Dear Jim,

Thanks for your attention. I am running a geostatistic analysis with geoR that is computational intense. At the end my analysis I call the function krige.control and krige.conv.  Do you have any idea how to improve the memory allocation in Linux?

Thanks,
Ricardo



De: jim holtman <jholtman@gmail.com>
Assunto: Re: [R] Memory Management under Linux
Para: "ricardo souza" <ricsouzabh@yahoo.com.br>
Cc: r-help@r-project.org
Data: Sexta-feira, 5 de Novembro de 2010, 10:21

It would be very useful if you would post some information about what
exactly you are doing.  There si something with the size of the data
object you are processing ('str' would help us understand it) and then
a portion of the script (both before and after the error message) so
we can understand the transformation that you are doing.  It is very
easy to generate a similar message:

> x <- matrix(0,20000, 20000)
Error: cannot allocate vector of size 3.0 Gb

but unless you know the context, it is almost impossible to give
advice.  It also depends on if you are in some function calls were
copies of objects may have been made, etc.

On Thu, Nov 4, 2010 at 7:52 PM, ricardo souza <ricsouzabh@yahoo.com.br> wrote:
> Dear all,
>
> I am using ubuntu linux 32 with 4 Gb.  I am running a very small script and I always got the same error message:  CAN NOT ALLOCATE A VECTOR OF SIZE 231.8 Mb.
>
> I have reading carefully the instruction in ?Memory.  Using the function gc() I got very low numbers of memory (please sea below).  I know that it has been posted several times at r-help (http://tolstoy.newcastle.edu.au/R/help/05/06/7565.html#7627qlink2).  However I did not find yet the solution to improve my memory issue in Linux.  Somebody cold please give some instruction how to improve my memory under linux?
>
>> gc()
>          used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 170934  4.6     350000  9.4   350000  9.4
> Vcells 195920  1.5     786432  6.0   781384  6.0
>
> INCREASING THE R MEMORY FOLLOWING THE INSTRUCTION IN  ?Memory
>
> I started R with:
>
> R --min-vsize=10M --max-vsize=4G --min-nsize=500k --max-nsize=900M
>> gc()
>          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
> Ncells 130433  3.5     500000 13.4      25200   500000 13.4
> Vcells  81138  0.7    1310720 10.0         NA   499143  3.9
>
> It increased but not so much!
>
> Please, please let me know.  I have read all r-help about this matter, but not solution. Thanks for your attention!
>
> Ricardo
>
>
>
>
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>
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>
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?



      
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