[R] "Error: cannot allocate vector of size 332.3 Mb"

[Jonathan Greenberg]

Steve: 

    Are you running R64.app?  If not, grab it from here:

http://r.research.att.com/R-2.9.0.pkg

(http://r.research.att.com/ under "Leopard build") .

    As far as I know (and I actually just tried it this morning), the 
standard R 2.9.1 package off the CRAN website is the 32 bit version, so 
you won't be able to access > 4GB of RAM.

--j

Steve Ellis wrote:
> Dear R-helpers,
>
> I am running R version 2.9.1 on a Mac Quad with 32Gb of RAM running 
> Mac OS X version 10.5.6.  With over 20Gb of RAM "free" (according to 
> the Activity Monitor) the following happens.
>
>     > x <- matrix(rep(0, 6600^2), ncol = 6600)
>
>     # So far so good.  But I need 3 matrices of this size.
>
>     > y <- matrix(rep(0, 6600^2), ncol = 6600)
>     R(3219) malloc: *** mmap(size=348483584) failed (error code=12)
>     *** error: can't allocate region
>     *** set a breakpoint in malloc_error_break to debug
>     R(3219) malloc: *** mmap(size=348483584) failed (error code=12)
>     *** error: can't allocate region
>     *** set a breakpoint in malloc_error_break to debug
>     Error: cannot allocate vector of size 332.3 Mb
>
> Now a 6600 x 6600 matrix should take up less than 400Mb of RAM.  So 
> the question is, with 20Gb of RAM free how come I can't create more 
> than one matrix of this size?  (In fact, sometimes R won't even create 
> one of them.)  More to the point, is there some simple remedy? 
> (Rewriting all my code to use the "Matrix" library, for example, is 
> not a simple remedy.)
>
> I tried launching R in a terminal with
>
>     R --min-vsize=10M --max-vsize=5G --min-nsize=500k --max-nsize=900M
>
> and that didn't work either.  Finally, let me remark that I had the 
> same problem with an older version of R.
>
>   -- Steve Ellis
>
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-- 

Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
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