can we manage memory usage to increase speed?

	  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                                   ">   \
 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

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Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

can we manage memory usage to increase speed?

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