perf(group): parallel queryname grouping for the correct/align/filter chains by nh13 · Pull Request #957 · fulcrumgenomics/fgumi

nh13 · 2026-09-13T18:15:00Z

Summary

fgumi correct's wall-clock floor was the serial GroupByQueryname step (~1.5 s of single-threaded CPU, flat across thread counts). This PR removes it: the source cutter now emits batches closed under queryname (no read-name run straddles a batch boundary), so grouping becomes a pure parallel map (AssembleTemplates) instead of a serial fold.

Verified on a 32-vCPU box (c8g.8xlarge, 20 M-record input): output is byte-identical at the record level, GroupByQueryname is gone from the pipeline, and correct is 1.70× faster at 16 threads and 5.85× at 32 threads (6.61 s → 1.13 s).

Stacked on #955 (nh/correct-scheduler-opt) — please review/merge that first. This branch targets that branch; the diff shown here is only this PR's commits.

Design

The key insight: records within a batch are already a contiguous, in-order slice of the queryname-grouped stream, and batches arrive in total order. FindBamBoundaries already carries the trailing partial record across blocks; if it carries the trailing partial queryname run instead, then no template straddles a batch and grouping is a pure per-batch function.

BatchCut::Queryname cut mode in the source cutters (FindBamBoundaries for BAM, ReadSamChunks for SAM): they carry the trailing queryname run to the next batch and coalesce up to blocks_per_batch blocks per emitted batch.
DecodedRecordBatch.closed_under_queryname flag, set by decode when the cutter ran the queryname cut. Inert until read downstream.
AssembleTemplates — a Parallel + ByItemOrdinal grouper: one BamTemplateBatch per input batch, no cross-batch state. Fails closed (InvalidData) on an unmarked batch.
Builder wiring: source_batch_cut() selects the queryname cut for the grouping-first stages (correct, align, filter --filter-by-template); append_queryname_grouper() picks AssembleTemplates (closed source) vs the serial GroupByQueryname (fallback).

Correctness

Identical templates. Both paths build every template over the same membership (a maximal run of adjacent same-name records); the cutter never splits a run.
Identical order. The cutter preserves byte order; decode maps records 1:1 and propagates batch_serial; the downstream ByItemOrdinal reorder restores emission order.
Fail-closed. The cutter self-checks once per emitted batch that the first record's name differs from the previous batch's last name; AssembleTemplates rejects any batch not marked closed.

Reading order

src/lib/pipeline/steps/boundaries/state.rs — the cut + the O(1) accumulator (subtlest file).
src/lib/pipeline/steps/group/assemble.rs — the parallel grouper (assemble_closed).
src/lib/pipeline/chains/builder.rs — the tail-kind refactor and the grouper sites.
src/lib/pipeline/steps/chain_tests.rs — the parity test (parallel path byte-matches serial GroupByQueryname) and the fail-closed test.

Benchmark gate (EC2)

c8g.8xlarge (Graviton4, 32 vCPU), 10 M templates / 20 M records, queryname-sorted, RX UMIs. correct -u <7 UMIs> --min-distance 1 --max-mismatches 2. Both binaries release builds from the same tree; before = base d1c1546b, after = this branch.

Byte-identity (fgumi compare bams --command correct, content mode): 16654106 vs 16654106, 0 content diffs, IDENTICAL. (Raw BGZF bytes differ because batch shaping is larger — non-contractual by design; every record's content and order is identical.)

Wall-clock (hyperfine, 1 warmup + 2 runs):

threads	before (s)	after (s)	speedup
1	12.77	12.18	1.05×
8	2.72	2.40	1.13×
16	2.22	1.31	1.70×
32	6.61	1.13	5.85×

GroupByQueryname is absent from the after telemetry; the hottest step is now the BGZF writer, the expected next limiter. (The before-binary's 6.61 s at 32 threads is the serial grouper's oversubscription behaviour that #955 addresses — which is why the after-path's monotonic scaling to 32 matters.)

Also in this PR: Template representation cleanups

Two perf cleanups to Template on the grouping hot path, each byte-output-preserving (Template.name is never serialized):

Read the query name on demand instead of storing an owned name: Vec<u8> — the field was a redundant per-template allocation copying bytes already in records[0], and heap_size double-counted them. Now Template::name() derives it from records[0].
Skip redundant re-verification for grouped runs. from_records_trusted skips the cross-record QNAME re-verify (both groupers build each template from a run that is same-named by construction), and skips the per-record truncation guard on that path (decode already enforces the identical check via validate_record_for_decode before any record reaches a grouper). Regression tests pin that a forced name_hash collision between two byte-different names still splits into separate templates.

Follow-ups (separate PRs)

Reuse the decode-time UMI cache on the pipeline correct path (currently populated by decode, then discarded by the grouper and re-scanned by correct) — coming as a PR stacked on this one.
Give the sort-merge the same backward-walk queryname cut so sort → filter --filter-by-template also runs the parallel path; then delete the now-unused serial GroupByQueryname.

Verification

cargo ci-fmt, cargo ci-lint (pedantic, -D warnings), cargo ci-doc, and cargo ci-test (10202 passed, 31 skipped) all green.

Risk: grouping output changes, but queryname-closed batching, serial fallback, collision-safe matching, and parity tests pin identical output; consensus, sort order, corrected UMIs, and metrics: none; unsafe: none, and no CLAUDE.md allowlist update is required; memory and scheduling: changed by the 256 MiB open-run bound, queue backpressure, and parallel worker scheduling.

Fix: Use AssembleTemplates for validated queryname-closed batches, with serial fallback.

Add queryname-aware BAM/SAM cuts with carry-over, coalescing, EOF handling, validation, and bounded open runs.
Propagate closure metadata through decoding and pipeline construction.
Add fail-closed parallel grouping with collision-safe matching and ordering.
Enable parallel grouping for correct, align, and template-filtering chains.
Simplify Template name storage and add trusted construction paths.
Add parity, boundary, backpressure, collision, and fail-closed tests.

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Walkthrough

The change removes stored template names, adds queryname-aware batch boundaries, and enables parallel template assembly for batches marked closed under queryname. Pipeline wiring selects parallel or serial grouping based on that metadata.

Changes

Queryname-aware grouping

Layer / File(s)	Summary
Template representation and API migration `src/lib/template.rs`, `src/lib/commands/`, `src/lib/pipeline/steps/`	`Template` derives names through `name()`. Empty templates use `Template::new()`. Verified and trusted constructors share construction logic.
Queryname batch boundaries and closure metadata `src/lib/pipeline/steps/boundaries/`, `src/lib/pipeline/steps/source/read_sam_chunks.rs`, `src/lib/pipeline/steps/parse/`, `src/lib/pipeline/steps/types.rs`	Batches support record or queryname cuts, carry open runs across blocks, and record whether queryname runs are closed.
Parallel template assembly `src/lib/pipeline/steps/group/*`, `src/lib/pipeline/steps/chain_tests.rs`	`AssembleTemplates` groups closed batches in parallel, preserves ordering and heap accounting, and rejects batches without closure metadata.
Closure-aware pipeline wiring `src/lib/pipeline/chains/builder.rs`	BAM, SAM, Correct, Align, Filter, consensus, and sort paths propagate closure metadata and select parallel or serial grouping accordingly.

Priority: ➖ Normal

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

Change: Refactor · Unblocks: 2 PRs

Sequence Diagram(s)

sequenceDiagram
  participant Source
  participant BoundaryState
  participant Decoder
  participant ChainBuilder
  participant Grouper
  Source->>BoundaryState: emit record or queryname-aligned batches
  BoundaryState->>Decoder: provide batch data
  Decoder->>ChainBuilder: attach closure metadata
  ChainBuilder->>Grouper: select parallel or serial grouping
  Grouper->>Grouper: produce ordered Template batches

Suggested labels: fgumi group

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nh13 · 2026-09-13T18:19:04Z

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coderabbitai · 2026-09-13T18:19:13Z

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`GroupByQueryname` is serial because a queryname run can straddle a batch boundary. `FindBamBoundaries` already carries the trailing partial *record* across blocks; teach it to carry the trailing partial *queryname run* instead, so every emitted `DecompressedBlock` is closed under queryname — a run lies entirely within one batch. A downstream grouper then needs no cross-batch state and can run as a pure parallel map (later commits). `BatchCut` (default `Record` = today's behaviour) selects the mode. Under `Queryname`, `apply_queryname_cut` walks backward from the last record while adjacent read names match, pulls the cursor back to the start of that trailing run, and carries it. `offsets.truncate` keeps the records counter counting each record exactly once (it derives from `offsets.len()`), so the carried run is counted when finally emitted, never twice. `min_emit_bytes` coalesces: one pipeline item is one ~64 KiB BGZF block, so a 1:1 grouper would emit ~114-template batches; the cutter holds closed runs until the emittable prefix reaches the target before emitting. `0` disables it. Fails closed, never silent: `record_name_in` guards the l_read_name/name bounds and returns `InvalidData` rather than letting `read_name` panic on a short record; a per-batch self-check remembers the last emitted name and errors if the next emitted batch begins with it — a straddle the parallel grouper cannot itself detect, caught at its source. EOF flush (`finish`) needs no change: the carried final run comes out as the last batch. `Record` mode is byte-for-byte unchanged; every non-grouping chain is untouched. Tests: run split across two blocks, a single run spanning three blocks, a run boundary exactly at a block end, single-record templates, coalescing to a byte target, byte-preservation across boundaries, and fail-closed on a too-short record.

The SAM analogue of the FindBamBoundaries queryname cut. `ReadSamChunks` already carries a trailing partial *line* across chunks; teach it to carry the trailing partial *queryname run* so every emitted `SamChunk` is closed under queryname, letting a downstream grouper run as a parallel map. `ReadSamState` gains a `BatchCut` mode (default `Record` = today's behaviour) and `min_emit_bytes`. Under `Queryname`, after `split_complete_lines`, `apply_queryname_cut` walks back over the complete lines comparing the QNAME field (bytes before the first tab, trailing `\n` stripped; a tab-less line is its own name), carries the trailing run's lines back into `leftover`, and truncates the offset table to the emitted prefix. `ReadSamChunks::new_queryname_cut` is the constructor the builder uses. Termination: when the whole chunk is one open run the cut emits nothing, so the read loop raises its effective target and reads more (otherwise the already-buffered leftover would keep satisfying the break gate and the reader would never advance to EOF). At EOF the trailing run is complete, so every line is emitted — which also stops an infinite carry when the final stream is one QNAME. The step skips a no-line chunk without minting a serial, keeping the downstream ordinal dense. Fail closed: a per-chunk self-check errors if a run straddles a chunk boundary (the first emitted line's QNAME equals the previous chunk's last). `Record` mode is byte-for-byte unchanged. Tests: run carried across chunks, single run over the whole stream, coalescing to a byte target, missing trailing newline flushed at EOF, and a tab-less line treated as its own QNAME.

Plumb the queryname-closure promise from the cutters (previous commits) through the decode step to the (future) parallel grouper. `DecodedRecordBatch` gains a private `closed_under_queryname` bool (default `false` via `new`), a `closed_under_queryname_marked(bool)` builder, and an accessor. The three decode steps that produce `DecodedRecordBatch` — `DecodeRecords`, `DecodeFromRecords`, `ParseSamChunk` — each gain a `closed_batches` field, a `with_closed_batches(bool)` builder, and mark every emitted batch with it. `Clone` (the parallel `new_worker_copy`) carries the flag so all worker clones agree. The flag is a producer-side promise the builder sets from the same decision that configures the cutter (`BatchCut::Queryname`), so the two cannot disagree. It is inert until a consumer reads it (the parallel `AssembleTemplates` grouper, next commit, which fails closed if the flag is clear). `false` everywhere today, so no behaviour changes.

When the source cutter runs in BatchCut::Queryname, every DecodedRecordBatch is closed under queryname (no run straddles a batch), so grouping needs no cross-batch state and can be a pure per-batch map. `AssembleTemplates` (StepKind::Parallel, ByItemOrdinal) replaces the serial GroupByQueryname on that path — one output batch per input batch, same batch_serial, each worker clone holding only its held slot. `assemble_closed` is the pure core: run-length group consecutive records by key.name_hash (with a read-name byte compare on hash-equal, matching GroupByQueryname's collision guard), build each run into a Template via Template::from_records, and return the templates plus the summed Template::heap_size so the caller builds the BamTemplateBatch via from_parts with no second heap walk. Fails closed: the step trusts the closure invariant it cannot itself verify (a batch cannot see its neighbours), so it errors InvalidData on the first batch whose closed_under_queryname flag is clear rather than silently splitting a straddling template — catching a builder mis-wiring immediately. Unit tests cover assemble_closed: grouped runs + summed heap, single-record templates, non-adjacent same-name runs kept separate, and empty. The step's fail-closed branch and end-to-end behaviour are covered by the chain-level parity test (next commit), matching the codebase's chain-level step-testing convention.

Add a chain-level parity test proving the parallel path (queryname-cut source + AssembleTemplates) produces byte-identical templates, in the same order, as the serial GroupByQueryname. Swept over thread counts {1,4}, template counts {1,50,300}, and payload sizes {64,4096}. Add a fail-closed test confirming AssembleTemplates rejects batches that are not marked closed_under_queryname with InvalidData.

…ilder Route the queryname-grouping chains (correct, align, filter --filter-by-template, zipper) through the parallel AssembleTemplates map when the source cut leaves batches closed under queryname, replacing the serial GroupByQueryname. - ChainTailKind::DecodedRecordBatch carries a closed_under_queryname flag, so every builder site that sets the record-stream tail must state closure. - source_batch_cut() selects BatchCut::Queryname for the queryname-grouping first stages (Correct/Align, Filter when --filter-by-template); all others keep the record cut. queryname_min_emit_bytes() coalesces up to blocks_per_batch BGZF blocks per emitted batch. - The BAM/SAM decode preambles thread the cut into FindBamBoundaries / ReadSamChunks and mark DecodeRecords / ParseSamChunk closed accordingly. - append_queryname_grouper() picks AssembleTemplates for a closed tail, else the pinned serial GroupByQueryname. - Consensus intermediate output is closed by construction, so its decode is marked closed for a downstream filter --filter-by-template. All chain, builder, and correct/align/zipper/filter/consensus/group/dedup/ clip/sort integration tests pass; correct-chain telemetry now shows AssembleTemplates in place of GroupByQueryname.

Point the field/method doc links at the fully-qualified BatchCut path so rustdoc resolves them; BatchCut is referenced by full path in this module, never imported.

The queryname coalescing cut re-scanned the entire carried record region on every call: when the closed prefix was below min_emit_bytes it rewound the cursor to the start of records and carried them all back into leftover, so the next block re-combined leftover+new and re-scanned every carried record's block_size prefix. With coalescing holding many blocks, this was O(n^2) and made FindBamBoundaries (still serial) ~28x slower than the record cut, regressing correct by 3-6x at 8/16 threads. Maintain a persistent scan accumulator (qn_buffer + qn_offsets) of complete, already-scanned records. Each call forward-scans only the new leftover+block, appends completed records to the accumulator, and decides the emit split on the accumulator (a backward walk bounded by the trailing run length, not the accumulator size). finish() flushes the accumulator at EOF. Record mode is unchanged. Adds regression tests: many-block coalescing preserves bytes exactly across repeated drain/rebase, and a long run spanning many coalesced blocks is carried whole.

…cation Two related cleanups to the Template representation and its construction, on the queryname-grouping hot path: 1. Drop the owned `name: Vec<u8>` field and derive the query name on demand via `Template::name()` from the first record's bytes. The field was a redundant per-template heap allocation copying bytes already held in `records[0]`, and `heap_size` double-counted those bytes. The name is never serialized, so BAM output is unchanged; the accessor returns an empty slice for a record-less template. 2. Add `Template::from_records_trusted`, which skips the cross-record QNAME consistency re-verification for callers that have already grouped records by read name. The parallel grouper (`assemble_closed`) and the serial one (`GroupByQueryname::flush_current_template`) both build each template from a run that is same-named by construction, so the re-check is pure overhead. For any valid same-named input it produces a template byte- and structure- identical to `from_records`; every other invariant (record truncation, at most one primary R1/R2) is still enforced. Adds parity tests (trusted vs verified construction), a name() accessor test, and reworks the heap_size/byte-budget tests to the record-only footprint.

…path `from_records_trusted` no longer re-runs the per-record truncation guard (len >= MIN_BAM_RECORD_LEN and read-name-region-in-bounds). Its only callers are the two queryname groupers, which are fed exclusively by `DecodeRecords`, and decode already enforces the identical check on every record via `validate_record_for_decode` before the record can reach a grouper. The guard is therefore redundant work on the grouping hot path. The guard is retained on the `from_records` (verify) path, whose callers do not carry decode's guarantee; the two truncation tests exercise that path and still pass. The trusted path's precondition (records are well-formed, as decode guarantees) is documented on `from_records_trusted`.

nh13 · 2026-09-13T20:28:01Z

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codecov · 2026-09-13T20:32:34Z

Codecov Report

❌ Patch coverage is 94.09006% with 63 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.07%. Comparing base (a9814c2) to head (7a5c074).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/lib/pipeline/steps/boundaries/state.rs	92.92%	24 Missing ⚠️
src/lib/pipeline/chains/builder.rs	87.91%	11 Missing ⚠️
src/lib/pipeline/steps/source/read_sam_chunks.rs	96.84%	11 Missing ⚠️
src/lib/pipeline/steps/group/assemble.rs	94.36%	8 Missing ⚠️
src/lib/pipeline/steps/align_and_merge.rs	42.85%	4 Missing ⚠️
src/lib/pipeline/steps/parse/decode.rs	81.25%	3 Missing ⚠️
src/lib/read_info.rs	0.00%	1 Missing ⚠️
src/lib/template.rs	98.38%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #957      +/-   ##
==========================================
+ Coverage   96.03%   96.07%   +0.04%     
==========================================
  Files         291      292       +1     
  Lines      143872   144996    +1124     
==========================================
+ Hits       138167   139306    +1139     
+ Misses       5705     5690      -15

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In `@src/lib/pipeline/steps/boundaries/state.rs`:
- Around line 475-476: Define and document an explicit byte ceiling for carried
queryname runs, using a separate limit unless MAX_CARRY_BYTES is formally
expanded to cover complete runs and supported large templates. Enforce the
ceiling independently in both BoundaryState’s qn_buffer path and ReadSamState’s
leftover path, including empty BAM names and SAM QNAME “*”, and return
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src/lib/commands/dedup.rs
src/lib/commands/group.rs
src/lib/commands/zipper.rs
src/lib/pipeline/chains/builder.rs
src/lib/pipeline/chains/commands/dedup.rs
src/lib/pipeline/chains/commands/group.rs
src/lib/pipeline/steps/align_and_merge.rs
src/lib/pipeline/steps/boundaries/bam.rs
src/lib/pipeline/steps/boundaries/state.rs
src/lib/pipeline/steps/chain_tests.rs
src/lib/pipeline/steps/extract.rs
src/lib/pipeline/steps/group/assemble.rs
src/lib/pipeline/steps/group/mod.rs
src/lib/pipeline/steps/group/queryname.rs
src/lib/pipeline/steps/parse/decode.rs
src/lib/pipeline/steps/parse/sam.rs
src/lib/pipeline/steps/serialize.rs
src/lib/pipeline/steps/source/read_sam_chunks.rs
src/lib/pipeline/steps/types.rs
src/lib/read_info.rs
src/lib/template.rs

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nh13 · 2026-09-14T04:44:15Z

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In `@src/lib/pipeline/steps/boundaries/state.rs`:
- Line 578: In emit_queryname_batch_inner, save the trailing queryname run’s
start index before the min_emit_bytes coalescing gate can reset j to 0, then
calculate carry_len from that saved boundary for the max_queryname_run_bytes
check. Preserve EOF flushing of the complete final run, and add a boundary test
where the closed prefix plus trailing run exceeds the cap but the trailing run
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nh13 · 2026-09-14T05:44:20Z

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In `@src/lib/pipeline/steps/source/read_sam_chunks.rs`:
- Line 371: Update the run-length calculation in the surrounding SAM chunk
validation method to use the end of the complete-line region rather than
self.leftover.len(), excluding the incomplete trailing line from the QNAME-run
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nh13 · 2026-09-14T08:16:04Z

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coderabbitai · 2026-09-14T08:16:09Z

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In `@src/lib/pipeline/steps/source/read_sam_chunks.rs`:
- Line 347: Update the EOF handling in the SAM chunk-reading logic to validate
the trailing QNAME run against max_queryname_run_bytes before assigning the EOF
emission result. Ensure an oversized run reaching EOF returns InvalidData rather
than bypassing the limit through the emit == 0 path, while preserving normal EOF
emission for valid runs.
- Line 375: Update the queryname carry/leftover handling in the SAM chunk reader
to measure the suffix after the last newline after each read and reject it with
InvalidData when it exceeds max_record_bytes, before carrying or returning
leftover. Repeat this validation before appending the synthetic EOF newline,
using the existing newline_at, fill_buf, and leftover logic.

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src/lib/pipeline/steps/source/read_sam_chunks.rs

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nh13 · 2026-09-14T15:16:53Z

@coderabbitai review

coderabbitai · 2026-09-14T15:17:00Z

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Inline comments:
In `@src/lib/pipeline/steps/source/read_sam_chunks.rs`:
- Line 266: Update the read flow around check_trailing_partial_record so
trailing newline-free data is tracked incrementally as chunks are appended
instead of rescanning the full suffix with memrchr after every fill_buf.
Accumulate the partial-record length from each newly appended chunk and reject
once it exceeds max_record_bytes, while preserving existing handling when a
newline terminates the record.

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src/lib/pipeline/steps/boundaries/state.rs
src/lib/pipeline/steps/source/read_sam_chunks.rs

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Under BatchCut::Queryname, BoundaryState::qn_buffer (BAM) and ReadSamState::leftover (SAM) retained every complete record of an open queryname run. min_emit_bytes gates only the closed prefix, and the incomplete-record backstops (MAX_CARRY_BYTES / MAX_RECORD_BYTES) never see a run of complete records, so a stream that never closes a run — every record sharing one read name, a run of empty BAM names (l_read_name == 1), or repeated SAM QNAME "*" — grew the carry until allocation failed. Add a documented MAX_QUERYNAME_RUN_BYTES ceiling, separate from the incomplete-record limits and exposed as a field so tests can drive the rejection with a small cap, to both cutters and return InvalidData once the carried run exceeds it.

nh13 · 2026-09-14T16:17:03Z

@coderabbitai review

coderabbitai · 2026-09-14T16:17:08Z

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nh13 force-pushed the nh/correct-scheduler-opt branch from 3129db6 to 223ee29 Compare September 13, 2026 18:18

nh13 mentioned this pull request Sep 13, 2026

perf(correct): resolve the template UMI from the primary read #958

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Base automatically changed from nh/correct-scheduler-opt to main September 13, 2026 19:43

nh13 added 10 commits September 13, 2026 13:23

docs(source): fix broken BatchCut intra-doc links in ReadSamChunks

d868f57

Point the field/method doc links at the fully-qualified BatchCut path so rustdoc resolves them; BatchCut is referenced by full path in this module, never imported.

nh13 force-pushed the nh/parallel-queryname-grouping branch from 0ba1fc6 to ebc44f1 Compare September 13, 2026 20:26

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nh13 force-pushed the nh/parallel-queryname-grouping branch from 55fb7e9 to 0987385 Compare September 14, 2026 05:17

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nh13 force-pushed the nh/parallel-queryname-grouping branch from 0987385 to 3a3a552 Compare September 14, 2026 06:08

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nh13 force-pushed the nh/parallel-queryname-grouping branch from 3a3a552 to d9e8ec1 Compare September 14, 2026 14:51

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nh13 force-pushed the nh/parallel-queryname-grouping branch from 13a415c to ece651a Compare September 14, 2026 15:44

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nh13 force-pushed the nh/parallel-queryname-grouping branch from ece651a to 7a5c074 Compare September 14, 2026 15:49

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nh13 deleted the nh/parallel-queryname-grouping branch September 14, 2026 17:44

nh13 mentioned this pull request Sep 14, 2026

chore: release v0.8.0 #868

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Summary

Design

Correctness

Reading order

Benchmark gate (EC2)

Also in this PR: Template representation cleanups

Follow-ups (separate PRs)

Verification

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