#pragma once #include "visited_list_pool.h" #include "hnswlib.h" #include #include #include #include #include #include namespace hnswlib { typedef unsigned int tableint; typedef unsigned int linklistsizeint; template class HierarchicalNSW : public AlgorithmInterface { public: static const tableint max_update_element_locks = 65536; HierarchicalNSW() : visited_list_pool_(nullptr), data_level0_memory_(nullptr), linkLists_(nullptr), cur_element_count(0) { } HierarchicalNSW(SpaceInterface *s) { } HierarchicalNSW(SpaceInterface *s, const std::string &location, bool nmslib = false, size_t max_elements=0) { loadIndex(location, s, max_elements); } HierarchicalNSW(SpaceInterface *s, size_t max_elements, size_t M = 16, size_t ef_construction = 200, size_t random_seed = 100) : link_list_locks_(max_elements), link_list_update_locks_(max_update_element_locks), element_levels_(max_elements) { max_elements_ = max_elements; num_deleted_ = 0; data_size_ = s->get_data_size(); fstdistfunc_ = s->get_dist_func(); dist_func_param_ = s->get_dist_func_param(); M_ = M; maxM_ = M_; maxM0_ = M_ * 2; ef_construction_ = std::max(ef_construction,M_); ef_ = 10; level_generator_.seed(random_seed); update_probability_generator_.seed(random_seed + 1); size_links_level0_ = maxM0_ * sizeof(tableint) + sizeof(linklistsizeint); size_data_per_element_ = size_links_level0_ + data_size_ + sizeof(labeltype); offsetData_ = size_links_level0_; label_offset_ = size_links_level0_ + data_size_; offsetLevel0_ = 0; data_level0_memory_ = (char *) malloc(max_elements_ * size_data_per_element_); if (data_level0_memory_ == nullptr) throw std::runtime_error("Not enough memory"); cur_element_count = 0; visited_list_pool_ = new VisitedListPool(1, max_elements); //initializations for special treatment of the first node enterpoint_node_ = -1; maxlevel_ = -1; linkLists_ = (char **) malloc(sizeof(void *) * max_elements_); if (linkLists_ == nullptr) throw std::runtime_error("Not enough memory: HierarchicalNSW failed to allocate linklists"); size_links_per_element_ = maxM_ * sizeof(tableint) + sizeof(linklistsizeint); mult_ = 1 / log(1.0 * M_); revSize_ = 1.0 / mult_; } struct CompareByFirst { constexpr bool operator()(std::pair const &a, std::pair const &b) const noexcept { return a.first < b.first; } }; ~HierarchicalNSW() { if (data_level0_memory_) free(data_level0_memory_); if (linkLists_) { for (tableint i = 0; i < cur_element_count; i++) { if (element_levels_[i] > 0) if (linkLists_[i]) free(linkLists_[i]); } free(linkLists_); } if (visited_list_pool_) delete visited_list_pool_; } size_t max_elements_; size_t cur_element_count; size_t size_data_per_element_; size_t size_links_per_element_; size_t num_deleted_; size_t M_; size_t maxM_; size_t maxM0_; size_t ef_construction_; double mult_, revSize_; int maxlevel_; VisitedListPool *visited_list_pool_; std::mutex cur_element_count_guard_; std::vector link_list_locks_; // Locks to prevent race condition during update/insert of an element at same time. // Note: Locks for additions can also be used to prevent this race condition if the querying of KNN is not exposed along with update/inserts i.e multithread insert/update/query in parallel. std::vector link_list_update_locks_; tableint enterpoint_node_; size_t size_links_level0_; size_t offsetData_, offsetLevel0_; char *data_level0_memory_; char **linkLists_; std::vector element_levels_; size_t data_size_; size_t label_offset_; DISTFUNC fstdistfunc_; void *dist_func_param_; std::unordered_map label_lookup_; std::default_random_engine level_generator_; std::default_random_engine update_probability_generator_; inline labeltype getExternalLabel(tableint internal_id) const { labeltype return_label; memcpy(&return_label,(data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_), sizeof(labeltype)); return return_label; } inline void setExternalLabel(tableint internal_id, labeltype label) const { memcpy((data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_), &label, sizeof(labeltype)); } inline labeltype *getExternalLabeLp(tableint internal_id) const { return (labeltype *) (data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_); } inline char *getDataByInternalId(tableint internal_id) const { return (data_level0_memory_ + internal_id * size_data_per_element_ + offsetData_); } int getRandomLevel(double reverse_size) { std::uniform_real_distribution distribution(0.0, 1.0); double r = -log(distribution(level_generator_)) * reverse_size; return (int) r; } std::priority_queue, std::vector>, CompareByFirst> searchBaseLayer(tableint ep_id, const void *data_point, int layer) { VisitedList *vl = visited_list_pool_->getFreeVisitedList(); vl_type *visited_array = vl->mass; vl_type visited_array_tag = vl->curV; std::priority_queue, std::vector>, CompareByFirst> top_candidates; std::priority_queue, std::vector>, CompareByFirst> candidateSet; dist_t lowerBound; if (!isMarkedDeleted(ep_id)) { dist_t dist = fstdistfunc_(data_point, getDataByInternalId(ep_id), dist_func_param_); top_candidates.emplace(dist, ep_id); lowerBound = dist; candidateSet.emplace(-dist, ep_id); } else { lowerBound = std::numeric_limits::max(); candidateSet.emplace(-lowerBound, ep_id); } visited_array[ep_id] = visited_array_tag; while (!candidateSet.empty()) { std::pair curr_el_pair = candidateSet.top(); if ((-curr_el_pair.first) > lowerBound && top_candidates.size() == ef_construction_) { break; } candidateSet.pop(); tableint curNodeNum = curr_el_pair.second; std::unique_lock lock(link_list_locks_[curNodeNum]); int *data;// = (int *)(linkList0_ + curNodeNum * size_links_per_element0_); if (layer == 0) { data = (int*)get_linklist0(curNodeNum); } else { data = (int*)get_linklist(curNodeNum, layer); // data = (int *) (linkLists_[curNodeNum] + (layer - 1) * size_links_per_element_); } size_t size = getListCount((linklistsizeint*)data); tableint *datal = (tableint *) (data + 1); #ifdef USE_SSE _mm_prefetch((char *) (visited_array + *(data + 1)), _MM_HINT_T0); _mm_prefetch((char *) (visited_array + *(data + 1) + 64), _MM_HINT_T0); _mm_prefetch(getDataByInternalId(*datal), _MM_HINT_T0); _mm_prefetch(getDataByInternalId(*(datal + 1)), _MM_HINT_T0); #endif for (size_t j = 0; j < size; j++) { tableint candidate_id = *(datal + j); // if (candidate_id == 0) continue; #ifdef USE_SSE _mm_prefetch((char *) (visited_array + *(datal + j + 1)), _MM_HINT_T0); _mm_prefetch(getDataByInternalId(*(datal + j + 1)), _MM_HINT_T0); #endif if (visited_array[candidate_id] == visited_array_tag) continue; visited_array[candidate_id] = visited_array_tag; char *currObj1 = (getDataByInternalId(candidate_id)); dist_t dist1 = fstdistfunc_(data_point, currObj1, dist_func_param_); if (top_candidates.size() < ef_construction_ || lowerBound > dist1) { candidateSet.emplace(-dist1, candidate_id); #ifdef USE_SSE _mm_prefetch(getDataByInternalId(candidateSet.top().second), _MM_HINT_T0); #endif if (!isMarkedDeleted(candidate_id)) top_candidates.emplace(dist1, candidate_id); if (top_candidates.size() > ef_construction_) top_candidates.pop(); if (!top_candidates.empty()) lowerBound = top_candidates.top().first; } } } visited_list_pool_->releaseVisitedList(vl); return top_candidates; } mutable std::atomic metric_distance_computations; mutable std::atomic metric_hops; template std::priority_queue, std::vector>, CompareByFirst> searchBaseLayerST(tableint ep_id, const void *data_point, size_t ef) const { VisitedList *vl = visited_list_pool_->getFreeVisitedList(); vl_type *visited_array = vl->mass; vl_type visited_array_tag = vl->curV; std::priority_queue, std::vector>, CompareByFirst> top_candidates; std::priority_queue, std::vector>, CompareByFirst> candidate_set; dist_t lowerBound; if (!has_deletions || !isMarkedDeleted(ep_id)) { dist_t dist = fstdistfunc_(data_point, getDataByInternalId(ep_id), dist_func_param_); lowerBound = dist; top_candidates.emplace(dist, ep_id); candidate_set.emplace(-dist, ep_id); } else { lowerBound = std::numeric_limits::max(); candidate_set.emplace(-lowerBound, ep_id); } visited_array[ep_id] = visited_array_tag; while (!candidate_set.empty()) { std::pair current_node_pair = candidate_set.top(); if ((-current_node_pair.first) > lowerBound && (top_candidates.size() == ef || has_deletions == false)) { break; } candidate_set.pop(); tableint current_node_id = current_node_pair.second; int *data = (int *) get_linklist0(current_node_id); size_t size = getListCount((linklistsizeint*)data); // bool cur_node_deleted = isMarkedDeleted(current_node_id); if(collect_metrics){ metric_hops++; metric_distance_computations+=size; } #ifdef USE_SSE _mm_prefetch((char *) (visited_array + *(data + 1)), _MM_HINT_T0); _mm_prefetch((char *) (visited_array + *(data + 1) + 64), _MM_HINT_T0); _mm_prefetch(data_level0_memory_ + (*(data + 1)) * size_data_per_element_ + offsetData_, _MM_HINT_T0); _mm_prefetch((char *) (data + 2), _MM_HINT_T0); #endif for (size_t j = 1; j <= size; j++) { int candidate_id = *(data + j); // if (candidate_id == 0) continue; #ifdef USE_SSE _mm_prefetch((char *) (visited_array + *(data + j + 1)), _MM_HINT_T0); _mm_prefetch(data_level0_memory_ + (*(data + j + 1)) * size_data_per_element_ + offsetData_, _MM_HINT_T0);//////////// #endif if (!(visited_array[candidate_id] == visited_array_tag)) { visited_array[candidate_id] = visited_array_tag; char *currObj1 = (getDataByInternalId(candidate_id)); dist_t dist = fstdistfunc_(data_point, currObj1, dist_func_param_); if (top_candidates.size() < ef || lowerBound > dist) { candidate_set.emplace(-dist, candidate_id); #ifdef USE_SSE _mm_prefetch(data_level0_memory_ + candidate_set.top().second * size_data_per_element_ + offsetLevel0_,/////////// _MM_HINT_T0);//////////////////////// #endif if (!has_deletions || !isMarkedDeleted(candidate_id)) top_candidates.emplace(dist, candidate_id); if (top_candidates.size() > ef) top_candidates.pop(); if (!top_candidates.empty()) lowerBound = top_candidates.top().first; } } } } visited_list_pool_->releaseVisitedList(vl); return top_candidates; } void getNeighborsByHeuristic2( std::priority_queue, std::vector>, CompareByFirst> &top_candidates, const size_t M) { if (top_candidates.size() < M) { return; } std::priority_queue> queue_closest; std::vector> return_list; while (top_candidates.size() > 0) { queue_closest.emplace(-top_candidates.top().first, top_candidates.top().second); top_candidates.pop(); } while (queue_closest.size()) { if (return_list.size() >= M) break; std::pair curent_pair = queue_closest.top(); dist_t dist_to_query = -curent_pair.first; queue_closest.pop(); bool good = true; for (std::pair second_pair : return_list) { dist_t curdist = fstdistfunc_(getDataByInternalId(second_pair.second), getDataByInternalId(curent_pair.second), dist_func_param_);; if (curdist < dist_to_query) { good = false; break; } } if (good) { return_list.push_back(curent_pair); } } for (std::pair curent_pair : return_list) { top_candidates.emplace(-curent_pair.first, curent_pair.second); } } linklistsizeint *get_linklist0(tableint internal_id) const { return (linklistsizeint *) (data_level0_memory_ + internal_id * size_data_per_element_ + offsetLevel0_); }; linklistsizeint *get_linklist0(tableint internal_id, char *data_level0_memory_) const { return (linklistsizeint *) (data_level0_memory_ + internal_id * size_data_per_element_ + offsetLevel0_); }; linklistsizeint *get_linklist(tableint internal_id, int level) const { return (linklistsizeint *) (linkLists_[internal_id] + (level - 1) * size_links_per_element_); }; linklistsizeint *get_linklist_at_level(tableint internal_id, int level) const { return level == 0 ? get_linklist0(internal_id) : get_linklist(internal_id, level); }; tableint mutuallyConnectNewElement(const void *data_point, tableint cur_c, std::priority_queue, std::vector>, CompareByFirst> &top_candidates, int level, bool isUpdate) { size_t Mcurmax = level ? maxM_ : maxM0_; getNeighborsByHeuristic2(top_candidates, M_); if (top_candidates.size() > M_) throw std::runtime_error("Should be not be more than M_ candidates returned by the heuristic"); std::vector selectedNeighbors; selectedNeighbors.reserve(M_); while (top_candidates.size() > 0) { selectedNeighbors.push_back(top_candidates.top().second); top_candidates.pop(); } tableint next_closest_entry_point = selectedNeighbors.back(); { linklistsizeint *ll_cur; if (level == 0) ll_cur = get_linklist0(cur_c); else ll_cur = get_linklist(cur_c, level); if (*ll_cur && !isUpdate) { throw std::runtime_error("The newly inserted element should have blank link list"); } setListCount(ll_cur,selectedNeighbors.size()); tableint *data = (tableint *) (ll_cur + 1); for (size_t idx = 0; idx < selectedNeighbors.size(); idx++) { if (data[idx] && !isUpdate) throw std::runtime_error("Possible memory corruption"); if (level > element_levels_[selectedNeighbors[idx]]) throw std::runtime_error("Trying to make a link on a non-existent level"); data[idx] = selectedNeighbors[idx]; } } for (size_t idx = 0; idx < selectedNeighbors.size(); idx++) { std::unique_lock lock(link_list_locks_[selectedNeighbors[idx]]); linklistsizeint *ll_other; if (level == 0) ll_other = get_linklist0(selectedNeighbors[idx]); else ll_other = get_linklist(selectedNeighbors[idx], level); size_t sz_link_list_other = getListCount(ll_other); if (sz_link_list_other > Mcurmax) throw std::runtime_error("Bad value of sz_link_list_other"); if (selectedNeighbors[idx] == cur_c) throw std::runtime_error("Trying to connect an element to itself"); if (level > element_levels_[selectedNeighbors[idx]]) throw std::runtime_error("Trying to make a link on a non-existent level"); tableint *data = (tableint *) (ll_other + 1); bool is_cur_c_present = false; if (isUpdate) { for (size_t j = 0; j < sz_link_list_other; j++) { if (data[j] == cur_c) { is_cur_c_present = true; break; } } } // If cur_c is already present in the neighboring connections of `selectedNeighbors[idx]` then no need to modify any connections or run the heuristics. if (!is_cur_c_present) { if (sz_link_list_other < Mcurmax) { data[sz_link_list_other] = cur_c; setListCount(ll_other, sz_link_list_other + 1); } else { // finding the "weakest" element to replace it with the new one dist_t d_max = fstdistfunc_(getDataByInternalId(cur_c), getDataByInternalId(selectedNeighbors[idx]), dist_func_param_); // Heuristic: std::priority_queue, std::vector>, CompareByFirst> candidates; candidates.emplace(d_max, cur_c); for (size_t j = 0; j < sz_link_list_other; j++) { candidates.emplace( fstdistfunc_(getDataByInternalId(data[j]), getDataByInternalId(selectedNeighbors[idx]), dist_func_param_), data[j]); } getNeighborsByHeuristic2(candidates, Mcurmax); int indx = 0; while (candidates.size() > 0) { data[indx] = candidates.top().second; candidates.pop(); indx++; } setListCount(ll_other, indx); // Nearest K: /*int indx = -1; for (int j = 0; j < sz_link_list_other; j++) { dist_t d = fstdistfunc_(getDataByInternalId(data[j]), getDataByInternalId(rez[idx]), dist_func_param_); if (d > d_max) { indx = j; d_max = d; } } if (indx >= 0) { data[indx] = cur_c; } */ } } } return next_closest_entry_point; } std::mutex global; size_t ef_; void setEf(size_t ef) { ef_ = ef; } std::priority_queue> searchKnnInternal(void *query_data, int k) { std::priority_queue> top_candidates; if (cur_element_count == 0) return top_candidates; tableint currObj = enterpoint_node_; dist_t curdist = fstdistfunc_(query_data, getDataByInternalId(enterpoint_node_), dist_func_param_); for (size_t level = maxlevel_; level > 0; level--) { bool changed = true; while (changed) { changed = false; int *data; data = (int *) get_linklist(currObj,level); int size = getListCount(data); tableint *datal = (tableint *) (data + 1); for (int i = 0; i < size; i++) { tableint cand = datal[i]; if (cand < 0 || cand > max_elements_) throw std::runtime_error("cand error"); dist_t d = fstdistfunc_(query_data, getDataByInternalId(cand), dist_func_param_); if (d < curdist) { curdist = d; currObj = cand; changed = true; } } } } if (num_deleted_) { std::priority_queue> top_candidates1=searchBaseLayerST(currObj, query_data, ef_); top_candidates.swap(top_candidates1); } else{ std::priority_queue> top_candidates1=searchBaseLayerST(currObj, query_data, ef_); top_candidates.swap(top_candidates1); } while (top_candidates.size() > k) { top_candidates.pop(); } return top_candidates; }; void resizeIndex(size_t new_max_elements){ if (new_max_elements(new_max_elements).swap(link_list_locks_); // Reallocate base layer char * data_level0_memory_new = (char *) realloc(data_level0_memory_, new_max_elements * size_data_per_element_); if (data_level0_memory_new == nullptr) throw std::runtime_error("Not enough memory: resizeIndex failed to allocate base layer"); data_level0_memory_ = data_level0_memory_new; // Reallocate all other layers char ** linkLists_new = (char **) realloc(linkLists_, sizeof(void *) * new_max_elements); if (linkLists_new == nullptr) throw std::runtime_error("Not enough memory: resizeIndex failed to allocate other layers"); linkLists_ = linkLists_new; max_elements_ = new_max_elements; } void saveIndex(const std::string &location) { std::ofstream output(location, std::ios::binary); std::streampos position; writeBinaryPOD(output, offsetLevel0_); writeBinaryPOD(output, max_elements_); writeBinaryPOD(output, cur_element_count); writeBinaryPOD(output, size_data_per_element_); writeBinaryPOD(output, label_offset_); writeBinaryPOD(output, offsetData_); writeBinaryPOD(output, maxlevel_); writeBinaryPOD(output, enterpoint_node_); writeBinaryPOD(output, maxM_); writeBinaryPOD(output, maxM0_); writeBinaryPOD(output, M_); writeBinaryPOD(output, mult_); writeBinaryPOD(output, ef_construction_); output.write(data_level0_memory_, cur_element_count * size_data_per_element_); for (size_t i = 0; i < cur_element_count; i++) { unsigned int linkListSize = element_levels_[i] > 0 ? size_links_per_element_ * element_levels_[i] : 0; writeBinaryPOD(output, linkListSize); if (linkListSize) output.write(linkLists_[i], linkListSize); } output.close(); } void loadIndex(const std::string &location, SpaceInterface *s, size_t max_elements_i=0) { std::ifstream input(location, std::ios::binary); if (!input.is_open()) throw std::runtime_error("Cannot open file"); // get file size: input.seekg(0,input.end); std::streampos total_filesize=input.tellg(); input.seekg(0,input.beg); readBinaryPOD(input, offsetLevel0_); readBinaryPOD(input, max_elements_); readBinaryPOD(input, cur_element_count); size_t max_elements = max_elements_i; if(max_elements < cur_element_count) max_elements = max_elements_; max_elements_ = max_elements; readBinaryPOD(input, size_data_per_element_); readBinaryPOD(input, label_offset_); readBinaryPOD(input, offsetData_); readBinaryPOD(input, maxlevel_); readBinaryPOD(input, enterpoint_node_); readBinaryPOD(input, maxM_); readBinaryPOD(input, maxM0_); readBinaryPOD(input, M_); readBinaryPOD(input, mult_); readBinaryPOD(input, ef_construction_); data_size_ = s->get_data_size(); fstdistfunc_ = s->get_dist_func(); dist_func_param_ = s->get_dist_func_param(); auto pos=input.tellg(); /// Optional - check if index is ok: input.seekg(cur_element_count * size_data_per_element_,input.cur); for (size_t i = 0; i < cur_element_count; i++) { if(input.tellg() < 0 || input.tellg()>=total_filesize){ throw std::runtime_error("Index seems to be corrupted or unsupported"); } unsigned int linkListSize; readBinaryPOD(input, linkListSize); if (linkListSize != 0) { input.seekg(linkListSize,input.cur); } } // throw exception if it either corrupted or old index if(input.tellg()!=total_filesize) throw std::runtime_error("Index seems to be corrupted or unsupported"); input.clear(); /// Optional check end input.seekg(pos,input.beg); data_level0_memory_ = (char *) malloc(max_elements * size_data_per_element_); if (data_level0_memory_ == nullptr) throw std::runtime_error("Not enough memory: loadIndex failed to allocate level0"); input.read(data_level0_memory_, cur_element_count * size_data_per_element_); size_links_per_element_ = maxM_ * sizeof(tableint) + sizeof(linklistsizeint); size_links_level0_ = maxM0_ * sizeof(tableint) + sizeof(linklistsizeint); std::vector(max_elements).swap(link_list_locks_); std::vector(max_update_element_locks).swap(link_list_update_locks_); visited_list_pool_ = new VisitedListPool(1, max_elements); linkLists_ = (char **) malloc(sizeof(void *) * max_elements); if (linkLists_ == nullptr) throw std::runtime_error("Not enough memory: loadIndex failed to allocate linklists"); element_levels_ = std::vector(max_elements); revSize_ = 1.0 / mult_; ef_ = 10; for (size_t i = 0; i < cur_element_count; i++) { label_lookup_[getExternalLabel(i)]=i; unsigned int linkListSize; readBinaryPOD(input, linkListSize); if (linkListSize == 0) { element_levels_[i] = 0; linkLists_[i] = nullptr; } else { element_levels_[i] = linkListSize / size_links_per_element_; linkLists_[i] = (char *) malloc(linkListSize); if (linkLists_[i] == nullptr) throw std::runtime_error("Not enough memory: loadIndex failed to allocate linklist"); input.read(linkLists_[i], linkListSize); } } for (size_t i = 0; i < cur_element_count; i++) { if(isMarkedDeleted(i)) num_deleted_ += 1; } input.close(); return; } template std::vector getDataByLabel(labeltype label) const { tableint label_c; auto search = label_lookup_.find(label); if (search == label_lookup_.end() || isMarkedDeleted(search->second)) { throw std::runtime_error("Label not found"); } label_c = search->second; char* data_ptrv = getDataByInternalId(label_c); size_t dim = *((size_t *) dist_func_param_); std::vector data; data_t* data_ptr = (data_t*) data_ptrv; for (int i = 0; i < dim; i++) { data.push_back(*data_ptr); data_ptr += 1; } return data; } static const unsigned char DELETE_MARK = 0x01; // static const unsigned char REUSE_MARK = 0x10; /** * Marks an element with the given label deleted, does NOT really change the current graph. * @param label */ void markDelete(labeltype label) { auto search = label_lookup_.find(label); if (search == label_lookup_.end()) { throw std::runtime_error("Label not found"); } tableint internalId = search->second; markDeletedInternal(internalId); } /** * Uses the first 8 bits of the memory for the linked list to store the mark, * whereas maxM0_ has to be limited to the lower 24 bits, however, still large enough in almost all cases. * @param internalId */ void markDeletedInternal(tableint internalId) { assert(internalId < cur_element_count); if (!isMarkedDeleted(internalId)) { unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2; *ll_cur |= DELETE_MARK; num_deleted_ += 1; } else { throw std::runtime_error("The requested to delete element is already deleted"); } } /** * Remove the deleted mark of the node, does NOT really change the current graph. * @param label */ void unmarkDelete(labeltype label) { auto search = label_lookup_.find(label); if (search == label_lookup_.end()) { throw std::runtime_error("Label not found"); } tableint internalId = search->second; unmarkDeletedInternal(internalId); } /** * Remove the deleted mark of the node. * @param internalId */ void unmarkDeletedInternal(tableint internalId) { assert(internalId < cur_element_count); if (isMarkedDeleted(internalId)) { unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2; *ll_cur &= ~DELETE_MARK; num_deleted_ -= 1; } else { throw std::runtime_error("The requested to undelete element is not deleted"); } } /** * Checks the first 8 bits of the memory to see if the element is marked deleted. * @param internalId * @return */ bool isMarkedDeleted(tableint internalId) const { unsigned char *ll_cur = ((unsigned char*)get_linklist0(internalId))+2; return *ll_cur & DELETE_MARK; } unsigned short int getListCount(linklistsizeint * ptr) const { return *((unsigned short int *)ptr); } void setListCount(linklistsizeint * ptr, unsigned short int size) const { *((unsigned short int*)(ptr))=*((unsigned short int *)&size); } void addPoint(const void *data_point, labeltype label) { addPoint(data_point, label,-1); } void updatePoint(const void *dataPoint, tableint internalId, float updateNeighborProbability) { // update the feature vector associated with existing point with new vector memcpy(getDataByInternalId(internalId), dataPoint, data_size_); int maxLevelCopy = maxlevel_; tableint entryPointCopy = enterpoint_node_; // If point to be updated is entry point and graph just contains single element then just return. if (entryPointCopy == internalId && cur_element_count == 1) return; int elemLevel = element_levels_[internalId]; std::uniform_real_distribution distribution(0.0, 1.0); for (int layer = 0; layer <= elemLevel; layer++) { std::unordered_set sCand; std::unordered_set sNeigh; std::vector listOneHop = getConnectionsWithLock(internalId, layer); if (listOneHop.size() == 0) continue; sCand.insert(internalId); for (auto&& elOneHop : listOneHop) { sCand.insert(elOneHop); if (distribution(update_probability_generator_) > updateNeighborProbability) continue; sNeigh.insert(elOneHop); std::vector listTwoHop = getConnectionsWithLock(elOneHop, layer); for (auto&& elTwoHop : listTwoHop) { sCand.insert(elTwoHop); } } for (auto&& neigh : sNeigh) { // if (neigh == internalId) // continue; std::priority_queue, std::vector>, CompareByFirst> candidates; size_t size = sCand.find(neigh) == sCand.end() ? sCand.size() : sCand.size() - 1; // sCand guaranteed to have size >= 1 size_t elementsToKeep = std::min(ef_construction_, size); for (auto&& cand : sCand) { if (cand == neigh) continue; dist_t distance = fstdistfunc_(getDataByInternalId(neigh), getDataByInternalId(cand), dist_func_param_); if (candidates.size() < elementsToKeep) { candidates.emplace(distance, cand); } else { if (distance < candidates.top().first) { candidates.pop(); candidates.emplace(distance, cand); } } } // Retrieve neighbours using heuristic and set connections. getNeighborsByHeuristic2(candidates, layer == 0 ? maxM0_ : maxM_); { std::unique_lock lock(link_list_locks_[neigh]); linklistsizeint *ll_cur; ll_cur = get_linklist_at_level(neigh, layer); size_t candSize = candidates.size(); setListCount(ll_cur, candSize); tableint *data = (tableint *) (ll_cur + 1); for (size_t idx = 0; idx < candSize; idx++) { data[idx] = candidates.top().second; candidates.pop(); } } } } repairConnectionsForUpdate(dataPoint, entryPointCopy, internalId, elemLevel, maxLevelCopy); }; void repairConnectionsForUpdate(const void *dataPoint, tableint entryPointInternalId, tableint dataPointInternalId, int dataPointLevel, int maxLevel) { tableint currObj = entryPointInternalId; if (dataPointLevel < maxLevel) { dist_t curdist = fstdistfunc_(dataPoint, getDataByInternalId(currObj), dist_func_param_); for (int level = maxLevel; level > dataPointLevel; level--) { bool changed = true; while (changed) { changed = false; unsigned int *data; std::unique_lock lock(link_list_locks_[currObj]); data = get_linklist_at_level(currObj,level); int size = getListCount(data); tableint *datal = (tableint *) (data + 1); #ifdef USE_SSE _mm_prefetch(getDataByInternalId(*datal), _MM_HINT_T0); #endif for (int i = 0; i < size; i++) { #ifdef USE_SSE _mm_prefetch(getDataByInternalId(*(datal + i + 1)), _MM_HINT_T0); #endif tableint cand = datal[i]; dist_t d = fstdistfunc_(dataPoint, getDataByInternalId(cand), dist_func_param_); if (d < curdist) { curdist = d; currObj = cand; changed = true; } } } } } if (dataPointLevel > maxLevel) throw std::runtime_error("Level of item to be updated cannot be bigger than max level"); for (int level = dataPointLevel; level >= 0; level--) { std::priority_queue, std::vector>, CompareByFirst> topCandidates = searchBaseLayer( currObj, dataPoint, level); std::priority_queue, std::vector>, CompareByFirst> filteredTopCandidates; while (topCandidates.size() > 0) { if (topCandidates.top().second != dataPointInternalId) filteredTopCandidates.push(topCandidates.top()); topCandidates.pop(); } // Since element_levels_ is being used to get `dataPointLevel`, there could be cases where `topCandidates` could just contains entry point itself. // To prevent self loops, the `topCandidates` is filtered and thus can be empty. if (filteredTopCandidates.size() > 0) { bool epDeleted = isMarkedDeleted(entryPointInternalId); if (epDeleted) { filteredTopCandidates.emplace(fstdistfunc_(dataPoint, getDataByInternalId(entryPointInternalId), dist_func_param_), entryPointInternalId); if (filteredTopCandidates.size() > ef_construction_) filteredTopCandidates.pop(); } currObj = mutuallyConnectNewElement(dataPoint, dataPointInternalId, filteredTopCandidates, level, true); } } } std::vector getConnectionsWithLock(tableint internalId, int level) { std::unique_lock lock(link_list_locks_[internalId]); unsigned int *data = get_linklist_at_level(internalId, level); int size = getListCount(data); std::vector result(size); tableint *ll = (tableint *) (data + 1); memcpy(result.data(), ll,size * sizeof(tableint)); return result; }; tableint addPoint(const void *data_point, labeltype label, int level) { tableint cur_c = 0; { // Checking if the element with the same label already exists // if so, updating it *instead* of creating a new element. std::unique_lock templock_curr(cur_element_count_guard_); auto search = label_lookup_.find(label); if (search != label_lookup_.end()) { tableint existingInternalId = search->second; templock_curr.unlock(); std::unique_lock lock_el_update(link_list_update_locks_[(existingInternalId & (max_update_element_locks - 1))]); if (isMarkedDeleted(existingInternalId)) { unmarkDeletedInternal(existingInternalId); } updatePoint(data_point, existingInternalId, 1.0); return existingInternalId; } if (cur_element_count >= max_elements_) { throw std::runtime_error("The number of elements exceeds the specified limit"); }; cur_c = cur_element_count; cur_element_count++; label_lookup_[label] = cur_c; } // Take update lock to prevent race conditions on an element with insertion/update at the same time. std::unique_lock lock_el_update(link_list_update_locks_[(cur_c & (max_update_element_locks - 1))]); std::unique_lock lock_el(link_list_locks_[cur_c]); int curlevel = getRandomLevel(mult_); if (level > 0) curlevel = level; element_levels_[cur_c] = curlevel; std::unique_lock templock(global); int maxlevelcopy = maxlevel_; if (curlevel <= maxlevelcopy) templock.unlock(); tableint currObj = enterpoint_node_; tableint enterpoint_copy = enterpoint_node_; memset(data_level0_memory_ + cur_c * size_data_per_element_ + offsetLevel0_, 0, size_data_per_element_); // Initialisation of the data and label memcpy(getExternalLabeLp(cur_c), &label, sizeof(labeltype)); memcpy(getDataByInternalId(cur_c), data_point, data_size_); if (curlevel) { linkLists_[cur_c] = (char *) malloc(size_links_per_element_ * curlevel + 1); if (linkLists_[cur_c] == nullptr) throw std::runtime_error("Not enough memory: addPoint failed to allocate linklist"); memset(linkLists_[cur_c], 0, size_links_per_element_ * curlevel + 1); } if ((signed)currObj != -1) { if (curlevel < maxlevelcopy) { dist_t curdist = fstdistfunc_(data_point, getDataByInternalId(currObj), dist_func_param_); for (int level = maxlevelcopy; level > curlevel; level--) { bool changed = true; while (changed) { changed = false; unsigned int *data; std::unique_lock lock(link_list_locks_[currObj]); data = get_linklist(currObj,level); int size = getListCount(data); tableint *datal = (tableint *) (data + 1); for (int i = 0; i < size; i++) { tableint cand = datal[i]; if (cand < 0 || cand > max_elements_) throw std::runtime_error("cand error"); dist_t d = fstdistfunc_(data_point, getDataByInternalId(cand), dist_func_param_); if (d < curdist) { curdist = d; currObj = cand; changed = true; } } } } } bool epDeleted = isMarkedDeleted(enterpoint_copy); for (int level = std::min(curlevel, maxlevelcopy); level >= 0; level--) { if (level > maxlevelcopy || level < 0) // possible? throw std::runtime_error("Level error"); std::priority_queue, std::vector>, CompareByFirst> top_candidates = searchBaseLayer( currObj, data_point, level); if (epDeleted) { top_candidates.emplace(fstdistfunc_(data_point, getDataByInternalId(enterpoint_copy), dist_func_param_), enterpoint_copy); if (top_candidates.size() > ef_construction_) top_candidates.pop(); } currObj = mutuallyConnectNewElement(data_point, cur_c, top_candidates, level, false); } } else { // Do nothing for the first element enterpoint_node_ = 0; maxlevel_ = curlevel; } //Releasing lock for the maximum level if (curlevel > maxlevelcopy) { enterpoint_node_ = cur_c; maxlevel_ = curlevel; } return cur_c; }; std::priority_queue> searchKnn(const void *query_data, size_t k) const { std::priority_queue> result; if (cur_element_count == 0) return result; tableint currObj = enterpoint_node_; dist_t curdist = fstdistfunc_(query_data, getDataByInternalId(enterpoint_node_), dist_func_param_); for (int level = maxlevel_; level > 0; level--) { bool changed = true; while (changed) { changed = false; unsigned int *data; data = (unsigned int *) get_linklist(currObj, level); int size = getListCount(data); metric_hops++; metric_distance_computations+=size; tableint *datal = (tableint *) (data + 1); for (int i = 0; i < size; i++) { tableint cand = datal[i]; if (cand < 0 || cand > max_elements_) throw std::runtime_error("cand error"); dist_t d = fstdistfunc_(query_data, getDataByInternalId(cand), dist_func_param_); if (d < curdist) { curdist = d; currObj = cand; changed = true; } } } } std::priority_queue, std::vector>, CompareByFirst> top_candidates; if (num_deleted_) { top_candidates=searchBaseLayerST( currObj, query_data, std::max(ef_, k)); } else{ top_candidates=searchBaseLayerST( currObj, query_data, std::max(ef_, k)); } while (top_candidates.size() > k) { top_candidates.pop(); } while (top_candidates.size() > 0) { std::pair rez = top_candidates.top(); result.push(std::pair(rez.first, getExternalLabel(rez.second))); top_candidates.pop(); } return result; }; void checkIntegrity(){ int connections_checked=0; std::vector inbound_connections_num(cur_element_count,0); for(int i = 0;i < cur_element_count; i++){ for(int l = 0;l <= element_levels_[i]; l++){ linklistsizeint *ll_cur = get_linklist_at_level(i,l); int size = getListCount(ll_cur); tableint *data = (tableint *) (ll_cur + 1); std::unordered_set s; for (int j=0; j 0); assert(data[j] < cur_element_count); assert (data[j] != i); inbound_connections_num[data[j]]++; s.insert(data[j]); connections_checked++; } assert(s.size() == size); } } if(cur_element_count > 1){ int min1=inbound_connections_num[0], max1=inbound_connections_num[0]; for(int i=0; i < cur_element_count; i++){ assert(inbound_connections_num[i] > 0); min1=std::min(inbound_connections_num[i],min1); max1=std::max(inbound_connections_num[i],max1); } std::cout << "Min inbound: " << min1 << ", Max inbound:" << max1 << "\n"; } std::cout << "integrity ok, checked " << connections_checked << " connections\n"; } }; }