A "strange" observation during ColVar calculations

From: Wang Yi (dexterwy_at_gmail.com)
Date: Mon Mar 21 2011 - 13:49:45 CDT


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~


Yi (Yves) Wang
Duke University

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