From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Dec 03 2014 - 02:31:26 CST
How many cores do you use along with the GPU?
What version of namd do you use, also build type (multicore/net…)?
What timestep do you use?
What fullelectfrequency do you use?
Have you tried “twoawayx yes”?
Look around for the apoa1 or stmv benchmark for which you will find data to compare yours against on the web.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Kshatresh Dutta Dubey
Gesendet: Mittwoch, 3. Dezember 2014 00:46
An: Josh Vermaas
Cc: NAMD list; Axel Kohlmeyer
Betreff: Re: namd-l: information about simulation speed
Hi,
I am using Nvidia GTX 680 gpu for namd (cuda version) run but simulation speed, as it shows 0.496354 days/ns (~2ns/day) while system has almost 54000 atoms including solvent. Isn't it very slow? Please suggest me to get proper benchmark.
Regards
Kshatresh
On Wed, Dec 3, 2014 at 1:35 AM, Kshatresh Dutta Dubey <kshatresh_at_gmail.com> wrote:
Thanks...I got.
On Wed, Dec 3, 2014 at 1:08 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
Grep around for a "Benchmark" line. They are there.
-Josh
On 12/02/2014 05:04 PM, Kshatresh Dutta Dubey wrote:
Yes, but I found like :
WallClock: 569.721008 CPUTime: 569.721008 Memory: 128.992188 MB,
Can we get information in simulation time like ns/day or ps/day?
On Wed, Dec 3, 2014 at 12:53 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
On Tue, Dec 2, 2014 at 5:50 PM, Kshatresh Dutta Dubey
<kshatresh_at_gmail.com> wrote:
> Dear User,
>
> Is there any way to get the information about the simulation speed in namd?
> I know some package like amber prints the speed of simulation in mdout.
have you looked at the NAMD output???
>
> Regards
> Kshatresh
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- With best regards ************************************************************************************************ Kshatresh Dutta Dubey Post Doctoral Researcher, Lise Meitner Center for Computational Quantum Chemistry Hebrew University of Jerusalem Israel Jerusalem, Israel -- With best regards ************************************************************************************************ Kshatresh Dutta Dubey Post Doctoral Researcher, Lise Meitner Center for Computational Quantum Chemistry Hebrew University of Jerusalem Israel Jerusalem, Israel -- With best regards ************************************************************************************************ Kshatresh Dutta Dubey Post Doctoral Researcher, Lise Meitner Center for Computational Quantum Chemistry Hebrew University of Jerusalem Israel Jerusalem, Israel
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