AMBER Archive (2008)

Subject: Re: AMBER: massively parallel computation

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Tue May 20 2008 - 09:28:24 CDT

A quick comment.. We observe increased performance on up to 1024 cores
on our cray xt4 for a system of ~600.000 atoms using pmemd. not
exactly linearly scaling that far though, but I expect even better
performance when we optimize the installation. so pmemd is most
definitively suited for use on several hundreds cpu's.
LS

On Tue, May 20, 2008 at 4:11 PM, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
> Oh man, you got yourself in trouble now ...
> Amber and more particularly PMEMD already use hundreds of cpus VERY
> efficiently !
>
> It might be time to post to this list the benchmarks showing how good pmemd
> really is against the other supposedly faster programs.
>
> Ross ?
> Bob ?
>
> Cheers
>
> Adrian
>
>
> Mingfeng Yang wrote:
>>
>> Recently, a few algorithms have been developed to enable massively
>> parallel
>> computation which can efficiently use hundreds of CPUs simultaneously for
>> MD
>> simulation. For example, J Comput Chem 26: 1318–1328, 2005.
>>
>> Is there a plan to implement such algorithm in Amber/PMEMD? As computer
>> cluster is getting cheaper and cheaper, the cluster size keeps expanding
>> quickly as well. Such algorithms should be very helpful and indispensable
>> to
>> reach >ms scale simulation.
>>
>> Thanks,
>> Mingfeng
>>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> ============================================================================
>
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-- 
mvh Lars Skjærven
Institutt for Biomedisin
Universitetet i Bergen
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