Running R on JASMIN
Running R on JASMIN
On the JASMIN sci servers and LOTUS, we support the use of R through the
“jasr” environment(s), as listed on the
Jaspy page.
In order to activate the R environment, you will need to use:
module load jasrNote that the Jaspy page lists all available environments. You can also list the R packages that are available in the environment by typing:
ls $CONDA_PREFIX/lib/R/library/Once you have activated the environment, you can start R, using:
R
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-conda-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.
Natural language support but running in an English locale
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.
[Previously saved workspace restored]
If you have an R script that you wish to run, you can use the “Rscript” command, such as:
Rscript <myscript>The following shows the options available when using “Rscript”:
Rscript --help
Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]
--options accepted are
--help Print usage and exit
--version Print version and exit
--verbose Print information on progress
--default-packages=list
Where 'list' is a comma-separated set
of package names, or 'NULL'
or options to R, in addition to --no-echo --no-restore, such as
--save Do save workspace at the end of the session
--no-environ Don't read the site and user environment files
--no-site-file Don't read the site-wide Rprofile
--no-init-file Don't read the user R profile
--restore Do restore previously saved objects at startup
--vanilla Combine --no-save, --no-restore, --no-site-file
--no-init-file and --no-environ
'file' may contain spaces but not shell metacharacters
Expressions (one or more '-e <expr>') may be used *instead* of 'file'
See also ?Rscript from within RThe version number (currently 4.0.5) is reported when you start R, or if you type:
R --version
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
Here are commands to do a simple plot to a file, which you can use to test running R either interactively or with “Rscript” as described above.
png("myplot.png")
x <- c(1,2,3,4)
y <- x*x
plot(x,y)
dev.off()(You could use the “display” command on JASMIN to view the output file.)
Here is a minimal example of using the “library” command to load one of the many add-on libraries that have been installed to supplement the core R distribution. It uses the “prettyunits” package to convert a number of bytes to human-readable format.
module load jasr
R --quietlibrary(prettyunits)
pretty_bytes(12345678)
[1] "12.35 MB"Finally, to quit R, type the following:
q()
Save workspace image? [y/n/c]: n