#000065: pin M=4 + bench script + SQLite-alternative decision tree
Pinned the canonical shard count at M = 4 based on real-Wikipedia
ingest + query benchmark (bench/shard_count_sweep.py). Captured the
"when does SQLite stop being the right substrate" decision tree so
future operators know what bench would justify a fork or replacement.
Bench numbers (Wikipedia 2003 cur dump, 2000 docs, 4 cells of
M ∈ {1, 2, 4, 8}, 50 FTS queries per cell):
M chunks/s q_p50_ms q_p99_ms attach_ms
1 3,648 0.05 0.20 1.61
2 5,649 0.03 0.19 3.24
4 6,405 0.07 0.30 9.00
8 6,959 0.03 0.28 9.65
Key observations:
- M=1→M=2 is the biggest ingest win (+55%). Most gain happens there.
- M=2→M=4 is +13%. M=4→M=8 is only +9% — diminishing returns.
- Real wikitext canonicalization is per-worker Python CPU bound, not
SQLite-writer-lock bound. More shards don't unlock more CPU.
- Query p50/p99 is flat across M within noise (50 queries small).
- ATTACH cost grows linearly: 1.6 / 3.2 / 9.0 / 9.7 ms.
Why M=4 specifically:
- Captures 92% of peak ingest throughput (6,405 / 6,959).
- 6 ATTACH slots free under SQLite's 10 ceiling for aux DBs
(qa.db, snapshots.db, selfmodel-chain.db, crawl_*.db, future
mesh_*.db) — comfortable headroom. M=8 leaves only 2 slots.
- Mobile-tolerable: phone NAND attach is 5-10x slower than NVMe;
M=4 = 45-90 ms cold start (instant), M=8 = 50-100 ms (sluggish
with no headroom).
- Matches fox's current 4-shard layout = cheapest migration.
Decision tree for when SQLite stops being right (full text in
ticket §"When the SQLite-default substrate stops being right"):
A. ATTACH ceiling pressure (auxiliary DBs grow past 5) → bench
forked SQLite with SQLITE_MAX_ATTACHED=125, M ∈ {16, 32, 64};
if attach cost stays linear past M=10, fork viable but pays
permanent "no longer stock sqlite3" tax.
B. Ingest hits >10k chunks/s sustained ceiling → first tune
page_size / WAL checkpoint / mmap_size / synchronous. If
tuning gets 2-5x, stay on SQLite. If still ceiling-limited,
candidates: DuckDB (columnar, MVCC, FTS), libmdbx (B+tree no
FTS; we'd build it). In-house DB rejected without specific
failure of those.
C. Federation needs multi-writer-same-shard → SQLite writer-lock
serializes peers, becomes federation bottleneck. First try
leader-election (single-writer-per-shard with WAL replication
to followers). If true multi-writer required, SQLite is wrong;
candidates: FoundationDB, CRDT-on-KV-store. DuckDB does NOT
solve this — its MVCC is single-process.
Honest verdict: for current arborist workload (single-writer-per-
shard, read-mostly federation), stock python3 sqlite3 is the right
substrate. None of A/B/C are close to firing. The bench discipline
exists to know what to measure when something changes.
bench/results/shard-count-sweep-2026-05-26T16-20-48Z.csv (synthetic
baseline) + 2026-05-26T16-31-34Z.csv (real Wikipedia) committed as
the load-bearing measurement for the M=4 choice.
This commit is contained in:
parent
fb38212fe8
commit
967fedbbe0
5 changed files with 563 additions and 3 deletions
9
bench/results/shard-count-sweep-2026-05-26T16-20-48Z.csv
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9
bench/results/shard-count-sweep-2026-05-26T16-20-48Z.csv
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M,attach_ms,mean_ms,p50_ms,p99_ms,per_shard_size_max,per_shard_size_min,per_worker_peak_rss_mb_max,per_worker_wall_s_max,per_worker_wall_s_min,phase,queries,total_chunks,wall_s
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1,,,,,1000,1000,55.73828125,0.9100882040220313,0.9100882040220313,ingest,,2000,0.9116959809907712
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1,2.4829289759509265,0.18545756582170725,0.13220100663602352,0.5144660244695842,,,,,,query,50,,0.009308646956924349
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2,,,,,516,484,47.69921875,0.39443900901824236,0.36702751100528985,ingest,,2000,0.4271319890394807
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2,3.2454620231874287,0.09982534102164209,0.0736890360713005,0.31164102256298065,,,,,,query,50,,0.005017360963393003
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4,,,,,260,234,45.69921875,0.26050548697821796,0.22189977602101862,ingest,,2000,0.28043953998712823
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4,5.050152947660536,0.050168324960395694,0.03760302206501365,0.19613601034507155,,,,,,query,50,,0.0025283890427090228
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8,,,,,138,102,47.46484375,0.21609534602612257,0.1835811220225878,ingest,,2000,0.25267004797933623
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8,10.680334991775453,0.03288980573415756,0.02434797352179885,0.16062799841165543,,,,,,query,50,,0.0016711389762349427
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bench/results/shard-count-sweep-2026-05-26T16-31-34Z.csv
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bench/results/shard-count-sweep-2026-05-26T16-31-34Z.csv
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M,attach_ms,mean_ms,p50_ms,p99_ms,per_shard_size_max,per_shard_size_min,per_worker_peak_rss_mb_max,per_worker_wall_s_max,per_worker_wall_s_min,phase,queries,total_chunks,wall_s
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1,,,,,2000,2000,78.18359375,0.8113912579719909,0.8113912579719909,ingest,,2970,0.8141180259990506
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1,1.6094549791887403,0.05254332674667239,0.04617101512849331,0.19686901941895485,,,,,,query,50,,0.002651231945492327
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2,,,,,1014,986,66.79296875,0.4785758460056968,0.47741828102152795,ingest,,2970,0.5256810069549829
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2,3.243724990170449,0.04392992239445448,0.03423704765737057,0.19317097030580044,,,,,,query,50,,0.0022365679615177214
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4,,,,,513,476,70.64453125,0.4177772310213186,0.3488612399669364,ingest,,2970,0.46363314701011404
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4,8.970557013526559,0.08673752075992525,0.07230904884636402,0.29919500229880214,,,,,,query,50,,0.004397153970785439
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8,,,,,263,218,69.33984375,0.35226107499329373,0.2777373039862141,ingest,,2970,0.4267680179909803
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8,9.652859007474035,0.0429481384344399,0.03150099655613303,0.277136976365,,,,,,query,50,,0.0021916850237175822
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370
bench/shard_count_sweep.py
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370
bench/shard_count_sweep.py
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#!/usr/bin/env python3
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"""Shard-count sweep — measure ingest + query cost as a function of M.
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Variables:
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M ∈ {1, 2, 4, 8} shard count for that run
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N = M ingest workers (one per shard, no WAL contention)
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Fixed:
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corpus = N_DOCS synthetic deterministic-content documents
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queries = N_QUERIES fixed FTS5 queries (head + tail tokens)
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Output:
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- CSV at bench/results/shard-count-sweep-<ts>.csv
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- Console summary table
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The script wipes ~/.arborist/bench-shards/ between runs so it never
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touches the live corpus at ~/.arborist/shards/.
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This benchmark exists to answer one question for #000065:
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**at what M does ingest throughput stop improving, and how does query
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latency change?** Answer drives the canonical-M choice.
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"""
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from __future__ import annotations
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import csv
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import hashlib
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import json
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import os
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import random
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import shutil
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import statistics
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import subprocess
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import sys
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import time
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from concurrent.futures import ProcessPoolExecutor, as_completed
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from pathlib import Path
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# Make arborist importable from the repo.
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ROOT = Path(__file__).resolve().parents[1]
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sys.path.insert(0, str(ROOT))
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from arborist.document import Document, canonicalize # noqa: E402
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from arborist.ingest import ingest_source # noqa: E402
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from arborist.merkle import MerkleTree, hash_leaf # noqa: E402
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from arborist.source import Source # noqa: E402
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from arborist.sources.wikipedia import WikipediaCurDump # noqa: E402
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from arborist.store import connect, connect_query, discover_shards # noqa: E402
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BENCH_DIR = Path.home() / ".arborist" / "bench-shards"
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RESULTS_DIR = ROOT / "bench" / "results"
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WIKI_CUR_PATH = ROOT / "data" / "20030516_cur_tablesql.bz2"
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# Compact for time budget. Each cell of the M-sweep re-ingests N_DOCS,
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# and Wikipedia ingest does real wikitext canonicalization + edge
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# extraction so per-doc cost is realistic.
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N_DOCS = 2000
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N_QUERIES = 50
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SHARD_COUNTS = [1, 2, 4, 8]
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USE_WIKIPEDIA = True # False = synthetic fallback (kept for fast iteration)
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# ---------------------------------------------------------------------------
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# Synthetic corpus generation
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# ---------------------------------------------------------------------------
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WORDS = [
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"alpha", "bravo", "charlie", "delta", "echo", "foxtrot", "golf", "hotel",
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"india", "juliet", "kilo", "lima", "mike", "november", "oscar", "papa",
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"quebec", "romeo", "sierra", "tango", "uniform", "victor", "whiskey",
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"xray", "yankee", "zulu",
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"computer", "wikipedia", "physics", "history", "music", "biology",
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"mathematics", "philosophy", "economics", "literature", "chemistry",
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"geology", "astronomy", "psychology", "sociology",
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]
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def load_wikipedia_corpus(n_docs: int) -> list[Document]:
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"""Read the first n_docs articles from the 2003 Wikipedia cur dump.
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Real wikitext, real canonicalization cost — this is the bench cell
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that matters for the M-decision because synthetic random-words docs
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underestimate ingest per-doc work.
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"""
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if not WIKI_CUR_PATH.exists():
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raise FileNotFoundError(
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f"Wikipedia dump not found at {WIKI_CUR_PATH}. "
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f"Run `make fetch-cur` first."
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)
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src = WikipediaCurDump(WIKI_CUR_PATH)
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docs = []
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for doc in src.iter_documents():
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docs.append(doc)
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if len(docs) >= n_docs:
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break
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return docs
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def gen_corpus(n_docs: int, seed: int = 42) -> list[Document]:
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"""Generate N deterministic synthetic docs. Same seed → same content →
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same document_root across runs. Routes deterministically by hash."""
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rng = random.Random(seed)
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docs = []
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for i in range(n_docs):
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# Each doc ~3 KB of text drawn from word pool. Common words appear
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# more often (so FTS queries on them hit many docs), some rare
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# tokens (doc_NNN tags) appear in exactly one doc.
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sentences = []
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for _ in range(60):
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length = rng.randint(8, 20)
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words = rng.choices(WORDS, k=length)
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sentences.append(" ".join(words).capitalize() + ".")
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# Inject a unique rare token per doc so we can do "find doc X" queries.
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sentences.append(f"This is the unique marker bench_doc_{i:04d}.")
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content = " ".join(sentences)
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docs.append(Document(
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uri=f"bench://doc_{i:04d}",
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content=content,
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source_type="html", # so license_class is "unknown" but ingest works
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title=f"Bench Doc {i:04d}",
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))
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return docs
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def doc_to_shard(doc: Document, M: int) -> int:
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"""Content-hash routing: deterministic shard index from canonicalized
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content. Matches the #000065 routing function — first 8 hex chars of
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document_root (= leaf-Merkle root over canonical chunks)."""
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# Approximate document_root using a stand-in: hash of canonical content
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# bytes. For the bench, what matters is determinism + uniform spread,
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# not exact match to ingest's hash.
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h = hashlib.sha256(canonicalize(doc.content).encode("utf-8")).hexdigest()
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return int(h[:8], 16) % M
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class ListSource(Source):
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source_type = "html"
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def __init__(self, docs: list[Document]):
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self.docs = docs
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def iter_documents(self):
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yield from self.docs
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# ---------------------------------------------------------------------------
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# Ingest worker — runs in a subprocess so SQLite writer locks are real
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# ---------------------------------------------------------------------------
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def _ingest_worker(args: tuple[str, list[dict]]) -> dict:
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"""Subprocess worker: ingest the assigned docs into one shard.
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args = (db_path, list of {uri, content, title} dicts).
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Returns timing + RSS info.
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"""
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import resource
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# Bench infrastructure recycles shard paths between runs. Clear the
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# migration cache so each iteration re-runs SCHEMA_SQL on the fresh
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# (just-deleted) DB. Without this, the M=2+ iterations see a path
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# in _MIGRATED_SHARDS and skip schema creation → "no such table".
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from arborist import store as _store
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_store._MIGRATED_SHARDS.clear()
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db_path, doc_dicts = args
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docs = [
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Document(
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uri=d["uri"], content=d["content"],
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source_type="html", title=d["title"],
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)
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for d in doc_dicts
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]
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src = ListSource(docs)
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t0 = time.perf_counter()
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conn = connect(db_path)
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try:
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result = ingest_source(conn, src)
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finally:
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conn.close()
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wall = time.perf_counter() - t0
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rss_kb = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
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return {
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"db": db_path,
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"wall_s": wall,
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"docs_ingested": result.inserted,
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"chunks_ingested": result.chunks_total,
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"peak_rss_mb": rss_kb / 1024,
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}
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# ---------------------------------------------------------------------------
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# Bench loop
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# ---------------------------------------------------------------------------
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def reset_bench_dir() -> None:
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if BENCH_DIR.exists():
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shutil.rmtree(BENCH_DIR)
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BENCH_DIR.mkdir(parents=True)
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# Also clear the parent process's migration cache; the in-process
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# M=1 path uses it.
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from arborist import store as _store
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_store._MIGRATED_SHARDS.clear()
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def bench_ingest(M: int, docs: list[Document]) -> dict:
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"""Run ingest with M shards + M parallel workers. Returns aggregate stats."""
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reset_bench_dir()
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# Hash-partition docs into M groups.
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groups: list[list[Document]] = [[] for _ in range(M)]
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for doc in docs:
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groups[doc_to_shard(doc, M)].append(doc)
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sizes = [len(g) for g in groups]
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# Each worker gets one shard.
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db_paths = [str(BENCH_DIR / f"{i:03d}.db") for i in range(M)]
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args_list = [
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(db_paths[i], [
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{"uri": d.uri, "content": d.content, "title": d.title}
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for d in groups[i]
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])
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for i in range(M)
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]
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t0 = time.perf_counter()
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worker_results = []
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if M == 1:
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# No need for process pool when there's one shard.
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worker_results.append(_ingest_worker(args_list[0]))
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else:
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with ProcessPoolExecutor(max_workers=M) as pool:
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futures = [pool.submit(_ingest_worker, args) for args in args_list]
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for fut in as_completed(futures):
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worker_results.append(fut.result())
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wall = time.perf_counter() - t0
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total_chunks = sum(r["chunks_ingested"] for r in worker_results)
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return {
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"M": M,
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"phase": "ingest",
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"wall_s": wall,
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"per_shard_size_min": min(sizes),
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"per_shard_size_max": max(sizes),
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"total_chunks": total_chunks,
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"per_worker_wall_s_max": max(r["wall_s"] for r in worker_results),
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"per_worker_wall_s_min": min(r["wall_s"] for r in worker_results),
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"per_worker_peak_rss_mb_max": max(r["peak_rss_mb"] for r in worker_results),
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}
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def gen_queries(rng_seed: int = 7) -> list[str]:
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"""Mix of head-term (common, hits many docs) and tail-term (one doc) queries."""
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rng = random.Random(rng_seed)
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queries = []
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# Half head queries: random common words.
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for _ in range(N_QUERIES // 2):
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n_words = rng.randint(1, 3)
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queries.append(" ".join(rng.choices(WORDS, k=n_words)))
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# Half tail queries: a specific bench_doc_NNNN marker.
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sample_docs = rng.sample(range(N_DOCS), N_QUERIES - N_QUERIES // 2)
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for i in sample_docs:
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queries.append(f"bench_doc_{i:04d}")
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return queries
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def bench_query(M: int, queries: list[str]) -> dict:
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"""Run query suite against the M-shard layout."""
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# Use connect_query which ATTACHes all the shards.
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snap_shards = discover_shards(BENCH_DIR)
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if not snap_shards:
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return {"M": M, "phase": "query", "wall_s": 0, "p50_ms": 0, "p99_ms": 0,
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"queries": 0, "error": "no_shards_discovered"}
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t_attach_0 = time.perf_counter()
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conn = connect_query(":memory:", shards_dir=BENCH_DIR)
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attach_ms = (time.perf_counter() - t_attach_0) * 1000
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try:
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latencies_ms = []
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t_total_0 = time.perf_counter()
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for q in queries:
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t0 = time.perf_counter()
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# FTS5 query across the union view.
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rows = conn.execute(
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"SELECT COUNT(*) FROM chunks_fts WHERE chunks_fts MATCH ?",
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(q,),
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).fetchall()
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latencies_ms.append((time.perf_counter() - t0) * 1000)
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total_wall = time.perf_counter() - t_total_0
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finally:
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conn.close()
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latencies_ms.sort()
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return {
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"M": M,
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"phase": "query",
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"wall_s": total_wall,
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"attach_ms": attach_ms,
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"p50_ms": latencies_ms[len(latencies_ms) // 2],
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"p99_ms": latencies_ms[int(len(latencies_ms) * 0.99)],
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"mean_ms": statistics.mean(latencies_ms),
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"queries": len(queries),
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}
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def main():
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print(f"== shard-count sweep ==")
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print(f" N_DOCS={N_DOCS}, N_QUERIES={N_QUERIES}, M ∈ {SHARD_COUNTS}")
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print(f" bench dir: {BENCH_DIR}")
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print()
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if USE_WIKIPEDIA:
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print(f" corpus: real Wikipedia ({WIKI_CUR_PATH.name}, first {N_DOCS} docs)")
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t_load = time.perf_counter()
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docs = load_wikipedia_corpus(N_DOCS)
|
||||
print(f" loaded {len(docs)} docs in {time.perf_counter() - t_load:.1f}s")
|
||||
else:
|
||||
print(f" corpus: synthetic ({N_DOCS} docs)")
|
||||
docs = gen_corpus(N_DOCS)
|
||||
queries = gen_queries()
|
||||
RESULTS_DIR.mkdir(parents=True, exist_ok=True)
|
||||
ts = time.strftime("%Y-%m-%dT%H-%M-%SZ", time.gmtime())
|
||||
csv_path = RESULTS_DIR / f"shard-count-sweep-{ts}.csv"
|
||||
|
||||
all_rows = []
|
||||
summary = []
|
||||
for M in SHARD_COUNTS:
|
||||
print(f"-- M={M} --")
|
||||
ingest = bench_ingest(M, docs)
|
||||
print(f" ingest: {ingest['wall_s']:.2f}s "
|
||||
f"chunks={ingest['total_chunks']} "
|
||||
f"worker_max={ingest['per_worker_wall_s_max']:.2f}s "
|
||||
f"peak_rss_mb={ingest['per_worker_peak_rss_mb_max']:.1f}")
|
||||
all_rows.append(ingest)
|
||||
query = bench_query(M, queries)
|
||||
print(f" query: {query['wall_s']:.2f}s for {query['queries']} qs "
|
||||
f"p50={query['p50_ms']:.2f}ms p99={query['p99_ms']:.2f}ms "
|
||||
f"attach={query['attach_ms']:.1f}ms")
|
||||
all_rows.append(query)
|
||||
summary.append({
|
||||
"M": M,
|
||||
"ingest_wall_s": ingest["wall_s"],
|
||||
"ingest_chunks_per_s": ingest["total_chunks"] / ingest["wall_s"],
|
||||
"query_p50_ms": query["p50_ms"],
|
||||
"query_p99_ms": query["p99_ms"],
|
||||
"query_attach_ms": query["attach_ms"],
|
||||
})
|
||||
|
||||
# Write CSV
|
||||
with open(csv_path, "w") as f:
|
||||
if all_rows:
|
||||
keys = set()
|
||||
for r in all_rows:
|
||||
keys.update(r.keys())
|
||||
w = csv.DictWriter(f, fieldnames=sorted(keys))
|
||||
w.writeheader()
|
||||
for r in all_rows:
|
||||
w.writerow(r)
|
||||
print()
|
||||
print(f"== summary ==")
|
||||
print(f"{'M':>2} {'ingest_wall_s':>14} {'chunks/s':>10} "
|
||||
f"{'q_p50_ms':>10} {'q_p99_ms':>10} {'attach_ms':>10}")
|
||||
for s in summary:
|
||||
print(f"{s['M']:>2} {s['ingest_wall_s']:>14.2f} "
|
||||
f"{s['ingest_chunks_per_s']:>10.1f} "
|
||||
f"{s['query_p50_ms']:>10.2f} {s['query_p99_ms']:>10.2f} "
|
||||
f"{s['query_attach_ms']:>10.2f}")
|
||||
print()
|
||||
print(f"results → {csv_path}")
|
||||
|
||||
# Tidy up bench dir.
|
||||
if BENCH_DIR.exists():
|
||||
shutil.rmtree(BENCH_DIR)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
|
|
@ -111,7 +111,7 @@ Newest first. Update on every open/close.
|
|||
|
||||
| ID | Title | Status | Opened | Directive |
|
||||
|----------|------------------------------------------------|-----------------------|------------|-----------|
|
||||
| #000065 | Canonical shard count `M` + content-hash routing (decouple ingest parallelism from ATTACH ceiling) | **open · scaffold + design · awaiting go/no-go** (2026-05-26; surfaced while sizing #000061's federation story). Today shard count conflates two roles: producer ingest parallelism (wants vCPU count) + consumer ATTACH fan-out (capped at SQLITE_MAX_ATTACHED=10 on stock python3 sqlite3). Producer with 16 vCPU → 16 shards → consumers fail to attach the 11th. Producer with 4 shards → 16-vCPU box runs 75% idle on ingest. Fix: pin a corpus-wide canonical M (default 8, ≤ ATTACH ceiling), introduce N (ingest workers) decoupled from M. Document → shard assignment becomes content-deterministic: `shard_idx = int(document_root[:8], 16) % M`. Same input → same output across every peer (today's "spray by ingest order" is non-deterministic across peers, a real federation weakness). Migration hard-constraint per fox: **content-addressed rebalance, NOT re-ingest** — every row is already addressed by `document_root` / `leaf_hash` / etc.; migration reads rows from the current 4 shards, computes each row's new shard via the routing function, INSERTs into M new shards. No source re-parse, no re-canonicalization, no re-chunking, no LLM. ~20–40 min I/O-bound vs. hours-to-days for true re-ingest. Audit chain consolidates to canonical shard 000 (re-numbered + re-hashed once) to preserve global event ordering. Phases: 0 design lock + pin M in meta table → 1 read path (connect_query honors M) → 2 ingest path (multi-shard write per worker) → 3 cold-pack restore re-routes on pull → 4 corpus migration tool. Open audit-chain re-numbering question (every shard has its own seq + event_hash; rebalancing splits a producer's chain across M consumer shards). Don't proliferate sub-tickets; the audit handling is part of this design lock. Out of scope: custom-built sqlite3 with higher MAX_ATTACHED (rejected: violates "python3 + venv + sqlite3 only" property from CLAUDE.md); topic-clustering shards (would break ingest determinism). | 2026-05-26 | — |
|
||||
| #000065 | Canonical shard count `M` + content-hash routing (decouple ingest parallelism from ATTACH ceiling) | **open · scaffold + design · awaiting go/no-go** (2026-05-26; surfaced while sizing #000061's federation story). Today shard count conflates two roles: producer ingest parallelism (wants vCPU count) + consumer ATTACH fan-out (capped at SQLITE_MAX_ATTACHED=10 on stock python3 sqlite3). Producer with 16 vCPU → 16 shards → consumers fail to attach the 11th. Producer with 4 shards → 16-vCPU box runs 75% idle on ingest. Fix: pin a corpus-wide canonical **M = 4** (decided 2026-05-26 from real-Wikipedia bench: M=4 captures 92% of peak ingest throughput, ATTACH cost 9 ms keeps mobile-tolerable, 6 free ATTACH slots under SQLite's 10 ceiling for auxiliary DBs), introduce N (ingest workers) decoupled from M. Document → shard assignment becomes content-deterministic: `shard_idx = int(document_root[:8], 16) % M`. Same input → same output across every peer (today's "spray by ingest order" is non-deterministic across peers, a real federation weakness). Migration hard-constraint per fox: **content-addressed rebalance, NOT re-ingest** — every row is already addressed by `document_root` / `leaf_hash` / etc.; migration reads rows from the current 4 shards, computes each row's new shard via the routing function, INSERTs into M new shards. No source re-parse, no re-canonicalization, no re-chunking, no LLM. ~20–40 min I/O-bound vs. hours-to-days for true re-ingest. Audit chain consolidates to canonical shard 000 (re-numbered + re-hashed once) to preserve global event ordering. Phases: 0 design lock + pin M in meta table → 1 read path (connect_query honors M) → 2 ingest path (multi-shard write per worker) → 3 cold-pack restore re-routes on pull → 4 corpus migration tool. Open audit-chain re-numbering question (every shard has its own seq + event_hash; rebalancing splits a producer's chain across M consumer shards). Don't proliferate sub-tickets; the audit handling is part of this design lock. Out of scope: custom-built sqlite3 with higher MAX_ATTACHED (rejected: violates "python3 + venv + sqlite3 only" property from CLAUDE.md); topic-clustering shards (would break ingest determinism). | 2026-05-26 | — |
|
||||
| #000064 | Cold-object operations toolkit (verify/diff/doctor/repair-fts/gc-plan + audit taxonomy) | **scaffold-only · awaiting go/no-go** (2026-05-26; from Dav1d #000061 review §11/§12/§14). Operator-facing observability + repair tools on top of #000061: `cold verify` (sample/full integrity check), `cold diff` (local vs remote manifest), `cold doctor` (one-shot health: connectivity / credentials / manifest age / missing-object count / tamper sample / audit-chain integrity), `cold repair-fts` (rebuild FTS5 from chunks.content), `cold gc-plan` (orphan bucket objects, read-only by default — destructive only with `--apply` + confirm). Plus expanded audit-event taxonomy: per-PUT/HEAD/GET success/failure events, manifest-pointer events, verify/doctor/gc events. All read-mostly; destructive ops require `--apply`. Bundled so the audit-taxonomy gets one design pass instead of five-way drift. Sequence: doctor → verify → diff → repair-fts → gc-plan. No code until #000061 closes. | 2026-05-26 | — |
|
||||
| #000063 | Cold-object private-ciphertext mode (mesh-keyed object keys) | **scaffold-only · awaiting go/no-go** (2026-05-26; from Dav1d #000061 review §9 / response A §13.3). Adds private mode to #000061 cold-object format so chunk bodies + manifest can be uploaded to public-read bucket without leaking corpus membership. Two strategies: (A) deterministic `object_key = HMAC(group_key, leaf_hash)` + AEAD-encrypted body — supports lookup-by-leaf-hash given the key; (B) random-key ciphertext + encrypted private manifest — stronger membership hiding, needs manifest fetch first. Strategy A default; B opt-in. Group key from existing `arborist/mesh/crypto.py`; pack manifest carries `epoch_id` for rotation. Verifier path unchanged: consumer decrypts, then `hash_leaf(plaintext) == leaf_hash` as in public mode. No code until (1) a real non-public corpus needs cold-object shipping, (2) mesh group-key ABI is stable enough to reference, (3) threat-model split between A vs B is settled by real adversary. | 2026-05-26 | — |
|
||||
| #000062 | Mechanistic Witness: governed diagnostic sidecar (CNA/SAE/Neuronpedia) | **scaffold-only · awaiting go/no-go** (2026-05-26; Dav1d de-novo review §4.7 / §9.1.F). Specification of a mechanistic-interpretability sidecar that produces a content-addressed `MechanisticWitnessRoot` over (model, prompts, capture policy, neurons/features, intervention deltas), used as a **diagnostic input** to SelfModel (#000014/#000017) + benchmark-fixture generation. **Hard constraint:** soft signals never enter the hard proof path — `audit_mode` does NOT move based on witness output, `providence_cache` is untouched, `governance_policy_hash` only moves via explicit ForkScore ACCEPT with M+C+X axes passing (#000060 §7). Four guardrails (diagnostic-only by default · sandbox intervention only · no production steering without governance · feature labels never semantic proof). Witness root TLV-encodes `model_config_root | activation_capture_policy_root | contrastive_prompt_set_root | feature_or_neuron_set_root | intervention_result_root | behavioral_delta_root | safety_policy_root`. Scaffold only — no code until a real falsifier-in-hand use case exists + the four guardrails are restated in CLAUDE.md as rules + #000060 H-ABCDEFG-M+C+X harness exists to gate promotion. Captured to keep mechanistic-interp tooling out of the substrate unless and until it earns its place; the dual-use risk (Pan et al. 2025 CNA: 0.1% MLP ablation breaks refusal in 72B models) makes the governance-first framing load-bearing. | 2026-05-26 | — |
|
||||
|
|
|
|||
|
|
@ -52,13 +52,75 @@ different shards. This makes federation gossip + content-addressing
|
|||
weaker than it should be — two peers' "shard 003.db" can have
|
||||
different contents.
|
||||
|
||||
## Design
|
||||
## Canonical M = 4 (decided 2026-05-26 from real-corpus bench)
|
||||
|
||||
The corpus-wide canonical shard count is **M = 4**. Reasoning grounded
|
||||
in two `bench/shard_count_sweep.py` runs (synthetic + real Wikipedia
|
||||
2003 cur dump, 2000 docs each, M ∈ {1, 2, 4, 8}).
|
||||
|
||||
### Real Wikipedia numbers (2026-05-26)
|
||||
|
||||
```
|
||||
M chunks/s q_p50_ms q_p99_ms attach_ms free ATTACH slots
|
||||
1 3,648 0.05 0.20 1.61 9
|
||||
2 5,649 0.03 0.19 3.24 8
|
||||
4 6,405 0.07 0.30 9.00 6
|
||||
8 6,959 0.03 0.28 9.65 2
|
||||
```
|
||||
|
||||
Full CSV: `bench/results/shard-count-sweep-2026-05-26T16-31-34Z.csv`.
|
||||
Synthetic-corpus comparison: `…T16-20-48Z.csv` (under-estimates per-
|
||||
doc work because random-word docs skip wikitext parsing + edge
|
||||
extraction — Wikipedia is the load-bearing measurement).
|
||||
|
||||
### Why M = 4
|
||||
|
||||
1. **Captures 92 % of peak ingest throughput** (6,405 / 6,959).
|
||||
Going from M=4 to M=8 buys only +9 % — diminishing-returns
|
||||
regime. The ingest bottleneck on real wikitext is Python CPU
|
||||
per worker (canonicalization + edge extraction), not SQLite
|
||||
writes; more shards don't unlock that.
|
||||
2. **Keeps 6 ATTACH slots free** under SQLite's 10-shard ceiling for
|
||||
`snapshots.db`, `qa.db`, `selfmodel-chain.db`, `crawl_*.db`,
|
||||
future `mesh_*.db` if extracted, and the manifest-pointer
|
||||
connection. M=8 leaves only 2 slots — operationally tight.
|
||||
3. **Mobile-tolerable.** Phone NAND attach is ~5–10× slower than
|
||||
NVMe. M=4 attach (9 ms on dev box) → ~45–90 ms cold-start on
|
||||
phone — feels instant. M=8 attach (9.65 ms) → ~50–100 ms; also
|
||||
fine but with no headroom for the slower mobile flash.
|
||||
4. **Matches fox's current 4-shard layout** = the cheapest migration.
|
||||
Most rows already hash-route to their existing shard with
|
||||
probability 1/M = 25 % (vs. uniform reshuffling at any other M).
|
||||
The teleport is partial, not total.
|
||||
5. **Query latency is flat across M within noise** at 2000-doc
|
||||
corpus. Larger query suites (n=1000+) on a populated corpus
|
||||
would tighten this; current data says shard count doesn't move
|
||||
p50 perceptibly when the FTS5 index fits in page cache.
|
||||
|
||||
### Why not M = 2
|
||||
|
||||
- Loses 13 % of peak ingest throughput vs M=4
|
||||
- ATTACH headroom (8 slots) overkill for current arborist's
|
||||
auxiliary DBs
|
||||
- Wider per-shard variance: 2 huge shards put more work behind
|
||||
one WAL writer lock during ingest spikes; 4 smaller shards
|
||||
spread the spike
|
||||
|
||||
### Why not M = 8
|
||||
|
||||
- +9 % ingest gain doesn't justify halving ATTACH headroom
|
||||
- Mobile attach cliff (10 shards + 8 corpus + qa + snapshots +
|
||||
mesh = right at the ceiling)
|
||||
- Federation peers with fewer vCPU than producer carry more
|
||||
per-shard work that doesn't pay back
|
||||
|
||||
### Design
|
||||
|
||||
Introduce two numbers, both explicit:
|
||||
|
||||
```
|
||||
N = ingest worker count — producer's vCPU choice
|
||||
M = canonical shard count — corpus-wide constant, M ≤ 8 by convention
|
||||
M = canonical shard count — corpus-wide constant, M = 4 by default
|
||||
```
|
||||
|
||||
**M is part of the corpus identity.** Pinned in the snapshot manifest +
|
||||
|
|
@ -244,6 +306,116 @@ in S3 as recovery rollback."
|
|||
shard is computable but the edges row still lives in src's
|
||||
shard. No change needed.
|
||||
|
||||
## When the SQLite-default substrate stops being right
|
||||
|
||||
The M=4 choice is correct **conditional on staying on stock python3
|
||||
sqlite3 with SQLITE_MAX_ATTACHED=10**. Three thresholds where that
|
||||
assumption breaks; each names what bench would justify moving:
|
||||
|
||||
### Threshold A: ATTACH-ceiling pressure forces a forked SQLite
|
||||
|
||||
**Signal:** auxiliary `.db` files (`qa.db`, `snapshots.db`,
|
||||
`selfmodel-chain.db`, `crawl_*.db`, future `mesh_*.db`) plus M=4
|
||||
canonical shards plus operator-facing connections push past 10 in
|
||||
practice. Today: 4 canonical + 3-4 auxiliary = 7-8, fits with M=4
|
||||
headroom. If auxiliary grows past 5, M=4 becomes the binding
|
||||
constraint.
|
||||
|
||||
**What to bench before the fork:**
|
||||
|
||||
1. Compile sqlite3 with `SQLITE_MAX_ATTACHED=125` (the spec maximum).
|
||||
2. Re-run `bench/shard_count_sweep.py` with M ∈ {16, 32, 64} on the
|
||||
real corpus.
|
||||
3. Measure: ATTACH cost growth (linear vs. super-linear?), query
|
||||
latency under wider UNION ALL, ingest throughput at higher M.
|
||||
4. **Decision criteria:**
|
||||
- If ATTACH cost stays roughly linear past M=10 → forked SQLite
|
||||
viable. Costs: a custom build to ship with arborist or a
|
||||
dependency on system-sqlite-with-this-flag (Debian / Fedora
|
||||
packages, mobile builds).
|
||||
- If ATTACH cost goes super-linear past M=10 → SQLite's
|
||||
architectural design doesn't expect wide multi-attach; need a
|
||||
different substrate.
|
||||
|
||||
**Cost of the fork:** ~1 day of build infrastructure. ~Permanent tax
|
||||
on every install: arborist no longer "just works" on stock sqlite3.
|
||||
Violates the CLAUDE.md "python3 + venv + sqlite3 is enough" property.
|
||||
Don't do it unless the bench says we have to.
|
||||
|
||||
### Threshold B: ingest throughput hits a wall
|
||||
|
||||
**Signal:** workload requires real-time ingest at > 10k chunks/s
|
||||
sustained (e.g., live mesh-replicated state across many peers). On
|
||||
this benchmark, real-Wikipedia ingest peaks at ~7,000 chunks/s
|
||||
regardless of M past 4. SQLite's single-writer-per-file model is the
|
||||
ceiling — adding more workers behind the same writer lock doesn't
|
||||
help.
|
||||
|
||||
**What to bench before considering alternatives:**
|
||||
|
||||
1. **Page size tuning.** Default 4 KB; arborist could rebuild shards
|
||||
with 16 KB or 64 KB pages. Bench: 4 KB vs 16 KB vs 64 KB on the
|
||||
same M=4 layout. Larger pages help wide-row tables (`edges`)
|
||||
especially.
|
||||
2. **WAL checkpoint interval.** Default auto-checkpoint at 1000
|
||||
frames. Bench: ingest throughput at 100, 1000, 10000-frame
|
||||
intervals.
|
||||
3. **`mmap_size` sweep.** Default 256 MB in arborist's `connect`.
|
||||
Bench: 0, 64 MB, 256 MB, 1 GB.
|
||||
4. **`synchronous=NORMAL` vs `OFF` for ingest workers.** NORMAL is
|
||||
the default + safe under WAL. OFF removes the per-commit fsync
|
||||
entirely and is faster but loses durability on power loss. For
|
||||
ingest from a deterministic dump (re-runnable), `OFF` might be
|
||||
acceptable.
|
||||
|
||||
**Decision criteria:**
|
||||
- If tuning gets us 2-5× more throughput → stay on SQLite, document
|
||||
the tuned pragmas in `connect()`.
|
||||
- If still ceiling-limited at 10k+ chunks/s → genuine substrate
|
||||
question. Candidates:
|
||||
- **DuckDB** (columnar, MVCC, multiple concurrent writers,
|
||||
supports SQLite-compatible SQL surface, has its own FTS).
|
||||
Bench against same harness.
|
||||
- **libmdbx / LMDB** (B+tree, MVCC, very fast reads). No FTS;
|
||||
we'd build it. Probably overkill for arborist's read patterns.
|
||||
- **In-house DB.** Too ambitious without a specific failure of
|
||||
the above to justify.
|
||||
|
||||
### Threshold C: federation needs multi-writer-same-shard
|
||||
|
||||
**Signal:** the mesh state evolves so that multiple peers can write
|
||||
to the same shard simultaneously (today: single-writer-per-shard
|
||||
is the assumption — mesh gossip pulls audit events but doesn't
|
||||
co-write). SQLite's writer lock serializes across peers — would
|
||||
become a federation bottleneck.
|
||||
|
||||
**What to bench before alternatives:**
|
||||
|
||||
1. Two peers writing to a network filesystem (NFS) backed shard with
|
||||
WAL — does SQLite's locking actually work, and what's throughput?
|
||||
(Spoiler: SQLite famously hates NFS; this fails.)
|
||||
2. Two peers writing to a shared block device (SAN) with WAL —
|
||||
similar story but better.
|
||||
3. Application-level coordination: only one peer is "leader" for a
|
||||
shard at a time; followers replicate the WAL frames.
|
||||
|
||||
**Decision criteria:**
|
||||
- If single-leader-per-shard works → stay on SQLite, build the
|
||||
leader-election layer above it.
|
||||
- If we need true multi-writer-same-shard → SQLite is wrong; needs
|
||||
a substrate with built-in MVCC + conflict resolution. **DuckDB
|
||||
doesn't solve this either** — its MVCC is single-process. The
|
||||
candidate becomes something like FoundationDB or a CRDT layer on
|
||||
any key-value store.
|
||||
|
||||
### Honest summary
|
||||
|
||||
For the current arborist workload (single-writer-per-shard, M=4,
|
||||
read-mostly federation), **stock python3 sqlite3 is the right
|
||||
substrate.** None of the three thresholds are close to firing. The
|
||||
bench discipline above exists so we know what to measure when
|
||||
something changes, not as a roadmap to leave SQLite.
|
||||
|
||||
## Scope boundaries
|
||||
|
||||
In scope:
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue