Merge branch 'query-refactor'

1 files changed, 371 insertions, 0 deletions

diff --git a/include/shard/AugBTree.h b/include/shard/AugBTree.h
new file mode 100644
index 0000000..e32ec64
--- /dev/null
+++ b/include/shard/AugBTree.h
@@ -0,0 +1,371 @@
+/*
+ * include/shard/AugBTree.h
+ *
+ * Copyright (C) 2023 Dong Xie <dongx@psu.edu>
+ *                    Douglas B. Rumbaugh <drumbaugh@psu.edu>
+ *
+ * All rights reserved. Published under the Modified BSD License.
+ *
+ */
+#pragma once
+
+
+#include <vector>
+#include <cassert>
+#include <queue>
+#include <memory>
+#include <concepts>
+
+#include "framework/ShardRequirements.h"
+
+#include "psu-ds/PriorityQueue.h"
+#include "util/Cursor.h"
+#include "psu-ds/Alias.h"
+#include "psu-ds/BloomFilter.h"
+#include "util/bf_config.h"
+
+using psudb::CACHELINE_SIZE;
+using psudb::BloomFilter;
+using psudb::PriorityQueue;
+using psudb::queue_record;
+using psudb::Alias;
+
+namespace de {
+
+thread_local size_t wirs_cancelations = 0;
+
+template <WeightedRecordInterface R>
+struct AugBTreeNode {
+    struct AugBTreeNode<R> *left, *right;
+    decltype(R::key) low, high;
+    decltype(R::weight) weight;
+    Alias* alias;
+};
+
+template <WeightedRecordInterface R>
+class AugBTree {
+private:
+    typedef decltype(R::key) K;
+    typedef decltype(R::value) V;
+    typedef decltype(R::weight) W;
+
+public:
+    AugBTree(MutableBuffer<R>* buffer)
+    : m_reccnt(0), m_tombstone_cnt(0), m_total_weight(0), m_root(nullptr) {
+        m_alloc_size = (buffer->get_record_count() * sizeof(Wrapped<R>)) + (CACHELINE_SIZE - (buffer->get_record_count() * sizeof(Wrapped<R>)) % CACHELINE_SIZE);
+        assert(m_alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Wrapped<R>*)std::aligned_alloc(CACHELINE_SIZE, m_alloc_size);
+
+        m_bf = new BloomFilter<R>(BF_FPR, buffer->get_tombstone_count(), BF_HASH_FUNCS);
+
+        size_t offset = 0;
+        m_reccnt = 0;
+        auto base = buffer->get_data();
+        auto stop = base + buffer->get_record_count();
+
+        std::sort(base, stop, std::less<Wrapped<R>>());
+
+        while (base < stop) {
+            if (!(base->is_tombstone()) && (base + 1) < stop) {
+                if (base->rec == (base + 1)->rec && (base + 1)->is_tombstone()) {
+                    base += 2;
+                    wirs_cancelations++;
+                    continue;
+                }
+            } else if (base->is_deleted()) {
+                base += 1;
+                continue;
+            }
+
+            // FIXME: this shouldn't be necessary, but the tagged record
+            // bypass doesn't seem to be working on this code-path, so this
+            // ensures that tagged records from the buffer are able to be
+            // dropped, eventually. It should only need to be &= 1
+            base->header &= 3;
+            m_data[m_reccnt++] = *base;
+            m_total_weight+= base->rec.weight;
+
+            if (m_bf && base->is_tombstone()) {
+                m_tombstone_cnt++;
+                m_bf->insert(base->rec);
+            }
+            
+            base++;
+        }
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+    }
+
+    AugBTree(AugBTree** shards, size_t len)
+    : m_reccnt(0), m_tombstone_cnt(0), m_total_weight(0), m_root(nullptr) {
+        std::vector<Cursor<Wrapped<R>>> cursors;
+        cursors.reserve(len);
+
+        PriorityQueue<Wrapped<R>> pq(len);
+
+        size_t attemp_reccnt = 0;
+        size_t tombstone_count = 0;
+        
+        for (size_t i = 0; i < len; ++i) {
+            if (shards[i]) {
+                auto base = shards[i]->get_data();
+                cursors.emplace_back(Cursor{base, base + shards[i]->get_record_count(), 0, shards[i]->get_record_count()});
+                attemp_reccnt += shards[i]->get_record_count();
+                tombstone_count += shards[i]->get_tombstone_count();
+                pq.push(cursors[i].ptr, i);
+            } else {
+                cursors.emplace_back(Cursor<Wrapped<R>>{nullptr, nullptr, 0, 0});
+            }
+        }
+
+        m_bf = new BloomFilter<R>(BF_FPR, tombstone_count, BF_HASH_FUNCS);
+
+        m_alloc_size = (attemp_reccnt * sizeof(Wrapped<R>)) + (CACHELINE_SIZE - (attemp_reccnt * sizeof(Wrapped<R>)) % CACHELINE_SIZE);
+        assert(m_alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Wrapped<R>*)std::aligned_alloc(CACHELINE_SIZE, m_alloc_size);
+        
+        while (pq.size()) {
+            auto now = pq.peek();
+            auto next = pq.size() > 1 ? pq.peek(1) : queue_record<Wrapped<R>>{nullptr, 0};
+            if (!now.data->is_tombstone() && next.data != nullptr &&
+                now.data->rec == next.data->rec && next.data->is_tombstone()) {
+                
+                pq.pop(); pq.pop();
+                auto& cursor1 = cursors[now.version];
+                auto& cursor2 = cursors[next.version];
+                if (advance_cursor<Wrapped<R>>(cursor1)) pq.push(cursor1.ptr, now.version);
+                if (advance_cursor<Wrapped<R>>(cursor2)) pq.push(cursor2.ptr, next.version);
+            } else {
+                auto& cursor = cursors[now.version];
+                if (!cursor.ptr->is_deleted()) {
+                    m_data[m_reccnt++] = *cursor.ptr;
+                    m_total_weight += cursor.ptr->rec.weight;
+                    if (m_bf && cursor.ptr->is_tombstone()) {
+                        ++m_tombstone_cnt;
+                        if (m_bf) m_bf->insert(cursor.ptr->rec);
+                    }
+                }
+                pq.pop();
+                
+                if (advance_cursor<Wrapped<R>>(cursor)) pq.push(cursor.ptr, now.version);
+            }
+        }
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+   }
+
+    ~AugBTree() {
+        if (m_data) free(m_data);
+        for (size_t i=0; i<m_alias.size(); i++) {
+            if (m_alias[i]) delete m_alias[i];
+        }
+
+        if (m_bf) delete m_bf;
+
+        free_tree(m_root);
+    }
+
+    Wrapped<R> *point_lookup(const R &rec, bool filter=false) {
+        if (filter && !m_bf->lookup(rec)) {
+            return nullptr;
+        }
+
+        size_t idx = get_lower_bound(rec.key);
+        if (idx >= m_reccnt) {
+            return nullptr;
+        }
+
+        while (idx < m_reccnt && m_data[idx].rec < rec) ++idx;
+
+        if (m_data[idx].rec == rec) {
+            return m_data + idx;
+        }
+
+        return nullptr;
+    }
+
+    Wrapped<R>* get_data() const {
+        return m_data;
+    }
+    
+    size_t get_record_count() const {
+        return m_reccnt;
+    }
+
+    size_t get_tombstone_count() const {
+        return m_tombstone_cnt;
+    }
+
+    const Wrapped<R>* get_record_at(size_t idx) const {
+        if (idx >= m_reccnt) return nullptr;
+        return m_data + idx;
+    }
+
+
+    size_t get_memory_usage() {
+        return m_alloc_size + m_node_cnt * sizeof(AugBTreeNode<Wrapped<R>>);
+    }
+
+    size_t get_aux_memory_usage() {
+        return 0;
+    }
+
+    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].rec.key) {
+                min = mid + 1;
+            } else {
+                max = mid;
+            }
+        }
+
+        return min;
+    }
+
+    W find_covering_nodes(K lower_key, K upper_key, std::vector<void *> &nodes, std::vector<W> &weights) {
+        W total_weight = 0;
+        
+        /* Simulate a stack to unfold recursion. */       
+        struct AugBTreeNode<R>* 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))) {
+                nodes.emplace_back(now);
+                weights.emplace_back(now->weight);
+                total_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;
+            }
+        }
+        
+
+        return total_weight;
+    }
+
+    Wrapped<R> *get_weighted_sample(K lower_key, K upper_key, void *internal_node, gsl_rng *rng) {
+        /* k -> sampling: three levels. 1. select a node -> select a fat point -> select a record. */
+
+        /* first level */ 
+        auto node = (AugBTreeNode<R>*) internal_node;
+
+        /* 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;
+
+        /* bounds rejection */
+        if (lower_key > record->rec.key || upper_key < record->rec.key) {
+            return nullptr;
+        } 
+
+        return record;
+    }
+
+private:
+
+    bool covered_by(struct AugBTreeNode<R>* 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].rec.key && m_data[high_index].rec.key < upper_key;
+    }
+
+    bool intersects(struct AugBTreeNode<R>* 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].rec.key && m_data[low_index].rec.key < upper_key;
+    }
+
+    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].rec.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_AugBTreeNode(weights, 0, n_groups-1);
+    }
+
+     struct AugBTreeNode<R>* construct_AugBTreeNode(const std::vector<W>& weights, size_t low, size_t high) {
+        if (low == high) {
+            return new AugBTreeNode<R>{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();
+        
+        m_node_cnt += 1; 
+        size_t mid = (low + high) / 2;
+        return new AugBTreeNode<R>{construct_AugBTreeNode(weights, low, mid),
+                                construct_AugBTreeNode(weights, mid + 1, high),
+                                low, high, sum, new Alias(node_weights)};
+    }
+
+    void free_tree(struct AugBTreeNode<R>* node) {
+        if (node) {
+            delete node->alias;
+            free_tree(node->left);
+            free_tree(node->right);
+            delete node;
+        }
+    }
+
+    Wrapped<R>* m_data;
+    std::vector<Alias *> m_alias;
+    AugBTreeNode<R>* m_root;
+    W m_total_weight;
+    size_t m_reccnt;
+    size_t m_tombstone_cnt;
+    size_t m_group_size;
+    size_t m_alloc_size;
+    size_t m_node_cnt;
+    BloomFilter<R> *m_bf;
+};
+}