[gmx-users] mdrun load sharing between dual processor machine
Lynne E. Bilston
l.bilston at unsw.edu.au
Thu May 2 05:24:16 CEST 2002
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?
Lynne E. Bilston, PhD
Senior Scientist, Prince of Wales Medical Research Institute, and
Conjoint Associate Professor, Faculty of Medicine, University of New South
Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924 Fax: +61-2-9382-2643
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