molclus调用orca进行优化计算时出现mpiexec -V；Segmentation fault (core dumped)

zikuzi · 发表于 Post on 2023-12-27 12:31:00

centos7系统下，采用社长的molclus调用orca进行优化计算时，出现错误，输出文件orca00001.out 最后是

orca.out (307.75 KB, 下载次数 Times of downloads: 0)

SHARK setup successfully completed in  71.6 seconds

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

SHARK setup successfully completed in  71.8 seconds

SHARK setup successfully completed in  71.8 seconds

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

SHARK setup successfully completed in  71.9 seconds

SHARK setup successfully completed in  72.0 seconds
done (  6.0 sec)
Calculating Nuclear repulsion             ... done (  0.0 sec) ENN=  53770.058246775217 Eh
done (  9.0 sec)
Calculating Nuclear repulsion             ... done (  0.0 sec) ENN=  53770.058246775217 Eh

SHARK setup successfully completed in  72.3 seconds

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

SHARK setup successfully completed in  72.3 seconds

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

Maximum memory used throughout the entire GTOINT-calculation: 1183.6 MB

ORCA finished by error termination in GTOInt
Calling Command: mpirun -np 36  /home/wl/orca/orca_gtoint_mpi orca.int.tmp orca
[file orca_tools/qcmsg.cpp, line 465]:
  .... aborting the run

第二个结构计算中开始出错，手动关闭后产生 orca.out文件

输入模板是
! r2SCAN-3c opt miniprint nopop noautostart
%maxcore 3000
%pal nprocs 36 end
* xyz 0 1
[GEOMETRY]
*

结构中含有C H O N S F 元素

出错后检查gcc gfortran 均正常，  mpiexec -V  显示 Segmentation fault (core dumped)
重启系统，重新安装 openmpi ，未能解决

orca模板和输出文件附上

orca00001.out (292.84 KB, 下载次数 Times of downloads: 2)

template.inp (107 Bytes, 下载次数 Times of downloads: 2)

sobereva · 发表于 Post on 2023-12-28 10:59:05

同样的信息重复输出多遍，通常是MPI并行不正常所致
用molclus调用ORCA之前先确保自己能手动正常并行运行ORCA
不正常的情况往往是当前机子里的MPI库和ORCA不兼容

zikuzi · 发表于 Post on 2023-12-28 11:30:21

本帖最后由 zikuzi 于 2023-12-28 11:33 编辑

sobereva 发表于 2023-12-28 10:59
同样的信息重复输出多遍，通常是MPI并行不正常所致
用molclus调用ORCA之前先确保自己能手动正常并行运行OR ...

非常感谢社长的回复，用的是ORCA5.0.4，openmpi 也是对应的 411，之前是可以正常使用的。
前两天按照您的教程在同个用户下安装了gromacs2018（非跨节点mpi版本），是不是因为这个原因导致的？
如果想要正常使用ORCA，是要卸载gmx么？还是有其他的解决方法？
麻烦社长多多指点

sobereva · 发表于 Post on 2023-12-29 04:35:04

zikuzi 发表于 2023-12-28 11:30
非常感谢社长的回复，用的是ORCA5.0.4，openmpi 也是对应的 411，之前是可以正常使用的。
前两天按照您 ...

原理上不会和gromacs有什么关系，毕竟不牵扯MPI的变动

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[ORCA] molclus调用orca进行优化计算时出现mpiexec -V；Segmentation fault (core dumped)