Re: amber-developers: amber performance

From: Adrian Roitberg <>
Date: Wed, 28 Feb 2007 22:16:05 -0500

Yong Duan wrote:
> I'd be more interested in their energy conservation trajectories but can't
> find information. Neither could I find a particularly compelling novel
> technique to enable their absurdly impressive performance which is about one
> order of magnitude better than others.
> yong
I had a long chat with Istvan K at Sanibel about this (Desmond).
Basically, we cannot expect to see the code for a while. In about a year
they plan to release it as executable only, free for academics, to run
under Schrodinger's Maestro free interface.

Their claim about changes is related to the use of single precision,
which drops messaging in half, and the fact that they do not communicate
too far and only send stuff to nearest neighbors. Please do not start
commenting on this issues, I am just transmitting what he told me and
have little or no real expertise on this.

They also claim that they can do better arithmetic with single precision
than others with double but being 'very careful'. I do not know what
this means !

One thing they claim really helped is mapping the coordinates WITHIN a
single processor (or a unit cell ?) to a number between -1 and 1 (maybe
0 and 1). They can later one trivially correct for this. It helps them
in being able to use parts of the register for other stuff.

They also wrote their own low level communication routines from scratch.
This will kill portability of course.

A recent paper by that group "A common, avoidable source of error in
molecular dynamics integrators" in J. Chem. Phys. 126, 046101 (2007)
might help a bit, but I have only glanced at it.


                            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
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Received on Sun Mar 04 2007 - 06:07:29 PST
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