From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Apr 26 2013 - 10:19:40 CDT
Did you perform a test between running with and without the GPUs? Even in
NAMD the biasing code only uses a single CPU.
On Fri, Apr 26, 2013 at 10:53 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Apr 26, 2013 at 4:46 PM, Francesco Pietra <chiendarret_at_gmail.com>
> > Hello:
> > This is to ask whether there is any plan to extend NAMD-CUDA to
> > bias-exchange metadynamics, temperature-exchange metadynamics, and
> > reconnaissance metadynamics. This is just to plan with my work.
> > I was not careful enough to appreaciate that PLUMED-NAMD is at a single
> > processor. I compiled NAMD2.9-CUDA4.0 with PLUMED1.3, including recon,
> > it seemed to run on multiple GPUs, by inserting commands for PLUMED into
> > NAMD conf file (just a "distance" job on a large protein I was engaged
> > with). According to nvidia-smi, all GPUs were involved, and the log file
> > showed PLUMED involved. Now, having been informed that PLUMED is at a
> > CPU with NAMD, it must have been fake success.
> it is not fake, it just shows that you know little about parallel
> programming, GPU acceleration, and code optimization.
> > Thanks
> > francesco pietra
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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