Hi,
I found that there is a problem when pbs job terminate unexpectedly (job killed manually / meet walltime), but galaxy shows the job still working.
And there are some error messages from log file below.
galaxy.jobs.runners.pbs DEBUG 2013-09-10 18:15:57,841 (3811/762.localhost) PBS job state changed from R to C galaxy.jobs.runners.pbs ERROR 2013-09-10 18:15:57,841 (3811/762.localhost) PBS job failed: Unknown error: -10 galaxy.jobs.runners ERROR 2013-09-10 18:15:57,841 (unknown) Unhandled exception calling fail_job Traceback (most recent call last): File "/mnt/RAID1/mirror/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 58, in run_next method(arg) File "/mnt/RAID1/mirror/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 560, in fail_job if pbs_job_state.stop_job: AttributeError: 'AsynchronousJobState' object has no attribute 'stop_job'
It seems that galaxy had received job status from pbs, but pbs.py can't handle message correctly. Is there any solution to solve this problem?
Thanks, Peter