Store the vectors in an HNSW in LMDB

Cargo.lock

@@ -1221,6 +1221,12 @@ dependencies = [
  "winapi",
 ]
 
+[[package]]
+name = "doc-comment"
+version = "0.3.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fea41bba32d969b513997752735605054bc0dfa92b4c56bf1189f2e174be7a10"
+
 [[package]]
 name = "dump"
 version = "1.2.0"
@@ -1725,6 +1731,15 @@ dependencies = [
  "byteorder",
 ]
 
+[[package]]
+name = "hashbrown"
+version = "0.11.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e"
+dependencies = [
+ "ahash 0.7.6",
+]
+
 [[package]]
 name = "hashbrown"
 version = "0.12.3"
@@ -1826,6 +1841,22 @@ dependencies = [
  "digest",
 ]
 
+[[package]]
+name = "hnsw"
+version = "0.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2b9740ebf8769ec4ad6762cc951ba18f39bba6dfbc2fbbe46285f7539af79752"
+dependencies = [
+ "ahash 0.7.6",
+ "hashbrown 0.11.2",
+ "libm",
+ "num-traits",
+ "rand_core",
+ "serde",
+ "smallvec",
+ "space",
+]
+
 [[package]]
 name = "http"
 version = "0.2.9"
@@ -1956,7 +1987,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
 dependencies = [
  "autocfg",
- "hashbrown",
+ "hashbrown 0.12.3",
  "serde",
 ]
 
@@ -2057,7 +2088,7 @@ checksum = "37228e06c75842d1097432d94d02f37fe3ebfca9791c2e8fef6e9db17ed128c1"
 dependencies = [
  "cedarwood",
  "fxhash",
- "hashbrown",
+ "hashbrown 0.12.3",
  "lazy_static",
  "phf",
  "phf_codegen",
@@ -2698,6 +2729,7 @@ dependencies = [
  "geoutils",
  "grenad",
  "heed",
+ "hnsw",
  "insta",
  "itertools",
  "json-depth-checker",
@@ -2712,6 +2744,7 @@ dependencies = [
  "once_cell",
  "ordered-float",
  "rand",
+ "rand_pcg",
  "rayon",
  "roaring",
  "rstar",
@@ -2721,6 +2754,7 @@ dependencies = [
  "smallstr",
  "smallvec",
  "smartstring",
+ "space",
  "tempfile",
  "thiserror",
  "time",
@@ -3273,6 +3307,16 @@ dependencies = [
  "getrandom",
 ]
 
+[[package]]
+name = "rand_pcg"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e"
+dependencies = [
+ "rand_core",
+ "serde",
+]
+
 [[package]]
 name = "rayon"
 version = "1.7.0"
@@ -3732,6 +3776,9 @@ name = "smallvec"
 version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
+dependencies = [
+ "serde",
+]
 
 [[package]]
 name = "smartstring"
@@ -3754,6 +3801,16 @@ dependencies = [
  "winapi",
 ]
 
+[[package]]
+name = "space"
+version = "0.17.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5ab9701ae895386d13db622abf411989deff7109b13b46b6173bb4ce5c1d123"
+dependencies = [
+ "doc-comment",
+ "num-traits",
+]
+
 [[package]]
 name = "spin"
 version = "0.5.2"
@@ -4405,7 +4462,7 @@ version = "0.16.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c531a2dc4c462b833788be2c07eef4e621d0e9edbd55bf280cc164c1c1aa043"
 dependencies = [
- "hashbrown",
+ "hashbrown 0.12.3",
  "once_cell",
 ]
 

milli/Cargo.toml

@@ -15,7 +15,7 @@ license.workspace = true
 bimap = { version = "0.6.3", features = ["serde"] }
 bincode = "1.3.3"
 bstr = "1.4.0"
-bytemuck = "1.13.1"
+bytemuck = { version = "1.13.1", features = ["extern_crate_alloc"] }
 byteorder = "1.4.3"
 charabia = { version = "0.7.2", default-features = false }
 concat-arrays = "0.1.2"
@@ -33,18 +33,21 @@ heed = { git = "https://github.com/meilisearch/heed", tag = "v0.12.6", default-f
     "lmdb",
     "sync-read-txn",
 ] }
+hnsw = { version = "0.11.0", features = ["serde1"] }
 json-depth-checker = { path = "../json-depth-checker" }
 levenshtein_automata = { version = "0.2.1", features = ["fst_automaton"] }
 memmap2 = "0.5.10"
 obkv = "0.2.0"
 once_cell = "1.17.1"
 ordered-float = "3.6.0"
+rand_pcg = { version = "0.3.1", features = ["serde1"] }
 rayon = "1.7.0"
 roaring = "0.10.1"
 rstar = { version = "0.10.0", features = ["serde"] }
 serde = { version = "1.0.160", features = ["derive"] }
 serde_json = { version = "1.0.95", features = ["preserve_order"] }
 slice-group-by = "0.3.0"
+space = "0.17.0"
 smallstr = { version = "0.3.0", features = ["serde"] }
 smallvec = "1.10.0"
 smartstring = "1.0.1"

milli/src/dot_product.rs

@@ -0,0 +1,16 @@
+use serde::{Deserialize, Serialize};
+use space::Metric;
+
+#[derive(Debug, Default, Clone, Copy, Serialize, Deserialize)]
+pub struct DotProduct;
+
+impl Metric<Vec<f32>> for DotProduct {
+    type Unit = u32;
+
+    // Following <https://docs.rs/space/0.17.0/space/trait.Metric.html>.
+    fn distance(&self, a: &Vec<f32>, b: &Vec<f32>) -> Self::Unit {
+        let dist: f32 = a.iter().zip(b).map(|(a, b)| a * b).sum();
+        debug_assert!(!dist.is_nan());
+        dist.to_bits()
+    }
+}

milli/src/index.rs

@@ -8,10 +8,12 @@ use charabia::{Language, Script};
 use heed::flags::Flags;
 use heed::types::*;
 use heed::{CompactionOption, Database, PolyDatabase, RoTxn, RwTxn};
+use rand_pcg::Pcg32;
 use roaring::RoaringBitmap;
 use rstar::RTree;
 use time::OffsetDateTime;
 
+use crate::dot_product::DotProduct;
 use crate::error::{InternalError, UserError};
 use crate::facet::FacetType;
 use crate::fields_ids_map::FieldsIdsMap;
@@ -26,6 +28,9 @@ use crate::{
     Result, RoaringBitmapCodec, RoaringBitmapLenCodec, Search, U8StrStrCodec, BEU16, BEU32,
 };
 
+/// The HNSW data-structure that we serialize, fill and search in.
+pub type Hnsw = hnsw::Hnsw<DotProduct, Vec<f32>, Pcg32, 12, 24>;
+
 pub const DEFAULT_MIN_WORD_LEN_ONE_TYPO: u8 = 5;
 pub const DEFAULT_MIN_WORD_LEN_TWO_TYPOS: u8 = 9;
 
@@ -42,6 +47,7 @@ pub mod main_key {
     pub const FIELDS_IDS_MAP_KEY: &str = "fields-ids-map";
     pub const GEO_FACETED_DOCUMENTS_IDS_KEY: &str = "geo-faceted-documents-ids";
     pub const GEO_RTREE_KEY: &str = "geo-rtree";
+    pub const VECTOR_HNSW_KEY: &str = "vector-hnsw";
     pub const HARD_EXTERNAL_DOCUMENTS_IDS_KEY: &str = "hard-external-documents-ids";
     pub const NUMBER_FACETED_DOCUMENTS_IDS_PREFIX: &str = "number-faceted-documents-ids";
     pub const PRIMARY_KEY_KEY: &str = "primary-key";
@@ -86,6 +92,7 @@ pub mod db_name {
     pub const FACET_ID_STRING_DOCIDS: &str = "facet-id-string-docids";
     pub const FIELD_ID_DOCID_FACET_F64S: &str = "field-id-docid-facet-f64s";
     pub const FIELD_ID_DOCID_FACET_STRINGS: &str = "field-id-docid-facet-strings";
+    pub const VECTOR_ID_DOCID: &str = "vector-id-docids";
     pub const DOCUMENTS: &str = "documents";
     pub const SCRIPT_LANGUAGE_DOCIDS: &str = "script_language_docids";
 }
@@ -149,6 +156,9 @@ pub struct Index {
     /// Maps the document id, the facet field id and the strings.
     pub field_id_docid_facet_strings: Database<FieldDocIdFacetStringCodec, Str>,
 
+    /// Maps a vector id to the document id that have it.
+    pub vector_id_docid: Database<OwnedType<BEU32>, OwnedType<BEU32>>,
+
     /// Maps the document id to the document as an obkv store.
     pub(crate) documents: Database<OwnedType<BEU32>, ObkvCodec>,
 }
@@ -162,7 +172,7 @@ impl Index {
     ) -> Result<Index> {
         use db_name::*;
 
-        options.max_dbs(23);
+        options.max_dbs(24);
         unsafe { options.flag(Flags::MdbAlwaysFreePages) };
 
         let env = options.open(path)?;
@@ -198,11 +208,11 @@ impl Index {
             env.create_database(&mut wtxn, Some(FACET_ID_IS_NULL_DOCIDS))?;
         let facet_id_is_empty_docids =
             env.create_database(&mut wtxn, Some(FACET_ID_IS_EMPTY_DOCIDS))?;
-
         let field_id_docid_facet_f64s =
             env.create_database(&mut wtxn, Some(FIELD_ID_DOCID_FACET_F64S))?;
         let field_id_docid_facet_strings =
             env.create_database(&mut wtxn, Some(FIELD_ID_DOCID_FACET_STRINGS))?;
+        let vector_id_docid = env.create_database(&mut wtxn, Some(VECTOR_ID_DOCID))?;
         let documents = env.create_database(&mut wtxn, Some(DOCUMENTS))?;
         wtxn.commit()?;
 
@@ -231,6 +241,7 @@ impl Index {
             facet_id_is_empty_docids,
             field_id_docid_facet_f64s,
             field_id_docid_facet_strings,
+            vector_id_docid,
             documents,
         })
     }
@@ -502,6 +513,26 @@ impl Index {
         }
     }
 
+    /* vector HNSW */
+
+    /// Writes the provided `hnsw`.
+    pub(crate) fn put_vector_hnsw(&self, wtxn: &mut RwTxn, hnsw: &Hnsw) -> heed::Result<()> {
+        self.main.put::<_, Str, SerdeBincode<Hnsw>>(wtxn, main_key::VECTOR_HNSW_KEY, hnsw)
+    }
+
+    /// Delete the `hnsw`.
+    pub(crate) fn delete_vector_hnsw(&self, wtxn: &mut RwTxn) -> heed::Result<bool> {
+        self.main.delete::<_, Str>(wtxn, main_key::VECTOR_HNSW_KEY)
+    }
+
+    /// Returns the `hnsw`.
+    pub fn vector_hnsw(&self, rtxn: &RoTxn) -> Result<Option<Hnsw>> {
+        match self.main.get::<_, Str, SerdeBincode<Hnsw>>(rtxn, main_key::VECTOR_HNSW_KEY)? {
+            Some(hnsw) => Ok(Some(hnsw)),
+            None => Ok(None),
+        }
+    }
+
     /* field distribution */
 
     /// Writes the field distribution which associates every field name with
@@ -1466,9 +1497,9 @@ pub(crate) mod tests {
 
         db_snap!(index, field_distribution,
             @r###"
-        age              1      |
+        age              1
-        id               2      |
+        id               2
-        name             2      |
+        name             2
         "###
         );
 
@@ -1486,9 +1517,9 @@ pub(crate) mod tests {
 
         db_snap!(index, field_distribution,
             @r###"
-        age              1      |
+        age              1
-        id               2      |
+        id               2
-        name             2      |
+        name             2
         "###
         );
 
@@ -1502,9 +1533,9 @@ pub(crate) mod tests {
 
         db_snap!(index, field_distribution,
             @r###"
-        has_dog          1      |
+        has_dog          1
-        id               2      |
+        id               2
-        name             2      |
+        name             2
         "###
         );
     }

milli/src/lib.rs

@@ -10,6 +10,7 @@ pub mod documents;
 
 mod asc_desc;
 mod criterion;
+pub mod dot_product;
 mod error;
 mod external_documents_ids;
 pub mod facet;

milli/src/update/clear_documents.rs

@@ -39,6 +39,7 @@ impl<'t, 'u, 'i> ClearDocuments<'t, 'u, 'i> {
             facet_id_is_empty_docids,
             field_id_docid_facet_f64s,
             field_id_docid_facet_strings,
+            vector_id_docid,
             documents,
         } = self.index;
 
@@ -57,6 +58,7 @@ impl<'t, 'u, 'i> ClearDocuments<'t, 'u, 'i> {
         self.index.put_field_distribution(self.wtxn, &FieldDistribution::default())?;
         self.index.delete_geo_rtree(self.wtxn)?;
         self.index.delete_geo_faceted_documents_ids(self.wtxn)?;
+        self.index.delete_vector_hnsw(self.wtxn)?;
 
         // We clean all the faceted documents ids.
         for field_id in faceted_fields {
@@ -95,6 +97,7 @@ impl<'t, 'u, 'i> ClearDocuments<'t, 'u, 'i> {
         facet_id_string_docids.clear(self.wtxn)?;
         field_id_docid_facet_f64s.clear(self.wtxn)?;
         field_id_docid_facet_strings.clear(self.wtxn)?;
+        vector_id_docid.clear(self.wtxn)?;
         documents.clear(self.wtxn)?;
 
         Ok(number_of_documents)

milli/src/update/delete_documents.rs

@@ -240,6 +240,7 @@ impl<'t, 'u, 'i> DeleteDocuments<'t, 'u, 'i> {
             facet_id_exists_docids,
             facet_id_is_null_docids,
             facet_id_is_empty_docids,
+            vector_id_docid,
             documents,
         } = self.index;
         // Remove from the documents database

milli/src/update/index_documents/typed_chunk.rs

@@ -4,10 +4,12 @@ use std::convert::TryInto;
 use std::fs::File;
 use std::io;
 
+use bytemuck::allocation::pod_collect_to_vec;
 use charabia::{Language, Script};
 use grenad::MergerBuilder;
 use heed::types::ByteSlice;
 use heed::RwTxn;
+use hnsw::Searcher;
 use roaring::RoaringBitmap;
 
 use super::helpers::{
@@ -17,7 +19,7 @@ use super::{ClonableMmap, MergeFn};
 use crate::facet::FacetType;
 use crate::update::facet::FacetsUpdate;
 use crate::update::index_documents::helpers::as_cloneable_grenad;
-use crate::{lat_lng_to_xyz, CboRoaringBitmapCodec, DocumentId, GeoPoint, Index, Result};
+use crate::{lat_lng_to_xyz, CboRoaringBitmapCodec, DocumentId, GeoPoint, Index, Result, BEU32};
 
 pub(crate) enum TypedChunk {
     FieldIdDocidFacetStrings(grenad::Reader<CursorClonableMmap>),
@@ -223,27 +225,19 @@ pub(crate) fn write_typed_chunk_into_index(
             index.put_geo_faceted_documents_ids(wtxn, &geo_faceted_docids)?;
         }
         TypedChunk::VectorPoints(vector_points) => {
-            // let mut rtree = index.geo_rtree(wtxn)?.unwrap_or_default();
+            let mut hnsw = index.vector_hnsw(wtxn)?.unwrap_or_default();
-            // let mut geo_faceted_docids = index.geo_faceted_documents_ids(wtxn)?;
+            let mut searcher = Searcher::new();
 
-            // let mut cursor = geo_points.into_cursor()?;
+            let mut cursor = vector_points.into_cursor()?;
-            // while let Some((key, value)) = cursor.move_on_next()? {
+            while let Some((key, value)) = cursor.move_on_next()? {
-            //     // convert the key back to a u32 (4 bytes)
+                // convert the key back to a u32 (4 bytes)
-            //     let docid = key.try_into().map(DocumentId::from_be_bytes).unwrap();
+                let docid = key.try_into().map(DocumentId::from_be_bytes).unwrap();
-
+                // convert the vector back to a Vec<f32>
-            //     // convert the latitude and longitude back to a f64 (8 bytes)
+                let vector: Vec<f32> = pod_collect_to_vec(value);
-            //     let (lat, tail) = helpers::try_split_array_at::<u8, 8>(value).unwrap();
+                let vector_id = hnsw.insert(vector, &mut searcher) as u32;
-            //     let (lng, _) = helpers::try_split_array_at::<u8, 8>(tail).unwrap();
+                index.vector_id_docid.put(wtxn, &BEU32::new(vector_id), &BEU32::new(docid))?;
-            //     let point = [f64::from_ne_bytes(lat), f64::from_ne_bytes(lng)];
+            }
-            //     let xyz_point = lat_lng_to_xyz(&point);
+            index.put_vector_hnsw(wtxn, &hnsw)?;
-
-            //     rtree.insert(GeoPoint::new(xyz_point, (docid, point)));
-            //     geo_faceted_docids.insert(docid);
-            // }
-            // index.put_geo_rtree(wtxn, &rtree)?;
-            // index.put_geo_faceted_documents_ids(wtxn, &geo_faceted_docids)?;
-
-            todo!("index vector points")
         }
         TypedChunk::ScriptLanguageDocids(hash_pair) => {
             let mut buffer = Vec::new();