[gmx-users] GPU low performance

[Justin Lemkul]

On 2/18/15 11:09 AM, Barnett, James W wrote:
> What's your exact command?
>

A full .log file would be even better; it would tell us everything we need to 
know :)

-Justin

> Have you reviewed this page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> James "Wes" Barnett
> Ph.D. Candidate
> Chemical and Biomolecular Engineering
>
> Tulane University
> Boggs Center for Energy and Biotechnology, Room 341-B
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Carmen Di Giovanni <cdigiova at unina.it>
> Sent: Wednesday, February 18, 2015 10:06 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] GPU low performance
>
> I post the message of a md run :
>
>
> Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677
> For optimal performance this ratio should be close to 1!
>
>
> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
>         performance loss, consider using a shorter cut-off and a finer PME grid.
>
> As can I solved this problem ?
> Thank you in advance
>
>
> --
> Carmen Di Giovanni, PhD
> Dept. of Pharmaceutical and Toxicological Chemistry
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigiova at unina.it
>
>
>
> Quoting Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 2/18/15 10:30 AM, Carmen Di Giovanni wrote:
>>> Daear all,
>>> I'm working on a machine with an INVIDIA Teska K20.
>>> After a minimization on a protein of 1925 atoms this is the mesage:
>>>
>>> Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
>>> For optimal performance this ratio should be close to 1!
>>>
>>
>> Minimization is a poor indicator of performance.  Do a real MD run.
>>
>>>
>>> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>>> performance loss.
>>>
>>> Core t (s) Wall t (s) (%)
>>> Time: 3289.010 205.891 1597.4
>>> (steps/hour)
>>> Performance: 8480.2
>>> Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
>>>
>>>
>>> Cai I improve the performance?
>>> At the moment in the forum I didn't full informations to solve this problem.
>>> In attachment there is the log. file
>>>
>>
>> The list does not accept attachments.  If you wish to share a file,
>> upload it to a file-sharing service and provide a URL.  The full
>> .log is quite important for understanding your hardware,
>> optimizations, and seeing full details of the performance breakdown.
>>   But again, base your assessment on MD, not EM.
>>
>> -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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-- 
==================================================

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

==================================================