[gmx-users] Optimal pme grid

[Mark Abraham]

Hi,

Yes this is expected. The number of ranks affects what grids may be chosen,
and thus the number of alternatives the optimizer might try. For such a
short run, the optimization is fairly useless, however.

Mark

On Fri, Aug 31, 2018 at 1:21 PM Mahmood Naderan <nt_mahmood at yahoo.com>
wrote:

> Hi
> It seems that changing the number of ntmpi and ntomp affects the number of
> steps that takes to calculate the optimal pme grid. Is that correct?
>
> Please see the following output
>
> gmx mdrun -nb gpu -ntmpi 1 -ntomp 16 -v -deffnm nvt
> Using 1 MPI thread
> Using 16 OpenMP threads
> step 2400: timed with pme grid 60 80 60, coulomb cutoff 1.037: 5708.7
> M-cycles
> step 2600: timed with pme grid 64 80 60, coulomb cutoff 1.000: 5382.6
> M-cycles
>               optimal pme grid 64 80 60, coulomb cutoff 1.000
> step 3900, remaining wall clock time:     1 s
>
>
>
> gmx mdrun -nb gpu -ntmpi 16 -ntomp 1 -v -deffnm nvtUsing 16 MPI threads
> Using 1 OpenMP thread per tMPI thread
> step 3800: timed with pme grid 56 72 56, coulomb cutoff 1.111: 21060.1
> M-cycles
> step 4000: timed with pme grid 60 72 56, coulomb cutoff 1.075: 21132.8
> M-cycles
>
> Writing final coordinates.
>
>
>
> I have intentionally limit the number of steps to 4000. As you can see, in
> the second run, the optimal value has not been reached.
>
>
>
>
>
>
> Regards,
> Mahmood
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