chore: bump LAMMPS to stable_22Jul2025 (#4861)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Chores**
* Updated all scripts, configuration files, and documentation to use the
latest LAMMPS stable release version (stable_22Jul2025) for building and
installing DeePMD-kit.
* Adjusted dependency specifications and environment variables to
reflect the new LAMMPS version.
* Revised installation instructions to reference the updated LAMMPS
source archive and directory names.
* Replaced external LAMMPS version extraction with a custom
implementation for improved version parsing.
* Removed obsolete environment variable settings related to C++ ABI
configuration.
* Updated build dependencies to conditionally include the MPI package
based on the build environment.
* Enhanced environment setup to properly handle CUDA and MPI library
paths across platforms during build and runtime.
* Improved library loading to explicitly load MPI libraries when
building with cibuildwheel.
* Clarified installation documentation to indicate automatic MPICH
installation without manual MPI setup.
* Added conditional interface to manage LAMMPS OP library directory
retrieval based on configuration.
* **Tests**
* Modified tests to restrict atom ID indexing to the subset of atoms
matching coordinate array lengths for consistency in validation.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

.devcontainer/build_cxx.sh

@@ -13,7 +13,7 @@ cmake -D ENABLE_TENSORFLOW=ON \
 	-D ENABLE_PYTORCH=ON \
 	-D ENABLE_PADDLE=ON \
 	-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
-	-D LAMMPS_VERSION=stable_29Aug2024_update1 \
+	-D LAMMPS_VERSION=stable_22Jul2025 \
 	-D CMAKE_BUILD_TYPE=Debug \
 	-D BUILD_TESTING:BOOL=TRUE \
 	-D TENSORFLOW_ROOT=${TENSORFLOW_ROOT} \

.devcontainer/devcontainer.json

@@ -11,7 +11,6 @@
     "PATH": "${containerEnv:PATH}:${containerWorkspaceFolder}/.venv/bin",
     "DP_ENABLE_PYTORCH": "1",
     "DP_VARIANT": "cpu",
-    "LMP_CXX11_ABI_0": "1",
     "UV_EXTRA_INDEX_URL": "https://download.pytorch.org/whl/cpu"
   }
 }

.github/workflows/test_cc.yml

@@ -41,7 +41,6 @@ jobs:
         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: ${{ matrix.check_memleak && '-fsanitize=leak' || '' }}
         LSAN_OPTIONS: suppressions=${{ github.workspace }}/.github/workflows/suppr.txt

.github/workflows/test_cuda.yml

@@ -30,10 +30,6 @@ jobs:
       with:
         python-version: '3.11'
         # cache: 'pip'
-    - name: Setup MPI
-      uses: mpi4py/setup-mpi@v1
-      with:
-        mpi: mpich
     - name: Install wget and unzip
       run: apt-get update && apt-get install -y wget unzip
     - uses: lukka/get-cmake@latest
@@ -74,7 +70,6 @@ jobs:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
-        LMP_CXX11_ABI_0: 1
         CMAKE_GENERATOR: Ninja
         DP_VARIANT: cuda
         DP_USE_MPICH2: 1

backend/dp_backend.py

@@ -1,6 +1,8 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """A PEP-517 backend to find TensorFlow."""
 
+import os
+
 from scikit_build_core import build as _orig
 
 from .find_pytorch import (
@@ -39,10 +41,15 @@ def __dir__() -> list[str]:
 def get_requires_for_build_wheel(
     config_settings: dict,
 ) -> list[str]:
+    if os.environ.get("CIBUILDWHEEL", "0") == "1":
+        cibw_deps = ["mpich"]
+    else:
+        cibw_deps = []
     return (
         _orig.get_requires_for_build_wheel(config_settings)
         + find_tensorflow()[1]
         + find_pytorch()[1]
+        + cibw_deps
     )
 
 

backend/find_pytorch.py

@@ -124,6 +124,11 @@ def get_pt_requirement(pt_version: str = "") -> dict:
             raise RuntimeError("Unsupported CUDA version") from None
     if pt_version == "":
         pt_version = os.environ.get("PYTORCH_VERSION", "")
+    if os.environ.get("CIBUILDWHEEL", "0") == "1":
+        # PyTorch OP library is built against mpich
+        mpi_requirement = ["mpich"]
+    else:
+        mpi_requirement = []
 
     return {
         "torch": [
@@ -134,7 +139,8 @@ def get_pt_requirement(pt_version: str = "") -> dict:
             f"torch=={Version(pt_version).base_version}.*"
             if pt_version != ""
             # https://github.com/pytorch/pytorch/commit/7e0c26d4d80d6602aed95cb680dfc09c9ce533bc
-            else "torch>=2.1.0"
+            else "torch>=2.1.0",
+            *mpi_requirement,
         ],
     }
 

backend/read_env.py

@@ -119,6 +119,7 @@ def get_argument_from_env() -> tuple[str, list, list, dict, str, str]:
 
     cmake_args = [
         "-DBUILD_PY_IF:BOOL=TRUE",
+        f"-DCIBUILDWHEEL={os.environ.get('CIBUILDWHEEL', '0')}",
         *cmake_args,
     ]
     return (

deepmd/lmp.py

@@ -81,7 +81,6 @@ def get_library_path(module: str, filename: str) -> list[str]:
 pt_dir = os.path.join(torch.__path__[0], "lib")
 op_dir = str(SHARED_LIB_DIR)
 
-
 cuda_library_paths = []
 if platform.system() == "Linux":
     cuda_library_paths.extend(

deepmd/lmp_check_build.py

@@ -0,0 +1,19 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+from deepmd.env import (
+    GLOBAL_CONFIG,
+)
+
+if GLOBAL_CONFIG.get("lammps_version", "") == "":
+
+    def get_op_dir() -> str:
+        """Get the directory of the deepmd-kit OP library."""
+        # empty
+        return ""
+else:
+    from deepmd.lmp import (
+        get_op_dir,
+    )
+
+__all__ = [
+    "get_op_dir",
+]

deepmd/pt/cxx_op.py

@@ -1,5 +1,12 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 import platform
+from ctypes import (
+    CDLL,
+    RTLD_GLOBAL,
+)
+from importlib import (
+    metadata,
+)
 
 import torch
 from packaging.version import (
@@ -87,6 +94,29 @@ def load_library(module_name: str) -> bool:
     return False
 
 
+def load_mpi_library() -> None:
+    """Load MPI library.
+
+    When building with cibuildwheel, the link to the MPI library is lost
+    after the wheel is repaired.
+    """
+    if platform.system() == "Linux":
+        libname = "libmpi.so.*"
+    elif platform.system() == "Darwin":
+        libname = "libmpi.*.dylib"
+    else:
+        raise RuntimeError("Unsupported platform")
+    MPI_LIB = next(p for p in metadata.files("mpich") if p.match(libname)).locate()
+    # use CDLL to load the library
+    CDLL(MPI_LIB, mode=RTLD_GLOBAL)
+
+
+if GLOBAL_CONFIG.get("cibuildwheel", "0") == "1" and platform.system() in (
+    "Linux",
+    "Darwin",
+):
+    load_mpi_library()
+
 ENABLE_CUSTOMIZED_OP = load_library("deepmd_op_pt")
 
 __all__ = [