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

himanshu khandelia hkhandelia at gmail.com
Tue Apr 15 10:15:28 CEST 2008


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

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.

Thank you,


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