From a02d6786015ff91890673f24081164812c4509f7 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 14:46:43 +0800
Subject: [PATCH 01/92] Test: Modify FindMKL.cmake

---
 .github/workflows/devcontainer.yml | 6 +++++-
 cmake/FindMKL.cmake                | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml
index ef9bbbfc84..f9fbdd47c0 100644
--- a/.github/workflows/devcontainer.yml
+++ b/.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
@@ -54,6 +57,7 @@ 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
diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
index f9cddfcf74..26dece3b44 100644
--- a/cmake/FindMKL.cmake
+++ b/cmake/FindMKL.cmake
@@ -4,7 +4,7 @@
 #  MKL_INCLUDE - where to find mkl.h, etc.
 #  MKL_FOUND        - True if mkl found.
 
-find_package(MKL NO_MODULE) # try using official module first
+# find_package(MKL NO_MODULE) # try using official module first
 if(NOT TARGET MKL::MKL)
 
 find_path(MKL_INCLUDE mkl_service.h HINTS ${MKLROOT}/include)

From 04bc224cb6e22e334ab33d472b54316cec87f353 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 16:10:44 +0800
Subject: [PATCH 02/92] Fix: Add condition to login to Aliyun Registry only for
 non-forked PRs

---
 .github/workflows/devcontainer.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml
index f9fbdd47c0..7eb4014364 100644
--- a/.github/workflows/devcontainer.yml
+++ b/.github/workflows/devcontainer.yml
@@ -44,10 +44,11 @@ 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 }}
 

From b8b78efc7729c745ea7108f335b70951cf78db3b Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 18:19:27 +0800
Subject: [PATCH 03/92] Update Dockerfile: streamline oneAPI installation and
 improve environment setup

---
 Dockerfile.intel | 107 ++++++++++++++++++++++++++++-------------------
 1 file changed, 65 insertions(+), 42 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 5bf6308e79..ed52e2c101 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -1,66 +1,89 @@
+# Base image
 FROM ubuntu:22.04
 
+# allow selecting oneAPI minor version at build time
+ARG ONEAPI_VER=2025.3
+ENV ONEAPI_VER=${ONEAPI_VER}
+
+# Basic build tools
 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
+    bc cmake git gnupg gcc g++ python3-numpy wget unzip ca-certificates \
+    vim sudo build-essential curl pkg-config \
+    libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev \
+ && rm -rf /var/lib/apt/lists/*
 
-# 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
+    | gpg --dearmor --yes -o /usr/share/keyrings/oneapi-archive-keyring.gpg \
+ && echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" \
+    > /etc/apt/sources.list.d/oneAPI.list
 
-# To save disk space, only install the essential components, but not the whole toolkit.
-RUN apt-get update && \
-    apt-get install -y \
+# Install essential oneAPI components (avoid pinning an exact mpi minor version)
+RUN apt-get update && apt-get install -y \
         intel-oneapi-compiler-dpcpp-cpp \
         intel-oneapi-compiler-fortran \
         intel-oneapi-mkl-devel \
-        intel-oneapi-mpi-devel="2021.11.*" \
-        intel-oneapi-vtune && \
-        rm /opt/intel/oneapi/mpi/latest && ln -s /opt/intel/oneapi/mpi/2021.11 /opt/intel/oneapi/mpi/latest
-ENV I_MPI_ROOT=/opt/intel/oneapi/mpi/latest \
-    LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib/:/opt/intel/oneapi/ippcp/latest/lib/:/opt/intel/oneapi/ipp/latest/lib:/opt/intel/oneapi/dpl/latest/lib:/opt/intel/oneapi/dnnl/latest/lib:/opt/intel/oneapi/dal/latest/lib:/opt/intel/oneapi/compiler/latest/lib:/opt/intel/oneapi/ccl/latest/lib/ \
-    LD_LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/opt/mpi/libfabric/lib:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib:/opt/intel/oneapi/itac/latest/slib:/opt/intel/oneapi/ippcp/latest/lib/:/opt/intel/oneapi/ipp/latest/lib:/opt/intel/oneapi/dpl/latest/lib:/opt/intel/oneapi/dnnl/latest/lib:/opt/intel/oneapi/debugger/latest/opt/debugger/lib:/opt/intel/oneapi/dal/latest/lib:/opt/intel/oneapi/compiler/latest/opt/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/latest/opt/compiler/lib:/opt/intel/oneapi/compiler/latest/lib:/opt/intel/oneapi/ccl/latest/lib/ \
-    PATH=/opt/intel/oneapi/vtune/latest/bin64:/opt/intel/oneapi/mpi/latest/opt/mpi/libfabric/bin:/opt/intel/oneapi/mpi/latest/bin:/opt/intel/oneapi/mkl/latest/bin/:/opt/intel/oneapi/itac/latest/bin:/opt/intel/oneapi/inspector/latest/bin64:/opt/intel/oneapi/dpcpp-ct/latest/bin:/opt/intel/oneapi/dev-utilities/latest/bin:/opt/intel/oneapi/debugger/latest/opt/debugger/bin:/opt/intel/oneapi/compiler/latest/opt/oclfpga/bin:/opt/intel/oneapi/compiler/latest/bin:/opt/intel/oneapi/advisor/latest/bin64:/opt/mamba/bin:/opt/mamba/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
-    MKLROOT=/opt/intel/oneapi/mkl/latest \
-    FI_PROVIDER_PATH=/opt/intel/oneapi/mpi/latest/opt/mpi/libfabric/lib/prov:/usr/lib/x86_64-linux-gnu/libfabric \
-    CMAKE_PREFIX_PATH=/opt/intel/oneapi/tbb/latest/env/..:/opt/intel/oneapi/mkl/latest/lib/cmake:/opt/intel/oneapi/ipp/latest/lib/cmake/ipp:/opt/intel/oneapi/dpl/latest/lib/cmake/oneDPL:/opt/intel/oneapi/dnnl/latest/lib/cmake:/opt/intel/oneapi/dal/latest:/opt/intel/oneapi/compiler/latest \
-    CMPLR_ROOT=/opt/intel/oneapi/compiler/latest
+        intel-oneapi-mpi-devel \
+        intel-oneapi-vtune \
+ && rm -rf /var/lib/apt/lists/*
+
+# Normalize 'latest' symlinks for mkl/mpi if possible; prefer requested ONEAPI_VER when present
+RUN set -eux; \
+    mkdir -p /opt/intel/oneapi; \
+    if [ -d "/opt/intel/oneapi/mkl/${ONEAPI_VER}" ]; then \
+        ln -sfn "/opt/intel/oneapi/mkl/${ONEAPI_VER}" /opt/intel/oneapi/mkl/latest; \
+    elif [ -d /opt/intel/oneapi/mkl ]; then \
+        ver=$(ls -1 /opt/intel/oneapi/mkl | sort -V | tail -n1 || true); \
+        [ -n "$ver" ] && ln -sfn "/opt/intel/oneapi/mkl/$ver" /opt/intel/oneapi/mkl/latest || true; \
+    fi; \
+    if [ -d "/opt/intel/oneapi/mpi/${ONEAPI_VER}" ]; then \
+        ln -sfn "/opt/intel/oneapi/mpi/${ONEAPI_VER}" /opt/intel/oneapi/mpi/latest; \
+    elif [ -d /opt/intel/oneapi/mpi ]; then \
+        ver=$(ls -1 /opt/intel/oneapi/mpi | sort -V | tail -n1 || true); \
+        [ -n "$ver" ] && ln -sfn "/opt/intel/oneapi/mpi/$ver" /opt/intel/oneapi/mpi/latest || true; \
+    fi; \
+    echo "MKL dirs:"; ls -la /opt/intel/oneapi/mkl || true; \
+    echo "MPI dirs:"; ls -la /opt/intel/oneapi/mpi || true
+
+# Set consistent envs referencing 'latest' symlink
+ENV I_MPI_ROOT=/opt/intel/oneapi/mpi/latest
+ENV MKLROOT=/opt/intel/oneapi/mkl/latest
+ENV LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
+ENV LD_LIBRARY_PATH=/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
+ENV PATH=/opt/intel/oneapi/mpi/latest/bin:/opt/intel/oneapi/mkl/latest/bin:$PATH
+ENV CMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl/latest/lib/cmake
 
 SHELL ["/bin/bash", "-c"]
 ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
-# https://elpa.mpcdf.mpg.de/software/tarball-archive/ELPA_TARBALL_ARCHIVE.html
-RUN source /opt/intel/oneapi/setvars.sh && \
+# Build ELPA (example dependency)
+RUN source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
     cd /tmp && \
-    ELPA_VER=2022.11.001 && \
+    ELPA_VER=2025.06.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    tar xzf elpa-$ELPA_VER.tar.gz  && rm elpa-$ELPA_VER.tar.gz && \
+    tar xzf elpa-$ELPA_VER.tar.gz && rm elpa-$ELPA_VER.tar.gz && \
     cd elpa-$ELPA_VER && mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
-    make -j`nproc` && \
-    make PREFIX=/usr/local install && \
-    ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
+    make -j"$(nproc)" && make PREFIX=/usr/local install && \
+    ln -sfn /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/elpa || true && \
     cd /tmp && rm -rf elpa-$ELPA_VER
 
-RUN cd /tmp && git clone https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ \
-    && rm -rf rapidjson
-
-RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip \
-        --no-check-certificate --quiet -O libtorch.zip && \
-    unzip -q libtorch.zip -d /opt  && rm libtorch.zip
-
-ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake
+# rapidjson and libtorch
+RUN cd /tmp && git clone --depth 1 https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ && rm -rf rapidjson
+RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip -O /tmp/libtorch.zip && \
+    unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
+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 source /opt/intel/oneapi/setvars.sh && \
-    git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+RUN set -eux; source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
+    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_RAPIDJSON=ON && \
-    cmake --build build -j`nproc` && \
+    cmake --build build -j"$(nproc)" && \
     cmake --install build && \
-    rm -rf build && \
-    abacus --version
-    #&& rm -rf abacus-develop
+    /usr/bin/abacus --version || true && \
+    rm -rf /tmp/abacus-develop /tmp/abacus-develop.tar.gz
+
+# Default entry
+CMD ["/bin/bash"]

From a393a725f1c1c2c08a697b2f2624575880fce2ad Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 19:17:46 +0800
Subject: [PATCH 04/92] Fix: Add gzip installation to Dockerfile for build
 tools

---
 Dockerfile.intel | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index ed52e2c101..2c4bf73e0b 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -8,6 +8,7 @@ ENV ONEAPI_VER=${ONEAPI_VER}
 # Basic build tools
 RUN apt-get update && apt-get install -y \
     bc cmake git gnupg gcc g++ python3-numpy wget unzip ca-certificates \
+    gzip \
     vim sudo build-essential curl pkg-config \
     libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev \
  && rm -rf /var/lib/apt/lists/*

From a81705f46fa9aa272ff1ae28a489c2ed22a14ed6 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 20:09:55 +0800
Subject: [PATCH 05/92] Update Dockerfile.intel

---
 .github/workflows/build_test_cmake.yml    | 2 +-
 .github/workflows/build_test_makefile.yml | 2 +-
 .github/workflows/cuda.yml                | 2 +-
 .github/workflows/devcontainer.yml        | 3 ++-
 .github/workflows/pytest.yml              | 3 ++-
 .github/workflows/test.yml                | 3 ++-
 Dockerfile.intel                          | 2 +-
 7 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build_test_cmake.yml b/.github/workflows/build_test_cmake.yml
index 22610fb454..a9ec3c8a6d 100644
--- a/.github/workflows/build_test_cmake.yml
+++ b/.github/workflows/build_test_cmake.yml
@@ -1,7 +1,7 @@
 name: Build Test
 on:
   push:
-  pull_request:
+  # pull_request:
 
 jobs:
   test:
diff --git a/.github/workflows/build_test_makefile.yml b/.github/workflows/build_test_makefile.yml
index 237d25ebf8..45ea727557 100644
--- a/.github/workflows/build_test_makefile.yml
+++ b/.github/workflows/build_test_makefile.yml
@@ -1,7 +1,7 @@
 name: Build Test
 on:
   push:
-  pull_request:
+  # pull_request:
 
 jobs:
   test:
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
index 14e829e546..2400fa4775 100644
--- a/.github/workflows/cuda.yml
+++ b/.github/workflows/cuda.yml
@@ -2,7 +2,7 @@ name: CUDA Test
 
 on:
   workflow_dispatch:
-  pull_request:
+  # pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml
index 7eb4014364..d3ff39b69f 100644
--- a/.github/workflows/devcontainer.yml
+++ b/.github/workflows/devcontainer.yml
@@ -17,7 +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
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 1e78dfb0a1..b0790c92a1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -1,7 +1,8 @@
 name: Pyabacus Build and Test
 
 on:
-  pull_request:
+  push:
+  # pull_request:
 
 jobs:
   test:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index df1dfb29dc..b87792a8db 100644
--- a/.github/workflows/test.yml
+++ b/.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 }}
diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2c4bf73e0b..604fd9b1b1 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -62,7 +62,7 @@ RUN source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
     cd /tmp && \
     ELPA_VER=2025.06.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    tar xzf elpa-$ELPA_VER.tar.gz && rm elpa-$ELPA_VER.tar.gz && \
+    tar xzf elpa-$ELPA_VER.tar.gz --no-same-owner --no-same-permissions && rm elpa-$ELPA_VER.tar.gz && \
     cd elpa-$ELPA_VER && mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
     make -j"$(nproc)" && make PREFIX=/usr/local install && \

From e6f7eff21950b1691a544efd65ddfbb7bd1273dc Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 28 Oct 2025 21:27:14 +0800
Subject: [PATCH 06/92] Fix: Update ELPA version to 2022.11.001 in Dockerfile

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 604fd9b1b1..0afac6434e 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -60,7 +60,7 @@ ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 # Build ELPA (example dependency)
 RUN source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
     cd /tmp && \
-    ELPA_VER=2025.06.001 && \
+    ELPA_VER=2022.11.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
     tar xzf elpa-$ELPA_VER.tar.gz --no-same-owner --no-same-permissions && rm elpa-$ELPA_VER.tar.gz && \
     cd elpa-$ELPA_VER && mkdir build && cd build && \

From d3cc27c6c4c912527d0b092f2580a38b58fd1227 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 14:05:56 +0800
Subject: [PATCH 07/92] Fix: Refactor Dockerfile.intel to streamline package
 installation and improve ELPA build process

---
 Dockerfile.intel | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 0afac6434e..67f6952e70 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -7,17 +7,14 @@ ENV ONEAPI_VER=${ONEAPI_VER}
 
 # Basic build tools
 RUN apt-get update && apt-get install -y \
-    bc cmake git gnupg gcc g++ python3-numpy wget unzip ca-certificates \
-    gzip \
-    vim sudo build-essential curl pkg-config \
-    libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev \
- && rm -rf /var/lib/apt/lists/*
+    bc cmake git gnupg gcc g++ python3-numpy sudo wget vim unzip \
+    libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev
 
 # Add Intel apt repo
 RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
-    | gpg --dearmor --yes -o /usr/share/keyrings/oneapi-archive-keyring.gpg \
- && echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" \
-    > /etc/apt/sources.list.d/oneAPI.list
+    | 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
 
 # Install essential oneAPI components (avoid pinning an exact mpi minor version)
 RUN apt-get update && apt-get install -y \
@@ -58,15 +55,16 @@ SHELL ["/bin/bash", "-c"]
 ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
 # Build ELPA (example dependency)
-RUN source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
+RUN source /opt/intel/oneapi/setvars.sh  \
     cd /tmp && \
     ELPA_VER=2022.11.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    tar xzf elpa-$ELPA_VER.tar.gz --no-same-owner --no-same-permissions && rm elpa-$ELPA_VER.tar.gz && \
+    tar xzf elpa-$ELPA_VER.tar.gz && rm elpa-$ELPA_VER.tar.gz && \
     cd elpa-$ELPA_VER && mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
-    make -j"$(nproc)" && make PREFIX=/usr/local install && \
-    ln -sfn /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/elpa || true && \
+    make -j`nproc` && \
+    make PREFIX=/usr/local install && \
+    ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
     cd /tmp && rm -rf elpa-$ELPA_VER
 
 # rapidjson and libtorch

From 7c6465c7edad9b78d8e28e9f8e9157ebc88d2687 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 16:51:48 +0800
Subject: [PATCH 08/92] Fix: Update ELPA build process in Dockerfile.intel to
 improve extraction and installation steps

---
 Dockerfile.intel | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 67f6952e70..9a06bb93e4 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -54,15 +54,20 @@ ENV CMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl/latest/lib/cmake
 SHELL ["/bin/bash", "-c"]
 ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
+RUN which gzip && ls -l $(which gzip)
+RUN ls -l /bin/gzip /usr/bin/gzip
+
 # Build ELPA (example dependency)
-RUN source /opt/intel/oneapi/setvars.sh  \
+RUN source /opt/intel/oneapi/setvars.sh && \
     cd /tmp && \
     ELPA_VER=2022.11.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    tar xzf elpa-$ELPA_VER.tar.gz && rm elpa-$ELPA_VER.tar.gz && \
-    cd elpa-$ELPA_VER && mkdir build && cd build && \
+    /bin/tar xzf elpa-$ELPA_VER.tar.gz && \
+    rm elpa-$ELPA_VER.tar.gz && \
+    cd elpa-$ELPA_VER && \
+    mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
-    make -j`nproc` && \
+    make -j$(nproc) && \
     make PREFIX=/usr/local install && \
     ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
     cd /tmp && rm -rf elpa-$ELPA_VER

From 4479db1e70770c616e0c9e639768019528f81773 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 17:12:16 +0800
Subject: [PATCH 09/92] Fix: Update ELPA extraction method in Dockerfile.intel
 to use gzip and tar commands

---
 Dockerfile.intel | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 9a06bb93e4..438042bafe 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -62,7 +62,8 @@ RUN source /opt/intel/oneapi/setvars.sh && \
     cd /tmp && \
     ELPA_VER=2022.11.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    /bin/tar xzf elpa-$ELPA_VER.tar.gz && \
+    gzip -d elpa-$ELPA_VER.tar.gz && \
+    tar xf elpa-$ELPA_VER.tar && \
     rm elpa-$ELPA_VER.tar.gz && \
     cd elpa-$ELPA_VER && \
     mkdir build && cd build && \

From eeb7e60d63553577164b352a79f082b2b7f008af Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 17:55:01 +0800
Subject: [PATCH 10/92] Fix: Correct file removal command in ELPA build process
 in Dockerfile.intel

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 438042bafe..72c9771761 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -64,7 +64,7 @@ RUN source /opt/intel/oneapi/setvars.sh && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
     gzip -d elpa-$ELPA_VER.tar.gz && \
     tar xf elpa-$ELPA_VER.tar && \
-    rm elpa-$ELPA_VER.tar.gz && \
+    rm elpa-$ELPA_VER.tar && \
     cd elpa-$ELPA_VER && \
     mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \

From fd422d63b9efee5869e826e64d7588e47f83e53d Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 18:49:26 +0800
Subject: [PATCH 11/92] Fix: Comment out LIBRARY_PATH and CC/CXX/FC environment
 variables in Dockerfile.intel

---
 Dockerfile.intel | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 72c9771761..a50e15c101 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -46,12 +46,13 @@ RUN set -eux; \
 # Set consistent envs referencing 'latest' symlink
 ENV I_MPI_ROOT=/opt/intel/oneapi/mpi/latest
 ENV MKLROOT=/opt/intel/oneapi/mkl/latest
-ENV LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
+# ENV LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
 ENV LD_LIBRARY_PATH=/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
 ENV PATH=/opt/intel/oneapi/mpi/latest/bin:/opt/intel/oneapi/mkl/latest/bin:$PATH
 ENV CMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl/latest/lib/cmake
 
 SHELL ["/bin/bash", "-c"]
+# ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
 ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
 RUN which gzip && ls -l $(which gzip)

From 296046a610bda638e77cb6272aff4da479c5725c Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 19:06:05 +0800
Subject: [PATCH 12/92] Fix: Update Dockerfile.intel to include pkg-config and
 kernel headers installation for vtune

---
 Dockerfile.intel | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index a50e15c101..2e7b38b67f 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -8,7 +8,8 @@ ENV ONEAPI_VER=${ONEAPI_VER}
 # Basic build tools
 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
+    libcereal-dev libxc-dev libgtest-dev libgmock-dev libbenchmark-dev \
+    pkg-config build-essential make ca-certificates
 
 # Add Intel apt repo
 RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
@@ -17,7 +18,13 @@ RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRO
     | sudo tee /etc/apt/sources.list.d/oneAPI.list
 
 # Install essential oneAPI components (avoid pinning an exact mpi minor version)
-RUN apt-get update && apt-get install -y \
+RUN apt-get update && \
+    # Ensure pkg-config and kernel headers are present before installing vtune (vtune's installer checks kernel headers)
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        pkg-config || true && \
+    # Try to install headers matching the build host kernel; fall back to generic headers if exact package not available.
+    DEBIAN_FRONTEND=noninteractive bash -lc "apt-get install -y --no-install-recommends linux-headers-$(uname -r) || apt-get install -y --no-install-recommends linux-headers-generic || true" && \
+    apt-get install -y \
         intel-oneapi-compiler-dpcpp-cpp \
         intel-oneapi-compiler-fortran \
         intel-oneapi-mkl-devel \

From 4c9d946f295c8352baecd6979a1ee722133cf90f Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 19:25:26 +0800
Subject: [PATCH 13/92] Fix: Correct environment variable assignments for
 compiler in Dockerfile.intel

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2e7b38b67f..5935ec7da5 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -60,7 +60,7 @@ ENV CMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl/latest/lib/cmake
 
 SHELL ["/bin/bash", "-c"]
 # ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
-ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
+ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
 
 RUN which gzip && ls -l $(which gzip)
 RUN ls -l /bin/gzip /usr/bin/gzip

From e31d91ad61e840a3a9ac9ddb66830aa5317e29c3 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 20:12:54 +0800
Subject: [PATCH 14/92] Fix: Update Dockerfile.intel to streamline oneAPI
 installation and improve package management

---
 Dockerfile.intel | 83 +++++++++++++++++++++---------------------------
 1 file changed, 37 insertions(+), 46 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 5935ec7da5..c3c685be99 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -1,15 +1,10 @@
 # Base image
 FROM ubuntu:22.04
 
-# allow selecting oneAPI minor version at build time
-ARG ONEAPI_VER=2025.3
-ENV ONEAPI_VER=${ONEAPI_VER}
-
-# Basic build tools
 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 make ca-certificates
+    pkg-config build-essential autoconf automake libtool
 
 # Add Intel apt repo
 RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
@@ -17,64 +12,60 @@ RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRO
     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
 
-# Install essential oneAPI components (avoid pinning an exact mpi minor version)
+# 安装oneAPI组件（使用更灵活的版本处理）
 RUN apt-get update && \
-    # Ensure pkg-config and kernel headers are present before installing vtune (vtune's installer checks kernel headers)
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-        pkg-config || true && \
-    # Try to install headers matching the build host kernel; fall back to generic headers if exact package not available.
-    DEBIAN_FRONTEND=noninteractive bash -lc "apt-get install -y --no-install-recommends linux-headers-$(uname -r) || apt-get install -y --no-install-recommends linux-headers-generic || true" && \
     apt-get install -y \
         intel-oneapi-compiler-dpcpp-cpp \
         intel-oneapi-compiler-fortran \
         intel-oneapi-mkl-devel \
         intel-oneapi-mpi-devel \
-        intel-oneapi-vtune \
- && rm -rf /var/lib/apt/lists/*
+        intel-oneapi-vtune && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# 设置oneAPI环境变量
+ENV ONEAPI_ROOT=/opt/intel/oneapi
+ENV I_MPI_ROOT=${ONEAPI_ROOT}/mpi/latest
+ENV MKLROOT=${ONEAPI_ROOT}/mkl/latest
+ENV CMPLR_ROOT=${ONEAPI_ROOT}/compiler/latest
 
-# Normalize 'latest' symlinks for mkl/mpi if possible; prefer requested ONEAPI_VER when present
-RUN set -eux; \
-    mkdir -p /opt/intel/oneapi; \
-    if [ -d "/opt/intel/oneapi/mkl/${ONEAPI_VER}" ]; then \
-        ln -sfn "/opt/intel/oneapi/mkl/${ONEAPI_VER}" /opt/intel/oneapi/mkl/latest; \
-    elif [ -d /opt/intel/oneapi/mkl ]; then \
-        ver=$(ls -1 /opt/intel/oneapi/mkl | sort -V | tail -n1 || true); \
-        [ -n "$ver" ] && ln -sfn "/opt/intel/oneapi/mkl/$ver" /opt/intel/oneapi/mkl/latest || true; \
-    fi; \
-    if [ -d "/opt/intel/oneapi/mpi/${ONEAPI_VER}" ]; then \
-        ln -sfn "/opt/intel/oneapi/mpi/${ONEAPI_VER}" /opt/intel/oneapi/mpi/latest; \
-    elif [ -d /opt/intel/oneapi/mpi ]; then \
-        ver=$(ls -1 /opt/intel/oneapi/mpi | sort -V | tail -n1 || true); \
-        [ -n "$ver" ] && ln -sfn "/opt/intel/oneapi/mpi/$ver" /opt/intel/oneapi/mpi/latest || true; \
-    fi; \
-    echo "MKL dirs:"; ls -la /opt/intel/oneapi/mkl || true; \
-    echo "MPI dirs:"; ls -la /opt/intel/oneapi/mpi || true
+# 设置库路径和包含路径
+ENV LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/intel64:${LIBRARY_PATH}
+ENV LD_LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/intel64:${LD_LIBRARY_PATH}
+ENV PATH=${ONEAPI_ROOT}/vtune/latest/bin64:${ONEAPI_ROOT}/mpi/latest/bin:${MKLROOT}/bin/intel64:${ONEAPI_ROOT}/compiler/latest/bin:${PATH}
+ENV CPATH=${MKLROOT}/include:${ONEAPI_ROOT}/mpi/latest/include:${CPATH}
+ENV PKG_CONFIG_PATH=${MKLROOT}/lib/pkgconfig:${ONEAPI_ROOT}/mpi/latest/lib/pkgconfig:${PKG_CONFIG_PATH}
 
-# Set consistent envs referencing 'latest' symlink
-ENV I_MPI_ROOT=/opt/intel/oneapi/mpi/latest
-ENV MKLROOT=/opt/intel/oneapi/mkl/latest
-# ENV LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
-ENV LD_LIBRARY_PATH=/opt/intel/oneapi/mpi/latest/lib:/opt/intel/oneapi/mkl/latest/lib
-ENV PATH=/opt/intel/oneapi/mpi/latest/bin:/opt/intel/oneapi/mkl/latest/bin:$PATH
-ENV CMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl/latest/lib/cmake
+# 设置CMAKE相关路径
+ENV CMAKE_PREFIX_PATH=${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"]
-# ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
+
+# 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=mpiifort
+
+SHELL ["/bin/bash", "-c"]
+# ENV CC=mpiicc CXX=mpiicpc FC=mpiifort
+ENV CC=mpiicx CXX=mpiicpx FC=mpiifx
 
-RUN which gzip && ls -l $(which gzip)
-RUN ls -l /bin/gzip /usr/bin/gzip
+# 验证oneAPI安装
+RUN source ${ONEAPI_ROOT}/setvars.sh && \
+    echo "=== 验证编译器 ===" && \
+    which mpiicc && mpiicc --version && \
+    echo "=== 验证MKL ===" && \
+    ls ${MKLROOT}/lib/intel64/ && \
+    echo "=== 验证MPI ===" && \
+    which mpirun && mpirun --version
 
 # Build ELPA (example dependency)
 RUN source /opt/intel/oneapi/setvars.sh && \
     cd /tmp && \
     ELPA_VER=2022.11.001 && \
     wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    gzip -d elpa-$ELPA_VER.tar.gz && \
-    tar xf elpa-$ELPA_VER.tar && \
-    rm elpa-$ELPA_VER.tar && \
-    cd elpa-$ELPA_VER && \
-    mkdir build && cd build && \
+    tar xzf elpa-$ELPA_VER.tar.gz  && rm elpa-$ELPA_VER.tar.gz && \
+    cd elpa-$ELPA_VER && mkdir build && cd build && \
     ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
     make -j$(nproc) && \
     make PREFIX=/usr/local install && \

From 47c555d79ab1d6efef82a606ab4bc40a2c9230b4 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Wed, 29 Oct 2025 20:29:40 +0800
Subject: [PATCH 15/92] Fix: Update compiler settings in Dockerfile.intel to
 use mpiicx for better compatibility

---
 Dockerfile.intel | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index c3c685be99..78274b3338 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -42,18 +42,14 @@ ENV CMAKE_PREFIX_PATH=${ONEAPI_ROOT}/tbb/latest:${MKLROOT}/lib/cmake:${ONEAPI_RO
 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=mpiifort
-
-SHELL ["/bin/bash", "-c"]
 # 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
 
 # 验证oneAPI安装
 RUN source ${ONEAPI_ROOT}/setvars.sh && \
     echo "=== 验证编译器 ===" && \
-    which mpiicc && mpiicc --version && \
+    which mpiicx && mpiicx --version && \
     echo "=== 验证MKL ===" && \
     ls ${MKLROOT}/lib/intel64/ && \
     echo "=== 验证MPI ===" && \

From 727b9ec5d729b5df7500dbfc406af2d4dc314ba8 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 13:35:32 +0800
Subject: [PATCH 16/92] Fix: Remove output redirection from oneAPI environment
 setup in Dockerfile.intel

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 78274b3338..da0cec5bb6 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -76,7 +76,7 @@ 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 set -eux; source /opt/intel/oneapi/setvars.sh >/dev/null 2>&1 || true; \
+RUN set -eux; source /opt/intel/oneapi/setvars.sh || true; \
     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_RAPIDJSON=ON && \

From d6368ba1cafaf7208bdab15f71f3ef7e0f0ace7b Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 13:56:52 +0800
Subject: [PATCH 17/92] Fix: Update Dockerfile.intel to enhance build command
 with error handling and clone abacus-develop repository

---
 Dockerfile.intel | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index da0cec5bb6..2eb179063b 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -76,7 +76,8 @@ 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 set -eux; source /opt/intel/oneapi/setvars.sh || true; \
+RUN set -ex; source /opt/intel/oneapi/setvars.sh || true; \
+    set -eux; \
     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_RAPIDJSON=ON && \

From 7fe731febe65f09770015b16a2a67198289023f9 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 14:23:44 +0800
Subject: [PATCH 18/92] Fix: Uncomment find_package for MKL to enable proper
 detection of MKL libraries

---
 cmake/FindMKL.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
index 26dece3b44..f9cddfcf74 100644
--- a/cmake/FindMKL.cmake
+++ b/cmake/FindMKL.cmake
@@ -4,7 +4,7 @@
 #  MKL_INCLUDE - where to find mkl.h, etc.
 #  MKL_FOUND        - True if mkl found.
 
-# find_package(MKL NO_MODULE) # try using official module first
+find_package(MKL NO_MODULE) # try using official module first
 if(NOT TARGET MKL::MKL)
 
 find_path(MKL_INCLUDE mkl_service.h HINTS ${MKLROOT}/include)

From f4cfdf83434d3d1b6488a83d1cb517de529880ab Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 15:12:17 +0800
Subject: [PATCH 19/92] Fix: Update CMake configuration in Dockerfile.intel to
 disable SYCL support for compatibility

---
 Dockerfile.intel | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2eb179063b..042af09ad3 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -80,7 +80,11 @@ RUN set -ex; source /opt/intel/oneapi/setvars.sh || true; \
     set -eux; \
     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_RAPIDJSON=ON && \
+    cmake -B build -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON\
+        -DMKL_ENABLE_SYCL=OFF \
+        -DENABLE_SYCL=OFF \
+        -DCMAKE_DISABLE_FIND_PACKAGE_SYCL=ON \
+        -DCMAKE_BUILD_TYPE=Release && \
     cmake --build build -j"$(nproc)" && \
     cmake --install build && \
     /usr/bin/abacus --version || true && \

From e6cf31535705b35fb89648446a97b893bb45d69d Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 16:11:06 +0800
Subject: [PATCH 20/92] Fix: Update abacus build process in Dockerfile.intel to
 set missing environment variables for SYCL compatibility

---
 Dockerfile.intel | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 042af09ad3..e5e3474e3b 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -76,19 +76,23 @@ 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 set -ex; source /opt/intel/oneapi/setvars.sh || true; \
-    set -eux; \
+RUN set -eux; \
+    export OCL_ICD_FILENAMES="" ; \
+    # 关键修复：在source setvars.sh之前设置缺失的变量
+    export mkl_sycl_distributed_dft_file="disabled" ; \
+    source /opt/intel/oneapi/setvars.sh > /dev/null 2>&1 || true; \
     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_RAPIDJSON=ON\
-        -DMKL_ENABLE_SYCL=OFF \
-        -DENABLE_SYCL=OFF \
-        -DCMAKE_DISABLE_FIND_PACKAGE_SYCL=ON \
+    cmake -B build \
+        -DENABLE_MLALGO=ON \
+        -DENABLE_LIBXC=ON \
+        -DENABLE_LIBRI=ON \
+        -DENABLE_RAPIDJSON=ON \
         -DCMAKE_BUILD_TYPE=Release && \
     cmake --build build -j"$(nproc)" && \
     cmake --install build && \
-    /usr/bin/abacus --version || true && \
-    rm -rf /tmp/abacus-develop /tmp/abacus-develop.tar.gz
+    (/usr/bin/abacus --version || echo "ABACUS installed but version check failed") && \
+    rm -rf /tmp/abacus-develop
 
 # Default entry
 CMD ["/bin/bash"]

From 825ed001791515fc11d0c341370234e54ed39f95 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 18:31:21 +0800
Subject: [PATCH 21/92] Fix: Remove unnecessary environment variable settings
 before cloning abacus in Dockerfile.intel

---
 Dockerfile.intel | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e5e3474e3b..4106fa3f2b 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -76,12 +76,7 @@ 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 set -eux; \
-    export OCL_ICD_FILENAMES="" ; \
-    # 关键修复：在source setvars.sh之前设置缺失的变量
-    export mkl_sycl_distributed_dft_file="disabled" ; \
-    source /opt/intel/oneapi/setvars.sh > /dev/null 2>&1 || true; \
-    cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+RUN cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \
         -DENABLE_MLALGO=ON \

From 38d1b065a07af9d93a10bf2240aece45159c53d1 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Thu, 30 Oct 2025 20:00:49 +0800
Subject: [PATCH 22/92] Fix: Comment out find_package for MKL to prevent
 conflicts with module detection

---
 cmake/FindMKL.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
index f9cddfcf74..26dece3b44 100644
--- a/cmake/FindMKL.cmake
+++ b/cmake/FindMKL.cmake
@@ -4,7 +4,7 @@
 #  MKL_INCLUDE - where to find mkl.h, etc.
 #  MKL_FOUND        - True if mkl found.
 
-find_package(MKL NO_MODULE) # try using official module first
+# find_package(MKL NO_MODULE) # try using official module first
 if(NOT TARGET MKL::MKL)
 
 find_path(MKL_INCLUDE mkl_service.h HINTS ${MKLROOT}/include)

From 6b31fe21cd2ae1004a52a859a8c87ce3083c60a4 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 10:26:00 +0800
Subject: [PATCH 23/92] Enhance Dockerfile with libraries installation: PEXSI
 and its DEPs

Added installation steps for GKlib, METIS, ParMETIS, SuperLU_DIST, and PEXSI to Dockerfile.
---
 Dockerfile.intel | 87 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 4106fa3f2b..1895940c0c 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -74,6 +74,93 @@ RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-
     unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
 ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 
+###### PEXSI PART: pexsi\gklib\metis\parmetis\superlu_dist ######
+ENV GKLIB_VERSION="master" # Although that is not good in CI/CD...
+ENV METIS_VERSION="master" # Although that is not good in CI/CD...
+ENV PARMETIS_VERSION="main" # Although that is not good in CI/CD...
+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-${GKLIB_VERSION} && \
+    make config cc=mpiicc shared=1 prefix=${GKLIB_ROOT} openmp=set && \
+    make -j$(nproc) && \
+    make install && \
+    cp ${GKLIB_ROOT}/lib64/*so ${GKLIB_ROOT}/lib/ \ #.so file CANNOT be found otherwise.
+    cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
+
+# 2. install METIS
+RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VERSION} -O METIS-${METIS_VERSION}.zip && \
+    unzip METIS-${METIS_VERSION}.zip && \
+    cd METIS-${METIS_VERSION} && \
+    make config cc=mpiicc shared=1 prefix=${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 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 cc=mpiicc 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;${GKLIB_ROOT}/lib64/libGKlib.so" \ # Although that is not good in CI/CD...
+    -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \ # Although that is not good in CI/CD...
+    -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
+    -DTPL_ENABLE_LAPACKLIB=ON \
+    -DTPL_ENABLE_COMBBLASLIB=OFF \
+    -DTPL_ENABLE_CUDALIB=OFF \
+    -DTPL_ENABLE_HIPLIB=OFF \
+    -Denable_complex16=ON \
+    -DXSDK_INDEX_SIZE=32 \
+    -DBUILD_SHARED_LIBS=ON \
+    -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
+    -DCMAKE_C_COMPILER=mpiicc \
+    -DCMAKE_CXX_COMPILER=mpiicpc \
+    -DCMAKE_C_FLAGS="-O3 -fopenmp" \
+    -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
+    -DXSDK_ENABLE_Fortran=ON \
+    -DCMAKE_Fortran_COMPILER=mpif90 && \                             
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf superlu_dist-${SUPERLU_DIST_VERSION} v${SUPERLU_DIST_VERSION}.tar.gz
+
+###     -DCMAKE_CUDA_COMPILER=nvcc \
+
+# 5. install PEXSI
+RUN wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
+    tar -xzf v${PEXSI_VERSION}.tar.gz && \
+    cd PEXSI-${PEXSI_VERSION} && \
+    mkdir build && cd build && \
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
+        -DPEXSI_ENABLE_OPENMP=ON \
+        -DPEXSI_ENABLE_FORTRAN=ON \
+        -DCMAKE_C_COMPILER=mpiicc \
+        -DCMAKE_CXX_COMPILER=mpiicpc \
+        -DCMAKE_FORTRAN_COMPILER=mpif90 && \
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+###### END of PEXSI PART ######
+
 # 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 cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \

From b8fcb701f8141ce499a1edbe0926db459727f666 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 10:32:39 +0800
Subject: [PATCH 24/92] Delete some #s to avoid errors

---
 Dockerfile.intel | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 1895940c0c..e0b3ab0066 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -74,10 +74,10 @@ RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-
     unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
 ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 
-###### PEXSI PART: pexsi\gklib\metis\parmetis\superlu_dist ######
-ENV GKLIB_VERSION="master" # Although that is not good in CI/CD...
-ENV METIS_VERSION="master" # Although that is not good in CI/CD...
-ENV PARMETIS_VERSION="main" # Although that is not good in CI/CD...
+###### 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-${GKLIB_VERSION}
@@ -159,7 +159,7 @@ RUN wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
-###### END of PEXSI PART ######
+###### END of PEXSI PART
 
 # 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

From da23327a9c7927316ab7f26c1de8df3a25bb8f94 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 11:18:12 +0800
Subject: [PATCH 25/92] Fix Dockerfile to ensure .so files are copied correctly

---
 Dockerfile.intel | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e0b3ab0066..e3c6ba2958 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -93,9 +93,9 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
     make config cc=mpiicc shared=1 prefix=${GKLIB_ROOT} openmp=set && \
     make -j$(nproc) && \
     make install && \
-    cp ${GKLIB_ROOT}/lib64/*so ${GKLIB_ROOT}/lib/ \ #.so file CANNOT be found otherwise.
+    cp ${GKLIB_ROOT}/lib64/*so ${GKLIB_ROOT}/lib/ && \
     cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
-
+    #.so file CANNOT be found otherwise.
 # 2. install METIS
 RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VERSION} -O METIS-${METIS_VERSION}.zip && \
     unzip METIS-${METIS_VERSION}.zip && \
@@ -121,8 +121,8 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     mkdir build && cd build && \
     cmake .. \
     -DTPL_ENABLE_PARMETISLIB=ON \
-    -DTPL_PARMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib64/libGKlib.so" \ # Although that is not good in CI/CD...
-    -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \ # Although that is not good in CI/CD...
+    -DTPL_PARMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib64/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 \

From 2171daf9b5ffdcdbb5296ab94f9b61457cf6b893 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 13:36:47 +0800
Subject: [PATCH 26/92] Refactor Dockerfile to simplify build commands: No icc
 now

Updated build commands in Dockerfile to remove specific compiler settings for MPI.
---
 Dockerfile.intel | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e3c6ba2958..e56a8319e2 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -90,7 +90,7 @@ ENV SUPERLU_DIST32_ROOT=/usr/local/superlu_dist32-${SUPERLU_DIST_VERSION}
 RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VERSION} -O GKlib-${GKLIB_VERSION}.zip && \
     unzip GKlib-${GKLIB_VERSION}.zip && \
     cd GKlib-${GKLIB_VERSION} && \
-    make config cc=mpiicc shared=1 prefix=${GKLIB_ROOT} openmp=set && \
+    make config shared=1 prefix=${GKLIB_ROOT} openmp=set && \
     make -j$(nproc) && \
     make install && \
     cp ${GKLIB_ROOT}/lib64/*so ${GKLIB_ROOT}/lib/ && \
@@ -100,7 +100,7 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
 RUN 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 cc=mpiicc shared=1 prefix=${METIS32_ROOT} gklib_path=${GKLIB_ROOT} && \
+    make config shared=1 prefix=${METIS32_ROOT} gklib_path=${GKLIB_ROOT} && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf METIS-${METIS_VERSION} METIS-${METIS_VERSION}.zip
@@ -109,7 +109,7 @@ RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VER
 RUN 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 cc=mpiicc shared=1 prefix=${PARMETIS32_ROOT} gklib_path=${GKLIB_ROOT} metis_path=${METIS32_ROOT} && \
+    make config shared=1 prefix=${PARMETIS32_ROOT} gklib_path=${GKLIB_ROOT} metis_path=${METIS32_ROOT} && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf ParMETIS-${PARMETIS_VERSION} ParMETIS-${PARMETIS_VERSION}.zip
@@ -132,8 +132,6 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     -DXSDK_INDEX_SIZE=32 \
     -DBUILD_SHARED_LIBS=ON \
     -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
-    -DCMAKE_C_COMPILER=mpiicc \
-    -DCMAKE_CXX_COMPILER=mpiicpc \
     -DCMAKE_C_FLAGS="-O3 -fopenmp" \
     -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
     -DXSDK_ENABLE_Fortran=ON \
@@ -142,6 +140,8 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     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
@@ -153,12 +153,13 @@ RUN wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
-        -DCMAKE_C_COMPILER=mpiicc \
-        -DCMAKE_CXX_COMPILER=mpiicpc \
         -DCMAKE_FORTRAN_COMPILER=mpif90 && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+
+###         -DCMAKE_C_COMPILER=mpiicc \
+###        -DCMAKE_CXX_COMPILER=mpiicpc \
 ###### END of PEXSI PART
 
 # Clone and build abacus (optional during image build; keep for CI image)

From 98fc4f4c7db61a8b1e6dd52fd33b2b175a9e7e32 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 14:04:27 +0800
Subject: [PATCH 27/92] Remove copying of .so files in Dockerfile

Removed the copying of shared object files to lib directory.
---
 Dockerfile.intel | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e56a8319e2..bf1ae354d6 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -93,9 +93,8 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
     make config shared=1 prefix=${GKLIB_ROOT} openmp=set && \
     make -j$(nproc) && \
     make install && \
-    cp ${GKLIB_ROOT}/lib64/*so ${GKLIB_ROOT}/lib/ && \
     cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
-    #.so file CANNOT be found otherwise.
+#.so file CANNOT be found otherwise.
 # 2. install METIS
 RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VERSION} -O METIS-${METIS_VERSION}.zip && \
     unzip METIS-${METIS_VERSION}.zip && \

From f135a015ac89450a75b03d6c38c3dce8c61ff9fb Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 14:36:15 +0800
Subject: [PATCH 28/92] Update Dockerfile to include library path exports

---
 Dockerfile.intel | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index bf1ae354d6..514a7e007a 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -96,7 +96,8 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
     cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
 #.so file CANNOT be found otherwise.
 # 2. install METIS
-RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VERSION} -O METIS-${METIS_VERSION}.zip && \
+RUN export LD_LIBRARY_PATH=${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=${GKLIB_ROOT} && \
@@ -105,7 +106,8 @@ RUN wget https://codeload.github.com/KarypisLab/METIS/zip/refs/heads/${METIS_VER
     cd / && rm -rf METIS-${METIS_VERSION} METIS-${METIS_VERSION}.zip
 
 # 3. install ParMETIS
-RUN wget https://codeload.github.com/KarypisLab/ParMETIS/zip/refs/heads/${PARMETIS_VERSION} -O ParMETIS-${PARMETIS_VERSION}.zip && \
+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} && \
@@ -144,7 +146,8 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 ###     -DCMAKE_CUDA_COMPILER=nvcc \
 
 # 5. install PEXSI
-RUN wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
+RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
     tar -xzf v${PEXSI_VERSION}.tar.gz && \
     cd PEXSI-${PEXSI_VERSION} && \
     mkdir build && cd build && \

From c3f0e4731d6336965715558fe7627632ea31651b Mon Sep 17 00:00:00 2001
From: Liang Sun <50293369+sunliang98@users.noreply.github.com>
Date: Mon, 3 Nov 2025 16:30:41 +0800
Subject: [PATCH 29/92] Update Dockerfile.intel

---
 Dockerfile.intel | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 514a7e007a..47baf413d4 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -93,6 +93,8 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
     make config shared=1 prefix=${GKLIB_ROOT} openmp=set && \
     make -j$(nproc) && \
     make install && \
+    ls ${GKLIB_ROOT}/lib && \
+    cp ${GKLIB_ROOT}/lib/libGKlib.so.5 ${GKLIB_ROOT}/lib/libGKlib.so && \ 
     cd / && rm -rf GKlib-${GKLIB_VERSION} GKlib-${GKLIB_VERSION}.zip
 #.so file CANNOT be found otherwise.
 # 2. install METIS

From ed44e786eee0f46e6129a25a5ce82c823aa783d6 Mon Sep 17 00:00:00 2001
From: Liang Sun <50293369+sunliang98@users.noreply.github.com>
Date: Mon, 3 Nov 2025 16:43:42 +0800
Subject: [PATCH 30/92] Update Dockerfile.intel

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 47baf413d4..e229436145 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -94,7 +94,7 @@ RUN wget https://codeload.github.com/KarypisLab/GKlib/zip/refs/heads/${GKLIB_VER
     make -j$(nproc) && \
     make install && \
     ls ${GKLIB_ROOT}/lib && \
-    cp ${GKLIB_ROOT}/lib/libGKlib.so.5 ${GKLIB_ROOT}/lib/libGKlib.so && \ 
+    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

From ac64756efb3422461819e9072076df35d77feb26 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Mon, 3 Nov 2025 16:51:16 +0800
Subject: [PATCH 31/92] Modify FindMKL.cmake to add support for finding and
 importing the MKL_CORE library.

---
 cmake/FindMKL.cmake | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
index 26dece3b44..e6ebc856f7 100644
--- a/cmake/FindMKL.cmake
+++ b/cmake/FindMKL.cmake
@@ -100,3 +100,17 @@ if(NOT TARGET MKL::MKL_SCALAPACK)
     )
   endif()
 endif()
+
+
+if(NOT TARGET MKL::CORE)
+  find_library(MKL_CORE NAMES mkl_core HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  message(STATUS "Found MKL_CORE: ${MKL_CORE}")
+  if(MKL_CORE)
+    # create an IMPORTED target that points to the discovered library file
+    add_library(MKL::CORE UNKNOWN IMPORTED)
+    set_target_properties(MKL::CORE PROPERTIES
+      IMPORTED_LOCATION "${MKL_CORE}"
+      INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE}"
+    )
+  endif()
+endif()
\ No newline at end of file

From b7ecb82b6ad7fe292513522d9a734a285478c1cb Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Mon, 3 Nov 2025 16:57:11 +0800
Subject: [PATCH 32/92] Turn off PEXSI

---
 Dockerfile.intel | 182 +++++++++++++++++++++++------------------------
 1 file changed, 91 insertions(+), 91 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e229436145..1d16727279 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -74,97 +74,97 @@ RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-
     unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
 ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 
-###### 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}/lib64/libGKlib.so" \
-    -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
-    -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
-    -DTPL_ENABLE_LAPACKLIB=ON \
-    -DTPL_ENABLE_COMBBLASLIB=OFF \
-    -DTPL_ENABLE_CUDALIB=OFF \
-    -DTPL_ENABLE_HIPLIB=OFF \
-    -Denable_complex16=ON \
-    -DXSDK_INDEX_SIZE=32 \
-    -DBUILD_SHARED_LIBS=ON \
-    -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
-    -DCMAKE_C_FLAGS="-O3 -fopenmp" \
-    -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
-    -DXSDK_ENABLE_Fortran=ON \
-    -DCMAKE_Fortran_COMPILER=mpif90 && \                             
-    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} && \
-    wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
-    tar -xzf v${PEXSI_VERSION}.tar.gz && \
-    cd PEXSI-${PEXSI_VERSION} && \
-    mkdir build && cd build && \
-    cmake .. \
-        -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
-        -DPEXSI_ENABLE_OPENMP=ON \
-        -DPEXSI_ENABLE_FORTRAN=ON \
-        -DCMAKE_FORTRAN_COMPILER=mpif90 && \
-    make -j$(nproc) && \
-    make install && \
-    cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
-
-###         -DCMAKE_C_COMPILER=mpiicc \
-###        -DCMAKE_CXX_COMPILER=mpiicpc \
-###### END of PEXSI PART
+# ###### PEXSI PART: pexsi and gklib and metis and parmetis and superlu_dist
+# ENV GKLIB_VERSION="master" 
+# ENV METIS_VERSION="master"
+# ENV PARMETIS_VERSION="main"
+# ENV SUPERLU_DIST_VERSION=7.2.0
+# ENV PEXSI_VERSION=2.0.0
+# ENV GKLIB_ROOT=/usr/local/gklib-${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}/lib64/libGKlib.so" \
+#     -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
+#     -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
+#     -DTPL_ENABLE_LAPACKLIB=ON \
+#     -DTPL_ENABLE_COMBBLASLIB=OFF \
+#     -DTPL_ENABLE_CUDALIB=OFF \
+#     -DTPL_ENABLE_HIPLIB=OFF \
+#     -Denable_complex16=ON \
+#     -DXSDK_INDEX_SIZE=32 \
+#     -DBUILD_SHARED_LIBS=ON \
+#     -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
+#     -DCMAKE_C_FLAGS="-O3 -fopenmp" \
+#     -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
+#     -DXSDK_ENABLE_Fortran=ON \
+#     -DCMAKE_Fortran_COMPILER=mpif90 && \                             
+#     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} && \
+#     wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
+#     tar -xzf v${PEXSI_VERSION}.tar.gz && \
+#     cd PEXSI-${PEXSI_VERSION} && \
+#     mkdir build && cd build && \
+#     cmake .. \
+#         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
+#         -DPEXSI_ENABLE_OPENMP=ON \
+#         -DPEXSI_ENABLE_FORTRAN=ON \
+#         -DCMAKE_FORTRAN_COMPILER=mpif90 && \
+#     make -j$(nproc) && \
+#     make install && \
+#     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+
+# ###         -DCMAKE_C_COMPILER=mpiicc \
+# ###        -DCMAKE_CXX_COMPILER=mpiicpc \
+# ###### END of PEXSI PART
 
 # 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

From 12d34786a2d0ef5efab980b0273cf2dcd38e11a7 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Mon, 3 Nov 2025 18:46:43 +0800
Subject: [PATCH 33/92] Update FindMKL.cmake and CMakeLists.txt

---
 CMakeLists.txt      | 2 +-
 cmake/FindMKL.cmake | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6e921dce23..0830d4d005 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -466,7 +466,7 @@ if(MKLROOT)
   find_package(MKL REQUIRED)
   add_definitions(-D__MKL)
   include_directories(${MKL_INCLUDE} ${MKL_INCLUDE}/fftw)
-  list(APPEND math_libs MKL::MKL MKL::MKL_SCALAPACK)
+  list(APPEND math_libs MKL::MKL)
   if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
     list(APPEND math_libs ifcore)
   endif()
diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
index e6ebc856f7..ca1147a432 100644
--- a/cmake/FindMKL.cmake
+++ b/cmake/FindMKL.cmake
@@ -70,7 +70,9 @@ if(MKL_FOUND)
     set_property(TARGET MKL::MKL PROPERTY
     INTERFACE_LINK_LIBRARIES
     "-Wl,--start-group"
-    MKL::INTEL MKL::INTEL_THREAD MKL::CORE)
+    MKL::INTEL MKL::INTEL_THREAD MKL::CORE
+    "-Wl,--end-group"
+    )
   endif()
 endif()
 

From 350a78e1d803e4a0c16403f40e743fc61a201511 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 21:03:50 +0800
Subject: [PATCH 34/92] Update Dockerfile.intel

---
 Dockerfile.intel | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 1d16727279..2b1c4e61d5 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -171,6 +171,10 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 RUN cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \
+        -DMKL_SYCL=OFF \
+        -DMKL_SYCL_INTERFACE_FULL=OFF \
+        -DMKL_SYCL_DISTRIBUTED_DFT=OFF \
+        -DMKL_SYCL_LINK=OFF \
         -DENABLE_MLALGO=ON \
         -DENABLE_LIBXC=ON \
         -DENABLE_LIBRI=ON \

From 1df9d5370e51d041eb87d16ed34c6f96a4d8e02a Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 3 Nov 2025 22:07:04 +0800
Subject: [PATCH 35/92] Update ABACUS version check path in Dockerfile

---
 Dockerfile.intel | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2b1c4e61d5..c52e63a4e0 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -174,7 +174,6 @@ RUN cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --de
         -DMKL_SYCL=OFF \
         -DMKL_SYCL_INTERFACE_FULL=OFF \
         -DMKL_SYCL_DISTRIBUTED_DFT=OFF \
-        -DMKL_SYCL_LINK=OFF \
         -DENABLE_MLALGO=ON \
         -DENABLE_LIBXC=ON \
         -DENABLE_LIBRI=ON \
@@ -182,7 +181,7 @@ RUN cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --de
         -DCMAKE_BUILD_TYPE=Release && \
     cmake --build build -j"$(nproc)" && \
     cmake --install build && \
-    (/usr/bin/abacus --version || echo "ABACUS installed but version check failed") && \
+    (/usr/local/bin/abacus --version || echo "ABACUS installed but version check failed") && \
     rm -rf /tmp/abacus-develop
 
 # Default entry

From d37f51d3a094e601312eb3d6be83e9cdf8f7645a Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 12:33:43 +0800
Subject: [PATCH 36/92] Update library paths in Dockerfile.intel

---
 Dockerfile.intel | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index c52e63a4e0..a8b3687713 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -30,8 +30,8 @@ ENV MKLROOT=${ONEAPI_ROOT}/mkl/latest
 ENV CMPLR_ROOT=${ONEAPI_ROOT}/compiler/latest
 
 # 设置库路径和包含路径
-ENV LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/intel64:${LIBRARY_PATH}
-ENV LD_LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/intel64:${LD_LIBRARY_PATH}
+ENV LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/:${LIBRARY_PATH}
+ENV LD_LIBRARY_PATH=${ONEAPI_ROOT}/tbb/latest/lib/intel64/gcc4.8:${ONEAPI_ROOT}/mpi/latest/lib:${MKLROOT}/lib/intel64:${ONEAPI_ROOT}/compiler/latest/lib/:${LD_LIBRARY_PATH}
 ENV PATH=${ONEAPI_ROOT}/vtune/latest/bin64:${ONEAPI_ROOT}/mpi/latest/bin:${MKLROOT}/bin/intel64:${ONEAPI_ROOT}/compiler/latest/bin:${PATH}
 ENV CPATH=${MKLROOT}/include:${ONEAPI_ROOT}/mpi/latest/include:${CPATH}
 ENV PKG_CONFIG_PATH=${MKLROOT}/lib/pkgconfig:${ONEAPI_ROOT}/mpi/latest/lib/pkgconfig:${PKG_CONFIG_PATH}

From 6cbc62af51568b47b89de4bab0bed3b689f92485 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 13:17:37 +0800
Subject: [PATCH 37/92] Uncomment PEXSI installation steps in Dockerfile

---
 Dockerfile.intel | 190 ++++++++++++++++++++++++-----------------------
 1 file changed, 96 insertions(+), 94 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index a8b3687713..def3edf257 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -74,107 +74,109 @@ RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-
     unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
 ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 
-# ###### 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}/lib64/libGKlib.so" \
-#     -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
-#     -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
-#     -DTPL_ENABLE_LAPACKLIB=ON \
-#     -DTPL_ENABLE_COMBBLASLIB=OFF \
-#     -DTPL_ENABLE_CUDALIB=OFF \
-#     -DTPL_ENABLE_HIPLIB=OFF \
-#     -Denable_complex16=ON \
-#     -DXSDK_INDEX_SIZE=32 \
-#     -DBUILD_SHARED_LIBS=ON \
-#     -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
-#     -DCMAKE_C_FLAGS="-O3 -fopenmp" \
-#     -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
-#     -DXSDK_ENABLE_Fortran=ON \
-#     -DCMAKE_Fortran_COMPILER=mpif90 && \                             
-#     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} && \
-#     wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
-#     tar -xzf v${PEXSI_VERSION}.tar.gz && \
-#     cd PEXSI-${PEXSI_VERSION} && \
-#     mkdir build && cd build && \
-#     cmake .. \
-#         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
-#         -DPEXSI_ENABLE_OPENMP=ON \
-#         -DPEXSI_ENABLE_FORTRAN=ON \
-#         -DCMAKE_FORTRAN_COMPILER=mpif90 && \
-#     make -j$(nproc) && \
-#     make install && \
-#     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
-
-# ###         -DCMAKE_C_COMPILER=mpiicc \
-# ###        -DCMAKE_CXX_COMPILER=mpiicpc \
-# ###### END of PEXSI PART
+###### PEXSI PART: pexsi and gklib and metis and parmetis and superlu_dist
+ENV GKLIB_VERSION="master" 
+ENV METIS_VERSION="master"
+ENV PARMETIS_VERSION="main"
+ENV SUPERLU_DIST_VERSION=7.2.0
+ENV PEXSI_VERSION=2.0.0
+ENV GKLIB_ROOT=/usr/local/gklib-${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}/lib64/libGKlib.so" \
+    -DTPL_PARMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
+    -DTPL_ENABLE_INTERNAL_BLASLIB=OFF \
+    -DTPL_ENABLE_LAPACKLIB=ON \
+    -DTPL_ENABLE_COMBBLASLIB=OFF \
+    -DTPL_ENABLE_CUDALIB=OFF \
+    -DTPL_ENABLE_HIPLIB=OFF \
+    -Denable_complex16=ON \
+    -DXSDK_INDEX_SIZE=32 \
+    -DBUILD_SHARED_LIBS=ON \
+    -DCMAKE_INSTALL_PREFIX=${SUPERLU_DIST32_ROOT} \
+    -DCMAKE_C_FLAGS="-O3 -fopenmp" \
+    -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
+    -DXSDK_ENABLE_Fortran=ON \
+    -DCMAKE_Fortran_COMPILER=mpif90 && \                             
+    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} && \
+    wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
+    tar -xzf v${PEXSI_VERSION}.tar.gz && \
+    cd PEXSI-${PEXSI_VERSION} && \
+    mkdir build && cd build && \
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
+        -DPEXSI_ENABLE_OPENMP=ON \
+        -DPEXSI_ENABLE_FORTRAN=ON \
+        -DCMAKE_FORTRAN_COMPILER=mpif90 && \
+    make -j$(nproc) && \
+    make install && \
+    cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+
+###         -DCMAKE_C_COMPILER=mpiicc \
+###        -DCMAKE_CXX_COMPILER=mpiicpc \
+###### END of PEXSI PART
+
 
 # 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 cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+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 CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH} && \
+    cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \
         -DMKL_SYCL=OFF \
-        -DMKL_SYCL_INTERFACE_FULL=OFF \
-        -DMKL_SYCL_DISTRIBUTED_DFT=OFF \
         -DENABLE_MLALGO=ON \
+        -DENABLE_PEXSI=ON \
         -DENABLE_LIBXC=ON \
         -DENABLE_LIBRI=ON \
         -DENABLE_RAPIDJSON=ON \

From e9f4086d441148ad6770207ecd0905da47b517ad Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 13:49:20 +0800
Subject: [PATCH 38/92] Change Fortran compiler from mpif90 to mpiifort

---
 Dockerfile.intel | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index def3edf257..acb48ccb6f 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -138,7 +138,7 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     -DCMAKE_C_FLAGS="-O3 -fopenmp" \
     -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
     -DXSDK_ENABLE_Fortran=ON \
-    -DCMAKE_Fortran_COMPILER=mpif90 && \                             
+    -DCMAKE_Fortran_COMPILER=mpiifort && \                             
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf superlu_dist-${SUPERLU_DIST_VERSION} v${SUPERLU_DIST_VERSION}.tar.gz
@@ -157,7 +157,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
-        -DCMAKE_FORTRAN_COMPILER=mpif90 && \
+        -DCMAKE_FORTRAN_COMPILER=mpiifort && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz

From 8947be15b79b74ebf11077c0fcc439475102e9f9 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 17:18:54 +0800
Subject: [PATCH 39/92] source setvar.sh

---
 Dockerfile.intel | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index acb48ccb6f..9d8d91f941 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -118,7 +118,8 @@ RUN export LD_LIBRARY_PATH=${METIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PA
     cd / && rm -rf ParMETIS-${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 && \
+RUN source ${ONEAPI_ROOT}/setvars.sh && \
+    wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
     tar -xzf v${SUPERLU_DIST_VERSION}.tar.gz && \
     cd superlu_dist-${SUPERLU_DIST_VERSION} && \
     mkdir build && cd build && \
@@ -148,7 +149,8 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 ###     -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} && \
+RUN source ${ONEAPI_ROOT}/setvars.sh && \
+    export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
     wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
     tar -xzf v${PEXSI_VERSION}.tar.gz && \
     cd PEXSI-${PEXSI_VERSION} && \

From 0ed15af44fc079fa9f8cea8f0c8813578d697262 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 18:01:47 +0800
Subject: [PATCH 40/92] Update Dockerfile to install SuperLU_DIST

---
 Dockerfile.intel | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 9d8d91f941..2752340174 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -119,6 +119,7 @@ RUN export LD_LIBRARY_PATH=${METIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PA
 
 # 4. install SuperLU_DIST 
 RUN source ${ONEAPI_ROOT}/setvars.sh && \
+    echo `which ifort` && \
     wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
     tar -xzf v${SUPERLU_DIST_VERSION}.tar.gz && \
     cd superlu_dist-${SUPERLU_DIST_VERSION} && \

From 221cd563ad4f6c3ea58285a2986cb50b1c36bd9c Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Tue, 4 Nov 2025 20:08:29 +0800
Subject: [PATCH 41/92] Update Dockerfile.intel

---
 Dockerfile.intel | 50 ++++++++++++++++++++++++++++--------------------
 1 file changed, 29 insertions(+), 21 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2752340174..1d40e7b632 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -55,25 +55,6 @@ RUN source ${ONEAPI_ROOT}/setvars.sh && \
     echo "=== 验证MPI ===" && \
     which mpirun && mpirun --version
 
-# Build ELPA (example dependency)
-RUN source /opt/intel/oneapi/setvars.sh && \
-    cd /tmp && \
-    ELPA_VER=2022.11.001 && \
-    wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
-    tar xzf elpa-$ELPA_VER.tar.gz  && rm elpa-$ELPA_VER.tar.gz && \
-    cd elpa-$ELPA_VER && mkdir build && cd build && \
-    ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
-    make -j$(nproc) && \
-    make PREFIX=/usr/local install && \
-    ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
-    cd /tmp && rm -rf elpa-$ELPA_VER
-
-# rapidjson and libtorch
-RUN cd /tmp && git clone --depth 1 https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ && rm -rf rapidjson
-RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip -O /tmp/libtorch.zip && \
-    unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
-ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
-
 ###### PEXSI PART: pexsi and gklib and metis and parmetis and superlu_dist
 ENV GKLIB_VERSION="master" 
 ENV METIS_VERSION="master"
@@ -118,8 +99,13 @@ RUN export LD_LIBRARY_PATH=${METIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PA
     cd / && rm -rf ParMETIS-${PARMETIS_VERSION} ParMETIS-${PARMETIS_VERSION}.zip
 
 # 4. install SuperLU_DIST 
-RUN source ${ONEAPI_ROOT}/setvars.sh && \
-    echo `which ifort` && \
+RUN echo "--- 检查 ifort 是否已安装 ---" && \
+    find /opt/intel -name "ifort" && \
+    echo "--- 检查 ifort 是否在 PATH 中 ---" && \
+    which ifort || echo "ifort 不在 PATH 中" && \
+    source ${ONEAPI_ROOT}/setvars.sh && \
+    echo "--- 激活后再次检查 ifort 是否在 PATH 中 ---" && \
+    which ifort || echo "激活后 ifort 仍然不在 PATH 中" && \
     wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
     tar -xzf v${SUPERLU_DIST_VERSION}.tar.gz && \
     cd superlu_dist-${SUPERLU_DIST_VERSION} && \
@@ -170,6 +156,28 @@ RUN source ${ONEAPI_ROOT}/setvars.sh && \
 ###### END of PEXSI PART
 
 
+# Build ELPA (example dependency)
+RUN source /opt/intel/oneapi/setvars.sh && \
+    cd /tmp && \
+    ELPA_VER=2022.11.001 && \
+    wget -q https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/$ELPA_VER/elpa-$ELPA_VER.tar.gz && \
+    tar xzf elpa-$ELPA_VER.tar.gz  && rm elpa-$ELPA_VER.tar.gz && \
+    cd elpa-$ELPA_VER && mkdir build && cd build && \
+    ../configure CFLAGS="-O3 -march=native" FCFLAGS="-O3 -qmkl=cluster" --enable-openmp && \
+    make -j$(nproc) && \
+    make PREFIX=/usr/local install && \
+    ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
+    cd /tmp && rm -rf elpa-$ELPA_VER
+
+# rapidjson and libtorch
+RUN cd /tmp && git clone --depth 1 https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ && rm -rf rapidjson
+RUN wget -q https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip -O /tmp/libtorch.zip && \
+    unzip -q /tmp/libtorch.zip -d /opt && rm -f /tmp/libtorch.zip
+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} && \

From 05bd604ffbe28a8106445cf9dd6e735dd8c02317 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 07:05:57 +0800
Subject: [PATCH 42/92] Update Fortran compiler from mpiifort to mpiifx

---
 Dockerfile.intel | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 1d40e7b632..a8154144c7 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -99,14 +99,7 @@ RUN export LD_LIBRARY_PATH=${METIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PA
     cd / && rm -rf ParMETIS-${PARMETIS_VERSION} ParMETIS-${PARMETIS_VERSION}.zip
 
 # 4. install SuperLU_DIST 
-RUN echo "--- 检查 ifort 是否已安装 ---" && \
-    find /opt/intel -name "ifort" && \
-    echo "--- 检查 ifort 是否在 PATH 中 ---" && \
-    which ifort || echo "ifort 不在 PATH 中" && \
-    source ${ONEAPI_ROOT}/setvars.sh && \
-    echo "--- 激活后再次检查 ifort 是否在 PATH 中 ---" && \
-    which ifort || echo "激活后 ifort 仍然不在 PATH 中" && \
-    wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
+RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${SUPERLU_DIST_VERSION} -O v${SUPERLU_DIST_VERSION}.tar.gz && \
     tar -xzf v${SUPERLU_DIST_VERSION}.tar.gz && \
     cd superlu_dist-${SUPERLU_DIST_VERSION} && \
     mkdir build && cd build && \
@@ -126,7 +119,7 @@ RUN echo "--- 检查 ifort 是否已安装 ---" && \
     -DCMAKE_C_FLAGS="-O3 -fopenmp" \
     -DCMAKE_CXX_FLAGS="-O3 -fopenmp" \
     -DXSDK_ENABLE_Fortran=ON \
-    -DCMAKE_Fortran_COMPILER=mpiifort && \                             
+    -DCMAKE_Fortran_COMPILER=mpiifx && \                             
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf superlu_dist-${SUPERLU_DIST_VERSION} v${SUPERLU_DIST_VERSION}.tar.gz
@@ -146,7 +139,7 @@ RUN source ${ONEAPI_ROOT}/setvars.sh && \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
-        -DCMAKE_FORTRAN_COMPILER=mpiifort && \
+        -DCMAKE_FORTRAN_COMPILER=mpiifx && \
     make -j$(nproc) && \
     make install && \
     cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz

From d9108e223a6c14cacdd310f26902b85194c30572 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 09:27:09 +0800
Subject: [PATCH 43/92] Fix library paths and RUN command in Dockerfile.intel

Updated library paths for PARMETIS in Dockerfile and removed source command from RUN instruction.
---
 Dockerfile.intel | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index a8154144c7..a00c371de0 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -105,7 +105,7 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     mkdir build && cd build && \
     cmake .. \
     -DTPL_ENABLE_PARMETISLIB=ON \
-    -DTPL_PARMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib64/libGKlib.so" \
+    -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 \
@@ -129,8 +129,7 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 ###     -DCMAKE_CUDA_COMPILER=nvcc \
 
 # 5. install PEXSI
-RUN source ${ONEAPI_ROOT}/setvars.sh && \
-    export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
     wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
     tar -xzf v${PEXSI_VERSION}.tar.gz && \
     cd PEXSI-${PEXSI_VERSION} && \

From c49741fb8f22ffcbf94ee1c8bf6eaa13c7cdc8b6 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 13:30:45 +0800
Subject: [PATCH 44/92] Update PEXSI download link and cleanup commands

---
 Dockerfile.intel | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index a00c371de0..6980f5aa65 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -130,9 +130,9 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 
 # 5. install PEXSI
 RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
-    wget https://github.com/ecrc/PEXSI/archive/v${PEXSI_VERSION}.tar.gz && \
+    wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz -O v${PEXSI_VERSION}.tar.gz  && \
     tar -xzf v${PEXSI_VERSION}.tar.gz && \
-    cd PEXSI-${PEXSI_VERSION} && \
+    cd v${PEXSI_VERSION} && \
     mkdir build && cd build && \
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
@@ -141,7 +141,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \
     make -j$(nproc) && \
     make install && \
-    cd / && rm -rf PEXSI-${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+    cd / && rm -rf v${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
 
 ###         -DCMAKE_C_COMPILER=mpiicc \
 ###        -DCMAKE_CXX_COMPILER=mpiicpc \

From d2fc1e8a9cbb5602bf5906fb01ac0142ffe4c60a Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 14:47:51 +0800
Subject: [PATCH 45/92] Fix download and extraction commands for PEXSI

---
 Dockerfile.intel | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 6980f5aa65..42bf862244 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -130,9 +130,9 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 
 # 5. install PEXSI
 RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
-    wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz -O v${PEXSI_VERSION}.tar.gz  && \
-    tar -xzf v${PEXSI_VERSION}.tar.gz && \
-    cd v${PEXSI_VERSION} && \
+    wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz && \
+    tar -xzf pexsi_v${PEXSI_VERSION}.tar.gz && \
+    cd pexsi_v${PEXSI_VERSION} && \
     mkdir build && cd build && \
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
@@ -141,7 +141,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \
     make -j$(nproc) && \
     make install && \
-    cd / && rm -rf v${PEXSI_VERSION} v${PEXSI_VERSION}.tar.gz
+    cd / && rm -rf pexsi_v${PEXSI_VERSION} pexsi_v${PEXSI_VERSION}.tar.gz
 
 ###         -DCMAKE_C_COMPILER=mpiicc \
 ###        -DCMAKE_CXX_COMPILER=mpiicpc \

From 67a7d2e9e7d380654ed96e3724fd31d53d0bce08 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 15:54:18 +0800
Subject: [PATCH 46/92] Add PEXSI installation to Dockerfile.intel

Updated the Dockerfile to include PEXSI installation steps.
---
 Dockerfile.intel | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 42bf862244..10f355b173 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -130,12 +130,15 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 
 # 5. install PEXSI
 RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    export CPATH=${SUPERLU_DIST32_ROOT}/include:${PARMETIS32_ROOT}/include:${METIS32_ROOT}/include:${GKLIB_ROOT}/include:${CPATH} && \
     wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz && \
     tar -xzf pexsi_v${PEXSI_VERSION}.tar.gz && \
     cd pexsi_v${PEXSI_VERSION} && \
     mkdir build && cd build && \
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
+        -DMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib/libGKlib.so" \
+        -DMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \

From a8a3d739d01c15d93b985855b223feda8fb8a5e2 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 16:35:49 +0800
Subject: [PATCH 47/92] Fix METIS_INCLUDE_DIRS to METIS_INCLUDE_DIR

---
 Dockerfile.intel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 10f355b173..e381a70475 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -138,7 +138,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
         -DMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib/libGKlib.so" \
-        -DMETIS_INCLUDE_DIRS="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
+        -DMETIS_INCLUDE_DIR="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \

From cd4984fb09c9ca5ce7cf03b2d5d82bf83a8750d4 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 18:04:52 +0800
Subject: [PATCH 48/92] Refactor CMake arguments in Dockerfile.intel

Removed METIS_LIBRARIES and METIS_INCLUDE_DIR from CMake arguments.
---
 Dockerfile.intel | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index e381a70475..c83c2fce94 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -130,6 +130,7 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 
 # 5. install PEXSI
 RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${GKLIB_ROOT}/lib:${LD_LIBRARY_PATH} && \
+    export PKG_CONFIG_PATH=${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:${CPATH} && \
     wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz && \
     tar -xzf pexsi_v${PEXSI_VERSION}.tar.gz && \
@@ -137,8 +138,6 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     mkdir build && cd build && \
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
-        -DMETIS_LIBRARIES="${PARMETIS32_ROOT}/lib/libparmetis.so;${METIS32_ROOT}/lib/libmetis.so;${GKLIB_ROOT}/lib/libGKlib.so" \
-        -DMETIS_INCLUDE_DIR="${PARMETIS32_ROOT}/include;${METIS32_ROOT}/include;${GKLIB_ROOT}/include" \
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \

From b141e1ae631b22200ec7efd782381890637cbc84 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 20:28:57 +0800
Subject: [PATCH 49/92] Add CMAKE_PREFIX_PATH

---
 Dockerfile.intel | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index c83c2fce94..8370532634 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -130,8 +130,10 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
 
 # 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:${GKLIB_ROOT}/include:${CPATH} && \
+    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}:${GKLIB_ROOT}:${CPATH} && \
     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} && \

From 08317d347adb077b19548c13c12c34f3ad32a9ad Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 21:31:39 +0800
Subject: [PATCH 50/92] Fix Dockerfile for Intel oneAPI and PEXSI build

---
 Dockerfile.intel | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 8370532634..810814819a 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -19,7 +19,8 @@ RUN apt-get update && \
         intel-oneapi-compiler-fortran \
         intel-oneapi-mkl-devel \
         intel-oneapi-mpi-devel \
-        intel-oneapi-vtune && \
+        intel-oneapi-vtune \
+        linux-headers-5.15.0-46-generic && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -111,7 +112,6 @@ RUN wget https://codeload.github.com/xiaoyeli/superlu_dist/tar.gz/refs/tags/v${S
     -DTPL_ENABLE_LAPACKLIB=ON \
     -DTPL_ENABLE_COMBBLASLIB=OFF \
     -DTPL_ENABLE_CUDALIB=OFF \
-    -DTPL_ENABLE_HIPLIB=OFF \
     -Denable_complex16=ON \
     -DXSDK_INDEX_SIZE=32 \
     -DBUILD_SHARED_LIBS=ON \
@@ -133,7 +133,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     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}:${GKLIB_ROOT}:${CPATH} && \
+    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} && \
@@ -143,7 +143,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
         -DPEXSI_ENABLE_OPENMP=ON \
         -DPEXSI_ENABLE_FORTRAN=ON \
         -DCMAKE_FORTRAN_COMPILER=mpiifx && \
-    make -j$(nproc) && \
+    make pexsi -j$(nproc) && \
     make install && \
     cd / && rm -rf pexsi_v${PEXSI_VERSION} pexsi_v${PEXSI_VERSION}.tar.gz
 
@@ -178,10 +178,12 @@ ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/develop /dev/null
 RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH} && \
     export CPATH=${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 \
         -DMKL_SYCL=OFF \
+        -DMKL_SYCL_LINK=OFF \
         -DENABLE_MLALGO=ON \
         -DENABLE_PEXSI=ON \
         -DENABLE_LIBXC=ON \

From 1eecf2337371092392fb114b1b41e9a4eb5363da Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 5 Nov 2025 22:25:46 +0800
Subject: [PATCH 51/92] Update Dockerfile.intel

---
 Dockerfile.intel | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 810814819a..25d3170210 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -19,8 +19,7 @@ RUN apt-get update && \
         intel-oneapi-compiler-fortran \
         intel-oneapi-mkl-devel \
         intel-oneapi-mpi-devel \
-        intel-oneapi-vtune \
-        linux-headers-5.15.0-46-generic && \
+        intel-oneapi-vtune && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 

From aa3fa474c6864d65fa5a7d9e3c1214483db464d1 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 06:57:59 +0800
Subject: [PATCH 52/92] Comment out add_executable in pexsi CMake files

Comment out add_executable lines in CMakeLists.txt for pexsi.
---
 Dockerfile.intel | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 25d3170210..c71ab96693 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -136,6 +136,8 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${PEXSI_VERSION}.tar.gz && \
     tar -xzf pexsi_v${PEXSI_VERSION}.tar.gz && \
     cd pexsi_v${PEXSI_VERSION} && \
+    sed -i 's/add_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} \

From 24388620543fa236d7588dfdc154ef90feead626 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:01:22 +0800
Subject: [PATCH 53/92] Disable Fortran support in Dockerfile.intel

---
 Dockerfile.intel | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index c71ab96693..2275bf2103 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -142,8 +142,7 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     cmake .. \
         -DCMAKE_INSTALL_PREFIX=${PEXSI32_ROOT} \
         -DPEXSI_ENABLE_OPENMP=ON \
-        -DPEXSI_ENABLE_FORTRAN=ON \
-        -DCMAKE_FORTRAN_COMPILER=mpiifx && \
+        -DPEXSI_ENABLE_FORTRAN=OFF && \
     make pexsi -j$(nproc) && \
     make install && \
     cd / && rm -rf pexsi_v${PEXSI_VERSION} pexsi_v${PEXSI_VERSION}.tar.gz

From c9cefbd5768a669b7a04b413fefab7afb304d6a7 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:38:28 +0800
Subject: [PATCH 54/92] Modify CMakeLists to comment out example executables

Comment out example executable additions in CMakeLists.
---
 Dockerfile.intel | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 2275bf2103..f98e64fe05 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -136,6 +136,8 @@ RUN export LD_LIBRARY_PATH=${SUPERLU_DIST32_ROOT}/lib:${METIS32_ROOT}/lib:${PARM
     wget https://bitbucket.org/berkeleylab/pexsi/downloads/pexsi_v${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 && \

From b2bdcd61dda038169cada257dd2c96a1e5da937d Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 19:01:54 +0800
Subject: [PATCH 55/92] Change abacus-develop retrieval method in Dockerfile

Replaced git clone with wget and unzip for abacus-develop.
---
 Dockerfile.intel | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index f98e64fe05..c081ed861a 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -181,8 +181,9 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 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 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 && \
+    cd /tmp && wget https://github.com/deepmodeling/abacus-develop/archive/refs/tags/v3.9.0.17.zip -O abacus-develop-3.9.0.17.zip && \
+    unzip abacus-develop-3.9.0.17.zip && \
+    cd abacus-develop-3.9.0.17 && \
     cmake -B build \
         -DMKL_SYCL=OFF \
         -DMKL_SYCL_LINK=OFF \

From a7c224594f02a8ebcc9f956964cba3d20931c9d5 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 20:01:56 +0800
Subject: [PATCH 56/92] Add include directive in edm.cpp for LCAO

---
 Dockerfile.intel | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index c081ed861a..d56ec53c5c 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -184,6 +184,7 @@ RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_RO
     cd /tmp && wget https://github.com/deepmodeling/abacus-develop/archive/refs/tags/v3.9.0.17.zip -O abacus-develop-3.9.0.17.zip && \
     unzip abacus-develop-3.9.0.17.zip && \
     cd abacus-develop-3.9.0.17 && \
+    sed -i '3i\#include "source_estate/elecstate_lcao.h"' source/source_lcao/edm.cpp && \
     cmake -B build \
         -DMKL_SYCL=OFF \
         -DMKL_SYCL_LINK=OFF \

From 95058348a1d2e7f7dcfa11cc0e87204f6456aafe Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 22:37:08 +0800
Subject: [PATCH 57/92] Update elecstate_lcao.cpp

---
 source/source_estate/elecstate_lcao.cpp | 34 +++++++++++--------------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/source/source_estate/elecstate_lcao.cpp b/source/source_estate/elecstate_lcao.cpp
index b0518d817e..a9578b228a 100644
--- a/source/source_estate/elecstate_lcao.cpp
+++ b/source/source_estate/elecstate_lcao.cpp
@@ -1,6 +1,5 @@
-#include "elecstate_lcao.h"
-
-#include "cal_dm.h"
+#include "source_estate/elecstate_lcao.h"
+#include "source_estate/cal_dm.h"
 #include "source_base/timer.h"
 #include "source_estate/module_dm/cal_dm_psi.h"
 #include "source_hamilt/module_xc/xc_functional.h"
@@ -15,12 +14,6 @@
 namespace elecstate
 {
 
-template <typename TK>
-void ElecStateLCAO<TK>::init_DM(const K_Vectors* kv, const Parallel_Orbitals* paraV, const int nspin)
-{
-    const int nspin_dm = nspin == 2 ? 2 : 1;
-    this->DM = new DensityMatrix<TK, double>(paraV, nspin_dm, kv->kvec_d, kv->get_nks() / nspin_dm);
-}
 
 template <>
 double ElecStateLCAO<double>::get_spin_constrain_energy()
@@ -37,9 +30,10 @@ double ElecStateLCAO<std::complex<double>>::get_spin_constrain_energy()
     return sc.cal_escon();
 }
 
-#ifdef __PEXSI
 template <>
-void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, std::vector<double*> pexsi_EDM)
+void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, 
+		std::vector<double*> pexsi_EDM,
+		DensityMatrix<double, double>* dm)
 {
     ModuleBase::timer::tick("ElecStateLCAO", "dm2Rho");
 
@@ -49,13 +43,15 @@ void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, std::vector<do
         nspin = 1;
     }
 
-    this->get_DM()->pexsi_EDM = pexsi_EDM;
+#ifdef __PEXSI
+    dm->pexsi_EDM = pexsi_EDM;
+#endif
 
     for (int is = 0; is < nspin; is++)
     {
-        this->DM->set_DMK_pointer(is, pexsi_DM[is]);
+        dm->set_DMK_pointer(is, pexsi_DM[is]);
     }
-    DM->cal_DMR();
+    dm->cal_DMR();
 
     for (int is = 0; is < PARAM.inp.nspin; is++)
     {
@@ -64,14 +60,14 @@ void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, std::vector<do
     }
 
     ModuleBase::GlobalFunc::NOTE("Calculate the charge on real space grid!");
-    ModuleGint::cal_gint_rho(this->DM->get_DMR_vector(), PARAM.inp.nspin, this->charge->rho);
+    ModuleGint::cal_gint_rho(dm->get_DMR_vector(), PARAM.inp.nspin, this->charge->rho);
     if (XC_Functional::get_ked_flag())
     {
         for (int is = 0; is < PARAM.inp.nspin; is++)
         {
             ModuleBase::GlobalFunc::ZEROS(this->charge->kin_r[0], this->charge->nrxx);
         }
-        ModuleGint::cal_gint_tau(this->DM->get_DMR_vector(), PARAM.inp.nspin, this->charge->kin_r);
+        ModuleGint::cal_gint_tau(dm->get_DMR_vector(), PARAM.inp.nspin, this->charge->kin_r);
     }
 
     this->charge->renormalize_rho();
@@ -81,13 +77,13 @@ void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, std::vector<do
 }
 
 template <>
-void ElecStateLCAO<std::complex<double>>::dm2rho(std::vector<std::complex<double>*> pexsi_DM,
-                                                  std::vector<std::complex<double>*> pexsi_EDM)
+void ElecStateLCAO<std::complex<double>>::dm2Rho(std::vector<std::complex<double>*> pexsi_DM,
+		std::vector<std::complex<double>*> pexsi_EDM,
+		DensityMatrix<std::complex<double>, double>* dm)
 {
     ModuleBase::WARNING_QUIT("ElecStateLCAO", "pexsi is not completed for multi-k case");
 }
 
-#endif
 
 template class ElecStateLCAO<double>;               // Gamma_only case
 template class ElecStateLCAO<std::complex<double>>; // multi-k case

From 14a698349601996d30ababc05a3d72fc694ed845 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 22:39:36 +0800
Subject: [PATCH 58/92] Update elecstate_lcao.h

---
 source/source_estate/elecstate_lcao.h | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/source/source_estate/elecstate_lcao.h b/source/source_estate/elecstate_lcao.h
index e9bb3077a5..eafc1e0a0d 100644
--- a/source/source_estate/elecstate_lcao.h
+++ b/source/source_estate/elecstate_lcao.h
@@ -27,27 +27,16 @@ class ElecStateLCAO : public ElecState
 
     virtual ~ElecStateLCAO()
     {
-        if (this->DM != nullptr)
-        {
-            delete this->DM;
-        }
     }
 
     // update charge density for next scf step
     // void getNewRho() override;
 
-    // initial density matrix
-    void init_DM(const K_Vectors* kv, const Parallel_Orbitals* paraV, const int nspin);
-    DensityMatrix<TK, double>* get_DM() const
-    {
-        return const_cast<DensityMatrix<TK, double>*>(this->DM);
-    }
     static int out_wfc_lcao;
     static bool need_psi_grid;
 
     double get_spin_constrain_energy() override;
 
-#ifdef __PEXSI
     // use for pexsi
 
     /**
@@ -56,10 +45,9 @@ class ElecStateLCAO : public ElecState
      * @param pexsi_EDM: pointers of energy-weighed density matrix (EDMK) calculated by pexsi, needed by MD, will be
      * stored in DensityMatrix::pexsi_EDM
      */
-    void dm2rho(std::vector<TK*> pexsi_DM, std::vector<TK*> pexsi_EDM);
-#endif
-
-    DensityMatrix<TK, double>* DM = nullptr;
+	void dm2Rho(std::vector<TK*> pexsi_DM, 
+			std::vector<TK*> pexsi_EDM, 
+			DensityMatrix<TK, double>* dm);
 
 };
 

From ee92dac7548ad07a03488db2926a707757f754bc Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Thu, 6 Nov 2025 22:49:55 +0800
Subject: [PATCH 59/92] Update Dockerfile.intel

---
 Dockerfile.intel | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index d56ec53c5c..1a66c18b4f 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -181,10 +181,8 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 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 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 && wget https://github.com/deepmodeling/abacus-develop/archive/refs/tags/v3.9.0.17.zip -O abacus-develop-3.9.0.17.zip && \
-    unzip abacus-develop-3.9.0.17.zip && \
-    cd abacus-develop-3.9.0.17 && \
-    sed -i '3i\#include "source_estate/elecstate_lcao.h"' source/source_lcao/edm.cpp && \
+    cd /tmp &&  git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
     cmake -B build \
         -DMKL_SYCL=OFF \
         -DMKL_SYCL_LINK=OFF \

From 2cf0a8dd3d9e31a1550e0c813801d4394f81e463 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Fri, 7 Nov 2025 09:05:43 +0800
Subject: [PATCH 60/92] Update elecstate_lcao.cpp

---
 source/source_estate/elecstate_lcao.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/source/source_estate/elecstate_lcao.cpp b/source/source_estate/elecstate_lcao.cpp
index a9578b228a..7bd32542ae 100644
--- a/source/source_estate/elecstate_lcao.cpp
+++ b/source/source_estate/elecstate_lcao.cpp
@@ -31,11 +31,11 @@ double ElecStateLCAO<std::complex<double>>::get_spin_constrain_energy()
 }
 
 template <>
-void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM, 
+void ElecStateLCAO<double>::dm2rho(std::vector<double*> pexsi_DM, 
 		std::vector<double*> pexsi_EDM,
 		DensityMatrix<double, double>* dm)
 {
-    ModuleBase::timer::tick("ElecStateLCAO", "dm2Rho");
+    ModuleBase::timer::tick("ElecStateLCAO", "dm2rho");
 
     int nspin = PARAM.inp.nspin;
     if (PARAM.inp.nspin == 4)
@@ -72,12 +72,12 @@ void ElecStateLCAO<double>::dm2Rho(std::vector<double*> pexsi_DM,
 
     this->charge->renormalize_rho();
 
-    ModuleBase::timer::tick("ElecStateLCAO", "dm2Rho");
+    ModuleBase::timer::tick("ElecStateLCAO", "dm2rho");
     return;
 }
 
 template <>
-void ElecStateLCAO<std::complex<double>>::dm2Rho(std::vector<std::complex<double>*> pexsi_DM,
+void ElecStateLCAO<std::complex<double>>::dm2rho(std::vector<std::complex<double>*> pexsi_DM,
 		std::vector<std::complex<double>*> pexsi_EDM,
 		DensityMatrix<std::complex<double>, double>* dm)
 {

From 899bc92455b685f0c0f15dac0199e01636231931 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Fri, 7 Nov 2025 09:07:28 +0800
Subject: [PATCH 61/92] Update elecstate_lcao.h


From c13df5ac4d1b6b220ba18e0cf0acc855133f775a Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Fri, 7 Nov 2025 14:07:00 +0800
Subject: [PATCH 62/92] Update Dockerfile.intel

---
 Dockerfile.intel | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 725dc40785..018bed6666 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -182,6 +182,8 @@ ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake:${CMAKE_PREFIX_PATH}
 ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/develop /dev/null
 RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH} && \
     export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH} && \
+    export CMAKE_PREFIX_PATH=${GKLIB_ROOT}:${METIS32_ROOT}:${PARMETIS32_ROOT}:${SUPERLU32_DIST_ROOT}:${PEXSI32_ROOT}:${CMAKE_PREFIX_PATH} && \
+    cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \

From d095f2f475cf6ac905407bf93b727474312de93d Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Fri, 7 Nov 2025 14:29:43 +0800
Subject: [PATCH 63/92] Update Dockerfile.intel

---
 Dockerfile.intel | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 018bed6666..1824cea2a3 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -184,7 +184,6 @@ RUN export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_RO
     export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH} && \
     export CMAKE_PREFIX_PATH=${GKLIB_ROOT}:${METIS32_ROOT}:${PARMETIS32_ROOT}:${SUPERLU32_DIST_ROOT}:${PEXSI32_ROOT}:${CMAKE_PREFIX_PATH} && \
     cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
-    cd /tmp && git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
     cmake -B build \
         -DENABLE_MLALGO=ON \

From 4983b0da7f31848f9a52edad3b86b360ff387863 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Fri, 7 Nov 2025 15:16:00 +0800
Subject: [PATCH 64/92] Update Dockerfile.intel

---
 Dockerfile.intel | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile.intel b/Dockerfile.intel
index 1824cea2a3..a85a50f2a3 100644
--- a/Dockerfile.intel
+++ b/Dockerfile.intel
@@ -181,8 +181,9 @@ 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:${CPATH} && \
-    export CMAKE_PREFIX_PATH=${GKLIB_ROOT}:${METIS32_ROOT}:${PARMETIS32_ROOT}:${SUPERLU32_DIST_ROOT}:${PEXSI32_ROOT}:${CMAKE_PREFIX_PATH} && \
+    export CMAKE_PREFIX_PATH=${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 \

From fbfa87e588e6af4aeda679b18fccd2d1f0ca8f83 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 20:49:21 +0800
Subject: [PATCH 65/92] Update devcontainer.yml

---
 .github/workflows/devcontainer.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml
index d3ff39b69f..762b34e16e 100644
--- a/.github/workflows/devcontainer.yml
+++ b/.github/workflows/devcontainer.yml
@@ -1,9 +1,9 @@
 name: Container
 
 on:
-  pull_request: # 当有 PR 指向 develop 分支时触发
-    branches:
-      - develop
+  #pull_request: # 当有 PR 指向 develop 分支时触发
+    #branches:
+    #  - develop
   push:
     branches:
       - develop

From 924e48e2e49ccd2154e2cfe42e0a6478c45f45f4 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 20:51:55 +0800
Subject: [PATCH 66/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index c664bf796c..eaeb96cabd 100644
--- a/.github/workflows/coverage.yml
+++ b/.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:

From cafd6fa40b4902322e110263d21ece82a17c70d1 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 20:56:34 +0800
Subject: [PATCH 67/92] Update CMakeLists.txt

---
 CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8ac95e45fd..ef32d94268 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -156,7 +156,8 @@ if(ENABLE_COVERAGE)
     include(FetchContent)
     FetchContent_Declare(
       cmakecodecov
-      URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
+      # URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
+      URL https://github.com/RWTH-HPC/CMake-codecov.git
     )
     FetchContent_Populate(cmakecodecov)
     list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)

From 31d8de816ca3e51cbd778b4a54d170a86f636fec Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 21:08:56 +0800
Subject: [PATCH 68/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index eaeb96cabd..a2568a7d40 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -19,6 +19,8 @@ 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: |
           cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON

From b1f0f68243015c79fe652539c07710d271335502 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 21:13:15 +0800
Subject: [PATCH 69/92] Update CMakeLists.txt

---
 CMakeLists.txt | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ef32d94268..511a3c3943 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -151,17 +151,18 @@ endif()
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 if(ENABLE_COVERAGE)
-  find_package(codecov)
-  if(NOT codecov_FOUND)
-    include(FetchContent)
-    FetchContent_Declare(
-      cmakecodecov
+  ##find_package(codecov)
+  ## if(NOT codecov_FOUND)
+  ##  include(FetchContent)
+   ## FetchContent_Declare(
+   #   cmakecodecov
       # URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
-      URL https://github.com/RWTH-HPC/CMake-codecov.git
-    )
-    FetchContent_Populate(cmakecodecov)
-    list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
-    find_package(codecov REQUIRED)
+   #   URL https://github.com/RWTH-HPC/CMake-codecov.git
+   # )
+   ## FetchContent_Populate(cmakecodecov)
+   ## list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
+   ## find_package(codecov REQUIRED)
+  set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/externals/CMake-codecov/cmake" ${CMAKE_MODULE_PATH})
   endif()
 endif()
 

From a49b42f9cae7005c7e782a77daeb7b71d8ce5352 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 21:24:53 +0800
Subject: [PATCH 70/92] Update CMakeLists.txt

---
 CMakeLists.txt | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 511a3c3943..3c46d6c86e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -151,18 +151,18 @@ endif()
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 if(ENABLE_COVERAGE)
-  ##find_package(codecov)
-  ## if(NOT codecov_FOUND)
-  ##  include(FetchContent)
-   ## FetchContent_Declare(
-   #   cmakecodecov
+  find_package(codecov)
+  if(NOT codecov_FOUND)
+    include(FetchContent)
+    FetchContent_Declare(
+      cmakecodecov
       # URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
-   #   URL https://github.com/RWTH-HPC/CMake-codecov.git
-   # )
-   ## FetchContent_Populate(cmakecodecov)
-   ## list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
-   ## find_package(codecov REQUIRED)
-  set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/externals/CMake-codecov/cmake" ${CMAKE_MODULE_PATH})
+      URL https://github.com/RWTH-HPC/CMake-codecov/archive/refs/heads/master.zip
+    )
+    FetchContent_Populate(cmakecodecov)
+    list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
+    find_package(codecov REQUIRED)
+  ##set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/externals/CMake-codecov/cmake" ${CMAKE_MODULE_PATH})
   endif()
 endif()
 

From e77fafb7a42e20961814a822e5369c79b04d3311 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 21:51:40 +0800
Subject: [PATCH 71/92] Update CMakeLists.txt

---
 CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3c46d6c86e..41bef6a632 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -157,7 +157,8 @@ if(ENABLE_COVERAGE)
     FetchContent_Declare(
       cmakecodecov
       # 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://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
     )
     FetchContent_Populate(cmakecodecov)
     list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)

From c910946d41e0f0f0639c0251df693a25584dad86 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Sun, 9 Nov 2025 21:57:38 +0800
Subject: [PATCH 72/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index a2568a7d40..af0ea88602 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -19,8 +19,8 @@ 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
+          # mkdir externals
+          # git submodule add git://github.com/RWTH-HPC/CMake-codecov.git externals/CMake-codecov
       - name: Building
         run: |
           cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON

From 8832d99402d8ee9261c26218c6656fa34d17b5df Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 09:57:00 +0800
Subject: [PATCH 73/92] Update CMakeLists.txt

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 41bef6a632..9b83fdbed6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -157,8 +157,8 @@ if(ENABLE_COVERAGE)
     FetchContent_Declare(
       cmakecodecov
       # 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
+      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
     )
     FetchContent_Populate(cmakecodecov)
     list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)

From 25b176919e675bbbc089aa06b791c0bab3c03439 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 10:27:56 +0800
Subject: [PATCH 74/92] Update CMakeLists.txt

---
 CMakeLists.txt | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9b83fdbed6..82a15f01d3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -156,9 +156,13 @@ if(ENABLE_COVERAGE)
     include(FetchContent)
     FetchContent_Declare(
       cmakecodecov
+      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://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)

From 273839c17e108c2f8dfe0e90ebfa08b7b01a1575 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 10:41:52 +0800
Subject: [PATCH 75/92] Update CMakeLists.txt

---
 CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 82a15f01d3..8eaf9c8c9b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -151,7 +151,7 @@ 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(
@@ -166,6 +166,7 @@ if(ENABLE_COVERAGE)
     )
     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()

From 8d12b64c126f2985bd730e4ce190cb68507a787f Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 10:52:32 +0800
Subject: [PATCH 76/92] Create Findcodecov.cmake

---
 cmake/Findcodecov.cmake | 275 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 275 insertions(+)
 create mode 100644 cmake/Findcodecov.cmake

diff --git a/cmake/Findcodecov.cmake b/cmake/Findcodecov.cmake
new file mode 100644
index 0000000000..004b086e70
--- /dev/null
+++ b/cmake/Findcodecov.cmake
@@ -0,0 +1,275 @@
+# This file is part of CMake-codecov.
+#
+# SPDX-FileCopyrightText: RWTH Aachen University, Federal Republic of Germany
+# SPDX-FileContributor: Alexander Haase, alexander.haase@rwth-aachen.de
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+# Add an option to choose, if coverage should be enabled or not. If enabled
+# marked targets will be build with coverage support and appropriate targets
+# will be added. If disabled coverage will be ignored for *ALL* targets.
+option(ENABLE_COVERAGE "Enable coverage build." OFF)
+
+set(COVERAGE_FLAG_CANDIDATES
+	# gcc and clang
+	"-O0 -g -fprofile-arcs -ftest-coverage"
+
+	# gcc and clang fallback
+	"-O0 -g --coverage"
+)
+
+
+# Add coverage support for target ${TNAME} and register target for coverage
+# evaluation. If coverage is disabled or not supported, this function will
+# simply do nothing.
+#
+# Note: This function is only a wrapper to define this function always, even if
+#   coverage is not supported by the compiler or disabled. This function must
+#   be defined here, because the module will be exited, if there is no coverage
+#   support by the compiler or it is disabled by the user.
+function (add_coverage TNAME)
+	# only add coverage for target, if coverage is support and enabled.
+	if (ENABLE_COVERAGE)
+		foreach (TNAME ${ARGV})
+			add_coverage_target(${TNAME})
+		endforeach ()
+	endif ()
+endfunction (add_coverage)
+
+
+# Add global target to gather coverage information after all targets have been
+# added. Other evaluation functions could be added here, after checks for the
+# specific module have been passed.
+#
+# Note: This function is only a wrapper to define this function always, even if
+#   coverage is not supported by the compiler or disabled. This function must
+#   be defined here, because the module will be exited, if there is no coverage
+#   support by the compiler or it is disabled by the user.
+function (coverage_evaluate)
+	# add lcov evaluation
+	if (LCOV_FOUND)
+		lcov_capture_initial()
+		lcov_capture()
+	endif (LCOV_FOUND)
+endfunction ()
+
+
+# Exit this module, if coverage is disabled. add_coverage is defined before this
+# return, so this module can be exited now safely without breaking any build-
+# scripts.
+if (NOT ENABLE_COVERAGE)
+	return()
+endif ()
+
+
+
+
+# Find the required flags foreach language.
+set(CMAKE_REQUIRED_QUIET_SAVE ${CMAKE_REQUIRED_QUIET})
+set(CMAKE_REQUIRED_QUIET ${codecov_FIND_QUIETLY})
+
+get_property(ENABLED_LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+foreach (LANG ${ENABLED_LANGUAGES})
+	if (NOT ${LANG} MATCHES "^(C|CXX|Fortran)$")
+		message(STATUS "Skipping coverage for unsupported language: ${LANG}")
+		continue()
+	endif ()
+
+	# Coverage flags are not dependent on language, but the used compiler. So
+	# instead of searching flags foreach language, search flags foreach compiler
+	# used.
+	set(COMPILER ${CMAKE_${LANG}_COMPILER_ID})
+	if (NOT COVERAGE_${COMPILER}_FLAGS)
+		foreach (FLAG ${COVERAGE_FLAG_CANDIDATES})
+			if(NOT CMAKE_REQUIRED_QUIET)
+				message(STATUS "Try ${COMPILER} code coverage flag = [${FLAG}]")
+			endif()
+
+			set(CMAKE_REQUIRED_FLAGS "${FLAG}")
+			unset(COVERAGE_FLAG_DETECTED CACHE)
+
+			if (${LANG} STREQUAL "C")
+				include(CheckCCompilerFlag)
+				check_c_compiler_flag("${FLAG}" COVERAGE_FLAG_DETECTED)
+
+			elseif (${LANG} STREQUAL "CXX")
+				include(CheckCXXCompilerFlag)
+				check_cxx_compiler_flag("${FLAG}" COVERAGE_FLAG_DETECTED)
+
+			elseif (${LANG} STREQUAL "Fortran")
+				# CheckFortranCompilerFlag was introduced in CMake 3.x. To be
+				# compatible with older Cmake versions, we will check if this
+				# module is present before we use it. Otherwise we will define
+				# Fortran coverage support as not available.
+				include(CheckFortranCompilerFlag OPTIONAL
+					RESULT_VARIABLE INCLUDED)
+				if (INCLUDED)
+					check_fortran_compiler_flag("${FLAG}"
+						COVERAGE_FLAG_DETECTED)
+				elseif (NOT CMAKE_REQUIRED_QUIET)
+					message("-- Performing Test COVERAGE_FLAG_DETECTED")
+					message("-- Performing Test COVERAGE_FLAG_DETECTED - Failed"
+						" (Check not supported)")
+				endif ()
+			endif()
+
+			unset(CMAKE_REQUIRED_FLAGS)
+
+			if (COVERAGE_FLAG_DETECTED)
+				set(COVERAGE_${COMPILER}_FLAGS "${FLAG}"
+					CACHE STRING "${COMPILER} flags for code coverage.")
+				mark_as_advanced(COVERAGE_${COMPILER}_FLAGS)
+				break()
+			elseif (NOT CMAKE_REQUIRED_QUIET)
+				message(WARNING "Code coverage is not available for ${COMPILER}"
+				        " compiler. Targets using this compiler will be "
+				        "compiled without it.")
+			endif ()
+		endforeach ()
+	endif ()
+endforeach ()
+
+set(CMAKE_REQUIRED_QUIET ${CMAKE_REQUIRED_QUIET_SAVE})
+
+
+
+
+# Helper function to get the language of a source file.
+function (codecov_lang_of_source FILE RETURN_VAR)
+	# Usually, only the last extension of the file should be checked, to avoid
+	# template files (i.e. *.t.cpp) are checked with the full file extension.
+	# However, this feature requires CMake 3.14 or later.
+	set(EXT_COMP "LAST_EXT")
+	if(${CMAKE_VERSION} VERSION_LESS "3.14.0")
+		set(EXT_COMP "EXT")
+	endif()
+
+	get_filename_component(FILE_EXT "${FILE}" ${EXT_COMP})
+	string(TOLOWER "${FILE_EXT}" FILE_EXT)
+	string(SUBSTRING "${FILE_EXT}" 1 -1 FILE_EXT)
+
+	get_property(ENABLED_LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+	foreach (LANG ${ENABLED_LANGUAGES})
+		list(FIND CMAKE_${LANG}_SOURCE_FILE_EXTENSIONS "${FILE_EXT}" TEMP)
+		if (NOT ${TEMP} EQUAL -1)
+			set(${RETURN_VAR} "${LANG}" PARENT_SCOPE)
+			return()
+		endif ()
+	endforeach()
+
+	set(${RETURN_VAR} "" PARENT_SCOPE)
+endfunction ()
+
+
+# Helper function to get the relative path of the source file destination path.
+# This path is needed by FindGcov and FindLcov cmake files to locate the
+# captured data.
+function (codecov_path_of_source FILE RETURN_VAR)
+	string(REGEX MATCH "TARGET_OBJECTS:([^ >]+)" _source ${FILE})
+
+	# If expression was found, SOURCEFILE is a generator-expression for an
+	# object library. Currently we found no way to call this function automatic
+	# for the referenced target, so it must be called in the directoryso of the
+	# object library definition.
+	if (NOT "${_source}" STREQUAL "")
+		set(${RETURN_VAR} "" PARENT_SCOPE)
+		return()
+	endif ()
+
+
+	string(REPLACE "${CMAKE_CURRENT_BINARY_DIR}/" "" FILE "${FILE}")
+	if(IS_ABSOLUTE ${FILE})
+		file(RELATIVE_PATH FILE ${CMAKE_CURRENT_SOURCE_DIR} ${FILE})
+	endif()
+
+	# get the right path for file
+	string(REPLACE ".." "__" PATH "${FILE}")
+
+	set(${RETURN_VAR} "${PATH}" PARENT_SCOPE)
+endfunction()
+
+
+
+
+# Add coverage support for target ${TNAME} and register target for coverage
+# evaluation.
+function(add_coverage_target TNAME)
+	# Check if all sources for target use the same compiler. If a target uses
+	# e.g. C and Fortran mixed and uses different compilers (e.g. clang and
+	# gfortran) this can trigger huge problems, because different compilers may
+	# use different implementations for code coverage.
+	get_target_property(TSOURCES ${TNAME} SOURCES)
+	set(TARGET_COMPILER "")
+	set(ADDITIONAL_FILES "")
+	foreach (FILE ${TSOURCES})
+		# If expression was found, FILE is a generator-expression for an object
+		# library. Object libraries will be ignored.
+		string(REGEX MATCH "TARGET_OBJECTS:([^ >]+)" _file ${FILE})
+		if ("${_file}" STREQUAL "")
+			codecov_lang_of_source(${FILE} LANG)
+			if (LANG)
+				list(APPEND TARGET_COMPILER ${CMAKE_${LANG}_COMPILER_ID})
+
+				list(APPEND ADDITIONAL_FILES "${FILE}.gcno")
+				list(APPEND ADDITIONAL_FILES "${FILE}.gcda")
+			endif ()
+		endif ()
+	endforeach ()
+
+	list(REMOVE_DUPLICATES TARGET_COMPILER)
+	list(LENGTH TARGET_COMPILER NUM_COMPILERS)
+
+	if (NUM_COMPILERS GREATER 1)
+		message(WARNING "Can't use code coverage for target ${TNAME}, because "
+		        "it will be compiled by incompatible compilers. Target will be "
+		        "compiled without code coverage.")
+		return()
+
+	elseif (NUM_COMPILERS EQUAL 0)
+		message(WARNING "Can't use code coverage for target ${TNAME}, because "
+		        "it uses an unknown compiler. Target will be compiled without "
+		        "code coverage.")
+		return()
+
+	elseif (NOT DEFINED "COVERAGE_${TARGET_COMPILER}_FLAGS")
+		# A warning has been printed before, so just return if flags for this
+		# compiler aren't available.
+		return()
+	endif()
+
+
+	# enable coverage for target
+	set_property(TARGET ${TNAME} APPEND_STRING
+		PROPERTY COMPILE_FLAGS " ${COVERAGE_${TARGET_COMPILER}_FLAGS}")
+	set_property(TARGET ${TNAME} APPEND_STRING
+		PROPERTY LINK_FLAGS " ${COVERAGE_${TARGET_COMPILER}_FLAGS}")
+
+
+	# Add gcov files generated by compiler to clean target.
+	set(CLEAN_FILES "")
+	foreach (FILE ${ADDITIONAL_FILES})
+		codecov_path_of_source(${FILE} FILE)
+		list(APPEND CLEAN_FILES "CMakeFiles/${TNAME}.dir/${FILE}")
+	endforeach()
+
+	if(${CMAKE_VERSION} VERSION_LESS "3.15.0")
+		set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
+			"${CLEAN_FILES}")
+	else()
+		set_directory_properties(PROPERTIES ADDITIONAL_CLEAN_FILES
+			"${CLEAN_FILES}")
+	endif()
+
+
+	add_gcov_target(${TNAME})
+	add_lcov_target(${TNAME})
+endfunction(add_coverage_target)
+
+
+
+
+# Include modules for parsing the collected data and output it in a readable
+# format (like gcov and lcov).
+find_package(Gcov)
+find_package(Lcov)

From 27f4dfc2fc46a3035740bc477e1db5abb20943af Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 11:13:17 +0800
Subject: [PATCH 77/92] Update CMakeLists.txt

---
 tests/integrate/CMakeLists.txt | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/tests/integrate/CMakeLists.txt b/tests/integrate/CMakeLists.txt
index 8da79197aa..d4cf1b5160 100644
--- a/tests/integrate/CMakeLists.txt
+++ b/tests/integrate/CMakeLists.txt
@@ -1,5 +1,12 @@
 find_program(BASH bash)
 find_package(Python3 REQUIRED)
+
+add_executable(sum_cube.exe ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
+install(TARGETS sum_cube.exe DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+if(ENABLE_COVERAGE)
+  add_coverage(sum_cube.exe)
+endif()
+
 if(ENABLE_ASAN)
     add_test(
         NAME integrated_test_with_asan
@@ -13,10 +20,4 @@ else()
         COMMAND ${BASH} Autotest.sh -a ${ABACUS_BIN_PATH} -n 4
         WORKING_DIRECTORY ${ABACUS_TEST_DIR}/integrate
     )
-    add_executable(sum_cube.exe ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
-    install(TARGETS sum_cube.exe DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
-
-    if(ENABLE_COVERAGE)
-      add_coverage(sum_cube.exe)
-    endif()
 endif()

From 05842bb8082eea0239ef541967af67d7a08f0247 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 12:16:02 +0800
Subject: [PATCH 78/92] Update CMakeLists.txt

---
 tests/integrate/CMakeLists.txt | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/integrate/CMakeLists.txt b/tests/integrate/CMakeLists.txt
index d4cf1b5160..106c179f90 100644
--- a/tests/integrate/CMakeLists.txt
+++ b/tests/integrate/CMakeLists.txt
@@ -1,10 +1,12 @@
 find_program(BASH bash)
 find_package(Python3 REQUIRED)
 
-add_executable(sum_cube.exe ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
-install(TARGETS sum_cube.exe DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+add_executable(sum_cube ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
+install(TARGETS sum_cube DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+message(STATUS "Target sum_cube has been defined in ${CMAKE_CURRENT_SOURCE_DIR}") # 添加此行
+    
 if(ENABLE_COVERAGE)
-  add_coverage(sum_cube.exe)
+  add_coverage(sum_cube)
 endif()
 
 if(ENABLE_ASAN)

From bd30a0ad514f1ba72d1f25e264549f66200e33dd Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 14:03:41 +0800
Subject: [PATCH 79/92] Update CMakeLists.txt

---
 source/source_cell/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/source_cell/CMakeLists.txt b/source/source_cell/CMakeLists.txt
index f9d4f0c535..ad3aefba42 100644
--- a/source/source_cell/CMakeLists.txt
+++ b/source/source_cell/CMakeLists.txt
@@ -3,7 +3,7 @@ add_subdirectory(module_neighbor)
 
 add_library(
     cell
-    OBJECT
+    STATIC
     atom_pseudo.cpp
     atom_spec.cpp
     pseudo.cpp

From feab2b003afbf1e923be600337c810c17587552c Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 14:32:44 +0800
Subject: [PATCH 80/92] Update CMakeLists.txt

---
 source/source_lcao/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/source_lcao/CMakeLists.txt b/source/source_lcao/CMakeLists.txt
index 5199625c41..5b7ad5e04a 100644
--- a/source/source_lcao/CMakeLists.txt
+++ b/source/source_lcao/CMakeLists.txt
@@ -54,7 +54,7 @@ if(ENABLE_LCAO)
 
     add_library(
         hamilt_lcao
-        OBJECT
+        STATIC
         ${objects}
     )
 

From 7fe71421e42b1f76ca104e0003fa7c280bcb9177 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 15:05:56 +0800
Subject: [PATCH 81/92] Update CMakeLists.txt

---
 source/source_lcao/module_hcontainer/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/source/source_lcao/module_hcontainer/CMakeLists.txt b/source/source_lcao/module_hcontainer/CMakeLists.txt
index 65db746a84..e0a5efe23b 100644
--- a/source/source_lcao/module_hcontainer/CMakeLists.txt
+++ b/source/source_lcao/module_hcontainer/CMakeLists.txt
@@ -12,7 +12,7 @@ list(APPEND objects
 
 add_library(
     hcontainer
-    OBJECT
+    STATIC
     ${objects}
 )
 
@@ -26,4 +26,4 @@ IF (BUILD_TESTING)
   endif()
 endif()
 
-endif()
\ No newline at end of file
+endif()

From 52d24d792e7b675a8222bed46a7b0d4312bb68f1 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 15:11:26 +0800
Subject: [PATCH 82/92] Update CMakeLists.txt

---
 source/source_lcao/module_rt/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/source_lcao/module_rt/CMakeLists.txt b/source/source_lcao/module_rt/CMakeLists.txt
index 58bc834a5f..4e794487db 100644
--- a/source/source_lcao/module_rt/CMakeLists.txt
+++ b/source/source_lcao/module_rt/CMakeLists.txt
@@ -19,7 +19,7 @@ if(ENABLE_LCAO)
 
     add_library(
         tddft
-        OBJECT
+        STATIC
         ${objects}
     )
 

From fd27fb3d3d037441a788477aee03d7ea2329680a Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 15:12:30 +0800
Subject: [PATCH 83/92] Update CMakeLists.txt

---
 source/source_lcao/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/source_lcao/CMakeLists.txt b/source/source_lcao/CMakeLists.txt
index 5b7ad5e04a..5199625c41 100644
--- a/source/source_lcao/CMakeLists.txt
+++ b/source/source_lcao/CMakeLists.txt
@@ -54,7 +54,7 @@ if(ENABLE_LCAO)
 
     add_library(
         hamilt_lcao
-        STATIC
+        OBJECT
         ${objects}
     )
 

From 50284f68534be00f20a5aad492c97dbffb10ed19 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 16:27:49 +0800
Subject: [PATCH 84/92] Update CMakeLists.txt

---
 CMakeLists.txt | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8eaf9c8c9b..f2cddc863c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -814,5 +814,22 @@ install(PROGRAMS ${ABACUS_BIN_PATH}
 )
 
 if(ENABLE_COVERAGE)
-  coverage_evaluate()
+  # coverage_evaluate()
+# ... 在所有 add_subdirectory() 之后 ...
+
+if(ENABLE_COVERAGE)
+    ## 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()

From ab10775cdadfe91af2d1f5db06bc90189e846876 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 16:31:39 +0800
Subject: [PATCH 85/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index af0ea88602..6dbde0025c 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -23,6 +23,8 @@ jobs:
           # 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
@@ -31,6 +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() }}

From df1329a1cca945ab3b42d4135025a18ecad354c1 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 17:02:27 +0800
Subject: [PATCH 86/92] Update CMakeLists.txt

---
 CMakeLists.txt | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f2cddc863c..235d44f7ea 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -813,10 +813,6 @@ install(PROGRAMS ${ABACUS_BIN_PATH}
         # DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
-if(ENABLE_COVERAGE)
-  # coverage_evaluate()
-# ... 在所有 add_subdirectory() 之后 ...
-
 if(ENABLE_COVERAGE)
     ## coverage_evaluate()
     add_custom_target(coverage

From d7257548c7bdf6186733d5ce4e2a7ce7b8c126fe Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 20:26:12 +0800
Subject: [PATCH 87/92] Create FindLcov.cmake

---
 cmake/FindLcov.cmake | 365 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 365 insertions(+)
 create mode 100644 cmake/FindLcov.cmake

diff --git a/cmake/FindLcov.cmake b/cmake/FindLcov.cmake
new file mode 100644
index 0000000000..1d48b55149
--- /dev/null
+++ b/cmake/FindLcov.cmake
@@ -0,0 +1,365 @@
+# This file is part of CMake-codecov.
+#
+# SPDX-FileCopyrightText: RWTH Aachen University, Federal Republic of Germany
+# SPDX-FileContributor: Alexander Haase, alexander.haase@rwth-aachen.de
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+# configuration
+set(LCOV_DATA_PATH "${CMAKE_BINARY_DIR}/lcov/data")
+set(LCOV_DATA_PATH_INIT "${LCOV_DATA_PATH}/init")
+set(LCOV_DATA_PATH_CAPTURE "${LCOV_DATA_PATH}/capture")
+set(LCOV_HTML_PATH "${CMAKE_BINARY_DIR}/lcov/html")
+
+set(GENINFO_EXTRA_FLAGS "" CACHE STRING "Additional flags to pass to geninfo.")
+string(REPLACE " " ";" GENINFO_EXTRA_FLAGS "${GENINFO_EXTRA_FLAGS}")
+set(LCOV_EXTRA_FLAGS "" CACHE STRING "Additional flags to pass to lcov.")
+string(REPLACE " " ";" LCOV_EXTRA_FLAGS "${LCOV_EXTRA_FLAGS}")
+
+
+# Search for Gcov which is used by Lcov.
+find_package(Gcov)
+
+
+
+
+# This function will add lcov evaluation for target <TNAME>. Only sources of
+# this target will be evaluated and no dependencies will be added. It will call
+# geninfo on any source file of <TNAME> once and store the info file in the same
+# directory.
+#
+# Note: This function is only a wrapper to define this function always, even if
+#   coverage is not supported by the compiler or disabled. This function must
+#   be defined here, because the module will be exited, if there is no coverage
+#   support by the compiler or it is disabled by the user.
+function (add_lcov_target TNAME)
+	if (LCOV_FOUND)
+		# capture initial coverage data
+		lcov_capture_initial_tgt(${TNAME})
+
+		# capture coverage data after execution
+		lcov_capture_tgt(${TNAME})
+	endif ()
+endfunction (add_lcov_target)
+
+
+
+
+# include required Modules
+include(FindPackageHandleStandardArgs)
+
+# Search for required lcov binaries.
+find_program(LCOV_BIN lcov)
+find_program(GENINFO_BIN geninfo)
+find_program(GENHTML_BIN genhtml)
+find_package_handle_standard_args(Lcov
+	REQUIRED_VARS LCOV_BIN GENINFO_BIN GENHTML_BIN
+)
+
+# enable genhtml C++ demangeling, if c++filt is found.
+set(GENHTML_CPPFILT_FLAG "")
+find_program(CPPFILT_BIN c++filt)
+if (NOT CPPFILT_BIN STREQUAL "")
+	set(GENHTML_CPPFILT_FLAG "--demangle-cpp")
+endif (NOT CPPFILT_BIN STREQUAL "")
+
+# enable no-external flag for lcov, if available.
+if (GENINFO_BIN AND NOT DEFINED GENINFO_EXTERN_FLAG)
+	set(FLAG "")
+	execute_process(COMMAND ${GENINFO_BIN} --help OUTPUT_VARIABLE GENINFO_HELP)
+	string(REGEX MATCH "external" GENINFO_RES "${GENINFO_HELP}")
+	if (GENINFO_RES)
+		set(FLAG "--no-external")
+	endif ()
+
+	set(GENINFO_EXTERN_FLAG "${FLAG}"
+		CACHE STRING "Geninfo flag to exclude system sources.")
+endif ()
+
+# If Lcov was not found, exit module now.
+if (NOT LCOV_FOUND)
+	return()
+endif (NOT LCOV_FOUND)
+
+
+
+
+# Create directories to be used.
+file(MAKE_DIRECTORY ${LCOV_DATA_PATH_INIT})
+file(MAKE_DIRECTORY ${LCOV_DATA_PATH_CAPTURE})
+
+set(LCOV_REMOVE_PATTERNS "")
+
+# This function will merge lcov files to a single target file. Additional lcov
+# flags may be set with setting LCOV_EXTRA_FLAGS before calling this function.
+function (lcov_merge_files OUTFILE ...)
+	# Remove ${OUTFILE} from ${ARGV} and generate lcov parameters with files.
+	list(REMOVE_AT ARGV 0)
+
+	# Generate merged file.
+	string(REPLACE "${CMAKE_BINARY_DIR}/" "" FILE_REL "${OUTFILE}")
+	add_custom_command(OUTPUT "${OUTFILE}.raw"
+		COMMAND cat ${ARGV} > ${OUTFILE}.raw
+		DEPENDS ${ARGV}
+		COMMENT "Generating ${FILE_REL}"
+	)
+
+	add_custom_command(OUTPUT "${OUTFILE}"
+		COMMAND ${LCOV_BIN} --quiet -a ${OUTFILE}.raw --output-file ${OUTFILE}
+			--base-directory ${PROJECT_SOURCE_DIR} ${LCOV_EXTRA_FLAGS}
+		COMMAND ${LCOV_BIN} --quiet -r ${OUTFILE} ${LCOV_REMOVE_PATTERNS}
+			--output-file ${OUTFILE} ${LCOV_EXTRA_FLAGS}
+		DEPENDS ${OUTFILE}.raw
+		COMMENT "Post-processing ${FILE_REL}"
+	)
+endfunction ()
+
+
+
+
+# Add a new global target to generate initial coverage reports for all targets.
+# This target will be used to generate the global initial info file, which is
+# used to gather even empty report data.
+if (NOT TARGET lcov-capture-init)
+	add_custom_target(lcov-capture-init)
+	set(LCOV_CAPTURE_INIT_FILES "" CACHE INTERNAL "")
+endif (NOT TARGET lcov-capture-init)
+
+
+# This function will add initial capture of coverage data for target <TNAME>,
+# which is needed to get also data for objects, which were not loaded at
+# execution time. It will call geninfo for every source file of <TNAME> once and
+# store the info file in the same directory.
+function (lcov_capture_initial_tgt TNAME)
+	# We don't have to check, if the target has support for coverage, thus this
+	# will be checked by add_coverage_target in Findcoverage.cmake. Instead we
+	# have to determine which gcov binary to use.
+	get_target_property(TSOURCES ${TNAME} SOURCES)
+	set(SOURCES "")
+	set(TCOMPILER "")
+	foreach (FILE ${TSOURCES})
+		codecov_path_of_source(${FILE} FILE)
+		if (NOT "${FILE}" STREQUAL "")
+			codecov_lang_of_source(${FILE} LANG)
+			if (NOT "${LANG}" STREQUAL "")
+				list(APPEND SOURCES "${FILE}")
+				set(TCOMPILER ${CMAKE_${LANG}_COMPILER_ID})
+			endif ()
+		endif ()
+	endforeach ()
+
+	# If no gcov binary was found, coverage data can't be evaluated.
+	if (NOT GCOV_${TCOMPILER}_BIN)
+		message(WARNING "No coverage evaluation binary found for ${TCOMPILER}.")
+		return()
+	endif ()
+
+	set(GCOV_BIN "${GCOV_${TCOMPILER}_BIN}")
+	set(GCOV_ENV "${GCOV_${TCOMPILER}_ENV}")
+
+
+	get_target_property(TBIN_DIR ${TNAME} BINARY_DIR)
+	set(TDIR ${TBIN_DIR}/CMakeFiles/${TNAME}.dir)
+
+	set(GENINFO_FILES "")
+	foreach(FILE ${SOURCES})
+		# generate empty coverage files
+		set(OUTFILE "${TDIR}/${FILE}.info.init")
+		list(APPEND GENINFO_FILES ${OUTFILE})
+
+		add_custom_command(OUTPUT ${OUTFILE} COMMAND ${GCOV_ENV} ${GENINFO_BIN}
+				--quiet --base-directory ${PROJECT_SOURCE_DIR} --initial
+				--gcov-tool ${GCOV_BIN} --output-filename ${OUTFILE}
+				${GENINFO_EXTERN_FLAG} ${TDIR}/${FILE}.gcno
+				${GENINFO_EXTRA_FLAGS}
+			DEPENDS ${TNAME}
+			COMMENT "Capturing initial coverage data for ${FILE}"
+		)
+	endforeach()
+
+	# Concatenate all files generated by geninfo to a single file per target.
+	set(OUTFILE "${LCOV_DATA_PATH_INIT}/${TNAME}.info")
+	list(APPEND LCOV_EXTRA_FLAGS "--initial")
+	lcov_merge_files("${OUTFILE}" ${GENINFO_FILES})
+	add_custom_target(${TNAME}-capture-init ALL DEPENDS ${OUTFILE})
+
+	# add geninfo file generation to global lcov-geninfo target
+	add_dependencies(lcov-capture-init ${TNAME}-capture-init)
+	set(LCOV_CAPTURE_INIT_FILES "${LCOV_CAPTURE_INIT_FILES}"
+		"${OUTFILE}" CACHE INTERNAL ""
+	)
+endfunction (lcov_capture_initial_tgt)
+
+
+# This function will generate the global info file for all targets. It has to be
+# called after all other CMake functions in the root CMakeLists.txt file, to get
+# a full list of all targets that generate coverage data.
+function (lcov_capture_initial)
+	# Skip this function (and do not create the following targets), if there are
+	# no input files.
+	if ("${LCOV_CAPTURE_INIT_FILES}" STREQUAL "")
+		return()
+	endif ()
+
+	# Add a new target to merge the files of all targets.
+	set(OUTFILE "${LCOV_DATA_PATH_INIT}/all_targets.info")
+	lcov_merge_files("${OUTFILE}" ${LCOV_CAPTURE_INIT_FILES})
+	add_custom_target(lcov-geninfo-init ALL	DEPENDS ${OUTFILE}
+		lcov-capture-init
+	)
+endfunction (lcov_capture_initial)
+
+
+
+
+# Add a new global target to generate coverage reports for all targets. This
+# target will be used to generate the global info file.
+if (NOT TARGET lcov-capture)
+	add_custom_target(lcov-capture)
+	set(LCOV_CAPTURE_FILES "" CACHE INTERNAL "")
+endif (NOT TARGET lcov-capture)
+
+
+# This function will add capture of coverage data for target <TNAME>, which is
+# needed to get also data for objects, which were not loaded at execution time.
+# It will call geninfo for every source file of <TNAME> once and store the info
+# file in the same directory.
+function (lcov_capture_tgt TNAME)
+	# We don't have to check, if the target has support for coverage, thus this
+	# will be checked by add_coverage_target in Findcoverage.cmake. Instead we
+	# have to determine which gcov binary to use.
+	get_target_property(TSOURCES ${TNAME} SOURCES)
+	set(SOURCES "")
+	set(TCOMPILER "")
+	foreach (FILE ${TSOURCES})
+		codecov_path_of_source(${FILE} FILE)
+		if (NOT "${FILE}" STREQUAL "")
+			codecov_lang_of_source(${FILE} LANG)
+			if (NOT "${LANG}" STREQUAL "")
+				list(APPEND SOURCES "${FILE}")
+				set(TCOMPILER ${CMAKE_${LANG}_COMPILER_ID})
+			endif ()
+		endif ()
+	endforeach ()
+
+	# If no gcov binary was found, coverage data can't be evaluated.
+	if (NOT GCOV_${TCOMPILER}_BIN)
+		message(WARNING "No coverage evaluation binary found for ${TCOMPILER}.")
+		return()
+	endif ()
+
+	set(GCOV_BIN "${GCOV_${TCOMPILER}_BIN}")
+	set(GCOV_ENV "${GCOV_${TCOMPILER}_ENV}")
+
+	get_target_property(TBIN_DIR ${TNAME} BINARY_DIR)
+	set(TDIR ${TBIN_DIR}/CMakeFiles/${TNAME}.dir)
+
+	set(GENINFO_FILES "")
+	foreach(FILE ${SOURCES})
+		# Generate coverage files. If no .gcda file was generated during
+		# execution, the empty coverage file will be used instead.
+		set(OUTFILE "${TDIR}/${FILE}.info")
+		list(APPEND GENINFO_FILES ${OUTFILE})
+
+		# Create an empty .gcda file, so the target capture file can have a dependency on it.
+		# The capture file will only use this .gcda if it has a non-zero size (test -s).
+		add_custom_command(OUTPUT "${TDIR}/${FILE}.gcda"
+			COMMAND "${CMAKE_COMMAND}" -E touch "${TDIR}/${FILE}.gcda"
+		)
+
+		add_custom_command(OUTPUT ${OUTFILE}
+			COMMAND test -s "${TDIR}/${FILE}.gcda"
+				&& ${GCOV_ENV} ${GENINFO_BIN} --quiet --base-directory
+					${PROJECT_SOURCE_DIR} --gcov-tool ${GCOV_BIN}
+					--output-filename ${OUTFILE} ${GENINFO_EXTERN_FLAG}
+					${TDIR}/${FILE}.gcda ${GENINFO_EXTRA_FLAGS}
+				|| cp ${OUTFILE}.init ${OUTFILE}
+			DEPENDS ${TNAME} ${TNAME}-capture-init "${TDIR}/${FILE}.gcda"
+			COMMENT "Capturing coverage data for ${FILE}"
+		)
+	endforeach()
+
+	# Concatenate all files generated by geninfo to a single file per target.
+	set(OUTFILE "${LCOV_DATA_PATH_CAPTURE}/${TNAME}.info")
+	lcov_merge_files("${OUTFILE}" ${GENINFO_FILES})
+	add_custom_target(${TNAME}-geninfo DEPENDS ${OUTFILE})
+
+	# add geninfo file generation to global lcov-capture target
+	add_dependencies(lcov-capture ${TNAME}-geninfo)
+	set(LCOV_CAPTURE_FILES "${LCOV_CAPTURE_FILES}" "${OUTFILE}" CACHE INTERNAL
+		""
+	)
+
+	# Add target for generating html output for this target only.
+	file(MAKE_DIRECTORY ${LCOV_HTML_PATH}/${TNAME})
+	add_custom_target(${TNAME}-genhtml
+		COMMAND ${GENHTML_BIN} --quiet --sort ${GENHTML_CPPFILT_FLAG}
+                        --prefix ${PROJECT_SOURCE_DIR}
+			--baseline-file ${LCOV_DATA_PATH_INIT}/${TNAME}.info
+			--output-directory ${LCOV_HTML_PATH}/${TNAME}
+			--title "${CMAKE_PROJECT_NAME} - target ${TNAME}"
+			${OUTFILE}
+		DEPENDS ${TNAME}-geninfo ${TNAME}-capture-init
+	)
+endfunction (lcov_capture_tgt)
+
+
+# This function will generate the global info file for all targets. It has to be
+# called after all other CMake functions in the root CMakeLists.txt file, to get
+# a full list of all targets that generate coverage data.
+function (lcov_capture)
+	# Skip this function (and do not create the following targets), if there are
+	# no input files.
+	if ("${LCOV_CAPTURE_FILES}" STREQUAL "")
+		return()
+	endif ()
+
+	# Add a new target to merge the files of all targets.
+	set(OUTFILE "${LCOV_DATA_PATH_CAPTURE}/all_targets.info")
+	lcov_merge_files("${OUTFILE}" ${LCOV_CAPTURE_FILES})
+	add_custom_target(lcov-geninfo DEPENDS ${OUTFILE} lcov-capture)
+
+	# Add a new global target for all lcov targets. This target could be used to
+	# generate the lcov html output for the whole project instead of calling
+	# <TARGET>-geninfo and <TARGET>-genhtml for each target. It will also be
+	# used to generate a html site for all project data together instead of one
+	# for each target.
+	if (NOT TARGET lcov)
+		file(MAKE_DIRECTORY ${LCOV_HTML_PATH}/all_targets)
+		add_custom_target(lcov
+			COMMAND ${GENHTML_BIN} --quiet --sort ${GENHTML_CPPFILT_FLAG}
+				--baseline-file ${LCOV_DATA_PATH_INIT}/all_targets.info
+				--output-directory ${LCOV_HTML_PATH}/all_targets
+				--title "${CMAKE_PROJECT_NAME}" --prefix "${PROJECT_SOURCE_DIR}"
+				${OUTFILE}
+			DEPENDS lcov-geninfo-init lcov-geninfo
+		)
+	endif ()
+endfunction (lcov_capture)
+
+
+
+
+# Add a new global target to generate the lcov html report for the whole project
+# instead of calling <TARGET>-genhtml for each target (to create an own report
+# for each target). Instead of the lcov target it does not require geninfo for
+# all targets, so you have to call <TARGET>-geninfo to generate the info files
+# the targets you'd like to have in your report or lcov-geninfo for generating
+# info files for all targets before calling lcov-genhtml.
+file(MAKE_DIRECTORY ${LCOV_HTML_PATH}/selected_targets)
+if (NOT TARGET lcov-genhtml)
+	add_custom_target(lcov-genhtml
+		COMMAND ${GENHTML_BIN}
+			--quiet
+			--output-directory ${LCOV_HTML_PATH}/selected_targets
+			--title \"${CMAKE_PROJECT_NAME} - targets  `find
+				${LCOV_DATA_PATH_CAPTURE} -name \"*.info\" ! -name
+				\"all_targets.info\" -exec basename {} .info \\\;`\"
+			--prefix ${PROJECT_SOURCE_DIR}
+			--sort
+			${GENHTML_CPPFILT_FLAG}
+			`find ${LCOV_DATA_PATH_CAPTURE} -name \"*.info\" ! -name
+				\"all_targets.info\"`
+	)
+endif (NOT TARGET lcov-genhtml)

From d5b3fde5ca16815c663d26163c5fe9accdabdbcd Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Mon, 10 Nov 2025 20:28:33 +0800
Subject: [PATCH 88/92] Create FindGcov.cmake

---
 cmake/FindGcov.cmake | 160 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100644 cmake/FindGcov.cmake

diff --git a/cmake/FindGcov.cmake b/cmake/FindGcov.cmake
new file mode 100644
index 0000000000..a6ef6fd5c8
--- /dev/null
+++ b/cmake/FindGcov.cmake
@@ -0,0 +1,160 @@
+# This file is part of CMake-codecov.
+#
+# SPDX-FileCopyrightText: RWTH Aachen University, Federal Republic of Germany
+# SPDX-FileContributor: Alexander Haase, alexander.haase@rwth-aachen.de
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+# include required Modules
+include(FindPackageHandleStandardArgs)
+
+
+# Search for gcov binary.
+set(CMAKE_REQUIRED_QUIET_SAVE ${CMAKE_REQUIRED_QUIET})
+set(CMAKE_REQUIRED_QUIET ${codecov_FIND_QUIETLY})
+
+get_property(ENABLED_LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+foreach (LANG ${ENABLED_LANGUAGES})
+	# Gcov evaluation is dependent on the used compiler. Check gcov support for
+	# each compiler that is used. If gcov binary was already found for this
+	# compiler, do not try to find it again.
+	if (NOT GCOV_${CMAKE_${LANG}_COMPILER_ID}_BIN)
+		get_filename_component(COMPILER_PATH "${CMAKE_${LANG}_COMPILER}" PATH)
+
+		if ("${CMAKE_${LANG}_COMPILER_ID}" STREQUAL "GNU")
+			# Some distributions like OSX (homebrew) ship gcov with the compiler
+			# version appended as gcov-x. To find this binary we'll build the
+			# suggested binary name with the compiler version.
+			string(REGEX MATCH "^[0-9]+" GCC_VERSION
+				"${CMAKE_${LANG}_COMPILER_VERSION}")
+
+			find_program(GCOV_BIN NAMES gcov-${GCC_VERSION} gcov
+				HINTS ${COMPILER_PATH})
+
+		elseif ("${CMAKE_${LANG}_COMPILER_ID}" MATCHES "^(Apple)?Clang$")
+			# Some distributions like Debian ship llvm-cov with the compiler
+			# version appended as llvm-cov-x.y or just llvm-cov-x. To find this binary we'll build
+			# the suggested binary name with the compiler version.
+			string(REGEX MATCH "^[0-9]+\.[0-9]+" LLVM_FULL_VERSION
+				"${CMAKE_${LANG}_COMPILER_VERSION}")
+			string(REGEX MATCH "^[0-9]+" LLVM_MAJOR_VERSION
+				"${CMAKE_${LANG}_COMPILER_VERSION}")
+
+			# llvm-cov prior version 3.5 seems to be not working with coverage
+			# evaluation tools, but these versions are compatible with the gcc
+			# gcov tool.
+			if(LLVM_FULL_VERSION VERSION_GREATER 3.4)
+				find_program(LLVM_COV_BIN NAMES "llvm-cov-${LLVM_FULL_VERSION}" "llvm-cov-${LLVM_MAJOR_VERSION}"
+					"llvm-cov" HINTS ${COMPILER_PATH})
+				mark_as_advanced(LLVM_COV_BIN)
+
+				if (LLVM_COV_BIN)
+					find_program(LLVM_COV_WRAPPER "llvm-cov-wrapper" PATHS
+						${CMAKE_MODULE_PATH})
+					if (LLVM_COV_WRAPPER)
+						set(GCOV_BIN "${LLVM_COV_WRAPPER}" CACHE FILEPATH "")
+
+						# set additional parameters
+						set(GCOV_${CMAKE_${LANG}_COMPILER_ID}_ENV
+							"LLVM_COV_BIN=${LLVM_COV_BIN}" CACHE STRING
+							"Environment variables for llvm-cov-wrapper.")
+						mark_as_advanced(GCOV_${CMAKE_${LANG}_COMPILER_ID}_ENV)
+					endif ()
+				endif ()
+			endif ()
+
+			if (NOT GCOV_BIN)
+				# Fall back to gcov binary if llvm-cov was not found or is
+				# incompatible. This is the default on OSX, but may crash on
+				# recent Linux versions.
+				find_program(GCOV_BIN gcov HINTS ${COMPILER_PATH})
+			endif ()
+		endif ()
+
+
+		if (GCOV_BIN)
+			set(GCOV_${CMAKE_${LANG}_COMPILER_ID}_BIN "${GCOV_BIN}" CACHE STRING
+				"${LANG} gcov binary.")
+
+			if (NOT CMAKE_REQUIRED_QUIET)
+				message("-- Found gcov evaluation for "
+				"${CMAKE_${LANG}_COMPILER_ID}: ${GCOV_BIN}")
+			endif()
+
+			unset(GCOV_BIN CACHE)
+		endif ()
+	endif ()
+endforeach ()
+
+
+
+
+# Add a new global target for all gcov targets. This target could be used to
+# generate the gcov files for the whole project instead of calling <TARGET>-gcov
+# for each target.
+if (NOT TARGET gcov)
+	add_custom_target(gcov)
+endif (NOT TARGET gcov)
+
+
+
+# This function will add gcov evaluation for target <TNAME>. Only sources of
+# this target will be evaluated and no dependencies will be added. It will call
+# Gcov on any source file of <TNAME> once and store the gcov file in the same
+# directory.
+function (add_gcov_target TNAME)
+	get_target_property(TBIN_DIR ${TNAME} BINARY_DIR)
+	set(TDIR ${TBIN_DIR}/CMakeFiles/${TNAME}.dir)
+
+	# We don't have to check, if the target has support for coverage, thus this
+	# will be checked by add_coverage_target in Findcoverage.cmake. Instead we
+	# have to determine which gcov binary to use.
+	get_target_property(TSOURCES ${TNAME} SOURCES)
+	set(SOURCES "")
+	set(TCOMPILER "")
+	foreach (FILE ${TSOURCES})
+		codecov_path_of_source(${FILE} FILE)
+		if (NOT "${FILE}" STREQUAL "")
+			codecov_lang_of_source(${FILE} LANG)
+			if (NOT "${LANG}" STREQUAL "")
+				list(APPEND SOURCES "${FILE}")
+				set(TCOMPILER ${CMAKE_${LANG}_COMPILER_ID})
+			endif ()
+		endif ()
+	endforeach ()
+
+	# If no gcov binary was found, coverage data can't be evaluated.
+	if (NOT GCOV_${TCOMPILER}_BIN)
+		message(WARNING "No coverage evaluation binary found for ${TCOMPILER}.")
+		return()
+	endif ()
+
+	set(GCOV_BIN "${GCOV_${TCOMPILER}_BIN}")
+	set(GCOV_ENV "${GCOV_${TCOMPILER}_ENV}")
+
+
+	set(BUFFER "")
+	set(NULL_DEVICE "/dev/null")
+	if(WIN32)
+		set(NULL_DEVICE "NUL")
+	endif()
+	foreach(FILE ${SOURCES})
+		get_filename_component(FILE_PATH "${TDIR}/${FILE}" PATH)
+
+		# call gcov
+		add_custom_command(OUTPUT ${TDIR}/${FILE}.gcov
+			COMMAND ${GCOV_ENV} ${GCOV_BIN} -p ${TDIR}/${FILE}.gcno > ${NULL_DEVICE}
+			DEPENDS ${TNAME} ${TDIR}/${FILE}.gcno
+			WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+		)
+
+		list(APPEND BUFFER ${TDIR}/${FILE}.gcov)
+	endforeach()
+
+
+	# add target for gcov evaluation of <TNAME>
+	add_custom_target(${TNAME}-gcov DEPENDS ${BUFFER})
+
+	# add evaluation target to the global gcov target.
+	add_dependencies(gcov ${TNAME}-gcov)
+endfunction (add_gcov_target)

From 9f484f0f69323a0a2caffe3d996340ca515dc7d7 Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 11 Nov 2025 16:04:48 +0800
Subject: [PATCH 89/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 91 +++++++++++++++++++++++++++++-----
 1 file changed, 78 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 6dbde0025c..e0d791e1cb 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -1,7 +1,7 @@
 name: Coverage Analysis
 
 on:
-  pull_request: # 当有 PR 指向 develop 分支时触发
+  pull_request:
     branches:
       - develop
   workflow_dispatch:
@@ -16,31 +16,96 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v5
+        with:
+          submodules: recursive
+      
       - 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
+          apt update && apt install -y curl jq ca-certificates python3-pip
+          wget https://github.com/linux-test-project/lcov/releases/download/v2.0/lcov-2.0.tar.gz
+          tar xzf lcov-2.0.tar.gz
+          cd lcov-2.0
+          make install
+          cd ..
+          lcov --version
+          pip3 install gcovr
+      
+      - name: Building with Coverage
         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
+          # 确保构建目录权限
+          mkdir -p build
+          chmod -R 755 build/
+          # 使用明确的覆盖率标志
+          cmake -B build \
+            -DENABLE_COVERAGE=ON \
+            -DBUILD_TESTING=ON \
+            -DENABLE_MLALGO=ON \
+            -DENABLE_LIBXC=ON \
+            -DENABLE_LIBRI=ON \
+            -DENABLE_GOOGLEBENCH=ON \
+            -DENABLE_RAPIDJSON=ON \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage" \
+            -DCMAKE_EXE_LINKER_FLAGS="--coverage"
+          cmake --build build -j`nproc` || echo "Some tests failed but continuing for coverage"
+          cmake --install build || echo "Some tests failed but continuing for coverage"
+      
       - name: Testing
         env:
           OMP_NUM_THREADS: 1
         run: |
-          cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
-      - name: Generate Coverage Report
+          # 运行测试前确保权限
+          chmod -R 755 build/
+          cmake --build build --target test ARGS="-V --timeout 21600" || echo "Some tests failed but continuing for coverage"
+      
+      - name: Generate Coverage Data
         run: |
-          cmake --build build --target coverage
+          cd build
+          # 检查 .gcno 和 .gcda 文件是否存在
+          echo "Checking for coverage files:"
+          find . -name "*.gcno" | head -10
+          find . -name "*.gcda" | head -10
+          
+          # 方法1: 使用更新后的 lcov
+          echo "Generating coverage with lcov..."
+          lcov --directory . --capture --output-file coverage.info || echo "lcov failed, will try gcovr"
+          
+          # 过滤覆盖率数据
+          lcov --remove coverage.info '/usr/*' '*/test/*' '*/external/*' '*/build/*' --output-file coverage.filtered.info || echo "lcov filtering failed"
+          
+          # 生成HTML报告用于检查
+          genhtml coverage.filtered.info --output-directory coverage-report || echo "genhtml failed"
+          
+          # # 方法2: 使用 gcovr 作为备用
+          # echo "Generating coverage with gcovr..."
+          # gcovr -r .. --html --html-details -o coverage-gcovr.html --print-summary || echo "gcovr failed"
+          
+          # # 同时生成 gcovr 的 XML 格式，Codecov 更喜欢这种格式
+          # gcovr -r .. --xml -o coverage.xml || echo "gcovr xml failed"
+          
+          cd ..
+      
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v5
         if: ${{ ! cancelled() }}
         with:
-          fail_ci_if_error: true
+          fail_ci_if_error: false  # 设置为 false 避免因覆盖率收集失败而整个 CI 失败
           token: ${{ secrets.CODECOV_TOKEN }}
-          skip_validation: true
+          files: ./build/coverage.xml,./build/coverage.info  # 提供多个文件选项
+          directory: ./build/
+          flags: unittests
+          name: codecov-umbrella
           verbose: true
+      
+      - name: Upload Coverage Report Artifact
+        uses: actions/upload-artifact@v4
+        if: always()  # 即使前面的步骤失败也上传，便于调试
+        with:
+          name: coverage-report
+          path: |
+            build/coverage-report/
+            build/coverage.info
+            build/coverage.xml
+          retention-days: 30
\ No newline at end of file

From 138a17ea5ab20e4907031ebe38d750885cbe104c Mon Sep 17 00:00:00 2001
From: sunliang98 <1700011430@pku.edu.cn>
Date: Tue, 11 Nov 2025 16:08:22 +0800
Subject: [PATCH 90/92] Update coverage.yml

---
 .github/workflows/coverage.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index e0d791e1cb..f57bb892ae 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -19,15 +19,16 @@ jobs:
         with:
           submodules: recursive
       
-      - name: Install Requirements for Coverage Testing
+      - name: Install Perl Dependencies and Coverage Tools
         run: |
           apt update && apt install -y curl jq ca-certificates python3-pip
-          wget https://github.com/linux-test-project/lcov/releases/download/v2.0/lcov-2.0.tar.gz
-          tar xzf lcov-2.0.tar.gz
-          cd lcov-2.0
-          make install
-          cd ..
+          # 首先安装系统版本的 lcov 和 Perl 依赖
+          apt install -y lcov perl-modules
+          # 安装必要的 Perl 模块
+          apt install -y libcapture-tiny-perl libdatetime-perl libjson-perl libperlio-gzip-perl
+          # 验证系统 lcov 是否工作
           lcov --version
+          # 同时安装 gcovr 作为备用方案
           pip3 install gcovr
       
       - name: Building with Coverage

From f0b9b2ce18236ab47b6de0c94360dc9ad0d6b5a5 Mon Sep 17 00:00:00 2001
From: Liang Sun <50293369+sunliang98@users.noreply.github.com>
Date: Tue, 18 Nov 2025 16:12:53 +0800
Subject: [PATCH 91/92] Update
 source_lcao/module_operator_lcao/test/CMakeLists.txt

---
 .../source_lcao/module_operator_lcao/test/CMakeLists.txt  | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/source/source_lcao/module_operator_lcao/test/CMakeLists.txt b/source/source_lcao/module_operator_lcao/test/CMakeLists.txt
index e39a3dac19..7d48538c5c 100644
--- a/source/source_lcao/module_operator_lcao/test/CMakeLists.txt
+++ b/source/source_lcao/module_operator_lcao/test/CMakeLists.txt
@@ -9,8 +9,8 @@ AddTest(
   ../../../source_basis/module_ao/parallel_orbitals.cpp 
   ../../../source_basis/module_ao/ORB_atomic_lm.cpp
   tmp_mocks.cpp ../../../source_hamilt/operator.cpp
-  ../../../source_lcao/module_rt/td_info.cpp
-  ../../../source_lcao/module_rt/td_folding.cpp
+  ../../module_rt/td_info.cpp
+  ../../module_rt/td_folding.cpp
   ../../../source_estate/module_pot/H_TDDFT_pw.cpp
 )
 
@@ -22,8 +22,8 @@ AddTest(
   ../../../source_basis/module_ao/parallel_orbitals.cpp 
   ../../../source_basis/module_ao/ORB_atomic_lm.cpp
   tmp_mocks.cpp ../../../source_hamilt/operator.cpp
-  ../../../source_lcao/module_rt/td_info.cpp
-  ../../../source_lcao/module_rt/td_folding.cpp
+  ../../module_rt/td_info.cpp
+  ../../module_rt/td_folding.cpp
   ../../../source_estate/module_pot/H_TDDFT_pw.cpp
 )
 

From 353ffe70b061c0ba448b90894ef923d3da099529 Mon Sep 17 00:00:00 2001
From: Liang Sun <50293369+sunliang98@users.noreply.github.com>
Date: Tue, 18 Nov 2025 16:13:51 +0800
Subject: [PATCH 92/92] Fix path for print_cell.cpp in CMakeLists.txt

---
 source/source_cell/test_pw/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/source_cell/test_pw/CMakeLists.txt b/source/source_cell/test_pw/CMakeLists.txt
index 68818a25ca..48893a14ae 100644
--- a/source/source_cell/test_pw/CMakeLists.txt
+++ b/source/source_cell/test_pw/CMakeLists.txt
@@ -15,7 +15,7 @@ AddTest(
   ../read_stru.cpp   ../read_atom_species.cpp
 	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/output.cpp
   ../../source_estate/read_pseudo.cpp ../../source_estate/cal_nelec_nband.cpp
-  ../../source_estate/read_orb.cpp    ../../source_cell/print_cell.cpp
+  ../../source_estate/read_orb.cpp    ../print_cell.cpp
   ../../source_estate/cal_wfc.cpp  ../sep.cpp   ../sep_cell.cpp
 )