galaxyproject / galaxyproject/pulsar
Node failure job with no `return_code` file still marked as successful in Galaxy
- Dominant language
- Python
- Stars
- 46
- Forks
- 62
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 15
Description
Running hifiasm on the VGP instance and the node it executed on appears to have failed and the job was terminated prematurely. As a result, nothing past a certain point in the job script was executed, including capturing/writing the tool return code to `return_code`. Despite this, none of the postprocessing failures were fatal (due to being work_dir outputs) and for some reason, Galaxy still treated this job as successful.
Contributor guide
Research direction
Trace how Pulsar handles a terminated job when the `return_code` file is absent, including whether failures in `work_dir` outputs affect the final status. Reproduce the hifiasm scenario if possible and verify that a job whose execution stops before writing `return_code` is reported as failed rather than successful.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend, distributed-systems
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100