On Tue, 2 Aug 2005, Spencer Graves wrote: > And you can identify inefficient code fairly easily taking snapshots > from "proc.time" and computing elapsed time for sections of your code.
Or use the profiler, which makes it much easier. There was a Programmers' Niche article about it in one of the first R Newsletters. -thomas > spencer graves > > Tuszynski, Jaroslaw W. wrote: > >> >> If you have a code that takes 2 weeks to run, than it might be a case of >> inefficient algorithm design. I was able to go from overnight runs (SELDI >> data analysis) to 20 minute runs by identifying single inefficient function >> that took most of the time, and writing it in C. >> >> Jarek >> ====================================================\======= >> >> Jarek Tuszynski, PhD. o / \ >> Science Applications International Corporation <\__,| >> (703) 676-4192 "> \ >> [EMAIL PROTECTED] ` \ >> >> >> -----Original Message----- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu >> Sent: Monday, August 01, 2005 8:28 PM >> To: r-help@stat.math.ethz.ch >> Subject: [R] can we manage memory usage to increase speed? >> >> Hi, >> >> Thanks for reading. >> >> I am running a process in R for microarray data analysis. RedHat Enterprise >> Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of >> <200M memory. And the CPU usage is total to ~110% for two. The program takes >> at least 2 weeks to run at the current speed. Is there some way we can >> increase the usage of CPUs and memories and speed up? Any suggestion is >> appreciated. >> >> Thanks again. >> >> Zhilin >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! >> http://www.R-project.org/posting-guide.html >> >> ______________________________________________ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- > Spencer Graves, PhD > Senior Development Engineer > PDF Solutions, Inc. > 333 West San Carlos Street Suite 700 > San Jose, CA 95110, USA > > [EMAIL PROTECTED] > www.pdf.com <http://www.pdf.com> > Tel: 408-938-4420 > Fax: 408-280-7915 > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html