Ubuntu20.04编译Gromacs时libstdc++.so.6链接错误求助

问题背景 #

Ubuntu 20.04全新机器（仅使用8小时），CMake配置Gromacs成功，但执行make时出现libstdc++.so.6相关链接错误。

初始错误信息 #

/usr/bin/ld: CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o: undefined reference to symbol '_ZSt20__throw_length_errorPKc@@GLIBCXX_3.4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make:87: bin/methane-water-integration] Error 1
make[1]: *** [CMakeFiles/Makefile2:4790: api/nblib/samples/CMakeFiles/methane-water-integration.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

系统libstdc++.so.6状态 #

检查/usr/lib/x86_64-linux-gnu和/lib/x86_64-linux-gnu目录，结果如下：

lrwxrwxrwx  2 root root        19 Apr 28  2021 libstdc++.so.6 -> libstdc++.so.6.0.29
-rw-r--r--  1 root root   2186464 Apr 28  2021 libstdc++.so.6.0.29

更新1：make VERBOSE=1详细输出 #

[ 95%] Linking CXX executable ../../../bin/methane-water-integration
cd /home/anthony/Downloads/gromacs-2022.3/build/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1
/usr/bin/gcc  -O3 -DNDEBUG   -Wl,-rpath,/home/anthony/anaconda3/lib   CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o  -o ../../../bin/methane-water-integration  -Wl,-rpath,"\$ORIGIN/../lib" ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/gcc/x86_64-linux-gnu/9/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so -Wl,-rpath-link,/home/anthony/Downloads/gromacs-2022.3/build/lib 
/usr/bin/ld: CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o: undefined reference to symbol '_ZSt20__throw_length_errorPKc@@GLIBCXX_3.4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make:87: bin/methane-water-integration] Error 1
make[2]: Leaving directory '/home/anthony/Downloads/gromacs-2022.3/build'
make[1]: *** [CMakeFiles/Makefile2:4790: api/nblib/samples/CMakeFiles/methane-water-integration.dir/all] Error 2
make[1]: Leaving directory '/home/anthony/Downloads/gromacs-2022.3/build'
make: *** [Makefile:163: all] Error 2

更新2：CMake检测到的编译器信息 #

-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /home/anthony/anaconda3/bin/python3.9 (found suitable version "3.9.12", minimum required is "3.7") found components: Interpreter Development 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  

解决方案 #

从make VERBOSE=1输出可见，链接命令使用gcc而非g++，导致未自动链接libstdc++.so，可按以下步骤解决：

• 重新指定C++编译器配置CMake
  删除现有build目录内容，重新运行CMake时明确指定CXX编译器：

  rm -rf build/*
  cd build
  cmake -DCMAKE_CXX_COMPILER=/usr/bin/g++ ..
  make
  

• 临时修改样本项目的CMake配置
  在Gromacs源码的api/nblib/samples/CMakeLists.txt中，为目标添加stdc++链接依赖：

  target_link_libraries(methane-water-integration PRIVATE nblib_gmx stdc++)
  

  修改后重新执行make。

• 排除Anaconda环境干扰
  链接命令中出现Anaconda的rpath，可能导致编译器路径混淆，可在纯净环境下编译：

  conda deactivate
  # 重新执行cmake和make
  

• 修复系统libstdc++依赖（可选）
  若怀疑系统库损坏，可重装相关依赖：

  sudo apt install --reinstall libstdc++6 gcc-9 g++-9
  

内容的提问来源于stack exchange，提问作者Anthony Nash