Installing Trilinos (in order to install peridigm) #1713
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@Chaztikov While I have not seen this error before, it seems that it looks for X11 headers/library and can't find any. Quick googling arounds seems to indicate that it is provided by |
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Thanks for your swift response, I am not sure, but think I need Matio for Peridigm? I specified X11's location correctly, I think but now receive errors, here is the CMakerErrors.log file: Performing C++ SOURCE FILE Test FINITE_VALUE_HAVE_GLOBAL_ISNAN failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_fb5dd/fast" Source file was: #include Performing C++ SOURCE FILE Test FINITE_VALUE_HAVE_GLOBAL_ISINF failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_88123/fast" Source file was: #include Performing C++ SOURCE FILE Test HAVE_GCC_ABI_DEMANGLE failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_50b7f/fast" Return value: 127 #include <cxxabi.h> int main() Performing C++ SOURCE FILE Test HAVE_TEUCHOS_BLASFLOAT failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_23deb/fast" Return value: 127 #define F77_BLAS_MANGLE(name,NAME) name ## _ #include #define SDOT_F77 F77_BLAS_MANGLE(sdot, SDOT) extern "C" { int main() val = SDOT_F77(&n, x, &incx, x, &incx); val = SASUM_F77(&n, x, &incx); val = SNRM2_F77(&n, x, &incx); val = SCASUM_F77(&n, xc, &incx); val = SCNRM2_F77(&n, xc, &incx); return 0; Performing C++ SOURCE FILE Test HAVE_TEUCHOS_BLASFLOAT_DOUBLE_RETURN failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_f6677/fast" Return value: 127 #define F77_BLAS_MANGLE(name,NAME) name ## _ #include #define SDOT_F77 F77_BLAS_MANGLE(sdot, SDOT) extern "C" { int main() val = SDOT_F77(&n, x, &incx, x, &incx); val = SASUM_F77(&n, x, &incx); val = SNRM2_F77(&n, x, &incx); val = SCASUM_F77(&n, xc, &incx); val = SCNRM2_F77(&n, xc, &incx); return 0; Performing C++ SOURCE FILE Test HAVE_TEUCHOS_LAPACKLARND failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_58c4b/fast" Return value: 1 #define F77_BLAS_MANGLE(name,NAME) name ## _ #define DLARND_F77 F77_BLAS_MANGLE(dlarnd,DLARND) extern "C" { double DLARND_F77(const int* idist, int* seed); } int main() const int idist = 1; double val = DLARND_F77(&idist, seed); return (val < 0.0 ? 1 : 0); } Performing C++ SOURCE FILE Test HAVE_CXX_PRAGMA_WEAK failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_29fdd/fast" Source file was: #include namespace A { int main() { Determining if the function dggsvd3 exists failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_24973/fast" Determining if the function DGGSVD3 exists failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_4053e/fast" Determining if the function DGGSVD3_ exists failed with the following output: Run Build Command:"/usr/bin/make" "cmTC_18f0d/fast" |
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@Chaztikov It looks strange that you set |
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Also, if you set |
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Thanks a bunch! It seems to have worked, nearly, now when I |
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I may see where this is coming from during the ./configure: -- HDF5_LIBRARY_NAMES='hdf5;z;hdf5_hl' Call Stack (most recent call first): -- NetCDF does not require HDF5 Setting up testing support ... -- CTEST_DROP_METHOD='http' Configuring individual enabled Trilinos packages ... |
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I seem to continue to have issues, possibly related to Is there a recommended order/way to install parallel netcdf with hdf5? |
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@Chaztikov What do the Peridigm developers recommend? I would suggest asking them about NetCDF etc. version issues. |
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Everything included in my configuration file seems to be what Peridigm recommends, I think I fixed one issue, now on to another Thanks by the way for all of your time! when I I get fairly far in the process but then: [ 87%] Building CXX object packages/rythmos/src/CMakeFiles/rythmos.dir/Rythmos_TimeStepNonlinearSolver.cpp.o |
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I updated my compiler to gcc-5, and now am getting this error: [ 86%] Building CXX object packages/tpetra/core/src/CMakeFiles/tpetra.dir/Tpetra_MultiVectorFiller.cpp.o I am using the mpicc installed by anaconda...could this cause an issue? |
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@Chaztikov If you do |
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I see [ 69%] Building CXX object packages/epetraext/src/CMakeFiles/epetraext.dir/inout/EpetraExt_HDF5.cpp.o |
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@Chaztikov This looks like an HDF5 version issue. Does your HDF5 version implement functions like |
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Many thanks again, it seems there is another underlying issue, I believe you can close this! |
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@Chaztikov Thanks! |
I am having a bear of a time trying to install Trilinos and its dependencies on Ubuntu to run in parallel, not sure why. Here is my configure file:
! /bin/bash
sudo rm -r -f CMakeCache.txt CMakeFiles/
-D MPI_BASE_DIR:PATH="/usr/local/openmpi/"
-D HDF5_INCLUDE_DIRS:PATH="/usr/local/hdf5/include"
-D HDF5_LIBRARY_DIRS:PATH="/usr/local/hdf5/lib"
-D Netcdf_INCLUDE_DIRS:PATH=/usr/local/netcdf/include
-D Netcdf_LIBRARY_DIRS:PATH=/usr/local/netcdf/lib
-D Boost_INCLUDE_DIRS:PATH=/usr/local/boost/include
-D Boost_LIBRARY_DIRS:PATH=/usr/local/boost/lib \
cmake \ -D CMAKE_BUILD_TYPE:STRING=RELEASE \ -DCMAKE_C_COMPILER=/usr/bin/mpicc \ -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \ -DCMAKE_Fortran_COMPILER=/usr/bin/mpif90 \ -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \ -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \ -D Trilinos_ENABLE_Teuchos:BOOL=ON \ -D Trilinos_ENABLE_Shards:BOOL=ON \ -D Trilinos_ENABLE_Sacado:BOOL=ON \ -D Trilinos_ENABLE_Epetra:BOOL=ON \ -D Trilinos_ENABLE_EpetraExt:BOOL=ON \ -D Trilinos_ENABLE_Ifpack:BOOL=ON \ -D Trilinos_ENABLE_AztecOO:BOOL=ON \ -D Trilinos_ENABLE_Amesos:BOOL=ON \ -D Trilinos_ENABLE_Anasazi:BOOL=ON \ -D Trilinos_ENABLE_Belos:BOOL=ON \ -D Trilinos_ENABLE_ML:BOOL=ON \ -D Trilinos_ENABLE_Phalanx:BOOL=ON \ -D Trilinos_ENABLE_Intrepid:BOOL=ON \ -D Trilinos_ENABLE_NOX:BOOL=ON \ -D Trilinos_ENABLE_Stratimikos:BOOL=ON \ -D Trilinos_ENABLE_Thyra:BOOL=ON \ -D Trilinos_ENABLE_Rythmos:BOOL=ON \ -D Trilinos_ENABLE_MOOCHO:BOOL=ON \ -D Trilinos_ENABLE_TriKota:BOOL=OFF \ -D Trilinos_ENABLE_Stokhos:BOOL=ON \ -D Trilinos_ENABLE_Zoltan:BOOL=ON \ -D Trilinos_ENABLE_Piro:BOOL=ON \ -D Trilinos_ENABLE_Teko:BOOL=ON \ -D Trilinos_ENABLE_SEACASIoss:BOOL=ON \ -D Trilinos_ENABLE_SEACAS:BOOL=ON \ -D Trilinos_ENABLE_SEACASBlot:BOOL=ON \ -D Trilinos_ENABLE_Pamgen:BOOL=ON \ -D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \ -D Trilinos_ENABLE_TESTS:BOOL=ON \ -D TPL_ENABLE_HDF5:BOOL=ON \ -D HDF5_INCLUDE_DIRS=/usr/include/hdf5 \ -D HDF5_INCLUDE_LIB=/usr/lib/x86_64-linux-gnu/hdf5/mpich \ -D Matio_LIBRARY_DIRS=/usr/lib/x86_64-linux-gnu \ -D Matio_LIBRARIES=/usr/lib/x86_64-linux-gnu/libmatio.a \ -D TPL_ENABLE_Netcdf:BOOL=ON \ -D TPL_Netcdf_Enables_Netcdf4:BOOL=ON \ -D TPL_ENABLE_MPI:BOOL=ON \ -D TPL_ENABLE_BLAS:BOOL=ON \ -D TPL_ENABLE_LAPACK:BOOL=ON \ -D TPL_ENABLE_Boost:BOOL=ON \ -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \ -D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \ -D X11_LIBRARY_DIRS=/usr/lib/X11 \ -D TPL_X11_INCLUDE_DIRS=/usr/include/X11 \ -D TPL_Netcdf_PARALLEL:BOOL=ON \ -D SEACAS_ENABLE_TESTS=ON \ ..
Here is the tail end of the output, seems it can't find X11, even though I specified where its libraries and include was...
Processing enabled TPL: X11 (enabled by SEACASSVDI, disable with -DTPL_ENABLE_X11=OFF) -- X11_LIBRARY_NAMES='X11' -- Searching for libs in X11_LIBRARY_DIRS='/usr/lib/X11' -- Searching for a lib in the set "X11": -- Searching for lib 'X11' ... -- NOTE: Did not find a lib in the lib set "X11" for the TPL 'X11'! -- ERROR: Could not find the libraries for the TPL 'X11'! -- TIP: If the TPL 'X11' is on your system then you can set: -DX11_LIBRARY_DIRS=';;...' to point to the directories where these libraries may be found. Or, just set: -DTPL_X11_LIBRARIES=';;...' to point to the full paths for the libraries which will bypass any search for libraries and these libraries will be used without question in the build. (But this will result in a build-time error if not all of the necessary symbols are found.) -- ERROR: Failed finding all of the parts of TPL 'X11' (see above), Aborting!
-- NOTE: The find module file for this failed TPL 'X11' is: /home/charles/Documents/code/Trilinos/cmake/TPLs/FindTPLX11.cmake which is pointed to in the file: /home/charles/Documents/code/Trilinos/TPLsList.cmake
TIP: One way to get past the configure failure for the TPL 'X11' is to simply disable it with: -DTPL_ENABLE_X11=OFF which will disable it and will recursively disable all of the downstream packages that have required dependencies on it, including the package 'SEACASSVDI' which triggered its enable. When you reconfigure, just grep the cmake stdout for 'X11' and then follow the disables that occur as a result to see what impact this TPL disable has on the configuration of Trilinos.
CMake Error at cmake/tribits/core/package_arch/TribitsProcessEnabledTpl.cmake:127 (MESSAGE): ERROR: TPL_X11_NOT_FOUND=TRUE, aborting! Call Stack (most recent call first): cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1659 (TRIBITS_PROCESS_ENABLED_TPL) cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:202 (TRIBITS_PROCESS_ENABLED_TPLS) cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL) CMakeLists.txt:93 (TRIBITS_PROJECT)
-- Configuring incomplete, errors occurred!
Thanks for reading!
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