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Diffstat (limited to 'include/shard/MemISAM.h')
| -rw-r--r-- | include/shard/MemISAM.h | 697 |
1 files changed, 0 insertions, 697 deletions
diff --git a/include/shard/MemISAM.h b/include/shard/MemISAM.h deleted file mode 100644 index a220792..0000000 --- a/include/shard/MemISAM.h +++ /dev/null @@ -1,697 +0,0 @@ -/* - * 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 "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> -struct irs_query_parms { - decltype(R::key) lower_bound; - decltype(R::key) upper_bound; - size_t sample_size; - gsl_rng *rng; -}; - -template <RecordInterface R, bool Rejection> -class IRSQuery; - -template <RecordInterface R> -struct IRSState { - size_t lower_bound; - size_t upper_bound; - size_t sample_size; - size_t total_weight; -}; - -template <RecordInterface R> -struct IRSBufferState { - size_t cutoff; - std::vector<Wrapped<R>> records; - size_t sample_size; -}; - -template <RecordInterface R> -struct ISAMRangeQueryParms { - decltype(R::key) lower_bound; - decltype(R::key) upper_bound; -}; - -template <RecordInterface R> -class ISAMRangeQuery; - -template <RecordInterface R> -struct ISAMRangeQueryState { - size_t start_idx; - size_t stop_idx; -}; - -template <RecordInterface R> -struct RangeQueryBufferState { - size_t cutoff; -}; - -template <RecordInterface R> -class MemISAM { -private: - friend class IRSQuery<R, true>; - friend class IRSQuery<R, false>; - friend class ISAMRangeQuery<R>; - -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 InMemISAMNode { - 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(InMemISAMNode) == inmem_isam_node_size, "node size does not match"); - -public: - MemISAM(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(); - } - - MemISAM(MemISAM** 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(); - } - } - - ~MemISAM() { - 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; - } - -private: - 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 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 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 Wrapped<R>* pos = reinterpret_cast<const Wrapped<R>*>(now); - while (pos < m_data + m_reccnt && pos->rec.key <= key) pos++; - - return pos - m_data; - } - - 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 = (InMemISAMNode*)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); - - InMemISAMNode* 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; - 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; - size_t m_alloc_size; -}; - -template <RecordInterface R, bool Rejection=true> -class IRSQuery { -public: - - constexpr static bool EARLY_ABORT=false; - constexpr static bool SKIP_DELETE_FILTER=false; - - static void *get_query_state(MemISAM<R> *isam, void *parms) { - auto res = new IRSState<R>(); - decltype(R::key) lower_key = ((irs_query_parms<R> *) parms)->lower_bound; - decltype(R::key) upper_key = ((irs_query_parms<R> *) parms)->upper_bound; - - res->lower_bound = isam->get_lower_bound(lower_key); - res->upper_bound = isam->get_upper_bound(upper_key); - - if (res->lower_bound == isam->get_record_count()) { - res->total_weight = 0; - } else { - res->total_weight = res->upper_bound - res->lower_bound; - } - - res->sample_size = 0; - return res; - } - - static void* get_buffer_query_state(MutableBuffer<R> *buffer, void *parms) { - auto res = new IRSBufferState<R>(); - - res->cutoff = buffer->get_record_count(); - res->sample_size = 0; - - if constexpr (Rejection) { - return res; - } - - auto lower_key = ((irs_query_parms<R> *) parms)->lower_bound; - auto upper_key = ((irs_query_parms<R> *) parms)->upper_bound; - - for (size_t i=0; i<res->cutoff; i++) { - if (((buffer->get_data() + i)->rec.key >= lower_key) && ((buffer->get_data() + i)->rec.key <= upper_key)) { - res->records.emplace_back(*(buffer->get_data() + i)); - } - } - - return res; - } - - static void process_query_states(void *query_parms, std::vector<void*> &shard_states, void *buff_state) { - auto p = (irs_query_parms<R> *) query_parms; - auto bs = (buff_state) ? (IRSBufferState<R> *) buff_state : nullptr; - - std::vector<size_t> shard_sample_sizes(shard_states.size()+1, 0); - size_t buffer_sz = 0; - - std::vector<size_t> weights; - if constexpr (Rejection) { - weights.push_back((bs) ? bs->cutoff : 0); - } else { - weights.push_back((bs) ? bs->records.size() : 0); - } - - size_t total_weight = 0; - for (auto &s : shard_states) { - auto state = (IRSState<R> *) s; - total_weight += state->total_weight; - weights.push_back(state->total_weight); - } - - // if no valid records fall within the query range, just - // set all of the sample sizes to 0 and bail out. - if (total_weight == 0) { - for (size_t i=0; i<shard_states.size(); i++) { - auto state = (IRSState<R> *) shard_states[i]; - state->sample_size = 0; - } - - return; - } - - std::vector<double> normalized_weights; - for (auto w : weights) { - normalized_weights.push_back((double) w / (double) total_weight); - } - - auto shard_alias = Alias(normalized_weights); - for (size_t i=0; i<p->sample_size; i++) { - auto idx = shard_alias.get(p->rng); - if (idx == 0) { - buffer_sz++; - } else { - shard_sample_sizes[idx - 1]++; - } - } - - if (bs) { - bs->sample_size = buffer_sz; - } - for (size_t i=0; i<shard_states.size(); i++) { - auto state = (IRSState<R> *) shard_states[i]; - state->sample_size = shard_sample_sizes[i+1]; - } - } - - static std::vector<Wrapped<R>> query(MemISAM<R> *isam, void *q_state, void *parms) { - auto lower_key = ((irs_query_parms<R> *) parms)->lower_bound; - auto upper_key = ((irs_query_parms<R> *) parms)->upper_bound; - auto rng = ((irs_query_parms<R> *) parms)->rng; - - auto state = (IRSState<R> *) q_state; - auto sample_sz = state->sample_size; - - std::vector<Wrapped<R>> result_set; - - if (sample_sz == 0 || state->lower_bound == isam->get_record_count()) { - return result_set; - } - - size_t attempts = 0; - size_t range_length = state->upper_bound - state->lower_bound; - do { - attempts++; - size_t idx = (range_length > 0) ? gsl_rng_uniform_int(rng, range_length) : 0; - result_set.emplace_back(*isam->get_record_at(state->lower_bound + idx)); - } while (attempts < sample_sz); - - return result_set; - } - - static std::vector<Wrapped<R>> buffer_query(MutableBuffer<R> *buffer, void *state, void *parms) { - auto st = (IRSBufferState<R> *) state; - auto p = (irs_query_parms<R> *) parms; - - std::vector<Wrapped<R>> result; - result.reserve(st->sample_size); - - if constexpr (Rejection) { - for (size_t i=0; i<st->sample_size; i++) { - auto idx = gsl_rng_uniform_int(p->rng, st->cutoff); - auto rec = buffer->get_data() + idx; - - if (rec->rec.key >= p->lower_bound && rec->rec.key <= p->upper_bound) { - result.emplace_back(*rec); - } - } - - return result; - } - - for (size_t i=0; i<st->sample_size; i++) { - auto idx = gsl_rng_uniform_int(p->rng, st->records.size()); - result.emplace_back(st->records[idx]); - } - - return result; - } - - static std::vector<R> merge(std::vector<std::vector<Wrapped<R>>> &results, void *parms) { - 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].rec); - } - } - - return output; - } - - static void delete_query_state(void *state) { - auto s = (IRSState<R> *) state; - delete s; - } - - static void delete_buffer_query_state(void *state) { - auto s = (IRSBufferState<R> *) state; - delete s; - } -}; - - -template <RecordInterface R> -class ISAMRangeQuery { -public: - - constexpr static bool EARLY_ABORT=false; - constexpr static bool SKIP_DELETE_FILTER=true; - - static void *get_query_state(MemISAM<R> *ts, void *parms) { - auto res = new ISAMRangeQueryState<R>(); - auto p = (ISAMRangeQueryParms<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 RangeQueryBufferState<R>(); - res->cutoff = buffer->get_record_count(); - - return res; - } - - static void process_query_states(void *query_parms, std::vector<void*> &shard_states, void *buff_state) { - return; - } - - static std::vector<Wrapped<R>> query(MemISAM<R> *ts, void *q_state, void *parms) { - std::vector<Wrapped<R>> records; - auto p = (ISAMRangeQueryParms<R> *) parms; - auto s = (ISAMRangeQueryState<R> *) q_state; - - // if the returned index is one past the end of the - // records for the PGM, then there are not records - // in the index falling into the specified range. - if (s->start_idx == ts->get_record_count()) { - return records; - } - - auto ptr = ts->get_record_at(s->start_idx); - - // roll the pointer forward to the first record that is - // greater than or equal to the lower bound. - while(ptr->rec.key < p->lower_bound) { - ptr++; - } - - while (ptr->rec.key <= p->upper_bound && ptr < ts->m_data + s->stop_idx) { - records.emplace_back(*ptr); - ptr++; - } - - return records; - } - - static std::vector<Wrapped<R>> buffer_query(MutableBuffer<R> *buffer, void *state, void *parms) { - auto p = (ISAMRangeQueryParms<R> *) parms; - auto s = (RangeQueryBufferState<R> *) state; - - std::vector<Wrapped<R>> records; - for (size_t i=0; i<s->cutoff; i++) { - auto rec = buffer->get_data() + i; - if (rec->rec.key >= p->lower_bound && rec->rec.key <= p->upper_bound) { - records.emplace_back(*rec); - } - } - - return records; - } - - static std::vector<R> merge(std::vector<std::vector<Wrapped<R>>> &results, void *parms) { - std::vector<Cursor<Wrapped<R>>> cursors; - cursors.reserve(results.size()); - - PriorityQueue<Wrapped<R>> pq(results.size()); - size_t total = 0; - size_t tmp_n = results.size(); - - - for (size_t i = 0; i < tmp_n; ++i) - if (results[i].size() > 0){ - auto base = results[i].data(); - cursors.emplace_back(Cursor{base, base + results[i].size(), 0, results[i].size()}); - assert(i == cursors.size() - 1); - total += results[i].size(); - pq.push(cursors[i].ptr, tmp_n - i - 1); - } else { - cursors.emplace_back(Cursor<Wrapped<R>>{nullptr, nullptr, 0, 0}); - } - - if (total == 0) { - return std::vector<R>(); - } - - std::vector<R> output; - output.reserve(total); - - 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[tmp_n - now.version - 1]; - auto& cursor2 = cursors[tmp_n - next.version - 1]; - 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[tmp_n - now.version - 1]; - if (!now.data->is_tombstone()) output.push_back(cursor.ptr->rec); - pq.pop(); - - if (advance_cursor<Wrapped<R>>(cursor)) pq.push(cursor.ptr, now.version); - } - } - - return output; - } - - static void delete_query_state(void *state) { - auto s = (ISAMRangeQueryState<R> *) state; - delete s; - } - - static void delete_buffer_query_state(void *state) { - auto s = (RangeQueryBufferState<R> *) state; - delete s; - } -}; - - - -} |