Re: A "strange" observation during ColVar calculations

From: Wang Yi (dexterwy_at_gmail.com)
Date: Tue Mar 22 2011 - 12:54:29 CDT

Hi Jerome,

I tried turning off the colvar output. It didn't appear to change the performance. I got the same benchmark time of 0.5 days/ns, on the same node, with colvarsTrajFrequency being 0 and 100. Therefore, it doesn't seem to be an I/O issue. Here is my colvar input:

colvarsTrajFrequency 100
colvar {
        name complex
        distance {
                group1 {atomNumbersRange 1 - 126}
                group2 {atomNumbersRange 127 - 156}
        }
}
harmonic {
        colvars complex
        centers 5.00
        forceConstant 45.0
}

Thanks.
___________________________

Yi (Yves) Wang
Duke University

在 2011-3-22,下午12:30, Jérôme Hénin 写道:

> 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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