RE: amber-developers: amber performance

From: Ross Walker <>
Date: Wed, 28 Feb 2007 16:15:49 -0800

Hi All,

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 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. There are
some other options etc in here that we could consider as well, such as
timesteps etc. Is 2fs really bleeding edge? Note: in the DeShaw paper they
use a 2.5fs time step with shake on just hydrogens.

This I think is a good plan since we can do these calculations and then put
something along the lines of - oh btw here is the performance of the
simulations on all the different codes etc.

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.


All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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> -----Original Message-----
> From:
> [] On Behalf Of Scott Brozell
> Sent: Wednesday, February 28, 2007 14:24
> To:
> 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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