#include #include #include #include #include #include #include #include #include "cmph_structs.h" #include "chd_structs_ph.h" #include "chd_ph.h" #include"miller_rabin.h" #include"bitbool.h" //#define DEBUG #include "debug.h" // NO_ELEMENT is equivalent to null pointer #ifndef NO_ELEMENT #define NO_ELEMENT UINT_MAX #endif // struct used to represent items at mapping, ordering and searching phases struct _chd_ph_item_t { cmph_uint32 f; cmph_uint32 h; }; typedef struct _chd_ph_item_t chd_ph_item_t; // struct to represent the items at mapping phase only. struct _chd_ph_map_item_t { cmph_uint32 f; cmph_uint32 h; cmph_uint32 bucket_num; }; typedef struct _chd_ph_map_item_t chd_ph_map_item_t; // struct to represent a bucket struct _chd_ph_bucket_t { cmph_uint32 items_list; // offset union { cmph_uint32 size; cmph_uint32 bucket_id; }; }; typedef struct _chd_ph_bucket_t chd_ph_bucket_t; struct _chd_ph_sorted_list_t { cmph_uint32 buckets_list; cmph_uint32 size; }; typedef struct _chd_ph_sorted_list_t chd_ph_sorted_list_t; static inline chd_ph_bucket_t * chd_ph_bucket_new(cmph_uint32 nbuckets); static inline void chd_ph_bucket_clean(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets); static inline void chd_ph_bucket_destroy(chd_ph_bucket_t * buckets); chd_ph_bucket_t * chd_ph_bucket_new(cmph_uint32 nbuckets) { chd_ph_bucket_t * buckets = (chd_ph_bucket_t *) calloc(nbuckets, sizeof(chd_ph_bucket_t)); return buckets; } void chd_ph_bucket_clean(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets) { register cmph_uint32 i = 0; assert(buckets); for(i = 0; i < nbuckets; i++) buckets[i].size = 0; } static cmph_uint8 chd_ph_bucket_insert(chd_ph_bucket_t * buckets,chd_ph_map_item_t * map_items, chd_ph_item_t * items, cmph_uint32 nbuckets,cmph_uint32 item_idx) { register cmph_uint32 i = 0; register chd_ph_item_t * tmp_item; register chd_ph_map_item_t * tmp_map_item = map_items + item_idx; register chd_ph_bucket_t * bucket = buckets + tmp_map_item->bucket_num; tmp_item = items + bucket->items_list; for(i = 0; i < bucket->size; i++) { if(tmp_item->f == tmp_map_item->f && tmp_item->h == tmp_map_item->h) { DEBUGP("Item not added\n"); return 0; }; tmp_item++; }; tmp_item->f = tmp_map_item->f; tmp_item->h = tmp_map_item->h; bucket->size++; return 1; }; void chd_ph_bucket_destroy(chd_ph_bucket_t * buckets) { free(buckets); } static inline cmph_uint8 chd_ph_mapping(cmph_config_t *mph, chd_ph_bucket_t * buckets, chd_ph_item_t * items, cmph_uint32 *max_bucket_size); static chd_ph_sorted_list_t * chd_ph_ordering(chd_ph_bucket_t ** _buckets,chd_ph_item_t ** items, cmph_uint32 nbuckets,cmph_uint32 nitems, cmph_uint32 max_bucket_size); static cmph_uint8 chd_ph_searching(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t *items , cmph_uint32 max_bucket_size, chd_ph_sorted_list_t *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table); static inline double chd_ph_space_lower_bound(cmph_uint32 _n, cmph_uint32 _r) { double r = _r, n = _n; return (1 + (r/n - 1.0 + 1.0/(2.0*n))*log(1 - n/r))/log(2); }; /* computes the entropy of non empty buckets.*/ static inline double chd_ph_get_entropy(cmph_uint32 * disp_table, cmph_uint32 n, cmph_uint32 max_probes) { register cmph_uint32 * probe_counts = (cmph_uint32 *) calloc(max_probes, sizeof(cmph_uint32)); register cmph_uint32 i; register double entropy = 0; for(i = 0; i < n; i++) { probe_counts[disp_table[i]]++; }; for(i = 0; i < max_probes; i++) { if(probe_counts[i] > 0) entropy -= probe_counts[i]*log((double)probe_counts[i]/(double)n)/log(2); }; free(probe_counts); return entropy; }; chd_ph_config_data_t *chd_ph_config_new(void) { chd_ph_config_data_t *chd_ph; chd_ph = (chd_ph_config_data_t *)malloc(sizeof(chd_ph_config_data_t)); assert(chd_ph); memset(chd_ph, 0, sizeof(chd_ph_config_data_t)); chd_ph->hashfunc = CMPH_HASH_JENKINS; chd_ph->cs = NULL; chd_ph->nbuckets = 0; chd_ph->n = 0; chd_ph->hl = NULL; chd_ph->m = 0; chd_ph->use_h = 1; chd_ph->keys_per_bin = 1; chd_ph->keys_per_bucket = 4; chd_ph->occup_table = 0; return chd_ph; } void chd_ph_config_destroy(cmph_config_t *mph) { chd_ph_config_data_t *data = (chd_ph_config_data_t *) mph->data; DEBUGP("Destroying algorithm dependent data\n"); if(data->occup_table) { free(data->occup_table); data->occup_table = NULL; } free(data); } void chd_ph_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs) { chd_ph_config_data_t *chd_ph = (chd_ph_config_data_t *)mph->data; CMPH_HASH *hashptr = hashfuncs; cmph_uint32 i = 0; while(*hashptr != CMPH_HASH_COUNT) { if (i >= 1) break; //chd_ph only uses one linear hash function chd_ph->hashfunc = *hashptr; ++i, ++hashptr; } } void chd_ph_config_set_b(cmph_config_t *mph, cmph_uint32 keys_per_bucket) { chd_ph_config_data_t *chd_ph; assert(mph); chd_ph = (chd_ph_config_data_t *)mph->data; if(keys_per_bucket < 1 || keys_per_bucket >= 15) { keys_per_bucket = 4; } chd_ph->keys_per_bucket = keys_per_bucket; } void chd_ph_config_set_keys_per_bin(cmph_config_t *mph, cmph_uint32 keys_per_bin) { chd_ph_config_data_t *chd_ph; assert(mph); chd_ph = (chd_ph_config_data_t *)mph->data; if(keys_per_bin <= 1 || keys_per_bin >= 128) { keys_per_bin = 1; } chd_ph->keys_per_bin = keys_per_bin; } cmph_uint8 chd_ph_mapping(cmph_config_t *mph, chd_ph_bucket_t * buckets, chd_ph_item_t * items, cmph_uint32 *max_bucket_size) { register cmph_uint32 i = 0, g = 0; cmph_uint32 hl[3]; chd_ph_config_data_t *chd_ph = (chd_ph_config_data_t *)mph->data; char * key = NULL; cmph_uint32 keylen = 0; chd_ph_map_item_t * map_item; chd_ph_map_item_t * map_items = malloc(chd_ph->m*sizeof(chd_ph_map_item_t)); register cmph_uint32 mapping_iterations = 1000; *max_bucket_size = 0; while(1) { mapping_iterations--; if (chd_ph->hl) hash_state_destroy(chd_ph->hl); chd_ph->hl = hash_state_new(chd_ph->hashfunc, chd_ph->m); chd_ph_bucket_clean(buckets, chd_ph->nbuckets); mph->key_source->rewind(mph->key_source->data); for(i = 0; i < chd_ph->m; i++) { mph->key_source->read(mph->key_source->data, &key, &keylen); hash_vector(chd_ph->hl, key, keylen, hl); map_item = (map_items + i); g = hl[0] % chd_ph->nbuckets; map_item->f = hl[1] % chd_ph->n; map_item->h = hl[2] % (chd_ph->n - 1) + 1; map_item->bucket_num=g; mph->key_source->dispose(mph->key_source->data, key, keylen); // if(buckets[g].size == (chd_ph->keys_per_bucket << 2)) // { // DEBUGP("BUCKET = %u -- SIZE = %u -- MAXIMUM SIZE = %u\n", g, buckets[g].size, (chd_ph->keys_per_bucket << 2)); // goto error; // } buckets[g].size++; if(buckets[g].size > *max_bucket_size) { *max_bucket_size = buckets[g].size; } } buckets[0].items_list = 0; for(i = 1; i < chd_ph->nbuckets; i++) { buckets[i].items_list = buckets[i-1].items_list + buckets[i - 1].size; buckets[i - 1].size = 0; }; buckets[i - 1].size = 0; for(i = 0; i < chd_ph->m; i++) { map_item = (map_items + i); if(!chd_ph_bucket_insert(buckets, map_items, items, chd_ph->nbuckets, i)) break; } if(i == chd_ph->m) { free(map_items); return 1; // SUCCESS } if(mapping_iterations == 0) { goto error; } } error: free(map_items); hash_state_destroy(chd_ph->hl); chd_ph->hl = NULL; return 0; // FAILURE } chd_ph_sorted_list_t * chd_ph_ordering(chd_ph_bucket_t ** _buckets, chd_ph_item_t ** _items, cmph_uint32 nbuckets, cmph_uint32 nitems, cmph_uint32 max_bucket_size) { chd_ph_sorted_list_t * sorted_lists = (chd_ph_sorted_list_t *) calloc(max_bucket_size + 1, sizeof(chd_ph_sorted_list_t)); chd_ph_bucket_t * input_buckets = (*_buckets); chd_ph_bucket_t * output_buckets; chd_ph_item_t * input_items = (*_items); chd_ph_item_t * output_items; register cmph_uint32 i, j, bucket_size, position, position2; // cmph_uint32 non_empty_buckets; DEBUGP("MAX BUCKET SIZE = %u\n", max_bucket_size); // Determine size of each list of buckets for(i = 0; i < nbuckets; i++) { bucket_size = input_buckets[i].size; if(bucket_size == 0) continue; sorted_lists[bucket_size].size++; }; sorted_lists[1].buckets_list = 0; // Determine final position of list of buckets into the contiguous array that will store all the buckets for(i = 2; i <= max_bucket_size; i++) { sorted_lists[i].buckets_list = sorted_lists[i-1].buckets_list + sorted_lists[i-1].size; sorted_lists[i-1].size = 0; }; sorted_lists[i-1].size = 0; // Store the buckets in a new array which is sorted by bucket sizes output_buckets = calloc(nbuckets, sizeof(chd_ph_bucket_t)); // everything is initialized with zero // non_empty_buckets = nbuckets; for(i = 0; i < nbuckets; i++) { bucket_size = input_buckets[i].size; if(bucket_size == 0) { // non_empty_buckets--; continue; }; position = sorted_lists[bucket_size].buckets_list + sorted_lists[bucket_size].size; output_buckets[position].bucket_id = i; output_buckets[position].items_list = input_buckets[i].items_list; sorted_lists[bucket_size].size++; }; /* for(i = non_empty_buckets; i < nbuckets; i++) output_buckets[i].size=0;*/ // Return the buckets sorted in new order and free the old buckets sorted in old order free(input_buckets); (*_buckets) = output_buckets; // Store the items according to the new order of buckets. output_items = (chd_ph_item_t*)calloc(nitems, sizeof(chd_ph_item_t)); position = 0; i = 0; for(bucket_size = 1; bucket_size <= max_bucket_size; bucket_size++) { for(i = sorted_lists[bucket_size].buckets_list; i < sorted_lists[bucket_size].size + sorted_lists[bucket_size].buckets_list; i++) { position2 = output_buckets[i].items_list; output_buckets[i].items_list = position; for(j = 0; j < bucket_size; j++) { output_items[position].f = input_items[position2].f; output_items[position].h = input_items[position2].h; position++; position2++; }; }; }; //Return the items sorted in new order and free the old items sorted in old order free(input_items); (*_items) = output_items; return sorted_lists; }; static inline cmph_uint8 place_bucket_probe(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t *items, cmph_uint32 probe0_num, cmph_uint32 probe1_num, cmph_uint32 bucket_num, cmph_uint32 size) { register cmph_uint32 i; register chd_ph_item_t * item; register cmph_uint32 position; item = items + buckets[bucket_num].items_list; // try place bucket with probe_num if(chd_ph->keys_per_bin > 1) { for(i = 0; i < size; i++) // placement { position = (cmph_uint32)((item->f + ((cmph_uint64)item->h)*probe0_num + probe1_num) % chd_ph->n); if(chd_ph->occup_table[position] >= chd_ph->keys_per_bin) { break; } (chd_ph->occup_table[position])++; item++; }; } else { for(i = 0; i < size; i++) // placement { position = (cmph_uint32)((item->f + ((cmph_uint64)item->h)*probe0_num + probe1_num) % chd_ph->n); if(GETBIT32(((cmph_uint32 *)chd_ph->occup_table), position)) { break; } SETBIT32(((cmph_uint32*)chd_ph->occup_table), position); item++; }; }; if(i != size) // Undo the placement { item = items + buckets[bucket_num].items_list; if(chd_ph->keys_per_bin > 1) { while(1) { if(i == 0) { break; } position = (cmph_uint32)((item->f + ((cmph_uint64 )item->h) * probe0_num + probe1_num) % chd_ph->n); (chd_ph->occup_table[position])--; item++; i--; }; } else { while(1) { if(i == 0) { break; } position = (cmph_uint32)((item->f + ((cmph_uint64 )item->h) * probe0_num + probe1_num) % chd_ph->n); UNSETBIT32(((cmph_uint32*)chd_ph->occup_table), position); // ([position/32]^=(1<<(position%32)); item++; i--; }; }; return 0; } return 1; }; static inline cmph_uint8 place_bucket(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t * items, cmph_uint32 max_probes, cmph_uint32 * disp_table, cmph_uint32 bucket_num, cmph_uint32 size) { register cmph_uint32 probe0_num, probe1_num, probe_num; probe0_num = 0; probe1_num = 0; probe_num = 0; while(1) { if(place_bucket_probe(chd_ph, buckets, items, probe0_num, probe1_num, bucket_num,size)) { disp_table[buckets[bucket_num].bucket_id] = probe0_num + probe1_num * chd_ph->n; return 1; } probe0_num++; if(probe0_num >= chd_ph->n) { probe0_num -= chd_ph->n; probe1_num++; }; probe_num++; if(probe_num >= max_probes || probe1_num >= chd_ph->n) { return 0; }; }; return 0; }; static inline cmph_uint8 place_buckets1(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t * buckets, chd_ph_item_t *items, cmph_uint32 max_bucket_size, chd_ph_sorted_list_t *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table) { register cmph_uint32 i = 0; register cmph_uint32 curr_bucket = 0; for(i = max_bucket_size; i > 0; i--) { curr_bucket = sorted_lists[i].buckets_list; while(curr_bucket < sorted_lists[i].size + sorted_lists[i].buckets_list) { if(!place_bucket(chd_ph, buckets, items, max_probes, disp_table, curr_bucket, i)) { return 0; } curr_bucket++; }; }; return 1; }; static inline cmph_uint8 place_buckets2(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t * items, cmph_uint32 max_bucket_size, chd_ph_sorted_list_t *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table) { register cmph_uint32 i,j, non_placed_bucket; register cmph_uint32 curr_bucket; register cmph_uint32 probe_num, probe0_num, probe1_num; cmph_uint32 sorted_list_size; #ifdef DEBUG cmph_uint32 items_list; cmph_uint32 bucket_id; #endif DEBUGP("USING HEURISTIC TO PLACE BUCKETS\n"); for(i = max_bucket_size; i > 0; i--) { probe_num = 0; probe0_num = 0; probe1_num = 0; sorted_list_size = sorted_lists[i].size; while(sorted_lists[i].size != 0) { curr_bucket = sorted_lists[i].buckets_list; for(j = 0, non_placed_bucket = 0; j < sorted_lists[i].size; j++) { // if bucket is successfully placed remove it from list if(place_bucket_probe(chd_ph, buckets, items, probe0_num, probe1_num, curr_bucket, i)) { disp_table[buckets[curr_bucket].bucket_id] = probe0_num + probe1_num * chd_ph->n; // DEBUGP("BUCKET %u PLACED --- DISPLACEMENT = %u\n", curr_bucket, disp_table[curr_bucket]); } else { // DEBUGP("BUCKET %u NOT PLACED\n", curr_bucket); #ifdef DEBUG items_list = buckets[non_placed_bucket + sorted_lists[i].buckets_list].items_list; bucket_id = buckets[non_placed_bucket + sorted_lists[i].buckets_list].bucket_id; #endif buckets[non_placed_bucket + sorted_lists[i].buckets_list].items_list = buckets[curr_bucket].items_list; buckets[non_placed_bucket + sorted_lists[i].buckets_list].bucket_id = buckets[curr_bucket].bucket_id; #ifdef DEBUG buckets[curr_bucket].items_list=items_list; buckets[curr_bucket].bucket_id=bucket_id; #endif non_placed_bucket++; } curr_bucket++; }; sorted_lists[i].size = non_placed_bucket; probe0_num++; if(probe0_num >= chd_ph->n) { probe0_num -= chd_ph->n; probe1_num++; }; probe_num++; if(probe_num >= max_probes || probe1_num >= chd_ph->n) { sorted_lists[i].size = sorted_list_size; return 0; }; }; sorted_lists[i].size = sorted_list_size; }; return 1; }; cmph_uint8 chd_ph_searching(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t *items , cmph_uint32 max_bucket_size, chd_ph_sorted_list_t *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table) { if(chd_ph->use_h) { return place_buckets2(chd_ph, buckets, items, max_bucket_size, sorted_lists, max_probes, disp_table); } else { return place_buckets1(chd_ph, buckets, items, max_bucket_size, sorted_lists, max_probes, disp_table); } } static inline cmph_uint8 chd_ph_check_bin_hashing(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, chd_ph_item_t *items, cmph_uint32 * disp_table, chd_ph_sorted_list_t * sorted_lists,cmph_uint32 max_bucket_size) { register cmph_uint32 bucket_size, i, j; register cmph_uint32 position, probe0_num, probe1_num; G_GNUC_UNUSED register cmph_uint32 m = 0; register chd_ph_item_t * item; if(chd_ph->keys_per_bin > 1) memset(chd_ph->occup_table, 0, chd_ph->n); else memset(chd_ph->occup_table, 0, ((chd_ph->n + 31)/32) * sizeof(cmph_uint32)); for(bucket_size = 1; bucket_size <= max_bucket_size; bucket_size++) for(i = sorted_lists[bucket_size].buckets_list; i < sorted_lists[bucket_size].size + sorted_lists[bucket_size].buckets_list; i++) { j = bucket_size; item = items + buckets[i].items_list; probe0_num = disp_table[buckets[i].bucket_id] % chd_ph->n; probe1_num = disp_table[buckets[i].bucket_id] / chd_ph->n; for(; j > 0; j--) { #ifdef DEBUG m++; #endif position = (cmph_uint32)((item->f + ((cmph_uint64 )item->h) * probe0_num + probe1_num) % chd_ph->n); if(chd_ph->keys_per_bin > 1) { if(chd_ph->occup_table[position] >= chd_ph->keys_per_bin) { return 0; } (chd_ph->occup_table[position])++; } else { if(GETBIT32(((cmph_uint32*)chd_ph->occup_table), position)) { return 0; } SETBIT32(((cmph_uint32*)chd_ph->occup_table), position); }; item++; }; }; DEBUGP("We were able to place m = %u keys\n", m); return 1; }; cmph_t *chd_ph_new(cmph_config_t *mph, double c) { cmph_t *mphf = NULL; chd_ph_data_t *chd_phf = NULL; chd_ph_config_data_t *chd_ph = (chd_ph_config_data_t *)mph->data; register double load_factor = c; register cmph_uint8 searching_success = 0; register cmph_uint32 max_probes = 1 << 20; // default value for max_probes register cmph_uint32 iterations = 100; chd_ph_bucket_t * buckets = NULL; chd_ph_item_t * items = NULL; register cmph_uint8 failure = 0; cmph_uint32 max_bucket_size = 0; chd_ph_sorted_list_t * sorted_lists = NULL; cmph_uint32 * disp_table = NULL; register double space_lower_bound = 0; #ifdef CMPH_TIMING double construction_time_begin = 0.0; double construction_time = 0.0; ELAPSED_TIME_IN_SECONDS(&construction_time_begin); #endif chd_ph->m = mph->key_source->nkeys; DEBUGP("m = %u\n", chd_ph->m); chd_ph->nbuckets = (cmph_uint32)(chd_ph->m/chd_ph->keys_per_bucket) + 1; DEBUGP("nbuckets = %u\n", chd_ph->nbuckets); if(load_factor < 0.5 ) { load_factor = 0.5; } if(load_factor >= 0.99) { load_factor = 0.99; } DEBUGP("load_factor = %.3f\n", load_factor); chd_ph->n = (cmph_uint32)(chd_ph->m/(chd_ph->keys_per_bin * load_factor)) + 1; //Round the number of bins to the prime immediately above if(chd_ph->n % 2 == 0) chd_ph->n++; for(;;) { if(check_primality(chd_ph->n) == 1) break; chd_ph->n += 2; // just odd numbers can be primes for n > 2 }; DEBUGP("n = %u \n", chd_ph->n); if(chd_ph->keys_per_bin == 1) { space_lower_bound = chd_ph_space_lower_bound(chd_ph->m, chd_ph->n); } if(mph->verbosity) { fprintf(stderr, "space lower bound is %.3f bits per key\n", space_lower_bound); } // We allocate the working tables buckets = chd_ph_bucket_new(chd_ph->nbuckets); items = (chd_ph_item_t *) calloc(chd_ph->m, sizeof(chd_ph_item_t)); max_probes = (cmph_uint32)(((log(chd_ph->m)/log(2))/20) * max_probes); if(chd_ph->keys_per_bin == 1) chd_ph->occup_table = (cmph_uint8 *) calloc(((chd_ph->n + 31)/32), sizeof(cmph_uint32)); else chd_ph->occup_table = (cmph_uint8 *) calloc(chd_ph->n, sizeof(cmph_uint8)); disp_table = (cmph_uint32 *) calloc(chd_ph->nbuckets, sizeof(cmph_uint32)); // // init_genrand(time(0)); while(1) { iterations --; if (mph->verbosity) { fprintf(stderr, "Starting mapping step for mph creation of %u keys with %u bins\n", chd_ph->m, chd_ph->n); } if(!chd_ph_mapping(mph, buckets, items, &max_bucket_size)) { if (mph->verbosity) { fprintf(stderr, "Failure in mapping step\n"); } failure = 1; goto cleanup; } if (mph->verbosity) { fprintf(stderr, "Starting ordering step\n"); } if(sorted_lists) { free(sorted_lists); } sorted_lists = chd_ph_ordering(&buckets, &items, chd_ph->nbuckets, chd_ph->m, max_bucket_size); if (mph->verbosity) { fprintf(stderr, "Starting searching step\n"); } searching_success = chd_ph_searching(chd_ph, buckets, items, max_bucket_size, sorted_lists, max_probes, disp_table); if(searching_success) break; // reset occup_table if(chd_ph->keys_per_bin > 1) memset(chd_ph->occup_table, 0, chd_ph->n); else memset(chd_ph->occup_table, 0, ((chd_ph->n + 31)/32) * sizeof(cmph_uint32)); if(iterations == 0) { // Cleanup memory if (mph->verbosity) { fprintf(stderr, "Failure because the max trials was exceeded\n"); } failure = 1; goto cleanup; }; } #ifdef DEBUG { if(!chd_ph_check_bin_hashing(chd_ph, buckets, items, disp_table,sorted_lists,max_bucket_size)) { DEBUGP("Error for bin packing generation"); failure = 1; goto cleanup; } } #endif if (mph->verbosity) { fprintf(stderr, "Starting compressing step\n"); } if(chd_ph->cs) { free(chd_ph->cs); } chd_ph->cs = (compressed_seq_t *) calloc(1, sizeof(compressed_seq_t)); compressed_seq_init(chd_ph->cs); compressed_seq_generate(chd_ph->cs, disp_table, chd_ph->nbuckets); #ifdef CMPH_TIMING ELAPSED_TIME_IN_SECONDS(&construction_time); register double entropy = chd_ph_get_entropy(disp_table, chd_ph->nbuckets, max_probes); DEBUGP("Entropy = %.4f\n", entropy/chd_ph->m); #endif cleanup: chd_ph_bucket_destroy(buckets); free(items); free(sorted_lists); free(disp_table); if(failure) { if(chd_ph->hl) { hash_state_destroy(chd_ph->hl); } chd_ph->hl = NULL; return NULL; } mphf = (cmph_t *)malloc(sizeof(cmph_t)); mphf->algo = mph->algo; chd_phf = (chd_ph_data_t *)malloc(sizeof(chd_ph_data_t)); chd_phf->cs = chd_ph->cs; chd_ph->cs = NULL; //transfer memory ownership chd_phf->hl = chd_ph->hl; chd_ph->hl = NULL; //transfer memory ownership chd_phf->n = chd_ph->n; chd_phf->nbuckets = chd_ph->nbuckets; mphf->data = chd_phf; mphf->size = chd_ph->n; DEBUGP("Successfully generated minimal perfect hash\n"); if (mph->verbosity) { fprintf(stderr, "Successfully generated minimal perfect hash function\n"); } #ifdef CMPH_TIMING register cmph_uint32 space_usage = chd_ph_packed_size(mphf)*8; construction_time = construction_time - construction_time_begin; fprintf(stdout, "%u\t%.2f\t%u\t%.4f\t%.4f\t%.4f\t%.4f\n", chd_ph->m, load_factor, chd_ph->keys_per_bucket, construction_time, space_usage/(double)chd_ph->m, space_lower_bound, entropy/chd_ph->m); #endif return mphf; } void chd_ph_load(FILE *fd, cmph_t *mphf) { char *buf = NULL; cmph_uint32 buflen; register size_t nbytes; chd_ph_data_t *chd_ph = (chd_ph_data_t *)malloc(sizeof(chd_ph_data_t)); DEBUGP("Loading chd_ph mphf\n"); mphf->data = chd_ph; nbytes = fread(&buflen, sizeof(cmph_uint32), (size_t)1, fd); DEBUGP("Hash state has %u bytes\n", buflen); buf = (char *)malloc((size_t)buflen); nbytes = fread(buf, (size_t)buflen, (size_t)1, fd); chd_ph->hl = hash_state_load(buf, buflen); free(buf); nbytes = fread(&buflen, sizeof(cmph_uint32), (size_t)1, fd); DEBUGP("Compressed sequence structure has %u bytes\n", buflen); buf = (char *)malloc((size_t)buflen); nbytes = fread(buf, (size_t)buflen, (size_t)1, fd); chd_ph->cs = (compressed_seq_t *) calloc(1, sizeof(compressed_seq_t)); compressed_seq_load(chd_ph->cs, buf, buflen); free(buf); // loading n and nbuckets DEBUGP("Reading n and nbuckets\n"); nbytes = fread(&(chd_ph->n), sizeof(cmph_uint32), (size_t)1, fd); nbytes = fread(&(chd_ph->nbuckets), sizeof(cmph_uint32), (size_t)1, fd); if (nbytes == 0 && ferror(fd)) { fprintf(stderr, "ERROR: %s\n", strerror(errno)); } } int chd_ph_dump(cmph_t *mphf, FILE *fd) { char *buf = NULL; cmph_uint32 buflen; register size_t nbytes; chd_ph_data_t *data = (chd_ph_data_t *)mphf->data; __cmph_dump(mphf, fd); hash_state_dump(data->hl, &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); compressed_seq_dump(data->cs, &buf, &buflen); DEBUGP("Dumping compressed sequence structure 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); // dumping n and nbuckets nbytes = fwrite(&(data->n), sizeof(cmph_uint32), (size_t)1, fd); nbytes = fwrite(&(data->nbuckets), sizeof(cmph_uint32), (size_t)1, fd); if (nbytes == 0 && ferror(fd)) { fprintf(stderr, "ERROR: %s\n", strerror(errno)); return 0; } return 1; } void chd_ph_destroy(cmph_t *mphf) { chd_ph_data_t *data = (chd_ph_data_t *)mphf->data; compressed_seq_destroy(data->cs); free(data->cs); hash_state_destroy(data->hl); free(data); free(mphf); } cmph_uint32 chd_ph_search(cmph_t *mphf, const char *key, cmph_uint32 keylen) { register chd_ph_data_t * chd_ph = mphf->data; cmph_uint32 hl[3]; register cmph_uint32 disp,position; register cmph_uint32 probe0_num,probe1_num; register cmph_uint32 f,g,h; hash_vector(chd_ph->hl, key, keylen, hl); g = hl[0] % chd_ph->nbuckets; f = hl[1] % chd_ph->n; h = hl[2] % (chd_ph->n-1) + 1; disp = compressed_seq_query(chd_ph->cs, g); probe0_num = disp % chd_ph->n; probe1_num = disp/chd_ph->n; position = (cmph_uint32)((f + ((cmph_uint64 )h)*probe0_num + probe1_num) % chd_ph->n); return position; } void chd_ph_pack(cmph_t *mphf, void *packed_mphf) { chd_ph_data_t *data = (chd_ph_data_t *)mphf->data; cmph_uint8 * ptr = packed_mphf; // packing hl type CMPH_HASH hl_type = hash_get_type(data->hl); *((cmph_uint32 *) ptr) = hl_type; ptr += sizeof(cmph_uint32); // packing hl hash_state_pack(data->hl, ptr); ptr += hash_state_packed_size(hl_type); // packing n *((cmph_uint32 *) ptr) = data->n; ptr += sizeof(data->n); // packing nbuckets *((cmph_uint32 *) ptr) = data->nbuckets; ptr += sizeof(data->nbuckets); // packing cs compressed_seq_pack(data->cs, ptr); //ptr += compressed_seq_packed_size(data->cs); } cmph_uint32 chd_ph_packed_size(cmph_t *mphf) { register chd_ph_data_t *data = (chd_ph_data_t *)mphf->data; register CMPH_HASH hl_type = hash_get_type(data->hl); register cmph_uint32 hash_state_pack_size = hash_state_packed_size(hl_type); register cmph_uint32 cs_pack_size = compressed_seq_packed_size(data->cs); return (cmph_uint32)(sizeof(CMPH_ALGO) + hash_state_pack_size + cs_pack_size + 3*sizeof(cmph_uint32)); } cmph_uint32 chd_ph_search_packed(void *packed_mphf, const char *key, cmph_uint32 keylen) { register CMPH_HASH hl_type = *(cmph_uint32 *)packed_mphf; register cmph_uint8 *hl_ptr = (cmph_uint8 *)(packed_mphf) + 4; register cmph_uint32 * ptr = (cmph_uint32 *)(hl_ptr + hash_state_packed_size(hl_type)); register cmph_uint32 n = *ptr++; register cmph_uint32 nbuckets = *ptr++; cmph_uint32 hl[3]; register cmph_uint32 disp,position; register cmph_uint32 probe0_num,probe1_num; register cmph_uint32 f,g,h; hash_vector_packed(hl_ptr, hl_type, key, keylen, hl); g = hl[0] % nbuckets; f = hl[1] % n; h = hl[2] % (n-1) + 1; disp = compressed_seq_query_packed(ptr, g); probe0_num = disp % n; probe1_num = disp/n; position = (cmph_uint32)((f + ((cmph_uint64 )h)*probe0_num + probe1_num) % n); return position; }