[gmx-users] GROMACS Parallel Runs
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 2 16:04:45 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?
at least twice the number of 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.
>> 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 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
>> Hope that helps,
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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