From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 22 2014 - 07:43:30 CDT
The basic idea is stated here:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132410000000000000
And there is an analysis of scaling and performance issues in this open
access paper:
http://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594#.U85b3v5Jy_8
If you have follow-up questions on that, feel free to ask them here!
Best,
Jerome
On 22 July 2014 14:33, Ivan Gregoretti <ivangreg_at_gmail.com> wrote:
> Hi Jérôme,
>
> Could you expand your answer a little bit?
>
> Thank you,
>
> Ivan
>
>
>
>
>
>
> On Tue, Jul 22, 2014 at 7:56 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
> > That is completely dependent on what variables you define, how many atoms
> > are involved, and the biases.
> >
> > Jerome
> >
> >
> >
> >
> > On 22 July 2014 13:27, George Patargias <gpat_at_bioacademy.gr> wrote:
> >>
> >> Hello,
> >>
> >> I am comparing the Benchmark times for a given system (~258,000 atoms)
> >> using
> >> NAMD_CVS-2014-06-02_Source version with and without the colvar module
> on.
> >>
> >> When the colvar module is *off* (equilibrium MD), I get something like
> >>
> >> Benchmark time: 256 CPUs 0.0268481 s/step 0.155371 days/ns 540.59 MB
> >> memory
> >>
> >> When the colvar module is *on* (moving harmonic restraint on an RMSD
> >> colvar calculated from 1981 C-alpha atoms), I get
> >>
> >> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns 569.555 MB
> memory
> >>
> >> which is 11-12 times slower.
> >>
> >> Is this the actual computational cost of a colvar calculation?
> >>
> >> Also the scaling of this particular colvar calculation is not good:
> >>
> >> Benchmark time: 48 CPUs 0.331787 s/step 1.92006 days/ns
> >> Benchmark time: 128 CPUs 0.322472 s/step 1.86616 days/ns
> >> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns
> >>
> >> Thanks in advance!
> >>
> >> George
> >>
> >> Dr. George Patargias
> >> Postdoctoral Research Fellow
> >> Biomedical Research Foundation
> >> Academy of Athens
> >> 4, Soranou Ephessiou
> >> 115 27
> >> Athens
> >> Greece
> >>
> >> Office: +302106597568
> >>
> >
>
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