NAMD on AMD Istanbul versus intel Nehalem with infiniband

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Fri Jan 22 2010 - 07:56:11 CST

Dear all,

I am currently configuring a small cluster 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 (approx. 10 double CPU nodes). I am
not an expert in hardware so unfortunately I cannot give many other
details.

I would be curious about your thoughts on the NAMD 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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Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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