[R-sig-hpc] Rmpi working with OpenMPI and PBSPro but snow fails
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>
More information about the R-sig-hpc