From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 26 2013 - 11:02:19 CDT
Not yet, I have to complete other work before getting really involved with
metadynamics.. Sorry for having misunderstood how the system works.
On Fri, Apr 26, 2013 at 5:19 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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 appreciate 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 the
>> > 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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