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Fix SDF computation with patchy potentials. #4687

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Fix SDF computation with patchy potentials.

Fix SDF computation with patchy potentials. #4687

Workflow file for this run

.github/workflows/test.yml at 7f98259
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
# 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/[email protected]
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: ${{ matrix.build_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ 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/[email protected]
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/[email protected]
with:
name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
path: build.tar
retention-days: 7
- name: 'Upload install'
uses: actions/[email protected]
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: ${{ matrix.test_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
strategy:
matrix:
include:
- {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
steps:
- name: Clean workspace
run: ( shopt -s dotglob nullglob; rm -rf ./* )
shell: bash
- name: Checkout
uses: actions/[email protected]
with:
path: code
submodules: true
- name: Download install
uses: actions/[email protected]
with:
name: install-${{ 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 -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 -x --pyargs hoomd -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 -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 -x --pyargs hoomd -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: ${{ matrix.test_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
strategy:
matrix:
include:
- {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
- {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
- {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
steps:
- name: Clean workspace
run: ( shopt -s dotglob nullglob; rm -rf ./* )
shell: bash
- name: Checkout
uses: actions/[email protected]
with:
path: code
submodules: true
- name: Download build
uses: actions/[email protected]
with:
name: build-${{ 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: ${{ matrix.test_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ 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: ${{ contains(github.event.pull_request.labels.*.name, 'validate') }}
steps:
- name: Clean workspace
run: ( shopt -s dotglob nullglob; rm -rf ./* )
shell: bash
- name: Checkout
uses: actions/[email protected]
with:
path: code
submodules: true
- name: Download install
uses: actions/[email protected]
with:
name: install-${{ 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 -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 -x --pyargs hoomd -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: ${{ matrix.build_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ 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/[email protected]
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/[email protected]
with:
name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
path: build.tar
retention-days: 7
- name: 'Upload install'
uses: actions/[email protected]
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: ${{ matrix.test_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ 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: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
steps:
- name: Clean workspace
run: ( shopt -s dotglob nullglob; rm -rf ./* )
shell: bash
- name: Checkout
uses: actions/[email protected]
with:
path: code
submodules: true
- name: Download install
uses: actions/[email protected]
with:
name: install-${{ 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 -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 -x --pyargs hoomd -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 -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 -x --pyargs hoomd -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: ${{ matrix.test_runner }}
container:
image: glotzerlab/ci:2023.10.09-${{ 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: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
steps:
- name: Clean workspace
run: ( shopt -s dotglob nullglob; rm -rf ./* )
shell: bash
- name: Checkout
uses: actions/[email protected]
with:
path: code
submodules: true
- name: Download build
uses: actions/[email protected]
with:
name: build-${{ 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!"