[gmx-users] GROMACS Parallel Runs

[Dallas B. Warren]

> 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 ....

>>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.