Provide a collapsed implementation of all pairs #3
Conversation
This file contains 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
This comment was marked as outdated.
This comment was marked as outdated.
Sorry, something went wrong.
|
@limefax let me know what you think :) |
|
These last two commits fix some of the issues you raised in #5:
|
This was referenced Jun 23, 2024
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Outdated suggestions cannot be applied.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.
This PR provides a collapsed implementation of the all pairs algorithm, processing one interaction per thread.
The interactions are accumulated using atomics, and we avoid having to reset the vector by using the thread assigned to the diagonal interaction to subtract the old acceleration.
On GPUs, the throughput of collapsed all-pairs is 3.3x higher than of all-pairs.
On CPUs, the throughput of collapsed all-pairs is 20x lower than of all-pairs.