[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:

http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

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

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