Merge pull request #1687 from IBAMR/mass_loss_redux #2
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| ## --------------------------------------------------------------------- | |
| ## | |
| ## Copyright (c) 2021 - 2021 by the IBAMR developers | |
| ## All rights reserved. | |
| ## | |
| ## This file is part of IBAMR. | |
| ## | |
| ## IBAMR is free software and is distributed under the 3-clause BSD | |
| ## license. The full text of the license can be found in the file | |
| ## COPYRIGHT at the top level directory of IBAMR. | |
| ## | |
| ## --------------------------------------------------------------------- | |
| name: Pull/push | |
| on: | |
| # Trigger the workflow on push or pull request, | |
| # but only when targeting the main branch | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| # build IBAMR with CMake and run tests | |
| build_ibamr: | |
| runs-on: ubuntu-latest | |
| name: Build IBAMR and run tests | |
| container: | |
| image: 'docker://wellsd2/ibamr:ibamr-0.14-bundled-deps' | |
| env: | |
| # For now, hardwire the configuration since we have only one. | |
| # This is used by ctest_configure.cmake to initialize the | |
| # CMake cache by including | |
| # `.github/cmake/configure_${CMAKE_CONFIGURATION}.cmake` | |
| # so it is possible to run the same container with different | |
| # values to build different configurations (e.g., release vs | |
| # debug, with/without in situ processing, static analysis). | |
| CMAKE_CONFIGURATION: fedora33 | |
| # If this variable is set, cause any build warnings to | |
| # be treated as an error (causing the build to fail before | |
| # testing and preventing merging). | |
| CTEST_NO_WARNINGS_ALLOWED: true | |
| # Delete old files in the cache (10G, the default limit, is GitHub's limit | |
| # for all cached artifacts) | |
| CCACHE_MAXSIZE: 250M | |
| CMAKE_GENERATOR: Unix Makefiles | |
| steps: | |
| - name: Checkout Source | |
| uses: actions/checkout@v3 | |
| id: git | |
| - name: Verify that clang-format was run | |
| id: format | |
| run: | | |
| git config --global --add safe.directory '*' | |
| ./scripts/formatting/download-clang-format | |
| ./scripts/formatting/check-indentation | |
| - name: Create keys | |
| id: keys | |
| run: | | |
| echo "key1=$(( ${{ github.run_number }} - 1))" >> $GITHUB_ENV | |
| echo "key2=$(( ${{ github.run_number }} - 2))" >> $GITHUB_ENV | |
| echo "key3=$(( ${{ github.run_number }} - 3))" >> $GITHUB_ENV | |
| echo "key4=$(( ${{ github.run_number }} - 4))" >> $GITHUB_ENV | |
| echo "key5=$(( ${{ github.run_number }} - 5))" >> $GITHUB_ENV | |
| - name: Populate ccache | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: ccache | |
| id: cache | |
| with: | |
| path: ~/.cache/ccache | |
| # A fundamental problem with the cache is that it is identified by a | |
| # single key and, should a cache with that key already exist, the | |
| # cache will not be updated. This makes sense for things like NPM but | |
| # not so much for ccache, since we get a new and unique cache each | |
| # time we rebuild the library with a new branch. | |
| # | |
| # To get around this, always make the key unique and rely on | |
| # restore-keys to find the highest-indexed key available. Explicitly | |
| # try to restore things from the most recent builds. | |
| key: ${{ runner.os }}-build-cmake-libmesh-${{ github.run_number }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-cmake-libmesh-${{ env.key1 }} | |
| ${{ runner.os }}-build-cmake-libmesh-${{ env.key2 }} | |
| ${{ runner.os }}-build-cmake-libmesh-${{ env.key3 }} | |
| ${{ runner.os }}-build-cmake-libmesh-${{ env.key4 }} | |
| ${{ runner.os }}-build-cmake-libmesh-${{ env.key5 }} | |
| ${{ runner.os }}-build-cmake-libmesh- | |
| ${{ runner.os }}-build-cmake | |
| - name: Configure IBAMR | |
| id: configure | |
| run: | | |
| # HDF5 is installed in a weird way on Fedora - since we aren't using | |
| # modules we have to intervene manually | |
| pushd ../ | |
| mkdir -p hdf5-shim | |
| ln -s /usr/include/mpich-x86_64 hdf5-shim/include | |
| ln -s /usr/lib64/mpich/lib hdf5-shim/lib | |
| export HDF5_ROOT=$(pwd)/hdf5-shim | |
| popd | |
| # If configuration fails we still want to save the output files: | |
| set +e | |
| bash -c "ctest -VV -S .github/cmake/ctest_configure.cmake" | |
| configure_status=$? | |
| set -e | |
| # The directory /build/ibamr is hardcoded in cmake/github_ci.cmake | |
| # | |
| # Archive doesn't like absolute paths to files so dump everything in ~/ | |
| find /build -name CMakeConfigureLog.yaml -exec cp {} ./ \; | |
| ccache --show-stats | |
| exit $configure_status | |
| - name: Archive CMakeConfigureLog.yaml | |
| if: always() | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: fedora33-CMakeError.log | |
| path: CMakeConfigureLog.yaml | |
| - name: Compile IBAMR | |
| id: build | |
| run: | | |
| cd /build/ibamr | |
| make -j2 tests examples | |
| ccache --show-stats | |
| - name: Test IBAMR | |
| id: test | |
| run: | | |
| bash -c "ctest --output-on-failure -VV -S .github/cmake/ctest_test.cmake" | |
| ccache --show-stats | |
| # build IBAMR with CMake, no libMesh, and run tests | |
| build_ibamr_no_libmesh: | |
| runs-on: ubuntu-latest | |
| name: Build IBAMR and run tests (no libMesh) | |
| container: | |
| image: 'docker://wellsd2/ibamr:ibamr-0.14-bundled-deps' | |
| env: | |
| CMAKE_CONFIGURATION: fedora33_no_libmesh | |
| # If this variable is set, cause any build warnings to | |
| # be treated as an error (causing the build to fail before | |
| # testing and preventing merging). | |
| CTEST_NO_WARNINGS_ALLOWED: true | |
| # Delete old files in the cache (10G, the default limit, is GitHub's limit | |
| # for all cached artifacts) | |
| CCACHE_MAXSIZE: 250M | |
| CMAKE_GENERATOR: Unix Makefiles | |
| steps: | |
| - name: Checkout Source | |
| uses: actions/checkout@v3 | |
| id: git | |
| - name: Verify that clang-format was run | |
| id: format | |
| run: | | |
| git config --global --add safe.directory '*' | |
| ./scripts/formatting/download-clang-format | |
| ./scripts/formatting/check-indentation | |
| - name: Create keys | |
| id: keys | |
| run: | | |
| echo "key1=$(( ${{ github.run_number }} - 1))" >> $GITHUB_ENV | |
| echo "key2=$(( ${{ github.run_number }} - 2))" >> $GITHUB_ENV | |
| echo "key3=$(( ${{ github.run_number }} - 3))" >> $GITHUB_ENV | |
| echo "key4=$(( ${{ github.run_number }} - 4))" >> $GITHUB_ENV | |
| echo "key5=$(( ${{ github.run_number }} - 5))" >> $GITHUB_ENV | |
| - name: Populate ccache | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: ccache | |
| id: cache | |
| with: | |
| path: ~/.cache/ccache | |
| key: ${{ runner.os }}-build-cmake-no-libmesh-${{ github.run_number }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-cmake-no-libmesh-${{ env.key1 }} | |
| ${{ runner.os }}-build-cmake-no-libmesh-${{ env.key2 }} | |
| ${{ runner.os }}-build-cmake-no-libmesh-${{ env.key3 }} | |
| ${{ runner.os }}-build-cmake-no-libmesh-${{ env.key4 }} | |
| ${{ runner.os }}-build-cmake-no-libmesh-${{ env.key5 }} | |
| ${{ runner.os }}-build-cmake-no-libmesh- | |
| - name: Configure IBAMR | |
| id: configure | |
| run: | | |
| # HDF5 is installed in a weird way on Fedora - since we aren't using | |
| # modules we have to intervene manually | |
| pushd ../ | |
| mkdir -p hdf5-shim | |
| ln -s /usr/include/mpich-x86_64 hdf5-shim/include | |
| ln -s /usr/lib64/mpich/lib hdf5-shim/lib | |
| export HDF5_ROOT=$(pwd)/hdf5-shim | |
| popd | |
| bash -c "ctest -VV -S .github/cmake/ctest_configure.cmake" | |
| ccache --show-stats | |
| - name: Compile IBAMR | |
| id: build | |
| run: | | |
| cd /build/ibamr | |
| make -j2 tests | |
| ccache --show-stats | |
| - name: Test IBAMR | |
| id: test | |
| run: | | |
| bash -c "ctest --output-on-failure -VV -S .github/cmake/ctest_test.cmake" | |
| - name: Compile IBAMR examples | |
| id: examples | |
| run: | | |
| cd /build/ibamr | |
| make -j2 examples | |
| ccache --show-stats | |
| # build IBAMR with autotools | |
| build_ibamr_autotools: | |
| runs-on: ubuntu-latest | |
| name: Build IBAMR (autotools) | |
| container: | |
| image: 'docker://wellsd2/ibamr:ibamr-0.14-bundled-deps' | |
| env: | |
| # Delete old files in the cache (10G, the default limit, is GitHub's limit | |
| # for all cached artifacts) | |
| CCACHE_MAXSIZE: 250M | |
| CMAKE_GENERATOR: Unix Makefiles | |
| steps: | |
| - name: Checkout Source | |
| uses: actions/checkout@v3 | |
| id: git | |
| - name: Verify that clang-format was run | |
| id: format | |
| run: | | |
| git config --global --add safe.directory '*' | |
| ./scripts/formatting/download-clang-format | |
| ./scripts/formatting/check-indentation | |
| - name: Create keys | |
| id: keys | |
| run: | | |
| echo "key1=$(( ${{ github.run_number }} - 1))" >> $GITHUB_ENV | |
| echo "key2=$(( ${{ github.run_number }} - 2))" >> $GITHUB_ENV | |
| echo "key3=$(( ${{ github.run_number }} - 3))" >> $GITHUB_ENV | |
| echo "key4=$(( ${{ github.run_number }} - 4))" >> $GITHUB_ENV | |
| echo "key5=$(( ${{ github.run_number }} - 5))" >> $GITHUB_ENV | |
| - name: Populate ccache | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: ccache | |
| id: cache | |
| with: | |
| path: ~/.cache/ccache | |
| # The same note on picking keys above applies here. | |
| key: ${{ runner.os }}-build-autotools-${{ github.run_number }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-autotools-${{ env.key1 }} | |
| ${{ runner.os }}-build-autotools-${{ env.key2 }} | |
| ${{ runner.os }}-build-autotools-${{ env.key3 }} | |
| ${{ runner.os }}-build-autotools-${{ env.key4 }} | |
| ${{ runner.os }}-build-autotools-${{ env.key5 }} | |
| ${{ runner.os }}-build-autotools- | |
| - name: Configure IBAMR (autotools) | |
| id: configure | |
| run: | | |
| source /etc/profile.d/modules.sh | |
| module load mpi | |
| export CC="ccache $(which mpicc)" | |
| export CXX="ccache $(which mpic++)" | |
| # we are just compiling things so go for speed | |
| export CFLAGS="-O0" | |
| export CXXFLAGS="-O0" | |
| export FFLAGS="-O0" | |
| mkdir build | |
| cd build | |
| ../configure PETSC_DIR=/petsc/ --with-samrai=/samrai \ | |
| --enable-libmesh --with-libmesh=/libmesh --with-libmesh-method=opt | |
| ccache --show-stats | |
| - name: archive | |
| if: always() | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: autotools-config.log | |
| path: build/config.log | |
| - name: Compile IBAMR (autotools) | |
| id: build | |
| run: | | |
| source /etc/profile.d/modules.sh | |
| module load mpi | |
| export CC="ccache $(which mpicc)" | |
| export CXX="ccache $(which mpic++)" | |
| echo "CC=${CC}" | |
| echo "CXX=${CXX}" | |
| cd build | |
| make -j2 tests examples | |
| ccache --show-stats | |
| # build IBAMR with CMake and run tests with our oldest dependencies on CENTOS 7 | |
| build_ibamr_centos: | |
| runs-on: ubuntu-latest | |
| name: Build IBAMR and run tests (CENTOS 7) | |
| container: | |
| image: 'docker://wellsd2/ibamr:ibamr-0.14-oldest-bundled-deps' | |
| env: | |
| CMAKE_CONFIGURATION: centos7 | |
| CTEST_NO_WARNINGS_ALLOWED: true | |
| CCACHE_MAXSIZE: 250M | |
| CMAKE_GENERATOR: Unix Makefiles | |
| steps: | |
| - name: Checkout Source | |
| uses: actions/checkout@v3 | |
| id: git | |
| # The version of git on centos is too old for our git script so skip that | |
| - name: Create keys | |
| id: keys | |
| run: | | |
| echo "key1=$(( ${{ github.run_number }} - 1))" >> $GITHUB_ENV | |
| echo "key2=$(( ${{ github.run_number }} - 2))" >> $GITHUB_ENV | |
| echo "key3=$(( ${{ github.run_number }} - 3))" >> $GITHUB_ENV | |
| echo "key4=$(( ${{ github.run_number }} - 4))" >> $GITHUB_ENV | |
| echo "key5=$(( ${{ github.run_number }} - 5))" >> $GITHUB_ENV | |
| - name: Populate ccache | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: ccache | |
| id: cache | |
| with: | |
| path: ~/.ccache/ | |
| key: ${{ runner.os }}-build-centos-cmake-${{ github.run_number }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-centos-cmake-${{ env.key1 }} | |
| ${{ runner.os }}-build-centos-cmake-${{ env.key2 }} | |
| ${{ runner.os }}-build-centos-cmake-${{ env.key3 }} | |
| ${{ runner.os }}-build-centos-cmake-${{ env.key4 }} | |
| ${{ runner.os }}-build-centos-cmake-${{ env.key5 }} | |
| ${{ runner.os }}-build-centos-cmake- | |
| - name: Configure IBAMR | |
| id: configure | |
| run: | | |
| # Don't bother with MPI/HDF5 paths and just let module handle it | |
| bash -c "source /etc/profile.d/modules.sh && module load mpi && ctest3 -VV -S .github/cmake/ctest_configure.cmake" | |
| ccache --show-stats | |
| - name: Compile IBAMR | |
| id: build | |
| run: | | |
| cd /build/ibamr | |
| # compile examples which depend on libMesh to verify that they still work with libMesh 1.1.0 | |
| make -j2 tests examples-IBFE examples-IBLevelSet examples-IIM examples-IMP examples-complex_fluids examples-fe_mechanics | |
| ccache --show-stats | |
| - name: Test IBAMR | |
| id: test | |
| run: | | |
| bash -c "ctest3 --output-on-failure -VV -S .github/cmake/ctest_test.cmake" | |
| ccache --show-stats | |
| - name: compile a sample project without installing IBAMR | |
| id: sampleproject | |
| run: | | |
| mkdir sample-project | |
| cd sample-project | |
| cp ../.github/project-template/CMakeLists.txt ./ | |
| cp ../.github/project-template/project.cpp ./ | |
| source /etc/profile.d/modules.sh | |
| module load mpi | |
| cmake3 -DIBAMR_ROOT=/build/ibamr . | |
| make | |
| ./project | |
| # build IBAMR with CMake when we use custom, not system, installations of dependencies | |
| build_ibamr_archlinux: | |
| runs-on: ubuntu-latest | |
| name: Build IBAMR with a non-system MPI | |
| container: | |
| image: 'docker://wellsd2/ibamr:ibamr-0.14-custom-deps' | |
| env: | |
| CMAKE_CONFIGURATION: archlinux | |
| CTEST_NO_WARNINGS_ALLOWED: true | |
| CCACHE_MAXSIZE: 250M | |
| CMAKE_GENERATOR: Unix Makefiles | |
| steps: | |
| - name: Checkout Source | |
| uses: actions/checkout@v3 | |
| id: git | |
| - name: Verify that clang-format was run | |
| id: format | |
| run: | | |
| git config --global --add safe.directory '*' | |
| ./scripts/formatting/download-clang-format | |
| ./scripts/formatting/check-indentation | |
| - name: Create keys | |
| id: keys | |
| run: | | |
| echo "key1=$(( ${{ github.run_number }} - 1))" >> $GITHUB_ENV | |
| echo "key2=$(( ${{ github.run_number }} - 2))" >> $GITHUB_ENV | |
| echo "key3=$(( ${{ github.run_number }} - 3))" >> $GITHUB_ENV | |
| echo "key4=$(( ${{ github.run_number }} - 4))" >> $GITHUB_ENV | |
| echo "key5=$(( ${{ github.run_number }} - 5))" >> $GITHUB_ENV | |
| - name: Populate ccache | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: ccache | |
| id: cache | |
| with: | |
| path: ~/.cache/ccache | |
| key: ${{ runner.os }}-build-archlinux-cmake-${{ github.run_number }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-archlinux-cmake-${{ env.key1 }} | |
| ${{ runner.os }}-build-archlinux-cmake-${{ env.key2 }} | |
| ${{ runner.os }}-build-archlinux-cmake-${{ env.key3 }} | |
| ${{ runner.os }}-build-archlinux-cmake-${{ env.key4 }} | |
| ${{ runner.os }}-build-archlinux-cmake-${{ env.key5 }} | |
| ${{ runner.os }}-build-archlinux-cmake- | |
| - name: Configure IBAMR | |
| id: configure | |
| run: | | |
| bash -c "ctest -VV -S .github/cmake/ctest_configure.cmake" | |
| ccache --show-stats | |
| - name: Compile IBAMR | |
| id: build | |
| run: | | |
| cd /build/ibamr | |
| make -j2 examples | |
| ccache --show-stats | |
| - name: Install IBAMR | |
| id: install | |
| run: | | |
| cd /build/ibamr | |
| make install | |
| - name: compile a sample project with an uninstalled IBAMR | |
| id: sampleproject1 | |
| run: | | |
| mkdir sample-project | |
| cd sample-project | |
| cp ../.github/project-template/CMakeLists.txt ./ | |
| cp ../.github/project-template/project.cpp ./ | |
| cmake -DIBAMR_ROOT=/build/ibamr . | |
| make | |
| ./project | |
| - name: compile a sample project with an installed IBAMR | |
| id: sampleproject2 | |
| run: | | |
| mkdir sample-project2 | |
| cd sample-project2 | |
| cp ../.github/project-template/CMakeLists.txt ./ | |
| cp ../.github/project-template/project.cpp ./ | |
| cmake -DIBAMR_ROOT=/ibamr . | |
| make | |
| ./project |