Bump numpy from 1.26.4 to 2.0.0 #5449
Workflow file for this run
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| name: Test | |
| # Edit the `test.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the | |
| # workflow. | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| types: [opened, labeled, reopened, synchronize] | |
| # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull | |
| # request source branch is in the same repository. | |
| push: | |
| branches: | |
| - "trunk-*" | |
| # Trigger on request. | |
| workflow_dispatch: | |
| env: | |
| # prevent deadlocked MPI tests from causing the job to cancel | |
| MPIEXEC_TIMEOUT: 3000 | |
| # allow mpirun to execute as root in the tests | |
| OMPI_ALLOW_RUN_AS_ROOT: 1 | |
| OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 | |
| # allow openmpi to oversubscribe cores | |
| OMPI_MCA_rmaps_base_oversubscribe: 1 | |
| # prevent errors from mis-configured openib systems | |
| OMPI_MCA_btl: "vader,self" | |
| # skip running the CPU tests in GPU builds | |
| _HOOMD_SKIP_CPU_TESTS_WHEN_GPUS_PRESENT_: 1 | |
| # Require GPU tests in GPU builds. | |
| _HOOMD_REQUIRE_GPU_TESTS_IN_GPU_BUILDS_: 1 | |
| # import HOOMD out of the build directory | |
| PYTHONPATH: ${{ github.workspace }}/install | |
| # Use multiple jobs to reduce the amount of time spent on GPU runners. Use CPU runners for | |
| # compiling all tests configurations (GPU and CPU), then upload the build directory (sans object | |
| # files) as an artifact. Test jobs depend on the build job, download the install directory, and run | |
| # the tests. Upload each build configuration to a separate artifact. | |
| # Github Actions does not support any form of templating at this time, not even YAML anchors. | |
| # To minimize the number of duplicated lines, encode the job configuration as an array in config: | |
| # [image, (mpi), (tbb)] | |
| jobs: | |
| start_action_runners: | |
| name: Start action runners | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Use jetstream2-admin/start | |
| uses: glotzerlab/jetstream2-admin/start@v1.2.5 | |
| with: | |
| OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }} | |
| OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }} | |
| build: | |
| name: Build [${{ join(matrix.config, '_') }}] | |
| runs-on: ${{ matrix.build_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| steps: | |
| - name: Set Werror on recent compilers | |
| run: | | |
| echo "CXXFLAGS=-Werror" >> $GITHUB_ENV | |
| if: ${{ !startsWith(matrix.config[0], 'gcc7') }} | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Configure | |
| run: | | |
| mkdir -p build | |
| cd build | |
| if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi | |
| echo "BUILD_TYPE=${BUILD_TYPE}" | |
| cmake ../code -GNinja \ | |
| -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ | |
| -DENABLE_GPU=${ENABLE_GPU:-"OFF"} \ | |
| -DENABLE_MPI=${ENABLE_MPI:-"OFF"} \ | |
| -DENABLE_TBB=${ENABLE_TBB:-"OFF"} \ | |
| -DENABLE_LLVM=${ENABLE_LLVM:-"OFF"} \ | |
| -DBUILD_MD=${BUILD_MD:-"ON"} \ | |
| -DBUILD_MPCD=${BUILD_MD:-"ON"} \ | |
| -DBUILD_METAL=${BUILD_MD:-"ON"} \ | |
| -DBUILD_HPMC=${BUILD_HPMC:-"ON"} \ | |
| -DCUDA_ARCH_LIST="60;70" \ | |
| -DENABLE_DEBUG_JIT=ON \ | |
| -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install \ | |
| -DPLUGINS="" | |
| env: | |
| ENABLE_GPU: ${{ contains(matrix.config[0], 'cuda') }} | |
| ENABLE_MPI: ${{ contains(matrix.config, 'mpi') }} | |
| ENABLE_TBB: ${{ contains(matrix.config, 'tbb') }} | |
| ENABLE_LLVM: ${{ contains(matrix.config, 'llvm') }} | |
| BUILD_MD: ${{ !contains(matrix.config, 'nomd') }} | |
| BUILD_HPMC: ${{ !contains(matrix.config, 'nohpmc') }} | |
| BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }} | |
| shell: bash | |
| - name: Build | |
| run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) | |
| working-directory: build | |
| - name: Configure plugins | |
| run : | | |
| mkdir -p build-example-plugins | |
| cd build-example-plugins | |
| if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi | |
| echo "BUILD_TYPE=${BUILD_TYPE}" | |
| CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake ../code/example_plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE} | |
| env: | |
| BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }} | |
| shell: bash | |
| - name: Build plugins | |
| run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) | |
| working-directory: build-example-plugins | |
| - name: Remove object files | |
| run: find build -type f -name '*.o' -delete | |
| # Tar the build directory to preserve permissions and reduce HTTP requests on upload. | |
| - name: 'Tar build' | |
| run: tar --use-compress-program='zstd -10 -T0' -cvf build.tar build | |
| - name: 'Tar install' | |
| run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install | |
| # Upload the tarballs. Retain the file for a limited time in case developers need to download | |
| # and run tests locally for further debugging. | |
| - name: 'Upload build' | |
| uses: actions/upload-artifact@v4.3.3 | |
| with: | |
| name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| path: build.tar | |
| retention-days: 7 | |
| - name: 'Upload install' | |
| uses: actions/upload-artifact@v4.3.3 | |
| with: | |
| name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| path: install.tar | |
| retention-days: 7 | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| pytest: | |
| name: Run pytest [${{ join(matrix.config, '_') }}] | |
| needs: build | |
| runs-on: ${{ matrix.test_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Download install | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| - name: Untar install | |
| run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar | |
| - name: Run pytest (serial) | |
| run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 | |
| - name: Run pytest (mpi) | |
| if: ${{ contains(matrix.config, 'mpi') }} | |
| run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 || (( cat pytest.out.1 && exit 1 )) | |
| - name: Run pytest (serial without cupy) | |
| if: ${{ contains(matrix.config[0], 'cuda') }} | |
| run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional | |
| env: | |
| _HOOMD_DISALLOW_CUPY_: 1 | |
| - name: Run pytest (mpi without cupy) | |
| if: ${{ contains(matrix.config[0], 'cuda') && contains(matrix.config, 'mpi') }} | |
| run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional || (( cat pytest.out.1 && exit 1 )) | |
| env: | |
| _HOOMD_DISALLOW_CUPY_: 1 | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| ctest: | |
| name: Run ctest [${{ join(matrix.config, '_') }}] | |
| needs: build | |
| runs-on: ${{ matrix.test_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Download build | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| - name: Untar build | |
| run: tar --use-compress-program='zstd -10 -T0' -xvf build.tar | |
| - name: Run tests | |
| run: >- | |
| ctest | |
| -T test | |
| --output-on-failure | |
| --test-output-size-failed 1048576 | |
| --test-output-size-passed 1048576 | |
| working-directory: build | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| validate: | |
| name: Validate [${{ join(matrix.config, '_') }}] | |
| needs: build | |
| runs-on: ${{ matrix.test_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') }} | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Download install | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| - name: Untar install | |
| run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar | |
| - name: Run pytest (serial) | |
| if: ${{ !contains(matrix.config, 'mpi') }} | |
| run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -p hoomd.pytest_plugin_validate -m validate --validate | |
| - name: Run pytest (mpi) | |
| if: ${{ contains(matrix.config, 'mpi') }} | |
| run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -p hoomd.pytest_plugin_validate -m validate --validate || (( cat pytest.out.1 && exit 1 )) | |
| - name: Run howto guides (serial) | |
| if: ${{ contains(matrix.config, 'llvm') }} # some examples require LLVM | |
| run: 'for i in *.py; do echo "Running howto: $i" && python3 $i || exit 1; done' | |
| working-directory: code/sphinx-doc/howto | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| build_release: | |
| name: Build [${{ join(matrix.config, '_') }}] | |
| runs-on: ${{ matrix.build_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda116_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda115_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda114_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda113_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda112_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda111_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [clang10_py38, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }} | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Configure | |
| run: | | |
| mkdir -p build | |
| cd build | |
| if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi | |
| echo "BUILD_TYPE=${BUILD_TYPE}" | |
| cmake ../code -GNinja \ | |
| -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ | |
| -DENABLE_GPU=${ENABLE_GPU:-"OFF"} \ | |
| -DENABLE_MPI=${ENABLE_MPI:-"OFF"} \ | |
| -DENABLE_TBB=${ENABLE_TBB:-"OFF"} \ | |
| -DENABLE_LLVM=${ENABLE_LLVM:-"OFF"} \ | |
| -DBUILD_MD=${BUILD_MD:-"ON"} \ | |
| -DBUILD_MPCD=${BUILD_MD:-"ON"} \ | |
| -DBUILD_METAL=${BUILD_MD:-"ON"} \ | |
| -DBUILD_HPMC=${BUILD_HPMC:-"ON"} \ | |
| -DCUDA_ARCH_LIST="60;70" \ | |
| -DENABLE_DEBUG_JIT=ON \ | |
| -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install \ | |
| -DPLUGINS="" | |
| env: | |
| ENABLE_GPU: ${{ contains(matrix.config[0], 'cuda') }} | |
| ENABLE_MPI: ${{ contains(matrix.config, 'mpi') }} | |
| ENABLE_TBB: ${{ contains(matrix.config, 'tbb') }} | |
| ENABLE_LLVM: ${{ contains(matrix.config, 'llvm') }} | |
| BUILD_MD: ${{ !contains(matrix.config, 'nomd') }} | |
| BUILD_HPMC: ${{ !contains(matrix.config, 'nohpmc') }} | |
| BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }} | |
| shell: bash | |
| - name: Build | |
| run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) | |
| working-directory: build | |
| - name: Configure plugins | |
| run : | | |
| mkdir -p build-example-plugins | |
| cd build-example-plugins | |
| if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi | |
| echo "BUILD_TYPE=${BUILD_TYPE}" | |
| CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake ../code/example_plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE} | |
| env: | |
| BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }} | |
| shell: bash | |
| - name: Build plugins | |
| run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) | |
| working-directory: build-example-plugins | |
| - name: Remove object files | |
| run: find build -type f -name '*.o' -delete | |
| # Tar the build directory to preserve permissions and reduce HTTP requests on upload. | |
| - name: 'Tar build' | |
| run: tar --use-compress-program='zstd -10 -T0' -cvf build.tar build | |
| - name: 'Tar install' | |
| run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install | |
| # Upload the tarballs. Retain the file for a limited time in case developers need to download | |
| # and run tests locally for further debugging. | |
| - name: 'Upload build' | |
| uses: actions/upload-artifact@v4.3.3 | |
| with: | |
| name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| path: build.tar | |
| retention-days: 7 | |
| - name: 'Upload install' | |
| uses: actions/upload-artifact@v4.3.3 | |
| with: | |
| name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| path: install.tar | |
| retention-days: 7 | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| pytest_release: | |
| name: Run pytest [${{ join(matrix.config, '_') }}] | |
| needs: build_release | |
| runs-on: ${{ matrix.test_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda116_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda115_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda114_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda113_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda112_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda111_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [clang10_py38, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }} | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Download install | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| - name: Untar install | |
| run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar | |
| - name: Run pytest (serial) | |
| run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 | |
| - name: Run pytest (mpi) | |
| if: ${{ contains(matrix.config, 'mpi') }} | |
| run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 || (( cat pytest.out.1 && exit 1 )) | |
| - name: Run pytest (serial without cupy) | |
| if: ${{ contains(matrix.config[0], 'cuda') }} | |
| run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional | |
| env: | |
| _HOOMD_DISALLOW_CUPY_: 1 | |
| - name: Run pytest (mpi without cupy) | |
| if: ${{ contains(matrix.config[0], 'cuda') && contains(matrix.config, 'mpi') }} | |
| run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional || (( cat pytest.out.1 && exit 1 )) | |
| env: | |
| _HOOMD_DISALLOW_CUPY_: 1 | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| ctest_release: | |
| name: Run ctest [${{ join(matrix.config, '_') }}] | |
| needs: build_release | |
| runs-on: ${{ matrix.test_runner }} | |
| container: | |
| image: glotzerlab/ci:2024.03.01-${{ matrix.config[0] }} | |
| options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES | |
| strategy: | |
| matrix: | |
| include: | |
| - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda116_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda115_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda114_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda113_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda112_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [cuda111_gcc9_py38, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' } | |
| - {config: [clang10_py38, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' } | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }} | |
| steps: | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.4 | |
| with: | |
| path: code | |
| submodules: true | |
| - name: Download build | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} | |
| - name: Untar build | |
| run: tar --use-compress-program='zstd -10 -T0' -xvf build.tar | |
| - name: Run tests | |
| run: >- | |
| ctest | |
| -T test | |
| --output-on-failure | |
| --test-output-size-failed 1048576 | |
| --test-output-size-passed 1048576 | |
| working-directory: build | |
| - name: Clean workspace | |
| run: ( shopt -s dotglob nullglob; rm -rf ./* ) | |
| shell: bash | |
| - name: Clean HOME | |
| run: ( shopt -s dotglob nullglob; rm -rf $HOME/* ) | |
| shell: bash | |
| # This job is used to provide a single requirement for branch merge conditions. GitHub considers | |
| # the check passing even if it is skipped, so this job raises errors when required jobs were not | |
| # run. | |
| unit_tests_complete: | |
| name: Unit test | |
| needs: [pytest, ctest, validate] | |
| if: ${{ always() && github.event_name == 'pull_request' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Error if pytest did not succeed | |
| if: needs.pytest.result != 'success' | |
| run: echo "::error ::pytest tests failed." && exit 1 | |
| - name: Error if ctest did not succeed | |
| if: needs.ctest.result != 'success' | |
| run: echo "::error ::ctest tests failed." && exit 1 | |
| - name: Warn if validate did not run | |
| if: needs.validate.result == 'skipped' | |
| run: echo "::warning ::Skipped validation tests." && exit 1 | |
| - name: Error if validate did not succeed | |
| if: needs.validate.result != 'success' | |
| run: echo "::error ::Validation tests failed." && exit 1 | |
| - run: echo "Done!" |