Hi David,
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] GROMACS Parallel Runs
Date: Mon, 02 Oct 2006 16:04:45 +0200
Sunny wrote:
Hi all,
Thanks for your proposed solutions. I will try to set fourier_nx to 64
first.
Do I also need to set fourier_nx to a bigger number, e.g. 256, when I want
to run on 128 CPUs?
at least twice the number of CPUs.
Sorry, I mean I will set fourier_nx to 128 first to see if it can work on 64
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.
You can easily do it yourself.
Do you mean I can install gmx in my user space instead of updating the
version under the root directory?
Sunny
Thanks,
Sunny
From: Carsten Kutzner <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] GROMACS Parallel Runs
Date: Mon, 02 Oct 2006 11:06:49 +0200
Hi,
the current version of gmx requires at least pme_order/2 grid points per
processor
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 not
useful for 32 or less CPUs though, because they would unnecessarily slow
down your
calculation.
Hope that helps,
Carsten
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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