Refactoring progress

1 files changed, 339 insertions, 0 deletions

diff --git a/include/shard/ISAMTree.h b/include/shard/ISAMTree.h
new file mode 100644
index 0000000..a610c09
--- /dev/null
+++ b/include/shard/ISAMTree.h
@@ -0,0 +1,339 @@
+/*
+ * include/shard/ISAMTree.h
+ *
+ * Copyright (C) 2023 Douglas B. Rumbaugh <drumbaugh@psu.edu> 
+ *                    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 "framework/ShardRequirements.h"
+
+#include "util/bf_config.h"
+#include "psu-ds/PriorityQueue.h"
+#include "util/Cursor.h"
+#include "psu-util/timer.h"
+
+using psudb::CACHELINE_SIZE;
+using psudb::BloomFilter;
+using psudb::PriorityQueue;
+using psudb::queue_record;
+using psudb::Alias;
+
+namespace de {
+
+thread_local size_t mrun_cancelations = 0;
+
+template <RecordInterface R>
+class ISAMTree {
+private:
+
+typedef decltype(R::key) K;
+typedef decltype(R::value) V;
+
+constexpr static size_t inmem_isam_node_size = 256;
+constexpr static size_t inmem_isam_fanout = inmem_isam_node_size / (sizeof(K) + sizeof(char*));
+
+struct InternalNode {
+    K keys[inmem_isam_fanout];
+    char* child[inmem_isam_fanout];
+};
+
+constexpr static size_t inmem_isam_leaf_fanout = inmem_isam_node_size / sizeof(R);
+constexpr static size_t inmem_isam_node_keyskip = sizeof(K) * inmem_isam_fanout;
+
+static_assert(sizeof(InternalNode) == inmem_isam_node_size, "node size does not match");
+
+public:
+    ISAMTree(MutableBuffer<R>* buffer)
+    :m_reccnt(0), m_tombstone_cnt(0), m_isam_nodes(nullptr), m_deleted_cnt(0) {
+
+        m_bf = new BloomFilter<R>(BF_FPR, buffer->get_tombstone_count(), BF_HASH_FUNCS);
+
+        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);
+
+        TIMER_INIT();
+
+        size_t offset = 0;
+        m_reccnt = 0;
+        auto base = buffer->get_data();
+        auto stop = base + buffer->get_record_count();
+
+        TIMER_START();
+        std::sort(base, stop, std::less<Wrapped<R>>());
+        TIMER_STOP();
+        auto sort_time = TIMER_RESULT();
+
+        TIMER_START();
+        while (base < stop) {
+            if (!base->is_tombstone() && (base + 1 < stop)
+                && base->rec == (base + 1)->rec  && (base + 1)->is_tombstone()) {
+                base += 2;
+                mrun_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;
+            if (m_bf && base->is_tombstone()) {
+                ++m_tombstone_cnt;
+                m_bf->insert(base->rec);
+            }
+
+            base++;
+        }
+        TIMER_STOP();
+        auto copy_time = TIMER_RESULT();
+
+        TIMER_START();
+        if (m_reccnt > 0) {
+            build_internal_levels();
+        }
+        TIMER_STOP();
+        auto level_time = TIMER_RESULT();
+    }
+
+    ISAMTree(ISAMTree** runs, size_t len)
+    : m_reccnt(0), m_tombstone_cnt(0), m_deleted_cnt(0), m_isam_nodes(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 (runs[i]) {
+                auto base = runs[i]->get_data();
+                cursors.emplace_back(Cursor{base, base + runs[i]->get_record_count(), 0, runs[i]->get_record_count()});
+                attemp_reccnt += runs[i]->get_record_count();
+                tombstone_count += runs[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);
+
+        size_t offset = 0;
+        
+        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(cursor1)) pq.push(cursor1.ptr, now.version);
+                if (advance_cursor(cursor2)) pq.push(cursor2.ptr, next.version);
+            } else {
+                auto& cursor = cursors[now.version];
+                if (!cursor.ptr->is_deleted()) {
+                    m_data[m_reccnt++] = *cursor.ptr;
+                    if (cursor.ptr->is_tombstone()) {
+                        ++m_tombstone_cnt;
+                        m_bf->insert(cursor.ptr->rec);
+                    }
+                }
+                pq.pop();
+                
+                if (advance_cursor(cursor)) pq.push(cursor.ptr, now.version);
+            }
+        }
+
+        if (m_reccnt > 0) {
+            build_internal_levels();
+        }
+    }
+
+    ~ISAMTree() {
+        if (m_data) free(m_data);
+        if (m_isam_nodes) free(m_isam_nodes);
+        if (m_bf) 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;
+    }
+
+    const Wrapped<R>* get_record_at(size_t idx) const {
+        return (idx < m_reccnt) ? m_data + idx : nullptr;
+    }
+
+    size_t get_memory_usage() {
+        return m_internal_node_cnt * inmem_isam_node_size + m_alloc_size;
+    }
+
+    size_t get_aux_memory_usage() {
+        return 0;
+    }
+
+    size_t get_lower_bound(const K& key) const {
+        const InternalNode* now = m_root;
+        while (!is_leaf(reinterpret_cast<const char*>(now))) {
+            const InternalNode* next = nullptr;
+            for (size_t i = 0; i < inmem_isam_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[inmem_isam_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 char*>(now))) {
+            const InternalNode* next = nullptr;
+            for (size_t i = 0; i < inmem_isam_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[inmem_isam_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;
+    }
+
+
+private:
+    void build_internal_levels() {
+        size_t n_leaf_nodes = m_reccnt / inmem_isam_leaf_fanout + (m_reccnt % inmem_isam_leaf_fanout != 0);
+        size_t level_node_cnt = n_leaf_nodes;
+        size_t node_cnt = 0;
+        do {
+            level_node_cnt = level_node_cnt / inmem_isam_fanout + (level_node_cnt % inmem_isam_fanout != 0);
+            node_cnt += level_node_cnt;
+        } while (level_node_cnt > 1);
+
+        m_alloc_size = (node_cnt * inmem_isam_node_size) + (CACHELINE_SIZE - (node_cnt * inmem_isam_node_size) % CACHELINE_SIZE);
+        assert(m_alloc_size % CACHELINE_SIZE == 0);
+
+        m_isam_nodes = (InternalNode*)std::aligned_alloc(CACHELINE_SIZE, m_alloc_size);
+        m_internal_node_cnt = node_cnt;
+        memset(m_isam_nodes, 0, node_cnt * inmem_isam_node_size);
+
+        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 < inmem_isam_fanout; ++i) {
+                auto rec_ptr = leaf_base + inmem_isam_leaf_fanout * i;
+                if (rec_ptr >= leaf_stop) break;
+                const Wrapped<R>* sep_key = std::min(rec_ptr + inmem_isam_leaf_fanout - 1, leaf_stop - 1);
+                current_node->keys[i] = sep_key->rec.key;
+                current_node->child[i] = (char*)rec_ptr;
+                ++fanout;
+            }
+            current_node++;
+            leaf_base += fanout * inmem_isam_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 < inmem_isam_fanout; ++i) {
+                    auto node_ptr = now + i;
+                    ++child_cnt;
+                    if (node_ptr >= level_stop) break;
+                    current_node->keys[i] = node_ptr->keys[inmem_isam_fanout - 1];
+                    current_node->child[i] = (char*)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 char* ptr) const {
+        return ptr >= (const char*)m_data && ptr < (const char*)(m_data + m_reccnt);
+    }
+
+    // Members: sorted data, internal ISAM levels, reccnt;
+    Wrapped<R>* m_data;
+    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;
+};
+}