Re: AMBER: amber8 parallel sander

From: Carlos Simmerling <>
Date: Thu, 22 Sep 2005 18:25:07 -0400

also watch out for 1-4 scaling factors in NAMD- the default may not be
for Amber ff.

Peter Gannett wrote:

>Oh, this is a different story. I've not tried PMEMD in a parallel
>environment. I did use Sander on both a cluster and at PSC (6 or 7, a
>few years ago) and after about 8 CPUs, things did not improve (speed).
>>>> 09/22 12:57 PM >>>
>Kathleen -
>Don't know who you were talking to on this one. PMEMD 8, which offers
>a subset of sander functionality (primarily pme explicit solvent calcs)
>scales well on good hardware out to about 128 procs, and has been
>competitive with namd on various platforms for top-end scaling.
>Versions under current development scale well out past 128 procs,
>depending once again on the h/w, though going over 200 procs is
>impractical with the current parallelization infrastructure. There has
>been an emphasis on getting good per processor performance, followed by
>scaling well up to reasonable numbers of processors, to yield good
>simulation througput. We can achieve on the order of 6-7 nsec/day
>simulating large (~100K atoms) explicit solvent systems with pme
>electrostatics; this is nothing to sneeze at. I don't actually know of
>many places where folks can get 256, 512, 1024 procs for days on end
>without obliterating their compute allocation.
>Regards - Bob Duke
> ----- Original Message -----
> From: Kathleen Erickson
> To:
> Sent: Thursday, September 22, 2005 12:44 PM
> Subject: Re: AMBER: amber8 parallel sander
> Peter: So are you saying that scaling efficiencies beyond 8 CPUs are
>better achieved with NAMD? In other words, is 8 CPUs the limit for most
>effiencient scaling on AMBER? I'd like to know at which point AMBER
>users find they need to switch to NAMD or some other MD package.
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Received on Thu Sep 22 2005 - 23:53:00 PDT
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