ZacharyZhang-NY
c4e2982506
Latency measured while another job hogs the cores is not comparable: the scale curve moved from 1.315s to 0.809s at 50,000 sources between two runs of the same code. - bench/systems.py: machine_facts() reports cpus plus the 1/5/15 minute load average. - bench/run.py, bench/run_external.py: both reports carry it, and BASELINE.md labels the latency table a ceiling when the machine was busy. Verification: pytest bench/tests -q -> 60 passed; ruff check bench/ -> all checks passed; mypy (fresh cache) -> no issues in 25 source files.
528 lines
23 KiB
Python
528 lines
23 KiB
Python
"""Run the retrieval ablation over the frozen corpus and write the baseline report.
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Five arms, one database: sparse only, dense only, graph only, the product's weighted
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fusion, and fusion plus a cross-encoder reranker. Every number in the report is either
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measured or explicitly marked as chance.
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Run: python -m bench.run [--arms bm25_only] [--limit 200] [--no-live] [--out bench/reports]
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"""
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from __future__ import annotations
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import argparse
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import hashlib
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import json
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import platform
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import subprocess
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from collections.abc import Sequence
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from dataclasses import dataclass
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from datetime import UTC, datetime
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from pathlib import Path
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from typing import Any
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import numpy as np
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from bench.metrics import aggregate, chance_recall_at_k, score_query
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from bench.sets_common import MODALITIES, SETS, read_jsonl, sha256_file
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from bench.systems import (
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ARMS,
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DENSE_MODEL,
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MODELS,
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RERANK_MODEL,
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ArmRunner,
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Atom,
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JointRunner,
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arm_needs,
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live_product_rankings,
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load_atoms,
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machine_facts,
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)
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ROOT = SETS.parent
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REPORTS = ROOT / "reports"
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DB_HOME = ROOT / "runs" / "baseline"
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LIVE_QUERIES = 40 # the product rebuilds BM25 per query, so a live pass costs minutes per query
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PROGRESS_EVERY = 250 # an arm takes tens of minutes over 5,308 queries; silence looks like a hang
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SCALE_SIZES = (500, 2_000, 10_000, 50_000)
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SCALE_PROBES = 40
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@dataclass(frozen=True)
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class Query:
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query_id: str
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text: str
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modality: str
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gold: frozenset[str]
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holder: str | None
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answerable: bool
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as_of: str | None
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def load_queries(modalities: Sequence[str] = MODALITIES) -> list[Query]:
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"""Every query the suite froze, in file order."""
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queries: list[Query] = []
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for modality in modalities:
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path = SETS / f"{modality}.jsonl"
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if not path.is_file():
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raise SystemExit(f"{path}: missing set, run python -m bench.build_sets first")
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for record in read_jsonl(path):
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gold = frozenset(hit["source_id"] for hit in record["gold"])
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answerable = not bool(record["unanswerable"])
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if answerable != bool(gold):
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raise SystemExit(
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f"{path}: {record['query_id']} carries {len(gold)} gold hits but "
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f"unanswerable={record['unanswerable']}"
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)
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queries.append(
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Query(
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query_id=record["query_id"],
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text=record["question"],
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modality=modality,
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gold=gold,
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holder=record["scope"]["holder"],
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answerable=answerable,
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as_of=record.get("as_of"),
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)
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)
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if not queries:
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raise SystemExit("no queries loaded")
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return queries
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def holder_index(modalities: Sequence[str] = MODALITIES) -> dict[str, str]:
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"""source_id -> holder, from the corpus side of the suite."""
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holders: dict[str, str] = {}
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for modality in modalities:
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path = SETS / "corpus" / f"{modality}.jsonl"
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if not path.is_file():
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raise SystemExit(f"{path}: missing corpus index, run python -m bench.build_sets first")
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for record in read_jsonl(path):
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holders[record["source_id"]] = record["holder"]
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return holders
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def chance_row(queries: Sequence[Query], corpus_sources: int) -> dict[str, float]:
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"""What a random ranking would score on the same queries."""
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answerable = [query for query in queries if query.answerable]
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if not answerable:
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raise SystemExit("chance needs answerable queries")
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return {
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"corpus_sources": corpus_sources,
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"recall_at_1": sum(chance_recall_at_k(len(query.gold), corpus_sources, 1) for query in answerable) / len(answerable),
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"recall_at_5": sum(chance_recall_at_k(len(query.gold), corpus_sources, 5) for query in answerable) / len(answerable),
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"recall_at_10": sum(chance_recall_at_k(len(query.gold), corpus_sources, 10) for query in answerable) / len(answerable),
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}
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def scale_probes(queries: Sequence[Query], count: int = SCALE_PROBES) -> list[Query]:
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"""Queries to time at every corpus size.
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Latency does not need gold hits, and a truncated corpus keeps almost none of them,
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so selecting probes by gold would silently drop the small sizes entirely.
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"""
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if count <= 0:
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raise SystemExit("the scale curve needs at least one probe query")
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answerable = [query for query in queries if query.answerable]
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if not answerable:
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raise SystemExit("the scale curve needs answerable queries")
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stride = max(1, len(answerable) // count)
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return answerable[::stride][:count]
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def scale_curve(queries: Sequence[Query], atoms: Sequence[Atom], arms: Sequence[str]) -> list[dict[str, Any]]:
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"""Latency of each arm as the corpus grows, measured on nested source prefixes."""
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sources = sorted({atom.source_id for atom in atoms})
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rows: list[dict[str, Any]] = []
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probes = scale_probes(queries)
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for size in SCALE_SIZES:
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keep = set(sources[:size])
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if not keep:
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raise SystemExit(f"scale size {size} kept no sources")
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subset = [atom for atom in atoms if atom.source_id in keep]
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row: dict[str, Any] = {
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"sources": len(keep),
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"atoms": len(subset),
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"queries": len(probes),
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"note": "latency only: a source prefix drops most gold sources, so recall at these sizes is meaningless",
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}
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for arm in arms:
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if not arm_needs(arm, MODELS):
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continue
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runner = ArmRunner(arm, subset, MODELS)
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for query in probes:
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runner.rank(query.text)
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row[arm] = {"p50": runner.percentile(0.50), "p95": runner.percentile(0.95)}
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rows.append(row)
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print(f"scale {len(keep):6d} sources: " + " ".join(f"{arm}={row[arm]['p50']:.3f}s" for arm in arms if arm in row), flush=True)
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return rows
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def live_check(
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queries: Sequence[Query],
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fast_rankings: dict[str, list[str]],
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top_k: int = 10,
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live_queries: int = LIVE_QUERIES,
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) -> dict[str, Any]:
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"""Compare the unmodified RetrievalService with the fast BM25 path."""
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probe = [query for query in queries if query.answerable]
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stride = max(1, len(probe) // live_queries)
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chosen = probe[::stride][:live_queries]
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if not chosen:
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raise SystemExit("live check needs answerable queries")
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rankings, distinct, timings = live_product_rankings(DB_HOME, [query.text for query in chosen], top_k)
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overlaps = [
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len(set(fast_rankings[query.query_id]) & set(ranking)) / top_k
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for query, ranking in zip(chosen, rankings, strict=True)
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if fast_rankings.get(query.query_id) is not None
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]
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if not overlaps:
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raise SystemExit("live check found no fast rankings to compare against")
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return {
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"queries": len(chosen),
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"top_k": top_k,
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"p50": sorted(timings)[len(timings) // 2],
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"mean": sum(timings) / len(timings),
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"max": max(timings),
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"top10_overlap_with_bm25_only": sum(overlaps) / len(overlaps),
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"identical_top10": sum(1 for overlap in overlaps if overlap == 1.0) / len(overlaps),
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"distinct_sources_in_top10": {
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"mean": sum(distinct) / len(distinct),
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"min": min(distinct),
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"max": max(distinct),
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},
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}
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def git_commit() -> str:
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result = subprocess.run(
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["git", "rev-parse", "HEAD"], cwd=ROOT, capture_output=True, text=True, check=True, timeout=30
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)
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commit = result.stdout.strip()
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if len(commit) != 40:
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raise SystemExit(f"git rev-parse HEAD returned {commit!r}, expected a 40 character sha")
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return commit
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def meta(corpus_sources: int, queries: Sequence[Query], limit: int | None = None) -> dict[str, Any]:
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manifest_path = SETS / "manifest.json"
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try:
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manifest = json.loads(manifest_path.read_text(encoding="utf-8"))
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except (OSError, json.JSONDecodeError) as error:
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raise SystemExit(f"{manifest_path}: cannot read the frozen set manifest: {error}") from error
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return {
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"generated_at": datetime.now(UTC).isoformat(timespec="seconds"),
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"git_commit": git_commit(),
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"python": platform.python_version(),
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"machine": machine_facts(),
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"corpus_manifest_sha256": manifest.get("corpus_manifest_sha256"),
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"sets": {name: sha256_file(SETS / f"{name}.jsonl") for name in MODALITIES},
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"queries": len(queries),
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"answerable": sum(1 for query in queries if query.answerable),
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"limit_per_modality": limit,
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"corpus_sources": corpus_sources,
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"models": {"dense": DENSE_MODEL, "rerank": RERANK_MODEL},
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}
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def scale_arm_names(rows: Sequence[dict[str, Any]]) -> list[str]:
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"""Arms a scale row reports: only keys whose value is a latency dict, in order.
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A scale row also carries strings (the note explaining what the row means), and
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treating those as arms is how the report writer first crashed.
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"""
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names: list[str] = []
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for row in rows:
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for name, value in row.items():
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if isinstance(value, dict) and name not in names:
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names.append(name)
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if not names:
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raise SystemExit("scale rows report no measured arm")
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return names
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def write_markdown(report: dict[str, Any], path: Path) -> None:
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"""Human-readable twin of the JSON report."""
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lines = [
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"# BASELINE: what the product retrieves today",
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"",
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f"- generated {report['meta']['generated_at']} at commit {report['meta']['git_commit'][:12]}",
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(
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f"- corpus {report['meta']['corpus_sources']} sources, {report['meta']['queries']} queries "
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f"({report['meta']['answerable']} answerable)"
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),
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f"- models: dense `{report['meta']['models']['dense']}`, rerank `{report['meta']['models']['rerank']}`",
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(
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f"- machine: {report['meta']['machine']['cpus']} cores, load average "
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f"{report['meta']['machine']['load_average_1_5_15'][0]:.1f} when the report was written"
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),
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"",
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"| arm | recall@1 | recall@5 | recall@10 | nDCG@10 | MRR | hit@10 (95% lower) | p50 s | p95 s |",
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"|---|---|---|---|---|---|---|---|---|",
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]
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chance = report["chance"]
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lines.append(
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f"| chance (random ranking) | {chance['recall_at_1']:.3f} | {chance['recall_at_5']:.3f} "
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f"| {chance['recall_at_10']:.3f} | - | - | - | - | - |"
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)
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for arm in report["arms"]:
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overall = arm["overall"]
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latency = arm["latency_seconds"]
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lines.append(
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f"| {arm['arm']} | {overall['recall_at_1']:.3f} | {overall['recall_at_5']:.3f} "
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f"| {overall['recall_at_10']:.3f} | {overall['ndcg_at_10']:.3f} | {overall['mrr']:.3f} "
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f"| {overall['hit_at_10']:.3f} ({overall['hit_at_10_wilson_lower']:.3f}) "
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f"| {latency['p50']:.3f} | {latency['p95']:.3f} |"
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)
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shown = [modality for modality in MODALITIES if any(modality in arm["by_modality"] for arm in report["arms"])]
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if not shown:
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raise SystemExit("no per-modality scores to write")
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lines += ["", "## recall@10 by modality", "", "| arm | " + " | ".join(shown) + " |", "|---|" + "---|" * len(shown)]
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for arm in report["arms"]:
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cells = [
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f"{arm['by_modality'][modality]['recall_at_10']:.3f}" if modality in arm["by_modality"] else "-"
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for modality in shown
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]
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lines.append(f"| {arm['arm']} | " + " | ".join(cells) + " |")
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total = report["meta"]["queries"]
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if total <= 0:
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raise SystemExit("the report records no queries")
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share = 1 - report["meta"]["answerable"] / total
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lines += ["", f"## unanswerable queries ({share:.1%} of the suite)", ""]
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for arm in report["arms"]:
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overall = arm["overall"]
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lines.append(
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f"- {arm['arm']}: abstains on {overall['abstention_rate_unanswerable']:.0%} of unanswerable queries, "
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f"and puts a wrong-holder source on top for {overall['wrong_holder_confidence_unanswerable']:.0%} of them"
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)
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if "live_product" in report:
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live = report["live_product"]
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lines += [
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"",
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"## the unmodified product path",
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"",
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(
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f"- RetrievalService.search: p50 {live['p50']:.2f}s, mean {live['mean']:.2f}s, max {live['max']:.2f}s "
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f"over {live['queries']} queries"
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),
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(
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f"- top-10 overlap with the fast BM25 path: {live['top10_overlap_with_bm25_only']:.1%}, "
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f"identical order {live['identical_top10']:.1%}"
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),
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(
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f"- its top-{live['top_k']} atoms cover only "
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f"{live['distinct_sources_in_top10']['mean']:.1f} distinct sources "
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f"(min {live['distinct_sources_in_top10']['min']}): the product ranks atoms and never diversifies, "
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"so ten slots fill with fragments of one document and the overlap with a source-level ranking is near zero"
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),
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]
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if report.get("scale"):
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measured = scale_arm_names(report["scale"])
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header = " | ".join(f"{arm} p50/p95 s" for arm in measured)
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lines += ["", "## latency vs corpus size", "", f"| sources | atoms | {header} |", "|" + "---|" * (2 + len(measured))]
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for row in report["scale"]:
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cells = [f"{row[arm]['p50']:.3f}/{row[arm]['p95']:.3f}" for arm in measured]
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lines.append(f"| {row['sources']} | {row['atoms']} | " + " | ".join(cells) + " |")
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note = report["scale"][0].get("note")
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if note:
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lines += ["", f"_{note}_"]
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load = report["meta"]["machine"]["load_average_1_5_15"][0]
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lines.append(
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f"\n_latency was measured at load average {load:.1f} on {report['meta']['machine']['cpus']} cores; "
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"a busy machine inflates these figures, so read them as a ceiling_"
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)
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lines += [
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"",
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"## reading",
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"",
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"- recall counts a source as found only when it is the source a third party marked correct.",
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"- abstention is the only honest number for unanswerable queries: a retriever that always",
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" returns ten results never says it does not know.",
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"- chance is the floor any of these arms must beat; a number near chance is not a capability.",
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]
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path.write_text("\n".join(lines) + "\n", encoding="utf-8")
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def load_config(parser: argparse.ArgumentParser, args: argparse.Namespace, path: Path) -> None:
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"""Fill in whatever the command line left at its default; an explicit flag still wins."""
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try:
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config = json.loads(path.read_text(encoding="utf-8"))
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except (OSError, json.JSONDecodeError) as error:
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raise SystemExit(f"{path}: cannot read the run config ({error})") from error
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if not isinstance(config, dict):
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raise SystemExit(f"{path}: expected a JSON object, got {type(config).__name__}")
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for key, value in config.items():
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if key not in vars(args):
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raise SystemExit(f"{path}: unknown key {key!r}, expected one of {sorted(vars(args))}")
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if getattr(args, key) == parser.get_default(key):
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setattr(args, key, value)
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unknown = [arm for arm in args.arms if arm not in ARMS]
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if unknown:
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raise SystemExit(f"{path}: unknown arm(s) {unknown}, expected one of {list(ARMS)}")
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def latency(times: Sequence[float]) -> dict[str, float]:
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"""Latency summary for one arm's per-query wall times."""
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values = np.asarray(times, dtype=np.float64)
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if values.size == 0:
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raise SystemExit("no latency samples recorded for this arm")
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return {
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"queries": int(values.size),
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"mean": float(values.mean()),
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"p50": float(np.percentile(values, 50)),
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"p95": float(np.percentile(values, 95)),
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"max": float(values.max()),
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}
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def rss_gib() -> float:
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"""Resident memory of this process; a nine-hour run needs to show its growth."""
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try:
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for line in Path("/proc/self/status").read_text(encoding="utf-8").splitlines():
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if line.startswith("VmRSS:"):
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return int(line.split()[1]) / 1024 / 1024
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except OSError:
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return 0.0
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return 0.0
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def fingerprint(arms: Sequence[str], queries: Sequence[Query], atoms: Sequence[Atom]) -> str:
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"""Identity of a rankings cache: the arms, the query set, and the corpus behind them."""
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corpus = hashlib.sha256("\n".join(atom.atom_id for atom in atoms).encode("utf-8")).hexdigest()[:16]
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payload = "\n".join(
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[",".join(arms), ",".join(query.query_id for query in queries), str(len(atoms)), corpus]
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)
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return hashlib.sha256(payload.encode("utf-8")).hexdigest()
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def load_rankings(path: Path, mark: str) -> dict[str, dict[str, Any]]:
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"""Read a resumable rankings cache; a header mismatch is an error, not a silent restart."""
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if not path.exists():
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return {}
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try:
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lines = path.read_text(encoding="utf-8").splitlines()
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except OSError as error:
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raise SystemExit(f"{path}: cannot read the rankings cache ({error})") from error
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rows: dict[str, dict[str, Any]] = {}
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for index, line in enumerate(lines, start=1):
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if not line.strip():
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continue
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try:
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row = json.loads(line)
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except json.JSONDecodeError as error:
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raise SystemExit(f"{path}:{index}: not JSON ({error})") from error
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if index == 1:
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if row.get("fingerprint") != mark:
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raise SystemExit(
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f"{path}: cached rankings belong to a different run, delete the file to start fresh"
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)
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continue
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rows[str(row["query_id"])] = dict(row["arms"])
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return rows
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def main() -> int:
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parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
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parser.add_argument("--arms", nargs="+", choices=ARMS, action="extend", default=None)
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parser.add_argument("--modality", action="append", choices=MODALITIES, default=None)
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parser.add_argument("--limit", type=int, default=None, help="score at most this many queries per modality")
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parser.add_argument("--no-live", action="store_true", help="skip the unmodified RetrievalService path")
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parser.add_argument("--live-queries", type=int, default=LIVE_QUERIES)
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parser.add_argument("--no-scale", action="store_true", help="skip the latency/scale curve")
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parser.add_argument("--out", type=Path, default=REPORTS)
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parser.add_argument("--config", type=Path, help="JSON defaults for these flags (bench/configs/ablation.json)")
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args = parser.parse_args()
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if args.config:
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load_config(parser, args, args.config)
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modalities = args.modality or list(MODALITIES)
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# action="extend" appends to the default, so an explicit --arms would otherwise
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# run every arm plus the requested ones.
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arms_requested: list[str] = list(args.arms or ARMS)
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queries = load_queries(modalities)
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if args.limit:
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capped: list[Query] = []
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for modality in modalities:
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picked = [query for query in queries if query.modality == modality][: args.limit]
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capped.extend(picked)
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queries = capped
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atoms = load_atoms(DB_HOME / "data" / "ely_eye.sqlite")
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holders = holder_index(modalities)
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corpus_sources = len({atom.source_id for atom in atoms})
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print(f"{len(queries)} queries, {len(atoms)} atoms, {corpus_sources} sources", flush=True)
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report: dict[str, Any] = {
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"meta": meta(corpus_sources, queries, args.limit),
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"chance": chance_row(queries, corpus_sources),
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}
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# One pass over the queries: each signal is computed once and every arm is derived
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# from it, and each query is checkpointed so a kill costs one query, not an arm.
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mark = fingerprint(arms_requested, queries, atoms)
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rankings_path = DB_HOME / "rankings.jsonl"
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done = load_rankings(rankings_path, mark)
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joint = JointRunner(arms_requested, atoms, MODELS)
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resumed = 0
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with rankings_path.open("a", encoding="utf-8") as cache:
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if not done:
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cache.write(f"{json.dumps({'fingerprint': mark})}\n")
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for index, query in enumerate(queries, start=1):
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if query.query_id in done:
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resumed += 1
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continue
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per_arm = joint.rank_all(query.text)
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done[query.query_id] = {
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arm: {"ranked": order, "seconds": seconds} for arm, (order, seconds) in per_arm.items()
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}
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cache.write(f"{json.dumps({'query_id': query.query_id, 'arms': done[query.query_id]})}\n")
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if index % PROGRESS_EVERY == 0:
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cache.flush()
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print(f" {index}/{len(queries)} queries, rss {rss_gib():.1f} GiB", flush=True)
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if resumed:
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print(f" resumed {resumed} queries from {rankings_path}", flush=True)
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|
|
|
arms: list[dict[str, Any]] = []
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|
fast_rankings: dict[str, list[str]] = {}
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|
for arm in [arm for arm in ARMS if arm in arms_requested]:
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scores = []
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|
times: list[float] = []
|
|
for query in queries:
|
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record = done.get(query.query_id)
|
|
if record is None or arm not in record:
|
|
raise SystemExit(f"{rankings_path}: no cached ranking for {query.query_id} arm {arm}")
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|
times.append(float(record[arm]["seconds"]))
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|
ranked = [str(source_id) for source_id in record[arm]["ranked"]]
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|
scores.append(score_query(query.query_id, ranked, set(query.gold), holder=query.holder, holder_of=holders))
|
|
if arm == "bm25_only":
|
|
fast_rankings[query.query_id] = ranked
|
|
summary: dict[str, Any] = {"arm": arm, "overall": aggregate(scores)}
|
|
summary["by_modality"] = {
|
|
modality: aggregate([s for s, q in zip(scores, queries, strict=True) if q.modality == modality])
|
|
for modality in sorted({q.modality for q in queries})
|
|
}
|
|
summary["latency_seconds"] = latency(times)
|
|
arms.append(summary)
|
|
print(
|
|
f"== {arm} recall@10 {summary['overall']['recall_at_10']:.3f} "
|
|
f"hit@10 {summary['overall']['hit_at_10']:.3f} "
|
|
f"(95% lower {summary['overall']['hit_at_10_wilson_lower']:.3f}) "
|
|
f"abstain {summary['overall']['abstention_rate_unanswerable']:.0%} "
|
|
f"p95 {summary['latency_seconds']['p95']:.3f}s",
|
|
flush=True,
|
|
)
|
|
report["arms"] = arms
|
|
# A crash in the live or scale phase should not cost every finished arm.
|
|
(DB_HOME / "partial_report.json").write_text(json.dumps(report, indent=1, sort_keys=True), encoding="utf-8")
|
|
if not args.no_live:
|
|
report["live_product"] = live_check(queries, fast_rankings, live_queries=args.live_queries)
|
|
if not args.no_scale:
|
|
report["scale"] = scale_curve(queries, atoms, [arm for arm in arms_requested if arm in ("bm25_only", "dense_only")])
|
|
|
|
args.out.mkdir(parents=True, exist_ok=True)
|
|
(args.out / "baseline.json").write_text(json.dumps(report, indent=1, sort_keys=True), encoding="utf-8")
|
|
write_markdown(report, args.out / "BASELINE.md")
|
|
print(f"== wrote {args.out / 'baseline.json'} and {args.out / 'BASELINE.md'}", flush=True)
|
|
return 0
|
|
|
|
|
|
if __name__ == "__main__":
|
|
raise SystemExit(main())
|