On 8/2/05, Spencer Graves <[EMAIL PROTECTED]> wrote: > And you can identify inefficient code fairly easily taking snapshots > from "proc.time" and computing elapsed time for sections of your code. > > spencer graves
Using Rprof may be a better choice. See ?Rprof > > 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 > ______________________________________________ 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