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
To:  "ngsflow@hygenomics.com"<ngsflow@hygenomics.com>;
Cc:  "galaxy-dev"<galaxy-dev@lists.bx.psu.edu>; "吴一雷"<wuyl@hygenomics.com>;
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, ngsflow@hygenomics.com
<ngsflow@hygenomics.com> 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。
> ________________________________
> ngsflow@hygenomics.com
>
> ___________________________________________________________
> 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/