Neko v0.8.0编译报错：undefined reference to MPI_Comm_f2c与ompi_mpi_byte

问题现象 #

执行make编译Neko v0.8.0时出现链接错误，报错信息如下：

comm/comm_wrapper.o: In function neko_comm_wrapper_init: 
/WORK/thuscc24team13_work/neko-0.8.0/src/comm/comm_wrapper.c:16:
undefined reference to MPI_Comm_f2c

gs/bcknd/device/device_mpi.o: In function device_mpi_isend:
/WORK/thuscc24team13_work/neko-0.8.0/src/gs/bcknd/device/device_mpi.c:66:
undefined reference to ompi_mpi_byte

gs/bcknd/device/device_mpi.o: In function device_mpi_irecv:
/WORK/thuscc24team13_work/neko-0.8.0/src/gs/bcknd/device/device_mpi.c:78:
undefined reference to ompi_mpi_byte

当前环境配置 #

已完成jsonfortran安装，导出相关环境变量，当前环境信息如下：

环境变量 #

$ echo $CC
mpiicc

$ echo $FC
mpiifort

$ echo $PKG_CONFIG_PATH
/home/thuscc24team13/WORK/json-fortran/main/lib64/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/vtune/2023.0.0/include/pkgconfig/lib64:
/apps/compilers/intel/oneapi/v2023.0.0.25537/vpl/2023.0.0/lib/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/tbb/2021.8.0/env/../lib/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/mpi/2021.8.0/lib/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/mkl/2023.0.0/lib/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/ippcp/2021.6.3/lib/pkgconfig:
/apps/compilers/intel/oneapi/v2023.0.0.25537/inspector/2023.0.0/include/pkgconfig/lib64:
/apps/compilers/intel/oneapi/v2023.0.0.25537/compiler/2023.0.0/lib/pkgconfig

已加载模块 #

$ module list
Currently Loaded Modulefiles:
1) compilers/intel/oneapi-2023/compiler/config    
2) compilers/intel/oneapi-2023/mkl/config    
3) compilers/intel/oneapi-2023/mpi/config   
4) tools/cmake/v3.25.2  
5) compilers/intel/oneapi-2023/config 
6) mpi/openmpi/v4.1.4 

解决步骤 #

这类链接错误源于MPI库链接不正确，或同时加载了不同MPI实现（Intel MPI与OpenMPI）导致冲突，按以下步骤处理：

1. 清理冲突MPI模块
   当前同时加载Intel oneAPI MPI和OpenMPI，先卸载OpenMPI模块：

   module unload mpi/openmpi/v4.1.4
   

2. 统一MPI环境变量
   确保编译工具链指向Intel MPI的编译器：

   export MPIFC=mpiifort
   export CC=mpiicc
   export FC=mpiifort
   

3. 重新配置编译环境
   进入Neko源码目录，清理旧编译文件后重新执行cmake配置：

   cd /WORK/thuscc24team13_work/neko-0.8.0
   make clean
   rm -rf CMakeCache.txt CMakeFiles/
   cmake . -DCMAKE_C_COMPILER=mpiicc -DCMAKE_Fortran_COMPILER=mpiifort -DJSONFORTRAN_DIR=/home/thuscc24team13/WORK/json-fortran/main
   

4. 重新编译
   执行多线程编译：

   make -j$(nproc)
   

额外排查方案 #

若上述步骤无效，检查pkg-config对MPI库的识别情况：

# 检查Intel MPI
pkg-config --libs intelmpi

若pkg-config无法正确识别，可手动在cmake时指定MPI库路径：

cmake . -DCMAKE_C_COMPILER=mpiicc -DCMAKE_Fortran_COMPILER=mpiifort -DMPI_C_LIBRARIES=/apps/compilers/intel/oneapi/v2023.0.0.25537/mpi/2021.8.0/lib/libmpi.so -DMPI_Fortran_LIBRARIES=/apps/compilers/intel/oneapi/v2023.0.0.25537/mpi/2021.8.0/lib/libmpi_mpifh.so

内容的提问来源于stack exchange，提问作者Just-lose-it