Re: AMBER: request for hardware recommendations

From: Carlos Simmerling <>
Date: Sat, 6 Oct 2007 13:00:13 -0400

are you thinking of using all 80 cores at once for runs, or will you usually
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. There
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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