[AMBER] GPU performance and GPU Direct

From: <steinbrt.rci.rutgers.edu>
Date: Wed, 7 Mar 2012 08:26:53 -0500 (EST)

Hi CUDA users,

I have a few short questions on running pmemd.cuda{,.MPI}:

- It is suggested to enable GPU Direct for running across multiple nodes.
Will this also affect performance for two GPU cards within the same node
or does it only concern Infiniband connects?

- My machine has only two GPUs, no onboard graphics. Therefore, GPU0
defaults to screen output, even at runlevel 3. If I boot up without a
screen attached, will one of my GPUs still handle displaying a useless
login screen? Does this affect performance? If yes, how to avoid?

- Scaling to 2 GPUs even in the same node gives about a 20% speedup
(comparable to the benchmarks). Is there a specific bottleneck for this,
like input file settings, system size etc? Did anyone see significantly
better scaling under some circumstances? Not that running 900 cores in a
single machine isn't awesome, but at the moment it seems running two
independent sims on each GPU would be preferable.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Mar 07 2012 - 05:30:05 PST
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