[gmx-users] Regarding parallel run in Gromacs 5.0

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Fri Dec 5 08:21:41 CET 2014

​​Dear All

I have upgraded my Gromacs v4.5.5 to 5.0. I am unable to run parallel
minimization and simulation in cluster. Previously (v4.5.5) I was
simulating using the command “mdrun –v –s em.tpr –nt 30 &” and
thus assigning 30 CPU’s for the system. However, in the new version it is
not working, and giving the below mentioned errors.  The command as per the
Dr. Justin tutorial “gmx mdrun -v -deffnm em” is also not working for my
cluster installation, but running fine in my local computer. Kindly help me
how to run minimization using mdrun in parallel.

GROMACS: gmx mdrun, VERSION 5.0
Executable: Bikash/cmake/gro/gro5.0/bin/gmx
Library dir: Bikash/cmake/gro/gro5.0/share/gromacs/top
Command line:
gmx mdrun -nt 30 -deffnm em

Back Off! I just backed up em.log to ./#em.log.1#

Number of hardware threads detected (288) does not match the number
reported by OpenMP (276).
Consider setting the launch configuration manually!
Reading file em.tpr, VERSION 5.0 (single precision)
The number of OpenMP threads was set by environment variable

Non-default thread affinity set, disabling internal thread affinity
Using 5 MPI threads
Segmentation fault

​Thanking you
In anticipation of your reply
Osaka, Japan​

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