feat(pipeline): park idle pool workers to fix the thread-oversubscription cliff by nh13 · Pull Request #955 · fulcrumgenomics/fgumi

nh13 · 2026-09-13T02:27:12Z

Summary

Fixes the thread-oversubscription cliff in the chain-builder pool: running a command with more worker threads than it has parallel work no longer slows it down.

The pool is replicated round-robin polling with no producer→consumer wakeup — an idle worker exponential-backoff sleeps then re-polls. When there are more workers than parallel work, the surplus churn poll→sleep→poll, and that churn actively slows the productive workers. On fgumi correct at 32 threads this was a hard regression: ~6.5s wall vs ~1.9s at 16 threads (pool 92% idle, 208s of aggregate idle churn), because a single serial grouping stage feeds the parallel work and nothing else can run.

Result

fgumi correct, 10M templates, c8g.8xlarge (32 vCPU):

threads	before	after
16	2.03s	1.90s
32	6.48s (1.9× vs 1 thread)	1.91s (6.4×)

The cliff is gone — throughput is now flat past the useful-parallelism point instead of collapsing. Aggregate idle dropped 208s → 35s (real parking, not spin-churn). Output is unchanged.

Approach (two layers)

L0 — remove the contention, take the cheap wins

Test-and-test-and-set on the Serial step mutex: parking_lot::try_lock writes (invalidates) the holder's cache line even on failure, so a surplus worker probing a held ceiling step stole that line every idle pass. Probe is_locked() (a shared load) first.
Raise the pool backoff floor 1µs → 20µs so a stray-success reset doesn't drop a surplus worker onto a per-microsecond re-poll ramp.

L2 — park the surplus (the real fix)

PoolEventCount: a Vyukov event-count over parking_lot Mutex/Condvar. Idle workers arm (register + SeqCst fence + snapshot), re-poll once, then block only if still empty; producers publish work then notify_one. When nobody is parked, notify_one is one fence + one read-shared load — no store, no lock, no wake. Correctness is the C++20 SeqCst-fence rule (arm fence and notify fence are totally ordered → no interleaving parks on a poppable item).
Notify seam is the driver's dispatch outcome: Progress → notify_one, Finished → notify_all. Using the outcome (not the queue push site) captures the reorder must-accept stash without threading the parker through every queue.
Concurrency ceiling gates notify_one on awake = n_pool − waiters < ceiling so the per-Progress cascade can't re-wake the whole surplus. Default = ungated; a controller can lower it later. notify_all (cancel/close/Finished) is never gated.
Pinned workers (Exclusive/sticky owners, Serial affinity targets) keep the old sleep-backoff — a shared notify_one can't target a specific worker. Detached drivers notify but don't wait. Cancel/error wake all parked workers via a late-bound Weak<PoolEventCount> on PipelineSignal. Only wired when n_threads > 1; single-thread/fused paths are behaviour-identical.

L1 (per-command) — pin the correct chain's serial GroupByQueryname to one worker (optional per-instance affinity, default unchanged for every other chain) so surplus workers Skip it instead of thrashing its mutex.

Testing

Full workspace suite green (9988 tests). New PoolEventCount unit tests incl. a no-lock-when-idle proof, a moved-generation test, and a 2000-iteration lost-wakeup stress; a TTAS test proving a held Serial step reports Contention without running.
Benchmarked on 32-vCPU Graviton: correct cliff gone; extract K=2 (push-heavy — the always-on notify canary) flat 16→32; sort (exercises the detached-driver notifier + pinned paths) scales cleanly with no regression.

Notes

Stacked on feat(pipeline): thread-utilization and per-step bandwidth telemetry for the chain-builder engine #951 (thread/bandwidth telemetry); base branch nh/pipeline-thread-telemetry.
This stops the cliff. It does not raise correct's ceiling — a single-threaded GroupByQueryname (~1.5s, runs end-to-end) still caps scaling past ~16 threads. Parallelizing that stage is separate follow-up work.
The concurrency-ceiling controller (feedback from edge depth) is deferred: the ungated ceiling was sufficient in benchmarks (the per-Progress cascade churn did not hurt).

Risk: output change none; unsafe change none, and no CLAUDE.md allowlist update is required; memory-bound and queue-capacity changes none, but worker backpressure changes through parking and wakeup limits.

Fix: Park idle workers, reduce serial-step lock contention, and pin GroupByQueryname in the correct chain.

Add PoolEventCount for coordinated worker parking and wakeups.
Handle progress, completion, cancellation, errors, pinned workers, and detached drivers.
Increase the minimum backoff and add test-and-test-and-set locking.
Preserve output and pass 9,988 workspace tests.
Improve reported 32-thread fgumi correct runtime from 6.48s to 1.91s.

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📒 Files selected for processing (4)

crates/fgumi-pipeline-core/src/builder.rs
crates/fgumi-pipeline-core/src/runtime/driver.rs
crates/fgumi-pipeline-core/src/runtime/event_count.rs
src/lib/pipeline/chains/builder.rs

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Walkthrough

The runtime adds coordinated event-count parking for eligible multi-worker pipelines. Pinned, detached, and single-worker paths retain backoff. Signals wake parked workers, and GroupByQueryname receives explicit affinity.

Changes

Pool parking coordination

Layer / File(s)	Summary
Event-count primitive `crates/fgumi-pipeline-core/src/runtime/event_count.rs`, `crates/fgumi-pipeline-core/src/runtime/mod.rs`	Adds `PoolEventCount`, wait outcomes, waiter registration, generation tracking, wakeup ceilings, notifications, and unit/stress coverage.
Worker parking and dispatch `crates/fgumi-pipeline-core/src/runtime/worker_core.rs`, `crates/fgumi-pipeline-core/src/runtime/driver.rs`	Adds event-count waiting for eligible workers. Pinned and single-worker paths retain backoff. Dispatch notifies peers after `Progress` and `Finished`. Serial dispatch detects held locks before returning `Contention`.
Pipeline wiring and affinity `crates/fgumi-pipeline-core/src/runtime/detached.rs`, `crates/fgumi-pipeline-core/src/runtime/builder.rs`, `crates/fgumi-pipeline-core/src/signal.rs`, `src/lib/pipeline/steps/group/queryname.rs`, `src/lib/pipeline/chains/builder.rs`	Creates and binds the multi-worker parker, passes it to workers and detached drivers, wakes workers on terminal signal transitions, and configures `GroupByQueryname` affinity.

Priority: ⬇️ Low

Estimated code review effort: 4 (Complex) | ~45 minutes

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant PipelineRun
  participant WorkerLoop
  participant PoolEventCount
  participant PipelineSignal
  PipelineRun->>WorkerLoop: provide parker and pinned flag
  WorkerLoop->>PoolEventCount: register and wait after idle recheck
  WorkerLoop->>PoolEventCount: notify_one after Progress
  WorkerLoop->>PoolEventCount: notify_all after Finished
  PipelineSignal->>PoolEventCount: wake parked workers on error or cancellation

Merge Risk: ⚪ Minimal · up to 223ee

Parked workers are woken for progress, completion, errors, and cancellation, including detached-driver activity. No concrete merge-blocking risk remains.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Title check	⚠️ Warning	The title uses a valid Conventional Commit type, a lowercase imperative description, and accurately describes the changes. However, the scope `pipeline` does not name an affected command or crate as r…	Use an affected crate or command as the scope, for example: `feat(fgumi-pipeline-core): park idle pool workers to fix the thread-oversubscription cliff`.

✅ Passed checks (2 passed)

Check name	Status	Explanation
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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Explanation

The title uses a valid Conventional Commit type, a lowercase imperative description, and accurately describes the changes. However, the scope pipeline does not name an affected command or crate as required.

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codecov · 2026-09-13T02:32:04Z

Codecov Report

❌ Patch coverage is 98.65952% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.02%. Comparing base (d757c77) to head (223ee29).

Files with missing lines	Patch %	Lines
crates/fgumi-pipeline-core/src/runtime/driver.rs	95.65%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #955      +/-   ##
==========================================
- Coverage   96.02%   96.02%   -0.01%     
==========================================
  Files         290      291       +1     
  Lines      143501   143872     +371     
==========================================
+ Hits       137796   138152     +356     
- Misses       5705     5720      +15

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nh13 · 2026-09-13T09:23:57Z

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Inline comments:
In `@crates/fgumi-pipeline-core/src/runtime/driver.rs`:
- Around line 262-265: Update the event-count wait branch in
round_robin_dispatch to arm and recheck first, then only when no progress
remains stamp the selected step Parked and initialize sleep_start immediately
before ec.wait. Ensure productive rechecks do not record idle time while the
board remains Running.

In `@crates/fgumi-pipeline-core/src/runtime/event_count.rs`:
- Around line 409-416: The stress test must verify that the wait completed
promptly rather than only confirming the producer stored work. Update the
synchronization around the wait outcome to use recv_timeout, or otherwise
preserve a timeout-distinguishable result from ec.wait, and assert that
completion was observed before the deadline; do not discard outcome or rely
solely on work.load(Ordering::SeqCst) after producer.join().
- Around line 115-116: Make WaitKey non-Copy so each token can be consumed only
once, while preserving its existing Debug, Clone, PartialEq, and Eq traits as
appropriate. Update wait and cancel_wait ownership handling and all in-tree call
sites to pass the key by value exactly once, preventing repeated decrements of
waiters.

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crates/fgumi-pipeline-core/src/builder.rs
crates/fgumi-pipeline-core/src/runtime/detached.rs
crates/fgumi-pipeline-core/src/runtime/driver.rs
crates/fgumi-pipeline-core/src/runtime/event_count.rs
crates/fgumi-pipeline-core/src/runtime/mod.rs
crates/fgumi-pipeline-core/src/runtime/worker_core.rs
crates/fgumi-pipeline-core/src/signal.rs
src/lib/pipeline/chains/builder.rs
src/lib/pipeline/steps/group/queryname.rs

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…liff The chain-builder pool is replicated round-robin polling with no producer->consumer wakeup: an idle worker (whole dispatch pass did no work) exponential-backoff *sleeps*, then re-polls. On an oversubscribed pipeline (more workers than available parallel work) the surplus workers churn poll->sleep->poll, and that churn actively slows the productive workers. On `fgumi correct` at 32 threads this was a hard cliff: ~6.5s wall vs ~1.9s at 16 threads (pool 92% idle, 208s of aggregate idle churn), because a single serial grouping stage feeds the parallel work and nothing else can run. Two layers: L0 — take the cheap wins, remove the contention: - Test-and-test-and-set on the Serial step mutex. `parking_lot::Mutex::try_lock` is a compare_exchange that writes (invalidates) the holder's cache line even when it fails; a surplus worker probing a held `Serial + Affinity::None` step (the throughput ceiling) stole that line every idle pass. Probe `is_locked()` (a shared load) first and report `Contention` without the write. - Raise the pool backoff floor 1us -> 20us so a surplus worker's stray-success reset does not drop it back onto a per-microsecond re-poll ramp. Wake latency for a worker that made progress is unaffected (it does not sleep). L2 — park the surplus (the real fix): - `PoolEventCount`, a Vyukov event-count over parking_lot Mutex/Condvar. An idle worker arms (`prepare_wait`: register + SeqCst fence + snapshot generation), re-polls its real condition one more pass, then blocks (`wait`) only if still empty; a producer publishes work then `notify_one` (SeqCst fence + a read-shared `waiters` load; when nobody is parked that is the whole cost — no store, no lock, no wake). Correctness is the C++20 SeqCst-fence rule: the arm fence and the notify fence are totally ordered, so no interleaving parks on a poppable item. Notify-under-lock gives the condvar the token a bare condvar lacks. - Notify seam is the driver's dispatch outcome, not the queue: `Progress` (pushed or held an item, including a reorder must-accept stash) -> notify_one; `Finished` (an output edge closed) -> notify_all. This captures the ordinal-unblocking stash without threading the parker through every queue. - Concurrency ceiling: notify_one wakes a parked worker only while `awake = n_pool - waiters < ceiling`, so the per-Progress cascade cannot re-wake the whole surplus. Default ceiling = n_pool (ungated); a controller can lower it later. notify_all (cancel/close/Finished) is never gated. - Pinned workers (Exclusive/sticky owners, and Serial affinity targets) keep the old sleep_backoff: a shared notify_one cannot target a specific worker, so a push meant for a pinned step's owner could wake a peer that Skips it. They are a handful of N and were never the problem. - Detached driver threads participate as notifiers (their pushes wake pool waiters via the same dispatch seam) but not as waiters (they keep their Park backoff). - Cancel/error wake every parked worker: `PipelineSignal` holds a late-bound Weak<PoolEventCount> (bound in `run` before any spawn, no Arc cycle) and calls notify_all after the terminal-state CAS in both `cancel` and `record_error` (a step Err calls only record_error, never cancel), so a parked worker observes is_done() instead of sleeping to its timeout. The wait deadline (the existing backoff) remains as a self-heal. - Only wired when `n_threads > 1`; the single-thread and fused paths pass `None` and keep the existing sleep-backoff idle (behaviour-identical off path). Result on `fgumi correct` at 32 threads: ~1.9s wall (from ~6.5s), flat vs 16 threads; aggregate idle 208s -> 35s (real parking, not spin-churn). `extract` K=2 (push-heavy) and `sort` (exercises the detached-driver notifier + pinned paths) show no regression.

`GroupByQueryname` is the throughput ceiling of the `correct` chain — the sole `Serial` feeder of the parallel `correct` step. Left as `Affinity::None` it is probed by every one of N workers on every idle pass; the engine's own bottleneck verdict flags a contended Serial step as an affinity/fuse/detach candidate. Give the step an optional per-instance affinity (default `Affinity::None`, so every other chain that uses it — align, dedup, filter-by-template — is unchanged) and, in `add_correct`, pin it to `Affinity::Worker(1)` (worker 1, not 0, which hosts the sticky reader source; clamped so `--threads 1` maps to worker 0 rather than requesting a non-existent worker). Surplus workers then `Skip` it entirely instead of thrashing its mutex. Pairs with the pool-worker parking in the engine: pinning stops the contention, parking stops the idle churn. Output is unchanged (pinning only selects which worker runs the serial step).

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nh13 deployed to github-actions September 13, 2026 02:27 — with GitHub Actions Active

nh13 force-pushed the nh/pipeline-thread-telemetry branch from bd44ae5 to 0f2c6d6 Compare September 13, 2026 03:50

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nh13 force-pushed the nh/correct-scheduler-opt branch from d1c1546 to 3129db6 Compare September 13, 2026 17:25

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nh13 mentioned this pull request Sep 13, 2026

perf(group): parallel queryname grouping for the correct/align/filter chains #957

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chore: release v0.8.0 #868

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perf(zipper): fold per-record PG/AS/XS aux scans into single-pass walks #964

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feat(pipeline): park idle pool workers to fix the thread-oversubscription cliff - #955

feat(pipeline): park idle pool workers to fix the thread-oversubscription cliff#955
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