AMBER Archive (2009)

Subject: Re: [AMBER] A good way to use an Amber force field with NAMD?

From: Robert Duke (
Date: Tue Mar 03 2009 - 22:26:59 CST

PMEMD generally won't scale well to 1024 running processors currently, BUT
you can generally use a smaller number and get more done than with namd at
the same processor count. I don't know the exact current comparison -
depends on run conditions, machine, problem size, how many processors you
use, how many processors per node you use, etc. etc. But we do pretty darn
well, all considered, and we do the amber ff absolutely correctly at full
precision. Ross has put benchmarks for the current release (10) on the website - a good thing to look at to get an idea of what you can
get (uses up to 512 cpu on bigger problems; actual allocated cpu's may be
higher for max production but this is less efficient). I still have
benchmarks for the pmemd 9 release out there on a broader spectrum of
machines; pmemd 10 is say roughly 20-50% faster, topend, for a number of
different setups than pmemd 9; one of the complexities in comparison is that
a lot of machines have actually gotten slower between the 9 and 10 release
(so take topsail here at unc - they doubled the processor count moving to
clovertown processors, but that decreased available interconnect bandwidth
per processor and the cpu clock rate was also dropped to about 2/3 of what
it was (so now you need 3 cpu's to get the same compute power you had with
2). So ask yourself, do you want to be able to claim that you are running
on 1024 cpu's, or do you want to get the number of nsec you need for your
simulation with minimal impact on your cpu allocation? Overall, I have been
avoiding doing a bunch of comparative benchmarks because 1) it takes lots of
time, 2) there are all sorts of apples and oranges problems with the
benchmarks (possible exception is JAC, but it is small and also competitors
change run conditions, accuracy, etc), and 3) folks tend to get upset with
each other over results in the competing camps about unfair comparisons and
wild claims.
Regards - Bob Duke

----- Original Message -----
From: "Sasha Buzko" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, March 03, 2009 9:55 PM
Subject: Re: [AMBER] A good way to use an Amber force field with NAMD?

> Thanks, Ross.
> Actually, I like this idea. Regarding scaling, though: do you know how
> well PMEMD scales on over 1024 processors compared to NAMD? I keep hearing
> that NAMD is considerably faster at these cpu numbers..
> If the scaling is comparable, I'd certainly try to do a local install (and
> could use your help in that case).
> Thanks again
> Sasha
> Ross Walker wrote:
>>> to answer your question about the requirement: we are trying to get some
>>> supercomputer time, and they only have NAMD installed. In any event,
>>> it's not our choice.
>> Just a quick question. Why not just install AMBER yourself. It builds on
>> every supercomputer I have ever used without issues. You can install it
>> in
>> your home directory as well.
>> To be honest even if I planned to use NAMD I'd do this. It can be pretty
>> brave to use the supercomputer center installed version unless you
>> implicitly trust the person who installed it.
>> If you let me know what machine it is I can probably install AMBER for
>> you
>> (or give you a suitable config file to use).
>> All the best
>> Ross
>> /\
>> \/
>> |\oss Walker
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- | |
>> | PGP Key available on request |
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