RE: AMBER: Sander slower on 16 processors than 8

From: Ross Walker <>
Date: Thu, 22 Feb 2007 14:10:57 -0800

Are you sure you aren't mistakenly using the serial version of the code?
Or perhaps a wireless connection between your nodes?


From: [] On Behalf Of
Martin Stennett
Sent: Thursday, February 22, 2007 13:11
Subject: Re: AMBER: Sander slower on 16 processors than 8

In my experience Sander slows dramatically with even two processors. The
message passing interface used means that it frequently drives itself into
bottlenecks, with one or more processors waiting for very long periods for
others to finish.
It also passes an extra-ordinary amount of data between threads, though with
your setup this shouldn't be as much of a factor as it was on my test
To me it seems that AMBER is great from the point of view of a chemist, and
very accessible should one want to change it. While from a computational
point of view needs a bit of optimisation and tweaking before it should be
considered as a serious solution.


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Received on Sun Feb 25 2007 - 06:07:24 PST
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