R help - Sep 2004 - memory problem under windows

I have (still) some memory problems, when trying to allocate a huge array:

WinXP pro, with 2G RAM

I start R by calling:	

Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ)

R.Version(): i386-pc-mingw32, 9.1, 21.6.2004

## and here the problem
x.dim <- 46
y.dim <- 58
slices <- 40
volumes <- 1040
a <- rep(0, x.dim * y.dim * slices * volumes)
dim(a) <- c(x.dim, y.dim, slices, volumes)

gives me: "Error: cannot allocate vector of size 850425 Kb"

even though

memory.limit(size = NA)
yields 	2147483648

and

memory.size()
gives 905838768

so why is that and what can I do against it?

Many thanks for your kind help

Cheers

Christoph

-- 
Christoph Lehmann                            Phone:  ++41 31 930 93 83
Department of Psychiatric Neurophysiology    Mobile: ++41 76 570 28 00
University Hospital of Clinical Psychiatry   Fax:    ++41 31 930 99 61
Waldau                                            lehmann at puk.unibe.ch
CH-3000 Bern 60         http://www.puk.unibe.ch/cl/pn_ni_cv_cl_03.html

Christoph Lehmann wrote:
> I have (still) some memory problems, when trying to allocate a huge array:
> 
> WinXP pro, with 2G RAM
> 
> I start R by calling:   
> 
> Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ)
Not sure that it actually says to use 2Gb there. You might try 
--max-mem-size=2000M, which seems to work better for me.

HTH,

Jim




-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

Did you read the *rest* of what the rw-FAQ says?

  Be aware though that Windows has (in most versions) a maximum amount of
  user virtual memory of 2Gb, and parts of this can be reserved by 
  processes but not used. The version of the memory manager used from R
  1.9.0 allocates large objects in their own memory areas and so is better
  able to make use of fragmented virtual memory than that used previously.

  R can be compiled to use a different memory manager which might be
  better at using large amounts of memory, but is substantially slower
  (making R several times slower on some tasks).

So, it tells you about memory fragmentation, and it tells you about making 
R aware of large-memory versions of Windows and that an alternative memory 
manager can be used.  If you actually tried those, the posting guide asks 
you to indicate it, so I presume you did not.

Also, take seriously the idea of using a more capable operating system 
that is better able to manage 2Gb of RAM.


On Tue, 14 Sep 2004, Christoph Lehmann wrote:
> I have (still) some memory problems, when trying to allocate a huge array:
> 
> WinXP pro, with 2G RAM
> 
> I start R by calling:	
> 
> Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ)
> 
> R.Version(): i386-pc-mingw32, 9.1, 21.6.2004
> 
> ## and here the problem
> x.dim <- 46
> y.dim <- 58
> slices <- 40
> volumes <- 1040
> a <- rep(0, x.dim * y.dim * slices * volumes)
> dim(a) <- c(x.dim, y.dim, slices, volumes)
> 
> gives me: "Error: cannot allocate vector of size 850425 Kb"
> 
> even though
> 
> memory.limit(size = NA)
> yields 	2147483648
> 
> and
> 
> memory.size()
> gives 905838768
> 
> so why is that and what can I do against it?
> 
> Many thanks for your kind help
> 
> Cheers
> 
> Christoph
> 
> 
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595