Merge devel into master

.github/labeler.yml

@@ -8,6 +8,7 @@ CUDA: source/lib/src/cuda/**/*
 ROCM: source/lib/src/rocm/**/*
 OP: source/op/**/*
 C++: source/api_cc/**/*
+C: source/api_c/**/*
 LAMMPS: source/lmp/**/*
 Gromacs: source/gmx/**/*
-i-Pi: source/ipi/**/*
+i-Pi: source/ipi/**/*

.github/workflows/build_cc.yml

@@ -3,26 +3,50 @@ on:
   pull_request:
 name: Build C++
 jobs:
-  testpython:
+  buildcc:
     name: Build C++
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
     strategy:  
       matrix:
         include:
         - variant: cpu
         - variant: cuda
+        - variant: rocm
+        - variant: clang
     steps:
     - name: work around permission issue
       run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@master
       with:
         submodules: true
-    - run: sudo apt update && sudo apt install g++-7
-    - run: sudo apt install nvidia-cuda-toolkit
+    - run: apt-get update && apt-get install -y nvidia-cuda-toolkit
       if: matrix.variant == 'cuda'
+    - 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 \
+         && printf 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | tee /etc/apt/preferences.d/rocm-pin-600 \
+         && curl -s https://repo.radeon.com/rocm/rocm.gpg.key | apt-key add - \
+         && apt-get update \
+         && 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'  
     - run: source/install/build_cc.sh
       env:
         DP_VARIANT: ${{ matrix.variant }}
-        CC: gcc-7
-        CXX: g++-7
-        CONDA_OVERRIDE_CUDA: 11.3
+        DOWNLOAD_TENSORFLOW: "FALSE"
+      if: matrix.variant != 'clang'
+    - run: source/install/build_cc.sh
+      env:
+        DP_VARIANT: cpu
+        DOWNLOAD_TENSORFLOW: "FALSE"
+        CC: clang
+        CXX: clang++
+      if: matrix.variant == 'clang'
+  pass:
+    name: Pass building C++
+    needs: [buildcc]
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "All jobs passed"

.github/workflows/build_wheel.yml

@@ -6,64 +6,83 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }}
+    name: Build wheels for cp${{ matrix.python }}-${{ matrix.platform_id }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-18.04]  #, windows-latest, macos-latest]
-
+        include:
+          # linux-64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: manylinux_x86_64
+            dp_variant: cuda
+          # macos-x86-64
+          - os: macos-latest
+            python: 310
+            platform_id: macosx_x86_64
+            dp_variant: cpu
+          # win-64
+          - os: windows-2019
+            python: 310
+            platform_id: win_amd64
+            dp_variant: cpu
+          # linux-aarch64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: manylinux_aarch64
+            dp_variant: cpu
     steps:
-      - name: work around permission issue
-        run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
       - uses: actions/checkout@v2
+        with:
+          submodules: true
+      - 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'
 
-      - name: Install cibuildwheel
-        run: |
-          python -m pip install cibuildwheel
-
+      - run: python -m pip install cibuildwheel==2.11.3
       - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-* cp310-*"
-          CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/deepmodeling/manylinux_2_28_x86_64_tensorflow
-          CIBW_BEFORE_BUILD: pip install tensorflow
-          CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
-        run: |
-          python -m cibuildwheel --output-dir wheelhouse
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_ARCHS: all
+          CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+          DP_VARIANT: ${{ matrix.dp_variant }}
       - uses: actions/upload-artifact@v2
         with:
           path: ./wheelhouse/*.whl
-
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
-      - run: pip install -U scikit-build tensorflow setuptools_scm
+          python-version: '3.10'
+      - run: python -m pip install build
       - name: Build sdist
-        run: python setup.py sdist
+        run: python -m build --sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
-    if: startsWith(github.event.ref, 'refs/tags/v')
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
-
       - uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__

.github/workflows/lint_python.yml

@@ -18,7 +18,7 @@ jobs:
       with:
         python-version: ${{ matrix.python }}
     - name: Install requirements
-      run: pip install -r requirements.txt
+      run: pip install .
     - uses: marian-code/python-lint-annotate@v2.5.0
       with:
         python-root-list: "./deepmd/*.py ./deepmd/*/*.py ./deepmd/*/*/*.py ./source/train/*.py ./source/tests/*.py ./source/op/*.py"

.github/workflows/package_c.yml

@@ -0,0 +1,26 @@
+name: Build C library
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build_c:
+    name: Build C library
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Package C library
+        run: ./source/install/docker_package_c.sh
+      - name: Test C library
+        run: ./source/install/docker_test_package_c.sh
+      # for download and debug
+      - name: Upload artifact
+        uses: actions/upload-artifact@v2
+        with:
+          path: ./libdeepmd_c.tar.gz
+      - name: Release
+        uses: softprops/action-gh-release@v1
+        if: startsWith(github.ref, 'refs/tags/')
+        with:
+          files: libdeepmd_c.tar.gz

.github/workflows/test_cc.yml

@@ -3,7 +3,7 @@ on:
   pull_request:
 name: Test C++
 jobs:
-  testpython:
+  testcc:
     name: Test C++
     runs-on: ubuntu-latest
     container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
@@ -13,5 +13,31 @@ jobs:
     - uses: actions/checkout@master
     - run: source/install/test_cc_local.sh
       env:
+        OMP_NUM_THREADS: 1
+        TF_INTRA_OP_PARALLELISM_THREADS: 1
+        TF_INTER_OP_PARALLELISM_THREADS: 1
         tensorflow_root: /usr/local
-    - run: source/install/codecov.sh
+    # test lammps
+    - run: apt-get update && apt-get install -y python3-pip python3-venv
+    - run: source/install/build_lammps.sh
+    - run: |
+        python -m pip install -U pip
+        python -m pip install -e .[cpu,test]
+      env:
+        DP_BUILD_TESTING: 1
+    - 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
+    - uses: codecov/codecov-action@v3
+      with:
+        gcov: true
+  pass:
+    name: Pass testing C++
+    needs: [testcc]
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "All jobs passed"

.github/workflows/test_python.yml

@@ -5,25 +5,10 @@ name: Test Python
 jobs:
   testpython:
     name: Test Python
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:  
       matrix:
         include:
-          - python: 3.6
-            gcc: 4.8
-            tf: 1.8
-          - python: 3.6
-            gcc: 4.8
-            tf: 1.12
-          - python: 3.6
-            gcc: 4.8
-            tf: 1.14
-          - python: 3.6
-            gcc: 5
-            tf: 1.14
-          - python: 3.6
-            gcc: 8
-            tf: 1.14
           - python: 3.7
             gcc: 5
             tf: 1.14
@@ -54,20 +39,21 @@ jobs:
     - name: work around permission issue
       run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@master
-    - name: pip cache
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key:
-          ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
     - run: python -m pip install -U pip>=21.3.1
-    - run: pip install -e .[cpu,test] codecov
+    - run: pip install -e .[cpu,test]
       env:
         CC: gcc-${{ matrix.gcc }}
         CXX: g++-${{ matrix.gcc }}
         TENSORFLOW_VERSION: ${{ matrix.tf }}
-        SETUPTOOLS_ENABLE_FEATURES: "legacy-editable"
+        DP_BUILD_TESTING: 1
     - run: dp --version
-    - run: pytest --cov=deepmd source/tests && codecov
+    - run: pytest --cov=deepmd source/tests --durations=0
+    - uses: codecov/codecov-action@v3
+      with:
+        gcov: true
+  pass:
+    name: Pass testing Python
+    needs: [testpython]
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "All jobs passed"

.gitignore

@@ -29,10 +29,16 @@ _templates
 API_CC
 doc/api_py/
 doc/api_core/
+doc/api_c/
 dp/
 dp_test/
 dp_test_cc/
+dp_test_c/
+dp_c/
 build_lammps/
 .idea/
 build_tests/
 build_cc_tests
+build_c_tests
+build_c/
+libdeepmd_c/