Adds HDF5 option to use subfiling #1089
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| concurrency: | |
| group: ${ {github.event_name }}-${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{github.event_name == 'pull_request'}} | |
| jobs: | |
| CI: | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| CCACHE_DIR: "${{ github.workspace }}/.ccache" | |
| CCACHE_MAXSIZE: "10G" | |
| CCACHE_CPP2: "true" | |
| ASAN_OPTIONS: "detect_leaks=0" | |
| strategy: | |
| matrix: | |
| distro: ['ubuntu:latest'] | |
| cxx: ['g++', 'clang++'] | |
| backend: ['OPENMP', 'SERIAL'] | |
| cmake_build_type: ['Debug', 'Release'] | |
| kokkos_ver: ['3.6.01'] | |
| bounds_check: ['OFF'] | |
| arborx: ['OFF'] | |
| heffte: ['OFF' ] | |
| hypre: ['OFF'] | |
| liball: ['OFF'] | |
| silo: ['OFF'] | |
| hdf5: ['OFF'] | |
| coverage: ['OFF'] | |
| include: | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'THREADS' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.7.00' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| silo: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:intel' | |
| cxx: 'icpx' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:intel' | |
| cxx: 'icpx' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:intel' | |
| cxx: 'icpx' | |
| backend: 'SERIAL' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:intel' | |
| cxx: 'icpx' | |
| backend: 'SERIAL' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:intel' | |
| cxx: 'icpx' | |
| backend: 'SERIAL' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'MKL' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '4.0.00' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| doxygen: 'ON' | |
| - distro: 'fedora:latest' | |
| cxx: 'clang++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '4.0.00' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'opensuse:latest' | |
| cxx: 'g++' | |
| cmake_build_type: 'Release' | |
| backend: 'OPENMP' | |
| kokkos_ver: '4.0.00' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'opensuse:latest' | |
| cxx: 'clang++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '4.0.00' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| hdf5: 'HDF5' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:rolling' | |
| cxx: 'g++' | |
| cmake_build_type: 'Release' | |
| backend: 'OPENMP' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:rolling' | |
| cxx: 'clang++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'fedora:nompi' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '4.0.00' | |
| arborx: 'ArborX' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'ArborX' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'FFTW' | |
| hypre: 'OFF' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Release' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| liball: 'libALL' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'HYPRE' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| silo: 'Silo' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'OFF' | |
| heffte: 'OFF' | |
| hypre: 'OFF' | |
| hdf5: 'HDF5' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'ArborX' | |
| heffte: 'FFTW' | |
| hypre: 'HYPRE' | |
| liball: 'libALL' | |
| silo: 'Silo' | |
| hdf5: 'HDF5' | |
| bounds_check: 'BoundsCheck' | |
| coverage: 'OFF' | |
| - distro: 'ubuntu:latest' | |
| cxx: 'g++' | |
| backend: 'OPENMP' | |
| cmake_build_type: 'Debug' | |
| kokkos_ver: '3.6.01' | |
| arborx: 'ArborX' | |
| heffte: 'FFTW' | |
| hypre: 'HYPRE' | |
| liball: 'libALL' | |
| silo: 'Silo' | |
| hdf5: 'HDF5' | |
| coverage: 'ON' | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: ghcr.io/ecp-copa/ci-containers/${{ matrix.distro }} | |
| options: --security-opt seccomp=unconfined | |
| steps: | |
| - name: Cache ccache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.CCACHE_DIR }} | |
| key: ccache-${{ matrix.distro }}-${{github.run_id}} | |
| restore-keys: ccache-${{ matrix.distro }} | |
| - name: Zero ccache stats | |
| run: | | |
| ccache -z | |
| - name: Checkout kokkos | |
| uses: actions/[email protected] | |
| with: | |
| repository: kokkos/kokkos | |
| ref: ${{ matrix.kokkos_ver }} | |
| path: kokkos | |
| - name: Build kokkos | |
| env: | |
| BOUNDS: ${{ matrix.bounds_check }} | |
| working-directory: kokkos | |
| run: | | |
| [[ ${{ matrix.backend }} == "OPENMP" ]] && kokkos_cmake_opts+=( -DKokkos_ENABLE_OPENMP==ON ) | |
| [[ ${{ matrix.backend }} == "THREADS" ]] && kokkos_cmake_opts+=( -DKokkos_ENABLE_THREADS==ON ) | |
| [[ ${BOUNDS} == "BoundsCheck" ]] && kokkos_cmake_opts+=( -DKokkos_ENABLE_DEBUG_BOUNDS_CHECK=ON ) | |
| cmake -B build \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/kokkos \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
| -DKokkos_ENABLE_HWLOC=ON \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} \ | |
| ${kokkos_cmake_opts[@]} | |
| cmake --build build --parallel 2 | |
| cmake --install build | |
| - name: Checkout arborx | |
| if: ${{ matrix.arborx == 'ArborX' }} | |
| uses: actions/[email protected] | |
| with: | |
| repository: arborx/ArborX | |
| ref: v1.2 | |
| path: arborx | |
| - name: Build arborx | |
| if: ${{ matrix.arborx == 'ArborX' }} | |
| working-directory: arborx | |
| run: | | |
| cmake -B build \ | |
| -DKokkos_ROOT=${HOME}/kokkos \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/arborx \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} | |
| cmake --build build --parallel 2 | |
| cmake --install build | |
| - name: Checkout heffte | |
| if: ${{ matrix.heffte != 'OFF' }} | |
| # actions/checkout doesn't work for external repos yet (actions/checkout#447) | |
| run: | | |
| git clone --depth 1 --branch v2.1.0 https://bitbucket.org/icl/heffte.git heffte | |
| - name: Build heffte | |
| if: ${{ matrix.heffte != 'OFF' }} | |
| working-directory: heffte | |
| run: | | |
| [[ ${{ matrix.heffte }} == "FFTW" ]] && heffte_cmake_opts+=( -DHeffte_ENABLE_FFTW=ON ) | |
| [[ ${{ matrix.heffte }} == "MKL" ]] && heffte_cmake_opts+=( -DHeffte_ENABLE_MKL=ON ) | |
| # FIXME: Remove MKL path below when we update heFFTe | |
| cmake -B build \ | |
| -DBUILD_SHARED_LIBS=ON \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/heffte \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} \ | |
| -DMKL_ROOT=/opt/intel/oneapi/mkl/latest \ | |
| -DHeffte_MKL_IOMP5=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin/libiomp5.so \ | |
| ${heffte_cmake_opts[@]} | |
| cmake --build build --parallel 2 | |
| cmake --install build | |
| - name: Checkout hypre | |
| if: ${{ matrix.hypre == 'HYPRE' }} | |
| uses: actions/[email protected] | |
| with: | |
| repository: hypre-space/hypre | |
| ref: v2.22.1 | |
| path: hypre | |
| - name: Build hypre | |
| if: ${{ matrix.hypre == 'HYPRE' }} | |
| working-directory: hypre/src | |
| run: | | |
| [[ ${{ matrix.backend }} == 'OPENMP' ]] && hypre_cmake_opts+=( -DHYPRE_WITH_OPENMP=ON ) | |
| cmake -B build \ | |
| -DHYPRE_INSTALL_PREFIX=$HOME/hypre \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} \ | |
| -DHYPRE_WITH_MPI=ON \ | |
| ${hypre_cmake_opts[@]} | |
| cmake --build build --parallel 2 | |
| cmake --install build | |
| - name: Checkout ALL | |
| if: ${{ matrix.liball == 'libALL' }} | |
| run: | | |
| git clone --depth 1 --branch v0.9.2 https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing ALL | |
| - name: Build ALL | |
| if: ${{ matrix.liball == 'libALL' }} | |
| working-directory: ALL | |
| run: | | |
| cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/ALL | |
| cmake --build build --parallel 2 | |
| cmake --install build | |
| - name: Checkout Cabana | |
| uses: actions/[email protected] | |
| - name: Build Cabana | |
| env: | |
| SANITIZER: ${{ matrix.sanitizer }} | |
| SILO: ${{ matrix.silo }} | |
| HDF5: ${{ matrix.hdf5 }} | |
| run: | | |
| if [[ ${SILO} == 'Silo' ]]; then | |
| cabana_cmake_opts+=( -DCabana_REQUIRE_SILO=ON ) | |
| else | |
| cabana_cmake_opts+=( -DCMAKE_DISABLE_FIND_PACKAGE_SILO=ON ) | |
| fi | |
| if [[ ${HDF5} == 'HDF5' ]]; then | |
| cabana_cmake_opts+=( -DCabana_REQUIRE_HDF5=ON ) | |
| else | |
| cabana_cmake_opts+=( -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON ) | |
| fi | |
| # FIXME: Add sanitizer for fedora when fixed | |
| if [[ ${SANITIZER} == 'MSAN' ]]; then | |
| cabana_cmake_opts+=( -DWITH_MSAN=ON ) | |
| elif [[ ${{ matrix.distro }} != *"fedora"* ]]; then | |
| cabana_cmake_opts+=( -DWITH_ASAN=ON ) | |
| fi | |
| #FIXME: Run valgrind for all builds once fixed/suppressed | |
| [[ ${{ matrix.distro }} == 'ubuntu:latest' || ${{ matrix.distro }} == 'ubuntu:rolling' || ${{ matrix.backend }} == OPENMP || ${{ matrix.cmake_build_type }} == Release ]] && cabana_cmake_opts+=( -DVALGRIND_EXECUTABLE=False ) | |
| cmake -B build \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/Cabana \ | |
| -DMPIEXEC_MAX_NUMPROCS=2 -DMPIEXEC_PREFLAGS="--oversubscribe" \ | |
| -DCMAKE_PREFIX_PATH="$HOME/kokkos;$HOME/arborx;$HOME/heffte;$HOME/hypre;$HOME/ALL" \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
| -DCMAKE_CXX_FLAGS="-Wall -Wextra -pedantic -Werror $([[ ${{ matrix.cxx }} == icpx ]] && echo -DCMAKE_CXX_FLAGS_DEBUG="-g -O0")" \ | |
| -DCabana_ENABLE_TESTING=ON \ | |
| -DCabana_ENABLE_EXAMPLES=ON \ | |
| -DCabana_ENABLE_PERFORMANCE_TESTING=ON \ | |
| -DCabana_PERFORMANCE_EXPECTED_FLOPS=0 \ | |
| -DCabana_ENABLE_COVERAGE_BUILD=${{ matrix.coverage }} \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} \ | |
| -DDOXYGEN_WARN_AS_ERROR=FAIL_ON_WARNINGS \ | |
| ${cabana_cmake_opts[@]} | |
| cmake --build build --parallel 2 --verbose | |
| CTEST_OUTPUT_ON_FAILURE=1 cmake --build build --target test | |
| cmake --install build | |
| - name: Test Cabana Export Target | |
| working-directory: example/core_tutorial/01_hello_world | |
| run: | | |
| cmake -B build \ | |
| -DCMAKE_PREFIX_PATH="$HOME/kokkos;$HOME/arborx;$HOME/heffte;$HOME/hypre;$HOME/Cabana" \ | |
| -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} | |
| cmake --build build | |
| - name: Build Doxygen | |
| if: ${{ matrix.doxygen == 'ON' }} | |
| run: cmake --build build --target doxygen | |
| - name: Show ccache stats | |
| run: | | |
| ccache -s | |
| - name: Upload Report to codecov.io | |
| if: ${{ matrix.coverage == 'ON' }} | |
| uses: codecov/codecov-action@v1 | |
| - name: Checkout gh-pages | |
| if: ${{ matrix.doxygen == 'ON' }} | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: 'gh-pages' | |
| path: 'html' | |
| - name: update and commit to gh-pages branch | |
| if: ${{ matrix.doxygen == 'ON' }} | |
| working-directory: html | |
| run: | | |
| rm -rf doxygen | |
| mv ../build/html doxygen | |
| git config --global user.name "Automatic Deployment (GitHub Action)"; | |
| git config --global user.email "[email protected]" | |
| git add --all | |
| git diff --quiet HEAD || git commit -m "Documentation Update" | |
| if [[ "${GITHUB_REF}" == 'refs/heads/master' ]]; then | |
| git push | |
| else | |
| git show | |
| fi |