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Published 20 hours ago • verified publisher icon panoptes-organization

When snakemake is manually cancelled the workflow remains as running

Open fgypas opened this issue 3 years ago • 3 comments

Describe the bug When a user manually kills (CTRL+C) a pipeline the process in panoptes stays forever as running

Expected behavior There are two solutions

  • The server periodically checks for workflows that are not updated (e.g. more than two days) and marks them as Cancellation or Error
  • The ideal solution would be that snakemake sends a signal before the CTRL+C takes place with the message Cancellation. I am not sure if this is possible though.

fgypas avatar Nov 09 '20 15:11 fgypas

How can we reproduce this? @fgypas For the moment, I'm running the workflow and I kill it with CTRL+C as suggested but the UI turns the workflow's status into "error".

dafentoulis avatar Dec 11 '20 12:12 dafentoulis

I think that @drekoumis added a fix for this at some point. @drekoumis Do you remember the commit/pull request? This is not completely fixed though, because when you kill the snakemake process with kill (e.g. kill -9 <process-id>) then it gets stack as running on the panoptes side. @dafentoulis Can you try this?

fgypas avatar Dec 11 '20 12:12 fgypas

I think that @drekoumis added a fix for this at some point. @drekoumis Do you remember the commit/pull request? This is not completely fixed though, because when you kill the snakemake process with kill (e.g. kill -9 <process-id>) then it gets stack as running on the panoptes side. @dafentoulis Can you try this?

I managed to reproduce it this way. Thank you. Indeed, manually cancelling with CTRL+C is not a problem anymore.

dafentoulis avatar Dec 11 '20 13:12 dafentoulis