[R] Running Rmpi/OpenMPI issues

[Tsai Li Ming]

Hi,

I have R 3.0.3 and OpenMPI 1.6.5.

Here’s my test script:
library(snow)

nbNodes <- 4
cl <- makeCluster(nbNodes, "MPI")
clusterCall(cl, function() Sys.info()[c("nodename","machine")])
mpi.quit()

And the mpirun command:
/opt/openmpi-1.6.5-intel/bin/mpirun -np 1 -H host1,host2,host3,host4 R --no-save < ~/test_mpi.R

Here’s the output:
> cl <- makeCluster(nbNodes, "MPI")
Loading required package: Rmpi
	4 slaves are spawned successfully. 0 failed.
> clusterCall(cl, function() Sys.info()[c("nodename","machine")])
[[1]]
    nodename      machine 
“host1"     "x86_64" 

[[2]]
    nodename      machine 
“host1"     "x86_64" 

[[3]]
    nodename      machine 
“host1"     "x86_64" 

[[4]]
    nodename      machine 
“host1"     "x86_64" 

> 
> mpi.quit()

I followed the instructions from:
http://www.statistik.uni-dortmund.de/useR-2008/tutorials/useR2008introhighperfR.pdf
, specifically to use -np 1

1. Why is it not running on the rest of the nodes? I can see all 4 processes on host1 and no orted daemon running.

What should be the correct way to run this? 

2. mpi.quit() just hangs there.

Thanks!