AMBER Archive (2007)

Subject: AMBER: request for hardware recommendations

From: Parish, Carol (cparish_at_richmond.edu)
Date: Sat Oct 06 2007 - 10:59:01 CDT

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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