Hey Eric, Odd - is MSI still using tool runner URLs in universe_wsgi.ini or have you guys transitioned to job_conf.xml. If you are using a job_conf.xml file - out of curiosity are you explicitly declaring an XML encoding at the top of it? Not that this would be the wrong thing to do - I am just trying to understand why you guys are the first to encounter this bug. Regardless, does this hack get you anywhere? https://gist.github.com/jmchilton/9353654 -John On Tue, Mar 4, 2014 at 12:46 PM, Eric Badger <badger@msi.umn.edu> wrote:
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
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