求助：gromacs跑em时出错no domain decomposition for 12 ranks that is compatibl...

不明嚼栗子

老师好，我用packmol建了个溶液体系，盒子是边长为4.1nm的立方体，结果报错
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Program:     gmx mdrun, version 2019
Source file: src/gromacs/domdec/domdec.cpp (line 2403)
MPI rank:    0 (out of 12)

Fatal error:
There is no domain decomposition for 12 ranks that is compatible with the
given box and a minimum cell size of 1.42027 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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请问这是怎么回事啊？谢谢老师！

sobereva

加上-ntmpi 1

不明嚼栗子

sobereva 发表于 2020-11-19 05:15
加上-ntmpi 1

感谢老师回复！但是加上-ntmpi 1后还是报错
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Program:     gmx mdrun, version 2019
Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 689)
MPI rank:    0 (out of 12)

Fatal error:
Setting the number of thread-MPI ranks is only supported with thread-MPI and
GROMACS was compiled without thread-MPI

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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我用的是天河1号自带的gromacs/2019.1，直接加载的模块。。

sobereva

不明嚼栗子 发表于 2020-11-19 11:42
感谢老师回复！但是加上-ntmpi 1后还是报错
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mpirun的时候用-np x，尝试不同的x直到能跑

Daniel_Arndt

不明嚼栗子 发表于 2020-11-19 11:42
感谢老师回复！但是加上-ntmpi 1后还是报错
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你可以找找客服。我在学校的超算中心遇到过类似情形，我问了一下当初编译gromacs这个模块的工作人员，他们直接告诉我一个合适的数字。