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

[Stefan Theussl]

Hi Gad,

Presumably you have installed an old implementation of MPI. 
mpi.comm.spawn has been supported since the MPI 1.2 standard as far as I 
remember. Can you pls tell us which implementation/version of MPI you 
use? (in case of LAM you may send us the output of 'laminfo')

Best,
Stefan

Gad Abraham wrote:
> 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
>