Re: A "strange" observation during ColVar calculations

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Mar 21 2011 - 15:46:27 CDT

Hello Yi, does the benchmark time have the same trend without colvars
enabled? And how many atoms did you include in the collective variables you
defined?

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Mon, Mar 21, 2011 at 2:49 PM, Wang Yi <dexterwy_at_gmail.com> wrote:

> NAMDers,
>
> Greetings from new subscriber, Yves.
>
> I have been using NAMD 2.7 Colvar for some umbrella sampling simulations.
> The system has about 3000 solvent molecules (water and DMSO) and the solute
> is about 1500 Da. What I observed as "strange" is the following:
>
> Say I submit the job to a node that has an 8-core CPU. And I request to use
> 6 cores. The benchmark time is about 0.6~0.8 days/ns. I have also tried
> requesting 4, 5, 7, 8 cores, the benchmark time all increased to about 2~3
> days/ns. I even tried to submit the job to a 12-core node, the benchmark
> time is still about 2 days/ns.
>
> The other observation is that: if my job is using 6 cores of an 8-core CPU,
> and another job is using 1 core on that CPU, my calculation would be
> significantly slowed down.
>
> I read on the Colvar manual that the Colvar functionality is not a
> parallelized process with the MD simulation. I'm speculating that this is
> the reason. But this is kind of frustrating, because, for an 8-core CPU, I
> can't use all 8 cores because it's gonna be slow. But if I use 6 cores and
> leave the other 2 cores open, someone might come in and use them, which will
> eventually slow my simulation down as well.
>
> I'm just wondering if anyone has similar experience, or hopefully a
> solution for that. Thanks a lot~
>
> Best,
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
>

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