perf(agent): open a store without copying the whole file

`read_from_disk` memory-mapped the file and then copied the entire
mapping into a `Vec` to hand to `File::from_bytes` — but `File::open`
memory-maps it itself whenever the facade's `mmap` feature is on, which
it is by default. So every open mapped the file, memcpy'd all of it, and
parsed the copy.

Store open at 100k x 384: 455 ms -> 327 ms, about 28% faster (two runs
after the change, 326.8 and 328.1 ms).

Peak memory is unchanged, which is worth saying because the opposite is
the natural assumption. The footprint harness now tracks a high-water
mark next to the retained figure, and it shows the peak falling after
the parse, during the index build — so a buffer allocated and freed
inside the parse never reaches it. Confirmed rather than assumed:
holding a deliberate extra copy of the whole file across the parse
leaves the peak exactly where it was, which is also what proved the
instrument was working before trusting its answer.

Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>

crates/clawhdf5-agent/src/storage.rs

@@ -113,13 +113,11 @@ pub type StoreState = (MemoryConfig, MemoryCache, SessionCache, KnowledgeCache);
 /// [`read_from_disk`], plus the checkpoint's [`WalMark`] (if any) so the
 /// caller can skip WAL entries this file already contains.
 pub fn read_from_disk_with_mark(path: &Path) -> Result<(StoreState, Option<WalMark>), MemoryError> {
-    let mmap = clawhdf5_io::MmapReader::open(path).map_err(MemoryError::Io)?;
-
-    // Advise the OS we'll need the whole file for parsing
-    mmap.advise_willneed(0, mmap.len());
-
-    // Parse the HDF5 file from the mmap'd bytes
-    let file = clawhdf5::File::from_bytes(mmap.as_bytes().to_vec())
+    // `File::open` memory-maps the file itself (the facade's `mmap` feature is
+    // on by default). Mapping it here and handing over `as_bytes().to_vec()`
+    // did the same work and then copied the whole store — a second full copy
+    // of the file, live for the whole parse, on top of the mapping.
+    let file = clawhdf5::File::open(path)
         .map_err(|e| MemoryError::Hdf5(format!("cannot open {}: {e}", path.display())))?;
 
     let (mut config, cache, sessions, knowledge) = schema::validate_and_load(&file)?;
@@ -133,9 +131,7 @@ pub fn read_from_disk_with_mark(path: &Path) -> Result<(StoreState, Option<WalMa
 pub fn read_from_disk_with_meta(
     path: &Path,
 ) -> Result<(StoreState, schema::CheckpointMeta), MemoryError> {
-    let mmap = clawhdf5_io::MmapReader::open(path).map_err(MemoryError::Io)?;
-    mmap.advise_willneed(0, mmap.len());
-    let file = clawhdf5::File::from_bytes(mmap.as_bytes().to_vec())
+    let file = clawhdf5::File::open(path)
         .map_err(|e| MemoryError::Hdf5(format!("cannot open {}: {e}", path.display())))?;
     let (mut config, cache, sessions, knowledge) = schema::validate_and_load(&file)?;
     config.path = path.to_path_buf();

crates/clawhdf5-bench/src/bin/search_harness.rs

@@ -230,13 +230,27 @@ struct CountingAllocator;
 
 static LIVE_BYTES: std::sync::atomic::AtomicI64 = std::sync::atomic::AtomicI64::new(0);
 
+/// High-water mark of [`LIVE_BYTES`] since it was last reset.
+///
+/// Live bytes at a checkpoint cannot see a buffer that was allocated and
+/// freed in between, and that is exactly the shape of a transient copy —
+/// which still has to fit in memory while it exists.
+static PEAK_BYTES: std::sync::atomic::AtomicI64 = std::sync::atomic::AtomicI64::new(0);
+
+fn note_peak(live: i64) {
+    PEAK_BYTES.fetch_max(live, std::sync::atomic::Ordering::Relaxed);
+}
+
 // SAFETY: every method forwards to the system allocator with the same layout
 // it was given, and only adds bookkeeping around it.
 unsafe impl std::alloc::GlobalAlloc for CountingAllocator {
     unsafe fn alloc(&self, layout: std::alloc::Layout) -> *mut u8 {
         let ptr = unsafe { std::alloc::System.alloc(layout) };
         if !ptr.is_null() {
-            LIVE_BYTES.fetch_add(layout.size() as i64, std::sync::atomic::Ordering::Relaxed);
+            let live = LIVE_BYTES
+                .fetch_add(layout.size() as i64, std::sync::atomic::Ordering::Relaxed)
+                + layout.size() as i64;
+            note_peak(live);
         }
         ptr
     }
@@ -249,10 +263,9 @@ unsafe impl std::alloc::GlobalAlloc for CountingAllocator {
     unsafe fn realloc(&self, ptr: *mut u8, layout: std::alloc::Layout, new_size: usize) -> *mut u8 {
         let new_ptr = unsafe { std::alloc::System.realloc(ptr, layout, new_size) };
         if !new_ptr.is_null() {
-            LIVE_BYTES.fetch_add(
-                new_size as i64 - layout.size() as i64,
-                std::sync::atomic::Ordering::Relaxed,
-            );
+            let delta = new_size as i64 - layout.size() as i64;
+            let live = LIVE_BYTES.fetch_add(delta, std::sync::atomic::Ordering::Relaxed) + delta;
+            note_peak(live);
         }
         new_ptr
     }
@@ -266,6 +279,19 @@ fn heap_bytes() -> u64 {
     LIVE_BYTES.load(std::sync::atomic::Ordering::Relaxed).max(0) as u64
 }
 
+/// Start watching for a new high-water mark from the current live total.
+fn reset_peak() {
+    PEAK_BYTES.store(
+        LIVE_BYTES.load(std::sync::atomic::Ordering::Relaxed),
+        std::sync::atomic::Ordering::Relaxed,
+    );
+}
+
+/// The highest live total seen since [`reset_peak`].
+fn peak_bytes() -> u64 {
+    PEAK_BYTES.load(std::sync::atomic::Ordering::Relaxed).max(0) as u64
+}
+
 fn mib(bytes: u64) -> f64 {
     bytes as f64 / (1 << 20) as f64
 }
@@ -580,19 +606,24 @@ fn bench_footprint(n: usize) {
     let path = mem.config().path.clone();
     drop(mem);
     let before_open = heap_bytes();
+    reset_peak();
     let reopened = HDF5Memory::open(&path).unwrap();
     let after_open = heap_bytes();
     let loaded = after_open.saturating_sub(before_open);
+    // Peak over the open, not just what it leaves behind: a buffer allocated
+    // and freed during the parse never shows up in the live total.
+    let peak = peak_bytes().saturating_sub(before_open);
     drop(reopened);
 
     let raw = (n * DIM * 4) as u64;
     println!(
-        "| {n} | {:.0} | {:.0} | {:.0} | {:.0} | {:.0} | {:.2}x |",
+        "| {n} | {:.0} | {:.0} | {:.0} | {:.0} | {:.0} | {:.0} | {:.2}x |",
         mib(raw),
         mib(after_entries.saturating_sub(base)),
         mib(after_store.saturating_sub(after_entries)),
         mib(after_indexes.saturating_sub(after_store)),
         mib(loaded),
+        mib(peak),
         loaded as f64 / raw as f64,
     );
 }
@@ -644,9 +675,9 @@ fn main() {
     if args.iter().any(|a| a == "--footprint") {
         println!("\n### Resident memory, {DIM}-dim f32\n");
         println!(
-            "| N | vectors (raw) | entries MiB | store MiB | indexes MiB | reopened MiB | reopened / raw |"
+            "| N | vectors (raw) | entries MiB | store MiB | indexes MiB | reopened MiB | peak during open MiB | reopened / raw |"
         );
-        println!("|---:|---:|---:|---:|---:|---:|---:|");
+        println!("|---:|---:|---:|---:|---:|---:|---:|---:|");
         for &n in sizes {
             bench_footprint(n);
         }