[R] Parallel: initializing SOCKET cluster

Ott Toomet otoomet at gmail.com
Wed Sep 2 02:16:24 CEST 2015

I am running R on TORQUE/MOAB cluster (I guess---as the documentation is

My problem is that I cannot start a slave node (using 'Rscript') before I
load the necessary modules first.  Just executing

cl <- makePSOCKcluster("n0470")

results in error:
/sw/r-3.2.0/lib64/R/bin/Rscript: error while loading shared libraries:
libiomp5.so: cannot open shared object file: No such file or directory

However, I can start it with the manual option and thereafter execute

[otoomet at n0470 ~]$ module load icc_15.0
[otoomet at n0470 ~]$ '/sw/r-3.2.0/lib64/R/bin/Rscript' -e
'parallel:::.slaveRSOCK()' MASTER=n0470 PORT=11985 TIMEOUT=2592000

and voila, it works.

Is there a way to execute initialization script on the nodes _before_
Rscript is started?  Or is there a better way to make cluster on such


Ott Toomet

Visiting Researcher
School of Information
Mary Gates Hall, Suite 095
University of Washington
Seattle, WA 98195

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