Dear all,
This error persists in the August release.
To reproduce:
- start workflows (and/or jobs)
- while jobs are running and/or waiting to run : restart galaxy
handler will now give these errors. Deleting the running/waiting jobs
and restarting galaxy resolves this.
Best,
Geert
On 04/03/2013 11:38 AM, Geert Vandeweyer wrote:
I was able to solve this by setting job state in the database from
queued and running to "failed" for two jobs that had a wrong state
after galaxy-restart.
best,
geert
On 04/02/2013 05:27 PM, Geert Vandeweyer wrote:
> Hi,
>
> I'm getting errors in the handler logs after upgrading galaxy stable
> to today's release.
>
> I specified the "dynamic" job runner as default, which returns a job
> for pbs.
>
> These errors appear as soon as the server is up and running. What
> could be the issue here?
>
> galaxy.jobs.runners ERROR 2013-04-02 17:24:23,411 Unhandled exception
> checking active jobs
> Traceback (most recent call last):
> File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 336, in monitor
> self.check_watched_items()
> File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line
> 382, in check_watched_items
> ( failures, statuses ) = self.check_all_jobs()
> File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line
> 463, in check_all_jobs
> pbs_server_name =
> self.__get_pbs_server(pbs_job_state.job_destination.params)
> File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line
> 221, in __get_pbs_server
> return job_destination_params['destination'].split('@')[-1]
> KeyError: 'destination'
>
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer(a)ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726