[gmx-users] GROMACS Parallel Runs
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 6 10:54:12 CEST 2006
>> 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.
>> >>the current version of gmx requires at least pme_order/2 grid points
>> >>for the x-dimension of the pme grid. With pme_order=4 and
>> >>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
>> >>are not
>> >>useful for 32 or less CPUs though, because they would unnecessarily
>> >>down your
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set all of them to 256
do not expect to get any performance gain though.
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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