[gmx-users] how to avoid multiple 'aprun' on batch job script?

Justin Lemkul jalemkul at vt.edu
Fri May 8 13:35:55 CEST 2015

On 5/8/15 1:31 AM, Satyabrata Das wrote:
> Dear All,
> Currently I am running simulation using Gromac-5.0.4 on Cray XC40.
> Its a protein in water system (100K), 300K, NPT ensemble, writing full
> precision output in every 2ps and compressed trajectory in 1ps.
> I have divided the run into 2ns bin, and the following command is used in
> a loop to run the job starting from 2ns:
> loop
> aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-$nt-to-$nt1.cpt -deffnm
> simu-$nt1-to-$nt2
> loop
> (aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-0-to-2.cpt -deffnm
> simu-2-to-4)
> ('tpr' files are generated by 'convert-tpr' program:
> gmx convert-tpr -s simu-0-to-2.tpr -o simu-2-to-4.tpr -extend 2000)
> Kindly suggest better way of doing this, if any.
> Since it is running on a loop, I need to invoke 'aprun' on every 2ns steps.
> Is it possible to run the loop by using 'aprun' only once?
> My admin is insisting to avoid multiple 'aprun' command on same job script.

Running in intervals of time like this does require a loop, but why is is 
necessary to run in 2-ns intervals?  If you're not running into wallclock 
limits, just run the whole interval you want.  It significantly cuts down on the 
complexity of your script and circumvents the issue entirely.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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