fastest version of BRZ
This commit is contained in:
fc_botelho
parent
1d07882eb3
commit
1dad589c00
152
src/brz.c
152
src/brz.c
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@ -14,11 +14,11 @@
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#include <stdio.h>
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#include <assert.h>
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#include <string.h>
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#define MAX_BUCKET_SIZE 255
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//#define DEBUG
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#include "debug.h"
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static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd);
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static int brz_gen_graphs(cmph_config_t *mph);
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static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n);
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static void flush_buffer(cmph_uint8 *buffer, cmph_uint32 *memory_usage, FILE * graphs_fd);
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static void save_in_disk(cmph_uint8 *buffer, cmph_uint8 * key, cmph_uint32 keylen, cmph_uint32 *memory_usage, cmph_uint32 memory_availability, FILE * graphs_fd);
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@ -137,16 +137,8 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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brz_data_t *brzf = NULL;
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cmph_uint32 i;
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cmph_uint32 iterations = 20;
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/* cmph_uint32 * disksize = NULL;
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cmph_uint32 * diskoffset = NULL;*/
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cmph_io_adapter_t *source = NULL;
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cmph_config_t *config = NULL;
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cmph_t *mphf_tmp = NULL;
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char ** keys_vd = NULL;
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FILE * graphs_fd = NULL;
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DEBUGP("c: %f\n", c);
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DEBUGP("c: %f\n");
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brz_config_data_t *brz = (brz_config_data_t *)mph->data;
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brz->c = c;
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brz->m = mph->key_source->nkeys;
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@ -160,13 +152,10 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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{
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fprintf(stderr, "Partioning the set of keys.\n");
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}
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graphs_fd = fopen("/mnt/hd4/fbotelho/cmph.tmp", "wb");
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if (graphs_fd == NULL)
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{
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free(brz->size);
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fprintf(stderr, "Unable to open file %s\n", "/mnt/hd4/fbotelho/cmph.tmp");
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return NULL;
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}
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brz->h1 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
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brz->h2 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
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brz->g = (cmph_uint8 **) malloc(sizeof(cmph_uint8 *) *brz->k);
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while(1)
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{
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@ -174,7 +163,7 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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DEBUGP("hash function 3\n");
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brz->h3 = hash_state_new(brz->hashfuncs[2], brz->k);
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DEBUGP("Generating graphs\n");
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ok = brz_gen_graphs(mph, graphs_fd);
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ok = brz_gen_graphs(mph);
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if (!ok)
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{
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--iterations;
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@ -189,7 +178,6 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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}
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else break;
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}
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fclose(graphs_fd);
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if (iterations == 0)
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{
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DEBUGP("Graphs with more than 255 keys were created in all 20 iterations\n");
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@ -204,44 +192,6 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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brz->offset[i] = brz->size[i-1] + brz->offset[i-1];
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}
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// codigo do algoritmo...
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graphs_fd = fopen("/mnt/hd4/fbotelho/cmph.tmp", "rb");
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brz->h1 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
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brz->h2 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
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brz->g = (cmph_uint8 **) malloc(sizeof(cmph_uint8 *) *brz->k);
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if (mph->verbosity)
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{
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fprintf(stderr, "\nGenerating mphf.\n");
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}
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DEBUGP("Generating mphf\n");
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for(i = 0; i < brz->k; i++)
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{
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if (mph->verbosity) fprintf(stderr, "\tMPHF %u in %u was generated.\n", i+1, brz->k);
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cmph_uint32 j;
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bmz_data_t * bmzf = NULL;
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cmph_uint8 nkeys = brz->size[i];
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if (nkeys == 0) continue;
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keys_vd = brz_read_keys_vd(graphs_fd, nkeys);
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// Source of keys
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source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)nkeys);
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config = cmph_config_new(source);
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cmph_config_set_algo(config, CMPH_BMZ);
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cmph_config_set_graphsize(config, c);
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//cmph_config_set_verbosity(config, 1);
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mphf_tmp = cmph_new(config);
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bmzf = (bmz_data_t *)mphf_tmp->data;
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//assert(brz_verify_mphf(mphf_tmp, source));
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brz_copy_partial_mphf(brz, bmzf, i, source);
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cmph_config_destroy(config);
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brz_destroy_keys_vd(keys_vd, nkeys);
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free(keys_vd);
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cmph_destroy(mphf_tmp);
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free(source);
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}
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fclose(graphs_fd);
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// Generating a mphf
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mphf = (cmph_t *)malloc(sizeof(cmph_t));
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mphf->algo = mph->algo;
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@ -271,12 +221,12 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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return mphf;
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}
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static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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static int brz_gen_graphs(cmph_config_t *mph)
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{
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#pragma pack(1)
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cmph_uint32 i, e;
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brz_config_data_t *brz = (brz_config_data_t *)mph->data;
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cmph_uint32 memory_availability = 209715200;//200MB //104857600;//100MB //524288000; // 500MB //209715200; // 200 MB
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cmph_uint32 memory_availability = 10485760; //10MB 209715200;//200MB //104857600;//100MB //524288000; // 500MB //209715200; // 200 MB
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cmph_uint32 memory_usage = 0;
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cmph_uint32 nkeys_in_buffer = 0;
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cmph_uint8 *buffer = (cmph_uint8 *)malloc(memory_availability);
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@ -292,6 +242,11 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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char *key = NULL;
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cmph_uint32 keylen;
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cmph_uint32 cur_bucket = 0;
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cmph_uint8 nkeys_vd = 0;
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char ** keys_vd = NULL;
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mph->key_source->rewind(mph->key_source->data);
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DEBUGP("Generating graphs from %u keys\n", brz->m);
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// Partitioning
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@ -302,7 +257,10 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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/* Buffers management */
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if (memory_usage + keylen + 1 > memory_availability) // flush buffers
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{
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fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
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if(mph->verbosity)
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{
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fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
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}
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cmph_uint32 value = buckets_size[0];
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cmph_uint32 sum = 0;
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@ -327,6 +285,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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memory_usage = memory_usage + keylen1 + 1;
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}
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sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
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/* sprintf(filename, "%u.cmph",nflushes);*/
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tmp_fd = fopen(filename, "wb");
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for(i = 0; i < nkeys_in_buffer; i++)
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{
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@ -339,13 +298,12 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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nflushes++;
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free(keys_index);
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fclose(tmp_fd);
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fprintf(stderr, "Flushing is over\n");
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}
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//fprintf(stderr, "Storing read Key\n");
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memcpy(buffer + memory_usage, key, keylen + 1);
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memory_usage = memory_usage + keylen + 1;
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h3 = hash(brz->h3, key, keylen) % brz->k;
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if (brz->size[h3] == 255)
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if (brz->size[h3] == MAX_BUCKET_SIZE)
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{
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free(buffer);
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free(buckets_size);
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@ -360,7 +318,10 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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if (memory_usage != 0) // flush buffers
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{
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fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
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if(mph->verbosity)
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{
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fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
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}
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cmph_uint32 value = buckets_size[0];
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cmph_uint32 sum = 0;
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cmph_uint32 keylen1 = 0;
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@ -383,6 +344,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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memory_usage = memory_usage + keylen1 + 1;
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}
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sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
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/* sprintf(filename, "%u.cmph",nflushes);*/
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tmp_fd = fopen(filename, "wb");
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for(i = 0; i < nkeys_in_buffer; i++)
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{
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@ -395,14 +357,16 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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nflushes++;
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free(keys_index);
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fclose(tmp_fd);
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fprintf(stderr, "Flushing is over\n");
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}
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free(buffer);
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free(buckets_size);
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if(nflushes > 1024) return 0; // Too many files generated.
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// Merging
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fprintf(stderr, "\nMerging files\n");
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// mphf generation
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if(mph->verbosity)
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{
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fprintf(stderr, "\nMPHF generation \n");
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}
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tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *));
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buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *));
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buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32));
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@ -410,6 +374,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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for(i = 0; i < nflushes; i++)
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{
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sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",i);
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/* sprintf(filename, "%u.cmph",i);*/
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tmp_fds[i] = fopen(filename, "rb");
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key = brz_read_key(tmp_fds[i]);
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keylen = strlen(key);
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@ -419,11 +384,15 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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memcpy(buffer_merge[i], key, keylen + 1);
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free(key);
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}
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e = 0;
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buffer = (cmph_uint8 *)malloc(memory_availability);
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keys_vd = (char **)calloc(MAX_BUCKET_SIZE, sizeof(char *));
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nkeys_vd = 0;
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//buffer = (cmph_uint8 *)malloc(memory_availability);
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while(e < brz->m)
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{
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i = brz_min_index(buffer_h3, nflushes);
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cur_bucket = buffer_h3[i];
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key = brz_read_key(tmp_fds[i]);
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if(key)
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{
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@ -431,20 +400,26 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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{
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keylen = strlen(key);
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h3 = hash(brz->h3, key, keylen) % brz->k;
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if (h3 != buffer_h3[i]) break;
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save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
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keys_vd[nkeys_vd++] = key;
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//save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
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//fwrite(key, 1, keylen + 1, graphs_fd);
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e++;
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free(key);
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//free(key);
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key = brz_read_key(tmp_fds[i]);
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}
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if (key)
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{
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save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
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//save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
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assert(nkeys_vd < brz->size[cur_bucket]);
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keys_vd[nkeys_vd++] = buffer_merge[i];
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//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
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e++;
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buffer_h3[i] = h3;
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free(buffer_merge[i]);
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//free(buffer_merge[i]);
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buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8));
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memcpy(buffer_merge[i], key, keylen + 1);
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free(key);
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@ -453,18 +428,43 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
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/* fprintf(stderr, "BOSTA %u %u e: %u\n", i, buffer_h3[i], e);*/
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if(!key)
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{
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save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
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assert(nkeys_vd < brz->size[cur_bucket]);
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keys_vd[nkeys_vd++] = buffer_merge[i];
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//save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
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//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
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e++;
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buffer_h3[i] = UINT_MAX;
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free(buffer_merge[i]);
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//free(buffer_merge[i]);
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buffer_merge[i] = NULL;
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}
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if(nkeys_vd == brz->size[cur_bucket]) // Generating mphf.
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{
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cmph_io_adapter_t *source = NULL;
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cmph_config_t *config = NULL;
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cmph_t *mphf_tmp = NULL;
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bmz_data_t * bmzf = NULL;
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// Source of keys
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//fprintf(stderr, "Generating mphf %u in %u \n",cur_bucket + 1, brz->k);
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source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)nkeys_vd);
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config = cmph_config_new(source);
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cmph_config_set_algo(config, CMPH_BMZ);
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cmph_config_set_graphsize(config, brz->c);
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mphf_tmp = cmph_new(config);
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bmzf = (bmz_data_t *)mphf_tmp->data;
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//assert(brz_verify_mphf(mphf_tmp, source));
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brz_copy_partial_mphf(brz, bmzf, cur_bucket, source);
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cmph_config_destroy(config);
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brz_destroy_keys_vd(keys_vd, nkeys_vd);
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cmph_destroy(mphf_tmp);
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free(source);
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nkeys_vd = 0;
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}
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}
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for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
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flush_buffer(buffer, &memory_usage, graphs_fd);
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//flush_buffer(buffer, &memory_usage, graphs_fd);
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free(tmp_fds);
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free(buffer);
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free(keys_vd);
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free(buffer_merge);
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free(buffer_h3);
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return 1;
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