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Merge pull request #4160 from meilisearch/diff-indexing-vector-points

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Diff Indexing for the vector points
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Many the fish 2023-11-02 16:01:51 +01:00 committed by GitHub
commit 2544bc1416
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2 changed files with 156 additions and 52 deletions
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127
milli/src/update/index_documents/extract/extract_vector_points.rs
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@ -1,15 +1,25 @@
use std::cmp::Ordering;
use std::convert::TryFrom;
use std::fs::File;
use std::io::{self, BufReader};
use std::io::{self, BufReader, BufWriter};
use std::mem::size_of;
use std::str::from_utf8;
use bytemuck::cast_slice;
use grenad::Writer;
use itertools::EitherOrBoth;
use ordered_float::OrderedFloat;
use serde_json::{from_slice, Value};
use super::helpers::{create_writer, writer_into_reader, GrenadParameters};
use crate::error::UserError;
use crate::update::del_add::{DelAdd, KvReaderDelAdd, KvWriterDelAdd};
use crate::update::index_documents::helpers::try_split_at;
use crate::{DocumentId, FieldId, InternalError, Result, VectorOrArrayOfVectors};
/// The length of the elements that are always in the buffer when inserting new values.
const TRUNCATE_SIZE: usize = size_of::<DocumentId>();
/// Extracts the embedding vector contained in each document under the `_vectors` field.
///
/// Returns the generated grenad reader containing the docid as key associated to the Vec<f32>
@ -27,45 +37,112 @@ pub fn extract_vector_points<R: io::Read + io::Seek>(
tempfile::tempfile()?,
);
let mut key_buffer = Vec::new();
let mut cursor = obkv_documents.into_cursor()?;
while let Some((key, value)) = cursor.move_on_next()? {
// this must always be serialized as (docid, external_docid);
let (docid_bytes, external_id_bytes) =
try_split_at(key, std::mem::size_of::<DocumentId>()).unwrap();
debug_assert!(std::str::from_utf8(external_id_bytes).is_ok());
debug_assert!(from_utf8(external_id_bytes).is_ok());
let obkv = obkv::KvReader::new(value);
key_buffer.clear();
key_buffer.extend_from_slice(docid_bytes);
// since we only needs the primary key when we throw an error we create this getter to
// lazily get it when needed
let document_id = || -> Value { std::str::from_utf8(external_id_bytes).unwrap().into() };
let document_id = || -> Value { from_utf8(external_id_bytes).unwrap().into() };
// first we retrieve the _vectors field
if let Some(vectors) = obkv.get(vectors_fid) {
// extract the vectors
let vectors = match from_slice(vectors) {
Ok(vectors) => VectorOrArrayOfVectors::into_array_of_vectors(vectors),
Err(_) => {
return Err(UserError::InvalidVectorsType {
document_id: document_id(),
value: from_slice(vectors).map_err(InternalError::SerdeJson)?,
}
.into())
}
};
if let Some(value) = obkv.get(vectors_fid) {
let vectors_obkv = KvReaderDelAdd::new(value);
if let Some(vectors) = vectors {
for (i, vector) in vectors.into_iter().enumerate().take(u16::MAX as usize) {
let index = u16::try_from(i).unwrap();
let mut key = docid_bytes.to_vec();
key.extend_from_slice(&index.to_be_bytes());
let bytes = cast_slice(&vector);
writer.insert(key, bytes)?;
}
}
// then we extract the values
let del_vectors = vectors_obkv
.get(DelAdd::Deletion)
.map(|vectors| extract_vectors(vectors, document_id))
.transpose()?
.flatten();
let add_vectors = vectors_obkv
.get(DelAdd::Addition)
.map(|vectors| extract_vectors(vectors, document_id))
.transpose()?
.flatten();
// and we finally push the unique vectors into the writer
push_vectors_diff(
&mut writer,
&mut key_buffer,
del_vectors.unwrap_or_default(),
add_vectors.unwrap_or_default(),
)?;
}
// else => the `_vectors` object was `null`, there is nothing to do
}
writer_into_reader(writer)
}
/// Computes the diff between both Del and Add numbers and
/// only inserts the parts that differ in the sorter.
fn push_vectors_diff(
writer: &mut Writer<BufWriter<File>>,
key_buffer: &mut Vec<u8>,
mut del_vectors: Vec<Vec<f32>>,
mut add_vectors: Vec<Vec<f32>>,
) -> Result<()> {
// We sort and dedup the vectors
del_vectors.sort_unstable_by(|a, b| compare_vectors(a, b));
add_vectors.sort_unstable_by(|a, b| compare_vectors(a, b));
del_vectors.dedup_by(|a, b| compare_vectors(a, b).is_eq());
add_vectors.dedup_by(|a, b| compare_vectors(a, b).is_eq());
let merged_vectors_iter =
itertools::merge_join_by(del_vectors, add_vectors, |del, add| compare_vectors(del, add));
// insert vectors into the writer
for (i, eob) in merged_vectors_iter.into_iter().enumerate().take(u16::MAX as usize) {
// Generate the key by extending the unique index to it.
key_buffer.truncate(TRUNCATE_SIZE);
let index = u16::try_from(i).unwrap();
key_buffer.extend_from_slice(&index.to_be_bytes());
match eob {
EitherOrBoth::Both(_, _) => (), // no need to touch anything
EitherOrBoth::Left(vector) => {
// We insert only the Del part of the Obkv to inform
// that we only want to remove all those vectors.
let mut obkv = KvWriterDelAdd::memory();
obkv.insert(DelAdd::Deletion, cast_slice(&vector))?;
let bytes = obkv.into_inner()?;
writer.insert(&key_buffer, bytes)?;
}
EitherOrBoth::Right(vector) => {
// We insert only the Add part of the Obkv to inform
// that we only want to remove all those vectors.
let mut obkv = KvWriterDelAdd::memory();
obkv.insert(DelAdd::Addition, cast_slice(&vector))?;
let bytes = obkv.into_inner()?;
writer.insert(&key_buffer, bytes)?;
}
}
}
Ok(())
}
/// Compares two vectors by using the OrderingFloat helper.
fn compare_vectors(a: &[f32], b: &[f32]) -> Ordering {
a.iter().copied().map(OrderedFloat).cmp(b.iter().copied().map(OrderedFloat))
}
/// Extracts the vectors from a JSON value.
fn extract_vectors(value: &[u8], document_id: impl Fn() -> Value) -> Result<Option<Vec<Vec<f32>>>> {
match from_slice(value) {
Ok(vectors) => Ok(VectorOrArrayOfVectors::into_array_of_vectors(vectors)),
Err(_) => Err(UserError::InvalidVectorsType {
document_id: document_id(),
value: from_slice(value).map_err(InternalError::SerdeJson)?,
}
.into()),
}
}

81
milli/src/update/index_documents/typed_chunk.rs
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@ -1,4 +1,4 @@
use std::collections::HashMap;
use std::collections::{HashMap, HashSet};
use std::convert::TryInto;
use std::fs::File;
use std::io::{self, BufReader};
@ -8,7 +8,9 @@ use charabia::{Language, Script};
use grenad::MergerBuilder;
use heed::types::ByteSlice;
use heed::RwTxn;
use log::error;
use obkv::{KvReader, KvWriter};
use ordered_float::OrderedFloat;
use roaring::RoaringBitmap;
use super::helpers::{self, merge_ignore_values, valid_lmdb_key, CursorClonableMmap};
@ -22,10 +24,9 @@ use crate::index::Hnsw;
use crate::update::del_add::{DelAdd, KvReaderDelAdd};
use crate::update::facet::FacetsUpdate;
use crate::update::index_documents::helpers::{as_cloneable_grenad, try_split_array_at};
use crate::update::index_documents::validate_document_id_value;
use crate::{
lat_lng_to_xyz, CboRoaringBitmapCodec, DocumentId, FieldId, GeoPoint, Index, InternalError,
Result, SerializationError, BEU32,
lat_lng_to_xyz, CboRoaringBitmapCodec, DocumentId, FieldId, GeoPoint, Index, Result,
SerializationError, BEU32,
};
pub(crate) enum TypedChunk {
@ -366,44 +367,70 @@ pub(crate) fn write_typed_chunk_into_index(
index.put_geo_faceted_documents_ids(wtxn, &geo_faceted_docids)?;
}
TypedChunk::VectorPoints(vector_points) => {
let (pids, mut points): (Vec<_>, Vec<_>) = match index.vector_hnsw(wtxn)? {
Some(hnsw) => hnsw.iter().map(|(pid, point)| (pid, point.clone())).unzip(),
None => Default::default(),
};
// Convert the PointIds into DocumentIds
let mut docids = Vec::new();
for pid in pids {
let docid =
index.vector_id_docid.get(wtxn, &BEU32::new(pid.into_inner()))?.unwrap();
docids.push(docid.get());
let mut vectors_set = HashSet::new();
// We extract and store the previous vectors
if let Some(hnsw) = index.vector_hnsw(wtxn)? {
for (pid, point) in hnsw.iter() {
let pid_key = BEU32::new(pid.into_inner());
let docid = index.vector_id_docid.get(wtxn, &pid_key)?.unwrap().get();
let vector: Vec<_> = point.iter().copied().map(OrderedFloat).collect();
vectors_set.insert((docid, vector));
}
}
let mut expected_dimensions = points.get(0).map(|p| p.len());
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 (left, _index) = try_split_array_at(key).unwrap();
let docid = DocumentId::from_be_bytes(left);
// convert the vector back to a Vec<f32>
let vector: Vec<f32> = pod_collect_to_vec(value);
// TODO Inform the user about the document that has a wrong `_vectors`
let found = vector.len();
let expected = *expected_dimensions.get_or_insert(found);
if expected != found {
return Err(UserError::InvalidVectorDimensions { expected, found }.into());
let vector_deladd_obkv = KvReaderDelAdd::new(value);
if let Some(value) = vector_deladd_obkv.get(DelAdd::Deletion) {
// convert the vector back to a Vec<f32>
let vector = pod_collect_to_vec(value).into_iter().map(OrderedFloat).collect();
let key = (docid, vector);
if !vectors_set.remove(&key) {
error!("Unable to delete the vector: {:?}", key.1);
}
}
if let Some(value) = vector_deladd_obkv.get(DelAdd::Addition) {
// convert the vector back to a Vec<f32>
let vector = pod_collect_to_vec(value).into_iter().map(OrderedFloat).collect();
vectors_set.insert((docid, vector));
}
points.push(NDotProductPoint::new(vector));
docids.push(docid);
}
assert_eq!(docids.len(), points.len());
// Extract the most common vector dimension
let expected_dimension_size = {
let mut dims = HashMap::new();
vectors_set.iter().for_each(|(_, v)| *dims.entry(v.len()).or_insert(0) += 1);
dims.into_iter().max_by_key(|(_, count)| *count).map(|(len, _)| len)
};
// Ensure that the vector lenghts are correct and
// prepare the vectors before inserting them in the HNSW.
let mut points = Vec::new();
let mut docids = Vec::new();
for (docid, vector) in vectors_set {
if expected_dimension_size.map_or(false, |expected| expected != vector.len()) {
return Err(UserError::InvalidVectorDimensions {
expected: expected_dimension_size.unwrap_or(vector.len()),
found: vector.len(),
}
.into());
} else {
let vector = vector.into_iter().map(OrderedFloat::into_inner).collect();
points.push(NDotProductPoint::new(vector));
docids.push(docid);
}
}
let hnsw_length = points.len();
let (new_hnsw, pids) = Hnsw::builder().build_hnsw(points);
assert_eq!(docids.len(), pids.len());
// Store the vectors in the point-docid relation database
index.vector_id_docid.clear(wtxn)?;
for (docid, pid) in docids.into_iter().zip(pids) {
index.vector_id_docid.put(