From: George Patargias (gpat_at_bioacademy.gr)
Date: Tue Jul 22 2014 - 06:27:52 CDT
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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