merge devel to master (v3.1.0) (#4798)

Author: njzjz

.devcontainer/build_cxx.sh

@@ -11,6 +11,7 @@ mkdir -p ${SCRIPT_PATH}/../buildcxx/
 cd ${SCRIPT_PATH}/../buildcxx/
 cmake -D ENABLE_TENSORFLOW=ON \
 	-D ENABLE_PYTORCH=ON \
+	-D ENABLE_PADDLE=ON \
 	-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
 	-D LAMMPS_VERSION=stable_29Aug2024_update1 \
 	-D CMAKE_BUILD_TYPE=Debug \

.devcontainer/download_libtorch.sh

@@ -4,5 +4,5 @@ set -ev
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 cd ${SCRIPT_PATH}/..
 
-wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.5.0%2Bcpu.zip -O ~/libtorch.zip
+wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.7.0%2Bcpu.zip -O ~/libtorch.zip
 unzip ~/libtorch.zip

.github/workflows/build_cc.yml

@@ -33,10 +33,7 @@ jobs:
     - uses: lukka/get-cmake@latest
     - run: python -m pip install uv
     - run: source/install/uv_with_retry.sh pip install --system 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: source/install/uv_with_retry.sh pip install --system 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
     - 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 \
@@ -52,22 +49,20 @@ jobs:
       env:
         DEBIAN_FRONTEND: noninteractive
     - run: |
-         echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.3/ jammy main' | sudo tee /etc/apt/sources.list.d/rocm.list \
+         echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/6.3/ jammy main' | sudo tee /etc/apt/sources.list.d/rocm.list \
          && printf 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | sudo tee /etc/apt/preferences.d/rocm-pin-600 \
          && curl -s https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add - \
          && sudo apt-get update \
          && sudo apt-get install -y rocm-dev hipcub-dev
       if: matrix.variant == 'rocm'
     - run: |
-        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
         source/install/build_cc.sh
       env:
         DP_VARIANT: ${{ matrix.dp_variant }}
         DOWNLOAD_TENSORFLOW: "FALSE"
         CMAKE_GENERATOR: Ninja
       if: matrix.variant != 'clang'
     - run: |
-        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
         source/install/build_cc.sh
       env:
         DP_VARIANT: cpu

.github/workflows/build_wheel.yml

@@ -14,24 +14,8 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  determine-arm64-runner:
-    runs-on: ubuntu-latest
-    permissions: read-all
-    outputs:
-      runner: ${{ steps.set-runner.outputs.runner }}
-    steps:
-      - name: Determine which runner to use for ARM64 build
-        id: set-runner
-        run: |
-          if [ "${{ github.repository_owner }}" == "deepmodeling" ]; then
-            echo "runner=[\"Linux\",\"ARM64\"]" >> $GITHUB_OUTPUT
-          else
-            echo "runner=\"ubuntu-latest\"" >> $GITHUB_OUTPUT
-          fi
-
   build_wheels:
     name: Build wheels for cp${{ matrix.python }}-${{ matrix.platform_id }}
-    needs: determine-arm64-runner
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -60,12 +44,12 @@ jobs:
             platform_id: macosx_arm64
             dp_variant: cpu
           # win-64
-          - os: windows-2019
+          - os: windows-2022
             python: 311
             platform_id: win_amd64
             dp_variant: cpu
           # linux-aarch64
-          - os: ${{ fromJson(needs.determine-arm64-runner.outputs.runner) }}
+          - os: ubuntu-24.04-arm
             python: 310
             platform_id: manylinux_aarch64
             dp_variant: cpu
@@ -86,7 +70,7 @@ jobs:
           rm -rf .git
         if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21
+        uses: pypa/cibuildwheel@v2.23
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all

.github/workflows/codeql.yml

@@ -41,8 +41,7 @@ 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
+        python -m pip install 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
       env:
         DEBIAN_FRONTEND: noninteractive
     # Initializes the CodeQL tools for scanning.
@@ -53,7 +52,6 @@ jobs:
         queries: security-extended,security-and-quality
     - name: "Run, Build Application using script"
       run: |
-        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
         source/install/build_cc.sh
       env:
         DP_VARIANT: cuda

.github/workflows/suppr.txt

@@ -0,0 +1 @@
+leak:libpaddle_inference

.github/workflows/test_cc.yml

@@ -29,21 +29,17 @@ jobs:
     - run: python -m pip install uv
     - name: Install Python dependencies
       run: |
-        source/install/uv_with_retry.sh pip install --system tensorflow-cpu
+        source/install/uv_with_retry.sh pip install --system tensorflow-cpu~=2.18.0 jax==0.5.0
         export TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
         source/install/uv_with_retry.sh pip install --system -e .[cpu,test,lmp,jax] mpi4py
+        source/install/uv_with_retry.sh pip install --system 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
     - name: Convert models
       run: source/tests/infer/convert-models.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
@@ -52,23 +48,32 @@ jobs:
         LMP_CXX11_ABI_0: 1
         CMAKE_GENERATOR: Ninja
         CXXFLAGS: ${{ matrix.check_memleak && '-fsanitize=leak' || '' }}
+        LSAN_OPTIONS: suppressions=${{ github.workspace }}/.github/workflows/suppr.txt
     # test lammps
-    - run: pytest --cov=deepmd source/lmp/tests
+    - run: |
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/paddle/lib/*.so ${{ github.workspace }}/dp_test/lib/
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/onednn/lib/* ${{ github.workspace }}/dp_test/lib/
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/mklml/lib/* ${{ github.workspace }}/dp_test/lib/
+        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: ${{ github.workspace }}/dp_test/lib:${{ github.workspace }}/libtorch/lib
+        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
       if: ${{ !matrix.check_memleak }}
     # test ipi
-    - run: pytest --cov=deepmd source/ipi/tests
+    - run: |
+        export PATH=${{ github.workspace }}/dp_test/bin:$PATH
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/paddle/lib/*.so ${{ github.workspace }}/dp_test/lib/
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/onednn/lib/* ${{ github.workspace }}/dp_test/lib/
+        cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/mklml/lib/* ${{ github.workspace }}/dp_test/lib/
+        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: ${{ github.workspace }}/dp_test/lib:${{ github.workspace }}/libtorch/lib
+        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
       if: ${{ !matrix.check_memleak }}
     - uses: codecov/codecov-action@v5
       env:

.github/workflows/test_cuda.yml

@@ -47,30 +47,27 @@ jobs:
          && sudo apt-get -y install cuda-12-3 libcudnn8=8.9.5.*-1+cuda12.3
       if: false  # skip as we use nvidia image
     - run: python -m pip install -U uv
-    - run: source/install/uv_with_retry.sh pip install --system "tensorflow~=2.18.0rc2" "torch~=2.5.0" "jax[cuda12]"
+    - run: source/install/uv_with_retry.sh pip install --system "tensorflow~=2.18.0rc2" "torch~=2.7.0" "jax[cuda12]==0.5.0"
     - run: |
         export PYTORCH_ROOT=$(python -c 'import torch;print(torch.__path__[0])')
         export TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
-        source/install/uv_with_retry.sh pip install --system -v -e .[gpu,test,lmp,cu12,torch,jax] mpi4py
+        pip install "paddlepaddle-gpu==3.0.0" -i https://www.paddlepaddle.org.cn/packages/stable/cu126/
+        source/install/uv_with_retry.sh pip install --system -v -e .[gpu,test,lmp,cu12,torch,jax] mpi4py --reinstall-package deepmd-kit
       env:
         DP_VARIANT: cuda
         DP_ENABLE_NATIVE_OPTIMIZATION: 1
         DP_ENABLE_PYTORCH: 1
     - run: dp --version
-    - run: python -m pytest source/tests --durations=0
+    - run: python -m pytest source/tests
       env:
         NUM_WORKERS: 0
         CUDA_VISIBLE_DEVICES: 0
         # See https://jax.readthedocs.io/en/latest/gpu_memory_allocation.html
         XLA_PYTHON_CLIENT_PREALLOCATE: false
+        XLA_PYTHON_CLIENT_ALLOCATOR: platform
     - name: Convert models
       run: source/tests/infer/convert-models.sh
-    - name: Download libtorch
-      run: |
-         wget https://download.pytorch.org/libtorch/cu124/libtorch-cxx11-abi-shared-with-deps-2.5.0%2Bcu124.zip -O libtorch.zip
-         unzip libtorch.zip
     - run: |
-        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
         export LD_LIBRARY_PATH=$CUDA_PATH/lib64:/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH
         source/install/test_cc_local.sh
       env:
@@ -82,8 +79,11 @@ jobs:
         DP_VARIANT: cuda
         DP_USE_MPICH2: 1
     - run: |
-        export LD_LIBRARY_PATH=$CUDA_PATH/lib64:/usr/lib/x86_64-linux-gnu/:$GITHUB_WORKSPACE/dp_test/lib:$GITHUB_WORKSPACE/libtorch/lib:$LD_LIBRARY_PATH
+        export LD_LIBRARY_PATH=$CUDA_PATH/lib64:/usr/lib/x86_64-linux-gnu/:$GITHUB_WORKSPACE/dp_test/lib:$LD_LIBRARY_PATH
         export PATH=$GITHUB_WORKSPACE/dp_test/bin:$PATH
+        cp $GITHUB_WORKSPACE/source/build_tests/paddle_inference_install_dir/paddle/lib/* $GITHUB_WORKSPACE/dp_test/lib/
+        cp $GITHUB_WORKSPACE/source/build_tests/paddle_inference_install_dir/third_party/install/onednn/lib/* $GITHUB_WORKSPACE/dp_test/lib/
+        cp $GITHUB_WORKSPACE/source/build_tests/paddle_inference_install_dir/third_party/install/mklml/lib/* $GITHUB_WORKSPACE/dp_test/lib/
         python -m pytest -s source/lmp/tests || (cat log.lammps && exit 1)
         python -m pytest source/ipi/tests
       env:

.github/workflows/test_python.yml

@@ -25,12 +25,14 @@ jobs:
         python-version: ${{ matrix.python }}
     - run: python -m pip install -U uv
     - run: |
-        source/install/uv_with_retry.sh pip install --system openmpi tensorflow-cpu
+        source/install/uv_with_retry.sh pip install --system openmpi tensorflow-cpu~=2.18.0
         source/install/uv_with_retry.sh pip install --system torch -i https://download.pytorch.org/whl/cpu
         export TENSORFLOW_ROOT=$(python -c 'import tensorflow;print(tensorflow.__path__[0])')
         export PYTORCH_ROOT=$(python -c 'import torch;print(torch.__path__[0])')
-        source/install/uv_with_retry.sh pip install --system -e .[test,jax] mpi4py
+        source/install/uv_with_retry.sh pip install --system -e .[test,jax] mpi4py "jax==0.5.0;python_version>='3.10'"
+        source/install/uv_with_retry.sh pip install --system -U setuptools
         source/install/uv_with_retry.sh pip install --system horovod --no-build-isolation
+        source/install/uv_with_retry.sh pip install --system --pre "paddlepaddle==3.0.0" -i https://www.paddlepaddle.org.cn/packages/stable/cpu/
       env:
         # Please note that uv has some issues with finding
         # existing TensorFlow package. Currently, it uses
@@ -42,6 +44,8 @@ jobs:
         HOROVOD_WITH_TENSORFLOW: 1
         HOROVOD_WITHOUT_PYTORCH: 1
         HOROVOD_WITH_MPI: 1
+        # https://cmake.org/cmake/help/latest/variable/CMAKE_POLICY_VERSION_MINIMUM.html
+        CMAKE_POLICY_VERSION_MINIMUM: 3.5
     - run: dp --version
     - name: Get durations from cache
       uses: actions/cache@v4
@@ -54,11 +58,11 @@ jobs:
         restore-keys: |
           test2-durations-combined-${{ matrix.python }}-${{ github.sha }}
           test2-durations-combined-${{ matrix.python }}
-    - run: pytest --cov=deepmd source/tests --durations=0 --splits 6 --group ${{ matrix.group }} --store-durations --clean-durations --durations-path=.test_durations --splitting-algorithm least_duration
+    - run: pytest --cov=deepmd source/tests  --splits 6 --group ${{ matrix.group }} --store-durations --clean-durations --durations-path=.test_durations --splitting-algorithm least_duration
       env:
         NUM_WORKERS: 0
     - name: Test TF2 eager mode
-      run: pytest --cov=deepmd --cov-append source/tests/consistent/io/test_io.py source/jax2tf_tests --durations=0
+      run: pytest --cov=deepmd --cov-append source/tests/consistent/io/test_io.py source/jax2tf_tests
       env:
         NUM_WORKERS: 0
         DP_TEST_TF2_ONLY: 1

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
         exclude: "^.+\\.pbtxt$"
       - id: end-of-file-fixer
-        exclude: "^.+\\.pbtxt$"
+        exclude: "^.+\\.pbtxt$|deeppot_sea.*\\.json$"
       - id: check-yaml
       - id: check-json
       - id: check-added-large-files
@@ -22,14 +22,14 @@ repos:
       - id: check-toml
   # Python
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
         files: \.py$
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.11.13
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -40,7 +40,7 @@ repos:
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pycqa/flake8
     # flake8 cannot autofix
-    rev: "7.1.1"
+    rev: "7.2.0"
     hooks:
       - id: flake8
         additional_dependencies:
@@ -60,10 +60,10 @@ repos:
       - id: blacken-docs
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.3
+    rev: v20.1.5
     hooks:
       - id: clang-format
-        exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$)
+        exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$|.+\.json$)
   # markdown, yaml, CSS, javascript
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
@@ -74,7 +74,7 @@ repos:
         exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
   # Shell
   - repo: https://github.com/scop/pre-commit-shfmt
-    rev: v3.10.0-1
+    rev: v3.11.0-1
     hooks:
       - id: shfmt
   # CMake
@@ -154,7 +154,7 @@ repos:
         exclude: .pre-commit-config.yaml|source/lmp
   # customized pylint rules
   - repo: https://github.com/pylint-dev/pylint/
-    rev: v3.3.1
+    rev: v3.3.7
     hooks:
       - id: pylint
         entry: env PYTHONPATH=source/checker pylint

.readthedocs.yml

@@ -10,5 +10,7 @@ build:
       - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
   apt_packages:
     - inkscape
+sphinx:
+  configuration: doc/conf.py
 formats:
   - pdf