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(New page: 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. <pre> $ cat 8GB.R x <-...) |
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| + | Those errors about tty and job control have something to do with shell startup and terminal settings, and are normal. | ||
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| + | ==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 | ||
Revision as of 20:49, 27 October 2011
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.
$ 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 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.o497 Warning: 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.
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
