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标题: 分享:安装plumed+cp2k+gromacs时遇到的一些坑 [打印本页]

作者
Author:
Lzzaya    时间: 2023-5-11 15:16
标题: 分享:安装plumed+cp2k+gromacs时遇到的一些坑
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

作者
Author:
Huschein    时间: 2023-5-11 22:08
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
作者
Author:
aw10279    时间: 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':



作者
Author:
cpp    时间: 2024-7-10 16:56
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
作者
Author:
cpp    时间: 2024-7-10 16:58
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?




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