[R-sig-hpc] Rmpi and mpirun

Ei-ji Nakama n@k@m@ @ending from ki@rim@or@jp
Fri Jul 13 07:17:46 CEST 2018


When you debug the OpenMPI process...
Read the result of the following command
$ ompi_info --param btl base --level 9

Maybe first time...try following command
$ mpirun --mca btl_base_verbose 40 -np 1 R --interactive
----<write script>----

Debugging parameter file can also be written below
$ mkdir -p ~/.openmpi
$ echo "btl_base_verbose = 40" > ~/.openmpi/mca-params.conf

2018-07-12 5:31 GMT+09:00 Vincent Boucher <vincent.boucher.u using gmail.com>:
> Hi,
> I'm running into an issue using Rmpi with Open MPI on a beowulf cluster.
> The installation of the package went without any issue. I have done the
> following:
> 'mpirun -n 1 --hostfile hostfile.txt R --interactive'
> then, 'library(Rmpi)
> when I do 'ns <- mpi.universe.size()' I get ns=12, which is what it is
> supposed to be. However, 'mpi.spawn.Rslaves(nslaves=ns)' fails and I get

Since you have already started the MPI master process,
          `mpi.universe.size() - 1'
will be the number of slaves that can be activated.

> the "not enough slots available..." message.
> It looks like when R opens, the nodes are already up and running (due to
> the mpirun) so mpi.spawn fails... I've tried to launch R directly (without
> mpirun) but then, I only get 1 node...

See below, orte_default_hostfile
ompi_info --params orte all --level 9

   $ echo 'orte_default_hostfile = "~/hostfile.txt"' >>

For the host file format, refer to the following.

> Am I missing something?
> many thanks
> Vincent
>         [[alternative HTML version deleted]]
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Best Regards,
Eiji NAKAMA <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>

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