[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

[Carlos Navarro Retamal]

Dear Justin (and everyone)
I tried using -pin parameters as following:
mdrun -nt 6 -pin on -pinoffset 0 -gpu_id 0 -deffnm test1 &
mdrun -nt 6 -pin on -pinoffset 7 -gpu_id 1 -deffnm test2 &

The performance increase a little bit (from ~17ns/day to 22ns/day) but i got the same warning message:

> Force evaluation time GPU/CPU: 2.206 ms/4.462 ms = 0.494
> For optimal performance this ratio should be close to 1!
>  
>  
> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>       performance loss.
>  
>                Core t (s)   Wall t (s)        (%)
>        Time:     2301.995      386.857      595.1
>                  (ns/day)    (hour/ns)
> Performance:       22.334        1.075
> Finished mdrun on rank 0 Tue Dec 30 16:49:14 2014




looking also into the nvidia settings, i saw that when i run only one mdrun process, the respective graphic card that is working on it showed a ~50% of performance, but when i run a new mdrun instance, the performance drop to about ~30% on each each graphic card ( i set a maximum performance mode).
Do you think this may be the problem?. and if this IS the issue, is there a way to solve it?
Kind regards,
Carlos

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl


On Tuesday, December 30, 2014 at 4:03 PM, Carlos Navarro Retamal wrote:

> Dear Justin,
> Thanks a lot for your reply.
> I tried with another system (~130k with the same results) 1GPU > 2 GPU’s
> In any case i’ll read the documentation you mention on your previous reply (and hopefully i’ll be able to run 2 process simultaneously .
> Kind regards,
> Carlos
>  
>  
> --  
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile   
> Teléfono: 56-71-201 798,  
> Fax: 56-71-201 561
> Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
>  
>  
> On Tuesday, December 30, 2014 at 3:40 PM, Justin Lemkul wrote:
>  
> >  
> >  
> > On 12/30/14 1:38 PM, Carlos Navarro Retamal wrote:
> > > Dear Justin,
> > > Thanks a lot for your reply.
> > >  
> > > > You can use the multiple cards to run
> > > > concurrent simulations on each (provided cooling is adequate to do this).
> > > >  
> > >  
> > >  
> > >  
> > >  
> > > I tried that. I launched 2 simulation at the same time, but on each i got the next warning at the end:
> > >  
> > > > Force evaluation time GPU/CPU: 3.177 ms/5.804 ms = 0.547
> > > > For optimal performance this ratio should be close to 1!
> > > >  
> > > >  
> > > > NOTE: The GPU has >25% less load than the CPU. This imbalance cause
> > > > performance loss.
> > > >  
> > >  
> > >  
> > > and i got really low performance ( ~ 17ns/day each)
> > > using the following commands:
> > >  
> > > > mdrun -deffnm test1 -gpu_id 0 -v
> > > > mdrun -deffnm test2 -gpu_id 1 -v
> > > >  
> > >  
> > >  
> > >  
> > >  
> > > Is there a better way to perform multiple md simulations at the same time?
> >  
> > In this case, both GPU are probably fighting for CPU resources (note how the CPU  
> > force evaluation is the limiting factor). You'll need to set -pin and  
> > -pinoffset suitably, IIRC. See discussion at
> >  
> > http://www.gromacs.org/Documentation/Acceleration_and_parallelization
> >  
> > -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 (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >  
> > ==================================================
> > --  
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