perf(progress): fast-path log_if_needed via cached next threshold by nh13 · Pull Request #345 · fulcrumgenomics/fgumi

nh13 · 2026-05-16T04:06:39Z

Stacked on #344.

Summary

Replace the divide-by-interval check in ProgressTracker::log_if_needed with a comparison against a cached next_threshold, saving ~30-60 cycles per call.
Mark the milestone-crossing branch #[cold] and re-read next_threshold under the EMA mutex so concurrent crossings can't double-log.

Why

log_if_needed(1) is called once per record on hot BAM paths. On a 16-thread sort at ~32 M calls/s this branch shows up as ~1 % of total CPU in profiles. The thresholds form a fixed arithmetic sequence, so caching the next one removes the division entirely on the predicted-not-taken fast path.

Test plan

cargo ci-test
cargo ci-fmt && cargo ci-lint
Spot-check a sort run logs progress at expected intervals

codecov · 2026-05-16T04:09:20Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.97%. Comparing base (c781d53) to head (5fb46c8).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #345   +/-   ##
=======================================
  Coverage   90.97%   90.97%           
=======================================
  Files          78       78           
  Lines       51017    51017           
=======================================
+ Hits        46412    46413    +1     
+ Misses       4605     4604    -1

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nh13 · 2026-05-16T14:00:43Z

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coderabbitai · 2026-05-16T14:00:49Z

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coderabbitai · 2026-05-16T14:00:52Z

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Run ID: 47149871-57ab-4b6d-a22e-cd42c0c34d55

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Reviewing files that changed from the base of the PR and between 9ed3d21 and 5fb46c8.

📒 Files selected for processing (1)

crates/fgumi-bam-io/src/progress.rs

📝 Walkthrough

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Walkthrough

ProgressTracker adds an atomic next_threshold to track the next milestone boundary and avoid per-call division. with_interval() stores the configured interval into that atomic. log_if_needed() performs an atomic fetch-and-add and quickly returns unless new_count reaches next_threshold; when reached it calls a slow-path that acquires the EMA mutex, re-checks the threshold, updates EMA if total is set, logs each crossed milestone with percentage/ETA, advances the threshold, and returns whether the call landed on the last logged milestone.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title accurately describes the main optimization: replacing a divide operation with a cached threshold comparison for performance improvement.
Description check	✅ Passed	Description clearly explains the optimization, motivation, and testing approach, directly related to the changeset.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Commit unit tests in branch nh/progress-next-threshold

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nh13 · 2026-05-16T14:57:28Z

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coderabbitai · 2026-05-16T14:57:33Z

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… path The fast path now compares `count` against a cached `next_threshold` instead of dividing by `interval`, saving ~30-60 cycles per call. At ~32 M `log_if_needed(1)` calls/s on a 16-thread sort, this is ~1 % of total CPU in profiles. Marked the slow path `#[cold]` and re-reads `next_threshold` under the EMA mutex so concurrent crossings can't double-log.

nh13 · 2026-05-20T01:36:41Z

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nh13 · 2026-05-20T01:41:49Z

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coderabbitai · 2026-05-20T01:42:00Z

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nh13 · 2026-05-20T01:56:34Z

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nh13 · 2026-05-20T01:56:35Z

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nh13 · 2026-05-20T02:02:06Z

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coderabbitai · 2026-05-20T02:02:13Z

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nh13 · 2026-05-20T16:06:26Z

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nh13 temporarily deployed to github-actions May 16, 2026 04:06 — with GitHub Actions Inactive

coderabbitai Bot approved these changes May 16, 2026

View reviewed changes

nh13 force-pushed the nh/perf-followups branch 2 times, most recently from 18ba353 to 77009a9 Compare May 18, 2026 15:42

Base automatically changed from nh/perf-followups to main May 18, 2026 15:46

nh13 force-pushed the nh/progress-next-threshold branch from 9ed3d21 to 5fb46c8 Compare May 18, 2026 15:56

nh13 temporarily deployed to github-actions May 18, 2026 15:57 — with GitHub Actions Inactive

nh13 merged commit 6b2f3f6 into main May 21, 2026
10 checks passed

nh13 deleted the nh/progress-next-threshold branch May 21, 2026 19:42

nh13 mentioned this pull request May 21, 2026

chore: release v0.3.0 #309

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nh13 commented May 16, 2026

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