error after pulling latest updates

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

error after pulling latest updates

Branden Timm-2
Hi All,
   Just did an update to HEAD, and upon restarting the daemons received
the following messages:

galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in
condor runner
Traceback (most recent call last):
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
     app = UniverseApplication( global_conf = global_conf, **kwargs )
   File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py", line
164, in __init__
     self.job_manager = manager.JobManager( self )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py", line
36, in __init__
     self.job_handler.start()
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
34, in start
     self.job_queue.start()
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
77, in start
     self.__check_jobs_at_startup()
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
125, in __check_jobs_at_startup
     self.dispatcher.recover( job, job_wrapper )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
620, in recover
     self.job_runners[runner_name].recover( job, job_wrapper )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py", line
243, in recover
     cjs.user_log = os.path.join(
self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag )
NameError: global name 'galaxy_id_tag' is not defined
Removing PID file main.pid

--
Branden Timm
[hidden email]
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: error after pulling latest updates

Branden Timm-2
I was able to work around this error by hacking the condor job runner,
there were two obvious errors.  First, in recover(), galaxy_id_tag was
not being set (hence the NameError).  Second, the same method was
invoking self.__old_job_state with one argument when it clearly expects
two.  The latter I just commented out.

243d242
<     galaxy_id_tag = job_wrapper.get_id_tag()
246c245
<         #self.__old_state_paths( cjs )
---
 >         self.__old_state_paths( cjs )

Obviously this is a hacky workaround, but I'd like to hear if anybody
knows the cause of these errors and whether a patch should be submitted.

--
Branden Timm
[hidden email]

On 6/5/2013 10:58 AM, Branden Timm wrote:

> Hi All,
>   Just did an update to HEAD, and upon restarting the daemons received
> the following messages:
>
> galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083
> in condor runner
> Traceback (most recent call last):
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py", line
> 164, in __init__
>     self.job_manager = manager.JobManager( self )
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py",
> line 36, in __init__
>     self.job_handler.start()
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py",
> line 34, in start
>     self.job_queue.start()
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py",
> line 77, in start
>     self.__check_jobs_at_startup()
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py",
> line 125, in __check_jobs_at_startup
>     self.dispatcher.recover( job, job_wrapper )
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py",
> line 620, in recover
>     self.job_runners[runner_name].recover( job, job_wrapper )
>   File
> "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py",
> line 243, in recover
>     cjs.user_log = os.path.join(
> self.app.config.cluster_files_directory, '%s.condor.log' %
> galaxy_id_tag )
> NameError: global name 'galaxy_id_tag' is not defined
> Removing PID file main.pid
>
> --
> Branden Timm
> [hidden email]
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: error after pulling latest updates

Nate Coraor (nate@bx.psu.edu)
On Jun 5, 2013, at 2:11 PM, Branden Timm wrote:

> I was able to work around this error by hacking the condor job runner, there were two obvious errors.  First, in recover(), galaxy_id_tag was not being set (hence the NameError).  Second, the same method was invoking self.__old_job_state with one argument when it clearly expects two.  The latter I just commented out.
>
> 243d242
> <     galaxy_id_tag = job_wrapper.get_id_tag()
> 246c245
> <         #self.__old_state_paths( cjs )
> ---
> >         self.__old_state_paths( cjs )
>
> Obviously this is a hacky workaround, but I'd like to hear if anybody knows the cause of these errors and whether a patch should be submitted.

Hi Branden,

I refactored all of the job runners but wasn't able to fully test all of the changes to the Condor runner, which is how this bug popped up.  I've committed the fix to the stable branch in galaxy-central.  Thanks for the fix and sorry for the inconvenience.

--nate

>
> --
> Branden Timm
> [hidden email]
>
> On 6/5/2013 10:58 AM, Branden Timm wrote:
>> Hi All,
>>  Just did an update to HEAD, and upon restarting the daemons received the following messages:
>>
>> galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in condor runner
>> Traceback (most recent call last):
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
>>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py", line 164, in __init__
>>    self.job_manager = manager.JobManager( self )
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py", line 36, in __init__
>>    self.job_handler.start()
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 34, in start
>>    self.job_queue.start()
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 77, in start
>>    self.__check_jobs_at_startup()
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 125, in __check_jobs_at_startup
>>    self.dispatcher.recover( job, job_wrapper )
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 620, in recover
>>    self.job_runners[runner_name].recover( job, job_wrapper )
>>  File "/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py", line 243, in recover
>>    cjs.user_log = os.path.join( self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag )
>> NameError: global name 'galaxy_id_tag' is not defined
>> Removing PID file main.pid
>>
>> --
>> Branden Timm
>> [hidden email]
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/