use python script to test CVODE, for approximate solution #298
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@v4 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}" | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v5 | |
| 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-13, windows-latest, ubuntu-latest, macos-14] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - name: checkout vcell-solvers repo | |
| uses: actions/checkout@v4 | |
| - name: Install Intel MacOS dependencies | |
| if: matrix.platform == 'macos-13' | |
| shell: bash | |
| run: | | |
| brew install boost | |
| brew install hdf5 | |
| brew install ninja | |
| brew install llvm | |
| echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile | |
| source /Users/runner/.bash_profile | |
| ln -s $(which gfortran-14) /usr/local/bin/gfortran | |
| gcc --version | |
| gfortran --version | |
| cmake --version | |
| brew info boost | |
| brew info hdf5 | |
| - name: Install ARM MacOS dependencies | |
| if: matrix.platform == 'macos-14' | |
| shell: bash | |
| run: | | |
| brew install boost | |
| brew install hdf5 | |
| brew install ninja | |
| brew install llvm | |
| echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile | |
| ln -s /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran | |
| gcc --version | |
| gfortran --version | |
| cmake --version | |
| brew info boost | |
| brew info hdf5 | |
| - name: Build Macos ARM | |
| if: matrix.platform == 'macos-14' | |
| run: | | |
| platform=macos | |
| echo "working dir is $PWD" | |
| mkdir build | |
| cd build | |
| export PATH="/opt/homebrew/opt/llvm/bin:$PATH" | |
| cmake \ | |
| -G Ninja \ | |
| -DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang \ | |
| -DCMAKE_CXX_COMPILER=/opt/homebrew/opt/llvm/bin/clang++ \ | |
| -DOPTION_MINGW=ON \ | |
| -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=ON \ | |
| -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| -B . -S .. | |
| ninja | |
| - name: Build Macos Intel | |
| if: matrix.platform == 'macos-13' | |
| 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_MINGW=ON \ | |
| -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=ON \ | |
| -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| -B . -S .. | |
| ninja | |
| - name: Test Macos | |
| if: matrix.platform == 'macos-13' || matrix.platform == 'macos-14' | |
| 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: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # with: | |
| # limit-access-to-actor: false | |
| - name: Install Windows Dependencies | |
| if: matrix.platform == 'windows-latest' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: CLANG64 | |
| update: true | |
| install: > | |
| zip | |
| git | |
| mingw-w64-clang-x86_64-curl | |
| 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 | |
| mingw-w64-clang-x86_64-zlib | |
| mingw-w64-clang-x86_64-libaec | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # with: | |
| # limit-access-to-actor: false | |
| - name: Build Windows | |
| if: matrix.platform == 'windows-latest' | |
| shell: msys2 {0} | |
| run: | | |
| platform=windows | |
| echo "working dir is $PWD" | |
| mkdir build | |
| cd build | |
| export PATH="/c/Program\ Files/LLVM/bin:$PATH" | |
| cmake \ | |
| -G Ninja \ | |
| -DCMAKE_C_COMPILER="clang.exe" \ | |
| -DCMAKE_CXX_COMPILER="clang++.exe" \ | |
| -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 \ | |
| -DOPTION_TARGET_DOCS=OFF \ | |
| -B . -S .. | |
| ninja -j 1 | |
| - name: Test Windows | |
| if: matrix.platform == 'windows-latest' | |
| shell: msys2 {0} | |
| run: | | |
| platform=windows | |
| echo "working dir is $PWD" | |
| cd build | |
| export PATH="/d/a/_temp/msys64/clang64/bin:$PATH" | |
| pacman -Sy --noconfirm diffutils | |
| 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 Linux Dependencies | |
| if: matrix.platform == 'ubuntu-latest' | |
| 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-latest' | |
| 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=ON \ | |
| -DOPTION_TARGET_SUNDIALS_SOLVER=ON \ | |
| -DOPTION_TARGET_HY3S_SOLVERS=OFF \ | |
| -B . -S .. | |
| ninja | |
| - name: Test Linux | |
| if: matrix.platform == 'ubuntu-latest' | |
| 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 | |
| - name: fix Macos shared object paths | |
| if: matrix.platform == 'macos-13' || matrix.platform == 'macos-14' | |
| shell: bash | |
| run: | | |
| mkdir build/upload | |
| cd build/bin | |
| rm hello_test TestVCellStoch testzip ziptool || true | |
| ls *_x64 | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true | |
| chmod u+w,+x * | |
| tar czvf ../upload/mac64_bad_paths.tgz . | |
| ../../.github/scripts/install_name_tool_macos.sh | |
| tar czvf ../upload/mac64.tgz --dereference . | |
| - name: handle shared object paths for Windows native build | |
| if: matrix.platform == 'windows-latest' | |
| shell: msys2 {0} | |
| run: | | |
| mkdir build/upload | |
| cd build/bin | |
| rm hello_test TestVCellStoch testzip ziptool || true | |
| ls *.exe | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| chmod u+w,+x * | |
| zip ../upload/win64.zip ./* | |
| cd ../.. | |
| # fi | |
| - name: handle shared object paths for Linux native build | |
| if: matrix.platform == 'ubuntu-latest' | |
| shell: bash | |
| run: | | |
| mkdir build/upload | |
| cd build/bin | |
| rm hello_test TestVCellStoch testzip ziptool || true | |
| ls *_x64 | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.so | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| ls *.so | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true | |
| chmod u+w,+x * | |
| tar czvf ../upload/linux64.tgz --dereference . | |
| cd ../.. | |
| - name: Upload Intel Macos binaries | |
| if: matrix.platform == 'macos-13' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: macos_x86_64.tgz | |
| path: build/upload/mac64.tgz | |
| - name: Upload ARM Macos binaries | |
| if: matrix.platform == 'macos-14' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: macos_arm64.tgz | |
| path: build/upload/mac64.tgz | |
| - name: Upload Windows binaries | |
| if: matrix.platform == 'windows-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: win64.zip | |
| path: build/upload/win64.zip | |
| - name: Upload Linux binaries | |
| if: matrix.platform == 'ubuntu-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linux64.tgz | |
| path: build/upload/linux64.tgz | |
| - name: Setup tmate session | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 | |
| with: | |
| limit-access-to-actor: false | |