no PID in database, unable to stop

Question: no PID in database, unable to stop

3.6 years ago by

United Kingdom

rich_jp • 0 wrote:

When I attempt to stop jobs on my local Galaxy server via the Admin>Manage Jobs section I get the following error message:

galaxy.jobs.handler DEBUG 2015-04-19 15:55:03,073 Stopping job 10374:

galaxy.jobs.handler DEBUG 2015-04-19 15:55:03,073 stopping job 10374 in local runner

galaxy.jobs.runners.local WARNING 2015-04-19 15:55:03,089 stop_job(): 10374: no PID in database for job, unable to stop

I have updated to the latest version of Galaxy (Galaxy 16119:02ddea42faad) and this has not solved the issue. I can of course 'kill' jobs via terminal commands and the Galaxy runner sees this and correctly sets the status to error. Has anyone else had this issue or know how to resolve it? It seems like it could be a database error (I use PostgreQSL 9.3) although all other connections to the database seem to be functioning correctly.

software error galaxy • 834 views

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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by rich_jp • 0

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

Was the job queued (grey) and not actually executing yet? This may fit the description of the situation. Just permanently delete the datasets and that will stop the processing.

Best, Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

3.6 years ago by

rich_jp • 0

United Kingdom

rich_jp • 0 wrote:

Hi Jen,

So I am talking about jobs that are already running (yellow) and then trying to kill them via Admin>Manage Jobs and submitting a kill request. Its then that I get the 'no PID in database for job error, unable to stop'.

Rich

ADD COMMENT • link written 3.6 years ago by rich_jp • 0

Hi Rich, So that you (and others) know, we were able to confirm the behavior here. More soon once the issue is sorted out. Thanks for reporting. Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, thanks to you (and others - Nate!) for checking on this for me. Just to add that I actually first observed this issue quite a while ago, importantly before I updated to the latest Galaxy (17052:28113eeee212 ). So it is not something specific to the latest release but has been around a while. Rich

ADD REPLY • link written 3.6 years ago by rich_jp • 0

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update: this was a true bug and it is now resolved in the current (15.03) release, through the latest incorporated sub-release. Updating against the distribution will incorporate the correction.

Thanks Rich for confirming the fix! Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen - thanks to you and Nate for taking a look and fixing this :)

ADD REPLY • link written 3.6 years ago by rich_jp • 0

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