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: cdigi...@unina.it
Quoting "Barnett, James W" <jbarn...@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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
Carmen Di Giovanni <cdigi...@unina.it>
Sent: Wednesday, February 18, 2015 10:06 AM
To: gromacs.org_gmx-users@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: cdigi...@unina.it
Quoting Justin Lemkul <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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