R
From FarmShare
Currently there's R 2.14.x installed from Ubuntu repos, and R 2.15.0 installed in FarmShare modules.
R Sample Job
Here's an example R file that generates a large array, fills it with some random numbers, then sleeps for 5mins. This happens to use up almost exactly 8GB of RAM.
[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh/R_test [0] $ cat 8GB.R x <- array(1:1073741824, dim=c(1024,1024,1024)) x <- gaussian() Sys.sleep(300)
Here's an example SGE submit script that runs that R file.
$ cat r_test.script #!/bin/bash # use the current directory #$ -cwd # mail this address #$ -M chekh@stanford.edu # send mail on begin, end, suspend #$ -m bes # get rid of spurious messages about tty/terminal types #$ -S /bin/sh R --vanilla --no-save < 8GB.R
You can submit it with just
qsub r_test.script
Here are the output files that I get, one from stderr, one from stdout
$ cat r_test.script.e497 tset: standard error: Function not implemented Undefined tty stdin: is not a tty
$ cat r_test.script.o497Warning: no access to tty (Bad file descriptor). Thus no job control in this shell.
R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
> x <- array(1:1073741824, dim=c(1024,1024,1024)) > x <- gaussian() > Sys.sleep(300) >
Those errors about tty and job control have something to do with shell startup and terminal settings, and are normal. Or specify the 'sh' shell in your job script
#get rid of spurious messages about tty/terminal types #$ -S /bin/sh
In the mail that you get about the ending of the job, the maxvmem number is actually incorrect, it is a known bug in this version of SGE. The R script on this page actually uses 8GB of vmem.
Installing CRAN Packages
Most CRAN packages can be installed per-user by running install.packages() in an interactive session:
install.packages("package_name", dependencies = TRUE)
R initially attempts to install to /usr/local/lib/R, but will prompt for the creation of a library subdirectory in ~/R (if necessary) and fall back to installation there when the initial attempt fails. If your package requires dependencies available from the standard Ubuntu repositories you can submit a HelpSU ticket requesting installation.
Links
Some other departments have some other more detailed examples:
- http://wiki.genomics.upenn.edu/index.php/HPC:ExamplesR
- http://me.eng.uab.edu/wiki/index.php?title=R-userinfo
- https://www.stanford.edu/dept/statistics/cgi-bin/projects/stat-sysadminwiki/index.php/R_Jobs