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fastest version of BRZ

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fc_botelho 2005-08-07 00:45:39 +00:00
parent 508ef470c8
commit 57126668ec
1 changed files with 80 additions and 80 deletions
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152
src/brz.c
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@ -14,11 +14,11 @@
#include <stdio.h> #include <stdio.h>
#include <assert.h> #include <assert.h>
#include <string.h> #include <string.h>
#define MAX_BUCKET_SIZE 255
//#define DEBUG //#define DEBUG
#include "debug.h" #include "debug.h"
static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd); static int brz_gen_graphs(cmph_config_t *mph);
static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n); static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n);
static void flush_buffer(cmph_uint8 *buffer, cmph_uint32 *memory_usage, FILE * graphs_fd); static void flush_buffer(cmph_uint8 *buffer, cmph_uint32 *memory_usage, FILE * graphs_fd);
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); 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);
@ -137,16 +137,8 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
brz_data_t *brzf = NULL; brz_data_t *brzf = NULL;
cmph_uint32 i; cmph_uint32 i;
cmph_uint32 iterations = 20; cmph_uint32 iterations = 20;
/* cmph_uint32 * disksize = NULL;
cmph_uint32 * diskoffset = NULL;*/
cmph_io_adapter_t *source = NULL; DEBUGP("c: %f\n");
cmph_config_t *config = NULL;
cmph_t *mphf_tmp = NULL;
char ** keys_vd = NULL;
FILE * graphs_fd = NULL;
DEBUGP("c: %f\n", c);
brz_config_data_t *brz = (brz_config_data_t *)mph->data; brz_config_data_t *brz = (brz_config_data_t *)mph->data;
brz->c = c; brz->c = c;
brz->m = mph->key_source->nkeys; brz->m = mph->key_source->nkeys;
@ -160,13 +152,10 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
{ {
fprintf(stderr, "Partioning the set of keys.\n"); fprintf(stderr, "Partioning the set of keys.\n");
} }
graphs_fd = fopen("/mnt/hd4/fbotelho/cmph.tmp", "wb");
if (graphs_fd == NULL) brz->h1 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
{ brz->h2 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
free(brz->size); brz->g = (cmph_uint8 **) malloc(sizeof(cmph_uint8 *) *brz->k);
fprintf(stderr, "Unable to open file %s\n", "/mnt/hd4/fbotelho/cmph.tmp");
return NULL;
}
while(1) while(1)
{ {
@ -174,7 +163,7 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
DEBUGP("hash function 3\n"); DEBUGP("hash function 3\n");
brz->h3 = hash_state_new(brz->hashfuncs[2], brz->k); brz->h3 = hash_state_new(brz->hashfuncs[2], brz->k);
DEBUGP("Generating graphs\n"); DEBUGP("Generating graphs\n");
ok = brz_gen_graphs(mph, graphs_fd); ok = brz_gen_graphs(mph);
if (!ok) if (!ok)
{ {
--iterations; --iterations;
@ -189,7 +178,6 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
} }
else break; else break;
} }
fclose(graphs_fd);
if (iterations == 0) if (iterations == 0)
{ {
DEBUGP("Graphs with more than 255 keys were created in all 20 iterations\n"); DEBUGP("Graphs with more than 255 keys were created in all 20 iterations\n");
@ -204,44 +192,6 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
brz->offset[i] = brz->size[i-1] + brz->offset[i-1]; brz->offset[i] = brz->size[i-1] + brz->offset[i-1];
} }
// codigo do algoritmo...
graphs_fd = fopen("/mnt/hd4/fbotelho/cmph.tmp", "rb");
brz->h1 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
brz->h2 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
brz->g = (cmph_uint8 **) malloc(sizeof(cmph_uint8 *) *brz->k);
if (mph->verbosity)
{
fprintf(stderr, "\nGenerating mphf.\n");
}
DEBUGP("Generating mphf\n");
for(i = 0; i < brz->k; i++)
{
if (mph->verbosity) fprintf(stderr, "\tMPHF %u in %u was generated.\n", i+1, brz->k);
cmph_uint32 j;
bmz_data_t * bmzf = NULL;
cmph_uint8 nkeys = brz->size[i];
if (nkeys == 0) continue;
keys_vd = brz_read_keys_vd(graphs_fd, nkeys);
// Source of keys
source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)nkeys);
config = cmph_config_new(source);
cmph_config_set_algo(config, CMPH_BMZ);
cmph_config_set_graphsize(config, c);
//cmph_config_set_verbosity(config, 1);
mphf_tmp = cmph_new(config);
bmzf = (bmz_data_t *)mphf_tmp->data;
//assert(brz_verify_mphf(mphf_tmp, source));
brz_copy_partial_mphf(brz, bmzf, i, source);
cmph_config_destroy(config);
brz_destroy_keys_vd(keys_vd, nkeys);
free(keys_vd);
cmph_destroy(mphf_tmp);
free(source);
}
fclose(graphs_fd);
// Generating a mphf // Generating a mphf
mphf = (cmph_t *)malloc(sizeof(cmph_t)); mphf = (cmph_t *)malloc(sizeof(cmph_t));
mphf->algo = mph->algo; mphf->algo = mph->algo;
@ -271,12 +221,12 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
return mphf; return mphf;
} }
static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd) static int brz_gen_graphs(cmph_config_t *mph)
{ {
#pragma pack(1) #pragma pack(1)
cmph_uint32 i, e; cmph_uint32 i, e;
brz_config_data_t *brz = (brz_config_data_t *)mph->data; brz_config_data_t *brz = (brz_config_data_t *)mph->data;
cmph_uint32 memory_availability = 209715200;//200MB //104857600;//100MB //524288000; // 500MB //209715200; // 200 MB cmph_uint32 memory_availability = 10485760; //10MB 209715200;//200MB //104857600;//100MB //524288000; // 500MB //209715200; // 200 MB
cmph_uint32 memory_usage = 0; cmph_uint32 memory_usage = 0;
cmph_uint32 nkeys_in_buffer = 0; cmph_uint32 nkeys_in_buffer = 0;
cmph_uint8 *buffer = (cmph_uint8 *)malloc(memory_availability); cmph_uint8 *buffer = (cmph_uint8 *)malloc(memory_availability);
@ -292,6 +242,11 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
char *key = NULL; char *key = NULL;
cmph_uint32 keylen; cmph_uint32 keylen;
cmph_uint32 cur_bucket = 0;
cmph_uint8 nkeys_vd = 0;
char ** keys_vd = NULL;
mph->key_source->rewind(mph->key_source->data); mph->key_source->rewind(mph->key_source->data);
DEBUGP("Generating graphs from %u keys\n", brz->m); DEBUGP("Generating graphs from %u keys\n", brz->m);
// Partitioning // Partitioning
@ -302,7 +257,10 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
/* Buffers management */ /* Buffers management */
if (memory_usage + keylen + 1 > memory_availability) // flush buffers if (memory_usage + keylen + 1 > memory_availability) // flush buffers
{ {
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer); if(mph->verbosity)
{
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
}
cmph_uint32 value = buckets_size[0]; cmph_uint32 value = buckets_size[0];
cmph_uint32 sum = 0; cmph_uint32 sum = 0;
@ -327,6 +285,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
memory_usage = memory_usage + keylen1 + 1; memory_usage = memory_usage + keylen1 + 1;
} }
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes); sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
/* sprintf(filename, "%u.cmph",nflushes);*/
tmp_fd = fopen(filename, "wb"); tmp_fd = fopen(filename, "wb");
for(i = 0; i < nkeys_in_buffer; i++) for(i = 0; i < nkeys_in_buffer; i++)
{ {
@ -339,13 +298,12 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
nflushes++; nflushes++;
free(keys_index); free(keys_index);
fclose(tmp_fd); fclose(tmp_fd);
fprintf(stderr, "Flushing is over\n");
} }
//fprintf(stderr, "Storing read Key\n"); //fprintf(stderr, "Storing read Key\n");
memcpy(buffer + memory_usage, key, keylen + 1); memcpy(buffer + memory_usage, key, keylen + 1);
memory_usage = memory_usage + keylen + 1; memory_usage = memory_usage + keylen + 1;
h3 = hash(brz->h3, key, keylen) % brz->k; h3 = hash(brz->h3, key, keylen) % brz->k;
if (brz->size[h3] == 255) if (brz->size[h3] == MAX_BUCKET_SIZE)
{ {
free(buffer); free(buffer);
free(buckets_size); free(buckets_size);
@ -360,7 +318,10 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
if (memory_usage != 0) // flush buffers if (memory_usage != 0) // flush buffers
{ {
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer); if(mph->verbosity)
{
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
}
cmph_uint32 value = buckets_size[0]; cmph_uint32 value = buckets_size[0];
cmph_uint32 sum = 0; cmph_uint32 sum = 0;
cmph_uint32 keylen1 = 0; cmph_uint32 keylen1 = 0;
@ -383,6 +344,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
memory_usage = memory_usage + keylen1 + 1; memory_usage = memory_usage + keylen1 + 1;
} }
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes); sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
/* sprintf(filename, "%u.cmph",nflushes);*/
tmp_fd = fopen(filename, "wb"); tmp_fd = fopen(filename, "wb");
for(i = 0; i < nkeys_in_buffer; i++) for(i = 0; i < nkeys_in_buffer; i++)
{ {
@ -395,14 +357,16 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
nflushes++; nflushes++;
free(keys_index); free(keys_index);
fclose(tmp_fd); fclose(tmp_fd);
fprintf(stderr, "Flushing is over\n");
} }
free(buffer); free(buffer);
free(buckets_size); free(buckets_size);
if(nflushes > 1024) return 0; // Too many files generated. if(nflushes > 1024) return 0; // Too many files generated.
// Merging // mphf generation
fprintf(stderr, "\nMerging files\n"); if(mph->verbosity)
{
fprintf(stderr, "\nMPHF generation \n");
}
tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *)); tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *));
buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *)); buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *));
buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32)); buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32));
@ -410,6 +374,7 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
for(i = 0; i < nflushes; i++) for(i = 0; i < nflushes; i++)
{ {
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",i); sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",i);
/* sprintf(filename, "%u.cmph",i);*/
tmp_fds[i] = fopen(filename, "rb"); tmp_fds[i] = fopen(filename, "rb");
key = brz_read_key(tmp_fds[i]); key = brz_read_key(tmp_fds[i]);
keylen = strlen(key); keylen = strlen(key);
@ -419,11 +384,15 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
memcpy(buffer_merge[i], key, keylen + 1); memcpy(buffer_merge[i], key, keylen + 1);
free(key); free(key);
} }
e = 0; e = 0;
buffer = (cmph_uint8 *)malloc(memory_availability); keys_vd = (char **)calloc(MAX_BUCKET_SIZE, sizeof(char *));
nkeys_vd = 0;
//buffer = (cmph_uint8 *)malloc(memory_availability);
while(e < brz->m) while(e < brz->m)
{ {
i = brz_min_index(buffer_h3, nflushes); i = brz_min_index(buffer_h3, nflushes);
cur_bucket = buffer_h3[i];
key = brz_read_key(tmp_fds[i]); key = brz_read_key(tmp_fds[i]);
if(key) if(key)
{ {
@ -431,20 +400,26 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
{ {
keylen = strlen(key); keylen = strlen(key);
h3 = hash(brz->h3, key, keylen) % brz->k; h3 = hash(brz->h3, key, keylen) % brz->k;
if (h3 != buffer_h3[i]) break; if (h3 != buffer_h3[i]) break;
save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
keys_vd[nkeys_vd++] = key;
//save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
//fwrite(key, 1, keylen + 1, graphs_fd); //fwrite(key, 1, keylen + 1, graphs_fd);
e++; e++;
free(key); //free(key);
key = brz_read_key(tmp_fds[i]); key = brz_read_key(tmp_fds[i]);
} }
if (key) if (key)
{ {
save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd); //save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
assert(nkeys_vd < brz->size[cur_bucket]);
keys_vd[nkeys_vd++] = buffer_merge[i];
//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd); //fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
e++; e++;
buffer_h3[i] = h3; buffer_h3[i] = h3;
free(buffer_merge[i]); //free(buffer_merge[i]);
buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8)); buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8));
memcpy(buffer_merge[i], key, keylen + 1); memcpy(buffer_merge[i], key, keylen + 1);
free(key); free(key);
@ -453,18 +428,43 @@ static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
/* fprintf(stderr, "BOSTA %u %u e: %u\n", i, buffer_h3[i], e);*/ /* fprintf(stderr, "BOSTA %u %u e: %u\n", i, buffer_h3[i], e);*/
if(!key) if(!key)
{ {
save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd); assert(nkeys_vd < brz->size[cur_bucket]);
keys_vd[nkeys_vd++] = buffer_merge[i];
//save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd); //fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
e++; e++;
buffer_h3[i] = UINT_MAX; buffer_h3[i] = UINT_MAX;
free(buffer_merge[i]); //free(buffer_merge[i]);
buffer_merge[i] = NULL; buffer_merge[i] = NULL;
} }
if(nkeys_vd == brz->size[cur_bucket]) // Generating mphf.
{
cmph_io_adapter_t *source = NULL;
cmph_config_t *config = NULL;
cmph_t *mphf_tmp = NULL;
bmz_data_t * bmzf = NULL;
// Source of keys
//fprintf(stderr, "Generating mphf %u in %u \n",cur_bucket + 1, brz->k);
source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)nkeys_vd);
config = cmph_config_new(source);
cmph_config_set_algo(config, CMPH_BMZ);
cmph_config_set_graphsize(config, brz->c);
mphf_tmp = cmph_new(config);
bmzf = (bmz_data_t *)mphf_tmp->data;
//assert(brz_verify_mphf(mphf_tmp, source));
brz_copy_partial_mphf(brz, bmzf, cur_bucket, source);
cmph_config_destroy(config);
brz_destroy_keys_vd(keys_vd, nkeys_vd);
cmph_destroy(mphf_tmp);
free(source);
nkeys_vd = 0;
}
} }
for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]); for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
flush_buffer(buffer, &memory_usage, graphs_fd); //flush_buffer(buffer, &memory_usage, graphs_fd);
free(tmp_fds); free(tmp_fds);
free(buffer); free(keys_vd);
free(buffer_merge); free(buffer_merge);
free(buffer_h3); free(buffer_h3);
return 1; return 1;