RE: RE: NAMD CUDA on dual Nvidia 295 GPUs

From: Sadhu, Shubho (NIH/NCI) [F] (
Date: Thu Jul 23 2009 - 12:14:42 CDT

For those without dedicated GPU cards, decreasing the time until the monitor is put to sleep and/or running simulations overnight will help. In Ubuntu, the monitor sleep time can be changed at system > preferences > power management. Since there's no output to the monitor when it's asleep, the GPU can focus on NAMD.

From: Axel Kohlmeyer []
Sent: Thursday, July 23, 2009 11:02 AM
To: Sadhu, Shubho (NIH/NCI) [F]
Subject: Re: namd-l: RE: NAMD CUDA on dual Nvidia 295 GPUs

On Thu, 2009-07-23 at 10:11 -0400, Sadhu, Shubho (NIH/NCI) [F] wrote:

> You could also use the +devices flag to specify certain GPU board(s)
> (you can find the numbers of the boards with the deviceQuery program
> in the Cuda SDK). I've found that if NAMD is using the same video card
> as the GUI, NAMD runs much slower. Use "grep binding <NAMD log file>"

this is an important point. particularly using the composite extension
and other x applications that cause many redraw events can cut the
performance of the GPU easily in half or worse. i found that vncviewer
is a very problematic application. in general it is good advice to
run everything but short tests on dedicated compute GPUs.


> to see which GPUs NAMD is running on. These lines are printed during
> startup. Hope this helps,

> Shubho
> ________________________________________
> From: [] On Behalf Of David Chalmers []
> Sent: Thursday, July 23, 2009 8:20 AM
> To:
> Subject: namd-l: NAMD CUDA on dual Nvidia 295 GPUs
> Dear All,
> We are trying out the CUDA version of NAMD (2.7b1 CVS version from a few
> days ago) on a machine with a quad core i7 cpu and two Geforce 295 GPUs. We
> are using Suse 11.1 with the most recent NVIDIA drivers and cuda toolkit
> installed.
> We are seeing a speed-up in NAMD running on a single core, but as far as we
> can tell, the speed up is only consistent with a single GPU being used.
> When we use the 'nvidia-settings' gui, the temperature of only one of the
> four GPUs is rising much.
> This leads me to a few questions:
> Can I use all four GPUs?
> Should I be using one, four (or some other number) of cores?
> Which version of NAMD should I be using, multicore or the charmrun version?
> Is there some way that I can better understand how many GPUs NAMD is using?
> Thanks for any advice,
> David
> ________________________________________________________________________
> David Chalmers
> Faculty of Pharmacy, Monash University
> 381 Royal Pde, Parkville, Vic 3053. Australia
> ________________________________________________________________________

Axel Kohlmeyer
   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.

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