Introduce PointStorage and support variable length

instant-distance-py/Cargo.toml

@@ -18,11 +18,11 @@ crate-type = ["cdylib", "lib"]
 name = "instant_distance"
 
 [dependencies]
+aligned-vec = { version = "0.5.0", features = ["serde"] }
 bincode = "1.3.1"
 instant-distance = { version = "0.6", path = "../instant-distance", features = ["with-serde"] }
 pyo3 = { version = "0.18.0", features = ["extension-module"] }
 serde = { version = "1", features = ["derive"] }
-serde-big-array = "0.5.0"
 
 [dev-dependencies]
 bencher = "0.1.5"

instant-distance-py/benches/all.rs

@@ -1,7 +1,8 @@
+use aligned_vec::avec;
 use bencher::{benchmark_group, benchmark_main, Bencher};
 
 use instant_distance::{Builder, Metric, Search};
-use instant_distance_py::{EuclidMetric, FloatArray};
+use instant_distance_py::{EuclidMetric, PointStorage};
 use rand::{rngs::StdRng, Rng, SeedableRng};
 
 benchmark_main!(benches);
@@ -9,8 +10,8 @@ benchmark_group!(benches, distance, build, query);
 
 fn distance(bench: &mut Bencher) {
     let mut rng = StdRng::seed_from_u64(SEED);
-    let point_a = FloatArray([rng.gen(); 300]);
+    let point_a = avec![rng.gen(); 304];
-    let point_b = FloatArray([rng.gen(); 300]);
+    let point_b = avec![rng.gen(); 304];
 
     bench.iter(|| EuclidMetric::distance(&point_a, &point_b));
 }
@@ -18,25 +19,25 @@ fn distance(bench: &mut Bencher) {
 fn build(bench: &mut Bencher) {
     let mut rng = StdRng::seed_from_u64(SEED);
     let points = (0..1024)
-        .map(|_| FloatArray([rng.gen(); 300]))
+        .map(|_| vec![rng.gen(); 304])
         .collect::<Vec<_>>();
 
     bench.iter(|| {
         Builder::default()
             .seed(SEED)
-            .build_hnsw::<_, _, EuclidMetric, Vec<FloatArray>>(points.clone())
+            .build_hnsw::<Vec<f32>, [f32], EuclidMetric, PointStorage>(points.clone())
     });
 }
 
 fn query(bench: &mut Bencher) {
     let mut rng = StdRng::seed_from_u64(SEED);
     let points = (0..1024)
-        .map(|_| FloatArray([rng.gen(); 300]))
+        .map(|_| vec![rng.gen(); 304])
         .collect::<Vec<_>>();
     let (hnsw, _) = Builder::default()
         .seed(SEED)
-        .build_hnsw::<_, _, EuclidMetric, Vec<FloatArray>>(points);
+        .build_hnsw::<Vec<f32>, [f32], EuclidMetric, PointStorage>(points);
-    let point = FloatArray([rng.gen(); 300]);
+    let point = avec![rng.gen(); 304];
 
     bench.iter(|| {
         let mut search = Search::default();

instant-distance-py/src/lib.rs

@@ -4,16 +4,17 @@
 use std::convert::TryFrom;
 use std::fs::File;
 use std::io::{BufReader, BufWriter};
-use std::iter::FromIterator;
+use std::iter::{repeat, FromIterator};
+use std::ops::Index;
 
-use instant_distance::Metric;
+use aligned_vec::{AVec, ConstAlign};
+use instant_distance::{Len, Metric, PointId};
 use pyo3::conversion::IntoPy;
-use pyo3::exceptions::{PyTypeError, PyValueError};
+use pyo3::exceptions::PyValueError;
 use pyo3::types::{PyList, PyModule, PyString};
 use pyo3::{pyclass, pymethods, pymodule};
 use pyo3::{Py, PyAny, PyErr, PyObject, PyRef, PyRefMut, PyResult, Python};
 use serde::{Deserialize, Serialize};
-use serde_big_array::BigArray;
 
 #[pymodule]
 #[pyo3(name = "instant_distance")]
@@ -29,7 +30,7 @@ fn instant_distance_py(_: Python, m: &PyModule) -> PyResult<()> {
 
 #[pyclass]
 struct HnswMap {
-    inner: instant_distance::HnswMap<FloatArray, EuclidMetric, MapValue, Vec<FloatArray>>,
+    inner: instant_distance::HnswMap<[f32], EuclidMetric, MapValue, PointStorage>,
 }
 
 #[pymethods]
@@ -39,7 +40,12 @@ impl HnswMap {
     fn build(points: &PyList, values: &PyList, config: &Config) -> PyResult<Self> {
         let points = points
             .into_iter()
-            .map(FloatArray::try_from)
+            .map(|v| {
+                v.iter()?
+                    .into_iter()
+                    .map(|x| x?.extract())
+                    .collect::<Result<Vec<_>, PyErr>>()
+            })
             .collect::<Result<Vec<_>, PyErr>>()?;
 
         let values = values
@@ -47,16 +53,21 @@ impl HnswMap {
             .map(MapValue::try_from)
             .collect::<Result<Vec<_>, PyErr>>()?;
 
-        let hsnw_map = instant_distance::Builder::from(config).build(points, values);
+        let hsnw_map = instant_distance::Builder::from(config)
+            .build::<Vec<_>, [f32], EuclidMetric, MapValue, PointStorage>(points, values);
         Ok(Self { inner: hsnw_map })
     }
 
     /// Load an index from the given file name
     #[staticmethod]
     fn load(fname: &str) -> PyResult<Self> {
-        let hnsw_map = bincode::deserialize_from::<_, instant_distance::HnswMap<_, _, _, _>>(
+        let hnsw_map = bincode::deserialize_from::<
-            BufReader::with_capacity(32 * 1024 * 1024, File::open(fname)?),
+            _,
-        )
+            instant_distance::HnswMap<[f32], EuclidMetric, MapValue, PointStorage>,
+        >(BufReader::with_capacity(
+            32 * 1024 * 1024,
+            File::open(fname)?,
+        ))
         .map_err(|e| PyValueError::new_err(format!("deserialization error: {e:?}")))?;
         Ok(Self { inner: hnsw_map })
     }
@@ -77,7 +88,7 @@ impl HnswMap {
     ///
     /// For best performance, reusing `Search` objects is recommended.
     fn search(slf: Py<Self>, point: &PyAny, search: &mut Search, py: Python<'_>) -> PyResult<()> {
-        let point = FloatArray::try_from(point)?;
+        let point = try_avec_from_py(point)?;
         let _ = slf.try_borrow(py)?.inner.search(&point, &mut search.inner);
         search.cur = Some((HnswType::Map(slf.clone_ref(py)), 0));
         Ok(())
@@ -90,7 +101,7 @@ impl HnswMap {
 /// with a squared Euclidean distance metric.
 #[pyclass]
 struct Hnsw {
-    inner: instant_distance::Hnsw<FloatArray, EuclidMetric, Vec<FloatArray>>,
+    inner: instant_distance::Hnsw<[f32], EuclidMetric, PointStorage>,
 }
 
 #[pymethods]
@@ -100,10 +111,16 @@ impl Hnsw {
     fn build(input: &PyList, config: &Config) -> PyResult<(Self, Vec<u32>)> {
         let points = input
             .into_iter()
-            .map(FloatArray::try_from)
+            .map(|v| {
+                v.iter()?
+                    .into_iter()
+                    .map(|x| x?.extract())
+                    .collect::<Result<Vec<_>, PyErr>>()
+            })
             .collect::<Result<Vec<_>, PyErr>>()?;
 
-        let (inner, ids) = instant_distance::Builder::from(config).build_hnsw(points);
+        let (inner, ids) = instant_distance::Builder::from(config)
+            .build_hnsw::<Vec<f32>, [f32], EuclidMetric, PointStorage>(points);
         let ids = Vec::from_iter(ids.into_iter().map(|pid| pid.into_inner()));
         Ok((Self { inner }, ids))
     }
@@ -111,9 +128,13 @@ impl Hnsw {
     /// Load an index from the given file name
     #[staticmethod]
     fn load(fname: &str) -> PyResult<Self> {
-        let hnsw = bincode::deserialize_from::<_, instant_distance::Hnsw<_, _, _>>(
+        let hnsw = bincode::deserialize_from::<
-            BufReader::with_capacity(32 * 1024 * 1024, File::open(fname)?),
+            _,
-        )
+            instant_distance::Hnsw<[f32], EuclidMetric, PointStorage>,
+        >(BufReader::with_capacity(
+            32 * 1024 * 1024,
+            File::open(fname)?,
+        ))
         .map_err(|e| PyValueError::new_err(format!("deserialization error: {e:?}")))?;
         Ok(Self { inner: hnsw })
     }
@@ -134,7 +155,7 @@ impl Hnsw {
     ///
     /// For best performance, reusing `Search` objects is recommended.
     fn search(slf: Py<Self>, point: &PyAny, search: &mut Search, py: Python<'_>) -> PyResult<()> {
-        let point = FloatArray::try_from(point)?;
+        let point = try_avec_from_py(point)?;
         let _ = slf.try_borrow(py)?.inner.search(&point, &mut search.inner);
         search.cur = Some((HnswType::Hnsw(slf.clone_ref(py)), 0));
         Ok(())
@@ -144,7 +165,7 @@ impl Hnsw {
 /// Search buffer and result set
 #[pyclass]
 struct Search {
-    inner: instant_distance::Search<FloatArray, EuclidMetric>,
+    inner: instant_distance::Search<[f32], EuclidMetric>,
     cur: Option<(HnswType, usize)>,
 }
 
@@ -345,42 +366,36 @@ impl Neighbor {
     }
 }
 
-#[repr(align(32))]
+fn try_avec_from_py(value: &PyAny) -> Result<AVec<f32, ConstAlign<ALIGNMENT>>, PyErr> {
-#[derive(Clone, Deserialize, Serialize)]
+    let mut new = AVec::new(ALIGNMENT);
-pub struct FloatArray(#[serde(with = "BigArray")] pub [f32; DIMENSIONS]);
+    for val in value.iter()? {
-
+        new.push(val?.extract::<f32>()?);
-impl TryFrom<&PyAny> for FloatArray {
-    type Error = PyErr;
-
-    fn try_from(value: &PyAny) -> Result<Self, Self::Error> {
-        let mut new = FloatArray([0.0; DIMENSIONS]);
-        for (i, val) in value.iter()?.enumerate() {
-            match i >= DIMENSIONS {
-                true => return Err(PyTypeError::new_err("point array too long")),
-                false => new.0[i] = val?.extract::<f32>()?,
     }
+    for _ in 0..PointStorage::padding(new.len()) {
+        new.push(0.0);
     }
     Ok(new)
-    }
 }
 
 #[derive(Clone, Copy, Deserialize, Serialize)]
 pub struct EuclidMetric;
 
-impl Metric<FloatArray> for EuclidMetric {
+impl Metric<[f32]> for EuclidMetric {
-    fn distance(lhs: &FloatArray, rhs: &FloatArray) -> f32 {
+    fn distance(lhs: &[f32], rhs: &[f32]) -> f32 {
+        debug_assert_eq!(lhs.len(), rhs.len());
+
         #[cfg(target_arch = "x86_64")]
         {
             use std::arch::x86_64::{
                 _mm256_castps256_ps128, _mm256_extractf128_ps, _mm256_fmadd_ps, _mm256_load_ps,
                 _mm256_setzero_ps, _mm256_sub_ps, _mm_add_ps, _mm_add_ss, _mm_cvtss_f32,
-                _mm_fmadd_ps, _mm_load_ps, _mm_movehl_ps, _mm_shuffle_ps, _mm_sub_ps,
+                _mm_movehl_ps, _mm_shuffle_ps,
             };
-            debug_assert_eq!(lhs.0.len() % 8, 4);
+            debug_assert_eq!(lhs.len() % 8, 0);
 
             unsafe {
                 let mut acc_8x = _mm256_setzero_ps();
-                for (lh_slice, rh_slice) in lhs.0.chunks_exact(8).zip(rhs.0.chunks_exact(8)) {
+                for (lh_slice, rh_slice) in lhs.chunks_exact(8).zip(rhs.chunks_exact(8)) {
                     let lh_8x = _mm256_load_ps(lh_slice.as_ptr());
                     let rh_8x = _mm256_load_ps(rh_slice.as_ptr());
                     let diff = _mm256_sub_ps(lh_8x, rh_8x);
@@ -391,11 +406,6 @@ impl Metric<FloatArray> for EuclidMetric {
                 let right = _mm256_castps256_ps128(acc_8x); // lower half
                 acc_4x = _mm_add_ps(acc_4x, right); // sum halves
 
-                let lh_4x = _mm_load_ps(lhs.0[DIMENSIONS - 4..].as_ptr());
-                let rh_4x = _mm_load_ps(rhs.0[DIMENSIONS - 4..].as_ptr());
-                let diff = _mm_sub_ps(lh_4x, rh_4x);
-                acc_4x = _mm_fmadd_ps(diff, diff, acc_4x);
-
                 let lower = _mm_movehl_ps(acc_4x, acc_4x);
                 acc_4x = _mm_add_ps(acc_4x, lower);
                 let upper = _mm_shuffle_ps(acc_4x, acc_4x, 0x1);
@@ -412,6 +422,114 @@ impl Metric<FloatArray> for EuclidMetric {
     }
 }
 
+#[derive(Debug, Deserialize, Serialize)]
+pub struct PointStorage {
+    point_len: usize,
+    points_data: AVec<f32>,
+}
+
+impl PointStorage {
+    const fn padding(len: usize) -> usize {
+        let floats_per_alignment = ALIGNMENT / std::mem::size_of::<f32>();
+        match len % floats_per_alignment {
+            0 => 0,
+            floats_over_alignment => floats_per_alignment - floats_over_alignment,
+        }
+    }
+
+    pub fn iter(&self) -> impl Iterator<Item = &[f32]> {
+        self.points_data.chunks_exact(self.point_len)
+    }
+}
+
+impl Default for PointStorage {
+    fn default() -> Self {
+        Self {
+            point_len: 1,
+            points_data: AVec::new(ALIGNMENT),
+        }
+    }
+}
+
+impl Index<usize> for PointStorage {
+    type Output = [f32];
+
+    fn index(&self, index: usize) -> &Self::Output {
+        let raw_idx = index * self.point_len;
+        &self.points_data[raw_idx..(raw_idx + self.point_len)]
+    }
+}
+
+impl Index<PointId> for PointStorage {
+    type Output = [f32];
+
+    fn index(&self, index: PointId) -> &Self::Output {
+        self.index(index.into_inner() as usize)
+    }
+}
+
+impl From<Vec<Vec<f32>>> for PointStorage {
+    fn from(value: Vec<Vec<f32>>) -> Self {
+        if let Some(point) = value.first() {
+            let point_len = point.len();
+            let padding = PointStorage::padding(point_len);
+            let mut points_data =
+                AVec::with_capacity(ALIGNMENT, value.len() * (point_len + padding));
+            for point in value {
+                // all points should have the same length
+                debug_assert_eq!(point.len(), point_len);
+                for v in point.into_iter().chain(repeat(0.0).take(padding)) {
+                    points_data.push(v);
+                }
+            }
+            Self {
+                point_len: point_len + padding,
+                points_data,
+            }
+        } else {
+            Default::default()
+        }
+    }
+}
+
+impl Len for PointStorage {
+    fn len(&self) -> usize {
+        self.points_data.len() / self.point_len
+    }
+}
+
+impl<'a> IntoIterator for &'a PointStorage {
+    type Item = &'a [f32];
+
+    type IntoIter = PointStorageIterator<'a>;
+
+    fn into_iter(self) -> Self::IntoIter {
+        PointStorageIterator {
+            storage: self,
+            next_idx: 0,
+        }
+    }
+}
+
+pub struct PointStorageIterator<'a> {
+    storage: &'a PointStorage,
+    next_idx: usize,
+}
+
+impl<'a> Iterator for PointStorageIterator<'a> {
+    type Item = &'a [f32];
+
+    fn next(&mut self) -> Option<Self::Item> {
+        if self.next_idx < self.storage.len() {
+            let result = &self.storage[self.next_idx];
+            self.next_idx += 1;
+            Some(result)
+        } else {
+            None
+        }
+    }
+}
+
 #[derive(Clone, Deserialize, Serialize)]
 enum MapValue {
     String(String),
@@ -433,4 +551,4 @@ impl IntoPy<Py<PyAny>> for &'_ MapValue {
     }
 }
 
-const DIMENSIONS: usize = 300;
+const ALIGNMENT: usize = 32;