add multilayer kmeans script, fix l2 simd

Signed-off-by: Keming <[email protected]>

Author: kemingy

scripts/cluster.py

@@ -0,0 +1,118 @@
+from struct import unpack, pack
+from sys import argv
+from functools import partial
+
+from faiss import Kmeans
+import numpy as np
+from tqdm import tqdm
+
+
+def default_filter(vec):
+    return True
+
+
+def reservoir_sampling(iterator, k: int):
+    """Reservoir sampling from an iterator."""
+    res = []
+    while len(res) < k:
+        res.append(next(iterator))
+    for i, vec in enumerate(iterator, k + 1):
+        j = np.random.randint(0, i)
+        if j < k:
+            res[j] = vec
+    return res
+
+
+def read_vec_yield(
+    filepath: str, vec_type: np.dtype = np.float32, filter=default_filter
+):
+    """Read vectors and yield an iterator."""
+    size = np.dtype(vec_type).itemsize
+    with open(filepath, "rb") as f:
+        while True:
+            try:
+                buf = f.read(4)
+                if len(buf) == 0:
+                    break
+                dim = unpack("<i", buf)[0]
+                vec = np.frombuffer(f.read(dim * size), dtype=vec_type)
+                if filter(vec):
+                    yield vec
+            except Exception as err:
+                print(err)
+                break
+
+
+def read_vec(filepath: str, vec_type: np.dtype = np.float32):
+    """Read vectors from a file. Support `fvecs`, `ivecs` and `bvecs` format.
+    Args:
+        filepath: The path of the file.
+        vec_type: The type of the vectors.
+    """
+    size = np.dtype(vec_type).itemsize
+    with open(filepath, "rb") as f:
+        vecs = []
+        while True:
+            try:
+                buf = f.read(4)
+                if len(buf) == 0:
+                    break
+                dim = unpack("<i", buf)[0]
+                vecs.append(np.frombuffer(f.read(dim * size), dtype=vec_type))
+            except Exception as err:
+                print(err)
+                break
+    return np.array(vecs)
+
+
+def write_vec(filepath: str, vecs: np.ndarray, vec_type: np.dtype = np.float32):
+    """Write vectors to a file. Support `fvecs`, `ivecs` and `bvecs` format."""
+    with open(filepath, "wb") as f:
+        for vec in vecs:
+            f.write(pack("<i", len(vec)))
+            f.write(vec.tobytes())
+
+
+def hierarchical_kmeans(vecs, n_cluster_top, n_cluster_down):
+    dim = vecs.shape[1]
+    top = Kmeans(dim, n_cluster_top)
+    top.train(vecs)
+    _, labels = top.assign(vecs)
+
+    centroids = []
+    for i in range(n_cluster_top):
+        down = Kmeans(dim, n_cluster_down)
+        down.train(vecs[labels == i])
+        centroids.append(down.centroids)
+
+    return np.vstack(centroids)
+
+
+if __name__ == "__main__":
+    filename = argv[1]
+    top_n = int(argv[2])
+    down_n = int(argv[3])
+    max_point_per_cluster = 256
+    top_points = reservoir_sampling(
+        read_vec_yield(filename), top_n * max_point_per_cluster
+    )
+    dim = top_points[0].shape[0]
+
+    top_cluster = Kmeans(dim, top_n)
+    top_cluster.train(top_points)
+
+    def filter_label(label, vec):
+        _, label = top_cluster.assign(vec.reshape((1, -1)))
+        return label[0] == label
+
+    centroids = []
+    for i in tqdm(range(top_n)):
+        down_points = reservoir_sampling(
+            read_vec_yield(filename, filter=partial(filter_label, i)),
+            down_n * max_point_per_cluster,
+        )
+        down_cluster = Kmeans(dim, down_n)
+        down_cluster.train(down_points)
+        centroids.append(down_cluster.centroids)
+
+    write_vec(f"centroids_{top_n}_{down_n}.fvecs", np.vstack(centroids))

src/simd.rs

@@ -20,12 +20,10 @@ pub unsafe fn l2_squared_distance(lhs: &[f32], rhs: &[f32]) -> f32 {
     assert_eq!(lhs.len(), rhs.len());
     let mut lhs_ptr = lhs.as_ptr();
     let mut rhs_ptr = rhs.as_ptr();
-    let block_16_num = lhs.len() >> 4;
-    let rest_num = lhs.len() & 0b1111;
     let (mut diff, mut vx, mut vy): (__m256, __m256, __m256);
     let mut sum = _mm256_setzero_ps();
 
-    for _ in 0..block_16_num {
+    for _ in 0..(lhs.len() / 16) {
         vx = _mm256_loadu_ps(lhs_ptr);
         vy = _mm256_loadu_ps(rhs_ptr);
         lhs_ptr = lhs_ptr.add(8);
@@ -41,7 +39,7 @@ pub unsafe fn l2_squared_distance(lhs: &[f32], rhs: &[f32]) -> f32 {
         sum = _mm256_fmadd_ps(diff, diff, sum);
     }
 
-    for _ in 0..rest_num / 8 {
+    for _ in 0..((lhs.len() & 0b1111) / 8) {
         vx = _mm256_loadu_ps(lhs_ptr);
         vy = _mm256_loadu_ps(rhs_ptr);
         lhs_ptr = lhs_ptr.add(8);
@@ -65,7 +63,7 @@ pub unsafe fn l2_squared_distance(lhs: &[f32], rhs: &[f32]) -> f32 {
     }
 
     let mut res = reduce_f32_256(sum);
-    for _ in 0..rest_num {
+    for _ in 0..(lhs.len() & 0b111) {
         let residual = *lhs_ptr - *rhs_ptr;
         res += residual * residual;
         lhs_ptr = lhs_ptr.add(1);