Common Output in GateToTree #1034
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: [ develop ] | |
| pull_request: | |
| branches: [ develop ] | |
| schedule: | |
| - cron: '0 0 * * 0,3' | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| options: [none, rtk, torch, optic] | |
| exclude: | |
| - os: macos-latest | |
| options: torch | |
| env: | |
| ROOT_VERSION: 'v6-32-02' | |
| GEANT4_VERSION: 'v11.2.1' | |
| ITK_VERSION: 'v5.3.0' | |
| ROOT_DIR: $(HOME)/software/root | |
| GEANT4_DIR: $(HOME)/software/geant4 | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Cache | |
| id: cache_gate_dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/software | |
| key: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1 | |
| restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1 | |
| - name: Install dependencies | |
| run: | | |
| if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then | |
| sudo apt-get update -qq | |
| sudo apt-get install -y gcc \ | |
| g++ \ | |
| make \ | |
| binutils \ | |
| libx11-dev \ | |
| libtbb-dev \ | |
| libxpm-dev \ | |
| libxft-dev \ | |
| libxext-dev \ | |
| qtbase5-dev \ | |
| qt5-qmake \ | |
| git \ | |
| cmake \ | |
| libssl-dev \ | |
| python3.8-dev \ | |
| ccache \ | |
| fftw3-dev | |
| gcc -v | |
| elif [ "${{ matrix.os }}" == "macos-latest" ]; then | |
| brew install python@3.12 || true | |
| brew link --overwrite python@3.12 | |
| #brew update | |
| brew cleanup | |
| brew config | |
| #rm -rf /usr/local/bin/python3.11-config /usr/local/bin/2to3-3.11 /usr/local/bin/idle3.11 /usr/local/bin/pydoc3.11 /usr/local/bin/python3.11 | |
| #rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3 | |
| brew install --force --verbose --overwrite --debug qt5 \ | |
| ccache \ | |
| tbb \ | |
| xrootd \ | |
| fftw | |
| brew link qt5 --force && sudo ln -s /usr/local/opt/qt/mkspecs /usr/local/mkspecs && sudo ln -s /usr/local/opt/qt/plugins /usr/local/plugins | |
| export PATH=/usr/local/opt/qt/bin:$PATH | |
| export LDFLAGS="-L/usr/local/opt/qt/lib -L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/qt/include -I/usr/local/opt/llvm/include -fopenmp" | |
| fi | |
| cd $HOME/ | |
| mkdir -p software option_dependencies | |
| cmake --version | |
| - name: Install root | |
| run: | | |
| if [ "${{ steps.cache_gate_dependencies.outputs.cache-hit }}" != 'true' ] && [ "${{ matrix.options }}" == 'none' ]; then | |
| cd $HOME/software | |
| mkdir root | |
| cd root | |
| mkdir src bin install | |
| git clone --branch $ROOT_VERSION https://github.com/root-project/root.git --depth 1 src | |
| cd bin | |
| cmake ../src -DCMAKE_CXX_STANDARD=17 \ | |
| -Dpython=OFF \ | |
| -Dpyroot=OFF \ | |
| -Dclad=OFF \ | |
| -Dxrootd=OFF \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/software/root/install | |
| make -j4 install | |
| cd .. | |
| rm -rf bin src | |
| fi | |
| - name: Install Geant4 | |
| run: | | |
| if [ "${{ steps.cache_gate_dependencies.outputs.cache-hit }}" != 'true' ] && [ "${{ matrix.options }}" == 'none' ]; then | |
| cd $HOME/software | |
| mkdir geant4 | |
| cd geant4 | |
| mkdir src bin install data | |
| git clone --branch $GEANT4_VERSION https://github.com/Geant4/geant4.git --depth 1 src | |
| cd bin | |
| cmake -DGEANT4_INSTALL_DATA=ON \ | |
| -DGEANT4_BUILD_MULTITHREADED=OFF \ | |
| -DGEANT4_INSTALL_DATADIR=$HOME/software/geant4/data \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/software/geant4/install \ | |
| ../src | |
| make -j4 install | |
| cd .. | |
| rm -rf src bin | |
| fi | |
| - name: Install option dependencies | |
| run: | | |
| if [ "${{ steps.cache_gate_dependencies.outputs.cache-hit }}" == 'true' ]; then | |
| cd $HOME/option_dependencies | |
| if [ "${{ matrix.options }}" == 'torch' ]; then | |
| if [ "${{ matrix.os }}" == 'ubuntu-latest' ]; then | |
| wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.10.1%2Bcpu.zip | |
| unzip libtorch-cxx11-abi-shared-with-deps-1.10.1+cpu.zip | |
| elif [ "${{ matrix.os }}" == 'macos-latest' ]; then | |
| wget https://download.pytorch.org/libtorch/cpu/libtorch-macos-arm64-2.2.0.zip | |
| unzip libtorch-macos-arm64-2.2.0.zip | |
| fi | |
| fi | |
| if [ "${{ matrix.options }}" == 'rtk' ]; then | |
| mkdir rtk | |
| cd rtk | |
| mkdir src bin | |
| git clone --branch $ITK_VERSION https://github.com/InsightSoftwareConsortium/ITK.git --depth 1 src | |
| cd bin | |
| cmake -DCMAKE_CXX_FLAGS="-std=c++17" -DBUILD_TESTING=OFF -DITK_USE_FFTWD=ON -DITK_USE_FFTWF=ON -DITK_USE_SYSTEM_FFTW:BOOL=ON -DITK_MINIMUM_COMPLIANCE_LEVEL=3 -DModule_RTK=ON -DREMOTE_GIT_TAG_RTK=master ../src | |
| make -j4 | |
| fi | |
| cd $HOME/option_dependencies | |
| ls | |
| else | |
| if [ "${{ matrix.options }}" != 'none' ]; then | |
| echo "Create the cache first and run the job again" | |
| exit 1 | |
| fi | |
| fi | |
| - name: Configure Gate | |
| run: | | |
| if [ "${{ steps.cache_gate_dependencies.outputs.cache-hit }}" == 'true' ]; then | |
| cd $HOME | |
| export ROOTSYS=$HOME/software/root/install | |
| export PATH=${ROOTSYS}:${PATH} | |
| source $HOME/software/root/install/bin/thisroot.sh | |
| source $HOME/software/geant4/install/bin/geant4.sh | |
| mkdir build | |
| cd build | |
| which cmake | |
| cmake --version | |
| export GATE_USE_TORCH=OFF | |
| export GATE_USE_RTK=OFF | |
| export GATE_USE_OPTICAL=OFF | |
| if [ "${{ matrix.options }}" == 'torch' ]; then | |
| export GATE_USE_TORCH=ON | |
| fi | |
| if [ "${{ matrix.options }}" == 'rtk' ]; then | |
| export GATE_USE_RTK=ON | |
| fi | |
| if [ "${{ matrix.options }}" == 'optic' ]; then | |
| export GATE_USE_OPTIC=ON | |
| fi | |
| cmake -DGATE_USE_TORCH=$GATE_USE_TORCH \ | |
| -DTorch_DIR=$HOME/option_dependencies/libtorch/share/cmake/Torch \ | |
| -DGATE_COMPILE_GATEDIGIT=ON \ | |
| -DGATE_USE_RTK=$GATE_USE_RTK \ | |
| -DITK_DIR=$HOME/option_dependencies/rtk/bin/ \ | |
| -DGATE_USE_OPTICAL=$GATE_USE_OPTICAL \ | |
| -DBUILD_TESTING=ON \ | |
| $GITHUB_WORKSPACE | |
| fi | |
| - name: Configure CTest | |
| if: steps.cache_gate_dependencies.outputs.cache-hit == 'true' | |
| run: | | |
| cd $HOME | |
| cat > dashboard.cmake << EOF | |
| set(CTEST_SITE "Github.macos-latest.none") | |
| file(TO_CMAKE_PATH "$HOME" CTEST_DASHBOARD_ROOT) | |
| file(TO_CMAKE_PATH "$GITHUB_WORKSPACE" CTEST_SOURCE_DIRECTORY) | |
| file(TO_CMAKE_PATH "$HOME/build" CTEST_BINARY_DIRECTORY) | |
| set(dashboard_source_name "$GITHUB_REPOSITORY") | |
| if("$GITHUB_REF" MATCHES "^refs/pull/") | |
| set(branch "") | |
| set(pr "-PR$GITHUB_REF") | |
| set(dashboard_model "Experimental") | |
| elseif("$GITHUB_REF" STREQUAL "refs/heads/develop") | |
| set(branch "-develop") | |
| set(pr "") | |
| set(dashboard_model "Continuous") | |
| else() | |
| set(branch "-BRANCH$GITHUB_REF") | |
| set(pr "") | |
| set(dashboard_model "Experimental") | |
| endif() | |
| set(CTEST_BUILD_NAME "github_macos-latest.none-Build$GITHUB_RUN_NUMBER\${pr}\${branch}") | |
| set(CTEST_UPDATE_VERSION_ONLY 1) | |
| set(CTEST_TEST_ARGS \${CTEST_TEST_ARGS} PARALLEL_LEVEL \${PARALLEL_LEVEL}) | |
| set(CTEST_CONFIGURATION_TYPE "Release") | |
| set(CTEST_CMAKE_GENERATOR "Unix Makefiles") | |
| set(CTEST_BUILD_FLAGS "\${CTEST_BUILD_FLAGS} -j4") | |
| set(CTEST_CUSTOM_WARNING_EXCEPTION | |
| \${CTEST_CUSTOM_WARNING_EXCEPTION} | |
| # macOS Azure Pipelines | |
| "ld: warning: text-based stub file" | |
| ) | |
| set(dashboard_no_clean 1) | |
| set(ENV{CC} $(cCompiler)) | |
| set(ENV{CXX} $(cxxCompiler)) | |
| string(TIMESTAMP build_date "%Y-%m-%d") | |
| message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}") | |
| message("CTEST_SITE = \${CTEST_SITE}") | |
| ctest_start("\${dashboard_model}") | |
| ctest_configure(CAPTURE_CMAKE_ERROR configure_errors RETURN_VALUE configure_Results) | |
| ctest_build(NUMBER_ERRORS build_errors RETURN_VALUE build_Results) | |
| ctest_submit(RETURN_VALUE submit_Results) | |
| if ((NOT \${configure_errors} EQUAL 0) OR (NOT \${configure_Results} EQUAL 0)) | |
| message( FATAL_ERROR "Configuration error" ) | |
| endif() | |
| if ((NOT \${build_errors} EQUAL 0) OR (NOT \${build_Results} EQUAL 0)) | |
| message( FATAL_ERROR "Build error" ) | |
| endif() | |
| if (NOT \${submit_Results} EQUAL 0) | |
| message( FATAL_ERROR "Submit error" ) | |
| endif() | |
| EOF | |
| cat dashboard.cmake | |
| - name: Build Gate | |
| run: | | |
| if [ "${{ steps.cache_gate_dependencies.outputs.cache-hit }}" == 'true' ]; then | |
| cd $HOME/build | |
| cp ../dashboard.cmake . | |
| export ROOTSYS=$HOME/software/root/install | |
| export PATH=${ROOTSYS}:${PATH} | |
| source $HOME/software/root/install/bin/thisroot.sh | |
| source $HOME/software/geant4/install/bin/geant4.sh | |
| ctest -S dashboard.cmake -VV | |
| if [ ! $? -eq 0 ]; then | |
| exit 1 | |
| fi | |
| fi | |
| # ssh_session: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout github repo | |
| # uses: actions/checkout@v3 | |
| # with: | |
| # lfs: true | |
| # - name: Checkout LFS objects | |
| # run: git lfs checkout | |
| # - name: Start SSH session | |
| # uses: luchihoratiu/debug-via-ssh@main | |
| # with: | |
| # NGROK_AUTH_TOKEN: ${{ secrets.NGROK_AUTH_TOKEN }} | |
| # SSH_PASS: ${{ secrets.SSH_PASS }} | |
| benchmarks: | |
| runs-on: ubuntu-latest | |
| needs: [build] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| strategy_name: [t1_edep_profiles, | |
| t2_edep_vox, | |
| t3_range_e+, | |
| t4_necr, | |
| t6_dpk, | |
| t8_LETActor, | |
| t10_SpectroGamma, | |
| t11_EMField, | |
| t12_tessellated_volume, | |
| t13_phsp, | |
| t15_optical, | |
| t16_decay, | |
| t17_extended_source, | |
| t18_movement_benchmark, | |
| t19_acollinearity, | |
| t20_digi_adder, | |
| t22_merged_actor, | |
| t23_digi_readout, | |
| t26_CoinSorter, | |
| t27_Hits_2SD, | |
| t28_Singles_2SD, | |
| t29_optical_digi, | |
| t30_dna, | |
| t31_vpgTLE-tt, | |
| t33_invert_filter, | |
| t34_biodose_actor] | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y gcc \ | |
| g++ \ | |
| make \ | |
| binutils \ | |
| libx11-dev \ | |
| libxpm-dev \ | |
| libxft-dev \ | |
| libxext-dev \ | |
| qtbase5-dev \ | |
| qt5-qmake \ | |
| git \ | |
| cmake \ | |
| libssl-dev \ | |
| python3.8-dev \ | |
| ccache \ | |
| fftw3-dev | |
| gcc -v | |
| cd | |
| - name: Run the test in docker | |
| run: | | |
| mkdir gate_benchmarks | |
| export GIT_SSL_NO_VERIFY=1 | |
| git clone --recursive https://github.com/OpenGATE/GateBenchmarks.git gate_benchmarks | |
| docker run --rm -e "TEST=${{ matrix.strategy_name }}" -v $GITHUB_WORKSPACE:/src -v $GITHUB_WORKSPACE/gate_benchmarks:/home tbaudier/gatebenchmarks:9.4 /home/.github/workflows/runTest.sh | |