NAMD on AMD Istanbul versus intel Nehalem with infiniband

From: Vlad Cojocaru (
Date: Fri Jan 22 2010 - 08:47:58 CST

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 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

Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter (

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