Ported over IRS with unit tests

3 files changed, 392 insertions, 2 deletions

diff --git a/include/framework/MutableBuffer.h b/include/framework/MutableBuffer.h
index b3acfee..42bc9a7 100644
--- a/include/framework/MutableBuffer.h
+++ b/include/framework/MutableBuffer.h
@@ -14,6 +14,7 @@
 #include <cassert>
 #include <numeric>
 #include <algorithm>
+#include <type_traits>
 
 #include "util/base.h"
 #include "util/bf_config.h"
@@ -46,7 +47,32 @@ public:
         if (m_tombstone_filter) delete m_tombstone_filter;
     }
 
-    int append(const K& key, const V& value, W weight = 1, bool is_tombstone = false) {
+    template <typename W_=W,
+              typename =std::enable_if_t<std::is_same<W_, void>::value>>
+    int append(const K& key, const V& value, bool is_tombstone = false) {
+        static_assert(std::is_same<W_, void>::value);
+        if (is_tombstone && m_tombstonecnt + 1 > m_tombstone_cap) return 0;
+
+        int32_t pos = 0;
+        if ((pos = try_advance_tail()) == -1) return 0;
+
+        m_data[pos].key = key;
+        m_data[pos].value = value;
+        m_data[pos].header = ((pos << 2) | (is_tombstone ? 1 : 0));
+
+        if (is_tombstone) {
+            m_tombstonecnt.fetch_add(1);
+            if (m_tombstone_filter) m_tombstone_filter->insert(key);
+        }
+
+        m_weight.fetch_add(1);
+        return 1;     
+    }
+
+    template <typename W_=W,
+              typename = std::enable_if_t<!std::is_same<W_, void>::value>>
+    int append(const K& key, const V& value, W_ weight=1, bool is_tombstone = false) {
+        static_assert(!std::is_same<W_, void>::value);
         if (is_tombstone && m_tombstonecnt + 1 > m_tombstone_cap) return 0;
 
         int32_t pos = 0;
@@ -82,6 +108,7 @@ public:
         return 1;     
     }
 
+
     bool truncate() {
         m_tombstonecnt.store(0);
         m_reccnt.store(0);
diff --git a/include/shard/MemISAM.h b/include/shard/MemISAM.h
new file mode 100644
index 0000000..6d97f95
--- /dev/null
+++ b/include/shard/MemISAM.h
@@ -0,0 +1,363 @@
+/*
+ * include/shard/MemISAM.h
+ *
+ * Copyright (C) 2023 Douglas 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/MutableBuffer.h"
+#include "ds/PriorityQueue.h"
+#include "util/Cursor.h"
+#include "util/timer.h"
+
+namespace de {
+
+thread_local size_t mrun_cancelations = 0;
+
+template <typename K, typename V>
+class MemISAM {
+private:
+typedef Record<K, V> Rec;
+
+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 InMemISAMNode {
+    K keys[inmem_isam_fanout];
+    char* child[inmem_isam_fanout];
+};
+
+constexpr static size_t inmem_isam_leaf_fanout = inmem_isam_node_size / sizeof(Rec);
+constexpr static size_t inmem_isam_node_keyskip = sizeof(K) * inmem_isam_fanout;
+
+static_assert(sizeof(InMemISAMNode) == inmem_isam_node_size, "node size does not match");
+
+
+public:
+    MemISAM(std::string data_fname, size_t record_cnt, size_t tombstone_cnt, BloomFilter *bf, bool tagging)
+    : m_reccnt(record_cnt), m_tombstone_cnt(tombstone_cnt), m_deleted_cnt(0), m_tagging(tagging) {
+
+        // read the stored data file the file
+        size_t alloc_size = (record_cnt * sizeof(Rec)) + (CACHELINE_SIZE - (record_cnt * sizeof(Rec)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Rec*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+
+        FILE *file = fopen(data_fname.c_str(), "rb");
+        assert(file);
+        auto res = fread(m_data, sizeof(Rec), m_reccnt, file);
+        assert (res == m_reccnt);
+        fclose(file);
+
+        // We can't really persist the internal structure, as it uses
+        // pointers, which are invalidated by the move. So we'll just
+        // rebuild it.
+        this->build_internal_levels();
+
+        // rebuild the bloom filter
+        for (size_t i=0; i<m_reccnt; i++) {
+            auto rec = this->get_record_at(i);
+            if (rec->is_tombstone()) {
+                bf->insert(rec->key);
+            }
+        }
+    }
+
+    MemISAM(MutableBuffer<K,V>* buffer, BloomFilter* bf, bool tagging)
+    :m_reccnt(0), m_tombstone_cnt(0), m_isam_nodes(nullptr), m_deleted_cnt(0), m_tagging(tagging) {
+
+        size_t alloc_size = (buffer->get_record_count() * sizeof(Rec)) + (CACHELINE_SIZE - (buffer->get_record_count() * sizeof(Rec)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Rec*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+
+        TIMER_INIT();
+
+        size_t offset = 0;
+        m_reccnt = 0;
+        TIMER_START();
+        Rec* base = buffer->sorted_output();
+        TIMER_STOP();
+
+        auto sort_time = TIMER_RESULT();
+        Rec* stop = base + buffer->get_record_count();
+
+        TIMER_START();
+        while (base < stop) {
+            if (!m_tagging) {
+                if (!base->is_tombstone() && (base + 1 < stop)
+                    && base->match(base + 1) && (base + 1)->is_tombstone()) {
+                    base += 2;
+                    mrun_cancelations++;
+                    continue;
+                } 
+            } else if (base->get_delete_status()) {
+                base += 1;
+                continue;
+            }
+
+            //Masking off the ts.
+            base->header &= 1;
+            m_data[m_reccnt++] = *base;
+            if (bf && base->is_tombstone()) {
+                ++m_tombstone_cnt;
+                bf->insert(base->key);
+            }
+
+            base++;
+        }
+        TIMER_STOP();
+        auto copy_time = TIMER_RESULT();
+
+        TIMER_START();
+        if (m_reccnt > 0) {
+            build_internal_levels();
+        }
+        TIMER_STOP();
+        auto level_time = TIMER_RESULT();
+
+        fprintf(stdout, "%ld %ld %ld\n", sort_time, copy_time, level_time);
+    }
+
+    MemISAM(MemISAM** runs, size_t len, BloomFilter* bf, bool tagging)
+    :m_reccnt(0), m_tombstone_cnt(0), m_deleted_cnt(0), m_isam_nodes(nullptr), m_tagging(tagging) {
+        std::vector<Cursor<K,V>> cursors;
+        cursors.reserve(len);
+
+        PriorityQueue<K,V> pq(len);
+
+        size_t attemp_reccnt = 0;
+        
+        for (size_t i = 0; i < len; ++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<K,V>{nullptr, nullptr, 0, 0});
+            }
+        }
+
+        size_t alloc_size = (attemp_reccnt * sizeof(Rec)) + (CACHELINE_SIZE - (attemp_reccnt * sizeof(Rec)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Rec*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+
+        size_t offset = 0;
+        
+        while (pq.size()) {
+            auto now = pq.peek();
+            auto next = pq.size() > 1 ? pq.peek(1) : queue_record<K,V>{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;
+                    if (cursor.ptr->is_tombstone()) {
+                        ++m_tombstone_cnt;
+                        bf->insert(cursor.ptr->key);
+                    }
+                }
+                pq.pop();
+                
+                if (advance_cursor(cursor)) pq.push(cursor.ptr, now.version);
+            }
+        }
+
+        if (m_reccnt > 0) {
+            build_internal_levels();
+        }
+    }
+
+    ~MemISAM() {
+        if (m_data) free(m_data);
+        if (m_isam_nodes) free(m_isam_nodes);
+    }
+
+    Rec* 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;
+    }
+
+    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;
+    }
+
+    const Rec* get_record_at(size_t idx) const {
+        return (idx < m_reccnt) ? m_data + idx : nullptr;
+    }
+
+    size_t get_lower_bound(const K& key) const {
+        const InMemISAMNode* now = m_root;
+        while (!is_leaf(reinterpret_cast<const char*>(now))) {
+            const InMemISAMNode* 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<InMemISAMNode*>(now->child[i]);
+                    break;
+                }
+            }
+
+            now = next ? next : reinterpret_cast<const InMemISAMNode*>(now->child[inmem_isam_fanout - 1]);
+        }
+
+        const Rec* pos = reinterpret_cast<const Rec*>(now);
+        while (pos < m_data + m_reccnt && pos->key < key) pos++;
+
+        return pos - m_data;
+    }
+
+    size_t get_upper_bound(const K& key) const {
+        const InMemISAMNode* now = m_root;
+        while (!is_leaf(reinterpret_cast<const char*>(now))) {
+            const InMemISAMNode* 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<InMemISAMNode*>(now->child[i]);
+                    break;
+                }
+            }
+
+            now = next ? next : reinterpret_cast<const InMemISAMNode*>(now->child[inmem_isam_fanout - 1]);
+        }
+
+        const Rec* pos = reinterpret_cast<const Rec*>(now);
+        while (pos < m_data + m_reccnt && pos->key <= key) pos++;
+
+        return pos - m_data;
+    }
+
+    bool check_tombstone(const K& key, const V& val) const {
+        size_t idx = get_lower_bound(key);
+        if (idx >= m_reccnt) {
+            return false;
+        }
+
+        Rec* ptr = m_data + idx;
+
+        while (ptr < m_data + m_reccnt && ptr->lt(key, val)) ptr++;
+        return ptr->match(key, val, true);
+    }
+
+    size_t get_memory_utilization() {
+        return m_reccnt * sizeof(Rec) + m_internal_node_cnt * inmem_isam_node_size;
+    }
+
+    void persist_to_file(std::string data_fname) {
+        FILE *file = fopen(data_fname.c_str(), "wb");
+        assert(file);
+        fwrite(m_data, sizeof(Rec), m_reccnt, file);
+        fclose(file);
+    }
+    
+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);
+
+        size_t alloc_size = (node_cnt * inmem_isam_node_size) + (CACHELINE_SIZE - (node_cnt * inmem_isam_node_size) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+
+        m_isam_nodes = (InMemISAMNode*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+        m_internal_node_cnt = node_cnt;
+        memset(m_isam_nodes, 0, node_cnt * inmem_isam_node_size);
+
+        InMemISAMNode* current_node = m_isam_nodes;
+
+        const Rec* leaf_base = m_data;
+        const Rec* 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 Rec* sep_key = std::min(rec_ptr + inmem_isam_leaf_fanout - 1, leaf_stop - 1);
+                current_node->keys[i] = sep_key->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;
+    Rec* m_data;
+    InMemISAMNode* m_isam_nodes;
+    InMemISAMNode* m_root;
+    size_t m_reccnt;
+    size_t m_tombstone_cnt;
+    size_t m_internal_node_cnt;
+    size_t m_deleted_cnt;
+    bool m_tagging;
+};
+
+}
diff --git a/include/util/Cursor.h b/include/util/Cursor.h
index b9093f4..2339800 100644
--- a/include/util/Cursor.h
+++ b/include/util/Cursor.h
@@ -14,7 +14,7 @@
 #include "io/PagedFile.h"
 
 namespace de {
-template<typename K, typename V, typename W>
+template<typename K, typename V, typename W=void>
 struct Cursor {
     Record<K,V,W> *ptr;
     const Record<K,V,W> *end;