[TYPO]

.gitattributes

@@ -1,2 +1,3 @@
 # do not show up detailed difference on GitHub
 source/3rdparty/* linguist-generated=true
+source/3rdparty/README.md linguist-generated=false

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: dropdown

.github/ISSUE_TEMPLATE/generic-issue.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: textarea

.github/labeler.yml

@@ -1,39 +1,38 @@
-Python:
-- changed-files:
-  - any-glob-to-any-file:
-    - deepmd/**/*
-    - deepmd_utils/**/*
-    - source/tests/**/*
-Docs:
-- changed-files:
-  - any-glob-to-any-file: doc/**/*
-Examples:
-- changed-files:
-  - any-glob-to-any-file: examples/**/*
-Core:
-- changed-files:
-  - any-glob-to-any-file: source/lib/**/*
-CUDA:
-- changed-files:
-  - any-glob-to-any-file: source/lib/src/gpu/**/*
-ROCM:
-- changed-files:
-  - any-glob-to-any-file: source/lib/src/gpu/**/*
-OP:
-- changed-files:
-  - any-glob-to-any-file: source/op/**/*
-C++:
-- changed-files:
-  - any-glob-to-any-file: source/api_cc/**/*
-C:
-- changed-files:
-  - any-glob-to-any-file: source/api_c/**/*
-LAMMPS:
-- changed-files:
-  - any-glob-to-any-file: source/lmp/**/*
-Gromacs:
-- changed-files:
-  - any-glob-to-any-file: source/gmx/**/*
-i-Pi:
-- changed-files:
-  - any-glob-to-any-file: source/ipi/**/*
+Python:
+  - changed-files:
+      - any-glob-to-any-file:
+          - deepmd/**/*
+          - source/tests/**/*
+Docs:
+  - changed-files:
+      - any-glob-to-any-file: doc/**/*
+Examples:
+  - changed-files:
+      - any-glob-to-any-file: examples/**/*
+Core:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/**/*
+CUDA:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/src/gpu/**/*
+ROCM:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/src/gpu/**/*
+OP:
+  - changed-files:
+      - any-glob-to-any-file: source/op/**/*
+C++:
+  - changed-files:
+      - any-glob-to-any-file: source/api_cc/**/*
+C:
+  - changed-files:
+      - any-glob-to-any-file: source/api_c/**/*
+LAMMPS:
+  - changed-files:
+      - any-glob-to-any-file: source/lmp/**/*
+Gromacs:
+  - changed-files:
+      - any-glob-to-any-file: source/gmx/**/*
+i-Pi:
+  - changed-files:
+      - any-glob-to-any-file: source/ipi/**/*

.github/workflows/build_cc.yml

@@ -1,6 +1,12 @@
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
   pull_request:
+  merge_group:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 name: Build C++
 jobs:
   buildcc:
@@ -27,6 +33,10 @@ jobs:
         cache: 'pip'
     - uses: lukka/get-cmake@latest
     - run: python -m pip install tensorflow
+    - name: Download libtorch
+      run: |
+         wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.1.2%2Bcpu.zip -O libtorch.zip
+         unzip libtorch.zip
     - run: |
          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
          && sudo dpkg -i cuda-keyring_1.0-1_all.deb \
@@ -48,13 +58,17 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get install -y rocm-dev hipcub-dev
       if: matrix.variant == 'rocm'
-    - run: source/install/build_cc.sh
+    - run: |
+        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+        source/install/build_cc.sh
       env:
         DP_VARIANT: ${{ matrix.dp_variant }}
         DOWNLOAD_TENSORFLOW: "FALSE"
         CMAKE_GENERATOR: Ninja
       if: matrix.variant != 'clang'
-    - run: source/install/build_cc.sh
+    - run: |
+        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+        source/install/build_cc.sh
       env:
         DP_VARIANT: cpu
         DOWNLOAD_TENSORFLOW: "FALSE"

.github/workflows/build_wheel.yml

@@ -2,7 +2,16 @@ name: Build and upload to PyPI
 
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
+    tags:
+      - "v*"
   pull_request:
+  merge_group:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 
 jobs:
   determine-arm64-runner:
@@ -41,12 +50,12 @@ jobs:
             cuda_version: 11.8
             dp_pkg_name: deepmd-kit-cu11
           # macos-x86-64
-          - os: macos-latest
+          - os: macos-13
             python: 311
             platform_id: macosx_x86_64
             dp_variant: cpu
           # macos-arm64
-          - os: macos-latest
+          - os: macos-14
             python: 311
             platform_id: macosx_arm64
             dp_variant: cpu
@@ -68,8 +77,20 @@ jobs:
       - uses: docker/setup-qemu-action@v3
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64' && matrix.os == 'ubuntu-latest'
+      # detect version in advance. See #3168
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+        if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
+      - run: |
+          python -m pip install setuptools_scm
+          python -c "from setuptools_scm import get_version;print('SETUPTOOLS_SCM_PRETEND_VERSION='+get_version())" >> $GITHUB_ENV
+          rm -rf .git
+        if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16
+        uses: pypa/cibuildwheel@v2.17
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -136,20 +157,20 @@ jobs:
           path: source/install/docker/dist
           merge-multiple: true
       - name: Log in to the Container registry
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@dbef88086f6cef02e264edb7dbf63250c17cef6c
+        uses: docker/metadata-action@v5
         with:
           images: ghcr.io/deepmodeling/deepmd-kit
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@4a13e500e55cf31b7a5d59a38ab2040ab0f42f56
+        uses: docker/build-push-action@v5
         with:
           context: source/install/docker
           push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' && github.actor != 'dependabot[bot]' }}

.github/workflows/codeql.yml

@@ -2,10 +2,14 @@ name: "CodeQL"
 
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
   pull_request:
   schedule:
     - cron: '45 2 * * 2'
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 jobs:
   analyze:
     name: Analyze
@@ -37,6 +41,8 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get -y install cuda-cudart-dev-12-2 cuda-nvcc-12-2
         python -m pip install tensorflow
+        wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.1.2%2Bcpu.zip -O libtorch.zip
+        unzip libtorch.zip
       env:
         DEBIAN_FRONTEND: noninteractive
     # Initializes the CodeQL tools for scanning.
@@ -46,7 +52,9 @@ jobs:
         languages: ${{ matrix.language }}
         queries: security-extended,security-and-quality
     - name: "Run, Build Application using script"
-      run: source/install/build_cc.sh
+      run: |
+        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+        source/install/build_cc.sh
       env:
         DP_VARIANT: cuda
         DOWNLOAD_TENSORFLOW: "FALSE"

.github/workflows/labeler.yml

@@ -11,4 +11,4 @@ jobs:
     steps:
     - uses: actions/labeler@v5
       with:
-        repo-token: "${{ secrets.GITHUB_TOKEN }}"
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/package_c.yml

@@ -2,8 +2,15 @@ name: Build C library
 
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
+    tags:
+      - "v*"
   pull_request:
-
+  merge_group:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 jobs:
   build_c:
     name: Build C library
@@ -35,7 +42,7 @@ jobs:
       - name: Test C library
         run: ./source/install/docker_test_package_c.sh
       - name: Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: ${{ matrix.filename }}

.github/workflows/test_cc.yml

@@ -1,11 +1,20 @@
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
   pull_request:
+  merge_group:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 name: Test C++
 jobs:
   testcc:
     name: Test C++
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        check_memleak: [true, false]
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -18,39 +27,53 @@ jobs:
         mpi: mpich
     - uses: lukka/get-cmake@latest
     - run: python -m pip install tensorflow
-    - run: source/install/test_cc_local.sh
+    - name: Download libtorch
+      run: |
+         wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.1.2%2Bcpu.zip -O libtorch.zip
+         unzip libtorch.zip
+    # https://github.com/actions/runner-images/issues/9491
+    - name: Fix kernel mmap rnd bits
+      run: sudo sysctl vm.mmap_rnd_bits=28
+      if: ${{ matrix.check_memleak }}
+    - run: |
+         export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+         source/install/test_cc_local.sh
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
         LMP_CXX11_ABI_0: 1
         CMAKE_GENERATOR: Ninja
+        CXXFLAGS: ${{ matrix.check_memleak && '-fsanitize=leak' || '' }}
     # test lammps
     # ASE issue: https://gitlab.com/ase/ase/-/merge_requests/2843
     # TODO: remove ase version when ase has new release
     - run: |
         python -m pip install -U pip
-        python -m pip install -e .[cpu,test,lmp] "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
+        python -m pip install -e .[cpu,test,lmp] mpi4py "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
       env:
         DP_BUILD_TESTING: 1
+      if: ${{ !matrix.check_memleak }}
     - run: pytest --cov=deepmd source/lmp/tests
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
         LAMMPS_PLUGIN_PATH: ${{ github.workspace }}/dp_test/lib/deepmd_lmp
-        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
+        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib:${{ github.workspace }}/libtorch/lib
+      if: ${{ !matrix.check_memleak }}
     # test ipi
     - run: pytest --cov=deepmd source/ipi/tests
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
         PATH: ${{ github.workspace }}/dp_test/bin:$PATH
-        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
-    - uses: codecov/codecov-action@v3
-      with:
-        gcov: true
+        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib:${{ github.workspace }}/libtorch/lib
+      if: ${{ !matrix.check_memleak }}
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pass:
     name: Pass testing C++
     needs: [testcc]