Re: amber-developers: amber performance

From: Ken Merz <>
Date: Wed, 28 Feb 2007 19:04:36 -0500


  Why not run a competition testing the performance of the plethora
of MD codes? How about testing them for consistency of results at the
same time? If AMBER hosts it then we can lay down the ground rules
like trajectory file writing frequencies. Otherwise we have the
current situation where no one knows who has the fastest code given a
particular situation. DEShaw is going to smoke us all... ;-)! This is
a problem in the QM area as well (the code that one cannot benchmark
doesn't help the situation here).


On Feb 28, 2007, at 6:32 PM, Adrian Roitberg wrote:

> Robert Duke wrote:
>> Yong -
>> Don't fret about the ntwx 250; it is a matter of history, and as
>> we move forward we can change it to look more competitive. I have
>> kept the values so far in the factor ix benchmark for backward
>> compatibility with older results. Also, by cranking the write
>> frequency up, I actually am actively looking to push the disk i/o
>> a bit harder to see where it will be a bottleneck (so if I can get
>> away with ntwx 250 at 300 processors, then I should be able to get
>> away with ntwx 1000 on 1200 processors). I do feel that it is
>> really only a fair benchmark if you DO write a trajectory though,
>> as most folks want at least a trajectory. If we handle our file i/
>> o efficiently, then we can end up having a competitive advantage
>> here (so the guys competing against us need to write trajectories
>> too).
>> Regards - Bob
> I agree with Bob, BUT (big one also) the 'guys competing against
> us' might not be writing as often, and it is unlikely we can
> convince them to run fair benchmarks.
> So, it would be cool if you could rerun the benchmarks writing
> every 500 or 1000 steps and tell us what they look like, so we can
> show off your stuff !
> --
> 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
> ======================================================================
> ======
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt

Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435


Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376
Received on Sun Mar 04 2007 - 06:07:26 PST
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