compressed hash and displace method added

src/Makefile

@@ -60,7 +60,8 @@ libcmph_la_LIBADD =
 am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \
 	graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \
 	bdz_ph.lo buffer_manager.lo buffer_entry.lo brz.lo fch.lo \
-	fch_buckets.lo select.lo compressed_seq.lo
+	fch_buckets.lo select.lo compressed_seq.lo chd_ph.lo \
+	miller_rabin.lo
 libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS)
 libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
@@ -207,7 +208,8 @@ libcmph_la_SOURCES = hash.c jenkins_hash.c\
 		      chm.c bmz.c bmz8.c bdz.c bdz_ph.c\
 		      buffer_manager.c buffer_entry.c\
 		      brz.c fch.c fch_buckets.c \
-		      select.c compressed_seq.c 
+		      select.c compressed_seq.c \
+		      chd_ph.c miller_rabin.c
 
 libcmph_la_LDFLAGS = -version-info 0:0:0
 cmph_SOURCES = main.c wingetopt.h wingetopt.c
@@ -319,6 +321,7 @@ include ./$(DEPDIR)/bmz8.Plo
 include ./$(DEPDIR)/brz.Plo
 include ./$(DEPDIR)/buffer_entry.Plo
 include ./$(DEPDIR)/buffer_manager.Plo
+include ./$(DEPDIR)/chd_ph.Plo
 include ./$(DEPDIR)/chm.Plo
 include ./$(DEPDIR)/cmph.Plo
 include ./$(DEPDIR)/cmph_structs.Plo
@@ -329,6 +332,7 @@ include ./$(DEPDIR)/graph.Plo
 include ./$(DEPDIR)/hash.Plo
 include ./$(DEPDIR)/jenkins_hash.Plo
 include ./$(DEPDIR)/main.Po
+include ./$(DEPDIR)/miller_rabin.Plo
 include ./$(DEPDIR)/select.Plo
 include ./$(DEPDIR)/vqueue.Plo
 include ./$(DEPDIR)/vstack.Plo

src/Makefile.am

@@ -7,7 +7,8 @@ libcmph_la_SOURCES =  hash.c jenkins_hash.c\
 		      chm.c bmz.c bmz8.c bdz.c bdz_ph.c\
 		      buffer_manager.c buffer_entry.c\
 		      brz.c fch.c fch_buckets.c \
-		      select.c compressed_seq.c 
+		      select.c compressed_seq.c \
+		      chd_ph.c miller_rabin.c
 
 libcmph_la_LDFLAGS = -version-info 0:0:0
 

src/Makefile.in

@@ -60,7 +60,8 @@ libcmph_la_LIBADD =
 am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \
 	graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \
 	bdz_ph.lo buffer_manager.lo buffer_entry.lo brz.lo fch.lo \
-	fch_buckets.lo select.lo compressed_seq.lo
+	fch_buckets.lo select.lo compressed_seq.lo chd_ph.lo \
+	miller_rabin.lo
 libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS)
 libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
@@ -207,7 +208,8 @@ libcmph_la_SOURCES = hash.c jenkins_hash.c\
 		      chm.c bmz.c bmz8.c bdz.c bdz_ph.c\
 		      buffer_manager.c buffer_entry.c\
 		      brz.c fch.c fch_buckets.c \
-		      select.c compressed_seq.c 
+		      select.c compressed_seq.c \
+		      chd_ph.c miller_rabin.c
 
 libcmph_la_LDFLAGS = -version-info 0:0:0
 cmph_SOURCES = main.c wingetopt.h wingetopt.c
@@ -319,6 +321,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/brz.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/buffer_entry.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/buffer_manager.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chd_ph.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chm.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cmph.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cmph_structs.Plo@am__quote@
@@ -329,6 +332,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hash.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/jenkins_hash.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/miller_rabin.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/select.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/vqueue.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/vstack.Plo@am__quote@

src/bdz_ph.c

@@ -484,13 +484,6 @@ void bdz_ph_load(FILE *f, cmph_t *mphf)
 	bdz_ph->g = (cmph_uint8 *)calloc((size_t)sizeg, sizeof(cmph_uint8));
 	nbytes = fread(bdz_ph->g, sizeg*sizeof(cmph_uint8), (size_t)1, f);
 
-/*	#ifdef DEBUG
-	cmph_uint32 i;
-	fprintf(stderr, "G: ");
-	for (i = 0; i < bdz_ph->n; ++i) fprintf(stderr, "%u ", GETVALUE(bdz_ph->g,i));
-	fprintf(stderr, "\n");
-	#endif
-*/	
 	return;
 }
 		

src/brz.c

@@ -105,6 +105,10 @@ void brz_config_set_mphf_fd(cmph_config_t *mph, FILE *mphf_fd)
 void brz_config_set_b(cmph_config_t *mph, cmph_uint32 b)
 {
 	brz_config_data_t *brz = (brz_config_data_t *)mph->data;
+	if(b <= 64 || b >= 175) 
+	{
+		b =  128;
+	}
 	brz->b = b;
 }
 

src/chd_ph.c

@@ -0,0 +1,833 @@
+#include<stdio.h>
+#include<stdlib.h>
+#include<string.h>
+#include<math.h>
+#include<time.h>
+#include<assert.h>
+#include<limits.h>
+
+#include "cmph_structs.h"
+#include "chd_structs_ph.h"
+#include "chd_ph.h"
+#include"miller_rabin.h"
+
+#define DEBUG
+#include "debug.h"
+
+// NO_ELEMENT is equivalent to null pointer
+#ifndef NO_ELEMENT
+#define NO_ELEMENT UINT_MAX
+#endif
+
+// struct to represents the buckets items
+struct _chd_ph_item_t
+{
+	cmph_uint32 f;
+	cmph_uint32 h;
+	struct _chd_ph_item_t * next;
+};
+typedef struct _chd_ph_item_t chd_ph_item_t;
+
+
+// struct to represent a bucket
+struct _chd_ph_bucket_t
+{
+	cmph_uint32 size;
+	chd_ph_item_t * items_list;
+	cmph_uint32 next_in_list;
+};
+typedef struct _chd_ph_bucket_t chd_ph_bucket_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 cmph_uint8 chd_ph_bucket_insert(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets, cmph_uint32 g, chd_ph_item_t * item);
+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;
+		buckets[i].items_list = 0;
+		buckets[i].next_in_list = NO_ELEMENT;
+	};
+}
+
+cmph_uint8 chd_ph_bucket_insert(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets, cmph_uint32 g, chd_ph_item_t * item)
+{
+	chd_ph_item_t * item1, * prior_item1;
+	item1 = buckets[g].items_list;
+	prior_item1 = 0;
+	while(item1 != 0 && (item1->f < item->f || (item1->f == item->f && item1->h < item->h)) )
+	{
+		prior_item1 = item1;
+		item1 = item1->next;
+	};
+	
+	if(item1 != 0 && item1->f == item->f && item1->h == item->h)
+	{
+		DEBUGP("Item not added\n");
+		return 0;
+	};
+	item->next = item1;
+	if(prior_item1 == 0)
+		buckets[g].items_list = item;
+	else
+		prior_item1->next = item;
+	
+	buckets[g].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 inline cmph_uint32 * chd_ph_ordering(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets, cmph_uint32 max_bucket_size);
+
+static inline cmph_uint8 chd_ph_searching(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, cmph_uint32 max_bucket_size,
+                                          cmph_uint32 *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table, 
+					  cmph_uint8 * occup_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()
+{
+	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;
+	
+	//The following fields are used just for statistics
+	chd_ph->space_usage = 0;
+	chd_ph->entropy = 0.0;
+	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");
+	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)
+{
+	assert(mph);
+	chd_ph_config_data_t *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)
+{
+	assert(mph);
+	chd_ph_config_data_t *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_item_t * item;
+	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);
+			
+			item = (items + i);
+
+			g = hl[0] % chd_ph->nbuckets;
+			item->f = hl[1] % chd_ph->n;
+			item->h = hl[2] % (chd_ph->n - 1) + 1;
+			
+			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;
+// 			}
+			
+			if(!chd_ph_bucket_insert(buckets, chd_ph->nbuckets, g, item))
+			{
+				break;
+			}
+			
+			if(buckets[g].size > *max_bucket_size)
+			{
+				  *max_bucket_size = buckets[g].size;
+			}
+		}
+		
+		if(i == chd_ph->m)
+		{
+			return 1; // SUCCESS
+		}
+		
+		if(mapping_iterations == 0)
+		{
+		      goto error;
+		}
+	}
+error:
+	hash_state_destroy(chd_ph->hl);
+	chd_ph->hl = NULL;
+	return 0; // FAILURE
+
+}
+
+cmph_uint32 * chd_ph_ordering(chd_ph_bucket_t * buckets, cmph_uint32 nbuckets, cmph_uint32 max_bucket_size)
+{
+	cmph_uint32 * sorted_lists = (cmph_uint32 *) calloc(max_bucket_size + 1, sizeof(cmph_uint32));
+	register cmph_uint32 i, size;
+	DEBUGP("MAX BUCKET SIZE = %u\n", max_bucket_size);
+	for(i = 0; i <= max_bucket_size; i++)
+	{
+		sorted_lists[i] = NO_ELEMENT;
+	}
+	for(i = 0; i < nbuckets; i++)
+	{
+		size = buckets[i].size;
+		if(size == 0)
+			continue;
+		buckets[i].next_in_list = sorted_lists[size];
+		sorted_lists[size] = i;
+	};
+
+	return sorted_lists;
+}
+
+static inline cmph_uint8 place_bucket_probe(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, cmph_uint8 * occup_table, 
+                                            cmph_uint32 probe0_num, cmph_uint32 probe1_num, cmph_uint32 bucket_num)
+{
+	register cmph_uint32 i;
+	register cmph_uint32 size = buckets[bucket_num].size;
+	register chd_ph_item_t * item;
+	register cmph_uint32 position;
+
+	item = buckets[bucket_num].items_list;
+	// try place bucket with probe_num
+	for(i = 0; i < size; i++) // placement
+	{
+		position = (item->f + ((cmph_uint64)item->h)*probe0_num + probe1_num) % chd_ph->n;
+		
+		if(occup_table[position] >= chd_ph->keys_per_bin)
+		{
+			break;
+		}
+		occup_table[position]++;
+		
+		item = item->next;
+	};
+	
+	if(i != size) // Undo the placement
+	{
+		item = buckets[bucket_num].items_list;
+		while(1)
+		{
+			if(i == 0)
+			{
+				break;
+			}
+			position = (item->f + ((cmph_uint64 )item->h) * probe0_num + probe1_num) % chd_ph->n;
+			occup_table[position]--;
+			item = item->next;
+			i--;
+		};
+		return 0;
+	};	
+	return 1;
+};
+
+static inline cmph_uint8 place_bucket(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, cmph_uint32 max_probes, 
+                                      cmph_uint32 * disp_table, cmph_uint8 * occup_table, cmph_uint32 bucket_num)
+				      
+{
+	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, occup_table, probe0_num, probe1_num, bucket_num))
+		{
+			disp_table[bucket_num] = 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, cmph_uint32 max_bucket_size,
+                                        cmph_uint32 *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table, 
+					cmph_uint8 * occup_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];
+		while(curr_bucket != NO_ELEMENT)
+		{
+			if(!place_bucket(chd_ph, buckets, max_probes, disp_table, occup_table, curr_bucket))
+			{
+				return 0;
+			}
+			curr_bucket = buckets[curr_bucket].next_in_list;
+		};
+	
+	};
+	return 1;
+};
+
+static inline cmph_uint8 place_buckets2(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, cmph_uint32 max_bucket_size,
+                                        cmph_uint32 *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table, 
+					cmph_uint8 * occup_table)
+{
+	register cmph_uint32 i;
+	register cmph_uint32 curr_bucket, prev_bucket;
+	register cmph_uint32 probe_num, probe0_num, probe1_num;
+	DEBUGP("USING HEURISTIC TO PLACE BUCKETS\n");
+	for(i = max_bucket_size; i > 0; i--)
+	{
+		probe_num = 0;
+		probe0_num = 0;
+		probe1_num = 0;
+		while(sorted_lists[i] != NO_ELEMENT)
+		{
+			prev_bucket = NO_ELEMENT;
+			curr_bucket = sorted_lists[i];
+			while(curr_bucket != NO_ELEMENT)
+			{
+				// if bucket is successfully placed remove it from list
+				if(place_bucket_probe(chd_ph, buckets, occup_table, probe0_num, probe1_num, curr_bucket))
+				{	
+					disp_table[curr_bucket] = probe0_num + probe1_num * chd_ph->n;
+// 					DEBUGP("BUCKET %u PLACED --- DISPLACEMENT = %u\n", curr_bucket, disp_table[curr_bucket]);
+					if(prev_bucket == NO_ELEMENT)
+					{
+						sorted_lists[i] = buckets[curr_bucket].next_in_list;
+					}
+					else
+					{
+						buckets[prev_bucket].next_in_list = buckets[curr_bucket].next_in_list;
+					}
+						
+				} 
+				else
+				{
+// 					DEBUGP("BUCKET %u NOT PLACED\n", curr_bucket);
+					prev_bucket = curr_bucket;
+				}
+				curr_bucket = buckets[curr_bucket].next_in_list;
+			};
+			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 1;
+};
+
+cmph_uint8 chd_ph_searching(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, cmph_uint32 max_bucket_size,
+                            cmph_uint32 *sorted_lists, cmph_uint32 max_probes, cmph_uint32 * disp_table, 
+			    cmph_uint8 * occup_table)
+{
+	if(chd_ph->use_h)
+	{
+		return place_buckets2(chd_ph, buckets, max_bucket_size, sorted_lists, max_probes, disp_table, occup_table);
+	}
+	else
+	{
+		return place_buckets1(chd_ph, buckets, max_bucket_size, sorted_lists, max_probes, disp_table, occup_table);
+	}
+
+}
+
+static inline cmph_uint8 chd_ph_check_bin_hashing(chd_ph_config_data_t *chd_ph, chd_ph_bucket_t *buckets, 
+                                                  cmph_uint32 * disp_table, cmph_uint8 * occup_table)
+{
+	register cmph_uint32 i, j;
+	register cmph_uint32 position, probe0_num, probe1_num;
+	register cmph_uint32 m = 0;
+	register chd_ph_item_t * item;
+
+	memset(occup_table, 0, chd_ph->n);
+	for(i = 0; i < chd_ph->nbuckets; i++)
+	{
+		j = buckets[i].size;
+		item = buckets[i].items_list;
+		probe0_num = disp_table[i] % chd_ph->n;
+		probe1_num = disp_table[i] / chd_ph->n;
+		for(; j > 0; j--)
+		{
+			if(item == 0)
+			{
+				return 0;
+			}
+			m++;
+			position = (item->f + ((cmph_uint64 )item->h) * probe0_num + probe1_num) % chd_ph->n;
+			if(occup_table[position] >= chd_ph->keys_per_bin)
+			{
+				return 0;
+			}
+			occup_table[position]++;
+			item = item->next;
+		};
+	};
+	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 << 18; // 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;
+	cmph_uint32 * sorted_lists = NULL;
+	cmph_uint32 * disp_table = NULL;
+	cmph_uint8 * occup_table;
+	
+	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(mph->verbosity && chd_ph->keys_per_bin == 1)
+	{
+		fprintf(stderr, "space lower bound is %.3f bits per key", chd_ph_space_lower_bound(chd_ph->m, chd_ph->n));
+	}
+
+       	// 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);
+	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, chd_ph->nbuckets, max_bucket_size);
+		
+		if (mph->verbosity)
+		{
+			fprintf(stderr, "Starting searching step\n");
+		}
+		
+		searching_success = chd_ph_searching(chd_ph, buckets, max_bucket_size, sorted_lists, max_probes, disp_table, occup_table);
+			
+		if(searching_success) break;
+		
+		// reset occup_table
+		memset(occup_table, 0, chd_ph->n);
+		if(iterations == 0)
+		{
+			// Cleanup memory
+			if (mph->verbosity)
+			{
+				fprintf(stderr, "Failure because the max trials was exceeded\n");
+			}
+			failure = 1;
+			goto cleanup;
+		};
+	}
+
+	#ifdef DEBUG	
+	chd_ph->entropy = chd_ph_get_entropy(disp_table, chd_ph->nbuckets, max_probes);
+	DEBUGP("Entropy = %.4f\n", chd_ph->entropy/chd_ph->m);
+
+	if(!chd_ph_check_bin_hashing(chd_ph, buckets, disp_table, occup_table))
+	{
+	
+		DEBUGP("Error for bin packing generation");
+		return NULL;
+	};
+	#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);
+	chd_ph->space_usage = compressed_seq_get_space_usage(chd_ph->cs);
+	chd_ph->space_usage += 64;
+	DEBUGP("space_usage/key = %.4f\n", chd_ph->space_usage/(double)chd_ph->m);
+	
+cleanup:
+	chd_ph_bucket_destroy(buckets); 
+	free(items);
+	free(sorted_lists);
+	free(disp_table);
+	free(occup_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");
+	}
+
+	return mphf;
+}
+
+
+
+void chd_ph_load(FILE *fd, cmph_t *mphf)
+{
+	char *buf = NULL;
+	cmph_uint32 buflen;
+	register cmph_uint32 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);	
+}
+
+int chd_ph_dump(cmph_t *mphf, FILE *fd)
+{
+	char *buf = NULL;
+	cmph_uint32 buflen;
+	register cmph_uint32 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);
+	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 = (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 (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 = (f + ((cmph_uint64 )h)*probe0_num + probe1_num) % n;
+	return position;
+}
+
+
+

src/chd_ph.h

@@ -0,0 +1,59 @@
+#ifndef _CMPH_CHD_PH_H__
+#define _CMPH_CHD_PH_H__
+
+#include "cmph.h"
+
+typedef struct __chd_ph_data_t chd_ph_data_t;
+typedef struct __chd_ph_config_data_t chd_ph_config_data_t;
+
+/* Config API */
+chd_ph_config_data_t *chd_ph_config_new();
+void chd_ph_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs);
+
+/** \fn void chd_ph_config_set_keys_per_bin(cmph_config_t *mph, cmph_uint32 keys_per_bin);
+ *  \brief Allows to set the number of keys per bin.
+ *  \param mph pointer to the configuration structure
+ *  \param keys_per_bin value for the number of keys per bin 
+ */
+void chd_ph_config_set_keys_per_bin(cmph_config_t *mph, cmph_uint32 keys_per_bin);
+
+/** \fn void chd_ph_config_set_b(cmph_config_t *mph, cmph_uint32 keys_per_bucket);
+ *  \brief Allows to set the number of keys per bucket.
+ *  \param mph pointer to the configuration structure
+ *  \param keys_per_bucket value for the number of keys per bucket 
+ */
+void chd_ph_config_set_b(cmph_config_t *mph, cmph_uint32 keys_per_bucket);
+void chd_ph_config_destroy(cmph_config_t *mph);
+
+
+/* Chd algorithm API */
+cmph_t *chd_ph_new(cmph_config_t *mph, double c);
+void chd_ph_load(FILE *fd, cmph_t *mphf);
+int chd_ph_dump(cmph_t *mphf, FILE *fd);
+void chd_ph_destroy(cmph_t *mphf);
+cmph_uint32 chd_ph_search(cmph_t *mphf, const char *key, cmph_uint32 keylen);
+
+/** \fn void chd_ph_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 chd_ph_pack(cmph_t *mphf, void *packed_mphf);
+
+/** \fn cmph_uint32 chd_ph_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 chd_ph_packed_size(cmph_t *mphf);
+
+/** cmph_uint32 chd_ph_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 chd_ph_search_packed(void *packed_mphf, const char *key, cmph_uint32 keylen);
+
+#endif

src/chd_structs_ph.h

@@ -0,0 +1,32 @@
+#ifndef __CMPH_CHD_PH_STRUCTS_H__
+#define __CMPH_CHD_PH_STRUCTS_H__
+
+#include "hash_state.h"
+#include "compressed_seq.h"
+
+struct __chd_ph_data_t
+{
+	compressed_seq_t * cs;	// compressed displacement values
+	cmph_uint32 nbuckets;	// number of buckets
+	cmph_uint32 n;		// number of bins
+	hash_state_t *hl;	// linear hash function
+};
+
+struct __chd_ph_config_data_t
+{
+	CMPH_HASH hashfunc;	// linear hash function to be used
+	compressed_seq_t * cs;	// compressed displacement values
+	cmph_uint32 nbuckets;	// number of buckets
+	cmph_uint32 n;		// number of bins
+	hash_state_t *hl;	// linear hash function
+	
+	cmph_uint32 m;		// number of keys
+	cmph_uint8 use_h;	// flag to indicate the of use of a heuristic (use_h = 1)
+	cmph_uint32 keys_per_bin;//maximum number of keys per bin 
+	cmph_uint32 keys_per_bucket; // average number of keys per bucket
+
+	//The following fields are used just for statistics
+	cmph_uint32 space_usage;
+	double entropy;
+};
+#endif

src/cmph.c

@@ -7,6 +7,7 @@
 #include "fch.h" /* included -- Fabiano */
 #include "bdz.h" /* included -- Fabiano */
 #include "bdz_ph.h" /* included -- Fabiano */
+#include "chd_ph.h" /* included -- Fabiano */
 
 #include <stdlib.h>
 #include <assert.h>
@@ -14,8 +15,7 @@
 //#define DEBUG
 #include "debug.h"
 
-const char *cmph_names[] = {"bmz", "bmz8", "chm", "brz", "fch", "bdz", 
+const char *cmph_names[] = {"bmz", "bmz8", "chm", "brz", "fch", "bdz", "bdz_ph", "chd_ph", NULL }; /* included -- Fabiano */
-							"bdz_ph", NULL }; /* included -- Fabiano */
 
 typedef struct 
 {
@@ -322,6 +322,9 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
 			case CMPH_BDZ_PH:
 				bdz_ph_config_destroy(mph);
 				break;
+			case CMPH_CHD_PH:
+				chd_ph_config_destroy(mph);
+				break;
 			default:
 				assert(0);
 		}
@@ -348,6 +351,9 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
 			case CMPH_BDZ_PH:
 				mph->data = bdz_ph_config_new();
 				break;
+			case CMPH_CHD_PH:
+				mph->data = chd_ph_config_new();
+				break;
 			default:
 				assert(0);
 		}
@@ -382,6 +388,18 @@ void cmph_config_set_b(cmph_config_t *mph, cmph_uint32 b)
 	{
 		bdz_config_set_b(mph, b);
 	}
+	else if (mph->algo == CMPH_CHD_PH) 
+	{
+		chd_ph_config_set_b(mph, b);
+	}
+}
+
+void cmph_config_set_keys_per_bin(cmph_config_t *mph, cmph_uint32 keys_per_bin)
+{
+	if (mph->algo == CMPH_CHD_PH) 
+	{
+		chd_ph_config_set_keys_per_bin(mph, keys_per_bin);
+	}
 }
 
 void cmph_config_set_memory_availability(cmph_config_t *mph, cmph_uint32 memory_availability)
@@ -420,6 +438,9 @@ void cmph_config_destroy(cmph_config_t *mph)
 			case CMPH_BDZ_PH: /* included -- Fabiano */
 				bdz_ph_config_destroy(mph);
 				break;
+			case CMPH_CHD_PH: /* included -- Fabiano */
+				chd_ph_config_destroy(mph);
+				break;
 			default:
 				assert(0);
 		}
@@ -457,6 +478,9 @@ void cmph_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs)
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			bdz_ph_config_set_hashfuncs(mph, hashfuncs);
 			break;
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			chd_ph_config_set_hashfuncs(mph, hashfuncs);
+			break;
 		default:
 			break;
 	}
@@ -506,6 +530,10 @@ cmph_t *cmph_new(cmph_config_t *mph)
 			DEBUGP("Creating bdz_ph hash\n");
 			mphf = bdz_ph_new(mph, c);
 			break;
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			DEBUGP("Creating chd_ph hash\n");
+			mphf = chd_ph_new(mph, c);
+			break;
 		default:
 			assert(0);
 	}
@@ -530,6 +558,8 @@ int cmph_dump(cmph_t *mphf, FILE *f)
 			return bdz_dump(mphf, f);
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			return bdz_ph_dump(mphf, f);
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			return chd_ph_dump(mphf, f);
 		default:
 			assert(0);
 	}
@@ -573,6 +603,10 @@ cmph_t *cmph_load(FILE *f)
 			DEBUGP("Loading bdz_ph algorithm dependent parts\n");
 			bdz_ph_load(f, mphf);
 			break;
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			DEBUGP("Loading chd_ph algorithm dependent parts\n");
+			chd_ph_load(f, mphf);
+			break;
 		default:
 			assert(0);
 	}
@@ -606,6 +640,9 @@ cmph_uint32 cmph_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 		        DEBUGP("bdz_ph algorithm search\n");		         
 		        return bdz_ph_search(mphf, key, keylen);
+		case CMPH_CHD_PH: /* included -- Fabiano */
+		        DEBUGP("chd_ph algorithm search\n");		         
+		        return chd_ph_search(mphf, key, keylen);
 		default:
 			assert(0);
 	}
@@ -643,6 +680,9 @@ void cmph_destroy(cmph_t *mphf)
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			bdz_ph_destroy(mphf);
 			return;
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			chd_ph_destroy(mphf);
+			return;
 		default: 
 			assert(0);
 	}
@@ -685,6 +725,9 @@ void cmph_pack(cmph_t *mphf, void *packed_mphf)
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			bdz_ph_pack(mphf, ptr);
 			break;
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			chd_ph_pack(mphf, ptr);
+			break;
 		default: 
 			assert(0);
 	}
@@ -714,6 +757,8 @@ cmph_uint32 cmph_packed_size(cmph_t *mphf)
 			return bdz_packed_size(mphf);
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			return bdz_ph_packed_size(mphf);
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			return chd_ph_packed_size(mphf);
 		default: 
 			assert(0);
 	}
@@ -747,6 +792,8 @@ cmph_uint32 cmph_search_packed(void *packed_mphf, const char *key, cmph_uint32 k
 			return bdz_search_packed(++ptr, key, keylen);
 		case CMPH_BDZ_PH: /* included -- Fabiano */
 			return bdz_ph_search_packed(++ptr, key, keylen);
+		case CMPH_CHD_PH: /* included -- Fabiano */
+			return chd_ph_search_packed(++ptr, key, keylen);
 		default: 
 			assert(0);
 	}

src/cmph.h

@@ -54,6 +54,7 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo);
 void cmph_config_set_tmp_dir(cmph_config_t *mph, cmph_uint8 *tmp_dir);
 void cmph_config_set_mphf_fd(cmph_config_t *mph, FILE *mphf_fd);
 void cmph_config_set_b(cmph_config_t *mph, cmph_uint32 b);
+void cmph_config_set_keys_per_bin(cmph_config_t *mph, cmph_uint32 keys_per_bin);
 void cmph_config_set_memory_availability(cmph_config_t *mph, cmph_uint32 memory_availability);
 void cmph_config_destroy(cmph_config_t *mph);
 

src/cmph_types.h

@@ -35,7 +35,7 @@ typedef unsigned int cmph_uint32;
 typedef enum { CMPH_HASH_JENKINS, CMPH_HASH_COUNT } CMPH_HASH;
 extern const char *cmph_hash_names[];
 typedef enum { CMPH_BMZ, CMPH_BMZ8, CMPH_CHM, CMPH_BRZ, CMPH_FCH,
-               CMPH_BDZ, CMPH_BDZ_PH, CMPH_COUNT } CMPH_ALGO; /* included -- Fabiano */
+               CMPH_BDZ, CMPH_BDZ_PH, CMPH_CHD_PH, CMPH_COUNT } CMPH_ALGO; /* included -- Fabiano */
 extern const char *cmph_names[];
 
 #endif

src/main.c

@@ -22,17 +22,18 @@
 
 void usage(const char *prg)
 {
-	fprintf(stderr, "usage: %s [-v] [-h] [-V] [-k nkeys] [-f hash_function] [-g [-c value][-s seed] ] [-a algorithm] [-M memory_in_MB] [-b BRZ_parameter] [-d tmp_dir] [-m file.mph]  keysfile\n", prg);   
+	fprintf(stderr, "usage: %s [-v] [-h] [-V] [-k nkeys] [-f hash_function] [-g [-c algorithm_dependent_value][-s seed] ] [-a algorithm] [-M memory_in_MB] [-b algorithm_dependent_value] [-t keys_per_bin] [-d tmp_dir] [-m file.mph]  keysfile\n", prg);   
 }
 void usage_long(const char *prg)
 {
 	cmph_uint32 i;
-	fprintf(stderr, "usage: %s [-v] [-h] [-V] [-k nkeys] [-f hash_function] [-g [-c value][-s seed] ] [-a algorithm] [-M memory_in_MB] [-b BRZ_parameter] [-d tmp_dir] [-m file.mph] keysfile\n", prg);   
+	fprintf(stderr, "usage: %s [-v] [-h] [-V] [-k nkeys] [-f hash_function] [-g [-c algorithm_dependent_value][-s seed] ] [-a algorithm] [-M memory_in_MB] [-b algorithm_dependent_value] [-t keys_per_bin] [-d tmp_dir] [-m file.mph] keysfile\n", prg);   
 	fprintf(stderr, "Minimum perfect hashing tool\n\n"); 
 	fprintf(stderr, "  -h\t print this help message\n");
 	fprintf(stderr, "  -c\t c value determines:\n");
 	fprintf(stderr, "    \t   the number of vertices in the graph for the algorithms BMZ and CHM\n");
 	fprintf(stderr, "    \t   the number of bits per key required in the FCH algorithm\n");
+	fprintf(stderr, "    \t   the load factor in the CHD_PH algorithm\n");
 	fprintf(stderr, "  -a\t algorithm - valid values are\n");
 	for (i = 0; i < CMPH_COUNT; ++i) fprintf(stderr, "    \t  * %s\n", cmph_names[i]);
 	fprintf(stderr, "  -f\t hash function (may be used multiple times) - valid values are\n");
@@ -51,7 +52,12 @@ void usage_long(const char *prg)
 	fprintf(stderr, "    \t In this case its value should be an integer in the range [64,175].\n");
 	fprintf(stderr, "    \t If BDZ algorithm is selected in option -a, than it is used to\n");
 	fprintf(stderr, "    \t determine the size of some precomputed rank information and\n");
-	fprintf(stderr, "    \t its value should be an integer in the range [3,10]\n");
+	fprintf(stderr, "    \t its value should be an integer in the range [3,10].\n");
+	fprintf(stderr, "    \t If CHD_PH algorithm is selected in option -a, than it is used to\n");
+	fprintf(stderr, "    \t set average number of keys per bucket and its value should be an\n");
+	fprintf(stderr, "    \t an integer in the range [1,32].\n");
+	fprintf(stderr, "  -t\t set the number of keys per bin for a t-perfect hashing function.\n");	
+	fprintf(stderr, "    \t A t-perfect hashing function allows at most t collisions in a given bin.\n");
 	fprintf(stderr, "  keysfile\t line separated file with keys\n");
 }
 
@@ -75,10 +81,11 @@ int main(int argc, char **argv)
 	char * tmp_dir = NULL;
 	cmph_io_adapter_t *source;
 	cmph_uint32 memory_availability = 0;
-	cmph_uint32 b = 128;
+	cmph_uint32 b = 0;
+	cmph_uint32 keys_per_bin = 0;
 	while (1)
 	{
-		char ch = getopt(argc, argv, "hVvgc:k:a:M:b:f:m:d:s:");
+		char ch = getopt(argc, argv, "hVvgc:k:a:M:b:t:f:m:d:s:");
 		if (ch == -1) break;
 		switch (ch)
 		{
@@ -141,6 +148,16 @@ int main(int argc, char **argv)
 					}
 				}
 				break;
+			case 't':
+				{
+					char *cptr;
+					keys_per_bin = strtoul(optarg, &cptr, 10);
+					if(*cptr != 0) {
+						fprintf(stderr, "Parameter t was not found: %s\n", optarg);
+						exit(1);
+					}
+				}
+				break;
 			case 'v':
 				++verbosity;
 				break;
@@ -237,6 +254,8 @@ int main(int argc, char **argv)
 		cmph_config_set_mphf_fd(config, mphf_fd);
 		cmph_config_set_memory_availability(config, memory_availability);
 		cmph_config_set_b(config, b);
+		cmph_config_set_keys_per_bin(config, keys_per_bin);
+		
 		//if((mph_algo == CMPH_BMZ || mph_algo == CMPH_BRZ) && c >= 2.0) c=1.15;
 		if(mph_algo == CMPH_BMZ  && c >= 2.0) c=1.15;
 		if (c != 0) cmph_config_set_graphsize(config, c);

src/miller_rabin.c

@@ -0,0 +1,67 @@
+#include "miller_rabin.h"
+
+static inline cmph_uint64 int_pow(cmph_uint64 a, cmph_uint64 d, cmph_uint64 n)
+{
+	cmph_uint64 a_pow = a;
+	cmph_uint64 res = 1;
+	while(d > 0)
+	{
+		if((d & 1) == 1)
+			res =(((cmph_uint64)res) * a_pow) % n;
+		a_pow = (((cmph_uint64)a_pow) * a_pow) % n;
+		d /= 2;
+	};
+	return res;
+};
+
+static inline cmph_uint8 check_witness(cmph_uint64 a_exp_d, cmph_uint64 n, cmph_uint64 s)
+{
+	cmph_uint64 i;
+	cmph_uint64 a_exp = a_exp_d;
+	if(a_exp == 1 || a_exp == (n - 1))
+		return 1;
+	for(i = 1; i < s; i++)
+	{
+		a_exp = (((cmph_uint64)a_exp) * a_exp) % n;
+		if(a_exp == (n - 1))
+			return 1;
+	};
+	return 0;
+};
+
+cmph_uint8 check_primality(cmph_uint64 n)
+{
+	cmph_uint64 a, d, s, a_exp_d;
+	if((n % 2) == 0)
+		return 0;
+	if((n % 3) == 0)
+		return 0;
+	if((n % 5) == 0)
+		return 0;
+	if((n % 7 ) == 0)
+		return 0;
+	//we decompoe the number n - 1 into 2^s*d
+	s = 0;
+	d = n - 1;
+	do 
+	{
+		s++;
+		d /= 2;
+	}while((d % 2) == 0);
+
+	a = 2;
+	a_exp_d = int_pow(a, d, n);
+	if(check_witness(a_exp_d, n, s) == 0)
+		return 0;
+	a = 7;
+	a_exp_d = int_pow(a, d, n);
+	if(check_witness(a_exp_d, n, s) == 0)
+		return 0;
+	a = 61;
+	a_exp_d = int_pow(a, d, n);
+	if(check_witness(a_exp_d, n, s) == 0)
+		return 0;
+	return 1;
+};
+
+

src/miller_rabin.h

@@ -0,0 +1,5 @@
+#ifndef _CMPH_MILLER_RABIN_H__ 
+#define _CMPH_MILLER_RABIN_H__ 
+#include "cmph_types.h"
+cmph_uint8 check_primality(cmph_uint64 n);
+#endif

tests/packed_mphf_tests.c

@@ -164,7 +164,6 @@ int main(int argc, char **argv)
 		}
 		source->dispose(source->data, buf, buflen);
 	}
-	
 	free(packed_mphf);
 	cmph_destroy(mphf);	
 	free(hashtable);