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 <maech...@stat.math.ethz.ch>: >>>>>> "MZ" == Mauricio Zambrano <hzambran.newsgro...@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 > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.