perf(svar2): rebalance sharded VCF worker budget - #140
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Adds a reproducible sweep over the sub-contig sharded VCF reader budget (reader_workers x per-shard HTSlib threads x OVERSHARD_FACTOR) to evaluate PR #140, plus BENCH-ONLY env hooks in orchestrator.rs so one build covers the whole space (GENORAY_READER_WORKERS / GENORAY_SHARD_HTSLIB / GENORAY_OVERSHARD). Unset, they leave the planner untouched. Every configuration is gated by a whole-store byte-identity oracle; all 60+ swept configurations matched, confirming sharding does not perturb output at any worker count. Findings are written up in scripts/bench_sharded_vcf/README.md. Co-Authored-By: Claude Opus 5 <[email protected]>
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Summary
reader_workersallocation for indexed/sharded VCF conversionMotivation
A real single-contig AoU chr22 conversion on a 16-CPU VM consistently used only ~299% CPU. The existing planner produced 8 HTSlib threads plus 3
processing_threads, but the sharded VCF branch uses onlyprocessing_threadsas its shard-worker count and does not use the separately reserved 8-thread monolithic HTSlib pool.With this change, the same 16-core/one-contig budget becomes:
The allocation is per concurrent contig, so the multi-contig case remains bounded (for example, 65 cores / 10 active contigs yields 2 readers per contig and 60 planned sharded-path threads total).
Verification
cargo test --no-default-features --features conversion— 310 unit tests plus all Rust E2E suites passprek run --all-files --show-diff-on-failurepasses, including fmt, check, Clippy (-D warnings), and Pyreflycargo check --no-default-featurespassesThe active Verily run was not interrupted; runtime benchmarking of this branch can follow after CI.