Phase D0 — measure-first build probe: the build is SA-workspace-bound (CONFIRM) - #23
Merged
Conversation
First Phase-D increment after the kernel pivot (√t/Cook-Mertz retired as the construction mechanism, kept as framing; native external-memory constructor is the target). D0 instruments the existing build to emit a build receipt (realized peak RSS + a logical n-scale SA-IS accountant), runs it on E. coli + yeast, and records a pre-registered verdict (±25% of ~185 MiB AND ≥70% SA-workspace attribution) that gates D1. Pure instrumentation + measurement + a focused OPEN_PROBLEMS reframing. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…e-bound) + OPEN_PROBLEMS √t-as-framing reframing (D0)
3 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The first Phase-D increment, after the scoping workflow pivoted the kernel: the literal √t/Cook–Mertz combiner is retired as the construction mechanism (stubbed and discarded on the correctness path; SA-IS produces a permutation with no low-degree-extension structure; Cook–Mertz is super-polynomial with no systems realization). Phase D's real target is a native, polynomial-time, budget-tunable external-memory SA/BWT constructor along a measured space/time curve, wrapped in the shipped contract; √t is kept as honest theoretical framing.
D0 is the cheap, decisive measure-first gate before any external-memory work.
Result — CONFIRM
rosalind indexnow emits a build receipt: realized peak RSS (util/rss.rs) + a code-grounded n-scaleBuildMemoryModelaccountant (from the realsais_implallocations) + the attribution ratio.Pre-registered gate (all met): E. coli peak within ±25% of ~185 MiB (182, −1.6%); ≥70% attributable (model envelopes realized); bytes/base identical (41) across a 2.6× size jump → the peak is the SA-construction workspace, scaling with n, not a fixed overhead. → D1 (blocked external-memory SA construction) greenlit; baseline curve point b=n = 41 B/base.
What's included
BuildMemoryModel(genomics/index/report.rs) — pure, unit-tested n-scale accountant.rosalind indexbuild receipt (realized peak + model breakdown + attribution).scripts/build_memory_probe.sh— reproducible (E. coli + yeast, build-only).docs/findings/2026-06-02-d0-build-memory-probe.md— the recorded verdict.docs/OPEN_PROBLEMS.mdreframed: √t = framing, native-EM = mechanism, no new-bound claim.No construction-algorithm change; no
sa_sample_rateknob (shrinks query, not build); MSRV 1.72; no new deps. Full suite green, 0 warnings (debug + release),fmtclean.🤖 Generated with Claude Code