On 6 February 2009 at 05:15, Ingeborg Schmidt wrote: | Hello, | I seem to be unable to get Lam/Mpi to work with Rmpi on Debian 5.
The Debian Rmpi package (ie r-cran-rmpi) switched to Open MPI instead of LAM/MPI quite some time ago as LAM/MPI is no longer actively developed, and the LAM/MPI team itself recommends switching to Open MPI. So recent versions of r-cran-rmpi will not work with LAM/MPI. | Following the readme file, I installed the packages r-cran-rmpi and lam3 lam3-dev lam-runtime . The lam-bhost.def is configured like this: You can of course uninstall r-cran-rmpi, and then use the LAM/MPI development package (currently called liblam4 on my Debian testing system) to locally intall Rmpi into /usr/local/lib/R/site-packages via R CMD INSTALL. You will have have to follow the instruction in the Rmpi sources. | hn01 | cn01 cpu=4 | cn02 cpu=4 | | Lam seems to be fine with this: | | >lamboot -v | n-1<13746> ssi:boot:base:linear: booting n0 (hn01) | n-1<13746> ssi:boot:base:linear: booting n1 (cn01) | n-1<13746> ssi:boot:base:linear: booting n2 (cn02) | n-1<13746> ssi:boot:base:linear: finished | | However, Rmpi 0.5.5 is not: | | > library("Rmpi") | [hn01:30424] mca: base: component_find: unable to open osc pt2pt: file These are __Open MPI__ error messages. You are mixing systems. There is a mailing list r-sig-hpc for these question. Please consider subscribing and posting there. Hth, Dirk | not found (ignored) | > mpi.spawn.Rslaves() | 1 slaves are spawned successfully. 0 failed. | master (rank 0, comm 1) of size 2 is running on: hn01 | slave1 (rank 1, comm 1) of size 2 is running on: hn01 | > mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size())) | $slave1 | [1] "I am 1 of 2" | > mpi.close.Rslaves() | [1] 1 | > mpi.quit() | | Note how only one slave is spawned. Trials with mpiexec -n 3 R --no-save -q and the .Rprofile in place started R on multiple nodes, but produced this output: | | [hn01:04612] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) | > [cn01:30306] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) | [cn01:30304] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) | [cn01:30305] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) | > | [1]> | [1]> | [1] "Please use mpi.quit() to quit R" | "Please use mpi.quit() to quit R" | "Please use mpi.quit() to quit R" | ----------------------------------------------------------------------------- | It seems that [at least] one of the processes that was started with | mpirun did not invoke MPI_INIT before quitting (it is possible that | more than one process did not invoke MPI_INIT -- mpirun was only | notified of the first one, which was on node n0). | | mpirun can *only* be used with MPI programs (i.e., programs that | invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program | to run non-MPI programs over the lambooted nodes. | ----------------------------------------------------------------------------- | mpirun failed with exit status 252 | | Do you have any suggestions? | | Cheers, | Ingeborg Schmidt | | | | | | ______________________________________________ | R-help@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-help | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html | and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.