[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

[Justin Lemkul]

On 2/24/15 8:09 AM, Harry Mark Greenblatt wrote:
> BS"D
>
> Dear David,
>
>
> Hey Harry,
>
> Thanks for the caveat. Carsten Kutzner posted these results a few days ago.
> This is what he said :
>
> I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test
> system using a 2 fs time step I get
> 24 ns/d on 64 AMD   cores 6272
> 16 ns/d on 32 AMD   cores 6380
> 36 ns/d on 32 AMD   cores 6380   with 1x GTX 980
> 40 ns/d on 32 AMD   cores 6380   with 2x GTX 980
> 27 ns/d on 20 Intel cores 2680v2
> 52 ns/d on 20 Intel cores 2680v2 with 1x GTX 980
> 62 ns/d on 20 Intel cores 2680v2 with 2x GTX 980
>
>
> I think 20 Intel cores means 2 x 10 cores each.
>
> Yes, the 2680v2 is a 10 core processor.  The "interference" I mentioned is not apparent across sockets, only within.
>
>
>
>
> But Szilard just mentioned in this same thread :
>
> If you can afford them get the 14/16 or 18 core v3 Haswells, those are
> *really* fast, but a pair can cost as much as a decent car.
>
>
>
> Perhaps he has seen some real results that do not show issues at 16 or 18 cores/socket, in which case they would be advantageous, if one can afford them.  I am only going on what the manager of our cluster mentioned to me in his tests.  But his tests were based on many different software packages, so perhaps Gromacs is less/not affected.
>

When running multiple jobs simultaneously on multi-core nodes, was pinning done 
properly so the jobs don't interfere with one another?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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