Re: A "strange" observation during ColVar calculations

From: Wang Yi (dexterwy_at_gmail.com)
Date: Mon Mar 28 2011 - 08:40:51 CDT

Hi Jérôme,

I checked the "new feature" page of the 2.8b1 release. The ColVar part didn't say about the parallelization improvement. So I'm a bit doubtful. But as you said, I will definitely give it a shot and I will keep you guys updated. Thanks again for the kind help~

Best,
___________________________

Yi (Yves) Wang
Duke University

在 2011-3-28,上午9:33, Jérôme Hénin 写道:

> Hi Yi,
>
> There have been improvements in this respect recently. Can you try
> again with 2.8b1?
>
> Thanks,
> Jerome
>
> On 22 March 2011 18:54, Wang Yi <dexterwy_at_gmail.com> wrote:
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:50 CST