[gmx-users] mdrun load sharing between dual processor machine

[Lynne E. Bilston]

Hi,

I''ve just noticed that when I run the normal version of gromacs (mdrun) on 
my new dual athlon linux machines, that it doesn't fully load both 
processors. According to top, although I'm getting 99.9% cpu usage for 
mdrun, it also says that cpu0 is working at about 80% and cpu1 is working 
at only about 20%. This adds up to 100% of one cpu. Does this mean I need 
to use the mpi version to fully utilise both processors?

And if I want to share a run across, say, 3 dual processor machines, what 
parameters should I use? Do I specify that each node has 2 processors in 
the lam hosts file, and then just do the usual with 3 nodes?

Also, does ssh slows down the interconnect compared to rsh?

Thanks,

Lynne
________________________________________________________________________________
Lynne E. Bilston, PhD
Senior Scientist, Prince of Wales Medical Research Institute, and
Conjoint Associate Professor, Faculty of Medicine, University of New South 
Wales
Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924	Fax: +61-2-9382-2643
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