[gmx-users] Running GROMACS in PBS

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 31 22:15:58 CEST 2007

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,
> 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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#PBS -l nodes=1:ppn=4

mpirun -c 4 mdrun

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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