Enable compatibility of GNU compilers + MKL (#7139)

* Enable compatibility of GNU compilers + MKL

* Fix issue with OpenMPI

* Update toolchain/README.md

Author: Growl1234

CMakeLists.txt

@@ -322,7 +322,7 @@ if(DEBUG_INFO)
 endif()
 
 if(ENABLE_MPI)
-  find_package(MPI REQUIRED)
+  find_package(MPI COMPONENTS CXX REQUIRED)
   include_directories(${MPI_CXX_INCLUDE_PATH})
   target_link_libraries(${ABACUS_BIN_NAME} MPI::MPI_CXX)
   add_compile_definitions(__MPI)

cmake/FindMKL.cmake

@@ -9,39 +9,54 @@ if(NOT TARGET MKL::MKL)
 
 find_path(MKL_INCLUDE mkl_service.h HINTS ${MKLROOT}/include)
 
-find_library(MKL_INTEL NAMES mkl_intel_lp64 HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
-find_library(MKL_INTEL_THREAD NAMES mkl_intel_thread HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
 find_library(MKL_CORE NAMES mkl_core HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
-find_library(MKL_IOMP5 NAMES iomp5
-  HINTS ENV CMPLR_ROOT
-  PATH_SUFFIXES lib lib/intel64 linux/compiler/lib/intel64_lin
-)
+if(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+  find_library(MKL_INTERFACE_LIB NAMES mkl_intel_lp64 HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  find_library(MKL_THREAD NAMES mkl_intel_thread HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  find_library(MKL_IOMP5 NAMES iomp5
+    HINTS ENV CMPLR_ROOT
+    PATH_SUFFIXES lib lib/intel64 linux/compiler/lib/intel64_lin
+  )
+else()
+  find_library(MKL_INTERFACE_LIB NAMES mkl_gf_lp64 HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  find_library(MKL_THREAD NAMES mkl_gnu_thread HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  # With GCC we use system-installed GNU OpenMP
+endif()
+
 if(ENABLE_MPI)
+  execute_process(COMMAND ${MPI_CXX_COMPILER} --showme:version
+                  OUTPUT_VARIABLE MPI_VER_OUT
+                  ERROR_VARIABLE MPI_VER_ERR)
+  if(MPI_VER_OUT MATCHES "Open MPI" OR MPI_VER_ERR MATCHES "Open MPI")
+    set(MKL_BLACS_LIB_NAME "mkl_blacs_openmpi_lp64")
+  else()
+    set(MKL_BLACS_LIB_NAME "mkl_blacs_intelmpi_lp64")
+  endif()
   find_library(MKL_SCALAPACK NAMES mkl_scalapack_lp64 HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
-  find_library(MKL_BLACS_INTELMPI NAMES mkl_blacs_intelmpi_lp64 HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
+  find_library(MKL_BLACS NAMES ${MKL_BLACS_LIB_NAME} HINTS ${MKLROOT}/lib ${MKLROOT}/lib/intel64)
 endif()
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
 # if all listed variables are TRUE
 
 if(ENABLE_MPI)
-  find_package_handle_standard_args(MKL DEFAULT_MSG MKL_INTEL MKL_INTEL_THREAD MKL_CORE MKL_SCALAPACK MKL_BLACS_INTELMPI MKL_INCLUDE)
+  find_package_handle_standard_args(MKL DEFAULT_MSG MKL_INTERFACE_LIB MKL_THREAD MKL_CORE MKL_SCALAPACK MKL_BLACS MKL_INCLUDE)
 else()
-  find_package_handle_standard_args(MKL MKL_INTEL MKL_INTEL_THREAD MKL_CORE MKL_INCLUDE)
+  find_package_handle_standard_args(MKL MKL_INTERFACE_LIB MKL_THREAD MKL_CORE MKL_INCLUDE)
 endif()
 
 if(MKL_FOUND)
-  if(NOT TARGET MKL::INTEL)
-    add_library(MKL::INTEL UNKNOWN IMPORTED)
-    set_target_properties(MKL::INTEL PROPERTIES
-      IMPORTED_LOCATION "${MKL_INTEL}"
+  if(NOT TARGET MKL::INTERFACE_LIB)
+    add_library(MKL::INTERFACE_LIB UNKNOWN IMPORTED)
+    set_target_properties(MKL::INTERFACE_LIB PROPERTIES
+      IMPORTED_LOCATION "${MKL_INTERFACE_LIB}"
       INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE}")
   endif()
-  if(NOT TARGET MKL::INTEL_THREAD)
-    add_library(MKL::INTEL_THREAD UNKNOWN IMPORTED)
-    set_target_properties(MKL::INTEL_THREAD PROPERTIES
-      IMPORTED_LOCATION "${MKL_INTEL_THREAD}"
+  if(NOT TARGET MKL::THREAD)
+    add_library(MKL::THREAD UNKNOWN IMPORTED)
+    set_target_properties(MKL::THREAD PROPERTIES
+      IMPORTED_LOCATION "${MKL_THREAD}"
       INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE}")
   endif()
   if(NOT TARGET MKL::CORE)
@@ -56,10 +71,10 @@ if(MKL_FOUND)
       IMPORTED_LOCATION "${MKL_SCALAPACK}"
       INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE}")
   endif()
-  if(NOT TARGET MKL::BLACS_INTELMPI)
-    add_library(MKL::BLACS_INTELMPI UNKNOWN IMPORTED)
-    set_target_properties(MKL::BLACS_INTELMPI PROPERTIES
-      IMPORTED_LOCATION "${MKL_BLACS_INTELMPI}"
+  if(ENABLE_MPI AND NOT TARGET MKL::BLACS)
+    add_library(MKL::BLACS UNKNOWN IMPORTED)
+    set_target_properties(MKL::BLACS PROPERTIES
+      IMPORTED_LOCATION "${MKL_BLACS}"
       INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE}")
   endif()
   if(MKL_IOMP5 AND NOT TARGET MKL::IOMP5)
@@ -72,14 +87,14 @@ if(MKL_FOUND)
     set_property(TARGET MKL::MKL PROPERTY
     INTERFACE_LINK_LIBRARIES
     "-Wl,--start-group"
-    MKL::INTEL MKL::INTEL_THREAD MKL::CORE MKL::MKL_SCALAPACK MKL::BLACS_INTELMPI
+    MKL::INTERFACE_LIB MKL::THREAD MKL::CORE MKL::MKL_SCALAPACK MKL::BLACS
     "-Wl,--end-group"
     )
   else()
     set_property(TARGET MKL::MKL PROPERTY
     INTERFACE_LINK_LIBRARIES
     "-Wl,--start-group"
-    MKL::INTEL MKL::INTEL_THREAD MKL::CORE
+    MKL::INTERFACE_LIB MKL::THREAD MKL::CORE
     "-Wl,--end-group"
     )
   endif()
@@ -90,9 +105,9 @@ if(MKL_FOUND)
 endif()
 
 if(ENABLE_MPI)
-  mark_as_advanced(MKL_INCLUDE MKL_INTEL MKL_INTEL_THREAD MKL_CORE MKL_SCALAPACK MKL_BLACS_INTELMPI)
+  mark_as_advanced(MKL_INCLUDE MKL_INTERFACE_LIB MKL_THREAD MKL_CORE MKL_SCALAPACK MKL_BLACS)
 else()
-  mark_as_advanced(MKL_INCLUDE MKL_INTEL MKL_INTEL_THREAD MKL_CORE)
+  mark_as_advanced(MKL_INCLUDE MKL_INTERFACE_LIB MKL_THREAD MKL_CORE)
 endif()
 
 endif() # MKL::MKL

toolchain/README.md

@@ -57,8 +57,9 @@ For new users, start with one of these pre-configured toolchains:
 # GNU toolchain (GCC + OpenMPI + OpenBLAS)
 ./toolchain_gnu.sh
 
-# Intel toolchain (Intel compilers + Intel MPI + MKL)
-./toolchain_intel.sh
+# Intel toolchain
+./toolchain_gcc-mkl.sh # GCC + OpenMPI + MKL
+./toolchain_intel.sh # Intel compilers + Intel MPI + MKL
 
 # AMD toolchain options
 ./toolchain_gcc-aocl.sh    # GCC + AMD AOCL
@@ -342,10 +343,6 @@ Related discussion here [#4976](https://github.com/deepmodeling/abacus-develop/i
 
 Notice: `icc` and `icpc` from Intel Classic Compiler of Intel-oneAPI are not supported for 2024.0 and newer version. And Intel-OneAPI 2023.2.0 can be found in QE website. You need to download Base-toolkit for MKL and HPC-toolkit for MPi and compiler for Intel-OneAPI 2023.2.0, while in Intel-OneAPI 2024.x, only the HPC-toolkit is needed.
 
-#### Gcc-MKL Issues
-
-You cannot use gcc as compiler while using MKL as math library for compile ABACUS, there will be lots of error in the lask linking step. See [#3198](https://github.com/deepmodeling/abacus-develop/issues/3198)
-
 #### AMD AOCC-AOCL problem
 
 Use AOCC-AOCL to compile dependencies is permitted and usually get boosting in ABACUS efficiency. But you need to get rid of `flang` while compiling ELPA. Toolchain itself helps you make this `flang` shade in default of `aocc-aocl` toolchain, and you can manually use `flang` by setting `--with-flang=yes` in `toolchain_aocc-aocl.sh` to have a try, while toolchain helps you to bypass the possible errors in compiling ELPA with AOCC-AOCL, but the computing efficiency will be relatively lower compared to `gnu` or `gcc-aocl` toolchain. There are some issues related to the numeric instability of ABACUS compiled by AOCC-AOCL toolchain, see [#6420](https://github.com/deepmodeling/abacus-develop/issues/6420)

toolchain/build_abacus_gcc-mkl.sh

@@ -0,0 +1,79 @@
+#!/bin/bash -e
+#SBATCH -J build_abacus_aocl
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o install.log
+#SBATCH -e install.err
+
+# Build ABACUS by gcc-mkl toolchain
+
+# load system env modules at first
+# module load mkl compiler mpi
+# source path/to/setvars.sh
+
+ABACUS_DIR=..
+TOOL=$(pwd)
+INSTALL_DIR=$TOOL/install
+source $INSTALL_DIR/setup
+cd $ABACUS_DIR
+ABACUS_DIR=$(pwd)
+
+BUILD_DIR=build_abacus_gcc_mkl
+rm -rf $BUILD_DIR
+
+PREFIX=$ABACUS_DIR
+ELPA=$INSTALL_DIR/elpa-2025.06.001/cpu
+# ELPA=$INSTALL_DIR/elpa-2025.06.001/nvidia # for elpa-gpu
+CEREAL=$INSTALL_DIR/cereal-master/include/cereal
+LIBXC=$INSTALL_DIR/libxc-7.0.0
+RAPIDJSON=$INSTALL_DIR/rapidjson-master
+LIBRI=$INSTALL_DIR/LibRI-master
+LIBCOMM=$INSTALL_DIR/LibComm-master
+USE_CUDA=OFF  # set ON to enable gpu-abacus
+# NEP_DIR=$INSTALL_DIR/NEP_CPU-main
+# LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
+# LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd
+
+cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
+        -DCMAKE_CXX_COMPILER=g++ \
+        -DMPI_CXX_COMPILER=mpicxx \
+        -DMKLROOT=$MKLROOT \
+        -DELPA_DIR=$ELPA \
+        -DCEREAL_INCLUDE_DIR=$CEREAL \
+        -DLibxc_DIR=$LIBXC \
+        -DENABLE_LCAO=ON \
+        -DENABLE_LIBXC=ON \
+        -DUSE_OPENMP=ON \
+        -DUSE_ELPA=ON \
+        -DENABLE_RAPIDJSON=ON \
+        -DRapidJSON_DIR=$RAPIDJSON \
+        -DENABLE_LIBRI=ON \
+        -DLIBRI_DIR=$LIBRI \
+        -DLIBCOMM_DIR=$LIBCOMM \
+        -DUSE_CUDA=$USE_CUDA \
+#         -DCMAKE_CUDA_COMPILER=/path/to/cuda/bin/nvcc \
+#         -DNEP_DIR=$NEP_DIR \
+#         -DENABLE_MLALGO=1 \
+#         -DTorch_DIR=$LIBTORCH \
+#         -Dlibnpy_INCLUDE_DIR=$LIBNPY \
+# 	      -DDeePMD_DIR=$DEEPMD \
+#         -DENABLE_CUSOLVERMP=ON \
+
+cmake --build $BUILD_DIR -j `nproc`
+cmake --install $BUILD_DIR 2>/dev/null
+
+# generate abacus_env.sh
+cat << EOF > "${TOOL}/abacus_env.sh"
+#!/bin/bash
+source $INSTALL_DIR/setup
+export PATH="${PREFIX}/bin":\${PATH}
+EOF
+
+# generate information
+cat << EOF
+========================== usage =========================
+Done!
+To use the installed ABACUS version
+You need to source ${TOOL}/abacus_env.sh first !
+EOF

toolchain/install_abacus_toolchain_new.sh

@@ -201,6 +201,7 @@ EOF
     ui_print_color "${UI_GREEN}${UI_BOLD}" "🚀 Build ABACUS with your preferred toolchain:"
     ui_print_color "${UI_WHITE}" "   ./build_abacus_gnu.sh        # GNU toolchain (GCC + OpenBLAS)"
     ui_print_color "${UI_WHITE}" "   ./build_abacus_intel.sh      # Intel toolchain (ICC + MKL)"
+    ui_print_color "${UI_WHITE}" "   ./build_abacus_gcc-mkl.sh    # GCC + MKL"
     ui_print_color "${UI_WHITE}" "   ./build_abacus_gcc-aocl.sh   # AMD GCC + AOCL"
     ui_print_color "${UI_WHITE}" "   ./build_abacus_aocc-aocl.sh  # AMD AOCC + AOCL"
     echo ""
@@ -220,4 +221,4 @@ EOF
 }
 
 # Run main function with all arguments
-main "$@"
+main "$@"

toolchain/toolchain_gcc-mkl.sh

@@ -0,0 +1,114 @@
+#!/bin/bash
+#SBATCH -J install
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o compile.log
+#SBATCH -e compile.err
+
+# Users can easily modify these parameters to customize the build
+# Before running this script, ensure you have loaded your system packages
+
+# Compiler Configuration
+TOOLCHAIN_COMPILER="gcc-mkl"
+WITH_GCC="system"
+WITH_AMD="no"
+WITH_INTEL="no"
+
+# Math Libraries (Intel MKL recommended)
+MATH_MODE="mkl"
+WITH_MKL="system"
+
+# MPI Implementation (OpenMPI recommended)
+MPI_MODE="openmpi"
+WITH_OPENMPI="install"
+WITH_4TH_OPENMPI="no"  # Set to "yes" for OpenMPI v4, deprecated
+WITH_MPICH="no"
+
+# Core Dependencies
+WITH_CMAKE="install"
+WITH_SCALAPACK="system"  # MKL provides ScaLAPACK
+WITH_FFTW="system"       # MKL provides FFTW
+WITH_LIBXC="install"
+WITH_ELPA="install"
+
+# Utility Libraries
+WITH_CEREAL="install"
+WITH_RAPIDJSON="install"
+
+# Advanced Features (EXX calculations)
+WITH_LIBRI="install"
+WITH_LIBCOMM="install"
+
+# Optional Features (MLALGO support)
+WITH_LIBTORCH="no"
+WITH_LIBNPY="no"
+WITH_NEP="no"
+
+# ELPA-GPU Support (uncomment and modify as needed)
+# ENABLE_CUDA="yes"
+# GPU_VERSION="75"  # Check your GPU compute capability
+# export CUDA_PATH="/usr/local/cuda"
+
+# ============================================================================
+# Execution Mode Control
+# ============================================================================
+# Dry-run mode: Show what would be done without actually executing
+DRY_RUN_MODE="no"   # Set to "yes" to enable dry-run mode
+
+# Pack-run mode: Only check and install required packages
+PACK_RUN_MODE="no"  # Set to "yes" to enable pack-run mode
+
+# ============================================================================
+# Package Version Selection (main/alt versions)
+# ============================================================================
+# Choose between main (latest stable) and alt (alternative/legacy) versions
+# Refer to scripts/package_versions.sh for specific version numbers
+
+CMAKE_VERSION="main"        # main=3.31.7, alt=3.30.5
+OPENMPI_VERSION="main"      # main=5.0.8, alt=4.1.6
+ELPA_VERSION="main"         # main=2025.06.001, alt=2024.05.001
+LIBXC_VERSION="main"        # main=7.0.0, alt=6.2.2
+# Optional Libraries
+LIBTORCH_VERSION="main"     # main=2.1.2, alt=1.12.1 (use alt for older GLIBC)
+# Note: main(2.1.2) version of LibTorch need glibc > 2.27
+# Note: alt(1.12.1) version of LibTorch cannot support DeePMD-Torch for DPA
+
+# Note: GCC-MKL toolchain uses MKL for math libraries (FFTW, ScaLAPACK)
+# so OpenBLAS and ScaLAPACK version selections are not applicable
+
+# ============================================================================
+# Execute Installation (DO NOT MODIFY BELOW THIS LINE)
+# ============================================================================
+
+# Call the main installation script with configured parameters
+exec ./install_abacus_toolchain_new.sh \
+  --with-gcc="$WITH_GCC" \
+  --math-mode="$MATH_MODE" \
+  --mpi-mode="$MPI_MODE" \
+  --with-mkl="$WITH_MKL" \
+  --with-openmpi="$WITH_OPENMPI" \
+  --with-mpich="$WITH_MPICH" \
+  --with-cmake="$WITH_CMAKE" \
+  --with-scalapack="$WITH_SCALAPACK" \
+  --with-libxc="$WITH_LIBXC" \
+  --with-fftw="$WITH_FFTW" \
+  --with-elpa="$WITH_ELPA" \
+  --with-cereal="$WITH_CEREAL" \
+  --with-rapidjson="$WITH_RAPIDJSON" \
+  --with-libtorch="$WITH_LIBTORCH" \
+  --with-nep="$WITH_NEP" \
+  --with-libnpy="$WITH_LIBNPY" \
+  --with-libri="$WITH_LIBRI" \
+  --with-libcomm="$WITH_LIBCOMM" \
+  --with-4th-openmpi="$WITH_4TH_OPENMPI" \
+  --package-version cmake:"$CMAKE_VERSION" \
+  --package-version openmpi:"$OPENMPI_VERSION" \
+  --package-version elpa:"$ELPA_VERSION" \
+  --package-version libxc:"$LIBXC_VERSION" \
+  --package-version libtorch:"$LIBTORCH_VERSION" \
+  ${DRY_RUN_MODE:+$([ "$DRY_RUN_MODE" = "yes" ] && echo "--dry-run")} \
+  ${PACK_RUN_MODE:+$([ "$PACK_RUN_MODE" = "yes" ] && echo "--pack-run")} \
+  ${ENABLE_CUDA:+--enable-cuda} \
+  ${GPU_VERSION:+--gpu-ver="$GPU_VERSION"} \
+  "$@" \
+  | tee compile.log