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`toil kill` doesn't cancel batch system jobs
See original GitHub issueAs noted in https://gitter.im/bd2k-genomics-toil/Lobby?at=618eb0f3fb3dcd4e88818830, toil kill doesn’t seem to be using the normal shared file machinery to find pid.log, and when we reorganized where shared files live, it lost the ability to find it.
We should change toil kill to use the normal shared file read code, so it will always be able to find the files it is looking for, no matter where we store them.
┆Issue is synchronized with this Jira Story ┆friendlyId: TOIL-1087
Issue Analytics
- State:
- Created 2 years ago
- Comments:9 (8 by maintainers)
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We don’t necessarily have a way to find the workers. We could do something like the services do and have a terminate flag file in the job store that gets polled, and make the workers (and leader, for when it’s on another machine) have a thread to poll it and self-terminate.
➤ Melaina Legaspi commented:
Lon Blauvelt : “Try to get the PID from the job store and then kill it with a gentle kill. Then kill all the workers. Toil kill should monitor to make sure all the workers are eliminated.“