GPU cluster

From: Matthew B. Roark (
Date: Tue Jun 19 2012 - 14:07:58 CDT

I currently use CHARMM on several Rocks clusters and I am looking to try out GPGPU. I am looking into buying either a small GPU cluster or a few stand-alone workstations to use CUDA enabled NAMD. I wanted to see what people are using and what people suggest.

(1) My main concern is that I need to have something that will positively work with NAMD. Is there any hardware or vendors I should stay away from? Are there vendors with "out-of-the-box' compatibility?

(2) How does scaling and efficiency work across multiple GPUs in the same server? That is, how many GPUs can a server really make good use of? I plan on testing with an 80k atom simulation.

(3) How much CPU power do I need to make use of multiple GPUs? Will 8 or 16 cores suffice?

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