On Sat, Feb 14, 2009 at 00:17,  <ashrafi@ucdavis.edu> wrote:

Hi,

I was trying to read ~400 chips in an affybatch and I got the same message.
Could you find a remedy for that. My server has 128 GB of RAM. However, R
halted ever before it uses the memory.

I have been able to load upto 250 CEL files but this time I wanted to test
what would happen if I want to normalize 400 chips.

 

Thanks for your prompt response.

 

Hamid

> 

> 

> 

> Martin Maechler wrote:

>> 

>>>>>>> "VK" == Vadim Kutsyy <vadim@kutsyy.com>

>>>>>>>     on Fri, 01 Aug 2008 07:35:01 -0700 writes:

>> 

>>     VK> Martin Maechler wrote:

>>     >>

>>     VK> The problem is in array.c, where allocMatrix check for

>>     VK> "if ((double)nrow * (double)ncol > INT_MAX)".  But why

>>     VK> itn is used and not long int for indexing? (max int is

>>     VK> 2147483647, max long int is 9223372036854775807)

>>     >>

>>     >> Well, Brian gave you all info:

>>     >>

>>     VK> exactly, and given that most modern system used for

>>     VK> computations (i.e.  64bit system) have long int which is

>>     VK> much larger than int, I am wondering why long int is not

>>     VK> used for indexing (I don't think that 4 bit vs 8 bit

>>     VK> storage is an issue).

>>     >> Did you really carefully read ?Memory-limits ??

>>     >>

>>     VK> Yes, it is specify that 4 bit int is used for indexing

>>     VK> in all version of R, but why? I think 2147483647

>>     VK> elements for a single vector is OK, but not as total

>>     VK> number of elements for the matrix.  I am running out of

>>     VK> indexing at mere 10% memory consumption.

>> 

>> Hmm, do you have 160 GBytes of RAM?

>> But anyway, let's move this topic from R-help to R-devel.

>> 

>>    [...........]

>> 

>>     VK> PS: I have no problem to go and modify C code, but I am

>>     VK> just wondering what are the reasons for having such

>>     VK> limitation.

>> 

>> This limitation and its possible remedies are an interesting topic, 

>> but really not for R-help:

>> 

>> It will be a lot about C programming the internal represenation of R 

>> objects, etc.

>> Very fascinating .... but for R-devel.

>> 

>> "See you there!"

>> Martin

>> 

>> ______________________________________________

>> R-help@r-project.org mailing list

>> https://stat.ethz.ch/mailman/listinfo/r-help

>> PLEASE do read the posting guide

>> http://www.R-project.org/posting-guide.html

>> and provide commented, minimal, self-contained, reproducible code.

>> 

>> 

> Quoted from:

> http://www.nabble.com/allocMatrix-limits-tp18763791p18776531.html

> 

> 

 


	[[alternative HTML version deleted]]

