As the doctor gone rogue

May 19, 2010

Personal R library on the cluster

Filed under: R — Tags: , — hypotheses @ 4:50 pm

I’m trying to set up my own personal R library on our HPCCC. The current configuration does not allow me to use .Renviron to specify the location of my library as the home directory on the compute node is set up to be different from the home directory on the frontend node [side note: I wish our HPCCC admin is smarter than what he is now, and set this up correctly, so that we won’t have all these troubles again and again.

So, the only solution I have is to install my personal library on the frontend node. Then, add the path to this folder in all my R script that I want to run.
This can be done by first : Find out what is the full path of my personal R library on the frontend node

.libPaths()
[1] "/users/bhoom/Rlibs"
[2] "/usr/bin/lib/Rlib/" # <- this is the default of my HPCCC

I then have to combine the output from the above command with what exist on the system already.

.libPaths(c(.libPaths(),"/users/bhoom/Rlibs"))

This way, on the compute node, my personal R library can still be located.

Ref http://www.biostat.jhsph.edu/bit/R-personal-library.html

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