R help - May 2013 - tree in tree package - Error: cannot allocate vector of size 2.0 Gb

R version 3.0.0 (2013-04-03)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=C                LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


6GB RAM, intel core2 quad, Scientific Linux 6.4

I am using tree in the tree package.  and I get the following error:

Error: cannot allocate vector of size 2.0 Gb

shouldn't I be able to allocate more memory than 2GB?  I am sure that I 
am missing something.  Any help would be greatly appreciated.
kind regards,

-- 
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************

Let's not spend our time and resources thinking about things that are so 
little or so large that all they really do for us is puff us up and make 
us feel like gods.  We are mammals, and have not exhausted the annoying 
little problems of being mammals.

                                 -K. Mullis

"A big computer, a complex algorithm and a long time does not equal 
science."

                               -Robert Gentleman

Hi,

On Fri, May 31, 2013 at 5:38 PM, Stephen Sefick <sas0025 at auburn.edu>
wrote:
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=C                LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> 6GB RAM, intel core2 quad, Scientific Linux 6.4
>
> I am using tree in the tree package.  and I get the following error:
>
> Error: cannot allocate vector of size 2.0 Gb
>
> shouldn't I be able to allocate more memory than 2GB?  I am sure that I
am
> missing something.  Any help would be greatly appreciated.
I don't remember who on the R list had previously put it this way, but
it puts it best, I think:

The 2gb is the straw that broke the camel's back.

R has likely been allocating more and more memory for whatever it's
trying to do and at some point it asked the OS for another 2gb more,
and *bam* ... toasted.

If you look at top (or htop) and monitor the R process as it's
running, I reckon that's what you'll see, too.

HTH,

-stee

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech

On May 31, 2013, at 2:38 PM, Stephen Sefick wrote:
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=C                LC_NAME=C
> [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> 6GB RAM, intel core2 quad, Scientific Linux 6.4
> 
> I am using tree in the tree package.  and I get the following error:
> 
> Error: cannot allocate vector of size 2.0 Gb
> 
> shouldn't I be able to allocate more memory than 2GB?
I believe that should be read as "unable to allocate contiguous block of
memory for a new object of size 2Gb".

The general rule is that you should have at least 3 times the free
(non-OS/non-other-running-applications) RAM as the size of your largest objects.
You seem to be in violation of that rule.

-- 

David Winsemius
Alameda, CA, USA