hpc documentation - software:r:r-simple

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== R script in batch ======

==== matmul.R script ====

Consider the simple R script file to multiply a small 3x3 matrix

<file R matmul.R>
# Calculate and print small matrix AA'
a <- matrix(1:12,3,4);
a%*%t(a)
</file>

Let's test this R script using ''Rscript'' from the command line on a compute node.  Don't forget to set your [[general/userguide/04_compute_environ?&#using-workgroup-and-directories|workgroup]] to define your cluster group or //investing-entity// compute nodes before you use ''qlogin'' to get on a compute node. For example,

<code bash>
workgroup -g it_css
qlogin
vpkg_require r/3
Rscript matmul.R
</code>

The output to the screen:

<code>
     [,1] [,2] [,3]
[1,]  166  188  210
[2,]  188  214  240
[3,]  210  240  270
</code>

To return to the head node, type
<code bash>
exit
</code>

==== matmul.qs file ====

To run a R script in batch instead of on the command line has nearly the same steps.
Consider the queue submission script file:

<file matmul.qs>
#$ -N matmultiply

# Add vpkg_require commands after this line:
vpkg_require r/3

# Syntax: Rscript [options] filename.R [arguments]
Rscript matmul.R 
</file>

Now to run the R script simply submit the job from the head node with the
''qsub'' command.

<code>
qsub matmul.qs
</code>

You should see a notification that your job was submitted.  Something like this

<code bash>
Your job 2283886 ("matmultiply") has been submitted
</code>

After the code completes the output of the script will appear in the file
''matmultiply.o2283886'' because ''-N matmultiply'' defines the name of the job in ''matmul.qs'' and appears in the notification above as ''("matmultiply")'' with ''2283886'' assigned as the job ID. Type 

<code>
more matmultiply.o2283886
</code>

to display the contents of the output file on the screen.  For example,

<code>
Adding dependency `x11/RHEL6.1` to your environment
Adding package `r/3.0.2` to your environment
     [,1] [,2] [,3]
[1,]  166  188  210
[2,]  188  214  240
[3,]  210  240  270
</code>