PGM-based shard

1 files changed, 345 insertions, 0 deletions

diff --git a/include/shard/PGM.h b/include/shard/PGM.h
new file mode 100644
index 0000000..9fad8d0
--- /dev/null
+++ b/include/shard/PGM.h
@@ -0,0 +1,345 @@
+/*
+ * include/shard/PGM.h
+ *
+ * Copyright (C) 2023 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 "pgm/pgm_index.hpp"
+#include "ds/PriorityQueue.h"
+#include "util/Cursor.h"
+#include "ds/BloomFilter.h"
+#include "util/bf_config.h"
+#include "framework/MutableBuffer.h"
+#include "framework/RecordInterface.h"
+#include "framework/ShardInterface.h"
+#include "framework/QueryInterface.h"
+
+namespace de {
+
+template <RecordInterface R>
+struct ts_range_query_parms {
+    decltype(R::key) lower_bound;
+    decltype(R::key) upper_bound;
+};
+
+template <RecordInterface R, bool Rejection>
+class PGMLookup;
+
+template <RecordInterface R>
+struct PGMState {
+    size_t start_idx;
+    size_t stop_idx;
+};
+
+template <RecordInterface R>
+struct PGMBufferState {
+    size_t cutoff;
+    Alias* alias;
+    decltype(R::weight) max_weight;
+
+    ~PGMBufferState() {
+        delete alias;
+    }
+
+};
+
+template <RecordInterface R>
+class PGM {
+private:
+    typedef decltype(R::key) K;
+    typedef decltype(R::value) V;
+
+public:
+
+    // FIXME: there has to be a better way to do this
+    friend class PGMLookup<R, true>;
+    friend class PGMLookup<R, false>;
+
+    PGM(MutableBuffer<R>* buffer)
+    : m_reccnt(0), m_tombstone_cnt(0) {
+
+        size_t alloc_size = (buffer->get_record_count() * sizeof(Wrapped<R>)) + (CACHELINE_SIZE - (buffer->get_record_count() * sizeof(Wrapped<R>)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Wrapped<R>*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+        std::vector<K> keys;
+
+        m_bf = new BloomFilter<K>(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>>());
+
+        K min_key = base->rec.key;
+        K max_key = (stop - 1)->rec.key;
+
+        while (base < stop) {
+            if (!(base->is_tombstone()) && (base + 1) < stop) {
+                if (base->rec == (base + 1)->rec && (base + 1)->is_tombstone()) {
+                    base += 2;
+                    continue;
+                }
+            } else if (base->is_deleted()) {
+                base += 1;
+                continue;
+            }
+
+            base->header &= 1;
+            m_data[m_reccnt++] = *base;
+            keys.emplace_back(base->rec.key);
+
+            if (m_bf && base->is_tombstone()) {
+                m_tombstone_cnt++;
+                m_bf->insert(base->rec.key);
+            }
+            
+            base++;
+        }
+
+        if (m_reccnt > 0) {
+            m_pgm = pgm::PGMIndex<K>(keys);
+        }
+    }
+
+    PGM(PGM** shards, size_t len)
+    : m_reccnt(0), m_tombstone_cnt(0) {
+        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<K>(BF_FPR, tombstone_count, BF_HASH_FUNCS);
+
+        size_t alloc_size = (attemp_reccnt * sizeof(Wrapped<R>)) + (CACHELINE_SIZE - (attemp_reccnt * sizeof(Wrapped<R>)) % CACHELINE_SIZE);
+        assert(alloc_size % CACHELINE_SIZE == 0);
+        m_data = (Wrapped<R>*)std::aligned_alloc(CACHELINE_SIZE, alloc_size);
+
+        std::vector<K> keys;
+
+        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;
+                    keys.emplace_back(cursor.ptr->rec.key);
+                    if (m_bf && cursor.ptr->is_tombstone()) {
+                        ++m_tombstone_cnt;
+                        if (m_bf) m_bf->insert(cursor.ptr->rec.key);
+                    }
+                }
+                pq.pop();
+                
+                if (advance_cursor<Wrapped<R>>(cursor)) pq.push(cursor.ptr, now.version);
+            }
+        }
+
+        if (m_reccnt > 0) {
+            m_pgm = pgm::PGMIndex<K>(keys);
+        }
+   }
+
+    ~PGM() {
+        if (m_data) free(m_data);
+        if (m_bf) delete m_bf;
+
+    }
+
+    Wrapped<R> *point_lookup(const R &rec, bool filter=false) {
+        if (filter && !m_bf->lookup(rec.key)) {
+            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 0;
+    }
+
+private:
+
+    // FIXME: depending upon the size of the returned bound,
+    // it may be better to switch between binary search and
+    // linear scan.
+    size_t get_lower_bound(const K& key) const {
+        auto bound = m_pgm.search(key);
+        size_t idx = bound.lo;
+
+        if (idx >= m_reccnt) {
+            return m_reccnt;
+        }
+
+        // if the found location _is_ the key, we're done.
+        if (m_data[idx].rec.key == key) {
+            return idx;
+        }
+
+        // if the found location is larger than the key, we need to
+        // move backwards towards the beginning of the array
+        if (m_data[idx].rec.key > key) {
+            for (ssize_t i=idx; i>=0; i--) {
+                if (m_data[i].rec.key < key) {
+                    return i+1;
+                }
+            }
+        // otherwise, we move forward towards the end
+        } else {
+            for (size_t i=idx; i<m_reccnt; i++) {
+                if (m_data[i].rec.key >= key) {
+                    return i - 1;
+                }
+            }
+        }
+
+        return m_reccnt;
+    }
+
+    Wrapped<R>* m_data;
+    size_t m_reccnt;
+    size_t m_tombstone_cnt;
+    K m_max_key;
+    K m_min_key;
+    pgm::PGMIndex<K> m_pgm;
+    BloomFilter<K> *m_bf;
+};
+
+
+template <RecordInterface R>
+class PGMRangeQuery {
+public:
+    static void *get_query_state(PGM<R> *ts, void *parms) {
+        auto res = new PGMState<R>();
+        auto p = (ts_range_query_parms<R> *) parms;
+
+        res->start_idx = ts->get_lower_bound(p->lower_bound);
+        res->stop_idx = ts->get_record_count();
+
+        return res;
+    }
+
+    static void* get_buffer_query_state(MutableBuffer<R> *buffer, void *parms) {
+        auto res = new PGMBufferState<R>();
+        res.cutoff = buffer->get_record_count();
+
+        return res;
+    }
+
+    static std::vector<Wrapped<R>> query(PGM<R> *ts, void *q_state, void *parms) {
+        std::vector<Wrapped<R>> records;
+        auto p = (ts_range_query_parms<R> *) parms;
+        auto s = (PGMState<R> *) q_state;
+        auto ptr = ts->get_record_at(s->lower_bound);
+        size_t i = 0;
+        while (ptr->rec.key <= p->upper_bound && i < s->stop_idx) {
+            records.emplace_back(ptr[i]);
+            i++;
+        }
+
+        return records;
+    }
+
+    static std::vector<Wrapped<R>> buffer_query(MutableBuffer<R> *buffer, void *state, void *parms) {
+        auto p = (ts_range_query_parms<R> *) parms;
+        auto s = (PGMBufferState<R> *) state;
+
+
+
+    }
+
+    static std::vector<R> merge(std::vector<std::vector<R>> &results) {
+        std::vector<R> output;
+
+        for (size_t i=0; i<results.size(); i++) {
+            for (size_t j=0; j<results[i].size(); j++) {
+                output.emplace_back(results[i][j]);
+            }
+        }
+
+        return output;
+    }
+
+    static void delete_query_state(void *state) {
+        auto s = (PGMState<R> *) state;
+        delete s;
+    }
+
+    static void delete_buffer_query_state(void *state) {
+        auto s = (PGMBufferState<R> *) state;
+        delete s;
+    }
+
+
+    //{q.get_buffer_query_state(p, p)};
+    //{q.buffer_query(p, p)};
+
+};
+
+}