Re: AMBER: request for hardware recommendations

From: Andy Purkiss <>
Date: Sat, 6 Oct 2007 18:53:23 +0100

One further thing to add, using dual quad core setups might lead to memory
bandwidth problems. See the information in a thread in the archives from August
and especially the comment by Ross Walker linked here

It appears that implicit solvent simulations run locally are OK, but that
explicit solvent simulations are not so good on quad cores.

Just something else to think about.

Quoting Carlos Simmerling <>:

> Carol,
> 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
> restraints,
> 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.
> Carlos
> 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
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to
> > To unsubscribe, send "unsubscribe amber" to
> >

"We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry."
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail                   |
This message was sent using IMP, the Internet Messaging Program.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 07 2007 - 06:08:01 PDT
Custom Search