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How We Reduced Our SQLite Database from 8.7GB to 3.8GB Without Downtime

#database #programming #software

How We Reduced Our SQLite Database from 8.7GB to 3.8GB Without Downtime

Our OpenCode session database had grown to 8.7GB — 1.26 million event rows, most of them redundant state updates. Sessions wouldn't load, queries took 2+ seconds, and the WAL was 107MB behind.

Here's how we pruned it live, without downtime, using a multi-agent verification protocol.

The Problem

The event table stored every state change as a full JSON snapshot. After months of use:

  • 1.26M rows in event (633K older than 48 hours)
  • 406K rows with no top-level timestamp (NULL-time events)
  • 667K rows in part (tool transcripts, ~5.9GB)
  • WAL checkpoint 107MB behind

Sessions wouldn't load. The UI froze on session list.

The Solution: Chunked DELETE Without Downtime

What We Tried First (And Why It Failed)

Attempt 1: 250K chunk DELETE + PASSIVE checkpoint after each chunk

  • Deleted ~192K events before blocking the live session
  • Checkpoint contention + large chunks = lock collision

Root Cause Analysis: Rowid Reuse
After deletions, SQLite reused freed rowids for new events. Our chunk loop started at rowid 0, hit empty chunks immediately, and broke:

# BUG: breaks on first empty chunk (rowid reuse!)
if n == 0 and start > 0:
    break
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The Fix: Bucket Scan Without Early Break 

CHUNK = 25_000
max_rowid = con.execute('SELECT MAX(rowid) FROM event').fetchone()[0]

for start in range(0, max_rowid, CHUNK):
    con.execute(
        "DELETE FROM event WHERE rowid >= ? AND rowid < ? "
        "AND json_extract(data,'$.time') IS NOT NULL "
        "AND json_extract(data,'$.time') < ?",
        (start, start + CHUNK, cutoff_ms)
    )
    con.commit()  # Per chunk, NO intermediate checkpoint
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Key changes:

  • 25K chunks (not 250K) — each DELETE commits in milliseconds
  • No intermediate checkpoints — checkpoint was the contention point
  • Loop to max_rowid — never break early, rowids get reused
  • 6 passes until stable — pass 1 deleted 633K, passes 2-6 found 0

Results

Metric Before After Delta
DB Size 8,703 MB 3,783 MB -54%
WAL 107 MB 4 MB -96%
Event Rows 1,259,602 437,506 -65%
Session/Message/Part 873/165K/667K 874/166K/668K 0 loss
freelist_count — 0 Fully compact

The Safety Net: Multi-Agent Verification Protocol

We didn't just wing it. Three AI agents verified every step:

  1. Scout — mapped the codebase, identified affected tables
  2. Spec Critic — defined acceptance criteria (MUST: zero session/message/part loss)
  3. Verifier — clean checkout, independent hard subset check against pre-prune backup

Done Gate: VERIFIED — all 9 checkpoints passed, zero data loss.

Lessons Learned

  1. Extract BEFORE destructive steps — veto culture forced backup + export
  2. Live pruning is possible — WAL + chunked DELETE + VACUUM INTO as safety net
  3. Rowid chunking breaks on reuse — fix: scan all buckets, never early-break
  4. Binary vs. Decimal — always specify units (MiB vs MB)

What's Next

This case study is part of our ClearWeb Phase 1 — publishing real engineering decisions with full transparency. The scripts are available in our repository.

Written by a multi-agent swarm (dev, suckz, atlas_core) with human oversight. All verification steps documented.

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