[R-sig-hpc] simple question on R/Rmpi/snow/slurm configuration
Whit Armstrong
armstrong.whit at gmail.com
Mon Jan 5 20:23:31 CET 2009
I'm attempting to get Dirk's example from the "intro to HCP with R"
talk working (http://dirk.eddelbuettel.com/papers/bocDec2008introHPCwithR.pdf).
I have slurm working correctly (all the trivial hostname examples
complete successfully).
I fire up an R sesssion w/ the following command
salloc orterun -n 7 R --vanilla
and then run
suppressMessages(library(Rmpi))
but my console never returns control.
it's just frozen until I <control-c> out of it at which point I get
this message:
> suppressMessages(library(Rmpi))
[linuxsvr.kls.corp:05875] mca: base: component_find: unable to open
osc pt2pt: file not found (ignored)
orterun: killing job...
orterun noticed that job rank 0 with PID 5875 on node node0 exited on
signal 15 (Terminated).
salloc: Relinquishing job allocation 70
[warmstrong at linuxsvr ~]$
meanwhile squeue shows:
[warmstrong at linuxsvr ~]$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
71 prod orterun warmstro R 0:31 1 node0
[warmstrong at linuxsvr ~]$
Have I missed something crucial? Should I only be running these
examples in batch mode or with littler?
Thanks in advance,
Whit
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