[gmx-users] GPU acceleration

[Justin Lemkul]

On 6/27/16 8:49 AM, יוכבד wrote:
> Hi
> I've recently installed GROMACS 5.1.2.
> I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
> using 4GPUs and 32 CPU and I got the performances of ~330ns/day
>
> Now I'm tring to run my system but I don't see any acceleration (a 500ps
> nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs and
> 15 CPUs.
>
> What am I missing here?
>
> attached is my mdp file and the command used was

The list does not accept attachments.  The .log files are the most informative 
as the end contains a full performance breakdown; if you wish to share them, 
upload them to a file sharing service and provide a URL.

The actual performance depends largely on the content/size of the system. 
Perhaps you have a bottleneck due to the size of the system such that you cannot 
efficiently utilize all 4 GPU and 15 CPUs (an odd combination, anyway) 
simultaneously.

-Justin

-- 
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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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