[gmx-users] running MD on gpu (Fatal error)

[Andrew Bostick]

Dear Gromacs users,

I am running MD on gpu using following command line:

gmx_mpi mdrun -nb gpu -v -deffnm gpu_md

But, I encountered with:

GROMACS version:    VERSION 5.1.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
"gpu_md.log" 319L, 14062C                                     1,1
Top
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
grpopts:
   nrdf:     16999.9      999171
   ref-t:         300         300
   tau-t:           1           1
annealing:          No          No
annealing-npoints:           0           0
   acc:            0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0 0 0 0
   energygrp-flags[  1]: 0 0 0 0
   energygrp-flags[  2]: 0 0 0 0
   energygrp-flags[  3]: 0 0 0 0

Using 1 MPI process
Using 192 OpenMP threads


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.3
Source code file:
/root/gromacs_source/gromacs-5.1.3/src/programs/mdrun/resource-division.cpp,
line: 571

Fatal error:
Your choice of 1 MPI rank and the use of 192 total threads leads to the use
of 192 OpenMP threads, whereas we expect the optimum to be with more MPI
ranks with 1 to 6 OpenMP threads. If you want to run with this many OpenMP
threads, specify the -ntomp option. But we suggest to increase the number
of MPI ranks.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


What is the reason of this error?

How to fix it?

Best,
Andrew