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

From: Thomas Lumley <tlumley_at_u.washington.edu>
Date: Wed 03 Aug 2005 - 04:08:29 EST

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@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
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>
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>
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>

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

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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 04:12:35 2005

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