Feat/seed from energy default#53
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XLA compile dominates cold tune_chains (~85% of stage-1 wall on GPU; the actual sampling of both probes is <1s) because each probe at a new chain count recompiles the round loop at new shapes. Two changes make the whole autotune share a single compiled loop: 1. Chain masking: nrpt(pad_chains_to=) pads the ladder to a fixed length with copies of the coldest chain and passes the true count into the jitted loop as TRACED data. Swaps beyond the live prefix are forced-rejected (identity permutation — DEO coupling is nearest-neighbour, so the padding is fully decoupled), attempt counters and the round-trip "top" are masked to the live prefix, and all outputs are sliced back to the true count, so optimize_schedule and every downstream consumer see unpadded semantics. tune_chains(pad_probes=) pads every probe to max_chains; autotune(pad_probes=None) auto-enables on accelerator + template mode (padding Gibbs work is ~free on a dispatch-bound GPU, real compute on CPU) and then runs the polish/production stage masked too. 2. Stage-1 probes run at the final n_expl when it is already known (pinned or the deterministic device default): scan length does not change compile time, so stage 3 reuses stage 1's executable instead of recompiling the loop at a new sweep count. The opt-in wall-timed exploration search still probes at n_expl=1. Because JAX's threefry key/uniform streams are prefix-stable, the live prefix of a masked run is BIT-IDENTICAL to the unpadded run — same states, same accept/reject decisions, same discovered N/Lambda/schedule. Regression-tested (TestChainMasking) and verified exactly on the full planted-Ising benchmark suite (L=16/24/32 lps=2, L=24 lps=6 seeds 0-3, lps=10): masked == unmasked on every config, ground-state hit-rate 1.0 preserved, brute-force --verify OK. Measured (RTX 5080, 22x22 grid): cold autotune 7.4s -> 6.0s, warm (persistent cache) 2.9s -> 2.4s; glassy multi-probe search (planted L=24 lps=6 seed=1) 9.0s -> 5.9s (-34%). Full suite 370 passed / 1 skipped on GPU; pre-commit (ruff check/format 0.15.20, pyright 1.1.411) clean. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Refresh the NRPT section: reproducible-by-default tuning, robust chain-count discovery (max_chains pilot, running-max Lambda, R-hat-gated energy seed), deterministic device-calibrated n_expl (wall-timed search now opt-in), and the identifiability gate. Rework "What makes Hamon fast" around the actual bottleneck — XLA compilation — covering chain-masked probes, structure-keyed jit caches, and the default-on persistent compile cache. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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