Merge devel into master (#2380)

deepmodeling · Mar 14, 2023 · 6cdc5bf · 6cdc5bf
2 parents 89d0d23 + a34e680
commit 6cdc5bf
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diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,4 @@
+---
+BasedOnStyle: Google
+BinPackParameters: false
+...
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,3 @@
+# .git-blame-ignore-revs
+# pre-commit
+97c38bb4235c9a440bd61a2459e330dba78269fa
diff --git a/.github/ISSUE_TEMPLATE/bug-report.yml b/.github/ISSUE_TEMPLATE/bug-report.yml
@@ -9,7 +9,7 @@ body:
     attributes:
       label: Bug summary
       description: Please provide a clear and concise description of what the bug is.
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -45,7 +45,7 @@ body:
     attributes:
       label: Input Files, Running Commands, Error Log, etc.
       description: "Please provide necessary information including input file, running commands, error log , etc., AS  DETAILED AS POSSIBLE to help locate and reproduce your problem. WARNING: Do not use image to show error log! Paste texts in a code block instead."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -54,7 +54,7 @@ body:
     attributes:
       label: Steps to Reproduce
       description: "Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -63,7 +63,7 @@ body:
     attributes:
       label: Further Information, Files, and Links
       description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: false
diff --git a/.github/ISSUE_TEMPLATE/feature-request.yml b/.github/ISSUE_TEMPLATE/feature-request.yml
@@ -9,7 +9,7 @@ body:
     attributes:
       label: Summary
       description: "Please provide a brief and concise description of the suggested feature or change"
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -18,7 +18,7 @@ body:
     attributes:
       label: Detailed Description
       description: "Please explain how you would like to see deepmd-kit enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -27,7 +27,7 @@ body:
     attributes:
       label: Further Information, Files, and Links
       description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: false
diff --git a/.github/ISSUE_TEMPLATE/generic-issue.yml b/.github/ISSUE_TEMPLATE/generic-issue.yml
@@ -9,7 +9,7 @@ body:
     attributes:
       label: Summary
       description: "Please provide a clear and concise description of what the question is."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -32,7 +32,7 @@ body:
     attributes:
       label: Python Version, CUDA Version, GCC Version, LAMMPS Version, etc
       description: "If applicable, specify what platform you are running on."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: false
@@ -41,7 +41,7 @@ body:
     attributes:
       label: Details
       description: "Please explain the issue in detail here."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
diff --git a/.github/ISSUE_TEMPLATE/parameters.yml b/.github/ISSUE_TEMPLATE/parameters.yml
@@ -9,7 +9,7 @@ body:
     attributes:
       label: Summary
       description: "Please provide a clear and concise description of what your request is."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -18,7 +18,7 @@ body:
     attributes:
       label: Detailed Description
       description: "Please explain how you would like to see deepmd-kit enhanced. Specify your material system, and exactly what behaviors or properties you are looking for, or what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation."
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: true
@@ -27,7 +27,7 @@ body:
     attributes:
       label: Further Information, Files, and Links
       description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications
-      placeholder: 
+      placeholder:
       value:
     validations:
       required: false
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "devel"
diff --git a/.github/workflows/build_cc.yml b/.github/workflows/build_cc.yml
@@ -7,21 +7,37 @@ jobs:
     name: Build C++
     runs-on: ubuntu-latest
     container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
-    strategy:  
+    strategy:
       matrix:
         include:
         - variant: cpu
+          dp_variant: cpu
         - variant: cuda
+          dp_variant: cuda
+        - variant: cuda120
+          dp_variant: cuda
         - variant: rocm
+          dp_variant: rocm
         - variant: clang
+          dp_variant: clang
     steps:
     - name: work around permission issue
       run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         submodules: true
     - run: apt-get update && apt-get install -y nvidia-cuda-toolkit
       if: matrix.variant == 'cuda'
+    - run: |
+         apt-get update \
+         && apt-get -y install wget \
+         && wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
+         && dpkg -i cuda-keyring_1.0-1_all.deb \
+         && apt-get update \
+         && apt-get -y install cuda-12-0
+      if: matrix.variant == 'cuda120'
+      env:
+        DEBIAN_FRONTEND: noninteractive
     - run: |
          apt-get update && apt-get install -y gnupg2 \
          && echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.3/ jammy main' | tee /etc/apt/sources.list.d/rocm.list \
@@ -31,10 +47,10 @@ jobs:
          && apt-get install -y rocm-dev hipcub-dev
       if: matrix.variant == 'rocm'
     - run: apt-get update && apt-get install -y clang
-      if: matrix.variant == 'clang'  
+      if: matrix.variant == 'clang'
     - run: source/install/build_cc.sh
       env:
-        DP_VARIANT: ${{ matrix.variant }}
+        DP_VARIANT: ${{ matrix.dp_variant }}
         DOWNLOAD_TENSORFLOW: "FALSE"
       if: matrix.variant != 'clang'
     - run: source/install/build_cc.sh
@@ -44,9 +60,22 @@ jobs:
         CC: clang
         CXX: clang++
       if: matrix.variant == 'clang'
+    - name: Test files exist
+      run: |
+        test -f dp/bin/dp_ipi &&
+        test -f dp/lib/libdeepmd_cc.so &&
+        test -f dp/lib/libdeepmd_c.so &&
+        test -f dp/lib/libdeepmd_op.so &&
+        test -f dp/lib/libdeepmd_ipi.so &&
+        test -f dp/lib/libdeepmd_lmp.so &&
+        test -f dp/lib/libdeepmd.so
   pass:
     name: Pass building C++
     needs: [buildcc]
     runs-on: ubuntu-latest
+    if: always()
     steps:
-      - run: echo "All jobs passed"
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
@@ -36,17 +36,13 @@ jobs:
       - uses: actions/checkout@v2
         with:
           submodules: true
+          # https://github.com/pypa/setuptools_scm/issues/480
+          fetch-depth: 0
       - uses: docker/setup-qemu-action@v2
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64'
-      - uses: actions/setup-python@v2
-        name: Install Python
-        with:
-          python-version: '3.8'
-
-      - run: python -m pip install cibuildwheel==2.11.3
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
+        uses: pypa/cibuildwheel@v2.11.3
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -83,7 +79,49 @@ jobs:
         with:
           name: artifact
           path: dist
-      - uses: pypa/gh-action-pypi-publish@master
+      - uses: pypa/gh-action-pypi-publish@v4
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}
+
+  build_docker:
+    # use the already built wheels to build docker
+    needs: [build_wheels]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: source/install/docker/dist
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ghcr.io/deepmodeling/deepmd-kit
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: source/install/docker
+          push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+  pass:
+    name: Pass testing build wheels
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: always()
+    steps:
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
@@ -11,4 +11,4 @@ jobs:
     steps:
     - uses: actions/labeler@v4
       with:
-        repo-token: "${{ secrets.GITHUB_TOKEN }}"
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/lint_python.yml b/.github/workflows/lint_python.yml
diff --git a/.github/workflows/test_cc.yml b/.github/workflows/test_cc.yml
@@ -10,7 +10,7 @@ jobs:
     steps:
     - name: work around permission issue
       run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: source/install/test_cc_local.sh
       env:
         OMP_NUM_THREADS: 1
@@ -39,5 +39,9 @@ jobs:
     name: Pass testing C++
     needs: [testcc]
     runs-on: ubuntu-latest
+    if: always()
     steps:
-      - run: echo "All jobs passed"
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/.github/workflows/test_python.yml b/.github/workflows/test_python.yml
@@ -6,7 +6,7 @@ jobs:
   testpython:
     name: Test Python
     runs-on: ubuntu-latest
-    strategy:  
+    strategy:
       matrix:
         include:
           - python: 3.7
@@ -38,8 +38,9 @@ jobs:
     steps:
     - name: work around permission issue
       run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
-    - uses: actions/checkout@master
-    - run: python -m pip install -U pip>=21.3.1
+    - uses: actions/checkout@v3
+    # https://github.com/pypa/pip/issues/11770
+    - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
     - run: pip install -e .[cpu,test]
       env:
         CC: gcc-${{ matrix.gcc }}
@@ -55,5 +56,9 @@ jobs:
     name: Pass testing Python
     needs: [testpython]
     runs-on: ubuntu-latest
+    if: always()
     steps:
-      - run: echo "All jobs passed"
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,7 @@
 *.gz
 *.bz2
 *.pyc
+*.pb
 tmp*
 CMakeCache.txt
 CMakeFiles