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

collection_from_pathlist is much slower than the other methods #220

Closed
ctb opened this issue Feb 17, 2024 · 0 comments · Fixed by #221
Closed

collection_from_pathlist is much slower than the other methods #220

ctb opened this issue Feb 17, 2024 · 0 comments · Fixed by #221

Comments

@ctb
Copy link
Collaborator

ctb commented Feb 17, 2024

In the new load_collection framework, it looks like collection_from_pathlist introduced in #211 does not read sketches in parallel, leading to extremely long load times for pathlists.

Here is the relevant benchmark result from #214:

Screenshot 2024-02-17 at 3 08 21 PM

We would still expect it to be slower, but maybe by a factor of two - not 18x! :)
@ctb ctb changed the title collection_from_pathlist does not read sketches in parallel collection_from_pathlist is much slower than the other methods Feb 17, 2024
@ctb ctb mentioned this issue Feb 17, 2024
Merged
@ctb ctb closed this as completed in #221 Feb 18, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

MRG: parallelize collection_from_pathlist sourmash-bio/sourmash_plugin_branchwater
1 participant
@ctb