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

[Douglas Bates]

On 8/2/05, Spencer Graves <spencer.graves at 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 at saic.com                     `    \
> >
> >
> > -----Original Message-----
> > From: r-help-bounces at stat.math.ethz.ch
> > [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Zhilin Liu
> > Sent: Monday, August 01, 2005 8:28 PM
> > To: r-help at 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.
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> 
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