On Sun, 13 Dec 2020 at 04:27, <luke-tier...@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-tier...@uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Iñaki Úcar ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
