[gmx-users] GROMACS Parallel Runs

[Sunny]

Hi David,

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>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 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 <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
>>>
>>>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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>>
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>
>--
>David.
>________________________________________________________________________
>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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