[gmx-users] cpu utilization

Dean Johnson dtj at uberh4x0r.org
Fri Oct 17 19:37:00 CEST 2003

Howdy all,
I have started running some benchmarks using the latest of all the 
required software (with vanilla MPICH). Its a 16 node Dell dual 1.7 & 
1.8Ghz xeons with gigE. When I am running Amber I get pretty much full 
cpu utillization when I run two 16 cpu (16x1) jobs and slightly less 
with a single 32 cpu (16x2)  job. Running GROMACS, I can only get 
utilization up close to 40% when I try larger jobs. The nodes have 
plenty of memory and the systems are pretty quiet. Is this consistent 
with what people are seeing?

Also, perhaps a bit of evidence, it has a real hard time cleaning up 
after itself. The output indicating performance and stuff comes *way* 
before the jobs eventually die and some never die. I had to write a 
simple  'killgro' command to nuke everything for good. Any ideas?


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