[gmx-users] GROMACS Parallel Runs
ge_sunny at hotmail.com
Fri Oct 6 10:34:07 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:
could not find a grid spacing with nx and ny divisible by the number of
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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