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-rwxr-xr-xgirepository/cmph/bdz.c703
1 files changed, 703 insertions, 0 deletions
diff --git a/girepository/cmph/bdz.c b/girepository/cmph/bdz.c
new file mode 100755
index 00000000..f422c8f9
--- /dev/null
+++ b/girepository/cmph/bdz.c
@@ -0,0 +1,703 @@
+#include "bdz.h"
+#include "cmph_structs.h"
+#include "bdz_structs.h"
+#include "hash.h"
+#include "bitbool.h"
+
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+#include <string.h>
+//#define DEBUG
+#include "debug.h"
+#define UNASSIGNED 3U
+#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((size_t)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,(size_t)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;i<nedges;i++){
+ printf("\nedge %d %d %d %d ",i,graph3->edges[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;i<nvertices;i++){
+ printf("\nfirst for vertice %d %d ",i,graph3->first_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((size_t)(nedges >> 3) + 1);
+ memset(marked_edge, 0, (size_t)(nedges >> 3) + 1);
+
+ for(i=0;i<nedges;i++){
+ v0=graph3->edges[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 (int)(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(cmph_uint32 b, cmph_uint32 * ranktable, cmph_uint8 * g, 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_uint32 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 = (cmph_uint8)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, double 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;
+ #ifdef CMPH_TIMING
+ double construction_time_begin = 0.0;
+ double construction_time = 0.0;
+ ELAPSED_TIME_IN_SECONDS(&construction_time_begin);
+ #endif
+
+
+ if (c == 0) c = 1.23; // validating restrictions over parameter c.
+ DEBUGP("c: %f\n", c);
+ bdz->m = mph->key_source->nkeys;
+ bdz->r = (cmph_uint32)ceil((c * mph->key_source->nkeys)/3);
+ if ((bdz->r % 2) == 0) bdz->r+=1;
+ bdz->n = 3*bdz->r;
+
+ bdz->k = (1U << bdz->b);
+ DEBUGP("b: %u -- k: %u\n", bdz->b, bdz->k);
+
+ bdz->ranktablesize = (cmph_uint32)ceil(bdz->n/(double)bdz->k);
+ 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);
+ #ifdef CMPH_TIMING
+ ELAPSED_TIME_IN_SECONDS(&construction_time);
+ #endif
+ 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");
+ }
+
+
+ #ifdef CMPH_TIMING
+ register cmph_uint32 space_usage = bdz_packed_size(mphf)*8;
+ register cmph_uint32 keys_per_bucket = 1;
+ construction_time = construction_time - construction_time_begin;
+ fprintf(stdout, "%u\t%.2f\t%u\t%.4f\t%.4f\n", bdz->m, bdz->m/(double)bdz->n, keys_per_bucket, construction_time, space_usage/(double)bdz->m);
+ #endif
+
+ 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((size_t)(bdz->n >> 3) + 1);
+ cmph_uint32 sizeg = (cmph_uint32)ceil(bdz->n/4.0);
+ bdz->g = (cmph_uint8 *)calloc((size_t)(sizeg), sizeof(cmph_uint8));
+ memset(marked_vertices, 0, (size_t)(bdz->n >> 3) + 1);
+ memset(bdz->g, 0xff, (size_t)(sizeg));
+
+ 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 = 0U, count = 0U, size = (bdz->k >> 2U), nbytes_total = (cmph_uint32)ceil(bdz->n/4.0), nbytes;
+ bdz->ranktable = (cmph_uint32 *)calloc((size_t)bdz->ranktablesize, sizeof(cmph_uint32));
+ // ranktable computation
+ bdz->ranktable[0] = 0;
+ i = 1;
+ while(1)
+ {
+ if(i == bdz->ranktablesize) break;
+ nbytes = size < nbytes_total? size : nbytes_total;
+ for(j = 0; j < nbytes; j++)
+ {
+ count += bdz_lookup_table[*(bdz->g + offset + j)];
+ }
+ bdz->ranktable[i] = count;
+ offset += nbytes;
+ nbytes_total -= size;
+ i++;
+ }
+}
+
+
+int bdz_dump(cmph_t *mphf, FILE *fd)
+{
+ char *buf = NULL;
+ cmph_uint32 buflen;
+ register size_t nbytes;
+ 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);
+ 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->r), sizeof(cmph_uint32), (size_t)1, fd);
+
+ cmph_uint32 sizeg = (cmph_uint32)ceil(data->n/4.0);
+ nbytes = fwrite(data->g, sizeof(cmph_uint8)*sizeg, (size_t)1, fd);
+
+ nbytes = fwrite(&(data->k), sizeof(cmph_uint32), (size_t)1, fd);
+ nbytes = fwrite(&(data->b), sizeof(cmph_uint8), (size_t)1, fd);
+ nbytes = fwrite(&(data->ranktablesize), sizeof(cmph_uint32), (size_t)1, fd);
+
+ nbytes = fwrite(data->ranktable, sizeof(cmph_uint32)*(data->ranktablesize), (size_t)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, sizeg;
+ register size_t nbytes;
+ bdz_data_t *bdz = (bdz_data_t *)malloc(sizeof(bdz_data_t));
+
+ DEBUGP("Loading bdz mphf\n");
+ mphf->data = bdz;
+
+ 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);
+ bdz->hl = hash_state_load(buf, buflen);
+ free(buf);
+
+
+ DEBUGP("Reading m and n\n");
+ nbytes = fread(&(bdz->n), sizeof(cmph_uint32), (size_t)1, f);
+ nbytes = fread(&(bdz->m), sizeof(cmph_uint32), (size_t)1, f);
+ nbytes = fread(&(bdz->r), sizeof(cmph_uint32), (size_t)1, f);
+ sizeg = (cmph_uint32)ceil(bdz->n/4.0);
+ bdz->g = (cmph_uint8 *)calloc((size_t)(sizeg), sizeof(cmph_uint8));
+ nbytes = fread(bdz->g, sizeg*sizeof(cmph_uint8), (size_t)1, f);
+
+ nbytes = fread(&(bdz->k), sizeof(cmph_uint32), (size_t)1, f);
+ nbytes = fread(&(bdz->b), sizeof(cmph_uint8), (size_t)1, f);
+ nbytes = fread(&(bdz->ranktablesize), sizeof(cmph_uint32), (size_t)1, f);
+
+ bdz->ranktable = (cmph_uint32 *)calloc((size_t)bdz->ranktablesize, sizeof(cmph_uint32));
+ nbytes = fread(bdz->ranktable, sizeof(cmph_uint32)*(bdz->ranktablesize), (size_t)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(cmph_uint32 b, cmph_uint32 * ranktable, cmph_uint8 * g, cmph_uint32 vertex)
+{
+ register cmph_uint32 index = vertex >> b;
+ register cmph_uint32 base_rank = ranktable[index];
+ register cmph_uint32 beg_idx_v = index << b;
+ register cmph_uint32 beg_idx_b = beg_idx_v >> 2;
+ register cmph_uint32 end_idx_b = vertex >> 2;
+ while(beg_idx_b < end_idx_b)
+ {
+ base_rank += bdz_lookup_table[*(g + beg_idx_b++)];
+
+ }
+ beg_idx_v = beg_idx_b << 2;
+ while(beg_idx_v < vertex)
+ {
+ if(GETVALUE(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)
+{
+ register cmph_uint32 vertex;
+ register bdz_data_t *bdz = mphf->data;
+ cmph_uint32 hl[3];
+ hash_vector(bdz->hl, key, keylen, hl);
+ 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->b, bdz->ranktable, bdz->g, 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);
+}
+
+/** \fn void bdz_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 bdz_pack(cmph_t *mphf, void *packed_mphf)
+{
+ bdz_data_t *data = (bdz_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 r
+ *((cmph_uint32 *) ptr) = data->r;
+ ptr += sizeof(data->r);
+
+ // packing ranktablesize
+ *((cmph_uint32 *) ptr) = data->ranktablesize;
+ ptr += sizeof(data->ranktablesize);
+
+ // packing ranktable
+ memcpy(ptr, data->ranktable, sizeof(cmph_uint32)*(data->ranktablesize));
+ ptr += sizeof(cmph_uint32)*(data->ranktablesize);
+
+ // packing b
+ *ptr++ = data->b;
+
+ // packing g
+ cmph_uint32 sizeg = (cmph_uint32)ceil(data->n/4.0);
+ memcpy(ptr, data->g, sizeof(cmph_uint8)*sizeg);
+}
+
+/** \fn cmph_uint32 bdz_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 bdz_packed_size(cmph_t *mphf)
+{
+ bdz_data_t *data = (bdz_data_t *)mphf->data;
+
+ CMPH_HASH hl_type = hash_get_type(data->hl);
+
+ return (cmph_uint32)(sizeof(CMPH_ALGO) + hash_state_packed_size(hl_type) + 3*sizeof(cmph_uint32) + sizeof(cmph_uint32)*(data->ranktablesize) + sizeof(cmph_uint8) + sizeof(cmph_uint8)* (cmph_uint32)(ceil(data->n/4.0)));
+}
+
+/** cmph_uint32 bdz_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 bdz_search_packed(void *packed_mphf, const char *key, cmph_uint32 keylen)
+{
+
+ register cmph_uint32 vertex;
+ register CMPH_HASH hl_type = *(cmph_uint32 *)packed_mphf;
+ register cmph_uint8 *hl_ptr = (cmph_uint8 *)(packed_mphf) + 4;
+
+ register cmph_uint32 *ranktable = (cmph_uint32*)(hl_ptr + hash_state_packed_size(hl_type));
+
+ register cmph_uint32 r = *ranktable++;
+ register cmph_uint32 ranktablesize = *ranktable++;
+ register cmph_uint8 * g = (cmph_uint8 *)(ranktable + ranktablesize);
+ register cmph_uint8 b = *g++;
+
+ cmph_uint32 hl[3];
+ hash_vector_packed(hl_ptr, hl_type, key, keylen, hl);
+ hl[0] = hl[0] % r;
+ hl[1] = hl[1] % r + r;
+ hl[2] = hl[2] % r + (r << 1);
+ vertex = hl[(GETVALUE(g, hl[0]) + GETVALUE(g, hl[1]) + GETVALUE(g, hl[2])) % 3];
+ return rank(b, ranktable, g, vertex);
+}
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