#include "graph.h" #include "bmz.h" #include "cmph_structs.h" #include "bmz_structs.h" #include "hash.h" #include "vqueue.h" #include "bitbool.h" #include #include #include #include #include //#define DEBUG #include "debug.h" static int bmz_gen_edges(cmph_config_t *mph); static cmph_uint8 bmz_traverse_critical_nodes(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited); static cmph_uint8 bmz_traverse_critical_nodes_heuristic(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited); static void bmz_traverse_non_critical_nodes(bmz_config_data_t *bmz, cmph_uint8 * used_edges, cmph_uint8 * visited); bmz_config_data_t *bmz_config_new(void) { bmz_config_data_t *bmz = NULL; bmz = (bmz_config_data_t *)malloc(sizeof(bmz_config_data_t)); assert(bmz); memset(bmz, 0, sizeof(bmz_config_data_t)); bmz->hashfuncs[0] = CMPH_HASH_JENKINS; bmz->hashfuncs[1] = CMPH_HASH_JENKINS; bmz->g = NULL; bmz->graph = NULL; bmz->hashes = NULL; return bmz; } void bmz_config_destroy(cmph_config_t *mph) { bmz_config_data_t *data = (bmz_config_data_t *)mph->data; DEBUGP("Destroying algorithm dependent data\n"); free(data); } void bmz_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs) { bmz_config_data_t *bmz = (bmz_config_data_t *)mph->data; CMPH_HASH *hashptr = hashfuncs; cmph_uint32 i = 0; while(*hashptr != CMPH_HASH_COUNT) { if (i >= 2) break; //bmz only uses two hash functions bmz->hashfuncs[i] = *hashptr; ++i, ++hashptr; } } cmph_t *bmz_new(cmph_config_t *mph, double c) { cmph_t *mphf = NULL; bmz_data_t *bmzf = NULL; cmph_uint32 i; cmph_uint32 iterations; cmph_uint32 iterations_map = 20; cmph_uint8 *used_edges = NULL; cmph_uint8 restart_mapping = 0; cmph_uint8 * visited = NULL; bmz_config_data_t *bmz = (bmz_config_data_t *)mph->data; if (c == 0) c = 1.15; // validating restrictions over parameter c. DEBUGP("c: %f\n", c); bmz->m = mph->key_source->nkeys; bmz->n = (cmph_uint32)ceil(c * mph->key_source->nkeys); DEBUGP("m (edges): %u n (vertices): %u c: %f\n", bmz->m, bmz->n, c); bmz->graph = graph_new(bmz->n, bmz->m); DEBUGP("Created graph\n"); bmz->hashes = (hash_state_t **)malloc(sizeof(hash_state_t *)*3); for(i = 0; i < 3; ++i) bmz->hashes[i] = NULL; do { // Mapping step cmph_uint32 biggest_g_value = 0; cmph_uint32 biggest_edge_value = 1; 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); } while(1) { int ok; DEBUGP("hash function 1\n"); bmz->hashes[0] = hash_state_new(bmz->hashfuncs[0], bmz->n); DEBUGP("hash function 2\n"); bmz->hashes[1] = hash_state_new(bmz->hashfuncs[1], bmz->n); DEBUGP("Generating edges\n"); ok = bmz_gen_edges(mph); if (!ok) { --iterations; hash_state_destroy(bmz->hashes[0]); bmz->hashes[0] = NULL; hash_state_destroy(bmz->hashes[1]); bmz->hashes[1] = NULL; DEBUGP("%u iterations remaining\n", iterations); if (mph->verbosity) { fprintf(stderr, "simple graph creation failure - %u iterations remaining\n", iterations); } if (iterations == 0) break; } else break; } if (iterations == 0) { graph_destroy(bmz->graph); return NULL; } // Ordering step if (mph->verbosity) { fprintf(stderr, "Starting ordering step\n"); } graph_obtain_critical_nodes(bmz->graph); // Searching step if (mph->verbosity) { fprintf(stderr, "Starting Searching step.\n"); fprintf(stderr, "\tTraversing critical vertices.\n"); } DEBUGP("Searching step\n"); visited = (cmph_uint8 *)malloc((size_t)bmz->n/8 + 1); memset(visited, 0, (size_t)bmz->n/8 + 1); used_edges = (cmph_uint8 *)malloc((size_t)bmz->m/8 + 1); memset(used_edges, 0, (size_t)bmz->m/8 + 1); free(bmz->g); bmz->g = (cmph_uint32 *)calloc((size_t)bmz->n, sizeof(cmph_uint32)); assert(bmz->g); for (i = 0; i < bmz->n; ++i) // critical nodes { if (graph_node_is_critical(bmz->graph, i) && (!GETBIT(visited,i))) { if(c > 1.14) restart_mapping = bmz_traverse_critical_nodes(bmz, i, &biggest_g_value, &biggest_edge_value, used_edges, visited); else restart_mapping = bmz_traverse_critical_nodes_heuristic(bmz, i, &biggest_g_value, &biggest_edge_value, used_edges, visited); if(restart_mapping) break; } } if(!restart_mapping) { if (mph->verbosity) { fprintf(stderr, "\tTraversing non critical vertices.\n"); } bmz_traverse_non_critical_nodes(bmz, used_edges, visited); // non_critical_nodes } else { iterations_map--; if (mph->verbosity) fprintf(stderr, "Restarting mapping step. %u iterations remaining.\n", iterations_map); } free(used_edges); free(visited); }while(restart_mapping && iterations_map > 0); graph_destroy(bmz->graph); bmz->graph = 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)); bmzf->g = bmz->g; bmz->g = NULL; //transfer memory ownership bmzf->hashes = bmz->hashes; bmz->hashes = NULL; //transfer memory ownership bmzf->n = bmz->n; bmzf->m = bmz->m; mphf->data = bmzf; mphf->size = bmz->m; DEBUGP("Successfully generated minimal perfect hash\n"); if (mph->verbosity) { fprintf(stderr, "Successfully generated minimal perfect hash function\n"); } return mphf; } static cmph_uint8 bmz_traverse_critical_nodes(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited) { cmph_uint32 next_g; cmph_uint32 u; /* Auxiliary vertex */ cmph_uint32 lav; /* lookahead vertex */ cmph_uint8 collision; vqueue_t * q = vqueue_new((cmph_uint32)(graph_ncritical_nodes(bmz->graph)) + 1); graph_iterator_t it, it1; DEBUGP("Labelling critical vertices\n"); bmz->g[v] = (cmph_uint32)ceil ((double)(*biggest_edge_value)/2) - 1; SETBIT(visited, v); next_g = (cmph_uint32)floor((double)(*biggest_edge_value/2)); /* next_g is incremented in the do..while statement*/ vqueue_insert(q, v); while(!vqueue_is_empty(q)) { v = vqueue_remove(q); it = graph_neighbors_it(bmz->graph, v); while ((u = graph_next_neighbor(bmz->graph, &it)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, u) && (!GETBIT(visited,u))) { collision = 1; while(collision) // lookahead to resolve collisions { next_g = *biggest_g_value + 1; it1 = graph_neighbors_it(bmz->graph, u); collision = 0; while((lav = graph_next_neighbor(bmz->graph, &it1)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, lav) && GETBIT(visited,lav)) { if(next_g + bmz->g[lav] >= bmz->m) { vqueue_destroy(q); return 1; // restart mapping step. } if (GETBIT(used_edges, (next_g + bmz->g[lav]))) { collision = 1; break; } } } if (next_g > *biggest_g_value) *biggest_g_value = next_g; } // Marking used edges... it1 = graph_neighbors_it(bmz->graph, u); while((lav = graph_next_neighbor(bmz->graph, &it1)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, lav) && GETBIT(visited, lav)) { SETBIT(used_edges,(next_g + bmz->g[lav])); if(next_g + bmz->g[lav] > *biggest_edge_value) *biggest_edge_value = next_g + bmz->g[lav]; } } bmz->g[u] = next_g; // Labelling vertex u. SETBIT(visited,u); vqueue_insert(q, u); } } } vqueue_destroy(q); return 0; } static cmph_uint8 bmz_traverse_critical_nodes_heuristic(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited) { cmph_uint32 next_g; cmph_uint32 u; /* Auxiliary vertex */ cmph_uint32 lav; /* lookahead vertex */ cmph_uint8 collision; cmph_uint32 * unused_g_values = NULL; cmph_uint32 unused_g_values_capacity = 0; cmph_uint32 nunused_g_values = 0; vqueue_t * q = vqueue_new((cmph_uint32)(0.5*graph_ncritical_nodes(bmz->graph))+1); graph_iterator_t it, it1; DEBUGP("Labelling critical vertices\n"); bmz->g[v] = (cmph_uint32)ceil ((double)(*biggest_edge_value)/2) - 1; SETBIT(visited, v); next_g = (cmph_uint32)floor((double)(*biggest_edge_value/2)); /* next_g is incremented in the do..while statement*/ vqueue_insert(q, v); while(!vqueue_is_empty(q)) { v = vqueue_remove(q); it = graph_neighbors_it(bmz->graph, v); while ((u = graph_next_neighbor(bmz->graph, &it)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, u) && (!GETBIT(visited,u))) { cmph_uint32 next_g_index = 0; collision = 1; while(collision) // lookahead to resolve collisions { if (next_g_index < nunused_g_values) { next_g = unused_g_values[next_g_index++]; } else { next_g = *biggest_g_value + 1; next_g_index = UINT_MAX; } it1 = graph_neighbors_it(bmz->graph, u); collision = 0; while((lav = graph_next_neighbor(bmz->graph, &it1)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, lav) && GETBIT(visited,lav)) { if(next_g + bmz->g[lav] >= bmz->m) { vqueue_destroy(q); free(unused_g_values); return 1; // restart mapping step. } if (GETBIT(used_edges, (next_g + bmz->g[lav]))) { collision = 1; break; } } } if(collision && (next_g > *biggest_g_value)) // saving the current g value stored in next_g. { if(nunused_g_values == unused_g_values_capacity) { unused_g_values = (cmph_uint32 *)realloc(unused_g_values, (unused_g_values_capacity + BUFSIZ)*sizeof(cmph_uint32)); unused_g_values_capacity += BUFSIZ; } unused_g_values[nunused_g_values++] = next_g; } if (next_g > *biggest_g_value) *biggest_g_value = next_g; } next_g_index--; if (next_g_index < nunused_g_values) unused_g_values[next_g_index] = unused_g_values[--nunused_g_values]; // Marking used edges... it1 = graph_neighbors_it(bmz->graph, u); while((lav = graph_next_neighbor(bmz->graph, &it1)) != GRAPH_NO_NEIGHBOR) { if (graph_node_is_critical(bmz->graph, lav) && GETBIT(visited, lav)) { SETBIT(used_edges,(next_g + bmz->g[lav])); if(next_g + bmz->g[lav] > *biggest_edge_value) *biggest_edge_value = next_g + bmz->g[lav]; } } bmz->g[u] = next_g; // Labelling vertex u. SETBIT(visited, u); vqueue_insert(q, u); } } } vqueue_destroy(q); free(unused_g_values); return 0; } static cmph_uint32 next_unused_edge(bmz_config_data_t *bmz, cmph_uint8 * used_edges, cmph_uint32 unused_edge_index) { while(1) { assert(unused_edge_index < bmz->m); if(GETBIT(used_edges, unused_edge_index)) unused_edge_index ++; else break; } return unused_edge_index; } static void bmz_traverse(bmz_config_data_t *bmz, cmph_uint8 * used_edges, cmph_uint32 v, cmph_uint32 * unused_edge_index, cmph_uint8 * visited) { graph_iterator_t it = graph_neighbors_it(bmz->graph, v); cmph_uint32 neighbor = 0; 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); 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); } } static void bmz_traverse_non_critical_nodes(bmz_config_data_t *bmz, cmph_uint8 * used_edges, cmph_uint8 * visited) { cmph_uint32 i, v1, v2, unused_edge_index = 0; DEBUGP("Labelling non critical vertices\n"); for(i = 0; i < bmz->m; i++) { v1 = graph_vertex_id(bmz->graph, i, 0); v2 = graph_vertex_id(bmz->graph, i, 1); if((GETBIT(visited,v1) && GETBIT(visited,v2)) || (!GETBIT(visited,v1) && !GETBIT(visited,v2))) continue; if(GETBIT(visited,v1)) bmz_traverse(bmz, used_edges, v1, &unused_edge_index, visited); else bmz_traverse(bmz, used_edges, v2, &unused_edge_index, visited); } for(i = 0; i < bmz->n; i++) { if(!GETBIT(visited,i)) { bmz->g[i] = 0; SETBIT(visited, i); bmz_traverse(bmz, used_edges, i, &unused_edge_index, visited); } } } static int bmz_gen_edges(cmph_config_t *mph) { cmph_uint32 e; bmz_config_data_t *bmz = (bmz_config_data_t *)mph->data; cmph_uint8 multiple_edges = 0; DEBUGP("Generating edges for %u vertices\n", bmz->n); graph_clear_edges(bmz->graph); mph->key_source->rewind(mph->key_source->data); for (e = 0; e < mph->key_source->nkeys; ++e) { cmph_uint32 h1, h2; cmph_uint32 keylen; char *key = NULL; mph->key_source->read(mph->key_source->data, &key, &keylen); // if (key == NULL)fprintf(stderr, "key = %s -- read BMZ\n", key); h1 = hash(bmz->hashes[0], key, keylen) % bmz->n; h2 = hash(bmz->hashes[1], key, keylen) % bmz->n; if (h1 == h2) if (++h2 >= bmz->n) h2 = 0; if (h1 == h2) { if (mph->verbosity) fprintf(stderr, "Self loop for key %u\n", e); mph->key_source->dispose(mph->key_source->data, key, keylen); return 0; } //DEBUGP("Adding edge: %u -> %u for key %s\n", h1, h2, key); mph->key_source->dispose(mph->key_source->data, key, keylen); // fprintf(stderr, "key = %s -- dispose BMZ\n", key); multiple_edges = graph_contains_edge(bmz->graph, h1, h2); if (mph->verbosity && multiple_edges) fprintf(stderr, "A non simple graph was generated\n"); if (multiple_edges) return 0; // checking multiple edge restriction. graph_add_edge(bmz->graph, h1, h2); } return !multiple_edges; } int bmz_dump(cmph_t *mphf, FILE *fd) { char *buf = NULL; cmph_uint32 buflen; cmph_uint32 two = 2; //number of hash functions bmz_data_t *data = (bmz_data_t *)mphf->data; register size_t nbytes; __cmph_dump(mphf, fd); nbytes = fwrite(&two, sizeof(cmph_uint32), (size_t)1, fd); hash_state_dump(data->hashes[0], &buf, &buflen); DEBUGP("Dumping hash state with %u bytes to disk\n", buflen); nbytes = fwrite(&buflen, sizeof(cmph_uint32), (size_t)1, fd); nbytes = fwrite(buf, (size_t)buflen, (size_t)1, fd); free(buf); hash_state_dump(data->hashes[1], &buf, &buflen); DEBUGP("Dumping hash state with %u bytes to disk\n", buflen); nbytes = fwrite(&buflen, sizeof(cmph_uint32), (size_t)1, fd); nbytes = fwrite(buf, (size_t)buflen, (size_t)1, fd); free(buf); nbytes = fwrite(&(data->n), sizeof(cmph_uint32), (size_t)1, fd); nbytes = fwrite(&(data->m), sizeof(cmph_uint32), (size_t)1, fd); nbytes = fwrite(data->g, sizeof(cmph_uint32)*(data->n), (size_t)1, fd); #ifdef DEBUG cmph_uint32 i; fprintf(stderr, "G: "); for (i = 0; i < data->n; ++i) fprintf(stderr, "%u ", data->g[i]); fprintf(stderr, "\n"); #endif return 1; } void bmz_load(FILE *f, cmph_t *mphf) { cmph_uint32 nhashes; char *buf = NULL; cmph_uint32 buflen; cmph_uint32 i; bmz_data_t *bmz = (bmz_data_t *)malloc(sizeof(bmz_data_t)); register size_t nbytes; DEBUGP("Loading bmz mphf\n"); mphf->data = bmz; nbytes = fread(&nhashes, sizeof(cmph_uint32), (size_t)1, f); bmz->hashes = (hash_state_t **)malloc(sizeof(hash_state_t *)*(nhashes + 1)); bmz->hashes[nhashes] = NULL; DEBUGP("Reading %u hashes\n", nhashes); for (i = 0; i < nhashes; ++i) { hash_state_t *state = NULL; nbytes = fread(&buflen, sizeof(cmph_uint32), (size_t)1, f); DEBUGP("Hash state has %u bytes\n", buflen); buf = (char *)malloc((size_t)buflen); nbytes = fread(buf, (size_t)buflen, (size_t)1, f); state = hash_state_load(buf, buflen); bmz->hashes[i] = state; free(buf); } DEBUGP("Reading m and n\n"); nbytes = fread(&(bmz->n), sizeof(cmph_uint32), (size_t)1, f); nbytes = fread(&(bmz->m), sizeof(cmph_uint32), (size_t)1, f); bmz->g = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*bmz->n); nbytes = fread(bmz->g, bmz->n*sizeof(cmph_uint32), (size_t)1, f); #ifdef DEBUG fprintf(stderr, "G: "); for (i = 0; i < bmz->n; ++i) fprintf(stderr, "%u ", bmz->g[i]); fprintf(stderr, "\n"); #endif return; } cmph_uint32 bmz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen) { bmz_data_t *bmz = mphf->data; cmph_uint32 h1 = hash(bmz->hashes[0], key, keylen) % bmz->n; cmph_uint32 h2 = hash(bmz->hashes[1], key, keylen) % bmz->n; DEBUGP("key: %s h1: %u h2: %u\n", key, h1, h2); if (h1 == h2 && ++h2 > bmz->n) h2 = 0; DEBUGP("key: %s g[h1]: %u g[h2]: %u edges: %u\n", key, bmz->g[h1], bmz->g[h2], bmz->m); return bmz->g[h1] + bmz->g[h2]; } void bmz_destroy(cmph_t *mphf) { bmz_data_t *data = (bmz_data_t *)mphf->data; free(data->g); hash_state_destroy(data->hashes[0]); hash_state_destroy(data->hashes[1]); free(data->hashes); free(data); free(mphf); } /** \fn void bmz_pack(cmph_t *mphf, void *packed_mphf); * \brief Support the ability to pack a perfect hash function into a preallocated contiguous memory space pointed by packed_mphf. * \param mphf pointer to the resulting mphf * \param packed_mphf pointer to the contiguous memory area used to store the resulting mphf. The size of packed_mphf must be at least cmph_packed_size() */ void bmz_pack(cmph_t *mphf, void *packed_mphf) { bmz_data_t *data = (bmz_data_t *)mphf->data; cmph_uint8 * ptr = packed_mphf; // packing h1 type CMPH_HASH h1_type = hash_get_type(data->hashes[0]); *((cmph_uint32 *) ptr) = h1_type; ptr += sizeof(cmph_uint32); // packing h1 hash_state_pack(data->hashes[0], ptr); ptr += hash_state_packed_size(h1_type); // packing h2 type CMPH_HASH h2_type = hash_get_type(data->hashes[1]); *((cmph_uint32 *) ptr) = h2_type; ptr += sizeof(cmph_uint32); // packing h2 hash_state_pack(data->hashes[1], ptr); ptr += hash_state_packed_size(h2_type); // packing n *((cmph_uint32 *) ptr) = data->n; ptr += sizeof(data->n); // packing g memcpy(ptr, data->g, sizeof(cmph_uint32)*data->n); } /** \fn cmph_uint32 bmz_packed_size(cmph_t *mphf); * \brief Return the amount of space needed to pack mphf. * \param mphf pointer to a mphf * \return the size of the packed function or zero for failures */ cmph_uint32 bmz_packed_size(cmph_t *mphf) { bmz_data_t *data = (bmz_data_t *)mphf->data; CMPH_HASH h1_type = hash_get_type(data->hashes[0]); CMPH_HASH h2_type = hash_get_type(data->hashes[1]); return (cmph_uint32)(sizeof(CMPH_ALGO) + hash_state_packed_size(h1_type) + hash_state_packed_size(h2_type) + 3*sizeof(cmph_uint32) + sizeof(cmph_uint32)*data->n); } /** cmph_uint32 bmz_search(void *packed_mphf, const char *key, cmph_uint32 keylen); * \brief Use the packed mphf to do a search. * \param packed_mphf pointer to the packed mphf * \param key key to be hashed * \param keylen key legth in bytes * \return The mphf value */ cmph_uint32 bmz_search_packed(void *packed_mphf, const char *key, cmph_uint32 keylen) { register cmph_uint8 *h1_ptr = packed_mphf; register CMPH_HASH h1_type = *((cmph_uint32 *)h1_ptr); h1_ptr += 4; register cmph_uint8 *h2_ptr = h1_ptr + hash_state_packed_size(h1_type); register CMPH_HASH h2_type = *((cmph_uint32 *)h2_ptr); h2_ptr += 4; register cmph_uint32 *g_ptr = (cmph_uint32 *)(h2_ptr + hash_state_packed_size(h2_type)); register cmph_uint32 n = *g_ptr++; register cmph_uint32 h1 = hash_packed(h1_ptr, h1_type, key, keylen) % n; register cmph_uint32 h2 = hash_packed(h2_ptr, h2_type, key, keylen) % n; if (h1 == h2 && ++h2 > n) h2 = 0; return (g_ptr[h1] + g_ptr[h2]); }