[R] R and Openmpi

From: Paul Hewson <paul.hewson_at_plymouth.ac.uk>
Date: Fri, 30 May 2008 15:47:04 +0100


We have R working with Rmpi/openmpi, but I'm a little worried. Specifically, (a) the -np flag doesn't seem to override the hostfile (it works fine with fortran hello world) and (b) I appear to have twice as many processes running as I think I should.

Rmpi version 0.5.5
Openmpi version 1.1
Viglen HPC with (effectively) 9 blades and 8 nodes on each blade. myhosts file contains details of the 9 blades, but specifies that there are 4 slots on each blade (to make sure I leave room for other users).

When running mpirun -bynode -np 2 -hostfile myhosts R --slave --vanilla task_pull.R

  1. I get as many R slaves as there slots defined in my myhosts file (there are 36 slots defined, and I get 36 slaves, regardless of the setting of -np, the master goes on the first machine in the myhosts file.
  2. The .Rout file confirms that I have 1 comm with 1 master and 36 slaves
  3. When I top each blade it indicates that there are in fact 8 processes running on each blade and
  4. When I pstree each blade it indicates that there are two orted processes, each with 4 subprocesses.

>From the point of view of getting a job done this ***seems*** OK (it's running very quickly), but it doesn't seem quite right - given I'm sharing the machine with other users and so on. Is there something I've missed in the useage of mpirun with R/Rmpi.

Many thanks


Paul Hewson
Lecturer in Statistics
University of Plymouth
Drake Circus
Plymouth PL4 8AA

tel ++44(0)1752 232778
email paul.hewson_at_plymouth.ac.uk
web http://www.plymouth.ac.uk/staff/phewson

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