AMBER Archive (2007)

Subject: RE: AMBER: Sander slower on 16 processors than 8

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Feb 22 2007 - 16:10:57 CST

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

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Martin Stennett
Sent: Thursday, February 22, 2007 13:11
To: amber_at_scripps.edu
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
system.
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.
Martin

 

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