[gmx-users] Regarding Performance Tuning for GROMACS
pall.szilard at gmail.com
Thu Jul 17 20:10:59 CEST 2014
Benchmarking and tuning is generally quite machine-specific, but you
could have a look at this great work done by Carsten Kutzner on
On Thu, Jul 17, 2014 at 7:24 PM, Justin Lemkul <jalemkul at 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
>> 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
> 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
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users