DiamondLightSource / DiamondLightSource/python-dlstbx

Better handle failed processing jobs when terminated by cluster

Open
#289 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
2
Forks
2
Avg merge
1d 11h
Merged PRs (30d)
2

Description

Raised by Mark; this collection has a permanent spinning cog: https://ispyb.diamond.ac.uk/dc/visit/mx37593-40/id/18159036

This corresponds to a reprocessing run that combined several datasets:

![Image](https://github.com/user-attachments/assets/bbad1ac7-bdf0-40d0-820a-58afa91c9597)

The log file shows it terminating in the middle of integration (I assume due to OOM errors):
```
...
oooooooooooooooooooooooooooooooooo.ooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => good "%" => ok "!" => bad rmsd
"O" => overloaded "#" => many bad "." => weak
"@" => abandoned
Mosaic spread: 0.413 < 0.413 < 0.413
-------------------- Spotfinding SWEEP2 --------------------
67030 spots found on 3600 images (max 1798 / bin)
***
******
********* ****
************* *********
* ******************* *** ************* ***
** ***************************** ******************** ****
************************************************************
************************************************************
************************************************************
************************************************************
1 image 3600
------------------- Autoindexing SWEEP2 --------------------
All possible indexing solutions:
aP 40.40 57.05 77.35 102.77 94.67 100.11
Indexing solution:
aP 40.40 57.05 77.35 102.77 94.67 100.11
-------------------- Integrating SWEEP2 --------------------
```

possibly we need to have a service that occasionally checks the cluster status for known reprocessing jobs, and marks it as failed if the cluster job has gone away but no status update written?

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.