[OOD-users] Setting up Proper Environments

[Dominic Daninger]

Hi All, We are going through our first setup of ood and have a question regarding environments.  If I were to submit a job outside of the ood browser using a submission script like this to PBS:

#!/bin/bash
#PBS -V
#PBS -l select=1:ncpus=2:mpiprocs=2
#PBS -l walltime=01:00
#PBS -N hostname.pbs
#PBS -j oe

module load prun/1.1 gnu7/7.1.0 openmpi/1.10.7 ohpc
mpirun hostname

Resulting in an output file similar to this:
compute-0-1
compute-0-1

If I submit the same job through the ood console using the Job Composer I end up getting this error:
/var/spool/pbs/mom_priv/jobs/29.vbcluster1.nor-tech.com.SC: line 9: module: command not found
/var/spool/pbs/mom_priv/jobs/29.vbcluster1.nor-tech.com.SC: line 11: mpirun: command not found

I have been able to get around this issue by sourcing the lmod init script inside my job script like this:

#!/bin/bash
#PBS -V
#PBS -l select=1:ncpus=2:mpiprocs=2
#PBS -N hostname.pbs
#PBS -j oe

export MODULEPATH=/opt/ohpc/pub/moduledeps/gnu7-openmpi:/opt/ohpc/pub/moduledeps/gnu7:/opt/ohpc/pub/modulefiles
source /opt/ohpc/admin/lmod/lmod/init/bash
module load prun/1.1 gnu7/7.1.0 openmpi/1.10.7 ohpc

mpirun hostname

Is there a way to pass the user's full environment to the job so we don't have to do the sourcing above?  Usually in PBS you'd use the '#PBS -V' option but that is not working with the ood.


Dominic Daninger | domd at nor-tech.com<mailto:domd at nor-tech.com>
Vice President of Engineering
Direct 952-229-2070 | Cell 612 251 3505 | Fax 952-229-2061
[NT logo.jpg]Burnsville, Minn.
People Friendly Technology with a Global Reach

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