Re: AMBER: massively parallel computation

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 20 May 2008 10:11:46 -0400

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.qtp.ufl.edu
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Received on Wed May 21 2008 - 06:07:47 PDT
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