[gmx-users] GROMACS Parallel Runs

Sunny ge_sunny at hotmail.com
Mon Oct 2 15:34:38 CEST 2006

Hi all,

Thanks for your proposed solutions.  I will try to set fourier_nx to 64 

Do I also need to set fourier_nx to a bigger number, e.g. 256, when I want 
to run on 128 CPUs?

As I am using a regional supercomputing system, it might be not easy to have 
gmx updated to the CVS version in short time. I will contact the system 
support to see if they would do the update.



>From: Carsten Kutzner <ckutzne at gwdg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] GROMACS Parallel Runs
>Date: Mon, 02 Oct 2006 11:06:49 +0200
>the current version of gmx requires at least pme_order/2 grid points per 
>for the x-dimension of the pme grid. With pme_order=4 and fourier_nx=64 you 
>end up with
>only one grid point per processor. On 64 CPUs you would have to set 
>fourier_nx to 128
>then (or alternatively choose a smaller fourierspacing). These settings are 
>useful for 32 or less CPUs though, because they would unnecessarily slow 
>down your
>Hope that helps,
>   Carsten

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