[R-sig-hpc] Rmpi working with OpenMPI and PBSPro but snow fails

Ei-ji Nakama nakama at ki.rim.or.jp
Thu Mar 5 03:24:02 CET 2009


To see whether your Open MPI installation has been configured to
use the PBS launcher

$ ompi_info | grep tm

2009/3/4 Huw Lynes <lynesh at cardiff.ac.uk>:
> WARNING: ignoring environment value of R_HOME

Please imagine the working of openmpi and PBS when MPI_spawn.

> module load apps/R
> module load libs/R-mpi

You try to define the environment variable in the shell of PBS.
set it before qsub.

$ man qsub       # It might be different in your environment.
  -V    Declares that all environment variables in the qsub command's
         environment are to be exported to the batch job.

$ module load apps/R
$ module load libs/R-mpi
$ qsub -V pbsshell.sh

EI-JI Nakama  <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>

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