Torque.py Bug

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Torque.py Bug

ngsflow@hygenomics.com
Hi,
 
base:
os:centos6.4
torque:4.2.7
 
I built a glaxy cluster today,and then I found the job completion status of torque queue is 'c',but the need state of galalxy is "ok".So I modified the torque.py file and solved this error. I do, right?
 
 
diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py
--- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013 -0500
+++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014 +0800
@@ -117,6 +117,8 @@
                 if id in job_ids:
                     state = job.find('job_state').text
                     # map PBS job states to Galaxy job states.
+                    if state == u'C' :
+                        state = 'ok'
                     rval[id] = self.__get_job_state(state)
         return rval
 


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Re: Torque.py Bug

John Chilton-4
Thanks for the bug report, that is indeed a problem - I am not sure
how the torque runner here would ever reach a complete job state. I
prefer the following fix however, if you would be willing to verify it
fixes the problem you are encountering I would be happy to apply it to
Galaxy's stable branch.

diff -r 6a633b37c4c4 lib/galaxy/jobs/runners/cli_job/torque.py
--- a/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:52:52 2014 -0500
+++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:32:41 2014 -0600
@@ -131,4 +131,5 @@
     def __get_job_state(self, state):
         return { 'E' : job_states.RUNNING,
                  'R' : job_states.RUNNING,
-                 'Q' : job_states.QUEUED }.get(state, state)
+                 'Q' : job_states.QUEUED,
+                 'C' : job_states.OK }.get(state, state)

-John


On Fri, Feb 28, 2014 at 12:13 AM, [hidden email]
<[hidden email]> wrote:

> Hi,
>
> base:
> os:centos6.4
> torque:4.2.7
>
> I built a glaxy cluster today,and then I found the job completion status of
> torque queue is 'c',but the need state of galalxy is "ok".So I modified the
> torque.py file and solved this error. I do, right?
>
>
> diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py
> --- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013
> -0500
> +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014
> +0800
> @@ -117,6 +117,8 @@
>                  if id in job_ids:
>                      state = job.find('job_state').text
>                      # map PBS job states to Galaxy job states.
> +                    if state == u'C' :
> +                        state = 'ok'
>                      rval[id] = self.__get_job_state(state)
>          return rval
>
> ________________________________
> [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.py Bug

John Chilton-4
Great, thanks for testing. This fix has been merged into stable and
default branches of galaxy-central.

-John

On Mon, Mar 3, 2014 at 7:58 PM, [hidden email]
<[hidden email]> wrote:

> hi,John :
> It's ok.
>
> ________________________________
> [hidden email]
>
> From: John Chilton
> Date: 2014-02-28 22:36
> To: [hidden email]
> CC: galaxy-dev
> Subject: Re: [galaxy-dev] Torque.py Bug
> Thanks for the bug report, that is indeed a problem - I am not sure
> how the torque runner here would ever reach a complete job state. I
> prefer the following fix however, if you would be willing to verify it
> fixes the problem you are encountering I would be happy to apply it to
> Galaxy's stable branch.
>
> diff -r 6a633b37c4c4 lib/galaxy/jobs/runners/cli_job/torque.py
> --- a/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:52:52 2014
> -0500
> +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:32:41 2014
> -0600
> @@ -131,4 +131,5 @@
>      def __get_job_state(self, state):
>          return { 'E' : job_states.RUNNING,
>                   'R' : job_states.RUNNING,
> -                 'Q' : job_states.QUEUED }.get(state, state)
> +                 'Q' : job_states.QUEUED,
> +                 'C' : job_states.OK }.get(state, state)
>
> -John
>
>
> On Fri, Feb 28, 2014 at 12:13 AM, [hidden email]
> <[hidden email]> wrote:
>> Hi,
>>
>> base:
>> os:centos6.4
>> torque:4.2.7
>>
>> I built a glaxy cluster today,and then I found the job completion status
>> of
>> torque queue is 'c',but the need state of galalxy is "ok".So I modified
>> the
>> torque.py file and solved this error. I do, right?
>>
>>
>> diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py
>> --- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013
>> -0500
>> +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014
>> +0800
>> @@ -117,6 +117,8 @@
>>                  if id in job_ids:
>>                      state = job.find('job_state').text
>>                      # map PBS job states to Galaxy job states.
>> +                    if state == u'C' :
>> +                        state = 'ok'
>>                      rval[id] = self.__get_job_state(state)
>>          return rval
>>
>> ________________________________
>> [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/