HDF5 interface and support for stochastic reading #156
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| name: CI | |
| on: | |
| push: | |
| branches: [ development ] | |
| pull_request: | |
| # CI runs when new commits are pushed or when draft PR is marked ready for review | |
| types: [opened, synchronize, reopened, ready_for_review] | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Release | |
| OMP_NUM_THREADS: 2 | |
| jobs: | |
| build: | |
| # Skip CI if PR is a draft | |
| if: github.event.pull_request.draft == false | |
| name: build (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}}) | |
| # The CMake configure and build commands are platform agnostic and should work equally | |
| # well on Windows or Mac. You can convert this to a matrix build if you need | |
| # cross-platform coverage. | |
| # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix | |
| runs-on: ${{matrix.os}} | |
| env: | |
| CC: ${{ matrix.cc }} | |
| CXX: ${{ matrix.cxx }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-22.04 | |
| - macos-14 | |
| cc: | |
| - gcc-12 | |
| - clang | |
| cxx: | |
| - g++-12 | |
| - clang++ | |
| mpi: | |
| - "ON" | |
| - "OFF" | |
| omp: | |
| - "ON" | |
| - "OFF" | |
| exclude: | |
| - os: ubuntu-22.04 | |
| cc: clang | |
| - os: ubuntu-22.04 | |
| cxx: clang++ | |
| - os: macos-14 | |
| cc: gcc-12 | |
| - os: macos-14 | |
| cxx: g++-12 | |
| - os: macos-14 | |
| mpi: "ON" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # Enable tmate debugging of manually-triggered workflows if the input option was provided | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }} | |
| - name: Prepare ccache timestamp | |
| id: ccache_cache_timestamp | |
| run: echo "{date_and_time}={$(date +'%Y-%m-%d-%H;%M;%S')}" >> $GITHUB_OUTPUT | |
| - name: Set ccache cache directory | |
| shell: bash | |
| run: echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}" | |
| - name: Cache ccache files | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{runner.workspace}}/.ccache | |
| key: ${{matrix.os}}-${{matrix.cxx}}-${{matrix.mpi}}-${{matrix.omp}}-${{ steps.ccache_cache_timestamp.outputs.date_and_time }} | |
| restore-keys: | | |
| ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }} | |
| ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }} | |
| ${{ matrix.os }}-${{ matrix.cxx }} | |
| ${{ matrix.os }} | |
| # - name: Clear ccache | |
| # run: ccache --clear | |
| - name: Install Dependencies on Ubunutu | |
| if: ${{ contains(matrix.os, 'ubuntu') }} | |
| run: | | |
| sudo apt update | |
| sudo apt install openmpi-bin libopenmpi-dev libyaml-cpp-dev libeigen3-dev libtiff-dev ccache | |
| - name: Install Dependencies on MacOS | |
| if: ${{ contains(matrix.os, 'macos') }} | |
| run: | | |
| brew install open-mpi libomp yaml-cpp eigen cfitsio ccache onnxruntime | |
| echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV | |
| echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH | |
| - name: Checkout Catch2 | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: catchorg/Catch2.git | |
| path: Catch2 | |
| ref: v3.4.0 | |
| - name: Build Catch2 | |
| run: | | |
| mkdir Catch2/build | |
| cd Catch2/build | |
| cmake .. -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local | |
| make -j$(nproc --ignore 1) install | |
| - name: Install FFTW | |
| run: | | |
| wget --no-check-certificate --no-verbose http://www.fftw.org/fftw-3.3.10.tar.gz -O- | tar --no-same-owner -xz; | |
| cd fftw-3.3.10 | |
| ./configure --prefix=${{github.workspace}}/local --enable-shared | |
| make -j$(nproc --ignore 1) install CFLAGS=-fPIC | |
| # Fix bug in FFT3 (cf. https://github.com/FFTW/fftw3/issues/332) | |
| sed -i -e 's/^.*FFTW3LibraryDepends.cmake.*$//1' ${{github.workspace}}/local/lib*/cmake/*/FFTW3Config.cmake | |
| - name: Install HDF5 | |
| run: | | |
| wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.gz -O- | tar --no-same-owner -xz; | |
| cd hdf5-1.14.3/ | |
| mkdir build && cd build | |
| #CC=`which mpicc` CXX=`which mpicxx` ./configure --prefix=${{github.workspace}}/local --enable-parallel --enable-shared --enable-cxx | |
| CC=`which mpicc` CXX=`which mpicxx` cmake .. -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -DHDF5_ENABLE_PARALLEL:BOOL=ON -DALLOW_UNSUPPORTED:BOOL=ON -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=ON -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF | |
| make -j$(nproc --ignore 2) install | |
| - name: Checkout SOPT | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: astro-informatics/sopt.git | |
| path: sopt | |
| ref: development | |
| - name: Build sopt | |
| run: | | |
| export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH | |
| mkdir -p ${{github.workspace}}/sopt/build | |
| cd ${{github.workspace}}/sopt/build | |
| cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=OFF -Dexamples=OFF | |
| make -j$(nproc --ignore 1) install | |
| - name: Pack dependencies | |
| run: | | |
| cd ${{github.workspace}} | |
| tar cfv dependencies.tar local | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }} | |
| path: ${{github.workspace}}/dependencies.tar | |
| retention-days: 5 | |
| test: | |
| needs: | |
| build | |
| name: test (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}}) | |
| runs-on: ${{matrix.os}} | |
| env: | |
| CC: ${{ matrix.cc }} | |
| CXX: ${{ matrix.cxx }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-22.04 | |
| - macos-14 | |
| cc: | |
| - gcc-12 | |
| - clang | |
| cxx: | |
| - g++-12 | |
| - clang++ | |
| mpi: | |
| - "ON" | |
| - "OFF" | |
| omp: | |
| - "ON" | |
| - "OFF" | |
| exclude: | |
| - os: ubuntu-22.04 | |
| cc: clang | |
| - os: ubuntu-22.04 | |
| cxx: clang++ | |
| - os: macos-14 | |
| cc: gcc-12 | |
| - os: macos-14 | |
| cxx: g++-12 | |
| - os: macos-14 | |
| mpi: "ON" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }} | |
| - name: Unpack dependencies | |
| run: tar xfv dependencies.tar | |
| - name: Install Dependencies on Ubunutu | |
| if: ${{ contains(matrix.os, 'ubuntu') }} | |
| run: | | |
| sudo apt update | |
| sudo apt install openmpi-bin libopenmpi-dev ccache graphviz libeigen3-dev libtiff-dev libcfitsio-dev libboost-all-dev libyaml-cpp-dev | |
| - name: Install Dependencies on MacOS | |
| if: ${{ contains(matrix.os, 'macos') }} | |
| run: | | |
| brew install open-mpi libomp eigen ccache cfitsio boost yaml-cpp onnxruntime | |
| echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV | |
| echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH | |
| - name: Build tests | |
| # Build your program with the given configuration | |
| run: | | |
| export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH | |
| #export PATH=${{github.workspace}}/local:$PATH | |
| mkdir -p ${{github.workspace}}/build | |
| cd ${{github.workspace}}/build | |
| cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Dhdf5=ON -Ddocasa=OFF -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=ON | |
| make -j$(nproc --ignore 1) install | |
| - name: Test | |
| working-directory: ${{github.workspace}}/build | |
| # Execute tests defined by the CMake configuration. | |
| # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail | |
| run: | | |
| export LD_LIBRARY_PATH=${{github.workspace}}/local/lib:${{github.workspace}}/local/external/lib:${LD_LIBRARY_PATH} | |
| ctest -C ${{env.BUILD_TYPE}} --output-on-failure | |
| doc: | |
| needs: | |
| build | |
| name: doc (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}}) | |
| runs-on: ${{matrix.os}} | |
| env: | |
| CC: ${{ matrix.cc }} | |
| CXX: ${{ matrix.cxx }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-22.04 | |
| cc: | |
| - gcc-12 | |
| cxx: | |
| - g++-12 | |
| mpi: | |
| - "OFF" | |
| omp: | |
| - "OFF" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }} | |
| - name: Unpack dependencies | |
| run: tar xfv dependencies.tar | |
| - name: Install Dependencies on Ubunutu | |
| if: ${{ contains(matrix.os, 'ubuntu') }} | |
| run: | | |
| sudo apt update | |
| sudo apt install ccache doxygen graphviz libeigen3-dev libtiff-dev libcfitsio-dev libboost-all-dev libyaml-cpp-dev | |
| - name: Install Dependencies on MacOS | |
| if: ${{ contains(matrix.os, 'macos') }} | |
| run: | | |
| brew install gcc libtiff eigen libyaml ccache cfitsio boost yaml-cpp onnxruntime | |
| echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV | |
| echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH | |
| - name: Build docs | |
| run: | | |
| export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH | |
| mkdir -p ${{github.workspace}}/build | |
| cd ${{github.workspace}}/build | |
| cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Dhdf5=ON -Ddompi=OFF -Dopenmp=OFF -Ddocs=ON | |
| make -j$(nproc --ignore 1) install | |
| - name: Deploy to GH pages | |
| if: ${{github.event_name == 'push'}} | |
| uses: JamesIves/[email protected] | |
| with: | |
| branch: gh-pages # The branch the action should deploy to. | |
| folder: build/cpp/docs/html # The folder the action should deploy. |