merge devel to master (v3.0.0) (deepmodeling#4407)

.devcontainer/Dockerfile

@@ -0,0 +1,3 @@
+FROM mcr.microsoft.com/devcontainers/cpp:1-ubuntu-24.04
+
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/

.devcontainer/README.md

@@ -0,0 +1,40 @@
+# DeePMD-kit devcontainer environment
+
+This [devcontainer](https://vscode.js.cn/docs/devcontainers/devcontainer-cli) environment setups Python and C++ environment to develop DeePMD-kit.
+One can setup locally or use [GitHub Codespaces](https://docs.github.com/en/codespaces) by clicking the Code button on the DeePMD-kit repository page.
+The whole setup process requires about 10 minutes, so one needs to be patient.
+
+## Python environment
+
+The following packages are installed into the Python environment `.venv`:
+
+- DeePMD-kit (in edit mode)
+- Backends including TensorFlow, PyTorch, JAX
+- LAMMPS
+- MPICH
+- CMake
+- pre-commit (including hooks)
+- Test packages including pytest
+- Doc packages including sphinx
+
+## C++ interface
+
+The C++ interface with TensorFlow and PyTorch support is installed into `dp` directory.
+
+When calling and debuging LAMMPS with DeePMD-kit, use the following scripts instead of the regular `lmp`:
+
+- `.devcontainer/lmp`
+- `.devcontainer/gdb_lmp`
+
+Use the following scripts for `pytest` with LAMMPS:
+
+- `.devcontainer/pytest_lmp`
+- `.devcontainer/gdb_pytest_lmp`
+
+## Rebuild
+
+Usually the Python package does not need to reinstall.
+But when one wants to recompile the C++ code, the following scripts can be executed.
+
+- `.devcontainer/build_cxx.sh`
+- `.devcontainer/build_py.sh`

.devcontainer/build_cxx.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+set -ev
+
+NPROC=$(nproc --all)
+SCRIPT_PATH=$(dirname $(realpath -s $0))
+
+export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
+TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+
+mkdir -p ${SCRIPT_PATH}/../buildcxx/
+cd ${SCRIPT_PATH}/../buildcxx/
+cmake -D ENABLE_TENSORFLOW=ON \
+	-D ENABLE_PYTORCH=ON \
+	-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
+	-D LAMMPS_VERSION=stable_29Aug2024_update1 \
+	-D CMAKE_BUILD_TYPE=Debug \
+	-D BUILD_TESTING:BOOL=TRUE \
+	-D TENSORFLOW_ROOT=${TENSORFLOW_ROOT} \
+	${SCRIPT_PATH}/../source
+cmake --build . -j${NPROC}
+cmake --install .

.devcontainer/build_py.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -ev
+
+SCRIPT_PATH=$(dirname $(realpath -s $0))
+cd ${SCRIPT_PATH}/..
+
+uv sync --dev --python 3.12 --extra cpu --extra torch --extra jax --extra lmp --extra test --extra docs
+pre-commit install

.devcontainer/devcontainer.json

@@ -0,0 +1,17 @@
+{
+  "name": "DeePMD-kit",
+  "build": {
+    "dockerfile": "Dockerfile"
+  },
+  "features": {
+    "ghcr.io/devcontainers/features/github-cli:1": {}
+  },
+  "postCreateCommand": ".devcontainer/build_py.sh && .devcontainer/download_libtorch.sh && .devcontainer/build_cxx.sh && pre-commit install-hooks",
+  "remoteEnv": {
+    "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"
+  }
+}

.devcontainer/download_libtorch.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+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
+unzip ~/libtorch.zip

.devcontainer/gdb_lmp

@@ -0,0 +1,9 @@
+#!/bin/bash
+SCRIPT_PATH=$(dirname $(realpath -s $0))
+
+export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
+TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+
+env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
+	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
+	gdb ${SCRIPT_PATH}/../.venv/lib/python3.12/site-packages/lammps/lmp "$@"

.devcontainer/gdb_pytest_lmp

@@ -0,0 +1,9 @@
+#!/bin/bash
+SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
+
+export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
+TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+
+env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
+	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
+	gdb --args python -m pytest -s "$@"

.devcontainer/lmp

@@ -0,0 +1,9 @@
+#!/bin/bash
+SCRIPT_PATH=$(dirname $(realpath -s $0))
+
+export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
+TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+
+env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
+	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
+	${SCRIPT_PATH}/../.venv/bin/lmp "$@"

.devcontainer/pytest_lmp

@@ -0,0 +1,9 @@
+#!/bin/bash
+SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
+
+export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
+TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+
+env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
+	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
+	python -m pytest "$@"

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -1,2 +1,4 @@
 # do not show up detailed difference on GitHub
 source/3rdparty/* linguist-generated=true
+source/3rdparty/README.md linguist-generated=false
+.git_archival.txt  export-subst

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: dropdown

.github/ISSUE_TEMPLATE/generic-issue.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: textarea

.github/labeler.yml

@@ -1,39 +1,38 @@
-Python:
-- changed-files:
-  - any-glob-to-any-file:
-    - deepmd/**/*
-    - deepmd_utils/**/*
-    - source/tests/**/*
-Docs:
-- changed-files:
-  - any-glob-to-any-file: doc/**/*
-Examples:
-- changed-files:
-  - any-glob-to-any-file: examples/**/*
-Core:
-- changed-files:
-  - any-glob-to-any-file: source/lib/**/*
-CUDA:
-- changed-files:
-  - any-glob-to-any-file: source/lib/src/gpu/**/*
-ROCM:
-- changed-files:
-  - any-glob-to-any-file: source/lib/src/gpu/**/*
-OP:
-- changed-files:
-  - any-glob-to-any-file: source/op/**/*
-C++:
-- changed-files:
-  - any-glob-to-any-file: source/api_cc/**/*
-C:
-- changed-files:
-  - any-glob-to-any-file: source/api_c/**/*
-LAMMPS:
-- changed-files:
-  - any-glob-to-any-file: source/lmp/**/*
-Gromacs:
-- changed-files:
-  - any-glob-to-any-file: source/gmx/**/*
-i-Pi:
-- changed-files:
-  - any-glob-to-any-file: source/ipi/**/*
+Python:
+  - changed-files:
+      - any-glob-to-any-file:
+          - deepmd/**/*
+          - source/tests/**/*
+Docs:
+  - changed-files:
+      - any-glob-to-any-file: doc/**/*
+Examples:
+  - changed-files:
+      - any-glob-to-any-file: examples/**/*
+Core:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/**/*
+CUDA:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/src/gpu/**/*
+ROCM:
+  - changed-files:
+      - any-glob-to-any-file: source/lib/src/gpu/**/*
+OP:
+  - changed-files:
+      - any-glob-to-any-file: source/op/**/*
+C++:
+  - changed-files:
+      - any-glob-to-any-file: source/api_cc/**/*
+C:
+  - changed-files:
+      - any-glob-to-any-file: source/api_c/**/*
+LAMMPS:
+  - changed-files:
+      - any-glob-to-any-file: source/lmp/**/*
+Gromacs:
+  - changed-files:
+      - any-glob-to-any-file: source/gmx/**/*
+i-PI:
+  - changed-files:
+      - any-glob-to-any-file: source/ipi/**/*

.github/workflows/build_cc.yml

@@ -1,11 +1,17 @@
 on:
   push:
+    branches-ignore:
+      - "gh-readonly-queue/**"
   pull_request:
+  merge_group:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
 name: Build C++
 jobs:
   buildcc:
     name: Build C++
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         include:
@@ -24,9 +30,13 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: '3.11'
-        cache: 'pip'
     - uses: lukka/get-cmake@latest
-    - run: python -m pip install tensorflow
+    - 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: |
          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 \
@@ -48,13 +58,17 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get install -y rocm-dev hipcub-dev
       if: matrix.variant == 'rocm'
-    - run: source/install/build_cc.sh
+    - run: |
+        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+        source/install/build_cc.sh
       env:
         DP_VARIANT: ${{ matrix.dp_variant }}
         DOWNLOAD_TENSORFLOW: "FALSE"
         CMAKE_GENERATOR: Ninja
       if: matrix.variant != 'clang'
-    - run: source/install/build_cc.sh
+    - run: |
+        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
+        source/install/build_cc.sh
       env:
         DP_VARIANT: cpu
         DOWNLOAD_TENSORFLOW: "FALSE"