[R] "cannot allocate vector of size ..." in RHLE5 PAE kernel

[Martin Maechler]

>>>>> "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