Opened 29 hours ago
Closed 7 hours ago
#1655 closed defect (fixed)
Sequencing job is registered as failed
| Reported by: | Nicklas Nordborg | Owned by: | |
|---|---|---|---|
| Priority: | critical | Milestone: | Job scheduler extension v1.16 |
| Component: | net.sf.basedb.opengrid | Keywords: | |
| Cc: |
Description
The error message is:
sacct: fatal: Bad job/step specified: HF2FHBGYW
A sequencing job is registered as a non-grid job to begin with and it should not use squeue or sacct to get information about it. There are custom scritpts in Reggie (eg. nextseq_status.sh that should be used instead).
Exactly how this is happening needs to be investigate. It is most likely related to #1646.
The effect of this bug is that the auto-confirmation in Reggie is not working and the sequencing need to be manually registered as ended.
Change History (3)
comment:1 by , 27 hours ago
comment:3 by , 7 hours ago
| Resolution: | → fixed |
|---|---|
| Status: | new → closed |
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It seems like this issue is related to changing the signal handler for a job when the status changes. This change is needed by #1646 since different signals are supported when a job is waiting, paused or executing.
But the signal handler is changed also for non-grid jobs which leads to the system thinks that it is a grid-job for the next update and then it fails because grid jobs have a numeric id.