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,
0.0%st
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
--
Regards,
Tyler Smit
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