[gmx-users] Regarding Performance Tuning for GROMACS

[Szilárd Páll]

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 <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
>>
>>
>> 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
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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