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].
