On Jul 1, 2009, at 4:43 PM, Jonathan Greenberg wrote:
By the way, you'll probably have to reinstall some or all of your
packages (and dependencies) if you are using R64.app, probably
downgrading them in the process.
--j
This really ought to be on the r-sig-mac list. I am copying that list
and follow-ups to any of these comments ought to trim the r-help
address.
It is certainly true that packages will need to be reinstalled, but I
am puzzled by the comment about "probably downgrading". My experience
is that current versions of packages are almost always available on
CRAN. The R.app 64 bit GUI provides for compiling from source and only
a few packages fail to compile for the Mac OS X 10.5.x 64-bit
architecture.
--
DW
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.
Correct. On a Mac:
x <- matrix(rep(0, 6600^2), ncol = 6600)
> object.size(x)
[1] 348480200
So the question is, with 20Gb of RAM free how come I can't create
more than one matrix of this size?
I am unable to reproduce that problem with "only" 10GB installed.
(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.)
Some part of your installation is faulty. You should not need to use
the 64 bit version to get those matrices created. Discuss further on
the r-sig-mac list.
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
__________________________________
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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