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

Mark Abraham mark.j.abraham at gmail.com
Mon May 11 12:05:08 CEST 2015


You should check out the other recent discussion in this list on
performance variation. Getting your GROMACS nodes allocated close together
is an important part of mitigating such problems.

Rather than manually splitting your job into small pieces, you can have
mdrun do that automatically for you. Make the initial .tpr do the full run
length that you plan, and have mdrun -maxh 24 stop the job just before the

You should also not be writing the .trr file at all unless you know exactly
why you will benefit from full-precision coordinates and/or velocities.


On Sat, May 9, 2015 at 8:41 AM Satyabrata Das <satyabratad04 at gmail.com>

> Thank you Justin, indeed wallclock limit is there, there are
> heterogeneity on performance (40 ns to 120 ns for 24:00:00)
> also and to avoid the very large trr file we do follow the smaller bin.
> One need to submit few time same job.
> Regarding heterogeneity: in order to balance PP:PME load imbalance
>  I do use -npme to allocate required no. of cpus for PME. For
> different run with similar load imbalance (~ <4%) overall performance
> vary. Any suggestions?
> With best regards,
> Satyabrata Das
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