Use an optimized version to rebuild all graph links

Cargo.lock

@@ -580,7 +580,7 @@ source = "git+https://github.com/meilisearch/bbqueue#e8af4a4bccc8eb36b2b0442c4a9
 
 [[package]]
 name = "benchmarks"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "bumpalo",
@@ -790,7 +790,7 @@ dependencies = [
 
 [[package]]
 name = "build-info"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "time",
@@ -1786,7 +1786,7 @@ dependencies = [
 
 [[package]]
 name = "dump"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "big_s",
@@ -2018,7 +2018,7 @@ checksum = "37909eebbb50d72f9059c3b6d82c0463f2ff062c9e95845c43a6c9c0355411be"
 
 [[package]]
 name = "file-store"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "tempfile",
  "thiserror 2.0.17",
@@ -2040,7 +2040,7 @@ dependencies = [
 
 [[package]]
 name = "filter-parser"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "insta",
  "levenshtein_automata",
@@ -2068,7 +2068,7 @@ dependencies = [
 
 [[package]]
 name = "flatten-serde-json"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "criterion",
  "serde_json",
@@ -2231,7 +2231,7 @@ dependencies = [
 
 [[package]]
 name = "fuzzers"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "arbitrary",
  "bumpalo",
@@ -2698,9 +2698,8 @@ dependencies = [
 
 [[package]]
 name = "hannoy"
-version = "0.1.0-nested-rtxns"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "be82bf3f2108ddc8885e3d306fcd7f4692066bfe26065ca8b42ba417f3c26dd1"
+version = "0.1.2-nested-rtxns"
+source = "git+https://github.com/nnethercott/hannoy?branch=use-heed-nested-rtxns#41f375e3080f311a5bef30eb647a2162262b5abd"
 dependencies = [
  "bytemuck",
  "byteorder",
@@ -3185,7 +3184,7 @@ dependencies = [
 
 [[package]]
 name = "index-scheduler"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "backoff",
@@ -3449,7 +3448,7 @@ dependencies = [
 
 [[package]]
 name = "json-depth-checker"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "criterion",
  "serde_json",
@@ -3939,7 +3938,7 @@ checksum = "ae960838283323069879657ca3de837e9f7bbb4c7bf6ea7f1b290d5e9476d2e0"
 
 [[package]]
 name = "meili-snap"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "insta",
  "md5 0.8.0",
@@ -3950,7 +3949,7 @@ dependencies = [
 
 [[package]]
 name = "meilisearch"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "actix-cors",
  "actix-http",
@@ -4048,7 +4047,7 @@ dependencies = [
 
 [[package]]
 name = "meilisearch-auth"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "base64 0.22.1",
  "enum-iterator",
@@ -4067,7 +4066,7 @@ dependencies = [
 
 [[package]]
 name = "meilisearch-types"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "actix-web",
  "anyhow",
@@ -4105,7 +4104,7 @@ dependencies = [
 
 [[package]]
 name = "meilitool"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "clap",
@@ -4139,7 +4138,7 @@ dependencies = [
 
 [[package]]
 name = "milli"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "arroy",
  "bbqueue",
@@ -4718,7 +4717,7 @@ checksum = "9b4f627cb1b25917193a259e49bdad08f671f8d9708acfd5fe0a8c1455d87220"
 
 [[package]]
 name = "permissive-json-pointer"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "big_s",
  "serde_json",
@@ -7758,7 +7757,7 @@ dependencies = [
 
 [[package]]
 name = "xtask"
-version = "1.30.0"
+version = "1.30.1"
 dependencies = [
  "anyhow",
  "build-info",

Cargo.toml

@@ -23,7 +23,7 @@ members = [
 ]
 
 [workspace.package]
-version = "1.30.0"
+version = "1.30.1"
 authors = [
     "Quentin de Quelen <quentin@dequelen.me>",
     "Clément Renault <clement@meilisearch.com>",

crates/milli/Cargo.toml

@@ -91,7 +91,7 @@ rhai = { version = "1.23.6", features = [
     "sync",
 ] }
 arroy = "0.6.4-nested-rtxns"
-hannoy = { version = "0.1.0-nested-rtxns", features = ["arroy"] }
+hannoy = { git = "https://github.com/nnethercott/hannoy", branch = "use-heed-nested-rtxns", features = ["arroy"] }
 rand = "0.8.5"
 tracing = "0.1.41"
 ureq = { version = "2.12.1", features = ["json"] }

crates/milli/src/update/upgrade/mod.rs

@@ -3,6 +3,7 @@ mod v1_13;
 mod v1_14;
 mod v1_15;
 mod v1_16;
+mod v1_30_1;
 
 use heed::RwTxn;
 use v1_12::{FixFieldDistribution, RecomputeStats};
@@ -10,6 +11,7 @@ use v1_13::AddNewStats;
 use v1_14::UpgradeArroyVersion;
 use v1_15::RecomputeWordFst;
 use v1_16::SwitchToMultimodal;
+use v1_30_1::RebuildHannoyGraph;
 
 use crate::constants::{VERSION_MAJOR, VERSION_MINOR, VERSION_PATCH};
 use crate::progress::{Progress, VariableNameStep};
@@ -33,6 +35,7 @@ const UPGRADE_FUNCTIONS: &[&dyn UpgradeIndex] = &[
     &UpgradeArroyVersion {},
     &RecomputeWordFst {},
     &SwitchToMultimodal {},
+    &RebuildHannoyGraph,
 ];
 
 /// Return true if the cached stats of the index must be regenerated
@@ -58,12 +61,12 @@ where
             return Err(crate::Error::InternalError(InternalError::AbortedIndexation));
         }
         if upgrade.must_upgrade(initial_version) {
-            regenerate_stats |= upgrade.upgrade(wtxn, index, progress.clone())?;
             progress.update_progress(VariableNameStep::<UpgradeVersion>::new(
                 upgrade.description(),
                 i as u32,
                 upgrade_functions.len() as u32,
             ));
+            regenerate_stats |= upgrade.upgrade(wtxn, index, progress.clone())?;
         } else {
             progress.update_progress(VariableNameStep::<UpgradeVersion>::new(
                 "Skipping migration that must not be applied",

crates/milli/src/update/upgrade/v1_30_1.rs

@@ -0,0 +1,50 @@
+use heed::RwTxn;
+use rand::SeedableRng as _;
+
+use super::UpgradeIndex;
+use crate::progress::Progress;
+use crate::vector::VectorStore;
+use crate::{Index, Result};
+
+/// Rebuilds the hannoy graph and do not touch to the embeddings.
+///
+/// This follows a bug in hannoy v0.0.9 and v0.1.0 where the graph
+/// was not built correctly.
+pub(super) struct RebuildHannoyGraph;
+
+impl UpgradeIndex for RebuildHannoyGraph {
+    fn upgrade(&self, wtxn: &mut RwTxn, index: &Index, progress: Progress) -> Result<bool> {
+        let embedders = index.embedding_configs();
+        let backend = index.get_vector_store(wtxn)?.unwrap_or_default();
+
+        for config in embedders.embedding_configs(wtxn)? {
+            let embedder_info = embedders.embedder_info(wtxn, &config.name)?.unwrap();
+            let mut vector_store = VectorStore::new(
+                backend,
+                index.vector_store,
+                embedder_info.embedder_id,
+                config.config.quantized(),
+            );
+
+            let seed = rand::random();
+            let mut rng = rand::rngs::StdRng::seed_from_u64(seed);
+            vector_store.rebuild_graph(
+                wtxn,
+                progress.clone(),
+                &mut rng,
+                vector_store.dimensions(wtxn)?.unwrap(),
+                &|| false,
+            )?;
+        }
+
+        Ok(false)
+    }
+
+    fn must_upgrade(&self, initial_version: (u32, u32, u32)) -> bool {
+        initial_version < (1, 30, 1)
+    }
+
+    fn description(&self) -> &'static str {
+        "Rebuilding graph links"
+    }
+}

crates/milli/src/vector/store.rs

@@ -246,6 +246,32 @@ impl VectorStore {
         Ok(())
     }
 
+    pub fn rebuild_graph<R: rand::Rng + rand::SeedableRng>(
+        &mut self,
+        wtxn: &mut RwTxn,
+        progress: Progress,
+        rng: &mut R,
+        dimension: usize,
+        cancel: &(impl Fn() -> bool + Sync + Send),
+    ) -> Result<(), crate::Error> {
+        for index in vector_store_range_for_embedder(self.embedder_index) {
+            if self.backend == VectorStoreBackend::Hannoy {
+                if self.quantized {
+                    let writer = hannoy::Writer::new(self._hannoy_quantized_db(), index, dimension);
+                    if !writer.is_empty(wtxn)? {
+                        hannoy_rebuild_graph(wtxn, &progress, rng, cancel, &writer)?;
+                    }
+                } else {
+                    let writer = hannoy::Writer::new(self._hannoy_angular_db(), index, dimension);
+                    if !writer.is_empty(wtxn)? {
+                        hannoy_rebuild_graph(wtxn, &progress, rng, cancel, &writer)?;
+                    }
+                }
+            }
+        }
+        Ok(())
+    }
+
     /// Overwrite all the embeddings associated with the index and item ID.
     /// /!\ It won't remove embeddings after the last passed embedding, which can leave stale embeddings.
     ///     You should call `del_items` on the `item_id` before calling this method.
@@ -1185,6 +1211,25 @@ where
     Ok(())
 }
 
+fn hannoy_rebuild_graph<R, D>(
+    wtxn: &mut RwTxn<'_>,
+    progress: &Progress,
+    rng: &mut R,
+    cancel: &(impl Fn() -> bool + Sync + Send),
+    writer: &hannoy::Writer<D>,
+) -> Result<(), crate::Error>
+where
+    R: rand::Rng + rand::SeedableRng,
+    D: hannoy::Distance,
+{
+    let mut builder = writer.builder(rng).progress(progress.clone());
+    builder
+        .cancel(cancel)
+        .ef_construction(HANNOY_EF_CONSTRUCTION)
+        .force_rebuild::<HANNOY_M, HANNOY_M0>(wtxn)?;
+    Ok(())
+}
+
 #[derive(Debug, Default, Clone)]
 pub struct VectorStoreStats {
     pub number_of_embeddings: u64,