分享：安装plumed+cp2k+gromacs时遇到的一些坑

Lzzaya

本人在安装plumed+cp2k+gromacs遇到了大量未知问题，特此记录并形成相关文档，帮助后续人员能顺利完成安装。
整体流程如http://bbs.keinsci.com/thread-21783-1-1.html本贴所示，但在实际安装过程中，任然存在不少的坑，让我挣扎了整整三天。相关完善的流程在附件中被展示，希望大家都可以顺利安装

Huschein

近段时间也正在打算自己手动尝试一边gromacs-cp2k的编译，如果可以的话，咱们可以加联系方式私聊

aw10279

想咨询一下，我按照你的这个流程，提前安装了所有相关软件，然后严格的做下来，最后在编译到100%的地方还是报错如下。看提示适合MPI有关，但我已经提前安装好了MPICH和OPENMPI，不知道还有什么问题。我是在WSL下安装的，请问楼主见没见过这个报错，该如何解决？谢谢！

[100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o
[100%] Built target gmx_objlib
[100%] Linking CXX executable ../../bin/gmx_d
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_stop':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.F:1166: undefined reference to `mpi_error_string_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_iallgatherv_iv_internal.constprop.0':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: undefined reference to `mpi_iallgatherv_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_iallgatherv_lv_internal.constprop.0':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: undefined reference to `mpi_iallgatherv_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_iallgatherv_dv_internal.constprop.0':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: undefined reference to `mpi_iallgatherv_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_iallgatherv_rv_internal.constprop.0':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: undefined reference to `mpi_iallgatherv_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_iallgatherv_zv_internal.constprop.0':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: undefined reference to `mpi_iallgatherv_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o):/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:2609: more undefined references to `mpi_iallgatherv_' follow
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_type_make_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3974: undefined reference to `mpi_get_address_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_read_at_all_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3942: undefined reference to `mpi_file_read_at_all_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_read_at_all_cv':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3917: undefined reference to `mpi_file_read_at_all_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_write_at_all_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3827: undefined reference to `mpi_file_write_at_all_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_write_at_all_cv':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3802: undefined reference to `mpi_file_write_at_all_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_write_at_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3770: undefined reference to `mpi_file_write_at_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_file_write_at_cv':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3745: undefined reference to `mpi_file_write_at_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_deallocate_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:4041: undefined reference to `mpi_free_mem_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_allocate_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:4007: undefined reference to `mpi_type_size_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `mp_alloc_mem_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3995: undefined reference to `mpi_alloc_mem_cptr_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_type_indexed_make_c':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3633: undefined reference to `mpi_type_indexed_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3618: undefined reference to `mpi_type_commit_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_rget_cv':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3575: undefined reference to `mpi_rget_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_win_create_cv':
/home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3503: undefined reference to `mpi_win_create_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/src/mpiwrap/message_passing.fypp:3505: undefined reference to `mpi_win_create_'
/usr/bin/ld: /home/fyy/soft/cp2k-2023.1/lib/local/psmp/libcp2k.a(message_passing.o): in function `__message_passing_MOD_mp_irecv_cm4':

cpp

aw10279 发表于 2023-7-20 19:28
想咨询一下，我按照你的这个流程，提前安装了所有相关软件，然后严格的做下来，最后在编译到100%的地方还是 ...

大概率是MPI库指定有问题

cpp

群主，您好，我成功编译安装了，并且gmx_mpi_d 能正常运行，但是gmx_mpi_d grompp -f em.mdp -p topol.top -c conf.gro -o nma-em.tpr 之后，并没有出现nma-em.inp文件，请问这是怎么回事呢？