From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Aug 19 2014 - 11:15:29 CDT
I think he wants something with more atoms, so that scaling with more GPUs
is more evident.
I suggest looking at the AMBER benchmark page, they have for instance a
ribosomal subunit or something massive like that.
On Tue, Aug 19, 2014 at 12:10 PM, Phil Greer <pgreer_at_structbio.pitt.edu>
> In the apoa1.namd file edit the numsteps parameter to 10000 or higher.
> -Phil Greer
> On Aug 19, 2014, at 11:48 AM, Maxime Boissonneault <
> maxime.boissonneault_at_calculquebec.ca> wrote:
> > Hi,
> > I am running the apoa1 benchmark on our GPU cluster. Each node has 8
> GPUs and 20 cores. I am compiling Namd with MPI and SMP support. It seems I
> reach a limit of about ~0.01s/step with one node, and cannot go quicker
> with more than one node.
> > Is there a larger benchmark out there that would scale better on this
> type of system ?
> > Thanks,
> > --
> > ---------------------------------
> > Maxime Boissonneault
> > Analyste de calcul - Calcul Québec, Université Laval
> > Ph. D. en physique
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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