/Cuda/Kokkos_Cuda_Locks.cpp | 24 +- .../core/src/Cuda/Kokkos_Cuda_Locks.hpp | 22 +- .../core/src/Cuda/Kokkos_Cuda_Parallel.hpp | 207 +- .../core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp | 176 +- .../kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp | 107 +- .../kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp | 223 +- .../src/Cuda/Kokkos_Cuda_Vectorization.hpp | 17 +- .../Kokkos_Cuda_Version_9_8_Compatibility.hpp | 49 - .../HIP/Kokkos_HIP_BlockSize_Deduction.hpp | 324 ++- .../kokkos/core/src/HIP/Kokkos_HIP_Error.hpp | 20 +- .../core/src/HIP/Kokkos_HIP_Instance.cpp | 87 +- .../core/src/HIP/Kokkos_HIP_Instance.hpp | 66 +- .../core/src/HIP/Kokkos_HIP_KernelLaunch.hpp | 350 ++- .../kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp | 18 +- .../kokkos/core/src/HIP/Kokkos_HIP_Locks.hpp | 21 +- .../core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp | 3 +- .../src/HIP/Kokkos_HIP_Parallel_MDRange.hpp | 125 +- .../src/HIP/Kokkos_HIP_Parallel_Range.hpp | 162 +- .../core/src/HIP/Kokkos_HIP_Parallel_Team.hpp | 230 +- .../kokkos/core/src/HIP/Kokkos_HIP_Space.cpp | 134 +- .../kokkos/core/src/HIP/Kokkos_HIP_Team.hpp | 192 -- packages/kokkos/core/src/HPX/Kokkos_HPX.cpp | 3 + .../kokkos/core/src/HPX/Kokkos_HPX_Task.hpp | 6 +- .../src/HPX/Kokkos_HPX_WorkGraphPolicy.hpp | 4 +- .../kokkos/core/src/KokkosExp_InterOp.hpp | 147 ++ .../core/src/KokkosExp_MDRangePolicy.hpp | 28 +- packages/kokkos/core/src/Kokkos_Atomic.hpp | 92 + .../Kokkos_Atomics_Desul_Volatile_Wrapper.hpp | 189 ++ .../core/src/Kokkos_Atomics_Desul_Wrapper.hpp | 271 +++ packages/kokkos/core/src/Kokkos_Complex.hpp | 80 +- packages/kokkos/core/src/Kokkos_Concepts.hpp | 91 +- packages/kokkos/core/src/Kokkos_CopyViews.hpp | 464 ++-- packages/kokkos/core/src/Kokkos_Core.hpp | 42 + packages/kokkos/core/src/Kokkos_Core_fwd.hpp | 11 +- packages/kokkos/core/src/Kokkos_Crs.hpp | 8 +- packages/kokkos/core/src/Kokkos_Cuda.hpp | 27 +- packages/kokkos/core/src/Kokkos_CudaSpace.hpp | 365 +--- .../kokkos/core/src/Kokkos_DetectionIdiom.hpp | 116 + .../kokkos/core/src/Kokkos_ExecPolicy.hpp | 1 - packages/kokkos/core/src/Kokkos_HBWSpace.hpp | 13 +- packages/kokkos/core/src/Kokkos_HIP.hpp | 1 - packages/kokkos/core/src/Kokkos_HIP_Space.hpp | 243 +-- packages/kokkos/core/src/Kokkos_HPX.hpp | 49 +- packages/kokkos/core/src/Kokkos_HostSpace.hpp | 22 +- packages/kokkos/core/src/Kokkos_Layout.hpp | 55 +- packages/kokkos/core/src/Kokkos_Macros.hpp | 63 +- .../kokkos/core/src/Kokkos_MasterLock.hpp | 4 + .../core/src/Kokkos_MathematicalFunctions.hpp | 308 ++- .../Kokkos_MathematicalSpecialFunctions.hpp | 1280 +++++++++++ .../kokkos/core/src/Kokkos_MemoryPool.hpp | 37 +- .../kokkos/core/src/Kokkos_MemoryTraits.hpp | 10 +- .../kokkos/core/src/Kokkos_NumericTraits.hpp | 62 +- packages/kokkos/core/src/Kokkos_OpenMP.hpp | 8 +- .../kokkos/core/src/Kokkos_OpenMPTarget.hpp | 9 +- .../core/src/Kokkos_OpenMPTargetSpace.hpp | 48 +- packages/kokkos/core/src/Kokkos_Parallel.hpp | 114 +- .../core/src/Kokkos_Parallel_Reduce.hpp | 71 +- .../Kokkos_Rank.hpp} | 29 +- packages/kokkos/core/src/Kokkos_SYCL.hpp | 42 +- .../kokkos/core/src/Kokkos_SYCL_Space.hpp | 151 +- .../kokkos/core/src/Kokkos_ScratchSpace.hpp | 8 +- packages/kokkos/core/src/Kokkos_Serial.hpp | 188 +- .../kokkos/core/src/Kokkos_TaskPolicy.hpp | 4 + .../kokkos/core/src/Kokkos_TaskScheduler.hpp | 11 +- packages/kokkos/core/src/Kokkos_Threads.hpp | 7 +- packages/kokkos/core/src/Kokkos_Tuners.hpp | 114 +- packages/kokkos/core/src/Kokkos_View.hpp | 21 +- .../core/src/Kokkos_WorkGraphPolicy.hpp | 12 +- .../core/src/OpenMP/Kokkos_OpenMP_Exec.cpp | 11 +- .../core/src/OpenMP/Kokkos_OpenMP_Exec.hpp | 13 +- .../core/src/OpenMP/Kokkos_OpenMP_Task.hpp | 5 - .../OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp | 5 +- .../OpenMPTarget/Kokkos_OpenMPTarget_Exec.hpp | 230 +- 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100644 packages/kokkos/core/src/desul/src/Lock_Array_HIP.cpp create mode 100644 packages/kokkos/core/src/impl/Kokkos_QuadPrecisionMath.hpp delete mode 100644 packages/kokkos/core/src/impl/Kokkos_Tags.hpp create mode 100644 packages/kokkos/core/src/traits/Kokkos_PolicyTraitMatcher.hpp create mode 100644 packages/kokkos/core/unit_test/TestDetectionIdiom.cpp create mode 100644 packages/kokkos/core/unit_test/TestExecSpacePartitioning.hpp rename packages/kokkos/core/unit_test/{cuda/TestCudaHostPinned_ViewAPI_c.cpp => TestExecutionSpace.hpp} (68%) create mode 100644 packages/kokkos/core/unit_test/TestInterOp.cpp create mode 100644 packages/kokkos/core/unit_test/TestMathematicalSpecialFunctions.hpp create mode 100644 packages/kokkos/core/unit_test/TestQuadPrecisionMath.hpp create mode 100644 packages/kokkos/core/unit_test/TestTypeList.cpp rename packages/kokkos/core/unit_test/{cuda/TestCudaHostPinned_ViewAPI_a.cpp => category_files/TestSYCLHostUSM_Category.hpp} (89%) rename packages/kokkos/core/unit_test/category_files/{TestSYCLSharedUSMSpace_Category.hpp => TestSYCLSharedUSM_Category.hpp} (100%) delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewAPI_d.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewAPI_e.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewCopy_a.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewCopy_b.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewMapping_a.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewMapping_b.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewMapping_subview.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewAPI_a.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewAPI_b.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewAPI_c.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewAPI_d.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewAPI_e.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewCopy_a.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewCopy_b.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewMapping_a.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewMapping_b.cpp delete mode 100644 packages/kokkos/core/unit_test/cuda/TestCudaUVM_ViewMapping_subview.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewAPI_a.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewAPI_b.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewAPI_c.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewAPI_d.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewAPI_e.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewCopy_a.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewCopy_b.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewMapping_a.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewMapping_b.cpp delete mode 100644 packages/kokkos/core/unit_test/hip/TestHIPHostPinned_ViewMapping_subview.cpp create mode 100644 packages/kokkos/core/unit_test/hip/TestHIP_BlocksizeDeduction.cpp create mode 100644 packages/kokkos/core/unit_test/sycl/TestSYCL_Spaces.cpp rename packages/kokkos/core/unit_test/{cuda/TestCudaUVM_SharedAlloc.cpp => sycl/TestSYCL_Task.cpp} (96%) create mode 100644 packages/kokkos/core/unit_test/sycl/TestSYCL_TeamScratchStreams.cpp create mode 100644 packages/kokkos/core/unit_test/tools/TestBuiltinTuners.cpp create mode 100644 packages/kokkos/core/unit_test/tools/TestCategoricalTuner.cpp rename packages/kokkos/core/unit_test/{cuda/TestCudaHostPinned_SharedAlloc.cpp => tools/TestEventCorrectness.cpp} (94%) create mode 100644 packages/kokkos/core/unit_test/tools/TestEventCorrectness.hpp diff --git a/packages/kokkos/.clang-format-ignore b/packages/kokkos/.clang-format-ignore index b163a2bfeaf4..43d242c3106a 100644 --- a/packages/kokkos/.clang-format-ignore +++ b/packages/kokkos/.clang-format-ignore @@ -1,2 +1,3 @@ core/unit_test/config/results/* tpls/gtest/gtest/* +core/src/desul/* diff --git a/packages/kokkos/.clang-tidy b/packages/kokkos/.clang-tidy index 207a105c5bdf..2b0d6e51d438 100644 --- a/packages/kokkos/.clang-tidy +++ b/packages/kokkos/.clang-tidy @@ -1,3 +1,3 @@ -Checks: '-*,kokkos-*,modernize-use-using,modernize-use-nullptr' +Checks: '-*,kokkos-*,modernize-use-using,modernize-use-nullptr,cppcoreguidelines-pro-type-cstyle-cast' FormatStyle: file HeaderFilterRegex: '.*/*.hpp' diff --git a/packages/kokkos/.jenkins b/packages/kokkos/.jenkins index 001171d648e7..09e8515e96f2 100644 --- a/packages/kokkos/.jenkins +++ b/packages/kokkos/.jenkins @@ -5,9 +5,12 @@ pipeline { CCACHE_DIR = '/tmp/ccache' CCACHE_MAXSIZE = '10G' CCACHE_CPP2 = 'true' - BUILD_JOBS = 8 - SITE = 'Jenkins' } + + options { + timeout(time: 6, unit: 'HOURS') + } + stages { stage('Clang-Format') { agent { @@ -36,7 +39,7 @@ pipeline { } steps { sh 'ccache --zero-stats' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ @@ -44,13 +47,15 @@ pipeline { -DCMAKE_CXX_FLAGS="-Werror -Wno-unknown-cuda-version -Wno-gnu-zero-variadic-macro-arguments" \ -DKokkos_ARCH_VOLTA70=ON \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ -DKokkos_ENABLE_EXAMPLES=ON \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_SYCL=ON \ -DKokkos_ENABLE_UNSUPPORTED_ARCHS=ON \ -DCMAKE_CXX_STANDARD=17 \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake''' + .. && \ + make -j8 && ctest --verbose''' } post { always { @@ -58,12 +63,12 @@ pipeline { } } } - stage('HIP-ROCm-3.8-C++14') { + stage('HIP-ROCm-4.2-C++14') { agent { dockerfile { filename 'Dockerfile.hipcc' dir 'scripts/docker' - additionalBuildArgs '--build-arg BASE=rocm/dev-ubuntu-20.04:3.8' + additionalBuildArgs '--build-arg BASE=rocm/dev-ubuntu-20.04:4.2' label 'rocm-docker && vega' args '-v /tmp/ccache.kokkos:/tmp/ccache --device=/dev/kfd --device=/dev/dri --security-opt seccomp=unconfined --group-add video --env HIP_VISIBLE_DEVICES=$HIP_VISIBLE_DEVICES' } @@ -72,24 +77,23 @@ pipeline { OMP_NUM_THREADS = 8 OMP_PLACES = 'threads' OMP_PROC_BIND = 'spread' - LC_ALL = 'C' } steps { sh 'ccache --zero-stats' sh 'echo "/opt/rocm/llvm/lib" > /etc/ld.so.conf.d/llvm.conf && ldconfig' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Debug \ -DCMAKE_CXX_COMPILER=hipcc \ -DCMAKE_CXX_FLAGS="-Werror -Wno-unused-command-line-argument -DNDEBUG" \ -DCMAKE_CXX_STANDARD=14 \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_HIP=ON \ - -DKokkos_ARCH_VEGA906=ON \ -DKokkos_ENABLE_OPENMP=ON \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake''' + .. && \ + make -j8 && ctest --verbose''' } post { always { @@ -97,33 +101,73 @@ pipeline { } } } - stage('HIP-ROCm-3.8-C++17') { + stage('HIP-ROCm-4.2-C++17') { agent { dockerfile { filename 'Dockerfile.hipcc' dir 'scripts/docker' - additionalBuildArgs '--build-arg BASE=rocm/dev-ubuntu-20.04:3.8' + additionalBuildArgs '--build-arg BASE=rocm/dev-ubuntu-20.04:4.2' label 'rocm-docker && vega' args '-v /tmp/ccache.kokkos:/tmp/ccache --device=/dev/kfd --device=/dev/dri --security-opt seccomp=unconfined --group-add video --env HIP_VISIBLE_DEVICES=$HIP_VISIBLE_DEVICES' } } - environment { - LC_ALL = 'C' - } steps { sh 'ccache --zero-stats' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=RelWithDebInfo \ -DCMAKE_CXX_COMPILER=hipcc \ -DCMAKE_CXX_FLAGS="-Werror -Wno-unused-command-line-argument" \ -DCMAKE_CXX_STANDARD=17 \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_HIP=ON \ + .. && \ + make -j8 && ctest --verbose''' + } + post { + always { + sh 'ccache --show-stats' + } + } + } + stage('OPENMPTARGET-ROCm-4.2') { + agent { + dockerfile { + filename 'Dockerfile.hipcc' + dir 'scripts/docker' + additionalBuildArgs '--build-arg BASE=rocm/dev-ubuntu-20.04:4.2' + label 'rocm-docker && vega && AMD_Radeon_Instinct_MI60' + args '-v /tmp/ccache.kokkos:/tmp/ccache --device=/dev/kfd --device=/dev/dri --security-opt seccomp=unconfined --group-add video --env HIP_VISIBLE_DEVICES=$HIP_VISIBLE_DEVICES' + } + } + environment { + OMP_NUM_THREADS = 8 + OMP_PLACES = 'threads' + OMP_PROC_BIND = 'spread' + LC_ALL = 'C' + } + steps { + sh 'ccache --zero-stats' + sh 'echo "/opt/rocm/llvm/lib" > /etc/ld.so.conf.d/llvm.conf && ldconfig' + sh '''rm -rf build && \ + cmake \ + -Bbuild \ + -DCMAKE_BUILD_TYPE=Debug \ + -DCMAKE_CXX_COMPILER=/opt/rocm/llvm/bin/clang++ \ + -DCMAKE_CXX_STANDARD=17 \ + -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=OFF \ + -DKokkos_ENABLE_TESTS=ON \ + -DKokkos_ENABLE_OPENMPTARGET=ON \ + -DKokkos_ENABLE_OPENMP=ON \ -DKokkos_ARCH_VEGA906=ON \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake''' + && \ + cmake --build build --parallel ${BUILD_JOBS} && \ + cd build && ctest --output-on-failure + ''' } post { always { @@ -142,19 +186,21 @@ pipeline { } steps { sh 'ccache --zero-stats' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=RelWithDebInfo \ -DCMAKE_CXX_COMPILER=clang++ \ -DCMAKE_CXX_FLAGS="-Wno-unknown-cuda-version -Werror -Wno-undefined-internal -Wno-pass-failed" \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_TUNING=ON \ -DKokkos_ENABLE_OPENMPTARGET=ON \ -DKokkos_ARCH_VOLTA70=ON \ -DCMAKE_CXX_STANDARD=17 \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake''' + .. && \ + make -j8 && ctest --verbose''' } post { always { @@ -173,7 +219,7 @@ pipeline { } steps { sh 'ccache --zero-stats' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_CLANG_TIDY="clang-tidy;-warnings-as-errors=*" \ @@ -182,13 +228,15 @@ pipeline { -DCMAKE_CXX_FLAGS=-Werror \ -DCMAKE_CXX_STANDARD=14 \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_CUDA=ON \ -DKokkos_ENABLE_CUDA_LAMBDA=ON \ -DKokkos_ENABLE_TUNING=ON \ -DKokkos_ARCH_VOLTA70=ON \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake''' + .. && \ + make -j8 && ctest --verbose''' } post { always { @@ -244,7 +292,7 @@ pipeline { steps { sh 'ccache --zero-stats' sh '''rm -rf install && mkdir -p install && \ - rm -rf build && \ + rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_COMPILER=g++-8 \ @@ -256,10 +304,12 @@ pipeline { -DKokkos_ENABLE_CUDA_LAMBDA=OFF \ -DKokkos_ENABLE_CUDA_UVM=ON \ -DKokkos_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE=ON \ - -DCMAKE_INSTALL_PREFIX=${PWD}/install \ - -DBUILD_NAME=${STAGE_NAME} \ - -DTARGET=install \ - -P cmake/KokkosCI.cmake && \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ + -DCMAKE_INSTALL_PREFIX=${PWD}/../install \ + .. && \ + make -j8 install && \ + cd .. && \ rm -rf build-tests && mkdir -p build-tests && cd build-tests && \ export CMAKE_PREFIX_PATH=${PWD}/../install && \ cmake \ @@ -302,7 +352,7 @@ pipeline { } steps { sh 'ccache --zero-stats' - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Debug \ -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ @@ -312,14 +362,14 @@ pipeline { -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ -DKokkos_ENABLE_DEBUG=ON \ -DKokkos_ENABLE_DEBUG_BOUNDS_CHECK=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_CUDA=ON \ -DKokkos_ENABLE_CUDA_LAMBDA=ON \ -DKokkos_ENABLE_LIBDL=OFF \ - -DBUILD_NAME=${STAGE_NAME} \ - -DTARGET=install \ - -P cmake/KokkosCI.cmake && \ - cd example/build_cmake_in_tree && \ + .. && \ + make -j8 && ctest --verbose && \ + cd ../example/build_cmake_in_tree && \ rm -rf build && mkdir -p build && cd build && \ cmake -DCMAKE_CXX_STANDARD=14 .. && make -j8 && ctest --verbose''' } @@ -342,18 +392,21 @@ pipeline { OMP_PROC_BIND = 'true' } steps { - sh '''rm -rf build && \ + sh '''rm -rf build && mkdir -p build && cd build && \ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_STANDARD=14 \ -DCMAKE_CXX_FLAGS=-Werror \ -DKokkos_ENABLE_COMPILER_WARNINGS=ON \ + -DKokkos_ENABLE_DEPRECATED_CODE_3=ON \ + -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF \ -DKokkos_ENABLE_TESTS=ON \ -DKokkos_ENABLE_OPENMP=ON \ -DKokkos_ENABLE_LIBDL=OFF \ - -DBUILD_NAME=${STAGE_NAME} \ - -P cmake/KokkosCI.cmake && \ - gcc -I$PWD/core/src core/unit_test/tools/TestCInterface.c''' + -DKokkos_ENABLE_LIBQUADMATH=ON \ + -DCMAKE_PREFIX_PATH=/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0 \ + .. && \ + make -j8 && ctest --verbose && gcc -I$PWD/../core/src/ ../core/unit_test/tools/TestCInterface.c''' } } } diff --git a/packages/kokkos/.travis.yml b/packages/kokkos/.travis.yml index 04ef01c1602c..87d0fd5cf6ed 100644 --- a/packages/kokkos/.travis.yml +++ b/packages/kokkos/.travis.yml @@ -67,14 +67,13 @@ install: before_script: - ccache -z - - if [[ ${COVERAGE} ]]; then export CXX="${CXX} --coverage"; export BUILD_NAME_SUFFIX="-Coverage"; fi + - if [[ ${COVERAGE} ]]; then export CXX="${CXX} --coverage"; fi - if [[ ! ${CMAKE_BUILD_TYPE} ]]; then export CXXFLAGS="${CXXFLAGS} -O2"; fi script: - export OMP_NUM_THREADS=2 - export OMP_PLACES=threads - export OMP_PROC_BIND=spread - - export BUILD_JOBS=2 # LD_LIBRARY_PATH workaround to find clang's libomp: https://github.com/travis-ci/travis-ci/issues/8613 - if [[ ${CC} = clang ]]; then export LD_LIBRARY_PATH=/usr/local/clang/lib${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH; fi # enable ccache for clang on linux and add CCACHE_CPP2 to avoid 'Argument unused during compilation -I...' warning @@ -82,17 +81,17 @@ script: ln -s /usr/bin/ccache $HOME/bin/clang++; export CCACHE_CPP2=yes; fi - - cmake + - mkdir build && + pushd build && + cmake .. ${BACKEND:+-DKokkos_ENABLE_${BACKEND}=On} -DCMAKE_CXX_FLAGS="${CXXFLAGS} -Werror" -DCMAKE_CXX_STANDARD=14 -DKokkos_ENABLE_COMPILER_WARNINGS=ON -DKokkos_ENABLE_TESTS=On - ${CMAKE_BUILD_TYPE:+-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}} - -DBUILD_NAME="${CC}-${BACKEND}${BUILD_NAME_SUFFIX}" - -DSITE=Travis - -P cmake/KokkosCI.cmake && - pushd build && + ${CMAKE_BUILD_TYPE:+-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}} && + make VERBOSE=1 -j2 && + travis_wait 60 make test CTEST_OUTPUT_ON_FAILURE=1 && make install DESTDIR=${PWD}/install && rm -rf ${PWD}/install/usr/local && rmdir ${PWD}/install/usr && popd diff --git a/packages/kokkos/CHANGELOG.md b/packages/kokkos/CHANGELOG.md index 7bb6de4cd924..2e779791dde2 100644 --- a/packages/kokkos/CHANGELOG.md +++ b/packages/kokkos/CHANGELOG.md @@ -1,5 +1,165 @@ # Change Log +## [3.5.00](https://github.com/kokkos/kokkos/tree/3.5.00) (2021-10-19) +[Full Changelog](https://github.com/kokkos/kokkos/compare/3.4.01...3.5.00) + +### Features: + +- Add support for quad-precision math functions/traits [\#4098](https://github.com/kokkos/kokkos/pull/4098) +- Adding ExecutionSpace partitioning function [\#4096](https://github.com/kokkos/kokkos/pull/4096) +- Improve Python Interop Capabilities [\#4065](https://github.com/kokkos/kokkos/pull/4065) +- Add half_t Kokkos::rand specialization [\#3922](https://github.com/kokkos/kokkos/pull/3922) +- Add math special functions: erf, erfcx, expint1, Bessel functions, Hankel functions [\#3920](https://github.com/kokkos/kokkos/pull/3920) +- Add missing common mathematical functions [\#4043](https://github.com/kokkos/kokkos/pull/4043) [\#4036](https://github.com/kokkos/kokkos/pull/4036) [\#4034](https://github.com/kokkos/kokkos/pull/4034) +- Let the numeric traits be SFINAE-friendly [\#4038](https://github.com/kokkos/kokkos/pull/4038) +- Add Desul atomics - enabling memory-order and memory-scope parameters [\#3247](https://github.com/kokkos/kokkos/pull/3247) +- Add detection idiom from the C++ standard library extension version 2 [\#3980](https://github.com/kokkos/kokkos/pull/3980) +- Fence Profiling Support in all backends [\#3966](https://github.com/kokkos/kokkos/pull/3966) [\#4304](https://github.com/kokkos/kokkos/pull/4304) [\#4258](https://github.com/kokkos/kokkos/pull/4258) [\#4232](https://github.com/kokkos/kokkos/pull/4232) +- Significant SYCL enhancements (see below) + +### Deprecations: + +- Deprecate CUDA_SAFE_CALL and HIP_SAFE_CALL [\#4249](https://github.com/kokkos/kokkos/pull/4249) +- Deprecate Kokkos::Impl::Timer (Kokkos::Timer has been available for a long time) [\#4201](https://github.com/kokkos/kokkos/pull/4201) +- Deprecate Experimental::MasterLock [\#4094](https://github.com/kokkos/kokkos/pull/4094) +- Deprecate Kokkos_TaskPolicy.hpp (headers got reorganized, doesn't remove functionality) [\#4011](https://github.com/kokkos/kokkos/pull/4011) +- Deprecate backward compatibility features [\#3978](https://github.com/kokkos/kokkos/pull/3978) +- Update and deprecate is_space::host_memory/execution/mirror_space [\#3973](https://github.com/kokkos/kokkos/pull/3973) + + +### Backends and Archs Enhancements: + +- Enabling constbitset constructors in kernels [\#4296](https://github.com/kokkos/kokkos/pull/4296) +- Use ZeroMemset in View constructor to improve performance [\#4226](https://github.com/kokkos/kokkos/pull/4226) +- Use memset in deep_copy [\#3944](https://github.com/kokkos/kokkos/pull/3944) +- Add missing fence() calls in resize(View) that effectively do deep_copy(resized, orig) [\#4212](https://github.com/kokkos/kokkos/pull/4212) +- Avoid allocations in resize and realloc [\#4207](https://github.com/kokkos/kokkos/pull/4207) +- StaticCsrGraph: use device type instead of execution space to construct views [\#3991](https://github.com/kokkos/kokkos/pull/3991) +- Consider std::sort when view is accessible from host [\#3929](https://github.com/kokkos/kokkos/pull/3929) +- Fix CPP20 warnings except for volatile [\#4312](https://github.com/kokkos/kokkos/pull/4312) + +#### SYCL: +- Introduce SYCLHostUSMSpace [\#4268](https://github.com/kokkos/kokkos/pull/4268) +- Implement SYCL TeamPolicy for vector_size > 1 [\#4183](https://github.com/kokkos/kokkos/pull/4183) +- Enable 64bit ranges for SYCL [\#4211](https://github.com/kokkos/kokkos/pull/4211) +- Don't print SYCL device info in execution space intialization [\#4168](https://github.com/kokkos/kokkos/pull/4168) +- Improve SYCL MDRangePolicy performance [\#4161](https://github.com/kokkos/kokkos/pull/4161) +- Use sub_groups in SYCL parallel_scan [\#4147](https://github.com/kokkos/kokkos/pull/4147) +- Implement subgroup reduction for SYCL RangePolicy parallel_reduce [\#3940](https://github.com/kokkos/kokkos/pull/3940) +- Use DPC++ broadcast extension in SYCL team_broadcast [\#4103](https://github.com/kokkos/kokkos/pull/4103) +- Only fence in SYCL parallel_reduce for non-device-accessible result_ptr [\#4089](https://github.com/kokkos/kokkos/pull/4089) +- Improve fencing behavior in SYCL backend [\#4088](https://github.com/kokkos/kokkos/pull/4088) +- Fence all registered SYCL queues before deallocating memory [\#4086](https://github.com/kokkos/kokkos/pull/4086) +- Implement SYCL::print_configuration [\#3992](https://github.com/kokkos/kokkos/pull/3992) +- Reuse scratch memory in parallel_scan and TeamPolicy (decreases memory footprint) [\#3899](https://github.com/kokkos/kokkos/pull/3899) [\#3889](https://github.com/kokkos/kokkos/pull/3889) + +#### CUDA: +- Cuda improve heuristic for blocksize [\#4271](https://github.com/kokkos/kokkos/pull/4271) +- Don't use [[deprecated]] for nvcc [\#4229](https://github.com/kokkos/kokkos/pull/4229) +- Improve error message for NVHPC as host compiler [\#4227](https://github.com/kokkos/kokkos/pull/4227) +- Update support for cuda reductions to work with types < 4bytes [\#4156](https://github.com/kokkos/kokkos/pull/4156) +- Fix incompatible team size deduction in rare cases parallel_reduce [\#4142](https://github.com/kokkos/kokkos/pull/4142) +- Remove UVM usage in DynamicView [\#4129](https://github.com/kokkos/kokkos/pull/4129) +- Remove dependency between core and containers [\#4114](https://github.com/kokkos/kokkos/pull/4114) +- Adding opt-in CudaMallocSync support when using CUDA version >= 11.2 [\#4026](https://github.com/kokkos/kokkos/pull/4026) [\#4233](https://github.com/kokkos/kokkos/pull/4233) +- Fix a potential race condition in the CUDA backend [\#3999](https://github.com/kokkos/kokkos/pull/3999) + +#### HIP: +- Implement new blocksize deduction method for HIP Backend [\#3953](https://github.com/kokkos/kokkos/pull/3953) +- Add multiple LaunchMechanism [\#3820](https://github.com/kokkos/kokkos/pull/3820) +- Make HIP backend thread-safe [\#4170](https://github.com/kokkos/kokkos/pull/4170) + +#### Serial: +- Refactor Serial backend and fix thread-safety issue [\#4053](https://github.com/kokkos/kokkos/pull/4053) + +#### OpenMPTarget: +- OpenMPTarget: support array reductions in RangePolicy [\#4040](https://github.com/kokkos/kokkos/pull/4040) +- OpenMPTarget: add MDRange parallel_reduce [\#4032](https://github.com/kokkos/kokkos/pull/4032) +- OpenMPTarget: Fix bug in for the case of a reducer. [\#4044](https://github.com/kokkos/kokkos/pull/4044) +- OpenMPTarget: verify process fix [\#4041](https://github.com/kokkos/kokkos/pull/4041) + +### Implemented enhancements BuildSystem + +#### Important BuildSystem Updates: +- Use hipcc architecture autodetection when Kokkos_ARCH is not set [\#3941](https://github.com/kokkos/kokkos/pull/3941) +- Introduce Kokkos_ENABLE_DEPRECATION_WARNINGS and remove deprecated code with Kokkos_ENABLE_DEPRECATED_CODE_3 [\#4106](https://github.com/kokkos/kokkos/pull/4106) [\#3855](https://github.com/kokkos/kokkos/pull/3855) + +#### Other Improvements: +- Add allow-unsupported-compiler flag to nvcc-wrapper [\#4298](https://github.com/kokkos/kokkos/pull/4298) +- nvcc_wrapper: fix errors in argument handling [\#3993](https://github.com/kokkos/kokkos/pull/3993) +- Adds support for -time= and -time in nvcc_wrapper [\#4015](https://github.com/kokkos/kokkos/pull/4015) +- nvcc_wrapper: suppress duplicates of GPU architecture and RDC flags [\#3968](https://github.com/kokkos/kokkos/pull/3968) +- Fix TMPDIR support in nvcc_wrapper [\#3792](https://github.com/kokkos/kokkos/pull/3792) +- NVHPC: update PGI compiler arch flags [\#4133](https://github.com/kokkos/kokkos/pull/4133) +- Replace PGI with NVHPC (works for both) [\#4196](https://github.com/kokkos/kokkos/pull/4196) +- Make sure that KOKKOS_CXX_HOST_COMPILER_ID is defined [\#4235](https://github.com/kokkos/kokkos/pull/4235) +- Add options to Makefile builds for deprecated code and warnings [\#4215](https://github.com/kokkos/kokkos/pull/4215) +- Use KOKKOS_CXX_HOST_COMPILER_ID for identifying CPU arch flags [\#4199](https://github.com/kokkos/kokkos/pull/4199) +- Added support for Cray Clang to Makefile.kokkos [\#4176](https://github.com/kokkos/kokkos/pull/4176) +- Add XLClang as compiler [\#4120](https://github.com/kokkos/kokkos/pull/4120) +- Keep quoted compiler flags when passing to Trilinos [\#3987](https://github.com/kokkos/kokkos/pull/3987) +- Add support for AMD Zen3 CPU architecture [\#3972](https://github.com/kokkos/kokkos/pull/3972) +- Rename IntelClang to IntelLLVM [\#3945](https://github.com/kokkos/kokkos/pull/3945) +- Add cppcoreguidelines-pro-type-cstyle-cast to clang-tidy [\#3522](https://github.com/kokkos/kokkos/pull/3522) +- Add sve bit size definition for A64FX [\#3947](https://github.com/kokkos/kokkos/pull/3947) [\#3946](https://github.com/kokkos/kokkos/pull/3946) +- Remove KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES [\#4150](https://github.com/kokkos/kokkos/pull/4150) + +### Other Changes: + +#### Tool Enhancements: + +- Retrieve original value from a point in a MultidimensionalSparseTuningProblem [\#3977](https://github.com/kokkos/kokkos/pull/3977) +- Allow extension of built-in tuners with additional tuning axes [\#3961](https://github.com/kokkos/kokkos/pull/3961) +- Added a categorical tuner [\#3955](https://github.com/kokkos/kokkos/pull/3955) + + +#### Miscellaneous: + +- hpcbind: Use double quotes around $@ when invoking user command [\#4284](https://github.com/kokkos/kokkos/pull/4284) +- Add file and line to error message [\#3985](https://github.com/kokkos/kokkos/pull/3985) +- Fix compiler warnings when compiling with nvc++ [\#4198](https://github.com/kokkos/kokkos/pull/4198) +- Add OpenMPTarget CI build on AMD GPUs [\#4055](https://github.com/kokkos/kokkos/pull/4055) +- CI: icpx is now part of intel container [\#4002](https://github.com/kokkos/kokkos/pull/4002) + +### Incompatibilities: + +- Remove pre CUDA 9 KOKKOS_IMPL_CUDA_* macros [\#4138](https://github.com/kokkos/kokkos/pull/4138) + +### Bug Fixes: +- UnorderedMap::clear() should zero the size() [\#4130](https://github.com/kokkos/kokkos/pull/4130) +- Add memory fence for HostSharedPtr::cleanup() [\#4144](https://github.com/kokkos/kokkos/pull/4144) +- SYCL: Fix race conditions in TeamPolicy::parallel_reduce [\#4418](https://github.com/kokkos/kokkos/pull/4418) +- Adding missing memory fence to serial exec space fence. [\#4292](https://github.com/kokkos/kokkos/pull/4292) +- Fix using external SYCL queues in tests [\#4291](https://github.com/kokkos/kokkos/pull/4291) +- Fix digits10 bug [\#4281](https://github.com/kokkos/kokkos/pull/4281) +- Fixes constexpr errors with frounding-math on gcc < 10. [\#4278](https://github.com/kokkos/kokkos/pull/4278) +- Fix compiler flags for PGI/NVHPC [\#4264](https://github.com/kokkos/kokkos/pull/4264) +- Fix Zen2/3 also implying Zen Arch with Makefiles [\#4260](https://github.com/kokkos/kokkos/pull/4260) +- Kokkos_Cuda.hpp: Fix shadow warning with cuda/11.0 [\#4252](https://github.com/kokkos/kokkos/pull/4252) +- Fix issue w/ static initialization of function attributes [\#4242](https://github.com/kokkos/kokkos/pull/4242) +- Disable long double hypot test on Power systems [\#4221](https://github.com/kokkos/kokkos/pull/4221) +- Fix false sharing in random pool [\#4218](https://github.com/kokkos/kokkos/pull/4218) +- Fix a missing memory_fence for debug shared alloc code [\#4216](https://github.com/kokkos/kokkos/pull/4216) +- Fix two xl issues [\#4179](https://github.com/kokkos/kokkos/pull/4179) +- Makefile.kokkos: fix (standard_in) 1: syntax error [\#4173](https://github.com/kokkos/kokkos/pull/4173) +- Fixes for query_device example [\#4172](https://github.com/kokkos/kokkos/pull/4172) +- Fix a bug when using HIP atomic with Kokkos::Complex [\#4159](https://github.com/kokkos/kokkos/pull/4159) +- Fix mistaken logic in pthread creation [\#4157](https://github.com/kokkos/kokkos/pull/4157) +- Define KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION when requesting Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON [\#4107](https://github.com/kokkos/kokkos/pull/4107) +- Fix compilation with latest MSVC version [\#4102](https://github.com/kokkos/kokkos/pull/4102) +- Fix incorrect macro definitions when compiling with Intel compiler on Windows [\#4087](https://github.com/kokkos/kokkos/pull/4087) +- Fixup global buffer overflow in hand rolled string manipulation [\#4070](https://github.com/kokkos/kokkos/pull/4070) +- Fixup heap buffer overflow in cmd line args parsing unit tests [\#4069](https://github.com/kokkos/kokkos/pull/4069) +- Only add quotes in compiler flags for Trilinos if necessary [\#4067](https://github.com/kokkos/kokkos/pull/4067) +- Fixed invocation of tools init callbacks [\#4061](https://github.com/kokkos/kokkos/pull/4061) +- Work around SYCL JIT compiler issues with static variables [\#4013](https://github.com/kokkos/kokkos/pull/4013) +- Fix TestDetectionIdiom.cpp test inclusion for Trilinos/TriBITS [\#4010](https://github.com/kokkos/kokkos/pull/4010) +- Fixup allocation headers with OpenMPTarget backend [\#4003](https://github.com/kokkos/kokkos/pull/4003) +- Add missing specialization for OMPT to Kokkos Random [\#3967](https://github.com/kokkos/kokkos/pull/3967) +- Disable hypot long double test on power arches [\#3962](https://github.com/kokkos/kokkos/pull/3962) +- Use different EBO workaround for MSVC (rebased) [\#3924](https://github.com/kokkos/kokkos/pull/3924) +- Fix SYCL Kokkos::Profiling::(de)allocateData calls [\#3928](https://github.com/kokkos/kokkos/pull/3928) + ## [3.4.01](https://github.com/kokkos/kokkos/tree/3.4.01) (2021-05-19) [Full Changelog](https://github.com/kokkos/kokkos/compare/3.4.00...3.4.01) diff --git a/packages/kokkos/CMakeLists.txt b/packages/kokkos/CMakeLists.txt index 600b7bff9506..1b6753f983db 100644 --- a/packages/kokkos/CMakeLists.txt +++ b/packages/kokkos/CMakeLists.txt @@ -111,8 +111,8 @@ ENDIF() set(Kokkos_VERSION_MAJOR 3) -set(Kokkos_VERSION_MINOR 4) -set(Kokkos_VERSION_PATCH 01) +set(Kokkos_VERSION_MINOR 5) +set(Kokkos_VERSION_PATCH 00) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") diff --git a/packages/kokkos/Makefile.kokkos b/packages/kokkos/Makefile.kokkos index bda8572073a3..7ab18f5894e8 100644 --- a/packages/kokkos/Makefile.kokkos +++ b/packages/kokkos/Makefile.kokkos @@ -1,19 +1,19 @@ # Default settings common options. KOKKOS_VERSION_MAJOR = 3 -KOKKOS_VERSION_MINOR = 4 -KOKKOS_VERSION_PATCH = 01 +KOKKOS_VERSION_MINOR = 5 +KOKKOS_VERSION_PATCH = 00 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) -# Options: Cuda,HIP,OpenMP,Pthread,Serial +# Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Pthread,Serial #KOKKOS_DEVICES ?= "OpenMP" KOKKOS_DEVICES ?= "Pthread" -# Options: +# Options: # Intel: KNC,KNL,SNB,HSW,BDW,SKX # NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86 # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX # IBM: BGQ,Power7,Power8,Power9 -# AMD-GPUS: Vega900,Vega906,Vega908 +# AMD-GPUS: Vega900,Vega906,Vega908,Vega90A # AMD-CPUS: AMDAVX,Zen,Zen2,Zen3 KOKKOS_ARCH ?= "" # Options: yes,no @@ -22,7 +22,7 @@ KOKKOS_DEBUG ?= "no" KOKKOS_USE_TPLS ?= "" # Options: c++14,c++1y,c++17,c++1z,c++2a KOKKOS_CXX_STANDARD ?= "c++14" -# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align +# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align,disable_deprecated_code,enable_deprecation_warnings KOKKOS_OPTIONS ?= "" KOKKOS_CMAKE ?= "no" KOKKOS_TRIBITS ?= "no" @@ -70,7 +70,7 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),exper # Check for advanced settings. KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings) -KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization) +KOKKOS_INTERNAL_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization) KOKKOS_INTERNAL_ENABLE_TUNING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_tuning) KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_complex_align) KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check) @@ -82,6 +82,9 @@ KOKKOS_INTERNAL_CUDA_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda) KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_constexpr) KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH := $(call kokkos_has_string,$(KOKKOS_HPX_OPTIONS),enable_async_dispatch) +KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_desul_atomics) +KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_deprecated_code) +KOKKOS_INTERNAL_ENABLE_DEPRECATION_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_deprecation_warnings) KOKKOS_INTERNAL_HIP_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_HIP_OPTIONS),rdc) @@ -102,6 +105,7 @@ endif # Check for other Execution Spaces. KOKKOS_INTERNAL_USE_CUDA := $(call kokkos_has_string,$(KOKKOS_DEVICES),Cuda) KOKKOS_INTERNAL_USE_HIP := $(call kokkos_has_string,$(KOKKOS_DEVICES),HIP) +KOKKOS_INTERNAL_USE_SYCL := $(call kokkos_has_string,$(KOKKOS_DEVICES),SYCL) KOKKOS_INTERNAL_USE_OPENMPTARGET := $(call kokkos_has_string,$(KOKKOS_DEVICES),OpenMPTarget) KOKKOS_DEVICELIST = @@ -123,11 +127,18 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) KOKKOS_DEVICELIST += HIP endif +KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER := $(shell expr $(KOKKOS_INTERNAL_ENABLE_CXX17) \ + + $(KOKKOS_INTERNAL_ENABLE_CXX20) \ + + $(KOKKOS_INTERNAL_ENABLE_CXX2A)) +ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1) + KOKKOS_DEVICELIST += SYCL + ifneq ($(KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER), 1) + $(error SYCL backend requires C++17 or newer) + endif + +endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) KOKKOS_DEVICELIST += OPENMPTARGET - KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER := $(shell expr $(KOKKOS_INTERNAL_ENABLE_CXX17) \ - + $(KOKKOS_INTERNAL_ENABLE_CXX20) \ - + $(KOKKOS_INTERNAL_ENABLE_CXX2A)) ifneq ($(KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER), 1) $(error OpenMPTarget backend requires C++17 or newer) endif @@ -158,6 +169,8 @@ KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2 KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "CC-")) KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep -c nvcc)>0" | bc)) KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang) +KOKKOS_INTERNAL_COMPILER_CRAY_CLANG := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "clang++")) +KOKKOS_INTERNAL_COMPILER_INTEL_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),oneAPI) KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple clang) KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC) KOKKOS_INTERNAL_COMPILER_GCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),GCC) @@ -237,7 +250,11 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -mp else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY_CLANG), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + else KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp + endif else ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp @@ -249,7 +266,11 @@ else # OpenMP is turned on by default in Cray compiler environment. KOKKOS_INTERNAL_OPENMP_FLAG := else - KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL_CLANG), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -fiopenmp + else + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + endif endif endif endif @@ -307,6 +328,13 @@ KOKKOS_INTERNAL_USE_ARCH_BDW := $(call kokkos_has_string,$(KOKKOS_ARCH),BDW) KOKKOS_INTERNAL_USE_ARCH_SKX := $(call kokkos_has_string,$(KOKKOS_ARCH),SKX) KOKKOS_INTERNAL_USE_ARCH_KNL := $(call kokkos_has_string,$(KOKKOS_ARCH),KNL) +KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen) +KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen9) +KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen11) +KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen12LP) +KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelDG1) +KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelXeHP) + # NVIDIA based. NVCC_WRAPPER := $(KOKKOS_PATH)/bin/nvcc_wrapper KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler30) @@ -374,20 +402,25 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX) KOKKOS_INTERNAL_USE_ARCH_ZEN3 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen3) KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2) -KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 0) + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 0) + KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) + endif +endif KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900) KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906) KOKKOS_INTERNAL_USE_ARCH_VEGA908 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega908) +KOKKOS_INTERNAL_USE_ARCH_VEGA90A := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega90A) # Any AVX? KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM)) KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)) -KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) +KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL)) KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX)) # Decide what ISA level we are able to support. -KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) +KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC)) KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9)) KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7)) @@ -396,8 +429,8 @@ KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POW KOKKOS_INTERNAL_USE_TM := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_SKX)) # Incompatible flags? -KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1" | bc )) -KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1" | bc)) +KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1") | bc) +KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1") | bc) ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MULTIHOST), 1) $(error Defined Multiple Host architectures: KOKKOS_ARCH=$(KOKKOS_ARCH) ) @@ -432,6 +465,10 @@ KOKKOS_LINK_FLAGS = KOKKOS_SRC = KOKKOS_HEADERS = +#ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1) + KOKKOS_LIBS += -latomic +#endif + # Generating the KokkosCore_config.h file. KOKKOS_INTERNAL_CONFIG_TMP=KokkosCore_config.tmp @@ -468,6 +505,10 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_HIP') endif +ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1) + tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_SYCL') +endif + ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_OPENMPTARGET') ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1) @@ -523,6 +564,12 @@ endif #only add the c++ standard flags if this is not CMake tmp := $(call kokkos_append_header,"/* General Settings */") +ifneq ($(KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEPRECATED_CODE_3") +endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_DEPRECATION_WARNINGS), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEPRECATION_WARNINGS") +endif ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1) ifneq ($(KOKKOS_STANDALONE_CMAKE), yes) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG) @@ -625,8 +672,10 @@ endif tmp := $(call kokkos_append_header,"/* Optimization Settings */") -ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1) +ifeq ($(KOKKOS_INTERNAL_AGGRESSIVE_VECTORIZATION), 1) + # deprecated tmp := $(call kokkos_append_header,"$H""define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION") endif tmp := $(call kokkos_append_header,"/* Cuda Settings */") @@ -1156,6 +1205,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA908") KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx908 endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA90A), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 90A") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA90A") + KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx90a + endif KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp) @@ -1174,6 +1228,52 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) endif endif +# Figure out the architecture flag for SYCL. +ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1) + # Lets start with adding architecture defines + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9-" + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN9") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9" + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN11") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen11" + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN12LP") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen12lp" + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_DG1") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device dg1" + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_XEHP") + KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device xehp" + endif + + KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/SYCL/*.cpp) + KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/SYCL/*.hpp) + + KOKKOS_CXXFLAGS+=-fsycl -fno-sycl-id-queries-fit-in-int -fsycl-unnamed-lambda + KOKKOS_CXXFLAGS+=$(KOKKOS_INTERNAL_SYCL_ARCH_FLAG) + KOKKOS_LDFLAGS+=-fsycl + KOKKOS_LDFLAGS+=$(KOKKOS_INTERNAL_SYCL_ARCH_FLAG) +endif + +ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_IMPL_DESUL_ATOMICS") +endif KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h 2>&1) @@ -1185,57 +1285,63 @@ endif ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0) tmp := $(shell cp KokkosCore_config.tmp KokkosCore_config.h) -endif -# Functions for generating config header file -kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1) -kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3) -kokkos_append_config_header = $(shell echo $1 >> $2)) -tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp") -tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp") -tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp") -tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp") -tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp") -tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp") -tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp") -tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp") -ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") - ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) - else - endif -endif -ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") -endif -ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + # Functions for generating config header file + kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1) + kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3) + kokkos_append_config_header = $(shell echo $1 >> $2)) + tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp") + tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp") + tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp") + tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp") + tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp") + tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp") + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) + else + endif + endif + ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif endif + KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/containers/src/*.hpp) @@ -1247,6 +1353,9 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp) + ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1) + KOKKOS_SRC += $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp + endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) ifneq ($(CUDA_PATH),) KOKKOS_CPPLAGS += -I$(CUDA_PATH)/include diff --git a/packages/kokkos/Makefile.targets b/packages/kokkos/Makefile.targets index cf9fc242420e..93854d0cf150 100644 --- a/packages/kokkos/Makefile.targets +++ b/packages/kokkos/Makefile.targets @@ -48,6 +48,17 @@ Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cu $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp +Lock_Array_CUDA.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp +endif + +ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1) +Kokkos_SYCL.o : $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL.cpp +Kokkos_SYCL_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Space.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Space.cpp +Kokkos_SYCL_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Instance.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Instance.cpp endif ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) diff --git a/packages/kokkos/README.md b/packages/kokkos/README.md index d55ef2caac93..673f46271252 100644 --- a/packages/kokkos/README.md +++ b/packages/kokkos/README.md @@ -7,7 +7,7 @@ applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources. It currently can use -CUDA, HPX, OpenMP and Pthreads as backend programming models with several other +CUDA, HIP, SYCL, HPX, OpenMP and C++ threads as backend programming models with several other backends in development. Kokkos Core is part of the Kokkos C++ Performance Portability Programming EcoSystem, @@ -16,29 +16,19 @@ profiling and debugging tools (https://github.com/kokkos/kokkos-tools). # Learning about Kokkos -A programming guide can be found on the Wiki, the API reference is under development. +The best way to start learning about Kokkos is going through the Kokkos Lectures. +They are online available at https://kokkos.link/the-lectures and contain a mix +of lecture videos and hands-on exercises covering all the important Kokkos Ecosystem +capabilities. + +A programming guide and API reference can be found on the Wiki +(https://github.com/kokkos/kokkos/wiki). For questions find us on Slack: https://kokkosteam.slack.com or open a github issue. For non-public questions send an email to crtrott(at)sandia.gov -A separate repository with extensive tutorial material can be found under -https://github.com/kokkos/kokkos-tutorials. - -Furthermore, the 'example/tutorial' directory provides step by step tutorial -examples which explain many of the features of Kokkos. They work with -simple Makefiles. To build with g++ and OpenMP simply type 'make' -in the 'example/tutorial' directory. This will build all examples in the -subfolders. To change the build options refer to the Programming Guide -in the compilation section. - -To learn more about Kokkos consider watching one of our presentations: -* GTC 2015: - - http://on-demand.gputechconf.com/gtc/2015/video/S5166.html - - http://on-demand.gputechconf.com/gtc/2015/presentation/S5166-H-Carter-Edwards.pdf - - # Contributing to Kokkos We are open and try to encourage contributions from external developers. @@ -53,57 +43,40 @@ For specifics see the LICENSE file contained in the repository or distribution. # Requirements -### Primary tested compilers on X86 are: -* GCC 5.3.0 -* GCC 5.4.0 -* GCC 5.5.0 -* GCC 6.1.0 -* GCC 7.2.0 -* GCC 7.3.0 -* GCC 8.1.0 -* Intel 17.0.1 -* Intel 17.4.196 -* Intel 18.2.128 -* Clang 4.0.0 -* Clang 6.0.0 for CUDA (CUDA Toolkit 9.0) -* Clang 7.0.0 for CUDA (CUDA Toolkit 9.1) -* Clang 8.0.0 for CUDA (CUDA Toolkit 9.2) -* PGI 18.7 -* NVCC 9.1 for CUDA (with gcc 6.1.0) -* NVCC 9.2 for CUDA (with gcc 7.2.0) -* NVCC 10.0 for CUDA (with gcc 7.4.0) -* NVCC 10.1 for CUDA (with gcc 7.4.0) -* NVCC 11.0 for CUDA (with gcc 8.4.0) - -### Primary tested compilers on Power 8 are: -* GCC 6.4.0 (OpenMP,Serial) -* GCC 7.2.0 (OpenMP,Serial) -* IBM XL 16.1.0 (OpenMP, Serial) -* NVCC 9.2.88 for CUDA (with gcc 7.2.0 and XL 16.1.0) - -### Primary tested compilers on Intel KNL are: -* Intel 17.2.174 (with gcc 6.2.0 and 6.4.0) -* Intel 18.2.199 (with gcc 6.2.0 and 6.4.0) - -### Primary tested compilers on ARM (Cavium ThunderX2) -* GCC 7.2.0 -* ARM/Clang 18.4.0 - -### Other compilers working: -* X86: - * Cygwin 2.1.0 64bit with gcc 4.9.3 - * GCC 8.1.0 (not warning free) - -### Known non-working combinations: -* Power8: - * Pthreads backend -* ARM - * Pthreads backend +### Minimum Compiler Versions + +Generally Kokkos should work with all compiler versions newer than the minimum. +However as in all sufficiently complex enough code, we have to work around compiler +bugs with almost all compilers. So compiler versions we don't test may have issues +we are unaware off. + +* GCC: 5.3.0 +* Clang: 4.0.0 +* Intel: 17.0.1 +* NVCC: 9.2.88 +* NVC++: 21.5 +* ROCM: 4.3 +* MSVC: 19.29 +* IBM XL: 16.1.1 +* Fujitsu: 4.5.0 +* ARM/Clang 20.1 + +### Primary Tested Compilers + +* GCC: 5.3.0, 6.1.0, 7.3.0, 8.3, 9.2, 10.0 +* NVCC: 9.2.88, 10.1, 11.0 +* Clang: 8.0.0, 9.0.0, 10.0.0, 12.0.0 +* Intel 17.4, 18.1, 19.5 +* MSVC: 19.29 +* ARM/Clang: 20.1 +* IBM XL: 16.1.1 +* ROCM: 4.3.0 ### Build system: -* CMake >= 3.10: required -* CMake >= 3.13: recommended + +* CMake >= 3.16: required * CMake >= 3.18: Fortran linkage. This does not affect most mixed Fortran/Kokkos builds. See [build issues](BUILD.md#KnownIssues). +* CMake >= 3.21.1 for NVC++ Primary tested compiler are passing in release mode with warnings as errors. They also are tested with a comprehensive set of @@ -153,7 +126,6 @@ cmake $srcdir \ -DCMAKE_INSTALL_PREFIX=$path_to_install \ -DKokkos_ENABLE_OPENMP=On \ -DKokkos_ARCH_HSW=On \ - -DKokkos_ENABLE_HWLOC=On \ -DKokkos_HWLOC_DIR=$path_to_hwloc ```` then simply type `make install`. The Kokkos CMake package will then be installed in `$path_to_install` to be used by downstream packages. @@ -212,23 +184,8 @@ where `...` is the unique spec identifying the particular Kokkos configuration a Some more details can found in the Kokkos spack [documentation](Spack.md) or the Spack [website](https://spack.readthedocs.io/en/latest). ## Raw Makefile -A bash script is provided to generate raw makefiles. -To install Kokkos as a library create a build directory and run the following -````bash -> $KOKKOS_PATH/generate_makefile.bash --prefix=$path_to_install -```` -Once the Makefile is generated, run: -````bash -> make kokkoslib -> make install -```` -To additionally run the unit tests: -````bash -> make build-test -> make test -```` -Run `generate_makefile.bash --help` for more detailed options such as -changing the device type for which to build. + +Raw Makefiles are only supported via inline builds. See below. ## Inline Builds vs. Installed Package For individual projects, it may be preferable to build Kokkos inline rather than link to an installed package. @@ -268,6 +225,35 @@ more than a single GPU is used by a single process. If you publish work which mentions Kokkos, please cite the following paper: +````BibTex +@ARTICLE{9485033, + author={Trott, Christian R. and Lebrun-Grandié, Damien and Arndt, Daniel and Ciesko, Jan and Dang, Vinh and Ellingwood, Nathan and Gayatri, Rahulkumar and Harvey, Evan and Hollman, Daisy S. and Ibanez, Dan and Liber, Nevin and Madsen, Jonathan and Miles, Jeff and Poliakoff, David and Powell, Amy and Rajamanickam, Sivasankaran and Simberg, Mikael and Sunderland, Dan and Turcksin, Bruno and Wilke, Jeremiah}, + journal={IEEE Transactions on Parallel and Distributed Systems}, + title={Kokkos 3: Programming Model Extensions for the Exascale Era}, + year={2022}, + volume={33}, + number={4}, + pages={805-817}, + doi={10.1109/TPDS.2021.3097283}} +```` + +If you use more than one Kokkos EcoSystem package, please also cite: + +````BibTex +@ARTICLE{9502936, + author={Trott, Christian and Berger-Vergiat, Luc and Poliakoff, David and Rajamanickam, Sivasankaran and Lebrun-Grandie, Damien and Madsen, Jonathan and Al Awar, Nader and Gligoric, Milos and Shipman, Galen and Womeldorff, Geoff}, + journal={Computing in Science Engineering}, + title={The Kokkos EcoSystem: Comprehensive Performance Portability for High Performance Computing}, + year={2021}, + volume={23}, + number={5}, + pages={10-18}, + doi={10.1109/MCSE.2021.3098509}} +```` + + +And if you feel generous: feel free to cite the original Kokkos paper which describes most of the basic Kokkos concepts: + ````BibTeX @article{CarterEdwards20143202, title = "Kokkos: Enabling manycore performance portability through polymorphic memory access patterns ", diff --git a/packages/kokkos/algorithms/CMakeLists.txt b/packages/kokkos/algorithms/CMakeLists.txt index 4df76a1dbbd1..eb54db8a5564 100644 --- a/packages/kokkos/algorithms/CMakeLists.txt +++ b/packages/kokkos/algorithms/CMakeLists.txt @@ -5,9 +5,7 @@ KOKKOS_SUBPACKAGE(Algorithms) IF (NOT Kokkos_INSTALL_TESTING) ADD_SUBDIRECTORY(src) ENDIF() -IF(NOT (KOKKOS_ENABLE_OPENMPTARGET - AND (KOKKOS_CXX_COMPILER_ID STREQUAL PGI OR - KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC))) +IF(NOT (KOKKOS_ENABLE_OPENMPTARGET AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC)) KOKKOS_ADD_TEST_DIRECTORIES(unit_tests) ENDIF() diff --git a/packages/kokkos/algorithms/src/Kokkos_Random.hpp b/packages/kokkos/algorithms/src/Kokkos_Random.hpp index 55ce19971faf..46b8ab87fabf 100644 --- a/packages/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/packages/kokkos/algorithms/src/Kokkos_Random.hpp @@ -447,6 +447,25 @@ struct rand { } }; +#if defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT +template +struct rand { + using half = Kokkos::Experimental::half_t; + KOKKOS_INLINE_FUNCTION + static half max() { return half(1.0); } + KOKKOS_INLINE_FUNCTION + static half draw(Generator& gen) { return half(gen.frand()); } + KOKKOS_INLINE_FUNCTION + static half draw(Generator& gen, const half& range) { + return half(gen.frand(float(range))); + } + KOKKOS_INLINE_FUNCTION + static half draw(Generator& gen, const half& start, const half& end) { + return half(gen.frand(float(start), float(end))); + } +}; +#endif // defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT + template struct rand { KOKKOS_INLINE_FUNCTION @@ -600,7 +619,7 @@ struct Random_XorShift1024_UseCArrayState template struct Random_UniqueIndex { - using locks_view_type = View; + using locks_view_type = View; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type) { #ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST @@ -615,7 +634,7 @@ struct Random_UniqueIndex { #ifdef KOKKOS_ENABLE_CUDA template <> struct Random_UniqueIndex { - using locks_view_type = View; + using locks_view_type = View; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type& locks_) { #ifdef __CUDA_ARCH__ @@ -625,7 +644,7 @@ struct Random_UniqueIndex { blockDim.x * blockDim.y * blockDim.z + i_offset) % locks_.extent(0); - while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) { + while (Kokkos::atomic_compare_exchange(&locks_(i, 0), 0, 1)) { i += blockDim.x * blockDim.y * blockDim.z; if (i >= static_cast(locks_.extent(0))) { i = i_offset; @@ -643,7 +662,7 @@ struct Random_UniqueIndex { #ifdef KOKKOS_ENABLE_HIP template <> struct Random_UniqueIndex { - using locks_view_type = View; + using locks_view_type = View; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type& locks_) { #ifdef __HIP_DEVICE_COMPILE__ @@ -653,7 +672,7 @@ struct Random_UniqueIndex { blockDim.x * blockDim.y * blockDim.z + i_offset) % locks_.extent(0); - while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) { + while (Kokkos::atomic_compare_exchange(&locks_(i, 0), 0, 1)) { i += blockDim.x * blockDim.y * blockDim.z; if (i >= static_cast(locks_.extent(0))) { i = i_offset; @@ -671,15 +690,15 @@ struct Random_UniqueIndex { #ifdef KOKKOS_ENABLE_SYCL template <> struct Random_UniqueIndex { - using locks_view_type = View; + using locks_view_type = View; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type& locks_) { -#ifdef KOKKOS_ARCH_INTEL_GEN +#ifdef KOKKOS_ARCH_INTEL_GPU int i = Kokkos::Impl::clock_tic() % locks_.extent(0); #else int i = 0; #endif - while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) { + while (Kokkos::atomic_compare_exchange(&locks_(i, 0), 0, 1)) { i = (i + 1) % static_cast(locks_.extent(0)); } return i; @@ -690,14 +709,14 @@ struct Random_UniqueIndex { #ifdef KOKKOS_ENABLE_OPENMPTARGET template <> struct Random_UniqueIndex { - using locks_view_type = View; + using locks_view_type = View; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type& locks) { const int team_size = omp_get_num_threads(); int i = omp_get_team_num() * team_size + omp_get_thread_num(); const int lock_size = locks.extent_int(0); - while (Kokkos::atomic_compare_exchange(&locks(i), 0, 1)) { + while (Kokkos::atomic_compare_exchange(&locks(i, 0), 0, 1)) { i = (i + 1) % lock_size; } return i; @@ -856,18 +875,22 @@ template class Random_XorShift64_Pool { private: using execution_space = typename DeviceType::execution_space; - using locks_type = View; - using state_data_type = View; + using locks_type = View; + using state_data_type = View; locks_type locks_; state_data_type state_; int num_states_; + int padding_; public: using generator_type = Random_XorShift64; using device_type = DeviceType; KOKKOS_INLINE_FUNCTION - Random_XorShift64_Pool() { num_states_ = 0; } + Random_XorShift64_Pool() { + num_states_ = 0; + padding_ = 0; + } Random_XorShift64_Pool(uint64_t seed) { num_states_ = 0; @@ -883,16 +906,22 @@ class Random_XorShift64_Pool { locks_ = src.locks_; state_ = src.state_; num_states_ = src.num_states_; + padding_ = src.padding_; return *this; } void init(uint64_t seed, int num_states) { if (seed == 0) seed = uint64_t(1318319); - + // I only want to pad on CPU like archs (less than 1000 threads). 64 is a + // magic number, or random number I just wanted something not too large and + // not too small. 64 sounded fine. + padding_ = num_states < 1000 ? 64 : 1; num_states_ = num_states; - locks_ = locks_type("Kokkos::Random_XorShift64::locks", num_states_); - state_ = state_data_type("Kokkos::Random_XorShift64::state", num_states_); + locks_ = + locks_type("Kokkos::Random_XorShift64::locks", num_states, padding_); + state_ = state_data_type("Kokkos::Random_XorShift64::state", num_states_, + padding_); typename state_data_type::HostMirror h_state = create_mirror_view(state_); typename locks_type::HostMirror h_lock = create_mirror_view(locks_); @@ -902,15 +931,15 @@ class Random_XorShift64_Pool { gen(seed, 0); for (int i = 0; i < 17; i++) gen.rand(); for (int i = 0; i < num_states_; i++) { - int n1 = gen.rand(); - int n2 = gen.rand(); - int n3 = gen.rand(); - int n4 = gen.rand(); - h_state(i) = (((static_cast(n1)) & 0xffff) << 00) | - (((static_cast(n2)) & 0xffff) << 16) | - (((static_cast(n3)) & 0xffff) << 32) | - (((static_cast(n4)) & 0xffff) << 48); - h_lock(i) = 0; + int n1 = gen.rand(); + int n2 = gen.rand(); + int n3 = gen.rand(); + int n4 = gen.rand(); + h_state(i, 0) = (((static_cast(n1)) & 0xffff) << 00) | + (((static_cast(n2)) & 0xffff) << 16) | + (((static_cast(n3)) & 0xffff) << 32) | + (((static_cast(n4)) & 0xffff) << 48); + h_lock(i, 0) = 0; } deep_copy(state_, h_state); deep_copy(locks_, h_lock); @@ -920,19 +949,19 @@ class Random_XorShift64_Pool { Random_XorShift64 get_state() const { const int i = Impl::Random_UniqueIndex::get_state_idx(locks_); - return Random_XorShift64(state_(i), i); + return Random_XorShift64(state_(i, 0), i); } // NOTE: state_idx MUST be unique and less than num_states KOKKOS_INLINE_FUNCTION Random_XorShift64 get_state(const int state_idx) const { - return Random_XorShift64(state_(state_idx), state_idx); + return Random_XorShift64(state_(state_idx, 0), state_idx); } KOKKOS_INLINE_FUNCTION void free_state(const Random_XorShift64& state) const { - state_(state.state_idx_) = state.state_; - locks_(state.state_idx_) = 0; + state_(state.state_idx_, 0) = state.state_; + locks_(state.state_idx_, 0) = 0; } }; @@ -1092,14 +1121,15 @@ template class Random_XorShift1024_Pool { private: using execution_space = typename DeviceType::execution_space; - using locks_type = View; - using int_view_type = View; + using locks_type = View; + using int_view_type = View; using state_data_type = View; locks_type locks_; state_data_type state_; int_view_type p_; int num_states_; + int padding_; friend class Random_XorShift1024; public: @@ -1129,15 +1159,21 @@ class Random_XorShift1024_Pool { state_ = src.state_; p_ = src.p_; num_states_ = src.num_states_; + padding_ = src.padding_; return *this; } inline void init(uint64_t seed, int num_states) { if (seed == 0) seed = uint64_t(1318319); + // I only want to pad on CPU like archs (less than 1000 threads). 64 is a + // magic number, or random number I just wanted something not too large and + // not too small. 64 sounded fine. + padding_ = num_states < 1000 ? 64 : 1; num_states_ = num_states; - locks_ = locks_type("Kokkos::Random_XorShift1024::locks", num_states_); + locks_ = + locks_type("Kokkos::Random_XorShift1024::locks", num_states_, padding_); state_ = state_data_type("Kokkos::Random_XorShift1024::state", num_states_); - p_ = int_view_type("Kokkos::Random_XorShift1024::p", num_states_); + p_ = int_view_type("Kokkos::Random_XorShift1024::p", num_states_, padding_); typename state_data_type::HostMirror h_state = create_mirror_view(state_); typename locks_type::HostMirror h_lock = create_mirror_view(locks_); @@ -1158,8 +1194,8 @@ class Random_XorShift1024_Pool { (((static_cast(n3)) & 0xffff) << 32) | (((static_cast(n4)) & 0xffff) << 48); } - h_p(i) = 0; - h_lock(i) = 0; + h_p(i, 0) = 0; + h_lock(i, 0) = 0; } deep_copy(state_, h_state); deep_copy(locks_, h_lock); @@ -1169,20 +1205,20 @@ class Random_XorShift1024_Pool { Random_XorShift1024 get_state() const { const int i = Impl::Random_UniqueIndex::get_state_idx(locks_); - return Random_XorShift1024(state_, p_(i), i); + return Random_XorShift1024(state_, p_(i, 0), i); }; // NOTE: state_idx MUST be unique and less than num_states KOKKOS_INLINE_FUNCTION Random_XorShift1024 get_state(const int state_idx) const { - return Random_XorShift1024(state_, p_(state_idx), state_idx); + return Random_XorShift1024(state_, p_(state_idx, 0), state_idx); } KOKKOS_INLINE_FUNCTION void free_state(const Random_XorShift1024& state) const { for (int i = 0; i < 16; i++) state_(state.state_idx_, i) = state.state_[i]; - p_(state.state_idx_) = state.p_; - locks_(state.state_idx_) = 0; + p_(state.state_idx_, 0) = state.p_; + locks_(state.state_idx_, 0) = 0; } }; diff --git a/packages/kokkos/algorithms/src/Kokkos_Sort.hpp b/packages/kokkos/algorithms/src/Kokkos_Sort.hpp index d17c02776ff5..7c1ce4c4cd8e 100644 --- a/packages/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/packages/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -319,7 +319,7 @@ class BinSort { Kokkos::RangePolicy(0, len), functor); } - execution_space().fence(); + execution_space().fence("Kokkos::Sort: fence after sorting"); } template @@ -492,7 +492,8 @@ bool try_std_sort(ViewType view) { view.stride_3(), view.stride_4(), view.stride_5(), view.stride_6(), view.stride_7()}; possible = possible && - std::is_same::value; + SpaceAccessibility::accessible; possible = possible && (ViewType::Rank == 1); possible = possible && (stride[0] == 1); if (possible) { diff --git a/packages/kokkos/algorithms/unit_tests/TestRandom.hpp b/packages/kokkos/algorithms/unit_tests/TestRandom.hpp index c37e779c9927..3dffce7df4f8 100644 --- a/packages/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/packages/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -47,7 +47,7 @@ #include #include #include -#include +#include #include #include #include @@ -198,11 +198,50 @@ struct test_random_functor { static_cast(1.0 * HIST_DIM3D * tmp2 / theMax); const uint64_t ind3_3d = static_cast(1.0 * HIST_DIM3D * tmp3 / theMax); - +// Workaround Intel 17 compiler bug which sometimes add random +// instruction alignment which makes the lock instruction +// illegal. Seems to be mostly just for unsigned int atomics. +// Looking at the assembly the compiler +// appears to insert cache line alignment for the instruction. +// Isn't restricted to specific archs. Seen it on SNB and SKX, but for +// different code. Another occurrence was with Desul atomics in +// a different unit test. This one here happens without desul atomics. +// Inserting an assembly nop instruction changes the alignment and +// works round this. +// +// 17.0.4 for 64bit Random works with 1/1/1/2/1 +// 17.0.4 for 1024bit Random works with 1/1/1/1/1 +#ifdef KOKKOS_COMPILER_INTEL +#if (KOKKOS_COMPILER_INTEL < 1800) + asm volatile("nop\n"); +#endif +#endif atomic_fetch_add(&density_1d(ind1_1d), 1); +#ifdef KOKKOS_COMPILER_INTEL +#if (KOKKOS_COMPILER_INTEL < 1800) + asm volatile("nop\n"); +#endif +#endif atomic_fetch_add(&density_1d(ind2_1d), 1); +#ifdef KOKKOS_COMPILER_INTEL +#if (KOKKOS_COMPILER_INTEL < 1800) + asm volatile("nop\n"); +#endif +#endif atomic_fetch_add(&density_1d(ind3_1d), 1); +#ifdef KOKKOS_COMPILER_INTEL +#if (KOKKOS_COMPILER_INTEL < 1800) + if (std::is_same>::value) + asm volatile("nop\n"); + asm volatile("nop\n"); +#endif +#endif atomic_fetch_add(&density_3d(ind1_3d, ind2_3d, ind3_3d), 1); +#ifdef KOKKOS_COMPILER_INTEL +#if (KOKKOS_COMPILER_INTEL < 1800) + asm volatile("nop\n"); +#endif +#endif } rand_pool.free_state(rand_gen); } @@ -338,9 +377,11 @@ struct test_random_scalar { using functor_type = test_histogram1d_functor; parallel_reduce(HIST_DIM1D, functor_type(density_1d, num_draws), result); - - double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D); - double mean_expect = 1.0 * num_draws * 3 / HIST_DIM1D; + double mean_eps_expect = 0.0001; + double variance_eps_expect = 0.07; + double covariance_eps_expect = 0.06; + double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D); + double mean_expect = 1.0 * num_draws * 3 / HIST_DIM1D; double variance_expect = 1.0 * num_draws * 3 / HIST_DIM1D * (1.0 - 1.0 / HIST_DIM1D); double covariance_expect = -1.0 * num_draws * 3 / HIST_DIM1D / HIST_DIM1D; @@ -349,11 +390,26 @@ struct test_random_scalar { variance_expect / (result.variance / HIST_DIM1D) - 1.0; double covariance_eps = (result.covariance / HIST_DIM1D - covariance_expect) / mean_expect; - pass_hist1d_mean = ((-0.0001 < mean_eps) && (0.0001 > mean_eps)) ? 1 : 0; - pass_hist1d_var = - ((-0.07 < variance_eps) && (0.07 > variance_eps)) ? 1 : 0; - pass_hist1d_covar = - ((-0.06 < covariance_eps) && (0.06 > covariance_eps)) ? 1 : 0; + +#if defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT + if (std::is_same::value) { + mean_eps_expect = 0.0003; + variance_eps_expect = 1.0; + covariance_eps_expect = 5.0e4; + } +#endif + + pass_hist1d_mean = + ((-mean_eps_expect < mean_eps) && (mean_eps_expect > mean_eps)) ? 1 + : 0; + pass_hist1d_var = ((-variance_eps_expect < variance_eps) && + (variance_eps_expect > variance_eps)) + ? 1 + : 0; + pass_hist1d_covar = ((-covariance_eps_expect < covariance_eps) && + (covariance_eps_expect > covariance_eps)) + ? 1 + : 0; cout << "Density 1D: " << mean_eps << " " << variance_eps << " " << (result.covariance / HIST_DIM1D / HIST_DIM1D) << " || " @@ -371,8 +427,9 @@ struct test_random_scalar { test_histogram3d_functor; parallel_reduce(HIST_DIM1D, functor_type(density_3d, num_draws), result); - double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D); - double mean_expect = 1.0 * num_draws / HIST_DIM1D; + double variance_factor = 1.2; + double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D); + double mean_expect = 1.0 * num_draws / HIST_DIM1D; double variance_expect = 1.0 * num_draws / HIST_DIM1D * (1.0 - 1.0 / HIST_DIM1D); double covariance_expect = -1.0 * num_draws / HIST_DIM1D / HIST_DIM1D; @@ -381,15 +438,23 @@ struct test_random_scalar { variance_expect / (result.variance / HIST_DIM1D) - 1.0; double covariance_eps = (result.covariance / HIST_DIM1D - covariance_expect) / mean_expect; + +#if defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT + if (std::is_same::value) { + variance_factor = 7; + } +#endif + pass_hist3d_mean = ((-tolerance < mean_eps) && (tolerance > mean_eps)) ? 1 : 0; - pass_hist3d_var = ((-1.2 * tolerance < variance_eps) && - (1.2 * tolerance > variance_eps)) + pass_hist3d_var = ((-variance_factor * tolerance < variance_eps) && + (variance_factor * tolerance > variance_eps)) ? 1 : 0; - pass_hist3d_covar = - ((-tolerance < covariance_eps) && (tolerance > covariance_eps)) ? 1 - : 0; + pass_hist3d_covar = ((-variance_factor * tolerance < covariance_eps) && + (variance_factor * tolerance > covariance_eps)) + ? 1 + : 0; cout << "Density 3D: " << mean_eps << " " << variance_eps << " " << result.covariance / HIST_DIM1D / HIST_DIM1D << " || " << tolerance @@ -471,6 +536,21 @@ void test_random(unsigned int num_draws) { deep_copy(density_1d, 0); deep_copy(density_3d, 0); + cout << "Test Scalar=half" << endl; + test_random_scalar test_half( + density_1d, density_3d, pool, num_draws); + ASSERT_EQ(test_half.pass_mean, 1); + ASSERT_EQ(test_half.pass_var, 1); + ASSERT_EQ(test_half.pass_covar, 1); + ASSERT_EQ(test_half.pass_hist1d_mean, 1); + ASSERT_EQ(test_half.pass_hist1d_var, 1); + ASSERT_EQ(test_half.pass_hist1d_covar, 1); + ASSERT_EQ(test_half.pass_hist3d_mean, 1); + ASSERT_EQ(test_half.pass_hist3d_var, 1); + ASSERT_EQ(test_half.pass_hist3d_covar, 1); + deep_copy(density_1d, 0); + deep_copy(density_3d, 0); + cout << "Test Scalar=float" << endl; test_random_scalar test_float(density_1d, density_3d, pool, num_draws); diff --git a/packages/kokkos/appveyor.yml b/packages/kokkos/appveyor.yml index e8763c0b665c..73a0d3187596 100644 --- a/packages/kokkos/appveyor.yml +++ b/packages/kokkos/appveyor.yml @@ -3,4 +3,8 @@ image: clone_folder: c:\projects\source build_script: - cmd: >- - cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON -DCMAKE_CXX_FLAGS="/W0 /EHsc /d1reportClassLayoutChanges" -DCTEST_ARGS="-C Debug -V --output-on-failure" -DBUILD_NAME=MSVC-2019 -DBUILD_TYPE=Debug -DSITE=AppVeyor -DTARGET=install -P cmake/KokkosCI.cmake + mkdir build && + cd build && + cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON -DCMAKE_CXX_FLAGS="/W0 /EHsc" -DKokkos_ENABLE_DEPRECATED_CODE_3=ON -DKokkos_ENABLE_DEPRECATION_WARNINGS=OFF && + cmake --build . --target install && + ctest -C Debug --output-on-failure diff --git a/packages/kokkos/benchmarks/atomic/main.cpp b/packages/kokkos/benchmarks/atomic/main.cpp index 7b5caa1aee16..cc0d3e41e85a 100644 --- a/packages/kokkos/benchmarks/atomic/main.cpp +++ b/packages/kokkos/benchmarks/atomic/main.cpp @@ -1,12 +1,12 @@ #include -#include +#include #include template double test_atomic(int L, int N, int M, int K, int R, Kokkos::View offsets) { Kokkos::View output("Output", N); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int r = 0; r < R; r++) Kokkos::parallel_for( @@ -28,7 +28,7 @@ template double test_no_atomic(int L, int N, int M, int K, int R, Kokkos::View offsets) { Kokkos::View output("Output", N); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; for (int r = 0; r < R; r++) Kokkos::parallel_for( L, KOKKOS_LAMBDA(const int& i) { diff --git a/packages/kokkos/benchmarks/bytes_and_flops/bench.hpp b/packages/kokkos/benchmarks/bytes_and_flops/bench.hpp index 62d7ef4a4cf3..4fc6ca2c68b3 100644 --- a/packages/kokkos/benchmarks/bytes_and_flops/bench.hpp +++ b/packages/kokkos/benchmarks/bytes_and_flops/bench.hpp @@ -43,7 +43,7 @@ */ #include -#include +#include template struct Run { diff --git a/packages/kokkos/benchmarks/bytes_and_flops/main.cpp b/packages/kokkos/benchmarks/bytes_and_flops/main.cpp index 6da2407a08b7..75f30a340938 100644 --- a/packages/kokkos/benchmarks/bytes_and_flops/main.cpp +++ b/packages/kokkos/benchmarks/bytes_and_flops/main.cpp @@ -43,7 +43,7 @@ */ #include -#include +#include #include #include diff --git a/packages/kokkos/benchmarks/gather/main.cpp b/packages/kokkos/benchmarks/gather/main.cpp index 5f10e4dcc1aa..dd502faaa480 100644 --- a/packages/kokkos/benchmarks/gather/main.cpp +++ b/packages/kokkos/benchmarks/gather/main.cpp @@ -43,7 +43,7 @@ */ #include -#include +#include #include #include diff --git a/packages/kokkos/benchmarks/stream/stream-kokkos.cpp b/packages/kokkos/benchmarks/stream/stream-kokkos.cpp index e7ef67e0805c..311947c197cb 100644 --- a/packages/kokkos/benchmarks/stream/stream-kokkos.cpp +++ b/packages/kokkos/benchmarks/stream/stream-kokkos.cpp @@ -52,35 +52,33 @@ #define HLINE "-------------------------------------------------------------\n" -#if defined(KOKKOS_ENABLE_CUDA) -using StreamHostArray = Kokkos::View::HostMirror; -using StreamDeviceArray = Kokkos::View; -#else -using StreamHostArray = Kokkos::View::HostMirror; -using StreamDeviceArray = Kokkos::View; -#endif +using StreamDeviceArray = + Kokkos::View>; +using StreamHostArray = typename StreamDeviceArray::HostMirror; using StreamIndex = int; +using Policy = Kokkos::RangePolicy>; -double now() { - struct timeval now; - gettimeofday(&now, nullptr); +void perform_set(StreamDeviceArray& a, const double scalar) { + Kokkos::parallel_for( + "set", Policy(0, a.extent(0)), + KOKKOS_LAMBDA(const StreamIndex i) { a[i] = scalar; }); - return (double)now.tv_sec + ((double)now.tv_usec * 1.0e-6); + Kokkos::fence(); } -void perform_copy(StreamDeviceArray& a, StreamDeviceArray& b, - StreamDeviceArray& c) { +void perform_copy(StreamDeviceArray& a, StreamDeviceArray& b) { Kokkos::parallel_for( - "copy", a.extent(0), KOKKOS_LAMBDA(const StreamIndex i) { c[i] = a[i]; }); + "copy", Policy(0, a.extent(0)), + KOKKOS_LAMBDA(const StreamIndex i) { b[i] = a[i]; }); Kokkos::fence(); } -void perform_scale(StreamDeviceArray& a, StreamDeviceArray& b, - StreamDeviceArray& c, const double scalar) { +void perform_scale(StreamDeviceArray& b, StreamDeviceArray& c, + const double scalar) { Kokkos::parallel_for( - "copy", a.extent(0), + "scale", Policy(0, b.extent(0)), KOKKOS_LAMBDA(const StreamIndex i) { b[i] = scalar * c[i]; }); Kokkos::fence(); @@ -89,7 +87,7 @@ void perform_scale(StreamDeviceArray& a, StreamDeviceArray& b, void perform_add(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c) { Kokkos::parallel_for( - "add", a.extent(0), + "add", Policy(0, a.extent(0)), KOKKOS_LAMBDA(const StreamIndex i) { c[i] = a[i] + b[i]; }); Kokkos::fence(); @@ -98,7 +96,7 @@ void perform_add(StreamDeviceArray& a, StreamDeviceArray& b, void perform_triad(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c, const double scalar) { Kokkos::parallel_for( - "triad", a.extent(0), + "triad", Policy(0, a.extent(0)), KOKKOS_LAMBDA(const StreamIndex i) { a[i] = b[i] + scalar * c[i]; }); Kokkos::fence(); @@ -184,6 +182,7 @@ int run_benchmark() { const double scalar = 3.0; + double setTime = std::numeric_limits::max(); double copyTime = std::numeric_limits::max(); double scaleTime = std::numeric_limits::max(); double addTime = std::numeric_limits::max(); @@ -191,13 +190,10 @@ int run_benchmark() { printf("Initializing Views...\n"); -#if defined(KOKKOS_HAVE_OPENMP) - Kokkos::parallel_for( - "init", Kokkos::RangePolicy(0, STREAM_ARRAY_SIZE), -#else Kokkos::parallel_for( - "init", Kokkos::RangePolicy(0, STREAM_ARRAY_SIZE), -#endif + "init", + Kokkos::RangePolicy(0, + STREAM_ARRAY_SIZE), KOKKOS_LAMBDA(const int i) { a[i] = 1.0; b[i] = 2.0; @@ -209,26 +205,30 @@ int run_benchmark() { Kokkos::deep_copy(dev_b, b); Kokkos::deep_copy(dev_c, c); - double start; - printf("Starting benchmarking...\n"); + Kokkos::Timer timer; + for (StreamIndex k = 0; k < STREAM_NTIMES; ++k) { - start = now(); - perform_copy(dev_a, dev_b, dev_c); - copyTime = std::min(copyTime, (now() - start)); + timer.reset(); + perform_set(dev_c, 1.5); + setTime = std::min(setTime, timer.seconds()); + + timer.reset(); + perform_copy(dev_a, dev_c); + copyTime = std::min(copyTime, timer.seconds()); - start = now(); - perform_scale(dev_a, dev_b, dev_c, scalar); - scaleTime = std::min(scaleTime, (now() - start)); + timer.reset(); + perform_scale(dev_b, dev_c, scalar); + scaleTime = std::min(scaleTime, timer.seconds()); - start = now(); + timer.reset(); perform_add(dev_a, dev_b, dev_c); - addTime = std::min(addTime, (now() - start)); + addTime = std::min(addTime, timer.seconds()); - start = now(); + timer.reset(); perform_triad(dev_a, dev_b, dev_c, scalar); - triadTime = std::min(triadTime, (now() - start)); + triadTime = std::min(triadTime, timer.seconds()); } Kokkos::deep_copy(a, dev_a); @@ -240,6 +240,9 @@ int run_benchmark() { printf(HLINE); + printf("Set %11.2f MB/s\n", + (1.0e-06 * 1.0 * (double)sizeof(double) * (double)STREAM_ARRAY_SIZE) / + setTime); printf("Copy %11.2f MB/s\n", (1.0e-06 * 2.0 * (double)sizeof(double) * (double)STREAM_ARRAY_SIZE) / copyTime); diff --git a/packages/kokkos/bin/hpcbind b/packages/kokkos/bin/hpcbind index 6af091a7d8b6..43f8a745da27 100755 --- a/packages/kokkos/bin/hpcbind +++ b/packages/kokkos/bin/hpcbind @@ -634,15 +634,15 @@ elif [[ ${HPCBIND_HAS_COMMAND} -eq 1 ]]; then > ${HPCBIND_OUT} if [[ ${HPCBIND_TEE} -eq 0 ]]; then if [[ ${HPCBIND_ENABLE_HWLOC_BIND} -eq 1 ]]; then - hwloc-bind "${HPCBIND_HWLOC_CPUSET}" -- $@ > ${HPCBIND_OUT} 2> ${HPCBIND_ERR} + hwloc-bind "${HPCBIND_HWLOC_CPUSET}" -- "$@" > ${HPCBIND_OUT} 2> ${HPCBIND_ERR} else - eval $@ > ${HPCBIND_OUT} 2> ${HPCBIND_ERR} + eval "$@" > ${HPCBIND_OUT} 2> ${HPCBIND_ERR} fi else if [[ ${HPCBIND_ENABLE_HWLOC_BIND} -eq 1 ]]; then - hwloc-bind "${HPCBIND_HWLOC_CPUSET}" -- $@ > >(tee ${HPCBIND_OUT}) 2> >(tee ${HPCBIND_ERR} >&2) + hwloc-bind "${HPCBIND_HWLOC_CPUSET}" -- "$@" > >(tee ${HPCBIND_OUT}) 2> >(tee ${HPCBIND_ERR} >&2) else - eval $@ > >(tee ${HPCBIND_OUT}) 2> >(tee ${HPCBIND_ERR} >&2) + eval "$@" > >(tee ${HPCBIND_OUT}) 2> >(tee ${HPCBIND_ERR} >&2) fi fi fi diff --git a/packages/kokkos/bin/nvcc_wrapper b/packages/kokkos/bin/nvcc_wrapper index 4e52e4d09f4f..ba2c55508aca 100755 --- a/packages/kokkos/bin/nvcc_wrapper +++ b/packages/kokkos/bin/nvcc_wrapper @@ -96,7 +96,7 @@ replace_pragma_ident=0 first_xcompiler_arg=1 # Allow for setting temp dir without setting TMPDIR in parent (see https://docs.olcf.ornl.gov/systems/summit_user_guide.html#setting-tmpdir-causes-jsm-jsrun-errors-job-state-flip-flop) -if [[ ! -z ${NVCC_WRAPPER_TMPDIR+x} ]]; then +if [[ -z ${NVCC_WRAPPER_TMPDIR+x} ]]; then temp_dir=${TMPDIR:-/tmp} else temp_dir=${NVCC_WRAPPER_TMPDIR+x} @@ -226,14 +226,14 @@ do cuda_args="$cuda_args $1" ;; #Handle more known nvcc args - --expt-extended-lambda|--expt-relaxed-constexpr|--Wno-deprecated-gpu-targets|-Wno-deprecated-gpu-targets) + --expt-extended-lambda|--expt-relaxed-constexpr|--Wno-deprecated-gpu-targets|-Wno-deprecated-gpu-targets|-allow-unsupported-compiler|--allow-unsupported-compiler) cuda_args="$cuda_args $1" ;; #Handle known nvcc args that have an argument - -maxrregcount=*|--maxrregcount=*) + -maxrregcount=*|--maxrregcount=*|-time=*) cuda_args="$cuda_args $1" ;; - -maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include) + -maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include|-time) cuda_args="$cuda_args $1 $2" shift ;; @@ -552,14 +552,14 @@ if [ $host_only -eq 1 ]; then $host_command elif [ -n "$nvcc_depfile_command" ]; then if [ "$NVCC_WRAPPER_SHOW_COMMANDS_BEING_RUN" == "1" ] ; then - echo "$nvcc_command && $nvcc_depfile_command" + echo "TMPDIR=${temp_dir} $nvcc_command && TMPDIR=${temp_dir} $nvcc_depfile_command" fi - $nvcc_command && $nvcc_depfile_command + TMPDIR=${temp_dir} $nvcc_command && TMPDIR=${temp_dir} $nvcc_depfile_command else if [ "$NVCC_WRAPPER_SHOW_COMMANDS_BEING_RUN" == "1" ] ; then - echo "$nvcc_command" + echo "TMPDIR=${temp_dir} $nvcc_command" fi - $nvcc_command + TMPDIR=${temp_dir} $nvcc_command fi error_code=$? diff --git a/packages/kokkos/cmake/CTestConfig.cmake.in b/packages/kokkos/cmake/CTestConfig.cmake.in deleted file mode 100644 index 1f82c0d64d15..000000000000 --- a/packages/kokkos/cmake/CTestConfig.cmake.in +++ /dev/null @@ -1,91 +0,0 @@ -#----------------------------------------------------------------------------------------# -# -# CTestConfig.cmake template for Kokkos -# -#----------------------------------------------------------------------------------------# - -# -# dash-board related -# -set(CTEST_PROJECT_NAME "Kokkos") -set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC") -set(CTEST_DROP_METHOD "https") -set(CTEST_DROP_SITE "cdash.nersc.gov") -set(CTEST_DROP_LOCATION "/submit.php?project=${CTEST_PROJECT_NAME}") -set(CTEST_CDASH_VERSION "1.6") -set(CTEST_CDASH_QUERY_VERSION TRUE) -set(CTEST_SUBMIT_RETRY_COUNT "1") -set(CTEST_SUBMIT_RETRY_DELAY "30") - -# -# configure/build related -# -set(CTEST_BUILD_NAME "@BUILD_NAME@") -set(CTEST_MODEL "@MODEL@") -set(CTEST_SITE "@SITE@") -set(CTEST_CONFIGURATION_TYPE "@BUILD_TYPE@") -set(CTEST_SOURCE_DIRECTORY "@SOURCE_REALDIR@") -set(CTEST_BINARY_DIRECTORY "@BINARY_REALDIR@") - -# -# configure/build related -# -set(CTEST_UPDATE_TYPE "git") -set(CTEST_UPDATE_VERSION_ONLY ON) -# set(CTEST_GENERATOR "") -# set(CTEST_GENERATOR_PLATFORM "") - -# -# testing related -# -set(CTEST_TIMEOUT "7200") -set(CTEST_TEST_TIMEOUT "7200") -set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_ERRORS "100") -set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS "100") -set(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "1048576") - -# -# coverage related -# -set(CTEST_CUSTOM_COVERAGE_EXCLUDE ".*tpls/.*;/usr/.*;.*unit_test/.*;.*unit_tests/.*;.*perf_test/.*") - -# -# commands -# -if(NOT "@CHECKOUT_COMMAND@" STREQUAL "") - set(CTEST_CHECKOUT_COMMAND "@CHECKOUT_COMMAND@") -endif() -set(CTEST_UPDATE_COMMAND "@GIT_EXECUTABLE@") -set(CTEST_CONFIGURE_COMMAND "@CMAKE_COMMAND@ -DCMAKE_BUILD_TYPE=@BUILD_TYPE@ -DKokkos_ENABLE_TESTS=ON @CONFIG_ARGS@ @SOURCE_REALDIR@") -set(CTEST_BUILD_COMMAND "@CMAKE_COMMAND@ --build @BINARY_REALDIR@ --target @TARGET@") -if(NOT WIN32) - set(CTEST_BUILD_COMMAND "${CTEST_BUILD_COMMAND} -- -j@BUILD_JOBS@") -endif() -set(CTEST_COVERAGE_COMMAND "gcov") -set(CTEST_MEMORYCHECK_COMMAND "valgrind") -set(CTEST_GIT_COMMAND "@GIT_EXECUTABLE@") - -# -# various configs -# -set(APPEND_VALUE @APPEND@) -if(APPEND_VALUE) - set(APPEND_CTEST APPEND) -endif() - -macro(SET_TEST_PROP VAR) - if(NOT "${ARGS}" STREQUAL "") - set(${VAR}_CTEST ${VAR} ${ARGN}) - endif() -endmacro() - -set_test_prop(START @START@) -set_test_prop(END @END@) -set_test_prop(STRIDE @STRIDE@) -set_test_prop(INCLUDE @INCLUDE@) -set_test_prop(EXCLUDE @EXCLUDE@) -set_test_prop(INCLUDE_LABEL @INCLUDE_LABEL@) -set_test_prop(EXCLUDE_LABEL @EXCLUDE_LABEL@) -set_test_prop(PARALLEL_LEVEL @PARALLEL_LEVEL@) -set_test_prop(STOP_TIME @STOP_TIME@) -set_test_prop(COVERAGE_LABELS @LABELS@) diff --git a/packages/kokkos/cmake/KokkosCI.cmake b/packages/kokkos/cmake/KokkosCI.cmake deleted file mode 100644 index e8c9af37ad54..000000000000 --- a/packages/kokkos/cmake/KokkosCI.cmake +++ /dev/null @@ -1,350 +0,0 @@ -cmake_minimum_required(VERSION 3.16 FATAL_ERROR) - -message(STATUS "") - -get_cmake_property(_cached_vars CACHE_VARIABLES) -set(KOKKOS_CMAKE_ARGS) -set(EXCLUDED_VARIABLES "CMAKE_COMMAND" "CMAKE_CPACK_COMMAND" "CMAKE_CTEST_COMMAND" "CMAKE_ROOT" - "CTEST_ARGS" "BUILD_NAME" "CMAKE_CXX_FLAGS" "CMAKE_BUILD_TYPE") -list(SORT _cached_vars) -foreach(_var ${_cached_vars}) - if(NOT "${_var}" IN_LIST EXCLUDED_VARIABLES) - list(APPEND KOKKOS_CMAKE_ARGS ${_var}) - if("${_var}" STREQUAL "CMAKE_BUILD_TYPE") - set(BUILD_TYPE "${CMAKE_BUILD_TYPE}") - endif() - endif() -endforeach() - - -#----------------------------------------------------------------------------------------# -# -# Macros and variables -# -#----------------------------------------------------------------------------------------# - -macro(CHECK_REQUIRED VAR) - if(NOT DEFINED ${VAR}) - message(FATAL_ERROR "Error! Variable '${VAR}' must be defined") - endif() -endmacro() - -# require the build name variable -CHECK_REQUIRED(BUILD_NAME) - -# uses all args -macro(SET_DEFAULT VAR) - if(NOT DEFINED ${VAR}) - set(${VAR} ${ARGN}) - endif() - # remove these ctest configuration variables from the defines - # passed to the Kokkos configuration - if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) - list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") - endif() -endmacro() - -# uses first arg -- useful for selecting via priority from multiple -# potentially defined variables, e.g.: -# -# set_default_arg1(BUILD_NAME ${TRAVIS_BUILD_NAME} ${BUILD_NAME}) -# -macro(SET_DEFAULT_ARG1 VAR) - if(NOT DEFINED ${VAR}) - foreach(_ARG ${ARGN}) - if(NOT "${_ARG}" STREQUAL "") - set(${VAR} ${_ARG}) - break() - endif() - endforeach() - endif() - # remove these ctest configuration variables from the defines - # passed to the Kokkos configuration - if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) - list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") - endif() -endmacro() - -# determine the default working directory -if(NOT "$ENV{WORKSPACE}" STREQUAL "") - set(WORKING_DIR "$ENV{WORKSPACE}") -else() - get_filename_component(WORKING_DIR ${CMAKE_CURRENT_LIST_DIR} DIRECTORY) -endif() - -# determine the hostname -execute_process(COMMAND hostname - OUTPUT_VARIABLE HOSTNAME - OUTPUT_STRIP_TRAILING_WHITESPACE) - -SET_DEFAULT(HOSTNAME "$ENV{HOSTNAME}") - -# get the number of processors -include(ProcessorCount) -ProcessorCount(NUM_PROCESSORS) - -# find git -find_package(Git QUIET) -if(NOT GIT_EXECUTABLE) - unset(GIT_EXECUTABLE CACHE) - unset(GIT_EXECUTABLE) -endif() - -function(EXECUTE_GIT_COMMAND VAR) - set(${VAR} "" PARENT_SCOPE) - execute_process(COMMAND ${GIT_EXECUTABLE} ${ARGN} - OUTPUT_VARIABLE VAL - RESULT_VARIABLE RET - OUTPUT_STRIP_TRAILING_WHITESPACE - WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} - ERROR_QUIET) - string(REPLACE ";" " " _CMD "${GIT_EXECUTABLE} ${ARGN}") - set(LAST_GIT_COMMAND "${_CMD}" PARENT_SCOPE) - if(RET EQUAL 0) - set(${VAR} "${VAL}" PARENT_SCOPE) - endif() -endfunction() - -# just gets the git branch name if available -function(GET_GIT_BRANCH_NAME VAR) - execute_git_command(GIT_BRANCH branch --show-current) - set(_INVALID "%D" "HEAD") - if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) - execute_git_command(GIT_BRANCH show -s --format=%D) - if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) - execute_git_command(GIT_BRANCH --describe all) - endif() - endif() - # - if(GIT_BRANCH) - string(REPLACE " " ";" _DESC "${GIT_BRANCH}") - # just set it to last one via loop instead of wonky cmake index manip - foreach(_ITR ${_DESC}) - set(GIT_BRANCH "${_ITR}") - endforeach() - set(${VAR} "${GIT_BRANCH}" PARENT_SCOPE) - message(STATUS "GIT BRANCH via '${LAST_GIT_COMMAND}': ${GIT_BRANCH}") - endif() -endfunction() - -# just gets the git branch name if available -function(GET_GIT_AUTHOR_NAME VAR) - execute_git_command(GIT_AUTHOR show -s --format=%an) - if(GIT_AUTHOR) - string(LENGTH "${GIT_AUTHOR}" STRLEN) - # if the build name gets too long, this can cause submission errors - if(STRLEN GREATER 24) - # remove middle initial - string(REGEX REPLACE " [A-Z]\. " " " GIT_AUTHOR "${GIT_AUTHOR}") - # get first and sur name - string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\1" F_NAME "${GIT_AUTHOR}") - string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\2" S_NAME "${GIT_AUTHOR}") - if(S_NAME) - set(GIT_AUTHOR "${S_NAME}") - elseif(F_NAME) - set(GIT_AUTHOR "${F_NAME}") - endif() - endif() - # remove any spaces, quotes, periods, etc. - string(REGEX REPLACE "[ ',;_\.\"]+" "" GIT_AUTHOR "${GIT_AUTHOR}") - set(${VAR} "${GIT_AUTHOR}" PARENT_SCOPE) - message(STATUS "GIT AUTHOR via '${LAST_GIT_COMMAND}': ${GIT_AUTHOR}") - endif() -endfunction() - -# get the name of the branch -GET_GIT_BRANCH_NAME(GIT_BRANCH) -# get the name of the author -GET_GIT_AUTHOR_NAME(GIT_AUTHOR) -# author, prefer git method for consistency -SET_DEFAULT_ARG1(AUTHOR ${GIT_AUTHOR} $ENV{GIT_AUTHOR} $ENV{AUTHOR}) -# SLUG == owner_name/repo_name -SET_DEFAULT_ARG1(SLUG $ENV{TRAVIS_PULL_REQUEST_SLUG} $ENV{TRAVIS_REPO_SLUG} $ENV{APPVEYOR_REPO_NAME} $ENV{PULL_REQUEST_SLUG} $ENV{REPO_SLUG}) -# branch name -SET_DEFAULT_ARG1(BRANCH $ENV{TRAVIS_PULL_REQUEST_BRANCH} $ENV{TRAVIS_BRANCH} $ENV{APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH} $ENV{APPVEYOR_REPO_BRANCH} $ENV{GIT_BRANCH} $ENV{BRANCH_NAME} $ENV{BRANCH} ${GIT_BRANCH}) -# pull request number -SET_DEFAULT_ARG1(PULL_REQUEST_NUM $ENV{TRAVIS_PULL_REQUEST} $ENV{CHANGE_ID} $ENV{APPVEYOR_PULL_REQUEST_NUMBER} $ENV{PULL_REQUEST_NUM}) -# get the event type, e.g. push, pull_request, api, cron, etc. -SET_DEFAULT_ARG1(EVENT_TYPE $ENV{TRAVIS_EVENT_TYPE} ${EVENT_TYPE}) - -if("${BRANCH}" STREQUAL "") - message(STATUS "Checked: environment variables for Travis, Appveyor, Jenkins (git plugin), BRANCH_NAME, BRANCH and 'git branch --show-current'") - message(FATAL_ERROR "Error! Git branch could not be determined. Please provide -DBRANCH=") -endif() - -#----------------------------------------------------------------------------------------# -# -# Set default values if not provided on command-line -# -#----------------------------------------------------------------------------------------# - -SET_DEFAULT(SOURCE_DIR "${WORKING_DIR}") # source directory -SET_DEFAULT(BINARY_DIR "${WORKING_DIR}/build") # build directory -SET_DEFAULT(BUILD_TYPE "${CMAKE_BUILD_TYPE}") # Release, Debug, etc. -SET_DEFAULT(MODEL "Continuous") # Continuous, Nightly, or Experimental -SET_DEFAULT(JOBS 1) # number of parallel ctests -SET_DEFAULT(CTEST_COMMAND "${CMAKE_CTEST_COMMAND}") # just in case -SET_DEFAULT(CTEST_ARGS "-V --output-on-failure") # extra arguments when ctest is called -SET_DEFAULT(GIT_EXECUTABLE "git") # ctest_update -SET_DEFAULT(TARGET "all") # build target -SET_DEFAULT_ARG1(SITE "$ENV{SITE}" - "${HOSTNAME}") # update site -SET_DEFAULT_ARG1(BUILD_JOBS "$ENV{BUILD_JOBS}" - "${NUM_PROCESSORS}") # number of parallel compile jobs -# -# The variable below correspond to ctest arguments, i.e. START,END,STRIDE are -# '-I START,END,STRIDE' -# -SET_DEFAULT(START "") -SET_DEFAULT(END "") -SET_DEFAULT(STRIDE "") -SET_DEFAULT(INCLUDE "") -SET_DEFAULT(EXCLUDE "") -SET_DEFAULT(INCLUDE_LABEL "") -SET_DEFAULT(EXCLUDE_LABEL "") -SET_DEFAULT(PARALLEL_LEVEL "") -SET_DEFAULT(STOP_TIME "") -SET_DEFAULT(LABELS "") -SET_DEFAULT(NOTES "") - -# default static build tag for Nightly -set(BUILD_TAG "${BRANCH}") - -if(NOT BUILD_TYPE) - # default for kokkos if not specified - set(BUILD_TYPE "RelWithDebInfo") -endif() - -# generate dynamic name if continuous or experimental model -if(NOT "${MODEL}" STREQUAL "Nightly") - if(EVENT_TYPE AND PULL_REQUEST_NUM) - # e.g. pull_request/123 - if(AUTHOR) - set(BUILD_TAG "${AUTHOR}/${EVENT_TYPE}/${PULL_REQUEST_NUM}") - else() - set(BUILD_TAG "${EVENT_TYPE}/${PULL_REQUEST_NUM}") - endif() - elseif(SLUG) - # e.g. owner_name/repo_name - set(BUILD_TAG "${SLUG}") - elseif(AUTHOR) - set(BUILD_TAG "${AUTHOR}/${BRANCH}") - endif() - if(EVENT_TYPE AND NOT PULL_REQUEST_NUM) - set(BUILD_TAG "${BUILD_TAG}-${EVENT_TYPE}") - endif() -endif() - -# unnecessary -string(REPLACE "/remotes/" "/" BUILD_TAG "${BUILD_TAG}") -string(REPLACE "/origin/" "/" BUILD_TAG "${BUILD_TAG}") - -message(STATUS "BUILD_TAG: ${BUILD_TAG}") - -set(BUILD_NAME "[${BUILD_TAG}] [${BUILD_NAME}-${BUILD_TYPE}]") - -# colons in build name create extra (empty) entries in CDash -string(REPLACE ":" "-" BUILD_NAME "${BUILD_NAME}") -# unnecessary info -string(REPLACE "/merge]" "]" BUILD_NAME "${BUILD_NAME}") -# consistency -string(REPLACE "/pr/" "/pull/" BUILD_NAME "${BUILD_NAME}") -string(REPLACE "pull_request/" "pull/" BUILD_NAME "${BUILD_NAME}") -# miscellaneous from missing fields -string(REPLACE "--" "-" BUILD_NAME "${BUILD_NAME}") -string(REPLACE "-]" "]" BUILD_NAME "${BUILD_NAME}") - -# check binary directory -if(EXISTS ${BINARY_DIR}) - if(NOT IS_DIRECTORY "${BINARY_DIR}") - message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not a directory!") - endif() - file(GLOB BINARY_DIR_FILES "${BINARY_DIR}/*") - if(NOT "${BINARY_DIR_FILES}" STREQUAL "") - message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not empty!") - endif() -endif() - -get_filename_component(SOURCE_REALDIR ${SOURCE_DIR} REALPATH) -get_filename_component(BINARY_REALDIR ${BINARY_DIR} REALPATH) - -#----------------------------------------------------------------------------------------# -# -# Generate the CTestConfig.cmake -# -#----------------------------------------------------------------------------------------# - -set(CONFIG_ARGS) -foreach(_ARG ${KOKKOS_CMAKE_ARGS}) - if(NOT "${${_ARG}}" STREQUAL "") - get_property(_ARG_TYPE CACHE ${_ARG} PROPERTY TYPE) - if("${_ARG_TYPE}" STREQUAL "UNINITIALIZED") - if("${${_ARG}}" STREQUAL "ON" OR "${${_ARG}}" STREQUAL "OFF") - set(_ARG_TYPE "BOOL") - elseif(EXISTS "${${_ARG}}" AND NOT IS_DIRECTORY "${${_ARG}}") - set(_ARG_TYPE "FILEPATH") - elseif(EXISTS "${${_ARG}}" AND IS_DIRECTORY "${${_ARG}}") - set(_ARG_TYPE "PATH") - elseif(NOT "${${_ARG}}" STREQUAL "") - set(_ARG_TYPE "STRING") - endif() - endif() - set(CONFIG_ARGS "${CONFIG_ARGS}set(${_ARG} \"${${_ARG}}\" CACHE ${_ARG_TYPE} \"\")\n") - endif() -endforeach() - -file(WRITE ${BINARY_REALDIR}/initial-cache.cmake -" -set(CMAKE_CXX_FLAGS \"${CMAKE_CXX_FLAGS}\" CACHE STRING \"\") -${CONFIG_ARGS} -") - -file(READ ${BINARY_REALDIR}/initial-cache.cmake _CACHE_INFO) -message(STATUS "Initial cache:\n${_CACHE_INFO}") - -# initialize the cache -set(CONFIG_ARGS "-C ${BINARY_REALDIR}/initial-cache.cmake") - - -# generate the CTestConfig.cmake -configure_file( - ${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake.in - ${BINARY_REALDIR}/CTestConfig.cmake - @ONLY) - -# copy/generate the dashboard script -configure_file( - ${CMAKE_CURRENT_LIST_DIR}/KokkosCTest.cmake.in - ${BINARY_REALDIR}/KokkosCTest.cmake - @ONLY) - -# custom CTest settings go in ${BINARY_DIR}/CTestCustom.cmake -execute_process( - COMMAND ${CMAKE_COMMAND} -E touch CTestCustom.cmake - WORKING_DIRECTORY ${BINARY_REALDIR} - ) - -#----------------------------------------------------------------------------------------# -# -# Execute CTest -# -#----------------------------------------------------------------------------------------# - -message(STATUS "") -message(STATUS "BUILD_NAME: ${BUILD_NAME}") -message(STATUS "Executing '${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS}'...") -message(STATUS "") - -# e.g. -DCTEST_ARGS="--output-on-failure -VV" should really be -DCTEST_ARGS="--output-on-failure;-VV" -string(REPLACE " " ";" CTEST_ARGS "${CTEST_ARGS}") - -execute_process( - COMMAND ${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS} - RESULT_VARIABLE RET - WORKING_DIRECTORY ${BINARY_REALDIR} - ) - -# ensure that any non-zero result variable gets propagated -if(NOT RET EQUAL 0) - message(FATAL_ERROR "CTest return non-zero exit code: ${RET}") -endif() diff --git a/packages/kokkos/cmake/KokkosCTest.cmake.in b/packages/kokkos/cmake/KokkosCTest.cmake.in deleted file mode 100644 index b6917f3cc189..000000000000 --- a/packages/kokkos/cmake/KokkosCTest.cmake.in +++ /dev/null @@ -1,261 +0,0 @@ -cmake_minimum_required(VERSION 3.16 FATAL_ERROR) - -if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") - include("${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") -endif() - -include(ProcessorCount) -ProcessorCount(CTEST_PROCESSOR_COUNT) - -cmake_policy(SET CMP0009 NEW) -cmake_policy(SET CMP0011 NEW) - -# ---------------------------------------------------------------------------- # -# -- Commands -# ---------------------------------------------------------------------------- # -find_program(CTEST_CMAKE_COMMAND NAMES cmake) -find_program(CTEST_UNAME_COMMAND NAMES uname) - -find_program(CTEST_BZR_COMMAND NAMES bzr) -find_program(CTEST_CVS_COMMAND NAMES cvs) -find_program(CTEST_GIT_COMMAND NAMES git) -find_program(CTEST_HG_COMMAND NAMES hg) -find_program(CTEST_P4_COMMAND NAMES p4) -find_program(CTEST_SVN_COMMAND NAMES svn) - -find_program(VALGRIND_COMMAND NAMES valgrind) -find_program(GCOV_COMMAND NAMES gcov) -find_program(LCOV_COMMAND NAMES llvm-cov) -find_program(MEMORYCHECK_COMMAND NAMES valgrind ) - -set(MEMORYCHECK_TYPE Valgrind) -# set(MEMORYCHECK_TYPE Purify) -# set(MEMORYCHECK_TYPE BoundsChecker) -# set(MEMORYCHECK_TYPE ThreadSanitizer) -# set(MEMORYCHECK_TYPE AddressSanitizer) -# set(MEMORYCHECK_TYPE LeakSanitizer) -# set(MEMORYCHECK_TYPE MemorySanitizer) -# set(MEMORYCHECK_TYPE UndefinedBehaviorSanitizer) -set(MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --leak-check=full") - -# ---------------------------------------------------------------------------- # -# -- Settings -# ---------------------------------------------------------------------------- # -## -- Process timeout in seconds -set(CTEST_TIMEOUT "7200") -## -- Set output to English -set(ENV{LC_MESSAGES} "en_EN" ) - - -# ---------------------------------------------------------------------------- # -# -- Copy ctest configuration file -# ---------------------------------------------------------------------------- # -macro(COPY_CTEST_CONFIG_FILES) - - foreach(_FILE CTestConfig.cmake CTestCustom.cmake) - - # if current directory is not binary or source directory - if(NOT "${CMAKE_CURRENT_LIST_DIR}" STREQUAL "${CTEST_BINARY_DIRECTORY}" AND - NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") - - # if file exists in current directory - if(EXISTS ${CMAKE_CURRENT_LIST_DIR}/${_FILE}) - configure_file(${CMAKE_CURRENT_LIST_DIR}/${_FILE} - ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) - endif() - - # if source and binary differ - elseif(NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") - - # if file exists in source directory but not in binary directory - if(EXISTS ${CTEST_SOURCE_DIRECTORY}/${_FILE} AND - NOT EXISTS ${CTEST_BINARY_DIRECTORY}/${_FILE}) - configure_file(${CTEST_SOURCE_DIRECTORY}/${_FILE} - ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) - endif() - - endif() - endforeach() - -endmacro() - -ctest_read_custom_files("${CMAKE_CURRENT_LIST_DIR}") - -message(STATUS "CTEST_MODEL: ${CTEST_MODEL}") - -#-------------------------------------------------------------------------# -# Start -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running START_CTEST stage...") -message(STATUS "") - -ctest_start(${CTEST_MODEL} TRACK ${CTEST_MODEL} ${APPEND_CTEST} - ${CTEST_SOURCE_DIRECTORY} ${CTEST_BINARY_DIRECTORY}) - - -#-------------------------------------------------------------------------# -# Config -# -copy_ctest_config_files() -ctest_read_custom_files("${CTEST_BINARY_DIRECTORY}") - - -#-------------------------------------------------------------------------# -# Update -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_UPDATE stage...") -message(STATUS "") - -ctest_update(SOURCE "${CTEST_SOURCE_DIRECTORY}" - RETURN_VALUE up_ret) - - -#-------------------------------------------------------------------------# -# Configure -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_CONFIGURE stage...") -message(STATUS "") - -ctest_configure(BUILD "${CTEST_BINARY_DIRECTORY}" - SOURCE ${CTEST_SOURCE_DIRECTORY} - ${APPEND_CTEST} - OPTIONS "${CTEST_CONFIGURE_OPTIONS}" - RETURN_VALUE config_ret) - - -#-------------------------------------------------------------------------# -# Echo configure log bc Damien wants to delay merging this PR for eternity -# -file(GLOB _configure_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastConfigure*.log") -# should only have one but loop just for safety -foreach(_LOG ${_configure_log}) - file(READ ${_LOG} _LOG_MESSAGE) - message(STATUS "Configure Log: ${_LOG}") - message(STATUS "\n${_LOG_MESSAGE}\n") -endforeach() - - -#-------------------------------------------------------------------------# -# Build -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_BUILD stage...") -message(STATUS "") - -ctest_build(BUILD "${CTEST_BINARY_DIRECTORY}" - ${APPEND_CTEST} - RETURN_VALUE build_ret) - - -#-------------------------------------------------------------------------# -# Echo build log bc Damien wants to delay merging this PR for eternity -# -file(GLOB _build_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastBuild*.log") -# should only have one but loop just for safety -foreach(_LOG ${_build_log}) - file(READ ${_LOG} _LOG_MESSAGE) - message(STATUS "Build Log: ${_LOG}") - message(STATUS "\n${_LOG_MESSAGE}\n") -endforeach() - - -#-------------------------------------------------------------------------# -# Test -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_TEST stage...") -message(STATUS "") - -ctest_test(RETURN_VALUE test_ret - ${APPEND_CTEST} - ${START_CTEST} - ${END_CTEST} - ${STRIDE_CTEST} - ${INCLUDE_CTEST} - ${EXCLUDE_CTEST} - ${INCLUDE_LABEL_CTEST} - ${EXCLUDE_LABEL_CTEST} - ${PARALLEL_LEVEL_CTEST} - ${STOP_TIME_CTEST} - SCHEDULE_RANDOM OFF) - - -#-------------------------------------------------------------------------# -# Coverage -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_COVERAGE stage...") -message(STATUS "") - -execute_process(COMMAND ${CTEST_COVERAGE_COMMAND} ${CTEST_COVERAGE_EXTRA_FLAGS} - WORKING_DIRECTORY ${CTEST_BINARY_DIRECTORY} - ERROR_QUIET) - -ctest_coverage(${APPEND_CTEST} - ${CTEST_COVERAGE_LABELS} - RETURN_VALUE cov_ret) - - -#-------------------------------------------------------------------------# -# MemCheck -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_MEMCHECK stage...") -message(STATUS "") - -ctest_memcheck(RETURN_VALUE mem_ret - ${APPEND_CTEST} - ${START_CTEST} - ${END_CTEST} - ${STRIDE_CTEST} - ${INCLUDE_CTEST} - ${EXCLUDE_CTEST} - ${INCLUDE_LABEL_CTEST} - ${EXCLUDE_LABEL_CTEST} - ${PARALLEL_LEVEL_CTEST}) - - -#-------------------------------------------------------------------------# -# Submit -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_SUBMIT stage...") -message(STATUS "") - -file(GLOB_RECURSE NOTE_FILES "${CTEST_BINARY_DIRECTORY}/*CTestNotes.cmake") -foreach(_FILE ${NOTE_FILES}) - message(STATUS "Including CTest notes files: \"${_FILE}\"...") - include("${_FILE}") -endforeach() - -# capture submit error so it doesn't fail because of a submission error -ctest_submit(RETURN_VALUE submit_ret - RETRY_COUNT 2 - RETRY_DELAY 10 - CAPTURE_CMAKE_ERROR submit_err) - -#-------------------------------------------------------------------------# -# Submit -# -message(STATUS "") -message(STATUS "[${CTEST_BUILD_NAME}] Finished ${CTEST_MODEL} Stages (${STAGES})") -message(STATUS "") - - -#-------------------------------------------------------------------------# -# Non-zero exit codes for important errors -# -if(NOT config_ret EQUAL 0) - message(FATAL_ERROR "Error during configuration! Exit code: ${config_ret}") -endif() - -if(NOT build_ret EQUAL 0) - message(FATAL_ERROR "Error during build! Exit code: ${build_ret}") -endif() - -if(NOT test_ret EQUAL 0) - message(FATAL_ERROR "Error during testing! Exit code: ${test_ret}") -endif() diff --git a/packages/kokkos/cmake/KokkosCore_config.h.in b/packages/kokkos/cmake/KokkosCore_config.h.in index 3455b0cb42e7..07baa0a5f09a 100644 --- a/packages/kokkos/cmake/KokkosCore_config.h.in +++ b/packages/kokkos/cmake/KokkosCore_config.h.in @@ -41,6 +41,7 @@ #cmakedefine KOKKOS_ENABLE_CUDA_LAMBDA #cmakedefine KOKKOS_ENABLE_CUDA_CONSTEXPR #cmakedefine KOKKOS_ENABLE_CUDA_LDG_INTRINSIC +#cmakedefine KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC #cmakedefine KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE #cmakedefine KOKKOS_ENABLE_HPX_ASYNC_DISPATCH #cmakedefine KOKKOS_ENABLE_DEBUG @@ -49,17 +50,21 @@ #cmakedefine KOKKOS_ENABLE_COMPILER_WARNINGS #cmakedefine KOKKOS_ENABLE_PROFILING_LOAD_PRINT #cmakedefine KOKKOS_ENABLE_TUNING -#cmakedefine KOKKOS_ENABLE_DEPRECATED_CODE +#cmakedefine KOKKOS_ENABLE_DEPRECATED_CODE_3 +#cmakedefine KOKKOS_ENABLE_DEPRECATION_WARNINGS #cmakedefine KOKKOS_ENABLE_LARGE_MEM_TESTS #cmakedefine KOKKOS_ENABLE_DUALVIEW_MODIFY_CHECK #cmakedefine KOKKOS_ENABLE_COMPLEX_ALIGN -#cmakedefine KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION +#cmakedefine KOKKOS_ENABLE_IMPL_DESUL_ATOMICS +#cmakedefine KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION // deprecated +#cmakedefine KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION /* TPL Settings */ #cmakedefine KOKKOS_ENABLE_HWLOC #cmakedefine KOKKOS_USE_LIBRT #cmakedefine KOKKOS_ENABLE_HBWSPACE #cmakedefine KOKKOS_ENABLE_LIBDL +#cmakedefine KOKKOS_ENABLE_LIBQUADMATH #cmakedefine KOKKOS_IMPL_CUDA_CLANG_WORKAROUND #cmakedefine KOKKOS_COMPILER_CUDA_VERSION @KOKKOS_COMPILER_CUDA_VERSION@ @@ -79,6 +84,12 @@ #cmakedefine KOKKOS_ARCH_POWER8 #cmakedefine KOKKOS_ARCH_POWER9 #cmakedefine KOKKOS_ARCH_INTEL_GEN +#cmakedefine KOKKOS_ARCH_INTEL_DG1 +#cmakedefine KOKKOS_ARCH_INTEL_GEN9 +#cmakedefine KOKKOS_ARCH_INTEL_GEN11 +#cmakedefine KOKKOS_ARCH_INTEL_GEN12LP +#cmakedefine KOKKOS_ARCH_INTEL_XEHP +#cmakedefine KOKKOS_ARCH_INTEL_GPU #cmakedefine KOKKOS_ARCH_KEPLER #cmakedefine KOKKOS_ARCH_KEPLER30 #cmakedefine KOKKOS_ARCH_KEPLER32 @@ -95,6 +106,7 @@ #cmakedefine KOKKOS_ARCH_VOLTA70 #cmakedefine KOKKOS_ARCH_VOLTA72 #cmakedefine KOKKOS_ARCH_TURING75 +#cmakedefine KOKKOS_ARCH_AMPERE #cmakedefine KOKKOS_ARCH_AMPERE80 #cmakedefine KOKKOS_ARCH_AMPERE86 #cmakedefine KOKKOS_ARCH_AMD_ZEN diff --git a/packages/kokkos/cmake/Modules/FindTPLCUDA.cmake b/packages/kokkos/cmake/Modules/FindTPLCUDA.cmake index 8d58d9641580..0c825c59e042 100644 --- a/packages/kokkos/cmake/Modules/FindTPLCUDA.cmake +++ b/packages/kokkos/cmake/Modules/FindTPLCUDA.cmake @@ -29,7 +29,12 @@ ELSE() ENDIF() include(FindPackageHandleStandardArgs) -FIND_PACKAGE_HANDLE_STANDARD_ARGS(TPLCUDA DEFAULT_MSG FOUND_CUDART FOUND_CUDA_DRIVER) +IF(KOKKOS_CXX_HOST_COMPILER_ID STREQUAL PGI) + SET(KOKKOS_CUDA_ERROR "Using NVHPC as host compiler requires at least CMake 3.20.1") +ELSE() + SET(KOKKOS_CUDA_ERROR DEFAULT_MSG) +ENDIF() +FIND_PACKAGE_HANDLE_STANDARD_ARGS(TPLCUDA ${KOKKOS_CUDA_ERROR} FOUND_CUDART FOUND_CUDA_DRIVER) IF (FOUND_CUDA_DRIVER AND FOUND_CUDART) KOKKOS_CREATE_IMPORTED_TPL(CUDA INTERFACE LINK_LIBRARIES CUDA::cuda_driver CUDA::cudart diff --git a/packages/kokkos/cmake/Modules/FindTPLLIBQUADMATH.cmake b/packages/kokkos/cmake/Modules/FindTPLLIBQUADMATH.cmake new file mode 100644 index 000000000000..be70b711e0f9 --- /dev/null +++ b/packages/kokkos/cmake/Modules/FindTPLLIBQUADMATH.cmake @@ -0,0 +1 @@ +KOKKOS_FIND_IMPORTED(LIBQUADMATH HEADER quadmath.h LIBRARY quadmath) diff --git a/packages/kokkos/cmake/deps/quadmath.cmake b/packages/kokkos/cmake/deps/quadmath.cmake new file mode 100644 index 000000000000..826f5021d359 --- /dev/null +++ b/packages/kokkos/cmake/deps/quadmath.cmake @@ -0,0 +1,46 @@ +# @HEADER +# ************************************************************************ +# +# Kokkos v. 3.0 +# Copyright (2020) National Technology & Engineering +# Solutions of Sandia, LLC (NTESS). +# +# Under the terms of Contract DE-NA0003525 with NTESS, +# the U.S. Government retains certain rights in this software. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# 1. Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# 3. Neither the name of the Corporation nor the names of the +# contributors may be used to endorse or promote products derived from +# this software without specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY +# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE +# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# Questions? Contact Christian R. Trott (crtrott@sandia.gov) +# +# ************************************************************************ +# @HEADER + +KOKKOS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( quadmath + REQUIRED_HEADERS quadmath.h + REQUIRED_LIBS_NAMES quadmath +) diff --git a/packages/kokkos/cmake/kokkos_arch.cmake b/packages/kokkos/cmake/kokkos_arch.cmake index e8b85542c633..c4637339f31f 100644 --- a/packages/kokkos/cmake/kokkos_arch.cmake +++ b/packages/kokkos/cmake/kokkos_arch.cmake @@ -67,8 +67,13 @@ KOKKOS_ARCH_OPTION(ZEN3 HOST "AMD Zen3 architecture") KOKKOS_ARCH_OPTION(VEGA900 GPU "AMD GPU MI25 GFX900") KOKKOS_ARCH_OPTION(VEGA906 GPU "AMD GPU MI50/MI60 GFX906") KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU MI100 GFX908") +KOKKOS_ARCH_OPTION(VEGA90A GPU "" ) KOKKOS_ARCH_OPTION(INTEL_GEN GPU "Intel GPUs Gen9+") - +KOKKOS_ARCH_OPTION(INTEL_DG1 GPU "Intel Iris XeMAX GPU") +KOKKOS_ARCH_OPTION(INTEL_GEN9 GPU "Intel GPU Gen9") +KOKKOS_ARCH_OPTION(INTEL_GEN11 GPU "Intel GPU Gen11") +KOKKOS_ARCH_OPTION(INTEL_GEN12LP GPU "Intel GPU Gen12LP") +KOKKOS_ARCH_OPTION(INTEL_XEHP GPU "Intel GPU Xe-HP") IF(KOKKOS_ENABLE_COMPILER_WARNINGS) @@ -76,6 +81,12 @@ IF(KOKKOS_ENABLE_COMPILER_WARNINGS) "-Wall" "-Wunused-parameter" "-Wshadow" "-pedantic" "-Wsign-compare" "-Wtype-limits" "-Wuninitialized") + # NOTE KOKKOS_ prefixed variable (all uppercase) is not set yet because TPLs are processed after ARCH + IF(Kokkos_ENABLE_LIBQUADMATH) + # warning: non-standard suffix on floating constant [-Wpedantic] + LIST(REMOVE_ITEM COMMON_WARNINGS "-pedantic") + ENDIF() + # OpenMPTarget compilers give erroneous warnings about sign comparison in loops IF(KOKKOS_ENABLE_OPENMPTARGET) LIST(REMOVE_ITEM COMMON_WARNINGS "-Wsign-compare") @@ -86,7 +97,7 @@ IF(KOKKOS_ENABLE_COMPILER_WARNINGS) COMPILER_SPECIFIC_FLAGS( COMPILER_ID CMAKE_CXX_COMPILER_ID - PGI NO-VALUE-SPECIFIED + NVHPC NO-VALUE-SPECIFIED GNU ${GNU_WARNINGS} DEFAULT ${COMMON_WARNINGS} ) @@ -158,16 +169,18 @@ ENDIF() IF (KOKKOS_ARCH_ARMV80) COMPILER_SPECIFIC_FLAGS( - Cray NO-VALUE-SPECIFIED - PGI NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + Cray NO-VALUE-SPECIFIED + NVHPC NO-VALUE-SPECIFIED DEFAULT -march=armv8-a ) ENDIF() IF (KOKKOS_ARCH_ARMV81) COMPILER_SPECIFIC_FLAGS( - Cray NO-VALUE-SPECIFIED - PGI NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + Cray NO-VALUE-SPECIFIED + NVHPC NO-VALUE-SPECIFIED DEFAULT -march=armv8.1-a ) ENDIF() @@ -175,8 +188,9 @@ ENDIF() IF (KOKKOS_ARCH_ARMV8_THUNDERX) SET(KOKKOS_ARCH_ARMV80 ON) #Not a cache variable COMPILER_SPECIFIC_FLAGS( - Cray NO-VALUE-SPECIFIED - PGI NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + Cray NO-VALUE-SPECIFIED + NVHPC NO-VALUE-SPECIFIED DEFAULT -march=armv8-a -mtune=thunderx ) ENDIF() @@ -184,23 +198,28 @@ ENDIF() IF (KOKKOS_ARCH_ARMV8_THUNDERX2) SET(KOKKOS_ARCH_ARMV81 ON) #Not a cache variable COMPILER_SPECIFIC_FLAGS( - Cray NO-VALUE-SPECIFIED - PGI NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + Cray NO-VALUE-SPECIFIED + NVHPC NO-VALUE-SPECIFIED DEFAULT -mcpu=thunderx2t99 -mtune=thunderx2t99 ) ENDIF() IF (KOKKOS_ARCH_A64FX) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + NVHPC NO-VALUE-SPECIFIED DEFAULT -march=armv8.2-a+sve - Clang -march=armv8.2-a+sve -msve-vector-bits=512 - GCC -march=armv8.2-a+sve -msve-vector-bits=512 + Clang -march=armv8.2-a+sve -msve-vector-bits=512 + GCC -march=armv8.2-a+sve -msve-vector-bits=512 ) ENDIF() IF (KOKKOS_ARCH_ZEN) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -mavx2 + NVHPC -tp=zen DEFAULT -march=znver1 -mtune=znver1 ) SET(KOKKOS_ARCH_AMD_ZEN ON) @@ -209,7 +228,9 @@ ENDIF() IF (KOKKOS_ARCH_ZEN2) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -mavx2 + NVHPC -tp=zen2 DEFAULT -march=znver2 -mtune=znver2 ) SET(KOKKOS_ARCH_AMD_ZEN2 ON) @@ -218,7 +239,9 @@ ENDIF() IF (KOKKOS_ARCH_ZEN3) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -mavx2 + NVHPC -tp=zen2 DEFAULT -march=znver3 -mtune=znver3 ) SET(KOKKOS_ARCH_AMD_ZEN3 ON) @@ -227,8 +250,9 @@ ENDIF() IF (KOKKOS_ARCH_WSM) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -xSSE4.2 - PGI -tp=nehalem + NVHPC -tp=px Cray NO-VALUE-SPECIFIED DEFAULT -msse4.2 ) @@ -238,8 +262,9 @@ ENDIF() IF (KOKKOS_ARCH_SNB OR KOKKOS_ARCH_AMDAVX) SET(KOKKOS_ARCH_AVX ON) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -mavx - PGI -tp=sandybridge + NVHPC -tp=sandybridge Cray NO-VALUE-SPECIFIED DEFAULT -mavx ) @@ -248,8 +273,9 @@ ENDIF() IF (KOKKOS_ARCH_HSW) SET(KOKKOS_ARCH_AVX2 ON) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -xCORE-AVX2 - PGI -tp=haswell + NVHPC -tp=haswell Cray NO-VALUE-SPECIFIED DEFAULT -march=core-avx2 -mtune=core-avx2 ) @@ -258,8 +284,9 @@ ENDIF() IF (KOKKOS_ARCH_BDW) SET(KOKKOS_ARCH_AVX2 ON) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -xCORE-AVX2 - PGI -tp=haswell + NVHPC -tp=haswell Cray NO-VALUE-SPECIFIED DEFAULT -march=core-avx2 -mtune=core-avx2 -mrtm ) @@ -269,8 +296,9 @@ IF (KOKKOS_ARCH_KNL) #avx512-mic SET(KOKKOS_ARCH_AVX512MIC ON) #not a cache variable COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -xMIC-AVX512 - PGI NO-VALUE-SPECIFIED + NVHPC -tp=knl Cray NO-VALUE-SPECIFIED DEFAULT -march=knl -mtune=knl ) @@ -279,6 +307,7 @@ ENDIF() IF (KOKKOS_ARCH_KNC) SET(KOKKOS_USE_ISA_KNC ON) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID DEFAULT -mmic ) ENDIF() @@ -287,8 +316,9 @@ IF (KOKKOS_ARCH_SKX) #avx512-xeon SET(KOKKOS_ARCH_AVX512XEON ON) COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Intel -xCORE-AVX512 - PGI NO-VALUE-SPECIFIED + NVHPC -tp=skylake Cray NO-VALUE-SPECIFIED DEFAULT -march=skylake-avx512 -mtune=skylake-avx512 -mrtm ) @@ -304,7 +334,8 @@ ENDIF() IF (KOKKOS_ARCH_POWER7) COMPILER_SPECIFIC_FLAGS( - PGI NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + NVHPC NO-VALUE-SPECIFIED DEFAULT -mcpu=power7 -mtune=power7 ) SET(KOKKOS_USE_ISA_POWERPCBE ON) @@ -312,16 +343,16 @@ ENDIF() IF (KOKKOS_ARCH_POWER8) COMPILER_SPECIFIC_FLAGS( - PGI NO-VALUE-SPECIFIED - NVIDIA NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + NVHPC -tp=pwr8 DEFAULT -mcpu=power8 -mtune=power8 ) ENDIF() IF (KOKKOS_ARCH_POWER9) COMPILER_SPECIFIC_FLAGS( - PGI NO-VALUE-SPECIFIED - NVIDIA NO-VALUE-SPECIFIED + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + NVHPC -tp=pwr9 DEFAULT -mcpu=power9 -mtune=power9 ) ENDIF() @@ -368,7 +399,7 @@ ENDIF() IF (KOKKOS_ENABLE_SYCL) COMPILER_SPECIFIC_FLAGS( - DEFAULT -fsycl + DEFAULT -fsycl -fno-sycl-id-queries-fit-in-int ) COMPILER_SPECIFIC_OPTIONS( DEFAULT -fsycl-unnamed-lambda @@ -443,20 +474,58 @@ ENDFUNCTION() CHECK_AMDGPU_ARCH(VEGA900 gfx900) # Radeon Instinct MI25 CHECK_AMDGPU_ARCH(VEGA906 gfx906) # Radeon Instinct MI50 and MI60 CHECK_AMDGPU_ARCH(VEGA908 gfx908) +CHECK_AMDGPU_ARCH(VEGA90A gfx90a) IF(KOKKOS_ENABLE_HIP AND NOT AMDGPU_ARCH_ALREADY_SPECIFIED) - MESSAGE(SEND_ERROR "HIP enabled but no AMD GPU architecture currently enabled. " - "Please enable one AMD GPU architecture via -DKokkos_ARCH_{..}=ON'.") + IF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + FIND_PROGRAM(ROCM_ENUMERATOR rocm_agent_enumerator) + EXECUTE_PROCESS(COMMAND ${ROCM_ENUMERATOR} OUTPUT_VARIABLE GPU_ARCHS) + STRING(LENGTH "${GPU_ARCHS}" len_str) + # enumerator always output gfx000 as the first line + IF(${len_str} LESS 8) + MESSAGE(SEND_ERROR "HIP enabled but no AMD GPU architecture currently enabled. " + "Please enable one AMD GPU architecture via -DKokkos_ARCH_{..}=ON'.") + ENDIF() + ELSE() + MESSAGE(SEND_ERROR "HIP enabled but no AMD GPU architecture currently enabled. " + "Please enable one AMD GPU architecture via -DKokkos_ARCH_{..}=ON'.") + ENDIF() +ENDIF() + +MACRO(CHECK_MULTIPLE_INTEL_ARCH) + IF(KOKKOS_ARCH_INTEL_GPU) + MESSAGE(FATAL_ERROR "Specifying multiple Intel GPU architectures is not allowed!") + ENDIF() + SET(KOKKOS_ARCH_INTEL_GPU ON) +ENDMACRO() + +IF(KOKKOS_ARCH_INTEL_GEN) + CHECK_MULTIPLE_INTEL_ARCH() +ENDIF() +IF(KOKKOS_ARCH_INTEL_DG1) + CHECK_MULTIPLE_INTEL_ARCH() +ENDIF() +IF(KOKKOS_ARCH_INTEL_GEN9) + CHECK_MULTIPLE_INTEL_ARCH() +ENDIF() +IF(KOKKOS_ARCH_INTEL_GEN11) + CHECK_MULTIPLE_INTEL_ARCH() +ENDIF() +IF(KOKKOS_ARCH_INTEL_GEN12LP) + CHECK_MULTIPLE_INTEL_ARCH() +ENDIF() +IF(KOKKOS_ARCH_INTEL_XEHP) + CHECK_MULTIPLE_INTEL_ARCH() ENDIF() IF (KOKKOS_ENABLE_OPENMPTARGET) SET(CLANG_CUDA_ARCH ${KOKKOS_CUDA_ARCH_FLAG}) IF (CLANG_CUDA_ARCH) - STRING(REPLACE "sm_" "cc" PGI_CUDA_ARCH ${CLANG_CUDA_ARCH}) + STRING(REPLACE "sm_" "cc" NVHPC_CUDA_ARCH ${CLANG_CUDA_ARCH}) COMPILER_SPECIFIC_FLAGS( Clang -Xopenmp-target -march=${CLANG_CUDA_ARCH} -fopenmp-targets=nvptx64-nvidia-cuda - XL -qtgtarch=${KOKKOS_CUDA_ARCH_FLAG} - PGI -gpu=${PGI_CUDA_ARCH} + XL -qtgtarch=${KOKKOS_CUDA_ARCH_FLAG} + NVHPC -gpu=${NVHPC_CUDA_ARCH} ) ENDIF() SET(CLANG_AMDGPU_ARCH ${KOKKOS_AMDGPU_ARCH_FLAG}) @@ -465,7 +534,7 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) Clang -Xopenmp-target=amdgcn-amd-amdhsa -march=${CLANG_AMDGPU_ARCH} -fopenmp-targets=amdgcn-amd-amdhsa ) ENDIF() - IF (KOKKOS_ARCH_INTEL_GEN) + IF (KOKKOS_ARCH_INTEL_GPU) COMPILER_SPECIFIC_FLAGS( IntelLLVM -fopenmp-targets=spir64 -D__STRICT_ANSI__ ) @@ -485,7 +554,27 @@ IF (KOKKOS_ENABLE_SYCL) ENDIF() ELSEIF(KOKKOS_ARCH_INTEL_GEN) COMPILER_SPECIFIC_FLAGS( - DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device skl" + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9-" + ) + ELSEIF(KOKKOS_ARCH_INTEL_GEN9) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9" + ) + ELSEIF(KOKKOS_ARCH_INTEL_GEN11) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen11" + ) + ELSEIF(KOKKOS_ARCH_INTEL_GEN12LP) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen12lp" + ) + ELSEIF(KOKKOS_ARCH_INTEL_DG1) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device dg1" + ) + ELSEIF(KOKKOS_ARCH_INTEL_XEHP) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device xehp" ) ENDIF() ENDIF() diff --git a/packages/kokkos/cmake/kokkos_compiler_id.cmake b/packages/kokkos/cmake/kokkos_compiler_id.cmake index 23847263a952..5afed4fb0e7b 100644 --- a/packages/kokkos/cmake/kokkos_compiler_id.cmake +++ b/packages/kokkos/cmake/kokkos_compiler_id.cmake @@ -137,7 +137,7 @@ SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang 4.0.0 or higher" SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 5.3.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 17.0.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n NVCC 9.2.88 or higher") -SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n HIPCC 3.8.0 or higher") +SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n HIPCC 4.2.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n PGI 17.4 or higher\n") IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) @@ -158,13 +158,23 @@ ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) ENDIF() SET(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Kokkos turns off CXX extensions" FORCE) ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) - IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.8.0) + IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 4.2.0) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 17.4) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() + # Treat PGI internally as NVHPC to simplify handling both compilers. + # Before CMake 3.20 NVHPC was identified as PGI, nvc++ is + # backward-compatible to pgc++. + SET(KOKKOS_CXX_COMPILER_ID NVHPC CACHE STRING INTERNAL FORCE) +ENDIF() + +IF(NOT DEFINED KOKKOS_CXX_HOST_COMPILER_ID) + SET(KOKKOS_CXX_HOST_COMPILER_ID ${KOKKOS_CXX_COMPILER_ID}) +ELSEIF(KOKKOS_CXX_HOST_COMPILER_ID STREQUAL PGI) + SET(KOKKOS_CXX_HOST_COMPILER_ID NVHPC CACHE STRING INTERNAL FORCE) ENDIF() STRING(REPLACE "." ";" VERSION_LIST ${KOKKOS_CXX_COMPILER_VERSION}) diff --git a/packages/kokkos/cmake/kokkos_enable_devices.cmake b/packages/kokkos/cmake/kokkos_enable_devices.cmake index d7f83ddbdf87..7fd079403645 100644 --- a/packages/kokkos/cmake/kokkos_enable_devices.cmake +++ b/packages/kokkos/cmake/kokkos_enable_devices.cmake @@ -62,7 +62,7 @@ IF(KOKKOS_ENABLE_OPENMP) COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Clang -Xcompiler ${ClangOpenMPFlag} IntelLLVM -Xcompiler -fiopenmp - PGI -Xcompiler -mp + NVHPC -Xcompiler -mp Cray NO-VALUE-SPECIFIED XL -Xcompiler -qsmp=omp DEFAULT -Xcompiler -fopenmp @@ -72,7 +72,7 @@ IF(KOKKOS_ENABLE_OPENMP) Clang ${ClangOpenMPFlag} IntelLLVM -fiopenmp AppleClang -Xpreprocessor -fopenmp - PGI -mp + NVHPC -mp Cray NO-VALUE-SPECIFIED XL -qsmp=omp DEFAULT -fopenmp @@ -94,7 +94,7 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) Clang ${ClangOpenMPFlag} -Wno-openmp-mapping IntelLLVM -fiopenmp -Wno-openmp-mapping XL -qsmp=omp -qoffload -qnoeh - PGI -mp=gpu + NVHPC -mp=gpu DEFAULT -fopenmp ) COMPILER_SPECIFIC_DEFS( diff --git a/packages/kokkos/cmake/kokkos_enable_options.cmake b/packages/kokkos/cmake/kokkos_enable_options.cmake index 95bce66c7bee..4cb8bd20f5ec 100644 --- a/packages/kokkos/cmake/kokkos_enable_options.cmake +++ b/packages/kokkos/cmake/kokkos_enable_options.cmake @@ -26,9 +26,16 @@ KOKKOS_CFG_DEPENDS(OPTIONS COMPILER_ID) # Put a check in just in case people are using this option KOKKOS_DEPRECATED_LIST(OPTIONS ENABLE) +# Set the Default for Desul Atomics usage. +set(_DESUL_ATOMICS_DEFAULT ON) + KOKKOS_ENABLE_OPTION(CUDA_RELOCATABLE_DEVICE_CODE OFF "Whether to enable relocatable device code (RDC) for CUDA") KOKKOS_ENABLE_OPTION(CUDA_UVM OFF "Whether to use unified memory (UM) for CUDA by default") KOKKOS_ENABLE_OPTION(CUDA_LDG_INTRINSIC OFF "Whether to use CUDA LDG intrinsics") +# As of 08/12/2021 CudaMallocAsync causes issues if UCX is used as MPI communication layer. +KOKKOS_ENABLE_OPTION(IMPL_CUDA_MALLOC_ASYNC OFF "Whether to enable CudaMallocAsync (requires CUDA Toolkit 11.2)") +KOKKOS_ENABLE_OPTION(DEPRECATED_CODE_3 ON "Whether code deprecated in major release 3 is available" ) +KOKKOS_ENABLE_OPTION(DEPRECATION_WARNINGS ON "Whether to emit deprecation warnings" ) KOKKOS_ENABLE_OPTION(HIP_RELOCATABLE_DEVICE_CODE OFF "Whether to enable relocatable device code (RDC) for HIP") KOKKOS_ENABLE_OPTION(HPX_ASYNC_DISPATCH OFF "Whether HPX supports asynchronous dispatch") KOKKOS_ENABLE_OPTION(TESTS OFF "Whether to build the unit tests") @@ -50,6 +57,9 @@ KOKKOS_ENABLE_OPTION(TUNING OFF "Whether to create bindings for tu KOKKOS_ENABLE_OPTION(AGGRESSIVE_VECTORIZATION OFF "Whether to aggressively vectorize loops") KOKKOS_ENABLE_OPTION(LAUNCH_COMPILER ON "Whether to potentially use the launch compiler") +# This option will go away eventually, but allows fallback to old implementation when needed. +KOKKOS_ENABLE_OPTION(IMPL_DESUL_ATOMICS ON "Whether to use desul based atomics - option only during beta") + IF (KOKKOS_ENABLE_CUDA) SET(KOKKOS_COMPILER_CUDA_VERSION "${KOKKOS_COMPILER_VERSION_MAJOR}${KOKKOS_COMPILER_VERSION_MINOR}") ENDIF() diff --git a/packages/kokkos/cmake/kokkos_functions.cmake b/packages/kokkos/cmake/kokkos_functions.cmake index e1a3e5f8bd00..02c9a911b1b8 100644 --- a/packages/kokkos/cmake/kokkos_functions.cmake +++ b/packages/kokkos/cmake/kokkos_functions.cmake @@ -773,7 +773,7 @@ FUNCTION(kokkos_link_tpl TARGET) ENDFUNCTION() FUNCTION(COMPILER_SPECIFIC_OPTIONS_HELPER) - SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelLLVM GNU HIPCC Fujitsu) + SET(COMPILERS NVIDIA NVHPC XL XLClang DEFAULT Cray Intel Clang AppleClang IntelLLVM GNU HIPCC Fujitsu) CMAKE_PARSE_ARGUMENTS( PARSE "LINK_OPTIONS;COMPILE_OPTIONS;COMPILE_DEFINITIONS;LINK_LIBRARIES" diff --git a/packages/kokkos/cmake/kokkos_test_cxx_std.cmake b/packages/kokkos/cmake/kokkos_test_cxx_std.cmake index 707fb000af52..1eb0592c7f05 100644 --- a/packages/kokkos/cmake/kokkos_test_cxx_std.cmake +++ b/packages/kokkos/cmake/kokkos_test_cxx_std.cmake @@ -140,7 +140,7 @@ IF (NOT KOKKOS_CXX_STANDARD_FEATURE) IF(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) INCLUDE(${KOKKOS_SRC_PATH}/cmake/cray.cmake) kokkos_set_cray_flags(${KOKKOS_CXX_STANDARD} ${KOKKOS_CXX_INTERMEDIATE_STANDARD}) - ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) INCLUDE(${KOKKOS_SRC_PATH}/cmake/pgi.cmake) kokkos_set_pgi_flags(${KOKKOS_CXX_STANDARD} ${KOKKOS_CXX_INTERMEDIATE_STANDARD}) ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) diff --git a/packages/kokkos/cmake/kokkos_tpls.cmake b/packages/kokkos/cmake/kokkos_tpls.cmake index d8d044c9d753..51bad521c487 100644 --- a/packages/kokkos/cmake/kokkos_tpls.cmake +++ b/packages/kokkos/cmake/kokkos_tpls.cmake @@ -67,6 +67,12 @@ SET(PTHREAD_DEFAULT OFF) ENDIF() KOKKOS_TPL_OPTION(PTHREAD ${PTHREAD_DEFAULT} TRIBITS Pthread) +IF(Trilinos_ENABLE_Kokkos AND TPL_ENABLE_quadmath) + SET(LIBQUADMATH_DEFAULT ON) +ELSE() + SET(LIBQUADMATH_DEFAULT OFF) +ENDIF() +KOKKOS_TPL_OPTION(LIBQUADMATH ${LIBQUADMATH_DEFAULT} TRIBITS quadmath) #Make sure we use our local FindKokkosCuda.cmake KOKKOS_IMPORT_TPL(HPX INTERFACE) @@ -78,6 +84,7 @@ KOKKOS_IMPORT_TPL(LIBDL) KOKKOS_IMPORT_TPL(MEMKIND) KOKKOS_IMPORT_TPL(PTHREAD INTERFACE) KOKKOS_IMPORT_TPL(ROCM INTERFACE) +KOKKOS_IMPORT_TPL(LIBQUADMATH) #Convert list to newlines (which CMake doesn't always like in cache variables) STRING(REPLACE ";" "\n" KOKKOS_TPL_EXPORT_TEMP "${KOKKOS_TPL_EXPORTS}") diff --git a/packages/kokkos/cmake/tpls/FindTPLquadmath.cmake b/packages/kokkos/cmake/tpls/FindTPLquadmath.cmake new file mode 100644 index 000000000000..1f7587da808f --- /dev/null +++ b/packages/kokkos/cmake/tpls/FindTPLquadmath.cmake @@ -0,0 +1,46 @@ +# @HEADER +# ************************************************************************ +# +# Kokkos v. 3.0 +# Copyright (2020) National Technology & Engineering +# Solutions of Sandia, LLC (NTESS). +# +# Under the terms of Contract DE-NA0003525 with NTESS, +# the U.S. Government retains certain rights in this software. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# 1. Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# 3. Neither the name of the Corporation nor the names of the +# contributors may be used to endorse or promote products derived from +# this software without specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY +# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE +# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# Questions? Contact Christian R. Trott (crtrott@sandia.gov) +# +# ************************************************************************ +# @HEADER + +TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( quadmath + REQUIRED_HEADERS quadmath.h + REQUIRED_LIBS_NAMES quadmath +) diff --git a/packages/kokkos/containers/performance_tests/TestDynRankView.hpp b/packages/kokkos/containers/performance_tests/TestDynRankView.hpp index 8c507c76621d..7ed9a0271a51 100644 --- a/packages/kokkos/containers/performance_tests/TestDynRankView.hpp +++ b/packages/kokkos/containers/performance_tests/TestDynRankView.hpp @@ -48,7 +48,7 @@ #include #include -#include +#include // Compare performance of DynRankView to View, specific focus on the parenthesis // operators diff --git a/packages/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp b/packages/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp index 65de551b2715..16b74a4997e5 100644 --- a/packages/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp +++ b/packages/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp @@ -48,7 +48,7 @@ #include #include -#include +#include // This test will simulate global ids diff --git a/packages/kokkos/containers/performance_tests/TestScatterView.hpp b/packages/kokkos/containers/performance_tests/TestScatterView.hpp index 0f3ba103efc5..8a23f59d32cd 100644 --- a/packages/kokkos/containers/performance_tests/TestScatterView.hpp +++ b/packages/kokkos/containers/performance_tests/TestScatterView.hpp @@ -46,7 +46,7 @@ #define KOKKOS_TEST_SCATTER_VIEW_HPP #include -#include +#include namespace Perf { diff --git a/packages/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp b/packages/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp index c31412552ad6..4547d5c35758 100644 --- a/packages/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp +++ b/packages/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp @@ -43,7 +43,7 @@ #ifndef KOKKOS_TEST_UNORDERED_MAP_PERFORMANCE_HPP #define KOKKOS_TEST_UNORDERED_MAP_PERFORMANCE_HPP -#include +#include #include #include diff --git a/packages/kokkos/containers/src/Kokkos_Bitset.hpp b/packages/kokkos/containers/src/Kokkos_Bitset.hpp index ea1d6dde5d26..c5b66f05a3ce 100644 --- a/packages/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/packages/kokkos/containers/src/Kokkos_Bitset.hpp @@ -76,20 +76,25 @@ class Bitset { using execution_space = Device; using size_type = unsigned int; - enum { BIT_SCAN_REVERSE = 1u }; - enum { MOVE_HINT_BACKWARD = 2u }; - - enum { - BIT_SCAN_FORWARD_MOVE_HINT_FORWARD = 0u, - BIT_SCAN_REVERSE_MOVE_HINT_FORWARD = BIT_SCAN_REVERSE, - BIT_SCAN_FORWARD_MOVE_HINT_BACKWARD = MOVE_HINT_BACKWARD, - BIT_SCAN_REVERSE_MOVE_HINT_BACKWARD = BIT_SCAN_REVERSE | MOVE_HINT_BACKWARD - }; + static constexpr unsigned BIT_SCAN_REVERSE = 1u; + static constexpr unsigned MOVE_HINT_BACKWARD = 2u; + + static constexpr unsigned BIT_SCAN_FORWARD_MOVE_HINT_FORWARD = 0u; + static constexpr unsigned BIT_SCAN_REVERSE_MOVE_HINT_FORWARD = + BIT_SCAN_REVERSE; + static constexpr unsigned BIT_SCAN_FORWARD_MOVE_HINT_BACKWARD = + MOVE_HINT_BACKWARD; + static constexpr unsigned BIT_SCAN_REVERSE_MOVE_HINT_BACKWARD = + BIT_SCAN_REVERSE | MOVE_HINT_BACKWARD; private: - enum { block_size = static_cast(sizeof(unsigned) * CHAR_BIT) }; - enum { block_mask = block_size - 1u }; - enum { block_shift = Kokkos::Impl::integral_power_of_two(block_size) }; + enum : unsigned { + block_size = static_cast(sizeof(unsigned) * CHAR_BIT) + }; + enum : unsigned { block_mask = block_size - 1u }; + enum : unsigned { + block_shift = Kokkos::Impl::integral_power_of_two(block_size) + }; public: /// constructor @@ -317,14 +322,18 @@ class ConstBitset { enum { block_shift = Kokkos::Impl::integral_power_of_two(block_size) }; public: + KOKKOS_FUNCTION ConstBitset() : m_size(0) {} + KOKKOS_FUNCTION ConstBitset(Bitset const& rhs) : m_size(rhs.m_size), m_blocks(rhs.m_blocks) {} + KOKKOS_FUNCTION ConstBitset(ConstBitset const& rhs) : m_size(rhs.m_size), m_blocks(rhs.m_blocks) {} + KOKKOS_FUNCTION ConstBitset& operator=(Bitset const& rhs) { this->m_size = rhs.m_size; this->m_blocks = rhs.m_blocks; @@ -332,6 +341,7 @@ class ConstBitset { return *this; } + KOKKOS_FUNCTION ConstBitset& operator=(ConstBitset const& rhs) { this->m_size = rhs.m_size; this->m_blocks = rhs.m_blocks; diff --git a/packages/kokkos/containers/src/Kokkos_DualView.hpp b/packages/kokkos/containers/src/Kokkos_DualView.hpp index 45710d1f737c..f55d0f2b7f3f 100644 --- a/packages/kokkos/containers/src/Kokkos_DualView.hpp +++ b/packages/kokkos/containers/src/Kokkos_DualView.hpp @@ -597,8 +597,10 @@ class DualView : public ViewTraits { } if (std::is_same::value) { - typename t_dev::execution_space().fence(); - typename t_host::execution_space().fence(); + typename t_dev::execution_space().fence( + "Kokkos::DualView<>::sync: fence after syncing DualView"); + typename t_host::execution_space().fence( + "Kokkos::DualView<>::sync: fence after syncing DualView"); } } @@ -776,10 +778,11 @@ class DualView : public ViewTraits { /// If \c Device is the same as this DualView's device type, then /// mark the device's data as modified. Otherwise, mark the host's /// data as modified. - template + template * = + nullptr> void modify() { if (modified_flags.data() == nullptr) return; - if (impl_dualview_is_single_device::value) return; int dev = get_device_side(); if (dev == 1) { // if Device is the same as DualView's device type @@ -811,8 +814,17 @@ class DualView : public ViewTraits { #endif } + template < + class Device, class Dummy = DualView, + std::enable_if_t* = nullptr> + void modify() { + return; + } + + template * = + nullptr> inline void modify_host() { - if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(0) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) @@ -832,8 +844,17 @@ class DualView : public ViewTraits { } } + template < + class Dummy = DualView, + std::enable_if_t* = nullptr> + inline void modify_host() { + return; + } + + template * = + nullptr> inline void modify_device() { - if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(1) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) @@ -853,6 +874,13 @@ class DualView : public ViewTraits { } } + template < + class Dummy = DualView, + std::enable_if_t* = nullptr> + inline void modify_device() { + return; + } + inline void clear_sync_state() { if (modified_flags.data() != nullptr) modified_flags(1) = modified_flags(0) = 0; @@ -875,8 +903,15 @@ class DualView : public ViewTraits { const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG) { - ::Kokkos::realloc(d_view, n0, n1, n2, n3, n4, n5, n6, n7); - h_view = create_mirror_view(d_view); + const size_t new_extents[8] = {n0, n1, n2, n3, n4, n5, n6, n7}; + const bool sizeMismatch = + Impl::size_mismatch(h_view, h_view.rank_dynamic, new_extents); + + if (sizeMismatch) { + ::Kokkos::realloc(d_view, n0, n1, n2, n3, n4, n5, n6, n7); + h_view = create_mirror_view(d_view); + } else + ::Kokkos::deep_copy(d_view, typename t_dev::value_type{}); /* Reset dirty flags */ if (modified_flags.data() == nullptr) { @@ -897,41 +932,31 @@ class DualView : public ViewTraits { const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG) { + const size_t new_extents[8] = {n0, n1, n2, n3, n4, n5, n6, n7}; + const bool sizeMismatch = + Impl::size_mismatch(h_view, h_view.rank_dynamic, new_extents); + if (modified_flags.data() == nullptr) { modified_flags = t_modified_flags("DualView::modified_flags"); } if (modified_flags(1) >= modified_flags(0)) { /* Resize on Device */ - ::Kokkos::resize(d_view, n0, n1, n2, n3, n4, n5, n6, n7); - h_view = create_mirror_view(d_view); - - /* Mark Device copy as modified */ - modified_flags(1) = modified_flags(1) + 1; + if (sizeMismatch) { + ::Kokkos::resize(d_view, n0, n1, n2, n3, n4, n5, n6, n7); + h_view = create_mirror_view(d_view); + /* Mark Device copy as modified */ + modified_flags(1) = modified_flags(1) + 1; + } } else { /* Realloc on Device */ - - ::Kokkos::realloc(d_view, n0, n1, n2, n3, n4, n5, n6, n7); - - const bool sizeMismatch = - (h_view.extent(0) != n0) || (h_view.extent(1) != n1) || - (h_view.extent(2) != n2) || (h_view.extent(3) != n3) || - (h_view.extent(4) != n4) || (h_view.extent(5) != n5) || - (h_view.extent(6) != n6) || (h_view.extent(7) != n7); - if (sizeMismatch) + if (sizeMismatch) { ::Kokkos::resize(h_view, n0, n1, n2, n3, n4, n5, n6, n7); + d_view = create_mirror_view(typename t_dev::execution_space(), h_view); - t_host temp_view = create_mirror_view(d_view); - - /* Remap on Host */ - Kokkos::deep_copy(temp_view, h_view); - - h_view = temp_view; - - d_view = create_mirror_view(typename t_dev::execution_space(), h_view); - - /* Mark Host copy as modified */ - modified_flags(0) = modified_flags(0) + 1; + /* Mark Host copy as modified */ + modified_flags(0) = modified_flags(0) + 1; + } } } diff --git a/packages/kokkos/containers/src/Kokkos_DynRankView.hpp b/packages/kokkos/containers/src/Kokkos_DynRankView.hpp index c6323fef9369..b673c53a4ef8 100644 --- a/packages/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/packages/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -1140,7 +1140,8 @@ class DynRankView : public ViewTraits { // to avoid incomplete type errors from usng Kokkos::Cuda directly. if (std::is_same::value) { - typename traits::device_type::memory_space::execution_space().fence(); + typename traits::device_type::memory_space::execution_space().fence( + "Kokkos::DynRankView<>::DynRankView: fence before UVM allocation"); } #endif //------------------------------------------------------------ @@ -1154,7 +1155,8 @@ class DynRankView : public ViewTraits { #if defined(KOKKOS_ENABLE_CUDA) if (std::is_same::value) { - typename traits::device_type::memory_space::execution_space().fence(); + typename traits::device_type::memory_space::execution_space().fence( + "Kokkos::DynRankView<>::DynRankView: fence after UVM allocation"); } #endif //------------------------------------------------------------ @@ -1404,7 +1406,7 @@ class ViewMapping< template struct apply { - static_assert(Kokkos::Impl::is_memory_traits::value, ""); + static_assert(Kokkos::is_memory_traits::value, ""); using traits_type = Kokkos::ViewTraits& lhs, namespace Kokkos { namespace Impl { -template +template struct DynRankViewFill { using const_value_type = typename OutputView::traits::const_value_type; @@ -1693,9 +1695,11 @@ inline void deep_copy( typename ViewTraits::value_type>::value, "deep_copy requires non-const type"); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::deep_copy(DynRankView, value_type): fence before filling view"); Kokkos::Impl::DynRankViewFill >(dst, value); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::deep_copy(DynRankView, value_type): fence after filling view"); } /** \brief Deep copy into a value in Host memory from a view. */ @@ -1711,10 +1715,13 @@ inline void deep_copy( using src_traits = ViewTraits; using src_memory_space = typename src_traits::memory_space; - Kokkos::fence(); + Kokkos::fence( + "Kokkos::deep_copy(value_type, DynRankView): fence before copying " + "value"); Kokkos::Impl::DeepCopy(&dst, src.data(), sizeof(ST)); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::deep_copy(value_type, DynRankView): fence after copying value"); } //---------------------------------------------------------------------------- @@ -1744,14 +1751,14 @@ inline void deep_copy( enum { DstExecCanAccessSrc = - Kokkos::Impl::SpaceAccessibility::accessible + Kokkos::SpaceAccessibility::accessible }; enum { SrcExecCanAccessDst = - Kokkos::Impl::SpaceAccessibility::accessible + Kokkos::SpaceAccessibility::accessible }; if ((void*)dst.data() != (void*)src.data()) { @@ -1762,10 +1769,14 @@ inline void deep_copy( // memory then can byte-wise copy if (rank(src) == 0 && rank(dst) == 0) { using value_type = typename dst_type::value_type; - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence before " + "copying rank-0 views"); Kokkos::Impl::DeepCopy( dst.data(), src.data(), sizeof(value_type)); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence after " + "copying rank-0 views"); } else if (std::is_same< typename DstType::traits::value_type, typename SrcType::traits::non_const_value_type>::value && @@ -1787,10 +1798,14 @@ inline void deep_copy( dst.extent(6) == src.extent(6) && dst.extent(7) == src.extent(7)) { const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span(); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence before " + "copying rank-1 views"); Kokkos::Impl::DeepCopy( dst.data(), src.data(), nbytes); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence after " + "copying rank-1 views"); } else if (std::is_same< typename DstType::traits::value_type, typename SrcType::traits::non_const_value_type>::value && @@ -1817,29 +1832,43 @@ inline void deep_copy( dst.stride_6() == src.stride_6() && dst.stride_7() == src.stride_7()) { const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span(); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence before " + "copying rank-1 views"); Kokkos::Impl::DeepCopy( dst.data(), src.data(), nbytes); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence after " + "copying rank-1 views"); } else if (DstExecCanAccessSrc) { // Copying data between views in accessible memory spaces and either // non-contiguous or incompatible shape. - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence before " + "remapping views of incompatible shape"); Kokkos::Impl::DynRankViewRemap(dst, src); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence after " + "remapping views of incompatible shape"); } else if (SrcExecCanAccessDst) { // Copying data between views in accessible memory spaces and either // non-contiguous or incompatible shape. - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence before " + "remapping views of incompatible shape"); Kokkos::Impl::DynRankViewRemap( dst, src); - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence after " + "remapping views of incompatible shape"); } else { Kokkos::Impl::throw_runtime_exception( "deep_copy given views that would require a temporary allocation"); } } else { - Kokkos::fence(); + Kokkos::fence( + "Kokkos::Impl::DeepCopy(DynRankView, DynRankView): fence due to same " + "src and dst"); } } diff --git a/packages/kokkos/containers/src/Kokkos_DynamicView.hpp b/packages/kokkos/containers/src/Kokkos_DynamicView.hpp index cc949d4c556a..2c764f535c58 100644 --- a/packages/kokkos/containers/src/Kokkos_DynamicView.hpp +++ b/packages/kokkos/containers/src/Kokkos_DynamicView.hpp @@ -53,36 +53,201 @@ namespace Kokkos { namespace Experimental { -// Simple metafunction for choosing memory space -// In the current implementation, if memory_space == CudaSpace, -// use CudaUVMSpace for the chunk 'array' allocation, which -// contains will contain pointers to chunks of memory allocated -// in CudaSpace namespace Impl { -template -struct ChunkArraySpace { - using memory_space = MemSpace; -}; -#ifdef KOKKOS_ENABLE_CUDA -template <> -struct ChunkArraySpace { - using memory_space = typename Kokkos::CudaUVMSpace; -}; -#endif -#ifdef KOKKOS_ENABLE_HIP -template <> -struct ChunkArraySpace { - using memory_space = typename Kokkos::Experimental::HIPHostPinnedSpace; -}; -#endif -#ifdef KOKKOS_ENABLE_SYCL -template <> -struct ChunkArraySpace { - using memory_space = typename Kokkos::Experimental::SYCLSharedUSMSpace; +/// Utility class to manage memory for chunked arrays on the host and +/// device. Allocates/deallocates memory on both the host and device along with +/// providing utilities for creating mirrors and deep copying between them. +template +struct ChunkedArrayManager { + using value_type = ValueType; + using pointer_type = ValueType*; + using track_type = Kokkos::Impl::SharedAllocationTracker; + + ChunkedArrayManager() = default; + ChunkedArrayManager(ChunkedArrayManager const&) = default; + ChunkedArrayManager(ChunkedArrayManager&&) = default; + ChunkedArrayManager& operator=(ChunkedArrayManager&&) = default; + ChunkedArrayManager& operator=(const ChunkedArrayManager&) = default; + + template + friend struct ChunkedArrayManager; + + template + inline ChunkedArrayManager(const ChunkedArrayManager& rhs) + : m_valid(rhs.m_valid), + m_chunk_max(rhs.m_chunk_max), + m_chunks((ValueType**)(rhs.m_chunks)), + m_track(rhs.m_track), + m_chunk_size(rhs.m_chunk_size) { + static_assert( + Kokkos::Impl::MemorySpaceAccess::assignable, + "Incompatible ChunkedArrayManager copy construction"); + } + + ChunkedArrayManager(const unsigned arg_chunk_max, + const unsigned arg_chunk_size) + : m_chunk_max(arg_chunk_max), m_chunk_size(arg_chunk_size) {} + + private: + struct ACCESSIBLE_TAG {}; + struct INACCESSIBLE_TAG {}; + + ChunkedArrayManager(ACCESSIBLE_TAG, pointer_type* arg_chunks, + const unsigned arg_chunk_max) + : m_valid(true), m_chunk_max(arg_chunk_max), m_chunks(arg_chunks) {} + + ChunkedArrayManager(INACCESSIBLE_TAG, const unsigned arg_chunk_max, + const unsigned arg_chunk_size) + : m_chunk_max(arg_chunk_max), m_chunk_size(arg_chunk_size) {} + + public: + template + struct IsAccessibleFrom; + + template + struct IsAccessibleFrom< + Space, typename std::enable_if_t::accessible>> : std::true_type {}; + + template + struct IsAccessibleFrom< + Space, typename std::enable_if_t::accessible>> : std::false_type {}; + + template + static ChunkedArrayManager create_mirror( + ChunkedArrayManager const& other, + typename std::enable_if::value>::type* = + nullptr) { + return ChunkedArrayManager{ + ACCESSIBLE_TAG{}, other.m_chunks, other.m_chunk_max}; + } + + template + static ChunkedArrayManager create_mirror( + ChunkedArrayManager const& other, + typename std::enable_if::value>::type* = + nullptr) { + using tag_type = + typename ChunkedArrayManager::INACCESSIBLE_TAG; + return ChunkedArrayManager{tag_type{}, other.m_chunk_max, + other.m_chunk_size}; + } + + public: + void allocate_device(const std::string& label) { + if (m_chunks == nullptr) { + m_chunks = reinterpret_cast(MemorySpace().allocate( + label.c_str(), (sizeof(pointer_type) * (m_chunk_max + 2)))); + } + } + + void initialize() { + for (unsigned i = 0; i < m_chunk_max + 2; i++) { + m_chunks[i] = nullptr; + } + m_valid = true; + } + + private: + /// Custom destroy functor for deallocating array chunks along with a linked + /// allocation + template + struct Destroy { + Destroy() = default; + Destroy(Destroy&&) = default; + Destroy(const Destroy&) = default; + Destroy& operator=(Destroy&&) = default; + Destroy& operator=(const Destroy&) = default; + + Destroy(std::string label, value_type** arg_chunk, + const unsigned arg_chunk_max, const unsigned arg_chunk_size, + value_type** arg_linked) + : m_label(label), + m_chunks(arg_chunk), + m_linked(arg_linked), + m_chunk_max(arg_chunk_max), + m_chunk_size(arg_chunk_size) {} + + void execute() { + // Destroy the array of chunk pointers. + // Two entries beyond the max chunks are allocation counters. + for (unsigned i = 0; i < m_chunk_max; i++) { + Space().deallocate(m_label.c_str(), m_chunks[i], + sizeof(value_type) * m_chunk_size); + } + // Destroy the linked allocation if we have one. + if (m_linked != nullptr) { + Space().deallocate(m_label.c_str(), m_linked, + (sizeof(value_type*) * (m_chunk_max + 2))); + } + } + + void destroy_shared_allocation() { execute(); } + + std::string m_label; + value_type** m_chunks = nullptr; + value_type** m_linked = nullptr; + unsigned m_chunk_max; + unsigned m_chunk_size; + }; + + public: + template + void allocate_with_destroy(const std::string& label, + pointer_type* linked_allocation = nullptr) { + using destroy_type = Destroy; + using record_type = + Kokkos::Impl::SharedAllocationRecord; + + // Allocate + 2 extra slots so that *m_chunk[m_chunk_max] == + // num_chunks_alloc and *m_chunk[m_chunk_max+1] == extent This must match in + // Destroy's execute(...) method + record_type* const record = record_type::allocate( + MemorySpace(), label, (sizeof(pointer_type) * (m_chunk_max + 2))); + m_chunks = static_cast(record->data()); + m_track.assign_allocated_record_to_uninitialized(record); + + record->m_destroy = destroy_type(label, m_chunks, m_chunk_max, m_chunk_size, + linked_allocation); + } + + pointer_type* get_ptr() const { return m_chunks; } + + template + typename std::enable_if::value>::type deep_copy_to( + ChunkedArrayManager const& other) { + Kokkos::Impl::DeepCopy( + other.m_chunks, m_chunks, sizeof(pointer_type) * (m_chunk_max + 2)); + } + + template + typename std::enable_if::value>::type deep_copy_to( + ChunkedArrayManager const&) { + // no-op + } + + KOKKOS_INLINE_FUNCTION + pointer_type* operator+(int i) const { return m_chunks + i; } + + KOKKOS_INLINE_FUNCTION + pointer_type& operator[](int i) const { return m_chunks[i]; } + + track_type const& track() const { return m_track; } + + KOKKOS_INLINE_FUNCTION + bool valid() const { return m_valid; } + + private: + bool m_valid = false; + unsigned m_chunk_max = 0; + pointer_type* m_chunks = nullptr; + track_type m_track; + unsigned m_chunk_size = 0; }; -#endif -} // end namespace Impl + +} /* end namespace Impl */ /** \brief Dynamic views are restricted to rank-one and no layout. * Resize only occurs on host outside of parallel_regions. @@ -93,6 +258,13 @@ class DynamicView : public Kokkos::ViewTraits { public: using traits = Kokkos::ViewTraits; + using value_type = typename traits::value_type; + using device_space = typename traits::memory_space; + using host_space = + typename Kokkos::Impl::HostMirror::Space::memory_space; + using device_accessor = Impl::ChunkedArrayManager; + using host_accessor = Impl::ChunkedArrayManager; + private: template friend class DynamicView; @@ -108,7 +280,7 @@ class DynamicView : public Kokkos::ViewTraits { "DynamicView only implemented for non-specialized View type"); template ::accessible> + Space, device_space>::accessible> struct verify_space { KOKKOS_FORCEINLINE_FUNCTION static void check() {} }; @@ -123,9 +295,8 @@ class DynamicView : public Kokkos::ViewTraits { }; private: - track_type m_track; - typename traits::value_type** m_chunks = - nullptr; // array of pointers to 'chunks' of memory + device_accessor m_chunks; + host_accessor m_chunks_host; unsigned m_chunk_shift; // ceil(log2(m_chunk_size)) unsigned m_chunk_mask; // m_chunk_size - 1 unsigned m_chunk_max; // number of entries in the chunk array - each pointing @@ -173,7 +344,8 @@ class DynamicView : public Kokkos::ViewTraits { KOKKOS_INLINE_FUNCTION size_t allocation_extent() const noexcept { - uintptr_t n = *reinterpret_cast(m_chunks + m_chunk_max); + uintptr_t n = + *reinterpret_cast(m_chunks_host + m_chunk_max); return (n << m_chunk_shift); } @@ -183,7 +355,7 @@ class DynamicView : public Kokkos::ViewTraits { KOKKOS_INLINE_FUNCTION size_t size() const noexcept { size_t extent_0 = - *reinterpret_cast(m_chunks + m_chunk_max + 1); + *reinterpret_cast(m_chunks_host + m_chunk_max + 1); return extent_0; } @@ -215,10 +387,10 @@ class DynamicView : public Kokkos::ViewTraits { // Allocation tracking properties KOKKOS_INLINE_FUNCTION - int use_count() const { return m_track.use_count(); } + int use_count() const { return m_chunks_host.track().use_count(); } inline const std::string label() const { - return m_track.template get_label(); + return m_chunks_host.track().template get_label(); } //---------------------------------------------------------------------- @@ -285,13 +457,7 @@ class DynamicView : public Kokkos::ViewTraits { * up to the maximum number of chunks * */ template - inline typename std::enable_if< - std::is_integral::value && - Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - typename Impl::ChunkArraySpace< - typename traits::memory_space>::memory_space>::accessible>::type - resize_serial(IntType const& n) { + inline void resize_serial(IntType const& n) { using local_value_type = typename traits::value_type; using value_pointer_type = local_value_type*; @@ -304,37 +470,40 @@ class DynamicView : public Kokkos::ViewTraits { } // *m_chunks[m_chunk_max] stores the current number of chunks being used - uintptr_t* const pc = reinterpret_cast(m_chunks + m_chunk_max); - std::string _label = - m_track.template get_label(); + uintptr_t* const pc = + reinterpret_cast(m_chunks_host + m_chunk_max); + std::string _label = m_chunks_host.track().template get_label(); + if (*pc < NC) { while (*pc < NC) { - m_chunks[*pc] = reinterpret_cast( - typename traits::memory_space().allocate( + m_chunks_host[*pc] = + reinterpret_cast(device_space().allocate( _label.c_str(), sizeof(local_value_type) << m_chunk_shift)); ++*pc; } } else { while (NC + 1 <= *pc) { --*pc; - typename traits::memory_space().deallocate( - _label.c_str(), m_chunks[*pc], - sizeof(local_value_type) << m_chunk_shift); - m_chunks[*pc] = nullptr; + device_space().deallocate(_label.c_str(), m_chunks_host[*pc], + sizeof(local_value_type) << m_chunk_shift); + m_chunks_host[*pc] = nullptr; } } - // *m_chunks[m_chunk_max+1] stores the 'extent' requested by resize + // *m_chunks_host[m_chunk_max+1] stores the 'extent' requested by resize *(pc + 1) = n; + + m_chunks_host.deep_copy_to(m_chunks); } KOKKOS_INLINE_FUNCTION bool is_allocated() const { - if (m_chunks == nullptr) { - return false; - } else { - // *m_chunks[m_chunk_max] stores the current number of chunks being used + if (m_chunks_host.valid()) { + // *m_chunks_host[m_chunk_max] stores the current number of chunks being + // used uintptr_t* const pc = - reinterpret_cast(m_chunks + m_chunk_max); + reinterpret_cast(m_chunks_host + m_chunk_max); return (*(pc + 1) > 0); + } else { + return false; } } @@ -349,8 +518,8 @@ class DynamicView : public Kokkos::ViewTraits { template DynamicView(const DynamicView& rhs) - : m_track(rhs.m_track), - m_chunks((typename traits::value_type**)rhs.m_chunks), + : m_chunks(rhs.m_chunks), + m_chunks_host(rhs.m_chunks_host), m_chunk_shift(rhs.m_chunk_shift), m_chunk_mask(rhs.m_chunk_mask), m_chunk_max(rhs.m_chunk_max), @@ -361,63 +530,6 @@ class DynamicView : public Kokkos::ViewTraits { "Incompatible DynamicView copy construction"); } - //---------------------------------------------------------------------- - - struct Destroy { - using local_value_type = typename traits::value_type; - std::string m_label; - local_value_type** m_chunks; - unsigned m_chunk_max; - bool m_destroy; - unsigned m_chunk_size; - - // Initialize or destroy array of chunk pointers. - // Two entries beyond the max chunks are allocation counters. - inline void operator()(unsigned i) const { - if (m_destroy && i < m_chunk_max && nullptr != m_chunks[i]) { - typename traits::memory_space().deallocate( - m_label.c_str(), m_chunks[i], - sizeof(local_value_type) * m_chunk_size); - } - m_chunks[i] = nullptr; - } - - void execute(bool arg_destroy) { - using Range = Kokkos::RangePolicy; - - m_destroy = arg_destroy; - - Kokkos::Impl::ParallelFor closure( - *this, - Range(0, m_chunk_max + 2)); // Add 2 to 'destroy' extra slots storing - // num_chunks and extent; previously + 1 - - closure.execute(); - - typename traits::execution_space().fence(); - // Impl::ChunkArraySpace< typename traits::memory_space - // >::memory_space::execution_space().fence(); - } - - void construct_shared_allocation() { execute(false); } - - void destroy_shared_allocation() { execute(true); } - - Destroy() = default; - Destroy(Destroy&&) = default; - Destroy(const Destroy&) = default; - Destroy& operator=(Destroy&&) = default; - Destroy& operator=(const Destroy&) = default; - - Destroy(std::string label, typename traits::value_type** arg_chunk, - const unsigned arg_chunk_max, const unsigned arg_chunk_size) - : m_label(label), - m_chunks(arg_chunk), - m_chunk_max(arg_chunk_max), - m_destroy(false), - m_chunk_size(arg_chunk_size) {} - }; - /**\brief Allocation constructor * * Memory is allocated in chunks @@ -427,10 +539,7 @@ class DynamicView : public Kokkos::ViewTraits { explicit inline DynamicView(const std::string& arg_label, const unsigned min_chunk_size, const unsigned max_extent) - : m_track(), - m_chunks(nullptr) - // The chunk size is guaranteed to be a power of two - , + : // The chunk size is guaranteed to be a power of two m_chunk_shift(Kokkos::Impl::integral_power_of_two_that_contains( min_chunk_size)) // div ceil(log2(min_chunk_size)) , @@ -440,28 +549,22 @@ class DynamicView : public Kokkos::ViewTraits { m_chunk_shift) // max num pointers-to-chunks in array , m_chunk_size(2 << (m_chunk_shift - 1)) { - using chunk_array_memory_space = typename Impl::ChunkArraySpace< - typename traits::memory_space>::memory_space; - // A functor to deallocate all of the chunks upon final destruction - using record_type = - Kokkos::Impl::SharedAllocationRecord; - - // Allocate chunk pointers and allocation counter - record_type* const record = - record_type::allocate(chunk_array_memory_space(), arg_label, - (sizeof(pointer_type) * (m_chunk_max + 2))); - // Allocate + 2 extra slots so that *m_chunk[m_chunk_max] == - // num_chunks_alloc and *m_chunk[m_chunk_max+1] == extent This must match in - // Destroy's execute(...) method - - m_chunks = reinterpret_cast(record->data()); - - record->m_destroy = Destroy(arg_label, m_chunks, m_chunk_max, m_chunk_size); + m_chunks = device_accessor(m_chunk_max, m_chunk_size); - // Initialize to zero - record->m_destroy.construct_shared_allocation(); - - m_track.assign_allocated_record_to_uninitialized(record); + if (device_accessor::template IsAccessibleFrom::value) { + m_chunks.template allocate_with_destroy(arg_label); + m_chunks.initialize(); + m_chunks_host = + device_accessor::template create_mirror(m_chunks); + } else { + m_chunks.allocate_device(arg_label); + m_chunks_host = + device_accessor::template create_mirror(m_chunks); + m_chunks_host.template allocate_with_destroy( + arg_label, m_chunks.get_ptr()); + m_chunks_host.initialize(); + m_chunks_host.deep_copy_to(m_chunks); + } } }; @@ -487,8 +590,8 @@ inline void deep_copy(const View& dst, enum { DstExecCanAccessSrc = - Kokkos::Impl::SpaceAccessibility::accessible + Kokkos::SpaceAccessibility::accessible }; if (DstExecCanAccessSrc) { @@ -512,8 +615,8 @@ inline void deep_copy(const Kokkos::Experimental::DynamicView& dst, enum { DstExecCanAccessSrc = - Kokkos::Impl::SpaceAccessibility::accessible + Kokkos::SpaceAccessibility::accessible }; if (DstExecCanAccessSrc) { diff --git a/packages/kokkos/containers/src/Kokkos_ErrorReporter.hpp b/packages/kokkos/containers/src/Kokkos_ErrorReporter.hpp index fbfaed9b1bcd..18f026dc6ffc 100644 --- a/packages/kokkos/containers/src/Kokkos_ErrorReporter.hpp +++ b/packages/kokkos/containers/src/Kokkos_ErrorReporter.hpp @@ -187,7 +187,8 @@ template void ErrorReporter::resize(const size_t new_size) { m_reports.resize(new_size); m_reporters.resize(new_size); - typename DeviceType::execution_space().fence(); + typename DeviceType::execution_space().fence( + "Kokkos::Experimental::ErrorReporter::resize: fence after resizing"); } } // namespace Experimental diff --git a/packages/kokkos/containers/src/Kokkos_OffsetView.hpp b/packages/kokkos/containers/src/Kokkos_OffsetView.hpp index 0f21a08ba3ba..57bf745d4038 100644 --- a/packages/kokkos/containers/src/Kokkos_OffsetView.hpp +++ b/packages/kokkos/containers/src/Kokkos_OffsetView.hpp @@ -116,8 +116,7 @@ KOKKOS_INLINE_FUNCTION void offsetview_verify_operator_bounds( This check should cover the case of Views that don't have the Unmanaged trait but were initialized by pointer. */ if (tracker.has_record()) { - Kokkos::Impl::operator_bounds_error_on_device( - map, Kokkos::Impl::has_printable_label_typedef()); + Kokkos::Impl::operator_bounds_error_on_device(map); } else { Kokkos::abort("OffsetView bounds error"); } @@ -1244,7 +1243,8 @@ class OffsetView : public ViewTraits { // to avoid incomplete type errors from usng Kokkos::Cuda directly. if (std::is_same::value) { - typename traits::device_type::memory_space::execution_space().fence(); + typename traits::device_type::memory_space::execution_space().fence( + "Kokkos::OffsetView::OffsetView(): fence before UVM allocation"); } #endif //------------------------------------------------------------ @@ -1256,7 +1256,8 @@ class OffsetView : public ViewTraits { #if defined(KOKKOS_ENABLE_CUDA) if (std::is_same::value) { - typename traits::device_type::memory_space::execution_space().fence(); + typename traits::device_type::memory_space::execution_space().fence( + "Kokkos::OffsetView::OffsetView(): fence after UVM allocation"); } #endif //------------------------------------------------------------ diff --git a/packages/kokkos/containers/src/Kokkos_ScatterView.hpp b/packages/kokkos/containers/src/Kokkos_ScatterView.hpp index dcd4cf73e5d7..79bc43b7393d 100644 --- a/packages/kokkos/containers/src/Kokkos_ScatterView.hpp +++ b/packages/kokkos/containers/src/Kokkos_ScatterView.hpp @@ -834,7 +834,7 @@ class ScatterView::value, "ScatterView contribute destination has different layout"); static_assert( - Kokkos::Impl::SpaceAccessibility< + Kokkos::SpaceAccessibility< execution_space, typename dest_type::memory_space>::accessible, "ScatterView contribute destination memory space not accessible"); if (dest.data() == internal_view.data()) return; @@ -1061,7 +1061,7 @@ class ScatterView::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::SpaceAccessibility< + Kokkos::SpaceAccessibility< execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); bool is_equal = (dest.data() == internal_view.data()); @@ -1290,7 +1290,7 @@ class ScatterView::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::SpaceAccessibility< + Kokkos::SpaceAccessibility< execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); auto extent = internal_view.extent(internal_view_type::rank - 1); diff --git a/packages/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp b/packages/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp index 81be3ee2d3e8..cd633e403101 100644 --- a/packages/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp +++ b/packages/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp @@ -405,7 +405,9 @@ class StaticCrsGraph { Kokkos::parallel_for("Kokkos::StaticCrsGraph::create_block_partitioning", Kokkos::RangePolicy(0, numRows()), partitioner); - typename device_type::execution_space().fence(); + typename device_type::execution_space().fence( + "Kokkos::StaticCrsGraph::create_block_partitioning:: fence after " + "partition"); row_block_offsets = block_offsets; } diff --git a/packages/kokkos/containers/src/Kokkos_UnorderedMap.hpp b/packages/kokkos/containers/src/Kokkos_UnorderedMap.hpp index edb0e7261da9..a1601eee3586 100644 --- a/packages/kokkos/containers/src/Kokkos_UnorderedMap.hpp +++ b/packages/kokkos/containers/src/Kokkos_UnorderedMap.hpp @@ -345,7 +345,8 @@ class UnorderedMap { const impl_value_type tmp = impl_value_type(); Kokkos::deep_copy(m_values, tmp); } - { Kokkos::deep_copy(m_scalars, 0); } + Kokkos::deep_copy(m_scalars, 0); + m_size = 0; } KOKKOS_INLINE_FUNCTION constexpr bool is_allocated() const { @@ -393,9 +394,9 @@ class UnorderedMap { /// /// This method has undefined behavior when erasable() is true. /// - /// Note that this is not a device function; it cannot be called in + /// Note that this is not a device function; it cannot be called in /// a parallel kernel. The value is not stored as a variable; it - /// must be computed. + /// must be computed. m_size is a mutable cache of that value. size_type size() const { if (capacity() == 0u) return 0u; if (modified()) { @@ -419,9 +420,13 @@ class UnorderedMap { bool begin_erase() { bool result = !erasable(); if (is_insertable_map && result) { - execution_space().fence(); + execution_space().fence( + "Kokkos::UnorderedMap::begin_erase: fence before setting erasable " + "flag"); set_flag(erasable_idx); - execution_space().fence(); + execution_space().fence( + "Kokkos::UnorderedMap::begin_erase: fence after setting erasable " + "flag"); } return result; } @@ -429,10 +434,12 @@ class UnorderedMap { bool end_erase() { bool result = erasable(); if (is_insertable_map && result) { - execution_space().fence(); + execution_space().fence( + "Kokkos::UnorderedMap::end_erase: fence before erasing"); Impl::UnorderedMapErase f(*this); f.apply(); - execution_space().fence(); + execution_space().fence( + "Kokkos::UnorderedMap::end_erase: fence after erasing"); reset_flag(erasable_idx); } return result; diff --git a/packages/kokkos/containers/src/Kokkos_Vector.hpp b/packages/kokkos/containers/src/Kokkos_Vector.hpp index a1fbba6b21c7..88721bd89eb2 100644 --- a/packages/kokkos/containers/src/Kokkos_Vector.hpp +++ b/packages/kokkos/containers/src/Kokkos_Vector.hpp @@ -119,12 +119,14 @@ class vector : public DualView { if (DV::template need_sync()) { set_functor_host f(DV::h_view, val); parallel_for("Kokkos::vector::assign", n, f); - typename DV::t_host::execution_space().fence(); + typename DV::t_host::execution_space().fence( + "Kokkos::vector::assign: fence after assigning values"); DV::template modify(); } else { set_functor f(DV::d_view, val); parallel_for("Kokkos::vector::assign", n, f); - typename DV::t_dev::execution_space().fence(); + typename DV::t_dev::execution_space().fence( + "Kokkos::vector::assign: fence after assigning values"); DV::template modify(); } } diff --git a/packages/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp b/packages/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp index 6047e60f3dd0..9512f2d4a20e 100644 --- a/packages/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp +++ b/packages/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp @@ -57,22 +57,10 @@ namespace Kokkos { namespace Impl { -KOKKOS_FORCEINLINE_FUNCTION -unsigned rotate_left(unsigned i, int r) { - constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); - return r ? ((i << r) | (i >> (size - r))) : i; -} - KOKKOS_FORCEINLINE_FUNCTION unsigned rotate_right(unsigned i, int r) { constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); - // FIXME_SYCL llvm.fshr.i32 missing - // (https://github.com/intel/llvm/issues/3308) -#ifdef __SYCL_DEVICE_ONLY__ - return rotate_left(i, size - r); -#else return r ? ((i >> r) | (i << (size - r))) : i; -#endif } template diff --git a/packages/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp b/packages/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp index 367ab3385720..fdd78e4e5f99 100644 --- a/packages/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp +++ b/packages/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp @@ -75,7 +75,7 @@ uint32_t fmix32(uint32_t h) { KOKKOS_INLINE_FUNCTION uint32_t MurmurHash3_x86_32(const void* key, int len, uint32_t seed) { - const uint8_t* data = (const uint8_t*)key; + const uint8_t* data = static_cast(key); const int nblocks = len / 4; uint32_t h1 = seed; diff --git a/packages/kokkos/containers/unit_tests/TestDualView.hpp b/packages/kokkos/containers/unit_tests/TestDualView.hpp index 3eee85ed10bd..e22564aa5c24 100644 --- a/packages/kokkos/containers/unit_tests/TestDualView.hpp +++ b/packages/kokkos/containers/unit_tests/TestDualView.hpp @@ -49,7 +49,7 @@ #include #include #include -#include +#include #include namespace Test { diff --git a/packages/kokkos/containers/unit_tests/TestDynViewAPI.hpp b/packages/kokkos/containers/unit_tests/TestDynViewAPI.hpp index dd0199ed81c7..a8d62bd24cad 100644 --- a/packages/kokkos/containers/unit_tests/TestDynViewAPI.hpp +++ b/packages/kokkos/containers/unit_tests/TestDynViewAPI.hpp @@ -702,6 +702,11 @@ class TestDynViewAPI { using View0 = Kokkos::View; using View1 = Kokkos::View; + using View2 = Kokkos::View; + using View3 = Kokkos::View; + using View4 = Kokkos::View; + using View5 = Kokkos::View; + using View6 = Kokkos::View; using View7 = Kokkos::View; using host_view_space = typename View0::host_mirror_space; @@ -1065,7 +1070,7 @@ class TestDynViewAPI { dView0 d_uninitialized( Kokkos::view_alloc(Kokkos::WithoutInitializing, "uninit"), 10, 20); - ASSERT_TRUE(d_uninitialized.data() != nullptr); + ASSERT_NE(d_uninitialized.data(), nullptr); ASSERT_EQ(d_uninitialized.rank(), 2); ASSERT_EQ(d_uninitialized.extent(0), 10); ASSERT_EQ(d_uninitialized.extent(1), 20); @@ -1075,14 +1080,14 @@ class TestDynViewAPI { hView0 hx, hy, hz; ASSERT_TRUE(Kokkos::is_dyn_rank_view::value); - ASSERT_FALSE(Kokkos::is_dyn_rank_view >::value); - - ASSERT_TRUE(dx.data() == nullptr); // Okay with UVM - ASSERT_TRUE(dy.data() == nullptr); // Okay with UVM - ASSERT_TRUE(dz.data() == nullptr); // Okay with UVM - ASSERT_TRUE(hx.data() == nullptr); - ASSERT_TRUE(hy.data() == nullptr); - ASSERT_TRUE(hz.data() == nullptr); + ASSERT_FALSE(Kokkos::is_dyn_rank_view>::value); + + ASSERT_EQ(dx.data(), nullptr); // Okay with UVM + ASSERT_EQ(dy.data(), nullptr); // Okay with UVM + ASSERT_EQ(dz.data(), nullptr); // Okay with UVM + ASSERT_EQ(hx.data(), nullptr); + ASSERT_EQ(hy.data(), nullptr); + ASSERT_EQ(hz.data(), nullptr); ASSERT_EQ(dx.extent(0), 0u); // Okay with UVM ASSERT_EQ(dy.extent(0), 0u); // Okay with UVM ASSERT_EQ(dz.extent(0), 0u); // Okay with UVM @@ -1153,11 +1158,11 @@ class TestDynViewAPI { ASSERT_EQ(dx.use_count(), size_t(2)); - ASSERT_FALSE(dx.data() == nullptr); - ASSERT_FALSE(const_dx.data() == nullptr); - ASSERT_FALSE(unmanaged_dx.data() == nullptr); - ASSERT_FALSE(unmanaged_from_ptr_dx.data() == nullptr); - ASSERT_FALSE(dy.data() == nullptr); + ASSERT_NE(dx.data(), nullptr); + ASSERT_NE(const_dx.data(), nullptr); + ASSERT_NE(unmanaged_dx.data(), nullptr); + ASSERT_NE(unmanaged_from_ptr_dx.data(), nullptr); + ASSERT_NE(dy.data(), nullptr); ASSERT_NE(dx, dy); ASSERT_EQ(dx.extent(0), unsigned(N0)); @@ -1317,17 +1322,17 @@ class TestDynViewAPI { ASSERT_NE(dx, dz); dx = dView0(); - ASSERT_TRUE(dx.data() == nullptr); - ASSERT_FALSE(dy.data() == nullptr); - ASSERT_FALSE(dz.data() == nullptr); + ASSERT_EQ(dx.data(), nullptr); + ASSERT_NE(dy.data(), nullptr); + ASSERT_NE(dz.data(), nullptr); dy = dView0(); - ASSERT_TRUE(dx.data() == nullptr); - ASSERT_TRUE(dy.data() == nullptr); - ASSERT_FALSE(dz.data() == nullptr); + ASSERT_EQ(dx.data(), nullptr); + ASSERT_EQ(dy.data(), nullptr); + ASSERT_NE(dz.data(), nullptr); dz = dView0(); - ASSERT_TRUE(dx.data() == nullptr); - ASSERT_TRUE(dy.data() == nullptr); - ASSERT_TRUE(dz.data() == nullptr); + ASSERT_EQ(dx.data(), nullptr); + ASSERT_EQ(dy.data(), nullptr); + ASSERT_EQ(dz.data(), nullptr); // View - DynRankView Interoperability tests // deep_copy from view to dynrankview @@ -1367,7 +1372,7 @@ class TestDynViewAPI { static void check_auto_conversion_to_const( const Kokkos::DynRankView& arg_const, const Kokkos::DynRankView& arg) { - ASSERT_TRUE(arg_const == arg); + ASSERT_EQ(arg_const, arg); } static void run_test_allocated() { @@ -1396,8 +1401,8 @@ class TestDynViewAPI { const_typeX xc = x; const_typeR xr = x; - ASSERT_TRUE(xc == x); - ASSERT_TRUE(x == xc); + ASSERT_EQ(xc, x); + ASSERT_EQ(x, xc); // For CUDA the constant random access View does not return // an lvalue reference due to retrieving through texture cache @@ -1406,7 +1411,7 @@ class TestDynViewAPI { if (!std::is_same::value) #endif { - ASSERT_TRUE(x.data() == xr.data()); + ASSERT_EQ(x.data(), xr.data()); } // typeX xf = xc ; // setting non-const from const must not compile @@ -1659,29 +1664,29 @@ class TestDynViewAPI { const_svector_right_type cvr3 = Kokkos::subdynrankview(mv, Kokkos::ALL(), 2); - ASSERT_TRUE(&v1[0] == &v1(0)); - ASSERT_TRUE(&v1[0] == &mv(0, 0)); - ASSERT_TRUE(&v2[0] == &mv(0, 1)); - ASSERT_TRUE(&v3[0] == &mv(0, 2)); - - ASSERT_TRUE(&cv1[0] == &mv(0, 0)); - ASSERT_TRUE(&cv2[0] == &mv(0, 1)); - ASSERT_TRUE(&cv3[0] == &mv(0, 2)); - - ASSERT_TRUE(&vr1[0] == &mv(0, 0)); - ASSERT_TRUE(&vr2[0] == &mv(0, 1)); - ASSERT_TRUE(&vr3[0] == &mv(0, 2)); - - ASSERT_TRUE(&cvr1[0] == &mv(0, 0)); - ASSERT_TRUE(&cvr2[0] == &mv(0, 1)); - ASSERT_TRUE(&cvr3[0] == &mv(0, 2)); - - ASSERT_TRUE(&mv1(0, 0) == &mv(1, 2)); - ASSERT_TRUE(&mv1(1, 1) == &mv(2, 3)); - ASSERT_TRUE(&mv1(3, 2) == &mv(4, 4)); - ASSERT_TRUE(&mvr1(0, 0) == &mv_right(1, 2)); - ASSERT_TRUE(&mvr1(1, 1) == &mv_right(2, 3)); - ASSERT_TRUE(&mvr1(3, 2) == &mv_right(4, 4)); + ASSERT_EQ(&v1[0], &v1(0)); + ASSERT_EQ(&v1[0], &mv(0, 0)); + ASSERT_EQ(&v2[0], &mv(0, 1)); + ASSERT_EQ(&v3[0], &mv(0, 2)); + + ASSERT_EQ(&cv1[0], &mv(0, 0)); + ASSERT_EQ(&cv2[0], &mv(0, 1)); + ASSERT_EQ(&cv3[0], &mv(0, 2)); + + ASSERT_EQ(&vr1[0], &mv(0, 0)); + ASSERT_EQ(&vr2[0], &mv(0, 1)); + ASSERT_EQ(&vr3[0], &mv(0, 2)); + + ASSERT_EQ(&cvr1[0], &mv(0, 0)); + ASSERT_EQ(&cvr2[0], &mv(0, 1)); + ASSERT_EQ(&cvr3[0], &mv(0, 2)); + + ASSERT_EQ(&mv1(0, 0), &mv(1, 2)); + ASSERT_EQ(&mv1(1, 1), &mv(2, 3)); + ASSERT_EQ(&mv1(3, 2), &mv(4, 4)); + ASSERT_EQ(&mvr1(0, 0), &mv_right(1, 2)); + ASSERT_EQ(&mvr1(1, 1), &mv_right(2, 3)); + ASSERT_EQ(&mvr1(3, 2), &mv_right(4, 4)); const_svector_type c_cv1(v1); typename svector_type::const_type c_cv2(v2); diff --git a/packages/kokkos/containers/unit_tests/TestDynamicView.hpp b/packages/kokkos/containers/unit_tests/TestDynamicView.hpp index f018793dd6f3..023bf92f62b4 100644 --- a/packages/kokkos/containers/unit_tests/TestDynamicView.hpp +++ b/packages/kokkos/containers/unit_tests/TestDynamicView.hpp @@ -52,7 +52,7 @@ #include #include -#include +#include namespace Test { diff --git a/packages/kokkos/containers/unit_tests/TestOffsetView.hpp b/packages/kokkos/containers/unit_tests/TestOffsetView.hpp index 9ddc226e291f..24a43e1ebc72 100644 --- a/packages/kokkos/containers/unit_tests/TestOffsetView.hpp +++ b/packages/kokkos/containers/unit_tests/TestOffsetView.hpp @@ -50,7 +50,7 @@ #include #include #include -#include +#include #include #include diff --git a/packages/kokkos/containers/unit_tests/TestScatterView.hpp b/packages/kokkos/containers/unit_tests/TestScatterView.hpp index fdbce2d49200..342ce2af48af 100644 --- a/packages/kokkos/containers/unit_tests/TestScatterView.hpp +++ b/packages/kokkos/containers/unit_tests/TestScatterView.hpp @@ -118,11 +118,51 @@ struct test_scatter_view_impl_cls sizes(LENGTH); - size_t total_length = 0; - for (size_t i = 0; i < LENGTH; ++i) { sizes[i] = rand() % 1000; } @@ -189,10 +187,6 @@ void run_test_graph3(size_t B, size_t N) { sizes[1] = N; sizes[1998] = N; - for (size_t i = 0; i < LENGTH; ++i) { - total_length += sizes[i]; - } - int C = 0; dView dx = Kokkos::create_staticcrsgraph("test", sizes); dx.create_block_partitioning(B, C); diff --git a/packages/kokkos/containers/unit_tests/TestUnorderedMap.hpp b/packages/kokkos/containers/unit_tests/TestUnorderedMap.hpp index 4413cfbc80e3..8009b9965663 100644 --- a/packages/kokkos/containers/unit_tests/TestUnorderedMap.hpp +++ b/packages/kokkos/containers/unit_tests/TestUnorderedMap.hpp @@ -295,10 +295,8 @@ void test_deep_copy(uint32_t num_nodes) { } // FIXME_SYCL wrong results on Nvidia GPUs but correct on Host and Intel GPUs -// FIXME_HIP // WORKAROUND MSVC -#if !(defined(KOKKOS_ENABLE_HIP) && (HIP_VERSION < 401)) && \ - !defined(_WIN32) && !defined(KOKKOS_ENABLE_SYCL) +#if !defined(_WIN32) && !defined(KOKKOS_ENABLE_SYCL) TEST(TEST_CATEGORY, UnorderedMap_insert) { for (int i = 0; i < 500; ++i) { test_insert(100000, 90000, 100, true); @@ -329,6 +327,23 @@ TEST(TEST_CATEGORY, UnorderedMap_valid_empty) { ASSERT_TRUE(n.is_allocated()); } +TEST(TEST_CATEGORY, UnorderedMap_clear_zero_size) { + using Map = + Kokkos::UnorderedMap; + + Map m(11); + ASSERT_EQ(0u, m.size()); + + m.insert(2); + m.insert(3); + m.insert(5); + m.insert(7); + ASSERT_EQ(4u, m.size()); + + m.clear(); + ASSERT_EQ(0u, m.size()); +} + } // namespace Test #endif // KOKKOS_TEST_UNORDERED_MAP_HPP diff --git a/packages/kokkos/core/cmake/KokkosCore_config.h.in b/packages/kokkos/core/cmake/KokkosCore_config.h.in deleted file mode 100644 index f0835772b864..000000000000 --- a/packages/kokkos/core/cmake/KokkosCore_config.h.in +++ /dev/null @@ -1,104 +0,0 @@ -/* The trivial 'src/build_common.sh' creates a config - * that must stay in sync with this file. - */ -#cmakedefine KOKKOS_FOR_SIERRA - -#if !defined(KOKKOS_FOR_SIERRA) - -#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H) -#error \ - "Don't include KokkosCore_config.h directly; include Kokkos_Macros.hpp instead." -#else -#define KOKKOS_CORE_CONFIG_H -#endif - -#cmakedefine KOKKOS_ENABLE_CUDA -#cmakedefine KOKKOS_ENABLE_HIP -#cmakedefine KOKKOS_ENABLE_OPENMP -#cmakedefine KOKKOS_ENABLE_THREADS -#cmakedefine KOKKOS_ENABLE_SERIAL -#cmakedefine KOKKOS_ENABLE_Winthread - -#cmakedefine KOKKOS_ENABLE_HWLOC -#cmakedefine KOKKOS_ENABLE_HBWSPACE -#cmakedefine KOKKOS_ENABLE_LIBRT - -#cmakedefine KOKKOS_ENABLE_DEBUG -#cmakedefine KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK -#cmakedefine KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK -#cmakedefine KOKKOS_ENABLE_PROFILING_LOAD_PRINT -#cmakedefine KOKKOS_ENABLE_TUNING - -#cmakedefine KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION - -#ifdef KOKKOS_ENABLE_CUDA - -#cmakedefine KOKKOS_ENABLE_CUDA_LDG_INTRINSIC - -// mfh 16 Sep 2014: If passed in on the command line, that overrides -// any value of KOKKOS_USE_CUDA_UVM here. Doing this should prevent build -// warnings like this one: -// -// packages/kokkos/core/src/KokkosCore_config.h:13:1: warning: -// "KOKKOS_USE_CUDA_UVM" redefined -// -// At some point, we should edit the test-build scripts in -// Trilinos/cmake/ctest/drivers/perseus/, and take -// -DKOKKOS_USE_CUDA_UVM from the command-line arguments there. I -// hesitate to do that now, because I'm not sure if all the files are -// including KokkosCore_config.h (or a header file that includes it) like -// they should. -#ifndef KOKKOS_USE_CUDA_UVM -#cmakedefine KOKKOS_USE_CUDA_UVM -#endif - -#cmakedefine KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE - -#cmakedefine KOKKOS_ENABLE_CUDA_LAMBDA - -#endif - -#cmakedefine KOKKOS_IMPL_CUDA_CLANG_WORKAROUND - -#ifndef __CUDA_ARCH__ -#cmakedefine KOKKOS_ENABLE_ISA_X86_64 -#cmakedefine KOKKOS_ENABLE_ISA_KNC -#cmakedefine KOKKOS_ENABLE_ISA_POWERPCLE -#endif - -#ifdef KOKKOS_ENABLE_HIP -#cmakedefine KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE -#endif - -#cmakedefine KOKKOS_ARCH_ARMV80 1 -#cmakedefine KOKKOS_ARCH_ARMV81 1 -#cmakedefine KOKKOS_ARCH_ARMV8_THUNDERX 1 -#cmakedefine KOKKOS_ARCH_AVX 1 -#cmakedefine KOKKOS_ARCH_AVX2 1 -#cmakedefine KOKKOS_ARCH_AVX512MIC 1 -#cmakedefine KOKKOS_ARCH_AVX512XEON 1 -#cmakedefine KOKKOS_ARCH_KNC 1 -#cmakedefine KOKKOS_ARCH_POWER8 1 -#cmakedefine KOKKOS_ARCH_POWER9 1 -#cmakedefine KOKKOS_ARCH_KEPLER 1 -#cmakedefine KOKKOS_ARCH_KEPLER30 1 -#cmakedefine KOKKOS_ARCH_KEPLER32 1 -#cmakedefine KOKKOS_ARCH_KEPLER35 1 -#cmakedefine KOKKOS_ARCH_KEPLER37 1 -#cmakedefine KOKKOS_ARCH_MAXWELL 1 -#cmakedefine KOKKOS_ARCH_MAXWELL50 1 -#cmakedefine KOKKOS_ARCH_MAXWELL52 1 -#cmakedefine KOKKOS_ARCH_MAXWELL53 1 -#cmakedefine KOKKOS_ARCH_PASCAL 1 -#cmakedefine KOKKOS_ARCH_PASCAL60 1 -#cmakedefine KOKKOS_ARCH_PASCAL61 1 -#cmakedefine KOKKOS_ARCH_VOLTA70 1 - -// TODO: These are currently not used in Kokkos. Should they be removed? -#cmakedefine KOKKOS_ENABLE_MPI -#cmakedefine KOKKOS_ENABLE_CUSPARSE - -// TODO: No longer options in Kokkos. Need to be removed. -#cmakedefine KOKKOS_USING_DEPRECATED_VIEW - -#endif // !defined(KOKKOS_FOR_SIERRA) diff --git a/packages/kokkos/core/perf_test/CMakeLists.txt b/packages/kokkos/core/perf_test/CMakeLists.txt index 9ff4b6006da8..a7c57a94346d 100644 --- a/packages/kokkos/core/perf_test/CMakeLists.txt +++ b/packages/kokkos/core/perf_test/CMakeLists.txt @@ -10,9 +10,7 @@ #INCLUDE_DIRECTORIES("${CMAKE_CURRENT_SOURCE_DIR}/../../algorithms/src") # FIXME_OPENMPTARGET - the NVIDIA HPC compiler nvc++ in the OpenMPTarget backend does not pass the perf_tests. -IF (KOKKOS_ENABLE_OPENMPTARGET - AND (KOKKOS_CXX_COMPILER_ID STREQUAL PGI - OR KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC)) +IF (KOKKOS_ENABLE_OPENMPTARGET AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) RETURN() ENDIF() diff --git a/packages/kokkos/core/perf_test/PerfTestGramSchmidt.cpp b/packages/kokkos/core/perf_test/PerfTestGramSchmidt.cpp index dee21fd7a575..b534c32c52c6 100644 --- a/packages/kokkos/core/perf_test/PerfTestGramSchmidt.cpp +++ b/packages/kokkos/core/perf_test/PerfTestGramSchmidt.cpp @@ -231,7 +231,7 @@ void run_test_gramschmidt(int exp_beg, int exp_end, int num_trials, std::cout << label_gramschmidt << " , " << parallel_work_length << " , " << min_seconds << " , " << (min_seconds / parallel_work_length) - << std::endl; + << ", " << avg_seconds << std::endl; } } diff --git a/packages/kokkos/core/perf_test/PerfTestHexGrad.cpp b/packages/kokkos/core/perf_test/PerfTestHexGrad.cpp index c431c2b0c86d..24c1898e0a16 100644 --- a/packages/kokkos/core/perf_test/PerfTestHexGrad.cpp +++ b/packages/kokkos/core/perf_test/PerfTestHexGrad.cpp @@ -280,7 +280,7 @@ void run_test_hexgrad(int exp_beg, int exp_end, int num_trials, std::cout << label_hexgrad << " , " << parallel_work_length << " , " << min_seconds << " , " << (min_seconds / parallel_work_length) - << std::endl; + << avg_seconds << std::endl; } } diff --git a/packages/kokkos/core/perf_test/PerfTest_ExecSpacePartitioning.cpp b/packages/kokkos/core/perf_test/PerfTest_ExecSpacePartitioning.cpp index 50bbc78a6b75..5b7c2a7a0390 100644 --- a/packages/kokkos/core/perf_test/PerfTest_ExecSpacePartitioning.cpp +++ b/packages/kokkos/core/perf_test/PerfTest_ExecSpacePartitioning.cpp @@ -205,7 +205,7 @@ TEST(default_exec, overlap_range_policy) { double time_end = timer.seconds(); if (SpaceInstance::overlap()) { - ASSERT_TRUE((time_end > 1.5 * time_overlap)); + ASSERT_GT(time_end, 1.5 * time_overlap); } printf("Time RangePolicy: NonOverlap: %lf Time Overlap: %lf\n", time_end, time_overlap); @@ -238,7 +238,7 @@ TEST(default_exec, overlap_range_policy) { double time_not_fenced = timer.seconds(); Kokkos::fence(); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_fenced > 2.0 * time_not_fenced); + ASSERT_GT(time_fenced, 2.0 * time_not_fenced); } timer.reset(); @@ -280,7 +280,7 @@ TEST(default_exec, overlap_range_policy) { ASSERT_EQ(h_result2(), h_result()); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_overlapped_reduce < 1.5 * time_no_overlapped_reduce); + ASSERT_LT(time_overlapped_reduce, 1.5 * time_no_overlapped_reduce); } printf("Time RangePolicy Reduce: NonOverlap: %lf Time Overlap: %lf\n", time_no_overlapped_reduce, time_overlapped_reduce); @@ -378,7 +378,7 @@ TEST(default_exec, overlap_mdrange_policy) { double time_end = timer.seconds(); if (SpaceInstance::overlap()) { - ASSERT_TRUE((time_end > 1.5 * time_overlap)); + ASSERT_GT(time_end, 1.5 * time_overlap); } printf("Time MDRangePolicy: NonOverlap: %lf Time Overlap: %lf\n", time_end, time_overlap); @@ -413,7 +413,7 @@ TEST(default_exec, overlap_mdrange_policy) { double time_not_fenced = timer.seconds(); Kokkos::fence(); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_fenced > 2.0 * time_not_fenced); + ASSERT_GT(time_fenced, 2.0 * time_not_fenced); } timer.reset(); @@ -459,7 +459,7 @@ TEST(default_exec, overlap_mdrange_policy) { ASSERT_EQ(h_result2(), h_result()); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_overlapped_reduce < 1.5 * time_no_overlapped_reduce); + ASSERT_LT(time_overlapped_reduce, 1.5 * time_no_overlapped_reduce); } printf("Time MDRangePolicy Reduce: NonOverlap: %lf Time Overlap: %lf\n", time_no_overlapped_reduce, time_overlapped_reduce); @@ -548,7 +548,7 @@ TEST(default_exec, overlap_team_policy) { double time_end = timer.seconds(); if (SpaceInstance::overlap()) { - ASSERT_TRUE((time_end > 1.5 * time_overlap)); + ASSERT_GT(time_end, 1.5 * time_overlap); } printf("Time TeamPolicy: NonOverlap: %lf Time Overlap: %lf\n", time_end, time_overlap); @@ -581,7 +581,7 @@ TEST(default_exec, overlap_team_policy) { double time_not_fenced = timer.seconds(); Kokkos::fence(); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_fenced > 2.0 * time_not_fenced); + ASSERT_GT(time_fenced, 2.0 * time_not_fenced); } timer.reset(); Kokkos::parallel_reduce( @@ -622,7 +622,7 @@ TEST(default_exec, overlap_team_policy) { ASSERT_EQ(h_result2(), h_result()); if (SpaceInstance::overlap()) { - ASSERT_TRUE(time_overlapped_reduce < 1.5 * time_no_overlapped_reduce); + ASSERT_LT(time_overlapped_reduce, 1.5 * time_no_overlapped_reduce); } printf("Time TeamPolicy Reduce: NonOverlap: %lf Time Overlap: %lf\n", time_no_overlapped_reduce, time_overlapped_reduce); diff --git a/packages/kokkos/core/perf_test/PerfTest_ViewAllocate.cpp b/packages/kokkos/core/perf_test/PerfTest_ViewAllocate.cpp index 550316bec997..555a05ea279c 100644 --- a/packages/kokkos/core/perf_test/PerfTest_ViewAllocate.cpp +++ b/packages/kokkos/core/perf_test/PerfTest_ViewAllocate.cpp @@ -120,7 +120,8 @@ void run_allocateview_tests(int N, int R) { { Kokkos::Timer timer; for (int r = 0; r < R; r++) { - double* a_ptr = (double*)Kokkos::kokkos_malloc("A", sizeof(double) * N8); + double* a_ptr = + static_cast(Kokkos::kokkos_malloc("A", sizeof(double) * N8)); Kokkos::parallel_for( N8, KOKKOS_LAMBDA(const int& i) { a_ptr[i] = 0.0; }); Kokkos::fence(); diff --git a/packages/kokkos/core/perf_test/PerfTest_ViewResize_8.cpp b/packages/kokkos/core/perf_test/PerfTest_ViewResize_8.cpp index afeeb643569e..b0562f2fd122 100644 --- a/packages/kokkos/core/perf_test/PerfTest_ViewResize_8.cpp +++ b/packages/kokkos/core/perf_test/PerfTest_ViewResize_8.cpp @@ -47,10 +47,18 @@ namespace Test { TEST(default_exec, ViewResize_Rank8) { +// FIXME_SYCL Avoid running out of resources on the CUDA GPU used in the CI +#ifdef KOKKOS_ENABLE_SYCL + printf("Resize View Performance for LayoutLeft:\n"); + run_resizeview_tests8(9, 1); + printf("Resize View Performance for LayoutRight:\n"); + run_resizeview_tests8(9, 1); +#else printf("Resize View Performance for LayoutLeft:\n"); run_resizeview_tests8(10, 1); printf("Resize View Performance for LayoutRight:\n"); run_resizeview_tests8(10, 1); +#endif } } // namespace Test diff --git a/packages/kokkos/core/perf_test/test_atomic.cpp b/packages/kokkos/core/perf_test/test_atomic.cpp index 59820f3bdd2e..54824e5b39b9 100644 --- a/packages/kokkos/core/perf_test/test_atomic.cpp +++ b/packages/kokkos/core/perf_test/test_atomic.cpp @@ -47,7 +47,7 @@ #include #include -#include +#include using exec_space = Kokkos::DefaultExecutionSpace; @@ -401,7 +401,7 @@ template void Loop(int loop, int test, const char* type_name) { LoopVariant(loop, test); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; T res = LoopVariant(loop, test); double time = timer.seconds(); diff --git a/packages/kokkos/core/perf_test/test_atomic_minmax_simple.cpp b/packages/kokkos/core/perf_test/test_atomic_minmax_simple.cpp index eec1c8eacc77..4086ef58163f 100644 --- a/packages/kokkos/core/perf_test/test_atomic_minmax_simple.cpp +++ b/packages/kokkos/core/perf_test/test_atomic_minmax_simple.cpp @@ -12,13 +12,13 @@ #include #include -#include +#include using exec_space = Kokkos::DefaultExecutionSpace; template void test(const int length) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; using vector = Kokkos::View; diff --git a/packages/kokkos/core/perf_test/test_mempool.cpp b/packages/kokkos/core/perf_test/test_mempool.cpp index 9aab119774c4..7887d4ba5519 100644 --- a/packages/kokkos/core/perf_test/test_mempool.cpp +++ b/packages/kokkos/core/perf_test/test_mempool.cpp @@ -48,7 +48,7 @@ #include #include -#include +#include using ExecSpace = Kokkos::DefaultExecutionSpace; using MemorySpace = Kokkos::DefaultExecutionSpace::memory_space; @@ -100,7 +100,7 @@ struct TestFunctor { const unsigned size_alloc = chunk * (1 + (j % chunk_span)); - ptrs(j) = (uintptr_t)pool.allocate(size_alloc); + ptrs(j) = reinterpret_cast(pool.allocate(size_alloc)); if (ptrs(j)) ++update; } @@ -129,7 +129,7 @@ struct TestFunctor { const unsigned size_alloc = chunk * (1 + (j % chunk_span)); - pool.deallocate((void*)ptrs(j), size_alloc); + pool.deallocate(reinterpret_cast(ptrs(j)), size_alloc); } } @@ -153,9 +153,9 @@ struct TestFunctor { for (unsigned k = 0; k < repeat_inner; ++k) { const unsigned size_alloc = chunk * (1 + (j % chunk_span)); - pool.deallocate((void*)ptrs(j), size_alloc); + pool.deallocate(reinterpret_cast(ptrs(j)), size_alloc); - ptrs(j) = (uintptr_t)pool.allocate(size_alloc); + ptrs(j) = reinterpret_cast(pool.allocate(size_alloc)); if (0 == ptrs(j)) update++; } @@ -266,7 +266,7 @@ int main(int argc, char* argv[]) { TestFunctor functor(total_alloc_size, min_superblock_size, number_alloc, fill_stride, chunk_span, repeat_inner); - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; if (!functor.test_fill()) { Kokkos::abort("fill "); diff --git a/packages/kokkos/core/perf_test/test_taskdag.cpp b/packages/kokkos/core/perf_test/test_taskdag.cpp index b2f936a955ec..49957ae9323d 100644 --- a/packages/kokkos/core/perf_test/test_taskdag.cpp +++ b/packages/kokkos/core/perf_test/test_taskdag.cpp @@ -56,7 +56,7 @@ int main() { return 0; } #include #include -#include +#include using ExecSpace = Kokkos::DefaultExecutionSpace; @@ -220,7 +220,7 @@ int main(int argc, char* argv[]) { double time_sum = 0; for (int i = 0; i < test_repeat_outer; ++i) { - Kokkos::Impl::Timer timer; + Kokkos::Timer timer; Functor::FutureType ftmp = Kokkos::host_spawn(Kokkos::TaskSingle(sched), Functor(fib_input)); diff --git a/packages/kokkos/core/src/CMakeLists.txt b/packages/kokkos/core/src/CMakeLists.txt index 2ab098980572..499736c60d55 100644 --- a/packages/kokkos/core/src/CMakeLists.txt +++ b/packages/kokkos/core/src/CMakeLists.txt @@ -9,6 +9,8 @@ INSTALL (DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/" DESTINATION ${KOKKOS_HEADER_DIR} FILES_MATCHING + PATTERN "*.inc" + PATTERN "*.inc_*" PATTERN "*.hpp" PATTERN "*.h" ) @@ -65,6 +67,15 @@ IF (KOKKOS_ENABLE_SYCL) APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/SYCL/*.hpp) ENDIF() +IF (KOKKOS_ENABLE_IMPL_DESUL_ATOMICS) + APPEND_GLOB(KOKKOS_CORE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/desul/src/*.cpp) + APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/desul/*.hpp) + APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/desul/*/*.hpp) + APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/desul/*/*/*.hpp) + APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/desul/*/*/*.inc) +ENDIF() + + KOKKOS_ADD_LIBRARY( kokkoscore SOURCES ${KOKKOS_CORE_SRCS} @@ -86,3 +97,15 @@ KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBDL) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBRT) KOKKOS_LINK_TPL(kokkoscore PUBLIC PTHREAD) KOKKOS_LINK_TPL(kokkoscore PUBLIC ROCM) + +# FIXME: We need a proper solution to figure out whether to enable +# libatomic +# XL requires libatomic even for 64 bit CAS, most others only for 128 +# I (CT) had removed 128bit CAS from desul to not need libatomic. +IF (KOKKOS_ENABLE_IMPL_DESUL_ATOMICS AND + (KOKKOS_ENABLE_OPENMPTARGET OR (CMAKE_CXX_COMPILER_ID STREQUAL XLClang))) + target_link_libraries(kokkoscore PUBLIC atomic) +ENDIF() + + +KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBQUADMATH) diff --git a/packages/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/packages/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp index 916f109758de..f6b276240316 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp @@ -90,43 +90,25 @@ static std::atomic num_uvm_allocations(0); } // namespace -DeepCopy::DeepCopy(void *dst, const void *src, - size_t n) { - CUDA_SAFE_CALL(cudaMemcpy(dst, src, n, cudaMemcpyDefault)); +void DeepCopyCuda(void *dst, const void *src, size_t n) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMemcpy(dst, src, n, cudaMemcpyDefault)); } -DeepCopy::DeepCopy(void *dst, const void *src, - size_t n) { - CUDA_SAFE_CALL(cudaMemcpy(dst, src, n, cudaMemcpyDefault)); -} - -DeepCopy::DeepCopy(void *dst, const void *src, - size_t n) { - CUDA_SAFE_CALL(cudaMemcpy(dst, src, n, cudaMemcpyDefault)); -} - -DeepCopy::DeepCopy(const Cuda &instance, void *dst, - const void *src, size_t n) { - CUDA_SAFE_CALL( - cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, instance.cuda_stream())); -} - -DeepCopy::DeepCopy(const Cuda &instance, void *dst, - const void *src, size_t n) { - CUDA_SAFE_CALL( - cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, instance.cuda_stream())); -} - -DeepCopy::DeepCopy(const Cuda &instance, void *dst, - const void *src, size_t n) { - CUDA_SAFE_CALL( +void DeepCopyAsyncCuda(const Cuda &instance, void *dst, const void *src, + size_t n) { + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, instance.cuda_stream())); } void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { cudaStream_t s = cuda_get_deep_copy_stream(); - CUDA_SAFE_CALL(cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, s)); - cudaStreamSynchronize(s); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, s)); + Impl::cuda_stream_synchronize( + s, + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + DeepCopyResourceSynchronization, + "Kokkos::Impl::DeepCopyAsyncCuda: Deep Copy Stream Sync"); } } // namespace Impl @@ -137,6 +119,7 @@ void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { namespace Kokkos { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 KOKKOS_DEPRECATED void CudaSpace::access_error() { const std::string msg( "Kokkos::CudaSpace::access_error attempt to execute Cuda function from " @@ -150,6 +133,7 @@ KOKKOS_DEPRECATED void CudaSpace::access_error(const void *const) { "non-Cuda space"); Kokkos::Impl::throw_runtime_exception(msg); } +#endif /*--------------------------------------------------------------------------*/ @@ -164,9 +148,11 @@ bool CudaUVMSpace::available() { /*--------------------------------------------------------------------------*/ +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 int CudaUVMSpace::number_of_allocations() { return Kokkos::Impl::num_uvm_allocations.load(); } +#endif #ifdef KOKKOS_IMPL_DEBUG_CUDA_PIN_UVM_TO_HOST // The purpose of the following variable is to allow a state-based choice // for pinning UVM allocations to the CPU. For now this is considered @@ -204,6 +190,8 @@ CudaUVMSpace::CudaUVMSpace() : m_device(Kokkos::Cuda().cuda_device()) {} CudaHostPinnedSpace::CudaHostPinnedSpace() {} +int memory_threshold_g = 40000; // 40 kB + //============================================================================== // {{{1 @@ -221,7 +209,19 @@ void *CudaSpace::impl_allocate( const Kokkos::Tools::SpaceHandle arg_handle) const { void *ptr = nullptr; +#ifndef CUDART_VERSION +#error CUDART_VERSION undefined! +#elif (defined(KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC) && CUDART_VERSION >= 11020) + cudaError_t error_code; + if (arg_alloc_size >= memory_threshold_g) { + error_code = cudaMallocAsync(&ptr, arg_alloc_size, 0); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); + } else { + error_code = cudaMalloc(&ptr, arg_alloc_size); + } +#else auto error_code = cudaMalloc(&ptr, arg_alloc_size); +#endif if (error_code != cudaSuccess) { // TODO tag as unlikely branch cudaGetLastError(); // This is the only way to clear the last error, which // we should do here since we're turning it into an @@ -253,7 +253,8 @@ void *CudaUVMSpace::impl_allocate( const Kokkos::Tools::SpaceHandle arg_handle) const { void *ptr = nullptr; - Cuda::impl_static_fence(); + Cuda::impl_static_fence( + "Kokkos::CudaUVMSpace::impl_allocate: Pre UVM Allocation"); if (arg_alloc_size > 0) { Kokkos::Impl::num_uvm_allocations++; @@ -276,7 +277,8 @@ void *CudaUVMSpace::impl_allocate( CudaMallocManaged); } } - Cuda::impl_static_fence(); + Cuda::impl_static_fence( + "Kokkos::CudaUVMSpace::impl_allocate: Post UVM Allocation"); if (Kokkos::Profiling::profileLibraryLoaded()) { const size_t reported_size = (arg_logical_size > 0) ? arg_logical_size : arg_alloc_size; @@ -337,9 +339,20 @@ void CudaSpace::impl_deallocate( Kokkos::Profiling::deallocateData(arg_handle, arg_label, arg_alloc_ptr, reported_size); } - try { - CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); +#ifndef CUDART_VERSION +#error CUDART_VERSION undefined! +#elif (defined(KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC) && CUDART_VERSION >= 11020) + if (arg_alloc_size >= memory_threshold_g) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFreeAsync(arg_alloc_ptr, 0)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); + } else { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); + } +#else + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); +#endif } catch (...) { } } @@ -362,7 +375,8 @@ void CudaUVMSpace::impl_deallocate( , const size_t arg_logical_size, const Kokkos::Tools::SpaceHandle arg_handle) const { - Cuda::impl_static_fence(); + Cuda::impl_static_fence( + "Kokkos::CudaUVMSpace::impl_deallocate: Pre UVM Deallocation"); if (Kokkos::Profiling::profileLibraryLoaded()) { const size_t reported_size = (arg_logical_size > 0) ? arg_logical_size : arg_alloc_size; @@ -372,11 +386,12 @@ void CudaUVMSpace::impl_deallocate( try { if (arg_alloc_ptr != nullptr) { Kokkos::Impl::num_uvm_allocations--; - CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); } } catch (...) { } - Cuda::impl_static_fence(); + Cuda::impl_static_fence( + "Kokkos::CudaUVMSpace::impl_deallocate: Post UVM Deallocation"); } void CudaHostPinnedSpace::deallocate(void *const arg_alloc_ptr, @@ -401,7 +416,7 @@ void CudaHostPinnedSpace::impl_deallocate( reported_size); } try { - CUDA_SAFE_CALL(cudaFreeHost(arg_alloc_ptr)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFreeHost(arg_alloc_ptr)); } catch (...) { } } @@ -462,7 +477,7 @@ SharedAllocationRecord::attach_texture_object( resDesc.res.linear.sizeInBytes = alloc_size; resDesc.res.linear.devPtr = alloc_ptr; - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaCreateTextureObject(&tex_obj, &resDesc, &texDesc, nullptr)); return tex_obj; @@ -581,7 +596,7 @@ void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, bool to_device) { if ((ptr == nullptr) || (bytes == 0)) return; cudaPointerAttributes attr; - CUDA_SAFE_CALL(cudaPointerGetAttributes(&attr, ptr)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaPointerGetAttributes(&attr, ptr)); // I measured this and it turns out prefetching towards the host slows // DualView syncs down. Probably because the latency is not too bad in the // first place for the pull down. If we want to change that provde @@ -593,8 +608,8 @@ void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, #endif if (to_device && is_managed && space.cuda_device_prop().concurrentManagedAccess) { - CUDA_SAFE_CALL(cudaMemPrefetchAsync(ptr, bytes, space.cuda_device(), - space.cuda_stream())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMemPrefetchAsync( + ptr, bytes, space.cuda_device(), space.cuda_stream())); } } diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp index 0f4259072d97..993c8d1bbadc 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp @@ -134,7 +134,12 @@ inline int cuda_deduce_block_size(bool early_termination, } if (blocks_per_sm >= min_blocks_per_sm) { - if (threads_per_sm >= opt_threads_per_sm) { + // The logic prefers smaller block sizes over larger ones to + // give more flexibility to the scheduler. + // But don't go below 128 where performance suffers significantly + // for simple copy/set kernels. + if ((threads_per_sm > opt_threads_per_sm) || + ((block_size >= 128) && (threads_per_sm == opt_threads_per_sm))) { opt_block_size = block_size; opt_threads_per_sm = threads_per_sm; } diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp index 4759001d81f9..36df0d2564ae 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp @@ -49,13 +49,19 @@ #ifdef KOKKOS_ENABLE_CUDA #include - +#include #include namespace Kokkos { namespace Impl { -void cuda_device_synchronize(); +void cuda_stream_synchronize( + const cudaStream_t stream, + Kokkos::Tools::Experimental::SpecialSynchronizationCases reason, + const std::string& name); +void cuda_device_synchronize(const std::string& name); +void cuda_stream_synchronize(const cudaStream_t stream, + const std::string& name); void cuda_internal_error_throw(cudaError e, const char* name, const char* file = nullptr, const int line = 0); @@ -68,9 +74,24 @@ inline void cuda_internal_safe_call(cudaError e, const char* name, } } -#define CUDA_SAFE_CALL(call) \ +#define KOKKOS_IMPL_CUDA_SAFE_CALL(call) \ Kokkos::Impl::cuda_internal_safe_call(call, #call, __FILE__, __LINE__) +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 + +KOKKOS_DEPRECATED +inline void cuda_internal_safe_call_deprecated(cudaError e, const char* name, + const char* file = nullptr, + const int line = 0) { + cuda_internal_safe_call(e, name, file, line); +} + +#define CUDA_SAFE_CALL(call) \ + Kokkos::Impl::cuda_internal_safe_call_deprecated(call, #call, __FILE__, \ + __LINE__) + +#endif + } // namespace Impl namespace Experimental { diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Graph_Impl.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Graph_Impl.hpp index 3de7a6991613..bd514f5e88d9 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Graph_Impl.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Graph_Impl.hpp @@ -60,6 +60,7 @@ #include #include +#include namespace Kokkos { namespace Impl { @@ -82,8 +83,8 @@ struct GraphImpl { constexpr size_t error_log_size = 256; cudaGraphNode_t error_node = nullptr; char error_log[error_log_size]; - CUDA_SAFE_CALL(cudaGraphInstantiate(&m_graph_exec, m_graph, &error_node, - error_log, error_log_size)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGraphInstantiate( + &m_graph_exec, m_graph, &error_node, error_log, error_log_size)); // TODO @graphs print out errors } @@ -107,26 +108,27 @@ struct GraphImpl { // TODO @graphs we need to somehow indicate the need for a fence in the // destructor of the GraphImpl object (so that we don't have to // just always do it) - m_execution_space.fence(); + m_execution_space.fence("Kokkos::GraphImpl::~GraphImpl: Graph Destruction"); KOKKOS_EXPECTS(bool(m_graph)) if (bool(m_graph_exec)) { - CUDA_SAFE_CALL(cudaGraphExecDestroy(m_graph_exec)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGraphExecDestroy(m_graph_exec)); } - CUDA_SAFE_CALL(cudaGraphDestroy(m_graph)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGraphDestroy(m_graph)); }; explicit GraphImpl(Kokkos::Cuda arg_instance) : m_execution_space(std::move(arg_instance)) { - CUDA_SAFE_CALL(cudaGraphCreate(&m_graph, cuda_graph_flags_t{0})); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGraphCreate(&m_graph, cuda_graph_flags_t{0})); } void add_node(std::shared_ptr const& arg_node_ptr) { // All of the predecessors are just added as normal, so all we need to // do here is add an empty node - CUDA_SAFE_CALL(cudaGraphAddEmptyNode(&(arg_node_ptr->node_details_t::node), - m_graph, - /* dependencies = */ nullptr, - /* numDependencies = */ 0)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGraphAddEmptyNode(&(arg_node_ptr->node_details_t::node), m_graph, + /* dependencies = */ nullptr, + /* numDependencies = */ 0)); } template @@ -171,7 +173,7 @@ struct GraphImpl { auto /*const*/& cuda_node = arg_node_ptr->node_details_t::node; KOKKOS_EXPECTS(bool(cuda_node)) - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaGraphAddDependencies(m_graph, &pred_cuda_node, &cuda_node, 1)); } @@ -179,7 +181,7 @@ struct GraphImpl { if (!bool(m_graph_exec)) { _instantiate_graph(); } - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaGraphLaunch(m_graph_exec, m_execution_space.cuda_stream())); } @@ -192,9 +194,10 @@ struct GraphImpl { KOKKOS_EXPECTS(!bool(m_graph_exec)) auto rv = std::make_shared( get_execution_space(), _graph_node_is_root_ctor_tag{}); - CUDA_SAFE_CALL(cudaGraphAddEmptyNode(&(rv->node_details_t::node), m_graph, - /* dependencies = */ nullptr, - /* numDependencies = */ 0)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGraphAddEmptyNode(&(rv->node_details_t::node), m_graph, + /* dependencies = */ nullptr, + /* numDependencies = */ 0)); KOKKOS_ENSURES(bool(rv->node_details_t::node)) return rv; } diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp index ec9c434fe663..c81286eb1004 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp @@ -51,6 +51,9 @@ !(defined(KOKKOS_ARCH_KEPLER) || defined(KOKKOS_ARCH_MAXWELL50) || \ defined(KOKKOS_ARCH_MAXWELL52)) #include +#include // istream & ostream for extraction and insertion ops +#include +#include // reduction_identity #ifndef KOKKOS_IMPL_HALF_TYPE_DEFINED // Make sure no one else tries to define half_t @@ -127,7 +130,7 @@ KOKKOS_INLINE_FUNCTION std::enable_if_t::value, T> cast_from_half(half_t); -class half_t { +class alignas(2) half_t { public: using impl_type = Kokkos::Impl::half_impl_t::type; @@ -138,6 +141,22 @@ class half_t { KOKKOS_FUNCTION half_t() : val(0.0F) {} + // Copy constructors + KOKKOS_DEFAULTED_FUNCTION + half_t(const half_t&) noexcept = default; + + KOKKOS_INLINE_FUNCTION + half_t(const volatile half_t& rhs) { +#ifdef __CUDA_ARCH__ + val = rhs.val; +#else + const volatile uint16_t* rv_ptr = + reinterpret_cast(&rhs.val); + const uint16_t rv_val = *rv_ptr; + val = reinterpret_cast(rv_val); +#endif // __CUDA_ARCH__ + } + // Don't support implicit conversion back to impl_type. // impl_type is a storage only type on host. KOKKOS_FUNCTION @@ -219,7 +238,7 @@ class half_t { #ifdef __CUDA_ARCH__ tmp.val = +tmp.val; #else - tmp.val = __float2half(+__half2float(tmp.val)); + tmp.val = __float2half(+__half2float(tmp.val)); #endif return tmp; } @@ -230,7 +249,7 @@ class half_t { #ifdef __CUDA_ARCH__ tmp.val = -tmp.val; #else - tmp.val = __float2half(-__half2float(tmp.val)); + tmp.val = __float2half(-__half2float(tmp.val)); #endif return tmp; } @@ -241,7 +260,7 @@ class half_t { #ifdef __CUDA_ARCH__ ++val; #else - float tmp = __half2float(val); + float tmp = __half2float(val); ++tmp; val = __float2half(tmp); #endif @@ -255,7 +274,7 @@ class half_t { #else float tmp = __half2float(val); --tmp; - val = __float2half(tmp); + val = __float2half(tmp); #endif return *this; } @@ -290,7 +309,10 @@ class half_t { template KOKKOS_FUNCTION void operator=(T rhs) volatile { - val = cast_to_half(rhs).val; + impl_type new_val = cast_to_half(rhs).val; + volatile uint16_t* val_ptr = + reinterpret_cast(const_cast(&val)); + *val_ptr = reinterpret_cast(new_val); } // Compound operators @@ -299,30 +321,21 @@ class half_t { #ifdef __CUDA_ARCH__ val += rhs.val; #else - val = __float2half(__half2float(val) + __half2float(rhs.val)); + val = __float2half(__half2float(val) + __half2float(rhs.val)); #endif return *this; } KOKKOS_FUNCTION - volatile half_t& operator+=(half_t rhs) volatile { -#ifdef __CUDA_ARCH__ - // Cuda 10 supports __half volatile stores but not volatile arithmetic - // operands. Cast away volatile-ness of val for arithmetic but not for store - // location. - val = const_cast(val) + rhs.val; -#else - // Use non-volatile val_ref to suppress: - // "warning: implicit dereference will not access object of type ‘volatile - // __half’ in statement" - auto val_ref = const_cast(val); - val_ref = __float2half(__half2float(const_cast(val)) + - __half2float(rhs.val)); -#endif - return *this; + void operator+=(const volatile half_t& rhs) volatile { + half_t tmp_rhs = rhs; + half_t tmp_lhs = *this; + + tmp_lhs += tmp_rhs; + *this = tmp_lhs; } - // Compund operators: upcast overloads for += + // Compound operators: upcast overloads for += template KOKKOS_FUNCTION std::enable_if_t< std::is_same::value || std::is_same::value, T> friend @@ -350,27 +363,18 @@ class half_t { #ifdef __CUDA_ARCH__ val -= rhs.val; #else - val = __float2half(__half2float(val) - __half2float(rhs.val)); + val = __float2half(__half2float(val) - __half2float(rhs.val)); #endif return *this; } KOKKOS_FUNCTION - volatile half_t& operator-=(half_t rhs) volatile { -#ifdef __CUDA_ARCH__ - // Cuda 10 supports __half volatile stores but not volatile arithmetic - // operands. Cast away volatile-ness of val for arithmetic but not for store - // location. - val = const_cast(val) - rhs.val; -#else - // Use non-volatile val_ref to suppress: - // "warning: implicit dereference will not access object of type ‘volatile - // __half’ in statement" - auto val_ref = const_cast(val); - val_ref = __float2half(__half2float(const_cast(val)) - - __half2float(rhs.val)); -#endif - return *this; + void operator-=(const volatile half_t& rhs) volatile { + half_t tmp_rhs = rhs; + half_t tmp_lhs = *this; + + tmp_lhs -= tmp_rhs; + *this = tmp_lhs; } // Compund operators: upcast overloads for -= @@ -401,27 +405,18 @@ class half_t { #ifdef __CUDA_ARCH__ val *= rhs.val; #else - val = __float2half(__half2float(val) * __half2float(rhs.val)); + val = __float2half(__half2float(val) * __half2float(rhs.val)); #endif return *this; } KOKKOS_FUNCTION - volatile half_t& operator*=(half_t rhs) volatile { -#ifdef __CUDA_ARCH__ - // Cuda 10 supports __half volatile stores but not volatile arithmetic - // operands. Cast away volatile-ness of val for arithmetic but not for store - // location. - val = const_cast(val) * rhs.val; -#else - // Use non-volatile val_ref to suppress: - // "warning: implicit dereference will not access object of type ‘volatile - // __half’ in statement" - auto val_ref = const_cast(val); - val_ref = __float2half(__half2float(const_cast(val)) * - __half2float(rhs.val)); -#endif - return *this; + void operator*=(const volatile half_t& rhs) volatile { + half_t tmp_rhs = rhs; + half_t tmp_lhs = *this; + + tmp_lhs *= tmp_rhs; + *this = tmp_lhs; } // Compund operators: upcast overloads for *= @@ -452,27 +447,18 @@ class half_t { #ifdef __CUDA_ARCH__ val /= rhs.val; #else - val = __float2half(__half2float(val) / __half2float(rhs.val)); + val = __float2half(__half2float(val) / __half2float(rhs.val)); #endif return *this; } KOKKOS_FUNCTION - volatile half_t& operator/=(half_t rhs) volatile { -#ifdef __CUDA_ARCH__ - // Cuda 10 supports __half volatile stores but not volatile arithmetic - // operands. Cast away volatile-ness of val for arithmetic but not for store - // location. - val = const_cast(val) / rhs.val; -#else - // Use non-volatile val_ref to suppress: - // "warning: implicit dereference will not access object of type ‘volatile - // __half’ in statement" - auto val_ref = const_cast(val); - val_ref = __float2half(__half2float(const_cast(val)) / - __half2float(rhs.val)); -#endif - return *this; + void operator/=(const volatile half_t& rhs) volatile { + half_t tmp_rhs = rhs; + half_t tmp_lhs = *this; + + tmp_lhs /= tmp_rhs; + *this = tmp_lhs; } // Compund operators: upcast overloads for /= @@ -504,7 +490,7 @@ class half_t { #ifdef __CUDA_ARCH__ lhs.val += rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); #endif return lhs; } @@ -529,7 +515,7 @@ class half_t { #ifdef __CUDA_ARCH__ lhs.val -= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); #endif return lhs; } @@ -554,7 +540,7 @@ class half_t { #ifdef __CUDA_ARCH__ lhs.val *= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); #endif return lhs; } @@ -579,7 +565,7 @@ class half_t { #ifdef __CUDA_ARCH__ lhs.val /= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); #endif return lhs; } @@ -683,6 +669,62 @@ class half_t { return __half2float(val) >= __half2float(rhs.val); #endif } + + KOKKOS_FUNCTION + friend bool operator==(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs == tmp_rhs; + } + + KOKKOS_FUNCTION + friend bool operator!=(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs != tmp_rhs; + } + + KOKKOS_FUNCTION + friend bool operator<(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs < tmp_rhs; + } + + KOKKOS_FUNCTION + friend bool operator>(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs > tmp_rhs; + } + + KOKKOS_FUNCTION + friend bool operator<=(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs <= tmp_rhs; + } + + KOKKOS_FUNCTION + friend bool operator>=(const volatile half_t& lhs, + const volatile half_t& rhs) { + half_t tmp_lhs = lhs, tmp_rhs = rhs; + return tmp_lhs >= tmp_rhs; + } + + // Insertion and extraction operators + friend std::ostream& operator<<(std::ostream& os, const half_t& x) { + const std::string out = std::to_string(static_cast(x)); + os << out; + return os; + } + + friend std::istream& operator>>(std::istream& is, half_t& x) { + std::string in; + is >> in; + x = std::stod(in); + return is; + } }; // CUDA before 11.1 only has the half <-> float conversions marked host device @@ -943,6 +985,25 @@ KOKKOS_INLINE_FUNCTION } #endif } // namespace Experimental + +// use float as the return type for sum and prod since cuda_fp16.h +// has no constexpr functions for casting to __half +template <> +struct reduction_identity { + KOKKOS_FORCEINLINE_FUNCTION constexpr static float sum() noexcept { + return 0.0F; + } + KOKKOS_FORCEINLINE_FUNCTION constexpr static float prod() noexcept { + return 1.0F; + } + KOKKOS_FORCEINLINE_FUNCTION constexpr static float max() noexcept { + return -65504.0F; + } + KOKKOS_FORCEINLINE_FUNCTION constexpr static float min() noexcept { + return 65504.0F; + } +}; + } // namespace Kokkos #endif // KOKKOS_IMPL_HALF_TYPE_DEFINED #endif // KOKKOS_ENABLE_CUDA diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp index 016cb6cdcbdd..6964d5b41b72 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp @@ -119,7 +119,7 @@ int cuda_kernel_arch() { int arch = 0; int *d_arch = nullptr; - cudaMalloc((void **)&d_arch, sizeof(int)); + cudaMalloc(reinterpret_cast(&d_arch), sizeof(int)); cudaMemcpy(d_arch, &arch, sizeof(int), cudaMemcpyDefault); query_cuda_kernel_arch<<<1, 1>>>(d_arch); @@ -141,7 +141,36 @@ bool cuda_launch_blocking() { } // namespace -void cuda_device_synchronize() { CUDA_SAFE_CALL(cudaDeviceSynchronize()); } +void cuda_device_synchronize(const std::string &name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event( + name, + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + GlobalDeviceSynchronization, + []() { // TODO: correct device ID + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); + }); +} + +void cuda_stream_synchronize(const cudaStream_t stream, const CudaInternal *ptr, + const std::string &name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event( + name, + Kokkos::Tools::Experimental::Impl::DirectFenceIDHandle{ + ptr->impl_get_instance_id()}, + [&]() { // TODO: correct device ID + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamSynchronize(stream)); + }); +} + +void cuda_stream_synchronize( + const cudaStream_t stream, + Kokkos::Tools::Experimental::SpecialSynchronizationCases reason, + const std::string &name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event( + name, reason, [&]() { // TODO: correct device ID + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamSynchronize(stream)); + }); +} void cuda_internal_error_throw(cudaError e, const char *name, const char *file, const int line) { @@ -221,7 +250,7 @@ CudaInternalDevices::CudaInternalDevices() { // See 'cudaSetDeviceFlags' for host-device thread interaction // Section 4.4.2.6 of the CUDA Toolkit Reference Manual - CUDA_SAFE_CALL(cudaGetDeviceCount(&m_cudaDevCount)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&m_cudaDevCount)); if (m_cudaDevCount > MAXIMUM_DEVICE_COUNT) { Kokkos::abort( @@ -229,7 +258,7 @@ CudaInternalDevices::CudaInternalDevices() { "have. Please report this to github.com/kokkos/kokkos."); } for (int i = 0; i < m_cudaDevCount; ++i) { - CUDA_SAFE_CALL(cudaGetDeviceProperties(m_cudaProp + i, i)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceProperties(m_cudaProp + i, i)); } } @@ -277,25 +306,27 @@ CudaInternal::~CudaInternal() { << std::endl; } - m_cudaDev = -1; - m_cudaArch = -1; - m_multiProcCount = 0; - m_maxWarpCount = 0; - m_maxBlock = 0; - m_maxSharedWords = 0; - m_maxConcurrency = 0; - m_scratchSpaceCount = 0; - m_scratchFlagsCount = 0; - m_scratchUnifiedCount = 0; - m_scratchUnifiedSupported = 0; - m_streamCount = 0; - m_scratchSpace = nullptr; - m_scratchFlags = nullptr; - m_scratchUnified = nullptr; - m_scratchConcurrentBitset = nullptr; - m_stream = nullptr; - m_team_scratch_current_size = 0; - m_team_scratch_ptr = nullptr; + m_cudaDev = -1; + m_cudaArch = -1; + m_multiProcCount = 0; + m_maxWarpCount = 0; + m_maxBlock = 0; + m_maxSharedWords = 0; + m_maxConcurrency = 0; + m_scratchSpaceCount = 0; + m_scratchFlagsCount = 0; + m_scratchUnifiedCount = 0; + m_scratchUnifiedSupported = 0; + m_streamCount = 0; + m_scratchSpace = nullptr; + m_scratchFlags = nullptr; + m_scratchUnified = nullptr; + m_scratchConcurrentBitset = nullptr; + m_stream = nullptr; + for (int i = 0; i < m_n_team_scratch; ++i) { + m_team_scratch_current_size[i] = 0; + m_team_scratch_ptr[i] = nullptr; + } } int CudaInternal::verify_is_initialized(const char *const label) const { @@ -305,16 +336,20 @@ int CudaInternal::verify_is_initialized(const char *const label) const { } return 0 <= m_cudaDev; } - +uint32_t CudaInternal::impl_get_instance_id() const { return m_instance_id; } CudaInternal &CudaInternal::singleton() { static CudaInternal self; return self; } +void CudaInternal::fence(const std::string &name) const { + Impl::cuda_stream_synchronize(m_stream, this, name); +} void CudaInternal::fence() const { - CUDA_SAFE_CALL(cudaStreamSynchronize(m_stream)); + fence("Kokkos::CudaInternal::fence(): Unnamed Instance Fence"); } -void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { +void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream, + bool manage_stream) { if (was_finalized) Kokkos::abort("Calling Cuda::initialize after Cuda::finalize is illegal\n"); was_initialized = true; @@ -350,8 +385,9 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { m_cudaDev = cuda_device_id; m_deviceProp = cudaProp; - CUDA_SAFE_CALL(cudaSetDevice(m_cudaDev)); - Kokkos::Impl::cuda_device_synchronize(); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_cudaDev)); + Kokkos::Impl::cuda_device_synchronize( + "Kokkos::CudaInternal::initialize: Fence on space initialization"); // Query what compute capability architecture a kernel executes: m_cudaArch = cuda_kernel_arch(); @@ -464,8 +500,8 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { m_scratchConcurrentBitset = reinterpret_cast(r->data()); - CUDA_SAFE_CALL(cudaMemset(m_scratchConcurrentBitset, 0, - sizeof(uint32_t) * buffer_bound)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMemset(m_scratchConcurrentBitset, 0, + sizeof(uint32_t) * buffer_bound)); } //---------------------------------- @@ -535,15 +571,19 @@ Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default // Allocate a staging buffer for constant mem in pinned host memory // and an event to avoid overwriting driver for previous kernel launches if (stream == nullptr) { - CUDA_SAFE_CALL(cudaMallocHost((void **)&constantMemHostStaging, - CudaTraits::ConstantMemoryUsage)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMallocHost(reinterpret_cast(&constantMemHostStaging), + CudaTraits::ConstantMemoryUsage)); - CUDA_SAFE_CALL(cudaEventCreate(&constantMemReusable)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaEventCreate(&constantMemReusable)); } - m_stream = stream; - m_team_scratch_current_size = 0; - m_team_scratch_ptr = nullptr; + m_stream = stream; + m_manage_stream = manage_stream; + for (int i = 0; i < m_n_team_scratch; ++i) { + m_team_scratch_current_size[i] = 0; + m_team_scratch_ptr[i] = nullptr; + } } //---------------------------------------------------------------------------- @@ -569,7 +609,7 @@ Cuda::size_type *CudaInternal::scratch_flags(const Cuda::size_type size) const { m_scratchFlags = reinterpret_cast(r->data()); - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaMemset(m_scratchFlags, 0, m_scratchFlagsCount * sizeScratchGrain)); } @@ -645,20 +685,37 @@ Cuda::size_type *CudaInternal::scratch_functor( return m_scratchFunctor; } -void *CudaInternal::resize_team_scratch_space(std::int64_t bytes, - bool force_shrink) { - if (m_team_scratch_current_size == 0) { - m_team_scratch_current_size = bytes; - m_team_scratch_ptr = Kokkos::kokkos_malloc( - "Kokkos::CudaSpace::TeamScratchMemory", m_team_scratch_current_size); +std::pair CudaInternal::resize_team_scratch_space( + std::int64_t bytes, bool force_shrink) { + // Multiple ParallelFor/Reduce Teams can call this function at the same time + // and invalidate the m_team_scratch_ptr. We use a pool to avoid any race + // condition. + + int current_team_scratch = 0; + int zero = 0; + int one = 1; + while (m_team_scratch_pool[current_team_scratch].compare_exchange_weak( + zero, one, std::memory_order_release, std::memory_order_relaxed)) { + current_team_scratch = (current_team_scratch + 1) % m_n_team_scratch; } - if ((bytes > m_team_scratch_current_size) || - ((bytes < m_team_scratch_current_size) && (force_shrink))) { - m_team_scratch_current_size = bytes; - m_team_scratch_ptr = Kokkos::kokkos_realloc( - m_team_scratch_ptr, m_team_scratch_current_size); + if (m_team_scratch_current_size[current_team_scratch] == 0) { + m_team_scratch_current_size[current_team_scratch] = bytes; + m_team_scratch_ptr[current_team_scratch] = + Kokkos::kokkos_malloc( + "Kokkos::CudaSpace::TeamScratchMemory", + m_team_scratch_current_size[current_team_scratch]); } - return m_team_scratch_ptr; + if ((bytes > m_team_scratch_current_size[current_team_scratch]) || + ((bytes < m_team_scratch_current_size[current_team_scratch]) && + (force_shrink))) { + m_team_scratch_current_size[current_team_scratch] = bytes; + m_team_scratch_ptr[current_team_scratch] = + Kokkos::kokkos_realloc( + m_team_scratch_ptr[current_team_scratch], + m_team_scratch_current_size[current_team_scratch]); + } + return std::make_pair(m_team_scratch_ptr[current_team_scratch], + current_team_scratch); } //---------------------------------------------------------------------------- @@ -685,36 +742,43 @@ void CudaInternal::finalize() { if (m_scratchFunctorSize > 0) RecordCuda::decrement(RecordCuda::get_record(m_scratchFunctor)); - if (m_team_scratch_current_size > 0) - Kokkos::kokkos_free(m_team_scratch_ptr); - - m_cudaDev = -1; - m_multiProcCount = 0; - m_maxWarpCount = 0; - m_maxBlock = 0; - m_maxSharedWords = 0; - m_scratchSpaceCount = 0; - m_scratchFlagsCount = 0; - m_scratchUnifiedCount = 0; - m_streamCount = 0; - m_scratchSpace = nullptr; - m_scratchFlags = nullptr; - m_scratchUnified = nullptr; - m_scratchConcurrentBitset = nullptr; - m_stream = nullptr; - m_team_scratch_current_size = 0; - m_team_scratch_ptr = nullptr; + for (int i = 0; i < m_n_team_scratch; ++i) { + if (m_team_scratch_current_size[i] > 0) + Kokkos::kokkos_free(m_team_scratch_ptr[i]); + } + + if (m_manage_stream && m_stream != nullptr) + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamDestroy(m_stream)); + + m_cudaDev = -1; + m_multiProcCount = 0; + m_maxWarpCount = 0; + m_maxBlock = 0; + m_maxSharedWords = 0; + m_scratchSpaceCount = 0; + m_scratchFlagsCount = 0; + m_scratchUnifiedCount = 0; + m_streamCount = 0; + m_scratchSpace = nullptr; + m_scratchFlags = nullptr; + m_scratchUnified = nullptr; + m_scratchConcurrentBitset = nullptr; + m_stream = nullptr; + for (int i = 0; i < m_n_team_scratch; ++i) { + m_team_scratch_current_size[i] = 0; + m_team_scratch_ptr[i] = nullptr; + } } // only destroy these if we're finalizing the singleton if (this == &singleton()) { - cudaFreeHost(constantMemHostStaging); - cudaEventDestroy(constantMemReusable); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFreeHost(constantMemHostStaging)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaEventDestroy(constantMemReusable)); auto &deep_copy_space = Kokkos::Impl::cuda_get_deep_copy_space(/*initialize*/ false); if (deep_copy_space) deep_copy_space->impl_internal_space_instance()->finalize(); - cudaStreamDestroy(cuda_get_deep_copy_stream()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamDestroy(cuda_get_deep_copy_stream())); } } @@ -823,7 +887,7 @@ Cuda::Cuda() "Cuda instance constructor"); } -Cuda::Cuda(cudaStream_t stream) +Cuda::Cuda(cudaStream_t stream, bool manage_stream) : m_space_instance(new Impl::CudaInternal, [](Impl::CudaInternal *ptr) { ptr->finalize(); delete ptr; @@ -831,18 +895,31 @@ Cuda::Cuda(cudaStream_t stream) Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); m_space_instance->initialize(Impl::CudaInternal::singleton().m_cudaDev, - stream); + stream, manage_stream); } void Cuda::print_configuration(std::ostream &s, const bool) { Impl::CudaInternal::singleton().print_configuration(s); } -void Cuda::impl_static_fence() { Kokkos::Impl::cuda_device_synchronize(); } +void Cuda::impl_static_fence(const std::string &name) { + Kokkos::Impl::cuda_device_synchronize(name); +} +void Cuda::impl_static_fence() { + impl_static_fence("Kokkos::Cuda::impl_static_fence(): Unnamed Static Fence"); +} -void Cuda::fence() const { m_space_instance->fence(); } +void Cuda::fence() const { + fence("Kokkos::Cuda::fence(): Unnamed Instance Fence"); +} +void Cuda::fence(const std::string &name) const { + m_space_instance->fence(name); +} const char *Cuda::name() { return "Cuda"; } +uint32_t Cuda::impl_instance_id() const noexcept { + return m_space_instance->impl_get_instance_id(); +} cudaStream_t Cuda::cuda_stream() const { return m_space_instance->m_stream; } int Cuda::cuda_device() const { return m_space_instance->m_cudaDev; } @@ -877,7 +954,15 @@ void CudaSpaceInitializer::finalize(bool all_spaces) { } } -void CudaSpaceInitializer::fence() { Kokkos::Cuda::impl_static_fence(); } +void CudaSpaceInitializer::fence() { + Kokkos::Cuda::impl_static_fence( + "Kokkos::CudaSpaceInitializer::fence: Initializer Fence"); +} +void CudaSpaceInitializer::fence(const std::string &name) { + // Kokkos::Cuda::impl_static_fence("Kokkos::CudaSpaceInitializer::fence: + // "+name); //TODO: or this + Kokkos::Cuda::impl_static_fence(name); +} void CudaSpaceInitializer::print_configuration(std::ostream &msg, const bool detail) { @@ -916,12 +1001,6 @@ void CudaSpaceInitializer::print_configuration(std::ostream &msg, msg << "yes\n"; #else msg << "no\n"; -#endif - msg << " KOKKOS_ENABLE_CUSPARSE: "; -#ifdef KOKKOS_ENABLE_CUSPARSE - msg << "yes\n"; -#else - msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA: "; #ifdef KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp index aaec2c29260a..7eb169838c05 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp @@ -3,6 +3,9 @@ #include #include +#include +#include + //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- // These functions fulfill the purpose of allowing to work around @@ -114,10 +117,14 @@ class CudaInternal { mutable size_type* m_scratchFunctor; uint32_t* m_scratchConcurrentBitset; cudaStream_t m_stream; + uint32_t m_instance_id; + bool m_manage_stream; // Team Scratch Level 1 Space - mutable int64_t m_team_scratch_current_size; - mutable void* m_team_scratch_ptr; + int m_n_team_scratch = 10; + mutable int64_t m_team_scratch_current_size[10]; + mutable void* m_team_scratch_ptr[10]; + mutable std::atomic_int m_team_scratch_pool[10]; bool was_initialized = false; bool was_finalized = false; @@ -135,7 +142,8 @@ class CudaInternal { return nullptr != m_scratchSpace && nullptr != m_scratchFlags; } - void initialize(int cuda_device_id, cudaStream_t stream = nullptr); + void initialize(int cuda_device_id, cudaStream_t stream = nullptr, + bool manage_stream = false); void finalize(); void print_configuration(std::ostream&) const; @@ -145,6 +153,7 @@ class CudaInternal { static void cuda_set_serial_execution(bool); #endif + void fence(const std::string&) const; void fence() const; ~CudaInternal(); @@ -175,20 +184,68 @@ class CudaInternal { m_scratchFunctor(nullptr), m_scratchConcurrentBitset(nullptr), m_stream(nullptr), - m_team_scratch_current_size(0), - m_team_scratch_ptr(nullptr) {} + m_instance_id( + Kokkos::Tools::Experimental::Impl::idForInstance( + reinterpret_cast(this))) { + for (int i = 0; i < m_n_team_scratch; ++i) { + m_team_scratch_current_size[i] = 0; + m_team_scratch_ptr[i] = nullptr; + m_team_scratch_pool[i] = 0; + } + } // Resizing of reduction related scratch spaces size_type* scratch_space(const size_type size) const; size_type* scratch_flags(const size_type size) const; size_type* scratch_unified(const size_type size) const; size_type* scratch_functor(const size_type size) const; - + uint32_t impl_get_instance_id() const; // Resizing of team level 1 scratch - void* resize_team_scratch_space(std::int64_t bytes, - bool force_shrink = false); + std::pair resize_team_scratch_space(std::int64_t bytes, + bool force_shrink = false); }; } // Namespace Impl + +namespace Experimental { +// Partitioning an Execution Space: expects space and integer arguments for +// relative weight +// Customization point for backends +// Default behavior is to return the passed in instance + +namespace Impl { +inline void create_Cuda_instances(std::vector& instances) { + for (int s = 0; s < int(instances.size()); s++) { + cudaStream_t stream; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamCreate(&stream)); + instances[s] = Cuda(stream, true); + } +} +} // namespace Impl + +template +std::vector partition_space(const Cuda&, Args...) { +#ifdef __cpp_fold_expressions + static_assert( + (... && std::is_arithmetic_v), + "Kokkos Error: partitioning arguments must be integers or floats"); +#endif + std::vector instances(sizeof...(Args)); + Impl::create_Cuda_instances(instances); + return instances; +} + +template +std::vector partition_space(const Cuda&, std::vector& weights) { + static_assert( + std::is_arithmetic::value, + "Kokkos Error: partitioning arguments must be integers or floats"); + + std::vector instances(weights.size()); + Impl::create_Cuda_instances(instances); + return instances; +} +} // namespace Experimental + } // Namespace Kokkos #endif diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp index d892a893b330..4b01798f5e2c 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp @@ -167,7 +167,7 @@ inline void configure_shmem_preference(KernelFuncPtr const& func, #ifndef KOKKOS_ARCH_KEPLER // On Kepler the L1 has no benefit since it doesn't cache reads auto set_cache_config = [&] { - CUDA_SAFE_CALL(cudaFuncSetCacheConfig( + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFuncSetCacheConfig( func, (prefer_shmem ? cudaFuncCachePreferShared : cudaFuncCachePreferL1))); return prefer_shmem; @@ -372,14 +372,15 @@ struct CudaParallelLaunchKernelInvoker< params.kernelParams = (void**)args; params.extra = nullptr; - CUDA_SAFE_CALL(cudaGraphAddKernelNode( + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGraphAddKernelNode( &graph_node, graph, /* dependencies = */ nullptr, /* numDependencies = */ 0, ¶ms)); } else { // We still need an empty node for the dependency structure - CUDA_SAFE_CALL(cudaGraphAddEmptyNode(&graph_node, graph, - /* dependencies = */ nullptr, - /* numDependencies = */ 0)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGraphAddEmptyNode(&graph_node, graph, + /* dependencies = */ nullptr, + /* numDependencies = */ 0)); } KOKKOS_ENSURES(bool(graph_node)) } @@ -475,14 +476,15 @@ struct CudaParallelLaunchKernelInvoker< params.kernelParams = (void**)args; params.extra = nullptr; - CUDA_SAFE_CALL(cudaGraphAddKernelNode( + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGraphAddKernelNode( &graph_node, graph, /* dependencies = */ nullptr, /* numDependencies = */ 0, ¶ms)); } else { // We still need an empty node for the dependency structure - CUDA_SAFE_CALL(cudaGraphAddEmptyNode(&graph_node, graph, - /* dependencies = */ nullptr, - /* numDependencies = */ 0)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGraphAddEmptyNode(&graph_node, graph, + /* dependencies = */ nullptr, + /* numDependencies = */ 0)); } KOKKOS_ENSURES(bool(graph_node)) } @@ -538,7 +540,8 @@ struct CudaParallelLaunchKernelInvoker< dim3 const& block, int shmem, CudaInternal const* cuda_instance) { // Wait until the previous kernel that uses the constant buffer is done - CUDA_SAFE_CALL(cudaEventSynchronize(cuda_instance->constantMemReusable)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaEventSynchronize(cuda_instance->constantMemReusable)); // Copy functor (synchronously) to staging buffer in pinned host memory unsigned long* staging = cuda_instance->constantMemHostStaging; @@ -554,8 +557,9 @@ struct CudaParallelLaunchKernelInvoker< get_kernel_func())<<m_stream>>>(); // Record an event that says when the constant buffer can be reused - CUDA_SAFE_CALL(cudaEventRecord(cuda_instance->constantMemReusable, - cudaStream_t(cuda_instance->m_stream))); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaEventRecord(cuda_instance->constantMemReusable, + cudaStream_t(cuda_instance->m_stream))); } #ifdef KOKKOS_CUDA_ENABLE_GRAPHS @@ -637,8 +641,9 @@ struct CudaParallelLaunchImpl< base_t::invoke_kernel(driver, grid, block, shmem, cuda_instance); #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) - CUDA_SAFE_CALL(cudaGetLastError()); - cuda_instance->fence(); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); + cuda_instance->fence( + "Kokkos::Impl::launch_kernel: Debug Only Check for Execution Error"); #endif } } @@ -650,7 +655,7 @@ struct CudaParallelLaunchImpl< // the code and the result is visible. auto wrap_get_attributes = []() -> cudaFuncAttributes { cudaFuncAttributes attr_tmp; - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaFuncGetAttributes(&attr_tmp, base_t::get_kernel_func())); return attr_tmp; }; diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp index ff3164954403..1f3024f3186a 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp @@ -81,22 +81,34 @@ namespace Impl { CudaLockArrays g_host_cuda_lock_arrays = {nullptr, nullptr, 0}; void initialize_host_cuda_lock_arrays() { +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + desul::Impl::init_lock_arrays(); + + DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE(); +#endif if (g_host_cuda_lock_arrays.atomic != nullptr) return; - CUDA_SAFE_CALL(cudaMalloc(&g_host_cuda_lock_arrays.atomic, - sizeof(int) * (CUDA_SPACE_ATOMIC_MASK + 1))); - CUDA_SAFE_CALL(cudaMalloc(&g_host_cuda_lock_arrays.scratch, - sizeof(int) * (Cuda::concurrency()))); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMalloc(&g_host_cuda_lock_arrays.atomic, + sizeof(int) * (CUDA_SPACE_ATOMIC_MASK + 1))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMalloc(&g_host_cuda_lock_arrays.scratch, + sizeof(int) * (Cuda::concurrency()))); + Impl::cuda_device_synchronize( + "Kokkos::Impl::initialize_host_cuda_lock_arrays: Pre Init Lock Arrays"); g_host_cuda_lock_arrays.n = Cuda::concurrency(); KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE(); init_lock_array_kernel_atomic<<<(CUDA_SPACE_ATOMIC_MASK + 1 + 255) / 256, 256>>>(); init_lock_array_kernel_threadid<<<(Kokkos::Cuda::concurrency() + 255) / 256, 256>>>(Kokkos::Cuda::concurrency()); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::initialize_host_cuda_lock_arrays: Post Init Lock Arrays"); } void finalize_host_cuda_lock_arrays() { +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + desul::Impl::finalize_lock_arrays(); +#endif + if (g_host_cuda_lock_arrays.atomic == nullptr) return; cudaFree(g_host_cuda_lock_arrays.atomic); g_host_cuda_lock_arrays.atomic = nullptr; diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp index 7640b8084d16..04fb7cb345a2 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp @@ -53,6 +53,10 @@ #include +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS +#include +#endif + namespace Kokkos { namespace Impl { @@ -150,13 +154,14 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } } // namespace } // namespace Impl } // namespace Kokkos + /* Dan Ibanez: it is critical that this code be a macro, so that it will capture the right address for Kokkos::Impl::g_device_cuda_lock_arrays! putting this in an inline function will NOT do the right thing! */ #define KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE() \ { \ if (::Kokkos::Impl::lock_array_copied == 0) { \ - CUDA_SAFE_CALL( \ + KOKKOS_IMPL_CUDA_SAFE_CALL( \ cudaMemcpyToSymbol(Kokkos::Impl::g_device_cuda_lock_arrays, \ &Kokkos::Impl::g_host_cuda_lock_arrays, \ sizeof(Kokkos::Impl::CudaLockArrays))); \ @@ -164,6 +169,8 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } lock_array_copied = 1; \ } +#ifndef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE #define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() #else @@ -171,6 +178,19 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE() #endif +#else + +#ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE +#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() +#else +// Still Need COPY_CUDA_LOCK_ARRAYS for team scratch etc. +#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() \ + KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE() \ + DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() +#endif + +#endif /* defined( KOKKOS_ENABLE_IMPL_DESUL_ATOMICS ) */ + #endif /* defined( KOKKOS_ENABLE_CUDA ) */ #endif /* #ifndef KOKKOS_CUDA_LOCKS_HPP */ diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp index 2834e6f3de01..f83b43e60885 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp @@ -62,7 +62,6 @@ #include #include #include -#include #include #include @@ -240,9 +239,11 @@ class TeamPolicyInternal //---------------------------------------- +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 KOKKOS_DEPRECATED inline int vector_length() const { return impl_vector_length(); } +#endif inline int impl_vector_length() const { return m_vector_length; } inline int team_size() const { return m_team_size; } inline int league_size() const { return m_league_size; } @@ -687,6 +688,7 @@ class ParallelFor, int m_shmem_size; void* m_scratch_ptr[2]; int m_scratch_size[2]; + int m_scratch_pool_id = -1; template __device__ inline @@ -797,15 +799,19 @@ class ParallelFor, // Functor's reduce memory, team scan memory, and team shared memory depend // upon team size. m_scratch_ptr[0] = nullptr; - m_scratch_ptr[1] = - m_team_size <= 0 - ? nullptr - : m_policy.space() - .impl_internal_space_instance() - ->resize_team_scratch_space( - static_cast(m_scratch_size[1]) * - static_cast(Cuda::concurrency() / - (m_team_size * m_vector_size))); + if (m_team_size <= 0) { + m_scratch_ptr[1] = nullptr; + } else { + auto scratch_ptr_id = + m_policy.space() + .impl_internal_space_instance() + ->resize_team_scratch_space( + static_cast(m_scratch_size[1]) * + (static_cast(Cuda::concurrency() / + (m_team_size * m_vector_size)))); + m_scratch_ptr[1] = scratch_ptr_id.first; + m_scratch_pool_id = scratch_ptr_id.second; + } const int shmem_size_total = m_shmem_begin + m_shmem_size; if (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < @@ -829,6 +835,14 @@ class ParallelFor, "Kokkos::Impl::ParallelFor< Cuda > requested too large team size.")); } } + + ~ParallelFor() { + if (m_scratch_pool_id >= 0) { + m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_pool[m_scratch_pool_id] = 0; + } + } }; } // namespace Impl @@ -870,9 +884,24 @@ class ParallelReduce, ReducerType, using value_type = typename ValueTraits::value_type; using reference_type = typename ValueTraits::reference_type; using functor_type = FunctorType; - using size_type = Kokkos::Cuda::size_type; - using index_type = typename Policy::index_type; - using reducer_type = ReducerType; + // Conditionally set word_size_type to int16_t or int8_t if value_type is + // smaller than int32_t (Kokkos::Cuda::size_type) + // word_size_type is used to determine the word count, shared memory buffer + // size, and global memory buffer size before the reduction is performed. + // Within the reduction, the word count is recomputed based on word_size_type + // and when calculating indexes into the shared/global memory buffers for + // performing the reduction, word_size_type is used again. + // For scalars > 4 bytes in size, indexing into shared/global memory relies + // on the block and grid dimensions to ensure that we index at the correct + // offset rather than at every 4 byte word; such that, when the join is + // performed, we have the correct data that was copied over in chunks of 4 + // bytes. + using word_size_type = typename std::conditional< + sizeof(value_type) < sizeof(Kokkos::Cuda::size_type), + typename std::conditional::type, + Kokkos::Cuda::size_type>::type; + using index_type = typename Policy::index_type; + using reducer_type = ReducerType; // Algorithmic constraints: blockSize is a power of two AND blockDim.y == // blockDim.z == 1 @@ -883,9 +912,11 @@ class ParallelReduce, ReducerType, const pointer_type m_result_ptr; const bool m_result_ptr_device_accessible; const bool m_result_ptr_host_accessible; - size_type* m_scratch_space; - size_type* m_scratch_flags; - size_type* m_unified_space; + word_size_type* m_scratch_space; + // m_scratch_flags must be of type Cuda::size_type due to use of atomics + // for tracking metadata in Kokkos_Cuda_ReduceScan.hpp + Cuda::size_type* m_scratch_flags; + word_size_type* m_unified_space; // Shall we use the shfl based reduction or not (only use it for static sized // types of more than 128bit) @@ -924,16 +955,16 @@ class ParallelReduce, ReducerType, __device__ inline void run(const DummySHMEMReductionType& ) const {*/ - const integral_nonzero_constant + const integral_nonzero_constant< + word_size_type, ValueTraits::StaticValueSize / sizeof(word_size_type)> word_count(ValueTraits::value_size( ReducerConditional::select(m_functor, m_reducer)) / - sizeof(size_type)); + sizeof(word_size_type)); { reference_type value = ValueInit::init(ReducerConditional::select(m_functor, m_reducer), - kokkos_impl_cuda_shared_memory() + + kokkos_impl_cuda_shared_memory() + threadIdx.y * word_count.value); // Number of blocks is bounded so that the reduction can be limited to two @@ -958,11 +989,12 @@ class ParallelReduce, ReducerType, // This is the final block with the final result at the final threads' // location - size_type* const shared = kokkos_impl_cuda_shared_memory() + - (blockDim.y - 1) * word_count.value; - size_type* const global = + word_size_type* const shared = + kokkos_impl_cuda_shared_memory() + + (blockDim.y - 1) * word_count.value; + word_size_type* const global = m_result_ptr_device_accessible - ? reinterpret_cast(m_result_ptr) + ? reinterpret_cast(m_result_ptr) : (m_unified_space ? m_unified_space : m_scratch_space); if (threadIdx.y == 0) { @@ -985,17 +1017,17 @@ class ParallelReduce, ReducerType, if (cuda_single_inter_block_reduce_scan( ReducerConditional::select(m_functor, m_reducer), blockIdx.x, - gridDim.x, kokkos_impl_cuda_shared_memory(), + gridDim.x, kokkos_impl_cuda_shared_memory(), m_scratch_space, m_scratch_flags)) { // This is the final block with the final result at the final threads' // location - size_type* const shared = - kokkos_impl_cuda_shared_memory() + + word_size_type* const shared = + kokkos_impl_cuda_shared_memory() + (blockDim.y - 1) * word_count.value; - size_type* const global = + word_size_type* const global = m_result_ptr_device_accessible - ? reinterpret_cast(m_result_ptr) + ? reinterpret_cast(m_result_ptr) : (m_unified_space ? m_unified_space : m_scratch_space); if (threadIdx.y == 0) { @@ -1100,15 +1132,21 @@ class ParallelReduce, ReducerType, KOKKOS_ASSERT(block_size > 0); - m_scratch_space = cuda_internal_scratch_space( + // TODO: down casting these uses more space than required? + m_scratch_space = (word_size_type*)cuda_internal_scratch_space( m_policy.space(), ValueTraits::value_size(ReducerConditional::select( m_functor, m_reducer)) * block_size /* block_size == max block_count */); - m_scratch_flags = - cuda_internal_scratch_flags(m_policy.space(), sizeof(size_type)); - m_unified_space = cuda_internal_scratch_unified( - m_policy.space(), ValueTraits::value_size(ReducerConditional::select( - m_functor, m_reducer))); + + // Intentionally do not downcast to word_size_type since we use Cuda + // atomics in Kokkos_Cuda_ReduceScan.hpp + m_scratch_flags = cuda_internal_scratch_flags(m_policy.space(), + sizeof(Cuda::size_type)); + m_unified_space = + reinterpret_cast(cuda_internal_scratch_unified( + m_policy.space(), + ValueTraits::value_size( + ReducerConditional::select(m_functor, m_reducer)))); // REQUIRED ( 1 , N , 1 ) dim3 block(1, block_size, 1); @@ -1139,7 +1177,9 @@ class ParallelReduce, ReducerType, false); // copy to device and execute if (!m_result_ptr_device_accessible) { - m_policy.space().fence(); + m_policy.space().fence( + "Kokkos::Impl::ParallelReduce::execute: Result " + "Not Device Accessible"); if (m_result_ptr) { if (m_unified_space) { @@ -1459,7 +1499,9 @@ class ParallelReduce, ReducerType, false); // copy to device and execute if (!m_result_ptr_device_accessible) { - m_policy.space().fence(); + m_policy.space().fence( + "Kokkos::Impl::ParallelReduce::execute: " + "Result Not Device Accessible"); if (m_result_ptr) { if (m_unified_space) { @@ -1580,6 +1622,7 @@ class ParallelReduce, size_type m_shmem_size; void* m_scratch_ptr[2]; int m_scratch_size[2]; + int m_scratch_pool_id = -1; const size_type m_league_size; int m_team_size; const size_type m_vector_size; @@ -1821,7 +1864,9 @@ class ParallelReduce, true); // copy to device and execute if (!m_result_ptr_device_accessible) { - m_policy.space().fence(); + m_policy.space().fence( + "Kokkos::Impl::ParallelReduce::execute: Result " + "Not Device Accessible"); if (m_result_ptr) { if (m_unified_space) { @@ -1895,16 +1940,19 @@ class ParallelReduce, FunctorTeamShmemSize::value(arg_functor, m_team_size); m_scratch_size[0] = m_shmem_size; m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); - m_scratch_ptr[1] = - m_team_size <= 0 - ? nullptr - : m_policy.space() - .impl_internal_space_instance() - ->resize_team_scratch_space( - static_cast(m_scratch_size[1]) * - (static_cast( - Cuda::concurrency() / - (m_team_size * m_vector_size)))); + if (m_team_size <= 0) { + m_scratch_ptr[1] = nullptr; + } else { + auto scratch_ptr_id = + m_policy.space() + .impl_internal_space_instance() + ->resize_team_scratch_space( + static_cast(m_scratch_size[1]) * + (static_cast(Cuda::concurrency() / + (m_team_size * m_vector_size)))); + m_scratch_ptr[1] = scratch_ptr_id.first; + m_scratch_pool_id = scratch_ptr_id.second; + } // The global parallel_reduce does not support vector_length other than 1 at // the moment @@ -1973,6 +2021,8 @@ class ParallelReduce, cudaFuncAttributes attr = CudaParallelLaunch::get_cuda_func_attributes(); + + // Valid team size not provided, deduce team size m_team_size = m_team_size >= 0 ? m_team_size @@ -1994,15 +2044,19 @@ class ParallelReduce, FunctorTeamShmemSize::value(arg_functor, m_team_size); m_scratch_size[0] = m_shmem_size; m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); - m_scratch_ptr[1] = - m_team_size <= 0 - ? nullptr - : m_policy.space() - .impl_internal_space_instance() - ->resize_team_scratch_space( - static_cast(m_scratch_size[1]) * - static_cast(Cuda::concurrency() / - (m_team_size * m_vector_size))); + if (m_team_size <= 0) { + m_scratch_ptr[1] = nullptr; + } else { + auto scratch_ptr_id = + m_policy.space() + .impl_internal_space_instance() + ->resize_team_scratch_space( + static_cast(m_scratch_size[1]) * + (static_cast(Cuda::concurrency() / + (m_team_size * m_vector_size)))); + m_scratch_ptr[1] = scratch_ptr_id.first; + m_scratch_pool_id = scratch_ptr_id.second; + } // The global parallel_reduce does not support vector_length other than 1 at // the moment @@ -2030,13 +2084,28 @@ class ParallelReduce, Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< Cuda > bad team size")); } - if (int(m_team_size) > - arg_policy.team_size_max(m_functor, m_reducer, ParallelReduceTag())) { + + size_type team_size_max = + Kokkos::Impl::cuda_get_max_block_size( + m_policy.space().impl_internal_space_instance(), attr, m_functor, + m_vector_size, m_policy.team_scratch_size(0), + m_policy.thread_scratch_size(0)) / + m_vector_size; + + if ((int)m_team_size > (int)team_size_max) { Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too " "large team size.")); } } + + ~ParallelReduce() { + if (m_scratch_pool_id >= 0) { + m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_pool[m_scratch_pool_id] = 0; + } + } }; } // namespace Impl @@ -2167,9 +2236,7 @@ class ParallelScan, Kokkos::Cuda> { for (typename Policy::member_type iwork_base = range.begin(); iwork_base < range.end(); iwork_base += blockDim.y) { -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned MASK = KOKKOS_IMPL_CUDA_ACTIVEMASK; -#endif + unsigned MASK = __activemask(); const typename Policy::member_type iwork = iwork_base + threadIdx.y; __syncthreads(); // Don't overwrite previous iteration values until they @@ -2182,11 +2249,7 @@ class ParallelScan, Kokkos::Cuda> { for (unsigned i = threadIdx.y; i < word_count.value; ++i) { shared_data[i + word_count.value] = shared_data[i] = shared_accum[i]; } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(MASK); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(MASK); if (CudaTraits::WarpSize < word_count.value) { __syncthreads(); } // Protect against large scan values. @@ -2457,9 +2520,7 @@ class ParallelScanWithTotal, for (typename Policy::member_type iwork_base = range.begin(); iwork_base < range.end(); iwork_base += blockDim.y) { -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned MASK = KOKKOS_IMPL_CUDA_ACTIVEMASK; -#endif + unsigned MASK = __activemask(); const typename Policy::member_type iwork = iwork_base + threadIdx.y; @@ -2474,11 +2535,7 @@ class ParallelScanWithTotal, shared_data[i + word_count.value] = shared_data[i] = shared_accum[i]; } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(MASK); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(MASK); if (CudaTraits::WarpSize < word_count.value) { __syncthreads(); } // Protect against large scan values. diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp index fc9fc3770bea..e5b05bcc64f1 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp @@ -191,48 +191,28 @@ __device__ bool cuda_inter_block_reduction( value_type tmp = Kokkos::shfl_down(value, 1, 32); if (id + 1 < int(gridDim.x)) join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask(); + int active = __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 2) { value_type tmp = Kokkos::shfl_down(value, 2, 32); if (id + 2 < int(gridDim.x)) join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 4) { value_type tmp = Kokkos::shfl_down(value, 4, 32); if (id + 4 < int(gridDim.x)) join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 8) { value_type tmp = Kokkos::shfl_down(value, 8, 32); if (id + 8 < int(gridDim.x)) join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 16) { value_type tmp = Kokkos::shfl_down(value, 16, 32); if (id + 16 < int(gridDim.x)) join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); } } // The last block has in its thread=0 the global reduction value through @@ -388,48 +368,28 @@ __device__ inline value_type tmp = Kokkos::shfl_down(value, 1, 32); if (id + 1 < int(gridDim.x)) reducer.join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; - int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - int active = KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + unsigned int mask = __activemask(); + int active = __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 2) { value_type tmp = Kokkos::shfl_down(value, 2, 32); if (id + 2 < int(gridDim.x)) reducer.join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 4) { value_type tmp = Kokkos::shfl_down(value, 4, 32); if (id + 4 < int(gridDim.x)) reducer.join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 8) { value_type tmp = Kokkos::shfl_down(value, 8, 32); if (id + 8 < int(gridDim.x)) reducer.join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); if (int(blockDim.x * blockDim.y) > 16) { value_type tmp = Kokkos::shfl_down(value, 16, 32); if (id + 16 < int(gridDim.x)) reducer.join(value, tmp); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask, 1); -#else - active += KOKKOS_IMPL_CUDA_BALLOT(1); -#endif + active += __ballot_sync(mask, 1); } } @@ -573,23 +533,17 @@ struct CudaReductionsFunctor { // part of the reduction const int width) // How much of the warp participates { -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK unsigned mask = width == 32 ? 0xffffffff : ((1 << width) - 1) << ((threadIdx.y * blockDim.x + threadIdx.x) / width) * width; -#endif const int lane_id = (threadIdx.y * blockDim.x + threadIdx.x) % 32; for (int delta = skip_vector ? blockDim.x : 1; delta < width; delta *= 2) { if (lane_id + delta < 32) { ValueJoin::join(functor, value, value + delta); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(mask); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(mask); } *value = *(value - lane_id); } @@ -612,17 +566,18 @@ struct CudaReductionsFunctor { const unsigned int delta = (threadIdx.y * blockDim.x + threadIdx.x) * 32; if (delta < blockDim.x * blockDim.y) *my_shared_team_buffer_element = shared_team_buffer_element[delta]; - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); scalar_intra_warp_reduction(functor, my_shared_team_buffer_element, false, blockDim.x * blockDim.y / 32); if (threadIdx.x + threadIdx.y == 0) *result = *shared_team_buffer_element; } } + template __device__ static inline bool scalar_inter_block_reduction( const FunctorType& functor, const Cuda::size_type /*block_id*/, - const Cuda::size_type block_count, Cuda::size_type* const shared_data, - Cuda::size_type* const global_data, Cuda::size_type* const global_flags) { + const Cuda::size_type block_count, SizeType* const shared_data, + SizeType* const global_data, Cuda::size_type* const global_flags) { Scalar* const global_team_buffer_element = ((Scalar*)global_data); Scalar* const my_global_team_buffer_element = global_team_buffer_element + blockIdx.x; @@ -713,17 +668,17 @@ __device__ void cuda_intra_block_reduce_scan( const pointer_type tdata_intra = base_data + value_count * threadIdx.y; { // Intra-warp reduction: - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_REDUCE_STEP(rtid_intra, tdata_intra, 0) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_REDUCE_STEP(rtid_intra, tdata_intra, 1) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_REDUCE_STEP(rtid_intra, tdata_intra, 2) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_REDUCE_STEP(rtid_intra, tdata_intra, 3) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_REDUCE_STEP(rtid_intra, tdata_intra, 4) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); } __syncthreads(); // Wait for all warps to reduce @@ -732,57 +687,31 @@ __device__ void cuda_intra_block_reduce_scan( const unsigned rtid_inter = (threadIdx.y ^ BlockSizeMask) << CudaTraits::WarpIndexShift; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - unsigned inner_mask = - KOKKOS_IMPL_CUDA_BALLOT_MASK(0xffffffff, (rtid_inter < blockDim.y)); -#endif + unsigned inner_mask = __ballot_sync(0xffffffff, (rtid_inter < blockDim.y)); if (rtid_inter < blockDim.y) { const pointer_type tdata_inter = base_data + value_count * (rtid_inter ^ BlockSizeMask); -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK if ((1 << 5) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); + __syncwarp(inner_mask); BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 5) } if ((1 << 6) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); + __syncwarp(inner_mask); BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 6) } if ((1 << 7) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); + __syncwarp(inner_mask); BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 7) } if ((1 << 8) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); + __syncwarp(inner_mask); BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 8) } if ((1 << 9) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); + __syncwarp(inner_mask); BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 9) } -#else - if ((1 << 5) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP; - BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 5) - } - if ((1 << 6) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP; - BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 6) - } - if ((1 << 7) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP; - BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 7) - } - if ((1 << 8) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP; - BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 8) - } - if ((1 << 9) < BlockSizeMask) { - KOKKOS_IMPL_CUDA_SYNCWARP; - BLOCK_REDUCE_STEP(rtid_inter, tdata_inter, 9) - } -#endif if (DoScan) { int n = @@ -795,25 +724,14 @@ __device__ void cuda_intra_block_reduce_scan( if (!(rtid_inter + n < blockDim.y)) n = 0; -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); - BLOCK_SCAN_STEP(tdata_inter, n, 8) - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); - BLOCK_SCAN_STEP(tdata_inter, n, 7) - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); - BLOCK_SCAN_STEP(tdata_inter, n, 6) - KOKKOS_IMPL_CUDA_SYNCWARP_MASK(inner_mask); - BLOCK_SCAN_STEP(tdata_inter, n, 5) -#else - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(inner_mask); BLOCK_SCAN_STEP(tdata_inter, n, 8) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(inner_mask); BLOCK_SCAN_STEP(tdata_inter, n, 7) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(inner_mask); BLOCK_SCAN_STEP(tdata_inter, n, 6) - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(inner_mask); BLOCK_SCAN_STEP(tdata_inter, n, 5) -#endif } } } @@ -832,17 +750,17 @@ __device__ void cuda_intra_block_reduce_scan( : ((rtid_intra & 16) ? 16 : 0)))); if (!(rtid_intra + n < blockDim.y)) n = 0; - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_SCAN_STEP(tdata_intra, n, 4) __threadfence_block(); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_SCAN_STEP(tdata_intra, n, 3) __threadfence_block(); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_SCAN_STEP(tdata_intra, n, 2) __threadfence_block(); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_SCAN_STEP(tdata_intra, n, 1) __threadfence_block(); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); BLOCK_SCAN_STEP(tdata_intra, n, 0) __threadfence_block(); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); } #undef BLOCK_SCAN_STEP @@ -858,12 +776,13 @@ __device__ void cuda_intra_block_reduce_scan( * Global reduce result is in the last threads' 'shared_data' location. */ -template +template __device__ bool cuda_single_inter_block_reduce_scan2( const FunctorType& functor, const Cuda::size_type block_id, - const Cuda::size_type block_count, Cuda::size_type* const shared_data, - Cuda::size_type* const global_data, Cuda::size_type* const global_flags) { - using size_type = Cuda::size_type; + const Cuda::size_type block_count, SizeType* const shared_data, + SizeType* const global_data, Cuda::size_type* const global_flags) { + using size_type = SizeType; using ValueTraits = FunctorValueTraits; using ValueJoin = FunctorValueJoin; using ValueInit = FunctorValueInit; @@ -953,11 +872,12 @@ __device__ bool cuda_single_inter_block_reduce_scan2( return is_last_block; } -template +template __device__ bool cuda_single_inter_block_reduce_scan( const FunctorType& functor, const Cuda::size_type block_id, - const Cuda::size_type block_count, Cuda::size_type* const shared_data, - Cuda::size_type* const global_data, Cuda::size_type* const global_flags) { + const Cuda::size_type block_count, SizeType* const shared_data, + SizeType* const global_data, Cuda::size_type* const global_flags) { using ValueTraits = FunctorValueTraits; if (!DoScan && ValueTraits::StaticValueSize > 0) return Kokkos::Impl::CudaReductionsFunctor< diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp index 2004edbeacdb..88ac0d1878a9 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp @@ -54,11 +54,27 @@ #include #include -#include // CUDA_SAFE_CALL +#include // KOKKOS_IMPL_CUDA_SAFE_CALL #include //---------------------------------------------------------------------------- +#if defined(__CUDA_ARCH__) +#define KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN(MSG) \ + { \ + __syncwarp(); \ + const unsigned b = __activemask(); \ + if (b != 0xffffffff) { \ + printf(" SYNCWARP AT %s (%d,%d,%d) (%d,%d,%d) failed %x\n", MSG, \ + blockIdx.x, blockIdx.y, blockIdx.z, threadIdx.x, threadIdx.y, \ + threadIdx.z, b); \ + return; \ + } \ + } +#else +#define KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN(MSG) +#endif + namespace Kokkos { namespace Impl { namespace { @@ -138,13 +154,13 @@ class TaskQueueSpecialization> { // Broadcast task pointer: // Sync before the broadcast - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); // pretend it's an int* for shuffle purposes ((int*)¤t_task)[0] = - KOKKOS_IMPL_CUDA_SHFL(((int*)¤t_task)[0], 0, 32); + __shfl_sync(0xffffffff, ((int*)¤t_task)[0], 0, 32); ((int*)¤t_task)[1] = - KOKKOS_IMPL_CUDA_SHFL(((int*)¤t_task)[1], 0, 32); + __shfl_sync(0xffffffff, ((int*)¤t_task)[1], 0, 32); if (current_task) { KOKKOS_ASSERT(!current_task->as_runnable_task().get_respawn_flag()); @@ -168,7 +184,7 @@ class TaskQueueSpecialization> { // Synchronize threads of the warp and insure memory // writes are visible to all threads in the warp. - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); if (shared_memory_task_copy->is_team_runnable()) { // Thread Team Task @@ -182,7 +198,7 @@ class TaskQueueSpecialization> { // Synchronize threads of the warp and insure memory // writes are visible to all threads in the warp. - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); // if(warp_lane < b % CudaTraits::WarpSize) b += CudaTraits::WarpSize; // b -= b % CudaTraits::WarpSize; @@ -196,7 +212,7 @@ class TaskQueueSpecialization> { // writes are visible to root thread of the warp for // respawn or completion. - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); if (warp_lane == 0) { // If respawn requested copy respawn data back to main memory @@ -249,12 +265,14 @@ class TaskQueueSpecialization> { auto& queue = scheduler.queue(); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecialization::execute: Pre Task Execution"); // Query the stack size, in bytes: size_t previous_stack_size = 0; - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaDeviceGetLimit(&previous_stack_size, cudaLimitStackSize)); // If not large enough then set the stack size, in bytes: @@ -262,18 +280,21 @@ class TaskQueueSpecialization> { const size_t larger_stack_size = 1 << 11; if (previous_stack_size < larger_stack_size) { - CUDA_SAFE_CALL(cudaDeviceSetLimit(cudaLimitStackSize, larger_stack_size)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaDeviceSetLimit(cudaLimitStackSize, larger_stack_size)); } cuda_task_queue_execute<<>>( scheduler, shared_per_warp); - CUDA_SAFE_CALL(cudaGetLastError()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecialization::execute: Post Task Execution"); if (previous_stack_size < larger_stack_size) { - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaDeviceSetLimit(cudaLimitStackSize, previous_stack_size)); } } @@ -295,13 +316,17 @@ class TaskQueueSpecialization> { destroy_type* dtor_ptr = (destroy_type*)((char*)storage + sizeof(function_type)); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecialization::execute: Pre Get Function Pointer for Tasks"); set_cuda_task_base_apply_function_pointer <<<1, 1>>>(ptr_ptr, dtor_ptr); - CUDA_SAFE_CALL(cudaGetLastError()); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecialization::execute: Post Get Function Pointer for Tasks"); ptr = *ptr_ptr; dtor = *dtor_ptr; @@ -372,23 +397,20 @@ class TaskQueueSpecializationConstrained< // count of 0 also. Otherwise, returns a task from another queue // or `end` if one couldn't be popped task_ptr = team_queue.attempt_to_steal_task(); -#if 0 - if(task != no_more_tasks_sentinel && task != end) { - std::printf("task stolen on rank %d\n", team_exec.league_rank()); - } -#endif } } // Synchronize warp with memory fence before broadcasting task pointer: // KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN( "A" ); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); // Broadcast task pointer: - ((int*)&task_ptr)[0] = KOKKOS_IMPL_CUDA_SHFL(((int*)&task_ptr)[0], 0, 32); - ((int*)&task_ptr)[1] = KOKKOS_IMPL_CUDA_SHFL(((int*)&task_ptr)[1], 0, 32); + ((int*)&task_ptr)[0] = + __shfl_sync(0xffffffff, ((int*)&task_ptr)[0], 0, 32); + ((int*)&task_ptr)[1] = + __shfl_sync(0xffffffff, ((int*)&task_ptr)[1], 0, 32); #if defined(KOKKOS_ENABLE_DEBUG) KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN("TaskQueue CUDA task_ptr"); @@ -418,7 +440,7 @@ class TaskQueueSpecializationConstrained< // writes are visible to all threads in the warp. // KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN( "B" ); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); if (task_root_type::TaskTeam == task_shmem->m_task_type) { // Thread Team Task @@ -432,7 +454,7 @@ class TaskQueueSpecializationConstrained< // writes are visible to all threads in the warp. // KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN( "C" ); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); // copy task closure from shared to global memory: @@ -445,7 +467,7 @@ class TaskQueueSpecializationConstrained< // respawn or completion. // KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN( "D" ); - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); // If respawn requested copy respawn data back to main memory @@ -475,12 +497,14 @@ class TaskQueueSpecializationConstrained< auto& queue = scheduler.queue(); queue.initialize_team_queues(warps_per_block * grid.x); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecializationConstrained::execute: Pre Execute Task"); // Query the stack size, in bytes: size_t previous_stack_size = 0; - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaDeviceGetLimit(&previous_stack_size, cudaLimitStackSize)); // If not large enough then set the stack size, in bytes: @@ -488,18 +512,21 @@ class TaskQueueSpecializationConstrained< const size_t larger_stack_size = 2048; if (previous_stack_size < larger_stack_size) { - CUDA_SAFE_CALL(cudaDeviceSetLimit(cudaLimitStackSize, larger_stack_size)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaDeviceSetLimit(cudaLimitStackSize, larger_stack_size)); } cuda_task_queue_execute<<>>( scheduler, shared_per_warp); - CUDA_SAFE_CALL(cudaGetLastError()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecializationConstrained::execute: Post Execute Task"); if (previous_stack_size < larger_stack_size) { - CUDA_SAFE_CALL( + KOKKOS_IMPL_CUDA_SAFE_CALL( cudaDeviceSetLimit(cudaLimitStackSize, previous_stack_size)); } } @@ -516,13 +543,17 @@ class TaskQueueSpecializationConstrained< destroy_type* dtor_ptr = (destroy_type*)((char*)storage + sizeof(function_type)); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecializationConstrained::get_function_pointer: Pre Get Function Pointer"); set_cuda_task_base_apply_function_pointer <<<1, 1>>>(ptr_ptr, dtor_ptr); - CUDA_SAFE_CALL(cudaGetLastError()); - CUDA_SAFE_CALL(cudaDeviceSynchronize()); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); + Impl::cuda_device_synchronize( + "Kokkos::Impl::TaskQueueSpecializationConstrained::get_function_pointer: Post Get Function Pointer"); ptr = *ptr_ptr; dtor = *dtor_ptr; @@ -609,7 +640,7 @@ class TaskExec { __device__ void team_barrier() const { if (1 < m_team_size) { - KOKKOS_IMPL_CUDA_SYNCWARP; + __syncwarp(0xffffffff); } } @@ -1205,5 +1236,7 @@ KOKKOS_INLINE_FUNCTION void single( //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- +#undef KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN + #endif /* #if defined( KOKKOS_ENABLE_TASKDAG ) */ #endif /* #ifndef KOKKOS_IMPL_CUDA_TASK_HPP */ diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp index e7806390155d..922b980a2545 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp @@ -340,191 +340,6 @@ class CudaTeamMember { #endif } - //-------------------------------------------------------------------------- - /**\brief Global reduction across all blocks - * - * Return !0 if reducer contains the final value - */ - template - KOKKOS_INLINE_FUNCTION static - typename std::enable_if::value, int>::type - global_reduce(ReducerType const& reducer, int* const global_scratch_flags, - void* const global_scratch_space, void* const shmem, - int const shmem_size) { -#ifdef __CUDA_ARCH__ - - using value_type = typename ReducerType::value_type; - using pointer_type = value_type volatile*; - - // Number of shared memory entries for the reduction: - const int nsh = shmem_size / sizeof(value_type); - - // Number of CUDA threads in the block, rank within the block - const int nid = blockDim.x * blockDim.y * blockDim.z; - const int tid = - threadIdx.x + blockDim.x * (threadIdx.y + blockDim.y * threadIdx.z); - - // Reduces within block using all available shared memory - // Contributes if it is the root "vector lane" - - // wn == number of warps in the block - // wx == which lane within the warp - // wy == which warp within the block - - const int wn = - (nid + CudaTraits::WarpIndexMask) >> CudaTraits::WarpIndexShift; - const int wx = tid & CudaTraits::WarpIndexMask; - const int wy = tid >> CudaTraits::WarpIndexShift; - - //------------------------ - { // Intra warp shuffle reduction from contributing CUDA threads - - value_type tmp(reducer.reference()); - - for (int i = CudaTraits::WarpSize; (int)blockDim.x <= (i >>= 1);) { - Impl::in_place_shfl_down(reducer.reference(), tmp, i, - CudaTraits::WarpSize); - - // Root of each vector lane reduces "thread" contribution - if (0 == threadIdx.x && wx < i) { - reducer.join(&tmp, reducer.data()); - } - } - - // Reduce across warps using shared memory. - // Number of warps may not be power of two. - - __syncthreads(); // Wait before shared data write - - // Number of shared memory entries for the reduction - // is at most one per warp - const int nentry = wn < nsh ? wn : nsh; - - if (0 == wx && wy < nentry) { - // Root thread of warp 'wy' has warp's value to contribute - ((value_type*)shmem)[wy] = tmp; - } - - __syncthreads(); // Wait for write to be visible to block - - // When more warps than shared entries - // then warps must take turns joining their contribution - // to the designated shared memory entry. - for (int i = nentry; i < wn; i += nentry) { - const int k = wy - i; - - if (0 == wx && i <= wy && k < nentry) { - // Root thread of warp 'wy' has warp's value to contribute - reducer.join(((value_type*)shmem) + k, &tmp); - } - - __syncthreads(); // Wait for write to be visible to block - } - - // One warp performs the inter-warp reduction: - - if (0 == wy) { - // Start fan-in at power of two covering nentry - - for (int i = (1 << (32 - __clz(nentry - 1))); (i >>= 1);) { - const int k = wx + i; - if (wx < i && k < nentry) { - reducer.join(((pointer_type)shmem) + wx, ((pointer_type)shmem) + k); - __threadfence_block(); // Wait for write to be visible to warp - } - } - } - } - //------------------------ - { // Write block's value to global_scratch_memory - - int last_block = 0; - - if (0 == wx) { - reducer.copy(((pointer_type)global_scratch_space) + - blockIdx.x * reducer.length(), - reducer.data()); - - __threadfence(); // Wait until global write is visible. - - last_block = (int)gridDim.x == - 1 + Kokkos::atomic_fetch_add(global_scratch_flags, 1); - - // If last block then reset count - if (last_block) *global_scratch_flags = 0; - } - - last_block = __syncthreads_or(last_block); - - if (!last_block) return 0; - } - //------------------------ - // Last block reads global_scratch_memory into shared memory. - - const int nentry = nid < gridDim.x ? (nid < nsh ? nid : nsh) - : (gridDim.x < nsh ? gridDim.x : nsh); - - // nentry = min( nid , nsh , gridDim.x ) - - // whole block reads global memory into shared memory: - - if (tid < nentry) { - const int offset = tid * reducer.length(); - - reducer.copy(((pointer_type)shmem) + offset, - ((pointer_type)global_scratch_space) + offset); - - for (int i = nentry + tid; i < (int)gridDim.x; i += nentry) { - reducer.join( - ((pointer_type)shmem) + offset, - ((pointer_type)global_scratch_space) + i * reducer.length()); - } - } - - __syncthreads(); // Wait for writes to be visible to block - - if (0 == wy) { - // Iterate to reduce shared memory to single warp fan-in size - - const int nreduce = - CudaTraits::WarpSize < nentry ? CudaTraits::WarpSize : nentry; - - // nreduce = min( CudaTraits::WarpSize , nsh , gridDim.x ) - - if (wx < nreduce && nreduce < nentry) { - for (int i = nreduce + wx; i < nentry; i += nreduce) { - reducer.join(((pointer_type)shmem) + wx, ((pointer_type)shmem) + i); - } - __threadfence_block(); // Wait for writes to be visible to warp - } - - // Start fan-in at power of two covering nentry - - for (int i = (1 << (32 - __clz(nreduce - 1))); (i >>= 1);) { - const int k = wx + i; - if (wx < i && k < nreduce) { - reducer.join(((pointer_type)shmem) + wx, ((pointer_type)shmem) + k); - __threadfence_block(); // Wait for writes to be visible to warp - } - } - - if (0 == wx) { - reducer.copy(reducer.data(), (pointer_type)shmem); - return 1; - } - } - return 0; - -#else - (void)reducer; - (void)global_scratch_flags; - (void)global_scratch_space; - (void)shmem; - (void)shmem_size; - return 0; -#endif - } - //---------------------------------------- // Private for the driver @@ -533,7 +348,7 @@ class CudaTeamMember { void* scratch_level_1_ptr, const int scratch_level_1_size, const int arg_league_rank, const int arg_league_size) : m_team_reduce(shared), - m_team_shared(((char*)shared) + shared_begin, shared_size, + m_team_shared(static_cast(shared) + shared_begin, shared_size, scratch_level_1_ptr, scratch_level_1_size), m_team_reduce_size(shared_begin), m_league_rank(arg_league_rank), @@ -854,14 +669,10 @@ KOKKOS_INLINE_FUNCTION void parallel_for( i += blockDim.x) { closure(i); } -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK( - blockDim.x == 32 ? 0xffffffff - : ((1 << blockDim.x) - 1) - << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(blockDim.x == 32 + ? 0xffffffff + : ((1 << blockDim.x) - 1) + << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); #endif } @@ -1100,14 +911,10 @@ KOKKOS_INLINE_FUNCTION void single( (void)lambda; #ifdef __CUDA_ARCH__ if (threadIdx.x == 0) lambda(); -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK( - blockDim.x == 32 ? 0xffffffff - : ((1 << blockDim.x) - 1) - << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(blockDim.x == 32 + ? 0xffffffff + : ((1 << blockDim.x) - 1) + << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); #endif } @@ -1118,14 +925,10 @@ KOKKOS_INLINE_FUNCTION void single( (void)lambda; #ifdef __CUDA_ARCH__ if (threadIdx.x == 0 && threadIdx.y == 0) lambda(); -#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK - KOKKOS_IMPL_CUDA_SYNCWARP_MASK( - blockDim.x == 32 ? 0xffffffff - : ((1 << blockDim.x) - 1) - << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); -#else - KOKKOS_IMPL_CUDA_SYNCWARP; -#endif + __syncwarp(blockDim.x == 32 + ? 0xffffffff + : ((1 << blockDim.x) - 1) + << (threadIdx.y % (32 / blockDim.x)) * blockDim.x); #endif } diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Vectorization.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Vectorization.hpp index 7f7b7b6e78ad..31d3c47e1c9c 100644 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Vectorization.hpp +++ b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Vectorization.hpp @@ -48,7 +48,12 @@ #ifdef KOKKOS_ENABLE_CUDA #include -#include + +#if !defined(KOKKOS_COMPILER_CLANG) +#define KOKKOS_IMPL_CUDA_MAX_SHFL_SIZEOF sizeof(long long) +#else +#define KOKKOS_IMPL_CUDA_MAX_SHFL_SIZEOF sizeof(int) +#endif namespace Kokkos { @@ -61,7 +66,7 @@ constexpr unsigned shfl_all_mask = 0xffffffffu; // Shuffle operations require input to be a register (stack) variable // Derived implements do_shfl_op(unsigned mask, T& in, int lane, int width), -// which turns in to one of KOKKOS_IMPL_CUDA_SHFL(_UP_|_DOWN_|_)MASK +// which turns in to one of __shfl_sync(_up|_down) // Since the logic with respect to value sizes, etc., is the same everywhere, // put it all in one place. template @@ -157,7 +162,7 @@ struct in_place_shfl_fn : in_place_shfl_op { (void)val; (void)lane; (void)width; - return KOKKOS_IMPL_CUDA_SHFL_MASK(mask, val, lane, width); + return __shfl_sync(mask, val, lane, width); } }; template @@ -170,7 +175,7 @@ struct in_place_shfl_up_fn : in_place_shfl_op { __device__ KOKKOS_IMPL_FORCEINLINE T do_shfl_op(unsigned mask, T& val, int lane, int width) const noexcept { - return KOKKOS_IMPL_CUDA_SHFL_UP_MASK(mask, val, lane, width); + return __shfl_up_sync(mask, val, lane, width); } }; template @@ -188,7 +193,7 @@ struct in_place_shfl_down_fn : in_place_shfl_op { (void)val; (void)lane; (void)width; - return KOKKOS_IMPL_CUDA_SHFL_DOWN_MASK(mask, val, lane, width); + return __shfl_down_sync(mask, val, lane, width); } }; template @@ -228,5 +233,7 @@ __device__ inline T shfl_up(const T& val, int delta, int width, } // end namespace Kokkos +#undef KOKKOS_IMPL_CUDA_MAX_SHFL_SIZEOF + #endif // defined( KOKKOS_ENABLE_CUDA ) #endif // !defined( KOKKOS_CUDA_VECTORIZATION_HPP ) diff --git a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Version_9_8_Compatibility.hpp b/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Version_9_8_Compatibility.hpp deleted file mode 100644 index 0cdd84ce2715..000000000000 --- a/packages/kokkos/core/src/Cuda/Kokkos_Cuda_Version_9_8_Compatibility.hpp +++ /dev/null @@ -1,49 +0,0 @@ -#include - -#if defined(__CUDA_ARCH__) -#define KOKKOS_IMPL_CUDA_ACTIVEMASK __activemask() -#define KOKKOS_IMPL_CUDA_SYNCWARP __syncwarp(0xffffffff) -#define KOKKOS_IMPL_CUDA_SYNCWARP_MASK(m) __syncwarp(m) -#define KOKKOS_IMPL_CUDA_BALLOT(x) __ballot_sync(__activemask(), x) -#define KOKKOS_IMPL_CUDA_BALLOT_MASK(m, x) __ballot_sync(m, x) -#define KOKKOS_IMPL_CUDA_SHFL(x, y, z) __shfl_sync(0xffffffff, x, y, z) -#define KOKKOS_IMPL_CUDA_SHFL_MASK(m, x, y, z) __shfl_sync(m, x, y, z) -#define KOKKOS_IMPL_CUDA_SHFL_UP(x, y, z) __shfl_up_sync(0xffffffff, x, y, z) -#define KOKKOS_IMPL_CUDA_SHFL_UP_MASK(m, x, y, z) __shfl_up_sync(m, x, y, z) -#define KOKKOS_IMPL_CUDA_SHFL_DOWN(x, y, z) \ - __shfl_down_sync(0xffffffff, x, y, z) -#define KOKKOS_IMPL_CUDA_SHFL_DOWN_MASK(m, x, y, z) __shfl_down_sync(m, x, y, z) -#else -#define KOKKOS_IMPL_CUDA_ACTIVEMASK 0 -#define KOKKOS_IMPL_CUDA_SYNCWARP -#define KOKKOS_IMPL_CUDA_SYNCWARP_MASK(m) (void)m -#define KOKKOS_IMPL_CUDA_BALLOT(x) 0 -#define KOKKOS_IMPL_CUDA_BALLOT_MASK(m, x) 0 -#define KOKKOS_IMPL_CUDA_SHFL(x, y, z) 0 -#define KOKKOS_IMPL_CUDA_SHFL_MASK(m, x, y, z) 0 -#define KOKKOS_IMPL_CUDA_SHFL_UP(x, y, z) 0 -#define KOKKOS_IMPL_CUDA_SHFL_DOWN(x, y, z) 0 -#define KOKKOS_IMPL_CUDA_SHFL_DOWN_MASK(m, x, y, z) 0 -#endif - -#if !defined(KOKKOS_COMPILER_CLANG) -#define KOKKOS_IMPL_CUDA_MAX_SHFL_SIZEOF sizeof(long long) -#else -#define KOKKOS_IMPL_CUDA_MAX_SHFL_SIZEOF sizeof(int) -#endif - -#if defined(__CUDA_ARCH__) -#define KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN(MSG) \ - { \ - __syncwarp(); \ - const unsigned b = __activemask(); \ - if (b != 0xffffffff) { \ - printf(" SYNCWARP AT %s (%d,%d,%d) (%d,%d,%d) failed %x\n", MSG, \ - blockIdx.x, blockIdx.y, blockIdx.z, threadIdx.x, threadIdx.y, \ - threadIdx.z, b); \ - return; \ - } \ - } -#else -#define KOKKOS_IMPL_CUDA_SYNCWARP_OR_RETURN(MSG) -#endif diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp index 9278d1bdc9ef..7eb3e1e9f70f 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp @@ -45,6 +45,7 @@ #ifndef KOKKOS_HIP_BLOCKSIZE_DEDUCTION_HPP #define KOKKOS_HIP_BLOCKSIZE_DEDUCTION_HPP +#include #include #if defined(__HIPCC__) @@ -56,118 +57,239 @@ namespace Kokkos { namespace Experimental { namespace Impl { -template -void hipOccupancy(int *numBlocks, int blockSize, int sharedmem) { - // FIXME_HIP - currently the "constant" path is unimplemented. - // we should look at whether it's functional, and - // perform some simple scaling studies to see when / - // if the constant launcher outperforms the current - // pass by pointer shared launcher - HIP_SAFE_CALL(hipOccupancyMaxActiveBlocksPerMultiprocessor( - numBlocks, - hip_parallel_launch_local_memory, - blockSize, sharedmem)); -} +enum class BlockType { Max, Preferred }; -template -void hipOccupancy(int *numBlocks, int blockSize, int sharedmem) { - hipOccupancy( - numBlocks, blockSize, sharedmem); +template , + HIPLaunchMechanism LaunchMechanism = + DeduceHIPLaunchMechanism::launch_mechanism> +unsigned get_preferred_blocksize_impl() { + // FIXME_HIP - could be if constexpr for c++17 + if (!HIPParallelLaunch::default_launchbounds()) { + // use the user specified value + return LaunchBounds::maxTperB; + } else { + if (HIPParallelLaunch::get_scratch_size() > 0) { + return HIPTraits::ConservativeThreadsPerBlock; + } + return HIPTraits::MaxThreadsPerBlock; + } } -template -int hip_internal_get_block_size(const F &condition_check, - const HIPInternal *hip_instance, - const hipFuncAttributes &attr, - const FunctorType &f, - const size_t vector_length, - const size_t shmem_block, - const size_t shmem_thread) { - const int min_blocks_per_sm = - LaunchBounds::minBperSM == 0 ? 1 : LaunchBounds::minBperSM; - const int max_threads_per_block = LaunchBounds::maxTperB == 0 - ? HIPTraits::MaxThreadsPerBlock - : LaunchBounds::maxTperB; - - const int regs_per_wavefront = std::max(attr.numRegs, 1); - const int regs_per_sm = hip_instance->m_regsPerSM; - const int shmem_per_sm = hip_instance->m_shmemPerSM; - const int max_shmem_per_block = hip_instance->m_maxShmemPerBlock; - const int max_blocks_per_sm = hip_instance->m_maxBlocksPerSM; - const int max_threads_per_sm = hip_instance->m_maxThreadsPerSM; - - int block_size = max_threads_per_block; - KOKKOS_ASSERT(block_size > 0); - const int blocks_per_warp = - (block_size + HIPTraits::WarpSize - 1) / HIPTraits::WarpSize; - - int functor_shmem = ::Kokkos::Impl::FunctorTeamShmemSize::value( - f, block_size / vector_length); - int total_shmem = shmem_block + shmem_thread * (block_size / vector_length) + - functor_shmem + attr.sharedSizeBytes; - int max_blocks_regs = regs_per_sm / (regs_per_wavefront * blocks_per_warp); - int max_blocks_shmem = - (total_shmem < max_shmem_per_block) - ? (total_shmem > 0 ? shmem_per_sm / total_shmem : max_blocks_regs) - : 0; - int blocks_per_sm = std::min(max_blocks_regs, max_blocks_shmem); - int threads_per_sm = blocks_per_sm * block_size; - if (threads_per_sm > max_threads_per_sm) { - blocks_per_sm = max_threads_per_sm / block_size; - threads_per_sm = blocks_per_sm * block_size; +// FIXME_HIP - entire function could be constexpr for c++17 +template , + HIPLaunchMechanism LaunchMechanism = + DeduceHIPLaunchMechanism::launch_mechanism> +unsigned get_max_blocksize_impl() { + // FIXME_HIP - could be if constexpr for c++17 + if (!HIPParallelLaunch::default_launchbounds()) { + // use the user specified value + return LaunchBounds::maxTperB; + } else { + // we can always fit 1024 threads blocks if we only care about registers + // ... and don't mind spilling + return HIPTraits::MaxThreadsPerBlock; } - int opt_block_size = - (blocks_per_sm >= min_blocks_per_sm) ? block_size : min_blocks_per_sm; - int opt_threads_per_sm = threads_per_sm; - block_size -= HIPTraits::WarpSize; - while (condition_check(blocks_per_sm) && - (block_size >= HIPTraits::WarpSize)) { - functor_shmem = ::Kokkos::Impl::FunctorTeamShmemSize::value( - f, block_size / vector_length); - total_shmem = shmem_block + shmem_thread * (block_size / vector_length) + - functor_shmem + attr.sharedSizeBytes; - max_blocks_regs = regs_per_sm / (regs_per_wavefront * blocks_per_warp); - max_blocks_shmem = - (total_shmem < max_shmem_per_block) - ? (total_shmem > 0 ? shmem_per_sm / total_shmem : max_blocks_regs) - : 0; - blocks_per_sm = std::min(max_blocks_regs, max_blocks_shmem); - threads_per_sm = blocks_per_sm * block_size; - if (threads_per_sm > max_threads_per_sm) { - blocks_per_sm = max_threads_per_sm / block_size; - threads_per_sm = blocks_per_sm * block_size; - } - if ((blocks_per_sm >= min_blocks_per_sm) && - (blocks_per_sm <= max_blocks_per_sm)) { - if (threads_per_sm >= opt_threads_per_sm) { - opt_block_size = block_size; - opt_threads_per_sm = threads_per_sm; +} + +// convenience method to select and return the proper function attributes +// for a kernel, given the launch bounds et al. +template , + BlockType BlockSize = BlockType::Max, + HIPLaunchMechanism LaunchMechanism = + DeduceHIPLaunchMechanism::launch_mechanism> +hipFuncAttributes get_hip_func_attributes_impl() { + // FIXME_HIP - could be if constexpr for c++17 + if (!HIPParallelLaunch::default_launchbounds()) { + // for user defined, we *always* honor the request + return HIPParallelLaunch::get_hip_func_attributes(); + } else { + // FIXME_HIP - could be if constexpr for c++17 + if (BlockSize == BlockType::Max) { + return HIPParallelLaunch< + DriverType, Kokkos::LaunchBounds, + LaunchMechanism>::get_hip_func_attributes(); + } else { + const int blocksize = + get_preferred_blocksize_impl(); + if (blocksize == HIPTraits::MaxThreadsPerBlock) { + return HIPParallelLaunch< + DriverType, Kokkos::LaunchBounds, + LaunchMechanism>::get_hip_func_attributes(); + } else { + return HIPParallelLaunch< + DriverType, + Kokkos::LaunchBounds, + LaunchMechanism>::get_hip_func_attributes(); } } - block_size -= HIPTraits::WarpSize; } - return opt_block_size; } -template -int hip_get_max_block_size(const HIPInternal *hip_instance, - const hipFuncAttributes &attr, const FunctorType &f, - const size_t vector_length, const size_t shmem_block, - const size_t shmem_thread) { - return hip_internal_get_block_size( - [](int x) { return x == 0; }, hip_instance, attr, f, vector_length, - shmem_block, shmem_thread); +// Given an initial block-size limitation based on register usage +// determine the block size to select based on LDS limitation +template +unsigned hip_internal_get_block_size(const HIPInternal *hip_instance, + const ShmemFunctor &f, + const unsigned tperb_reg) { + // translate LB from CUDA to HIP + const unsigned min_waves_per_eu = + LaunchBounds::minBperSM ? LaunchBounds::minBperSM : 1; + const unsigned min_threads_per_sm = min_waves_per_eu * HIPTraits::WarpSize; + const unsigned shmem_per_sm = hip_instance->m_shmemPerSM; + unsigned block_size = tperb_reg; + do { + unsigned total_shmem = f(block_size); + // find how many threads we can fit with this blocksize based on LDS usage + unsigned tperb_shmem = total_shmem > shmem_per_sm ? 0 : block_size; + + // FIXME_HIP - could be if constexpr for c++17 + if (BlockSize == BlockType::Max) { + // we want the maximum blocksize possible + // just wait until we get a case where we can fit the LDS per SM + if (tperb_shmem) return block_size; + } else { + if (block_size == tperb_reg && tperb_shmem >= tperb_reg) { + // fast path for exit on first iteration if registers are more limiting + // than LDS usage, just use the register limited size + return tperb_reg; + } + // otherwise we need to apply a heuristic to choose the blocksize + // the current launchbound selection scheme is: + // 1. If no spills, choose 1024 [MaxThreadsPerBlock] + // 2. Otherwise, choose 256 [ConservativeThreadsPerBlock] + // + // For blocksizes between 256 and 1024, we'll be forced to use the 1024 LB + // and we'll already have pretty decent occupancy, thus dropping to 256 + // *probably* isn't a concern + const unsigned blocks_per_cu_shmem = shmem_per_sm / total_shmem; + const unsigned tperb = tperb_shmem < tperb_reg ? tperb_shmem : tperb_reg; + + // for anything with > 4 WF's & can fit multiple blocks + // we're probably not occupancy limited so just return that + if (blocks_per_cu_shmem > 1 && + tperb > HIPTraits::ConservativeThreadsPerBlock) { + return block_size; + } + + // otherwise, it's probably better to drop to the first valid size that + // fits in the ConservativeThreadsPerBlock + if (tperb >= min_threads_per_sm) return block_size; + } + block_size >>= 1; + } while (block_size >= HIPTraits::WarpSize); + // TODO: return a negative, add an error to kernel launch + return 0; +} + +// Standardized blocksize deduction for parallel constructs with no LDS usage +// Returns the preferred blocksize as dictated by register usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_preferred_blocksize() { + return get_preferred_blocksize_impl(); +} + +// Standardized blocksize deduction for parallel constructs with no LDS usage +// Returns the max blocksize as dictated by register usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_max_blocksize() { + return get_max_blocksize_impl(); +} + +// Standardized blocksize deduction for non-teams parallel constructs with LDS +// usage Returns the 'preferred' blocksize, as determined by the heuristics in +// hip_internal_get_block_size +// +// The ShmemFunctor takes a single argument of the current blocksize under +// consideration, and returns the LDS usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_preferred_blocksize(HIPInternal const *hip_instance, + ShmemFunctor const &f) { + // get preferred blocksize limited by register usage + const unsigned tperb_reg = + hip_get_preferred_blocksize(); + return hip_internal_get_block_size(hip_instance, f, tperb_reg); +} + +// Standardized blocksize deduction for teams-based parallel constructs with LDS +// usage Returns the 'preferred' blocksize, as determined by the heuristics in +// hip_internal_get_block_size +// +// The ShmemTeamsFunctor takes two arguments: the hipFunctionAttributes and +// the current blocksize under consideration, and returns the LDS usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_preferred_team_blocksize(HIPInternal const *hip_instance, + ShmemTeamsFunctor const &f) { + hipFuncAttributes attr = + get_hip_func_attributes_impl(); + // get preferred blocksize limited by register usage + using namespace std::placeholders; + const unsigned tperb_reg = + hip_get_preferred_blocksize(); + return hip_internal_get_block_size( + hip_instance, std::bind(f, attr, _1), tperb_reg); +} + +// Standardized blocksize deduction for non-teams parallel constructs with LDS +// usage Returns the maximum possible blocksize, as determined by the heuristics +// in hip_internal_get_block_size +// +// The ShmemFunctor takes a single argument of the current blocksize under +// consideration, and returns the LDS usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_max_blocksize(HIPInternal const *hip_instance, + ShmemFunctor const &f) { + // get max blocksize limited by register usage + const unsigned tperb_reg = hip_get_max_blocksize(); + return hip_internal_get_block_size( + hip_instance, f, tperb_reg); } -template -int hip_get_opt_block_size(HIPInternal const *hip_instance, - hipFuncAttributes const &attr, FunctorType const &f, - size_t const vector_length, size_t const shmem_block, - size_t const shmem_thread) { - return hip_internal_get_block_size( - [](int) { return true; }, hip_instance, attr, f, vector_length, - shmem_block, shmem_thread); +// Standardized blocksize deduction for teams-based parallel constructs with LDS +// usage Returns the maximum possible blocksize, as determined by the heuristics +// in hip_internal_get_block_size +// +// The ShmemTeamsFunctor takes two arguments: the hipFunctionAttributes and +// the current blocksize under consideration, and returns the LDS usage +// +// Note: a returned block_size of zero indicates that the algorithm could not +// find a valid block size. The caller is responsible for error handling. +template +unsigned hip_get_max_team_blocksize(HIPInternal const *hip_instance, + ShmemTeamsFunctor const &f) { + hipFuncAttributes attr = + get_hip_func_attributes_impl(); + // get max blocksize + using namespace std::placeholders; + const unsigned tperb_reg = hip_get_max_blocksize(); + return hip_internal_get_block_size( + hip_instance, std::bind(f, attr, _1), tperb_reg); } } // namespace Impl diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Error.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Error.hpp index b3480bcad00c..a75e7a4a6c93 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Error.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Error.hpp @@ -66,12 +66,30 @@ inline void hip_internal_safe_call(hipError_t e, const char* name, } } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 + +KOKKOS_DEPRECATED +inline void hip_internal_safe_call_deprecated(hipError_t e, const char* name, + const char* file = nullptr, + const int line = 0) { + hip_internal_safe_call(e, name, file, line); +} + +#endif + } // namespace Impl } // namespace Kokkos -#define HIP_SAFE_CALL(call) \ +#define KOKKOS_IMPL_HIP_SAFE_CALL(call) \ Kokkos::Impl::hip_internal_safe_call(call, #call, __FILE__, __LINE__) +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 +#define HIP_SAFE_CALL(call) \ + Kokkos::Impl::hip_internal_safe_call_deprecated(call, #call, __FILE__, \ + __LINE__) + +#endif + namespace Kokkos { namespace Experimental { diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp index 18ef10e22cd3..336ac8c6987c 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp @@ -77,7 +77,7 @@ class HIPInternalDevices { }; HIPInternalDevices::HIPInternalDevices() { - HIP_SAFE_CALL(hipGetDeviceCount(&m_hipDevCount)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&m_hipDevCount)); if (m_hipDevCount > MAXIMUM_DEVICE_COUNT) { Kokkos::abort( @@ -85,7 +85,7 @@ HIPInternalDevices::HIPInternalDevices() { "have. Please report this to github.com/kokkos/kokkos."); } for (int i = 0; i < m_hipDevCount; ++i) { - HIP_SAFE_CALL(hipGetDeviceProperties(m_hipProp + i, i)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceProperties(m_hipProp + i, i)); } } @@ -95,6 +95,9 @@ const HIPInternalDevices &HIPInternalDevices::singleton() { } } // namespace +unsigned long *Impl::HIPInternal::constantMemHostStaging = nullptr; +hipEvent_t Impl::HIPInternal::constantMemReusable = nullptr; + namespace Impl { //---------------------------------------------------------------------------- @@ -154,6 +157,9 @@ int HIPInternal::verify_is_initialized(const char *const label) const { return 0 <= m_hipDev; } +uint32_t HIPInternal::impl_get_instance_id() const noexcept { + return m_instance_id; +} HIPInternal &HIPInternal::singleton() { static HIPInternal *self = nullptr; if (!self) { @@ -163,12 +169,23 @@ HIPInternal &HIPInternal::singleton() { } void HIPInternal::fence() const { - HIP_SAFE_CALL(hipStreamSynchronize(m_stream)); - // can reset our cycle id now as well - m_cycleId = 0; + fence("Kokkos::HIPInternal::fence: Unnamed Internal Fence"); +} +void HIPInternal::fence(const std::string &name) const { + Kokkos::Tools::Experimental::Impl::profile_fence_event< + Kokkos::Experimental::HIP>( + name, + Kokkos::Tools::Experimental::Impl::DirectFenceIDHandle{ + impl_get_instance_id()}, + [&]() { + KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamSynchronize(m_stream)); + // can reset our cycle id now as well + m_cycleId = 0; + }); } -void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { +void HIPInternal::initialize(int hip_device_id, hipStream_t stream, + bool manage_stream) { if (was_finalized) Kokkos::abort("Calling HIP::initialize after HIP::finalize is illegal\n"); @@ -197,9 +214,10 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { m_hipDev = hip_device_id; m_deviceProp = hipProp; - HIP_SAFE_CALL(hipSetDevice(m_hipDev)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipSetDevice(m_hipDev)); m_stream = stream; + m_manage_stream = manage_stream; m_team_scratch_current_size = 0; m_team_scratch_ptr = nullptr; @@ -222,7 +240,7 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { // theoretically, we can get 40 WF's / CU, but only can sustain 32 // see // https://github.com/ROCm-Developer-Tools/HIP/blob/a0b5dfd625d99af7e288629747b40dd057183173/vdi/hip_platform.cpp#L742 - m_maxBlocksPerSM = 32; + m_maxWavesPerCU = 32; // FIXME_HIP - Nick to implement this upstream // Register count comes from Sec. 2.2. "Data Sharing" of the // Vega 7nm ISA document (see the diagram) @@ -232,7 +250,7 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { m_regsPerSM = 65536; m_shmemPerSM = hipProp.maxSharedMemoryPerMultiProcessor; m_maxShmemPerBlock = hipProp.sharedMemPerBlock; - m_maxThreadsPerSM = m_maxBlocksPerSM * HIPTraits::WarpSize; + m_maxThreadsPerSM = m_maxWavesPerCU * HIPTraits::WarpSize; //---------------------------------- // Multiblock reduction uses scratch flags for counters // and scratch space for partial reduction values. @@ -265,8 +283,8 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { m_scratchConcurrentBitset = reinterpret_cast(r->data()); - HIP_SAFE_CALL(hipMemset(m_scratchConcurrentBitset, 0, - sizeof(uint32_t) * buffer_bound)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipMemset(m_scratchConcurrentBitset, 0, + sizeof(uint32_t) * buffer_bound)); } //---------------------------------- @@ -287,6 +305,15 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { // Init the array for used for arbitrarily sized atomics if (m_stream == nullptr) ::Kokkos::Impl::initialize_host_hip_lock_arrays(); + + // Allocate a staging buffer for constant mem in pinned host memory + // and an event to avoid overwriting driver for previous kernel launches + if (m_stream == nullptr) { + KOKKOS_IMPL_HIP_SAFE_CALL(hipHostMalloc((void **)&constantMemHostStaging, + HIPTraits::ConstantMemoryUsage)); + + KOKKOS_IMPL_HIP_SAFE_CALL(hipEventCreate(&constantMemReusable)); + } } //---------------------------------------------------------------------------- @@ -339,7 +366,7 @@ Kokkos::Experimental::HIP::size_type *HIPInternal::scratch_flags( m_scratchFlags = reinterpret_cast(r->data()); - HIP_SAFE_CALL( + KOKKOS_IMPL_HIP_SAFE_CALL( hipMemset(m_scratchFlags, 0, m_scratchFlagsCount * sizeScratchGrain)); } @@ -365,7 +392,7 @@ void *HIPInternal::resize_team_scratch_space(std::int64_t bytes, //---------------------------------------------------------------------------- void HIPInternal::finalize() { - this->fence(); + this->fence("Kokkos::HIPInternal::finalize: fence on finalization"); was_finalized = true; if (nullptr != m_scratchSpace || nullptr != m_scratchFlags) { using RecordHIP = @@ -378,6 +405,9 @@ void HIPInternal::finalize() { if (m_team_scratch_current_size > 0) Kokkos::kokkos_free(m_team_scratch_ptr); + if (m_manage_stream && m_stream != nullptr) + KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamDestroy(m_stream)); + m_hipDev = -1; m_hipArch = -1; m_multiProcCount = 0; @@ -395,28 +425,36 @@ void HIPInternal::finalize() { m_team_scratch_ptr = nullptr; } if (nullptr != d_driverWorkArray) { - HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); d_driverWorkArray = nullptr; } + + // only destroy these if we're finalizing the singleton + if (this == &singleton()) { + KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(constantMemHostStaging)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipEventDestroy(constantMemReusable)); + } } char *HIPInternal::get_next_driver(size_t driverTypeSize) const { std::lock_guard const lock(m_mutexWorkArray); if (d_driverWorkArray == nullptr) { - HIP_SAFE_CALL( + KOKKOS_IMPL_HIP_SAFE_CALL( hipHostMalloc(&d_driverWorkArray, m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), hipHostMallocNonCoherent)); } if (driverTypeSize > m_maxDriverTypeSize) { // fence handles the cycle id reset for us - fence(); - HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + fence( + "Kokkos::HIPInternal::get_next_driver: fence before reallocating " + "resources"); + KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); m_maxDriverTypeSize = driverTypeSize; if (m_maxDriverTypeSize % 128 != 0) m_maxDriverTypeSize = m_maxDriverTypeSize + 128 - m_maxDriverTypeSize % 128; - HIP_SAFE_CALL( + KOKKOS_IMPL_HIP_SAFE_CALL( hipHostMalloc(&d_driverWorkArray, m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), hipHostMallocNonCoherent)); @@ -424,7 +462,9 @@ char *HIPInternal::get_next_driver(size_t driverTypeSize) const { m_cycleId = (m_cycleId + 1) % m_maxDriverCycles; if (m_cycleId == 0) { // ensure any outstanding kernels are completed before we wrap around - fence(); + fence( + "Kokkos::HIPInternal::get_next_driver: fence before reusing first " + "driver"); } } return &d_driverWorkArray[m_maxDriverTypeSize * m_cycleId]; @@ -462,7 +502,14 @@ Kokkos::Experimental::HIP::size_type *hip_internal_scratch_flags( namespace Kokkos { namespace Impl { -void hip_device_synchronize() { HIP_SAFE_CALL(hipDeviceSynchronize()); } +void hip_device_synchronize(const std::string &name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event< + Kokkos::Experimental::HIP>( + name, + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + GlobalDeviceSynchronization, + [&]() { KOKKOS_IMPL_HIP_SAFE_CALL(hipDeviceSynchronize()); }); +} void hip_internal_error_throw(hipError_t e, const char *name, const char *file, const int line) { diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp index f4f88628e313..967c6fdd4be6 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp @@ -48,6 +48,7 @@ #define KOKKOS_HIP_INSTANCE_HPP #include +#include #include @@ -59,10 +60,12 @@ struct HIPTraits { static int constexpr WarpSize = 64; static int constexpr WarpIndexMask = 0x003f; /* hexadecimal for 63 */ static int constexpr WarpIndexShift = 6; /* WarpSize == 1 << WarpShift*/ + static int constexpr ConservativeThreadsPerBlock = + 256; // conservative fallback blocksize in case of spills static int constexpr MaxThreadsPerBlock = - 1024; // FIXME_HIP -- assumed constant for now - + 1024; // the maximum we can fit in a block static int constexpr ConstantMemoryUsage = 0x008000; /* 32k bytes */ + static int constexpr KernelArgumentLimit = 0x001000; /* 4k bytes */ static int constexpr ConstantMemoryUseThreshold = 0x000200; /* 512 bytes */ }; @@ -90,7 +93,7 @@ class HIPInternal { unsigned m_multiProcCount = 0; unsigned m_maxWarpCount = 0; unsigned m_maxBlock = 0; - unsigned m_maxBlocksPerSM = 0; + unsigned m_maxWavesPerCU = 0; unsigned m_maxSharedWords = 0; int m_regsPerSM; int m_shmemPerSM = 0; @@ -108,6 +111,8 @@ class HIPInternal { mutable int m_cycleId = 0; // mutex to access d_driverWorkArray mutable std::mutex m_mutexWorkArray; + // mutex to access shared memory + mutable std::mutex m_mutexSharedMemory; // Scratch Spaces for Reductions size_type m_scratchSpaceCount = 0; @@ -119,7 +124,10 @@ class HIPInternal { hipDeviceProp_t m_deviceProp; - hipStream_t m_stream = nullptr; + hipStream_t m_stream = nullptr; + uint32_t m_instance_id = Kokkos::Tools::Experimental::Impl::idForInstance< + Kokkos::Experimental::HIP>(reinterpret_cast(this)); + bool m_manage_stream = false; // Team Scratch Level 1 Space mutable int64_t m_team_scratch_current_size = 0; @@ -128,18 +136,25 @@ class HIPInternal { bool was_finalized = false; + // FIXME_HIP: these want to be per-device, not per-stream... use of 'static' + // here will break once there are multiple devices though + static unsigned long *constantMemHostStaging; + static hipEvent_t constantMemReusable; + static HIPInternal &singleton(); int verify_is_initialized(const char *const label) const; int is_initialized() const { return m_hipDev >= 0; } - void initialize(int hip_device_id, hipStream_t stream = nullptr); + void initialize(int hip_device_id, hipStream_t stream = nullptr, + bool manage_stream = false); void finalize(); void print_configuration(std::ostream &) const; void fence() const; + void fence(const std::string &) const; // returns the next driver type pointer in our work array char *get_next_driver(size_t driverTypeSize) const; @@ -151,13 +166,52 @@ class HIPInternal { // Resizing of reduction related scratch spaces size_type *scratch_space(const size_type size); size_type *scratch_flags(const size_type size); - + uint32_t impl_get_instance_id() const noexcept; // Resizing of team level 1 scratch void *resize_team_scratch_space(std::int64_t bytes, bool force_shrink = false); }; } // namespace Impl + +// Partitioning an Execution Space: expects space and integer arguments for +// relative weight +// Customization point for backends +// Default behavior is to return the passed in instance + +namespace Impl { +inline void create_HIP_instances(std::vector &instances) { + for (int s = 0; s < int(instances.size()); s++) { + hipStream_t stream; + KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamCreate(&stream)); + instances[s] = HIP(stream, true); + } +} +} // namespace Impl + +template +std::vector partition_space(const HIP &, Args...) { +#ifdef __cpp_fold_expressions + static_assert( + (... && std::is_arithmetic_v), + "Kokkos Error: partitioning arguments must be integers or floats"); +#endif + + std::vector instances(sizeof...(Args)); + Impl::create_HIP_instances(instances); + return instances; +} + +template +std::vector partition_space(const HIP &, std::vector &weights) { + static_assert( + std::is_arithmetic::value, + "Kokkos Error: partitioning arguments must be integers or floats"); + + std::vector instances(weights.size()); + Impl::create_HIP_instances(instances); + return instances; +} } // namespace Experimental } // namespace Kokkos diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp index f774423b378b..f209edf7c04e 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp @@ -52,6 +52,7 @@ #include #include #include +#include // Must use global variable on the device with HIP-Clang #ifdef __HIP__ @@ -64,7 +65,7 @@ namespace Kokkos { namespace Experimental { template inline __device__ T *kokkos_impl_hip_shared_memory() { - HIP_DYNAMIC_SHARED(HIPSpace::size_type, sh); + extern __shared__ Kokkos::Experimental::HIPSpace::size_type sh[]; return (T *)sh; } } // namespace Experimental @@ -74,10 +75,12 @@ namespace Kokkos { namespace Experimental { namespace Impl { +// The hip_parallel_launch_*_memory code is identical to the cuda code template __global__ static void hip_parallel_launch_constant_memory() { const DriverType &driver = *(reinterpret_cast( kokkos_impl_hip_constant_memory_buffer)); + driver(); } @@ -87,12 +90,13 @@ __global__ __launch_bounds__( const DriverType &driver = *(reinterpret_cast( kokkos_impl_hip_constant_memory_buffer)); - driver->operator()(); + driver(); } template __global__ static void hip_parallel_launch_local_memory( const DriverType *driver) { + // FIXME_HIP driver() pass by copy driver->operator()(); } @@ -101,6 +105,21 @@ __global__ __launch_bounds__( maxTperB, minBperSM) static void hip_parallel_launch_local_memory(const DriverType *driver) { + // FIXME_HIP driver() pass by copy + driver->operator()(); +} + +template +__global__ static void hip_parallel_launch_global_memory( + const DriverType *driver) { + driver->operator()(); +} + +template +__global__ __launch_bounds__( + maxTperB, + minBperSM) static void hip_parallel_launch_global_memory(const DriverType + *driver) { driver->operator()(); } @@ -127,33 +146,238 @@ struct HIPDispatchProperties { HIPLaunchMechanism launch_mechanism = l; }; +// Use local memory up to ConstantMemoryUseThreshold +// Use global memory above ConstantMemoryUsage +// In between use ConstantMemory +// The following code is identical to the cuda code +template +struct DeduceHIPLaunchMechanism { + static constexpr Kokkos::Experimental::WorkItemProperty::HintLightWeight_t + light_weight = Kokkos::Experimental::WorkItemProperty::HintLightWeight; + static constexpr Kokkos::Experimental::WorkItemProperty::HintHeavyWeight_t + heavy_weight = Kokkos::Experimental::WorkItemProperty::HintHeavyWeight; + static constexpr typename DriverType::Policy::work_item_property property = + typename DriverType::Policy::work_item_property(); + + static constexpr HIPLaunchMechanism valid_launch_mechanism = + // BuildValidMask + (sizeof(DriverType) < HIPTraits::KernelArgumentLimit + ? HIPLaunchMechanism::LocalMemory + : HIPLaunchMechanism::Default) | + (sizeof(DriverType) < HIPTraits::ConstantMemoryUsage + ? HIPLaunchMechanism::ConstantMemory + : HIPLaunchMechanism::Default) | + HIPLaunchMechanism::GlobalMemory; + + static constexpr HIPLaunchMechanism requested_launch_mechanism = + (((property & light_weight) == light_weight) + ? HIPLaunchMechanism::LocalMemory + : HIPLaunchMechanism::ConstantMemory) | + HIPLaunchMechanism::GlobalMemory; + + static constexpr HIPLaunchMechanism default_launch_mechanism = + // BuildValidMask + (sizeof(DriverType) < HIPTraits::ConstantMemoryUseThreshold) + ? HIPLaunchMechanism::LocalMemory + : ((sizeof(DriverType) < HIPTraits::ConstantMemoryUsage) + ? HIPLaunchMechanism::ConstantMemory + : HIPLaunchMechanism::GlobalMemory); + + // None LightWeight HeavyWeight + // F +struct HIPParallelLaunchKernelFuncData { + static unsigned int get_scratch_size( + hipFuncAttributes const &hip_func_attributes) { + return hip_func_attributes.localSizeBytes; + } + + static hipFuncAttributes get_hip_func_attributes(void const *kernel_func) { + static hipFuncAttributes attr = [=]() { + hipFuncAttributes attr; + KOKKOS_IMPL_HIP_SAFE_CALL(hipFuncGetAttributes(&attr, kernel_func)); + return attr; + }(); + return attr; + } +}; + +//---------------------------------------------------------------// +// HIPParallelLaunchKernelFunc structure and its specializations // +//---------------------------------------------------------------// template struct HIPParallelLaunchKernelFunc; +// HIPLaunchMechanism::LocalMemory specializations template struct HIPParallelLaunchKernelFunc< DriverType, Kokkos::LaunchBounds, HIPLaunchMechanism::LocalMemory> { + using funcdata_t = HIPParallelLaunchKernelFuncData< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory>; static auto get_kernel_func() { return hip_parallel_launch_local_memory; } + + static constexpr auto default_launchbounds() { return false; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); + } }; template struct HIPParallelLaunchKernelFunc, HIPLaunchMechanism::LocalMemory> { + using funcdata_t = + HIPParallelLaunchKernelFuncData, + HIPLaunchMechanism::LocalMemory>; + static auto get_kernel_func() { + return HIPParallelLaunchKernelFunc< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory>::get_kernel_func(); + } + + static constexpr auto default_launchbounds() { return true; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); + } +}; + +// HIPLaunchMechanism::GlobalMemory specializations +template +struct HIPParallelLaunchKernelFunc< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::GlobalMemory> { + using funcdata_t = HIPParallelLaunchKernelFuncData< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::GlobalMemory>; + static auto get_kernel_func() { + return hip_parallel_launch_global_memory; + } + + static constexpr auto default_launchbounds() { return false; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); + } +}; + +template +struct HIPParallelLaunchKernelFunc, + HIPLaunchMechanism::GlobalMemory> { + using funcdata_t = + HIPParallelLaunchKernelFuncData, + HIPLaunchMechanism::GlobalMemory>; + static auto get_kernel_func() { + return hip_parallel_launch_global_memory; + } + + static constexpr auto default_launchbounds() { return true; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); + } +}; + +// HIPLaunchMechanism::ConstantMemory specializations +template +struct HIPParallelLaunchKernelFunc< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::ConstantMemory> { + using funcdata_t = HIPParallelLaunchKernelFuncData< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::ConstantMemory>; static auto get_kernel_func() { - return hip_parallel_launch_local_memory; + return hip_parallel_launch_constant_memory; + } + + static constexpr auto default_launchbounds() { return false; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); } }; +template +struct HIPParallelLaunchKernelFunc, + HIPLaunchMechanism::ConstantMemory> { + using funcdata_t = + HIPParallelLaunchKernelFuncData, + HIPLaunchMechanism::ConstantMemory>; + static auto get_kernel_func() { + return hip_parallel_launch_constant_memory; + } + static constexpr auto default_launchbounds() { return true; } + + static auto get_scratch_size() { + return funcdata_t::get_scratch_size(get_hip_func_attributes()); + } + + static hipFuncAttributes get_hip_func_attributes() { + return funcdata_t::get_hip_func_attributes( + reinterpret_cast(get_kernel_func())); + } +}; + +//------------------------------------------------------------------// +// HIPParallelLaunchKernelInvoker structure and its specializations // +//------------------------------------------------------------------// template struct HIPParallelLaunchKernelInvoker; +// HIPLaunchMechanism::LocalMemory specialization template struct HIPParallelLaunchKernelInvoker @@ -170,21 +394,83 @@ struct HIPParallelLaunchKernelInvoker +struct HIPParallelLaunchKernelInvoker + : HIPParallelLaunchKernelFunc { + using base_t = HIPParallelLaunchKernelFunc; + + // FIXME_HIP the code is different than cuda because driver cannot be passed + // by copy + static void invoke_kernel(DriverType const *driver, dim3 const &grid, + dim3 const &block, int shmem, + HIPInternal const *hip_instance) { + (base_t::get_kernel_func())<<m_stream>>>( + driver); + } +}; + +// HIPLaunchMechanism::ConstantMemory specializations +template +struct HIPParallelLaunchKernelInvoker + : HIPParallelLaunchKernelFunc { + using base_t = + HIPParallelLaunchKernelFunc; + static_assert(sizeof(DriverType) < HIPTraits::ConstantMemoryUsage, + "Kokkos Error: Requested HIPLaunchConstantMemory with a " + "Functor larger than 32kB."); + + static void invoke_kernel(DriverType const *driver, dim3 const &grid, + dim3 const &block, int shmem, + HIPInternal const *hip_instance) { + // Wait until the previous kernel that uses the constant buffer is done + KOKKOS_IMPL_HIP_SAFE_CALL( + hipEventSynchronize(hip_instance->constantMemReusable)); + + // Copy functor (synchronously) to staging buffer in pinned host memory + unsigned long *staging = hip_instance->constantMemHostStaging; + std::memcpy((void *)staging, (void *)driver, sizeof(DriverType)); + + // Copy functor asynchronously from there to constant memory on the device + KOKKOS_IMPL_HIP_SAFE_CALL(hipMemcpyToSymbolAsync( + HIP_SYMBOL(kokkos_impl_hip_constant_memory_buffer), staging, + sizeof(DriverType), 0, hipMemcpyHostToDevice, hip_instance->m_stream)); + + // Invoke the driver function on the device + (base_t:: + get_kernel_func())<<m_stream>>>(); + + // Record an event that says when the constant buffer can be reused + KOKKOS_IMPL_HIP_SAFE_CALL(hipEventRecord(hip_instance->constantMemReusable, + hip_instance->m_stream)); + } +}; + +//-----------------------------// +// HIPParallelLaunch structure // +//-----------------------------// template , - HIPLaunchMechanism LaunchMechanism = HIPLaunchMechanism::LocalMemory> + HIPLaunchMechanism LaunchMechanism = + DeduceHIPLaunchMechanism::launch_mechanism> struct HIPParallelLaunch; template + unsigned int MinBlocksPerSM, HIPLaunchMechanism LaunchMechanism> struct HIPParallelLaunch< DriverType, Kokkos::LaunchBounds, - HIPLaunchMechanism::LocalMemory> + LaunchMechanism> : HIPParallelLaunchKernelInvoker< DriverType, Kokkos::LaunchBounds, - HIPLaunchMechanism::LocalMemory> { + LaunchMechanism> { using base_t = HIPParallelLaunchKernelInvoker< DriverType, Kokkos::LaunchBounds, - HIPLaunchMechanism::LocalMemory>; + LaunchMechanism>; HIPParallelLaunch(const DriverType &driver, const dim3 &grid, const dim3 &block, const int shmem, @@ -205,22 +491,48 @@ struct HIPParallelLaunch< base_t::invoke_kernel(d_driver, grid, block, shmem, hip_instance); #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) - HIP_SAFE_CALL(hipGetLastError()); - hip_instance->fence(); + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetLastError()); + hip_instance->fence( + "Kokkos::Experimental::Impl::HIParallelLaunch: Debug Only Check for " + "Execution Error"); #endif } } +}; - static hipFuncAttributes get_hip_func_attributes() { - static hipFuncAttributes attr = []() { - hipFuncAttributes attr; - HIP_SAFE_CALL(hipFuncGetAttributes( - &attr, reinterpret_cast(base_t::get_kernel_func()))); - return attr; - }(); - return attr; +// convenience method to launch the correct kernel given the launch bounds et +// al. +template , + HIPLaunchMechanism LaunchMechanism = + DeduceHIPLaunchMechanism::launch_mechanism> +void hip_parallel_launch(const DriverType &driver, const dim3 &grid, + const dim3 &block, const int shmem, + const HIPInternal *hip_instance, + const bool prefer_shmem) { + // FIXME_HIP - could be if constexpr for c++17 + if (!HIPParallelLaunch::default_launchbounds()) { + // for user defined, we *always* honor the request + HIPParallelLaunch( + driver, grid, block, shmem, hip_instance, prefer_shmem); + } else { + // we can do what we like + const unsigned flat_block_size = block.x * block.y * block.z; + if (flat_block_size <= HIPTraits::ConservativeThreadsPerBlock) { + // we have to use the large blocksize + HIPParallelLaunch< + DriverType, + Kokkos::LaunchBounds, + LaunchMechanism>(driver, grid, block, shmem, hip_instance, + prefer_shmem); + } else { + HIPParallelLaunch, + LaunchMechanism>(driver, grid, block, shmem, + hip_instance, prefer_shmem); + } } -}; +} } // namespace Impl } // namespace Experimental } // namespace Kokkos diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp index 4f5271b6f644..c4292d35eca7 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp @@ -84,11 +84,17 @@ namespace Impl { HIPLockArrays g_host_hip_lock_arrays = {nullptr, nullptr, 0}; void initialize_host_hip_lock_arrays() { +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + desul::Impl::init_lock_arrays(); + + DESUL_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); +#endif + if (g_host_hip_lock_arrays.atomic != nullptr) return; - HIP_SAFE_CALL(hipMalloc( + KOKKOS_IMPL_HIP_SAFE_CALL(hipMalloc( &g_host_hip_lock_arrays.atomic, sizeof(std::int32_t) * (KOKKOS_IMPL_HIP_SPACE_ATOMIC_MASK + 1))); - HIP_SAFE_CALL(hipMalloc( + KOKKOS_IMPL_HIP_SAFE_CALL(hipMalloc( &g_host_hip_lock_arrays.scratch, sizeof(std::int32_t) * (::Kokkos::Experimental::HIP::concurrency()))); @@ -103,10 +109,14 @@ void initialize_host_hip_lock_arrays() { } void finalize_host_hip_lock_arrays() { +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + desul::Impl::finalize_lock_arrays(); +#endif + if (g_host_hip_lock_arrays.atomic == nullptr) return; - HIP_SAFE_CALL(hipFree(g_host_hip_lock_arrays.atomic)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipFree(g_host_hip_lock_arrays.atomic)); g_host_hip_lock_arrays.atomic = nullptr; - HIP_SAFE_CALL(hipFree(g_host_hip_lock_arrays.scratch)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipFree(g_host_hip_lock_arrays.scratch)); g_host_hip_lock_arrays.scratch = nullptr; g_host_hip_lock_arrays.n = 0; #ifdef KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.hpp index f34f85f43b0b..71b104c2e4b6 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Locks.hpp @@ -51,6 +51,10 @@ #include +#ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS +#include +#endif + namespace Kokkos { namespace Impl { @@ -147,7 +151,7 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } #define KOKKOS_COPY_HIP_LOCK_ARRAYS_TO_DEVICE() \ { \ if (::Kokkos::Impl::lock_array_copied == 0) { \ - HIP_SAFE_CALL(hipMemcpyToSymbol( \ + KOKKOS_IMPL_HIP_SAFE_CALL(hipMemcpyToSymbol( \ HIP_SYMBOL(::Kokkos::Impl::g_device_hip_lock_arrays), \ &::Kokkos::Impl::g_host_hip_lock_arrays, \ sizeof(::Kokkos::Impl::HIPLockArrays))); \ @@ -155,6 +159,8 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } ::Kokkos::Impl::lock_array_copied = 1; \ } +#ifndef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS + #ifdef KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE #define KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE() #else @@ -162,6 +168,19 @@ inline int eliminate_warning_for_lock_array() { return lock_array_copied; } KOKKOS_COPY_HIP_LOCK_ARRAYS_TO_DEVICE() #endif +#else + +#ifdef KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE +#define KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE() +#else +// Still Need COPY_CUDA_LOCK_ARRAYS for team scratch etc. +#define KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE() \ + KOKKOS_COPY_HIP_LOCK_ARRAYS_TO_DEVICE() \ + DESUL_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE() +#endif + +#endif /* defined( KOKKOS_ENABLE_IMPL_DESUL_ATOMICS ) */ + #endif /* defined( __HIPCC__ ) */ #endif /* #ifndef KOKKOS_HIP_LOCKS_HPP */ diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp index ce1aff9586d2..acb538e1cb39 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp @@ -28,7 +28,8 @@ inline TileSizeProperties get_tile_size_properties( space.impl_internal_space_instance()->m_maxThreadsPerSM; properties.default_largest_tile_size = 16; properties.default_tile_size = 4; - properties.max_total_tile_size = 1024; + properties.max_total_tile_size = + Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock; return properties; } diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp index 35e7d6fb853a..eae323dd913d 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp @@ -81,6 +81,8 @@ class ParallelFor, } inline void execute() const { + using ClosureType = + ParallelFor; if (m_policy.m_num_tiles == 0) return; array_index_type const maxblocks = static_cast( m_policy.space().impl_internal_space_instance()->m_maxBlock); @@ -94,7 +96,8 @@ class ParallelFor, block.y, maxblocks), 1); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } else if (Policy::rank == 3) { @@ -110,7 +113,8 @@ class ParallelFor, std::min((m_policy.m_upper[2] - m_policy.m_lower[2] + block.z - 1) / block.z, maxblocks)); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } else if (Policy::rank == 4) { @@ -128,7 +132,8 @@ class ParallelFor, std::min((m_policy.m_upper[3] - m_policy.m_lower[3] + block.z - 1) / block.z, maxblocks)); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } else if (Policy::rank == 5) { @@ -147,7 +152,8 @@ class ParallelFor, std::min((m_policy.m_upper[4] - m_policy.m_lower[4] + block.z - 1) / block.z, maxblocks)); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } else if (Policy::rank == 6) { @@ -165,7 +171,8 @@ class ParallelFor, std::min(static_cast(m_policy.m_tile_end[4] * m_policy.m_tile_end[5]), static_cast(maxblocks))); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } else { @@ -178,22 +185,18 @@ class ParallelFor, : m_functor(arg_functor), m_policy(arg_policy) {} template - static int max_tile_size_product(const Policy& pol, const Functor&) { + static int max_tile_size_product(const Policy&, const Functor&) { using closure_type = ParallelFor, Kokkos::Experimental::HIP>; - hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, LaunchBounds>::get_hip_func_attributes(); - auto const& prop = pol.space().hip_device_prop(); - // Limits due to registers/SM, MDRange doesn't have - // shared memory constraints - int const regs_per_sm = prop.regsPerMultiprocessor; - int const regs_per_thread = attr.numRegs; - int const max_threads_per_sm = regs_per_sm / regs_per_thread; - return std::min( - max_threads_per_sm, - static_cast( - Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + unsigned block_size = + Kokkos::Experimental::Impl::hip_get_max_blocksize(); + if (block_size == 0) + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelFor< HIP > could not find a valid " + "tile size.")); + return block_size; } }; @@ -242,6 +245,9 @@ class ParallelReduce, ReducerType, const bool m_result_ptr_device_accessible; size_type* m_scratch_space; size_type* m_scratch_flags; + // Only let one Parallel/Scan modify the shared memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_shared_memory_lock; using DeviceIteratePattern = typename Kokkos::Impl::Reduce::DeviceIterateTile< Policy::rank, Policy, FunctorType, WorkTag, reference_type>; @@ -307,32 +313,30 @@ class ParallelReduce, ReducerType, // Determine block size constrained by shared memory: // This is copy/paste from Kokkos_HIP_Parallel_Range inline unsigned local_block_size(const FunctorType& f) { - unsigned int n = - ::Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock; - int shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< - false, FunctorType, WorkTag>(f, n); - using closure_type = Impl::ParallelReduce; - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, LaunchBounds>::get_hip_func_attributes(); - while ( - (n && - (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < - shmem_size)) || - (n > - static_cast( - ::Kokkos::Experimental::Impl::hip_get_max_block_size( - m_policy.space().impl_internal_space_instance(), attr, f, 1, - shmem_size, 0)))) { - n >>= 1; - shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< - false, FunctorType, WorkTag>(f, n); + const auto& instance = m_policy.space().impl_internal_space_instance(); + auto shmem_functor = [&f](unsigned n) { + return hip_single_inter_block_reduce_scan_shmem(f, n); + }; + using closure_type = ParallelReduce; + + unsigned block_size = + Kokkos::Experimental::Impl::hip_get_preferred_blocksize( + instance, shmem_functor); + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " + "valid tile size.")); } - return n; + return block_size; } inline void execute() { - const int nwork = m_policy.m_num_tiles; + using ClosureType = ParallelReduce; + const int nwork = m_policy.m_num_tiles; if (nwork) { int block_size = m_policy.m_prod_tile_dims; // CONSTRAINT: Algorithm requires block_size >= product of tile dimensions @@ -366,14 +370,16 @@ class ParallelReduce, ReducerType, ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< false, FunctorType, WorkTag>(m_functor, block.y); - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem, m_policy.space().impl_internal_space_instance(), false); // copy to device and execute if (!m_result_ptr_device_accessible) { - m_policy.space().fence(); + m_policy.space().fence( + "Kokkos::Impl::ParallelReduce: fence because " + "reduction can't access result storage location"); if (m_result_ptr) { const int size = ValueTraits::value_size( @@ -403,7 +409,10 @@ class ParallelReduce, ReducerType, MemorySpaceAccess::accessible), m_scratch_space(nullptr), - m_scratch_flags(nullptr) {} + m_scratch_flags(nullptr), + m_shared_memory_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexSharedMemory) {} ParallelReduce(const FunctorType& arg_functor, const Policy& arg_policy, const ReducerType& reducer) @@ -416,23 +425,25 @@ class ParallelReduce, ReducerType, typename ReducerType::result_view_type:: memory_space>::accessible), m_scratch_space(nullptr), - m_scratch_flags(nullptr) {} + m_scratch_flags(nullptr), + m_shared_memory_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexSharedMemory) {} + template - static int max_tile_size_product(const Policy& pol, const Functor&) { + static int max_tile_size_product(const Policy&, const Functor&) { using closure_type = ParallelReduce, ReducerType, Kokkos::Experimental::HIP>; - hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, LaunchBounds>::get_hip_func_attributes(); - auto const& prop = pol.space().hip_device_prop(); - // Limits due do registers/SM - int const regs_per_sm = prop.regsPerMultiprocessor; - int const regs_per_thread = attr.numRegs; - int const max_threads_per_sm = regs_per_sm / regs_per_thread; - return std::min( - max_threads_per_sm, - static_cast( - Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + unsigned block_size = + Kokkos::Experimental::Impl::hip_get_max_blocksize(); + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " + "valid tile size.")); + } + return block_size; } }; } // namespace Impl diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp index 7d2825eeb4c6..e02ead1e9901 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp @@ -108,16 +108,21 @@ class ParallelFor, inline void execute() const { const typename Policy::index_type nwork = m_policy.end() - m_policy.begin(); + using DriverType = + ParallelFor; const int block_size = - LaunchBounds::maxTperB - ? LaunchBounds::maxTperB - : ::Kokkos::Experimental::Impl::HIPTraits:: - MaxThreadsPerBlock; // FIXME_HIP Choose block_size better + Kokkos::Experimental::Impl::hip_get_preferred_blocksize(); const dim3 block(1, block_size, 1); const dim3 grid( typename Policy::index_type((nwork + block.y - 1) / block.y), 1, 1); - Kokkos::Experimental::Impl::HIPParallelLaunch( + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelFor< HIP > could not find a " + "valid execution configuration.")); + } + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), false); } @@ -173,15 +178,12 @@ class ParallelReduce, ReducerType, const bool m_result_ptr_host_accessible; size_type* m_scratch_space = nullptr; size_type* m_scratch_flags = nullptr; + // Only let one ParallelReduce/Scan modify the shared memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_shared_memory_lock; -#if HIP_VERSION < 401 - static bool constexpr UseShflReduction = - ((sizeof(value_type) > 2 * sizeof(double)) && - static_cast(ValueTraits::StaticValueSize)); -#else static bool constexpr UseShflReduction = static_cast(ValueTraits::StaticValueSize); -#endif private: struct ShflReductionTag {}; @@ -328,30 +330,15 @@ class ParallelReduce, ReducerType, // Determine block size constrained by shared memory: inline unsigned local_block_size(const FunctorType& f) { - unsigned int n = - ::Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock; - int shmem_size = - hip_single_inter_block_reduce_scan_shmem( - f, n); - using closure_type = Impl::ParallelReduce; - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, LaunchBounds>::get_hip_func_attributes(); - while ( - (n && - (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < - shmem_size)) || - (n > - static_cast( - ::Kokkos::Experimental::Impl::hip_get_max_block_size( - m_policy.space().impl_internal_space_instance(), attr, f, 1, - shmem_size, 0)))) { - n >>= 1; - shmem_size = - hip_single_inter_block_reduce_scan_shmem( - f, n); - } - return n; + const auto& instance = m_policy.space().impl_internal_space_instance(); + auto shmem_functor = [&f](unsigned n) { + return hip_single_inter_block_reduce_scan_shmem(f, n); + }; + using DriverType = ParallelReduce; + return Kokkos::Experimental::Impl::hip_get_preferred_blocksize< + DriverType, LaunchBounds>(instance, shmem_functor); } inline void execute() { @@ -362,7 +349,11 @@ class ParallelReduce, ReducerType, !std::is_same::value; if ((nwork > 0) || need_device_set) { const int block_size = local_block_size(m_functor); - KOKKOS_ASSERT(block_size > 0); + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " + "valid execution configuration.")); + } m_scratch_space = ::Kokkos::Experimental::Impl::hip_internal_scratch_space( @@ -391,14 +382,17 @@ class ParallelReduce, ReducerType, WorkTag>(m_functor, block.y); - Kokkos::Experimental::Impl::HIPParallelLaunch( + using DriverType = ParallelReduce; + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem, m_policy.space().impl_internal_space_instance(), false); // copy to device and execute if (!m_result_ptr_device_accessible) { - m_policy.space().impl_internal_space_instance()->fence(); + m_policy.space().impl_internal_space_instance()->fence( + "Kokkos::Impl::ParallelReduce: fence because " + "reduction can't access result storage location"); if (m_result_ptr) { const int size = ValueTraits::value_size( @@ -429,7 +423,10 @@ class ParallelReduce, ReducerType, typename ViewType::memory_space>::accessible), m_result_ptr_host_accessible( MemorySpaceAccess::accessible) {} + typename ViewType::memory_space>::accessible), + m_shared_memory_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexSharedMemory) {} ParallelReduce(const FunctorType& arg_functor, const Policy& arg_policy, const ReducerType& reducer) @@ -444,7 +441,10 @@ class ParallelReduce, ReducerType, m_result_ptr_host_accessible( MemorySpaceAccess::accessible) {} + memory_space>::accessible), + m_shared_memory_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexSharedMemory) {} }; template @@ -482,6 +482,9 @@ class ParallelScanHIPBase { size_type* m_scratch_flags = nullptr; size_type m_final = false; int m_grid_x = 0; + // Only let one ParallelReduce/Scan modify the shared memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_shared_memory_lock; private: template @@ -624,22 +627,7 @@ class ParallelScanHIPBase { } // Determine block size constrained by shared memory: - inline unsigned local_block_size(const FunctorType& f) { - // blockDim.y must be power of two = 128 (2 warps) or 256 (4 warps) or - // 512 (8 warps) gridDim.x <= blockDim.y * blockDim.y - // - // TODO check best option - - unsigned n = Experimental::Impl::HIPTraits::WarpSize * 4; - while (n && static_cast(m_policy.space() - .impl_internal_space_instance() - ->m_maxShmemPerBlock) < - hip_single_inter_block_reduce_scan_shmem(f, n)) { - n >>= 1; - } - return n; - } + virtual inline unsigned local_block_size(const FunctorType& f) = 0; inline void impl_execute() { const index_type nwork = m_policy.end() - m_policy.begin(); @@ -649,7 +637,11 @@ class ParallelScanHIPBase { const int gridMaxComputeCapability_2x = 0x01fff; const int block_size = static_cast(local_block_size(m_functor)); - KOKKOS_ASSERT(block_size > 0); + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelScan< HIP > could not find a " + "valid execution configuration.")); + } const int grid_max = std::min(block_size * block_size, gridMaxComputeCapability_2x); @@ -674,15 +666,16 @@ class ParallelScanHIPBase { const int shmem = ValueTraits::value_size(m_functor) * (block_size + 2); m_final = false; - Kokkos::Experimental::Impl::HIPParallelLaunch( + // these ones are OK to be just the base because the specializations + // do not modify the kernel at all + using DriverType = ParallelScanHIPBase; + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem, m_policy.space().impl_internal_space_instance(), false); // copy to device and execute m_final = true; - Kokkos::Experimental::Impl::HIPParallelLaunch( + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem, m_policy.space().impl_internal_space_instance(), false); // copy to device and execute @@ -690,13 +683,17 @@ class ParallelScanHIPBase { } ParallelScanHIPBase(const FunctorType& arg_functor, const Policy& arg_policy) - : m_functor(arg_functor), m_policy(arg_policy) {} + : m_functor(arg_functor), + m_policy(arg_policy), + m_shared_memory_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexSharedMemory) {} }; template class ParallelScan, Kokkos::Experimental::HIP> - : private ParallelScanHIPBase { + : public ParallelScanHIPBase { public: using Base = ParallelScanHIPBase; using Base::operator(); @@ -706,6 +703,23 @@ class ParallelScan, ParallelScan(const FunctorType& arg_functor, const typename Base::Policy& arg_policy) : Base(arg_functor, arg_policy) {} + + inline unsigned local_block_size(const FunctorType& f) { + // blockDim.y must be power of two = 128 (2 warps) or 256 (4 warps) or + // 512 (8 warps) gridDim.x <= blockDim.y * blockDim.y + + const auto& instance = + Base::m_policy.space().impl_internal_space_instance(); + auto shmem_functor = [&f](unsigned n) { + return hip_single_inter_block_reduce_scan_shmem( + f, n); + }; + using DriverType = ParallelScan; + return Kokkos::Experimental::Impl::hip_get_preferred_blocksize< + DriverType, typename Base::LaunchBounds>(instance, shmem_functor); + } }; //---------------------------------------------------------------------------- @@ -713,7 +727,7 @@ class ParallelScan, template class ParallelScanWithTotal, ReturnType, Kokkos::Experimental::HIP> - : private ParallelScanHIPBase { + : public ParallelScanHIPBase { public: using Base = ParallelScanHIPBase; using Base::operator(); @@ -737,6 +751,24 @@ class ParallelScanWithTotal, const typename Base::Policy& arg_policy, ReturnType& arg_returnvalue) : Base(arg_functor, arg_policy), m_returnvalue(arg_returnvalue) {} + + inline unsigned local_block_size(const FunctorType& f) { + // blockDim.y must be power of two = 128 (2 warps) or 256 (4 warps) or + // 512 (8 warps) gridDim.x <= blockDim.y * blockDim.y + + const auto& instance = + Base::m_policy.space().impl_internal_space_instance(); + auto shmem_functor = [&f](unsigned n) { + return hip_single_inter_block_reduce_scan_shmem( + f, n); + }; + using DriverType = + ParallelScanWithTotal; + return Kokkos::Experimental::Impl::hip_get_preferred_blocksize< + DriverType, typename Base::LaunchBounds>(instance, shmem_functor); + } }; } // namespace Impl diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp index 96c3ff2a7510..b794f5bc0371 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp @@ -56,20 +56,20 @@ namespace Kokkos { namespace Impl { + template class TeamPolicyInternal : public PolicyTraits { public: using execution_policy = TeamPolicyInternal; - using traits = PolicyTraits; + using traits = PolicyTraits; + using BlockType = Kokkos::Experimental::Impl::BlockType; template friend class TeamPolicyInternal; private: - static int constexpr MAX_WARP = 8; - typename traits::execution_space m_space; int m_league_size; int m_team_size; @@ -101,17 +101,9 @@ class TeamPolicyInternal template int team_size_max(FunctorType const& f, ParallelForTag const&) const { using closure_type = - Impl::ParallelFor >; - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, - typename traits::launch_bounds>::get_hip_func_attributes(); - int const block_size = ::Kokkos::Experimental::Impl::hip_get_max_block_size< - FunctorType, typename traits::launch_bounds>( - space().impl_internal_space_instance(), attr, f, - static_cast(impl_vector_length()), - static_cast(team_scratch_size(0)) + 2 * sizeof(double), - static_cast(thread_scratch_size(0)) + sizeof(double)); - return block_size / impl_vector_length(); + Impl::ParallelFor>; + + return internal_team_size_common(f); } template @@ -129,8 +121,8 @@ class TeamPolicyInternal return internal_team_size_max(f); } - template - inline int team_size_max(const FunctorType& f, const ReducerType& /*r*/, + template + inline int team_size_max(const FunctorType& f, const ReducerType&, const ParallelReduceTag&) const { using closure_type = Impl::ParallelReduce, @@ -141,17 +133,9 @@ class TeamPolicyInternal template int team_size_recommended(FunctorType const& f, ParallelForTag const&) const { using closure_type = - Impl::ParallelFor >; - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, - typename traits::launch_bounds>::get_hip_func_attributes(); - int const block_size = ::Kokkos::Experimental::Impl::hip_get_opt_block_size< - FunctorType, typename traits::launch_bounds>( - space().impl_internal_space_instance(), attr, f, - static_cast(impl_vector_length()), - static_cast(team_scratch_size(0)) + 2 * sizeof(double), - static_cast(thread_scratch_size(0)) + sizeof(double)); - return block_size / impl_vector_length(); + Impl::ParallelFor>; + + return internal_team_size_common(f); } template @@ -169,7 +153,7 @@ class TeamPolicyInternal return internal_team_size_recommended(f); } - template + template int team_size_recommended(FunctorType const& f, ReducerType const&, ParallelReduceTag const&) const { using closure_type = @@ -177,6 +161,7 @@ class TeamPolicyInternal ReducerType>; return internal_team_size_recommended(f); } + inline bool impl_auto_vector_length() const { return m_tune_vector_length; } inline bool impl_auto_team_size() const { return m_tune_team_size; } static int vector_length_max() { @@ -211,7 +196,10 @@ class TeamPolicyInternal inline void impl_set_vector_length(size_t size) { m_vector_length = size; } inline void impl_set_team_size(size_t size) { m_team_size = size; } int impl_vector_length() const { return m_vector_length; } + +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 KOKKOS_DEPRECATED int vector_length() const { return impl_vector_length(); } +#endif int team_size() const { return m_team_size; } @@ -266,7 +254,8 @@ class TeamPolicyInternal "space."); // Make sure total block size is permissible - if (m_team_size * m_vector_length > 1024) { + if (m_team_size * m_vector_length > + ::Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock) { Impl::throw_runtime_exception( std::string("Kokkos::TeamPolicy< HIP > the team size is too large. " "Team size x vector length must be smaller than 1024.")); @@ -363,26 +352,84 @@ class TeamPolicyInternal using member_type = Kokkos::Impl::HIPTeamMember; protected: - template - int internal_team_size_common(const FunctorType& f, - BlockSizeCallable&& block_size_callable) const { - using closure_type = ClosureType; + template + int internal_team_size_common(const FunctorType& f) const { + // FIXME_HIP: this could be unified with the + // internal_team_size_common_reduce + // once we can turn c++17 constexpr on by default. + // The problem right now is that we can't turn off the evaluation + // of the functor_value_traits's valuesize / StaticValueSize + + const unsigned shmem_block = team_scratch_size(0) + 2 * sizeof(double); + const unsigned shmem_thread = thread_scratch_size(0) + sizeof(double); + const int vector_length = impl_vector_length(); + + const auto functor = [&f, shmem_block, shmem_thread, vector_length]( + const hipFuncAttributes& attr, int block_size) { + int functor_shmem = + ::Kokkos::Impl::FunctorTeamShmemSize::value( + f, block_size / vector_length); + return shmem_block + shmem_thread * (block_size / vector_length) + + functor_shmem + attr.sharedSizeBytes; + }; + int block_size; + // FIXME_HIP - could be if constexpr for c++17 + if (BlockSize == BlockType::Max) { + block_size = ::Kokkos::Experimental::Impl::hip_get_max_team_blocksize< + ClosureType, typename traits::launch_bounds>( + space().impl_internal_space_instance(), functor); + } else { + block_size = + ::Kokkos::Experimental::Impl::hip_get_preferred_team_blocksize< + ClosureType, typename traits::launch_bounds>( + space().impl_internal_space_instance(), functor); + } + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelFor< HIP > could not find a valid " + "team size.")); + } + return block_size / impl_vector_length(); + } + + template + int internal_team_size_common_reduce(const FunctorType& f) const { using functor_value_traits = Impl::FunctorValueTraits; - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - closure_type, - typename traits::launch_bounds>::get_hip_func_attributes(); - const int block_size = std::forward(block_size_callable)( - space().impl_internal_space_instance(), attr, f, - static_cast(impl_vector_length()), - static_cast(team_scratch_size(0)) + 2 * sizeof(double), - static_cast(thread_scratch_size(0)) + sizeof(double) + - ((functor_value_traits::StaticValueSize != 0) - ? 0 - : functor_value_traits::value_size(f))); - KOKKOS_ASSERT(block_size > 0); + const unsigned shmem_block = team_scratch_size(0) + 2 * sizeof(double); + const unsigned shmem_thread = thread_scratch_size(0) + sizeof(double) + + ((functor_value_traits::StaticValueSize != 0) + ? 0 + : functor_value_traits::value_size(f)); + const int vector_length = impl_vector_length(); + + const auto functor = [&f, shmem_block, shmem_thread, vector_length]( + const hipFuncAttributes& attr, int block_size) { + int functor_shmem = + ::Kokkos::Impl::FunctorTeamShmemSize::value( + f, block_size / vector_length); + return shmem_block + shmem_thread * (block_size / vector_length) + + functor_shmem + attr.sharedSizeBytes; + }; + int block_size; + // FIXME_HIP - could be if constexpr for c++17 + if (BlockSize == BlockType::Max) { + block_size = ::Kokkos::Experimental::Impl::hip_get_max_team_blocksize< + ClosureType, typename traits::launch_bounds>( + space().impl_internal_space_instance(), functor); + } else { + block_size = + ::Kokkos::Experimental::Impl::hip_get_preferred_team_blocksize< + ClosureType, typename traits::launch_bounds>( + space().impl_internal_space_instance(), functor); + } + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " + "valid team size.")); + } // Currently we require Power-of-2 team size for reductions. int p2 = 1; while (p2 <= block_size) p2 *= 2; @@ -392,16 +439,13 @@ class TeamPolicyInternal template int internal_team_size_max(const FunctorType& f) const { - return internal_team_size_common( - f, ::Kokkos::Experimental::Impl::hip_get_max_block_size< - FunctorType, typename traits::launch_bounds>); + return internal_team_size_common_reduce(f); } template int internal_team_size_recommended(const FunctorType& f) const { - return internal_team_size_common( - f, ::Kokkos::Experimental::Impl::hip_get_opt_block_size< - FunctorType, typename traits::launch_bounds>); + return internal_team_size_common_reduce( + f); } }; @@ -505,7 +549,11 @@ class ParallelFor, dim3 const block(static_cast(m_vector_size), static_cast(m_team_size), 1); - ::Kokkos::Experimental::Impl::HIPParallelLaunch( + using closure_type = + ParallelFor, + Kokkos::Experimental::HIP>; + ::Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem_size_total, m_policy.space().impl_internal_space_instance(), true); // copy to device and execute @@ -520,17 +568,9 @@ class ParallelFor, m_scratch_lock(m_policy.space() .impl_internal_space_instance() ->m_team_scratch_mutex) { - hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< - ParallelFor, launch_bounds>::get_hip_func_attributes(); - m_team_size = - m_team_size >= 0 - ? m_team_size - : ::Kokkos::Experimental::Impl::hip_get_opt_block_size< - FunctorType, launch_bounds>( - m_policy.space().impl_internal_space_instance(), attr, - m_functor, m_vector_size, m_policy.team_scratch_size(0), - m_policy.thread_scratch_size(0)) / - m_vector_size; + m_team_size = m_team_size >= 0 ? m_team_size + : arg_policy.team_size_recommended( + arg_functor, ParallelForTag()); m_shmem_begin = (sizeof(double) * (m_team_size + 2)); m_shmem_size = @@ -556,23 +596,12 @@ class ParallelFor, int const shmem_size_total = m_shmem_begin + m_shmem_size; if (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < shmem_size_total) { - printf( - "%i %i\n", - m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock, - shmem_size_total); Kokkos::Impl::throw_runtime_exception(std::string( "Kokkos::Impl::ParallelFor< HIP > insufficient shared memory")); } - if (static_cast(m_team_size) > - static_cast( - ::Kokkos::Experimental::Impl::hip_get_max_block_size( - m_policy.space().impl_internal_space_instance(), attr, - arg_functor, arg_policy.impl_vector_length(), - arg_policy.team_scratch_size(0), - arg_policy.thread_scratch_size(0)) / - arg_policy.impl_vector_length())) { + size_t max_size = arg_policy.team_size_max(arg_functor, ParallelForTag()); + if (static_cast(m_team_size) > static_cast(max_size)) { Kokkos::Impl::throw_runtime_exception(std::string( "Kokkos::Impl::ParallelFor< HIP > requested too large team size.")); } @@ -839,8 +868,11 @@ class ParallelReduce, } const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; - Kokkos::Experimental::Impl::HIPParallelLaunch( + using closure_type = + ParallelReduce, + ReducerType, Kokkos::Experimental::HIP>; + Kokkos::Experimental::Impl::hip_parallel_launch( *this, grid, block, shmem_size_total, m_policy.space().impl_internal_space_instance(), true); // copy to device and execute @@ -890,17 +922,9 @@ class ParallelReduce, m_scratch_lock(m_policy.space() .impl_internal_space_instance() ->m_team_scratch_mutex) { - hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< - ParallelReduce, launch_bounds>::get_hip_func_attributes(); - m_team_size = - m_team_size >= 0 - ? m_team_size - : Kokkos::Experimental::Impl::hip_get_opt_block_size( - m_policy.space().impl_internal_space_instance(), attr, - m_functor, m_vector_size, m_policy.team_scratch_size(0), - m_policy.thread_scratch_size(0)) / - m_vector_size; + m_team_size = m_team_size >= 0 ? m_team_size + : arg_policy.team_size_recommended( + arg_functor, ParallelReduceTag()); m_team_begin = UseShflReduction @@ -958,8 +982,9 @@ class ParallelReduce, "L0 scratch memory")); } - if (static_cast(m_team_size) > - arg_policy.team_size_max(m_functor, m_reducer, ParallelReduceTag())) { + size_t max_size = + arg_policy.team_size_max(arg_functor, ParallelReduceTag()); + if (static_cast(m_team_size) > static_cast(max_size)) { Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< HIP > requested too " "large team size.")); @@ -992,18 +1017,10 @@ class ParallelReduce, m_scratch_lock(m_policy.space() .impl_internal_space_instance() ->m_team_scratch_mutex) { - hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< - ParallelReduce, launch_bounds>::get_hip_func_attributes(); - m_team_size = - m_team_size >= 0 - ? m_team_size - : Kokkos::Experimental::Impl::hip_get_opt_block_size( - m_policy.space().impl_internal_space_instance(), attr, - m_functor, m_vector_size, m_policy.team_scratch_size(0), - m_policy.thread_scratch_size(0)) / - m_vector_size; - + m_team_size = m_team_size >= 0 + ? m_team_size + : arg_policy.team_size_recommended(arg_functor, reducer, + ParallelReduceTag()); m_team_begin = UseShflReduction ? 0 @@ -1046,7 +1063,6 @@ class ParallelReduce, // upon team size. const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; - if ((!Kokkos::Impl::is_integral_power_of_two(m_team_size) && !UseShflReduction) || m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < @@ -1054,8 +1070,10 @@ class ParallelReduce, Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< HIP > bad team size")); } - if (static_cast(m_team_size) > - arg_policy.team_size_max(m_functor, m_reducer, ParallelReduceTag())) { + + size_t max_size = + arg_policy.team_size_max(arg_functor, reducer, ParallelReduceTag()); + if (static_cast(m_team_size) > static_cast(max_size)) { Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< HIP > requested too " "large team size.")); diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp index 15ca089d1474..e25ebe2ab355 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp @@ -67,102 +67,32 @@ namespace { hipStream_t get_deep_copy_stream() { static hipStream_t s = nullptr; if (s == nullptr) { - HIP_SAFE_CALL(hipStreamCreate(&s)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamCreate(&s)); } return s; } } // namespace -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); +void DeepCopyHIP(void* dst, void const* src, size_t n) { + KOKKOS_IMPL_HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); } -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); -} - -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); -} - -DeepCopy::DeepCopy(const Kokkos::Experimental::HIP& - instance, - void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL( - hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); -} - -DeepCopy:: - DeepCopy(const Kokkos::Experimental::HIP& instance, void* dst, - const void* src, size_t n) { - HIP_SAFE_CALL( - hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); -} - -DeepCopy:: - DeepCopy(const Kokkos::Experimental::HIP& instance, void* dst, - const void* src, size_t n) { - HIP_SAFE_CALL( - hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); -} - -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); -} - -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); -} - -DeepCopy::DeepCopy(void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL(hipMemcpy(dst, src, n, hipMemcpyDefault)); -} - -DeepCopy:: - DeepCopy(const Kokkos::Experimental::HIP& instance, void* dst, - const void* src, size_t n) { - HIP_SAFE_CALL( - hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); -} - -DeepCopy::DeepCopy(const Kokkos::Experimental::HIP& - instance, - void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL( - hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); -} - -DeepCopy::DeepCopy(const Kokkos::Experimental::HIP& - instance, - void* dst, const void* src, - size_t n) { - HIP_SAFE_CALL( +void DeepCopyAsyncHIP(const Kokkos::Experimental::HIP& instance, void* dst, + void const* src, size_t n) { + KOKKOS_IMPL_HIP_SAFE_CALL( hipMemcpyAsync(dst, src, n, hipMemcpyDefault, instance.hip_stream())); } void DeepCopyAsyncHIP(void* dst, void const* src, size_t n) { hipStream_t s = get_deep_copy_stream(); - HIP_SAFE_CALL(hipMemcpyAsync(dst, src, n, hipMemcpyDefault, s)); - HIP_SAFE_CALL(hipStreamSynchronize(s)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipMemcpyAsync(dst, src, n, hipMemcpyDefault, s)); + Kokkos::Tools::Experimental::Impl::profile_fence_event< + Kokkos::Experimental::HIP>( + "Kokkos::Impl::DeepCopyAsyncHIP: Post Deep Copy Fence on Deep-Copy " + "stream", + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + DeepCopyResourceSynchronization, + [&]() { KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamSynchronize(s)); }); } } // namespace Impl @@ -171,6 +101,7 @@ void DeepCopyAsyncHIP(void* dst, void const* src, size_t n) { /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 namespace Kokkos { KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error() { @@ -188,6 +119,7 @@ KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error(const void* const) { } } // namespace Kokkos +#endif /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ @@ -283,7 +215,7 @@ void HIPSpace::impl_deallocate( Kokkos::Profiling::deallocateData(arg_handle, arg_label, arg_alloc_ptr, reported_size); } - HIP_SAFE_CALL(hipFree(arg_alloc_ptr)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipFree(arg_alloc_ptr)); } void HIPHostPinnedSpace::deallocate(void* const arg_alloc_ptr, @@ -307,7 +239,7 @@ void HIPHostPinnedSpace::impl_deallocate( Kokkos::Profiling::deallocateData(arg_handle, arg_label, arg_alloc_ptr, reported_size); } - HIP_SAFE_CALL(hipHostFree(arg_alloc_ptr)); + KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(arg_alloc_ptr)); } } // namespace Experimental @@ -427,23 +359,42 @@ HIP::HIP() "HIP instance constructor"); } -HIP::HIP(hipStream_t const stream) +HIP::HIP(hipStream_t const stream, bool manage_stream) : m_space_instance(new Impl::HIPInternal, [](Impl::HIPInternal* ptr) { ptr->finalize(); delete ptr; }) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); - m_space_instance->initialize(Impl::HIPInternal::singleton().m_hipDev, stream); + m_space_instance->initialize(Impl::HIPInternal::singleton().m_hipDev, stream, + manage_stream); } void HIP::print_configuration(std::ostream& s, const bool) { Impl::HIPInternal::singleton().print_configuration(s); } -void HIP::impl_static_fence() { HIP_SAFE_CALL(hipDeviceSynchronize()); } +uint32_t HIP::impl_instance_id() const noexcept { + return m_space_instance->impl_get_instance_id(); +} +void HIP::impl_static_fence(const std::string& name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event< + Kokkos::Experimental::HIP>( + name, + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + GlobalDeviceSynchronization, + [&]() { KOKKOS_IMPL_HIP_SAFE_CALL(hipDeviceSynchronize()); }); +} +void HIP::impl_static_fence() { + impl_static_fence("Kokkos::HIP::impl_static_fence: Unnamed Static Fence"); +} -void HIP::fence() const { m_space_instance->fence(); } +void HIP::fence(const std::string& name) const { + m_space_instance->fence(name); +} +void HIP::fence() const { + fence("Kokkos::HIP::fence(): Unnamed Instance Fence"); +} hipStream_t HIP::hip_stream() const { return m_space_instance->m_stream; } @@ -489,6 +440,9 @@ void HIPSpaceInitializer::finalize(const bool all_spaces) { void HIPSpaceInitializer::fence() { Kokkos::Experimental::HIP::impl_static_fence(); } +void HIPSpaceInitializer::fence(const std::string& name) { + Kokkos::Experimental::HIP::impl_static_fence(name); +} void HIPSpaceInitializer::print_configuration(std::ostream& msg, const bool detail) { diff --git a/packages/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp b/packages/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp index fe52886ced7c..fb67a25c5e7f 100644 --- a/packages/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp +++ b/packages/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp @@ -316,198 +316,6 @@ class HIPTeamMember { #endif } - //-------------------------------------------------------------------------- - /**\brief Global reduction across all blocks - * - * Return !0 if reducer contains the final value - */ - template - KOKKOS_INLINE_FUNCTION static - typename std::enable_if::value, int>::type - global_reduce(ReducerType const& reducer, int* const global_scratch_flags, - void* const global_scratch_space, void* const shmem, - int const shmem_size) { -#ifdef __HIP_DEVICE_COMPILE__ - using value_type = typename ReducerType::value_type; - using pointer_type = value_type volatile*; - - // Number of shared memory entries for the reduction: - const int nsh = shmem_size / sizeof(value_type); - - // Number of HIP threads in the block, rank within the block - const int nid = blockDim.x * blockDim.y * blockDim.z; - const int tid = - threadIdx.x + blockDim.x * (threadIdx.y + blockDim.y * threadIdx.z); - - // Reduces within block using all available shared memory - // Contributes if it is the root "vector lane" - - // wn == number of warps in the block - // wx == which lane within the warp - // wy == which warp within the block - - const int wn = (nid + Experimental::Impl::HIPTraits::WarpIndexMask) >> - Experimental::Impl::HIPTraits::WarpIndexShift; - const int wx = tid & Experimental::Impl::HIPTraits::WarpIndexMask; - const int wy = tid >> Experimental::Impl::HIPTraits::WarpIndexShift; - - //------------------------ - { // Intra warp shuffle reduction from contributing HIP threads - - value_type tmp(reducer.reference()); - - int constexpr warp_size = - ::Kokkos::Experimental::Impl::HIPTraits::WarpSize; - for (int i = warp_size; static_cast(blockDim.x) <= (i >>= 1);) { - Experimental::Impl::in_place_shfl_down(reducer.reference(), tmp, i, - warp_size); - - // Root of each vector lane reduces "thread" contribution - if (0 == threadIdx.x && wx < i) { - reducer.join(&tmp, reducer.data()); - } - } - - // Reduce across warps using shared memory. - // Number of warps may not be power of two. - - __syncthreads(); // Wait before shared data write - - // Number of shared memory entries for the reduction - // is at most one per warp - const int nentry = wn < nsh ? wn : nsh; - - if (0 == wx && wy < nentry) { - // Root thread of warp 'wy' has warp's value to contribute - (reinterpret_cast(shmem))[wy] = tmp; - } - - __syncthreads(); // Wait for write to be visible to block - - // When more warps than shared entries - // then warps must take turns joining their contribution - // to the designated shared memory entry. - for (int i = nentry; i < wn; i += nentry) { - const int k = wy - i; - - if (0 == wx && i <= wy && k < nentry) { - // Root thread of warp 'wy' has warp's value to contribute - reducer.join((reinterpret_cast(shmem)) + k, &tmp); - } - - __syncthreads(); // Wait for write to be visible to block - } - - // One warp performs the inter-warp reduction: - - if (0 == wy) { - // Start fan-in at power of two covering nentry - - for (int i = (1 << (warp_size - __clz(nentry - 1))); (i >>= 1);) { - const int k = wx + i; - if (wx < i && k < nentry) { - reducer.join((reinterpret_cast(shmem)) + wx, - (reinterpret_cast(shmem)) + k); - __threadfence_block(); // Wait for write to be visible to warp - } - } - } - } - //------------------------ - { // Write block's value to global_scratch_memory - - int last_block = 0; - - if (0 == wx) { - reducer.copy((reinterpret_cast(global_scratch_space)) + - blockIdx.x * reducer.length(), - reducer.data()); - - __threadfence(); // Wait until global write is visible. - - last_block = static_cast(gridDim.x) == - 1 + Kokkos::atomic_fetch_add(global_scratch_flags, 1); - - // If last block then reset count - if (last_block) *global_scratch_flags = 0; - } - - // FIXME hip does not support __syncthreads_or so we need to do it by hand - // last_block = __syncthreads_or(last_block); - - __shared__ int last_block_shared; - if (last_block) last_block_shared = last_block; - __threadfence_block(); - - if (!last_block_shared) return 0; - } - //------------------------ - // Last block reads global_scratch_memory into shared memory. - - const int nentry = nid < gridDim.x ? (nid < nsh ? nid : nsh) - : (gridDim.x < nsh ? gridDim.x : nsh); - - // nentry = min( nid , nsh , gridDim.x ) - - // whole block reads global memory into shared memory: - - if (tid < nentry) { - const int offset = tid * reducer.length(); - - reducer.copy( - (reinterpret_cast(shmem)) + offset, - (reinterpret_cast(global_scratch_space)) + offset); - - for (int i = nentry + tid; i < static_cast(gridDim.x); i += nentry) { - reducer.join((reinterpret_cast(shmem)) + offset, - (reinterpret_cast(global_scratch_space)) + - i * reducer.length()); - } - } - - __syncthreads(); // Wait for writes to be visible to block - - if (0 == wy) { - // Iterate to reduce shared memory to single warp fan-in size - - int constexpr warp_size = - ::Kokkos::Experimental::Impl::HIPTraits::WarpSize; - const int nreduce = warp_size < nentry ? warp_size : nentry; - - if (wx < nreduce && nreduce < nentry) { - for (int i = nreduce + wx; i < nentry; i += nreduce) { - reducer.join(((pointer_type)shmem) + wx, ((pointer_type)shmem) + i); - } - __threadfence_block(); // Wait for writes to be visible to warp - } - - // Start fan-in at power of two covering nentry - - for (int i = (1 << (warp_size - __clz(nreduce - 1))); (i >>= 1);) { - const int k = wx + i; - if (wx < i && k < nreduce) { - reducer.join((reinterpret_cast(shmem)) + wx, - (reinterpret_cast(shmem)) + k); - __threadfence_block(); // Wait for writes to be visible to warp - } - } - - if (0 == wx) { - reducer.copy(reducer.data(), reinterpret_cast(shmem)); - return 1; - } - } - return 0; -#else - (void)reducer; - (void)global_scratch_flags; - (void)global_scratch_space; - (void)shmem; - (void)shmem_size; - return 0; -#endif - } - //---------------------------------------- // Private for the driver diff --git a/packages/kokkos/core/src/HPX/Kokkos_HPX.cpp b/packages/kokkos/core/src/HPX/Kokkos_HPX.cpp index 910d5e52e6ac..d9cb66e11f46 100644 --- a/packages/kokkos/core/src/HPX/Kokkos_HPX.cpp +++ b/packages/kokkos/core/src/HPX/Kokkos_HPX.cpp @@ -191,6 +191,9 @@ void HPXSpaceInitializer::finalize(const bool all_spaces) { } void HPXSpaceInitializer::fence() { Kokkos::Experimental::HPX().fence(); } +void HPXSpaceInitializer::fence(const std::string &name) { + Kokkos::Experimental::HPX().fence(name); +} void HPXSpaceInitializer::print_configuration(std::ostream &msg, const bool detail) { diff --git a/packages/kokkos/core/src/HPX/Kokkos_HPX_Task.hpp b/packages/kokkos/core/src/HPX/Kokkos_HPX_Task.hpp index df09e026fd9b..7bb3ca5d0070 100644 --- a/packages/kokkos/core/src/HPX/Kokkos_HPX_Task.hpp +++ b/packages/kokkos/core/src/HPX/Kokkos_HPX_Task.hpp @@ -82,7 +82,9 @@ class TaskQueueSpecialization< task_queue.scheduler = &scheduler; Kokkos::Impl::dispatch_execute_task(&task_queue, Kokkos::Experimental::HPX()); - Kokkos::Experimental::HPX().fence(); + Kokkos::Experimental::HPX().fence( + "Kokkos::Impl::TaskQueueSpecialization::execute: fence " + "after task execution"); } // Must provide task queue execution function @@ -214,7 +216,7 @@ class TaskQueueSpecializationConstrained< task_queue.scheduler = &scheduler; Kokkos::Impl::dispatch_execute_task(&task_queue, Kokkos::Experimental::HPX()); - Kokkos::Experimental::HPX().fence(); + Kokkos::Experimental::HPX().fence()"Kokkos::Impl::TaskQueueSpecializationConstrained::execute: fence after task execution"; } // Must provide task queue execution function diff --git a/packages/kokkos/core/src/HPX/Kokkos_HPX_WorkGraphPolicy.hpp b/packages/kokkos/core/src/HPX/Kokkos_HPX_WorkGraphPolicy.hpp index 527fe12ad937..d7e13e28f054 100644 --- a/packages/kokkos/core/src/HPX/Kokkos_HPX_WorkGraphPolicy.hpp +++ b/packages/kokkos/core/src/HPX/Kokkos_HPX_WorkGraphPolicy.hpp @@ -79,7 +79,9 @@ class ParallelFor, public: void execute() const { dispatch_execute_task(this, m_policy.space()); - m_policy.space().fence(); + m_policy.space().fence( + "Kokkos::Experimental::Impl::HPX::ParallelFor: fence " + "after kernel execution"); } void execute_task() const { diff --git a/packages/kokkos/core/src/KokkosExp_InterOp.hpp b/packages/kokkos/core/src/KokkosExp_InterOp.hpp new file mode 100644 index 000000000000..37c2088f88f0 --- /dev/null +++ b/packages/kokkos/core/src/KokkosExp_InterOp.hpp @@ -0,0 +1,147 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 3.0 +// Copyright (2020) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#ifndef KOKKOS_CORE_EXP_INTEROP_HPP +#define KOKKOS_CORE_EXP_INTEROP_HPP + +#include +#include +#include +#include +#include +#include + +namespace Kokkos { +namespace Impl { + +// ------------------------------------------------------------------ // +// this is used to convert +// Kokkos::Device to MemSpace +// +template +struct device_memory_space { + using type = Tp; +}; + +template +struct device_memory_space> { + using type = MemT; +}; + +template +using device_memory_space_t = typename device_memory_space::type; + +// ------------------------------------------------------------------ // +// this is the impl version which takes a view and converts to python +// view type +// +template +struct python_view_type_impl; + +template