[R] Cannot allocate large vectors (running out of memory?)

From: Ronnen Levinson <RML27_at_cornell.edu>
Date: Mon, 24 Mar 2008 14:39:55 -0700

   Hi.
   As shown in the simplified example below, I'm having trouble allocating    memory for large vectors, even though it would appear that there is more    than enough memory available. That is, even with a memory limit of 1500 MB,    R 2.6.1 (Win) will allocate memory for a first vector of 285 MB, but not for    a second vector of the same size. Forcing garbage collection does not seem    to solve the problem.
   Can anyone explain why is this happening, and how to fix it?    Thanks,
   Ronnen.
   P.S. E-mailed CCs of posted replies would be appreciated.
> rm(list=ls(all=TRUE))
> gc()

            used (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells 143465  3.9     350000   9.4    350000   9.4
   Vcells 88573 0.7 50380943 384.4 131023877 999.7
> memory.limit()

   [1] 1535.875
> n <- 8640 * 4320
> x=rep(1/3, n)
> memory.size()

   [1] 578.8543
> gc()
              used  (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells   143471   3.9     350000   9.4    350000   9.4
   Vcells 37413375 285.5 78720219 600.6 131023877 999.7
> y=rep(1/7, n)

   Error: cannot allocate vector of size 284.8 Mb
> memory.size()

   [1] 578.8543
> gc()
              used  (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells   143471   3.9     350000   9.4    350000   9.4
   Vcells 37413375 285.5 78720219 600.6 131023877 999.7
> version
                  _
   platform       i386-pc-mingw32
   arch           i386
   os             mingw32
   system         i386, mingw32
   status
   major          2
   minor          6.1
   year           2007
   month          11
   day            26
   svn rev        43537
   language       R

   version.string R version 2.6.1 (2007-11-26)

   --
   Ronnen Levinson, Ph.D.
   scientist, Lawrence Berkeley National Lab    The Onion horoscope: Pisces February 19 - March 20 You will soon be    unwillingly forced into a flurry of activity when you are chosen to host the    2014 Winter Olympiad.



R-help_at_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. Received on Mon 24 Mar 2008 - 22:01:56 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 24 Mar 2008 - 23:30:23 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive