RE: RE: NAMD CUDA on dual Nvidia 295 GPUs

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 23 2009 - 12:28:24 CDT

On Thu, 2009-07-23 at 13:14 -0400, Sadhu, Shubho (NIH/NCI) [F] wrote:

> 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.

or you can type into an xterm: xset dpms force off

or hit: Ctrl-Alt-F1
to switch to a text console.

cheers,
   axel.

> 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
> > ________________________________________________________________________
> >
> >
>
> --
> =======================================================================
> 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.
>

-- 
=======================================================================
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.

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