Thanks for the feedback, I have incorporated that previous patch into
galaxy-central.
As for the new warning message - I think this is fine. It is not
surprising the process doesn't have an exit code - the job script
itself never got to the point where that would have been written. If
there are no
Hi, John,
Actually, now that I am taking a look at this, I wanted to report
something. I am actually not sure if this is a problem or not (based on
what I can tell this is not causing any negative impact). The Galaxy log
data is actually reporting that the cleanup failed (for my testing I am
usi
Hi, John,
Based on my initial testing the application of your patch 2 successfully
conveys the job walltime exceeded error to the web UI. As far as I am
concerned you resolved this issue perfectly. Thank you so much for your
help with this. I will let you know if I experience any additional iss
On Tue, Nov 5, 2013 at 11:53 AM, Daniel Patrick Sullivan
wrote:
> Hi, John,
>
> Thank you for taking the time to help me look into this issue. I have
> applied the patch you provided and confirmed that it appears to help
> remediate the problem (when a walltime is exceeded feedback is in fact
> p
Hey Daniel,
Thanks so much for the details problem report, it was very helpful.
Reviewing the code there appears to be a bug in the PBS job runner -
in some cases pbs_job_state.stop_job is never set but is attempted to
be read. I don't have torque so I don't have a great test setup for
this proble
