[DiskBBQ] Use a HNSW graph to compute neighbours (elastic#134109)

Uses a HNSW structure to compute the neighbours when the number of centroid is over a threshold

Author: iverase

benchmarks/src/main/java/org/elasticsearch/benchmark/vector/ComputeNeighboursBenchmark.java

@@ -0,0 +1,77 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the "Elastic License
+ * 2.0", the "GNU Affero General Public License v3.0 only", and the "Server Side
+ * Public License v 1"; you may not use this file except in compliance with, at
+ * your election, the "Elastic License 2.0", the "GNU Affero General Public
+ * License v3.0 only", or the "Server Side Public License, v 1".
+ */
+
+package org.elasticsearch.benchmark.vector;
+
+import org.elasticsearch.common.logging.LogConfigurator;
+import org.elasticsearch.index.codec.vectors.cluster.NeighborHood;
+import org.openjdk.jmh.annotations.Benchmark;
+import org.openjdk.jmh.annotations.BenchmarkMode;
+import org.openjdk.jmh.annotations.Fork;
+import org.openjdk.jmh.annotations.Measurement;
+import org.openjdk.jmh.annotations.Mode;
+import org.openjdk.jmh.annotations.OutputTimeUnit;
+import org.openjdk.jmh.annotations.Param;
+import org.openjdk.jmh.annotations.Scope;
+import org.openjdk.jmh.annotations.Setup;
+import org.openjdk.jmh.annotations.State;
+import org.openjdk.jmh.annotations.Warmup;
+import org.openjdk.jmh.infra.Blackhole;
+
+import java.io.IOException;
+import java.util.Random;
+import java.util.concurrent.TimeUnit;
+
+@BenchmarkMode(Mode.AverageTime)
+@OutputTimeUnit(TimeUnit.SECONDS)
+@State(Scope.Benchmark)
+// first iteration is complete garbage, so make sure we really warmup
+@Warmup(iterations = 1, time = 1)
+// real iterations. not useful to spend tons of time here, better to fork more
+@Measurement(iterations = 3, time = 1)
+// engage some noise reduction
+@Fork(value = 1)
+public class ComputeNeighboursBenchmark {
+
+    static {
+        LogConfigurator.configureESLogging(); // native access requires logging to be initialized
+    }
+
+    @Param({ "1000", "2000", "3000", "5000", "10000", "20000", "50000" })
+    int numVectors;
+
+    @Param({ "384", "782", "1024" })
+    int dims;
+
+    float[][] vectors;
+    int clusterPerNeighbour = 128;
+
+    @Setup
+    public void setup() throws IOException {
+        Random random = new Random(123);
+        vectors = new float[numVectors][dims];
+        for (float[] vector : vectors) {
+            for (int i = 0; i < dims; i++) {
+                vector[i] = random.nextFloat();
+            }
+        }
+    }
+
+    @Benchmark
+    @Fork(jvmArgsPrepend = { "--add-modules=jdk.incubator.vector" })
+    public void bruteForce(Blackhole bh) {
+        bh.consume(NeighborHood.computeNeighborhoodsBruteForce(vectors, clusterPerNeighbour));
+    }
+
+    @Benchmark
+    @Fork(jvmArgsPrepend = { "--add-modules=jdk.incubator.vector" })
+    public void graph(Blackhole bh) throws IOException {
+        bh.consume(NeighborHood.computeNeighborhoodsGraph(vectors, clusterPerNeighbour));
+    }
+}

server/src/main/java/org/elasticsearch/index/codec/vectors/cluster/KMeansLocal.java

@@ -139,40 +139,40 @@ private static int getBestCentroidFromNeighbours(
         NeighborHood neighborhood,
         float[] distances
     ) {
-        final int limit = neighborhood.neighbors.length - 3;
+        final int limit = neighborhood.neighbors().length - 3;
         int bestCentroidOffset = centroidIdx;
         assert centroidIdx >= 0 && centroidIdx < centroids.length;
         float minDsq = VectorUtil.squareDistance(vector, centroids[centroidIdx]);
         int i = 0;
         for (; i < limit; i += 4) {
-            if (minDsq < neighborhood.maxIntraDistance) {
+            if (minDsq < neighborhood.maxIntraDistance()) {
                 // if the distance found is smaller than the maximum intra-cluster distance
                 // we don't consider it for further re-assignment
                 return bestCentroidOffset;
             }
             ESVectorUtil.squareDistanceBulk(
                 vector,
-                centroids[neighborhood.neighbors[i]],
-                centroids[neighborhood.neighbors[i + 1]],
-                centroids[neighborhood.neighbors[i + 2]],
-                centroids[neighborhood.neighbors[i + 3]],
+                centroids[neighborhood.neighbors()[i]],
+                centroids[neighborhood.neighbors()[i + 1]],
+                centroids[neighborhood.neighbors()[i + 2]],
+                centroids[neighborhood.neighbors()[i + 3]],
                 distances
             );
             for (int j = 0; j < distances.length; j++) {
                 float dsq = distances[j];
                 if (dsq < minDsq) {
                     minDsq = dsq;
-                    bestCentroidOffset = neighborhood.neighbors[i + j];
+                    bestCentroidOffset = neighborhood.neighbors()[i + j];
                 }
             }
         }
-        for (; i < neighborhood.neighbors.length; i++) {
-            if (minDsq < neighborhood.maxIntraDistance) {
+        for (; i < neighborhood.neighbors().length; i++) {
+            if (minDsq < neighborhood.maxIntraDistance()) {
                 // if the distance found is smaller than the maximum intra-cluster distance
                 // we don't consider it for further re-assignment
                 return bestCentroidOffset;
             }
-            int offset = neighborhood.neighbors[i];
+            int offset = neighborhood.neighbors()[i];
             // float score = neighborhood.scores[i];
             assert offset >= 0 && offset < centroids.length : "Invalid neighbor offset: " + offset;
             // compute the distance to the centroid
@@ -210,52 +210,6 @@ private static int getBestCentroid(float[][] centroids, float[] vector, float[]
         return bestCentroidOffset;
     }
 
-    private NeighborHood[] computeNeighborhoods(float[][] centers, int clustersPerNeighborhood) {
-        int k = centers.length;
-        assert k > clustersPerNeighborhood;
-        NeighborQueue[] neighborQueues = new NeighborQueue[k];
-        for (int i = 0; i < k; i++) {
-            neighborQueues[i] = new NeighborQueue(clustersPerNeighborhood, true);
-        }
-        final float[] scores = new float[4];
-        final int limit = k - 3;
-        for (int i = 0; i < k - 1; i++) {
-            float[] center = centers[i];
-            int j = i + 1;
-            for (; j < limit; j += 4) {
-                ESVectorUtil.squareDistanceBulk(center, centers[j], centers[j + 1], centers[j + 2], centers[j + 3], scores);
-                for (int h = 0; h < 4; h++) {
-                    neighborQueues[j + h].insertWithOverflow(i, scores[h]);
-                    neighborQueues[i].insertWithOverflow(j + h, scores[h]);
-                }
-            }
-            for (; j < k; j++) {
-                float dsq = VectorUtil.squareDistance(center, centers[j]);
-                neighborQueues[j].insertWithOverflow(i, dsq);
-                neighborQueues[i].insertWithOverflow(j, dsq);
-            }
-        }
-
-        NeighborHood[] neighborhoods = new NeighborHood[k];
-        for (int i = 0; i < k; i++) {
-            NeighborQueue queue = neighborQueues[i];
-            if (queue.size() == 0) {
-                // no neighbors, skip
-                neighborhoods[i] = NeighborHood.EMPTY;
-                continue;
-            }
-            // consume the queue into the neighbors array and get the maximum intra-cluster distance
-            int[] neighbors = new int[queue.size()];
-            float maxIntraDistance = queue.topScore();
-            int iter = 0;
-            while (queue.size() > 0) {
-                neighbors[neighbors.length - ++iter] = queue.pop();
-            }
-            neighborhoods[i] = new NeighborHood(neighbors, maxIntraDistance);
-        }
-        return neighborhoods;
-    }
-
     private void assignSpilled(
         FloatVectorValues vectors,
         KMeansIntermediate kmeansIntermediate,
@@ -299,8 +253,8 @@ private void assignSpilled(
             if (neighborhoods != null) {
                 assert neighborhoods[currAssignment] != null;
                 NeighborHood neighborhood = neighborhoods[currAssignment];
-                centroidCount = neighborhood.neighbors.length;
-                centroidOrds = c -> neighborhood.neighbors[c];
+                centroidCount = neighborhood.neighbors().length;
+                centroidOrds = c -> neighborhood.neighbors()[c];
             } else {
                 centroidCount = centroids.length - 1;
                 centroidOrds = c -> c < currAssignment ? c : c + 1; // skip the current centroid
@@ -344,10 +298,6 @@ private void assignSpilled(
         }
     }
 
-    record NeighborHood(int[] neighbors, float maxIntraDistance) {
-        static final NeighborHood EMPTY = new NeighborHood(new int[0], Float.POSITIVE_INFINITY);
-    }
-
     /**
      * cluster using a lloyd k-means algorithm that is not neighbor aware
      *
@@ -390,7 +340,7 @@ private void doCluster(FloatVectorValues vectors, KMeansIntermediate kMeansInter
         NeighborHood[] neighborhoods = null;
         // if there are very few centroids, don't bother with neighborhoods or neighbor aware clustering
         if (neighborAware && centroids.length > clustersPerNeighborhood) {
-            neighborhoods = computeNeighborhoods(centroids, clustersPerNeighborhood);
+            neighborhoods = NeighborHood.computeNeighborhoods(centroids, clustersPerNeighborhood);
         }
         cluster(vectors, kMeansIntermediate, neighborhoods);
         if (neighborAware && soarLambda >= 0) {