[gmx-developers] GPU acceleration on 48 core nodes

[Berk Hess]

Hi,

Currently you shouldn't use the HT cores as the thread pinning locks to 
the wrong cores.

The question on the AMD 48-core node is not specific enough. Performance 
does not
depend on the number of cores, but on the core/GPU ratio and the PCI-E 
connection(s).
If you have only one GPU I would suggest to use only one CPU with it on 
the AMD.

We have new kepler kernels in the making which should give a least a 
factor 1.5 improvement.

Cheers,

Berk

On 05/24/2012 03:11 PM, Carsten Kutzner wrote:
> Hi,
>
> does anyone have experiences with running the gpu-accelerated Gromacs
> on AMD 48-core nodes? Are there known performance issues?
>
> We are able to get good performance with a GTX680 when it is plugged
> in an Intel node (12 cores), but not when we plug it in an Interlagos
> (48 cores).
>
> With an 80k atom test system, PME 96x96x80, cutoffs @ 1 nm, GMX_NSTLIST=20-80,
> we get (I list results for the best performing NSTLIST value only, typically 40)
> ~  8.5 ns/day on the Intel node with HT
> ~ 13.5 ns/day on the Intel node with the GPU (with or without HT, similar performance)
> ~ 14.0 ns/day on the Intel node with TWO GPUs (with HT)
> ~ 17.0 ns/day on the Intel node with two GPUs _without HT_
> ~ 15.0 ns/day on the AMD Interlagos using 48 cores and no GPU
> ~ 10.0 ns/day on the AMD Interlagos using 48 cores and the GTX680.
>
> Is it possible to get a speedup from the GPU with Interlagos nodes?
>
> Thanks for any hints,
>    Carsten
>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>
>
>
>