[gmx-users] Running GROMACS on mini GPU cluster

Justin Lemkul jalemkul at vt.edu
Fri Jul 26 03:20:34 CEST 2013

On 7/25/13 6:09 PM, Tim Moore wrote:
> I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying to bench mark some systems, and I am getting this message:
> NOTE: The number of threads is not equal to the number of (logical) cores
>        and the -pin option is set to auto: will not pin thread to cores.
>        This can lead to significant performance degradation.
>        Consider using -pin on (and -pinoffset in case you run multiple jobs).
> Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set -nt 2. But since we have a queuing system, there is no way to know which cores will be available to set -pinoffset. Does anyone have a solution, or should I even be worrying about that at all?

You're probably not invoking mdrun correctly for your configuration.  The wiki 
page has some useful examples:




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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