[gmx-users] GROMACS Parallel Runs
ge_sunny at hotmail.com
Mon Oct 2 15:34:38 CEST 2006
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
>Hope that helps,
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