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Toil not parsing bjobs -l info for running jobs #209

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ionox0 opened this issue Jul 30, 2019 · 0 comments
Open

Toil not parsing bjobs -l info for running jobs #209

ionox0 opened this issue Jul 30, 2019 · 0 comments

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@ionox0
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ionox0 commented Jul 30, 2019

This logging means that this line:

https://github.com/DataBiosphere/toil/blob/master/src/toil/batchSystems/lsf.py#L122

is not being parsed correctly by lsf.py batch system.

however, it still works because default return value from that function is return None which is the same as return value for when job is running

however we need to fix this debug logging as it should be printing "bjobs detected job started but not completed: <job id>".

DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600
DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601
DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s
DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221600
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600
DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601
DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s
DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221600
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600
DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601
DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s
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