Last modified: 2014-08-27 23:16:18 UTC
When I run a python job using pywikibot it works with a simple jsub but fails to import pywikibot module when doing a jsub -once -continuous It's a problem of a missing environment variable, PYTHONPATH tools.phetools@tools-login:~$ cat .profile . ~/.bashrc export PYTHONPATH=/shared/pywikipedia/core:/shared/pywikipedia/core/externals/httplib2:/shared/pywikipedia/core/scripts ~/.bashrc contains also the same export trying a simple $ jsub -l h_vmem=512M -N test_env /bin/bash -c "env" show PYTHONPATH in ~/test_env.out but $ jsub -once -continuous -l h_vmem=512M -N test_env /bin/bash -c "env" doesn't show anything coming from ~/.profile or ~/.bashrc, same trouble with sh rather than /bin/bash. results are in /var/data/project/test_env.out.good / /var/data/project/test_env.out.bad the .err is always empty
typo, I meant /data/project/phetools/test_env.out.good and /data/project/phetools/test_env.out.bad
Looking the man page http://cf.ccmr.cornell.edu/cgi-bin/w3mman2html.cgi?qsub%281B%29 environment var are not exported to the job, it's the normal behavior, that docs says to use qsub -V to pass env variable, is it possible jsub doesn't pass -V to qsub when using -once -continuous ?
Actually, jsub passes -V in neither case; but the gridengine is really random about when it decides to start subshells or not. I strongly recommend that any dependency on the environment be sourced from the job script itself for that reason (or, possibly, by sourcing .bashrc explicitly as many have done).
