Stable version of BRZ algorithm
This commit is contained in:
fc_botelho
parent
3181ab91f2
commit
d2aeaae27c
52
INSTALL
52
INSTALL
|
|
@ -1,13 +1,16 @@
|
|||
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
|
||||
Foundation, Inc.
|
||||
Installation Instructions
|
||||
*************************
|
||||
|
||||
This file is free documentation; the Free Software Foundation gives
|
||||
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004 Free
|
||||
Software Foundation, Inc.
|
||||
|
||||
This file is free documentation; the Free Software Foundation gives
|
||||
unlimited permission to copy, distribute and modify it.
|
||||
|
||||
Basic Installation
|
||||
==================
|
||||
|
||||
These are generic installation instructions.
|
||||
These are generic installation instructions.
|
||||
|
||||
The `configure' shell script attempts to guess correct values for
|
||||
various system-dependent variables used during compilation. It uses
|
||||
|
|
@ -67,9 +70,9 @@ The simplest way to compile this package is:
|
|||
Compilers and Options
|
||||
=====================
|
||||
|
||||
Some systems require unusual options for compilation or linking that
|
||||
the `configure' script does not know about. Run `./configure --help'
|
||||
for details on some of the pertinent environment variables.
|
||||
Some systems require unusual options for compilation or linking that the
|
||||
`configure' script does not know about. Run `./configure --help' for
|
||||
details on some of the pertinent environment variables.
|
||||
|
||||
You can give `configure' initial values for configuration parameters
|
||||
by setting variables in the command line or in the environment. Here
|
||||
|
|
@ -82,7 +85,7 @@ is an example:
|
|||
Compiling For Multiple Architectures
|
||||
====================================
|
||||
|
||||
You can compile the package for more than one kind of computer at the
|
||||
You can compile the package for more than one kind of computer at the
|
||||
same time, by placing the object files for each architecture in their
|
||||
own directory. To do this, you must use a version of `make' that
|
||||
supports the `VPATH' variable, such as GNU `make'. `cd' to the
|
||||
|
|
@ -99,19 +102,19 @@ for another architecture.
|
|||
Installation Names
|
||||
==================
|
||||
|
||||
By default, `make install' will install the package's files in
|
||||
By default, `make install' will install the package's files in
|
||||
`/usr/local/bin', `/usr/local/man', etc. You can specify an
|
||||
installation prefix other than `/usr/local' by giving `configure' the
|
||||
option `--prefix=PATH'.
|
||||
option `--prefix=PREFIX'.
|
||||
|
||||
You can specify separate installation prefixes for
|
||||
architecture-specific files and architecture-independent files. If you
|
||||
give `configure' the option `--exec-prefix=PATH', the package will use
|
||||
PATH as the prefix for installing programs and libraries.
|
||||
give `configure' the option `--exec-prefix=PREFIX', the package will
|
||||
use PREFIX as the prefix for installing programs and libraries.
|
||||
Documentation and other data files will still use the regular prefix.
|
||||
|
||||
In addition, if you use an unusual directory layout you can give
|
||||
options like `--bindir=PATH' to specify different values for particular
|
||||
options like `--bindir=DIR' to specify different values for particular
|
||||
kinds of files. Run `configure --help' for a list of the directories
|
||||
you can set and what kinds of files go in them.
|
||||
|
||||
|
|
@ -122,7 +125,7 @@ option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
|
|||
Optional Features
|
||||
=================
|
||||
|
||||
Some packages pay attention to `--enable-FEATURE' options to
|
||||
Some packages pay attention to `--enable-FEATURE' options to
|
||||
`configure', where FEATURE indicates an optional part of the package.
|
||||
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
|
||||
is something like `gnu-as' or `x' (for the X Window System). The
|
||||
|
|
@ -137,11 +140,11 @@ you can use the `configure' options `--x-includes=DIR' and
|
|||
Specifying the System Type
|
||||
==========================
|
||||
|
||||
There may be some features `configure' cannot figure out
|
||||
automatically, but needs to determine by the type of machine the package
|
||||
will run on. Usually, assuming the package is built to be run on the
|
||||
_same_ architectures, `configure' can figure that out, but if it prints
|
||||
a message saying it cannot guess the machine type, give it the
|
||||
There may be some features `configure' cannot figure out automatically,
|
||||
but needs to determine by the type of machine the package will run on.
|
||||
Usually, assuming the package is built to be run on the _same_
|
||||
architectures, `configure' can figure that out, but if it prints a
|
||||
message saying it cannot guess the machine type, give it the
|
||||
`--build=TYPE' option. TYPE can either be a short name for the system
|
||||
type, such as `sun4', or a canonical name which has the form:
|
||||
|
||||
|
|
@ -167,9 +170,9 @@ eventually be run) with `--host=TYPE'.
|
|||
Sharing Defaults
|
||||
================
|
||||
|
||||
If you want to set default values for `configure' scripts to share,
|
||||
you can create a site shell script called `config.site' that gives
|
||||
default values for variables like `CC', `cache_file', and `prefix'.
|
||||
If you want to set default values for `configure' scripts to share, you
|
||||
can create a site shell script called `config.site' that gives default
|
||||
values for variables like `CC', `cache_file', and `prefix'.
|
||||
`configure' looks for `PREFIX/share/config.site' if it exists, then
|
||||
`PREFIX/etc/config.site' if it exists. Or, you can set the
|
||||
`CONFIG_SITE' environment variable to the location of the site script.
|
||||
|
|
@ -178,7 +181,7 @@ A warning: not all `configure' scripts look for a site script.
|
|||
Defining Variables
|
||||
==================
|
||||
|
||||
Variables not defined in a site shell script can be set in the
|
||||
Variables not defined in a site shell script can be set in the
|
||||
environment passed to `configure'. However, some packages may run
|
||||
configure again during the build, and the customized values of these
|
||||
variables may be lost. In order to avoid this problem, you should set
|
||||
|
|
@ -192,8 +195,7 @@ overridden in the site shell script).
|
|||
`configure' Invocation
|
||||
======================
|
||||
|
||||
`configure' recognizes the following options to control how it
|
||||
operates.
|
||||
`configure' recognizes the following options to control how it operates.
|
||||
|
||||
`--help'
|
||||
`-h'
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
file_adapter_ex2.o file_adapter_ex2.o: file_adapter_ex2.c ../src/cmph.h \
|
||||
/usr/include/stdlib.h /usr/include/features.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/gnu/stubs.h \
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stddef.h \
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stddef.h \
|
||||
/usr/include/sys/types.h /usr/include/bits/types.h \
|
||||
/usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \
|
||||
/usr/include/time.h /usr/include/endian.h /usr/include/bits/endian.h \
|
||||
|
|
@ -11,7 +11,7 @@ file_adapter_ex2.o file_adapter_ex2.o: file_adapter_ex2.c ../src/cmph.h \
|
|||
/usr/include/bits/sched.h /usr/include/alloca.h /usr/include/stdio.h \
|
||||
/usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
|
||||
/usr/include/bits/wchar.h /usr/include/gconv.h \
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stdarg.h \
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stdarg.h \
|
||||
/usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
|
||||
/usr/include/bits/stdio.h ../src/cmph_types.h
|
||||
|
||||
|
|
@ -25,7 +25,7 @@ file_adapter_ex2.o file_adapter_ex2.o: file_adapter_ex2.c ../src/cmph.h \
|
|||
|
||||
/usr/include/gnu/stubs.h:
|
||||
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stddef.h:
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stddef.h:
|
||||
|
||||
/usr/include/sys/types.h:
|
||||
|
||||
|
|
@ -69,7 +69,7 @@ file_adapter_ex2.o file_adapter_ex2.o: file_adapter_ex2.c ../src/cmph.h \
|
|||
|
||||
/usr/include/gconv.h:
|
||||
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stdarg.h:
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stdarg.h:
|
||||
|
||||
/usr/include/bits/stdio_lim.h:
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
vector_adapter_ex1.o vector_adapter_ex1.o: vector_adapter_ex1.c \
|
||||
../src/cmph.h /usr/include/stdlib.h /usr/include/features.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stddef.h \
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stddef.h \
|
||||
/usr/include/sys/types.h /usr/include/bits/types.h \
|
||||
/usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \
|
||||
/usr/include/time.h /usr/include/endian.h /usr/include/bits/endian.h \
|
||||
|
|
@ -11,7 +11,7 @@ vector_adapter_ex1.o vector_adapter_ex1.o: vector_adapter_ex1.c \
|
|||
/usr/include/bits/sched.h /usr/include/alloca.h /usr/include/stdio.h \
|
||||
/usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
|
||||
/usr/include/bits/wchar.h /usr/include/gconv.h \
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stdarg.h \
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stdarg.h \
|
||||
/usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
|
||||
/usr/include/bits/stdio.h ../src/cmph_types.h
|
||||
|
||||
|
|
@ -25,7 +25,7 @@ vector_adapter_ex1.o vector_adapter_ex1.o: vector_adapter_ex1.c \
|
|||
|
||||
/usr/include/gnu/stubs.h:
|
||||
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stddef.h:
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stddef.h:
|
||||
|
||||
/usr/include/sys/types.h:
|
||||
|
||||
|
|
@ -69,7 +69,7 @@ vector_adapter_ex1.o vector_adapter_ex1.o: vector_adapter_ex1.c \
|
|||
|
||||
/usr/include/gconv.h:
|
||||
|
||||
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/include/stdarg.h:
|
||||
/usr/lib/gcc/i386-redhat-linux/3.4.2/include/stdarg.h:
|
||||
|
||||
/usr/include/bits/stdio_lim.h:
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
# Makefile.in generated by automake 1.9.1 from Makefile.am.
|
||||
# Makefile.in generated by automake 1.9.2 from Makefile.am.
|
||||
# examples/Makefile. Generated from Makefile.in by configure.
|
||||
|
||||
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
|
||||
|
|
@ -36,8 +36,8 @@ POST_INSTALL = :
|
|||
NORMAL_UNINSTALL = :
|
||||
PRE_UNINSTALL = :
|
||||
POST_UNINSTALL = :
|
||||
build_triplet = i686-suse-linux
|
||||
host_triplet = i686-suse-linux
|
||||
build_triplet = i686-pc-linux-gnu
|
||||
host_triplet = i686-pc-linux-gnu
|
||||
noinst_PROGRAMS = vector_adapter_ex1$(EXEEXT) \
|
||||
file_adapter_ex2$(EXEEXT)
|
||||
subdir = examples
|
||||
|
|
@ -74,14 +74,14 @@ DIST_SOURCES = $(file_adapter_ex2_SOURCES) \
|
|||
ETAGS = etags
|
||||
CTAGS = ctags
|
||||
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
|
||||
ACLOCAL = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run aclocal-1.9
|
||||
ACLOCAL = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run aclocal-1.9
|
||||
AMDEP_FALSE = #
|
||||
AMDEP_TRUE =
|
||||
AMTAR = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run tar
|
||||
AMTAR = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run tar
|
||||
AR = ar
|
||||
AUTOCONF = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run autoconf
|
||||
AUTOHEADER = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run autoheader
|
||||
AUTOMAKE = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run automake-1.9
|
||||
AUTOCONF = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run autoconf
|
||||
AUTOHEADER = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run autoheader
|
||||
AUTOMAKE = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run automake-1.9
|
||||
AWK = gawk
|
||||
CC = gcc
|
||||
CCDEPMODE = depmode=gcc3
|
||||
|
|
@ -89,9 +89,9 @@ CFLAGS = -g -O2 -D_FILE_OFFSET_BITS=64
|
|||
CPP = gcc -E
|
||||
CPPFLAGS =
|
||||
CXX = g++
|
||||
CXXCPP = /lib/cpp
|
||||
CXXDEPMODE = depmode=none
|
||||
CXXFLAGS =
|
||||
CXXCPP = g++ -E
|
||||
CXXDEPMODE = depmode=gcc3
|
||||
CXXFLAGS = -g -O2
|
||||
CYGPATH_W = echo
|
||||
DEFS = -DHAVE_CONFIG_H
|
||||
DEPDIR = .deps
|
||||
|
|
@ -101,8 +101,8 @@ ECHO_N = -n
|
|||
ECHO_T =
|
||||
EGREP = grep -E
|
||||
EXEEXT =
|
||||
F77 =
|
||||
FFLAGS =
|
||||
F77 = g77
|
||||
FFLAGS = -g -O2
|
||||
GETCONF = getconf
|
||||
INSTALL_DATA = ${INSTALL} -m 644
|
||||
INSTALL_PROGRAM = ${INSTALL}
|
||||
|
|
@ -114,7 +114,7 @@ LIBS =
|
|||
LIBTOOL = $(SHELL) $(top_builddir)/libtool
|
||||
LN_S = ln -s
|
||||
LTLIBOBJS =
|
||||
MAKEINFO = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/cmph/missing --run makeinfo
|
||||
MAKEINFO = ${SHELL} /home/fbotelho/doutorado/algoritmos/cmph/missing --run makeinfo
|
||||
OBJEXT = o
|
||||
PACKAGE = cmph
|
||||
PACKAGE_BUGREPORT =
|
||||
|
|
@ -131,35 +131,35 @@ VERSION = 0.3
|
|||
ac_ct_AR = ar
|
||||
ac_ct_CC = gcc
|
||||
ac_ct_CXX = g++
|
||||
ac_ct_F77 =
|
||||
ac_ct_F77 = g77
|
||||
ac_ct_GETCONF = getconf
|
||||
ac_ct_RANLIB = ranlib
|
||||
ac_ct_STRIP = strip
|
||||
am__fastdepCC_FALSE = #
|
||||
am__fastdepCC_TRUE =
|
||||
am__fastdepCXX_FALSE =
|
||||
am__fastdepCXX_TRUE = #
|
||||
am__fastdepCXX_FALSE = #
|
||||
am__fastdepCXX_TRUE =
|
||||
am__include = include
|
||||
am__leading_dot = .
|
||||
am__quote =
|
||||
am__tar = ${AMTAR} chof - "$$tardir"
|
||||
am__untar = ${AMTAR} xf -
|
||||
bindir = ${exec_prefix}/bin
|
||||
build = i686-suse-linux
|
||||
build = i686-pc-linux-gnu
|
||||
build_alias =
|
||||
build_cpu = i686
|
||||
build_os = linux
|
||||
build_vendor = suse
|
||||
build_os = linux-gnu
|
||||
build_vendor = pc
|
||||
datadir = ${prefix}/share
|
||||
exec_prefix = ${prefix}
|
||||
host = i686-suse-linux
|
||||
host = i686-pc-linux-gnu
|
||||
host_alias =
|
||||
host_cpu = i686
|
||||
host_os = linux
|
||||
host_vendor = suse
|
||||
host_os = linux-gnu
|
||||
host_vendor = pc
|
||||
includedir = ${prefix}/include
|
||||
infodir = ${prefix}/info
|
||||
install_sh = /home/fbotelho/doutorado/algoritmos/cmph/cmph/install-sh
|
||||
install_sh = /home/fbotelho/doutorado/algoritmos/cmph/install-sh
|
||||
libdir = ${exec_prefix}/lib
|
||||
libexecdir = ${exec_prefix}/libexec
|
||||
localstatedir = ${prefix}/var
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
# Makefile.in generated by automake 1.9.1 from Makefile.am.
|
||||
# Makefile.in generated by automake 1.9.2 from Makefile.am.
|
||||
# @configure_input@
|
||||
|
||||
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
|
||||
|
|
|
|||
|
|
@ -15,13 +15,6 @@
|
|||
//#define DEBUG
|
||||
#include "debug.h"
|
||||
|
||||
//static cmph_uint32 UNDEFINED = UINT_MAX;
|
||||
|
||||
/* static const char bitmask[8] = { 1, 1 << 1, 1 << 2, 1 << 3, 1 << 4, 1 << 5, 1 << 6, 1 << 7 }; */
|
||||
/* #define GETBIT(array, i) (array[(i) / 8] & bitmask[(i) % 8]) */
|
||||
/* #define SETBIT(array, i) (array[(i) / 8] |= bitmask[(i) % 8]) */
|
||||
/* #define UNSETBIT(array, i) (array[(i) / 8] &= (~(bitmask[(i) % 8]))) */
|
||||
|
||||
static int bmz_gen_edges(cmph_config_t *mph);
|
||||
static cmph_uint8 bmz_traverse_critical_nodes(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited);
|
||||
static cmph_uint8 bmz_traverse_critical_nodes_heuristic(bmz_config_data_t *bmz, cmph_uint32 v, cmph_uint32 * biggest_g_value, cmph_uint32 * biggest_edge_value, cmph_uint8 * used_edges, cmph_uint8 * visited);
|
||||
|
|
@ -535,7 +528,7 @@ cmph_uint32 bmz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
|
|||
DEBUGP("key: %s h1: %u h2: %u\n", key, h1, h2);
|
||||
if (h1 == h2 && ++h2 > bmz->n) h2 = 0;
|
||||
DEBUGP("key: %s g[h1]: %u g[h2]: %u edges: %u\n", key, bmz->g[h1], bmz->g[h2], bmz->m);
|
||||
return (bmz->g[h1] + bmz->g[h2]);
|
||||
return bmz->g[h1] + bmz->g[h2];
|
||||
}
|
||||
void bmz_destroy(cmph_t *mphf)
|
||||
{
|
||||
|
|
|
|||
|
|
@ -375,9 +375,10 @@ static void bmz8_traverse(bmz8_config_data_t *bmz8, cmph_uint8 * used_edges, cmp
|
|||
while((neighbor = graph_next_neighbor(bmz8->graph, &it)) != GRAPH_NO_NEIGHBOR)
|
||||
{
|
||||
if(GETBIT(visited,neighbor)) continue;
|
||||
DEBUGP("Visiting neighbor %u\n", neighbor);
|
||||
//DEBUGP("Visiting neighbor %u\n", neighbor);
|
||||
*unused_edge_index = next_unused_edge(bmz8, used_edges, *unused_edge_index);
|
||||
bmz8->g[neighbor] = *unused_edge_index - bmz8->g[v];
|
||||
//if (bmz8->g[neighbor] >= bmz8->m) bmz8->g[neighbor] += bmz8->m;
|
||||
SETBIT(visited, neighbor);
|
||||
(*unused_edge_index)++;
|
||||
bmz8_traverse(bmz8, used_edges, neighbor, unused_edge_index, visited);
|
||||
|
|
@ -437,7 +438,7 @@ static int bmz8_gen_edges(cmph_config_t *mph)
|
|||
mph->key_source->dispose(mph->key_source->data, key, keylen);
|
||||
return 0;
|
||||
}
|
||||
DEBUGP("Adding edge: %u -> %u for key %s\n", h1, h2, key);
|
||||
//DEBUGP("Adding edge: %u -> %u for key %s\n", h1, h2, key);
|
||||
mph->key_source->dispose(mph->key_source->data, key, keylen);
|
||||
// fprintf(stderr, "key = %s -- dispose BMZ\n", key);
|
||||
multiple_edges = graph_contains_edge(bmz8->graph, h1, h2);
|
||||
|
|
|
|||
131
src/brz.c
131
src/brz.c
|
|
@ -1,7 +1,7 @@
|
|||
|
||||
#include "graph.h"
|
||||
#include "bmz.h"
|
||||
#include "bmz_structs.h"
|
||||
#include "bmz8.h"
|
||||
#include "bmz8_structs.h"
|
||||
#include "brz.h"
|
||||
#include "cmph_structs.h"
|
||||
#include "brz_structs.h"
|
||||
|
|
@ -22,7 +22,7 @@ static int brz_gen_graphs(cmph_config_t *mph);
|
|||
static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n);
|
||||
static char * brz_read_key(FILE * fd);
|
||||
static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys);
|
||||
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source);
|
||||
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source);
|
||||
|
||||
brz_config_data_t *brz_config_new()
|
||||
{
|
||||
|
|
@ -37,6 +37,7 @@ brz_config_data_t *brz_config_new()
|
|||
brz->h1 = NULL;
|
||||
brz->h2 = NULL;
|
||||
brz->h3 = NULL;
|
||||
brz->memory_availability = 1024*1024;
|
||||
brz->tmp_dir = (cmph_uint8 *)calloc(10, sizeof(cmph_uint8));
|
||||
strcpy(brz->tmp_dir, "/var/tmp/\0");
|
||||
assert(brz);
|
||||
|
|
@ -64,6 +65,12 @@ void brz_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs)
|
|||
}
|
||||
}
|
||||
|
||||
void brz_config_set_memory_availability(cmph_config_t *mph, cmph_uint32 memory_availability)
|
||||
{
|
||||
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
|
||||
brz->memory_availability = memory_availability*1024*1024;
|
||||
}
|
||||
|
||||
void brz_config_set_tmp_dir(cmph_config_t *mph, cmph_uint8 *tmp_dir)
|
||||
{
|
||||
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
|
||||
|
|
@ -84,73 +91,6 @@ void brz_config_set_tmp_dir(cmph_config_t *mph, cmph_uint8 *tmp_dir)
|
|||
|
||||
}
|
||||
}
|
||||
// static cmph_uint8 brz_verify_mphf(cmph_t * mphf, cmph_io_adapter_t *source)
|
||||
// {
|
||||
// cmph_uint8 * hashtable = NULL;
|
||||
// cmph_uint32 i;
|
||||
// hashtable = (cmph_uint8*)malloc(source->nkeys*sizeof(cmph_uint8));
|
||||
// source->rewind(source->data);
|
||||
// memset(hashtable, 0, source->nkeys);
|
||||
// //check all keys
|
||||
// for (i = 0; i < source->nkeys; ++i)
|
||||
// {
|
||||
// cmph_uint32 h;
|
||||
// char *buf;
|
||||
// cmph_uint32 buflen = 0;
|
||||
// source->read(source->data, &buf, &buflen);
|
||||
// h = cmph_search(mphf, buf, buflen);
|
||||
// if(hashtable[h])
|
||||
// {
|
||||
// fprintf(stderr, "collision: %u\n",h);
|
||||
// return 0;
|
||||
// }
|
||||
// //assert(hashtable[h]==0);
|
||||
// hashtable[h] = 1;
|
||||
// source->dispose(source->data, buf, buflen);
|
||||
// }
|
||||
// fprintf(stderr, "\n===============================================================================\n");
|
||||
// free(hashtable);
|
||||
// return 1;
|
||||
// }
|
||||
//
|
||||
// static cmph_uint8 brz_verify_mphf1(hash_state_t *h1, hash_state_t *h2, cmph_uint8 * g, cmph_uint32 n, cmph_io_adapter_t *source)
|
||||
// {
|
||||
// cmph_uint8 * hashtable = NULL;
|
||||
// cmph_uint32 i;
|
||||
// hashtable = (cmph_uint8*)calloc(source->nkeys, sizeof(cmph_uint8));
|
||||
// source->rewind(source->data);
|
||||
// //memset(hashtable, 0, source->nkeys);
|
||||
// //check all keys
|
||||
// for (i = 0; i < source->nkeys; ++i)
|
||||
// {
|
||||
// cmph_uint32 h1_v;
|
||||
// cmph_uint32 h2_v;
|
||||
// cmph_uint32 h;
|
||||
// char *buf;
|
||||
// cmph_uint32 buflen = 0;
|
||||
// source->read(source->data, &buf, &buflen);
|
||||
//
|
||||
// h1_v = hash(h1, buf, buflen) % n;
|
||||
//
|
||||
// h2_v = hash(h2, buf, buflen) % n;
|
||||
//
|
||||
// if (h1_v == h2_v && ++h2_v >= n) h2_v = 0;
|
||||
//
|
||||
// h = ((cmph_uint32)g[h1_v] + (cmph_uint32)g[h2_v]) % source->nkeys;
|
||||
//
|
||||
// if(hashtable[h])
|
||||
// {
|
||||
// fprintf(stderr, "collision: %u\n",h);
|
||||
// return 0;
|
||||
// }
|
||||
// //assert(hashtable[h]==0);
|
||||
// hashtable[h] = 1;
|
||||
// source->dispose(source->data, buf, buflen);
|
||||
//
|
||||
// }
|
||||
// free(hashtable);
|
||||
// return 1;
|
||||
// }
|
||||
|
||||
cmph_t *brz_new(cmph_config_t *mph, float c)
|
||||
{
|
||||
|
|
@ -244,13 +184,12 @@ cmph_t *brz_new(cmph_config_t *mph, float c)
|
|||
|
||||
static int brz_gen_graphs(cmph_config_t *mph)
|
||||
{
|
||||
#pragma pack(1)
|
||||
cmph_uint32 i, e;
|
||||
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
|
||||
cmph_uint32 memory_availability = 209715200;//200MB //104857600;//100MB //524288000; // 500MB //209715200; // 200 MB
|
||||
//cmph_uint32 memory_availability = 200*1024*1024;
|
||||
cmph_uint32 memory_usage = 0;
|
||||
cmph_uint32 nkeys_in_buffer = 0;
|
||||
cmph_uint8 *buffer = (cmph_uint8 *)malloc(memory_availability);
|
||||
cmph_uint8 *buffer = (cmph_uint8 *)malloc(brz->memory_availability);
|
||||
cmph_uint32 *buckets_size = (cmph_uint32 *)calloc(brz->k, sizeof(cmph_uint32));
|
||||
cmph_uint32 *keys_index = NULL;
|
||||
cmph_uint8 **buffer_merge = NULL;
|
||||
|
|
@ -276,7 +215,7 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
mph->key_source->read(mph->key_source->data, &key, &keylen);
|
||||
|
||||
/* Buffers management */
|
||||
if (memory_usage + keylen + 1 > memory_availability) // flush buffers
|
||||
if (memory_usage + keylen + 1 > brz->memory_availability) // flush buffers
|
||||
{
|
||||
if(mph->verbosity)
|
||||
{
|
||||
|
|
@ -305,7 +244,6 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
buckets_size[h3]++;
|
||||
memory_usage = memory_usage + keylen1 + 1;
|
||||
}
|
||||
// sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
|
||||
filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
|
||||
sprintf(filename, "%s%u.cmph",brz->tmp_dir, nflushes);
|
||||
tmp_fd = fopen(filename, "wb");
|
||||
|
|
@ -323,11 +261,10 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
free(keys_index);
|
||||
fclose(tmp_fd);
|
||||
}
|
||||
//fprintf(stderr, "Storing read Key\n");
|
||||
memcpy(buffer + memory_usage, key, keylen + 1);
|
||||
memory_usage = memory_usage + keylen + 1;
|
||||
h3 = hash(brz->h3, key, keylen) % brz->k;
|
||||
if (brz->size[h3] == MAX_BUCKET_SIZE)
|
||||
if ((brz->size[h3] == MAX_BUCKET_SIZE) || ((brz->c >= 1.0) && (cmph_uint8)(brz->c * brz->size[h3]) < brz->size[h3]))
|
||||
{
|
||||
free(buffer);
|
||||
free(buckets_size);
|
||||
|
|
@ -367,8 +304,6 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
buckets_size[h3]++;
|
||||
memory_usage = memory_usage + keylen1 + 1;
|
||||
}
|
||||
// sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",nflushes);
|
||||
// sprintf(filename, "/mnt/sd2/fbotelho/dados/%u.cmph",nflushes);
|
||||
filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
|
||||
sprintf(filename, "%s%u.cmph",brz->tmp_dir, nflushes);
|
||||
tmp_fd = fopen(filename, "wb");
|
||||
|
|
@ -401,8 +336,6 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
|
||||
for(i = 0; i < nflushes; i++)
|
||||
{
|
||||
// sprintf(filename, "/mnt/hd4/fbotelho/%u.cmph",i);
|
||||
// sprintf(filename, "/mnt/sd2/fbotelho/dados/%u.cmph",i);
|
||||
filename = (char *)calloc(strlen(brz->tmp_dir) + 11, sizeof(char));
|
||||
sprintf(filename, "%s%u.cmph",brz->tmp_dir, i);
|
||||
tmp_fds[i] = fopen(filename, "rb");
|
||||
|
|
@ -420,7 +353,6 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
e = 0;
|
||||
keys_vd = (char **)calloc(MAX_BUCKET_SIZE, sizeof(char *));
|
||||
nkeys_vd = 0;
|
||||
//buffer = (cmph_uint8 *)malloc(memory_availability);
|
||||
while(e < brz->m)
|
||||
{
|
||||
i = brz_min_index(buffer_h3, nflushes);
|
||||
|
|
@ -436,56 +368,43 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
if (h3 != buffer_h3[i]) break;
|
||||
|
||||
keys_vd[nkeys_vd++] = key;
|
||||
|
||||
//save_in_disk(buffer, key, keylen, &memory_usage, memory_availability, graphs_fd);
|
||||
//fwrite(key, 1, keylen + 1, graphs_fd);
|
||||
e++;
|
||||
//free(key);
|
||||
key = brz_read_key(tmp_fds[i]);
|
||||
}
|
||||
if (key)
|
||||
{
|
||||
//save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
|
||||
assert(nkeys_vd < brz->size[cur_bucket]);
|
||||
keys_vd[nkeys_vd++] = buffer_merge[i];
|
||||
//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
|
||||
e++;
|
||||
buffer_h3[i] = h3;
|
||||
//free(buffer_merge[i]);
|
||||
buffer_merge[i] = (cmph_uint8 *)calloc(keylen + 1, sizeof(cmph_uint8));
|
||||
memcpy(buffer_merge[i], key, keylen + 1);
|
||||
free(key);
|
||||
}
|
||||
}
|
||||
/* fprintf(stderr, "BOSTA %u %u e: %u\n", i, buffer_h3[i], e);*/
|
||||
if(!key)
|
||||
{
|
||||
assert(nkeys_vd < brz->size[cur_bucket]);
|
||||
keys_vd[nkeys_vd++] = buffer_merge[i];
|
||||
//save_in_disk(buffer, buffer_merge[i], strlen(buffer_merge[i]), &memory_usage, memory_availability, graphs_fd);
|
||||
//fwrite(buffer_merge[i], 1, strlen(buffer_merge[i]) + 1, graphs_fd);
|
||||
e++;
|
||||
buffer_h3[i] = UINT_MAX;
|
||||
//free(buffer_merge[i]);
|
||||
buffer_merge[i] = NULL;
|
||||
}
|
||||
|
||||
if(nkeys_vd == brz->size[cur_bucket]) // Generating mphf.
|
||||
if(nkeys_vd == brz->size[cur_bucket]) // Generating mphf for each bucket.
|
||||
{
|
||||
cmph_io_adapter_t *source = NULL;
|
||||
cmph_config_t *config = NULL;
|
||||
cmph_t *mphf_tmp = NULL;
|
||||
bmz_data_t * bmzf = NULL;
|
||||
bmz8_data_t * bmzf = NULL;
|
||||
// Source of keys
|
||||
//fprintf(stderr, "Generating mphf %u in %u \n",cur_bucket + 1, brz->k);
|
||||
if(nkeys_vd > max_size) max_size = nkeys_vd;
|
||||
source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)nkeys_vd);
|
||||
config = cmph_config_new(source);
|
||||
cmph_config_set_algo(config, CMPH_BMZ);
|
||||
cmph_config_set_algo(config, CMPH_BMZ8);
|
||||
cmph_config_set_graphsize(config, brz->c);
|
||||
mphf_tmp = cmph_new(config);
|
||||
bmzf = (bmz_data_t *)mphf_tmp->data;
|
||||
//assert(brz_verify_mphf(mphf_tmp, source));
|
||||
bmzf = (bmz8_data_t *)mphf_tmp->data;
|
||||
brz_copy_partial_mphf(brz, bmzf, cur_bucket, source);
|
||||
cmph_config_destroy(config);
|
||||
brz_destroy_keys_vd(keys_vd, nkeys_vd);
|
||||
|
|
@ -495,14 +414,12 @@ static int brz_gen_graphs(cmph_config_t *mph)
|
|||
}
|
||||
}
|
||||
for(i = 0; i < nflushes; i++) fclose(tmp_fds[i]);
|
||||
//flush_buffer(buffer, &memory_usage, graphs_fd);
|
||||
free(tmp_fds);
|
||||
free(keys_vd);
|
||||
free(buffer_merge);
|
||||
free(buffer_h3);
|
||||
fprintf(stderr, "Maximal Size: %u\n", max_size);
|
||||
return 1;
|
||||
#pragma pack()
|
||||
}
|
||||
|
||||
static cmph_uint32 brz_min_index(cmph_uint32 * vector, cmph_uint32 n)
|
||||
|
|
@ -541,7 +458,7 @@ static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys)
|
|||
for(i = 0; i < nkeys; i++) free(keys_vd[i]);
|
||||
}
|
||||
|
||||
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source)
|
||||
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz8_data_t * bmzf, cmph_uint32 index, cmph_io_adapter_t *source)
|
||||
{
|
||||
cmph_uint32 i;
|
||||
cmph_uint32 n = ceil(brz->c * brz->size[index]);
|
||||
|
|
@ -549,13 +466,11 @@ static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmp
|
|||
brz->g[index] = (cmph_uint8 *)calloc(n, sizeof(cmph_uint8));
|
||||
for(i = 0; i < n; i++)
|
||||
{
|
||||
brz->g[index][i] = (cmph_uint8) bmzf->g[i];
|
||||
brz->g[index][i] = bmzf->g[i];
|
||||
//fprintf(stderr, "gsrc[%u]: %u gdest: %u\n", i, (cmph_uint8) bmzf->g[i], brz->g[index][i]);
|
||||
}
|
||||
brz->h1[index] = hash_state_copy(bmzf->hashes[0]);
|
||||
brz->h2[index] = hash_state_copy(bmzf->hashes[1]);
|
||||
//brz->size[index] = bmzf->n;
|
||||
//assert(brz_verify_mphf1(brz->h1[index], brz->h2[index], brz->g[index], n, source));
|
||||
}
|
||||
|
||||
int brz_dump(cmph_t *mphf, FILE *fd)
|
||||
|
|
@ -675,11 +590,13 @@ cmph_uint32 brz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
|
|||
cmph_uint32 n = ceil(brz->c * m);
|
||||
cmph_uint32 h1 = hash(brz->h1[h3], key, keylen) % n;
|
||||
cmph_uint32 h2 = hash(brz->h2[h3], key, keylen) % n;
|
||||
cmph_uint8 mphf_bucket;
|
||||
if (h1 == h2 && ++h2 >= n) h2 = 0;
|
||||
mphf_bucket = brz->g[h3][h1] + brz->g[h3][h2];
|
||||
DEBUGP("key: %s h1: %u h2: %u h3: %u\n", key, h1, h2, h3);
|
||||
DEBUGP("key: %s g[h1]: %u g[h2]: %u offset[h3]: %u edges: %u\n", key, brz->g[h3][h1], brz->g[h3][h2], brz->offset[h3], brz->m);
|
||||
DEBUGP("Address: %u\n", (((cmph_uint32)brz->g[h3][h1] + (cmph_uint32)brz->g[h3][h2])% m + brz->offset[h3]));
|
||||
return (((cmph_uint32)brz->g[h3][h1] + (cmph_uint32)brz->g[h3][h2])% m + brz->offset[h3]);
|
||||
DEBUGP("Address: %u\n", mphf_bucket + brz->offset[h3]);
|
||||
return (mphf_bucket + brz->offset[h3]);
|
||||
}
|
||||
void brz_destroy(cmph_t *mphf)
|
||||
{
|
||||
|
|
|
|||
|
|
@ -28,6 +28,7 @@ struct __brz_config_data_t
|
|||
hash_state_t **h1;
|
||||
hash_state_t **h2;
|
||||
hash_state_t * h3;
|
||||
cmph_uint32 memory_availability;
|
||||
cmph_uint8 * tmp_dir; // temporary directory
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -173,10 +173,11 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
|
|||
mph->data = bmz_config_new();
|
||||
break;
|
||||
case CMPH_BMZ8:
|
||||
mph->data = (void*)bmz8_config_new();
|
||||
mph->data = bmz8_config_new();
|
||||
break;
|
||||
case CMPH_BRZ:
|
||||
mph->data = brz_config_new();
|
||||
break;
|
||||
default:
|
||||
assert(0);
|
||||
}
|
||||
|
|
@ -219,6 +220,7 @@ void cmph_config_destroy(cmph_config_t *mph)
|
|||
break;
|
||||
case CMPH_BRZ: /* included -- Fabiano */
|
||||
brz_config_destroy(mph);
|
||||
break;
|
||||
default:
|
||||
assert(0);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue