Re: Fat node

From: Jim Phillips (
Date: Tue Aug 29 2006 - 14:19:47 CDT

For NAMD I would suggest smaller nodes (dual socket, dual core seems to be
the sweet spot as far as price goes) with Myrinet or Infiniband. A fat
machine is useful if you have some large memory or shared memory jobs that
you want to run as well, but you'll definitely pay more for it. If you
would be buying more than one such node, then you would be sharing the
network between more processors and hence get worse performance than if
you got smaller nodes and spread the communication out more.

I can be more decisive if you ask a question like: "For my $XXX I can buy
A, B, or C. Which solution would give better NAMD performance for my
typical simulation of a YYY-atom system?"


On Mon, 28 Aug 2006, wrote:

> Hello everyone. I couldn't find any threads about this, so here it goes. We are
> about to buy new equipment for building a Linux cluster, and we have been
> suggested to buy a "fat node" with some 8 dual-core processors and 16GB or 32GB
> RAM. Does anyone have any experience with this kind of achitechture regarding
> parallel performance (e.g. with NAMD)? Our guess is that the latency within
> this single motherboard should be lower than on the same number of processors
> ("thin nodes") on Gbit ethernet, but how would it compare to Myrinet? Any
> comments are very much appreciated.
> J. Valencia
> ----------------------------------------------------------------
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