#include "bdz.h" #include "cmph_structs.h" #include "bdz_structs.h" #include "hash.h" #include "bitbool.h" #include #include #include #include #include //#define DEBUG #include "debug.h" #define UNASSIGNED 3 #define NULL_EDGE 0xffffffff //cmph_uint32 ngrafos = 0; //cmph_uint32 ngrafos_aciclicos = 0; // table used for looking up the number of assigned vertices a 8-bit integer const cmph_uint8 bdz_lookup_table[] = { 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 0 }; typedef struct { cmph_uint32 vertices[3]; cmph_uint32 next_edges[3]; }bdz_edge_t; typedef cmph_uint32 * bdz_queue_t; static void bdz_alloc_queue(bdz_queue_t * queuep, cmph_uint32 nedges) { (*queuep)=malloc(nedges*sizeof(cmph_uint32)); }; static void bdz_free_queue(bdz_queue_t * queue) { free(*queue); }; typedef struct { cmph_uint32 nedges; bdz_edge_t * edges; cmph_uint32 * first_edge; cmph_uint8 * vert_degree; }bdz_graph3_t; static void bdz_alloc_graph3(bdz_graph3_t * graph3, cmph_uint32 nedges, cmph_uint32 nvertices) { graph3->edges=malloc(nedges*sizeof(bdz_edge_t)); graph3->first_edge=malloc(nvertices*sizeof(cmph_uint32)); graph3->vert_degree=malloc(nvertices); }; static void bdz_init_graph3(bdz_graph3_t * graph3, cmph_uint32 nedges, cmph_uint32 nvertices) { memset(graph3->first_edge,0xff,nvertices*sizeof(cmph_uint32)); memset(graph3->vert_degree,0,nvertices); graph3->nedges=0; }; static void bdz_free_graph3(bdz_graph3_t *graph3) { free(graph3->edges); free(graph3->first_edge); free(graph3->vert_degree); }; static void bdz_partial_free_graph3(bdz_graph3_t *graph3) { free(graph3->first_edge); free(graph3->vert_degree); graph3->first_edge = NULL; graph3->vert_degree = NULL; }; static void bdz_add_edge(bdz_graph3_t * graph3, cmph_uint32 v0, cmph_uint32 v1, cmph_uint32 v2) { graph3->edges[graph3->nedges].vertices[0]=v0; graph3->edges[graph3->nedges].vertices[1]=v1; graph3->edges[graph3->nedges].vertices[2]=v2; graph3->edges[graph3->nedges].next_edges[0]=graph3->first_edge[v0]; graph3->edges[graph3->nedges].next_edges[1]=graph3->first_edge[v1]; graph3->edges[graph3->nedges].next_edges[2]=graph3->first_edge[v2]; graph3->first_edge[v0]=graph3->first_edge[v1]=graph3->first_edge[v2]=graph3->nedges; graph3->vert_degree[v0]++; graph3->vert_degree[v1]++; graph3->vert_degree[v2]++; graph3->nedges++; }; static void bdz_dump_graph(bdz_graph3_t* graph3, cmph_uint32 nedges, cmph_uint32 nvertices) { int i; for(i=0;iedges[i].vertices[0], graph3->edges[i].vertices[1],graph3->edges[i].vertices[2]); printf(" nexts %d %d %d",graph3->edges[i].next_edges[0], graph3->edges[i].next_edges[1],graph3->edges[i].next_edges[2]); }; for(i=0;ifirst_edge[i]); }; }; static void bdz_remove_edge(bdz_graph3_t * graph3, cmph_uint32 curr_edge) { cmph_uint32 i,j=0,vert,edge1,edge2; for(i=0;i<3;i++){ vert=graph3->edges[curr_edge].vertices[i]; edge1=graph3->first_edge[vert]; edge2=NULL_EDGE; while(edge1!=curr_edge&&edge1!=NULL_EDGE){ edge2=edge1; if(graph3->edges[edge1].vertices[0]==vert){ j=0; } else if(graph3->edges[edge1].vertices[1]==vert){ j=1; } else j=2; edge1=graph3->edges[edge1].next_edges[j]; }; if(edge1==NULL_EDGE){ printf("\nerror remove edge %d dump graph",curr_edge); bdz_dump_graph(graph3,graph3->nedges,graph3->nedges+graph3->nedges/4); exit(-1); }; if(edge2!=NULL_EDGE){ graph3->edges[edge2].next_edges[j] = graph3->edges[edge1].next_edges[i]; } else graph3->first_edge[vert]= graph3->edges[edge1].next_edges[i]; graph3->vert_degree[vert]--; }; }; static int bdz_generate_queue(cmph_uint32 nedges, cmph_uint32 nvertices, bdz_queue_t queue, bdz_graph3_t* graph3) { cmph_uint32 i,v0,v1,v2; cmph_uint32 queue_head=0,queue_tail=0; cmph_uint32 curr_edge; cmph_uint32 tmp_edge; cmph_uint8 * marked_edge =malloc((nedges >> 3) + 1); memset(marked_edge, 0, (nedges >> 3) + 1); for(i=0;iedges[i].vertices[0]; v1=graph3->edges[i].vertices[1]; v2=graph3->edges[i].vertices[2]; if(graph3->vert_degree[v0]==1 || graph3->vert_degree[v1]==1 || graph3->vert_degree[v2]==1){ if(!GETBIT(marked_edge,i)) { queue[queue_head++]=i; SETBIT(marked_edge,i); } }; }; while(queue_tail!=queue_head){ curr_edge=queue[queue_tail++]; bdz_remove_edge(graph3,curr_edge); v0=graph3->edges[curr_edge].vertices[0]; v1=graph3->edges[curr_edge].vertices[1]; v2=graph3->edges[curr_edge].vertices[2]; if(graph3->vert_degree[v0]==1 ) { tmp_edge=graph3->first_edge[v0]; if(!GETBIT(marked_edge,tmp_edge)) { queue[queue_head++]=tmp_edge; SETBIT(marked_edge,tmp_edge); }; }; if(graph3->vert_degree[v1]==1) { tmp_edge=graph3->first_edge[v1]; if(!GETBIT(marked_edge,tmp_edge)){ queue[queue_head++]=tmp_edge; SETBIT(marked_edge,tmp_edge); }; }; if(graph3->vert_degree[v2]==1){ tmp_edge=graph3->first_edge[v2]; if(!GETBIT(marked_edge,tmp_edge)){ queue[queue_head++]=tmp_edge; SETBIT(marked_edge,tmp_edge); }; }; }; free(marked_edge); return queue_head-nedges;/* returns 0 if successful otherwies return negative number*/ }; static int bdz_mapping(cmph_config_t *mph, bdz_graph3_t* graph3, bdz_queue_t queue); static void assigning(bdz_config_data_t *bdz, bdz_graph3_t* graph3, bdz_queue_t queue); static void ranking(bdz_config_data_t *bdz); static cmph_uint32 rank(bdz_data_t *bdz, cmph_uint32 vertex); bdz_config_data_t *bdz_config_new() { bdz_config_data_t *bdz; bdz = (bdz_config_data_t *)malloc(sizeof(bdz_config_data_t)); assert(bdz); memset(bdz, 0, sizeof(bdz_config_data_t)); bdz->hashfunc = CMPH_HASH_JENKINS; bdz->g = NULL; bdz->hl = NULL; bdz->k = 0; //kth index in ranktable, $k = log_2(n=3r)/\varepsilon$ bdz->b = 7; // number of bits of k bdz->ranktablesize = 0; //number of entries in ranktable, $n/k +1$ bdz->ranktable = NULL; // rank table return bdz; } void bdz_config_destroy(cmph_config_t *mph) { bdz_config_data_t *data = (bdz_config_data_t *)mph->data; DEBUGP("Destroying algorithm dependent data\n"); free(data); } void bdz_config_set_b(cmph_config_t *mph, cmph_uint8 b) { bdz_config_data_t *bdz = (bdz_config_data_t *)mph->data; if (b <= 2 || b > 10) b = 7; // validating restrictions over parameter b. bdz->b = b; DEBUGP("b: %u\n", b); } void bdz_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs) { bdz_config_data_t *bdz = (bdz_config_data_t *)mph->data; CMPH_HASH *hashptr = hashfuncs; cmph_uint32 i = 0; while(*hashptr != CMPH_HASH_COUNT) { if (i >= 1) break; //bdz only uses one linear hash function bdz->hashfunc = *hashptr; ++i, ++hashptr; } } cmph_t *bdz_new(cmph_config_t *mph, float c) { cmph_t *mphf = NULL; bdz_data_t *bdzf = NULL; cmph_uint32 iterations; bdz_queue_t edges; bdz_graph3_t graph3; bdz_config_data_t *bdz = (bdz_config_data_t *)mph->data; if (c == 0) c = 1.23; // validating restrictions over parameter c. DEBUGP("c: %f\n", c); bdz->m = mph->key_source->nkeys; bdz->r = ceil((c * mph->key_source->nkeys)/3); bdz->n = 3*bdz->r; bdz->k = (1 << bdz->b); DEBUGP("b: %u -- k: %u\n", bdz->b, bdz->k); bdz->ranktablesize = bdz->n/bdz->k + 2; DEBUGP("ranktablesize: %u\n", bdz->ranktablesize); bdz_alloc_graph3(&graph3, bdz->m, bdz->n); bdz_alloc_queue(&edges,bdz->m); DEBUGP("Created hypergraph\n"); DEBUGP("m (edges): %u n (vertices): %u r: %u c: %f \n", bdz->m, bdz->n, bdz->r, c); // Mapping step iterations = 1000; if (mph->verbosity) { fprintf(stderr, "Entering mapping step for mph creation of %u keys with graph sized %u\n", bdz->m, bdz->n); } while(1) { int ok; DEBUGP("linear hash function \n"); bdz->hl = hash_state_new(bdz->hashfunc, 15); ok = bdz_mapping(mph, &graph3, edges); //ok = 0; if (!ok) { --iterations; hash_state_destroy(bdz->hl); bdz->hl = NULL; DEBUGP("%u iterations remaining\n", iterations); if (mph->verbosity) { fprintf(stderr, "acyclic graph creation failure - %u iterations remaining\n", iterations); } if (iterations == 0) break; } else break; } if (iterations == 0) { bdz_free_queue(&edges); bdz_free_graph3(&graph3); return NULL; } bdz_partial_free_graph3(&graph3); // Assigning step if (mph->verbosity) { fprintf(stderr, "Entering assigning step for mph creation of %u keys with graph sized %u\n", bdz->m, bdz->n); } assigning(bdz, &graph3, edges); bdz_free_queue(&edges); bdz_free_graph3(&graph3); if (mph->verbosity) { fprintf(stderr, "Entering ranking step for mph creation of %u keys with graph sized %u\n", bdz->m, bdz->n); } ranking(bdz); mphf = (cmph_t *)malloc(sizeof(cmph_t)); mphf->algo = mph->algo; bdzf = (bdz_data_t *)malloc(sizeof(bdz_data_t)); bdzf->g = bdz->g; bdz->g = NULL; //transfer memory ownership bdzf->hl = bdz->hl; bdz->hl = NULL; //transfer memory ownership bdzf->ranktable = bdz->ranktable; bdz->ranktable = NULL; //transfer memory ownership bdzf->ranktablesize = bdz->ranktablesize; bdzf->k = bdz->k; bdzf->b = bdz->b; bdzf->n = bdz->n; bdzf->m = bdz->m; bdzf->r = bdz->r; mphf->data = bdzf; mphf->size = bdz->m; DEBUGP("Successfully generated minimal perfect hash\n"); if (mph->verbosity) { fprintf(stderr, "Successfully generated minimal perfect hash function\n"); } return mphf; } static int bdz_mapping(cmph_config_t *mph, bdz_graph3_t* graph3, bdz_queue_t queue) { cmph_uint32 e; int cycles = 0; cmph_uint32 hl[3]; bdz_config_data_t *bdz = (bdz_config_data_t *)mph->data; bdz_init_graph3(graph3, bdz->m, bdz->n); mph->key_source->rewind(mph->key_source->data); for (e = 0; e < mph->key_source->nkeys; ++e) { cmph_uint32 h0, h1, h2; cmph_uint32 keylen; char *key = NULL; mph->key_source->read(mph->key_source->data, &key, &keylen); hash_vector(bdz->hl, key, keylen,hl); h0 = hl[0] % bdz->r; h1 = hl[1] % bdz->r + bdz->r; h2 = hl[2] % bdz->r + (bdz->r << 1); mph->key_source->dispose(mph->key_source->data, key, keylen); bdz_add_edge(graph3,h0,h1,h2); } cycles = bdz_generate_queue(bdz->m, bdz->n, queue, graph3); return (cycles == 0); } static void assigning(bdz_config_data_t *bdz, bdz_graph3_t* graph3, bdz_queue_t queue) { cmph_uint32 i; cmph_uint32 nedges=graph3->nedges; cmph_uint32 curr_edge; cmph_uint32 v0,v1,v2; cmph_uint8 * marked_vertices =malloc((bdz->n >> 3) + 1); bdz->g = (cmph_uint8 *)calloc((bdz->n >> 2)+1, sizeof(cmph_uint8)); memset(marked_vertices, 0, (bdz->n >> 3) + 1); memset(bdz->g, 0xff, (bdz->n >> 2) + 1); for(i=nedges-1;i+1>=1;i--){ curr_edge=queue[i]; v0=graph3->edges[curr_edge].vertices[0]; v1=graph3->edges[curr_edge].vertices[1]; v2=graph3->edges[curr_edge].vertices[2]; DEBUGP("B:%u %u %u -- %u %u %u\n", v0, v1, v2, GETVALUE(bdz->g, v0), GETVALUE(bdz->g, v1), GETVALUE(bdz->g, v2)); if(!GETBIT(marked_vertices, v0)){ if(!GETBIT(marked_vertices,v1)) { SETVALUE1(bdz->g, v1, UNASSIGNED); SETBIT(marked_vertices, v1); } if(!GETBIT(marked_vertices,v2)) { SETVALUE1(bdz->g, v2, UNASSIGNED); SETBIT(marked_vertices, v2); } SETVALUE1(bdz->g, v0, (6-(GETVALUE(bdz->g, v1) + GETVALUE(bdz->g,v2)))%3); SETBIT(marked_vertices, v0); } else if(!GETBIT(marked_vertices, v1)) { if(!GETBIT(marked_vertices, v2)) { SETVALUE1(bdz->g, v2, UNASSIGNED); SETBIT(marked_vertices, v2); } SETVALUE1(bdz->g, v1, (7-(GETVALUE(bdz->g, v0)+GETVALUE(bdz->g, v2)))%3); SETBIT(marked_vertices, v1); }else { SETVALUE1(bdz->g, v2, (8-(GETVALUE(bdz->g,v0)+GETVALUE(bdz->g, v1)))%3); SETBIT(marked_vertices, v2); } DEBUGP("A:%u %u %u -- %u %u %u\n", v0, v1, v2, GETVALUE(bdz->g, v0), GETVALUE(bdz->g, v1), GETVALUE(bdz->g, v2)); }; free(marked_vertices); } static void ranking(bdz_config_data_t *bdz) { cmph_uint32 i, j, offset = 0, count = 0, size = (bdz->k >> 2), nbytes_total = (bdz->n >> 2)+1, nbytes; bdz->ranktable = (cmph_uint32 *)calloc(bdz->ranktablesize, sizeof(cmph_uint32)); // ranktable computation bdz->ranktable[0] = 0; i = 1; while(1) { nbytes = size < nbytes_total? size : nbytes_total; for(j = 0; j < nbytes; j++) { count += bdz_lookup_table[*(bdz->g + offset + j)]; } if(i == bdz->ranktablesize) fprintf(stderr, "i:%u == bdz->ranktablesize:%u\n", i, bdz->ranktablesize); assert(i < bdz->ranktablesize); bdz->ranktable[i] = count; offset += nbytes; if(size >= nbytes_total) break; nbytes_total -= size; i++; } } int bdz_dump(cmph_t *mphf, FILE *fd) { char *buf = NULL; cmph_uint32 buflen; bdz_data_t *data = (bdz_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); fwrite(&buflen, sizeof(cmph_uint32), 1, fd); fwrite(buf, buflen, 1, fd); free(buf); fwrite(&(data->n), sizeof(cmph_uint32), 1, fd); fwrite(&(data->m), sizeof(cmph_uint32), 1, fd); fwrite(&(data->r), sizeof(cmph_uint32), 1, fd); fwrite(data->g, sizeof(cmph_uint8)*((data->n >> 2) +1), 1, fd); fwrite(&(data->k), sizeof(cmph_uint32), 1, fd); fwrite(&(data->b), sizeof(cmph_uint8), 1, fd); fwrite(&(data->ranktablesize), sizeof(cmph_uint32), 1, fd); fwrite(data->ranktable, sizeof(cmph_uint32)*(data->ranktablesize), 1, fd); #ifdef DEBUG cmph_uint32 i; fprintf(stderr, "G: "); for (i = 0; i < data->n; ++i) fprintf(stderr, "%u ", GETVALUE(data->g, i)); fprintf(stderr, "\n"); #endif return 1; } void bdz_load(FILE *f, cmph_t *mphf) { char *buf = NULL; cmph_uint32 buflen; bdz_data_t *bdz = (bdz_data_t *)malloc(sizeof(bdz_data_t)); DEBUGP("Loading bdz mphf\n"); mphf->data = bdz; fread(&buflen, sizeof(cmph_uint32), 1, f); DEBUGP("Hash state has %u bytes\n", buflen); buf = (char *)malloc(buflen); fread(buf, buflen, 1, f); bdz->hl = hash_state_load(buf, buflen); free(buf); DEBUGP("Reading m and n\n"); fread(&(bdz->n), sizeof(cmph_uint32), 1, f); fread(&(bdz->m), sizeof(cmph_uint32), 1, f); fread(&(bdz->r), sizeof(cmph_uint32), 1, f); bdz->g = (cmph_uint8 *)calloc((bdz->n >> 2) + 1, sizeof(cmph_uint8)); fread(bdz->g, ((bdz->n >> 2) + 1)*sizeof(cmph_uint8), 1, f); fread(&(bdz->k), sizeof(cmph_uint32), 1, f); fread(&(bdz->b), sizeof(cmph_uint8), 1, f); fread(&(bdz->ranktablesize), sizeof(cmph_uint32), 1, f); bdz->ranktable = (cmph_uint32 *)calloc(bdz->ranktablesize, sizeof(cmph_uint32)); fread(bdz->ranktable, sizeof(cmph_uint32)*(bdz->ranktablesize), 1, f); #ifdef DEBUG cmph_uint32 i = 0; fprintf(stderr, "G: "); for (i = 0; i < bdz->n; ++i) fprintf(stderr, "%u ", GETVALUE(bdz->g,i)); fprintf(stderr, "\n"); #endif return; } cmph_uint32 bdz_search_ph(cmph_t *mphf, const char *key, cmph_uint32 keylen) { bdz_data_t *bdz = mphf->data; cmph_uint32 hl[3]; hash_vector(bdz->hl, key, keylen, hl); cmph_uint32 vertex; hl[0] = hl[0] % bdz->r; hl[1] = hl[1] % bdz->r + bdz->r; hl[2] = hl[2] % bdz->r + (bdz->r << 1); vertex = hl[(GETVALUE(bdz->g, hl[0]) + GETVALUE(bdz->g, hl[1]) + GETVALUE(bdz->g, hl[2])) % 3]; return vertex; } static inline cmph_uint32 rank(bdz_data_t *bdz, cmph_uint32 vertex) { cmph_uint32 index = vertex >> bdz->b; cmph_uint32 base_rank = bdz->ranktable[index]; cmph_uint32 beg_idx_v = index << bdz->b; cmph_uint32 beg_idx_b = beg_idx_v >> 2; cmph_uint32 end_idx_b = vertex >> 2; while(beg_idx_b < end_idx_b) { base_rank += bdz_lookup_table[*(bdz->g + beg_idx_b++)]; } beg_idx_v = beg_idx_b << 2; while(beg_idx_v < vertex) { if(GETVALUE(bdz->g, beg_idx_v) != UNASSIGNED) base_rank++; beg_idx_v++; } return base_rank; } cmph_uint32 bdz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen) { bdz_data_t *bdz = mphf->data; cmph_uint32 hl[3]; hash_vector(bdz->hl, key, keylen, hl); cmph_uint32 vertex; hl[0] = hl[0] % bdz->r; hl[1] = hl[1] % bdz->r + bdz->r; hl[2] = hl[2] % bdz->r + (bdz->r << 1); vertex = hl[(GETVALUE(bdz->g, hl[0]) + GETVALUE(bdz->g, hl[1]) + GETVALUE(bdz->g, hl[2])) % 3]; return rank(bdz, vertex); } void bdz_destroy(cmph_t *mphf) { bdz_data_t *data = (bdz_data_t *)mphf->data; free(data->g); hash_state_destroy(data->hl); free(data->ranktable); free(data); free(mphf); }