perf(placement): prefetch the table the scoring loop probes - #117
Merged
Conversation
computeChildMetrics prefetched seedFreqInReads and seedInverseGenomeCounts, but the hot per-seed loop reads neither -- it probes logReadCounts, which was never prefetched. So every per-seed lookup missed cache while bandwidth was spent prefetching two tables that are never read here. Prefetch logReadCounts instead (and drop the two dead prefetches). A/B (single-thread): TB place -17% at t1 (5.63 -> 4.66s), -6% at t8, -4% at t16; SARS place neutral (read-processing-bound, tables cache-resident). Placement output byte-identical; unit + e2e + examples pass. Found re-profiling the memory-bound scoring loop -- a single-socket taskset test ruled out NUMA, pointing at cache/bandwidth, and the prefetch/lookup mismatch was the culprit.
amkram
changed the title
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
No description provided.