Update ['pixdim'] after Spacing transform in meta dict. #16085
Workflow file for this run
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| # Jenkinsfile.monai-premerge | |
| name: premerge-gpu | |
| on: | |
| # quick tests for pull requests and the releasing branches | |
| push: | |
| branches: | |
| - main | |
| - releasing/* | |
| pull_request: | |
| types: [opened, synchronize, closed] | |
| concurrency: | |
| # automatically cancel the previously triggered workflows when there's a newer version | |
| group: build-gpu-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| GPU-quick-py3: # GPU with full dependencies | |
| # if: ${{ github.repository == 'Project-MONAI/MONAI' && github.event.pull_request.merged != true }} | |
| if: ${{ false }} # disable self-hosted job project-monai/monai#7039 | |
| strategy: | |
| matrix: | |
| environment: | |
| - "PT19+CUDA114DOCKER" | |
| - "PT110+CUDA111" | |
| - "PT112+CUDA118DOCKER" | |
| - "PT113+CUDA116" | |
| - "PT210+CUDA121DOCKER" | |
| include: | |
| # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes | |
| - environment: PT110+CUDA111 | |
| pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu111" | |
| base: "nvcr.io/nvidia/cuda:11.1.1-devel-ubuntu18.04" | |
| - environment: PT112+CUDA118DOCKER | |
| # 22.09: 1.13.0a0+d0d6b1f | |
| pytorch: "-h" # we explicitly set pytorch to -h to avoid pip install error | |
| base: "nvcr.io/nvidia/pytorch:22.09-py3" | |
| - environment: PT113+CUDA116 | |
| pytorch: "torch==1.13.1 torchvision==0.14.1" | |
| base: "nvcr.io/nvidia/cuda:11.6.1-devel-ubuntu18.04" | |
| - environment: PT210+CUDA121DOCKER | |
| # 23.08: 2.1.0a0+29c30b1 | |
| pytorch: "-h" # we explicitly set pytorch to -h to avoid pip install error | |
| base: "nvcr.io/nvidia/pytorch:23.08-py3" | |
| - environment: PT210+CUDA121DOCKER | |
| # 24.08: 2.3.0a0+40ec155e58.nv24.3 | |
| pytorch: "-h" # we explicitly set pytorch to -h to avoid pip install error | |
| base: "nvcr.io/nvidia/pytorch:24.08-py3" | |
| container: | |
| image: ${{ matrix.base }} | |
| options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true # workaround for unsatisfied condition: cuda>=11.6 | |
| runs-on: [self-hosted, linux, x64, common] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: apt install | |
| if: github.event.pull_request.merged != true | |
| run: | | |
| apt-get update | |
| apt-get install -y wget | |
| if [ ${{ matrix.environment }} = "PT110+CUDA111" ] || \ | |
| [ ${{ matrix.environment }} = "PT113+CUDA116" ] | |
| then | |
| PYVER=3.9 PYSFX=3 DISTUTILS=python3-distutils && \ | |
| apt-get update && apt-get install -y --no-install-recommends \ | |
| curl \ | |
| pkg-config \ | |
| python$PYVER \ | |
| python$PYVER-dev \ | |
| python$PYSFX-pip \ | |
| $DISTUTILS \ | |
| rsync \ | |
| swig \ | |
| unzip \ | |
| zip \ | |
| zlib1g-dev \ | |
| libboost-locale-dev \ | |
| libboost-program-options-dev \ | |
| libboost-system-dev \ | |
| libboost-thread-dev \ | |
| libboost-test-dev \ | |
| libgoogle-glog-dev \ | |
| libjsoncpp-dev \ | |
| cmake \ | |
| git && \ | |
| rm -rf /var/lib/apt/lists/* && \ | |
| export PYTHONIOENCODING=utf-8 LC_ALL=C.UTF-8 && \ | |
| rm -f /usr/bin/python && \ | |
| rm -f /usr/bin/python`echo $PYVER | cut -c1-1` && \ | |
| ln -s /usr/bin/python$PYVER /usr/bin/python && \ | |
| ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` && | |
| curl -O https://bootstrap.pypa.io/get-pip.py && \ | |
| python get-pip.py && \ | |
| rm get-pip.py; | |
| fi | |
| - if: matrix.environment == 'PT19+CUDA114DOCKER' | |
| name: Optional Cupy dependency (cuda114) | |
| run: echo "cupy-cuda114" >> requirements-dev.txt | |
| - name: Install dependencies | |
| if: github.event.pull_request.merged != true | |
| run: | | |
| which python | |
| python -m pip install --upgrade pip wheel | |
| # fixes preinstalled ruamel_yaml error from the docker image | |
| rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel* | |
| rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/llvmlite* #6377 | |
| python -m pip install ${{ matrix.pytorch }} | |
| python -m pip install -r requirements-dev.txt | |
| python -m pip list | |
| - name: Run quick tests (GPU) | |
| if: github.event.pull_request.merged != true | |
| run: | | |
| git clone --depth 1 \ | |
| https://github.com/Project-MONAI/MONAI-extra-test-data.git /MONAI-extra-test-data | |
| export MONAI_EXTRA_TEST_DATA="/MONAI-extra-test-data" | |
| nvidia-smi | |
| export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)") | |
| echo "Sleep $LAUNCH_DELAY" | |
| sleep $LAUNCH_DELAY | |
| export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils | tail -n 1) | |
| echo $CUDA_VISIBLE_DEVICES | |
| trap 'if pgrep python; then pkill python; fi;' ERR | |
| python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null & | |
| python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))" | |
| python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))' | |
| python -c "import monai; monai.config.print_config()" | |
| # build for the current self-hosted CI Tesla V100 | |
| BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --build --disttests | |
| ./runtests.sh --quick --unittests | |
| if [ ${{ matrix.environment }} = "PT113+CUDA116" ]; then | |
| # test the clang-format tool downloading once | |
| coverage run -m tests.clang_format_utils | |
| fi | |
| coverage xml --ignore-errors | |
| if pgrep python; then pkill python; fi | |
| shell: bash | |
| - name: Upload coverage | |
| if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }} | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| files: ./coverage.xml |