hnswlib 0.1.0
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- checksums.yaml +7 -0
- data/.github/workflows/build.yml +20 -0
- data/.gitignore +18 -0
- data/.rspec +3 -0
- data/CHANGELOG.md +5 -0
- data/CODE_OF_CONDUCT.md +84 -0
- data/Gemfile +10 -0
- data/LICENSE.txt +176 -0
- data/README.md +56 -0
- data/Rakefile +17 -0
- data/ext/hnswlib/extconf.rb +11 -0
- data/ext/hnswlib/hnswlibext.cpp +29 -0
- data/ext/hnswlib/hnswlibext.hpp +420 -0
- data/ext/hnswlib/src/LICENSE +201 -0
- data/ext/hnswlib/src/bruteforce.h +152 -0
- data/ext/hnswlib/src/hnswalg.h +1192 -0
- data/ext/hnswlib/src/hnswlib.h +108 -0
- data/ext/hnswlib/src/space_ip.h +282 -0
- data/ext/hnswlib/src/space_l2.h +281 -0
- data/ext/hnswlib/src/visited_list_pool.h +78 -0
- data/hnswlib.gemspec +35 -0
- data/lib/hnswlib.rb +154 -0
- data/lib/hnswlib/version.rb +9 -0
- metadata +69 -0
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#pragma once
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#include <unordered_map>
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#include <fstream>
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#include <mutex>
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#include <algorithm>
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namespace hnswlib {
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template<typename dist_t>
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class BruteforceSearch : public AlgorithmInterface<dist_t> {
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public:
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BruteforceSearch(SpaceInterface <dist_t> *s) {
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}
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BruteforceSearch(SpaceInterface<dist_t> *s, const std::string &location) {
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loadIndex(location, s);
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}
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BruteforceSearch(SpaceInterface <dist_t> *s, size_t maxElements) {
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maxelements_ = maxElements;
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data_size_ = s->get_data_size();
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fstdistfunc_ = s->get_dist_func();
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dist_func_param_ = s->get_dist_func_param();
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size_per_element_ = data_size_ + sizeof(labeltype);
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data_ = (char *) malloc(maxElements * size_per_element_);
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if (data_ == nullptr)
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std::runtime_error("Not enough memory: BruteforceSearch failed to allocate data");
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cur_element_count = 0;
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}
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~BruteforceSearch() {
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free(data_);
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}
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char *data_;
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size_t maxelements_;
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size_t cur_element_count;
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size_t size_per_element_;
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size_t data_size_;
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DISTFUNC <dist_t> fstdistfunc_;
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void *dist_func_param_;
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std::mutex index_lock;
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std::unordered_map<labeltype,size_t > dict_external_to_internal;
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void addPoint(const void *datapoint, labeltype label) {
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int idx;
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{
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std::unique_lock<std::mutex> lock(index_lock);
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auto search=dict_external_to_internal.find(label);
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if (search != dict_external_to_internal.end()) {
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idx=search->second;
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}
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else{
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if (cur_element_count >= maxelements_) {
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throw std::runtime_error("The number of elements exceeds the specified limit\n");
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}
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idx=cur_element_count;
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dict_external_to_internal[label] = idx;
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cur_element_count++;
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}
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}
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memcpy(data_ + size_per_element_ * idx + data_size_, &label, sizeof(labeltype));
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memcpy(data_ + size_per_element_ * idx, datapoint, data_size_);
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};
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void removePoint(labeltype cur_external) {
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size_t cur_c=dict_external_to_internal[cur_external];
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dict_external_to_internal.erase(cur_external);
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labeltype label=*((labeltype*)(data_ + size_per_element_ * (cur_element_count-1) + data_size_));
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dict_external_to_internal[label]=cur_c;
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memcpy(data_ + size_per_element_ * cur_c,
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data_ + size_per_element_ * (cur_element_count-1),
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data_size_+sizeof(labeltype));
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cur_element_count--;
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}
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std::priority_queue<std::pair<dist_t, labeltype >>
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searchKnn(const void *query_data, size_t k) const {
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std::priority_queue<std::pair<dist_t, labeltype >> topResults;
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if (cur_element_count == 0) return topResults;
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for (int i = 0; i < k; i++) {
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dist_t dist = fstdistfunc_(query_data, data_ + size_per_element_ * i, dist_func_param_);
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topResults.push(std::pair<dist_t, labeltype>(dist, *((labeltype *) (data_ + size_per_element_ * i +
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data_size_))));
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}
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dist_t lastdist = topResults.top().first;
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for (int i = k; i < cur_element_count; i++) {
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dist_t dist = fstdistfunc_(query_data, data_ + size_per_element_ * i, dist_func_param_);
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if (dist <= lastdist) {
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topResults.push(std::pair<dist_t, labeltype>(dist, *((labeltype *) (data_ + size_per_element_ * i +
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data_size_))));
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if (topResults.size() > k)
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topResults.pop();
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lastdist = topResults.top().first;
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}
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}
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return topResults;
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};
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void saveIndex(const std::string &location) {
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std::ofstream output(location, std::ios::binary);
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std::streampos position;
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writeBinaryPOD(output, maxelements_);
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writeBinaryPOD(output, size_per_element_);
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writeBinaryPOD(output, cur_element_count);
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output.write(data_, maxelements_ * size_per_element_);
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output.close();
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}
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void loadIndex(const std::string &location, SpaceInterface<dist_t> *s) {
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std::ifstream input(location, std::ios::binary);
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std::streampos position;
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readBinaryPOD(input, maxelements_);
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readBinaryPOD(input, size_per_element_);
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readBinaryPOD(input, cur_element_count);
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data_size_ = s->get_data_size();
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fstdistfunc_ = s->get_dist_func();
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dist_func_param_ = s->get_dist_func_param();
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size_per_element_ = data_size_ + sizeof(labeltype);
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data_ = (char *) malloc(maxelements_ * size_per_element_);
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if (data_ == nullptr)
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std::runtime_error("Not enough memory: loadIndex failed to allocate data");
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input.read(data_, maxelements_ * size_per_element_);
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input.close();
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}
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};
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}
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#pragma once
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#include "visited_list_pool.h"
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#include "hnswlib.h"
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#include <atomic>
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#include <random>
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#include <stdlib.h>
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#include <assert.h>
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#include <unordered_set>
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#include <list>
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namespace hnswlib {
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typedef unsigned int tableint;
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typedef unsigned int linklistsizeint;
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template<typename dist_t>
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class HierarchicalNSW : public AlgorithmInterface<dist_t> {
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public:
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static const tableint max_update_element_locks = 65536;
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HierarchicalNSW(SpaceInterface<dist_t> *s) {
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}
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HierarchicalNSW(SpaceInterface<dist_t> *s, const std::string &location, bool nmslib = false, size_t max_elements=0) {
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loadIndex(location, s, max_elements);
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}
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HierarchicalNSW(SpaceInterface<dist_t> *s, size_t max_elements, size_t M = 16, size_t ef_construction = 200, size_t random_seed = 100) :
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link_list_locks_(max_elements), link_list_update_locks_(max_update_element_locks), element_levels_(max_elements) {
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max_elements_ = max_elements;
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has_deletions_=false;
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data_size_ = s->get_data_size();
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fstdistfunc_ = s->get_dist_func();
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dist_func_param_ = s->get_dist_func_param();
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M_ = M;
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maxM_ = M_;
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maxM0_ = M_ * 2;
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ef_construction_ = std::max(ef_construction,M_);
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ef_ = 10;
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level_generator_.seed(random_seed);
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update_probability_generator_.seed(random_seed + 1);
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size_links_level0_ = maxM0_ * sizeof(tableint) + sizeof(linklistsizeint);
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size_data_per_element_ = size_links_level0_ + data_size_ + sizeof(labeltype);
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offsetData_ = size_links_level0_;
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label_offset_ = size_links_level0_ + data_size_;
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offsetLevel0_ = 0;
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data_level0_memory_ = (char *) malloc(max_elements_ * size_data_per_element_);
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if (data_level0_memory_ == nullptr)
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throw std::runtime_error("Not enough memory");
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cur_element_count = 0;
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visited_list_pool_ = new VisitedListPool(1, max_elements);
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//initializations for special treatment of the first node
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enterpoint_node_ = -1;
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maxlevel_ = -1;
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linkLists_ = (char **) malloc(sizeof(void *) * max_elements_);
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if (linkLists_ == nullptr)
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throw std::runtime_error("Not enough memory: HierarchicalNSW failed to allocate linklists");
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size_links_per_element_ = maxM_ * sizeof(tableint) + sizeof(linklistsizeint);
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mult_ = 1 / log(1.0 * M_);
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revSize_ = 1.0 / mult_;
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}
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struct CompareByFirst {
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constexpr bool operator()(std::pair<dist_t, tableint> const &a,
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std::pair<dist_t, tableint> const &b) const noexcept {
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return a.first < b.first;
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}
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};
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~HierarchicalNSW() {
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free(data_level0_memory_);
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for (tableint i = 0; i < cur_element_count; i++) {
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if (element_levels_[i] > 0)
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free(linkLists_[i]);
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}
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free(linkLists_);
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delete visited_list_pool_;
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}
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size_t max_elements_;
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size_t cur_element_count;
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size_t size_data_per_element_;
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size_t size_links_per_element_;
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size_t M_;
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size_t maxM_;
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size_t maxM0_;
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size_t ef_construction_;
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double mult_, revSize_;
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int maxlevel_;
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VisitedListPool *visited_list_pool_;
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std::mutex cur_element_count_guard_;
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std::vector<std::mutex> link_list_locks_;
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// Locks to prevent race condition during update/insert of an element at same time.
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// 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.
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std::vector<std::mutex> link_list_update_locks_;
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tableint enterpoint_node_;
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size_t size_links_level0_;
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size_t offsetData_, offsetLevel0_;
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char *data_level0_memory_;
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char **linkLists_;
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std::vector<int> element_levels_;
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size_t data_size_;
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bool has_deletions_;
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size_t label_offset_;
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DISTFUNC<dist_t> fstdistfunc_;
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void *dist_func_param_;
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std::unordered_map<labeltype, tableint> label_lookup_;
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std::default_random_engine level_generator_;
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std::default_random_engine update_probability_generator_;
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inline labeltype getExternalLabel(tableint internal_id) const {
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labeltype return_label;
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memcpy(&return_label,(data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_), sizeof(labeltype));
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return return_label;
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}
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inline void setExternalLabel(tableint internal_id, labeltype label) const {
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memcpy((data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_), &label, sizeof(labeltype));
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}
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inline labeltype *getExternalLabeLp(tableint internal_id) const {
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return (labeltype *) (data_level0_memory_ + internal_id * size_data_per_element_ + label_offset_);
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}
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inline char *getDataByInternalId(tableint internal_id) const {
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return (data_level0_memory_ + internal_id * size_data_per_element_ + offsetData_);
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}
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int getRandomLevel(double reverse_size) {
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std::uniform_real_distribution<double> distribution(0.0, 1.0);
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double r = -log(distribution(level_generator_)) * reverse_size;
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return (int) r;
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}
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std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst>
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searchBaseLayer(tableint ep_id, const void *data_point, int layer) {
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VisitedList *vl = visited_list_pool_->getFreeVisitedList();
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vl_type *visited_array = vl->mass;
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vl_type visited_array_tag = vl->curV;
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std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
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std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> candidateSet;
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dist_t lowerBound;
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if (!isMarkedDeleted(ep_id)) {
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dist_t dist = fstdistfunc_(data_point, getDataByInternalId(ep_id), dist_func_param_);
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top_candidates.emplace(dist, ep_id);
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lowerBound = dist;
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candidateSet.emplace(-dist, ep_id);
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} else {
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lowerBound = std::numeric_limits<dist_t>::max();
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candidateSet.emplace(-lowerBound, ep_id);
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}
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visited_array[ep_id] = visited_array_tag;
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while (!candidateSet.empty()) {
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std::pair<dist_t, tableint> curr_el_pair = candidateSet.top();
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if ((-curr_el_pair.first) > lowerBound) {
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break;
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}
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candidateSet.pop();
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tableint curNodeNum = curr_el_pair.second;
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192
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[curNodeNum]);
|
193
|
+
|
194
|
+
int *data;// = (int *)(linkList0_ + curNodeNum * size_links_per_element0_);
|
195
|
+
if (layer == 0) {
|
196
|
+
data = (int*)get_linklist0(curNodeNum);
|
197
|
+
} else {
|
198
|
+
data = (int*)get_linklist(curNodeNum, layer);
|
199
|
+
// data = (int *) (linkLists_[curNodeNum] + (layer - 1) * size_links_per_element_);
|
200
|
+
}
|
201
|
+
size_t size = getListCount((linklistsizeint*)data);
|
202
|
+
tableint *datal = (tableint *) (data + 1);
|
203
|
+
#ifdef USE_SSE
|
204
|
+
_mm_prefetch((char *) (visited_array + *(data + 1)), _MM_HINT_T0);
|
205
|
+
_mm_prefetch((char *) (visited_array + *(data + 1) + 64), _MM_HINT_T0);
|
206
|
+
_mm_prefetch(getDataByInternalId(*datal), _MM_HINT_T0);
|
207
|
+
_mm_prefetch(getDataByInternalId(*(datal + 1)), _MM_HINT_T0);
|
208
|
+
#endif
|
209
|
+
|
210
|
+
for (size_t j = 0; j < size; j++) {
|
211
|
+
tableint candidate_id = *(datal + j);
|
212
|
+
// if (candidate_id == 0) continue;
|
213
|
+
#ifdef USE_SSE
|
214
|
+
_mm_prefetch((char *) (visited_array + *(datal + j + 1)), _MM_HINT_T0);
|
215
|
+
_mm_prefetch(getDataByInternalId(*(datal + j + 1)), _MM_HINT_T0);
|
216
|
+
#endif
|
217
|
+
if (visited_array[candidate_id] == visited_array_tag) continue;
|
218
|
+
visited_array[candidate_id] = visited_array_tag;
|
219
|
+
char *currObj1 = (getDataByInternalId(candidate_id));
|
220
|
+
|
221
|
+
dist_t dist1 = fstdistfunc_(data_point, currObj1, dist_func_param_);
|
222
|
+
if (top_candidates.size() < ef_construction_ || lowerBound > dist1) {
|
223
|
+
candidateSet.emplace(-dist1, candidate_id);
|
224
|
+
#ifdef USE_SSE
|
225
|
+
_mm_prefetch(getDataByInternalId(candidateSet.top().second), _MM_HINT_T0);
|
226
|
+
#endif
|
227
|
+
|
228
|
+
if (!isMarkedDeleted(candidate_id))
|
229
|
+
top_candidates.emplace(dist1, candidate_id);
|
230
|
+
|
231
|
+
if (top_candidates.size() > ef_construction_)
|
232
|
+
top_candidates.pop();
|
233
|
+
|
234
|
+
if (!top_candidates.empty())
|
235
|
+
lowerBound = top_candidates.top().first;
|
236
|
+
}
|
237
|
+
}
|
238
|
+
}
|
239
|
+
visited_list_pool_->releaseVisitedList(vl);
|
240
|
+
|
241
|
+
return top_candidates;
|
242
|
+
}
|
243
|
+
|
244
|
+
mutable std::atomic<long> metric_distance_computations;
|
245
|
+
mutable std::atomic<long> metric_hops;
|
246
|
+
|
247
|
+
template <bool has_deletions, bool collect_metrics=false>
|
248
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst>
|
249
|
+
searchBaseLayerST(tableint ep_id, const void *data_point, size_t ef) const {
|
250
|
+
VisitedList *vl = visited_list_pool_->getFreeVisitedList();
|
251
|
+
vl_type *visited_array = vl->mass;
|
252
|
+
vl_type visited_array_tag = vl->curV;
|
253
|
+
|
254
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
|
255
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> candidate_set;
|
256
|
+
|
257
|
+
dist_t lowerBound;
|
258
|
+
if (!has_deletions || !isMarkedDeleted(ep_id)) {
|
259
|
+
dist_t dist = fstdistfunc_(data_point, getDataByInternalId(ep_id), dist_func_param_);
|
260
|
+
lowerBound = dist;
|
261
|
+
top_candidates.emplace(dist, ep_id);
|
262
|
+
candidate_set.emplace(-dist, ep_id);
|
263
|
+
} else {
|
264
|
+
lowerBound = std::numeric_limits<dist_t>::max();
|
265
|
+
candidate_set.emplace(-lowerBound, ep_id);
|
266
|
+
}
|
267
|
+
|
268
|
+
visited_array[ep_id] = visited_array_tag;
|
269
|
+
|
270
|
+
while (!candidate_set.empty()) {
|
271
|
+
|
272
|
+
std::pair<dist_t, tableint> current_node_pair = candidate_set.top();
|
273
|
+
|
274
|
+
if ((-current_node_pair.first) > lowerBound) {
|
275
|
+
break;
|
276
|
+
}
|
277
|
+
candidate_set.pop();
|
278
|
+
|
279
|
+
tableint current_node_id = current_node_pair.second;
|
280
|
+
int *data = (int *) get_linklist0(current_node_id);
|
281
|
+
size_t size = getListCount((linklistsizeint*)data);
|
282
|
+
// bool cur_node_deleted = isMarkedDeleted(current_node_id);
|
283
|
+
if(collect_metrics){
|
284
|
+
metric_hops++;
|
285
|
+
metric_distance_computations+=size;
|
286
|
+
}
|
287
|
+
|
288
|
+
#ifdef USE_SSE
|
289
|
+
_mm_prefetch((char *) (visited_array + *(data + 1)), _MM_HINT_T0);
|
290
|
+
_mm_prefetch((char *) (visited_array + *(data + 1) + 64), _MM_HINT_T0);
|
291
|
+
_mm_prefetch(data_level0_memory_ + (*(data + 1)) * size_data_per_element_ + offsetData_, _MM_HINT_T0);
|
292
|
+
_mm_prefetch((char *) (data + 2), _MM_HINT_T0);
|
293
|
+
#endif
|
294
|
+
|
295
|
+
for (size_t j = 1; j <= size; j++) {
|
296
|
+
int candidate_id = *(data + j);
|
297
|
+
// if (candidate_id == 0) continue;
|
298
|
+
#ifdef USE_SSE
|
299
|
+
_mm_prefetch((char *) (visited_array + *(data + j + 1)), _MM_HINT_T0);
|
300
|
+
_mm_prefetch(data_level0_memory_ + (*(data + j + 1)) * size_data_per_element_ + offsetData_,
|
301
|
+
_MM_HINT_T0);////////////
|
302
|
+
#endif
|
303
|
+
if (!(visited_array[candidate_id] == visited_array_tag)) {
|
304
|
+
|
305
|
+
visited_array[candidate_id] = visited_array_tag;
|
306
|
+
|
307
|
+
char *currObj1 = (getDataByInternalId(candidate_id));
|
308
|
+
dist_t dist = fstdistfunc_(data_point, currObj1, dist_func_param_);
|
309
|
+
|
310
|
+
if (top_candidates.size() < ef || lowerBound > dist) {
|
311
|
+
candidate_set.emplace(-dist, candidate_id);
|
312
|
+
#ifdef USE_SSE
|
313
|
+
_mm_prefetch(data_level0_memory_ + candidate_set.top().second * size_data_per_element_ +
|
314
|
+
offsetLevel0_,///////////
|
315
|
+
_MM_HINT_T0);////////////////////////
|
316
|
+
#endif
|
317
|
+
|
318
|
+
if (!has_deletions || !isMarkedDeleted(candidate_id))
|
319
|
+
top_candidates.emplace(dist, candidate_id);
|
320
|
+
|
321
|
+
if (top_candidates.size() > ef)
|
322
|
+
top_candidates.pop();
|
323
|
+
|
324
|
+
if (!top_candidates.empty())
|
325
|
+
lowerBound = top_candidates.top().first;
|
326
|
+
}
|
327
|
+
}
|
328
|
+
}
|
329
|
+
}
|
330
|
+
|
331
|
+
visited_list_pool_->releaseVisitedList(vl);
|
332
|
+
return top_candidates;
|
333
|
+
}
|
334
|
+
|
335
|
+
void getNeighborsByHeuristic2(
|
336
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> &top_candidates,
|
337
|
+
const size_t M) {
|
338
|
+
if (top_candidates.size() < M) {
|
339
|
+
return;
|
340
|
+
}
|
341
|
+
|
342
|
+
std::priority_queue<std::pair<dist_t, tableint>> queue_closest;
|
343
|
+
std::vector<std::pair<dist_t, tableint>> return_list;
|
344
|
+
while (top_candidates.size() > 0) {
|
345
|
+
queue_closest.emplace(-top_candidates.top().first, top_candidates.top().second);
|
346
|
+
top_candidates.pop();
|
347
|
+
}
|
348
|
+
|
349
|
+
while (queue_closest.size()) {
|
350
|
+
if (return_list.size() >= M)
|
351
|
+
break;
|
352
|
+
std::pair<dist_t, tableint> curent_pair = queue_closest.top();
|
353
|
+
dist_t dist_to_query = -curent_pair.first;
|
354
|
+
queue_closest.pop();
|
355
|
+
bool good = true;
|
356
|
+
|
357
|
+
for (std::pair<dist_t, tableint> second_pair : return_list) {
|
358
|
+
dist_t curdist =
|
359
|
+
fstdistfunc_(getDataByInternalId(second_pair.second),
|
360
|
+
getDataByInternalId(curent_pair.second),
|
361
|
+
dist_func_param_);;
|
362
|
+
if (curdist < dist_to_query) {
|
363
|
+
good = false;
|
364
|
+
break;
|
365
|
+
}
|
366
|
+
}
|
367
|
+
if (good) {
|
368
|
+
return_list.push_back(curent_pair);
|
369
|
+
}
|
370
|
+
}
|
371
|
+
|
372
|
+
for (std::pair<dist_t, tableint> curent_pair : return_list) {
|
373
|
+
top_candidates.emplace(-curent_pair.first, curent_pair.second);
|
374
|
+
}
|
375
|
+
}
|
376
|
+
|
377
|
+
|
378
|
+
linklistsizeint *get_linklist0(tableint internal_id) const {
|
379
|
+
return (linklistsizeint *) (data_level0_memory_ + internal_id * size_data_per_element_ + offsetLevel0_);
|
380
|
+
};
|
381
|
+
|
382
|
+
linklistsizeint *get_linklist0(tableint internal_id, char *data_level0_memory_) const {
|
383
|
+
return (linklistsizeint *) (data_level0_memory_ + internal_id * size_data_per_element_ + offsetLevel0_);
|
384
|
+
};
|
385
|
+
|
386
|
+
linklistsizeint *get_linklist(tableint internal_id, int level) const {
|
387
|
+
return (linklistsizeint *) (linkLists_[internal_id] + (level - 1) * size_links_per_element_);
|
388
|
+
};
|
389
|
+
|
390
|
+
linklistsizeint *get_linklist_at_level(tableint internal_id, int level) const {
|
391
|
+
return level == 0 ? get_linklist0(internal_id) : get_linklist(internal_id, level);
|
392
|
+
};
|
393
|
+
|
394
|
+
tableint mutuallyConnectNewElement(const void *data_point, tableint cur_c,
|
395
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> &top_candidates,
|
396
|
+
int level, bool isUpdate) {
|
397
|
+
size_t Mcurmax = level ? maxM_ : maxM0_;
|
398
|
+
getNeighborsByHeuristic2(top_candidates, M_);
|
399
|
+
if (top_candidates.size() > M_)
|
400
|
+
throw std::runtime_error("Should be not be more than M_ candidates returned by the heuristic");
|
401
|
+
|
402
|
+
std::vector<tableint> selectedNeighbors;
|
403
|
+
selectedNeighbors.reserve(M_);
|
404
|
+
while (top_candidates.size() > 0) {
|
405
|
+
selectedNeighbors.push_back(top_candidates.top().second);
|
406
|
+
top_candidates.pop();
|
407
|
+
}
|
408
|
+
|
409
|
+
tableint next_closest_entry_point = selectedNeighbors.back();
|
410
|
+
|
411
|
+
{
|
412
|
+
linklistsizeint *ll_cur;
|
413
|
+
if (level == 0)
|
414
|
+
ll_cur = get_linklist0(cur_c);
|
415
|
+
else
|
416
|
+
ll_cur = get_linklist(cur_c, level);
|
417
|
+
|
418
|
+
if (*ll_cur && !isUpdate) {
|
419
|
+
throw std::runtime_error("The newly inserted element should have blank link list");
|
420
|
+
}
|
421
|
+
setListCount(ll_cur,selectedNeighbors.size());
|
422
|
+
tableint *data = (tableint *) (ll_cur + 1);
|
423
|
+
for (size_t idx = 0; idx < selectedNeighbors.size(); idx++) {
|
424
|
+
if (data[idx] && !isUpdate)
|
425
|
+
throw std::runtime_error("Possible memory corruption");
|
426
|
+
if (level > element_levels_[selectedNeighbors[idx]])
|
427
|
+
throw std::runtime_error("Trying to make a link on a non-existent level");
|
428
|
+
|
429
|
+
data[idx] = selectedNeighbors[idx];
|
430
|
+
|
431
|
+
}
|
432
|
+
}
|
433
|
+
|
434
|
+
for (size_t idx = 0; idx < selectedNeighbors.size(); idx++) {
|
435
|
+
|
436
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[selectedNeighbors[idx]]);
|
437
|
+
|
438
|
+
linklistsizeint *ll_other;
|
439
|
+
if (level == 0)
|
440
|
+
ll_other = get_linklist0(selectedNeighbors[idx]);
|
441
|
+
else
|
442
|
+
ll_other = get_linklist(selectedNeighbors[idx], level);
|
443
|
+
|
444
|
+
size_t sz_link_list_other = getListCount(ll_other);
|
445
|
+
|
446
|
+
if (sz_link_list_other > Mcurmax)
|
447
|
+
throw std::runtime_error("Bad value of sz_link_list_other");
|
448
|
+
if (selectedNeighbors[idx] == cur_c)
|
449
|
+
throw std::runtime_error("Trying to connect an element to itself");
|
450
|
+
if (level > element_levels_[selectedNeighbors[idx]])
|
451
|
+
throw std::runtime_error("Trying to make a link on a non-existent level");
|
452
|
+
|
453
|
+
tableint *data = (tableint *) (ll_other + 1);
|
454
|
+
|
455
|
+
bool is_cur_c_present = false;
|
456
|
+
if (isUpdate) {
|
457
|
+
for (size_t j = 0; j < sz_link_list_other; j++) {
|
458
|
+
if (data[j] == cur_c) {
|
459
|
+
is_cur_c_present = true;
|
460
|
+
break;
|
461
|
+
}
|
462
|
+
}
|
463
|
+
}
|
464
|
+
|
465
|
+
// If cur_c is already present in the neighboring connections of `selectedNeighbors[idx]` then no need to modify any connections or run the heuristics.
|
466
|
+
if (!is_cur_c_present) {
|
467
|
+
if (sz_link_list_other < Mcurmax) {
|
468
|
+
data[sz_link_list_other] = cur_c;
|
469
|
+
setListCount(ll_other, sz_link_list_other + 1);
|
470
|
+
} else {
|
471
|
+
// finding the "weakest" element to replace it with the new one
|
472
|
+
dist_t d_max = fstdistfunc_(getDataByInternalId(cur_c), getDataByInternalId(selectedNeighbors[idx]),
|
473
|
+
dist_func_param_);
|
474
|
+
// Heuristic:
|
475
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> candidates;
|
476
|
+
candidates.emplace(d_max, cur_c);
|
477
|
+
|
478
|
+
for (size_t j = 0; j < sz_link_list_other; j++) {
|
479
|
+
candidates.emplace(
|
480
|
+
fstdistfunc_(getDataByInternalId(data[j]), getDataByInternalId(selectedNeighbors[idx]),
|
481
|
+
dist_func_param_), data[j]);
|
482
|
+
}
|
483
|
+
|
484
|
+
getNeighborsByHeuristic2(candidates, Mcurmax);
|
485
|
+
|
486
|
+
int indx = 0;
|
487
|
+
while (candidates.size() > 0) {
|
488
|
+
data[indx] = candidates.top().second;
|
489
|
+
candidates.pop();
|
490
|
+
indx++;
|
491
|
+
}
|
492
|
+
|
493
|
+
setListCount(ll_other, indx);
|
494
|
+
// Nearest K:
|
495
|
+
/*int indx = -1;
|
496
|
+
for (int j = 0; j < sz_link_list_other; j++) {
|
497
|
+
dist_t d = fstdistfunc_(getDataByInternalId(data[j]), getDataByInternalId(rez[idx]), dist_func_param_);
|
498
|
+
if (d > d_max) {
|
499
|
+
indx = j;
|
500
|
+
d_max = d;
|
501
|
+
}
|
502
|
+
}
|
503
|
+
if (indx >= 0) {
|
504
|
+
data[indx] = cur_c;
|
505
|
+
} */
|
506
|
+
}
|
507
|
+
}
|
508
|
+
}
|
509
|
+
|
510
|
+
return next_closest_entry_point;
|
511
|
+
}
|
512
|
+
|
513
|
+
std::mutex global;
|
514
|
+
size_t ef_;
|
515
|
+
|
516
|
+
void setEf(size_t ef) {
|
517
|
+
ef_ = ef;
|
518
|
+
}
|
519
|
+
|
520
|
+
|
521
|
+
std::priority_queue<std::pair<dist_t, tableint>> searchKnnInternal(void *query_data, int k) {
|
522
|
+
std::priority_queue<std::pair<dist_t, tableint >> top_candidates;
|
523
|
+
if (cur_element_count == 0) return top_candidates;
|
524
|
+
tableint currObj = enterpoint_node_;
|
525
|
+
dist_t curdist = fstdistfunc_(query_data, getDataByInternalId(enterpoint_node_), dist_func_param_);
|
526
|
+
|
527
|
+
for (size_t level = maxlevel_; level > 0; level--) {
|
528
|
+
bool changed = true;
|
529
|
+
while (changed) {
|
530
|
+
changed = false;
|
531
|
+
int *data;
|
532
|
+
data = (int *) get_linklist(currObj,level);
|
533
|
+
int size = getListCount(data);
|
534
|
+
tableint *datal = (tableint *) (data + 1);
|
535
|
+
for (int i = 0; i < size; i++) {
|
536
|
+
tableint cand = datal[i];
|
537
|
+
if (cand < 0 || cand > max_elements_)
|
538
|
+
throw std::runtime_error("cand error");
|
539
|
+
dist_t d = fstdistfunc_(query_data, getDataByInternalId(cand), dist_func_param_);
|
540
|
+
|
541
|
+
if (d < curdist) {
|
542
|
+
curdist = d;
|
543
|
+
currObj = cand;
|
544
|
+
changed = true;
|
545
|
+
}
|
546
|
+
}
|
547
|
+
}
|
548
|
+
}
|
549
|
+
|
550
|
+
if (has_deletions_) {
|
551
|
+
std::priority_queue<std::pair<dist_t, tableint >> top_candidates1=searchBaseLayerST<true>(currObj, query_data,
|
552
|
+
ef_);
|
553
|
+
top_candidates.swap(top_candidates1);
|
554
|
+
}
|
555
|
+
else{
|
556
|
+
std::priority_queue<std::pair<dist_t, tableint >> top_candidates1=searchBaseLayerST<false>(currObj, query_data,
|
557
|
+
ef_);
|
558
|
+
top_candidates.swap(top_candidates1);
|
559
|
+
}
|
560
|
+
|
561
|
+
while (top_candidates.size() > k) {
|
562
|
+
top_candidates.pop();
|
563
|
+
}
|
564
|
+
return top_candidates;
|
565
|
+
};
|
566
|
+
|
567
|
+
void resizeIndex(size_t new_max_elements){
|
568
|
+
if (new_max_elements<cur_element_count)
|
569
|
+
throw std::runtime_error("Cannot resize, max element is less than the current number of elements");
|
570
|
+
|
571
|
+
|
572
|
+
delete visited_list_pool_;
|
573
|
+
visited_list_pool_ = new VisitedListPool(1, new_max_elements);
|
574
|
+
|
575
|
+
|
576
|
+
element_levels_.resize(new_max_elements);
|
577
|
+
|
578
|
+
std::vector<std::mutex>(new_max_elements).swap(link_list_locks_);
|
579
|
+
|
580
|
+
// Reallocate base layer
|
581
|
+
char * data_level0_memory_new = (char *) realloc(data_level0_memory_, new_max_elements * size_data_per_element_);
|
582
|
+
if (data_level0_memory_new == nullptr)
|
583
|
+
throw std::runtime_error("Not enough memory: resizeIndex failed to allocate base layer");
|
584
|
+
data_level0_memory_ = data_level0_memory_new;
|
585
|
+
|
586
|
+
// Reallocate all other layers
|
587
|
+
char ** linkLists_new = (char **) realloc(linkLists_, sizeof(void *) * new_max_elements);
|
588
|
+
if (linkLists_new == nullptr)
|
589
|
+
throw std::runtime_error("Not enough memory: resizeIndex failed to allocate other layers");
|
590
|
+
linkLists_ = linkLists_new;
|
591
|
+
|
592
|
+
max_elements_ = new_max_elements;
|
593
|
+
}
|
594
|
+
|
595
|
+
void saveIndex(const std::string &location) {
|
596
|
+
std::ofstream output(location, std::ios::binary);
|
597
|
+
std::streampos position;
|
598
|
+
|
599
|
+
writeBinaryPOD(output, offsetLevel0_);
|
600
|
+
writeBinaryPOD(output, max_elements_);
|
601
|
+
writeBinaryPOD(output, cur_element_count);
|
602
|
+
writeBinaryPOD(output, size_data_per_element_);
|
603
|
+
writeBinaryPOD(output, label_offset_);
|
604
|
+
writeBinaryPOD(output, offsetData_);
|
605
|
+
writeBinaryPOD(output, maxlevel_);
|
606
|
+
writeBinaryPOD(output, enterpoint_node_);
|
607
|
+
writeBinaryPOD(output, maxM_);
|
608
|
+
|
609
|
+
writeBinaryPOD(output, maxM0_);
|
610
|
+
writeBinaryPOD(output, M_);
|
611
|
+
writeBinaryPOD(output, mult_);
|
612
|
+
writeBinaryPOD(output, ef_construction_);
|
613
|
+
|
614
|
+
output.write(data_level0_memory_, cur_element_count * size_data_per_element_);
|
615
|
+
|
616
|
+
for (size_t i = 0; i < cur_element_count; i++) {
|
617
|
+
unsigned int linkListSize = element_levels_[i] > 0 ? size_links_per_element_ * element_levels_[i] : 0;
|
618
|
+
writeBinaryPOD(output, linkListSize);
|
619
|
+
if (linkListSize)
|
620
|
+
output.write(linkLists_[i], linkListSize);
|
621
|
+
}
|
622
|
+
output.close();
|
623
|
+
}
|
624
|
+
|
625
|
+
void loadIndex(const std::string &location, SpaceInterface<dist_t> *s, size_t max_elements_i=0) {
|
626
|
+
|
627
|
+
|
628
|
+
std::ifstream input(location, std::ios::binary);
|
629
|
+
|
630
|
+
if (!input.is_open())
|
631
|
+
throw std::runtime_error("Cannot open file");
|
632
|
+
|
633
|
+
// get file size:
|
634
|
+
input.seekg(0,input.end);
|
635
|
+
std::streampos total_filesize=input.tellg();
|
636
|
+
input.seekg(0,input.beg);
|
637
|
+
|
638
|
+
readBinaryPOD(input, offsetLevel0_);
|
639
|
+
readBinaryPOD(input, max_elements_);
|
640
|
+
readBinaryPOD(input, cur_element_count);
|
641
|
+
|
642
|
+
size_t max_elements=max_elements_i;
|
643
|
+
if(max_elements < cur_element_count)
|
644
|
+
max_elements = max_elements_;
|
645
|
+
max_elements_ = max_elements;
|
646
|
+
readBinaryPOD(input, size_data_per_element_);
|
647
|
+
readBinaryPOD(input, label_offset_);
|
648
|
+
readBinaryPOD(input, offsetData_);
|
649
|
+
readBinaryPOD(input, maxlevel_);
|
650
|
+
readBinaryPOD(input, enterpoint_node_);
|
651
|
+
|
652
|
+
readBinaryPOD(input, maxM_);
|
653
|
+
readBinaryPOD(input, maxM0_);
|
654
|
+
readBinaryPOD(input, M_);
|
655
|
+
readBinaryPOD(input, mult_);
|
656
|
+
readBinaryPOD(input, ef_construction_);
|
657
|
+
|
658
|
+
|
659
|
+
data_size_ = s->get_data_size();
|
660
|
+
fstdistfunc_ = s->get_dist_func();
|
661
|
+
dist_func_param_ = s->get_dist_func_param();
|
662
|
+
|
663
|
+
auto pos=input.tellg();
|
664
|
+
|
665
|
+
|
666
|
+
/// Optional - check if index is ok:
|
667
|
+
|
668
|
+
input.seekg(cur_element_count * size_data_per_element_,input.cur);
|
669
|
+
for (size_t i = 0; i < cur_element_count; i++) {
|
670
|
+
if(input.tellg() < 0 || input.tellg()>=total_filesize){
|
671
|
+
throw std::runtime_error("Index seems to be corrupted or unsupported");
|
672
|
+
}
|
673
|
+
|
674
|
+
unsigned int linkListSize;
|
675
|
+
readBinaryPOD(input, linkListSize);
|
676
|
+
if (linkListSize != 0) {
|
677
|
+
input.seekg(linkListSize,input.cur);
|
678
|
+
}
|
679
|
+
}
|
680
|
+
|
681
|
+
// throw exception if it either corrupted or old index
|
682
|
+
if(input.tellg()!=total_filesize)
|
683
|
+
throw std::runtime_error("Index seems to be corrupted or unsupported");
|
684
|
+
|
685
|
+
input.clear();
|
686
|
+
|
687
|
+
/// Optional check end
|
688
|
+
|
689
|
+
input.seekg(pos,input.beg);
|
690
|
+
|
691
|
+
|
692
|
+
data_level0_memory_ = (char *) malloc(max_elements * size_data_per_element_);
|
693
|
+
if (data_level0_memory_ == nullptr)
|
694
|
+
throw std::runtime_error("Not enough memory: loadIndex failed to allocate level0");
|
695
|
+
input.read(data_level0_memory_, cur_element_count * size_data_per_element_);
|
696
|
+
|
697
|
+
|
698
|
+
|
699
|
+
|
700
|
+
size_links_per_element_ = maxM_ * sizeof(tableint) + sizeof(linklistsizeint);
|
701
|
+
|
702
|
+
|
703
|
+
size_links_level0_ = maxM0_ * sizeof(tableint) + sizeof(linklistsizeint);
|
704
|
+
std::vector<std::mutex>(max_elements).swap(link_list_locks_);
|
705
|
+
std::vector<std::mutex>(max_update_element_locks).swap(link_list_update_locks_);
|
706
|
+
|
707
|
+
|
708
|
+
visited_list_pool_ = new VisitedListPool(1, max_elements);
|
709
|
+
|
710
|
+
|
711
|
+
linkLists_ = (char **) malloc(sizeof(void *) * max_elements);
|
712
|
+
if (linkLists_ == nullptr)
|
713
|
+
throw std::runtime_error("Not enough memory: loadIndex failed to allocate linklists");
|
714
|
+
element_levels_ = std::vector<int>(max_elements);
|
715
|
+
revSize_ = 1.0 / mult_;
|
716
|
+
ef_ = 10;
|
717
|
+
for (size_t i = 0; i < cur_element_count; i++) {
|
718
|
+
label_lookup_[getExternalLabel(i)]=i;
|
719
|
+
unsigned int linkListSize;
|
720
|
+
readBinaryPOD(input, linkListSize);
|
721
|
+
if (linkListSize == 0) {
|
722
|
+
element_levels_[i] = 0;
|
723
|
+
|
724
|
+
linkLists_[i] = nullptr;
|
725
|
+
} else {
|
726
|
+
element_levels_[i] = linkListSize / size_links_per_element_;
|
727
|
+
linkLists_[i] = (char *) malloc(linkListSize);
|
728
|
+
if (linkLists_[i] == nullptr)
|
729
|
+
throw std::runtime_error("Not enough memory: loadIndex failed to allocate linklist");
|
730
|
+
input.read(linkLists_[i], linkListSize);
|
731
|
+
}
|
732
|
+
}
|
733
|
+
|
734
|
+
has_deletions_=false;
|
735
|
+
|
736
|
+
for (size_t i = 0; i < cur_element_count; i++) {
|
737
|
+
if(isMarkedDeleted(i))
|
738
|
+
has_deletions_=true;
|
739
|
+
}
|
740
|
+
|
741
|
+
input.close();
|
742
|
+
|
743
|
+
return;
|
744
|
+
}
|
745
|
+
|
746
|
+
template<typename data_t>
|
747
|
+
std::vector<data_t> getDataByLabel(labeltype label)
|
748
|
+
{
|
749
|
+
tableint label_c;
|
750
|
+
auto search = label_lookup_.find(label);
|
751
|
+
if (search == label_lookup_.end() || isMarkedDeleted(search->second)) {
|
752
|
+
throw std::runtime_error("Label not found");
|
753
|
+
}
|
754
|
+
label_c = search->second;
|
755
|
+
|
756
|
+
char* data_ptrv = getDataByInternalId(label_c);
|
757
|
+
size_t dim = *((size_t *) dist_func_param_);
|
758
|
+
std::vector<data_t> data;
|
759
|
+
data_t* data_ptr = (data_t*) data_ptrv;
|
760
|
+
for (int i = 0; i < dim; i++) {
|
761
|
+
data.push_back(*data_ptr);
|
762
|
+
data_ptr += 1;
|
763
|
+
}
|
764
|
+
return data;
|
765
|
+
}
|
766
|
+
|
767
|
+
static const unsigned char DELETE_MARK = 0x01;
|
768
|
+
// static const unsigned char REUSE_MARK = 0x10;
|
769
|
+
/**
|
770
|
+
* Marks an element with the given label deleted, does NOT really change the current graph.
|
771
|
+
* @param label
|
772
|
+
*/
|
773
|
+
void markDelete(labeltype label)
|
774
|
+
{
|
775
|
+
has_deletions_=true;
|
776
|
+
auto search = label_lookup_.find(label);
|
777
|
+
if (search == label_lookup_.end()) {
|
778
|
+
throw std::runtime_error("Label not found");
|
779
|
+
}
|
780
|
+
markDeletedInternal(search->second);
|
781
|
+
}
|
782
|
+
|
783
|
+
/**
|
784
|
+
* Uses the first 8 bits of the memory for the linked list to store the mark,
|
785
|
+
* whereas maxM0_ has to be limited to the lower 24 bits, however, still large enough in almost all cases.
|
786
|
+
* @param internalId
|
787
|
+
*/
|
788
|
+
void markDeletedInternal(tableint internalId) {
|
789
|
+
unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2;
|
790
|
+
*ll_cur |= DELETE_MARK;
|
791
|
+
}
|
792
|
+
|
793
|
+
/**
|
794
|
+
* Remove the deleted mark of the node.
|
795
|
+
* @param internalId
|
796
|
+
*/
|
797
|
+
void unmarkDeletedInternal(tableint internalId) {
|
798
|
+
unsigned char *ll_cur = ((unsigned char *)get_linklist0(internalId))+2;
|
799
|
+
*ll_cur &= ~DELETE_MARK;
|
800
|
+
}
|
801
|
+
|
802
|
+
/**
|
803
|
+
* Checks the first 8 bits of the memory to see if the element is marked deleted.
|
804
|
+
* @param internalId
|
805
|
+
* @return
|
806
|
+
*/
|
807
|
+
bool isMarkedDeleted(tableint internalId) const {
|
808
|
+
unsigned char *ll_cur = ((unsigned char*)get_linklist0(internalId))+2;
|
809
|
+
return *ll_cur & DELETE_MARK;
|
810
|
+
}
|
811
|
+
|
812
|
+
unsigned short int getListCount(linklistsizeint * ptr) const {
|
813
|
+
return *((unsigned short int *)ptr);
|
814
|
+
}
|
815
|
+
|
816
|
+
void setListCount(linklistsizeint * ptr, unsigned short int size) const {
|
817
|
+
*((unsigned short int*)(ptr))=*((unsigned short int *)&size);
|
818
|
+
}
|
819
|
+
|
820
|
+
void addPoint(const void *data_point, labeltype label) {
|
821
|
+
addPoint(data_point, label,-1);
|
822
|
+
}
|
823
|
+
|
824
|
+
void updatePoint(const void *dataPoint, tableint internalId, float updateNeighborProbability) {
|
825
|
+
// update the feature vector associated with existing point with new vector
|
826
|
+
memcpy(getDataByInternalId(internalId), dataPoint, data_size_);
|
827
|
+
|
828
|
+
int maxLevelCopy = maxlevel_;
|
829
|
+
tableint entryPointCopy = enterpoint_node_;
|
830
|
+
// If point to be updated is entry point and graph just contains single element then just return.
|
831
|
+
if (entryPointCopy == internalId && cur_element_count == 1)
|
832
|
+
return;
|
833
|
+
|
834
|
+
int elemLevel = element_levels_[internalId];
|
835
|
+
std::uniform_real_distribution<float> distribution(0.0, 1.0);
|
836
|
+
for (int layer = 0; layer <= elemLevel; layer++) {
|
837
|
+
std::unordered_set<tableint> sCand;
|
838
|
+
std::unordered_set<tableint> sNeigh;
|
839
|
+
std::vector<tableint> listOneHop = getConnectionsWithLock(internalId, layer);
|
840
|
+
if (listOneHop.size() == 0)
|
841
|
+
continue;
|
842
|
+
|
843
|
+
sCand.insert(internalId);
|
844
|
+
|
845
|
+
for (auto&& elOneHop : listOneHop) {
|
846
|
+
sCand.insert(elOneHop);
|
847
|
+
|
848
|
+
if (distribution(update_probability_generator_) > updateNeighborProbability)
|
849
|
+
continue;
|
850
|
+
|
851
|
+
sNeigh.insert(elOneHop);
|
852
|
+
|
853
|
+
std::vector<tableint> listTwoHop = getConnectionsWithLock(elOneHop, layer);
|
854
|
+
for (auto&& elTwoHop : listTwoHop) {
|
855
|
+
sCand.insert(elTwoHop);
|
856
|
+
}
|
857
|
+
}
|
858
|
+
|
859
|
+
for (auto&& neigh : sNeigh) {
|
860
|
+
// if (neigh == internalId)
|
861
|
+
// continue;
|
862
|
+
|
863
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> candidates;
|
864
|
+
size_t size = sCand.find(neigh) == sCand.end() ? sCand.size() : sCand.size() - 1; // sCand guaranteed to have size >= 1
|
865
|
+
size_t elementsToKeep = std::min(ef_construction_, size);
|
866
|
+
for (auto&& cand : sCand) {
|
867
|
+
if (cand == neigh)
|
868
|
+
continue;
|
869
|
+
|
870
|
+
dist_t distance = fstdistfunc_(getDataByInternalId(neigh), getDataByInternalId(cand), dist_func_param_);
|
871
|
+
if (candidates.size() < elementsToKeep) {
|
872
|
+
candidates.emplace(distance, cand);
|
873
|
+
} else {
|
874
|
+
if (distance < candidates.top().first) {
|
875
|
+
candidates.pop();
|
876
|
+
candidates.emplace(distance, cand);
|
877
|
+
}
|
878
|
+
}
|
879
|
+
}
|
880
|
+
|
881
|
+
// Retrieve neighbours using heuristic and set connections.
|
882
|
+
getNeighborsByHeuristic2(candidates, layer == 0 ? maxM0_ : maxM_);
|
883
|
+
|
884
|
+
{
|
885
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[neigh]);
|
886
|
+
linklistsizeint *ll_cur;
|
887
|
+
ll_cur = get_linklist_at_level(neigh, layer);
|
888
|
+
size_t candSize = candidates.size();
|
889
|
+
setListCount(ll_cur, candSize);
|
890
|
+
tableint *data = (tableint *) (ll_cur + 1);
|
891
|
+
for (size_t idx = 0; idx < candSize; idx++) {
|
892
|
+
data[idx] = candidates.top().second;
|
893
|
+
candidates.pop();
|
894
|
+
}
|
895
|
+
}
|
896
|
+
}
|
897
|
+
}
|
898
|
+
|
899
|
+
repairConnectionsForUpdate(dataPoint, entryPointCopy, internalId, elemLevel, maxLevelCopy);
|
900
|
+
};
|
901
|
+
|
902
|
+
void repairConnectionsForUpdate(const void *dataPoint, tableint entryPointInternalId, tableint dataPointInternalId, int dataPointLevel, int maxLevel) {
|
903
|
+
tableint currObj = entryPointInternalId;
|
904
|
+
if (dataPointLevel < maxLevel) {
|
905
|
+
dist_t curdist = fstdistfunc_(dataPoint, getDataByInternalId(currObj), dist_func_param_);
|
906
|
+
for (int level = maxLevel; level > dataPointLevel; level--) {
|
907
|
+
bool changed = true;
|
908
|
+
while (changed) {
|
909
|
+
changed = false;
|
910
|
+
unsigned int *data;
|
911
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[currObj]);
|
912
|
+
data = get_linklist_at_level(currObj,level);
|
913
|
+
int size = getListCount(data);
|
914
|
+
tableint *datal = (tableint *) (data + 1);
|
915
|
+
#ifdef USE_SSE
|
916
|
+
_mm_prefetch(getDataByInternalId(*datal), _MM_HINT_T0);
|
917
|
+
#endif
|
918
|
+
for (int i = 0; i < size; i++) {
|
919
|
+
#ifdef USE_SSE
|
920
|
+
_mm_prefetch(getDataByInternalId(*(datal + i + 1)), _MM_HINT_T0);
|
921
|
+
#endif
|
922
|
+
tableint cand = datal[i];
|
923
|
+
dist_t d = fstdistfunc_(dataPoint, getDataByInternalId(cand), dist_func_param_);
|
924
|
+
if (d < curdist) {
|
925
|
+
curdist = d;
|
926
|
+
currObj = cand;
|
927
|
+
changed = true;
|
928
|
+
}
|
929
|
+
}
|
930
|
+
}
|
931
|
+
}
|
932
|
+
}
|
933
|
+
|
934
|
+
if (dataPointLevel > maxLevel)
|
935
|
+
throw std::runtime_error("Level of item to be updated cannot be bigger than max level");
|
936
|
+
|
937
|
+
for (int level = dataPointLevel; level >= 0; level--) {
|
938
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> topCandidates = searchBaseLayer(
|
939
|
+
currObj, dataPoint, level);
|
940
|
+
|
941
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> filteredTopCandidates;
|
942
|
+
while (topCandidates.size() > 0) {
|
943
|
+
if (topCandidates.top().second != dataPointInternalId)
|
944
|
+
filteredTopCandidates.push(topCandidates.top());
|
945
|
+
|
946
|
+
topCandidates.pop();
|
947
|
+
}
|
948
|
+
|
949
|
+
// Since element_levels_ is being used to get `dataPointLevel`, there could be cases where `topCandidates` could just contains entry point itself.
|
950
|
+
// To prevent self loops, the `topCandidates` is filtered and thus can be empty.
|
951
|
+
if (filteredTopCandidates.size() > 0) {
|
952
|
+
bool epDeleted = isMarkedDeleted(entryPointInternalId);
|
953
|
+
if (epDeleted) {
|
954
|
+
filteredTopCandidates.emplace(fstdistfunc_(dataPoint, getDataByInternalId(entryPointInternalId), dist_func_param_), entryPointInternalId);
|
955
|
+
if (filteredTopCandidates.size() > ef_construction_)
|
956
|
+
filteredTopCandidates.pop();
|
957
|
+
}
|
958
|
+
|
959
|
+
currObj = mutuallyConnectNewElement(dataPoint, dataPointInternalId, filteredTopCandidates, level, true);
|
960
|
+
}
|
961
|
+
}
|
962
|
+
}
|
963
|
+
|
964
|
+
std::vector<tableint> getConnectionsWithLock(tableint internalId, int level) {
|
965
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[internalId]);
|
966
|
+
unsigned int *data = get_linklist_at_level(internalId, level);
|
967
|
+
int size = getListCount(data);
|
968
|
+
std::vector<tableint> result(size);
|
969
|
+
tableint *ll = (tableint *) (data + 1);
|
970
|
+
memcpy(result.data(), ll,size * sizeof(tableint));
|
971
|
+
return result;
|
972
|
+
};
|
973
|
+
|
974
|
+
tableint addPoint(const void *data_point, labeltype label, int level) {
|
975
|
+
|
976
|
+
tableint cur_c = 0;
|
977
|
+
{
|
978
|
+
// Checking if the element with the same label already exists
|
979
|
+
// if so, updating it *instead* of creating a new element.
|
980
|
+
std::unique_lock <std::mutex> templock_curr(cur_element_count_guard_);
|
981
|
+
auto search = label_lookup_.find(label);
|
982
|
+
if (search != label_lookup_.end()) {
|
983
|
+
tableint existingInternalId = search->second;
|
984
|
+
templock_curr.unlock();
|
985
|
+
|
986
|
+
std::unique_lock <std::mutex> lock_el_update(link_list_update_locks_[(existingInternalId & (max_update_element_locks - 1))]);
|
987
|
+
|
988
|
+
if (isMarkedDeleted(existingInternalId)) {
|
989
|
+
unmarkDeletedInternal(existingInternalId);
|
990
|
+
}
|
991
|
+
updatePoint(data_point, existingInternalId, 1.0);
|
992
|
+
|
993
|
+
return existingInternalId;
|
994
|
+
}
|
995
|
+
|
996
|
+
if (cur_element_count >= max_elements_) {
|
997
|
+
throw std::runtime_error("The number of elements exceeds the specified limit");
|
998
|
+
};
|
999
|
+
|
1000
|
+
cur_c = cur_element_count;
|
1001
|
+
cur_element_count++;
|
1002
|
+
label_lookup_[label] = cur_c;
|
1003
|
+
}
|
1004
|
+
|
1005
|
+
// Take update lock to prevent race conditions on an element with insertion/update at the same time.
|
1006
|
+
std::unique_lock <std::mutex> lock_el_update(link_list_update_locks_[(cur_c & (max_update_element_locks - 1))]);
|
1007
|
+
std::unique_lock <std::mutex> lock_el(link_list_locks_[cur_c]);
|
1008
|
+
int curlevel = getRandomLevel(mult_);
|
1009
|
+
if (level > 0)
|
1010
|
+
curlevel = level;
|
1011
|
+
|
1012
|
+
element_levels_[cur_c] = curlevel;
|
1013
|
+
|
1014
|
+
|
1015
|
+
std::unique_lock <std::mutex> templock(global);
|
1016
|
+
int maxlevelcopy = maxlevel_;
|
1017
|
+
if (curlevel <= maxlevelcopy)
|
1018
|
+
templock.unlock();
|
1019
|
+
tableint currObj = enterpoint_node_;
|
1020
|
+
tableint enterpoint_copy = enterpoint_node_;
|
1021
|
+
|
1022
|
+
|
1023
|
+
memset(data_level0_memory_ + cur_c * size_data_per_element_ + offsetLevel0_, 0, size_data_per_element_);
|
1024
|
+
|
1025
|
+
// Initialisation of the data and label
|
1026
|
+
memcpy(getExternalLabeLp(cur_c), &label, sizeof(labeltype));
|
1027
|
+
memcpy(getDataByInternalId(cur_c), data_point, data_size_);
|
1028
|
+
|
1029
|
+
|
1030
|
+
if (curlevel) {
|
1031
|
+
linkLists_[cur_c] = (char *) malloc(size_links_per_element_ * curlevel + 1);
|
1032
|
+
if (linkLists_[cur_c] == nullptr)
|
1033
|
+
throw std::runtime_error("Not enough memory: addPoint failed to allocate linklist");
|
1034
|
+
memset(linkLists_[cur_c], 0, size_links_per_element_ * curlevel + 1);
|
1035
|
+
}
|
1036
|
+
|
1037
|
+
if ((signed)currObj != -1) {
|
1038
|
+
|
1039
|
+
if (curlevel < maxlevelcopy) {
|
1040
|
+
|
1041
|
+
dist_t curdist = fstdistfunc_(data_point, getDataByInternalId(currObj), dist_func_param_);
|
1042
|
+
for (int level = maxlevelcopy; level > curlevel; level--) {
|
1043
|
+
|
1044
|
+
|
1045
|
+
bool changed = true;
|
1046
|
+
while (changed) {
|
1047
|
+
changed = false;
|
1048
|
+
unsigned int *data;
|
1049
|
+
std::unique_lock <std::mutex> lock(link_list_locks_[currObj]);
|
1050
|
+
data = get_linklist(currObj,level);
|
1051
|
+
int size = getListCount(data);
|
1052
|
+
|
1053
|
+
tableint *datal = (tableint *) (data + 1);
|
1054
|
+
for (int i = 0; i < size; i++) {
|
1055
|
+
tableint cand = datal[i];
|
1056
|
+
if (cand < 0 || cand > max_elements_)
|
1057
|
+
throw std::runtime_error("cand error");
|
1058
|
+
dist_t d = fstdistfunc_(data_point, getDataByInternalId(cand), dist_func_param_);
|
1059
|
+
if (d < curdist) {
|
1060
|
+
curdist = d;
|
1061
|
+
currObj = cand;
|
1062
|
+
changed = true;
|
1063
|
+
}
|
1064
|
+
}
|
1065
|
+
}
|
1066
|
+
}
|
1067
|
+
}
|
1068
|
+
|
1069
|
+
bool epDeleted = isMarkedDeleted(enterpoint_copy);
|
1070
|
+
for (int level = std::min(curlevel, maxlevelcopy); level >= 0; level--) {
|
1071
|
+
if (level > maxlevelcopy || level < 0) // possible?
|
1072
|
+
throw std::runtime_error("Level error");
|
1073
|
+
|
1074
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates = searchBaseLayer(
|
1075
|
+
currObj, data_point, level);
|
1076
|
+
if (epDeleted) {
|
1077
|
+
top_candidates.emplace(fstdistfunc_(data_point, getDataByInternalId(enterpoint_copy), dist_func_param_), enterpoint_copy);
|
1078
|
+
if (top_candidates.size() > ef_construction_)
|
1079
|
+
top_candidates.pop();
|
1080
|
+
}
|
1081
|
+
currObj = mutuallyConnectNewElement(data_point, cur_c, top_candidates, level, false);
|
1082
|
+
}
|
1083
|
+
|
1084
|
+
|
1085
|
+
} else {
|
1086
|
+
// Do nothing for the first element
|
1087
|
+
enterpoint_node_ = 0;
|
1088
|
+
maxlevel_ = curlevel;
|
1089
|
+
|
1090
|
+
}
|
1091
|
+
|
1092
|
+
//Releasing lock for the maximum level
|
1093
|
+
if (curlevel > maxlevelcopy) {
|
1094
|
+
enterpoint_node_ = cur_c;
|
1095
|
+
maxlevel_ = curlevel;
|
1096
|
+
}
|
1097
|
+
return cur_c;
|
1098
|
+
};
|
1099
|
+
|
1100
|
+
std::priority_queue<std::pair<dist_t, labeltype >>
|
1101
|
+
searchKnn(const void *query_data, size_t k) const {
|
1102
|
+
std::priority_queue<std::pair<dist_t, labeltype >> result;
|
1103
|
+
if (cur_element_count == 0) return result;
|
1104
|
+
|
1105
|
+
tableint currObj = enterpoint_node_;
|
1106
|
+
dist_t curdist = fstdistfunc_(query_data, getDataByInternalId(enterpoint_node_), dist_func_param_);
|
1107
|
+
|
1108
|
+
for (int level = maxlevel_; level > 0; level--) {
|
1109
|
+
bool changed = true;
|
1110
|
+
while (changed) {
|
1111
|
+
changed = false;
|
1112
|
+
unsigned int *data;
|
1113
|
+
|
1114
|
+
data = (unsigned int *) get_linklist(currObj, level);
|
1115
|
+
int size = getListCount(data);
|
1116
|
+
metric_hops++;
|
1117
|
+
metric_distance_computations+=size;
|
1118
|
+
|
1119
|
+
tableint *datal = (tableint *) (data + 1);
|
1120
|
+
for (int i = 0; i < size; i++) {
|
1121
|
+
tableint cand = datal[i];
|
1122
|
+
if (cand < 0 || cand > max_elements_)
|
1123
|
+
throw std::runtime_error("cand error");
|
1124
|
+
dist_t d = fstdistfunc_(query_data, getDataByInternalId(cand), dist_func_param_);
|
1125
|
+
|
1126
|
+
if (d < curdist) {
|
1127
|
+
curdist = d;
|
1128
|
+
currObj = cand;
|
1129
|
+
changed = true;
|
1130
|
+
}
|
1131
|
+
}
|
1132
|
+
}
|
1133
|
+
}
|
1134
|
+
|
1135
|
+
std::priority_queue<std::pair<dist_t, tableint>, std::vector<std::pair<dist_t, tableint>>, CompareByFirst> top_candidates;
|
1136
|
+
if (has_deletions_) {
|
1137
|
+
top_candidates=searchBaseLayerST<true,true>(
|
1138
|
+
currObj, query_data, std::max(ef_, k));
|
1139
|
+
}
|
1140
|
+
else{
|
1141
|
+
top_candidates=searchBaseLayerST<false,true>(
|
1142
|
+
currObj, query_data, std::max(ef_, k));
|
1143
|
+
}
|
1144
|
+
|
1145
|
+
while (top_candidates.size() > k) {
|
1146
|
+
top_candidates.pop();
|
1147
|
+
}
|
1148
|
+
while (top_candidates.size() > 0) {
|
1149
|
+
std::pair<dist_t, tableint> rez = top_candidates.top();
|
1150
|
+
result.push(std::pair<dist_t, labeltype>(rez.first, getExternalLabel(rez.second)));
|
1151
|
+
top_candidates.pop();
|
1152
|
+
}
|
1153
|
+
return result;
|
1154
|
+
};
|
1155
|
+
|
1156
|
+
void checkIntegrity(){
|
1157
|
+
int connections_checked=0;
|
1158
|
+
std::vector <int > inbound_connections_num(cur_element_count,0);
|
1159
|
+
for(int i = 0;i < cur_element_count; i++){
|
1160
|
+
for(int l = 0;l <= element_levels_[i]; l++){
|
1161
|
+
linklistsizeint *ll_cur = get_linklist_at_level(i,l);
|
1162
|
+
int size = getListCount(ll_cur);
|
1163
|
+
tableint *data = (tableint *) (ll_cur + 1);
|
1164
|
+
std::unordered_set<tableint> s;
|
1165
|
+
for (int j=0; j<size; j++){
|
1166
|
+
assert(data[j] > 0);
|
1167
|
+
assert(data[j] < cur_element_count);
|
1168
|
+
assert (data[j] != i);
|
1169
|
+
inbound_connections_num[data[j]]++;
|
1170
|
+
s.insert(data[j]);
|
1171
|
+
connections_checked++;
|
1172
|
+
|
1173
|
+
}
|
1174
|
+
assert(s.size() == size);
|
1175
|
+
}
|
1176
|
+
}
|
1177
|
+
if(cur_element_count > 1){
|
1178
|
+
int min1=inbound_connections_num[0], max1=inbound_connections_num[0];
|
1179
|
+
for(int i=0; i < cur_element_count; i++){
|
1180
|
+
assert(inbound_connections_num[i] > 0);
|
1181
|
+
min1=std::min(inbound_connections_num[i],min1);
|
1182
|
+
max1=std::max(inbound_connections_num[i],max1);
|
1183
|
+
}
|
1184
|
+
std::cout << "Min inbound: " << min1 << ", Max inbound:" << max1 << "\n";
|
1185
|
+
}
|
1186
|
+
std::cout << "integrity ok, checked " << connections_checked << " connections\n";
|
1187
|
+
|
1188
|
+
}
|
1189
|
+
|
1190
|
+
};
|
1191
|
+
|
1192
|
+
}
|