Re: [R] problem with mpiexec and Rmpi

From: Dirk Eddelbuettel <edd_at_debian.org>
Date: Tue, 01 Jul 2008 20:17:44 -0500

On 1 July 2008 at 19:47, Dirk Eddelbuettel wrote:
|
| 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:~$

That didn't survice a cut&paste very well. It should read

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:~$

Dirk  

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

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Received on Wed 02 Jul 2008 - 01:21:15 GMT

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