perf(sort): read ahead deeply on the file the merge is blocked on

[nh13]

The deep read allowance goes to the drain frontier — the lowest source that has not fully drained. That is the file the merge reaches next only when sources drain in order, which is what an input already in the requested order produces. It is the case #709 was built for, and it still works there.

A partially-correlated input breaks the assumption. Sorting an already-SO:coordinate BAM to template-coordinate interleaves at the median (p50 = 1 block per source) but still draws long solo runs from a source that is not the lowest undrained one (p99 = 512 consecutive blocks). The file the consumer is parked on therefore took the shallow allowance and went bare — the pool passed over it 93% of the time finding nothing read yet, while sitting 46% idle.

That is the common production shape: anyone re-sorting pipeline output hits it.

The fix

The consumer already knew which source it was parked on; it just never told the pool. It now publishes that index, and that file gets the deep allowance alongside the frontier. Both are single files, so the extra read-ahead is bounded by two deep FIFOs rather than by K.

Sizing it turned out to matter more than targeting it, and only in bytes. Only one worker may hold a file’s reader mutex, so a refill is a single sequential read whose cost is per-request-bound until it is large enough to stream. A "block" is ~64 KB for BGZF and up to 256 KB for a zstd frame, and its compressed size moves with --temp-compression, so any fixed block count is right for exactly one codec at one compression level. Measured on one input, template-coordinate spills averaged 10,448 B/block against queryname’s 14,407 B. The allowance is now a 2 MiB target divided by the block size the run actually observes.

Measured

1kg-wgs-HG00096, coordinate → template-coordinate, 89 spill runs, 8 threads, --max-memory 512M, c7g.4xlarge:

refill	batch	merge loop	pool util
4 blocks (before)	4	326.5s	54%
1 MiB	101	212.4s	83%
2 MiB (chosen)	201	197.5s	89%
4 MiB	402	194.5s	90%

2 MiB is the knee; 4 MiB buys 3s for twice the read-ahead. Total sort wall 10m17s → 8m16s.

Peak RSS is flat across the whole sweep (4793–4828 MB against a 4794 MB baseline) — the allowance is scoped to one file, and fewer stalls mean less transient buffering elsewhere.

Neither knob works alone. Batch 32 into a cap-8 FIFO measures 325.5s against a 326.5s baseline, because a batch larger than the FIFO is never admitted and silently degrades to the cap. Hence the cap multiple.

Correctness and no-regression

• compare bams --command sort against the unmodified sort: IDENTICAL — 779,820,469 records, zero sort-order violations, zero run-multiset mismatches. Re-verified on the final shipped defaults.
• Orders that already used the frontier path are unchanged: queryname → coordinate 184.0s → 185.0s, coordinate → queryname 228.4s → 229.3s, both at 97% utilization.

Instrumentation (first commit)

Included because it is what makes the rest arguable rather than asserted.

in_flight_at_park already collected concurrent decompressions on the awaited file but surfaced only the none and exactly one buckets — which cannot distinguish a pool running two deep from one at its cap, and that is exactly the difference between scheduling headroom and irreducible latency. Per-gate skip counters for the same file then say which of the four admission gates holds the depth where it is.

Three hypotheses died to these counters, each having looked plausible first:

1. Decompress latency is irreducible — refuted: the pool is 2+ deep on the awaited file in 59% of parks.
2. The scheduler is demand-blind — refuted: it is on the right file, just starved of supply.
3. try_lock contention serializes workers onto one file — refuted: 6% of skips, against raw-empty’s 93%.

Where the merge floor actually is

The earlier version of this section put the floor at worker_busy / threads ≈ 175s and said we were within ~13% of it. That arithmetic assumes workers are the constraint, and --merge-threads falsifies it: it predicts ~90s at 16 threads and measures 174.1s.

The real bound is the serial per-block decompress chain on the file the consumer is blocked on. At a p50 of 32 us per block over 5,368,248 blocks that is 171.8s, and it is the same number the 2026-08-03 investigation reached from output-compression worker-busy — two independent derivations agreeing.

run	merge loop	vs 171.8s
before this PR (t8)	326.5s	+90%
t8	201.4s	+17%
t16	174.1s	+1.3%

At t8 the residual is pool capacity: 87% utilization, and of the worker scans that find no work, 97% are backpressured, 2% contended, 0% waiting on a peer's read — there is no legal work left, not a scheduling bug. At t16 capacity stops binding (50% utilization) and the merge lands 1.3% above the block-latency floor.

The binding gate moves with it, which is the useful part for whoever picks this up next:

awaited-file skip reason	t8	t16
raw-lock	32%	6%
raw-empty	61%	47%
decomp-capped	2%	46%

PHASE2_DECOMP_CAP = 8 is irrelevant at t8 and binding half the time at t16, alongside 19% gap-filling on the awaited file — a reorder-buffer head-of-line stall, where the file's buffer holds later blocks while the consumer needs an earlier one. That cap is the only remaining candidate for going below 172s. More threads, deeper read-ahead, and a cheaper consumer are all now measured dead ends.

Reading order

1. read ahead deeply on the file the merge is blocked on — instrumentation + the fix. This is the whole wall-clock win.
2. skip retired sources before paying their try_locks — still unmeasured for wall impact. Kept deliberately; is_drained now short-circuits on the retired flag too, since retirement is terminal and retired files stay in every is_phase_complete scan.
3. measure the merge consumer's serial cost exactly — replaces a sampled estimator whose rows summed to 151% of loop wall with exact park/backpressure clocks, and counts how each record reaches the writer.
4. borrow keyed records in place during the merge — keyed spills reassembled 100% of records into scratch while the comment claimed the opposite. CPU-efficiency only: −19 to −21% consumer CPU, ~1% wall, because the saved time converts to park at both t8 and t16.

Risk: output changes none; unsafe changes none and the CLAUDE.md allowlist remains unchanged; memory and backpressure policy change through deep read-ahead bounded to two FIFOs.

Fix: prioritize the awaited source and drain-frontier file while sizing read-ahead toward 2 MiB from observed compressed block sizes.

• Skip retired sources before lock acquisition.
• Add diagnostics for decompression depth, backpressure, refill sizing, and admission skips.
• Preserve zero-copy presentation for contiguous keyed records.
• Add tests for scheduling, sizing, resets, depth metrics, and oversized records.
• Reduce merge-loop time from 326.5s to 180.6s and total sort time from 10m17s to 8m16s.
• Keep peak RSS flat and output equivalent to the unmodified sort.

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Walkthrough

The merge pipeline now records consumer, presentation, output backpressure, and read-ahead metrics. Phase 2 prioritizes awaited sources, retires drained files, sizes refills from measured blocks, and uses zero-copy keyed records when possible.

Changes

Merge pipeline diagnostics and scheduling

Layer / File(s)	Summary
Phase 2 state and read-ahead scheduling crates/fgumi-sort/src/worker_pool.rs, crates/fgumi-sort/src/external.rs	Phase 2 retires drained files, tracks awaited sources and skip causes, measures read volume, and applies byte-based refill allowances. Tests cover retirement, drain behavior, scheduling, and per-merge state reset.
Permit wait accounting crates/fgumi-sort/src/worker_pool.rs, crates/fgumi-sort/src/bgzf_io.rs, crates/fgumi-sort/src/pooled_bam_writer.rs	Permit acquisition records blocked duration and wait count. Staging and pooled writers expose these totals.
Zero-copy record presentation crates/fgumi-sort/src/external.rs	Contiguous keyed records borrow decompressed bytes. Records that cross block boundaries are reassembled. Oversized-record tests validate both paths and presentation counters.
Consumer and merge diagnostics crates/fgumi-sort/src/external.rs, crates/fgumi-sort/src/merge_trace.rs	Merge diagnostics report record presentation, output backpressure, consumer CPU, awaited-file depth, read-ahead depth, and concurrent decompression depth. Consumer trace tests cover depth counts, weighted means, and empty traces.

Estimated code review effort: 4 (Complex) | ~60 minutes

Merge Risk: 🟠 High · up to 0181a

The change adds deep read-ahead for the merge-blocked files, but its entry-based sizing can allow unexpectedly large compressed buffers and potentially exhaust memory, making the PR unsafe to merge until the read-ahead is bounded by bytes.

Sequence Diagram(s)

sequenceDiagram
  participant MergeConsumer
  participant SharedPipelineState
  participant SortWorkerPool
  participant Phase2FileState
  participant PooledBamWriter
  MergeConsumer->>SharedPipelineState: publish awaited source
  SortWorkerPool->>SharedPipelineState: read awaited source and sizing metrics
  SortWorkerPool->>Phase2FileState: schedule prioritized refill
  Phase2FileState-->>SortWorkerPool: provide decompressed blocks
  SortWorkerPool-->>MergeConsumer: provide merge records
  MergeConsumer->>PooledBamWriter: write merged output
  PooledBamWriter-->>MergeConsumer: report permit backpressure

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Suggested labels: fgumi sort

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title uses valid Conventional Commit syntax, names the sort scope, and accurately describes the read-ahead change.
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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Codecov Report

❌ Patch coverage is 98.17232% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.32%. Comparing base (effea0a) to head (51c396d).

Files with missing lines	Patch %	Lines
crates/fgumi-sort/src/external.rs	95.93%	5 Missing ⚠️
crates/fgumi-sort/src/merge_trace.rs	96.96%	1 Missing ⚠️
crates/fgumi-sort/src/worker_pool.rs	99.54%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #806      +/-   ##
==========================================
- Coverage   94.34%   94.32%   -0.02%     
==========================================
  Files         186      186              
  Lines      113146   113486     +340     
==========================================
+ Hits       106745   107046     +301     
- Misses       6401     6440      +39     

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[nh13]

Follow-up measurement, on the same host and input, on whether the residual under-utilization can be recovered by adding merge workers. Short answer: barely, and the reason is worth recording.

--merge-threads already exists, so this needed no code change. 1kg-wgs-HG00096, coordinate → template-coordinate, 89 spill runs, --threads 8, --max-memory 512M, c7g.4xlarge (16 vCPU):

--merge-threads	merge loop	worker util	consumer parked	peak RSS
8 (this PR)	197.5s	89%	56%	4793 MB
9	192.6s	82%	56%	4696 MB
12	185.9s	63%	—	4829 MB
16	180.6s	50%	50%	4855 MB

Doubling the pool buys 8.6% and halves efficiency. Total worker busy is pinned at ~1400–1435s regardless of thread count, so the added threads are not finding more work to do.

This corrects a claim in the PR description. I described the floor as worker_busy / threads ≈ 175s, which assumes the workers are the constraint. That arithmetic predicts ~90s at 16 threads; the measurement is 180.6s. The extra eight threads bought 12 seconds.

The actual limit is the single-threaded merge consumer. Its serial work barely moves with more workers — loser tree 40.6s → 56.1s, enqueue write 44.1s → 50.0s — and it still parks 90.7s of a 180.6s loop at 16 threads. Parks collapse 4x (2.92M → 709K) while wall clock moves 6%: the pool keeps up easily, the consumer cannot consume faster.

That also explains the cores-over-time trace cited in the description. The steady 7.49-of-8 with no ramp signature is not unrecoverable idle — it is workers waiting on a serial consumer.

No default change proposed. 2.5% for a thread the user did not ask for is a poor trade, and defaulting Phase 2 to threads + 1 would quietly make --threads N mean N+1. The flag is already there for anyone who wants it. The honest guidance is that Phase 2 scales weakly, because the merge consumer is serial — and going meaningfully below ~180s means parallelizing that consumer (e.g. range-partitioning the key space), not adding workers or read-ahead.

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Inline comments:
In `@crates/fgumi-sort/src/worker_pool.rs`:
- Around line 1027-1036: Update is_drained to return immediately when retired is
already set, before acquiring the decompressed mutex or performing other checks.
Preserve the existing drain detection and Release publication when the file is
not yet retired, so callers including is_phase_complete,
advance_phase2_frontier, and decompress_and_publish benefit without call-site
changes.
- Line 3105: Update set_phase2_files alongside the existing phase2_lowest_active
and phase2_awaited_source resets to also reset awaited_skips, phase2_read_bytes,
and phase2_read_blocks, ensuring reused pools start each new file set with fresh
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crates/fgumi-sort/src/worker_pool.rs (1)

2523-2527: 🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win

Count awaited deep reads as deep reads.

A non-frontier awaited source uses awaited_allowance_for at Lines 2467-2474. This counter records that batch as shallow. read_batch_split therefore no longer splits by allowance, and the merge diagnostics can misreport deep-read use.

Classify with phase2_deserves_deep_read(i, frontier, awaited). Rename downstream “frontier” labels to “deep” if they include awaited-source batches.

Proposed fix

-            let (batches, blocks) = if i == frontier {
+            let (batches, blocks) = if phase2_deserves_deep_read(i, frontier, awaited) {
                 (&shared.deep_read_batches, &shared.deep_read_blocks)
             } else {
                 (&shared.shallow_read_batches, &shared.shallow_read_blocks)
             };

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In `@crates/fgumi-sort/src/worker_pool.rs` around lines 2523 - 2527, Update the
batch classification around the shared deep_read_batches and
shallow_read_batches selection to use phase2_deserves_deep_read(i, frontier,
awaited), so awaited non-frontier sources are counted as deep reads. Rename
downstream “frontier” labels to “deep” where they include awaited-source
batches, including read_batch_split and merge diagnostics.

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Inline comments:
In `@crates/fgumi-sort/src/external.rs`:
- Around line 4291-4307: Update the ratio calculation near est_write so output
backpressure time is removed from the write estimate before forming ratio_total.
Subtract blocked_secs from est_write, clamp the resulting write component to a
nonnegative value if needed, and use that adjusted value for the enqueue-write
share and nanoseconds-per-record calculations.
- Around line 1209-1217: Replace the process-wide RECORD_BORROWED and
RECORD_REASSEMBLED atomics with counters owned by each merge operation, updating
them wherever records are borrowed or reassembled. Pass that merge’s final
counter snapshot into log_merge_sub_phases so each log reports only the current
merge, without resetting shared state or introducing concurrency races.

In `@crates/fgumi-sort/src/worker_pool.rs`:
- Around line 661-664: Update the performance-floor documentation near the
worker-pool timing explanation to identify the serial merge consumer and
awaited-file decompression chain as active limits, and remove the claim that
only output compression can improve performance. Keep the existing measured
timing context while avoiding wording that rules out consumer or
decompression-cap improvements.

---

Outside diff comments:
In `@crates/fgumi-sort/src/worker_pool.rs`:
- Around line 2523-2527: Update the batch classification around the shared
deep_read_batches and shallow_read_batches selection to use
phase2_deserves_deep_read(i, frontier, awaited), so awaited non-frontier sources
are counted as deep reads. Rename downstream “frontier” labels to “deep” where
they include awaited-source batches, including read_batch_split and merge
diagnostics.

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Addressed the outside-diff finding on `worker_pool.rs` (batch classification around lines 2523-2527): the deep/shallow read-batch counters now classify with `phase2_deserves_deep_read(i, frontier, awaited)`, so an awaited non-frontier source (which reads at the deep allowance via `awaited_allowance_for`) is counted as deep rather than shallow. The downstream `read_batch_split` log label was renamed from "frontier" to "deep" to match, and `set_phase2_files` now also resets the deep/shallow read-batch counters (sibling of the awaited-skip/read-byte resets) so a reused pool starts each merge fresh.

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Inline comments:
In `@crates/fgumi-sort/src/worker_pool.rs`:
- Around line 684-691: Clamp the derived batch in awaited_allowance_for to a
defined maximum before calculating raw_cap, so small mean_block_bytes values
cannot create unbounded read batches or allocations. Preserve the existing
zero-size fallback and minimum batch behavior, and ensure both returned
allowances use the clamped batch.
- Around line 2467-2480: Update the allowance selection around
phase2_read_allowance and awaited_allowance_for so both the frontier case and
the phase2_deserves_deep_read case use measured byte-based sizing from
read_blocks and read_bytes; retain the regular allowance only for non-deep
reads, including when frontier equals awaited.

Apply the same fix in `@crates/fgumi-sort/src/worker_pool.rs` around lines 634 -
668.

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In `@crates/fgumi-sort/src/worker_pool.rs`:
- Around line 693-704: Update the phase-2 starving-read flow around the batch
calculation and raw FIFO capacity so each deep FIFO and read batch is bounded by
an explicit compressed-byte budget, not only the entry-count limits from
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