I am running R on TORQUE/MOAB cluster (I guess---as the documentation is
terrific).
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@n0470 ~]$ module load icc_15.0
[otoomet@n0470 ~]$ '/sw/r-3.2.0/lib64/R/bin/Rscript' -e
'parallel:::.slaveRSOCK()' MASTER=n0470 PORT=11985 TIMEOUT=2592000
METHODS=TRUE XDR=TRUE
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
systems?
Cheers,
Ott
--
Ott Toomet
Visiting Researcher
School of Information
Mary Gates Hall, Suite 095
University of Washington
Seattle, WA 98195
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