can't ctrl-c toil

[gijzelaerr]

What is the proper way to kill toil?

If I ctrl-c a cwl toil (3.19.0) run it keeps on going. For now i'm using:

$ ps ax | grep toil | awk '{ print $1 }' | xargs kill

in a different console, but there must be a better way?

┆Issue is synchronized with this Jira Story ┆friendlyId: TOIL-40

[diekhans]

This is a known issue that needs to be address in the code:

http://www.regexprn.com/2010/05/killing-multithreaded-python-programs.html

I always used create threads with daemon = True approach.

In the mean time you can also ctrl-z toil it and kill %1

Gijs Molenaar [email protected] writes:

What is the proper way to kill toil?

If I ctrl-c a cwl toil run it keeps on going. For now i'm using:

$ ps ax | grep toil | awk '{ print $1 }' | xargs kill

in a different console, but there must be a better way?

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[mr-c]

In what PR was this fixed?

[adamnovak]

It looks like we set up a SIGTERM handler in #3779 which is at https://github.com/DataBiosphere/toil/blame/b5abd3c6565cee88edde94eb5546fa85909adbc3/src/toil/common.py#L928.

I think this ought to be working now, for cases where the Toil main thread is actually available to receive the signal and none of the other threads are hung.