[R-sig-hpc] mpi_comm_spawn error with Rmpi and snow on SGI Altix

[Gad Abraham]

Hi,

I'm running R-2.8.1 on SuSE linux (don't know which version, kernel 
2.6.16.60-0.27-default) on an SGI Altix cluster.

Rmpi 0.5-6 and snow 0.3-3 both installed OK, Rmpi is linked correctly AFAIK:
 > R CMD ldd Rmpi.so
linux-gate.so.1 =>  (0xa000000000000000)
libmpi.so => /usr/lib/libmpi.so (0x200000080008c000)
...

I'm trying to call the script testsnow.R:

library(snow)
cl <- makeCluster(4, "MPI")

fun <- function(i) {
    x <- matrix(rnorm(3e6), ncol=3)
    replicate(1000, crossprod(x))
}

system.time({
    r <- parLapply(cl, 1:4, fun)
})


I call it with another script submitted to qsub:
#!/bin/sh
#$ -cwd
#$ -pe mpi 2
mpirun -np 1 /home/gabraham/bin/R --vanilla < testsnow.R


This fails with the error:

Error calling job_getjid(): No such file or directory
Error in .Call("mpi_comm_spawn", as.character(slave), 
as.character(slavearg),  :
   C symbol name "mpi_comm_spawn" not in DLL for package "Rmpi"
Calls: makeCluster ... switch -> makeMPIcluster -> mpi.comm.spawn -> .Call
Execution halted
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job

Any idea what's happening?

Thanks,
Gad

-- 
Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham