Merge pull request #1 from dbrumbaugh/new-buffer

Initial Concurrency Implementation

1 files changed, 311 insertions, 0 deletions

diff --git a/include/shard/AugBTree.h b/include/shard/AugBTree.h
new file mode 100644
index 0000000..54931bd
--- /dev/null
+++ b/include/shard/AugBTree.h
@@ -0,0 +1,311 @@
+/*
+ * include/shard/AugBTree.h
+ *
+ * Copyright (C) 2023 Dong Xie <dongx@psu.edu>
+ *                    Douglas B. Rumbaugh <drumbaugh@psu.edu>
+ *
+ * Distributed under the Modified BSD License.
+ *
+ * A shard shim around the alias augmented B-tree. Designed to be 
+ * used along side the WIRS query in include/query/wirs.h, but
+ * also supports the necessary methods for other common query
+ * types.
+ *
+ * TODO: The code in this file is very poorly commented.
+ */
+#pragma once
+
+
+#include <vector>
+#include <cassert>
+
+#include "framework/ShardRequirements.h"
+
+#include "psu-ds/Alias.h"
+#include "psu-ds/BloomFilter.h"
+#include "util/bf_config.h"
+#include "util/SortedMerge.h"
+
+using psudb::CACHELINE_SIZE;
+using psudb::BloomFilter;
+using psudb::Alias;
+using psudb::byte;
+
+namespace de {
+
+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(BufferView<R> buffer)
+    : m_data(nullptr)
+    , m_root(nullptr)
+    , m_reccnt(0)
+    , m_tombstone_cnt(0)
+    , m_group_size(0)
+    , m_alloc_size(0)
+    , m_node_cnt(0)
+    , m_bf(new BloomFilter<R>(BF_FPR, buffer.get_tombstone_count(), BF_HASH_FUNCS))
+    {
+        m_alloc_size = psudb::sf_aligned_alloc(CACHELINE_SIZE, 
+                                               buffer.get_record_count() * 
+                                                 sizeof(Wrapped<R>), 
+                                               (byte**) &m_data);
+
+        auto res = sorted_array_from_bufferview(std::move(buffer), m_data, m_bf);
+        m_reccnt = res.record_count;
+        m_tombstone_cnt = res.tombstone_count;
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+    }
+
+    AugBTree(std::vector<AugBTree*> shards)
+    : m_data(nullptr)
+    , m_root(nullptr)
+    , m_reccnt(0)
+    , m_tombstone_cnt(0)
+    , m_group_size(0)
+    , m_alloc_size(0)
+    , m_node_cnt(0)
+    , m_bf(nullptr)
+    {
+        size_t attemp_reccnt = 0;
+        size_t tombstone_count = 0;
+        auto cursors = build_cursor_vec<R, AugBTree>(shards, &attemp_reccnt, &tombstone_count);
+
+        m_bf = new BloomFilter<R>(BF_FPR, tombstone_count, BF_HASH_FUNCS);
+        m_alloc_size = psudb::sf_aligned_alloc(CACHELINE_SIZE, 
+                                               attemp_reccnt * sizeof(Wrapped<R>),
+                                               (byte **) &m_data);
+
+        auto res = sorted_array_merge<R>(cursors, m_data, m_bf);
+        m_reccnt = res.record_count;
+        m_tombstone_cnt = res.tombstone_count;
+
+        if (m_reccnt > 0) {
+            build_wirs_structure();
+        }
+   }
+
+    ~AugBTree() {
+        free(m_data);
+        for (size_t i=0; i<m_alias.size(); i++) {
+            delete m_alias[i];
+        }
+
+        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-1) && 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 (m_bf) ? m_bf->memory_usage() : 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;
+    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;
+};
+}