Torque Exec Exception

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Torque Exec Exception

ngsflow@hygenomics.com

hi all:

 

galaxy.jobs.runners.cli_job.torque WARNING 2014-03-07 11:23:33,764 No valid qstat XML return from `qstat -x`, got the following:

galaxy.jobs.runners ERROR 2014-03-07 11:23:33,765 Unhandled exception checking active jobs

Traceback (most recent call last):

  File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/__init__.py", line 339, in monitor

    self.check_watched_items()

  File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 150, in check_watched_items

    job_states = self.__get_job_states()

  File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 202, in __get_job_states

    job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids))

TypeError: 'NoneType' object is not iterable

 
#qmgr -c "p q batch"
 
create queue batch
set queue batch queue_type = Execution
set queue batch enabled = True
set queue batch started = True
 
Finish the torque tasks , throw exceptions in the log file。


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Re: Torque Exec Exception

Nate Coraor (nate@bx.psu.edu)
Hello,

Are you able to run `qstat -x` on the command line on the remote
system? What's the output?

--nate

On Thu, Mar 6, 2014 at 1:01 PM, [hidden email]
<[hidden email]> wrote:

> hi all:
>
>
>
> galaxy.jobs.runners.cli_job.torque WARNING 2014-03-07 11:23:33,764 No valid
> qstat XML return from `qstat -x`, got the following:
>
> galaxy.jobs.runners ERROR 2014-03-07 11:23:33,765 Unhandled exception
> checking active jobs
>
> Traceback (most recent call last):
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/__init__.py", line
> 339, in monitor
>
>     self.check_watched_items()
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 150,
> in check_watched_items
>
>     job_states = self.__get_job_states()
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 202,
> in __get_job_states
>
>     job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids))
>
> TypeError: 'NoneType' object is not iterable
>
>
> #qmgr -c "p q batch"
>
> create queue batch
> set queue batch queue_type = Execution
> set queue batch enabled = True
> set queue batch started = True
>
> Finish the torque tasks , throw exceptions in the log file。
> ________________________________
> [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/

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Re: Torque Exec Exception

ngsflow@hygenomics.com
hi,

we can run 'qstat -x' on the command line successfully but nothing shows on terminal.

because we have no job submitted recently. (pbs only shows jobs traced back a certain time, not the entire history)

 

however, in case of nothing returns for 'qstat -x' command, there will be an error prompt in paster.log file, which we think it is not properly logged (although the command is actually successfully finished).

 

We will look into code to make sure for that if we have time. Just for your reference.

 
 
------------------ Original ------------------
Date:  Fri, Mar 7, 2014 10:34 PM
Cc:  "galaxy-dev"<[hidden email]>; "吴一雷"<[hidden email]>;
Subject:  Re: [galaxy-dev] Torque Exec Exception
 
Hello,

Are you able to run `qstat -x` on the command line on the remote
system? What's the output?

--nate

On Thu, Mar 6, 2014 at 1:01 PM, [hidden email]
<[hidden email]> wrote:

> hi all:
>
>
>
> galaxy.jobs.runners.cli_job.torque WARNING 2014-03-07 11:23:33,764 No valid
> qstat XML return from `qstat -x`, got the following:
>
> galaxy.jobs.runners ERROR 2014-03-07 11:23:33,765 Unhandled exception
> checking active jobs
>
> Traceback (most recent call last):
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/__init__.py", line
> 339, in monitor
>
>     self.check_watched_items()
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 150,
> in check_watched_items
>
>     job_states = self.__get_job_states()
>
>   File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 202,
> in __get_job_states
>
>     job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids))
>
> TypeError: 'NoneType' object is not iterable
>
>
> #qmgr -c "p q batch"
>
> create queue batch
> set queue batch queue_type = Execution
> set queue batch enabled = True
> set queue batch started = True
>
> Finish the torque tasks , throw exceptions in the log file。
> ________________________________
> [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/