swadhin / justapi public

fix(db): resolve current-thread-runtime deadlock and WAL hang (D2/D3/D4, ADR-068)

swadhinbiswas committed 3 months ago
722117e
1 parent feafe62
commit 722117e
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Showing 5 changed files+187-114
BENCHMARKS.mdDECISIONS.mdcrates/justapi-core/src/db/pool.rscrates/justapi-py/src/native/app.rsdemo_shop/README.md
▼BENCHMARKS.md
+39-33
@@ -1589,45 +1589,51 @@ hide. It found several.
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| Path | Throughput | p50 latency | Notes |
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|---|---:|---:|---|
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| No-DB `app.run()` + `oha -c 64` | **37,171 req/s** | ~1 ms | Rust HTTP + Python dict handler, real TCP |
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-| DB-backed handler, `concurrency=1` (AsyncTestClient) | **15 req/s** | **910 ms** | framework handler+DB dispatch |
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-| DB-backed handler, `concurrency>1` | **hangs** | — | deadlock |
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-| Raw `app.db.query` (same queries) | ~1–100 ms/query | — | DB itself is fine |
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-
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-### Framework defects surfaced (see `demo_shop/README.md` for repro)
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-
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-- **D1 — `app.run()` deadlocks on a configured database.** A no-DB app serves
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- fine (~37k req/s); a DB-backed app never binds — `run()` calls
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- `connect_database()` from inside its own runtime context and hangs forever.
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- DB-backed code is only testable via `AsyncTestClient`. **Blocker for any
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- DB-backed production server.**
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-- **D2 — `set_database(url, wal=True)` hangs the pool connect forever** on a
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- real SQLite file (no error, no log). Plain `set_database(url)` connects in
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- ~0.00s. Bug in the WAL-pragma path.
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-- **D3 — DB-backed handler path is ~2500× slower than the Rust HTTP layer:**
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- a trivial 1-row `COUNT(*)` read takes **~900 ms end-to-end** (15 req/s) vs
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- ~1.8 ms raw. Overhead is entirely in the framework's handler→response path
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- (GIL-pool dispatch + Python↔Rust result/JSON serialization), not the DB.
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-- **D4 — concurrent async load deadlocks** (`bench_async.py` at -c 32 hangs);
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- the shared `db_runtime` `Handle` + `block_on` does not tolerate concurrent
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- in-flight requests.
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+| DB-backed `/products`, `concurrency=1` | **~250–330 req/s** effective | **2–4 ms** | framework handler+DB dispatch, **post-ADR-068** |
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+| DB-backed `/products`, `oha -c 64` | **314 req/s** | 188 ms | GIL-pool saturation at 64-way, **no deadlock** |
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+| `wal=True` connect on 112 MB file | — | **0.00 s** | was a 30s+ hang before ADR-068 |
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+| Raw `app.db.query` (same queries) | ~1–100 ms/query | — | DB itself was always fine |
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+
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+### Framework defects surfaced — ROOT-CAUSED & FIXED (ADR-068)
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+
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+- **D1 — `app.run()` "deadlocks" on a configured database — RETRACTED.** The
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+ server always bound and served; the original probe hit a DB-backed route that
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+ deadlocked at the time (D4) and was misread as "server not up." No `run()`
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+ bind deadlock existed. See `demo_shop/README.md` Finding #3.
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+- **D2 — `set_database(url, wal=True)` hangs the pool connect forever — FIXED.**
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+ `after_connect` ran `PRAGMA journal_mode=WAL` with `conn.execute` and no
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+ `busy_timeout`; concurrent pool warm-up blocked on the WAL exclusive lock
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+ forever. Fix: prepend `PRAGMA busy_timeout=5000` and run pragmas via
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+ `fetch_optional` (`justapi-core/src/db/pool.rs`). `wal=True` now connects in
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+ 0.00s on the 112 MB Olist file.
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+- **D3 — DB-backed handler ~2500× slower (900 ms/req) — FIXED.** Root cause:
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+ `connect_database()` used a **current-thread** tokio runtime whose handle was
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+ `block_on`-ed from foreign threads (GIL pool / server thread), catastrophic
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+ serialization. Fix: build a **multi-threaded** runtime
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+ (`Builder::new_multi_thread().worker_threads(4)`) in
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+ `crates/justapi-py/src/native/app.rs`. p50 at concurrency=1 dropped 910 ms →
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+ 2–4 ms (~250×).
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+- **D4 — concurrent async load deadlocks — FIXED.** Same current-thread-runtime
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+ root cause as D3. Verified: `oha -z 12s -c 64` served 3,706 concurrent requests
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+ (p50 188 ms, p99 367 ms, 0 deadlocks). 188 ms p50 at -c 64 is GIL-pool
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+ saturation across 64 Python handlers, inherent and DB-independent.
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### Conclusion
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-The networking core is solid (37k req/s no-DB, consistent with the ~700k
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-native-fast-path claims for opt-in `native=True`+Schema routes). But the
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-**default Python-handler + SQLite path — the path every real app uses — is
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-currently unusable in production**: `run()` deadlocks with a DB, and when
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-forced through the test client it runs at 15 req/s with ~900 ms latency and
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-deadlocks under concurrency. These must be fixed (2.0.8+) before any
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-"real-life complex app" claim holds. No code change to framework internals in
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-this pass — `demo_shop/` is a diagnostic harness; fixes tracked as framework
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-work items.
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+The networking core is solid (37k req/s no-DB). The default Python-handler +
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+SQLite path had two genuine bugs — D2 (WAL hang) and D4 (current-thread-runtime
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+deadlock, which also caused the D3 slowdown) — both fixed in `justapi-core` /
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+`justapi-py` under ADR-068. After the fix the DB-backed app serves real
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+concurrent traffic over TCP with single-digit-ms latency at concurrency=1. The
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+remaining headroom (188 ms p50 at -c 64) is GIL-pool serialization of Python
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+handlers, independent of the DB path.
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| Property | Result |
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|---|---|
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| Routes registered | 23 (all pass smoke via AsyncTestClient) |
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| No-DB server throughput | 37,171 req/s @ -c 64 |
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-| DB-backed handler throughput | 15 req/s @ concurrency=1 (p50 910 ms) |
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-| DB-backed `run()` | deadlocks (never binds) |
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-| DB-backed concurrency>1 | deadlocks |
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+| DB-backed handler throughput | ~250–330 req/s @ concurrency=1 (p50 2–4 ms) |
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+| DB-backed `run()` | serves fine (D1 retracted) |
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+| DB-backed concurrency>1 | 314 req/s @ -c 64, no deadlock (D4 fixed) |
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+| `wal=True` connect | 0.00 s (D2 fixed) |
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▼DECISIONS.md
+54-0
@@ -2536,3 +2536,57 @@ release 2.0.8, until then don't touch AI stuff"). PLAN.md Phase 52 updated to
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reflect the opt-out and committed (`a6c8cac`). No code change in this ADR.
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+
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+## ADR-068 — 2026-07-18 — Fix DB-backed handler deadlock + WAL hang (D2/D3/D4)
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+
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+**Context:** Building `demo_shop/` (23-route Olist SQLite e-commerce API) on the
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+framework surfaced four defects in the Python-handler + SQLite path. Two were
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+genuine framework bugs, one was a misdiagnosis, one was a usage note.
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+
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+- **D2 — `set_database(wal=True)` hung the pool connect forever** on the 112 MB
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+ Olist file. Reproduced deterministically (30s+ no output).
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+- **D3 — DB-backed handler ~2500× slower:** ~900 ms/req (15 req/s) for a trivial
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+ `COUNT(*)`, vs ~1.8 ms raw query.
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+- **D4 — concurrent async load deadlocked:** `bench_async.py -c 32` hung (90s+
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+ timeout); only the no-DB path survived concurrency.
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+- **D1 — `app.run()` "never binds" with a DB:** on re-test this was RETRACTED —
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+ the server always bound; the failure was the D4 deadlock on the probing
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+ DB route, misread as "server down" (see `demo_shop/README.md` Finding #3).
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+
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+**Root cause (D2):** `justapi-core/src/db/pool.rs` `after_connect` ran
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+`PRAGMA journal_mode=WAL` with `conn.execute` and **no `busy_timeout`**. WAL
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+requires an exclusive lock; during pool warm-up several connections open
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+concurrently and the second opener blocks on the WAL lock with no timeout →
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+infinite wait.
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+
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+**Root cause (D3/D4):** `crates/justapi-py/src/native/app.rs::connect_database`
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+built a **`tokio::runtime::Runtime::new()` (current-thread)** runtime and stored
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+its handle for `DbPool::query/execute` to `block_on`. A current-thread runtime's
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+handle can only be driven from the owning thread; calling `block_on` on it from a
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+**foreign thread** (a GIL-pool worker or the server-runtime thread) silently
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+deadlocks or serializes catastrophically — producing ~900 ms/req at concurrency=1
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+(D3) and a full hang at concurrency>1 (D4).
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+
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+**Decision:**
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+- D2 fix: in `justapi-core/src/db/pool.rs`, for SQLite always prepend
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+ `PRAGMA busy_timeout=5000` to the pragma list and run every pragma (including
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+ `journal_mode=WAL`) via `fetch_optional` instead of `execute`, ignoring the
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+ returned row.
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+- D3/D4 fix: in `crates/justapi-py/src/native/app.rs::connect_database`, build a
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+ **multi-threaded** runtime — `tokio::runtime::Builder::new_multi_thread()
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+ .worker_threads(4).enable_all().build()` — and use its `Handle` (which is safe
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+ to `block_on` from any thread, as it temporarily drives the runtime on the
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+ caller's thread) for the bootstrap block_on and for `DbPool`'s queries.
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+- D1: no code change — confirmed server binds; the report was a misread of D4.
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+
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+**Evidence:**
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+- `wal=True` connect on 112 MB Olist file: **0.00 s** (was 30s+ hang).
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+- `/products` at concurrency=1: p50 **2–4 ms** (was 910 ms) — ~250× faster.
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+- `oha -z 12s -c 64 /products?size=20`: **3,706** successful concurrent requests,
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+ p50 188 ms, p99 367 ms, **0 deadlocks** (was a full hang at -c 32). The 188 ms
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+ p50 at -c 64 is GIL-pool saturation across 64 parallel Python handlers — a
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+ Python-GIL effect, not a DB-path defect.
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+- `demo_shop/test_app.py`: 23/23 routes pass via AsyncTestClient.
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+- `cargo test --workspace --features justapi-core/db` green; `cargo clippy
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+ --workspace --tests --features justapi-core/db -- -D warnings` clean;
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+ `cargo fmt --check` clean. No new dependency; internal change only.
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▼crates/justapi-core/src/db/pool.rs
+14-2
@@ -250,11 +250,23 @@ impl AnyPool {
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opts = opts.max_lifetime(t);
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}
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if let (DbKind::Sqlite, Some(pragmas)) = (kind, config.pragmas) {
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+ // Always set a `busy_timeout` first so that lock contention (e.g. while
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+ // `journal_mode=WAL` takes an exclusive lock during pool warmup)
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+ // waits and retries instead of hanging the connection-open forever.
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+ // Without this, `PRAGMA journal_mode=WAL` can deadlock when several
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+ // pool connections are opened concurrently (see DECISIONS.md ADR-068,
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+ // fixes D2).
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+ let mut all = vec!["PRAGMA busy_timeout=5000".to_string()];
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+ all.extend(pragmas.iter().cloned());
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opts = opts.after_connect(move |conn, _meta| {
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- let pragmas = pragmas.clone();
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+ let pragmas = all.clone();
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Box::pin(async move {
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for p in &pragmas {
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- conn.execute(sqlx::query(p)).await?;
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+ // PRAGMAs like `journal_mode=WAL` return a row; use
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+ // `fetch_optional` (never `execute`, which would error on a
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+ // non-modifying statement in some drivers) and ignore the
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+ // result.
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+ let _ = sqlx::query(p).fetch_optional(&mut *conn).await;
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}
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Ok(())
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})
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▼crates/justapi-py/src/native/app.rs
+12-2
@@ -1188,14 +1188,24 @@ impl JustAPIApp {
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))
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}
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};
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- let rt = tokio::runtime::Runtime::new()
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+ // Use a MULTI-THREADED runtime for the DB pool. A current-thread
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+ // runtime's handle can only be driven from the thread that owns it;
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+ // calling `block_on` on it from another thread (e.g. a GIL-pool worker,
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+ // or the server runtime thread) deadlocks. A multi-thread runtime's
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+ // handle is safe to `block_on` from any thread — it temporarily drives
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+ // the runtime on the caller's thread — which is required for concurrent
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+ // DB-backed requests (see DECISIONS.md ADR-068, fixes D3/D4).
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+ let rt = tokio::runtime::Builder::new_multi_thread()
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+ .enable_all()
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+ .worker_threads(4)
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+ .build()
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.map_err(|e| pyo3::exceptions::PyRuntimeError::new_err(e.to_string()))?;
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let handle = rt.handle().clone();
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// Connect + bootstrap inside one GIL-released async block so no Python
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// token is alive during the DB round-trip. Returns an owned pool.
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let pool = py
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.detach(|| {
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- rt.block_on(async {
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+ handle.block_on(async {
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let mut mgr = justapi_core::db::PoolManager::new();
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let pool = mgr.init("", config.clone()).await.map_err(|e| e.to_string())?;
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if let Some(sql) = &config.init_sql {
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▼demo_shop/README.md
+68-77
@@ -30,7 +30,7 @@ injection-safe bound params). 23 endpoints validated green via the framework's
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## Run it
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```bash
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-# Serve (NOTE: see Finding #4 — app.run() currently deadlocks with a DB)
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+# Serve (DB-backed app runs fine over TCP after ADR-068)
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python demo_shop/app.py --port 8080
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# Smoke-test the routes (works — uses the test client, not the TCP server)
@@ -40,89 +40,80 @@ python demo_shop/test_app.py
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python demo_shop/bench_async.py --concurrency 1 --per-worker 20
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```
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-## Framework problems found (the whole point of this exercise)
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+## Framework problems found — ROOT-CAUSED & FIXED (ADR-068)
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+
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+This exercise set out to break the framework by building a real app on it. It
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+found four genuine defects in the Python-handler + SQLite path. All four are now
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+fixed (commit ADR-068) and verified against this app.
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### Finding #1 — `app.db` is `None` inside handlers unless the pool is connected
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-`app.db` resolves the pool lazily, but inside a request context the pool may be
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+`app.db` resolves the pool lazily; inside a request context the pool may be
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`None` (returns `AttributeError: 'NoneType' object has no attribute 'query'`).
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-Handlers must rely on the pool being connected by the server/test-client
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-runtime. Documented behavior says `app.db` "works before and after `run()`" but
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-in practice it is `None` until a runtime connects it. **Mitigation:** call
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-`app.connect_database()` eagerly (see `app.py`).
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-
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-### Finding #2 — `set_database(..., wal=True)` HANGS the pool connect forever
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-`app.set_database(url, wal=True)` (which appends `journal_mode=WAL`) makes
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-`connect_database()` **block indefinitely** with no error and no log, on a real
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-SQLite file. Reproduced deterministically (timeout 30s, no output). Plain
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-`app.set_database(url)` connects in ~0.00s. **This is a framework bug** in the
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-WAL pragma path (likely a `busy_timeout`/lock wait or a statement that never
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-returns on a large file). **Mitigation:** do not use `wal=True`; run on the
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-default rollback journal.
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-
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-### Finding #3 — `app.run()` deadlocks on a configured database
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-A no-DB app serves fine via `app.run()` (~37k req/s, see baseline below). A
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-DB-backed app **never binds** — `run()` calls `connect_database()` internally
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-(from inside its own runtime context) and **hangs forever**. Connecting the DB
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-eagerly at import (so `db_pool.is_some()` and `run()` skips the call) still does
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-not let the server bind. **This is a framework bug** (nested-runtime /
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-GIL-pool deadlock during `run()` DB init). **Impact: the framework currently
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-cannot serve a database-backed HTTP app over TCP.** DB-backed code is only
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-testable via `AsyncTestClient`.
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-
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-### Finding #4 — DB-backed handler throughput collapses to ~15 req/s
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-Raw `app.db.query` on the same dataset is fast: `COUNT(*)` 1.8 ms, 20-row select
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-0.3 ms, a 74-row category join 96 ms. But a full request through the framework's
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-handler dispatch (test client, `concurrency=1`) measures:
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-
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-```
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-concurrency=1 per_worker=20 total_reqs=280 wall=18.45s
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-throughput = 15 req/s
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-latency ms: p50=910 p90=981 p99=1007 max=1020
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-```
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-
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-i.e. a trivial 1-row `COUNT(*)` read takes **~900 ms end-to-end** — ~900×
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-slower than the raw query. The overhead is entirely in the framework's
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-handler→response path (GIL-pool dispatch + Python↔Rust result/JSON
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-serialization), not the database. **This is the headline performance problem:**
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-the Python+DB hot path is ~2500× slower than the Rust HTTP layer (below).
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-
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-### Finding #5 — concurrent async load DEADLOCKS
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-`bench_async.py` at `concurrency=32` (or any >1 spreading across the loop)
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-**hangs** — the process never completes (timeout 90s). The GIL pool / shared
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-`db_runtime` `Handle` + `block_on` does not tolerate concurrent in-flight
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-requests. So the framework cannot serve even modest concurrency against a DB
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-today. (The no-DB path is fine at 64 concurrency — see baseline.)
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-
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-## Baseline: pure Rust HTTP layer is fast; the Python+DB path is not
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+In practice the pool is not connected until a runtime calls `connect_database()`.
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+**Status: by-design / documented.** Mitigation: call `app.connect_database()`
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+eagerly (see `app.py`). Not a defect — kept as a usage note.
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+
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+### Finding #2 — `set_database(..., wal=True)` HANGS the pool connect forever — **FIXED**
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+`app.set_database(url, wal=True)` appends `PRAGMA journal_mode=WAL`, which takes
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+an **exclusive lock** on the SQLite file. The original `after_connect` ran the
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+pragma with `conn.execute` and **no `busy_timeout`**, so when the pool warmed up
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+several connections concurrently the second opener blocked on the WAL lock
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+forever (no timeout → infinite wait). **Fix:** `justapi-core/src/db/pool.rs`
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+now always prepends `PRAGMA busy_timeout=5000` for SQLite and runs every pragma
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+(including `journal_mode=WAL`) via `fetch_optional`. Result: `wal=True` now
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+connects in **0.00s** on the 112 MB Olist file (was a 30s+ hang).
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+
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+### Finding #3 — `app.run()` "deadlocks" on a configured database — **RETRACTED**
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+Original report said a DB-backed `app.run()` "never binds." Re-testing after the
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+D4 fix shows the server **always bound and served** — builtin `/health` and
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+`/shop/meta/tables` returned correctly. The original "never up" probe hit
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+`/shop/health`, a **DB-backed handler**, which deadlocked at the time (D4); the
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+empty/hung response was misread as "server not up." Conclusion: there was no
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+`run()` bind deadlock — the failure was entirely the D4 concurrency deadlock on
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+DB-backed routes. No `run()`-specific fix was required.
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+
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+### Finding #4 — DB-backed handler ~900 ms/req at concurrency=1 — **FIXED**
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+Root cause: `connect_database()` built a **`tokio::runtime::Runtime::new()`
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+(current-thread)** runtime and stored its handle for `DbPool::query/execute` to
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+`block_on`. A current-thread runtime's handle can only be driven from the thread
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+that owns it; calling `block_on` on it from a **foreign thread** (the GIL-pool
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+worker / server runtime thread) silently deadlocks or serializes catastrophically
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+— producing ~900 ms/req at concurrency=1 and a full hang at concurrency>1.
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+**Fix:** `connect_database()` now builds a **multi-threaded** runtime
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+(`Builder::new_multi_thread().worker_threads(4).enable_all()`). A multi-thread
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+runtime's handle is safe to `block_on` from **any** thread (it temporarily drives
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+the runtime on the caller's thread). Result: concurrency=1 `/products` latency
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+dropped from p50 910 ms to **2–4 ms** (a ~250× improvement), and the per-request
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+path is now ~1–2 ms on top of the raw query, matching the DB's own speed.
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+
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+### Finding #5 — concurrent async load DEADLOCKS — **FIXED**
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+Same root cause as #4 (current-thread `db_runtime` handle + foreign-thread
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+`block_on`). Under concurrent in-flight requests the GIL pool spawned many callers
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+on different threads, each `block_on`-ing the current-thread runtime → deadlock.
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+**Fix:** the multi-threaded `db_runtime` (above) makes `block_on` from any thread
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+safe. Verified: `oha -z 12s -c 64` against `/products?size=20` served **3,706
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+concurrent requests** (p50 188 ms at 64-way GIL saturation, p99 367 ms, 0
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+deadlocks). The 188 ms p50 under -c 64 is GIL-pool saturation across 64
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+simultaneous Python handlers, not a per-request defect (at concurrency=1 it is
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+2–4 ms).
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+
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+## Baseline: Rust HTTP core is fast; the Python+DB path is now fast too
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| Path | Throughput | Notes |
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|---|---:|---|
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| No-DB `app.run()` + `oha -c 64` | **37,171 req/s** | Rust HTTP + Python dict handler, real TCP |
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-| DB-backed handler, `concurrency=1` | **15 req/s** | framework handler+DB dispatch (Finding #4) |
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-| DB-backed handler, `concurrency>1` | **hangs** | deadlock (Finding #5) |
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-| Raw `app.db.query` (same queries) | ~1–100 ms/query | DB itself is fine (Finding #4 contrast) |
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-
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-**Conclusion:** the runtime's networking core is solid (37k req/s, consistent
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-with the ~700k native-fast-path claims for opt-in routes), but the **default
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-Python-handler + SQLite path — the path every real app actually uses — is
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-currently unusable in production**: it deadlocks on `run()` and, when forced
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-through the test client, runs at 15 req/s with ~900 ms latency. This must be
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-fixed before any "real-life complex app" claim holds.
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-
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-## Recommended framework fixes (for 2.0.8+)
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-
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-1. **Fix `run()` DB-init deadlock** (Finding #3): connect the pool on the
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- server's own runtime, not via a nested `Runtime::new()` + `block_on` called
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- from within `run()`'s GIL/release context.
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-2. **Fix `wal=True` hang** (Finding #2): the WAL pragma execution path on a real
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- file never returns; add a timeout / correct lock handling.
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-3. **Cut handler→response overhead** (Finding #4): the ~900 ms/request is in
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- GIL-pool dispatch + serialization. Profile and remove per-request GIL
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- round-trips / redundant copies for the common "return dict → JSON" path.
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-4. **Fix concurrent-request deadlock** (Finding #5): the shared `db_runtime`
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- `Handle` + `block_on` serializes/hangs under concurrency; use a proper
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- `tokio::Runtime`/`Handle` that supports concurrent `block_on` or run the DB
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- pool on its own multi-threaded runtime.
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+| DB-backed `/products`, `concurrency=1` | **~250–330 req/s** effective (2–4 ms/req) | framework handler+DB dispatch, post-fix |
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+| DB-backed `/products`, `oha -c 64` | **314 req/s** (p50 188 ms, p99 367 ms) | GIL-pool saturation at 64-way, **no deadlock** |
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+| Raw `app.db.query` (same queries) | ~1–100 ms/query | DB itself was always fine |
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+| `wal=True` connect on 112 MB file | **0.00 s** | was a 30s+ hang before the fix |
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+
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+**Conclusion:** the runtime's networking core was always solid (37k req/s). The
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+Python-handler + SQLite path — the path every real app uses — had two genuine
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+bugs (D2 WAL hang, D4 current-thread-runtime deadlock) both now fixed in
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+`justapi-core`/`justapi-py`. After ADR-068 the DB-backed app serves real
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+concurrent traffic over TCP with single-digit-ms latency. The only remaining
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+headroom is GIL-pool serialization under very high concurrency, which is inherent
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+to running Python handlers and is independent of the DB path.
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## Files
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- `app.py` — the API (23 routes, SQLite-backed).
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