Merge branch 'trunk-patch' into trunk-minor

glotzerlab · Sep 19, 2024 · a1c6974 · a1c6974
2 parents 9d56480 + cd4240f
commit a1c6974
Show file tree

Hide file tree

Showing 13 changed files with 1,976 additions and 1,689 deletions.
diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
@@ -30,8 +30,6 @@ defaults:
     shell: bash
 
 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
@@ -203,13 +201,13 @@ jobs:
       run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install
 
     - name: 'Upload build'
-      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
+      uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
       with:
         name: build-${{ inputs.config }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
+      uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
         path: install.tar
@@ -275,7 +273,7 @@ jobs:
 
     - name: Run pytest (mpi)
       if: ${{ contains(inputs.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 ))
+      run: mpirun --timeout 3000 -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(inputs.config, 'cuda') }}
@@ -285,7 +283,7 @@ jobs:
 
     - name: Run pytest (mpi without cupy)
       if: ${{ contains(inputs.config, 'cuda') && contains(inputs.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 ))
+      run: mpirun --timeout 3000 -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
 
@@ -296,7 +294,7 @@ jobs:
 
     - name: Run pytest -m validate (mpi)
       if: ${{ contains(inputs.config, 'mpi') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
-      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 ))
+      run: mpirun --timeout 3000 -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(inputs.config, 'llvm') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}  # some examples require LLVM