Hi there,
I've run into an issue with the pbs runner involving pbs server name strings becoming 'unicode' rather than 'str'. The pbs_python lib can't pass unicode strings down to the C library, which results in this failure:
https://gist.github.com/anonymous/9352218
The very top line of log output in the above gist is due to a line I added to runners/pbs.py:
https://gist.github.com/anonymous/9352101#file-pbs-py-L16
I can reproduce this as follows:
1. Start a job using pbs runner. 2. While the job is still running, restart galaxy. 3. Error now appears in the logs.
It seems that this is happening because, when deserializing job.destination_params from the database, the strings are converted to unicode. The jobs in this state are effectively stuck, since galaxy can't connect to check on their status.
I'm not sure where the best place to address this would be; thoughts?
This is on an up to date galaxy-dist with Torque 2.5.13.
Thanks, Eric