[gmx-users] No scale up beyond 4 processors for 240000 atom system

[Berk Hess]

>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
>
>Hello,
>
>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, 
>2x
>Gigabit Ethernet
>
>GROMACS 3.3.1: 240000 atoms, PME, 1.0 nm real cutoff
>
>processors   ns/day
>1       0.141
>2       0.253
>4       0.409
>8       0.232
>16      0.107
>
>
>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,
>
>-Maria

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.

Berk.

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