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

disable HDF5 file locking #2314

Open
wants to merge 1 commit into
base: master
Choose a base branch
from

Conversation

cat-bro
Copy link
Collaborator

@cat-bro cat-bro commented Dec 3, 2024

There has been an error in gunicorn logs coming from the tool predictions API:

Dec 03 00:01:47 galaxy galaxyctl[2118437]:   File "h5py/h5f.pyx", line 102, in h5py.h5f.open
Dec 03 00:01:47 galaxy galaxyctl[2118437]: OSError: Unable to synchronously open file (file locking flag values don't match)

From a google search I found recommendations to use HDF5_USE_FILE_LOCKING: "FALSE". Checked out EU and Main infrastructure playbooks and found that they are already using this, and they have adopted it recently. (galaxyproject/usegalaxy-playbook@3724a13#diff-68bca5ccf2e9695dcca9925b36cce7bb8e7bd223d9c6531649be01986c661020R31)

I'm not sure if this means instances are individually compensating for something that has gone wrong in Galaxy

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

Successfully merging this pull request may close these issues.

1 participant