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main.yml
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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]
env:
ROOT_VERSION: 'v6-26-08'
GEANT4_VERSION: 'v11.1.1'
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 }}-build4
restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build4
- name: Install dependencies
run: |
if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
sudo apt-get update -qq
sudo apt-get install -y gcc \
g++ \
make \
binutils \
libx11-dev \
libxpm-dev \
libxft-dev \
libxext-dev \
qtbase5-dev \
qt5-qmake \
git \
cmake \
libssl-dev \
python3.8-dev \
ccache \
fftw3-dev
gcc -v
elif [ "${{ matrix.os }}" == "macos-latest" ]; then
brew update
brew cleanup
brew config
rm -rf /usr/local/bin/python3.11-config /usr/local/bin/2to3-3.11 /usr/local/bin/idle3.11 /usr/local/bin/pydoc3.11 /usr/local/bin/python3.11
rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3
brew install --force --verbose --overwrite --debug qt5 \
ccache \
tbb \
xrootd \
fftw
brew link qt5 --force && sudo ln -s /usr/local/opt/qt/mkspecs /usr/local/mkspecs && sudo ln -s /usr/local/opt/qt/plugins /usr/local/plugins
export PATH=/usr/local/opt/qt/bin:$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 $ROOT_VERSION https://github.com/root-project/root.git --depth 1 src
cd bin
cmake ../src -DCMAKE_CXX_STANDARD=17 \
-Dpython=OFF \
-Dpyroot=OFF \
-Dclad=OFF \
-DCMAKE_INSTALL_PREFIX=$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-1.10.1.zip
unzip libtorch-macos-1.10.1.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 [ ! $? -eq 0 ]; then
exit 1
fi
fi
benchmarks:
runs-on: ubuntu-latest
needs: [build]
strategy:
fail-fast: false
matrix:
strategy_name: [t1_edep_profiles,
t2_edep_vox,
t3_range_e+,
t4_necr,
t6_dpk,
t7_garf,
t8_LETActor,
t10_SpectroGamma,
t11_EMField,
t12_tessellated_volume,
t13_phsp,
t15_optical,
t16_decay,
t17_extended_source,
t18_movement_benchmark,
t19_acollinearity,
t20_digi_adder,
t22_merged_actor,
t23_digi_readout,
t26_CoinSorter,
t27_Hits_2SD,
t28_Singles_2SD,
t29_optical_digi,
t30_dna,
t31_vpgTLE-tt,
t32_isotopes,
t33_invert_filter]
steps:
- name: Checkout github repo
uses: actions/checkout@v3
with:
lfs: true
- name: Checkout LFS objects
run: git lfs checkout
- name: Checkout submodules
run: git submodule update --init --recursive
- name: Install dependencies
run: |
sudo apt-get update -qq
sudo apt-get install -y gcc \
g++ \
make \
binutils \
libx11-dev \
libxpm-dev \
libxft-dev \
libxext-dev \
qtbase5-dev \
qt5-qmake \
git \
cmake \
libssl-dev \
python3.8-dev \
ccache \
fftw3-dev
gcc -v
cd
- name: Run the test in docker
run: |
mkdir gate_benchmarks
export GIT_SSL_NO_VERIFY=1
git clone --recursive https://github.com/OpenGATE/GateBenchmarks.git gate_benchmarks
docker run --rm -e "TEST=${{ matrix.strategy_name }}" -v $GITHUB_WORKSPACE:/src -v $GITHUB_WORKSPACE/gate_benchmarks:/home tbaudier/gatebenchmarks:9.3 /home/.github/workflows/runTest.sh