Re: [R] can we manage memory usage to increase speed?

From: Douglas Bates <dmbates_at_gmail.com>
Date: Wed 03 Aug 2005 - 02:57:59 EST

On 8/2/05, Spencer Graves <spencer.graves@pdf.com> 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 "> \
> > Jaroslaw.W.Tuszynski@saic.com ` \
> >
> >
> > -----Original Message-----
> > From: r-help-bounces@stat.math.ethz.ch
> > [mailto:r-help-bounces@stat.math.ethz.ch] 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]]
> >
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>
> --
> Spencer Graves, PhD
> Senior Development Engineer
> PDF Solutions, Inc.
> 333 West San Carlos Street Suite 700
> San Jose, CA 95110, USA
>
> spencer.graves@pdf.com
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>
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>



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 Received on Wed Aug 03 03:01:31 2005

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