[Rd] allocMatrix error

From: Hamid Ashafi <ashrafi_at_ucdavis.edu>
Date: Tue, 17 Feb 2009 00:29:46 -0800


On Sat, Feb 14, 2009 at 00:17, <ashrafi_at_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_at_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_at_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

>

>  

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