Test: Modify FindMKL.cmake (DO NOT CLOSE OR MERGE)

.github/workflows/build_test_cmake.yml

@@ -1,7 +1,7 @@
 name: Build Test
 on:
   push:
-  pull_request:
+  # pull_request:
 
 jobs:
   test:

.github/workflows/build_test_makefile.yml

@@ -1,7 +1,7 @@
 name: Build Test
 on:
   push:
-  pull_request:
+  # pull_request:
 
 jobs:
   test:

.github/workflows/coverage.yml

@@ -1,6 +1,9 @@
 name: Coverage Analysis
 
 on:
+  pull_request: # 当有 PR 指向 develop 分支时触发
+    branches:
+      - develop
   workflow_dispatch:
   push:
     tags:
@@ -16,8 +19,12 @@ jobs:
       - name: Install Requirements for Coverage Testing
         run: |
           apt update && apt install -y lcov gpg curl jq ca-certificates
+          # mkdir externals
+          # git submodule add git://github.com/RWTH-HPC/CMake-codecov.git externals/CMake-codecov
       - name: Building
         run: |
+          rm -rf build/
+          rm -f CMakeCache.txt
           cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
           cmake --build build -j`nproc`
           cmake --install build
@@ -26,6 +33,9 @@ jobs:
           OMP_NUM_THREADS: 1
         run: |
           cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
+      - name: Generate Coverage Report
+        run: |
+          cmake --build build --target coverage
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v5
         if: ${{ ! cancelled() }}

.github/workflows/cuda.yml

@@ -2,7 +2,7 @@ name: CUDA Test
 
 on:
   workflow_dispatch:
-  pull_request:
+  # pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/devcontainer.yml

@@ -1,6 +1,9 @@
 name: Container
 
 on:
+  #pull_request: # 当有 PR 指向 develop 分支时触发
+    #branches:
+    #  - develop
   push:
     branches:
       - develop
@@ -14,7 +17,8 @@ jobs:
     if: github.repository_owner == 'deepmodeling'
     strategy:
       matrix:
-        dockerfile: ["gnu","intel","cuda"]
+        dockerfile: ["intel"]
+        # dockerfile: ["gnu","intel","cuda"]
     steps:
       - name: Checkout
         uses: actions/checkout@v5
@@ -41,10 +45,11 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Login to Aliyun Registry
+        # 只有在不是由 fork 的 PR 触发时才执行
+        if: github.event.pull_request.head.repo.full_name == github.repository
         uses: docker/login-action@v3
         with:
           registry: dp-harbor-registry.us-east-1.cr.aliyuncs.com
-            # AliCloud automatically mirrors to registry.dp.tech
           username: ${{ secrets.DP_HARBOR_USERNAME }}
           password: ${{ secrets.DP_HARBOR_PASSWORD }}
 
@@ -54,6 +59,7 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           file: Dockerfile.${{ matrix.dockerfile }}
-          push: true
+          # 只有在 develop 分支或打标签时才推送，PR时不推送
+          push: ${{ github.event_name != 'pull_request' }}
           cache-from: type=registry,ref=ghcr.io/deepmodeling/abacus-${{ matrix.dockerfile }}:latest
           cache-to: type=inline

.github/workflows/pytest.yml

@@ -1,7 +1,8 @@
 name: Pyabacus Build and Test
 
 on:
-  pull_request:
+  push:
+  # pull_request:
 
 jobs:
   test:

.github/workflows/test.yml

@@ -1,7 +1,8 @@
 name: Integration Test and Unit Test
 
 on:
-  pull_request:
+  push:
+  # pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

CMakeLists.txt

@@ -151,16 +151,24 @@ endif()
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 if(ENABLE_COVERAGE)
-  find_package(codecov)
+  find_package(codecov QUIET)
   if(NOT codecov_FOUND)
     include(FetchContent)
     FetchContent_Declare(
       cmakecodecov
-      URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
+      GIT_REPOSITORY https://github.com/RWTH-HPC/CMake-codecov.git
+      GIT_TAG master
+      # URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
+      # URL https://github.com/RWTH-HPC/CMake-codecov/archive/refs/heads/master.zip
+      # URL https://gitee.com/mirrors_rwth-elp/cmake-codecov/archive/refs/heads/master.zip
+      GIT_SHALLOW TRUE
+      GIT_PROGRESS TRUE
     )
     FetchContent_Populate(cmakecodecov)
     list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
+    set(CMAKE_MODULE_PATH "${cmakecodecov_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
     find_package(codecov REQUIRED)
+  ##set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/externals/CMake-codecov/cmake" ${CMAKE_MODULE_PATH})
   endif()
 endif()
 
@@ -806,5 +814,18 @@ install(PROGRAMS ${ABACUS_BIN_PATH}
 )
 
 if(ENABLE_COVERAGE)
-  coverage_evaluate()
+    ## coverage_evaluate()
+    add_custom_target(coverage
+        COMMAND ${CMAKE_COMMAND} -E echo "Capturing coverage data..."
+        COMMAND lcov --capture --directory ${CMAKE_BINARY_DIR} --output-file ${CMAKE_BINARY_DIR}/coverage.info
+        COMMAND ${CMAKE_COMMAND} -E echo "Filtering coverage data..."
+
+        COMMAND lcov --remove ${CMAKE_BINARY_DIR}/coverage.info '/usr/*' '*/test/*' '*/gtest/*' '*/gmock/*' --output-file ${CMAKE_BINARY_DIR}/coverage.info
+        COMMAND ${CMAKE_COMMAND} -E echo "Generating HTML report..."
+
+        COMMAND genhtml -o ${CMAKE_BINARY_DIR}/coverage_html ${CMAKE_BINARY_DIR}/coverage.info
+        COMMAND ${CMAKE_COMMAND} -E echo "Coverage report generated at: ${CMAKE_BINARY_DIR}/coverage_html/index.html"
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Generating code coverage report with lcov"
+    )
 endif()

Dockerfile.intel

@@ -1,17 +1,18 @@
+# Base image
 FROM ubuntu:22.04
 
 RUN apt-get update && apt-get install -y \
     bc cmake git gnupg gcc g++ python3-numpy sudo wget vim unzip \
     libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev \
     pkg-config build-essential autoconf automake libtool
 
-# Following steps by https://software.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html .
+# Add Intel apt repo
 RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
     | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null && \
     echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" \
     | sudo tee /etc/apt/sources.list.d/oneAPI.list
 
-# To save disk space, only install the essential components, but not the whole toolkit.
+# 安装oneAPI组件（使用更灵活的版本处理）
 RUN apt-get update && \
     apt-get install -y \
         intel-oneapi-compiler-dpcpp-cpp \
@@ -44,18 +45,121 @@ ENV PKG_CONFIG_PATH=${MKLROOT}/lib/pkgconfig:${ONEAPI_ROOT}/mpi/latest/lib/pkgco
 ENV CMAKE_PREFIX_PATH=${ONEAPI_ROOT}/tbb/latest:${MKLROOT}/lib/cmake:${ONEAPI_ROOT}/dpl/latest/lib/cmake:${ONEAPI_ROOT}/dnnl/latest/lib/cmake:${ONEAPI_ROOT}/dal/latest:${ONEAPI_ROOT}/compiler/latest:${CMAKE_PREFIX_PATH}
 
 SHELL ["/bin/bash", "-c"]
+
+# 设置编译器 - 使用更兼容的配置
+# ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
+# 备用设置（如果上面的不行）
 ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
-# Verify oneAPI installation
+# 验证oneAPI安装
 RUN source ${ONEAPI_ROOT}/setvars.sh && \
-    echo "=== Verify compiler ===" && \
+    echo "=== 验证编译器 ===" && \
     which mpiicx && mpiicx --version && \
-    echo "=== Verify MKL ===" && \
+    echo "=== 验证MKL ===" && \
     ls ${MKLROOT}/lib/intel64/ && \
-    echo "=== Verify MPI ===" && \
+    echo "=== 验证MPI ===" && \
     which mpirun && mpirun --version
 
-# https://elpa.mpcdf.mpg.de/software/tarball-archive/ELPA_TARBALL_ARCHIVE.html
+###### PEXSI PART: pexsi and gklib and metis and parmetis and superlu_dist
+ENV GKLIB_VERSION="master" 
+ENV METIS_VERSION="master"
+ENV PARMETIS_VERSION="main"
+ENV SUPERLU_DIST_VERSION=7.2.0
+ENV PEXSI_VERSION=2.0.0
+ENV GKLIB_ROOT=/usr/local/gklib-${GKLIB_VERSION}
+ENV METIS32_ROOT=/usr/local/metis32-${METIS_VERSION}
+ENV PARMETIS32_ROOT=/usr/local/parmetis32-${PARMETIS_VERSION}
+ENV PEXSI32_ROOT=/usr/local/pexsi32-${PEXSI_VERSION}
+ENV SUPERLU_DIST32_ROOT=/usr/local/superlu_dist32-${SUPERLU_DIST_VERSION}
+
+# 2. install GKlib
+RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VERSION} -O GKlib-${GKLIB_VERSION}.zip && \
+    unzip GKlib-${GKLIB_VERSION}.zip && \
+    cd GKlib-${GKLIB_VERSION} && \
+    make config shared=1 prefix=${GKLIB_ROOT} openmp=set && \
+    make -j$(nproc) && \
+    make install && \
+    ls ${GKLIB_ROOT}/lib && \
+    cp ${GKLIB_ROOT}/lib/libGKlib.so.0 ${GKLIB_ROOT}/lib/libGKlib.so && \ 
+    cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
+#.so file CANNOT be found otherwise.
+# 2. install METIS
+RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VERSION} -O METIS-${METIS_VERSION}.zip && \
+    unzip METIS-${METIS_VERSION}.zip && \
+    cd METIS-${METIS_VERSION} && \
+    make config shared=1 prefix=${METIS32_ROOT} gklib_path=${GKLIB_ROOT} && \
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf METIS-${METIS_VERSION} METIS-${METIS_VERSION}.zip
+
+# 3. install ParMETIS
+RUN export LD_LIBRARY_PATH=${METIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    wget https://codeload.github.com/KarypisLab/ParMETIS/zip/refs/heads/${PARMETIS_VERSION} -O ParMETIS-${PARMETIS_VERSION}.zip && \
+    unzip ParMETIS-${PARMETIS_VERSION}.zip && \
+    cd ParMETIS-${PARMETIS_VERSION} && \
+    make config shared=1 prefix=${PARMETIS32_ROOT} gklib_path=${GKLIB_ROOT} metis_path=${METIS32_ROOT} && \
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf ParMETIS-${PARMETIS_VERSION} ParMETIS-${PARMETIS_VERSION}.zip
+
+# 4. install SuperLU_DIST 
+RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
+    tar -xzf v${SUPERLU_DIST_VERSION}.tar.gz && \
+    cd superlu_dist-${SUPERLU_DIST_VERSION} && \
+    mkdir build && cd build && \
+    cmake .. \
+    -DTPL_ENABLE_PARMETISLIB=ON \
+    -DTPL_PARMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib/libGKlib.so" \
+    -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
+    -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
+    -DTPL_ENABLE_LAPACKLIB=ON \
+    -DTPL_ENABLE_COMBBLASLIB=OFF \
+    -DTPL_ENABLE_CUDALIB=OFF \
+    -Denable_complex16=ON \
+    -DXSDK_INDEX_SIZE=32 \
+    -DBUILD_SHARED_LIBS=ON \
+    -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
+    -DCMAKE_C_FLAGS="-O3 -fopenmp" \
+    -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
+    -DXSDK_ENABLE_Fortran=ON \
+    -DCMAKE_Fortran_COMPILER=mpiifx && \                             
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf superlu_dist-${SUPERLU_DIST_VERSION} v${SUPERLU_DIST_VERSION}.tar.gz
+
+###     -DCMAKE_C_COMPILER=mpiicc \
+###     -DCMAKE_CXX_COMPILER=mpiicpc \
+###     -DCMAKE_CUDA_COMPILER=nvcc \
+
+# 5. install PEXSI
+RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    export LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LIBRARY_PATH} && \
+    export PKG_CONFIG_PATH=${SUPERLU_DIST32_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${GKLIB_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH} && \
+    export CPATH=${SUPERLU_DIST32_ROOT}/include:${PARMETIS32_ROOT}/include:${METIS32_ROOT}/include:${GKLIB_ROOT}/include:${CMAKE_PREFIX_PATH} && \
+    export CMAKE_PREFIX_PATH=${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH} && \
+    wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz && \
+    tar -xzf pexsi_v${PEXSI_VERSION}.tar.gz && \
+    cd pexsi_v${PEXSI_VERSION} && \
+    sed -i 's/^add_pexsi_f_example_exe/# add_pexsi_f_example_exe/g' fortran/CMakeLists.txt && \
+    sed -i 's/^add_pexsi_example_exe/# add_pexsi_example_exe/g' examples/CMakeLists.txt && \
+    sed -i 's/add_executable/# add_executable/g' fortran/CMakeLists.txt && \
+    sed -i 's/add_executable/# add_executable/g' examples/CMakeLists.txt && \
+    mkdir build && cd build && \
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
+        -DPEXSI_ENABLE_OPENMP=ON \
+        -DPEXSI_ENABLE_FORTRAN=OFF && \
+    make pexsi -j$(nproc) && \
+    make install && \
+    cd / && rm -rf pexsi_v${PEXSI_VERSION} pexsi_v${PEXSI_VERSION}.tar.gz
+
+###         -DCMAKE_C_COMPILER=mpiicc \
+###        -DCMAKE_CXX_COMPILER=mpiicpc \
+###### END of PEXSI PART
+
+
+# Build ELPA (example dependency)
 RUN source /opt/intel/oneapi/setvars.sh && \
     cd /tmp && \
     ELPA_VER=2022.11.001 && \
@@ -77,13 +181,16 @@ ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 # Clone and build abacus (optional during image build; keep for CI image)
 ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/develop /dev/null
 RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH} && \
     export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH} && \
+    export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH} && \
     cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \
         -DENABLE_MLALGO=ON \
         -DENABLE_LIBXC=ON \
         -DENABLE_LIBRI=ON \
+        -DENABLE_PEXSI=ON \
         -DENABLE_RAPIDJSON=ON \
         -DCMAKE_BUILD_TYPE=Release && \
     cmake --build build -j"$(nproc)" && \