[R-sig-hpc] Rmpi working with OpenMPI and PBSPro but snow fails
lynesh at cardiff.ac.uk
Thu Mar 5 11:03:32 CET 2009
On Thu, 2009-03-05 at 11:24 +0900, Ei-ji Nakama wrote:
> 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.
Huw Lynes | Advanced Research Computing
HEC Sysadmin | Cardiff University
| Redwood Building,
Tel: +44 (0) 29208 70626 | King Edward VII Avenue, CF10 3NB
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