From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 22 2014 - 10:56:45 CDT
This isn't surprising, there are two factors leading to your poorer than
average results:
1) The RMSD colvar is a particularly computationally intensive one, since
it not only requires the calculation of the RMSD, but also the alignment to
the reference at every step. If you redo this test with a simpler colvar
like distance, or something intermediate like radius of gyration, you'll
get much less slow-down.
2) You are using a lot of cores. The colvar calculation occurs (at least
the last time I looked into these things) on a single core, so its speed is
more or less set and is a kind of upper limit on what you can expect. So
when you add cores to the rest of the calculation, you eventually hit the
wall at how long the colvar calculation takes.
If you want to improve things, don't use so many atoms in the colvar. For
instance, you could use just the C-alphas, or even every other or every
third C-alpha. This will likely give you a dramatic improvement.
On Tue, Jul 22, 2014 at 9:41 AM, Ivan Gregoretti <ivangreg_at_gmail.com> wrote:
> Thank you Jérôme.
>
>
>
>
>
>
>
> On Tue, Jul 22, 2014 at 8:44 AM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> > George.
> >
> > I never observed such drastic difference when I have used colvars (most
> > often distance and rgyr in NAMD 2.8 and 2.9). It is advisable to check
> your
> > input and the scalability of system with and without colvars So do not
> check
> > just benchmark time, but also wallclock and CPU time after some short
> > simulation. Generally 256 processors with 258000 atoms could be too
> much...
> >
> > Branko
> >
> >
> >
> > On 7/22/2014 2:33 PM, Ivan Gregoretti 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
> >>>>
> >
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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