On 2007-02-19, Tyler Smith <[EMAIL PROTECTED]> 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 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
