here's a link to the log file https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing
The computer is 4GPUs and 32 CPUs but some GPUs were in use hence only 15-16 were used. Thanks On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/27/16 8:49 AM, יוכבד wrote: > >> Hi >> I've recently installed GROMACS 5.1.2. >> I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine >> using 4GPUs and 32 CPU and I got the performances of ~330ns/day >> >> Now I'm tring to run my system but I don't see any acceleration (a 500ps >> nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs >> and >> 15 CPUs. >> >> What am I missing here? >> >> attached is my mdp file and the command used was >> > > The list does not accept attachments. The .log files are the most > informative as the end contains a full performance breakdown; if you wish > to share them, upload them to a file sharing service and provide a URL. > > The actual performance depends largely on the content/size of the system. > Perhaps you have a bottleneck due to the size of the system such that you > cannot efficiently utilize all 4 GPU and 15 CPUs (an odd combination, > anyway) simultaneously. > > -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 > > [email protected] | (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 [email protected]. -- 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 [email protected].
