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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Apr 15 11:29:00 CEST 2008


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.


 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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