[gmx-users] GPU low performance

[Barnett, James W]

What's your exact command?

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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