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

[Thomas Lumley]

On Tue, 2 Aug 2005, Spencer Graves wrote:

> 	  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
>>
>> 	[[alternative HTML version deleted]]
>>
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>
> -- 
> Spencer Graves, PhD
> Senior Development Engineer
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>
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>
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Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle