[R] problem with mpiexec and Rmpi

[Dirk Eddelbuettel]

On 1 July 2008 at 14:03, Erin Hodgess wrote: | I'm having some trouble with
mpiexec and Rmpi.
| 
| I would like to be able to pass in the number of "children" via the mpiexec
| command (from the command line).
| 
| this is in SUSE10.1, with R-2.7.1
| 
| Here are my files: cat eb.R library(Rmpi) mpi.remote.exec(paste("i
|  am",mpi.comm.rank(),"of",mpi.comm.size())) mpi.quit()
|  hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> cat e.in source("eb.R")
| 
| hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> mpiexec -n 3 ./R --no-save -q -f
| e.in >e.out Error in mpi.remote.exec(paste("i am", mpi.comm.rank(), "of",
| mpi.comm.size())) : It seems no slaves running.  Calls: source ->
| eval.with.vis -> eval.with.vis -> mpi.remote.exec Error in
| mpi.remote.exec(paste("i am", mpi.comm.rank(), "of", mpi.comm.size())) : It
| seems no slaves running.  Calls: source -> eval.with.vis -> eval.with.vis
| -> mpi.remote.exec Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
| "of", mpi.comm.size())) : It seems no slaves running.  Calls: source ->
| eval.with.vis -> eval.with.vis -> mpi.remote.exec
| hodgesse at erinstoy:~/Desktop/R-2.7.1/bin>
| 
| Does anyone have any suggestions, please?  The scary part: I can get this
| to work on Windows but not on SUSE10.1

Things do differ slightly between MPI imnplementations -- but I have no
difficulties with Open MPI on Debian and Ubuntu.  Open MPI is the successor
to LAM, it also renamed mpirun etc to orterun [ where orte stands for Open
Run Time Environment, as I recall ].  Anyway, using a one-line littler
invocation works for me;

edd at ron:~$ orterun -n 2 -H ron,joe r -lRmpi -e'cat("Hello", mpi.comm.rank(0),
"of", mpi.comm.size(), "on", mpi.get.processor.name(), "\n")' Hello 0 of 0 on
ron Hello 1 of 0 on joe edd at ron:~$

Here 'r' is littler; it uses the -l flag to load the specified library and
the -e flag to pass the string for evaluation.

'ron' is a Debian testing box, 'joe' is an Ubuntu hardy box, and both are
running the standard packages for Debian and Ubuntu:

	r-cran-rmpi for Rmpi libopenmpi1 for Open MPI littler for 'r'

I happen to maintain all of those in Debian and noticed that Open MPI was
broken in Ubuntu 'hardy' as they foobared the build; but that is now
fixed. Ubuntu users should get an updated package via hardy-updates.

As for your problem, you haven't told us which MPI toolkit you are running.
It may be LAM in which case you probably want to read up on lamboot and the
hosts file or argument -- but that is just a guess.

Hope this helps, Dirk

-- 
Three out of two people have difficulties with fractions.