stable version of BRZ using extenal memory to flush vector g
This commit is contained in:
parent
24dbad9bd3
commit
7352e08488
@ -16,8 +16,8 @@ libcmph_la_SOURCES = debug.h\
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cmph_structs.h cmph_structs.c\
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cmph_structs.h cmph_structs.c\
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chm.h chm_structs.h chm.c\
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chm.h chm_structs.h chm.c\
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bmz.h bmz_structs.h bmz.c\
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bmz.h bmz_structs.h bmz.c\
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bmz8.h bmz8_structs.h bmz8.c
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bmz8.h bmz8_structs.h bmz8.c\
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# brz.h brz_structs.h brz.c
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brz.h brz_structs.h brz.c
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libcmph_la_LDFLAGS = -version-info 0:0:0
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libcmph_la_LDFLAGS = -version-info 0:0:0
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@ -446,11 +446,8 @@ int bmz_dump(cmph_t *mphf, FILE *fd)
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{
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{
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint32 nbuflen;
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cmph_uint32 i;
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cmph_uint32 two = 2; //number of hash functions
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cmph_uint32 two = 2; //number of hash functions
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bmz_data_t *data = (bmz_data_t *)mphf->data;
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bmz_data_t *data = (bmz_data_t *)mphf->data;
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cmph_uint32 nn, nm;
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__cmph_dump(mphf, fd);
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__cmph_dump(mphf, fd);
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fwrite(&two, sizeof(cmph_uint32), 1, fd);
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fwrite(&two, sizeof(cmph_uint32), 1, fd);
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@ -453,10 +453,8 @@ int bmz8_dump(cmph_t *mphf, FILE *fd)
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{
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{
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint8 i;
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cmph_uint8 two = 2; //number of hash functions
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cmph_uint8 two = 2; //number of hash functions
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bmz8_data_t *data = (bmz8_data_t *)mphf->data;
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bmz8_data_t *data = (bmz8_data_t *)mphf->data;
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cmph_uint8 nn, nm;
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__cmph_dump(mphf, fd);
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__cmph_dump(mphf, fd);
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fwrite(&two, sizeof(cmph_uint8), 1, fd);
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fwrite(&two, sizeof(cmph_uint8), 1, fd);
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50
src/brz.c
50
src/brz.c
@ -1,4 +1,3 @@
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#include "graph.h"
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#include "graph.h"
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#include "bmz8.h"
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#include "bmz8.h"
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#include "bmz8_structs.h"
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#include "bmz8_structs.h"
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@ -23,7 +22,7 @@ static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n);
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static char * brz_read_key(FILE * fd);
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static char * brz_read_key(FILE * fd);
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static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys);
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static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys);
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static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source);
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static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source);
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static void brz_flush_g(brz_config_data_t *brz, cmph_uint32 *start_index, FILE * fd);
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brz_config_data_t *brz_config_new()
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brz_config_data_t *brz_config_new()
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{
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{
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brz_config_data_t *brz = NULL;
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brz_config_data_t *brz = NULL;
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@ -48,7 +47,6 @@ void brz_config_destroy(cmph_config_t *mph)
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{
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{
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brz_config_data_t *data = (brz_config_data_t *)mph->data;
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brz_config_data_t *data = (brz_config_data_t *)mph->data;
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DEBUGP("Destroying algorithm dependent data\n");
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DEBUGP("Destroying algorithm dependent data\n");
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free(data->tmp_dir);
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free(data);
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free(data);
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}
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}
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@ -81,12 +79,12 @@ void brz_config_set_tmp_dir(cmph_config_t *mph, cmph_uint8 *tmp_dir)
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if(tmp_dir[len-1] != '/')
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if(tmp_dir[len-1] != '/')
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{
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{
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brz->tmp_dir = calloc(len+2, sizeof(cmph_uint8));
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brz->tmp_dir = calloc(len+2, sizeof(cmph_uint8));
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sprintf(brz->tmp_dir, "%s/\0", tmp_dir);
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sprintf(brz->tmp_dir, "%s/", tmp_dir);
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}
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}
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else
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else
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{
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{
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brz->tmp_dir = calloc(len+1, sizeof(cmph_uint8));
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brz->tmp_dir = calloc(len+1, sizeof(cmph_uint8));
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sprintf(brz->tmp_dir, "%s\0", tmp_dir);
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sprintf(brz->tmp_dir, "%s", tmp_dir);
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}
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}
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}
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}
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@ -169,6 +167,8 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
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brz->size = NULL; //transfer memory ownership
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brz->size = NULL; //transfer memory ownership
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brzf->offset = brz->offset;
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brzf->offset = brz->offset;
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brz->offset = NULL; //transfer memory ownership
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brz->offset = NULL; //transfer memory ownership
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brzf->tmp_dir = brz->tmp_dir;
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brz->tmp_dir = NULL; //transfer memory ownership
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brzf->k = brz->k;
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brzf->k = brz->k;
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brzf->c = brz->c;
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brzf->c = brz->c;
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brzf->m = brz->m;
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brzf->m = brz->m;
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@ -204,6 +204,7 @@ static int brz_gen_graphs(cmph_config_t *mph)
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cmph_uint32 max_size = 0;
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cmph_uint32 max_size = 0;
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cmph_uint32 cur_bucket = 0;
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cmph_uint32 cur_bucket = 0;
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cmph_uint8 nkeys_vd = 0;
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cmph_uint8 nkeys_vd = 0;
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cmph_uint32 start_index = 0;
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char ** keys_vd = NULL;
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char ** keys_vd = NULL;
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@ -333,7 +334,11 @@ static int brz_gen_graphs(cmph_config_t *mph)
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tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *));
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tmp_fds = (FILE **)calloc(nflushes, sizeof(FILE *));
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buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *));
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buffer_merge = (cmph_uint8 **)calloc(nflushes, sizeof(cmph_uint8 *));
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buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32));
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buffer_h3 = (cmph_uint32 *)calloc(nflushes, sizeof(cmph_uint32));
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filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
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sprintf(filename, "%stmpg.cmph",brz->tmp_dir);
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tmp_fd = fopen(filename, "w");
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free(filename);
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memory_usage = 0;
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for(i = 0; i < nflushes; i++)
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for(i = 0; i < nflushes; i++)
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{
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{
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filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
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filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
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@ -406,6 +411,12 @@ static int brz_gen_graphs(cmph_config_t *mph)
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mphf_tmp = cmph_new(config);
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mphf_tmp = cmph_new(config);
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bmzf = (bmz8_data_t *)mphf_tmp->data;
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bmzf = (bmz8_data_t *)mphf_tmp->data;
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brz_copy_partial_mphf(brz, bmzf, cur_bucket, source);
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brz_copy_partial_mphf(brz, bmzf, cur_bucket, source);
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memory_usage += brz->size[cur_bucket];
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if((cur_bucket+1 == brz->k)||(memory_usage > brz->memory_availability))
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{
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brz_flush_g(brz, &start_index, tmp_fd);
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memory_usage = 0;
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}
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cmph_config_destroy(config);
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cmph_config_destroy(config);
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brz_destroy_keys_vd(keys_vd, nkeys_vd);
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brz_destroy_keys_vd(keys_vd, nkeys_vd);
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cmph_destroy(mphf_tmp);
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cmph_destroy(mphf_tmp);
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@ -413,6 +424,7 @@ static int brz_gen_graphs(cmph_config_t *mph)
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nkeys_vd = 0;
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nkeys_vd = 0;
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}
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}
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}
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}
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fclose(tmp_fd);
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for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
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for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
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free(tmp_fds);
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free(tmp_fds);
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free(keys_vd);
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free(keys_vd);
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@ -458,6 +470,17 @@ static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys)
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for(i = 0; i < nkeys; i++) free(keys_vd[i]);
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for(i = 0; i < nkeys; i++) free(keys_vd[i]);
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}
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}
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static void brz_flush_g(brz_config_data_t *brz, cmph_uint32 *start_index, FILE * fd)
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{
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while(*start_index < brz->k && brz->g[*start_index] != NULL)
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{
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fwrite(brz->g[*start_index], sizeof(cmph_uint8), brz->size[*start_index], fd);
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free(brz->g[*start_index]);
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brz->g[*start_index] = NULL;
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*start_index = *start_index + 1;
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}
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}
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static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source)
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static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source)
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{
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{
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cmph_uint32 i;
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cmph_uint32 i;
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@ -477,9 +500,14 @@ int brz_dump(cmph_t *mphf, FILE *fd)
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{
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{
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint32 nbuflen;
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cmph_uint32 i;
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cmph_uint32 i;
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brz_data_t *data = (brz_data_t *)mphf->data;
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brz_data_t *data = (brz_data_t *)mphf->data;
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FILE * tmpg_fd = NULL;
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char * filename = NULL;
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filename = (char *)calloc(strlen(data->tmp_dir) + 11, sizeof(char));
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sprintf(filename, "%stmpg.cmph",data->tmp_dir);
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tmpg_fd = fopen(filename, "rb");
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free(filename);
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DEBUGP("Dumping brzf\n");
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DEBUGP("Dumping brzf\n");
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__cmph_dump(mphf, fd);
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__cmph_dump(mphf, fd);
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@ -517,14 +545,17 @@ int brz_dump(cmph_t *mphf, FILE *fd)
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for(i = 0; i < data->k; i++)
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for(i = 0; i < data->k; i++)
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{
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{
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cmph_uint32 n = ceil(data->c * data->size[i]);
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cmph_uint32 n = ceil(data->c * data->size[i]);
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fwrite(data->g[i], sizeof(cmph_uint8)*n, 1, fd);
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buf = (char *)calloc(n, sizeof(cmph_uint8));
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fread(buf, sizeof(cmph_uint8), n, tmpg_fd);
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fwrite(buf, sizeof(cmph_uint8), n, fd);
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free(buf);
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}
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}
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fclose(tmpg_fd);
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return 1;
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return 1;
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}
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}
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void brz_load(FILE *f, cmph_t *mphf)
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void brz_load(FILE *f, cmph_t *mphf)
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{
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{
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cmph_uint32 nhashes;
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint32 i;
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cmph_uint32 i;
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@ -614,6 +645,7 @@ void brz_destroy(cmph_t *mphf)
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free(data->h2);
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free(data->h2);
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free(data->size);
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free(data->size);
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free(data->offset);
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free(data->offset);
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free(data->tmp_dir);
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free(data);
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free(data);
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free(mphf);
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free(mphf);
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}
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}
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@ -13,7 +13,8 @@ struct __brz_data_t
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cmph_uint32 k; // number of components
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cmph_uint32 k; // number of components
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hash_state_t **h1;
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hash_state_t **h1;
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hash_state_t **h2;
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hash_state_t **h2;
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hash_state_t * h3;
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hash_state_t * h3;
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cmph_uint8 * tmp_dir; // temporary directory
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};
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};
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struct __brz_config_data_t
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struct __brz_config_data_t
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@ -182,7 +182,7 @@ static int chm_gen_edges(cmph_config_t *mph)
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if (h1 == h2) if (++h2 >= chm->n) h2 = 0;
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if (h1 == h2) if (++h2 >= chm->n) h2 = 0;
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if (h1 == h2)
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if (h1 == h2)
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{
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{
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if (mph->verbosity) fprintf(stderr, "Self loop for key %e\n", e);
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if (mph->verbosity) fprintf(stderr, "Self loop for key %u\n", e);
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mph->key_source->dispose(mph->key_source->data, key, keylen);
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mph->key_source->dispose(mph->key_source->data, key, keylen);
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return 0;
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return 0;
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}
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}
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@ -201,7 +201,6 @@ int chm_dump(cmph_t *mphf, FILE *fd)
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{
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{
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint32 i;
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cmph_uint32 two = 2; //number of hash functions
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cmph_uint32 two = 2; //number of hash functions
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chm_data_t *data = (chm_data_t *)mphf->data;
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chm_data_t *data = (chm_data_t *)mphf->data;
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__cmph_dump(mphf, fd);
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__cmph_dump(mphf, fd);
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@ -234,11 +233,9 @@ int chm_dump(cmph_t *mphf, FILE *fd)
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void chm_load(FILE *f, cmph_t *mphf)
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void chm_load(FILE *f, cmph_t *mphf)
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{
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{
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cmph_uint32 nhashes;
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cmph_uint32 nhashes;
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char fbuf[BUFSIZ];
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char *buf = NULL;
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char *buf = NULL;
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cmph_uint32 buflen;
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cmph_uint32 buflen;
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cmph_uint32 i;
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cmph_uint32 i;
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hash_state_t *state;
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chm_data_t *chm = (chm_data_t *)malloc(sizeof(chm_data_t));
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chm_data_t *chm = (chm_data_t *)malloc(sizeof(chm_data_t));
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DEBUGP("Loading chm mphf\n");
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DEBUGP("Loading chm mphf\n");
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34
src/cmph.c
34
src/cmph.c
@ -3,11 +3,11 @@
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#include "chm.h"
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#include "chm.h"
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#include "bmz.h"
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#include "bmz.h"
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#include "bmz8.h" /* included -- Fabiano */
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#include "bmz8.h" /* included -- Fabiano */
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//#include "brz.h" /* included -- Fabiano */
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#include "brz.h" /* included -- Fabiano */
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#include <stdlib.h>
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#include <stdlib.h>
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#include <assert.h>
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#include <assert.h>
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#include <string.h>
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//#define DEBUG
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//#define DEBUG
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#include "debug.h"
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#include "debug.h"
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@ -159,7 +159,7 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
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bmz8_config_destroy(mph);
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bmz8_config_destroy(mph);
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break;
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break;
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case CMPH_BRZ:
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case CMPH_BRZ:
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// brz_config_destroy(mph);
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brz_config_destroy(mph);
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break;
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break;
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default:
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default:
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assert(0);
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assert(0);
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@ -176,7 +176,7 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
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mph->data = bmz8_config_new();
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mph->data = bmz8_config_new();
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break;
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break;
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case CMPH_BRZ:
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case CMPH_BRZ:
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// mph->data = brz_config_new();
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mph->data = brz_config_new();
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break;
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break;
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default:
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default:
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assert(0);
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assert(0);
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@ -196,7 +196,7 @@ void cmph_config_set_tmp_dir(cmph_config_t *mph, cmph_uint8 *tmp_dir)
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case CMPH_BMZ8: /* included -- Fabiano */
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case CMPH_BMZ8: /* included -- Fabiano */
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break;
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break;
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case CMPH_BRZ: /* included -- Fabiano */
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case CMPH_BRZ: /* included -- Fabiano */
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// brz_config_set_tmp_dir(mph, tmp_dir);
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brz_config_set_tmp_dir(mph, tmp_dir);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
@ -215,7 +215,7 @@ void cmph_config_set_memory_availability(cmph_config_t *mph, cmph_uint32 memory_
|
|||||||
case CMPH_BMZ8: /* included -- Fabiano */
|
case CMPH_BMZ8: /* included -- Fabiano */
|
||||||
break;
|
break;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
// brz_config_set_memory_availability(mph, memory_availability);
|
brz_config_set_memory_availability(mph, memory_availability);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
@ -238,7 +238,7 @@ void cmph_config_destroy(cmph_config_t *mph)
|
|||||||
bmz8_config_destroy(mph);
|
bmz8_config_destroy(mph);
|
||||||
break;
|
break;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
// brz_config_destroy(mph);
|
brz_config_destroy(mph);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
@ -265,7 +265,7 @@ void cmph_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs)
|
|||||||
bmz8_config_set_hashfuncs(mph, hashfuncs);
|
bmz8_config_set_hashfuncs(mph, hashfuncs);
|
||||||
break;
|
break;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
// brz_config_set_hashfuncs(mph, hashfuncs);
|
brz_config_set_hashfuncs(mph, hashfuncs);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
break;
|
break;
|
||||||
@ -302,9 +302,9 @@ cmph_t *cmph_new(cmph_config_t *mph)
|
|||||||
mphf = bmz8_new(mph, c);
|
mphf = bmz8_new(mph, c);
|
||||||
break;
|
break;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
/* DEBUGP("Creating brz hash\n");
|
DEBUGP("Creating brz hash\n");
|
||||||
if (c == 0) c = 1.15;
|
if (c == 0) c = 1.15;
|
||||||
mphf = brz_new(mph, c);*/
|
mphf = brz_new(mph, c);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
@ -323,8 +323,7 @@ int cmph_dump(cmph_t *mphf, FILE *f)
|
|||||||
case CMPH_BMZ8: /* included -- Fabiano */
|
case CMPH_BMZ8: /* included -- Fabiano */
|
||||||
return bmz8_dump(mphf, f);
|
return bmz8_dump(mphf, f);
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
break;
|
return brz_dump(mphf, f);
|
||||||
/* return brz_dump(mphf, f);*/
|
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
}
|
}
|
||||||
@ -353,8 +352,8 @@ cmph_t *cmph_load(FILE *f)
|
|||||||
bmz8_load(f, mphf);
|
bmz8_load(f, mphf);
|
||||||
break;
|
break;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
/* DEBUGP("Loading brz algorithm dependent parts\n");
|
DEBUGP("Loading brz algorithm dependent parts\n");
|
||||||
brz_load(f, mphf);*/
|
brz_load(f, mphf);
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
@ -378,9 +377,8 @@ cmph_uint32 cmph_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
|
|||||||
DEBUGP("bmz8 algorithm search\n");
|
DEBUGP("bmz8 algorithm search\n");
|
||||||
return bmz8_search(mphf, key, keylen);
|
return bmz8_search(mphf, key, keylen);
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
break;
|
DEBUGP("brz algorithm search\n");
|
||||||
/* DEBUGP("brz algorithm search\n");
|
return brz_search(mphf, key, keylen);
|
||||||
return brz_search(mphf, key, keylen);*/
|
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
}
|
}
|
||||||
@ -407,7 +405,7 @@ void cmph_destroy(cmph_t *mphf)
|
|||||||
bmz8_destroy(mphf);
|
bmz8_destroy(mphf);
|
||||||
return;
|
return;
|
||||||
case CMPH_BRZ: /* included -- Fabiano */
|
case CMPH_BRZ: /* included -- Fabiano */
|
||||||
/* brz_destroy(mphf);*/
|
brz_destroy(mphf);
|
||||||
return;
|
return;
|
||||||
default:
|
default:
|
||||||
assert(0);
|
assert(0);
|
||||||
|
@ -143,7 +143,7 @@ int main(int argc, char **argv)
|
|||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
if (!valid || mph_algo == CMPH_BRZ)
|
if (!valid)
|
||||||
{
|
{
|
||||||
fprintf(stderr, "Invalid mph algorithm: %s. It is not available in version %s\n", optarg, VERSION);
|
fprintf(stderr, "Invalid mph algorithm: %s. It is not available in version %s\n", optarg, VERSION);
|
||||||
return -1;
|
return -1;
|
||||||
|
Loading…
Reference in New Issue
Block a user