Re: A "strange" observation during ColVar calculations

From: Jrme Hnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Mar 22 2011 - 11:30:56 CDT

Hi,

This is strange indeed. Is it possible that the colvars are I/O bound
here. Are the colvars writing large volumes of data? Can you try
setting colvarsTrajFrequency to 0?

Also, you can generally request a full node even if you do not use all
cores. Indeed, job queuing systems often assume this (and accordingly,
they charge you for using the whole node).

If the performance problem persists, you can post your colvars input
file, we'll have a look.

Best,
Jerome

2011/3/21 Wang Yi <dexterwy_at_gmail.com>:
> 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
>
>
>
>
> 在 2011-3-21,下午4:46, Giacomo Fiorin 写道:
>
> 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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