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 issues.

Respectfully yours,

Dan Sullivan


On Tue, Nov 5, 2013 at 8:52 PM, John Chilton <chil...@msi.umn.edu> wrote:

> On Tue, Nov 5, 2013 at 11:53 AM, Daniel Patrick Sullivan
> <dansulli...@gmail.com> 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
> > provided via the Galaxy web UI; it no longer appears that jobs are
> running
> > indefinitely).    One thing I would like to note is that the error that
> is
> > provided to the user is generic, i.e. the web UI reports "An error
> occurred
> > with this dataset: Job cannot be completed due to a cluster error, please
> > retry it later".  So, the fact that a Walltime exceeded error actually
> > occurred is not presented to the user (I am not sure if this is
> intentional
> > or not).  Again, I appreciate you taking the time to verify and patch
> this
> > issue.  I have attached a screenshot of the output for your review.
>
> Glad we are making progress - I have committed that previous patch to
> galaxy-central. Lets see if we cannot improve the user feedback so
> they know they hit the maximum walltime. Can you try this new patch?
> The message about the timeout was being built but it was not being
> logged not set as the error message on the dataset - this should
> resolve that.
>
> >
> > I am probably going to be testing Galaxy with Torque 4.2.5 in the coming
> > weeks, I will let you know if I identify any additional problems.  Thank
> you
> > so much have a wonderful day.
>
> You too, thanks for working with me on fixing this!
>
> -John
>
> >
> > Dan Sullivan
> >
> >
> > On Tue, Nov 5, 2013 at 8:48 AM, John Chilton <chil...@msi.umn.edu>
> wrote:
> >>
> >> 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 problem, any chance you can make the following changes for me and
> >> let me know if they work?
> >>
> >> Between the following two lines:
> >>
> >>                     log.error( '(%s/%s) PBS job failed: %s' % (
> >> galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ),
> >> 'Unknown error: %s' % status.exit_status ) ) )
> >>                     self.work_queue.put( ( self.fail_job, pbs_job_state
> )
> >> )
> >>
> >>                     log.error( '(%s/%s) PBS job failed: %s' % (
> >> galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ),
> >> 'Unknown error: %s' % status.exit_status ) ) )
> >>                     pbs_job_state.stop_job = False
> >>                     self.work_queue.put( ( self.fail_job, pbs_job_state
> )
> >> )
> >>
> >> And at the top of the file can you add a -11 option to the
> >> JOB_EXIT_STATUS to indicate a job timeout.
> >>
> >> I have attached a patch that would apply against the latest stable -
> >> it will probably will work against your branch as well.
> >>
> >> If you would rather not act as my QC layer, I can try to come up with
> >> a way to do some testing on my end :).
> >>
> >> Thanks again,
> >> -John
> >>
> >>
> >> On Mon, Nov 4, 2013 at 10:10 AM, Daniel Patrick Sullivan
> >> <dansulli...@gmail.com> wrote:
> >> > Hi, Galaxy Developers,
> >> >
> >> > I have what I hops is somewhat of a basic question regarding Galaxy's
> >> > interaction with a pbs job cluster and information reported via the
> >> > webUI.
> >> > Basically, in certain situations, the walltime of a specific job is
> >> > exceeded.  This is of course to be expected and all fine and
> >> > understandeable.
> >> >
> >> > My problem is that the information is not being relayed back to the
> end
> >> > user
> >> > via the Galaxy web UI, which causes confusion in our Galaxy user
> >> > community.
> >> > Basically the Torque scheduler generates the following message when a
> >> > walltime is exceeded:
> >> >
> >> > 11/04/2013
> >> > 08:39:45;000d;PBS_Server.30621;Job;163.sctest.cri.uchicago.edu
> ;preparing
> >> > to
> >> > send 'a' mail for job 163.sctest.cri.uchicago.edu to
> >> > s.cri.gal...@crigalaxy-test.uchicago.edu (Job exceeded its walltime
> >> > limit.
> >> > Job was aborted
> >> > 11/04/2013
> >> > 08:39:45;0009;PBS_Server.30621;Job;163.sctest.cri.uchicago.edu;job
> exit
> >> > status -11 handled
> >> >
> >> > Now, my problem is that this status -11 return code is not being
> >> > correctly
> >> > handled by Galaxy.  What happens is that Galaxy throws an exception,
> >> > specificially:
> >> >
> >> > 10.135.217.178 - - [04/Nov/2013:08:39:42 -0500] "GET
> >> > /api/histories/90240358ebde1489 HTTP/1.1" 200 -
> >> > "https://crigalaxy-test.uchicago.edu/history"; "Mozilla/5.0 (X11;
> Linux
> >> > x86_64; rv:23.0) Gecko/20100101 Firefox/23.0"
> >> > galaxy.jobs.runners.pbs DEBUG 2013-11-04 08:39:46,137
> >> > (2150/163.sctest.cri.uchicago.edu) PBS job state changed from R to C
> >> > galaxy.jobs.runners.pbs ERROR 2013-11-04 08:39:46,139
> >> > (2150/163.sctest.cri.uchicago.edu) PBS job failed: Unknown error: -11
> >> > galaxy.jobs.runners ERROR 2013-11-04 08:39:46,139 (unknown) Unhandled
> >> > exception calling fail_job
> >> > Traceback (most recent call last):
> >> >   File
> >> > "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> >> > line 60, in run_next
> >> >     method(arg)
> >> >   File
> "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
> >> > line
> >> > 561, in fail_job
> >> >     if pbs_job_state.stop_job:
> >> > AttributeError: 'AsynchronousJobState' object has no attribute
> >> > 'stop_job'
> >> >
> >> > After this exception occurs, the Galaxy job status via the Web UI is
> >> > still
> >> > reported as "Job is currently running".  It appears that the job will
> >> > remain
> >> > in this state (from the end users perspective) indefinitely.  Has
> >> > anybody
> >> > seen this issue before?
> >> >
> >> > I noticed that return code -11 does not exist in
> >> > /group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py under
> the
> >> > JOB_EXIT_STATUS  dictionary.   I tried adding an entry for this,
> however
> >> > when I do the exception changes to:
> >> >
> >> > galaxy.jobs.runners.pbs ERROR 2013-11-04 10:02:17,274
> >> > (2151/164.sctest.cri.uchicago.edu) PBS job failed: job walltime
> exceeded
> >> > galaxy.jobs.runners ERROR 2013-11-04 10:02:17,275 (unknown) Unhandled
> >> > exception calling fail_job
> >> > Traceback (most recent call last):
> >> >   File
> >> > "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> >> > line 60, in run_next
> >> >     method(arg)
> >> >   File
> "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
> >> > line
> >> > 562, in fail_job
> >> >     if pbs_job_state.stop_job:
> >> > AttributeError: 'AsynchronousJobState' object has no attribute
> >> > 'stop_job'
> >> >
> >> > I am wondering if this is a bug or if it is just because I am using a
> >> > newer
> >> > version of TORQUE (I am using TORQUE 4.2.2).
> >> >
> >> > In terms of Galaxy, I am using:
> >> >
> >> > [s.cri.galaxy@crigalaxy-test galaxy-dist]$ hg parents
> >> > changeset:   10408:6822f41bc9bb
> >> > branch:      stable
> >> > parent:      10393:d05bf67aefa6
> >> > user:        Dave Bouvier <d...@bx.psu.edu>
> >> > date:        Mon Aug 19 13:06:17 2013 -0400
> >> > summary:     Fix for case where running functional tests might
> overwrite
> >> > certain files in database/files.
> >> >
> >> > [s.cri.galaxy@crigalaxy-test galaxy-dist]$
> >> >
> >> > Does anybody know how I could fix this such that walltime exceeded
> >> > messages
> >> > are correctly reporeted via the Galaxy web UI for TORQUE 4.2.2?  Thank
> >> > you
> >> > so much for your input and guidance, and for the ongoing development
> of
> >> > Galaxy.
> >> >
> >> > Dan Sullivan
> >> >
> >> > ___________________________________________________________
> >> > Please keep all replies on the list by using "reply all"
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> >> >
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> >
> >
> >
> >
> > ___________________________________________________________
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>
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