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

Satyabrata Das satyabratad04 at gmail.com
Fri May 8 07:31:50 CEST 2015

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:

aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-$nt-to-$nt1.cpt -deffnm
(aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-0-to-2.cpt -deffnm

('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.

Please help.

With best regards,

Satyabrata Das

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