And you can identify inefficient code fairly easily taking snapshots from "proc.time" and computing elapsed time for sections of your code.
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