Deleted jobs on the cloud keep running
Dear list, When running Galaxy/Cloudman on Amazon (on Ubuntu 12.04), I run into the following: - I start a job with <parallelism> in the tool.xml file. - Since I have use_tasked_jobs=True in universe_wsgi.ini, the job is split and divided over the instances on EC2 - I change my mind, and click on the delete button in the Galaxy UI. This removes the job from the UI. - I log in to an instance running my job, and see that it is still running (both its wrapper and the tool program). It keeps running, keeping my instances busy. - When tasks of this job finish (I assume), it is reported to galaxy, and my logfile says things like: galaxy.jobs DEBUG 2012-08-29 12:42:08,239 task 319 for job 25 ended galaxy.jobs DEBUG 2012-08-29 12:42:08,265 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-08-29 12:42:08,282 task 319 ended So I wonder if the default behaviour when deleting jobs in the UI is that they keep running but hidden, or is there something wrong in my config? Is there a way to change this with a setting? cheers, jorrit boekel
This should be fixed in 7443:f1eb04839053, but the cloud is (by default) at 7166:1744124f8ee4. The default installation on the cloud will be updated next time we do a galaxy-dist release, but until then you can certainly update your own instance through the admin panel (or via terminal). -Dannon On Aug 29, 2012, at 8:50 AM, Jorrit Boekel <jorrit.boekel@scilifelab.se> wrote:
Dear list,
When running Galaxy/Cloudman on Amazon (on Ubuntu 12.04), I run into the following:
- I start a job with <parallelism> in the tool.xml file. - Since I have use_tasked_jobs=True in universe_wsgi.ini, the job is split and divided over the instances on EC2 - I change my mind, and click on the delete button in the Galaxy UI. This removes the job from the UI. - I log in to an instance running my job, and see that it is still running (both its wrapper and the tool program). It keeps running, keeping my instances busy. - When tasks of this job finish (I assume), it is reported to galaxy, and my logfile says things like:
galaxy.jobs DEBUG 2012-08-29 12:42:08,239 task 319 for job 25 ended galaxy.jobs DEBUG 2012-08-29 12:42:08,265 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-08-29 12:42:08,282 task 319 ended
So I wonder if the default behaviour when deleting jobs in the UI is that they keep running but hidden, or is there something wrong in my config? Is there a way to change this with a setting?
cheers, jorrit boekel ___________________________________________________________ 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:
participants (2)
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Dannon Baker -
Jorrit Boekel