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

Mon, Jan 17, 2011 5:34 AM

Thanks for your answer Martin, but -unfortunately- the decision about
installing a 32 bits OS in the 64 bits machine, was taken by the IT
guys of my work and not by me.

By the way, due to strong limitations about software installation in
my work place, this problem didn't happen in Ubuntu, but in Red Hat
Enterprise 5. At home I have Ubuntu 10.10 32 bits, but I can not run
the code I need in that machine.


Cheers,

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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