Drastic simplification of Min-heap code and resultant Delta speedup.
This commit is contained in:
Moinak Ghosh
parent
0a1e3b39ef
commit
ddaa3b6b6d
5 changed files with 94 additions and 322 deletions
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@ -25,8 +25,8 @@
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PROG= pcompress
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PROG= pcompress
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MAINSRCS = main.c utils/utils.c allocator.c lzma_compress.c ppmd_compress.c \
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MAINSRCS = main.c utils/utils.c allocator.c lzma_compress.c ppmd_compress.c \
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adaptive_compress.c lzfx_compress.c lz4_compress.c none_compress.c \
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adaptive_compress.c lzfx_compress.c lz4_compress.c none_compress.c \
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utils/xxhash_base.c utils/heapq.c utils/cpuid.c
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utils/xxhash_base.c utils/heap.c utils/cpuid.c
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MAINHDRS = allocator.h pcompress.h utils/utils.h utils/xxhash.h utils/heapq.h \
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MAINHDRS = allocator.h pcompress.h utils/utils.h utils/xxhash.h utils/heap.h \
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utils/cpuid.h utils/xxhash.h
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utils/cpuid.h utils/xxhash.h
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MAINOBJS = $(MAINSRCS:.c=.o)
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MAINOBJS = $(MAINSRCS:.c=.o)
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@ -73,7 +73,7 @@
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#include <allocator.h>
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#include <allocator.h>
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#include <utils.h>
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#include <utils.h>
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#include <pthread.h>
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#include <pthread.h>
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#include <heapq.h>
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#include <heap.h>
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#include <xxhash.h>
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#include <xxhash.h>
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#include <qsort.h>
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#include <qsort.h>
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#include <lzma_crc.h>
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#include <lzma_crc.h>
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@ -475,7 +475,7 @@ dedupe_compress(dedupe_context_t *ctx, uchar_t *buf, uint64_t *size, uint64_t of
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uint64_t cur_roll_checksum, cur_pos_checksum;
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uint64_t cur_roll_checksum, cur_pos_checksum;
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uint32_t *ctx_heap;
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uint32_t *ctx_heap;
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rabin_blockentry_t **htab;
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rabin_blockentry_t **htab;
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heap_t heap;
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MinHeap heap;
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DEBUG_STAT_EN(uint32_t max_count);
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DEBUG_STAT_EN(uint32_t max_count);
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DEBUG_STAT_EN(max_count = 0);
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DEBUG_STAT_EN(max_count = 0);
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DEBUG_STAT_EN(double strt, en_1, en);
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DEBUG_STAT_EN(double strt, en_1, en);
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@ -672,17 +672,15 @@ dedupe_compress(dedupe_context_t *ctx, uchar_t *buf, uint64_t *size, uint64_t of
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* search engines to detect similar documents.
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* search engines to detect similar documents.
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*/
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*/
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if (ctx->delta_flag) {
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if (ctx->delta_flag) {
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memcpy(ctx_heap, buf1+last_offset, length);
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length /= 8;
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length /= 8;
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pc[1] = DELTA_NORMAL_PCT(length);
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pc[1] = DELTA_NORMAL_PCT(length);
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pc[2] = DELTA_EXTRA_PCT(length);
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pc[2] = DELTA_EXTRA_PCT(length);
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pc[3] = DELTA_EXTRA2_PCT(length);
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pc[3] = DELTA_EXTRA2_PCT(length);
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reset_heap(&heap, pc[ctx->delta_flag]);
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heap_nsmallest(&heap, (int64_t *)(buf1+last_offset),
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ksmallest((int64_t *)ctx_heap, length, &heap);
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(int64_t *)ctx_heap, pc[ctx->delta_flag], length);
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ctx->blocks[blknum]->similarity_hash =
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ctx->blocks[blknum]->similarity_hash =
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XXH32((const uchar_t *)ctx_heap, pc[ctx->delta_flag]*8, 0);
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XXH32((const uchar_t *)ctx_heap, heap_size(&heap)*8, 0);
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}
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}
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++blknum;
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++blknum;
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last_offset = i+1;
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last_offset = i+1;
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@ -713,16 +711,16 @@ dedupe_compress(dedupe_context_t *ctx, uchar_t *buf, uint64_t *size, uint64_t of
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uint64_t pc[4];
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uint64_t pc[4];
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if (length > ctx->rabin_poly_min_block_size) {
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if (length > ctx->rabin_poly_min_block_size) {
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memcpy(ctx_heap, buf1+last_offset, length);
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length /= 8;
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length /= 8;
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pc[1] = DELTA_NORMAL_PCT(length);
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pc[1] = DELTA_NORMAL_PCT(length);
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pc[2] = DELTA_EXTRA_PCT(length);
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pc[2] = DELTA_EXTRA_PCT(length);
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pc[3] = DELTA_EXTRA2_PCT(length);
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pc[3] = DELTA_EXTRA2_PCT(length);
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reset_heap(&heap, pc[ctx->delta_flag]);
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heap_nsmallest(&heap, (int64_t *)(buf1+last_offset),
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ksmallest((int64_t *)ctx_heap, length, &heap);
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(int64_t *)ctx_heap, pc[ctx->delta_flag], length);
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cur_sketch =
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cur_sketch =
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XXH32((const uchar_t *)ctx_heap, pc[ctx->delta_flag]*8, 0);
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XXH32((const uchar_t *)ctx_heap, heap_size(&heap)*8, 0);
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} else {
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} else {
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cur_sketch =
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cur_sketch =
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XXH32((const uchar_t *)(buf1+last_offset), length, 0);
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XXH32((const uchar_t *)(buf1+last_offset), length, 0);
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75
utils/heap.c
Normal file
75
utils/heap.c
Normal file
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@ -0,0 +1,75 @@
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/*
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* This file is a part of Pcompress, a chunked parallel multi-
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* algorithm lossless compression and decompression program.
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*
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* Copyright (C) 2012-2013 Moinak Ghosh. All rights reserved.
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* Use is subject to license terms.
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 3 of the License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this program.
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* If not, see <http://www.gnu.org/licenses/>.
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*
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* moinakg@belenix.org, http://moinakg.wordpress.com/
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*/
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/*
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* Functions for a rudimentary fast min-heap implementation.
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* Adapted from "Algorithms with C", Kyle Loudon, O'Reilly.
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*/
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#include <limits.h>
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#include <stdlib.h>
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#include <string.h>
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#include <sys/types.h>
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#include <stdint.h>
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#include <inttypes.h>
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#include "heap.h"
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#define heap_parent(npos) ((__TYPE)(((npos) - 1) / 2))
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#define heap_left(npos) (((npos) * 2) + 1)
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#define heap_right(npos) (((npos) * 2) + 2)
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static void
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heap_insert(MinHeap *heap, __TYPE data)
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{
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__TYPE temp;
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__TYPE ipos, ppos;
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heap->tree[heap_size(heap)] = data;
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ipos = heap_size(heap);
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ppos = heap_parent(ipos);
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while (ipos > 0 && heap->tree[ppos] > heap->tree[ipos]) {
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temp = heap->tree[ppos];
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heap->tree[ppos] = heap->tree[ipos];
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heap->tree[ipos] = temp;
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ipos = ppos;
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ppos = heap_parent(ipos);
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}
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if (heap->size < heap->totsize)
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heap->size++;
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}
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void
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heap_nsmallest(MinHeap *heap, __TYPE *data, __TYPE *heapbuf, __TYPE heapsize, __TYPE datasize)
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{
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__TYPE i;
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heap->size = 1;
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heap->totsize = heapsize;
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heap->tree = heapbuf;
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heap->tree[0] = data[0];
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for (i = 1; i < datasize; i++)
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heap_insert(heap, data[i]);
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}
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@ -27,14 +27,14 @@
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#define __HEAPQ_H_
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#define __HEAPQ_H_
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#define __TYPE int64_t
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#define __TYPE int64_t
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typedef struct {
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typedef struct Heap_ {
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__TYPE *ary;
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__TYPE size;
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__TYPE len;
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__TYPE totsize;
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__TYPE tot;
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__TYPE *tree;
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} heap_t;
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} MinHeap;
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int ksmallest(__TYPE *ary, __TYPE len, heap_t *heap);
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#define heap_size(heap) ((heap)->size)
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void reset_heap(heap_t *h, __TYPE tot);
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void heapify(heap_t *h, __TYPE *ary);
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void heap_nsmallest(MinHeap *heap, __TYPE *data, __TYPE *heapbuf, __TYPE heapsize, __TYPE datasize);
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#endif
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#endif
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301
utils/heapq.c
301
utils/heapq.c
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@ -1,301 +0,0 @@
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/*
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* This file is a part of Pcompress, a chunked parallel multi-
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* algorithm lossless compression and decompression program.
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*
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* Copyright (C) 2012-2013 Moinak Ghosh. All rights reserved.
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* Use is subject to license terms.
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 3 of the License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this program.
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* If not, see <http://www.gnu.org/licenses/>.
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*
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* moinakg@belenix.org, http://moinakg.wordpress.com/
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*/
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/*
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* Functions for a rudimentary fast min-heap implementation.
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* Derived from Python's _heapqmodule.c by way of drastic simplification
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* and a few optimizations.
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*/
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/*
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* Original Python _heapqmodule.c implementation was derived directly
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* from heapq.py in Py2.3 which was written by Kevin O'Connor, augmented
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* by Tim Peters, annotated by François Pinard, and converted to C by
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* Raymond Hettinger.
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*/
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#include <stdio.h>
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#include <limits.h>
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#include <stdlib.h>
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#include <string.h>
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#include <sys/types.h>
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#include <stdint.h>
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#include <inttypes.h>
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#include <heapq.h>
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#ifndef NDEBUG
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#define ERROR_CHK
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#endif
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void
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reset_heap(heap_t *heap, __TYPE tot)
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{
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if (heap) {
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heap->len = 0;
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heap->tot = tot;
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}
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}
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static int
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_siftdownmax(heap_t *h, __TYPE startpos, __TYPE pos)
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{
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__TYPE newitem, parent;
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__TYPE parentpos, *heap;
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#ifdef ERROR_CHK
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if (pos >= h->len) {
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fprintf(stderr, "_siftdownmax: index out of range\n");
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return -1;
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}
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#endif
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heap = h->ary;
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newitem = heap[pos];
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/* Follow the path to the root, moving parents down until finding
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a place newitem fits. */
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while (pos > startpos){
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parentpos = (pos - 1) >> 1;
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parent = heap[parentpos];
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if (parent < newitem)
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break;
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heap[pos] = parent;
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pos = parentpos;
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}
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heap[pos] = newitem;
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return 0;
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}
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static int
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_siftupmax(heap_t *h, __TYPE spos, __TYPE epos)
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{
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__TYPE endpos, childpos, rightpos;
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__TYPE newitem, *heap, pos;
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endpos = h->len;
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heap = h->ary;
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#ifdef ERROR_CHK
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if (spos >= endpos) {
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fprintf(stderr, "_siftupmax: index out of range: %" PRId64 ", len: %" PRId64 "\n", spos, endpos);
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return -1;
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}
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#endif
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do {
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pos = spos;
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/* Bubble up the smaller child until hitting a leaf. */
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newitem = heap[pos];
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childpos = (pos << 1) + 1; /* leftmost child position */
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while (childpos < endpos) {
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/* Set childpos to index of smaller child. */
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rightpos = childpos + 1;
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if (rightpos < endpos) {
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if (heap[rightpos] < heap[childpos])
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childpos = rightpos;
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}
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/* Move the smaller child up. */
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heap[pos] = heap[childpos];
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pos = childpos;
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childpos = (pos << 1) + 1;
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}
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/* The leaf at pos is empty now. Put newitem there, and and bubble
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it up to its final resting place (by sifting its parents down). */
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heap[pos] = newitem;
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#ifdef ERROR_CHK
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if (_siftdownmax(h, spos, pos) == -1)
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return (-1);
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#else
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_siftdownmax(h, spos, pos);
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#endif
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spos--;
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} while (spos >= epos);
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return (0);
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}
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static int
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_siftupmax_s(heap_t *h, __TYPE spos)
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{
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__TYPE endpos, childpos, rightpos;
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__TYPE newitem, *heap, pos;
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endpos = h->len;
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heap = h->ary;
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#ifdef ERROR_CHK
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if (spos >= endpos) {
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fprintf(stderr, "_siftupmax: index out of range: %" PRId64 ", len: %" PRId64 "\n", spos, endpos);
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return -1;
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}
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#endif
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pos = spos;
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/* Bubble up the smaller child until hitting a leaf. */
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newitem = heap[pos];
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childpos = (pos << 1) + 1; /* leftmost child position */
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while (childpos < endpos) {
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/* Set childpos to index of smaller child. */
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rightpos = childpos + 1;
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if (rightpos < endpos) {
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if (heap[rightpos] < heap[childpos])
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childpos = rightpos;
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}
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/* Move the smaller child up. */
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heap[pos] = heap[childpos];
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pos = childpos;
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childpos = (pos << 1) + 1;
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}
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/* The leaf at pos is empty now. Put newitem there, and and bubble
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it up to its final resting place (by sifting its parents down). */
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heap[pos] = newitem;
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return (_siftdownmax(h, spos, pos));
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}
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int
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ksmallest(__TYPE *ary, __TYPE len, heap_t *heap)
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{
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__TYPE elem, los;
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__TYPE i, *hp, n;
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__TYPE tmp;
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n = heap->tot;
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heap->ary = ary;
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hp = ary;
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heap->len = n;
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||||||
#ifdef ERROR_CHK
|
|
||||||
if(_siftupmax(heap, n/2-1, 0) == -1)
|
|
||||||
return (-1);
|
|
||||||
#else
|
|
||||||
_siftupmax(heap, n/2-1, 0);
|
|
||||||
#endif
|
|
||||||
|
|
||||||
los = hp[0];
|
|
||||||
for (i = n; i < len; i++) {
|
|
||||||
elem = ary[i];
|
|
||||||
if (elem >= los) {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
|
|
||||||
tmp = hp[0];
|
|
||||||
hp[0] = elem;
|
|
||||||
ary[i] = tmp;
|
|
||||||
#ifdef ERROR_CHK
|
|
||||||
if (_siftupmax_s(heap, 0) == -1)
|
|
||||||
return (-1);
|
|
||||||
#else
|
|
||||||
_siftupmax_s(heap, 0);
|
|
||||||
#endif
|
|
||||||
los = hp[0];
|
|
||||||
}
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
static int
|
|
||||||
_siftdown(heap_t *h, __TYPE startpos, __TYPE pos)
|
|
||||||
{
|
|
||||||
__TYPE newitem, parent, *heap;
|
|
||||||
__TYPE parentpos;
|
|
||||||
|
|
||||||
heap = h->ary;
|
|
||||||
#ifdef ERROR_CHK
|
|
||||||
if (pos >= h->tot) {
|
|
||||||
fprintf(stderr, "_siftdown: index out of range: %" PRId64 ", len: %" PRId64 "\n", pos, h->len);
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
#endif
|
|
||||||
|
|
||||||
/* Follow the path to the root, moving parents down until finding
|
|
||||||
a place newitem fits. */
|
|
||||||
newitem = heap[pos];
|
|
||||||
while (pos > startpos){
|
|
||||||
parentpos = (pos - 1) >> 1;
|
|
||||||
parent = heap[parentpos];
|
|
||||||
if (parent < newitem) {
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
heap[pos] = parent;
|
|
||||||
pos = parentpos;
|
|
||||||
}
|
|
||||||
heap[pos] = newitem;
|
|
||||||
return (0);
|
|
||||||
}
|
|
||||||
|
|
||||||
static int
|
|
||||||
_siftup(heap_t *h, __TYPE pos)
|
|
||||||
{
|
|
||||||
__TYPE startpos, endpos, childpos, rightpos;
|
|
||||||
__TYPE newitem, *heap;
|
|
||||||
|
|
||||||
endpos = h->tot;
|
|
||||||
heap = h->ary;
|
|
||||||
startpos = pos;
|
|
||||||
#ifdef ERROR_CHK
|
|
||||||
if (pos >= endpos) {
|
|
||||||
fprintf(stderr, "_siftup: index out of range: %" PRId64 ", len: %" PRId64 "\n", pos, endpos);
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
#endif
|
|
||||||
|
|
||||||
/* Bubble up the smaller child until hitting a leaf. */
|
|
||||||
newitem = heap[pos];
|
|
||||||
childpos = 2*pos + 1; /* leftmost child position */
|
|
||||||
while (childpos < endpos) {
|
|
||||||
/* Set childpos to index of smaller child. */
|
|
||||||
rightpos = childpos + 1;
|
|
||||||
if (rightpos < endpos) {
|
|
||||||
if (heap[rightpos] < heap[childpos])
|
|
||||||
childpos = rightpos;
|
|
||||||
}
|
|
||||||
/* Move the smaller child up. */
|
|
||||||
heap[pos] = heap[childpos];
|
|
||||||
pos = childpos;
|
|
||||||
childpos = 2*pos + 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* The leaf at pos is empty now. Put newitem there, and and bubble
|
|
||||||
it up to its final resting place (by sifting its parents down). */
|
|
||||||
heap[pos] = newitem;
|
|
||||||
return _siftdown(h, startpos, pos);
|
|
||||||
}
|
|
||||||
|
|
||||||
void
|
|
||||||
heapify(heap_t *h, __TYPE *ary)
|
|
||||||
{
|
|
||||||
__TYPE i, n;
|
|
||||||
|
|
||||||
n = h->tot;
|
|
||||||
h->ary = ary;
|
|
||||||
|
|
||||||
/* Transform bottom-up. The largest index there's any point to
|
|
||||||
looking at is the largest with a child index in-range, so must
|
|
||||||
have 2*i + 1 < n, or i < (n-1)/2. If n is even = 2*j, this is
|
|
||||||
(2*j-1)/2 = j-1/2 so j-1 is the largest, which is n//2 - 1. If
|
|
||||||
n is odd = 2*j+1, this is (2*j+1-1)/2 = j so j-1 is the largest,
|
|
||||||
and that's again n//2-1.
|
|
||||||
*/
|
|
||||||
for (i=n/2-1 ; i>=0 ; i--)
|
|
||||||
if(_siftup(h, i) == -1)
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
Loading…
Reference in a new issue