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Store the vectors in an HNSW in LMDB

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This commit is contained in:
Clément Renault 2023-06-08 12:19:06 +02:00
parent 7ac2f1489d
commit 4571e512d2
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GPG Key ID: 92ADA4E935E71FA4
8 changed files with 142 additions and 36 deletions
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63
Cargo.lock generated
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@ -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",
]

5
milli/Cargo.toml
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@ -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"

16
milli/src/dot_product.rs Normal file
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@ -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()
}
}

53
milli/src/index.rs
View File

@ -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 |
id 2 |
name 2 |
age 1
id 2
name 2
"###
);
@ -1486,9 +1517,9 @@ pub(crate) mod tests {
db_snap!(index, field_distribution,
@r###"
age 1 |
id 2 |
name 2 |
age 1
id 2
name 2
"###
);
@ -1502,9 +1533,9 @@ pub(crate) mod tests {
db_snap!(index, field_distribution,
@r###"
has_dog 1 |
id 2 |
name 2 |
has_dog 1
id 2
name 2
"###
);
}

1
milli/src/lib.rs
View File

@ -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;

3
milli/src/update/clear_documents.rs
View File

@ -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)

1
milli/src/update/delete_documents.rs
View File

@ -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

36
milli/src/update/index_documents/typed_chunk.rs
View File

@ -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 geo_faceted_docids = index.geo_faceted_documents_ids(wtxn)?;
let mut hnsw = index.vector_hnsw(wtxn)?.unwrap_or_default();
let mut searcher = Searcher::new();
// let mut cursor = geo_points.into_cursor()?;
// while let Some((key, value)) = cursor.move_on_next()? {
// // convert the key back to a u32 (4 bytes)
// let docid = key.try_into().map(DocumentId::from_be_bytes).unwrap();
// // convert the latitude and longitude back to a f64 (8 bytes)
// let (lat, tail) = helpers::try_split_array_at::<u8, 8>(value).unwrap();
// let (lng, _) = helpers::try_split_array_at::<u8, 8>(tail).unwrap();
// let point = [f64::from_ne_bytes(lat), f64::from_ne_bytes(lng)];
// let xyz_point = lat_lng_to_xyz(&point);
// 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")
let mut cursor = vector_points.into_cursor()?;
while let Some((key, value)) = cursor.move_on_next()? {
// convert the key back to a u32 (4 bytes)
let docid = key.try_into().map(DocumentId::from_be_bytes).unwrap();
// convert the vector back to a Vec<f32>
let vector: Vec<f32> = pod_collect_to_vec(value);
let vector_id = hnsw.insert(vector, &mut searcher) as u32;
index.vector_id_docid.put(wtxn, &BEU32::new(vector_id), &BEU32::new(docid))?;
}
index.put_vector_hnsw(wtxn, &hnsw)?;
}
TypedChunk::ScriptLanguageDocids(hash_pair) => {
let mut buffer = Vec::new();