RE: AMBER: request for hardware recommendations

From: Parish, Carol <>
Date: Sat, 6 Oct 2007 13:20:13 -0400

Thank very much. Judging by the timings in the Amber page, I think that
some of the time I'd want to run on at least 16 cores, maybe up to as
many as 40 cores, but most jobs would use 8 or so cores. I'd likely use
both pmemd and sander, but most of my longer jobs will likely be
REMD/sander. I'm starting to think that I'm sort of at the cusp; where
some of my jobs would do OK with gigE and some would benefit from
infiniband and I just need to choose a configuration? Thanks again,



From: [] On Behalf
Of Carlos Simmerling
Sent: Saturday, October 06, 2007 1:00 PM
Subject: Re: AMBER: request for hardware recommendations


are you thinking of using all 80 cores at once for runs, or will you
have multiple simulations going (multiple users)? For 80 cores on
a small number of simulations you probably won't get good scaling with
gigE. It also depends on whether you will use mostly pmemd, which scales
well, or sander, which doesn't scale as well but has more functionality.
pmemd is great for standard MD, but anything beyond that like most
free energy calculations, REMD, NEB, and so on will require sander.
Let us know how you'll be using it and we might be able to help more.
are also lots of benchmarks on the Amber page for various clusters.

On 10/6/07, Parish, Carol <> wrote:

Please forgive this hardware-recommendation related post. I looked
through the manual, the webpage and the reflectors and I didn't see any
recent information on this specific issue.

I would like to use AMBER for systems of about 200 residues in explicit
and implicit solvent. My budget will allow me to purchase either a
cluster of 10 dual quad core intels (80 cores) with gigE, or a much
smaller number of cores with infiniband. Should I invest in infiniband
or would gig E scale OK in the TIP3 calcs for a cluster this size? (10
boxes; 80 cores)

I have heard rumors that it can be difficult to install AMBER in
parallel on commodity clusters. Can anyone recommend linux
hardware/software combinations that work best?

Can anybody recommend a vendor who can install and test AMBER on a
gigE/intel cluster?

Can anyone recommend a good quality gigE switch? Does anyone know of a
HOWTO for configuring a switch to work optimally?

Thanks very much, Carol Parish

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Received on Sun Oct 07 2007 - 06:08:01 PDT
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