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Re: OT processes and cpu use

On 2007-02-19, Tyler Smith <tyler.smith@mail.mcgill.ca> wrote:
> Hi,
> I have a general question about processes in GNU/Linux. I'm working
> with PAUP, which is a command-line tool for calculating phylogenies
> from various data types (gene sequencies, proteins etc.). This sort of
> analysis routinely takes hours to days of processing. I find it is
> convenient to run paup in *shell* mode inside emacs -nw, allowing me to
> easily yank commands from various files into the paup process.
> When I check with top, it appears that paup is using 99% of the CPU
> when I do this, which is as it should be. I just wanted to check with
> more experienced people to verify that running paup from within emacs
> is not going to incur a performance hit. The analysis I have running
> at the moment (heuristic search) will take more than 5 hours, and if
> that works properly I'll be continuing on with a follow-up (bootstrap)
> that will take several days, so tweaking performance is a non-trivial
> concern.
> Any comments on my current set-up or suggestions for ways to tweak
> performance in any way would be most welcome!
Sorry for reposting, but I should add that my concern stems in part
from top reporting that 27% of the CPU is being used by users, and 73%
by system, which conflicts with the line item for paup, a user
process, which shows 99% CPU use. So I'm not sure if paup is using 99%
or 27% of the CPU:

Cpu(s): 26.7%us, 73.3%sy,  0.0%ni,  0.0%id,  0.0%wa,  0.0%hi,  0.0%si,

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND           
14385 tyler     25   0  141m 140m  660 R 99.7  9.3  82:34.35 paup  


Tyler Smit

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