/* HNSW (Hierarchical Navigable Small World) Implementation. * * Based on the paper by Yu. A. Malkov, D. A. Yashunin. * * Many details of this implementation, not covered in the paper, were * obtained simulating different workloads and checking the connection * quality of the graph. * * Notably, this implementation: * * 1. Only uses bi-directional links, implementing strategies in order to * link new nodes even when candidates are full, and our new node would * be not close enough to replace old links in candidate. * * 2. We normalize on-insert, making cosine similarity and dot product the * same. This means we can't use euclidean distance or alike here. * Together with quantization, this provides an important speedup that * makes HNSW more practical. * * 3. The quantization used is int8. And it is performed per-vector, so the * "range" (max abs value) is also stored alongside with the quantized data. * * 4. This library implements true elements deletion, not just marking the * element as deleted, but removing it (we can do it since our links are * bidirectional), and reliking the nodes orphaned of one link among * them. * * Copyright (c) 2009-Present, Redis Ltd. * All rights reserved. * * Licensed under your choice of (a) the Redis Source Available License 2.0 * (RSALv2); or (b) the Server Side Public License v1 (SSPLv1); or (c) the * GNU Affero General Public License v3 (AGPLv3). * Originally authored by: Salvatore Sanfilippo. */ #define _DEFAULT_SOURCE #define _POSIX_C_SOURCE 200809L #include #include #include #include #include #include /* for INFINITY if not in math.h */ #include #include "hnsw.h" #include "mixer.h" /* Check if we can compile SIMD code with function attributes */ #if defined (__x86_64__) && ((defined(__GNUC__) && __GNUC__ >= 5) || (defined(__clang__) && __clang_major__ >= 4)) #if defined(__has_attribute) && __has_attribute(target) #define HAVE_AVX2 #define HAVE_AVX512 #endif #endif #if defined (HAVE_AVX2) #define ATTRIBUTE_TARGET_AVX2 __attribute__((target("avx2,fma"))) #define VSET_USE_AVX2 (__builtin_cpu_supports("avx2") && __builtin_cpu_supports("fma")) #else #define ATTRIBUTE_TARGET_AVX2 #define VSET_USE_AVX2 0 #endif #if defined (HAVE_AVX512) #define ATTRIBUTE_TARGET_AVX512 __attribute__((target("avx512f,fma"))) #define VSET_USE_AVX512 (__builtin_cpu_supports("avx512f")) #else #define ATTRIBUTE_TARGET_AVX512 #define VSET_USE_AVX512 0 #endif /* Include SIMD headers when supported */ #if defined(HAVE_AVX2) || defined(HAVE_AVX512) #include #endif #if 0 #define debugmsg printf #else #define debugmsg if(0) printf #endif #ifndef INFINITY #define INFINITY (1.0/0.0) #endif #define MIN(a,b) ((a) < (b) ? (a) : (b)) /* Algorithm parameters. */ #define HNSW_P 0.25 /* Probability of level increase. */ #define HNSW_MAX_LEVEL 16 /* Max level nodes can reach. */ #define HNSW_EF_C 200 /* Default size of dynamic candidate list while * inserting a new node, in case 0 is passed to * the 'ef' argument while inserting. This is also * used when deleting nodes for the search step * needed sometimes to reconnect nodes that remain * orphaned of one link. */ static void (*hfree)(void *p) = free; static void *(*hmalloc)(size_t s) = malloc; static void *(*hrealloc)(void *old, size_t s) = realloc; void hnsw_set_allocator(void (*free_ptr)(void*), void *(*malloc_ptr)(size_t), void *(*realloc_ptr)(void*, size_t)) { hfree = free_ptr; hmalloc = malloc_ptr; hrealloc = realloc_ptr; } // Get a warning if you use the libc allocator functions for mistake. #define malloc use_hmalloc_instead #define realloc use_hrealloc_instead #define free use_hfree_instead /* ============================== Prototypes ================================ */ void hnsw_cursor_element_deleted(HNSW *index, hnswNode *deleted); /* ============================ Priority queue ================================ * We need a priority queue to take an ordered list of candidates. Right now * it is implemented as a linear array, since it is relatively small. * * You may find it to be odd that we take the best element (smaller distance) * at the end of the array, but this way popping from the pqueue is O(1), as * we need to just decrement the count, and this is a very used operation * in a critical code path. This makes the priority queue implementation a * bit more complex in the insertion, but for good reasons. */ /* Maximum number of candidates we'll ever need (cit. Bill Gates). */ #define HNSW_MAX_CANDIDATES 256 typedef struct { hnswNode *node; float distance; } pqitem; typedef struct { pqitem *items; /* Array of items. */ uint32_t count; /* Current number of items. */ uint32_t cap; /* Maximum capacity. */ } pqueue; /* The HNSW algorithms access the pqueue conceptually from nearest (index 0) * to farthest (larger indexes) node, so the following macros are used to * access the pqueue in this fashion, even if the internal order is * actually reversed. */ #define pq_get_node(q,i) ((q)->items[(q)->count-(i+1)].node) #define pq_get_distance(q,i) ((q)->items[(q)->count-(i+1)].distance) /* Create a new priority queue with given capacity. Adding to the * pqueue only retains 'capacity' elements with the shortest distance. */ pqueue *pq_new(uint32_t capacity) { pqueue *pq = hmalloc(sizeof(*pq)); if (!pq) return NULL; pq->items = hmalloc(sizeof(pqitem) * capacity); if (!pq->items) { hfree(pq); return NULL; } pq->count = 0; pq->cap = capacity; return pq; } /* Free a priority queue. */ void pq_free(pqueue *pq) { if (!pq) return; hfree(pq->items); hfree(pq); } /* Insert maintaining distance order (higher distances first). */ void pq_push(pqueue *pq, hnswNode *node, float distance) { if (pq->count < pq->cap) { /* Queue not full: shift right from high distances to make room. */ uint32_t i = pq->count; while (i > 0 && pq->items[i-1].distance < distance) { pq->items[i] = pq->items[i-1]; i--; } pq->items[i].node = node; pq->items[i].distance = distance; pq->count++; } else { /* Queue full: if new item is worse than worst, ignore it. */ if (distance >= pq->items[0].distance) return; /* Otherwise shift left from low distances to drop worst. */ uint32_t i = 0; while (i < pq->cap-1 && pq->items[i+1].distance > distance) { pq->items[i] = pq->items[i+1]; i++; } pq->items[i].node = node; pq->items[i].distance = distance; } } /* Remove and return the top (closest) element, which is at count-1 * since we store elements with higher distances first. * Runs in constant time. */ hnswNode *pq_pop(pqueue *pq, float *distance) { if (pq->count == 0) return NULL; pq->count--; *distance = pq->items[pq->count].distance; return pq->items[pq->count].node; } /* Get distance of the furthest element. * An empty priority queue has infinite distance as its furthest element, * note that this behavior is needed by the algorithms below. */ float pq_max_distance(pqueue *pq) { if (pq->count == 0) return INFINITY; return pq->items[0].distance; } /* ============================ HNSW algorithm ============================== */ #if defined(HAVE_AVX512) /* AVX512 optimized dot product for float vectors */ ATTRIBUTE_TARGET_AVX512 float vectors_distance_float_avx512(const float *x, const float *y, uint32_t dim) { __m512 sum = _mm512_setzero_ps(); uint32_t i; /* Process 16 floats at a time with AVX512 */ for (i = 0; i + 15 < dim; i += 16) { __m512 vx = _mm512_loadu_ps(&x[i]); __m512 vy = _mm512_loadu_ps(&y[i]); sum = _mm512_fmadd_ps(vx, vy, sum); } /* Horizontal sum of the 16 elements in sum */ float dot = _mm512_reduce_add_ps(sum); /* Handle remaining elements */ for (; i < dim; i++) { dot += x[i] * y[i]; } return 1.0f - dot; } #endif /* HAVE_AVX512 */ #if defined(HAVE_AVX2) /* AVX2 optimized dot product for float vectors */ ATTRIBUTE_TARGET_AVX2 float vectors_distance_float_avx2(const float *x, const float *y, uint32_t dim) { __m256 sum1 = _mm256_setzero_ps(); __m256 sum2 = _mm256_setzero_ps(); uint32_t i; /* Process 16 floats at a time with two AVX2 registers */ for (i = 0; i + 15 < dim; i += 16) { __m256 vx1 = _mm256_loadu_ps(&x[i]); __m256 vy1 = _mm256_loadu_ps(&y[i]); __m256 vx2 = _mm256_loadu_ps(&x[i + 8]); __m256 vy2 = _mm256_loadu_ps(&y[i + 8]); sum1 = _mm256_fmadd_ps(vx1, vy1, sum1); sum2 = _mm256_fmadd_ps(vx2, vy2, sum2); } /* Combine the two sums */ __m256 combined = _mm256_add_ps(sum1, sum2); /* Horizontal sum of the 8 elements */ __m128 sum_high = _mm256_extractf128_ps(combined, 1); __m128 sum_low = _mm256_castps256_ps128(combined); __m128 sum_128 = _mm_add_ps(sum_high, sum_low); sum_128 = _mm_hadd_ps(sum_128, sum_128); sum_128 = _mm_hadd_ps(sum_128, sum_128); float dot = _mm_cvtss_f32(sum_128); /* Handle remaining elements */ for (; i < dim; i++) { dot += x[i] * y[i]; } return 1.0f - dot; } #endif /* HAVE_AVX2 */ /* Optimized dot product: automatically selects best available implementation * Dot product: our vectors are already normalized. * Version for not quantized vectors of floats. */ float vectors_distance_float(const float *x, const float *y, uint32_t dim) { #if defined(HAVE_AVX512) if (dim >= 16 && VSET_USE_AVX512) { return vectors_distance_float_avx512(x, y, dim); } #endif #if defined(HAVE_AVX2) if (VSET_USE_AVX2 && dim >= 16) { return vectors_distance_float_avx2(x, y, dim); } #endif /* Fallback to original scalar implementation */ float dot0 = 0.0f, dot1 = 0.0f; uint32_t i; /* Use two accumulators to reduce dependencies among multiplications. * This provides a clear speed boost in Apple silicon, but should be * help in general. */ for (i = 0; i + 7 < dim; i += 8) { dot0 += x[i] * y[i] + x[i+1] * y[i+1] + x[i+2] * y[i+2] + x[i+3] * y[i+3]; dot1 += x[i+4] * y[i+4] + x[i+5] * y[i+5] + x[i+6] * y[i+6] + x[i+7] * y[i+7]; } /* Handle the remaining elements. These are a minority in the case * of a small vector, don't optimize this part. */ for (; i < dim; i++) dot0 += x[i] * y[i]; /* The following line may be counter intuitive. The dot product of * normalized vectors is equivalent to their cosine similarity. The * cosine will be from -1 (vectors facing opposite directions in the * N-dim space) to 1 (vectors are facing in the same direction). * * We kinda want a "score" of distance from 0 to 2 (this is a distance * function and we want minimize the distance for K-NN searches), so we * can't just add 1: that would return a number in the 0-2 range, with * 0 meaning opposite vectors and 2 identical vectors, so this is * similarity, not distance. * * Returning instead (1 - dotprod) inverts the meaning: 0 is identical * and 2 is opposite, hence it is their distance. * * Why don't normalize the similarity right now, and return from 0 to * 1? Because division is costly. */ return 1.0f - (dot0 + dot1); } /* Q8 quants dotproduct. We do integer math and later fix it by range. */ float vectors_distance_q8(const int8_t *x, const int8_t *y, uint32_t dim, float range_a, float range_b) { // Handle zero vectors special case. if (range_a == 0 || range_b == 0) { /* Zero vector distance from anything is 1.0 * (since 1.0 - dot_product where dot_product = 0). */ return 1.0f; } /* Each vector is quantized from [-max_abs, +max_abs] to [-127, 127] * where range = 2*max_abs. */ const float scale_product = (range_a/127) * (range_b/127); int32_t dot0 = 0, dot1 = 0; uint32_t i; // Process 8 elements at a time for better pipeline utilization. for (i = 0; i + 7 < dim; i += 8) { dot0 += ((int32_t)x[i]) * ((int32_t)y[i]) + ((int32_t)x[i+1]) * ((int32_t)y[i+1]) + ((int32_t)x[i+2]) * ((int32_t)y[i+2]) + ((int32_t)x[i+3]) * ((int32_t)y[i+3]); dot1 += ((int32_t)x[i+4]) * ((int32_t)y[i+4]) + ((int32_t)x[i+5]) * ((int32_t)y[i+5]) + ((int32_t)x[i+6]) * ((int32_t)y[i+6]) + ((int32_t)x[i+7]) * ((int32_t)y[i+7]); } // Handle remaining elements. for (; i < dim; i++) dot0 += ((int32_t)x[i]) * ((int32_t)y[i]); // Convert to original range. float dotf = (dot0 + dot1) * scale_product; float distance = 1.0f - dotf; // Clamp distance to [0, 2]. if (distance < 0) distance = 0; else if (distance > 2) distance = 2; return distance; } static inline int popcount64(uint64_t x) { x = (x & 0x5555555555555555) + ((x >> 1) & 0x5555555555555555); x = (x & 0x3333333333333333) + ((x >> 2) & 0x3333333333333333); x = (x & 0x0F0F0F0F0F0F0F0F) + ((x >> 4) & 0x0F0F0F0F0F0F0F0F); x = (x & 0x00FF00FF00FF00FF) + ((x >> 8) & 0x00FF00FF00FF00FF); x = (x & 0x0000FFFF0000FFFF) + ((x >> 16) & 0x0000FFFF0000FFFF); x = (x & 0x00000000FFFFFFFF) + ((x >> 32) & 0x00000000FFFFFFFF); return x; } /* Binary vectors distance. */ float vectors_distance_bin(const uint64_t *x, const uint64_t *y, uint32_t dim) { uint32_t len = (dim+63)/64; uint32_t opposite = 0; for (uint32_t j = 0; j < len; j++) { uint64_t xor = x[j]^y[j]; opposite += popcount64(xor); } return (float)opposite*2/dim; } /* Dot product between nodes. Will call the right version depending on the * quantization used. */ float hnsw_distance(HNSW *index, hnswNode *a, hnswNode *b) { switch(index->quant_type) { case HNSW_QUANT_NONE: return vectors_distance_float(a->vector,b->vector,index->vector_dim); case HNSW_QUANT_Q8: return vectors_distance_q8(a->vector,b->vector,index->vector_dim,a->quants_range,b->quants_range); case HNSW_QUANT_BIN: return vectors_distance_bin(a->vector,b->vector,index->vector_dim); default: assert(1 != 1); return 0; } } /* This do Q8 'range' quantization. * For people looking at this code thinking: Oh, I could use min/max * quants instead! Well: I tried with min/max normalization but the dot * product needs to accumulate the sum for later correction, and it's slower. */ void quantize_to_q8(float *src, int8_t *dst, uint32_t dim, float *rangeptr) { float max_abs = 0; for (uint32_t j = 0; j < dim; j++) { if (src[j] > max_abs) max_abs = src[j]; if (-src[j] > max_abs) max_abs = -src[j]; } if (max_abs == 0) { if (rangeptr) *rangeptr = 0; memset(dst, 0, dim); return; } const float scale = 127.0f / max_abs; // Scale to map to [-127, 127]. for (uint32_t j = 0; j < dim; j++) { dst[j] = (int8_t)roundf(src[j] * scale); } if (rangeptr) *rangeptr = max_abs; // Return max_abs instead of 2*max_abs. } /* Binary quantization of vector 'src' to 'dst'. We use full words of * 64 bit as smallest unit, we will just set all the unused bits to 0 * so that they'll be the same in all the vectors, and when xor+popcount * is used to compute the distance, such bits are not considered. This * allows to go faster. */ void quantize_to_bin(float *src, uint64_t *dst, uint32_t dim) { memset(dst,0,(dim+63)/64*sizeof(uint64_t)); for (uint32_t j = 0; j < dim; j++) { uint32_t word = j/64; uint32_t bit = j&63; /* Since cosine similarity checks the vector direction and * not magnitudo, we do likewise in the binary quantization and * just remember if the component is positive or negative. */ if (src[j] > 0) dst[word] |= 1ULL< HNSW_MAX_M) m = HNSW_MAX_M; index->M = m; index->quant_type = quant_type; index->enter_point = NULL; index->max_level = 0; index->vector_dim = vector_dim; index->node_count = 0; index->last_id = 0; index->head = NULL; index->cursors = NULL; /* Initialize epochs array. */ for (int i = 0; i < HNSW_MAX_THREADS; i++) index->current_epoch[i] = 0; /* Initialize locks. */ if (pthread_rwlock_init(&index->global_lock, NULL) != 0) { hfree(index); return NULL; } for (int i = 0; i < HNSW_MAX_THREADS; i++) { if (pthread_mutex_init(&index->slot_locks[i], NULL) != 0) { /* Clean up previously initialized mutexes. */ for (int j = 0; j < i; j++) pthread_mutex_destroy(&index->slot_locks[j]); pthread_rwlock_destroy(&index->global_lock); hfree(index); return NULL; } } /* Initialize atomic variables. */ index->next_slot = 0; index->version = 0; return index; } /* Fill 'vec' with the node vector, de-normalizing and de-quantizing it * as needed. Note that this function will return an approximated version * of the original vector. */ void hnsw_get_node_vector(HNSW *index, hnswNode *node, float *vec) { if (index->quant_type == HNSW_QUANT_NONE) { memcpy(vec,node->vector,index->vector_dim*sizeof(float)); } else if (index->quant_type == HNSW_QUANT_Q8) { int8_t *quants = node->vector; for (uint32_t j = 0; j < index->vector_dim; j++) vec[j] = (quants[j]*node->quants_range)/127; } else if (index->quant_type == HNSW_QUANT_BIN) { uint64_t *bits = node->vector; for (uint32_t j = 0; j < index->vector_dim; j++) { uint32_t word = j/64; uint32_t bit = j&63; vec[j] = (bits[word] & (1ULL<quant_type != HNSW_QUANT_BIN) { for (uint32_t j = 0; j < index->vector_dim; j++) vec[j] *= node->l2; } } /* Return the number of bytes needed to represent a vector in the index, * that is function of the dimension of the vectors and the quantization * type used. */ uint32_t hnsw_quants_bytes(HNSW *index) { switch(index->quant_type) { case HNSW_QUANT_NONE: return index->vector_dim * sizeof(float); case HNSW_QUANT_Q8: return index->vector_dim; case HNSW_QUANT_BIN: return (index->vector_dim+63)/64*8; default: assert(0 && "Quantization type not supported."); } } /* Create new node. Returns NULL on out of memory. * It is possible to pass the vector as floats or, in case this index * was already stored on disk and is being loaded, or serialized and * transmitted in any form, the already quantized version in * 'qvector'. * * Only vector or qvector should be non-NULL. The reason why passing * a quantized vector is useful, is that because re-normalizing and * re-quantizing several times the same vector may accumulate rounding * errors. So if you work with quantized indexes, you should save * the quantized indexes. * * Note that, together with qvector, the quantization range is needed, * since this library uses per-vector quantization. In case of quantized * vectors the l2 is considered to be '1', so if you want to restore * the right l2 (to use the API that returns an approximation of the * original vector) make sure to save the l2 on disk and set it back * after the node creation (see later for the serialization API that * handles this and more). */ hnswNode *hnsw_node_new(HNSW *index, uint64_t id, const float *vector, const int8_t *qvector, float qrange, uint32_t level, int normalize) { hnswNode *node = hmalloc(sizeof(hnswNode)+(sizeof(hnswNodeLayer)*(level+1))); if (!node) return NULL; if (id == 0) id = ++index->last_id; node->level = level; node->id = id; node->next = NULL; node->vector = NULL; node->l2 = 1; // Default in case of already quantized vectors. It is // up to the caller to fill this later, if needed. /* Initialize visited epoch array. */ for (int i = 0; i < HNSW_MAX_THREADS; i++) node->visited_epoch[i] = 0; if (qvector == NULL) { /* Copy input vector. */ node->vector = hmalloc(sizeof(float) * index->vector_dim); if (!node->vector) { hfree(node); return NULL; } memcpy(node->vector, vector, sizeof(float) * index->vector_dim); if (normalize) hnsw_normalize_vector(node->vector,&node->l2,index->vector_dim); /* Handle quantization. */ if (index->quant_type != HNSW_QUANT_NONE) { void *quants = hmalloc(hnsw_quants_bytes(index)); if (quants == NULL) { hfree(node->vector); hfree(node); return NULL; } // Quantize. switch(index->quant_type) { case HNSW_QUANT_Q8: quantize_to_q8(node->vector,quants,index->vector_dim,&node->quants_range); break; case HNSW_QUANT_BIN: quantize_to_bin(node->vector,quants,index->vector_dim); break; default: assert(0 && "Quantization type not handled."); break; } // Discard the full precision vector. hfree(node->vector); node->vector = quants; } } else { // We got the already quantized vector. Just copy it. assert(index->quant_type != HNSW_QUANT_NONE); uint32_t vector_bytes = hnsw_quants_bytes(index); node->vector = hmalloc(vector_bytes); node->quants_range = qrange; if (node->vector == NULL) { hfree(node); return NULL; } memcpy(node->vector,qvector,vector_bytes); } /* Initialize each layer. */ for (uint32_t i = 0; i <= level; i++) { uint32_t max_links = (i == 0) ? index->M*2 : index->M; node->layers[i].max_links = max_links; node->layers[i].num_links = 0; node->layers[i].worst_distance = 0; node->layers[i].worst_idx = 0; node->layers[i].links = hmalloc(sizeof(hnswNode*) * max_links); if (!node->layers[i].links) { for (uint32_t j = 0; j < i; j++) hfree(node->layers[j].links); hfree(node->vector); hfree(node); return NULL; } } return node; } /* Free a node. */ void hnsw_node_free(hnswNode *node) { if (!node) return; for (uint32_t i = 0; i <= node->level; i++) hfree(node->layers[i].links); hfree(node->vector); hfree(node); } /* Free the entire index. */ void hnsw_free(HNSW *index,void(*free_value)(void*value)) { if (!index) return; hnswNode *current = index->head; while (current) { hnswNode *next = current->next; if (free_value) free_value(current->value); hnsw_node_free(current); current = next; } /* Destroy locks */ pthread_rwlock_destroy(&index->global_lock); for (int i = 0; i < HNSW_MAX_THREADS; i++) { pthread_mutex_destroy(&index->slot_locks[i]); } hfree(index); } /* Add node to linked list of nodes. We may need to scan the whole * HNSW graph for several reasons. The list is doubly linked since we * also need the ability to remove a node without scanning the whole thing. */ void hnsw_add_node(HNSW *index, hnswNode *node) { node->next = index->head; node->prev = NULL; if (index->head) index->head->prev = node; index->head = node; index->node_count++; } /* Search the specified layer starting from the specified entry point * to collect 'ef' nodes that are near to 'query'. * * This function implements optional hybrid search, so that each node * can be accepted or not based on its associated value. In this case * a callback 'filter_callback' should be passed, together with a maximum * effort for the search (number of candidates to evaluate), since even * with a a low "EF" value we risk that there are too few nodes that satisfy * the provided filter, and we could trigger a full scan. */ pqueue *search_layer_with_filter( HNSW *index, hnswNode *query, hnswNode *entry_point, uint32_t ef, uint32_t layer, uint32_t slot, int (*filter_callback)(void *value, void *privdata), void *filter_privdata, uint32_t max_candidates) { // Mark visited nodes with a never seen epoch. index->current_epoch[slot]++; pqueue *candidates = pq_new(HNSW_MAX_CANDIDATES); pqueue *results = pq_new(ef); if (!candidates || !results) { if (candidates) pq_free(candidates); if (results) pq_free(results); return NULL; } // Take track of the total effort: only used when filtering via // a callback to have a bound effort. uint32_t evaluated_candidates = 1; // Add entry point. float dist = hnsw_distance(index, query, entry_point); pq_push(candidates, entry_point, dist); if (filter_callback == NULL || filter_callback(entry_point->value, filter_privdata)) { pq_push(results, entry_point, dist); } entry_point->visited_epoch[slot] = index->current_epoch[slot]; // Process candidates. while (candidates->count > 0) { // Max effort. If zero, we keep scanning. if (filter_callback && max_candidates && evaluated_candidates >= max_candidates) break; float cur_dist; hnswNode *current = pq_pop(candidates, &cur_dist); evaluated_candidates++; float furthest = pq_max_distance(results); if (results->count >= ef && cur_dist > furthest) break; /* Check neighbors. */ for (uint32_t i = 0; i < current->layers[layer].num_links; i++) { hnswNode *neighbor = current->layers[layer].links[i]; if (neighbor->visited_epoch[slot] == index->current_epoch[slot]) continue; // Already visited during this scan. neighbor->visited_epoch[slot] = index->current_epoch[slot]; float neighbor_dist = hnsw_distance(index, query, neighbor); furthest = pq_max_distance(results); if (filter_callback == NULL) { /* Original HNSW logic when no filtering: * Add to results if better than current max or * results not full. */ if (neighbor_dist < furthest || results->count < ef) { pq_push(candidates, neighbor, neighbor_dist); pq_push(results, neighbor, neighbor_dist); } } else { /* With filtering: we add candidates even if doesn't match * the filter, in order to continue to explore the graph. */ if (neighbor_dist < furthest || candidates->count < ef) { pq_push(candidates, neighbor, neighbor_dist); } /* Add results only if passes filter. */ if (filter_callback(neighbor->value, filter_privdata)) { if (neighbor_dist < furthest || results->count < ef) { pq_push(results, neighbor, neighbor_dist); } } } } } pq_free(candidates); return results; } /* Just a wrapper without hybrid search callback. */ pqueue *search_layer(HNSW *index, hnswNode *query, hnswNode *entry_point, uint32_t ef, uint32_t layer, uint32_t slot) { return search_layer_with_filter(index, query, entry_point, ef, layer, slot, NULL, NULL, 0); } /* This function is used in order to initialize a node allocated in the * function stack with the specified vector. The idea is that we can * easily use hnsw_distance() from a vector and the HNSW nodes this way: * * hnswNode myQuery; * hnsw_init_tmp_node(myIndex,&myQuery,0,some_vector); * hnsw_distance(&myQuery, some_hnsw_node); * * Make sure to later free the node with: * * hnsw_free_tmp_node(&myQuery,some_vector); * You have to pass the vector to the free function, because sometimes * hnsw_init_tmp_node() may just avoid allocating a vector at all, * just reusing 'some_vector' pointer. * * Return 0 on out of memory, 1 on success. */ int hnsw_init_tmp_node(HNSW *index, hnswNode *node, int is_normalized, const float *vector) { node->vector = NULL; /* Work on a normalized query vector if the input vector is * not normalized. */ if (!is_normalized) { node->vector = hmalloc(sizeof(float)*index->vector_dim); if (node->vector == NULL) return 0; memcpy(node->vector,vector,sizeof(float)*index->vector_dim); hnsw_normalize_vector(node->vector,NULL,index->vector_dim); } else { node->vector = (float*)vector; } /* If quantization is enabled, our query fake node should be * quantized as well. */ if (index->quant_type != HNSW_QUANT_NONE) { void *quants = hmalloc(hnsw_quants_bytes(index)); if (quants == NULL) { if (node->vector != vector) hfree(node->vector); return 0; } switch(index->quant_type) { case HNSW_QUANT_Q8: quantize_to_q8(node->vector, quants, index->vector_dim, &node->quants_range); break; case HNSW_QUANT_BIN: quantize_to_bin(node->vector, quants, index->vector_dim); } if (node->vector != vector) hfree(node->vector); node->vector = quants; } return 1; } /* Free the stack allocated node initialized by hnsw_init_tmp_node(). */ void hnsw_free_tmp_node(hnswNode *node, const float *vector) { if (node->vector != vector) hfree(node->vector); } /* Return approximated K-NN items. Note that neighbors and distances * arrays must have space for at least 'k' items. * norm_query should be set to 1 if the query vector is already * normalized, otherwise, if 0, the function will copy the vector, * L2-normalize the copy and search using the normalized version. * * If the filter_privdata callback is passed, only elements passing the * specified filter (invoked with privdata and the value associated * to the node as arguments) are returned. In such case, if max_candidates * is not NULL, it represents the maximum number of nodes to explore, since * the search may be otherwise unbound if few or no elements pass the * filter. */ int hnsw_search_with_filter (HNSW *index, const float *query_vector, uint32_t k, hnswNode **neighbors, float *distances, uint32_t slot, int query_vector_is_normalized, int (*filter_callback)(void *value, void *privdata), void *filter_privdata, uint32_t max_candidates) { if (!index || !query_vector || !neighbors || k == 0) return -1; if (!index->enter_point) return 0; // Empty index. /* Use a fake node that holds the query vector, this way we can * use our normal node to node distance functions when checking * the distance between query and graph nodes. */ hnswNode query; if (hnsw_init_tmp_node(index,&query,query_vector_is_normalized,query_vector) == 0) return -1; // Start searching from the entry point. hnswNode *curr_ep = index->enter_point; /* Start from higher layer to layer 1 (layer 0 is handled later) * in the next section. Descend to the most similar node found * so far. */ for (int lc = index->max_level; lc > 0; lc--) { pqueue *results = search_layer(index, &query, curr_ep, 1, lc, slot); if (!results) continue; if (results->count > 0) { curr_ep = pq_get_node(results,0); } pq_free(results); } /* Search bottom layer (the most densely populated) with ef = k */ pqueue *results = search_layer_with_filter( index, &query, curr_ep, k, 0, slot, filter_callback, filter_privdata, max_candidates); if (!results) { hnsw_free_tmp_node(&query, query_vector); return -1; } /* Copy results. */ uint32_t found = MIN(k, results->count); for (uint32_t i = 0; i < found; i++) { neighbors[i] = pq_get_node(results,i); if (distances) { distances[i] = pq_get_distance(results,i); } } pq_free(results); hnsw_free_tmp_node(&query, query_vector); return found; } /* Wrapper to hnsw_search_with_filter() when no filter is needed. */ int hnsw_search(HNSW *index, const float *query_vector, uint32_t k, hnswNode **neighbors, float *distances, uint32_t slot, int query_vector_is_normalized) { return hnsw_search_with_filter(index,query_vector,k,neighbors, distances,slot,query_vector_is_normalized, NULL,NULL,0); } /* Rescan a node and update the wortst neighbor index. * The followinng two functions are variants of this function to be used * when links are added or removed: they may do less work than a full scan. */ void hnsw_update_worst_neighbor(HNSW *index, hnswNode *node, uint32_t layer) { float worst_dist = 0; uint32_t worst_idx = 0; for (uint32_t i = 0; i < node->layers[layer].num_links; i++) { float dist = hnsw_distance(index, node, node->layers[layer].links[i]); if (dist > worst_dist) { worst_dist = dist; worst_idx = i; } } node->layers[layer].worst_distance = worst_dist; node->layers[layer].worst_idx = worst_idx; } /* Update node worst neighbor distance information when a new neighbor * is added. */ void hnsw_update_worst_neighbor_on_add(HNSW *index, hnswNode *node, uint32_t layer, uint32_t added_index, float distance) { (void) index; // Unused but here for API symmetry. if (node->layers[layer].num_links == 1 || // First neighbor? distance > node->layers[layer].worst_distance) // New worst? { node->layers[layer].worst_distance = distance; node->layers[layer].worst_idx = added_index; } } /* Update node worst neighbor distance information when a linked neighbor * is removed. */ void hnsw_update_worst_neighbor_on_remove(HNSW *index, hnswNode *node, uint32_t layer, uint32_t removed_idx) { if (node->layers[layer].num_links == 0) { node->layers[layer].worst_distance = 0; node->layers[layer].worst_idx = 0; } else if (removed_idx == node->layers[layer].worst_idx) { hnsw_update_worst_neighbor(index,node,layer); } else if (removed_idx < node->layers[layer].worst_idx) { // Just update index if we removed element before worst. node->layers[layer].worst_idx--; } } /* We have a list of candidate nodes to link to the new node, when inserting * one. This function selects which nodes to link and performs the linking. * * Parameters: * * - 'candidates' is the priority queue of potential good nodes to link to the * new node 'new_node'. * - 'required_links' is as many links we would like our new_node to get * at the specified layer. * - 'aggressive' changes the strategy used to find good neighbors as follows: * * This function is called with aggressive=0 for all the layers, including * layer 0. When called like that, it will use the diversity of links and * quality of links checks before linking our new node with some candidate. * * However if the insert function finds that at layer 0, with aggressive=0, * few connections were made, it calls this function again with aggressiveness * levels greater up to 2. * * At aggressive=1, the diversity checks are disabled, and the candidate * node for linking is accepted even if it is nearest to an already accepted * neighbor than it is to the new node. * * When we link our new node by replacing the link of a candidate neighbor * that already has the max number of links, inevitably some other node loses * a connection (to make space for our new node link). In this case: * * 1. If such "dropped" node would remain with too little links, we try with * some different neighbor instead, however as the 'aggressive' parameter * has incremental values (0, 1, 2) we are more and more willing to leave * the dropped node with fever connections. * 2. If aggressive=2, we will scan the candidate neighbor node links to * find a different linked-node to replace, one better connected even if * its distance is not the worse. * * Note: this function is also called during deletion of nodes in order to * provide certain nodes with additional links. */ void select_neighbors(HNSW *index, pqueue *candidates, hnswNode *new_node, uint32_t layer, uint32_t required_links, int aggressive) { for (uint32_t i = 0; i < candidates->count; i++) { hnswNode *neighbor = pq_get_node(candidates,i); if (neighbor == new_node) continue; // Don't link node with itself. /* Use our cached distance among the new node and the candidate. */ float dist = pq_get_distance(candidates,i); /* First of all, since our links are all bidirectional, if the * new node for any reason has no longer room, or if it accumulated * the required number of links, return ASAP. */ if (new_node->layers[layer].num_links >= new_node->layers[layer].max_links || new_node->layers[layer].num_links >= required_links) return; /* If aggressive is true, it is possible that the new node * already got some link among the candidates (see the top comment, * this function gets re-called in case of too few links). * So we need to check if this candidate is already linked to * the new node. */ if (aggressive) { int duplicated = 0; for (uint32_t j = 0; j < new_node->layers[layer].num_links; j++) { if (new_node->layers[layer].links[j] == neighbor) { duplicated = 1; break; } } if (duplicated) continue; } /* Diversity check. We accept new candidates * only if there is no element already accepted that is nearest * to the candidate than the new element itself. * However this check is disabled if we have pressure to find * new links (aggressive != 0) */ if (!aggressive) { int diversity_failed = 0; for (uint32_t j = 0; j < new_node->layers[layer].num_links; j++) { float link_dist = hnsw_distance(index, neighbor, new_node->layers[layer].links[j]); if (link_dist < dist) { diversity_failed = 1; break; } } if (diversity_failed) continue; } /* If potential neighbor node has space, simply add the new link. * We will have space as well. */ uint32_t n = neighbor->layers[layer].num_links; if (n < neighbor->layers[layer].max_links) { /* Link candidate to new node. */ neighbor->layers[layer].links[n] = new_node; neighbor->layers[layer].num_links++; /* Update candidate worst link info. */ hnsw_update_worst_neighbor_on_add(index,neighbor,layer,n,dist); /* Link new node to candidate. */ uint32_t new_links = new_node->layers[layer].num_links; new_node->layers[layer].links[new_links] = neighbor; new_node->layers[layer].num_links++; /* Update new node worst link info. */ hnsw_update_worst_neighbor_on_add(index,new_node,layer,new_links,dist); continue; } /* ==================================================================== * Replacing existing candidate neighbor link step. * ================================================================== */ /* If we are here, our accepted candidate for linking is full. * * If new node is more distant to candidate than its current worst link * then we skip it: we would not be able to establish a bidirectional * connection without compromising link quality of candidate. * * At aggressiveness > 0 we don't care about this check. */ if (!aggressive && dist >= neighbor->layers[layer].worst_distance) continue; /* We can add it: we are ready to replace the candidate neighbor worst * link with the new node, assuming certain conditions are met. */ hnswNode *worst_node = neighbor->layers[layer].links[neighbor->layers[layer].worst_idx]; /* The worst node linked to our candidate may remain too disconnected * if we remove the candidate node as its link. Let's check if * this is the case: */ if (aggressive == 0 && worst_node->layers[layer].num_links <= index->M/2) continue; /* Aggressive level = 1. It's ok if the node remains with just * HNSW_M/4 links. */ else if (aggressive == 1 && worst_node->layers[layer].num_links <= index->M/4) continue; /* If aggressive is set to 2, then the new node we are adding failed * to find enough neighbors. We can't insert an almost orphaned new * node, so let's see if the target node has some other link * that is well connected in the graph: we could drop it instead * of the worst link. */ if (aggressive == 2 && worst_node->layers[layer].num_links <= index->M/4) { /* Let's see if we can find at least a candidate link that * would remain with a few connections. Track the one * that is the farthest away (worst distance) from our candidate * neighbor (in order to remove the less interesting link). */ worst_node = NULL; uint32_t worst_idx = 0; float max_dist = 0; for (uint32_t j = 0; j < neighbor->layers[layer].num_links; j++) { hnswNode *to_drop = neighbor->layers[layer].links[j]; /* Skip this if it would remain too disconnected as well. * * NOTE about index->M/4 min connections requirement: * * It is not too strict, since leaving a node with just a * single link does not just leave it too weakly connected, but * also sometimes creates cycles with few disconnected * nodes linked among them. */ if (to_drop->layers[layer].num_links <= index->M/4) continue; float link_dist = hnsw_distance(index, neighbor, to_drop); if (worst_node == NULL || link_dist > max_dist) { worst_node = to_drop; max_dist = link_dist; worst_idx = j; } } if (worst_node != NULL) { /* We found a node that we can drop. Let's pretend this is * the worst node of the candidate to unify the following * code path. Later we will fix the worst node info anyway. */ neighbor->layers[layer].worst_distance = max_dist; neighbor->layers[layer].worst_idx = worst_idx; } else { /* Otherwise we have no other option than reallocating * the max number of links for this target node, and * ensure at least a few connections for our new node. */ uint32_t reallocation_limit = layer == 0 ? index->M * 3 : index->M *2; if (neighbor->layers[layer].max_links >= reallocation_limit) continue; uint32_t new_max_links = neighbor->layers[layer].max_links+1; hnswNode **new_links = hrealloc(neighbor->layers[layer].links, sizeof(hnswNode*) * new_max_links); if (new_links == NULL) continue; // Non critical. /* Update neighbor's link capacity. */ neighbor->layers[layer].links = new_links; neighbor->layers[layer].max_links = new_max_links; /* Establish bidirectional link. */ uint32_t n = neighbor->layers[layer].num_links; neighbor->layers[layer].links[n] = new_node; neighbor->layers[layer].num_links++; hnsw_update_worst_neighbor_on_add(index, neighbor, layer, n, dist); n = new_node->layers[layer].num_links; new_node->layers[layer].links[n] = neighbor; new_node->layers[layer].num_links++; hnsw_update_worst_neighbor_on_add(index, new_node, layer, n, dist); continue; } } // Remove backlink from the worst node of our candidate. for (uint64_t j = 0; j < worst_node->layers[layer].num_links; j++) { if (worst_node->layers[layer].links[j] == neighbor) { memmove(&worst_node->layers[layer].links[j], &worst_node->layers[layer].links[j+1], (worst_node->layers[layer].num_links - j - 1) * sizeof(hnswNode*)); worst_node->layers[layer].num_links--; hnsw_update_worst_neighbor_on_remove(index,worst_node,layer,j); break; } } /* Replace worst link with the new node. */ neighbor->layers[layer].links[neighbor->layers[layer].worst_idx] = new_node; /* Update the worst link in the target node, at this point * the link that we replaced may no longer be the worst. */ hnsw_update_worst_neighbor(index,neighbor,layer); // Add new node -> candidate link. uint32_t new_links = new_node->layers[layer].num_links; new_node->layers[layer].links[new_links] = neighbor; new_node->layers[layer].num_links++; // Update new node worst link. hnsw_update_worst_neighbor_on_add(index,new_node,layer,new_links,dist); } } /* This function implements node reconnection after a node deletion in HNSW. * When a node is deleted, other nodes at the specified layer lose one * connection (all the neighbors of the deleted node). This function attempts * to pair such nodes together in a way that maximizes connection quality * among the M nodes that were former neighbors of our deleted node. * * The algorithm works by first building a distance matrix among the nodes: * * N0 N1 N2 N3 * N0 0 1.2 0.4 0.9 * N1 1.2 0 0.8 0.5 * N2 0.4 0.8 0 1.1 * N3 0.9 0.5 1.1 0 * * For each potential pairing (i,j) we compute a score that combines: * 1. The direct cosine distance between the two nodes * 2. The average distance to other nodes that would no longer be * available for pairing if we select this pair * * We want to balance local node-to-node requirements and global requirements. * For instance sometimes connecting A with B, while optimal, would leave * C and D to be connected without other choices, and this could be a very * bad connection. Maybe instead A and C and B and D are both relatively high * quality connections. * * The formula used to calculate the score of each connection is: * * score[i,j] = W1*(2-distance[i,j]) + W2*((new_avg_i + new_avg_j)/2) * where new_avg_x is the average of distances in row x excluding distance[i,j] * * So the score is directly proportional to the SIMILARITY of the two nodes * and also directly proportional to the DISTANCE of the potential other * connections that we lost by pairign i,j. So we have a cost for missed * opportunities, or better, in this case, a reward if the missing * opportunities are not so good (big average distance). * * W1 and W2 are weights (defaults: 0.7 and 0.3) that determine the relative * importance of immediate connection quality vs future pairing potential. * * After the initial pairing phase, any nodes that couldn't be paired * (due to odd count or existing connections) are handled by searching * the broader graph using the standard HNSW neighbor selection logic. */ void hnsw_reconnect_nodes(HNSW *index, hnswNode **nodes, int count, uint32_t layer) { if (count <= 0) return; debugmsg("Reconnecting %d nodes\n", count); /* Step 1: Build the distance matrix between all nodes. * Since distance(i,j) = distance(j,i), we only compute the upper triangle * and mirror it to the lower triangle. */ float *distances = hmalloc((unsigned long) count * count * sizeof(float)); if (!distances) return; for (int i = 0; i < count; i++) { distances[i*count + i] = 0; // Distance to self is 0 for (int j = i+1; j < count; j++) { float dist = hnsw_distance(index, nodes[i], nodes[j]); distances[i*count + j] = dist; // Upper triangle. distances[j*count + i] = dist; // Lower triangle. } } /* Step 2: Calculate row averages (will be used in scoring): * please note that we just calculate row averages and not * columns averages since the matrix is symmetrical, so those * are the same: check the image in the top comment if you have any * doubt about this. */ float *row_avgs = hmalloc(count * sizeof(float)); if (!row_avgs) { hfree(distances); return; } for (int i = 0; i < count; i++) { float sum = 0; int valid_count = 0; for (int j = 0; j < count; j++) { if (i != j) { sum += distances[i*count + j]; valid_count++; } } row_avgs[i] = valid_count ? sum / valid_count : 0; } /* Step 3: Build scoring matrix. What we do here is to combine how * good is a given i,j nodes connection, with how badly connecting * i,j will affect the remaining quality of connections left to * pair the other nodes. */ float *scores = hmalloc((unsigned long) count * count * sizeof(float)); if (!scores) { hfree(distances); hfree(row_avgs); return; } /* Those weights were obtained manually... No guarantee that they * are optimal. However with these values the algorithm is certain * better than its greedy version that just attempts to pick the * best pair each time (verified experimentally). */ const float W1 = 0.7; // Weight for immediate distance. const float W2 = 0.3; // Weight for future potential. for (int i = 0; i < count; i++) { for (int j = 0; j < count; j++) { if (i == j) { scores[i*count + j] = -1; // Invalid pairing. continue; } // Check for existing connection between i and j. int already_linked = 0; for (uint32_t k = 0; k < nodes[i]->layers[layer].num_links; k++) { if (nodes[i]->layers[layer].links[k] == nodes[j]) { scores[i*count + j] = -1; // Already linked. already_linked = 1; break; } } if (already_linked) continue; float dist = distances[i*count + j]; /* Calculate new averages excluding this pair. * Handle edge case where we might have too few elements. * Note that it would be not very smart to recompute the average * each time scanning the row, we can remove the element * and adjust the average without it. */ float new_avg_i = 0, new_avg_j = 0; if (count > 2) { new_avg_i = (row_avgs[i] * (count-1) - dist) / (count-2); new_avg_j = (row_avgs[j] * (count-1) - dist) / (count-2); } /* Final weighted score: the more similar i,j, the better * the score. The more distant are the pairs we lose by * connecting i,j, the better the score. */ scores[i*count + j] = W1*(2-dist) + W2*((new_avg_i + new_avg_j)/2); } } // Step 5: Pair nodes greedily based on scores. int *used = hmalloc(count*sizeof(int)); memset(used,0,count*sizeof(int)); if (!used) { hfree(distances); hfree(row_avgs); hfree(scores); return; } /* Scan the matrix looking each time for the potential * link with the best score. */ while(1) { float max_score = -1; int best_j = -1, best_i = -1; // Seek best score i,j values. for (int i = 0; i < count; i++) { if (used[i]) continue; // Already connected. /* No space left? Not possible after a node deletion but makes * this function more future-proof. */ if (nodes[i]->layers[layer].num_links >= nodes[i]->layers[layer].max_links) continue; for (int j = 0; j < count; j++) { if (i == j) continue; // Same node, skip. if (used[j]) continue; // Already connected. float score = scores[i*count + j]; if (score < 0) continue; // Invalid link. /* If the target node has space, and its score is better * than any other seen so far... remember it is the best. */ if (score > max_score && nodes[j]->layers[layer].num_links < nodes[j]->layers[layer].max_links) { // Track the best connection found so far. max_score = score; best_j = j; best_i = i; } } } // Possible link found? Connect i and j. if (best_j != -1) { debugmsg("[%d] linking %d with %d: %f\n", layer, (int)best_i, (int)best_j, max_score); // Link i -> j. int link_idx = nodes[best_i]->layers[layer].num_links; nodes[best_i]->layers[layer].links[link_idx] = nodes[best_j]; nodes[best_i]->layers[layer].num_links++; // Update worst distance if needed. float dist = distances[best_i*count + best_j]; hnsw_update_worst_neighbor_on_add(index,nodes[best_i],layer,link_idx,dist); // Link j -> i. link_idx = nodes[best_j]->layers[layer].num_links; nodes[best_j]->layers[layer].links[link_idx] = nodes[best_i]; nodes[best_j]->layers[layer].num_links++; // Update worst distance if needed. hnsw_update_worst_neighbor_on_add(index,nodes[best_j],layer,link_idx,dist); // Mark connection as used. used[best_i] = used[best_j] = 1; } else { break; // No more valid connections available. } } /* Step 6: Handle remaining unpaired nodes using the standard HNSW * neighbor selection. */ for (int i = 0; i < count; i++) { if (used[i]) continue; // Skip if node is already at max connections. if (nodes[i]->layers[layer].num_links >= nodes[i]->layers[layer].max_links) continue; debugmsg("[%d] Force linking %d\n", layer, i); /* First, try with local nodes as candidates. * Some candidate may have space. */ pqueue *candidates = pq_new(count); if (!candidates) continue; /* Add all the local nodes having some space as candidates * to be linked with this node. */ for (int j = 0; j < count; j++) { if (i != j && // Must not be itself. nodes[j]->layers[layer].num_links < // Must not be full. nodes[j]->layers[layer].max_links) { float dist = distances[i*count + j]; pq_push(candidates, nodes[j], dist); } } /* Try local candidates first with aggressive = 1. * So we will link only if there is space. * We want one link more than the links we already have. */ uint32_t wanted_links = nodes[i]->layers[layer].num_links+1; if (candidates->count > 0) { select_neighbors(index, candidates, nodes[i], layer, wanted_links, 1); debugmsg("Final links after attempt with local nodes: %d (wanted: %d)\n", (int)nodes[i]->layers[layer].num_links, wanted_links); } // If still no connection, search the broader graph. if (nodes[i]->layers[layer].num_links != wanted_links) { debugmsg("No force linking possible with local candidates\n"); pq_free(candidates); // Find entry point for target layer by descending through levels. hnswNode *curr_ep = index->enter_point; for (uint32_t lc = index->max_level; lc > layer; lc--) { pqueue *results = search_layer(index, nodes[i], curr_ep, 1, lc, 0); if (results) { if (results->count > 0) { curr_ep = pq_get_node(results,0); } pq_free(results); } } if (curr_ep) { /* Search this layer for candidates. * Use the default EF_C in this case, since it's not an * "insert" operation, and we don't know the user * specified "EF". */ candidates = search_layer(index, nodes[i], curr_ep, HNSW_EF_C, layer, 0); if (candidates) { /* Try to connect with aggressiveness proportional to the * node linking condition. */ int aggressiveness = (nodes[i]->layers[layer].num_links > index->M / 2) ? 1 : 2; select_neighbors(index, candidates, nodes[i], layer, wanted_links, aggressiveness); debugmsg("Final links with broader search: %d (wanted: %d)\n", (int)nodes[i]->layers[layer].num_links, wanted_links); pq_free(candidates); } } } else { pq_free(candidates); } } // Cleanup. hfree(distances); hfree(row_avgs); hfree(scores); hfree(used); } /* This is an helper function in order to support node deletion. * It's goal is just to: * * 1. Remove the node from the bidirectional links of neighbors in the graph. * 2. Remove the node from the linked list of nodes. * 3. Fix the entry point in the graph. We just select one of the neighbors * of the deleted node at a lower level. If none is found, we do * a full scan. * 4. The node itself amd its aux value field are NOT freed. It's up to the * caller to do it, by using hnsw_node_free(). * 5. The node associated value (node->value) is NOT freed. * * Why this function will not free the node? Because in node updates it * could be a good idea to reuse the node allocation for different reasons * (currently not implemented). * In general it is more future-proof to be able to reuse the node if * needed. Right now this library reuses the node only when links are * not touched (see hnsw_update() for more information). */ void hnsw_unlink_node(HNSW *index, hnswNode *node) { if (!index || !node) return; index->version++; // This node may be missing in an already compiled list // of neighbors. Make optimistic concurrent inserts fail. /* Remove all bidirectional links at each level. * Note that in this implementation all the * links are guaranteed to be bedirectional. */ /* For each level of the deleted node... */ for (uint32_t level = 0; level <= node->level; level++) { /* For each linked node of the deleted node... */ for (uint32_t i = 0; i < node->layers[level].num_links; i++) { hnswNode *linked = node->layers[level].links[i]; /* Find and remove the backlink in the linked node */ for (uint32_t j = 0; j < linked->layers[level].num_links; j++) { if (linked->layers[level].links[j] == node) { /* Remove by shifting remaining links left */ memmove(&linked->layers[level].links[j], &linked->layers[level].links[j + 1], (linked->layers[level].num_links - j - 1) * sizeof(hnswNode*)); linked->layers[level].num_links--; hnsw_update_worst_neighbor_on_remove(index,linked,level,j); break; } } } } /* Update cursors pointing at this element. */ if (index->cursors) hnsw_cursor_element_deleted(index,node); /* Update the previous node's next pointer. */ if (node->prev) { node->prev->next = node->next; } else { /* If there's no previous node, this is the head. */ index->head = node->next; } /* Update the next node's prev pointer. */ if (node->next) node->next->prev = node->prev; /* Update node count. */ index->node_count--; /* If this node was the enter_point, we need to update it. */ if (node == index->enter_point) { /* Reset entry point - we'll find a new one (unless the HNSW is * now empty) */ index->enter_point = NULL; index->max_level = 0; /* Step 1: Try to find a replacement by scanning levels * from top to bottom. Under normal conditions, if there is * any other node at the same level, we have a link. Anyway * we descend levels to find any neighbor at the higher level * possible. */ for (int level = node->level; level >= 0; level--) { if (node->layers[level].num_links > 0) { index->enter_point = node->layers[level].links[0]; break; } } /* Step 2: If no links were found at any level, do a full scan. * This should never happen in practice if the HNSW is not * empty. */ if (!index->enter_point) { uint32_t new_max_level = 0; hnswNode *current = index->head; while (current) { if (current != node && current->level >= new_max_level) { new_max_level = current->level; index->enter_point = current; } current = current->next; } } /* Update max_level. */ if (index->enter_point) index->max_level = index->enter_point->level; } /* Clear the node's links but don't free the node itself */ node->prev = node->next = NULL; } /* Higher level API for hnsw_unlink_node() + hnsw_reconnect_nodes() actual work. * This will get the write lock, will delete the node, free it, * reconnect the node neighbors among themselves, and unlock again. * If free_value function pointer is not NULL, then the function provided is * used to free node->value. * * The function returns 0 on error (inability to acquire the lock), otherwise * 1 is returned. */ int hnsw_delete_node(HNSW *index, hnswNode *node, void(*free_value)(void*value)) { if (pthread_rwlock_wrlock(&index->global_lock) != 0) return 0; hnsw_unlink_node(index,node); if (free_value && node->value) free_value(node->value); /* Relink all the nodes orphaned of this node link. * Do it for all the levels. */ for (unsigned int j = 0; j <= node->level; j++) { hnsw_reconnect_nodes(index, node->layers[j].links, node->layers[j].num_links, j); } hnsw_node_free(node); pthread_rwlock_unlock(&index->global_lock); return 1; } /* ============================ Threaded API ================================ * Concurrent readers should use the following API to get a slot assigned * (and a lock, too), do their read-only call, and unlock the slot. * * There is a reason why read operations don't implement opaque transparent * locking directly on behalf of the user: when we return a result set * with hnsw_search(), we report a set of nodes. The caller will do something * with the nodes and the associated values, so the unlocking of the * slot should happen AFTER the result was already used, otherwise we may * have changes to the HNSW nodes as the result is being accessed. */ /* Try to acquire a read slot. Returns the slot number (0 to HNSW_MAX_THREADS-1) * on success, -1 on error (pthread mutex errors). */ int hnsw_acquire_read_slot(HNSW *index) { /* First try a non-blocking approach on all slots. */ for (uint32_t i = 0; i < HNSW_MAX_THREADS; i++) { if (pthread_mutex_trylock(&index->slot_locks[i]) == 0) { if (pthread_rwlock_rdlock(&index->global_lock) != 0) { pthread_mutex_unlock(&index->slot_locks[i]); return -1; } return i; } } /* All trylock attempts failed, use atomic increment to select slot. */ uint32_t slot = index->next_slot++ % HNSW_MAX_THREADS; /* Try to lock the selected slot. */ if (pthread_mutex_lock(&index->slot_locks[slot]) != 0) return -1; /* Get read lock. */ if (pthread_rwlock_rdlock(&index->global_lock) != 0) { pthread_mutex_unlock(&index->slot_locks[slot]); return -1; } return slot; } /* Release a previously acquired read slot: note that it is important that * nodes returned by hnsw_search() are accessed while the read lock is * still active, to be sure that nodes are not freed. */ void hnsw_release_read_slot(HNSW *index, int slot) { if (slot < 0 || slot >= HNSW_MAX_THREADS) return; pthread_rwlock_unlock(&index->global_lock); pthread_mutex_unlock(&index->slot_locks[slot]); } /* ============================ Nodes insertion ============================= * We have an optimistic API separating the read-only candidates search * and the write side (actual node insertion). We internally also use * this API to provide the plain hnsw_insert() function for code unification. */ struct InsertContext { pqueue *level_queues[HNSW_MAX_LEVEL]; /* Candidates for each level. */ hnswNode *node; /* Pre-allocated node ready for insertion */ uint64_t version; /* Index version at preparation time. This is used * for CAS-like locking during change commit. */ }; /* Optimistic insertion API. * * WARNING: Note that this is an internal function: users should call * hnsw_prepare_insert() instead. * * This is how it works: you use hnsw_prepare_insert() and it will return * a context where good candidate neighbors are already pre-selected. * This step only uses read locks. * * Then finally you try to actually commit the new node with * hnsw_try_commit_insert(): this time we will require a write lock, but * for less time than it would be otherwise needed if using directly * hnsw_insert(). When you try to commit the write, if no node was deleted in * the meantime, your operation will succeed, otherwise it will fail, and * you should try to just use the hnsw_insert() API, since there is * contention. * * See hnsw_node_new() for information about 'vector' and 'qvector' * arguments, and which one to pass. */ InsertContext *hnsw_prepare_insert_nolock(HNSW *index, const float *vector, const int8_t *qvector, float qrange, uint64_t id, int slot, int ef) { InsertContext *ctx = hmalloc(sizeof(*ctx)); if (!ctx) return NULL; memset(ctx, 0, sizeof(*ctx)); ctx->version = index->version; /* Crete a new node that we may be able to insert into the * graph later, when calling the commit function. */ uint32_t level = random_level(); ctx->node = hnsw_node_new(index, id, vector, qvector, qrange, level, 1); if (!ctx->node) { hfree(ctx); return NULL; } hnswNode *curr_ep = index->enter_point; /* Empty graph, no need to collect candidates. */ if (curr_ep == NULL) return ctx; /* Phase 1: Find good entry point on the highest level of the new * node we are going to insert. */ for (unsigned int lc = index->max_level; lc > level; lc--) { pqueue *results = search_layer(index, ctx->node, curr_ep, 1, lc, slot); if (results) { if (results->count > 0) curr_ep = pq_get_node(results,0); pq_free(results); } } /* Phase 2: Collect a set of potential connections for each layer of * the new node. */ for (int lc = MIN(level, index->max_level); lc >= 0; lc--) { pqueue *candidates = search_layer(index, ctx->node, curr_ep, ef, lc, slot); if (!candidates) continue; curr_ep = (candidates->count > 0) ? pq_get_node(candidates,0) : curr_ep; ctx->level_queues[lc] = candidates; } return ctx; } /* External API for hnsw_prepare_insert_nolock(), handling locking. */ InsertContext *hnsw_prepare_insert(HNSW *index, const float *vector, const int8_t *qvector, float qrange, uint64_t id, int ef) { InsertContext *ctx; int slot = hnsw_acquire_read_slot(index); ctx = hnsw_prepare_insert_nolock(index,vector,qvector,qrange,id,slot,ef); hnsw_release_read_slot(index,slot); return ctx; } /* Free an insert context and all its resources. */ void hnsw_free_insert_context(InsertContext *ctx) { if (!ctx) return; for (uint32_t i = 0; i < HNSW_MAX_LEVEL; i++) { if (ctx->level_queues[i]) pq_free(ctx->level_queues[i]); } if (ctx->node) hnsw_node_free(ctx->node); hfree(ctx); } /* Commit a prepared insert operation. This function is a low level API that * should not be called by the user. See instead hnsw_try_commit_insert(), that * will perform the CAS check and acquire the write lock. * * See the top comment in hnsw_prepare_insert() for more information * on the optimistic insertion API. * * This function can't fail and always returns the pointer to the * just inserted node. Out of memory is not possible since no critical * allocation is never performed in this code path: we populate links * on already allocated nodes. */ hnswNode *hnsw_commit_insert_nolock(HNSW *index, InsertContext *ctx, void *value) { hnswNode *node = ctx->node; node->value = value; /* Handle first node case. */ if (index->enter_point == NULL) { index->version++; // First node, make concurrent inserts fail. index->enter_point = node; index->max_level = node->level; hnsw_add_node(index, node); ctx->node = NULL; // So hnsw_free_insert_context() will not free it. hnsw_free_insert_context(ctx); return node; } /* Connect the node with near neighbors at each level. */ for (int lc = MIN(node->level,index->max_level); lc >= 0; lc--) { if (ctx->level_queues[lc] == NULL) continue; /* Try to provide index->M connections to our node. The call * is not guaranteed to be able to provide all the links we would * like to have for the new node: they must be bi-directional, obey * certain quality checks, and so forth, so later there are further * calls to force the hand a bit if needed. * * Let's start with aggressiveness = 0. */ select_neighbors(index, ctx->level_queues[lc], node, lc, index->M, 0); /* Layer 0 and too few connections? Let's be more aggressive. */ if (lc == 0 && node->layers[0].num_links < index->M/2) { select_neighbors(index, ctx->level_queues[lc], node, lc, index->M, 1); /* Still too few connections? Let's go to * aggressiveness level '2' in linking strategy. */ if (node->layers[0].num_links < index->M/4) { select_neighbors(index, ctx->level_queues[lc], node, lc, index->M/4, 2); } } } /* If new node level is higher than current max, update entry point. */ if (node->level > index->max_level) { index->version++; // Entry point changed, make concurrent inserts fail. index->enter_point = node; index->max_level = node->level; } /* Add node to the linked list. */ hnsw_add_node(index, node); ctx->node = NULL; // So hnsw_free_insert_context() will not free the node. hnsw_free_insert_context(ctx); return node; } /* If the context obtained with hnsw_prepare_insert() is still valid * (nodes not deleted in the meantime) then add the new node to the HNSW * index and return its pointer. Otherwise NULL is returned and the operation * should be either performed with the blocking API hnsw_insert() or attempted * again. */ hnswNode *hnsw_try_commit_insert(HNSW *index, InsertContext *ctx, void *value) { /* Check if the version changed since preparation. Note that we * should access index->version under the write lock in order to * be sure we can safely commit the write: this is just a fast-path * in order to return ASAP without acquiring the write lock in case * the version changed. */ if (ctx->version != index->version) { hnsw_free_insert_context(ctx); return NULL; } /* Try to acquire write lock. */ if (pthread_rwlock_wrlock(&index->global_lock) != 0) { hnsw_free_insert_context(ctx); return NULL; } /* Check version again under write lock. */ if (ctx->version != index->version) { pthread_rwlock_unlock(&index->global_lock); hnsw_free_insert_context(ctx); return NULL; } /* Commit the change: note that it's up to hnsw_commit_insert_nolock() * to free the insertion context. */ hnswNode *node = hnsw_commit_insert_nolock(index, ctx, value); /* Release the write lock. */ pthread_rwlock_unlock(&index->global_lock); return node; } /* Insert a new element into the graph. * See hnsw_node_new() for information about 'vector' and 'qvector' * arguments, and which one to pass. * * Return NULL on out of memory during insert. Otherwise the newly * inserted node pointer is returned. */ hnswNode *hnsw_insert(HNSW *index, const float *vector, const int8_t *qvector, float qrange, uint64_t id, void *value, int ef) { /* Write lock. We acquire the write lock even for the prepare() * operation (that is a read-only operation) since we want this function * to don't fail in the check-and-set stage of commit(). * * Basically here we are using the optimistic API in a non-optimistinc * way in order to have a single insertion code in the implementation. */ if (pthread_rwlock_wrlock(&index->global_lock) != 0) return NULL; // Prepare the insertion - note we pass slot 0 since we're single threaded. InsertContext *ctx = hnsw_prepare_insert_nolock(index, vector, qvector, qrange, id, 0, ef); if (!ctx) { pthread_rwlock_unlock(&index->global_lock); return NULL; } // Commit the prepared insertion without version checking. hnswNode *node = hnsw_commit_insert_nolock(index, ctx, value); // Release write lock and return our node pointer. pthread_rwlock_unlock(&index->global_lock); return node; } /* Helper function for qsort call in hnsw_should_reuse_node(). */ static int compare_floats(const float *a, const float *b) { if (*a < *b) return 1; if (*a > *b) return -1; return 0; } /* This function determines if a node can be reused with a new vector by: * * 1. Computing average of worst 25% of current distances. * 2. Checking if at least 50% of new distances stay below this threshold. * 3. Requiring a minimum number of links for the check to be meaningful. * * This check is useful when we want to just update a node that already * exists in the graph. Often the new vector is a learned embedding generated * by some model, and the embedding represents some document that perhaps * changed just slightly compared to the past, so the new embedding will * be very nearby. We need to find a way do determine if the current node * neighbors (practically speaking its location in the grapb) are good * enough even with the new vector. * * XXX: this function needs improvements: successive updates to the same * node with more and more distant vectors will make the node drift away * from its neighbors. One of the additional metrics used could be * neighbor-to-neighbor distance, that represents a more absolute check * of fit for the new vector. */ int hnsw_should_reuse_node(HNSW *index, hnswNode *node, int is_normalized, const float *new_vector) { /* Step 1: Not enough links? Advice to avoid reuse. */ const uint32_t min_links_for_reuse = 4; uint32_t layer0_connections = node->layers[0].num_links; if (layer0_connections < min_links_for_reuse) return 0; /* Step2: get all current distances and run our heuristic. */ float *old_distances = hmalloc(sizeof(float) * layer0_connections); if (!old_distances) return 0; // Temporary node with the new vector, to simplify the next logic. hnswNode tmp_node; if (hnsw_init_tmp_node(index,&tmp_node,is_normalized,new_vector) == 0) { hfree(old_distances); return 0; } /* Get old dinstances and sort them to access the 25% worst * (bigger) ones. */ for (uint32_t i = 0; i < layer0_connections; i++) { old_distances[i] = hnsw_distance(index, node, node->layers[0].links[i]); } qsort(old_distances, layer0_connections, sizeof(float), (int (*)(const void*, const void*))(&compare_floats)); uint32_t count = (layer0_connections+3)/4; // 25% approx to larger int. if (count > layer0_connections) count = layer0_connections; // Futureproof. float worst_avg = 0; // Compute average of 25% worst dinstances. for (uint32_t i = 0; i < count; i++) worst_avg += old_distances[i]; worst_avg /= count; hfree(old_distances); // Count how many new distances stay below the threshold. uint32_t good_distances = 0; for (uint32_t i = 0; i < layer0_connections; i++) { float new_dist = hnsw_distance(index, &tmp_node, node->layers[0].links[i]); if (new_dist <= worst_avg) good_distances++; } hnsw_free_tmp_node(&tmp_node,new_vector); /* At least 50% of the nodes should pass our quality test, for the * node to be reused. */ return good_distances >= layer0_connections/2; } /** * Return a random node from the HNSW graph. * * This function performs a random walk starting from the entry point, * using only level 0 connections for navigation. It uses log^2(N) steps * to ensure proper mixing time. */ hnswNode *hnsw_random_node(HNSW *index, int slot) { if (index->node_count == 0 || index->enter_point == NULL) return NULL; (void)slot; // Unused, but we need the caller to acquire the lock. /* First phase: descend from max level to level 0 taking random paths. * Note that we don't need a more conservative log^2(N) steps for * proper mixing, since we already descend to a random cluster here. */ hnswNode *current = index->enter_point; for (uint32_t level = index->max_level; level > 0; level--) { /* If current node doesn't have this level or no links, continue * to lower level. */ if (current->level < level || current->layers[level].num_links == 0) continue; /* Choose random neighbor at this level. */ uint32_t rand_neighbor = rand() % current->layers[level].num_links; current = current->layers[level].links[rand_neighbor]; } /* Second phase: at level 0, take log(N) * c random steps. */ const int c = 3; // Multiplier for more thorough exploration. double logN = log2(index->node_count + 1); uint32_t num_walks = (uint32_t)(logN * c); /* Avoid the ping-pong effect: imagine there are just two nodes and * the number of walks selected is even. We will select always the * first element of the graph; conversely, if it is odd, we will always * select the other element. One way to add more selection randomness is * to randomly add '1' or '0' to the number of walks to perform. */ num_walks += rand() & 1; // Perform random walk at level 0. for (uint32_t i = 0; i < num_walks; i++) { if (current->layers[0].num_links == 0) return current; // Choose random neighbor. uint32_t rand_neighbor = rand() % current->layers[0].num_links; current = current->layers[0].links[rand_neighbor]; } return current; } /* ============================= Serialization ============================== * * TO SERIALIZE * ============ * * To serialize on disk, you need to persist the vector dimension, number * of elements, and the quantization type index->quant_type. These are * global values for the whole index. * * Then, to serialize each node: * * call hnsw_serialize_node() with each node you find in the linked list * of nodes, starting at index->head (each node has a next pointer). * The function will return an hnswSerNode structure, you will need * to store the following on disk (for each node): * * - The sernode->vector data, that is sernode->vector_size bytes. * - The sernode->params array, that points to an array of uint64_t * integers. There are sernode->params_count total items. These * parameters contain everything there is to need about your node: how * many levels it has, its ID, the list of neighbors for each level (as node * IDs), and so forth. * * You need to to save your own node->value in some way as well, but it already * belongs to the user of the API, since, for this library, it's just a pointer, * so the user should know how to serialized its private data. * * RELOADING FROM DISK / NET * ========================= * * When reloading nodes, you first load the index vector dimension and * quantization type, and create the index with: * * HNSW *hnsw_new(uint32_t vector_dim, uint32_t quant_type); * * Then you load back, for each node (you stored how many nodes you had) * the vector and the params array / count. * You also load the value associated with your node. * * At this point you add back the loaded elements into the index with: * * hnsw_insert_serialized(HNSW *index, void *vector, uint64_t params, * uint32_t params_len, void *value); * * Once you added all the nodes back, you need to resolve the pointers * (since so far they are added just with the node IDs as reference), so * you call: * * hnsw_deserialize_index(index); * * The index is now ready to be used like if it has been always in memory. * * DESIGN NOTES * ============ * * Why this API does not just give you a binary blob to save? Because in * many systems (and in Redis itself) to save integers / floats can have * more interesting encodings that just storing a 64 bit value. Many vector * indexes will be small, and their IDs will be small numbers, so the storage * system can exploit that and use less disk space, less network bandwidth * and so forth. * * How is the data stored in these arrays of numbers? Oh well, we have * things that are obviously numbers like node ID, number of levels for the * node and so forth. Also each of our nodes have an unique incremental ID, * so we can store a node set of links in terms of linked node IDs. This * data is put directly in the loaded node pointer space! We just cast the * integer to the pointer (so THIS IS NOT SAFE for 32 bit systems). Then * we want to translate such IDs into pointers. To do that, we build an * hash table, then scan all the nodes again and fix all the links converting * the ID to the pointer. */ /* History of serialization versions: * version 0: the first implementation, lacking worst node id/info. * version 1: includes worst link id/info. */ #define HNSW_SERIALIZATION_VERSION 1 /* This is a special worst link index that is set when loading a serialized * node with version 0 (this version of the serialization lacked explicit * information about the worst link index/distance). This way, later, the * function that fixes a deserialized index will know to compute the worst * index info at runtime. */ #define HNSW_SER_WORSTLINK_MISSING UINT32_MAX /* Return the serialized node information as specified in the top comment * above. Note that the returned information is true as long as the node * provided is not deleted or modified, so this function should be called * when there are no concurrent writes. * * The function hnsw_serialize_node() should be called in order to * free the result of this function. */ hnswSerNode *hnsw_serialize_node(HNSW *index, hnswNode *node) { /* The first step is calculating the number of uint64_t parameters * that we need in order to serialize the node. */ uint32_t num_params = 0; num_params += 2; // node ID, number of layers. for (uint32_t i = 0; i <= node->level; i++) { num_params += 2; // max_links and num_links info for this layer. num_params += node->layers[i].num_links; // The IDs of linked nodes. num_params += 1; // worst link id/distance parameter. } /* We use another 64bit value to store two floats that are about * the vector: l2 and quantization range (that is only used if the * vector is quantized). */ num_params++; /* Allocate the return object and the parameters array. */ hnswSerNode *sn = hmalloc(sizeof(hnswSerNode)); if (sn == NULL) return NULL; sn->params = hmalloc(sizeof(uint64_t)*num_params); if (sn->params == NULL) { hfree(sn); return NULL; } /* Fill data. */ sn->params_count = num_params; sn->vector = node->vector; sn->vector_size = hnsw_quants_bytes(index); uint32_t param_idx = 0; sn->params[param_idx++] = node->id; /* The second parameter contains information about the serialization * version of this node, the node level and some unused field: * * +--------+--------+--------+--------+ * |VVVVVVVV|........|........|LLLLLLLL| * +--------+--------+--------+--------+ * * V is the version, 8 bits. * L is the node level, 8 bits (but actually 16 is the max so far). * The middle two bytes are reserved for future uses. */ sn->params[param_idx] = node->level & 0xff; sn->params[param_idx] |= HNSW_SERIALIZATION_VERSION << 24; param_idx++; for (uint32_t i = 0; i <= node->level; i++) { sn->params[param_idx++] = node->layers[i].num_links; sn->params[param_idx++] = node->layers[i].max_links; for (uint32_t j = 0; j < node->layers[i].num_links; j++) { sn->params[param_idx++] = node->layers[i].links[j]->id; } /* Since version 1: pack and store worst_idx and worst_distance. */ uint32_t worst_distance_bits; memcpy(&worst_distance_bits, &node->layers[i].worst_distance, sizeof(float)); uint64_t wi = (((uint64_t)worst_distance_bits) << 32) | node->layers[i].worst_idx; sn->params[param_idx++] = wi; } /* Store l2 and range as uint32_t, in a way that is endian-safe. * Note that in big endian archs both are reversed: integers and * also the bytes of floats, so they will match. */ uint64_t l2_and_range; uint32_t l2_bits, range_bits; memcpy(&l2_bits,&node->l2,sizeof(float)); memcpy(&range_bits,&node->quants_range,sizeof(float)); l2_and_range = ((uint64_t)range_bits<<32) | l2_bits; sn->params[param_idx++] = l2_and_range; /* Better safe than sorry: */ assert(param_idx == num_params); return sn; } /* This is needed in order to free hnsw_serialize_node() returned * structure. */ void hnsw_free_serialized_node(hnswSerNode *sn) { hfree(sn->params); hfree(sn); } /* Load a serialized node. See the top comment in this section of code * for the documentation about how to use this. * * The function returns NULL both on out of memory and if the remaining * parameters length does not match the number of links or other items * to load. */ hnswNode *hnsw_insert_serialized(HNSW *index, void *vector, uint64_t *params, uint32_t params_len, void *value) { if (params_len < 2) return NULL; uint64_t id = params[0]; /* Check the node serialization function for the specific layout * of param[1] fields. */ uint32_t level = params[1] & 0xff; // Node level. uint32_t version = (params[1] & 0xff000000) >> 24; // Format version. if (version > HNSW_SERIALIZATION_VERSION) return NULL; int has_worst_link_info = version > 0; /* Keep track of maximum ID seen while loading. */ if (id >= index->last_id) index->last_id = id; /* Create node, passing vector data directly based on quantization type. */ hnswNode *node; if (index->quant_type != HNSW_QUANT_NONE) { node = hnsw_node_new(index, id, NULL, vector, 0, level, 0); } else { node = hnsw_node_new(index, id, vector, NULL, 0, level, 0); } if (!node) return NULL; /* Load params array into the node. */ uint32_t param_idx = 2; for (uint32_t i = 0; i <= level; i++) { /* Sanity check. */ if (param_idx + 2 + has_worst_link_info > params_len) { hnsw_node_free(node); return NULL; } uint32_t num_links = params[param_idx++]; uint32_t max_links = params[param_idx++]; /* Sanity check: links should be less than max links and * in general a reasonable amount. */ if (num_links > max_links || max_links > HNSW_MAX_M*4) { hnsw_node_free(node); return NULL; } /* If max_links is larger than current allocation, reallocate. * It could happen in select_neighbors() that we over-allocate the * node under very unlikely to happen conditions. */ if (max_links > node->layers[i].max_links) { hnswNode **new_links = hrealloc(node->layers[i].links, sizeof(hnswNode*) * max_links); if (!new_links) { hnsw_node_free(node); return NULL; } node->layers[i].links = new_links; node->layers[i].max_links = max_links; } node->layers[i].num_links = num_links; /* Sanity check. */ if (param_idx + num_links + has_worst_link_info > params_len) { hnsw_node_free(node); return NULL; } /* Fill links for this layer with the IDs. Note that this * is going to not work in 32 bit systems. Deleting / adding-back * nodes can produce IDs larger than 2^32-1 even if we can't never * fit more than 2^32 nodes in a 32 bit system. */ for (uint32_t j = 0; j < num_links; j++) node->layers[i].links[j] = (hnswNode*)params[param_idx++]; if (has_worst_link_info) { uint64_t wi = params[param_idx++]; uint32_t worst_idx = wi & 0xffffffff; uint32_t worst_distance_bits = wi >> 32; float worst_distance; memcpy(&worst_distance,&worst_distance_bits,sizeof(float)); node->layers[i].worst_idx = worst_idx; node->layers[i].worst_distance = worst_distance; // Sanity check the worst ID range. if (node->layers[i].num_links > 0 && node->layers[i].worst_idx >= node->layers[i].num_links) { hnsw_node_free(node); return NULL; } } else { node->layers[i].worst_idx = HNSW_SER_WORSTLINK_MISSING; node->layers[i].worst_distance = 0; } } /* Get l2 and quantization range. */ if (param_idx >= params_len) { hnsw_node_free(node); return NULL; } /* Load l2 and range packed into an uint64_t in an endian safe way. */ uint64_t l2_and_range = params[param_idx]; uint32_t l2_bits, range_bits; l2_bits = l2_and_range & 0xffffffff; range_bits = l2_and_range >> 32; memcpy(&node->l2, &l2_bits, sizeof(float)); memcpy(&node->quants_range, &range_bits, sizeof(float)); node->value = value; hnsw_add_node(index, node); /* Keep track of higher node level and set the entry point to the * greatest level node seen so far: thanks to this check we don't * need to remember what our entry point was during serialization. */ if (index->enter_point == NULL || level > index->max_level) { index->max_level = level; index->enter_point = node; } return node; } /* Integer hashing, used by hnsw_deserialize_index(). * MurmurHash3's 64-bit finalizer function. */ uint64_t hnsw_hash_node_id(uint64_t id) { id ^= id >> 33; id *= 0xff51afd7ed558ccd; id ^= id >> 33; id *= 0xc4ceb9fe1a85ec53; id ^= id >> 33; return id; } /* Helper for duplicated link detection in hnsw_deserialize_index(). */ static int qsort_compare_pointers(const void *aptr, const void *bptr) { uintptr_t a = *((uintptr_t*)aptr); uintptr_t b = *((uintptr_t*)bptr); if (a > b) return 1; if (a < b) return -1; return 0; } /* Fix pointers of neighbors nodes: after loading the serialized nodes, the * neighbors links are just IDs (casted to pointers), instead of the actual * pointers. We need to resolve IDs into pointers. * * The two integers salt0 and salt1 are used to make the internal state * of the function unguessable to an external attacker, in order to protect * from corruptions. Show be two random numbers from /dev/urandom if possible * otherwise can be just 0,0 if the application is not security critical and * never processes untrusted inputs. * * Return 0 on error (out of memory or some ID that can't be resolved), 1 on * success. */ int hnsw_deserialize_index(HNSW *index, uint64_t salt0, uint64_t salt1) { /* We will use simple linear probing, so over-allocating is a good * idea: anyway this flat array of pointers will consume a fraction * of the memory of the loaded index. */ uint64_t min_size = index->node_count*2; uint64_t table_size = 1; while(table_size < min_size) table_size <<= 1; hnswNode **table = hmalloc(sizeof(hnswNode*) * table_size); if (table == NULL) return 0; memset(table,0,sizeof(hnswNode*) * table_size); /* First pass: populate the ID -> pointer hash table. */ hnswNode *node = index->head; while(node) { uint64_t bucket = hnsw_hash_node_id(node->id) & (table_size-1); for (uint64_t j = 0; j < table_size; j++) { if (table[bucket] == NULL) { table[bucket] = node; break; } bucket = (bucket+1) & (table_size-1); } node = node->next; } /* Second pass: fix pointers of all the neighbors links. * As we scan and fix the links, we also compute the accumulator * register "reciprocal", that is used in order to guarantee that all * the links are reciprocal. * * This is how it works, we hash (using a strong hash function) the * following key for each link that we see from A to B (or vice versa): * * hash(salt || A || B || link-level) * * We always sort A and B, so the same link from A to B and from B to A * will hash the same. The we xor the result into the 128 bit accumulator. * If each link has its own backlink, the accumulator is guaranteed to * be zero at the end. * * Collisions are extremely unlikely to happen, and an external attacker * can't easily control the hash function output, since the salt is * unknown, and also there would be to control the pointers. * * This algorithm is O(1) for each node so it is basically free for * us, as we scan the list of nodes, and runs on constant and very * small memory. */ uint64_t accumulator[2] = {0,0}; node = index->head; // Rewind. while(node) { uint64_t this_node_id = node->id; for (uint32_t i = 0; i <= node->level; i++) { // Check if there are duplicated links: those are // also corruptions of the on-disk serialization format. if (node->layers[i].num_links > 0) { qsort(node->layers[i].links, node->layers[i].num_links, sizeof(void*), qsort_compare_pointers); for (uint32_t j = 0; j < node->layers[i].num_links-1; j++) { if (node->layers[i].links[j] == node->layers[i].links[j+1]) goto corrupted; } } // Resolve pointers. for (uint32_t j = 0; j < node->layers[i].num_links; j++) { uint64_t linked_id = (uint64_t) node->layers[i].links[j]; // We can't link to our own node. if (linked_id == this_node_id) goto corrupted; // Compute accumulator for reciprocal links check. uint64_t mixed_h1, mixed_h2; secure_pair_mixer_128(salt0, salt1, this_node_id, linked_id, (uint64_t)i, &mixed_h1, &mixed_h2); accumulator[0] ^= mixed_h1; accumulator[1] ^= mixed_h2; // Fix links. uint64_t bucket = hnsw_hash_node_id(linked_id) & (table_size-1); hnswNode *neighbor = NULL; for (uint64_t k = 0; k < table_size; k++) { if (table[bucket] && table[bucket]->id == linked_id) { neighbor = table[bucket]; break; } bucket = (bucket+1) & (table_size-1); } /* The neighbor must exist and also exist at the right * level. */ if (neighbor == NULL || neighbor->level < i) { /* Unresolved link! Either a bug in this code * or broken serialization data. */ goto corrupted; } node->layers[i].links[j] = neighbor; } /* The worst link information was missing from older * serialization formats. Compute it on the fly if needed. */ if (node->layers[i].worst_idx == HNSW_SER_WORSTLINK_MISSING) { hnsw_update_worst_neighbor(index,node,i); } } node = node->next; } /* Check that links are reciprocal, otherwise fail. */ if (accumulator[0] || accumulator[1]) goto corrupted; /* Everything fine. Return success. */ hfree(table); return 1; corrupted: /* Some corruption error detected. */ hfree(table); return 0; } /* ================================ Iterator ================================ */ /* Get a cursor that can be used as argument of hnsw_cursor_next() to iterate * all the elements that remain there from the start to the end of the * iteration, excluding newly added elements. * * The function returns NULL on out of memory. */ hnswCursor *hnsw_cursor_init(HNSW *index) { if (pthread_rwlock_wrlock(&index->global_lock) != 0) return NULL; hnswCursor *cursor = hmalloc(sizeof(*cursor)); if (cursor == NULL) { pthread_rwlock_unlock(&index->global_lock); return NULL; } cursor->index = index; cursor->next = index->cursors; cursor->current = index->head; index->cursors = cursor; pthread_rwlock_unlock(&index->global_lock); return cursor; } /* Free the cursor. Can be called both at the end of the iteration, when * hnsw_cursor_next() returned NULL, or before. */ void hnsw_cursor_free(hnswCursor *cursor) { HNSW *index = cursor->index; if (pthread_rwlock_wrlock(&index->global_lock) != 0) { // No easy way to recover from that. We will leak memory. return; } hnswCursor *x = index->cursors; hnswCursor *prev = NULL; while(x) { if (x == cursor) { if (prev) prev->next = cursor->next; else index->cursors = cursor->next; hfree(cursor); break; } prev = x; x = x->next; } pthread_rwlock_unlock(&index->global_lock); } /* Acquire a lock to use the cursor. Returns 1 if the lock was acquired * with success, otherwise zero is returned. The returned element is * protected after calling hnsw_cursor_next() for all the time required to * access it, then hnsw_cursor_release_lock() should be called in order * to unlock the HNSW index. */ int hnsw_cursor_acquire_lock(hnswCursor *cursor) { return pthread_rwlock_rdlock(&cursor->index->global_lock) == 0; } /* Release the cursor lock, see hnsw_cursor_acquire_lock() top comment * for more information. */ void hnsw_cursor_release_lock(hnswCursor *cursor) { pthread_rwlock_unlock(&cursor->index->global_lock); } /* Return the next element of the HNSW. See hnsw_cursor_init() for * the guarantees of the function. */ hnswNode *hnsw_cursor_next(hnswCursor *cursor) { hnswNode *ret = cursor->current; if (ret) cursor->current = ret->next; return ret; } /* Called by hnsw_unlink_node() if there is at least an active cursor. * Will scan the cursors to see if any cursor is going to yield this * one, and in this case, updates the current element to the next. */ void hnsw_cursor_element_deleted(HNSW *index, hnswNode *deleted) { hnswCursor *x = index->cursors; while(x) { if (x->current == deleted) x->current = deleted->next; x = x->next; } } /* ============================ Debugging stuff ============================= */ /* Show stats about nodes connections. */ void hnsw_print_stats(HNSW *index) { if (!index || !index->head) { printf("Empty index or NULL pointer passed\n"); return; } long long total_links = 0; int min_links = -1; // We'll set this to first node's count. int isolated_nodes = 0; uint32_t node_count = 0; // Iterate through all nodes using the linked list. hnswNode *current = index->head; while (current) { // Count total links for this node across all layers. int node_total_links = 0; for (uint32_t layer = 0; layer <= current->level; layer++) node_total_links += current->layers[layer].num_links; // Update statistics. total_links += node_total_links; // Initialize or update minimum links. if (min_links == -1 || node_total_links < min_links) { min_links = node_total_links; } // Check if node is isolated (no links at all). if (node_total_links == 0) isolated_nodes++; node_count++; current = current->next; } // Print statistics printf("HNSW Graph Statistics:\n"); printf("----------------------\n"); printf("Total nodes: %u\n", node_count); if (node_count > 0) { printf("Average links per node: %.2f\n", (float)total_links / node_count); printf("Minimum links in a single node: %d\n", min_links); printf("Number of isolated nodes: %d (%.1f%%)\n", isolated_nodes, (float)isolated_nodes * 100 / node_count); } } /* Validate graph connectivity and link reciprocity. Takes pointers to store results: * - connected_nodes: will contain number of reachable nodes from entry point. * - reciprocal_links: will contain 1 if all links are reciprocal, 0 otherwise. * Returns 0 on success, -1 on error (NULL parameters and such). */ int hnsw_validate_graph(HNSW *index, uint64_t *connected_nodes, int *reciprocal_links) { if (!index || !connected_nodes || !reciprocal_links) return -1; if (!index->enter_point) { *connected_nodes = 0; *reciprocal_links = 1; // Empty graph is valid. return 0; } // Initialize connectivity check. index->current_epoch[0]++; *connected_nodes = 0; *reciprocal_links = 1; // Initialize node stack. uint64_t stack_size = index->node_count; hnswNode **stack = hmalloc(sizeof(hnswNode*) * stack_size); if (!stack) return -1; uint64_t stack_top = 0; // Start from entry point. index->enter_point->visited_epoch[0] = index->current_epoch[0]; (*connected_nodes)++; stack[stack_top++] = index->enter_point; // Process all reachable nodes. while (stack_top > 0) { hnswNode *current = stack[--stack_top]; // Explore all neighbors at each level. for (uint32_t level = 0; level <= current->level; level++) { for (uint64_t i = 0; i < current->layers[level].num_links; i++) { hnswNode *neighbor = current->layers[level].links[i]; // Check reciprocity. int found_backlink = 0; for (uint64_t j = 0; j < neighbor->layers[level].num_links; j++) { if (neighbor->layers[level].links[j] == current) { found_backlink = 1; break; } } if (!found_backlink) { *reciprocal_links = 0; } // If we haven't visited this neighbor yet. if (neighbor->visited_epoch[0] != index->current_epoch[0]) { neighbor->visited_epoch[0] = index->current_epoch[0]; (*connected_nodes)++; if (stack_top < stack_size) { stack[stack_top++] = neighbor; } else { // This should never happen in a valid graph. hfree(stack); return -1; } } } } } hfree(stack); // Now scan for unreachable nodes and print debug info. printf("\nUnreachable nodes debug information:\n"); printf("=====================================\n"); hnswNode *current = index->head; while (current) { if (current->visited_epoch[0] != index->current_epoch[0]) { printf("\nUnreachable node found:\n"); printf("- Node pointer: %p\n", (void*)current); printf("- Node ID: %llu\n", (unsigned long long)current->id); printf("- Node level: %u\n", current->level); // Print info about all its links at each level. for (uint32_t level = 0; level <= current->level; level++) { printf(" Level %u links (%u):\n", level, current->layers[level].num_links); for (uint64_t i = 0; i < current->layers[level].num_links; i++) { hnswNode *neighbor = current->layers[level].links[i]; // Check reciprocity for this specific link int found_backlink = 0; for (uint64_t j = 0; j < neighbor->layers[level].num_links; j++) { if (neighbor->layers[level].links[j] == current) { found_backlink = 1; break; } } printf(" - Link %llu: pointer=%p, id=%llu, visited=%s,recpr=%s\n", (unsigned long long)i, (void*)neighbor, (unsigned long long)neighbor->id, neighbor->visited_epoch[0] == index->current_epoch[0] ? "yes" : "no", found_backlink ? "yes" : "no"); } } } current = current->next; } printf("Total connected nodes: %llu\n", (unsigned long long)*connected_nodes); printf("All links are bi-directiona? %s\n", (*reciprocal_links)?"yes":"no"); return 0; } /* Test graph recall ability by verifying each node can be found searching * for its own vector. This helps validate that the majority of nodes are * properly connected and easily reachable in the graph structure. Every * unreachable node is reported. * * Normally only a small percentage of nodes will be not reachable when * visited. This is expected and part of the statistical properties * of HNSW. This happens especially with entries that have an ambiguous * meaning in the represented space, and are across two or multiple clusters * of items. * * The function works by: * 1. Iterating through all nodes in the linked list * 2. Using each node's vector to perform a search with specified EF * 3. Verifying the node can find itself as nearest neighbor * 4. Collecting and reporting statistics about reachability * * This is just a debugging function that reports stuff in the standard * output, part of the implementation because this kind of functions * provide some visibility on what happens inside the HNSW. */ void hnsw_test_graph_recall(HNSW *index, int test_ef, int verbose) { // Stats uint32_t total_nodes = 0; uint32_t unreachable_nodes = 0; uint32_t perfectly_reachable = 0; // Node finds itself as first result // For storing search results hnswNode **neighbors = hmalloc(sizeof(hnswNode*) * test_ef); float *distances = hmalloc(sizeof(float) * test_ef); float *test_vector = hmalloc(sizeof(float) * index->vector_dim); if (!neighbors || !distances || !test_vector) { hfree(neighbors); hfree(distances); hfree(test_vector); return; } // Get a read slot for searching (even if it's highly unlikely that // this test will be run threaded...). int slot = hnsw_acquire_read_slot(index); if (slot < 0) { hfree(neighbors); hfree(distances); return; } printf("\nTesting graph recall\n"); printf("====================\n"); // Process one node at a time using the linked list hnswNode *current = index->head; while (current) { total_nodes++; // If using quantization, we need to reconstruct the normalized vector if (index->quant_type == HNSW_QUANT_Q8) { int8_t *quants = current->vector; // Reconstruct normalized vector from quantized data for (uint32_t j = 0; j < index->vector_dim; j++) { test_vector[j] = (quants[j] * current->quants_range) / 127; } } else if (index->quant_type == HNSW_QUANT_NONE) { memcpy(test_vector,current->vector,sizeof(float)*index->vector_dim); } else { assert(0 && "Quantization type not supported."); } // Search using the node's own vector with high ef int found = hnsw_search(index, test_vector, test_ef, neighbors, distances, slot, 1); if (found == 0) continue; // Empty HNSW? // Look for the node itself in the results int found_self = 0; int self_position = -1; for (int i = 0; i < found; i++) { if (neighbors[i] == current) { found_self = 1; self_position = i; break; } } if (!found_self || self_position != 0) { unreachable_nodes++; if (verbose) { if (!found_self) printf("\nNode %s cannot find itself:\n", (char*)current->value); else printf("\nNode %s is not top result:\n", (char*)current->value); printf("- Node ID: %llu\n", (unsigned long long)current->id); printf("- Node level: %u\n", current->level); printf("- Found %d neighbors but self not among them\n", found); printf("- Closest neighbor distance: %f\n", distances[0]); printf("- Neighbors: "); for (uint32_t i = 0; i < current->layers[0].num_links; i++) { printf("%s ", (char*)current->layers[0].links[i]->value); } printf("\n"); printf("\nFound instead: "); for (int j = 0; j < found && j < 10; j++) { printf("%s ", (char*)neighbors[j]->value); } printf("\n"); } } else { perfectly_reachable++; } current = current->next; } // Release read slot hnsw_release_read_slot(index, slot); // Free resources hfree(neighbors); hfree(distances); hfree(test_vector); // Print final statistics printf("Total nodes tested: %u\n", total_nodes); printf("Perfectly reachable nodes: %u (%.1f%%)\n", perfectly_reachable, total_nodes ? (float)perfectly_reachable * 100 / total_nodes : 0); printf("Unreachable/suboptimal nodes: %u (%.1f%%)\n", unreachable_nodes, total_nodes ? (float)unreachable_nodes * 100 / total_nodes : 0); } /* Return exact K-NN items by performing a linear scan of all nodes. * This function has the same signature as hnsw_search_with_filter() but * instead of using the graph structure, it scans all nodes to find the * true nearest neighbors. * * Note that neighbors and distances arrays must have space for at least 'k' items. * norm_query should be set to 1 if the query vector is already normalized. * * If the filter_callback is passed, only elements passing the specified filter * are returned. The slot parameter is ignored but kept for API consistency. */ int hnsw_ground_truth_with_filter (HNSW *index, const float *query_vector, uint32_t k, hnswNode **neighbors, float *distances, uint32_t slot, int query_vector_is_normalized, int (*filter_callback)(void *value, void *privdata), void *filter_privdata) { /* Note that we don't really use the slot here: it's a linear scan. * Yet we want the user to acquire the slot as this will hold the * global lock in read only mode. */ (void) slot; /* Take our query vector into a temporary node. */ hnswNode query; if (hnsw_init_tmp_node(index, &query, query_vector_is_normalized, query_vector) == 0) return -1; /* Accumulate best results into a priority queue. */ pqueue *results = pq_new(k); if (!results) { hnsw_free_tmp_node(&query, query_vector); return -1; } /* Scan all nodes linearly. */ hnswNode *current = index->head; while (current) { /* Apply filter if needed. */ if (filter_callback && !filter_callback(current->value, filter_privdata)) { current = current->next; continue; } /* Calculate distance to query. */ float dist = hnsw_distance(index, &query, current); /* Add to results to pqueue. Will be accepted only if better than * the current worse or pqueue not full. */ pq_push(results, current, dist); current = current->next; } /* Copy results to output arrays. */ uint32_t found = MIN(k, results->count); for (uint32_t i = 0; i < found; i++) { neighbors[i] = pq_get_node(results, i); if (distances) distances[i] = pq_get_distance(results, i); } /* Clean up. */ pq_free(results); hnsw_free_tmp_node(&query, query_vector); return found; }