[Rd] [External] R crashes when using huge data sets with character string variables

[Arne Henningsen]

Dear all

Thanks a lot for your very helpful explanations and suggestions. I
have increased the size of my computer's "swapfile" and this solved my
problem, i.e., R no longer crashes when I work with character string
variables in my large data set (probably until I work with an even
larger data set).

Best wishes,
Arne



On Sun, 13 Dec 2020 at 11:17, Iñaki Ucar <iucar using fedoraproject.org> wrote:
>
> On Sun, 13 Dec 2020 at 04:27, <luke-tierney using uiowa.edu> wrote:
> >
> > If R is receiving a kill signal there is nothing it can do about it.
> >
> > I am guessing you are running into a memory over-commit issue in your OS.
> > https://en.wikipedia.org/wiki/Memory_overcommitment
> > https://engineering.pivotal.io/post/virtual_memory_settings_in_linux_-_the_problem_with_overcommit/
>
> Correct. And in particular, this is most probably the earlyoom [1]
> service in action, which, I believe, is installed and enabled by
> default in Ubuntu 20.04. It is a simple daemon that monitors memory,
> and when some conditions are reached (e.g., the system is about to
> start swapping), it looks for offending processes and kills them.
>
> [1] https://github.com/rfjakob/earlyoom
>
> Iñaki
>
> > If you have to run this close to your physical memory limits you might
> > try using your shell's facility (ulimit for bash, limit for some
> > others) to limit process memory/virtual memory use to your available
> > physical memory. You can also try setting the R_MAX_VSIZE environment
> > variable mentioned in ?Memory; that only affects the R heap, not
> > malloc() done elsewhere.
> >
> > Best,
> >
> > luke
> >
> > On Sat, 12 Dec 2020, Arne Henningsen wrote:
> >
> > > When working with a huge data set with character string variables, I
> > > experienced that various commands let R crash. When I run R in a
> > > Linux/bash console, R terminates with the message "Killed". When I use
> > > RStudio, I get the message "R Session Aborted. R encountered a fatal
> > > error. The session was terminated. Start New Session". If an object in
> > > the R workspace needs too much memory, I would expect that R would not
> > > crash but issue an error message "Error: cannot allocate vector of
> > > size ...".  A minimal reproducible example (at least on my computer)
> > > is:
> > >
> > > nObs <- 1e9
> > >
> > > date <- paste( round( runif( nObs, 1981, 2015 ) ), round( runif( nObs,
> > > 1, 12 ) ), round( runif( nObs, 1, 31 ) ), sep = "-" )
> > >
> > > Is this a bug or a feature of R?
> > >
> > > Some information about my R version, OS, etc:
> > >
> > > R> sessionInfo()
> > > R version 4.0.3 (2020-10-10)
> > > Platform: x86_64-pc-linux-gnu (64-bit)
> > > Running under: Ubuntu 20.04.1 LTS
> > >
> > > Matrix products: default
> > > BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
> > > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
> > >
> > > locale:
> > > [1] LC_CTYPE=en_DK.UTF-8       LC_NUMERIC=C
> > > [3] LC_TIME=en_DK.UTF-8        LC_COLLATE=en_DK.UTF-8
> > > [5] LC_MONETARY=en_DK.UTF-8    LC_MESSAGES=en_DK.UTF-8
> > > [7] LC_PAPER=en_DK.UTF-8       LC_NAME=C
> > > [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > > [11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C
> > >
> > > attached base packages:
> > > [1] stats     graphics  grDevices utils     datasets  methods   base
> > >
> > > loaded via a namespace (and not attached):
> > > [1] compiler_4.0.3
> > >
> > > /Arne
> > >
> > >
> >
> > --
> > Luke Tierney
> > Ralph E. Wareham Professor of Mathematical Sciences
> > University of Iowa                  Phone:             319-335-3386
> > Department of Statistics and        Fax:               319-335-3017
> >     Actuarial Science
> > 241 Schaeffer Hall                  email:   luke-tierney using uiowa.edu
> > Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Iñaki Úcar



-- 
Arne Henningsen
http://www.arne-henningsen.name