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.

Sign up for GitHub

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

Jump to bottom

Update ODK image to v1.4.3 in QC #3087

Merged
merged 11 commits into from
Oct 12, 2023
Merged

Update ODK image to v1.4.3 in QC #3087

merged 11 commits into from
Oct 12, 2023

Conversation

anitacaron
Copy link
Collaborator

@anitacaron anitacaron commented Oct 4, 2023 •
edited
Loading

Fixes #3084

@anitacaron anitacaron requested a review from gouttegd as a code owner October 4, 2023 15:33
@anitacaron anitacaron self-assigned this Oct 4, 2023
@anitacaron anitacaron mentioned this pull request Oct 4, 2023
Merged
@anitacaron anitacaron requested a review from matentzn October 4, 2023 15:52
@anitacaron
Copy link
Collaborator Author

QC failed with the message:

Exception in thread "elk-reasoner-thread-2" java.lang.OutOfMemoryError: Java heap space
make: *** [uberon.Makefile:128: uberon.owl] Error 1

I increased to 8GB the ENV ROBOT_JAVA_ARGS in the QC for testing.

This was referenced Oct 4, 2023
Merged
Merged
@cthoyt
Copy link
Contributor

cthoyt commented Oct 4, 2023

Looks like 8G wasn't enough

@cthoyt cthoyt mentioned this pull request Oct 10, 2023
Merged
3 tasks
@anitacaron
Copy link
Collaborator Author

We found out that the command robot materialize which is part of the rule that generates uberon.owl was causing the peak memory around 20G (on my macos machine).

We decided to remove this command when running QC because it will not bring unsats issues.

matentzn
matentzn approved these changes Oct 12, 2023
View reviewed changes
Copy link
Contributor

@matentzn matentzn left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Few changes, fantastic work!

@anitacaron anitacaron merged commit 54fbb3e into master Oct 12, 2023
@gouttegd gouttegd mentioned this pull request Oct 12, 2023
Merged
gouttegd added a commit that referenced this pull request Oct 12, 2023
@gouttegd
Merge pull request #3090 from obophenotype/update-odk-version
70256c0 
Add explanatory comment after #3087
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@gouttegd gouttegd gouttegd left review comments

@matentzn matentzn matentzn approved these changes

Assignees

@anitacaron anitacaron

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

CI failure, maybe due to overlapping synonyms
4 participants
@anitacaron @cthoyt @matentzn @gouttegd