Hello, I need help with killing a job. It is perpetually trying to run because I deleted the files before realizing that they were needed for the job to complete. This job cannot complete and is now making a log jamb and preventing any other job from running. Do I wait indefinitely for it to time out? or is there something else I can do.
Looking for help so far I’ve seen posts about using gxadmin. But, I am hesitant to use this and muck up galaxy more than I have already
Yes, purging the running dataset will usually work to kill an unwanted job. How this technically works as a user in the web application is that the next time the job needs to interact with the rest of the job running parts of the database (an input, or the history), a connection will “go wrong”, then the job fails. But this means letting the job process on the cluster node first.. unless it is still queued, then it will die before getting the final dispatch message.
Since this is your own Galaxy, you could kill the job wherever it is running, then clean up the database. This topic has what worked for another person (who didn’t have gxadmin set up due to the default database still be used). → How to kill a failed job without gxadmin?
The gxadmin command do all of this for you. This is a reply from the author.
Other than that, if you have the cluster resources available to run more jobs, I am wondering if you need to adjust how many concurrent processes are allowed. This is adjustable on the server and per user and we can share where to set these. The version of Galaxy and which database you are using might matter, so please include those.
You will need to be logged into an account with administrator permissions set in the galaxy.yml top level configuration file. The email address(s) here need to match the account email address.
# Administrative users - set this to a comma-separated list of valid
# Galaxy users (email addresses). These users will have access to the
# Admin section of the server, and will have access to create users,
# groups, roles, libraries, and more. For more information, see:
# https://galaxyproject.org/admin/
#admin_users: null
If you are using the default database, then the default/maximum is 4. But if you have upgraded then you can set these to a higher level.