[R] "cannot allocate vector of size ..." in RHLE5 PAE kernel
maechler at stat.math.ethz.ch
Mon Jan 17 12:36:12 CET 2011
>>>>> "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> \ 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.
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