VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jul 26 2009 - 18:22:59 CDT

On Sun, 2009-07-26 at 16:20 -0500, luc Renambot wrote:
> Hello,

luc,

>
> I just got a new Linux system with 4 Nvidia GPUs (and eventually 6 of
> them, 9800 GT 1GB RAM). I'd like to benchmark it.

i am curious. why so many? why not 2 or 3 GTX 275 cards instead
(and perhaps one 9800GT for the display)? transferring data across
the PCIe bus is one of the big bottlenecks in GPU computing and
- at least on paper - the GTX 275 should have about twice the
performance than the GT 9800 while needing in total much less power.

> I got VMD installed and it recognize all the GPUs. Nice !
> But I couldn't find on the web site a file or a benchmark to stress
> test my new system.

i don't have any example for VMD that you could use,
but have you tried other GPU accelerated codes?

> Would anybody like to share such a file or script ?
> I'd be happy to share results and configuration if anybody is
> interested.

i'd be interested to see how that machine works with
HOOMD. http://www.ameslab.gov/hoomd/benchmarks.html
n.b. the GPU parallelization in HOOMD is very simpleminded
and thus not very efficient (i've seen 20-40% speedup from
using a second GPU and next to nothing from a third),
but you could just run 4 individual benchmarks backgrounded
at the same time and tied to different GPUs via the
--gpu=# flag and that should give you a good estimate for
the best case scenario (i've been able to run with the
4 GPUs in a tesla S1070 on a single node machine with
two 8xPCIe-2.0 busses reasonably efficient at a 15% performance
hit, which is quite surprising given that it was on a
dell poweredge 1950 with a horrible memory and PCI bandwidth).

a second option would be to try the GPU accelerated
compilation of NAMD.

cheers,
   axel.

>
>
> Thanks,
>
> --
> Luc.
>
> renambot_at_gmail.com
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.