RE: amber-developers: amber performance

From: Yong Duan <>
Date: Wed, 28 Feb 2007 15:13:04 -0800

On the issue of comparison to other packages/programs, I think it makes
sense to publish a set of comparison using throughput (rather than the
dubious feeling-good scaling).

Although I am pretty sure Bob and everybody else has considered this, please
use a more realistic ntwx. 250-step/frame is just not the thing we do any
more (was probably common 20 years ago). This has absolutely nothing to do
with the notion of being "honest" or not. Ntwx=250 is just not realistic. In
fact, if my students save the frames that often he/she likely receives a
long and torturous lecture from me demanding an explanation.


-----Original Message-----
[] On Behalf Of Robert Duke
Sent: Wednesday, February 28, 2007 2:59 PM
Subject: Re: amber-developers: amber performance

Scott -
Great! I will be working for a little bit to get tip4p (actually I will
probably just go ahead and do full extra pnts support), remd, ti into a
checked in version of pmemd so the various amber developers can start
reaping the benefits; then I will go back to pushing performance and can
have pieces of that available for "pmemd 10 beta" performance comparison.
Right now, the code base I have is not significantly faster than 9; I have
been spending time on design issues, ff validity, electrostatic methods
validity, etc. But I'll have some of this stuff working hopefully before
too long.
Best Regards - Bob

----- Original Message -----
From: "Scott Brozell" <>
To: <>
Sent: Wednesday, February 28, 2007 5:24 PM
Subject: amber-developers: amber performance

> Hi,
> Today Kent Milfeld from TACC asked me about amber performance because
> he saw that there is work underway for charmm's performance.
> I told him about pmemd (which he had never heard of), namd, gromacs, etc.
> He was very receptive to the idea that namd has great advertising
> and might not be targeting the best science.
> This follows on the discussion we had at the amber meeting regarding
> a publication on good vs dubious science, pmemd, single vs double
> precision,
> scaling vs throughput, etc. I hope that the ball will be rolling soon.
> And I'm happy to help out.
> Scott
Received on Sun Mar 04 2007 - 06:07:26 PST
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