[gmx-users] No scale up beyond 4 processors for 240000 atom system
gmx3 at hotmail.com
Tue Oct 9 12:47:47 CEST 2007
>From: "maria goranovic" <mariagoranovic at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] No scale up beyond 4 processors for 240000 atom system
>Date: Tue, 9 Oct 2007 12:09:50 +0200
>I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16
>processors. Here are my benchmarks:
>Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram,
>GROMACS 3.3.1: 240000 atoms, PME, 1.0 nm real cutoff
>Do I need to recompile with some other options ? Or is this the best I can
>get ? Will another type of network improve performance ? It seems
>communication is the rate limiting step for 8 or 16 cores ?
>Thank you for the help,
So this is 4 cores sharing one ethernet connection?
With such a setup you will never get good scaling.
You need something like an Infiniband network.
Gromacs 4.0 will give a big improvement, but I don't know how much.
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