Axis 3 · Random access and the window law

axis3-W1

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  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
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  "schema": "window-law-verdict-v1",
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axis3-W1024

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axis3-W128

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  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
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  "schema": "window-law-verdict-v1",
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axis3-W16

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  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
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axis3-W16384

{
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  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W2

{
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  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W2048

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  "kind": "measured",
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  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W256

{
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  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W32

{
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  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W32768

{
  "axis": 3,
  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W4

{
  "axis": 3,
  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W4096

{
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  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
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}

axis3-W512

{
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  "domain": "uppercase-sequence-without-FASTA-framing",
  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W64

{
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  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W65536

{
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  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W8

{
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  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-W8192

{
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  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

axis3-Wnone

{
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  "kind": "measured",
  "machine": "ace-core",
  "protocol": "4a0027fec59b3252dc07b29458a57a5a451957f1b64b36f3927765cbc6be7a5c",
  "requests": "65409940b72d1d0e0368d2c04750b190c4736d780d5befeadb6750da836bd241",
  "samples_per_window": 10000,
  "schema": "window-law-verdict-v1",
  "scope": "cpu-in-process",
  "seed": 20261003,
  "threads": 1
}

Methodology, definitions and acceptance criteria

Complete source methodology · SHA-256 9b1ce9415146ebd7588791bdff318e58610dfd23afba3d5b40800f3e40b339e7

Compression access methodology

Status: review draft aligned with frozen protocol v1.1. This document does not authorize measurements, a release, a Pages update or an external publication.

Authority and immutable comparison contract

PROTOCOL_AXIS3.md is the frozen Axis 3 contract. PROTOCOL_AXIS5.md fixes the A7 synthetic Axis 5 experiment. PROTOCOL_FREEZE.json identifies its exact bytes. This methodology explains that contract; it does not replace or amend it. RUN.md describes implemented commands and their remaining limitations. If any implementation or supporting document disagrees with the frozen protocol, stop: do not publish non-comparable results with a qualification. A semantic change requires a new protocol version and full rerun.

Before an official run, freeze the protocol, runbook, ordered source manifest, exact request lists and optional diagnostic-W list. Record SHA-256 of their bytes and the codec build receipts in evidence. Never amend a measured row by silently replacing an input or a configuration. Old evidence stays historical and byte-identifiable. Synthetic CI evidence remains labelled synthetic; it must never become an ace-core performance row.

Stock and equal-granularity configurations

Use the competitor's best documented stock configuration for the declared workload. Record source pins, author-supported build instructions, compiler flags, library versions and environment settings before the run. Failure to reproduce that configuration produces FAILED with a reason, not a compromised score. AGC cohort construction uses one create with all selected assemblies, not a chain of append calls. Freeze input order and explicit sample/contig IDs. AGC noref uses the first cohort member as internal seed; AGC t2t includes the frozen external reference. N counts queried assemblies, not extra references.

Keep BGZF-default and BGZF-matched-g as separate configuration rows in the same execution scope. Neither replaces the other. The matched-g writer flushes at its declared raw input-byte boundary; the emitted block geometry, not a nominal limit, determines the decode granules. ISIZE counts raw FASTA bytes, not Q in canonical sequence bytes. Use the frozen FASTA-to-sequence mapping to obtain canonical bytes represented in each actual block. Preserve the geometry and its declared aggregation rule; do not relabel raw ISIZE as canonical Q.

Charge archives, frame indexes, FASTA .fai/.gzi sidecars, required references and other access dependencies. A shared reference is counted once, never omitted. Report total and per-queried-assembly stored bytes. Missing dependencies or unestablished independent decode geometry must not become a valid model row. Q is not the LZ lookback window; keep the latter in a separate column. AGC's nominal segment size is not evidence of its actual independently decoded Q.

Canonical bytes and coordinates

Truth is uppercase sequence bytes without FASTA headers or line separators. Preserve the original source objects unchanged. A common request is (assembly_id, contig_id, start0, end0), using zero-based half-open coordinates [start0,end0). It is valid iff 0 <= start0 < end0 <= contig_length; its length is exactly end0-start0. A request never crosses a contig boundary.

Adapters translate only at the library boundary:

Record both canonical and translated coordinates with their conventions in evidence. A native FASTA-aware reader may use a verified FASTA index internally; raw FASTA offsets are never substituted for canonical coordinates. The external request space is per contig even when a codec stores concatenated sequence bytes. Do not clip, substitute another contig, shrink W or repair an invalid/empty request. Such requests produce FAILED. Contigs shorter than W have no valid starts for that W; sampling excludes those starts, not failures after decoding.

Same machine and execution boundary

CPU in-process, GPU in-process and process-per-request CLI are separate scopes; never rank across them. CPU in-process uses one persistent library handle and one decode thread. Open/index/reference setup occurs outside window timing; the reader operation, including its required lookups and decoding, remains inside. Do not silently substitute a helper process, a decoded-data cache or a different machine. Declare residency and use the same access/cache policy for each comparable configuration.

The official host must be ace-core. Before running, retain hostname, uptime/load, one-second process CPU deltas, frequency policy and available storage. The gate requires load <0.5, storage >20,000,000,000 bytes, and no foreign process consuming 10% or more of one CPU over the sample interval. Keep thresholds and raw telemetry. A passing sample is not proof of continuous quiescence. A GitHub-hosted runner is not a substitute for ace-core, and a green PR does not authorize a measurement.

Requests, timing and truth

The initial official cohort is HPRC N=4; N=50/all require separate explicit plans. Freeze source URLs, source and FASTA hashes, assembly/contig IDs, lengths, ordering and references. Sample uniformly over valid starts in eligible contigs across the cohort. Use 10,000 requests per W, seed 20261003 and the recorded PRNG identity. Reuse the same frozen requests and per-answer SHA for all eligible formats.

Time the reader call only. Immediately outside that interval, check the length and SHA-256 of every canonical answer. Retain every request ID, canonical and translated coordinates, expected/observed SHA and raw nanoseconds. Report nearest-rank p50/p95/p99 and windows/s from the raw samples; do not drop slow or failed observations. W=1 uses the same nearest-rank p50 convention for calibration.

For D_Q, independently perform full sequential decode of the same corpus with the same format, configuration, archive, library and one decode thread. The accepted B run plan in tools/verdict_refrel3.py fixes three warmups and nine measured full decodes; verify every decode, including warmups. Retain all measured times, their median/min/max and both native and canonical output-byte counts. D_Q is canonical sequence bytes divided by the median measured full-decode time, in bytes/s.

D_Q and Q use the same canonical sequence-byte domain as W for every format. If native full decode emits serialized FASTA, framing removal, canonicalization and SHA validation occur outside the timed decode boundary. State both output domains and that boundary in evidence. A native sequence-byte full-decode path is also valid. If neither implements the required boundary, the row is FAILED. Do not count FASTA framing in D_Q's numerator or Q, or charge framing removal to one decoder's timer and exclude it for another.

Window law: primary B and secondary A

Let D_Q be the independent sequential throughput in canonical bytes/s and Q the observed canonical-byte decode granule. Times below are in seconds; convert to microseconds only for display. The primary model is B:

t_B(W) = c0 + (W+Q-1)/D_Q
c0 = median(t(W=1)) - Q/D_Q
t_A(W) = (W+Q-1)/D_Q
error_B_percent = 100 * (measured_p50 - predicted_B_p50) / predicted_B_p50

The c0 probe is a separate 10,000-request W=1 random-position experiment, using the same format, thread, corpus and seed rule. W=1 is excluded from the verdict set. No coefficients are fitted to the 1/8/64 KiB observations or to additional diagnostic windows. A changed codec or output domain needs its own c0 and D_Q; do not reuse historical values from another implementation, configuration or host.

Only W = {1024,8192,65536} contributes to the p50 model-B error verdict. The fixed criterion is |error_B_percent| <=20% inclusive at each of the three windows. Both signs of the boundary are included. Retain predictions from both models. An extra predeclared window is DIAGNOSTIC_ONLY: its prediction error does not change the aggregate verdict. Freeze that W list before execution; it cannot be selected from successful observations afterward.

Applicability and diagnostic fallback

If c0<0, model B is FAIL for that format and c0 is reported unchanged. Do not clamp it to zero, refit it, change the seed or discard the format. In this case use secondary model A as the diagnostic reference only, not as a replacement primary acceptance rule. Model A never affects the verdict. Its prediction may be printed beside B, but cannot turn a model-B FAIL into PASS. For c0=0, B remains applicable and its prediction equals A; the ordinary B criterion still applies.

The p50 prediction is a falsifiable model, not a theorem about medians. All windows must remain byte-correct even when a latency model is outside its domain. A negative c0 is a model failure, not by itself evidence of a decoding error.

Model verdict, correctness and comparison coverage

Distinguish model FAIL from data FAILED. Correct output can fail the latency prediction; retain that measured evidence with its model FAIL. A wrong SHA, short/extra output, decoder error, malformed metadata, missing reference/index, wrong pin/thread/scope or protocol drift makes the data row FAILED and suppresses valid performance fields. This also applies to CALIBRATION_ONLY and DIAGNOSTIC_ONLY observations: no correctness failure is waived as diagnostic. A successful evidence-integrity verification is not a model-B PASS.

Include at least four non-ACEAPEX format families with valid data. BGZF default and matched-g are two required configurations but one family, not two foreign formats. Candidate families are BGZF, zstd seekable, indexed LZ4, OpenZL-seg and AGC. Keep each configuration visible; do not cherry-pick successful variants or omit failed ones to meet coverage. A failed prediction remains visible; a missing or data-FAILED family does not count as valid coverage. The refrel3 comparison also requires q4k and q16k, as specified in the B job. No claim of refrel3 model success follows from synthetic tests, symbol checks or missing official logs.

Evidence-derived reports and other axes

Regenerate tables and graphs from validated evidence and raw logs. Captions contain source-log SHA-256. Keep the “where we lose” section, failures, exact commands and storage ledger; missing evidence is not a victory. Report memory only when the complete declared scope is captured. Do not invent times, peak memory or storage from estimates labelled as measurements.