On Mon, Feb 19, 2007 at 09:56:26PM +0000, Tyler Smith wrote: > Hi, 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 If your process is already taking the whole cpu, i don't see how you could improve its performance. > 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 if you're really looking at many days of processing, it may be worth your while to run some test in different configurations and timing them. Saving a few % here and there maybe worthwhile. All I can suggest is that you eliminate *every* process that you don't need in order to do your thing. If you're running emacs -nw, then you must be running X in some form, do you need it? If not, get rid of it -- X will on occaision demand some cpu. If it works out to a couple % over a couple days, you're looking at an h our or so. .02 A
Attachment:
signature.asc
Description: Digital signature