[gmx-users] Running GROMACS in PBS

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Apr 2 17:58:36 CEST 2007


On Saturday, 31. March 2007 22:10, Triguero, Luciano O wrote:
> Hello Everyone,
> I have a small problem here and need your help. Let start telling that I
> had spend some time trying to solve the problem with the recommendations I
> found in the internet, however my problem persist.
> I am running gromacs in a cluster and want to use one single machine with 4
> nodes. When I submit mpimdrun directly to one of the node as (mpimdrun -np
> 4 -s filename.tpr -N 4) the program runs without problems. However, when I
> do the same command inside a script and sibmit it to the PBS system. I mean
> (qsub -q long run.job), mpimdrun doesn't work. Is there anybody in the list
> who has experienced a similar problem and know how to solve it.
> Thank in advance,

try to submit an interactive job.

qsub -N gmx_test -l nodes=2:ppn=2 -I

than try after submitting to start gromacs interactivly

mpirun -np 4 mdrun -v 

(depends on your installation)

> Luciano
> Dr. Luciano Triguero College of Art and Science Department of Physics and
> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118
> Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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