Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Consider adding a retry mechanism for out-of-memory error codes #39

Open
jpalmer37 opened this issue Oct 21, 2024 · 0 comments
Open

Consider adding a retry mechanism for out-of-memory error codes #39

jpalmer37 opened this issue Oct 21, 2024 · 0 comments

Comments

@jpalmer37
Copy link

I have encountered rare cases where a run appears to fail due to running out of memory during the kraken process. It appears to be a consistent error code of 137.

For the FluViewer_nf pipeline, we temporarily implemented the following retry mechanism for a memory-heavy process. I was thinking something similar could be applicable here for kraken:

process kraken {
  memory  { (70 + 10 * task.attempt) GB }   # ** not tested **
  errorStrategy { (task.exitStatus == 137 && task.attempt <= maxRetries) ? 'retry' : 'ignore' } 
  maxRetries 3
  
  ...
}

This pattern is also referenced here: https://seqera.io/blog/error-recovery-and-automatic-resources-management/

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant