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 <[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: Fri, 06 Oct 2006 10:54:12 +0200
Sunny wrote:
From: "Dallas B. Warren" <[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: 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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