[gmx-developers] GPU acceleration on 48 core nodes

[Carsten Kutzner]

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