Sqlite Wal

SQLite Operational Guide

Concise operational pointers for deep SQLite tuning, WAL diagnosis, and multi-process correctness.

Assumes you already know SQL and basic SQLite usage (.dump, .schema, EXPLAIN QUERY PLAN). This skill covers the operational layer — WAL internals, fsync semantics, lock states, pragma defaults, FTS5/JSON1 quirks, network-FS hazards.

When to use

Load when the question is about:

• WAL mechanics, checkpointing, -wal/-shm file behavior
• SQLITE_BUSY / SQLITE_BUSY_SNAPSHOT diagnosis, busy_timeout tuning
• Multi-process or multi-host SQLite (and why most attempts corrupt)
• Pragma-level perf tuning (synchronous, cache_size, mmap_size, temp_store)
• FTS5 index design (tokenizers, contentless tables, vocab tables)
• JSON1 indexing via generated columns; JSONB choice (3.45+)
• Backup correctness (VACUUM INTO, backup API, sqlite3_rsync)
• Replication patterns: Litestream / LiteFS / rqlite tradeoffs

Do NOT load for: ordinary SELECT/INSERT writing, schema-first design, "what index should I add", basic CREATE TABLE syntax — those don't need this skill.

WAL mechanics

• Enable: PRAGMA journal_mode=WAL returns wal on success. Persists across connections in the file header — unlike every other journal mode. To revert: PRAGMA journal_mode=DELETE (default).
• Three files: name.db, name.db-wal (append-only log of new page versions), name.db-shm (mmap'd wal-index, ephemeral). All three are required while connections are open. Lost -shm is recoverable on next open.
• Concurrency model: many readers + one writer concurrent. Writers append to WAL; readers see a snapshot at txn start (their "end mark") and consult WAL pages newer than the main DB but ≤ their end mark. Rollback journal mode serializes everything; WAL does not.
• Checkpoint = fold WAL pages back into main DB. Not the same as commit. Commit just appends a frame to -wal.
• -shm is mmap-only — never required to be on disk. If the FS doesn't support shared mmap (most network FS), WAL fails. Workaround: PRAGMA locking_mode=EXCLUSIVE before first WAL access — -shm is then never created, but the connection holds the file exclusively.
• Format version bump: opening a WAL DB with an SQLite older than 3.7.0 fails — WAL bumps the file-format version from 1 to 2.

Checkpointing

• Auto-checkpoint default: PRAGMA wal_autocheckpoint=1000 (pages, ~4 MB at the default 4096-byte page size). Triggered at end of any commit that grows WAL ≥ N pages. Setting 0 disables.
• Manual modes: PRAGMA wal_checkpoint(MODE):
  • PASSIVE (default): does whatever it can without blocking; may not finish if readers/writers are active.
  • FULL: waits for writers, then checkpoints all committed frames; may block briefly.
  • RESTART: like FULL, then waits for readers past the checkpoint to finish; next writer starts at WAL offset 0 (file size unchanged).
  • TRUNCATE: like RESTART, then truncates -wal to zero bytes.
• Checkpoint starvation: a long-running read txn pins its end mark, blocking the checkpointer from advancing past unread frames. -wal grows unbounded. Symptom: -wal >> .db. Fix: kill the long reader; use PRAGMA journal_size_limit=N (default -1 = no limit) to bound the file post-checkpoint (does not prevent growth between checkpoints).
• Litestream/LiteFS pattern: app sets PRAGMA wal_autocheckpoint=0 and lets the replicator drive checkpoints, so frames aren't dropped before being shipped.
• WAL-reset bug (3.7.0–3.51.2): two concurrent connections checkpointing/writing could corrupt. Fixed in 3.51.3 / backported 3.50.7, 3.44.6. Verify version on production.

Synchronous and durability

• Defaults: PRAGMA synchronous=FULL (2) for rollback journal. WAL mode's effective default depends on the binary; always set explicitly.
• Recommended for WAL: PRAGMA synchronous=NORMAL (1). fsync's -wal only at checkpoint boundaries (not every commit). Power-loss safe because WAL is append-only and torn appended frames are detected and discarded on recovery. Throughput: typically 2–10× over FULL.
• FULL (2) under WAL: fsync after every commit and at checkpoint. Worst-case durability, lowest throughput. Use only if you cannot tolerate losing the last few committed transactions on power loss.
• OFF (0): no fsync ever. Unsafe under power loss — both rollback and WAL modes can corrupt. Acceptable only for ephemeral/derived data.
• macOS specific: stock fsync() does NOT flush the disk write cache. Set PRAGMA fullfsync=1 (default OFF, macOS-only) to use F_FULLFSYNC. Cost: large; benefit: actual durability on consumer SSDs.
• Linux ext4: default fsync is sufficient when the FS is mounted with barrier=1 (default since ~2010). USB sticks and consumer SD cards routinely lie about sync — corruption on power loss is the storage's fault, not SQLite's.
• Crash recovery: hot WAL is detected on next open; uncommitted frames are discarded. Do NOT delete -wal or -shm after a crash — it destroys committed-but-not-checkpointed transactions. Safe deletion requires a clean shutdown (last connection closes, checkpoint runs).

Locking and concurrency

• Rollback-journal lock states (UNLOCKED → SHARED → RESERVED → PENDING → EXCLUSIVE): WAL skips most of these. WAL writers acquire a write lock on a byte range in -shm; readers acquire a per-reader byte-range lock recording their end mark. Many readers + one writer truly concurrent.
• SQLITE_BUSY (5): another connection holds an incompatible lock right now. Resolved by waiting/retrying.
• SQLITE_BUSY_SNAPSHOT (517): WAL-specific. A read txn began with end-mark E; another connection wrote and committed beyond E; this connection now tries to upgrade its read txn to a write txn. Cannot proceed without restarting the txn — busy_timeout does not retry this. Fix: re-issue BEGIN IMMEDIATE and replay.
• PRAGMA busy_timeout=N (ms). Default 0 (return BUSY instantly). Production minimum: 5000. Implementation: short polling sleeps internally, retries on SQLITE_BUSY only — not on BUSY_SNAPSHOT.
• BEGIN modes:
  • BEGIN / BEGIN DEFERRED (default): acquires no lock until first statement. Read becomes write on first DML — that upgrade is where BUSY_SNAPSHOT happens.
  • BEGIN IMMEDIATE: acquires the write lock at BEGIN. If another writer is active, fails with BUSY now (recoverable via busy_timeout). Use this for any txn that will write.
  • BEGIN EXCLUSIVE: in WAL mode, identical to IMMEDIATE. In rollback mode, blocks readers too.
• Single-writer rule: SQLite serializes writes per database file. Multi-process writers ⇒ funnel writes through a single process or accept BUSY/SNAPSHOT retry storms. Keep write txns short (sub-second).
• Threading: SQLITE_THREADSAFE defaults to 1 (serialized) when compiled without flags. Mode 2 (multi-thread) is safe across threads only if each connection/prepared statement is touched by one thread at a time. Prepared statements are NOT thread-safe regardless of mode.

Network filesystems = corruption

• NFS, SMB, FUSE, sshfs, GCS Fuse, S3FS, EFS: do not host an active SQLite DB on these. POSIX advisory locking is buggy or unimplemented; -shm mmap does not synchronize across hosts; fsync() semantics are unreliable. Multi-host writes corrupt within minutes.
• Single-host on NFS: marginally safer with PRAGMA locking_mode=EXCLUSIVE (avoids -shm), but fsync reliability is still the FS's problem. Treat as best-effort, never authoritative.
• Hard/symlinks: opening the same DB through two distinct names yields two distinct -wal/-shm pairs ⇒ corruption.
• Backup-while-open: cp / rsync of an open DB captures inconsistent state. Always use VACUUM INTO, the backup API, or sqlite3_rsync (3.47+).

Pragma tuning

• cache_size: default -2000 (negative = KiB ⇒ 2 MB). Positive = pages. Production: -200000 (200 MB) is reasonable for read-heavy workloads. Per-connection.
• mmap_size: default 0 (off). Bytes of DB file the OS will mmap into the process for reads. Reduces syscalls; bounded per connection. Set to e.g. 268435456 (256 MB) on systems with the address space. Caveat: a stray pointer write into mmap'd region corrupts the DB.
• temp_store: default 0 (compile-time SQLITE_TEMP_STORE). Set 2 (MEMORY) to keep temp tables / indexes / sort scratch in RAM — large win for complex queries.
• page_size: default 4096 (since 3.12.0, 2016). Must be set before the first write to the DB; changing later requires VACUUM to rewrite. Powers of two 512–65536. 4096 is correct for nearly all workloads; 8192 occasionally helps for blob-heavy DBs.
• foreign_keys: default OFF (per-connection!) since 3.6.19. Re-enable on every new connection: PRAGMA foreign_keys=ON.
• recursive_triggers: default OFF. Triggers fire per-row; without this pragma, a trigger that modifies the same table will not re-fire.
• Production opening sequence (after every sqlite3_open):

  PRAGMA journal_mode=WAL;
  PRAGMA synchronous=NORMAL;
  PRAGMA busy_timeout=5000;
  PRAGMA cache_size=-200000;
  PRAGMA temp_store=MEMORY;
  PRAGMA foreign_keys=ON;
  PRAGMA mmap_size=268435456;  -- if address space allows
  

FTS5 quirks

• Content modes:
  • Default: full row stored in FTS5 shadow tables. Largest, simplest.
  • content=t1, content_rowid=a: external content. Index only; query joins back to source. Requires triggers (AFTER INSERT/UPDATE/DELETE) to keep in sync — easy to drift.
  • content='': contentless. Smallest. No UPDATE/DELETE (use INSERT INTO ft(ft, rowid) VALUES('delete', N)). 3.43+ adds contentless_delete=1 for true DELETE/INSERT-OR-REPLACE.
• Tokenizers:
  • unicode61 (default): case-insensitive, strips diacritics by default (remove_diacritics=1). Set 0 to preserve.
  • trigram: required for substring (%foo%) / LIKE / GLOB acceleration. 3-grams as tokens.
  • porter: English stemming wrapper (tokenize='porter unicode61').
  • ascii: ASCII-only fast path; non-ASCII becomes token chars.
• MATCH syntax: thr* (prefix), ^one (initial token), col : "phrase" (column filter), NEAR(a b, 5) (within N tokens, default 10), - (NOT). Implicit AND beats OR.
• detail knob (size vs query power):
  • full (default): rowid + col + offset. Supports NEAR, phrase, snippets.
  • column: rowid + col. ~50% smaller; no NEAR/phrase.
  • none: rowid only. ~80% smaller; no NEAR/phrase/column filter.
• Maintenance: INSERT INTO ft(ft) VALUES('optimize') merges all segments — slow; one-shot. INSERT INTO ft(ft, rank) VALUES('merge', N) does incremental work. automerge defaults to 4, crisismerge to 16.
• fts5vocab: virtual table exposing term/col/doc/cnt. Useful for token-distribution analysis and detecting tokenizer mismatches.

JSON and JSONB

• JSON1 is built-in since 3.38 (2022-02-22) — no extension load needed. Pre-3.38 builds need -DSQLITE_ENABLE_JSON1.
• -> and ->> operators since 3.38: data->'$.user' returns JSON text; data->>'$.user.name' returns SQL native (TEXT/INTEGER/REAL/NULL). Use ->> for WHERE clauses; -> for nested extraction.
• Indexed JSON queries require generated columns:

  ALTER TABLE events ADD COLUMN user_id TEXT
    GENERATED ALWAYS AS (data->>'$.user.id') VIRTUAL;
  CREATE INDEX events_user ON events(user_id);
  

  VIRTUAL (default) computes on read; STORED materializes on write. Index is identical either way; choose based on read/write ratio.
• JSONB (3.45+, 2024-01-15): binary on-disk format. jsonb_* functions return BLOB; storing JSONB columns avoids re-parsing on every read. Migration: rewrite columns with UPDATE t SET data = jsonb(data). Mixing text-JSON and JSONB columns is fine — accessor functions accept either.

Backups and replication

• VACUUM INTO 'file.db': atomic, online, transaction-consistent. Reads with shared lock; writes a fresh DB file with no -wal artifacts. Recommended default for app-level backups.
• Backup API (sqlite3_backup_init/step/finish): copies pages with concurrent writes allowed; restarts pages that change mid-copy. Library-level only.
• sqlite3_rsync (3.47+): rsync-style delta copy of an open DB. Designed for low-bandwidth replication.
• Plain file copy is safe ONLY when: journal_mode=DELETE and no connection is open. With WAL, copying just .db produces a stale snapshot — must copy .db + .db-wal + .db-shm atomically, which a plain cp cannot guarantee.
• Litestream: tails the WAL by reading -wal frames; ships them to S3/blob storage. Requires wal_autocheckpoint=0 so app-driven checkpoints don't truncate frames before shipment.
• LiteFS: FUSE FS that intercepts SQLite writes at the page level; multi-node primary-replica with per-DB leadership. Constraint: one writer per DB, replicas read-only.
• rqlite / dqlite: SQLite behind Raft. Each write is a Raft log entry; SQL is replayed on every node. Different correctness model — multi-master at the cost of write latency.

Common pitfalls

• INTEGER PRIMARY KEY IS the rowid — alias for the hidden 64-bit rowid. INT PRIMARY KEY is NOT (subtle: INT ≠ INTEGER in this one place). Inserting NULL auto-generates.
• Type affinity is hint-level in default tables — CREATE TABLE t(n INTEGER); INSERT INTO t VALUES('hello') succeeds. Use STRICT tables (3.37+, 2021-11-27) to enforce: CREATE TABLE t(n INTEGER) STRICT — only INT/INTEGER/REAL/TEXT/BLOB/ANY allowed; mismatches raise SQLITE_CONSTRAINT_DATATYPE.
• WITHOUT ROWID: requires explicit PRIMARY KEY (NOT NULL enforced). Single B-tree (no rowid index). Best for non-integer PKs and small rows (< 1/20 of page size, ~200 B at 4 KB pages). INTEGER PRIMARY KEY stops being a rowid alias here. No AUTOINCREMENT.
• ATTACH DATABASE: cross-DB queries work, but only the main DB's WAL handles atomicity. Multi-DB writes are NOT atomic across files in WAL mode — use rollback journal if cross-file atomicity is required.
• PRAGMA foreign_keys is per-connection: your migration tool may have it ON, your app OFF, your repl shell different again. Pin it on every open.
• Triggers: per-row, fire after each affected row's modification. recursive_triggers=OFF by default ⇒ a trigger that re-modifies the same table won't cascade. Surprising for ORM-style soft-delete patterns.
• Single-writer constraint: queue all writes through a dedicated process or a per-DB mutex in your app. Long write txns (> ~100 ms) starve readers via SNAPSHOT, even though "readers don't block writers." Break large writes into chunks.

Authoritative references

Official SQLite docs (sqlite.org):

• WAL mode
• PRAGMA reference
• File locking
• Transactions / BEGIN modes
• How To Corrupt An SQLite Database File
• Threading modes
• FTS5
• JSON1 / JSONB
• STRICT tables
• WITHOUT ROWID

Replication and operator deep-dives:

• Litestream tips — WAL settings, busy_timeout, autocheckpoint disable
• Fly.io: SQLite Internals: WAL — Ben Johnson on checkpoint dynamics
• LiteFS docs (fly.io/docs/litefs/) — FUSE-level page replication
• rqlite / dqlite project docs — Raft-over-SQLite tradeoffs

Guardrails

Before recommending a non-trivial pragma change or replication topology:

1. Quote the exact pragma name and its default value (per pragma.html).
2. Cite the official SQLite doc section.
3. Make the recommendation conditional on observed metrics — -wal size, SQLITE_BUSY count, txn duration.
4. Verify SQLite version (SELECT sqlite_version()). Many features (JSONB 3.45, STRICT 3.37, contentless_delete 3.43, sqlite3_rsync 3.47, WAL-reset fix 3.51.3) are version-gated.

Tuning without measurement, or porting a Postgres mental model wholesale to SQLite, is worse than defaults.