AMBER Archive (2004)

Subject: Re: AMBER: NEC and Regatta

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Jun 28 2004 - 07:38:27 CDT

Sorry - I neglected to mention that for the 3.0, 3.03, and 3.1 releases of
pmemd, the benchmarks are in the release and update notes, found under
src.pmemd in the gzipped tarball.
Regards - Bob Duke
----- Original Message -----
From: "Robert Duke" <rduke_at_email.unc.edu>
To: <amber_at_scripps.edu>
Sent: Monday, June 28, 2004 8:18 AM
Subject: Re: AMBER: NEC and Regatta

> There has been lots of work with pmemd on both the p690 and the
> alpha/quadrics (see amber.scripps.edu website for links to pmemd resource
> pre-amber8 releases of pmemd (3.0, 3.03, 3.1), pmemd 8 is part of the
amber
> 8 release). There were lots of benchmarks published for the 3/3.03/3.1
> releases for both of these platforms, and a lot of numbers are included
for
> the various versions of sander too. For amber 8, there are benchmarks for
> these platforms on the website, generally referencing pmemd or my name.
> Sorry, but I have no numbers on the NEC.
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Filip Lankas" <filip.lankas_at_epfl.ch>
> To: <amber_at_scripps.edu>
> Sent: Monday, June 28, 2004 7:47 AM
> Subject: AMBER: NEC and Regatta
>
>
> > Dear Amber users,
> >
> > does anyone have an experience with running Amber 7/8 on
> >
> > 1. NEC SX-5
> >
> > 2. IBM Regatta p690 (with Power4 CPUs)
> >
> > What speed and what scaling (with no. of atoms and no. of processors)
> > can one expect? How would it compare with, say, Alpha ES45 connected
> > with Quadrix? Are there some peculiarities to be aware of?
> >
> > I'm particularly interested in running explicit-solvent MD with PME.
> >
> > Thanks a lot in advance,
> >
> > Filip
> >
> > --
> > ---------------------------------------------
> > Dr. Filip Lankas
> > Bernoulli Institute for Mathematics
> > EPFL (Swiss Federal Institute of Technology)
> > CH-1015 Lausanne
> > Tel: +41 21 693 2593 Fax: +41 21 693 5530
> > ---------------------------------------------
> >
> >
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>
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