Merge branch 'master' into catalyst_api_2_structured_blocks

Conflicts: packages/seacas/libraries/ioss/src/catalyst/Iocatalyst_DatabaseIO.C
sandialabs · Jan 3, 2024 · b709940 · b709940
2 parents bcee062 + 9f9ac60
commit b709940
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diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml
@@ -23,7 +23,7 @@ jobs:
         compiler: [ gnu, clang, mpi ]
         hdf5: [ V18, V110, V114 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - uses: actions/checkout@v3
@@ -40,7 +40,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         if: steps.cache-TPL.outputs.cache-hit != 'true'
@@ -64,7 +64,7 @@ jobs:
         compiler: [ gnu, clang, mpi ]
         hdf5: [ V18, V110, V114 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - uses: actions/checkout@v3
@@ -78,7 +78,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Check Cache
         shell: bash -l {0}

diff --git a/.github/workflows/build_variant.yml b/.github/workflows/build_variant.yml
@@ -24,7 +24,7 @@ jobs:
         compiler: [ gnu, clang, mpi ]
         hdf5: [ V110 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - uses: actions/checkout@v3
@@ -41,7 +41,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         if: steps.cache-TPL.outputs.cache-hit != 'true'
@@ -62,7 +62,7 @@ jobs:
       matrix:
         hdf5: [ V110 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
         config:
         - {
             name: "Debug serial build",
@@ -317,7 +317,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v4-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Check Cache
         shell: bash -l {0}

diff --git a/.github/workflows/coverity-scan.yml b/.github/workflows/coverity-scan.yml
@@ -14,7 +14,7 @@ jobs:
         compiler: [ gnu ]
         hdf5: [ V110 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - uses: actions/checkout@v3
@@ -31,7 +31,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         if: steps.cache-TPL.outputs.cache-hit != 'true'
@@ -55,7 +55,7 @@ jobs:
         compiler: [ gnu ]
         hdf5: [ V110 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - uses: actions/checkout@v3
@@ -69,7 +69,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v1-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Check Cache
         shell: bash -l {0}

diff --git a/.github/workflows/intel-build.yml b/.github/workflows/intel-build.yml
@@ -23,7 +23,7 @@ jobs:
         compiler: [ intel, mpi ]
         hdf5: [ V114 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
 
     defaults:
       run:
@@ -67,7 +67,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-        key: TPL-v5intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+        key: TPL-v2intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
     - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
       if: steps.cache-TPL.outputs.cache-hit != 'true'
@@ -89,7 +89,7 @@ jobs:
         compiler: [ intel, mpi ]
         hdf5: [ V114 ]
         netcdf: [ 4.9.2 ]
-        cgns: [ 4.3.0 ]
+        cgns: [ 4.4.0 ]
     steps:
 
       - name: Maximize build space
@@ -126,7 +126,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v5intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
+          key: TPL-v2intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
 
       - name: Check Cache
         shell: bash -l {0}
@@ -149,6 +149,13 @@ jobs:
           mkdir build
           cd build
           source /opt/intel/oneapi/setvars.sh
+          echo "------------"
+          ls /opt/intel/oneapi/2024.0/
+          echo "------------"
+          ls /opt/intel/oneapi/2024.0/bin/
+          echo "------------"
+          export PATH=/opt/intel/oneapi/2024.0/bin/:$PATH
+          export LD_LIBRARY_PATH=/opt/intel/oneapi/2024.0/lib/:$LD_LIBRARY_PATH
           printenv >> $GITHUB_ENV
           NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config
 

diff --git a/README.md b/README.md
@@ -49,7 +49,8 @@ libraries using the `install-tpl.sh` script, or you can install them
 manually as detailed in
 [TPL-Manual-Install.md](TPL-Manual-Install.md).
 
-*  To use the script, simply type `./install-tpl.sh`
+*  The script requires bash and wget, which you may need to install.
+*  To use the script, simply type `bash ./install-tpl.sh`.
 *  The default behavior can be modified via a few environment variables:
 
 | Variable        | Values          | Default | Description |
@@ -77,7 +78,8 @@ manually as detailed in
 | KOKKOS          | YES, NO | NO  | Should Kokkos TPL be built. |
 | GNU_PARALLEL    | YES, NO | YES | Should GNU parallel script be built. |
 | FMT             | YES, NO | YES | Should Lib::FMT TPL be built. |
-| H5VERSION       | V114, V110, V18 | V110 | Use HDF5-1.14.X, HDF5-1.10.X or HDF5-1.8.X |
+| H5VERSION       | V114, V110, V18 | V114 | Use HDF5-1.14.X, HDF5-1.10.X or HDF5-1.8.X |
+| H5CPP           | YES, NO | NO  | Should the HDF5 C++ library be built/installed |
 | BB              | YES, NO | NO  | Enable Burst Buffer support in PnetCDF |
 | JOBS            | {count} |  2   | Number of "jobs" used for simultaneous compiles |
 | SUDO            | "" or sudo | "" | If need to be superuser to install |
@@ -92,7 +94,7 @@ to configure the SEACAS CMake build.
 *  `cd $ACCESS`
 *  `mkdir build`
 *  `cd build`
-*  edit the `${ACCESS}cmake-config` file and adjust compilers and other settings as needed.
+*  edit the `${ACCESS}/cmake-config` file and adjust compilers and other settings as needed.
 *  enter the command `../cmake-config` and cmake should configure everything for the build.
 *  `make && make install`
 *  If everything works, your applications should be in `${ACCESS}/bin`
@@ -284,7 +286,7 @@ in aprepro.
 ### Mac
 On a mac system, I use the `brew` system which provides all of the
 applications listed above.  The X11 system I use is `XQuartz`.  The
-Mac also requires `XCode`
+Mac also requires `Xcode`
 
 ### Linux
 On an ubuntu system, the following is used to set up the basic

diff --git a/TPL/hdf5/runcmake.sh b/TPL/hdf5/runcmake.sh
@@ -7,8 +7,6 @@ if [ "X$ACCESS" == "X" ] ; then
 fi
 INSTALL_PATH=${INSTALL_PATH:-${ACCESS}}
 
-H5VERSION=${H5VERSION:-V110}
-
 DEBUG="${DEBUG:-NO}"
 if [ "$DEBUG" == "YES" ]
 then
@@ -65,7 +63,7 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
 	 -DDEFAULT_API_VERSION=V18 \
 	 -DHDF5_ENABLE_PARALLEL:BOOL=${MPI} \
 	 -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
-	 -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
+	 -DHDF5_BUILD_CPP_LIB:BOOL=${H5CPP} \
 	 -DHDF5_BUILD_FORTRAN:BOOL=OFF \
 	 -DHDF5_BUILD_HL_LIB:BOOL=ON \
 	 -DHDF5_DISABLE_COMPILER_WARNINGS:BOOL=ON \

diff --git a/TPL/netcdf/runcmake.sh b/TPL/netcdf/runcmake.sh
@@ -66,6 +66,7 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          -DENABLE_CDF5=ON \
          -DENABLE_MMAP:BOOL=ON \
          -DENABLE_DAP:BOOL=OFF \
+         -DENABLE_BYTERANGE:BOOL=OFF \
          -DENABLE_V2_API:BOOL=OFF \
 	 -DENABLE_FILTER_TESTING:BOOL=OFF \
 	 -DENABLE_TESTS:BOOL=OFF \

diff --git a/cmake-config b/cmake-config
@@ -160,11 +160,11 @@ then
 
   if [ "$COMPILER" == "intel" ]
   then
-      CXX=icpc
-      CC=icc
-      FC=ifort
+      CXX=icpx
+      CC=icx
+      FC=ifx
       CFLAGS="-Wall -Wunused"
-      CXXFLAGS="-Wall -Wextra  -Wunused"
+      CXXFLAGS="-Wall -Wextra  -Wunused -DFMT_HEADER_ONLY"
   fi
 
   # When building:  "scan-build make -j8"
@@ -555,6 +555,7 @@ echo "        CXX: ${CXX}"
 echo "         FC: ${FC}"
 echo "        MPI: ${MPI}"
 echo "     SHARED: ${SHARED}"
+echo "    FORTRAN: ${FORTRAN}"
 echo " BUILD_TYPE: ${BUILD_TYPE}"
 echo " THREADSAFE: ${THREADSAFE}"
 echo "       CRAY: ${CRAY}"

diff --git a/install-tpl.sh b/install-tpl.sh
@@ -123,6 +123,9 @@ KOKKOS=${KOKKOS:-NO}
 KOKKOS=$(check_valid KOKKOS)
 
 H5VERSION=${H5VERSION:-V114}
+# Build/Install the HDF5 C++ library?
+H5CPP=${H5CPP:-NO}
+H5CPP=$(check_valid H5CPP)
 
 FAODEL=${FAODEL:-NO}
 FAODEL=$(check_valid FAODEL)
@@ -200,6 +203,7 @@ if [ $# -gt 0 ]; then
         echo "   PNETCDF      = ${PNETCDF}"
         echo "   HDF5         = ${HDF5}"
         echo "   H5VERSION    = ${H5VERSION}"
+        echo "   H5CPP        = ${H5CPP}"
         echo "   CGNS         = ${CGNS}"
         echo "   MATIO        = ${MATIO}"
         echo "   METIS        = ${METIS}"
@@ -423,7 +427,7 @@ then
             hdf_version="1.13.1"
             hdf_base="1.13"
 	elif [ "${H5VERSION}" == "V114" ]; then
-            hdf_version="1.14.2"
+            hdf_version="1.14.3"
             hdf_base="1.14"
 	    hdf_suffix=""
 	elif [ "${H5VERSION}" == "develop" ]; then
@@ -459,7 +463,7 @@ then
             rm -rf build
             mkdir build
             cd build || exit
-            CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash -x ../../runcmake.sh
+            CRAY=${CRAY} H5CPP=${H5CPP} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash -x ../../runcmake.sh
             #CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash ../runconfigure.sh
             if [[ $? != 0 ]]
             then
@@ -604,7 +608,7 @@ then
         then
             echo "${txtgrn}+++ Configuring, Building, and Installing...${txtrst}"
             cd CGNS || exit
-            git checkout v4.3.0
+            git checkout v4.4.0
             rm -rf build
             mkdir build
             cd build || exit
@@ -719,7 +723,7 @@ then
     check_exec automake
     check_exec autoconf
 
-    matio_version="1.5.23"
+    matio_version="v1.5.26"
     if [ "$FORCE" == "YES" ] || ! [ -e $INSTALL_PATH/lib/libmatio.${LD_EXT} ]
     then
         echo "${txtgrn}+++ MatIO${txtrst}"
@@ -766,7 +770,7 @@ then
         echo "${txtgrn}+++ FMT${txtrst}"
         cd $ACCESS || exit
         cd TPL/fmt || exit
-        fmt_version="10.1.0"
+        fmt_version="10.2.0"
 
         if [ "$DOWNLOAD" == "YES" ]
         then

diff --git a/packages/seacas/Jamfile b/packages/seacas/Jamfile
@@ -1508,6 +1508,7 @@ exe slice
     ioinit
   : <include>$(seacas-root)/applications/slice
     <define>USE_METIS
+    <define>USE_ZOLTAN
     <tag>@utility-exec-tag
   ;