Re: A "strange" observation during ColVar calculations

From: Wang Yi (dexterwy_at_gmail.com)
Date: Mon Mar 21 2011 - 15:58:17 CDT

Hi Giacomo,

Thanks for your reply.

The colvar has a harmonic potential restraining about 90 non-hydrogen atoms. It is weird because, without the colvar, I can scale up to 10~12 CPUs and get 0.18 days/ns benchmark time.

Best,
___________________________

Yi (Yves) Wang
Duke University

ÔÚ 2011-3-21£¬ÏÂÎç4:46£¬ Giacomo Fiorin дµÀ£º

> 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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