Merge pull request #1 from dbrumbaugh/new-buffer

Initial Concurrency Implementation

1 files changed, 277 insertions, 0 deletions

diff --git a/include/shard/ISAMTree.h b/include/shard/ISAMTree.h
new file mode 100644
index 0000000..3763271
--- /dev/null
+++ b/include/shard/ISAMTree.h
@@ -0,0 +1,277 @@
+/*
+ * include/shard/ISAMTree.h
+ *
+ * Copyright (C) 2023 Douglas B. Rumbaugh <drumbaugh@psu.edu> 
+ *                    Dong Xie <dongx@psu.edu>
+ *
+ * Distributed under the Modified BSD License.
+ *
+ * A shard shim around an in-memory ISAM tree.
+ *
+ * TODO: The code in this file is very poorly commented.
+ */
+#pragma once
+
+#include <vector>
+#include <cassert>
+
+#include "framework/ShardRequirements.h"
+
+#include "util/bf_config.h"
+#include "psu-ds/BloomFilter.h"
+#include "util/SortedMerge.h"
+
+using psudb::CACHELINE_SIZE;
+using psudb::BloomFilter;
+using psudb::PriorityQueue;
+using psudb::queue_record;
+using psudb::byte;
+
+namespace de {
+
+template <KVPInterface R>
+class ISAMTree {
+private:
+
+typedef decltype(R::key) K;
+typedef decltype(R::value) V;
+
+constexpr static size_t NODE_SZ = 256;
+constexpr static size_t INTERNAL_FANOUT = NODE_SZ / (sizeof(K) + sizeof(byte*));
+
+struct InternalNode {
+    K keys[INTERNAL_FANOUT];
+    byte* child[INTERNAL_FANOUT];
+};
+
+static_assert(sizeof(InternalNode) == NODE_SZ, "node size does not match");
+
+constexpr static size_t LEAF_FANOUT = NODE_SZ / sizeof(R);
+
+
+public:
+    ISAMTree(BufferView<R> buffer)
+        : m_bf(new BloomFilter<R>(BF_FPR, buffer.get_tombstone_count(), BF_HASH_FUNCS))
+        , m_isam_nodes(nullptr)
+        , m_root(nullptr)
+        , m_reccnt(0)
+        , m_tombstone_cnt(0)
+        , m_internal_node_cnt(0)
+        , m_deleted_cnt(0)
+        , m_alloc_size(0)
+        , m_data(nullptr)
+    {
+        m_alloc_size = psudb::sf_aligned_alloc(CACHELINE_SIZE, 
+                                               buffer.get_record_count() * 
+                                                 sizeof(Wrapped<R>), 
+                                               (byte**) &m_data);
+
+        /* 
+         * without this, gcc seems to hoist the building of the array
+         * _above_ its allocation under -O3, resulting in memfaults.
+         */
+        asm volatile ("" ::: "memory");
+
+        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_internal_levels();
+        }
+    }
+
+    ISAMTree(std::vector<ISAMTree*> &shards)
+        : m_bf(nullptr) 
+        , m_isam_nodes(nullptr)
+        , m_root(nullptr)
+        , m_reccnt(0)
+        , m_tombstone_cnt(0)
+        , m_internal_node_cnt(0)
+        , m_deleted_cnt(0)
+        , m_alloc_size(0)
+        , m_data(nullptr)
+    {
+        size_t attemp_reccnt = 0;
+        size_t tombstone_count = 0;
+        auto cursors = build_cursor_vec<R, ISAMTree>(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_internal_levels();
+        }
+    }
+
+    ~ISAMTree() {
+        free(m_data);
+        free(m_isam_nodes);
+        delete m_bf;
+    }
+
+    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;
+    }
+
+
+    size_t get_memory_usage() {
+        return m_alloc_size + m_internal_node_cnt * NODE_SZ;
+    }
+
+    size_t get_aux_memory_usage() {
+        return (m_bf) ? m_bf->memory_usage() : 0;
+    }
+
+    /* SortedShardInterface methods */
+    size_t get_lower_bound(const K& key) const {
+        const InternalNode* now = m_root;
+        while (!is_leaf(reinterpret_cast<const byte*>(now))) {
+            const InternalNode* next = nullptr;
+            for (size_t i = 0; i < INTERNAL_FANOUT - 1; ++i) {
+                if (now->child[i + 1] == nullptr || key <= now->keys[i]) {
+                    next = reinterpret_cast<InternalNode*>(now->child[i]);
+                    break;
+                }
+            }
+
+            now = next ? next : reinterpret_cast<const InternalNode*>(now->child[INTERNAL_FANOUT - 1]);
+        }
+
+        const Wrapped<R>* pos = reinterpret_cast<const Wrapped<R>*>(now);
+        while (pos < m_data + m_reccnt && pos->rec.key < key) pos++;
+
+        return pos - m_data;
+    }
+
+    size_t get_upper_bound(const K& key) const {
+        const InternalNode* now = m_root;
+        while (!is_leaf(reinterpret_cast<const byte*>(now))) {
+            const InternalNode* next = nullptr;
+            for (size_t i = 0; i < INTERNAL_FANOUT - 1; ++i) {
+                if (now->child[i + 1] == nullptr || key < now->keys[i]) {
+                    next = reinterpret_cast<InternalNode*>(now->child[i]);
+                    break;
+                }
+            }
+
+            now = next ? next : reinterpret_cast<const InternalNode*>(now->child[INTERNAL_FANOUT - 1]);
+        }
+
+        const Wrapped<R>* pos = reinterpret_cast<const Wrapped<R>*>(now);
+        while (pos < m_data + m_reccnt && pos->rec.key <= key) pos++;
+
+        return pos - m_data;
+    }
+
+    const Wrapped<R>* get_record_at(size_t idx) const {
+        return (idx < m_reccnt) ? m_data + idx : nullptr;
+    }
+
+private:
+    void build_internal_levels() {
+        size_t n_leaf_nodes = m_reccnt / LEAF_FANOUT + (m_reccnt % LEAF_FANOUT != 0);
+
+        size_t level_node_cnt = n_leaf_nodes;
+        size_t node_cnt = 0;
+        do {
+            level_node_cnt = level_node_cnt / INTERNAL_FANOUT + (level_node_cnt % INTERNAL_FANOUT != 0);
+            node_cnt += level_node_cnt;
+        } while (level_node_cnt > 1);
+
+        m_alloc_size += psudb::sf_aligned_calloc(CACHELINE_SIZE, node_cnt, NODE_SZ, (byte**) &m_isam_nodes);
+        m_internal_node_cnt = node_cnt;
+
+        InternalNode* current_node = m_isam_nodes;
+
+        const Wrapped<R>* leaf_base = m_data;
+        const Wrapped<R>* leaf_stop = m_data + m_reccnt;
+        while (leaf_base < leaf_stop) {
+            size_t fanout = 0;
+            for (size_t i = 0; i < INTERNAL_FANOUT; ++i) {
+                auto rec_ptr = leaf_base + LEAF_FANOUT * i;
+                if (rec_ptr >= leaf_stop) break;
+                const Wrapped<R>* sep_key = std::min(rec_ptr + LEAF_FANOUT - 1, leaf_stop - 1);
+                current_node->keys[i] = sep_key->rec.key;
+                current_node->child[i] = (byte*)rec_ptr;
+                ++fanout;
+            }
+            current_node++;
+            leaf_base += fanout * LEAF_FANOUT;
+        }
+
+        auto level_start = m_isam_nodes;
+        auto level_stop = current_node;
+        auto current_level_node_cnt = level_stop - level_start;
+        while (current_level_node_cnt > 1) {
+            auto now = level_start;
+            while (now < level_stop) {
+                size_t child_cnt = 0;
+                for (size_t i = 0; i < INTERNAL_FANOUT; ++i) {
+                    auto node_ptr = now + i;
+                    ++child_cnt;
+                    if (node_ptr >= level_stop) break;
+                    current_node->keys[i] = node_ptr->keys[INTERNAL_FANOUT - 1];
+                    current_node->child[i] = (byte*)node_ptr;
+                }
+                now += child_cnt;
+                current_node++;
+            }
+            level_start = level_stop;
+            level_stop = current_node;
+            current_level_node_cnt = level_stop - level_start;
+        }
+        
+        assert(current_level_node_cnt == 1);
+        m_root = level_start;
+    }
+
+    bool is_leaf(const byte* ptr) const {
+        return ptr >= (const byte*)m_data && ptr < (const byte*)(m_data + m_reccnt);
+    }
+
+    psudb::BloomFilter<R> *m_bf;
+    InternalNode* m_isam_nodes;
+    InternalNode* m_root;
+    size_t m_reccnt;
+    size_t m_tombstone_cnt;
+    size_t m_internal_node_cnt;
+    size_t m_deleted_cnt;
+    size_t m_alloc_size;
+
+    Wrapped<R>* m_data;
+};
+}