Merge remote-tracking branch 'upstream/devel' into devel

Author: SumGuo-88

.github/workflows/build_wheel.yml

@@ -86,7 +86,7 @@ jobs:
           rm -rf .git
         if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21
+        uses: pypa/cibuildwheel@v2.22
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all

.github/workflows/test_cuda.yml

@@ -51,6 +51,7 @@ jobs:
     - 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 --pre https://paddle-whl.bj.bcebos.com/nightly/cu123/paddlepaddle-gpu/paddlepaddle_gpu-3.0.0.dev20241126-cp311-cp311-linux_x86_64.whl
         source/install/uv_with_retry.sh pip install --system -v -e .[gpu,test,lmp,cu12,torch,jax] mpi4py
       env:
         DP_VARIANT: cuda

.github/workflows/test_python.yml

@@ -31,6 +31,7 @@ jobs:
         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 horovod --no-build-isolation
+        source/install/uv_with_retry.sh pip install --system --pre "paddlepaddle" -i https://www.paddlepaddle.org.cn/packages/nightly/cpu/
       env:
         # Please note that uv has some issues with finding
         # existing TensorFlow package. Currently, it uses

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.8.3
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -60,7 +60,7 @@ repos:
       - id: blacken-docs
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.3
+    rev: v19.1.5
     hooks:
       - id: clang-format
         exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$)
@@ -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: v3.10.0-2
     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: v3.3.2
     hooks:
       - id: pylint
         entry: env PYTHONPATH=source/checker pylint

CITATIONS.bib

@@ -128,26 +128,26 @@ @article{Zhang_NpjComputMater_2024_v10_p94
   doi          = {10.1038/s41524-024-01278-7},
 }
 
-@misc{Zhang_2023_DPA2,
+@article{Zhang_npjComputMater_2024_v10_p293,
   annote       = {DPA-2},
   author       = {
     Duo Zhang and Xinzijian Liu and Xiangyu Zhang and Chengqian Zhang and Chun
-    Cai and Hangrui Bi and Yiming Du and Xuejian Qin and Jiameng Huang and
-    Bowen Li and Yifan Shan and Jinzhe Zeng and Yuzhi Zhang and Siyuan Liu and
-    Yifan Li and Junhan Chang and Xinyan Wang and Shuo Zhou and Jianchuan Liu
-    and Xiaoshan Luo and Zhenyu Wang and Wanrun Jiang and Jing Wu and Yudi Yang
-    and Jiyuan Yang and Manyi Yang and Fu-Qiang Gong and Linshuang Zhang and
-    Mengchao Shi and Fu-Zhi Dai and Darrin M. York and Shi Liu and Tong Zhu and
-    Zhicheng Zhong and Jian Lv and Jun Cheng and Weile Jia and Mohan Chen and
-    Guolin Ke and Weinan E and Linfeng Zhang and Han Wang
+    Cai and Hangrui Bi and Yiming Du and Xuejian Qin and Anyang Peng and
+    Jiameng Huang and Bowen Li and Yifan Shan and Jinzhe Zeng and Yuzhi Zhang
+    and Siyuan Liu and Yifan Li and Junhan Chang and Xinyan Wang and Shuo Zhou
+    and Jianchuan Liu and Xiaoshan Luo and Zhenyu Wang and Wanrun Jiang and
+    Jing Wu and Yudi Yang and Jiyuan Yang and Manyi Yang and Fu-Qiang Gong and
+    Linshuang Zhang and Mengchao Shi and Fu-Zhi Dai and Darrin M. York and Shi
+    Liu and Tong Zhu and Zhicheng Zhong and Jian Lv and Jun Cheng and Weile Jia
+    and Mohan Chen and Guolin Ke and Weinan E and Linfeng Zhang and Han Wang
   },
-  title        = {
-    {DPA-2: Towards a universal large atomic model for molecular and material
-    simulation}
-  },
-  publisher    = {arXiv},
-  year         = 2023,
-  doi          = {10.48550/arXiv.2312.15492},
+  title        = {{DPA-2: a large atomic model as a multi-task learner}},
+  journal      = {npj Comput. Mater},
+  year         = 2024,
+  volume       = 10,
+  number       = 1,
+  pages        = 293,
+  doi          = {10.1038/s41524-024-01493-2},
 }
 
 @article{Zhang_PhysPlasmas_2020_v27_p122704,

backend/find_paddle.py

@@ -0,0 +1,133 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+import importlib
+import os
+import site
+from functools import (
+    lru_cache,
+)
+from importlib.machinery import (
+    FileFinder,
+)
+from importlib.util import (
+    find_spec,
+)
+from pathlib import (
+    Path,
+)
+from sysconfig import (
+    get_path,
+)
+from typing import (
+    Optional,
+    Union,
+)
+
+
+@lru_cache
+def find_paddle() -> tuple[Optional[str], list[str]]:
+    """Find PaddlePadle library.
+
+    Tries to find PaddlePadle in the order of:
+
+    1. Environment variable `PADDLE_ROOT` if set
+    2. The current Python environment.
+    3. user site packages directory if enabled
+    4. system site packages directory (purelib)
+
+    Considering the default PaddlePadle package still uses old CXX11 ABI, we
+    cannot install it automatically.
+
+    Returns
+    -------
+    str, optional
+        PaddlePadle library path if found.
+    list of str
+        Paddle requirement if not found. Empty if found.
+    """
+    if os.environ.get("DP_ENABLE_PADDLE", "0") == "0":
+        return None, []
+    requires = []
+    pd_spec = None
+
+    if (pd_spec is None or not pd_spec) and os.environ.get("PADDLE_ROOT") is not None:
+        site_packages = Path(os.environ.get("PADDLE_ROOT")).parent.absolute()
+        pd_spec = FileFinder(str(site_packages)).find_spec("paddle")
+
+    # get paddle spec
+    # note: isolated build will not work for backend
+    if pd_spec is None or not pd_spec:
+        pd_spec = find_spec("paddle")
+
+    if not pd_spec and site.ENABLE_USER_SITE:
+        # first search TF from user site-packages before global site-packages
+        site_packages = site.getusersitepackages()
+        if site_packages:
+            pd_spec = FileFinder(site_packages).find_spec("paddle")
+
+    if not pd_spec:
+        # purelib gets site-packages path
+        site_packages = get_path("purelib")
+        if site_packages:
+            pd_spec = FileFinder(site_packages).find_spec("paddle")
+
+    # get install dir from spec
+    try:
+        pd_install_dir = pd_spec.submodule_search_locations[0]  # type: ignore
+        # AttributeError if ft_spec is None
+        # TypeError if submodule_search_locations are None
+        # IndexError if submodule_search_locations is an empty list
+    except (AttributeError, TypeError, IndexError):
+        pd_install_dir = None
+        requires.extend(get_pd_requirement()["paddle"])
+    return pd_install_dir, requires
+
+
+@lru_cache
+def get_pd_requirement(pd_version: str = "") -> dict:
+    """Get PaddlePadle requirement when Paddle is not installed.
+
+    If pd_version is not given and the environment variable `PADDLE_VERSION` is set, use it as the requirement.
+
+    Parameters
+    ----------
+    pd_version : str, optional
+        Paddle version
+
+    Returns
+    -------
+    dict
+        PaddlePadle requirement.
+    """
+    if pd_version is None:
+        return {"paddle": []}
+    if pd_version == "":
+        pd_version = os.environ.get("PADDLE_VERSION", "")
+
+    return {
+        "paddle": [
+            "paddlepaddle>=3.0.0b1" if pd_version != "" else "paddlepaddle>=3.0.0b1",
+        ],
+    }
+
+
+@lru_cache
+def get_pd_version(pd_path: Optional[Union[str, Path]]) -> str:
+    """Get Paddle version from a Paddle Python library path.
+
+    Parameters
+    ----------
+    pd_path : str or Path
+        Paddle Python library path, e.g. "/python3.10/site-packages/paddle/"
+
+    Returns
+    -------
+    str
+        version
+    """
+    if pd_path is None or pd_path == "":
+        return ""
+    version_file = Path(pd_path) / "version" / "__init__.py"
+    spec = importlib.util.spec_from_file_location("paddle.version", version_file)
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module.full_version

deepmd/__init__.py

@@ -40,6 +40,6 @@ def DeepPotential(*args, **kwargs):
 
 
 __all__ = [
-    "__version__",
     "DeepPotential",
+    "__version__",
 ]

deepmd/backend/paddle.py

@@ -0,0 +1,124 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+from importlib.util import (
+    find_spec,
+)
+from typing import (
+    TYPE_CHECKING,
+    Callable,
+    ClassVar,
+)
+
+from deepmd.backend.backend import (
+    Backend,
+)
+
+if TYPE_CHECKING:
+    from argparse import (
+        Namespace,
+    )
+
+    from deepmd.infer.deep_eval import (
+        DeepEvalBackend,
+    )
+    from deepmd.utils.neighbor_stat import (
+        NeighborStat,
+    )
+
+
+@Backend.register("pd")
+@Backend.register("paddle")
+class PaddleBackend(Backend):
+    """Paddle backend."""
+
+    name = "Paddle"
+    """The formal name of the backend."""
+    features: ClassVar[Backend.Feature] = (
+        Backend.Feature.ENTRY_POINT
+        | Backend.Feature.DEEP_EVAL
+        | Backend.Feature.NEIGHBOR_STAT
+        | Backend.Feature.IO
+    )
+    """The features of the backend."""
+    suffixes: ClassVar[list[str]] = [".json", ".pd"]
+    """The suffixes of the backend."""
+
+    def is_available(self) -> bool:
+        """Check if the backend is available.
+
+        Returns
+        -------
+        bool
+            Whether the backend is available.
+        """
+        return find_spec("paddle") is not None
+
+    @property
+    def entry_point_hook(self) -> Callable[["Namespace"], None]:
+        """The entry point hook of the backend.
+
+        Returns
+        -------
+        Callable[[Namespace], None]
+            The entry point hook of the backend.
+        """
+        from deepmd.pd.entrypoints.main import main as deepmd_main
+
+        return deepmd_main
+
+    @property
+    def deep_eval(self) -> type["DeepEvalBackend"]:
+        """The Deep Eval backend of the backend.
+
+        Returns
+        -------
+        type[DeepEvalBackend]
+            The Deep Eval backend of the backend.
+        """
+        from deepmd.pd.infer.deep_eval import DeepEval as DeepEvalPD
+
+        return DeepEvalPD
+
+    @property
+    def neighbor_stat(self) -> type["NeighborStat"]:
+        """The neighbor statistics of the backend.
+
+        Returns
+        -------
+        type[NeighborStat]
+            The neighbor statistics of the backend.
+        """
+        from deepmd.pd.utils.neighbor_stat import (
+            NeighborStat,
+        )
+
+        return NeighborStat
+
+    @property
+    def serialize_hook(self) -> Callable[[str], dict]:
+        """The serialize hook to convert the model file to a dictionary.
+
+        Returns
+        -------
+        Callable[[str], dict]
+            The serialize hook of the backend.
+        """
+        from deepmd.pd.utils.serialization import (
+            serialize_from_file,
+        )
+
+        return serialize_from_file
+
+    @property
+    def deserialize_hook(self) -> Callable[[str, dict], None]:
+        """The deserialize hook to convert the dictionary to a model file.
+
+        Returns
+        -------
+        Callable[[str, dict], None]
+            The deserialize hook of the backend.
+        """
+        from deepmd.pd.utils.serialization import (
+            deserialize_to_file,
+        )
+
+        return deserialize_to_file