[gmx-users] GPU acceleration

[יוכבד]

here's a link to the log file
https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing

The  computer is 4GPUs and 32 CPUs but some GPUs were in use hence only
15-16 were used.

Thanks

On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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