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fc_botelho 2005-08-06 20:20:04 +00:00
parent fc61796452
commit 1d07882eb3
3 changed files with 286 additions and 121 deletions
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15
src/bmz.c
View File

@ -87,7 +87,7 @@ cmph_t *bmz_new(cmph_config_t *mph, float c)
// Mapping step
cmph_uint32 biggest_g_value = 0;
cmph_uint32 biggest_edge_value = 1;
iterations = 20;
iterations = 100;
if (mph->verbosity)
{
fprintf(stderr, "Entering mapping step for mph creation of %u keys with graph sized %u\n", bmz->m, bmz->n);
@ -143,7 +143,7 @@ cmph_t *bmz_new(cmph_config_t *mph, float c)
used_edges = (cmph_uint8 *)malloc(bmz->m/8 + 1);
memset(used_edges, 0, bmz->m/8 + 1);
free(bmz->g);
bmz->g = malloc(bmz->n * sizeof(cmph_uint32));
bmz->g = calloc(bmz->n, sizeof(cmph_uint32));
assert(bmz->g);
for (i = 0; i < bmz->n; ++i) // critical nodes
{
@ -172,7 +172,10 @@ cmph_t *bmz_new(cmph_config_t *mph, float c)
}while(restart_mapping && iterations_map > 0);
graph_destroy(bmz->graph);
bmz->graph = NULL;
if (iterations_map == 0) return NULL;
if (iterations_map == 0)
{
return NULL;
}
mphf = (cmph_t *)malloc(sizeof(cmph_t));
mphf->algo = mph->algo;
bmzf = (bmz_data_t *)malloc(sizeof(bmz_data_t));
@ -368,15 +371,13 @@ static void bmz_traverse(bmz_config_data_t *bmz, cmph_uint8 * used_edges, cmph_u
{
graph_iterator_t it = graph_neighbors_it(bmz->graph, v);
cmph_uint32 neighbor = 0;
cmph_uint32 gvalue;
while((neighbor = graph_next_neighbor(bmz->graph, &it)) != GRAPH_NO_NEIGHBOR)
{
if(GETBIT(visited,neighbor)) continue;
DEBUGP("Visiting neighbor %u\n", neighbor);
*unused_edge_index = next_unused_edge(bmz, used_edges, *unused_edge_index);
if(*unused_edge_index < bmz->g[v]) gvalue = *unused_edge_index + bmz->m;
else gvalue = *unused_edge_index;
bmz->g[neighbor] = gvalue - bmz->g[v];
bmz->g[neighbor] = *unused_edge_index - bmz->g[v];
if (bmz->g[neighbor] >= bmz->m) bmz->g[neighbor] += bmz->m;
SETBIT(visited, neighbor);
(*unused_edge_index)++;
bmz_traverse(bmz, used_edges, neighbor, unused_edge_index, visited);

391
src/brz.c
View File

@ -1,3 +1,4 @@
#include "graph.h"
#include "bmz.h"
#include "bmz_structs.h"
@ -17,8 +18,11 @@
//#define DEBUG
#include "debug.h"
static int brz_before_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset);
static void brz_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset, FILE * graphs_fd);
static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd);
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 save_in_disk(cmph_uint8 *buffer, cmph_uint8 * key, cmph_uint32 keylen, cmph_uint32 *memory_usage, cmph_uint32 memory_availability, FILE * graphs_fd);
static char * brz_read_key(FILE * fd);
static char ** brz_read_keys_vd(FILE * graphs_fd, cmph_uint8 nkeys);
static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys);
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source);
@ -83,6 +87,7 @@ static cmph_uint8 brz_verify_mphf(cmph_t * mphf, cmph_io_adapter_t *source)
hashtable[h] = 1;
source->dispose(source->data, buf, buflen);
}
fprintf(stderr, "\n===============================================================================\n");
free(hashtable);
return 1;
}
@ -132,8 +137,8 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
brz_data_t *brzf = NULL;
cmph_uint32 i;
cmph_uint32 iterations = 20;
cmph_uint32 * disksize = NULL;
cmph_uint32 * diskoffset = NULL;
/* cmph_uint32 * disksize = NULL;
cmph_uint32 * diskoffset = NULL;*/
cmph_io_adapter_t *source = NULL;
cmph_config_t *config = NULL;
@ -146,30 +151,30 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
brz->c = c;
brz->m = mph->key_source->nkeys;
DEBUGP("m: %u\n", brz->m);
brz->k = ceil(brz->m/128);
brz->k = ceil(brz->m/170);
DEBUGP("k: %u\n", brz->k);
brz->size = (cmph_uint8 *) malloc(sizeof(cmph_uint8)*brz->k);
brz->offset = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
brz->size = (cmph_uint8 *) calloc(brz->k, sizeof(cmph_uint8));
disksize = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
diskoffset = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
for(i = 0; i < brz->k; ++i)
// Clustering the keys by graph id.
if (mph->verbosity)
{
brz->size[i] = 0;
brz->offset[i] = 0;
disksize[i] = 0;
diskoffset[i] = 0;
fprintf(stderr, "Partioning the set of keys.\n");
}
graphs_fd = fopen("/mnt/hd4/fbotelho/cmph.tmp", "wb");
if (graphs_fd == NULL)
{
free(brz->size);
fprintf(stderr, "Unable to open file %s\n", "/mnt/hd4/fbotelho/cmph.tmp");
return NULL;
}
// Creating the external graphs.
while(1)
{
int ok;
DEBUGP("hash function 3\n");
brz->h3 = hash_state_new(brz->hashfuncs[2], brz->k);
DEBUGP("Generating graphs\n");
ok = brz_before_gen_graphs(mph, disksize, diskoffset);
ok = brz_gen_graphs(mph, graphs_fd);
if (!ok)
{
--iterations;
@ -184,59 +189,50 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
}
else break;
}
fclose(graphs_fd);
if (iterations == 0)
{
DEBUGP("Graphs with more than 255 keys were created in all 20 iterations\n");
free(brz->size);
free(brz->offset);
free(disksize);
free(diskoffset);
return NULL;
}
DEBUGP("Graphs generated\n");
brz->offset = (cmph_uint32 *)calloc(brz->k, sizeof(cmph_uint32));
for (i = 1; i < brz->k; ++i)
{
brz->offset[i] = brz->size[i-1] + brz->offset[i-1];
}
// graphs_fd = fopen("/colecao/fbotelho/cmph.tmp", "wb");
/* graphs_fd = fopen("cmph.tmp", "wb");*/
graphs_fd = fopen("/var/tmp/cmph.tmp", "wb");
if (graphs_fd == NULL)
{
free(brz->size);
free(brz->offset);
free(disksize);
free(diskoffset);
fprintf(stderr, "Unable to open file %s\n", "/colecao/fbotelho/cmph.tmp");
return NULL;
}
// Clustering the keys by graph id.
brz_gen_graphs(mph, disksize, diskoffset, graphs_fd);
free(disksize);
free(diskoffset);
DEBUGP("Graphs generated\n");
fclose(graphs_fd);
// graphs_fd = fopen("/colecao/fbotelho/cmph.tmp", "rb");
/* graphs_fd = fopen("cmph.tmp", "rb");*/
graphs_fd = fopen("/var/tmp/cmph.tmp", "rb");
// 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); // implementar
brz_copy_partial_mphf(brz, bmzf, i, source);
cmph_config_destroy(config);
brz_destroy_keys_vd(keys_vd, nkeys);
free(keys_vd);
@ -275,98 +271,265 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
return mphf;
}
static int brz_before_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset)
static int brz_gen_graphs(cmph_config_t *mph, FILE * graphs_fd)
{
cmph_uint32 e;
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
mph->key_source->rewind(mph->key_source->data);
DEBUGP("Generating information before the keys partition\n");
for (e = 0; e < brz->m; ++e)
{
cmph_uint32 h3;
cmph_uint32 keylen;
char *key;
mph->key_source->read(mph->key_source->data, &key, &keylen);
h3 = hash(brz->h3, key, keylen) % brz->k;
// if(h3 == 6)
// {
// DEBUGP("key = %s\n", key);
// DEBUGP("keylen = %u\n", keylen + 1);
// }
mph->key_source->dispose(mph->key_source->data, key, keylen);
if (brz->size[h3] == 255) return 0;
brz->size[h3] = brz->size[h3] + 1;
disksize[h3] = disksize[h3] + keylen + 1;
// if(h3 == 6)
// {
// DEBUGP("disksize[%u]=%u \n", h3, disksize[h3]);
// }
}
// DEBUGP("size:%u offset: %u\n", brz->size[0], brz->offset[0]);
for (e = 1; e < brz->k; ++e)
{
brz->offset[e] = brz->size[e-1] + brz->offset[e-1];
diskoffset[e] = disksize[e-1] + diskoffset[e-1];
/* DEBUGP("disksize[%u]=%u diskoffset[%u]: %u\n", e, disksize[e], e, diskoffset[e]);
DEBUGP("size[%u]=%u offset[%u]: %u\n", e, brz->size[e], e, brz->offset[e]);*/
}
return 1;
}
// disksize nao esta sendo usado ainda. Sera usado qd incluir os buffers.
static void brz_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset, FILE * graphs_fd)
{
cmph_uint32 e;
#pragma pack(1)
cmph_uint32 i, e;
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_usage = 0;
cmph_uint32 nkeys_in_buffer = 0;
cmph_uint8 *buffer = (cmph_uint8 *)malloc(memory_availability);
cmph_uint32 *buckets_size = (cmph_uint32 *)calloc(brz->k, sizeof(cmph_uint32));
cmph_uint32 *keys_index = NULL;
cmph_uint8 **buffer_merge = NULL;
cmph_uint32 *buffer_h3 = NULL;
cmph_uint32 nflushes = 0;
cmph_uint32 h3;
FILE * tmp_fd = NULL;
FILE ** tmp_fds = NULL;
char filename[100];
char *key = NULL;
cmph_uint32 keylen;
mph->key_source->rewind(mph->key_source->data);
DEBUGP("Generating graphs from %u keys\n", brz->m);
// Partitioning
for (e = 0; e < brz->m; ++e)
{
cmph_uint32 h3;
cmph_uint32 keylen;
char *key;
mph->key_source->read(mph->key_source->data, &key, &keylen);
/* Buffers management */
if (memory_usage + keylen + 1 > memory_availability) // flush buffers
{
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
cmph_uint32 value = buckets_size[0];
cmph_uint32 sum = 0;
cmph_uint32 keylen1 = 0;
buckets_size[0] = 0;
for(i = 1; i < brz->k; i++)
{
if(buckets_size[i] == 0) continue;
sum += value;
value = buckets_size[i];
buckets_size[i] = sum;
}
memory_usage = 0;
keys_index = (cmph_uint32 *)calloc(nkeys_in_buffer, sizeof(cmph_uint32));
for(i = 0; i < nkeys_in_buffer; i++)
{
keylen1 = strlen(buffer + memory_usage);
h3 = hash(brz->h3, buffer + memory_usage, keylen1) % brz->k;
keys_index[buckets_size[h3]] = memory_usage;
buckets_size[h3]++;
memory_usage = memory_usage + keylen1 + 1;
}
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
tmp_fd = fopen(filename, "wb");
for(i = 0; i < nkeys_in_buffer; i++)
{
keylen1 = strlen(buffer + keys_index[i]) + 1;
fwrite(buffer + keys_index[i], 1, keylen1, tmp_fd);
}
nkeys_in_buffer = 0;
memory_usage = 0;
bzero(buckets_size, brz->k*sizeof(cmph_uint32));
nflushes++;
free(keys_index);
fclose(tmp_fd);
fprintf(stderr, "Flushing is over\n");
}
//fprintf(stderr, "Storing read Key\n");
memcpy(buffer + memory_usage, key, keylen + 1);
memory_usage = memory_usage + keylen + 1;
h3 = hash(brz->h3, key, keylen) % brz->k;
/* if(h3 == 6)
if (brz->size[h3] == 255)
{
DEBUGP("key = %s\n", key);
DEBUGP("keylen = %u\n", keylen + 1);
}*/
fseek(graphs_fd, diskoffset[h3], SEEK_SET);
fwrite(key, sizeof(char), keylen + 1, graphs_fd);
/* if(h3 == 6)
{
DEBUGP("diskoffset[%u]=%u \n", h3, diskoffset[h3]);
}*/
diskoffset[h3] = diskoffset[h3] + keylen + 1;
free(buffer);
free(buckets_size);
return 0;
}
brz->size[h3] = brz->size[h3] + 1;
buckets_size[h3] ++;
nkeys_in_buffer++;
mph->key_source->dispose(mph->key_source->data, key, keylen);
}
if (memory_usage != 0) // flush buffers
{
fprintf(stderr, "Flushing %u\n", nkeys_in_buffer);
cmph_uint32 value = buckets_size[0];
cmph_uint32 sum = 0;
cmph_uint32 keylen1 = 0;
buckets_size[0] = 0;
for(i = 1; i < brz->k; i++)
{
if(buckets_size[i] == 0) continue;
sum += value;
value = buckets_size[i];
buckets_size[i] = sum;
}
memory_usage = 0;
keys_index = (cmph_uint32 *)calloc(nkeys_in_buffer, sizeof(cmph_uint32));
for(i = 0; i < nkeys_in_buffer; i++)
{
keylen1 = strlen(buffer + memory_usage);
h3 = hash(brz->h3, buffer + memory_usage, keylen1) % brz->k;
keys_index[buckets_size[h3]] = memory_usage;
buckets_size[h3]++;
memory_usage = memory_usage + keylen1 + 1;
}
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
tmp_fd = fopen(filename, "wb");
for(i = 0; i < nkeys_in_buffer; i++)
{
keylen1 = strlen(buffer + keys_index[i]) + 1;
fwrite(buffer + keys_index[i], 1, keylen1, tmp_fd);
}
nkeys_in_buffer = 0;
memory_usage = 0;
bzero(buckets_size, brz->k*sizeof(cmph_uint32));
nflushes++;
free(keys_index);
fclose(tmp_fd);
fprintf(stderr, "Flushing is over\n");
}
free(buffer);
free(buckets_size);
if(nflushes > 1024) return 0; // Too many files generated.
// Merging
fprintf(stderr, "\nMerging files\n");
tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *));
buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *));
buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32));
for(i = 0; i < nflushes; i++)
{
sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",i);
tmp_fds[i] = fopen(filename, "rb");
key = brz_read_key(tmp_fds[i]);
keylen = strlen(key);
h3 = hash(brz->h3, key, keylen) % brz->k;
buffer_h3[i] = h3;
buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8));
memcpy(buffer_merge[i], key, keylen + 1);
free(key);
}
e = 0;
buffer = (cmph_uint8 *)malloc(memory_availability);
while(e < brz->m)
{
i = brz_min_index(buffer_h3, nflushes);
key = brz_read_key(tmp_fds[i]);
if(key)
{
while(key)
{
keylen = strlen(key);
h3 = hash(brz->h3, key, keylen) % brz->k;
if (h3 != buffer_h3[i]) break;
save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
//fwrite(key, 1, keylen + 1, graphs_fd);
e++;
free(key);
key = brz_read_key(tmp_fds[i]);
}
if (key)
{
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);
e++;
buffer_h3[i] = h3;
free(buffer_merge[i]);
buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8));
memcpy(buffer_merge[i], key, keylen + 1);
free(key);
}
}
/* fprintf(stderr, "BOSTA %u %u e: %u\n", i, buffer_h3[i], e);*/
if(!key)
{
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);
e++;
buffer_h3[i] = UINT_MAX;
free(buffer_merge[i]);
buffer_merge[i] = NULL;
}
}
for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
flush_buffer(buffer, &memory_usage, graphs_fd);
free(tmp_fds);
free(buffer);
free(buffer_merge);
free(buffer_h3);
return 1;
#pragma pack()
}
static void flush_buffer(cmph_uint8 *buffer, cmph_uint32 *memory_usage, FILE * graphs_fd)
{
fwrite(buffer, 1, *memory_usage, graphs_fd);
*memory_usage = 0;
}
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)
{
if(*memory_usage + keylen + 1 > memory_availability)
{
flush_buffer(buffer, memory_usage, graphs_fd);
}
memcpy(buffer + *memory_usage, key, keylen + 1);
*memory_usage = *memory_usage + keylen + 1;
}
static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n)
{
cmph_uint32 i, min_index = 0;
for(i = 1; i < n; i++)
{
if(vector[i] < vector[min_index]) min_index = i;
}
return min_index;
}
static char * brz_read_key(FILE * fd)
{
char * buf = (char *)malloc(BUFSIZ);
cmph_uint32 buf_pos = 0;
char c;
while(1)
{
fread(&c, sizeof(char), 1, fd);
if(feof(fd))
{
free(buf);
return NULL;
}
buf[buf_pos++] = c;
if(c == '\0') break;
if(buf_pos % BUFSIZ == 0) buf = (char *)realloc(buf, buf_pos + BUFSIZ);
}
return buf;
}
static char ** brz_read_keys_vd(FILE * graphs_fd, cmph_uint8 nkeys)
{
char ** keys_vd = (char **)malloc(sizeof(char *)*nkeys);
cmph_uint8 i;
cmph_uint8 i;
for(i = 0; i < nkeys; i++)
{
char * buf = (char *)malloc(BUFSIZ);
cmph_uint32 buf_pos = 0;
char c;
while(1)
{
fread(&c, sizeof(char), 1, graphs_fd);
buf[buf_pos++] = c;
if(c == '\0') break;
if(buf_pos % BUFSIZ == 0) buf = (char *)realloc(buf, buf_pos + BUFSIZ);
}
char * buf = brz_read_key(graphs_fd);
keys_vd[i] = (char *)malloc(strlen(buf) + 1);
strcpy(keys_vd[i], buf);
free(buf);
}
free(buf);
}
return keys_vd;
}

1
src/main.c
View File

@ -248,6 +248,7 @@ int main(int argc, char **argv)
cmph_uint32 buflen = 0;
source->read(source->data, &buf, &buflen);
h = cmph_search(mphf, buf, buflen);
assert(h < source->nkeys);
if(hashtable[h])fprintf(stderr, "collision: %u\n",h);
assert(hashtable[h]==0);
hashtable[h] = 1;