do not require HDF5 1.8.11 #137
Workflow file for this run
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| name: CD | |
| on: [push, workflow_dispatch] | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| # build-and-push-image: | |
| # runs-on: ubuntu-latest | |
| # permissions: | |
| # contents: read | |
| # packages: write | |
| # | |
| # steps: | |
| # - name: Checkout repository | |
| # uses: actions/checkout@v3 | |
| # | |
| # - name: Log in to the Container registry | |
| # uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| # with: | |
| # registry: ${{ env.REGISTRY }} | |
| # username: ${{ github.actor }} | |
| # password: ${{ secrets.GITHUB_TOKEN }} | |
| # | |
| # - name: Extract metadata (tags, labels) for Docker | |
| # id: meta | |
| # uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| # with: | |
| # images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| # | |
| # - name: Build and push Docker image | |
| # uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| # with: | |
| # context: . | |
| # push: true | |
| # tags: ${{ steps.meta.outputs.tags }} | |
| # labels: ${{ steps.meta.outputs.labels }} | |
| native-build: | |
| name: | |
| native-build-${{ matrix.platform }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [macos-latest, windows-latest, ubuntu-18.04] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - name: checkout vcell-solvers repo | |
| uses: actions/checkout@v3 | |
| - name: Install MacOS dependencies | |
| if: matrix.platform == 'macos-latest' | |
| shell: bash | |
| run: | | |
| brew install boost | |
| brew install hdf5 | |
| brew install ninja | |
| brew install llvm | |
| echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile | |
| ln -s /usr/local/bin/gfortran-12 /usr/local/bin/gfortran | |
| gcc --version | |
| gfortran --version | |
| cmake --version | |
| brew info boost | |
| brew info hdf5 | |
| - name: Build Macos | |
| if: matrix.platform == 'macos-latest' | |
| run: | | |
| platform=macos | |
| echo "working dir is $PWD" | |
| mkdir build | |
| cd build | |
| export PATH="/usr/local/opt/llvm/bin:$PATH" | |
| cmake \ | |
| -G Ninja \ | |
| -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \ | |
| -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \ | |
| -DOPTION_TARGET_MESSAGING=OFF \ | |
| -DOPTION_TARGET_PARALLEL=OFF \ | |
| -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \ | |
| -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \ | |
| -DOPTION_TARGET_SMOLDYN_SOLVER=ON \ | |
| -DOPTION_TARGET_FV_SOLVER=ON \ | |
| -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \ | |
| -DOPTION_TARGET_NFSIM_SOLVER=ON \ | |
| -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \ | |
| -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| -B . -S .. | |
| ninja | |
| - name: Test Macos | |
| if: matrix.platform == 'macos-latest' | |
| run: | | |
| platform=macos | |
| echo "working dir is $PWD" | |
| cd build | |
| ctest -VV | |
| echo "------ running FiniteVolume_x64 ------" | |
| ./bin/FiniteVolume_x64 || true | |
| echo | |
| echo "------ running NFsim_x64 ------" | |
| ./bin/NFsim_x64 || true | |
| echo "------ running SundialsSolverStandalone_x64 ------" | |
| ./bin/SundialsSolverStandalone_x64 || true | |
| echo "------ running VCellStoch_x64 ------" | |
| ./bin/VCellStoch_x64 || true | |
| echo "------ running smoldyn_x64 ------" | |
| ./bin/smoldyn_x64 || true | |
| echo "------ running testzip ------" | |
| ./bin/testzip || true | |
| echo "------ running ziptool ------" | |
| ./bin/ziptool || true | |
| - name: Install Windows Dependencies | |
| if: matrix.platform == 'windows-latest' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: CLANG64 | |
| update: true | |
| install: > | |
| git | |
| mingw-w64-clang-x86_64-toolchain | |
| mingw-w64-clang-x86_64-flang | |
| mingw-w64-clang-x86_64-cmake | |
| mingw-w64-clang-x86_64-boost | |
| mingw-w64-clang-x86_64-hdf5 | |
| mingw-w64-clang-x86_64-libzip | |
| mingw-w64-clang-x86_64-netcdf | |
| - name: Build Windows | |
| if: matrix.platform == 'windows-latest' | |
| shell: msys2 {0} | |
| run: | | |
| platform=windows | |
| echo "working dir is $PWD" | |
| mkdir build | |
| cd build | |
| PATH="/c/Program Files/LLVM/bin:$PATH" | |
| cmake \ | |
| -G Ninja \ | |
| -DCMAKE_C_COMPILER=clang \ | |
| -DCMAKE_CXX_COMPILER=clang++ \ | |
| -DOPTION_TARGET_MESSAGING=OFF \ | |
| -DOPTION_TARGET_PARALLEL=OFF \ | |
| -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \ | |
| -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \ | |
| -DOPTION_TARGET_SMOLDYN_SOLVER=ON \ | |
| -DOPTION_TARGET_FV_SOLVER=ON \ | |
| -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \ | |
| -DOPTION_TARGET_NFSIM_SOLVER=ON \ | |
| -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \ | |
| -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| -B . -S .. | |
| ninja -j 1 | |
| - name: Test Windows | |
| if: matrix.platform == 'windows-latest' | |
| shell: msys2 {0} | |
| run: | | |
| platform=windows | |
| echo "working dir is $PWD" | |
| cd build | |
| ctest -VV | |
| echo "------ running FiniteVolume_x64 ------" | |
| ./bin/FiniteVolume_x64 || true | |
| echo | |
| echo "------ running NFsim_x64 ------" | |
| ./bin/NFsim_x64 || true | |
| echo "------ running SundialsSolverStandalone_x64 ------" | |
| ./bin/SundialsSolverStandalone_x64 || true | |
| echo "------ running VCellStoch_x64 ------" | |
| ./bin/VCellStoch_x64 || true | |
| echo "------ running smoldyn_x64 ------" | |
| ./bin/smoldyn_x64 || true | |
| echo "------ running testzip ------" | |
| ./bin/testzip || true | |
| echo "------ running ziptool ------" | |
| ./bin/ziptool || true | |
| - name: Setup tmate session | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 | |
| with: | |
| limit-access-to-actor: false | |
| # - name: Install Linux Dependencies | |
| # if: matrix.platform == 'ubuntu-18.04' | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install -y libboost-all-dev | |
| # sudo apt-get install -y libhdf5-dev | |
| # sudo apt-get install -y ninja-build | |
| # | |
| # gcc --version | |
| # gfortran --version | |
| # cmake --version | |
| # dpkg -s libboost-all-dev | |
| # dpkg -s libhdf5-dev | |
| # | |
| # - name: Build Linux | |
| # if: matrix.platform == 'ubuntu-18.04' | |
| # run: | | |
| # platform=linux | |
| # echo "working dir is $PWD" | |
| # | |
| # mkdir build | |
| # cd build | |
| # | |
| # cmake \ | |
| # -G Ninja \ | |
| # -DOPTION_TARGET_MESSAGING=OFF \ | |
| # -DOPTION_TARGET_PARALLEL=OFF \ | |
| # -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \ | |
| # -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \ | |
| # -DOPTION_TARGET_SMOLDYN_SOLVER=ON \ | |
| # -DOPTION_TARGET_FV_SOLVER=ON \ | |
| # -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \ | |
| # -DOPTION_TARGET_NFSIM_SOLVER=ON \ | |
| # -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \ | |
| # -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| # -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| # -B . -S .. | |
| # | |
| # ninja | |
| # | |
| # - name: Test Linux | |
| # if: matrix.platform == 'ubuntu-18.04' | |
| # run: | | |
| # platform=linux | |
| # echo "working dir is $PWD" | |
| # | |
| # cd build | |
| # | |
| # ctest -VV | |
| # | |
| # echo "------ running FiniteVolume_x64 ------" | |
| # ./bin/FiniteVolume_x64 || true | |
| # echo | |
| # echo "------ running NFsim_x64 ------" | |
| # ./bin/NFsim_x64 || true | |
| # echo "------ running SundialsSolverStandalone_x64 ------" | |
| # ./bin/SundialsSolverStandalone_x64 || true | |
| # echo "------ running VCellStoch_x64 ------" | |
| # ./bin/VCellStoch_x64 || true | |
| # echo "------ running smoldyn_x64 ------" | |
| # ./bin/smoldyn_x64 || true | |
| # echo "------ running testzip ------" | |
| # ./bin/testzip || true | |
| # echo "------ running ziptool ------" | |
| # ./bin/ziptool || true | |
| # |