[gmx-users] Why does "system is not well equilibrated" error come out when using multiple GPUs but not one GPUs?

孙业平 sunyeping at aliyun.com
Mon Sep 9 06:13:54 CEST 2019

Dear everyone, 

I am trying to run a MD simulation with gromacs-2019.3 on a workstation with multiple GPUs. When I run the simulation with only one GPU by the command:

      mpirun_mpi -np 1 gmx_mpi mdrun -ntomp 6 -gpu_id 0 -v -deffnm md

it can run normally. However, when I try to run the simulation with multiple GPUs by the command:
     gmx_mpi mdrun -v -deffnm md

It gives out the follow error information:

Fatal error:
atal error:
120 particles communicated to PME rank 4 are more than 2/3 times the cut-off

out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I am very confused that why the simulation can run with one GPU but cannot run with multiple GPUs. The error information seem to tell that the system is not been well equilibrated, but if it is really related to equilibration, why it also related to the number of GPUs? 

Could you tell me what causes the problem and how to solve it?

Best regard.
Yeping Sun


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