[gmx-users] Running GROMACS on mini GPU cluster
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.
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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