求助：计算溶剂化自由能换机器报错

xjtu_zk

sobereva 发表于 2021-11-18 05:20
了解一下并行机制

社长，我昨天已经尝试了不同的-ntomp的值，发现在6的时候速度最快。我也尝试了修改-ntmpi的值，但是发现只有1的时候可以运行，修改成其他值均报下面的错误。
Data prefix:  /usr/local/gromacs
Working dir:  /home/rlxt/gmxtrain/DINW3
Command line:
  gmx mdrun -deffnm min-0 -ntmpi 32 -ntomp 2 -pin on


Back Off! I just backed up min-0.log to ./#min-0.log.4#
Reading file min-0.tpr, VERSION 2020.1 (single precision)

-------------------------------------------------------
Program:     gmx mdrun, version 2020.1
Source file: src/gromacs/domdec/domdec.cpp (line 2277)
MPI rank:    0 (out of 32)

Fatal error:
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 1.17491 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

xjtu_zk

喵星大佬 发表于 2021-11-17 20:40
你要改ntomp和ntmpi啊。两个相乘=物理核数的时候优化

比如有32个物理核，那你可以用2mpi*16omp，4mpi*8o ...

我尝试了修改ntmpi的值，但是发现只有1的时候可以运行，改成其他值都报下面的错误：
Data prefix:  /usr/local/gromacs
Working dir:  /home/rlxt/gmxtrain/DINW3
Command line:
  gmx mdrun -deffnm min-0 -ntmpi 32 -ntomp 2 -pin on


Back Off! I just backed up min-0.log to ./#min-0.log.4#
Reading file min-0.tpr, VERSION 2020.1 (single precision)

-------------------------------------------------------
Program:     gmx mdrun, version 2020.1
Source file: src/gromacs/domdec/domdec.cpp (line 2277)
MPI rank:    0 (out of 32)

Fatal error:
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 1.17491 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

前辈帮忙看看是怎么回事啊？

喵星大佬

你的体系太小了，本来就只能这样了

sobereva

xjtu_zk 发表于 2021-11-18 09:49
我尝试了修改ntmpi的值，但是发现只有1的时候可以运行，改成其他值都报下面的错误：
Data prefix:  /usr ...

体系太小的话，本来就没法域分解

xjtu_zk

sobereva 发表于 2021-11-19 05:16
体系太小的话，本来就没法域分解

好的 明白了 社长 谢谢！