AMBER Archive (2007)

Subject: Re: AMBER: Improving pmemd parallel scaling

From: Mark Williamson (Mark.Williamson_at_imperial.ac.uk)
Date: Thu Jun 28 2007 - 11:19:06 CDT

Alessandro Nascimento wrote:
> I'm running amber9 (lam-mpi) on 6 Intel Xeon 3.4 processors in Gigabit
> network.
> Looking the processors usage with linux "top" over the machines when

I am not a heavyweight in this area, others will chime in with more
info, hence this is a quick note. There was a recent paper discussing
approaches on high-latency networks within GROMACS:

http://dx.doi.org/10.1002/jcc.20703

There are some hardware tips in there as well that may be applicable to
your situation.

regards,

Mark Williamson
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