multithreading_trial #24
Closed
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Owner
Author
|
Needs more work. Runtime is not significantly different from single threaded mode atm. Cols per second seem to slow toward end of the run for some reason. |
Owner
Author
|
I think the Biopython MSA data structure is not suitable for multithreaded processing. Try converting the alignment to a Polars dataframe before processing and then back to MSA afterwards. |
Owner
Author
|
Tested with numpy array as data structure. Speed is limited by complex dict lookups. RIP calculation step needs restructuring before multithreading will be useful. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Experimenting with multithreading of alignment processing.
*Did not end up using dask.