[gmx-users] gromacs analysis performance on a dual core suse box.

Stéphane Téletchéa stephane.teletchea at jouy.inra.fr
Tue Apr 15 14:27:40 CEST 2008

Florian Haberl a écrit :
> Hi,
> On Tuesday, 15. April 2008 10:15, himanshu khandelia wrote:
>> Hello,
>> I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis
>> and want to know what is the limiting factor in my machine's
>> performance.
>> When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of
>> my machine pretty much freezes up. A trjconv will use only 1 cpu, but
>> is it using all the memory of the machine as well for IO? If it is not
>> using all the memory, then why does the machine freeze? Of course, the
>> answers might lie in my local installation, but I was wondering if you
>> folks have some insights? I am running Suse 10.x.
>> A top command typically indicates a 20-35 % cpu usage while running
>> the trjconv.
> is your data on the local machine or it is mounted over nfs?
> Do you have gbit nics?
> Normally 100mbit cards or slow nfs server are the limiting factor.
> Greetings,
> Florian

I'd bet for your hard drive limiting the troughput, hard drives are
really slow in comparison with memory and cpu speed.
The fact that your machine seems frozen is another link to that.

In order to get a better response (i.e not complete freeze of the
machine), you could try another kernel scheduler (see the kernel option
elevator), but this will be a compromise between responsiveness and


Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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