ElmerGrid, add input checks when reading gmsh msh files. #548
Workflow file for this run
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| name: build | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths-ignore: | |
| - '**.nix' | |
| - 'flake.lock' | |
| pull_request: | |
| paths-ignore: | |
| - '**.nix' | |
| - 'flake.lock' | |
| concurrency: ci-ubuntu-${{ github.ref }} | |
| jobs: | |
| ubuntu: | |
| # For available GitHub-hosted runners, see: | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners | |
| runs-on: ubuntu-24.04 | |
| name: ubuntu (${{ matrix.compiler }} ${{ matrix.mpi }} MPI ${{ matrix.openmp }} OpenMP) | |
| strategy: | |
| # Allow other runners in the matrix to continue if some fail | |
| fail-fast: false | |
| matrix: | |
| compiler: [gcc] | |
| mpi: [with] | |
| openmp: [with] | |
| include: | |
| - compiler: gcc | |
| compiler-pkgs: "g++ gcc" | |
| cc: "gcc" | |
| cxx: "g++" | |
| openmp: with | |
| openmp-cmake-flags: "-DWITH_OpenMP=ON" | |
| - compiler: gcc | |
| compiler-pkgs: "g++ gcc" | |
| cc: "gcc" | |
| cxx: "g++" | |
| mpi: without | |
| openmp: with | |
| openmp-cmake-flags: "-DWITH_OpenMP=ON" | |
| - compiler: gcc | |
| compiler-pkgs: "g++ gcc" | |
| cc: "gcc" | |
| cxx: "g++" | |
| mpi: with | |
| openmp: without | |
| openmp-cmake-flags: "-DWITH_OpenMP=OFF" | |
| - compiler: clang | |
| compiler-pkgs: "clang" | |
| cc: "clang" | |
| cxx: "clang++" | |
| mpi: with | |
| openmp: without | |
| openmp-cmake-flags: "-DWITH_OpenMP=OFF" | |
| # - compiler: clang | |
| # compiler-pkgs: "clang libomp-dev" | |
| # cc: "clang" | |
| # cxx: "clang++" | |
| # mpi: with | |
| # openmp: with | |
| # openmp-cmake-flags: "-DWITH_OpenMP=ON -DOpenMP_C_FLAGS='-fopenmp=libgomp -D_OPENMP=201511' -DOpenMP_CXX_FLAGS='-fopenmp=libgomp -D_OPENMP=201511' -DOpenMP_C_LIB_NAMES='gomp;pthread' -DOpenMP_CXX_LIB_NAMES='gomp;pthread'" | |
| env: | |
| CC: ${{ matrix.cc }} | |
| CXX: ${{ matrix.cxx }} | |
| steps: | |
| - name: get CPU information | |
| run: lscpu | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: install dependencies | |
| run: | | |
| sudo apt -qq update | |
| sudo apt install -y ${{ matrix.compiler-pkgs }} cmake gfortran \ | |
| libopenblas-dev \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "libhypre-dev") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "libopenmpi-dev libmumps-dev libparmetis-dev") \ | |
| $([ "${{ matrix.compiler }}" == "gcc" ] && echo "libsuitesparse-dev") \ | |
| $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "librocalution-dev") \ | |
| libqwt-qt5-dev qtscript5-dev libqt5svg5-dev \ | |
| libvtk9-qt-dev libglvnd-dev \ | |
| occt-misc libocct-data-exchange-dev libocct-draw-dev \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "trilinos-all-dev libptscotch-dev") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "libnetcdff-dev") | |
| - name: configure | |
| # CHOLMOD and rocALUTION require a working OpenMP package. So, disable them for clang. | |
| run: | | |
| # work around error in the rocALUTION CMake config file distributed by Ubuntu | |
| if [ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ]; then | |
| sudo sed -i '/find_dependency(HIP)/d' /usr/lib/x86_64-linux-gnu/cmake/rocalution/rocalution-config.cmake | |
| fi | |
| mkdir ${GITHUB_WORKSPACE}/build | |
| cd ${GITHUB_WORKSPACE}/build | |
| cmake \ | |
| -DCMAKE_BUILD_TYPE="Release" \ | |
| -DCMAKE_INSTALL_PREFIX="${GITHUB_WORKSPACE}/usr" \ | |
| -DBLA_VENDOR="OpenBLAS" \ | |
| ${{ matrix.openmp-cmake-flags }} \ | |
| -DWITH_LUA=ON \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Zoltan=ON" || echo "-DWITH_Zoltan=OFF") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Mumps=ON" || echo "-DWITH_Mumps=OFF") \ | |
| $([ "${{ matrix.compiler }}" == "gcc" ] && echo "-DWITH_CHOLMOD=ON" || echo "-DWITH_CHOLMOD=OFF") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Hypre=ON -DHYPRE_INCLUDE_DIR=/usr/include/hypre" || echo "-DWITH_Hypre=OFF") \ | |
| $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ROCALUTION=ON" || echo "-DWITH_ROCALUTION=OFF") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ElmerIce=ON" || echo "-DWITH_ElmerIce=OFF") \ | |
| -DWITH_ELMERGUI=ON \ | |
| -DWITH_VTK=ON \ | |
| -DWITH_OCC=ON \ | |
| -DWITH_MATC=ON \ | |
| -DWITH_PARAVIEW=ON \ | |
| -DCREATE_PKGCONFIG_FILE=ON \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_MPI=ON -DMPI_TEST_MAXPROC=2 -DMPIEXEC_PREFLAGS=--allow-run-as-root" || echo "-DWITH_MPI=OFF") \ | |
| $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Trilinos=ON" || echo "-DWITH_Trilinos=OFF") \ | |
| .. | |
| - name: build | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/build | |
| cmake --build . -j$(nproc) | |
| - name: install | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/build | |
| cmake --install . | |
| - name: check | |
| id: run-ctest | |
| timeout-minutes: 150 | |
| env: | |
| CTEST_OUTPUT_ON_FAILURE: 1 | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/build | |
| ctest . \ | |
| -LE slow \ | |
| -j$(nproc) \ | |
| --timeout 300 | |
| - name: Re-run tests | |
| if: always() && (steps.run-ctest.outcome == 'failure') | |
| timeout-minutes: 60 | |
| env: | |
| CTEST_OUTPUT_ON_FAILURE: 1 | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/build | |
| # get names of failed tests and strip potential "_np*" suffix | |
| failed_tests=($(ctest . -N --rerun-failed | grep -E "Test\s+#.*" | awk '{print $3}' | sed -e 's/_np[0-9]*$//g')) | |
| # remove duplicate test names | |
| unique_failed_tests=($(echo "${failed_tests[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' ')) | |
| for test in "${unique_failed_tests[@]}"; do | |
| # check if test is from fem or ElmerIce | |
| if [ -d fem/tests/${test} ]; then | |
| test_root=fem/tests | |
| else | |
| test_root=elmerice/Tests | |
| fi | |
| echo "::group::Content of ${test_root}/${test}" | |
| echo ---- Files ---- | |
| ls -Rl ${test_root}/${test} | |
| if [ -f ${test_root}/${test}/test-stderr*.log ]; then | |
| echo ---- Content of test-stderr*.log ---- | |
| cat ${test_root}/${test}/test-stderr*.log | |
| fi | |
| if [ -f ${test_root}/${test}/test-stdout*.log ]; then | |
| echo ---- Content of test-stdout*.log ---- | |
| cat ${test_root}/${test}/test-stdout*.log | |
| fi | |
| echo "::endgroup::" | |
| done | |
| echo "::group::Re-run failing tests" | |
| ctest --rerun-failed --output-on-failure --timeout 180 || true | |
| echo "::endgroup::" | |
| echo "::group::Log from these tests" | |
| [ ! -f Testing/Temporary/LastTest.log ] || cat Testing/Temporary/LastTest.log | |
| echo "::endgroup::" |