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fix Brownian integrators when using anisotropic interactions and zeroing out elements of the moment of inertia tensor #5442

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fix Brownian integrators when using anisotropic interactions and zeroing out elements of the moment of inertia tensor

fix Brownian integrators when using anisotropic interactions and zeroing out elements of the moment of inertia tensor #5442

Workflow file for this run

.github/workflows/test.yml at a1d7435
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!"