Hi, Benchmarking and tuning is generally quite machine-specific, but you could have a look at this great work done by Carsten Kutzner on SuperMUC: http://www.mpibpc.mpg.de/11832367/kutzner13talk-Parco.pdf https://www.mpibpc.mpg.de/14613164/Kutzner_2014_ParCo-conf2013.pdf
On Thu, Jul 17, 2014 at 7:24 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/14, 12:39 PM, vidhya sankar wrote: >> >> Hai Justin Thank you for your Previous Reply >> >> Is there is Any Restrictions in usage of Number of Processor (in >> Clustering ) for Performance Tuning in gromacs 4 and After Version. >> especially when i use PME >> >> When I surf I got the Following Link >> >> >> http://www.mpibpc.mpg.de/262136/PosterHuenfeld2009.pdf >> >> >> >> >> Please give me the Brief Detail and Guidance. >> > > Benchmarking and tuning should always be done. There are limits to the > number of processors, but they are dependent upon system size and related to > DD. Generally Gromacs can scale to a few hundred atoms per core. Note that depending on the machine (especially network), simulation system (as well as the desired minimum parallel efficiency = definition of "scale"), as Carsten also showed, the limit can be even lower! Cheers, -- Szilárd > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > 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. -- 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.