[gmx-users] GROMACS Parallel Runs

[David van der Spoel]

Sunny wrote:
> Setting both fourier_nx and nkx to 256 and running grompp with -np 256 
> still produces the error:
> 
> could not find a grid spacing with nx and ny divisible by the number of 
> nodes (256)
> 
> Does it mean 256 nodes are not allowed?
> 
> Sunny
> 
>> 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: Fri, 06 Oct 2006 10:54:12 +0200
>>
>> Sunny wrote:
>>>> From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
>>>> 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: Fri, 06 Oct 2006 09:35:31 +1000
>>>>
>>>> > I have successfully run gmx on up to 128 cpus. When I scale
>>>> > to 256 cpus, the
>>>> > following error occurs. Does it mean that gmx can't be run on
>>>> > 256 nodes?
>>>> >
>>>> > Fatal error:
>>>> > could not find a grid spacing with nx and ny divisible by the
>>>> > number of
>>>> > nodes (256)
>>>>
>>>> Isn't that just due to the reasoning pointed out previously ....
>>>>
>>>
>>> I think that's not the same problem. This time I have set 
>>> fourier_nx=512 (or nkx=512, I've tried both setting). When running 
>>> grompp ... -np 256, it reports the error:
>>>
>>> Fatal error:
>>> could not find a grid spacing with nx and ny divisible by the number 
>>> of nodes (256)
>>>
>>> If I run the same grompp with the same .mdp file and less -np (i.e., 
>>> 128), the error doesn't occur.
>>>
>>> Thanks,
>>>
>>> Sunny
>>>
>>>> >>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.
> 
>> set all of them to 256
>>
>> do not expect to get any performance gain though.
>>
>> -- 
>> David.
> 
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you need to set nkx, nky, nkz manually in the mdp file

-- 
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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