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

Use HDF5 files for quantity logs. #72

Merged
merged 9 commits into from
Nov 9, 2023
Merged

Use HDF5 files for quantity logs. #72

merged 9 commits into from
Nov 9, 2023

Conversation

joaander
Copy link
Member

@joaander joaander commented Nov 6, 2023 •
edited
Loading

Description

Switch from GSD to HDF5 for thermodynamic logs.

Motivation and context

Reduce the time needed to run the analysis workflow steps.

How has this been tested?

  • Test entire workflow run.

Checklist:

@joaander
Copy link
Member Author

joaander commented Nov 7, 2023

I ran the complete workflow on Great Lakes. I didn't measure before/after timings, but the analysis step feels faster. The total output file size is also much smaller: 81M for 4 replicates.

@joaander joaander marked this pull request as ready for review November 7, 2023 20:23
@joaander joaander requested review from a team and tommy-waltmann and removed request for a team November 7, 2023 20:23
tommy-waltmann
tommy-waltmann requested changes Nov 9, 2023
View reviewed changes
Copy link
Collaborator

@tommy-waltmann tommy-waltmann left a comment

Choose a reason for hiding this comment

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

The changes look mostly good. There is just one comment which appears to have been copy/pasted in each validation test file which is no longer true.

hoomd_validation/hard_disk.py Show resolved Hide resolved
hoomd_validation/hard_sphere.py Show resolved Hide resolved
hoomd_validation/hard_sphere.py Show resolved Hide resolved
hoomd_validation/simple_polygon.py Show resolved Hide resolved
hoomd_validation/patchy_particle_pressure.py Show resolved Hide resolved
hoomd_validation/lj_union.py Show resolved Hide resolved
hoomd_validation/lj_fluid.py Show resolved Hide resolved
@joaander joaander merged commit af73bc6 into trunk Nov 9, 2023
2 checks passed
@joaander joaander deleted the log-hdf5 branch November 9, 2023 14:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@tommy-waltmann tommy-waltmann tommy-waltmann approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@joaander @tommy-waltmann