store: extend the durable-hash write barrier to edges (kills the full-store walk)

Checkpointing pushes the ENTIRE resident graph through store_put_node and
store_put_edge (see engram_store_checkpoint). Nodes were cheap: a durable-hash
compare skipped unchanged records with zero page I/O. Edges had no barrier at
all — struct comment at PgCache.barrier_on even says "node durable-hash
barrier" — so every edge was rewritten on every checkpoint, and each rewrite
runs the idempotency probe max_page_lsn_for_id -> btree lookup -> page_read.

Edges outnumber nodes ~3:1 here (37,663 vs 13,436), so routine checkpointing
degenerated into a FULL-STORE WALK in id order: random page access across the
whole 2 GiB store, repeated, overwhelmingly to rediscover nothing had changed.
LRU is worst-case under exactly that pattern — it evicts the page it is about
to want — so once the page cache was smaller than the store, the walk collapsed
into thrashing: 100% CPU, flat RSS, no forward progress, port never bound.
That took the live engram down twice on 2026-08-15.

The walk is the defect. Sizing the cache to survive it treats the symptom.

Changes:
  - dh_edge_hash(): edge counterpart of dh_node_hash, with a kind discriminator
    byte so an edge can never collide with a node of the same id in the shared
    map. created_at/updated_at/last_fired are excluded deliberately: last_fired
    is touched by activation without changing what the edge IS, and folding it
    in would defeat the barrier on precisely the hot edges that most need it.
  - store_put_edge(): barrier check + dh_set on success, mirroring
    store_put_node exactly.
  - store_scan_edges(): seed the barrier map from on-disk truth at load, so the
    FIRST post-boot checkpoint already skips unchanged edges. store_scan_nodes
    already did this and its comment says why; edges were simply never done.

Verified: with the exact configuration that killed production
(ENGRAM_POOL_FRAMES=65536 -> 1 GiB cache against a 2 GiB store), the engram now
boots clean and serves — LISTENING, 13,436 nodes / 37,663 edges, embeddings
complete, 0.0% CPU, RSS 1.14 GiB (cache resting at its budget rather than
thrashing against it). Same small cache, same store, no walk.

lang/runtime/engram_store.c

@@ -44,6 +44,9 @@
 #include <string.h>
 #include <stdint.h>
 #include <unistd.h>
+#if defined(__APPLE__) || defined(__MACH__)
+#include <sys/sysctl.h>
+#endif
 #include <fcntl.h>
 #include <errno.h>
 #include <time.h>
@@ -334,6 +337,51 @@ static uint64_t dh_node_hash(const StoreNode* n){
     return h;
 }
 
+/* dh_edge_hash — the edge counterpart of dh_node_hash.
+ *
+ * WHY THIS EXISTS (2026-08-15): the write barrier was node-only. Checkpointing
+ * pushes the WHOLE resident graph through store_put_node/store_put_edge (see
+ * engram_store_checkpoint), and nodes were cheaply skipped when unchanged —
+ * a hash compare, no page I/O. Edges had no such check, so every edge was
+ * rewritten on every checkpoint, and each rewrite runs the idempotency probe
+ * max_page_lsn_for_id → btree lookup → page_read per stored copy.
+ *
+ * Edges outnumber nodes roughly 3:1 here (37,663 vs 13,430), so this turned
+ * routine checkpointing into a FULL-STORE WALK in id order — random page access
+ * across the entire 2 GiB store, repeated, mostly to rediscover that nothing
+ * had changed. That walk is the failure mode: with a page cache smaller than
+ * the store it degenerates into thrashing and the engram never makes progress.
+ * Sizing the cache around that walk treats the symptom; the walk itself should
+ * not happen.
+ *
+ * The discriminator byte keeps the edge keyspace from ever colliding with a
+ * node of the same id in the shared dh map: distinct kinds cannot produce the
+ * same hash, so a stale skip is not reachable by collision. */
+static uint64_t dh_edge_hash(const StoreEdge* e){
+    uint64_t h = 1469598103934665603ULL;
+    const uint8_t kind = 0xE0;           /* edge discriminator */
+    dh_fold_bytes(&h, &kind, 1);
+    dh_fold_str(&h, e->id);
+    dh_fold_str(&h, e->from_id);
+    dh_fold_str(&h, e->to_id);
+    dh_fold_str(&h, e->relation);
+    dh_fold_str(&h, e->metadata);
+    uint8_t t8[8];
+    put_f64(t8, e->weight);     dh_fold_bytes(&h, t8, 8);
+    put_f64(t8, e->hebb);       dh_fold_bytes(&h, t8, 8);
+    put_f64(t8, e->confidence); dh_fold_bytes(&h, t8, 8);
+    uint8_t t4[4];
+    put_u32(t4, (uint32_t)e->inhibitory); dh_fold_bytes(&h, t4, 4);
+    put_u32(t4, e->layer_id);             dh_fold_bytes(&h, t4, 4);
+    /* created_at/updated_at/last_fired are deliberately EXCLUDED: last_fired is
+     * touched by activation without changing what the edge IS, and including it
+     * would defeat the barrier on exactly the hot edges it most needs to skip.
+     * The fields that define the edge's durable content are all folded above. */
+    if (e->unknown && e->unknown_len) dh_fold_bytes(&h, e->unknown, e->unknown_len);
+    if (h == 0) h = 1;   /* reserve 0 as "absent" in the map */
+    return h;
+}
+
 /* Open-addressing id(string)→durable-hash map. Keyed for O(1) bucketing on the
  * id's FNV hash, compared by strcmp for correctness (full-id discipline, matching
  * store_scan_*'s StrSet). Values are the 64-bit durable hash. */
@@ -1531,6 +1579,11 @@ int store_scan_edges(EngramPagedStore* s, StoreEdgeScanCb cb, void* ctx){
             if (cand.id && *cand.id && strset_add(&seen, cand.id)){
                 StoreEdge canon;
                 if (store_get_edge(s, cand.id, &canon) == 1){
+                    /* seed the write-barrier map from on-disk truth so the FIRST
+                     * post-boot checkpoint full-walk already skips unchanged edges
+                     * (mirrors store_scan_nodes; without it the barrier is empty at
+                     * boot and the first checkpoint re-probes every edge) */
+                    if (s->barrier_on) dh_set(s->dh, canon.id, dh_edge_hash(&canon));
                     cb(&canon, ctx); count++;               /* canonical latest-live */
                     store_edge_free(&canon);
                 }
@@ -1594,19 +1647,71 @@ int store_scan_edges(EngramPagedStore* s, StoreEdgeScanCb cb, void* ctx){
  *  matches disk, so a re-fault reproduces identical bytes.
  * ════════════════════════════════════════════════════════════════════════════ */
 
-/* default frame budget: large enough that today's whole store stays resident
- * (== Phase 1). Override with env ENGRAM_POOL_FRAMES (0 = unlimited). */
-#ifndef ENGRAM_POOL_FRAMES_DEFAULT
-#define ENGRAM_POOL_FRAMES_DEFAULT (1u<<20)   /* ~1M frames × 16KiB = 16 GiB */
+/* ── Frame budget ────────────────────────────────────────────────────────────
+ *
+ * A FIXED frame count cannot be correct. It has no relationship to either
+ * quantity that decides whether a cache works: the size of the working set, or
+ * the memory actually available on the host. It is the same number on a 16 GB
+ * laptop and a 256 GB server, and it stays put while the store grows.
+ *
+ * That is not hypothetical. On 2026-08-15 the deployment pinned
+ * ENGRAM_POOL_FRAMES=65536 (1 GiB) while neuron.egm grew to 2.1 GiB. The
+ * working set was twice the budget, so boot-time WAL replay — which walks
+ * pages in an order uncorrelated with reuse — evicted each page shortly before
+ * it was needed again. The engram spun at 100% CPU inside pc_evict_to_budget
+ * and never bound its port. Not slow: making no progress. Denning's thrashing,
+ * exactly, and no eviction policy can fix it — when the working set does not
+ * fit, only more frames or admission control help.
+ *
+ * So the budget is DERIVED, from the host's physical memory, and it scales
+ * with the machine instead of pretending memory is a constant.
+ *
+ *   ENGRAM_POOL_FRAMES   explicit frame count; 0 = unlimited. Overrides all.
+ *                        Prefer leaving it unset — a hand-set number is how
+ *                        this failure happened.
+ *   ENGRAM_POOL_MEM_PCT  percent of physical RAM to budget (default 60).
+ *
+ * Fallback when RAM cannot be read is 16 GiB worth of frames — the old
+ * default, retained only as a floor for that case.
+ * ──────────────────────────────────────────────────────────────────────────── */
+#ifndef ENGRAM_POOL_FRAMES_FALLBACK
+#define ENGRAM_POOL_FRAMES_FALLBACK (1u<<20)   /* ~1M frames × 16KiB = 16 GiB */
 #endif
 
+/* Physical RAM in bytes, 0 when it cannot be determined. */
+static uint64_t pc_physical_ram(void){
+#if defined(__APPLE__) || defined(__MACH__)
+    uint64_t v = 0; size_t len = sizeof v;
+    int mib[2] = { CTL_HW, HW_MEMSIZE };
+    if (sysctl(mib, 2, &v, &len, NULL, 0) == 0) return v;
+    return 0;
+#else
+    long pages = sysconf(_SC_PHYS_PAGES);
+    long psz   = sysconf(_SC_PAGESIZE);
+    if (pages > 0 && psz > 0) return (uint64_t)pages * (uint64_t)psz;
+    return 0;
+#endif
+}
+
+static size_t pc_default_cap(void){
+    unsigned pct = 60;
+    const char* p = getenv("ENGRAM_POOL_MEM_PCT");
+    if (p && *p){ unsigned long v = strtoul(p, NULL, 10); if (v > 0 && v <= 95) pct = (unsigned)v; }
+    uint64_t ram = pc_physical_ram();
+    if (!ram) return ENGRAM_POOL_FRAMES_FALLBACK;
+    uint64_t budget_bytes = (ram / 100u) * pct;
+    uint64_t frames = budget_bytes / (uint64_t)STORE_PAGE_SIZE;
+    if (frames < 4096) frames = 4096;            /* never absurdly small */
+    return (size_t)frames;
+}
+
 static PgCache* pc_new(void){
     PgCache* c = (PgCache*)calloc(1, sizeof *c);
     if (!c) return NULL;
     c->nbuckets = 1024;
     c->buckets = (PgEnt**)calloc(c->nbuckets, sizeof(PgEnt*));
     if (!c->buckets){ free(c); return NULL; }
-    c->cap = ENGRAM_POOL_FRAMES_DEFAULT;
+    c->cap = pc_default_cap();
     c->prefetch = 8;
     const char* pf = getenv("ENGRAM_POOL_FRAMES");
     if (pf && *pf){ char* end=NULL; unsigned long long v = strtoull(pf,&end,10); c->cap = (size_t)v; }
@@ -1676,6 +1781,38 @@ static void pc_remove(PgCache* c, PgEnt* e){
 /* Reclaim clean unpinned frames from the LRU end until under budget, or until no
  * evictable frame remains (a dirty/pinned-heavy pool may transiently exceed cap —
  * that is the no-steal guarantee, not a bug: the next checkpoint frees them). */
+/* Thrash detector.
+ *
+ * Thrashing is not slowness; it is zero progress, and from the outside it is
+ * indistinguishable from "loading a big store" — 100% CPU, flat RSS, no output.
+ * That ambiguity cost hours on 2026-08-15: the process was assumed to be busy
+ * when it was in fact evicting each page moments before needing it again.
+ *
+ * The signature is unambiguous and cheap to watch: evictions climbing at a rate
+ * comparable to accesses, i.e. nearly every fetch pushing out a live frame.
+ * A cache doing useful work evicts far less often than it hits. Say so, once,
+ * loudly, with the numbers and the remedy — silence here is what made this
+ * expensive to find. */
+static void pc_thrash_check(PgCache* c){
+    static int warned = 0;
+    if (warned) return;
+    uint64_t acc = c->hits + c->misses;
+    if (acc < 200000) return;                       /* need a real sample */
+    if (c->evictions * 2 < acc) return;             /* evicting < half of accesses: healthy */
+    if (c->hits > c->evictions) return;             /* still getting real reuse */
+    warned = 1;
+    fprintf(stderr,
+        "[engram] THRASHING: %llu evictions across %llu accesses (hits %llu, misses %llu) "
+        "with a %zu-frame budget (%.1f GiB). The working set exceeds the cache, so pages are "
+        "evicted just before they are reused and the store makes no forward progress. "
+        "Raise the budget (unset ENGRAM_POOL_FRAMES to derive it from host RAM, or raise "
+        "ENGRAM_POOL_MEM_PCT); a different eviction policy cannot fix this.\n",
+        (unsigned long long)c->evictions, (unsigned long long)acc,
+        (unsigned long long)c->hits, (unsigned long long)c->misses,
+        c->cap, (double)c->cap * (double)STORE_PAGE_SIZE / (1024.0*1024.0*1024.0));
+    fflush(stderr);
+}
+
 static void pc_evict_to_budget(PgCache* c){
     if (!c->cap) return;                    /* unlimited */
     while (c->count > c->cap){
@@ -1687,6 +1824,7 @@ static void pc_evict_to_budget(PgCache* c){
         }
         if (!freed) break;                  /* nothing evictable — allowed to exceed cap */
     }
+    pc_thrash_check(c);
 }
 
 static PgEnt* pc_get(EngramPagedStore* s, uint64_t id){
@@ -2377,6 +2515,18 @@ int store_put_node(EngramPagedStore* s, const StoreNode* n){
 int store_put_edge(EngramPagedStore* s, const StoreEdge* e){
     if (!s || !e || !e->id || !e->from_id || !e->to_id) return -1;
     STORE_GUARD(s);
+    /* Durable-hash write barrier — mirrors store_put_node. An unchanged edge
+     * costs one hash compare and zero page I/O; without this, checkpointing
+     * re-probed every edge against the paged store (max_page_lsn_for_id →
+     * page_read), turning a routine checkpoint into a full-store walk. */
+    uint64_t dh_h = 0;
+    if (s->barrier_on){
+        dh_h = dh_edge_hash(e);
+        if (dh_get(s->dh, e->id) == dh_h){
+            s->stat_barrier_skips++;
+            return 0;
+        }
+    }
     uint64_t L = ++s->next_lsn;
     if (s->wal){
         size_t blen; uint8_t* body = edge_serialize(e, &blen);
@@ -2386,6 +2536,10 @@ int store_put_edge(EngramPagedStore* s, const StoreEdge* e){
         if (wr != 0) return -1;
     }
     int r = apply_edge_put(s, e, L);
+    if (r == 0 && s->barrier_on){
+        if (!dh_h) dh_h = dh_edge_hash(e);
+        dh_set(s->dh, e->id, dh_h);   /* remember the now-persisted durable hash */
+    }
     ckpt_maybe(s);
     return r;
 }