RE: RE: NAMD CUDA on dual Nvidia 295 GPUs

From: Sadhu, Shubho (NIH/NCI) [F] (sadhusj_at_mail.nih.gov)
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.

Shubho
________________________________________
From: Axel Kohlmeyer [akohlmey_at_cmm.chem.upenn.edu]
Sent: Thursday, July 23, 2009 11:02 AM
To: Sadhu, Shubho (NIH/NCI) [F]
Cc: namd-l_at_ks.uiuc.edu; david.chalmers_at_vcp.monash.edu.au
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.

cheers,
   axel.

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

> Shubho
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of David Chalmers [david.chalmers_at_vcp.monash.edu.au]
> Sent: Thursday, July 23, 2009 8:20 AM
> To: namd-l_at_ks.uiuc.edu
> 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
> ________________________________________________________________________
>
>

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