simple question on R/Rmpi/snow/slurm configuration

library(Rmpi)

library(snow)

 cl <- getMPIcluster()

cl

 mpi.universe.size()

"Whit Armstrong" <armstrong.whit at gmail.com> writes:

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

I think you want to salloc your universe, and then run R on one node
of the universe

salloc -n 7 orterun -np 1 R --vanilla

then

library(Rmpi)
mpi.universe.size()

will report 7.

Martin

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

--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793