[gmx-users] GPU low performance

[Carmen Di Giovanni]

Dear James, this is the command:
gmx_mpi mdrun -s prod_30ns.tpr  -deffnm prod_30ns -gpu_id 0
where gpu_id = 0 is INVIDIA Tesla K20


-- 
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 "Barnett, James W" <jbarnet4 at tulane.edu>:

> 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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