Initial port of WIRS structure and mutable buffer

1 files changed, 440 insertions, 0 deletions

diff --git a/include/shard/WIRS.h b/include/shard/WIRS.h
new file mode 100644
index 0000000..5d6baeb
--- /dev/null
+++ b/include/shard/WIRS.h
@@ -0,0 +1,440 @@
+/*
+ * include/shard/WIRS.h
+ *
+ * Copyright (C) 2023 Dong Xie <dongx@psu.edu>
+ *
+ * All rights reserved. Published under the Modified BSD License.
+ *
+ */
+#pragma once
+
+#include <vector>
+#include <cassert>
+#include <queue>
+#include <memory>
+
+#include "ds/PriorityQueue.h"
+#include "util/Cursor.h"
+#include "ds/Alias.h"
+#include "ds/BloomFilter.h"
+#include "util/Record.h"
+#include "framework/MutableBuffer.h"
+
+namespace de {
+
+struct sample_state;
+template <typename K, typename V, typename W>
+bool check_deleted(Record<K, V, W>* record, sample_state *state);
+extern thread_local size_t bounds_rejections;
+extern thread_local size_t tombstone_rejections;
+
+
+
+thread_local size_t m_wirsrun_cancelations = 0;
+
+template <typename K, typename V, typename W>
+class WIRS {
+private:
+    struct wirs_node {
+        struct wirs_node *left, *right;
+        K low, high;
+        W weight;
+        Alias* alias;
+    };
+
+    struct WIRSState {
+        W tot_weight;
+        std::vector<wirs_node*> nodes;
+        Alias* top_level_alias;
+
+        ~WIRSState() {
+            if (top_level_alias) delete top_level_alias;
+        }
+    };
+
+public:
+    WIRS(MutableBuffer<K, V, W>* buffer, BloomFilter* bf, bool tagging)
+    : m_reccnt(0), m_tombstone_cnt(0), m_deleted_cnt(0), m_total_weight(0), m_rejection_cnt(0), 
+      m_ts_check_cnt(0), m_tagging(tagging), m_root(nullptr) {
+
+        size_t alloc_size = (buffer->get_record_count() * sizeof(Record<K, V, W>)) + (CACHELINE_SIZE - (buffer->get_record_count() * sizeof(Record<K, V, W>)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Record<K, V, W>*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+
+        size_t offset = 0;
+        m_reccnt = 0;
+        auto base = buffer->sorted_output();
+        auto stop = base + buffer->get_record_count();
+
+        while (base < stop) {
+            if (!m_tagging) {
+                if (!(base->is_tombstone()) && (base + 1) < stop) {
+                    if (base->match(base + 1) && (base + 1)->is_tombstone()) {
+                        base += 2;
+                        m_wirsrun_cancelations++;
+                        continue;
+                    }
+                }
+            } else if (base->get_delete_status()) {
+                base += 1;
+                continue;
+            }
+
+            base->header &= 1;
+            m_data[m_reccnt++] = *base;
+            m_total_weight+= base->weight;
+
+            if (bf && base->is_tombstone()) {
+                m_tombstone_cnt++;
+                bf->insert(base->key);
+            }
+            
+            base++;
+        }
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+    }
+
+    WIRS(WIRS** runs, size_t len, BloomFilter* bf, bool tagging)
+    : m_reccnt(0), m_tombstone_cnt(0), m_deleted_cnt(0), m_total_weight(0), m_rejection_cnt(0), m_ts_check_cnt(0), 
+      m_tagging(tagging), m_root(nullptr) {
+        std::vector<Cursor> cursors;
+        cursors.reserve(len);
+
+        PriorityQueue<K, V, W> pq(len);
+
+        size_t attemp_reccnt = 0;
+        
+        for (size_t i = 0; i < len; ++i) {
+            //assert(runs[i]);
+            if (runs[i]) {
+                auto base = runs[i]->sorted_output();
+                cursors.emplace_back(Cursor{base, base + runs[i]->get_record_count(), 0, runs[i]->get_record_count()});
+                attemp_reccnt += runs[i]->get_record_count();
+                pq.push(cursors[i].ptr, i);
+            } else {
+                cursors.emplace_back(Cursor{nullptr, nullptr, 0, 0});
+            }
+        }
+
+        size_t alloc_size = (attemp_reccnt * sizeof(Record<K, V, W>)) + (CACHELINE_SIZE - (attemp_reccnt * sizeof(Record<K, V, W>)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Record<K, V, W>*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+        
+        while (pq.size()) {
+            auto now = pq.peek();
+            auto next = pq.size() > 1 ? pq.peek(1) : queue_record<K, V, W>{nullptr, 0};
+            if (!m_tagging && !now.data->is_tombstone() && next.data != nullptr &&
+                now.data->match(next.data) && next.data->is_tombstone()) {
+                
+                pq.pop(); pq.pop();
+                auto& cursor1 = cursors[now.version];
+                auto& cursor2 = cursors[next.version];
+                if (advance_cursor(cursor1)) pq.push(cursor1.ptr, now.version);
+                if (advance_cursor(cursor2)) pq.push(cursor2.ptr, next.version);
+            } else {
+                auto& cursor = cursors[now.version];
+                if (!m_tagging || !cursor.ptr->get_delete_status()) {
+                    m_data[m_reccnt++] = *cursor.ptr;
+                    m_total_weight += cursor.ptr->weight;
+                    if (bf && cursor.ptr->is_tombstone()) {
+                        ++m_tombstone_cnt;
+                        if (bf) bf->insert(cursor.ptr->key);
+                    }
+                }
+                pq.pop();
+                
+                if (advance_cursor(cursor)) pq.push(cursor.ptr, now.version);
+            }
+        }
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+   }
+
+    ~WIRS() {
+        if (m_data) free(m_data);
+        for (size_t i=0; i<m_alias.size(); i++) {
+            if (m_alias[i]) delete m_alias[i];
+        }
+
+        free_tree(m_root);
+    }
+
+    bool delete_record(const K& key, const V& val) {
+        size_t idx = get_lower_bound(key);
+        if (idx >= m_reccnt) {
+            return false;
+        }
+
+        while (idx < m_reccnt && m_data[idx].lt(key, val)) ++idx;
+
+        if (m_data[idx].match(key, val, false)) {
+            m_data[idx].set_delete_status();
+            m_deleted_cnt++;
+            return true;
+        }
+
+        return false;
+    }
+
+    void free_tree(struct wirs_node* node) {
+        if (node) {
+            delete node->alias;
+            free_tree(node->left);
+            free_tree(node->right);
+            delete node;
+        }
+    }
+
+    Record<K, V, W>* sorted_output() const {
+        return m_data;
+    }
+    
+    size_t get_record_count() const {
+        return m_reccnt;
+    }
+
+    size_t get_tombstone_count() const {
+        return m_tombstone_cnt;
+    }
+
+    const Record<K, V, W>* get_record_at(size_t idx) const {
+        if (idx >= m_reccnt) return nullptr;
+        return m_data + idx;
+    }
+
+    // low - high -> decompose to a set of nodes.
+    // Build Alias across the decomposed nodes.
+    WIRSState* get_sample_run_state(const K& lower_key, const K& upper_key) {
+        WIRSState* res = new WIRSState();
+        //std::vector<struct wirs_node*> nodes;
+        //double tot_weight = decompose_node(m_root, lower_key, upper_key, res->nodes);
+
+        // Simulate a stack to unfold recursion.        
+        double tot_weight = 0.0;
+        struct wirs_node* st[64] = {0};
+        st[0] = m_root;
+        size_t top = 1;
+        while(top > 0) {
+            auto now = st[--top];
+            if (covered_by(now, lower_key, upper_key) ||
+                (now->left == nullptr && now->right == nullptr && intersects(now, lower_key, upper_key))) {
+                res->nodes.emplace_back(now);
+                tot_weight += now->weight;
+            } else {
+                if (now->left && intersects(now->left, lower_key, upper_key)) st[top++] = now->left;
+                if (now->right && intersects(now->right, lower_key, upper_key)) st[top++] = now->right;
+            }
+        }
+        
+        //assert(tot_weight > 0.0);
+        std::vector<double> weights;
+        for (const auto& node: res->nodes) {
+            weights.emplace_back(node->weight / tot_weight);
+        }
+        res->tot_weight = tot_weight;
+        res->top_level_alias = new Alias(weights);
+
+        return res;
+    }
+
+    // returns the number of records sampled
+    // NOTE: This operation returns records strictly between the lower and upper bounds, not
+    // including them.
+    size_t get_samples(WIRSState* run_state, Record<K, V, W> *sample_set, const K& lower_key, const K& upper_key, size_t sample_sz, sample_state *state, gsl_rng *rng) {
+        if (sample_sz == 0) {
+            return 0;
+        }
+
+        // k -> sampling: three levels. 1. select a node -> select a fat point -> select a record.
+        size_t cnt = 0;
+        size_t attempts = 0;
+        do {
+            ++attempts;
+            // first level....
+            auto node = run_state->nodes[run_state->top_level_alias->get(rng)];
+            // second level...
+            auto fat_point = node->low + node->alias->get(rng);
+            // third level...
+            size_t rec_offset = fat_point * m_group_size + m_alias[fat_point]->get(rng);
+            auto record = m_data + rec_offset;
+
+            if (lower_key > record->key || upper_key < record->key) {
+                // bounds rejection
+                bounds_rejections++;
+                continue;
+            } else if (record->is_tombstone() || (state && check_deleted(record, state))) {
+                // tombstone/delete rejection
+                tombstone_rejections++;
+                continue;
+            }
+
+            sample_set[cnt++] = *record;
+            
+        } while (attempts < sample_sz);
+
+        return cnt;
+    }
+
+    size_t get_lower_bound(const K& key) const {
+        size_t min = 0;
+        size_t max = m_reccnt - 1;
+
+        const char * record_key;
+        while (min < max) {
+            size_t mid = (min + max) / 2;
+
+            if (key > m_data[mid].key) {
+                min = mid + 1;
+            } else {
+                max = mid;
+            }
+        }
+
+        return min;
+    }
+
+    bool check_delete(K key, V val) {
+        size_t idx = get_lower_bound(key);
+        if (idx >= m_reccnt) {
+            return false;
+        }
+
+        auto ptr = m_data + get_lower_bound(key);
+
+        while (ptr < m_data + m_reccnt && ptr->lt(key, val)) {
+            ptr ++;
+        }
+
+        bool result = (m_tagging) ? ptr->get_delete_status()
+                                  : ptr->match(key, val, true);
+        m_rejection_cnt += result;
+        return result;
+    }
+
+    bool check_tombstone(const K& key, const V& val) {
+        m_ts_check_cnt++;
+        size_t idx = get_lower_bound(key);
+        if (idx >= m_reccnt) {
+            return false;
+        }
+
+        auto ptr = m_data + get_lower_bound(key);
+
+        while (ptr < m_data + m_reccnt && ptr->lt(key, val)) {
+            ptr ++;
+        }
+
+        bool result = ptr->match(key, val, true);
+        m_rejection_cnt += result;
+
+        return result;
+    }
+
+
+    size_t get_memory_utilization() {
+        return 0;
+    }
+
+
+    size_t get_rejection_count() {
+        return m_rejection_cnt;
+    }
+
+    size_t get_ts_check_count() {
+        return m_ts_check_cnt;
+    }
+    
+private:
+
+    bool covered_by(struct wirs_node* node, const K& lower_key, const K& upper_key) {
+        auto low_index = node->low * m_group_size;
+        auto high_index = std::min((node->high + 1) * m_group_size - 1, m_reccnt - 1);
+        return lower_key < m_data[low_index].key && m_data[high_index].key < upper_key;
+    }
+
+    bool intersects(struct wirs_node* node, const K& lower_key, const K& upper_key) {
+        auto low_index = node->low * m_group_size;
+        auto high_index = std::min((node->high + 1) * m_group_size - 1, m_reccnt - 1);
+        return lower_key < m_data[high_index].key && m_data[low_index].key < upper_key;
+    }
+    
+    struct wirs_node* construct_wirs_node(const std::vector<W>& weights, size_t low, size_t high) {
+        if (low == high) {
+            return new wirs_node{nullptr, nullptr, low, high, weights[low], new Alias({1.0})};
+        } else if (low > high) return nullptr;
+
+        std::vector<double> node_weights;
+        W sum = 0;
+        for (size_t i = low; i < high; ++i) {
+            node_weights.emplace_back(weights[i]);
+            sum += weights[i];
+        }
+
+        for (auto& w: node_weights)
+            if (sum) w /= sum;
+            else w = 1.0 / node_weights.size();
+        
+        
+        size_t mid = (low + high) / 2;
+        return new wirs_node{construct_wirs_node(weights, low, mid),
+                             construct_wirs_node(weights, mid + 1, high),
+                             low, high, sum, new Alias(node_weights)};
+    }
+
+
+    void build_wirs_structure() {
+        m_group_size = std::ceil(std::log(m_reccnt));
+        size_t n_groups = std::ceil((double) m_reccnt / (double) m_group_size);
+        
+        // Fat point construction + low level alias....
+        double sum_weight = 0.0;
+        std::vector<W> weights;
+        std::vector<double> group_norm_weight;
+        size_t i = 0;
+        size_t group_no = 0;
+        while (i < m_reccnt) {
+            double group_weight = 0.0;
+            group_norm_weight.clear();
+            for (size_t k = 0; k < m_group_size && i < m_reccnt; ++k, ++i) {
+                auto w = m_data[i].weight;
+                group_norm_weight.emplace_back(w);
+                group_weight += w;
+                sum_weight += w;
+            }
+
+            for (auto& w: group_norm_weight)
+                if (group_weight) w /= group_weight;
+                else w = 1.0 / group_norm_weight.size();
+            m_alias.emplace_back(new Alias(group_norm_weight));
+
+            
+            weights.emplace_back(group_weight);
+        }
+
+        assert(weights.size() == n_groups);
+
+        m_root = construct_wirs_node(weights, 0, n_groups-1);
+    }
+
+    Record<K, V, W>* m_data;
+    std::vector<Alias *> m_alias;
+    wirs_node* m_root;
+    bool m_tagging;
+    W m_total_weight;
+    size_t m_reccnt;
+    size_t m_tombstone_cnt;
+    size_t m_group_size;
+    size_t m_ts_check_cnt;
+    size_t m_deleted_cnt;
+
+    // The number of rejections caused by tombstones
+    // in this WIRS.
+    size_t m_rejection_cnt;
+};
+
+}