[R-sig-hpc] Encapsulated R for cluster use

Daryl Waggott Daryl.Waggott at oicr.on.ca
Sat Nov 5 03:02:48 CET 2011

Hello R HPC list,

In order to use any software tool in our production cluster environment we need to fully *bundle* or encapsulate all dependencies.  This is due to a policy of reproducible and logged research which is not at the whims of a heterogeneous computing environment.  My general question is --- are there any recommended strategies for compiling R with a set of packages that do not depend on (potentially changing) dynamically linked libraries?  Static linking doesn't look practical in R, so I have been attempting to aggregate all the dependencies determined by the function *ldd* and putting them in a a directory that is referenced by setting the LD_LIBRARY_PATH environment variable.  Needless to say, I haven't had much luck.  The cluster is all 64 bit Debian.  Are there any strategies at compile time that might be helpful?  My knowledge of the ins and outs of all the configure and make parameters is a work in progress.  Thank  you for any advice or pointers to documentation.


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