[R] increase the usage of CPU and Memory

[Oliver Ruebenacker]

     Hello Xi,

  If a program has input or output to disk or network, this may cause
it to wait and not use the available CPU.

  Output is usually buffered, but may cause delay if the buffer gets
full (I'm not sure though whether this is an issue with plenty of
memory available)

     Take care
     Oliver

On Mon, Jun 25, 2012 at 8:07 PM, Xi <amzhangxi at gmail.com> wrote:
> Dear All,
>
> I have been searching online for help increasing my R code more efficiently
> for almost a whole day, however, there is no solution to my case. So if
> anyone could give any clue to solve my problem, I would be very appreciate
> for you help. Thanks in advance.
>
> Here is my issue:
>
> My desktop is with i7-950 Quad-core CPU with 24Gb memory, and a  NVIDIA GTX
> 480  graphic card, and I am using a 64-bit version of R under 64-bit Windows
> .
>
> I am running a "for" loop to generate a 461*5 matrix data, which is coming
> from the coefficients of 5 models. The loop would produce 5 values one
> time, and it will run 461 times in total. I have tried to run the code
> inside the loop just once, it will cost almost 10 seconds, so if
> we intuitively calculate the time of the whole loop will cost, it would be
> 4610 seconds, equal to almost one and a half hours, which is exactly the
> whole loop taking indeed. But I have to run this kinda loop for
> 30 data-sets!
>
> Although I thought I am using a not-bad at all desktop, I checked the usage
> of CPU and memory during my running R code, and found out the whole code
> just used 15% of CPU and 10% of memory. Does anyone have the same issue
> with me? or Does anyone know some methods to shorten the running time and
> increase the usage of CPU and memory?
>
> Many thanks,
> Xi
>
>        [[alternative HTML version deleted]]
>
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-- 
Oliver Ruebenacker, Bioinformatics and Network Analysis Consultant
President and Founder of Knowomics
(http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Consultant at Predictive Medicine
(http://predmed.com/people/oliverruebenacker.html)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)