FastPathology Ubuntu 18.04 #23
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: FastPathology Ubuntu 18.04 | |
| on: | |
| workflow_dispatch: | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Release | |
| jobs: | |
| build: | |
| name: Build | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: ubuntu:18.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| apt update && apt install -y sudo | |
| # Get a newer version of cmake | |
| sudo apt install -y gpg wget software-properties-common lsb-release | |
| 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 | |
| - 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 | |
| # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make. | |
| # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type | |
| run: | | |
| cmake -B build \ | |
| -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}\ | |
| -DFAST_MODULE_OpenVINO=ON \ | |
| -DFAST_MODULE_Dicom=OFF \ | |
| -DFAST_MODULE_WholeSlideImaging=ON \ | |
| -DFAST_MODULE_OpenIGTLink=OFF \ | |
| -DFAST_MODULE_Clarius=OFF \ | |
| -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=OFF \ | |
| -DFAST_MODULE_RealSense=OFF \ | |
| -DFAST_BUILD_TESTS=ON \ | |
| -DFAST_BUILD_EXAMPLES=OFF | |
| - name: Build | |
| # Build your program with the given configuration | |
| run: cmake --build build --config ${{env.BUILD_TYPE}} -j 4 | |
| - name: Package | |
| run: | | |
| cmake --build build --config ${{env.BUILD_TYPE}} --target package -j 4 | |
| mv build/fast_*.tar.xz build/fast_ubuntu18.04.tar.xz | |
| - name: Upload archive package | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Archive package (tar.xz) | |
| path: ${{github.workspace}}/build/fast_ubuntu18.04.tar.xz | |
| if-no-files-found: error | |
| - name: Upload package to external repo release | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_name: AICAN-Research/FAST-Pathology-dependencies | |
| repo_token: ${{ secrets.FAST_PATHOLOGY_PUSH_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_ubuntu18.04.tar.xz | |
| asset_name: fast_ubuntu18.04.tar.xz | |
| file_glob: true | |
| tag: v1.0.0 | |
| overwrite: true | |
| 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/* |