umappp 0.1.2

data/vendor/hnswlib/hnswalg.h

@@ -0,0 +1,1192 @@
+#pragma once
+
+#include "visited_list_pool.h"
+#include "hnswlib.h"
+#include <atomic>
+#include <random>
+#include <stdlib.h>
+#include <assert.h>
+#include <unordered_set>
+#include <list>
+
+namespace hnswlib {
+    typedef unsigned int tableint;
+    typedef unsigned int linklistsizeint;
+
+    template<typename dist_t>
+    class HierarchicalNSW : public AlgorithmInterface<dist_t> {
+    public:
+        static const tableint max_update_element_locks = 65536;
+        HierarchicalNSW(SpaceInterface<dist_t> *s) {
+
+        }
+
+        HierarchicalNSW(SpaceInterface<dist_t> *s, const std::string &location, bool nmslib = false, size_t max_elements=0) {
+            loadIndex(location, s, max_elements);
+        }
+
+        HierarchicalNSW(SpaceInterface<dist_t> *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;
+
+            has_deletions_=false;
+            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<dist_t, tableint> const &a,
+                                      std::pair<dist_t, tableint> const &b) const noexcept {
+                return a.first < b.first;
+            }
+        };
+
+        ~HierarchicalNSW() {
+
+            free(data_level0_memory_);
+            for (tableint i = 0; i < cur_element_count; i++) {
+                if (element_levels_[i] > 0)
+                    free(linkLists_[i]);
+            }
+            free(linkLists_);
+            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 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<std::mutex> 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<std::mutex> link_list_update_locks_;
+        tableint enterpoint_node_;
+
+
+        size_t size_links_level0_;
+        size_t offsetData_, offsetLevel0_;
+
+
+        char *data_level0_memory_;
+        char **linkLists_;
+        std::vector<int> element_levels_;
+
+        size_t data_size_;
+
+        bool has_deletions_;
+
+
+        size_t label_offset_;
+        DISTFUNC<dist_t> fstdistfunc_;
+        void *dist_func_param_;
+        std::unordered_map<labeltype, tableint> 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<double> distribution(0.0, 1.0);
+            double r = -log(distribution(level_generator_)) * reverse_size;
+            return (int) r;
+        }
+
+
+        std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
+            std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<dist_t>::max();
+                candidateSet.emplace(-lowerBound, ep_id);
+            }
+            visited_array[ep_id] = visited_array_tag;
+
+            while (!candidateSet.empty()) {
+                std::pair<dist_t, tableint> curr_el_pair = candidateSet.top();
+                if ((-curr_el_pair.first) > lowerBound) {
+                    break;
+                }
+                candidateSet.pop();
+
+                tableint curNodeNum = curr_el_pair.second;
+
+                std::unique_lock <std::mutex> 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<long> metric_distance_computations;
+        mutable std::atomic<long> metric_hops;
+
+        template <bool has_deletions, bool collect_metrics=false>
+        std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
+            std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<dist_t>::max();
+                candidate_set.emplace(-lowerBound, ep_id);
+            }
+
+            visited_array[ep_id] = visited_array_tag;
+
+            while (!candidate_set.empty()) {
+
+                std::pair<dist_t, tableint> current_node_pair = candidate_set.top();
+
+                if ((-current_node_pair.first) > lowerBound) {
+                    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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> &top_candidates,
+        const size_t M) {
+            if (top_candidates.size() < M) {
+                return;
+            }
+
+            std::priority_queue<std::pair<dist_t, tableint>> queue_closest;
+            std::vector<std::pair<dist_t, tableint>> 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<dist_t, tableint> curent_pair = queue_closest.top();
+                dist_t dist_to_query = -curent_pair.first;
+                queue_closest.pop();
+                bool good = true;
+
+                for (std::pair<dist_t, tableint> 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<dist_t, tableint> 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<tableint> 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 <std::mutex> 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<std::pair<dist_t, tableint>> searchKnnInternal(void *query_data, int k) {
+            std::priority_queue<std::pair<dist_t, tableint  >> 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 (has_deletions_) {
+                std::priority_queue<std::pair<dist_t, tableint  >> top_candidates1=searchBaseLayerST<true>(currObj, query_data,
+                                                                                                           ef_);
+                top_candidates.swap(top_candidates1);
+            }
+            else{
+                std::priority_queue<std::pair<dist_t, tableint  >> top_candidates1=searchBaseLayerST<false>(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<cur_element_count)
+                throw std::runtime_error("Cannot resize, max element is less than the current number of elements");
+
+
+            delete visited_list_pool_;
+            visited_list_pool_ = new VisitedListPool(1, new_max_elements);
+
+
+            element_levels_.resize(new_max_elements);
+
+            std::vector<std::mutex>(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<dist_t> *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<std::mutex>(max_elements).swap(link_list_locks_);
+            std::vector<std::mutex>(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<int>(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);
+                }
+            }
+
+            has_deletions_=false;
+
+            for (size_t i = 0; i < cur_element_count; i++) {
+                if(isMarkedDeleted(i))
+                    has_deletions_=true;
+            }
+
+            input.close();
+
+            return;
+        }
+
+        template<typename data_t>
+        std::vector<data_t> 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_t> 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)
+        {
+            has_deletions_=true;
+            auto search = label_lookup_.find(label);
+            if (search == label_lookup_.end()) {
+                throw std::runtime_error("Label not found");
+            }
+            markDeletedInternal(search->second);
+        }
+
+        /**
+         * 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) {
+            unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2;
+            *ll_cur |= DELETE_MARK;
+        }
+
+        /**
+         * Remove the deleted mark of the node.
+         * @param internalId
+         */
+        void unmarkDeletedInternal(tableint internalId) {
+            unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2;
+            *ll_cur &= ~DELETE_MARK;
+        }
+
+        /**
+         * 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<float> distribution(0.0, 1.0);
+            for (int layer = 0; layer <= elemLevel; layer++) {
+                std::unordered_set<tableint> sCand;
+                std::unordered_set<tableint> sNeigh;
+                std::vector<tableint> 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<tableint> listTwoHop = getConnectionsWithLock(elOneHop, layer);
+                    for (auto&& elTwoHop : listTwoHop) {
+                        sCand.insert(elTwoHop);
+                    }
+                }
+
+                for (auto&& neigh : sNeigh) {
+//                    if (neigh == internalId)
+//                        continue;
+
+                    std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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 <std::mutex> 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 <std::mutex> 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> topCandidates = searchBaseLayer(
+                        currObj, dataPoint, level);
+
+                std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<tableint> getConnectionsWithLock(tableint internalId, int level) {
+            std::unique_lock <std::mutex> lock(link_list_locks_[internalId]);
+            unsigned int *data = get_linklist_at_level(internalId, level);
+            int size = getListCount(data);
+            std::vector<tableint> 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 <std::mutex> 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 <std::mutex> 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 <std::mutex> lock_el_update(link_list_update_locks_[(cur_c & (max_update_element_locks - 1))]);
+            std::unique_lock <std::mutex> lock_el(link_list_locks_[cur_c]);
+            int curlevel = getRandomLevel(mult_);
+            if (level > 0)
+                curlevel = level;
+
+            element_levels_[cur_c] = curlevel;
+
+
+            std::unique_lock <std::mutex> 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 <std::mutex> 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, 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<std::pair<dist_t, labeltype >>
+        searchKnn(const void *query_data, size_t k) const {
+            std::priority_queue<std::pair<dist_t, labeltype >> 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::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
+            if (has_deletions_) {
+                top_candidates=searchBaseLayerST<true,true>(
+                        currObj, query_data, std::max(ef_, k));
+            }
+            else{
+                top_candidates=searchBaseLayerST<false,true>(
+                        currObj, query_data, std::max(ef_, k));
+            }
+
+            while (top_candidates.size() > k) {
+                top_candidates.pop();
+            }
+            while (top_candidates.size() > 0) {
+                std::pair<dist_t, tableint> rez = top_candidates.top();
+                result.push(std::pair<dist_t, labeltype>(rez.first, getExternalLabel(rez.second)));
+                top_candidates.pop();
+            }
+            return result;
+        };
+
+        void checkIntegrity(){
+            int connections_checked=0;
+            std::vector <int > 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<tableint> s;
+                    for (int j=0; j<size; j++){
+                        assert(data[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";
+
+        }
+
+    };
+
+}