Removed use of omp get wall time functions #526
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| name: CI Ubuntu 18.04 | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| release: | |
| types: [ published ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Release | |
| jobs: | |
| build: | |
| name: Build | |
| # 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: ubuntu-20.04 | |
| container: | |
| image: ubuntu:18.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| apt update && apt install -y sudo | |
| mkdir -p ${{github.workspace}}/artifacts | |
| # Get a newer version of cmake | |
| sudo apt install -y gpg wget software-properties-common lsb-release ca-certificates | |
| wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | sudo tee /usr/share/keyrings/kitware-archive-keyring.gpg >/dev/null | |
| echo 'deb [signed-by=/usr/share/keyrings/kitware-archive-keyring.gpg] https://apt.kitware.com/ubuntu/ bionic main' | sudo tee /etc/apt/sources.list.d/kitware.list >/dev/null | |
| sudo apt-get update | |
| sudo rm /usr/share/keyrings/kitware-archive-keyring.gpg | |
| sudo apt-get install kitware-archive-keyring | |
| sudo apt install -y cmake | |
| sudo apt install -y g++ patchelf | |
| sudo apt install -y '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev | |
| sudo apt install -y libopenslide-dev libjpeg-turbo8-dev # Needed for WSI module | |
| sudo apt install -y pkgconf libusb-1.0-0-dev # Needed for realsense | |
| sudo apt install -y python3 libpython3-dev python3-pip python3-setuptools | |
| sudo pip3 install --upgrade pip | |
| pip3 install numpy==1.19.5 pylddwrap==1.2.0 twine wheel==0.37.1 | |
| - name: Install CUDA and TensorRT | |
| run: | | |
| wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin | |
| sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600 | |
| sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub | |
| sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub | |
| sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /" | |
| sudo apt-get update | |
| sudo apt-get install -y cuda-toolkit-11-0 libcudnn8 libnvinfer-dev libnvonnxparsers-dev libnvparsers-dev | |
| - name: Configure CMake | |
| run: | | |
| cmake -B build \ | |
| -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}\ | |
| -DFAST_MODULE_OpenVINO=ON \ | |
| -DFAST_MODULE_Dicom=ON \ | |
| -DFAST_MODULE_WholeSlideImaging=ON \ | |
| -DFAST_MODULE_OpenIGTLink=ON \ | |
| -DFAST_MODULE_Clarius=ON \ | |
| -DFAST_MODULE_TensorFlow=ON \ | |
| -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda/" \ | |
| -DFAST_MODULE_TensorRT=ON \ | |
| -DFAST_MODULE_HDF5=ON \ | |
| -DFAST_MODULE_Plotting=ON \ | |
| -DFAST_MODULE_Python=ON \ | |
| -DFAST_MODULE_RealSense=ON \ | |
| -DFAST_BUILD_EXAMPLES=ON | |
| - name: Build | |
| # Build your program with the given configuration | |
| run: cmake --build build --config ${{env.BUILD_TYPE}} -j 4 | |
| - name: Build Python wheel | |
| run: | | |
| cmake --build build --config ${{env.BUILD_TYPE}} --target python-wheel -j 4 | |
| - name: Package | |
| run: | | |
| cmake --build build --config ${{env.BUILD_TYPE}} --target package -j 4 | |
| - name: Upload Debian package | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Debian package | |
| path: ${{github.workspace}}/build/fast_*.deb | |
| if-no-files-found: error | |
| - name: Upload archive package | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Archive package (tar.xz) | |
| path: ${{github.workspace}}/build/fast_*.tar.xz | |
| if-no-files-found: error | |
| - name: Upload Python wheel | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Python wheel | |
| path: ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| if-no-files-found: error | |
| - name: Upload Debian package to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_*.deb | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload archive package to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_*.tar.xz | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload Python wheel to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload Python wheel to PyPi | |
| if: ${{ github.event_name == 'release' && !contains(github.ref, 'rc') }} | |
| run: | | |
| twine upload --username smistad --password ${{ secrets.PYPI_PASSWORD }} ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| - name: Test PyPi upload | |
| if: ${{ github.event_name == 'release' && !contains(github.ref, 'rc') }} | |
| run: | | |
| sleep 60 | |
| pip3 install pyfast==${GITHUB_REF#refs/tags/v} | |
| shell: bash | |
| test-cpp: | |
| name: Run C++ Tests | |
| needs: [build] | |
| runs-on: [self-hosted, linux] | |
| steps: | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: 'Archive package (tar.xz)' | |
| path: ${{github.workspace}}/download/ | |
| - name: Extract artifact | |
| run: | | |
| mkdir -p ${{github.workspace}}/download/ | |
| cd ${{github.workspace}}/download/ | |
| tar -xf fast_*.tar.xz -C ${{github.workspace}} | |
| - name: Download test data | |
| run: | | |
| cd ${{github.workspace}} | |
| cd fast* | |
| cd fast/bin/ | |
| ./downloadTestData | |
| - name: Run tests | |
| env: | |
| DISPLAY: ':1' | |
| run: | | |
| cd ${{github.workspace}} | |
| cd fast_* | |
| cd fast/bin/ | |
| ./testFAST ~[visual] | |
| - name: Cleanup | |
| if: always() | |
| run: | | |
| rm -Rf ${{github.workspace}} | |
| rm -Rf $HOME/FAST/kernel_binaries/* | |
| test-python: | |
| name: Run Python Tests | |
| needs: [build] | |
| runs-on: [self-hosted, linux] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: 'Python wheel' | |
| path: ${{github.workspace}}/download/ | |
| - name: Create environment and install python packages | |
| run: | | |
| cd ${{github.workspace}} | |
| mkdir tmp | |
| cd tmp | |
| virtualenv -p python3 venv | |
| source venv/bin/activate | |
| pip3 install pytest | |
| pip3 install ${{github.workspace}}/download/pyFAST-*.whl | |
| - name: Run tests | |
| env: | |
| DISPLAY: ':1' | |
| run: | | |
| cd ${{github.workspace}}/tmp/ | |
| source venv/bin/activate | |
| pytest ../source/FAST/ | |
| - name: Cleanup | |
| if: always() | |
| run: | | |
| rm -Rf ${{github.workspace}}/download/ | |
| rm -Rf ${{github.workspace}}/tmp/ | |
| rm -Rf $HOME/FAST/kernel_binaries/* | |