"cannot allocate vector of size ..." in RHLE5 PAE kernel

Mon, Jan 17, 2011 7:42 AM

Following the advice a colleague, I put the gc() and gcinfo(TRUE)
commands just before the line I got the problem, and their output
were:

                 used (Mb) gc trigger  (Mb)  max used   (Mb)
Ncells  471485 12.6    1704095  45.6   7920371  211.5
Vcells 6408885 48.9  113919753 869.2 347651599 2652.4

Garbage collection 538 = 323+101+114 (level 2) ...
13.0 Mbytes of cons cells used (29%)
49.0 Mbytes of vectors used (7%)

Error: cannot allocate vector of size 238.1 Mb


If I understood correctly, I should have enough memory for allocating
the new matrix (Q.obs <- matrix(NA, nrow=6940,  MZ> ncol=9000) ))

Thanks in advance for any help,

Mauricio

===============================
Linux user #454569 -- Ubuntu user #17469
===============================

2011/1/17 Martin Maechler <maechler at stat.math.ethz.ch>:
>>>>>> "MZ" == Mauricio Zambrano <hzambran.newsgroups at gmail.com>
>>>>>> ? ? on Mon, 17 Jan 2011 11:46:44 +0100 writes:
>
> ? ?MZ> Dear R community,
> ? ?MZ> I'm running R 32 bits in a 64-bits machine (with 16Gb of Ram) using a
> ? ?MZ> PAE kernel, as you can see here:
>
> ? ?MZ> $ uname -a
> ? ?MZ> Linux mymachine 2.6.18-238.el5PAE #1 SMP Sun Dec 19 14:42:44 EST 2010
> ? ?MZ> i686 i686 i386 GNU/Linux
>
>
> ? ?MZ> When I try to create a large matrix ( Q.obs <- matrix(NA, nrow=6940,
> ? ?MZ> ncol=9000) ), I got the following error:
>
>
> ? ?>> Error: cannot allocate vector of size 238.3 Mb
>
>
> ? ?MZ> However, the amount of free memory in my machine seems to be much
> ? ?MZ> larger than this:
>
> ? ?MZ> system("free")
> ? ?MZ> \ ? ? ? ? ? ? total ? ? ? used ? ? ? free ? ? shared ? ?buffers ? ? cached
> ? ?MZ> Mem: ? ? ?12466236 ? ?6354116 ? ?6112120 ? ? ? ? ?0 ? ? ?67596 ? ?2107556
> ? ?MZ> -/+ buffers/cache: ? ?4178964 ? ?8287272
> ? ?MZ> Swap: ? ? 12582904 ? ? ? ? ?0 ? 12582904
>
>
> ? ?MZ> I tried to increase the memory limit available for R by using:
>
> ? ?MZ> $ R --min-vsize=10M --max-vsize=5000M --min-nsize=500k --max-nsize=5000M
>
>
> ? ?MZ> but it didn't work.
>
>
> ? ?MZ> Any hint about how can I get R using all the memory available in the machine ?
>
> Install a 64-bit version of Linux, i.e., ubuntu in your case
> and work from there.
> I don't think there's a way around that.
>
> Martin
>

"cannot allocate vector of size ..." in RHLE5 PAE kernel

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