Oh, that sounds worrying... I know other people used our machines in the past for parallel computing. I'll investigate your suggestion, though, and will confirm if that's the case. Thanks very much again!
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 25 December 2012 06:37
To: AMBER Mailing List
Subject: Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD
On Mon, Dec 24, 2012, Amparo Garcia Lopez wrote:
> The script and my files run normally in one machhine (4 processors). Speed is 5.21 ns/day. The output file says "running Amber/MPI on 4 nodes"
>
> When I run the script on several machines in parallel the speed doesn't
> increase (or it can get even lower),
This is very common. Unless you have an infiband (or equivalent) connection,
it is likely that you may not be able to scale pmemd beyond a single node.
Gigabit ethernet is not enough, at least for most problems. Basically, you
are being limited by the speed at which coordinates can be communicated
between nodes.
....good luck....dac
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Received on Tue Dec 25 2012 - 15:00:02 PST
