Re: amber-developers: amber performance

From: Scott Brozell <>
Date: Thu, 1 Mar 2007 13:17:06 -0800


If Dave's comments are only worth $0.02 then mine surely will be
valueless, due to inflation, by the time you finish reading this :)

I started the sunday night conversation between Ross, Tom C, and Mike
because I am an Amber representative and I do not have enough expertise
to explain in detail to people like Kent Milfeld and other higher ups
why the well advertised NAMD and Gromacs are not the best performing MD
codes. Of course, I can mention throughput vs scaling and everybody gets
it, but the tradeoffs between single and double precision vis-a-vis
energy conservation, and other good vs dubious science issues are
more involved.

Thus, I think that we do need publications, not just benchmarks,
that underscore the tradeoffs. I see the pedagogical value of such
work as much greater than its Amber advertising value.


ps and in the category of free advice,

It reads like Bob has quite a bit of work that could be
published - this could be a case of not following Knuth's quote:
Premature optimization is the root of all evil.
In other words, you may due more communal good by publishing than
optimizing pmemd for feature x on platform y or beating namd
performance yet again.

On Thu, 1 Mar 2007, David A. Case wrote:

> On Wed, Feb 28, 2007, Ross Walker wrote:
> >
> > Tom C and I spent some time talking about this on Sunday evening. We pretty
> > much came to the conclusion that we want to do is design a series of
> > calculations that attempt to address the various issues that people simply
> > "believe" at present. I.e. find something that is sensitive to single vs
> > double precision and see if we can address whether single precision is okay
> > or not.
> In my view, this could very easily become a time sink where you don't get
> any definitive results and just waste time and create controvesy. The way in
> which gromacs and desmond use single precision is quite different, and both
> would be different from trying to compile sander in single precision.
> > In addition we thought about answering PME vs force switch
> > simulations. Here a salt water solution simulation might be useful as this
> > would be an extreme test of the electrostatics and we could address whether
> > a force switch cutoff is actually okay or if you really need pme.
> Bob has already answered this, pointing out quite eloquently ways in which
> this could become another wild-goose chase. And, since he already has so much
> data in this area, starting some new effort here doesn't seem very productive.
> >
> > A straight benchmark paper is unlikely to get published so I think wrapping
> > it up in a paper that attempts to address issues regarding PME, time step,
> > single vs double precision etc is a good way to go.
> We don't necessarily need a paper on benchmarks: a good web site that collects
> numbers we already have lying around (plus some new calculations) would go a
> long way in my view. A key need: someone in the Amber community needs to be
> able to run gromacs and namd, so we can do our own side-by-side comparisons.
> The usual $.02 disclaimers go here.
Received on Sun Mar 04 2007 - 06:07:45 PST
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