[AMBER] AMBER on AMD Istanbul versus intel Nehalem with infiniband

From: Vlad Cojocaru <Vlad.Cojocaru.h-its.org>
Date: Fri, 22 Jan 2010 15:45:28 +0100

Dear all,

I am currently configuring a small cluster (approx. 10 double CPU nodes)
on which I would like to run mainly AMBER/NAMD/GROMACS.

The choice seems to be between the latest AMD Istanbul and Intel Nehalem
chips with infiniband interconnect. I am not an expert in hardware so
unfortunately I cannot give many other details.

I would be curious about your thoughts on the AMBER (especially PMEMD
but also SANDER since PMEMD has still limited functionality) performance
on the 2 chips. Is there anything in particular that one should consider
? Would there be any reason (except price) to go for slightly older chips?

Is there anything one should consider about the infiniband inter connect
? Could one replace the inifiniband with 10 Gbits ethernet ?

Thanks for your thoughts
Vlad

-- 
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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
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69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Fri Jan 22 2010 - 07:00:03 PST