fix(db,resolution): WAL file cap + cgroup cache credit + pool/parse sizing corrections from the instrumented kernel-scale runs (#1335)

Four §7a.1 instrumented-run findings, each measured:

1. File-size trigger + truncate-at-barrier: a fully-backfilled WAL still
   grows the FILE without bound — the writer only restarts at frame 0 when a
   commit finds zero reader marks, which the instrumented run showed never
   happens (file marched 361→721MB through two COMPLETE backfills; 22GB by
   phase end). backpressure() now also trips at 4× the soft cap on raw file
   size and TRUNCATEs at the parked barrier; the timer path truncates
   opportunistically after complete backfills. Dubbo peak: 251MB → 69MB at
   the same 16MB valve; dumps byte-identical under aggressive folding.

2. cgroup memory credit: memory.current counts reclaimable page cache — a
   post-parse container read 57MB of headroom on a 6GB box and silently
   disabled the pool. inactive_file is credited back (the docker-stats
   working-set convention); the same run now reads a sane 4.4GB budget.

3. Pool at 2 cores reversed: sequential resolution measured FASTER than
   pooled-6-on-2 at kernel scale (853s vs 1,150s), and synthesis is
   Amdahl-bound by cFnPtrEdges (306s of 358s) so pooling it bought nothing.
   cpuCap = min(ap−1, 6), no floor: ap=2 → sequential is the fast path.

4. Parse floor of 2: one parse worker at a 2-cpuset measured 34% slower
   (493s vs 369s) — main + store-worker don't fill the second core. Floor
   restores the baseline (373.5s measured).

Plus the observability §7a.1 burned three 25-minute cycles for: valve
armed/fire/timer-pass/heartbeat lines, checkpoint-worker error capture,
pool sizing decisions (incl. the disabled path), backpressure-hook
presence — all behind CODEGRAPH_SYNTH_TIMINGS / CODEGRAPH_WAL_VALVE_DEBUG.

Suite: 2,490 passed / 4 skipped (kernel required). Kernel-scale record
runs with this build follow in the migration plan §7a.1.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/db/index.ts

@@ -395,6 +395,7 @@ export class DatabaseConnection {
       const workerSource = `
         const { workerData, parentPort } = require('node:worker_threads');
         let row = null;
+        let err = null;
         try {
           const { DatabaseSync } = require('node:sqlite');
           const db = new DatabaseSync(workerData.dbPath);
@@ -402,10 +403,10 @@ export class DatabaseConnection {
           try {
             if (mode === 'TRUNCATE') db.exec('PRAGMA busy_timeout = 2000');
             row = db.prepare('PRAGMA wal_checkpoint(' + mode + ')').get();
-          } catch {}
+          } catch (e) { err = String(e && e.message || e); }
           try { db.close(); } catch {}
-        } catch {}
-        parentPort.postMessage({ row });
+        } catch (e) { err = err || String(e && e.message || e); }
+        parentPort.postMessage({ row, err });
       `;
       return await new Promise((resolve) => {
         let settled = false;
@@ -416,7 +417,13 @@ export class DatabaseConnection {
         };
         try {
           const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath, mode } });
-          worker.once('message', (m: { row?: Record<string, number> | null }) => { void worker.terminate(); finish(m?.row ?? null); });
+          worker.once('message', (m: { row?: Record<string, number> | null; err?: string | null }) => {
+            if (m?.err && process.env.CODEGRAPH_WAL_VALVE_DEBUG) {
+              console.error(`[wal-valve] checkpoint worker (${mode}): ${m.err}`);
+            }
+            void worker.terminate();
+            finish(m?.row ?? null);
+          });
           worker.once('error', () => { void worker.terminate(); finish(null); });
           worker.once('exit', () => finish(null));
         } catch {

src/db/wal-valve.ts

@@ -50,6 +50,8 @@ import type { DatabaseConnection } from './index';
 const DEFAULT_WAL_VALVE_MB = 256;
 /** Hard cap = this × soft threshold; past it the writer pauses for a full backfill. */
 const HARD_CAP_MULTIPLIER = 2;
+/** File cap = this × soft threshold; past it the barrier also TRUNCATEs the file. */
+const FILE_CAP_MULTIPLIER = 4;
 /** Passes attempted per writer pause before giving up (a pinned reader could stall forever). */
 const MAX_PAUSED_BACKFILL_PASSES = 20;
 /** How often the timer looks at the WAL file size. */
@@ -80,6 +82,7 @@ export class WalCheckpointValve {
   private sizeAtLastFullBackfill = 0;
   private readonly softBytes: number;
   private readonly hardBytes: number;
+  private readonly fileCapBytes: number;
 
   /**
    * Futility latch: consecutive backfill give-ups (a reader pinning the WAL)
@@ -102,6 +105,7 @@ export class WalCheckpointValve {
   ) {
     this.softBytes = softMb * 1024 * 1024;
     this.hardBytes = this.softBytes * HARD_CAP_MULTIPLIER;
+    this.fileCapBytes = this.softBytes * FILE_CAP_MULTIPLIER;
     // CODEGRAPH_WAL_VALVE_DEBUG=1 surfaces valve decisions to stderr without
     // needing the caller's verbose plumbing — the observability gap that let
     // §7a.1 run 1 fail silently (give-ups were verbose-gated and invisible).
@@ -124,7 +128,19 @@ export class WalCheckpointValve {
   /** Begin watching the WAL. Idempotent; the timer never holds the loop open. */
   start(): void {
     if (this.timer) return;
-    this.timer = setInterval(() => this.check(), this.intervalMs);
+    // One armed line per run under either diagnostics env: §7a.1's failed
+    // kernel-scale runs burned three 25-minute cycles before "is the valve
+    // even alive?" could be answered.
+    if (process.env.CODEGRAPH_SYNTH_TIMINGS || process.env.CODEGRAPH_WAL_VALVE_DEBUG) {
+      console.error(`[wal-valve] armed soft=${this.mb(this.softBytes)} hard=${this.mb(this.hardBytes)} wal=${this.mb(this.db.getWalSizeBytes())}`);
+    }
+    let ticks = 0;
+    this.timer = setInterval(() => {
+      if ((++ticks % 15) === 0) {
+        this.log(`alive: wal=${this.mb(this.db.getWalSizeBytes())} baseline=${this.mb(this.sizeAtLastFullBackfill)} inflight=${this.inflight ? 'y' : 'n'} paused=${this.pause ? 'y' : 'n'}`);
+      }
+      this.check();
+    }, this.intervalMs);
     this.timer.unref?.();
   }
 
@@ -150,7 +166,15 @@ export class WalCheckpointValve {
   backpressure(): Promise<void> | null {
     if (this.pause) return this.pause;
     if (Date.now() < this.futileUntil) return null; // pinned reader — parking is churn, not progress
-    if (this.growthBytes() <= this.hardBytes) return null;
+    // Two independent triggers:
+    //  - growth: un-backfilled BACKLOG past the hard cap (the original valve).
+    //  - file size: a WAL can stay fully backfilled and still grow without
+    //    bound — the writer only restarts at frame 0 if a commit finds no
+    //    reader marks, which §7a.1's instrumented run showed never happens
+    //    in practice (file marched 361→721MB through two COMPLETE
+    //    backfills). Past the file cap, park and TRUNCATE at the barrier —
+    //    the backfill part is instant when the backlog is already folded.
+    if (this.growthBytes() <= this.hardBytes && this.db.getWalSizeBytes() <= this.fileCapBytes) return null;
     this.log(`backpressure: wal=${this.mb(this.db.getWalSizeBytes())} baseline=${this.mb(this.sizeAtLastFullBackfill)} — pausing writer for full backfill`);
     const t0 = Date.now();
     this.pause = this.backfillFully().finally(() => {
@@ -226,9 +250,11 @@ export class WalCheckpointValve {
   }
 
   private fire(): void {
+    this.log(`fire: wal=${this.mb(this.db.getWalSizeBytes())} baseline=${this.mb(this.sizeAtLastFullBackfill)}`);
     const p = this.db
       .checkpointWalPassive()
       .then((res) => {
+        this.log(`timer pass: ${res ? `busy=${res.busy} log=${res.log} checkpointed=${res.checkpointed}` : 'null (machinery unavailable)'} wal=${this.mb(this.db.getWalSizeBytes())}`);
         // Full backfill (busy 0, every log frame checkpointed) ⇒ the writer's
         // next commit wraps the WAL; the file's current size becomes the new
         // growth baseline. A partial pass (writer appended during it, or a
@@ -237,6 +263,16 @@ export class WalCheckpointValve {
         // SQLite reports log = checkpointed = -1, which is harmless here.
         if (res && res.busy === 0 && res.log === res.checkpointed) {
           this.sizeAtLastFullBackfill = this.db.getWalSizeBytes();
+          // Opportunistic file chop while everything is folded: best-effort —
+          // an active writer/reader turns it into a busy no-op, and the
+          // barrier-path truncate (backpressure file cap) remains the
+          // deterministic bound.
+          if (this.db.getWalSizeBytes() > this.softBytes * 2) {
+            return this.db.checkpointWalTruncate().then((t) => {
+              if (t) this.log(`timer truncate: busy=${t.busy} wal=${this.mb(this.db.getWalSizeBytes())}`);
+              this.sizeAtLastFullBackfill = this.db.getWalSizeBytes();
+            });
+          }
         }
       })
       .catch(() => { /* best-effort */ })

src/extraction/index.ts

@@ -1619,8 +1619,11 @@ export class ExtractionOrchestrator {
       // with cores from availableParallelism — cpuset/affinity-honest, where
       // os.cpus() enumerates the host's CPUs and spawned 8 wasm workers (and
       // their grammar heaps) inside a 2-CPU container for zero extra
-      // throughput (§7a.1).
-      const poolSize = resolveParsePoolSize(process.env.CODEGRAPH_PARSE_WORKERS, os.availableParallelism());
+      // throughput (§7a.1). Floored so a 2-core box still gets 2 workers:
+      // parse is worker-side CPU, and 1 worker measured 34% slower than the
+      // old oversubscribed pool on the kernel-scale 2-cpuset envelope
+      // (493s vs 369s) — main + store-worker don't fill the second core.
+      const poolSize = resolveParsePoolSize(process.env.CODEGRAPH_PARSE_WORKERS, Math.max(3, os.availableParallelism()));
       // Read each needed grammar's WASM ONCE here and hand the bytes to every
       // worker, so spawns/respawns load grammars from memory instead of
       // re-reading them from disk (#1231: on an HDD, respawn re-reads amplify

src/resolution/index.ts

@@ -1358,6 +1358,10 @@ export class ReferenceResolver {
     // window to fire; see ./cooperative-yield.
     const maybeYield = createYielder();
 
+    if (process.env.CODEGRAPH_SYNTH_TIMINGS) {
+      console.error(`[pool-timing] backpressure hook: ${parallel?.backpressure ? 'present' : 'absent'}`);
+    }
+
     await this.warmCachesYielding(maybeYield);
 
     const total = this.queries.getUnresolvedReferencesCount();

src/resolution/memory-budget.ts

@@ -24,9 +24,26 @@ function readCgroupBytes(path: string): number | null {
   }
 }
 
+/** `inactive_file` from a cgroup memory.stat file — reclaimable page cache. */
+function readInactiveFile(statPath: string): number {
+  try {
+    const m = /^inactive_file (\d+)$/m.exec(fs.readFileSync(statPath, 'utf8'));
+    return m ? Number.parseInt(m[1]!, 10) : 0;
+  } catch {
+    return 0;
+  }
+}
+
 /**
  * Available headroom under the cgroup memory limit (v2 then v1), or null
  * when uncontained (no limit, non-Linux, or unreadable). Never throws.
+ *
+ * Reclaimable page cache (`inactive_file`) is credited back: `memory.current`
+ * counts it as usage, but the kernel reclaims it on demand — after a bulk
+ * parse the cache is stuffed with the DB's own pages, and the naive
+ * `max − current` read 57MB of headroom on a 6GB container and silently
+ * disabled the resolver pool (§7a.1 diagnostic run). This is the same
+ * working-set convention `docker stats` uses.
  */
 export function cgroupMemoryAvailable(): number | null {
   if (process.platform !== 'linux') return null;
@@ -34,7 +51,8 @@ export function cgroupMemoryAvailable(): number | null {
   const v2Max = readCgroupBytes('/sys/fs/cgroup/memory.max');
   if (v2Max !== null) {
     const current = readCgroupBytes('/sys/fs/cgroup/memory.current') ?? 0;
-    return Math.max(0, v2Max - current);
+    const reclaimable = readInactiveFile('/sys/fs/cgroup/memory.stat');
+    return Math.max(0, v2Max - Math.max(0, current - reclaimable));
   }
   // v1
   const v1Limit = readCgroupBytes('/sys/fs/cgroup/memory/memory.limit_in_bytes');
@@ -42,7 +60,8 @@ export function cgroupMemoryAvailable(): number | null {
   // anything at or beyond half the address-space-ish range as uncontained.
   if (v1Limit !== null && v1Limit < 2 ** 60) {
     const usage = readCgroupBytes('/sys/fs/cgroup/memory/memory.usage_in_bytes') ?? 0;
-    return Math.max(0, v1Limit - usage);
+    const reclaimable = readInactiveFile('/sys/fs/cgroup/memory/memory.stat');
+    return Math.max(0, v1Limit - Math.max(0, usage - reclaimable));
   }
   return null;
 }

src/resolution/resolver-pool.ts

@@ -95,7 +95,12 @@ export class ResolverPool {
         return Math.min(n, 16);
       }
     }
-    const cpuCap = Math.max(2, Math.min(opts.availableParallelism - 1, 6));
+    // No floor: at ap=2 the pool LOSES to sequential outright — measured on
+    // the kernel-scale 2-cpuset envelope: resolution 853s sequential vs
+    // 1,150s pooled-6-on-2 (§7a.1), and synthesis is Amdahl-bound by its
+    // dominant pass (cFnPtrEdges 306s of 358s) so pooling it bought nothing.
+    // ap−1 < 2 ⇒ sequential is the fast path, not a fallback.
+    const cpuCap = Math.min(opts.availableParallelism - 1, 6);
     const perWorker = Math.min(Math.max(opts.dbSizeBytes * 0.2, 256 * 1024 * 1024), 1.5 * 1024 * 1024 * 1024);
     const memCap = Math.floor((opts.memoryBudget * 0.7) / perWorker);
     const size = Math.min(cpuCap, memCap);
@@ -117,18 +122,22 @@ export class ResolverPool {
     try {
       dbSizeBytes = fs.statSync(dbPath).size;
     } catch { /* fresh/missing file — the 256MB per-worker floor applies */ }
+    const ap = os.availableParallelism();
+    const budget = memoryBudgetBytes();
     const size = ResolverPool.resolvePoolSize({
       explicit: process.env.CODEGRAPH_RESOLVE_WORKERS,
-      availableParallelism: os.availableParallelism(),
-      memoryBudget: memoryBudgetBytes(),
+      availableParallelism: ap,
+      memoryBudget: budget,
       dbSizeBytes,
     });
-    if (size === null) return null;
+    // Both outcomes log under SYNTH_TIMINGS — a silent null is how §7a.1's
+    // diagnostic run hid the memory-term misfire for a whole 25-minute cycle.
     if (process.env.CODEGRAPH_SYNTH_TIMINGS) {
       console.error(
-        `[pool-timing] pool size=${size} (ap=${os.availableParallelism()} budget=${Math.round(memoryBudgetBytes() / 1024 / 1024)}MB db=${Math.round(dbSizeBytes / 1024 / 1024)}MB)`
+        `[pool-timing] pool ${size === null ? 'disabled' : `size=${size}`} (ap=${ap} budget=${Math.round(budget / 1024 / 1024)}MB db=${Math.round(dbSizeBytes / 1024 / 1024)}MB)`
       );
     }
+    if (size === null) return null;
     try {
       return new ResolverPool(workerScript, dbPath, projectRoot, size);
     } catch {