From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 22 2014 - 06:56:42 CDT
That is completely dependent on what variables you define, how many atoms
are involved, and the biases.
On 22 July 2014 13:27, George Patargias <gpat_at_bioacademy.gr> wrote:
> I am comparing the Benchmark times for a given system (~258,000 atoms)
> 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!
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Office: +302106597568
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