[gmx-users] Cuda CC 2.0 restrictions

[Mark Abraham]

On Fri, Sep 5, 2014 at 11:24 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:

> I've run into a problem with an older card (GTX-580)
> which is CC 2.0. On a larger box size, mdrun stops
> with:
>
>    Fatal error:
>    Watch out, the input system is too large to simulate!
>    The number of nonbonded work units (=number of super-clusters)
>    exceeds themaximum grid size in x dimension (86276 > 65535)!
>
>
> This seems to refer to the CUDA "grid of thread blocks per dimension",
> limitation specific for CC below 3.0 (I know this system worked already
> on a CC 3.0 device).
>
> My question: can this grid count calculated by mdrun be "manipulated"
> somehow by mdp options (nstlist, rvdw, rlist)?
>

The number of super-clusters grows as the size of the neighbour list, i.e.
something like rlist^3. By default, rlist is set based on a complex
diffusion-based heuristic using T, max(rvdw,rcoulomb),
verlet-buffer-tolerance and nstlist. The minimum value for nstlist is set
in the .mdp file, but gets increased based on the hardware using other
heuristics. Using a smaller nstlist will require a smaller buffer and thus
smaller rlist. This can be done with mdrun -nstlist x, which requires mdrun
to use x for nstlist, rather than the .mdp value or its own choice. That's
going to perform relatively worse than the default, because the CPU-only
neighbour searching will happen accordingly more often, but it's better
than not running at all :-D.

You could also mess around with reducing max(rcouloumb,rvdw) and
corresponding buffs to PME parameters, but demonstrating correctness and
achieving CPU-GPU load balance is less straightforward than the above.

Mark

Thanks,
>
> M.
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