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

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Mon, 24 Mar 2008 22:12:08 +0000 (GMT)

See ?"Memory-limits" and rw-FAQ Q2.9. Since you have already used more than 1Gb of what is presumably a 2Gb address space (we don't know your Windows version), it is not surprising that there is no 285Mb hole left.

On Mon, 24 Mar 2008, Ronnen Levinson wrote:

>
> 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.
>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Mon 24 Mar 2008 - 22:19:49 GMT

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