panoptes
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When snakemake is manually cancelled the workflow remains as running
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
orError
- 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.
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".
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 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 asrunning
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.