AMBER Archive (2006)

Subject: Re: AMBER: timing estimates

From: Robert Duke (
Date: Wed Apr 19 2006 - 19:06:59 CDT

Well, without putting a lot of thought into a response, I would quickly say
that I would not use GB ethernet with more than about 8 cpu's, but I would
use a good infiniband implementation on up to maybe 128 cpus; certainly 96
(typically these are dual cpu nodes). For pmemd I test/bench on a large
opteron/infiniband cluster and a intel em64t/infiniband cluster (both
pushing out around 1000 cpu's); for both I can get up to around 6-7 nsec/day
for the factor ix benchmark (~90K atoms) on 128 cpu's. The interconnect
really really does matter, GB ethernet is not very good, and a good
infiniband really is rather nice, all considered. I say a "good infiniband"
because I am aware that infiniband comes in different brands and speeds, and
I don't have the hard data on the two clusters that I do use (this is the
sort of detail that seems to get neglected); I would expect that these
clusters that perform well are using top-end infiniband implementations
Regards - Bob Duke

----- Original Message -----
From: "Ed Pate" <>
To: <>
Sent: Wednesday, April 19, 2006 7:10 PM
Subject: AMBER: timing estimates

> Dear Amber users:
> This is a somewhat poorly posed question. Are there any timing estimates
> available or rules of thumb for computational speed running an amber
> molecular dynamics simulation with infinband interconnects as
> opposed to ethernet? Does infiniband give significant speedup? The
> application would be a large protein in a box of explicit water molecules.
> Thanks for the help.
> Ed Pate
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