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Toil can hang on the GI Slurm cluster in a way that lsof fixes #5214

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adamnovak opened this issue Feb 19, 2025 · 0 comments · May be fixed by #5215
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Toil can hang on the GI Slurm cluster in a way that lsof fixes #5214

adamnovak opened this issue Feb 19, 2025 · 0 comments · May be fixed by #5215
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adamnovak commented Feb 19, 2025 •
edited by unito-bot
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@glennhickey has had Toil jobs start on the GI Slurm cluster and hang apparently forever around the point where they would be reading the job from the FileJobStore.

He's also noticed that logging into the node and running lsof on the Toil process seems to unstick it.

We should add a workaround feature to Toil to try and take advantage of this to prevent the workers from getting stuck.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1699
@adamnovak adamnovak self-assigned this Feb 19, 2025
@adamnovak adamnovak linked a pull request Feb 19, 2025 that will close this issue
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Add worker unstick-ing thread DataBiosphere/toil
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