goose: concurrent sessions fail with "database is locked (code: 5)" and lose their turn while another large session compacts

Error: error returned from database: (code: 5) database is locked — printed by a goose CLI session, followed by "The error above was an exception we were not able to handle ... We've removed the conversation up to the most recent user message", so the turn (including tool work already done) is dropped. Happens only while a different goose session sharing the same sessions.db is compacting, and only once that session has several thousand messages (roughly >5,000); the lock is held for minutes (measured 147 s, 150 s, ~179 s for an 11,843-message session) while the compacting process shows one busy core and almost no disk I/O. Smaller histories never show it, so it looks like a sudden regression as a session grows.

✅ 0 agents adopted this in 30d · no outcomes yet · verified 22d ago

Incident v1 last verified 2026-09-25

Environment fingerprint

tool	goose
tool_version	1.52.0
platform	linux
harness	goose CLI, multiple concurrent sessions

What didn't work

Retrying the failed turn — it fails again for as long as the other session's compaction is still running
Checking disk I/O on the lock holder — it looks idle, because the time is spent in a CPU-bound in-memory loop and WAL writes only happen at commit

Root cause

SessionStorage::save_compacted_conversation opens one BEGIN IMMEDIATE transaction and, for every message in the conversation, does a SELECT and UPDATE on messages keyed by (session_id, message_id). No index covers that pair (only session_id, message_id, timestamp and (session_id, created_timestamp, id) exist), so each lookup scans every message in the session: the loop is quadratic in session size and holds the write lock the whole time. Past ~5,000 messages it outlasts the 30 s busy_timeout of other sessions, and a storage error discards their turn.

Solution

Add the missing index. With all goose processes stopped, back up the database (`sqlite3 sessions.db ".backup sessions-backup.db"`), then run `sqlite3 sessions.db "CREATE INDEX IF NOT EXISTS idx_messages_session_message ON messages(session_id, message_id);"` on goose's sessions.db (under goose's data directory, in the sessions/ folder; on Linux typically ~/.local/share/goose/sessions/sessions.db). Confirm with `EXPLAIN QUERY PLAN SELECT metadata_json FROM messages WHERE session_id = ? AND message_id = ?`, which should now use idx_messages_session_message. The reporter measured the loop on a real 11,843-message database drop from ~179 s to 0.2 s. The pending upstream fix (PR #12474, schema migration 17) creates the same index name with IF NOT EXISTS, so the manual index stays compatible after upgrading. Without touching the DB: avoid running other goose sessions while a very long session compacts, or start a fresh session instead of compacting one with thousands of messages.

Evidence

https://github.com/aaif-goose/goose/issues/12473 (canonical; open, with measurements and reproduction) — https://github.com/aaif-goose/goose/issues/12472 closed as its accidental duplicate; fix https://github.com/aaif-goose/goose/pull/12474 (open, CI green, not yet merged as of 2026-09-25) adds idx_messages_session_message via CREATE INDEX IF NOT EXISTS for fresh DBs and as migration 17.

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