Merge remote-tracking branch 'origin/trunk-minor' into feature-virtua…

…l-move-monte-carlo
glotzerlab · Dec 12, 2024 · e8281d8 · e8281d8
2 parents d052302 + dcf270d
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.8.2
+current_version = 5.0.0
 commit = False
 tag = False
 parse = ^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P<number>0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$
@@ -14,16 +14,10 @@ values =
 
 [bumpversion:file:INSTALLING.rst]
 
-[bumpversion:file:BUILDING.rst]
-
 [bumpversion:file:CMakeLists.txt]
 
 [bumpversion:file:sphinx-doc/conf.py]
 
-[bumpversion:file:hoomd/hpmc/pair/user.py]
-
-[bumpversion:file:hoomd/hpmc/external/user.py]
-
 [bumpversion:file:.github/ISSUE_TEMPLATE/bug_report.yml]
 
 [bumpversion:file:.github/ISSUE_TEMPLATE/release.md]
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -56,13 +56,11 @@ body:
         - Compiled from source
         - Conda-forge package
         - glotzerlab-software package
-    validations:
-      required: true
   - type: input
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 4.8.2
+      placeholder: 5.0.0
     validations:
       required: true
   - type: markdown

diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md
@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.8.2'
+title: 'Release 5.0.0'
 labels: ''
 assignees: 'joaander'
 
@@ -20,12 +20,13 @@ Minor and major releases:
 
 All releases:
 
-- [ ] Update change log.
-  - ``git log --format=oneline --first-parent $(git log -n 1 --pretty=format:%H -- CHANGELOG.rst)...``
+- [ ] Review change log.
 - [ ] Check readthedocs build, especially change log formatting.
 - [ ] Run *bumpversion*.
 - [ ] Tag and push.
 - [ ] Update conda-forge recipe.
 - [ ] Update *glotzerlab-software*.
 - [ ] Update *hoomd-component-template*.
+- [ ] Update *hoomd-md-pair-template*.
+- [ ] Update *hoomd-hpmc-shape-template*.
 - [ ] Update *hpmc-energy-template*.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -21,15 +21,9 @@ Resolves #???
 <!--- Please build the sphinx documentation and check that any changes to
       documentation display properly. -->
 
-## Change log
-
-<!-- Propose a change log entry. -->
-```
-
-```
-
 ## Checklist:
 
 - [ ] I have reviewed the [**Contributor Guidelines**](https://github.com/glotzerlab/hoomd-blue/blob/trunk-minor/CONTRIBUTING.rst).
 - [ ] I agree with the terms of the [**HOOMD-blue Contributor Agreement**](https://github.com/glotzerlab/hoomd-blue/blob/trunk-minor/ContributorAgreement.md).
 - [ ] My name is on the list of contributors (`sphinx-doc/credits.rst`) in the pull request source branch.
+- [ ] I have summarized these changes in `CHANGELOG.rst` following the established format.
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
@@ -118,15 +116,15 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
         path: code
         submodules: true
 
     - name: Create Python Environment
-      uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0
+      uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
       with:
-        micromamba-version: '1.5.8-0'
+        micromamba-version: '2.0.2-2'
         environment-name: test
         environment-file: code/.github/workflows/environments/py${{ inputs.python }}-conda-lock.yml
         post-cleanup: all
@@ -158,21 +156,16 @@ jobs:
                                -DCMAKE_BUILD_TYPE=${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(inputs.config, 'cuda') }}
         ENABLE_MPI: ${{ contains(inputs.config, 'mpi') }}
-        ENABLE_TBB: ${{ contains(inputs.config, 'tbb') }}
-        ENABLE_LLVM: ${{ contains(inputs.config, 'llvm') }}
         BUILD_MD: ${{ !contains(inputs.config, 'nomd') }}
         BUILD_HPMC: ${{ !contains(inputs.config, 'nohpmc') }}
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
@@ -181,18 +174,6 @@ jobs:
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
       working-directory: build
 
-    - name: Configure plugins
-      run : |
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake -S code/example_plugins -B build-example-plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
-      env:
-        BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
-
-    - name: Build plugins
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
-      working-directory: build-example-plugins
-
     - name: Remove object files
       run: find build -type f -name '*.o' -delete
 
@@ -203,13 +184,13 @@ 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@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
       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@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
         path: install.tar
@@ -233,14 +214,14 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
         path: code
 
     - name: Create Python Environment
-      uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0
+      uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
       with:
-        micromamba-version: '1.5.8-0'
+        micromamba-version: '2.0.2-2'
         environment-name: test
         environment-file: code/.github/workflows/environments/py${{ inputs.python }}-conda-lock.yml
         post-cleanup: all
@@ -275,7 +256,7 @@ 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') }}
@@ -285,21 +266,36 @@ 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
 
+    ### compute-sanitizer checks: These checks are slow, so run them only when validation is
+    # requested, but no on the actual long validation tests. Every class's basic test should ensure
+    # that the GPU kernel is called for at least a few timesteps for these checks to be effective.
+    - name: Run memcheck
+      if: ${{ contains(inputs.config, 'cuda') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' && !contains(inputs.config, 'mpi')}}
+      run: compute-sanitizer --tool memcheck --error-exitcode 1 python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1
+
+    - name: Run racecheck
+      if: ${{ contains(inputs.config, 'cuda') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' && !contains(inputs.config, 'mpi')}}
+      run: compute-sanitizer --tool racecheck --error-exitcode 1 python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1
+
+    - name: Run synccheck
+      if: ${{ contains(inputs.config, 'cuda') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' && !contains(inputs.config, 'mpi')}}
+      run: compute-sanitizer --tool synccheck --error-exitcode 1 python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1
+
     ### Validation tests
     - name: Run pytest -m validate (serial)
       if: ${{ !contains(inputs.config, 'mpi') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
       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 -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
+      if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
       run: 'for i in *.py; do echo "Running howto: $i" && python3 $i || exit 1; done'
       working-directory: code/sphinx-doc/howto
 

diff --git a/.github/workflows/environments/environment.yaml b/.github/workflows/environments/environment.yaml
@@ -1,5 +1,4 @@
 channels:
-- conda-forge/label/numpy_rc
 - conda-forge
 dependencies:
 - cereal
@@ -8,7 +7,7 @@ dependencies:
 - gsd
 - h5py
 - ninja
-- numpy>=2.0.0rc1
+- numpy>=2.0.0
 - mpi4py
 - openmpi
 - pybind11