Rmpi working with OpenMPI and PBSPro but snow fails

Hi

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

$ ompi_info | grep tm

Yes it is.

[scmhl2 at arccacluster8 Rmpi_tests]$ ompi_info | grep tm
              MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.3)
                 MCA ras: tm (MCA v2.0, API v2.0, Component v1.3)
                 MCA plm: tm (MCA v2.0, API v2.0, Component v1.3)

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.

I'm not sure I understand what you mean. Could you elaborate?

You try to define the environment variable in the shell of PBS.

In this instance the shell of PBS is just a bash script launched by
pbs_mom so setting environment here or in the login shell is
functionally equivalent except that PBS isn't entirely reliable when it
comes to sending complex environments through.

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

Behaves exactly the same. Including the warnings about R_HOME.

Thanks,
Huw

Huw Lynes                       | Advanced Research Computing
HEC Sysadmin                    | Cardiff University
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