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.navarr...@gmail.com or cnava...@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.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or > cnava...@utalca.cl (mailto:cnava...@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 > > > > jalem...@outerbanks.umaryland.edu > > (mailto:jalem...@outerbanks.umaryland.edu) | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > > a mail to gmx-users-requ...@gromacs.org > > (mailto:gmx-users-requ...@gromacs.org). > > > > > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
