Re: Running NAMD on Forge (CUDA)

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Jul 12 2012 - 13:41:16 CDT

Hi Aron,

Thanks for the explanations. I don't know whether I'm doing everything
right. I don't see any speed advantage running on the CUDA cluster (Forge)
versus running on a non-CUDA cluster.

I did the following benchmarks on Forge (the system has 127,000 atoms
and ran for 1000 steps):

np 1: 506 sec
np 2: 281 sec
np 4: 163 sec
np 6: 136 sec
np 12: 218 sec

On the other hand, running the same system on 16 cores of Trestles (AMD
Magny Cours) takes 129 sec. It seems that I'm not really making good use
of SUs by running on the CUDA cluster. Or, maybe I'm doing something
wrong? I'm using the ibverbs-smp-CUDA pre-compiled version of NAMD 2.9.

Thanks,

      Gianluca

On Tue, 10 Jul 2012, Aron Broom wrote:

> if it is truly just one node, you can use the multicore-CUDA version and avoid the
> MPI charmrun stuff.  Still, it boils down to much the same thing I think.  If you do
> what you've done below, you are running one job with 12 CPU cores and all GPUs.  If
> you don't specify the +devices, NAMD will automatically find the available GPUs, so I
> think the main benefit of specifying them is when you are running more than one job
> and don't want the jobs sharing GPUs.
>
> I'm not sure you'll see great scaling across 6 GPUs for a single job, but that would
> be great if you did.
>
> ~Aron
>
> On Tue, Jul 10, 2012 at 1:14 PM, Gianluca Interlandi <gianluca_at_u.washington.edu>
> wrote:
> Hi,
>
> I have a question concerning running NAMD on a CUDA cluster.
>
> NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. If I
> want to use all 6 CUDA devices in a node, how many processes is it
> recommended to spawn? Do I need to specify "+devices"?
>
> So, if for example I want to spawn 12 processes, do I need to specify:
>
> charmrun +p12 -machinefile $PBS_NODEFILE +devices 0,1,2,3,4,5 namd2
> +idlepoll
>
> Thanks,
>
>      Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>                     +1 (206) 685 4435
>                     http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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