diogo
/
yap-6.3
Archived
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

lbfgs 

memory leaks with _output_
improve configure
This commit is contained in:
Vitor Santos Costa 2018-10-19 14:56:49 +01:00
parent 3786de19de
commit 8fcf3eb008
15 changed files with 731 additions and 660 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
.configure-custom.sh
View File

@ -12,11 +12,15 @@ WITH_VARS="swig|yes|WITH_SWIG \
mpi|yes|WITH_MPI \ mpi|yes|WITH_MPI \
gecode|yes|WITH_GECODE \ gecode|yes|WITH_GECODE \
docs|yes|WITH_DOCS \ docs|yes|WITH_DOCS \
r|yes|WITH_REAL \ r|yes|WITH_R \
myddas|yes|WITH_MYDDAS \
cudd|yes|WITH_CUDD \ cudd|yes|WITH_CUDD \
xml2|yes|WITH_XML2 \ xml2|yes|WITH_XML2 \
raptor|yes|WITH_RAPTOR \ raptor|yes|WITH_RAPTOR \
python|yes|WITH_PYTHON \ python|yes|WITH_PYTHON \
openssl|yes|WITH_OPENSSL\ openssl|yes|WITH_OPENSSL\
java|yes|WITH_JAVA
lbfgs|yes|WITH_LBFGS
extensions|yes|WITH_EXTENSIONS
readline|yes|WITH_READLINE \ readline|yes|WITH_READLINE \
gmp|yes|WITH_GMP" gmp|yes|WITH_GMP"

21
C/c_interface.c
View File

@ -1811,27 +1811,6 @@ X_API bool YAP_RetryGoal(YAP_dogoalinfo *dgi) {
return out; return out;
} }
static void completeInnerCall(bool on_cut, yamop *old_CP, yamop *old_P) {
if (on_cut) {
P = old_P;
ENV = (CELL *)ENV[E_E];
CP = old_CP;
LOCAL_AllowRestart = TRUE;
// we are back to user code again, need slots */
} else {
P = old_P;
ENV = B->cp_env;
ENV = (CELL *)ENV[E_E];
CP = old_CP;
HR = B->cp_h;
TR = B->cp_tr;
B = B->cp_b;
LOCAL_AllowRestart = FALSE;
SET_ASP(ENV, E_CB * sizeof(CELL));
// make sure the slots are ok.
}
}
X_API bool YAP_LeaveGoal(bool successful, YAP_dogoalinfo *dgi) { X_API bool YAP_LeaveGoal(bool successful, YAP_dogoalinfo *dgi) {
CACHE_REGS CACHE_REGS
choiceptr myB, handler; choiceptr myB, handler;

2
C/dbase.c
View File

@ -25,7 +25,7 @@ static char SccsId[] = "%W% %G%";
* *
* @brief record and other forms of storing terms. * @brief record and other forms of storing terms.
* *
* / */
/** @defgroup Internal_Database Internal Data Base /** @defgroup Internal_Database Internal Data Base

119
C/text.c
View File

@ -59,54 +59,6 @@ typedef struct TextBuffer_manager {
} text_buffer_t; } text_buffer_t;
int AllocLevel(void) { return LOCAL_TextBuffer->lvl; } int AllocLevel(void) { return LOCAL_TextBuffer->lvl; }
int push_text_stack__(USES_REGS1) {
int i = LOCAL_TextBuffer->lvl;
i++;
LOCAL_TextBuffer->lvl = i;
return i;
}
int pop_text_stack__(int i) {
int lvl = LOCAL_TextBuffer->lvl;
while (lvl >= i) {
struct mblock *p = LOCAL_TextBuffer->first[lvl];
while (p) {
struct mblock *np = p->next;
free(p);
p = np;
}
LOCAL_TextBuffer->first[lvl] = NULL;
LOCAL_TextBuffer->last[lvl] = NULL;
lvl--;
}
LOCAL_TextBuffer->lvl = lvl;
return lvl;
}
void *pop_output_text_stack__(int i, const void *export) {
int lvl = LOCAL_TextBuffer->lvl;
while (lvl >= i) {
struct mblock *p = LOCAL_TextBuffer->first[lvl];
while (p) {
struct mblock *np = p->next;
if (p + 1 == export) {
size_t sz = p->sz - sizeof(struct mblock);
memmove(p, p + 1, sz);
export = p;
} else {
free(p);
}
p = np;
}
LOCAL_TextBuffer->first[lvl] = NULL;
LOCAL_TextBuffer->last[lvl] = NULL;
lvl--;
}
LOCAL_TextBuffer->lvl = lvl;
return (void *)export;
}
// void pop_text_stack(int i) { LOCAL_TextBuffer->lvl = i; } // void pop_text_stack(int i) { LOCAL_TextBuffer->lvl = i; }
void insert_block(struct mblock *o) { void insert_block(struct mblock *o) {
int lvl = o->lvl; int lvl = o->lvl;
@ -138,6 +90,68 @@ void release_block(struct mblock *o) {
o->next->prev = o->prev; o->next->prev = o->prev;
} }
int push_text_stack__(USES_REGS1) {
int i = LOCAL_TextBuffer->lvl;
i++;
LOCAL_TextBuffer->lvl = i;
return i;
}
int pop_text_stack__(int i) {
int lvl = LOCAL_TextBuffer->lvl;
while (lvl >= i) {
struct mblock *p = LOCAL_TextBuffer->first[lvl];
while (p) {
struct mblock *np = p->next;
free(p);
p = np;
}
LOCAL_TextBuffer->first[lvl] = NULL;
LOCAL_TextBuffer->last[lvl] = NULL;
lvl--;
}
LOCAL_TextBuffer->lvl = lvl;
return lvl;
}
void *pop_output_text_stack__(int i, const void *export) {
int lvl = LOCAL_TextBuffer->lvl;
bool found = false;
while (lvl >= i) {
struct mblock *p = LOCAL_TextBuffer->first[lvl];
while (p) {
struct mblock *np = p->next;
if (p + 1 == export) {
found = true;
} else {
free(p);
}
p = np;
}
LOCAL_TextBuffer->first[lvl] = NULL;
LOCAL_TextBuffer->last[lvl] = NULL;
lvl--;
}
LOCAL_TextBuffer->lvl = lvl;
if (found) {
if (lvl) {
struct mblock *o = (struct mblock *)export-1;
o->lvl = lvl;
o->prev = o->next = 0;
insert_block(o);
} else {
struct mblock *p = (struct mblock *)export-1;
size_t sz = p->sz - sizeof(struct mblock);
memmove(p, p + 1, sz);
export = p;
}
}
return (void *)export;
}
void *Malloc(size_t sz USES_REGS) { void *Malloc(size_t sz USES_REGS) {
int lvl = LOCAL_TextBuffer->lvl; int lvl = LOCAL_TextBuffer->lvl;
if (sz == 0) if (sz == 0)
@ -1027,10 +1041,11 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
void **bufv; void **bufv;
unsigned char *buf; unsigned char *buf;
int i, j; int i, j;
// int lvl = push_text_stack();
int lvl = push_text_stack();
bufv = Malloc(tot * sizeof(unsigned char *)); bufv = Malloc(tot * sizeof(unsigned char *));
if (!bufv) { if (!bufv) {
// pop_text_stack(lvl); pop_text_stack(lvl);
return NULL; return NULL;
} }
for (i = 0, j = 0; i < tot; i++) { for (i = 0, j = 0; i < tot; i++) {
@ -1038,7 +1053,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
unsigned char *nbuf = Yap_readText(inp + i PASS_REGS); unsigned char *nbuf = Yap_readText(inp + i PASS_REGS);
if (!nbuf) { if (!nbuf) {
// pop_text_stack(lvl); pop_text_stack(lvl);
return NULL; return NULL;
} }
// if (!nbuf[0]) // if (!nbuf[0])
@ -1054,7 +1069,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
buf = concat(tot, bufv PASS_REGS); buf = concat(tot, bufv PASS_REGS);
} }
bool rc = write_Text(buf, out PASS_REGS); bool rc = write_Text(buf, out PASS_REGS);
// pop_text_stack( lvl ); pop_text_stack( lvl );
return rc; return rc;
} }

257
CMakeLists.txt
View File

@ -67,7 +67,62 @@ if (POLICY CMP0068)
cmake_policy(SET CMP0068 NEW) cmake_policy(SET CMP0068 NEW)
endif () endif ()
## options: compilation flags
option(BUILD_SHARED_LIBS "Build shared library" ON) option(BUILD_SHARED_LIBS "Build shared library" ON)
CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_MMAP "Use MMAP for shared memory allocation" ON "NOT WITH_YAPOR_THOR" OFF)
CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_SHM "Use SHM for shared memory allocation" ON "NOT WITH_YAPOR_THOR; NOT WITH_SYSTEM_MMAP" OFF)
OPTION(WITH_CALL_TRACER "support for procedure-call tracing" ${DEBUG})
option(WITH_YAP_DLL "compile YAP as a DLL" ON)
option(WITH_YAP_STATIC "compile YAP statically" OFF)
option(WITH_YAP_CONDOR "allow YAP to be used from condor" OFF)
option(WITH_YAP_DLL "compile YAP as a DLL" ON)
if (WITH_YAP_CONDOR)
set(WITH_YAP_STATIC ON)
set(WITH_YAP_DLL OFF)
endif ()
## options: libraries
option(WITH_THREADED_CODE "threaded code" ON)
option(WITH_MPI "Interface to OpenMPI/MPICH" ON)
option(WITH_READLINE "use readline or libedit" ON)
option(WITH_JIT "just in Time Clause Compilation" OFF)
if (APPLE)
option(WITH_BREW "brew" ON)
if (not WITH_BREW)
option(WITH_MACPORTS "mac-ports" ON)
endif()
endif()
option (WITH_EXTENSIONS "packages and libraries that add value to YAP" ON)
if (ANDROID)
OPTION(WITH_MYDDAS " Enable MYDDAS driver" ON)
OPTION(WITH_SQLITE3 " Enable MYDDAS SQLITE3 driver" ON)
elseif(WITH_EXTENSIONS)
if (WITH_MYDDAS)
OPTION(WITH_MYSQL " Enable MYDDAS MYSQL driver" ON)
OPTION(WITH_ODBC " Enable MYDDAS ODBC driver" ON)
OPTION(WITH_POSTGRES " Enable MYDDAS POSTGRES driver" ON)
OPTION(WITH_SQLITE3 " Enable MYDDAS SQLITE3 driver" ON)
endif()
OPTION(WITH_SWIG " Enable SWIG interfaces to foreign languages" ON)
OPTION(WITH_RAPTOR " Enable the RAPTOR RDF library" ON)
OPTION(WITH_XML2 " Enable the RAPTOR XML2 library" ON)
OPTION(WITH_XML " Enable the Prolog XML library" ON)
OPTION(WITH_CLPBN" Enable the CLPBN and PFL probabilistic languages" ON)
IF (WITH_CLPBN)
OPTION(WITH_HORUS " Enable the HORUS inference libraray for CLPBN and PFL" ON)
ENDIF()
option(WITH_PROBLOG "include Problog-I." ON)
OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON)
option(WITH_GECODE "interface gecode constraint solver" ON)
option(WITH_LBFGS "interface with lbfgs" ON)
option(WITH_PRISM "use PRISM system in YAP" ON)
option(WITH_PYTHON "Allow Python->YAP and YAP->Python" ON)
option(WITH_R "Use R Interface" ON)
option(WITH_JAVA "Try to use Java (currently Java 6,7,8)" ON)
endif()
set(CMAKE_POSITION_INDEPENDENT_CODE TRUE) set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
@ -218,7 +273,7 @@ if ($ENV{CONDA_BUILD}x STREQUAL "1x" )
${PREFIX}/include ${PREFIX}/include
${SYS_PREFIX}/include ${SYS_PREFIX}/include
) )
set(YAP_IS_MOVABLE 1) set(YAP_IS_MOVABLE 1)
endif() endif()
@ -232,13 +287,12 @@ if (APPLE)
set(PATH $ENV{PATH}) set(PATH $ENV{PATH})
option(WITH_BREW "brew" ON)
if (WITH_MACPORTS) if (WITH_MACPORTS)
# Add MacPorts # Add MacPorts
# Detect if the "port" command is valid on this system; if so, return full path # Detect if the "port" command is valid on this system; if so, return full path
EXECUTE_PROCESS(COMMAND which port RESULT_VARIABLE DETECT_MACPORTS OUTPUT_VARIABLE MACPORTS_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) EXECUTE_PROCESS(COMMAND which port RESULT_VARIABLE DETECT_MACPORTS OUTPUT_VARIABLE MACPORTS_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
IF (${DETECT_MACPORTS} EQUAL 0) IF (${DETECT_MACPORTS} EQUAL 0)
# "/opt/local/bin/port" doesn't have libs, so we get the parent directory # "/opt/local/bin/port" doesn't have libs, so we get the parent directory
GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY) GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY)
@ -249,21 +303,20 @@ IF (${DETECT_MACPORTS} EQUAL 0)
LINK_DIRECTORIES(${LINK DIRECTORIES} ${MACPORTS_PREFIX}/lib) LINK_DIRECTORIES(${LINK DIRECTORIES} ${MACPORTS_PREFIX}/lib)
MESSAGE("WINNING!: ${MACPORTS_PREFIX}/lib") MESSAGE("WINNING!: ${MACPORTS_PREFIX}/lib")
ENDIF() ENDIF()
ENDIF() ENDIF()
option(WITH_BREW "brew" ON)
if (WITH_BREW) if (WITH_BREW)
EXECUTE_PROCESS(COMMAND brew --prefix RESULT_VARIABLE DETECT_BREW OUTPUT_VARIABLE BREW_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) EXECUTE_PROCESS(COMMAND brew --prefix RESULT_VARIABLE DETECT_BREW OUTPUT_VARIABLE BREW_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
IF (${DETECT_BREW} EQUAL 0) IF (${DETECT_BREW} EQUAL 0)
# "/opt/local" is where MacPorts lives, add `/lib` suffix and link # "/opt/local" is where MacPorts lives, add `/lib` suffix and link
LINK_DIRECTORIES( ${BREW_PREFIX}/lib) LINK_DIRECTORIES( ${BREW_PREFIX}/lib)
MESSAGE("BREW!: ${BREW_PREFIX}/lib") MESSAGE("BREW!: ${BREW_PREFIX}/lib")
ENDIF() ENDIF()
list(INSERT CMAKE_PREFIX_PATH pos list(INSERT CMAKE_PREFIX_PATH pos
@ -344,23 +397,22 @@ if (GMP_FOUND)
endif (GMP_FOUND) endif (GMP_FOUND)
option(WITH_READLINE "use readline or libedit" ON)
if (WITH_READLINE) if (WITH_READLINE)
include(FindReadline) include(FindReadline)
List(APPEND YAP_SYSTEM_OPTIONS readline) List(APPEND YAP_SYSTEM_OPTIONS readline)
# include subdirectories configuration # include subdirectories configuration
## after we have all functionality in ## after we have all functionality in
# #
# ADD_SUBDIRECTORY(console/terminal) # ADD_SUBDIRECTORY(console/terminal)
if (READLINE_FOUND) if (READLINE_FOUND)
include_directories(${READLINE_INCLUDE_DIR}) include_directories(${READLINE_INCLUDE_DIR})
# required for configure # required for configure
list(APPEND CMAKE_REQUIRED_LIBRARIES ${READLINE_LIBRARIES}) list(APPEND CMAKE_REQUIRED_LIBRARIES ${READLINE_LIBRARIES})
list(APPEND CMAKE_REQUIRED_INCLUDES ${READLINE_INCLUDE_DIR}) list(APPEND CMAKE_REQUIRED_INCLUDES ${READLINE_INCLUDE_DIR})
endif () endif ()
endif() endif()
#MPI STUFF #MPI STUFF
@ -475,10 +527,10 @@ endif ()
#ENDIF("${isSystemDir}" STREQUAL "-1") #ENDIF("${isSystemDir}" STREQUAL "-1")
# #
IF(NOT WIN32 AND NOT APPLE) IF(NOT WIN32 AND NOT APPLE)
LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib/Yap) LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib/Yap)
LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib) LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib)
LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../../../lib) LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../../../lib)
ELSE() ELSE()
LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib/Yap) LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib/Yap)
LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
@ -500,7 +552,6 @@ endif ()
# set_property( DIRECTORY APPEND_STRING PROPERTY -fsanitize=memory;-fsanitize-memory-track-origins=2) # set_property( DIRECTORY APPEND_STRING PROPERTY -fsanitize=memory;-fsanitize-memory-track-origins=2)
if (HAVE_GCC) if (HAVE_GCC)
# replace instructions codes by the address of their code # replace instructions codes by the address of their code
option(WITH_THREADED_CODE "threaded code" ON)
if (WITH_THREADED_CODE) if (WITH_THREADED_CODE)
set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS THREADED_CODE=1) set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS THREADED_CODE=1)
endif (WITH_THREADED_CODE) endif (WITH_THREADED_CODE)
@ -509,8 +560,6 @@ endif (HAVE_GCC)
# #
#option (YAP_SWI_IO ON) #option (YAP_SWI_IO ON)
OPTION(WITH_CALL_TRACER
"support for procedure-call tracing" ON)
#TODO: #TODO:
if (WITH_CALL_TRACER) if (WITH_CALL_TRACER)
list(APPEND YAP_SYSTEM_OPTIONS "call_tracer " ${YAP_SYSTEM_OPTIONS}) list(APPEND YAP_SYSTEM_OPTIONS "call_tracer " ${YAP_SYSTEM_OPTIONS})
@ -523,25 +572,27 @@ include_directories(utf8proc packages/myddas packages/myddas/sqlite3/src )
set_property(SOURCE ${LIBYAP_SOURCES} APPEND PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1) set_property(SOURCE ${LIBYAP_SOURCES} APPEND PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1)
add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
if (ANDROID) IF (WITH_MYDDAS)
if (ANDROID)
else() else()
if (MYSQL_FOUND) add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
if (MYSQL_FOUND)
add_definitions(= -DMYDDAS_MYSQL=1) add_definitions(= -DMYDDAS_MYSQL=1)
endif () endif ()
if (ODBC_FOUND) if (ODBC_FOUND)
add_definitions(= -DMYDDAS_ODBC=1) add_definitions(= -DMYDDAS_ODBC=1)
endif () endif ()
if (MYSQL_POSTGRES) if (MYSQL_POSTGRES)
add_definitions(= -DMYDDAS_POSTGRES=1) add_definitions(= -DMYDDAS_POSTGRES=1)
endif () endif ()
endif() endif(ANDROID)
endif(WITH_MYDDAS)
OPTION(WITH_SWIG " Enable SWIG interfaces to foreign languages" ON)
IF (WITH_SWIG) IF (WITH_SWIG)
find_host_package(SWIG) find_host_package(SWIG)
@ -551,19 +602,15 @@ IF (WITH_SWIG)
ENDIF (WITH_SWIG) ENDIF (WITH_SWIG)
option(WITH_PYTHON
"Allow Python->YAP and YAP->Python" ON)
IF (WITH_PYTHON) IF (WITH_PYTHON)
include(python ) include(python )
ENDIF (WITH_PYTHON) ENDIF (WITH_PYTHON)
option(WITH_R
"Use R Interface" ON)
IF (WITH_R) IF (WITH_R)
find_host_package(LibR) find_host_package(LibR)
add_subDIRECTORY(packages/real) add_subDIRECTORY(packages/real)
ENDIF (WITH_R) ENDIF (WITH_R)
@ -580,8 +627,8 @@ if (WIN32 OR ANDROID)
if (ANDROID) if (ANDROID)
List(APPEND YLIBS $<TARGET_OBJECTS:YAPsqlite3>) List(APPEND YLIBS $<TARGET_OBJECTS:YAPsqlite3>)
List(APPEND YLIBS $<TARGET_OBJECTS:YAPJava>) List(APPEND YLIBS $<TARGET_OBJECTS:YAPJava>)
endif ()
endif () endif ()
endif ()
include(Sources) include(Sources)
@ -694,7 +741,7 @@ set_target_properties(libYap
if (WITH_PYTHON AND PYTHONLIBS_FOUND AND SWIG_FOUND) if (WITH_PYTHON AND PYTHONLIBS_FOUND AND SWIG_FOUND)
set( ENV{PYTHONPATH} ${CMAKE_BINARY_DIR}/packages/python/swig:${CMAKE_BINARY_DIR}/packages/python/yap_kernel:. ) set( ENV{PYTHONPATH} ${CMAKE_BINARY_DIR}/packages/python/swig:${CMAKE_BINARY_DIR}/packages/python/yap_kernel:. )
add_subdirectory(packages/python/swig) add_subdirectory(packages/python/swig)
include(FindPythonModule) include(FindPythonModule)
@ -733,26 +780,24 @@ if (NOT WIN32)
endif () endif ()
option(WITH_JIT
"just in Time Clause Compilation" OFF)
if (WITH_JIT) if (WITH_JIT)
add_subDIRECTORY(JIT) add_subDIRECTORY(JIT)
endif (WITH_JIT) endif (WITH_JIT)
add_subDIRECTORY(packages/raptor)
add_subDIRECTORY(packages/xml) if (WITH_XML2 OR WITH_RAPTOR)
add_subDIRECTORY(packages/raptor)
endif()
OPTION(WITH_CLPBN " Enable the CLPBN and PFL probabilistic languages" ON) if (WITH_XML)
OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON) add_subDIRECTORY(packages/xml)
OPTION(WITH_HORUS " Enable the CLPBN and PFL probabilistic languages" ON) endif ()
find_host_package(Doxygen)
option(WITH_DOCS "Create and install the HTML based API documentation (requires Doxygen)" ${DOXYGEN_FOUND})
IF (WITH_CLPBN) IF (WITH_CLPBN)
add_subDIRECTORY(packages/CLPBN) add_subDIRECTORY(packages/CLPBN)
@ -762,50 +807,40 @@ IF (WITH_CPLINT)
add_subDIRECTORY(packages/cplint) add_subDIRECTORY(packages/cplint)
ENDIF (WITH_CPLINT) ENDIF (WITH_CPLINT)
# please install doxygen for prolog first
# git clone http://www.github.com/vscosta/doxygen-yap
# cd doxygen-yap
# mkdir -p build
# cd build
# make; sudo make install
option(WITH_DOCS
"generate YAP docs" OFF)
IF (WITH_DOCS) IF (WITH_DOCS)
get_target_property(YAP_SOURCES libYap SOURCES) get_target_property(YAP_SOURCES libYap SOURCES)
add_subDIRECTORY(docs) add_subDIRECTORY(docs)
find_host_package(Doxygen)
ENDIF (WITH_DOCS) ENDIF (WITH_DOCS)
# add_subDIRECTORY (packages/cuda) # add_subDIRECTORY (packages/cuda)
option(WITH_GECODE
"interface gecode constraint solver" ON)
if (WITH_GECODE) if (WITH_GECODE)
add_subDIRECTORY(packages/gecode) add_subDIRECTORY(packages/gecode)
endif () endif ()
option(WITH_LBFGS
"interface with lbfgs" ON)
if (WITH_LBFGS) if (WITH_LBFGS)
add_subDIRECTORY(packages/yap-lbfgs) add_subDIRECTORY(packages/yap-lbfgs)
endif () endif ()
option(WITH_JAVA "Try to use Java (currently Java 6,7,8)" ON)
if (WITH_JAVA) if (WITH_JAVA)
#detect java setup, as it is shared between different installations. #detect java setup, as it is shared between different installations.
find_package(Java COMPONENTS Runtime Development) find_package(Java COMPONENTS Runtime Development)
# find_package(Java COMPONENTS Development) # find_package(Java COMPONENTS Development)
# find_package(Java COMPONENTS Runtime) # find_package(Java COMPONENTS Runtime)
#find_package(JavaLibs) #find_package(JavaLibs)
if (Java_Development_FOUND) if (Java_Development_FOUND)
set (STD_CMAKE_FIND_FRAMEWORK ${CMAKE_FIND_FRAMEWORK}) set (STD_CMAKE_FIND_FRAMEWORK ${CMAKE_FIND_FRAMEWORK})
set (CMAKE_FIND_FRAMEWORK LAST) # CMake will find the Java returned by /usr/libexec/java_home. set (CMAKE_FIND_FRAMEWORK LAST) # CMake will find the Java returned by /usr/libexec/java_home.
@ -817,7 +852,7 @@ if (Java_Development_FOUND)
if (JNI_FOUND) if (JNI_FOUND)
get_filename_component(JAVA_HOME ${JAVA_INCLUDE_PATH} DIRECTORY) get_filename_component(JAVA_HOME ${JAVA_INCLUDE_PATH} DIRECTORY)
include(UseJava) include(UseJava)
@ -853,21 +888,38 @@ get_filename_component(JAVA_HOME ${JAVA_INCLUDE_PATH} DIRECTORY)
# JAVA_AWT_INCLUDE_PATH = the include path to jawt.h # JAVA_AWT_INCLUDE_PATH = the include path to jawt.h
endif (JNI_FOUND) endif (JNI_FOUND)
endif (Java_Development_FOUND) endif (Java_Development_FOUND)
add_subDIRECTORY(packages/jpl)
endif(WITH_JAVA) endif(WITH_JAVA)
add_subDIRECTORY(packages/jpl) if (WITH_CUDD)
add_subDIRECTORY(packages/bdd) add_subDIRECTORY(packages/bdd)
add_subDIRECTORY(packages/ProbLog) endif()
add_subDIRECTORY(packages/swi-minisat2) if (WITH_PROBLOG)
add_subDIRECTORY(packages/clpqr) add_subDIRECTORY(packages/ProbLog)
endif()
if (WITH_MINISAT)
add_subDIRECTORY(packages/swi-minisat2)
endif()
if (WITH_CLPQR)
add_subDIRECTORY(packages/clpqr)
endif()
#todo: use cmake target builds #todo: use cmake target builds
@ -886,28 +938,9 @@ add_subDIRECTORY(packages/clpqr)
# option (USE_CYGWIN # option (USE_CYGWIN
# "use cygwin library in WIN32" OFF) # "use cygwin library in WIN32" OFF)
option(WITH_PRISM
"use PRISM system in YAP" ON)
#TODO: #TODO:
option(WITH_YAP_DLL
"compile YAP as a DLL" ON)
#TODO:
option(WITH_YAP_STATIC
"compile YAP statically" OFF)
#TODO:
option(WITH_YAP_CONDOR
"allow YAP to be used from condor" OFF)
if (WITH_YAP_CONDOR)
# use default allocator
set(YAP_STATIC ON)
set(YAP_DLL OFF)
endif ()
#TODO: detect arch before allow this option #TODO: detect arch before allow this option
# OPTION(WIN64 # OPTION(WIN64
# "compile YAP for win64" OFF) # "compile YAP for win64" OFF)
@ -952,20 +985,12 @@ install(TARGETS libYap yap-bin
) )
CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_MMAP "Use MMAP for shared memory allocation" ON if (WITH_MPI)
"NOT WITH_YAPOR_THOR" OFF)
CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_SHM "Use SHM for shared memory allocation" ON add_subDIRECTORY(library/lammpi)
"NOT WITH_YAPOR_THOR; NOT WITH_SYSTEM_MMAP" OFF)
if (NOT ANDROID) if (MPI_C_FOUND)
add_subDIRECTORY(library/lammpi)
if (MPI_C_FOUND)
CMAKE_DEPENDENT_OPTION(WITH_MPI ON "Interface to OpenMPI/MPICH"
"MPI_C_FOUND" OFF)
macro_optional_add_subDIRECTORY(library/mpi) macro_optional_add_subDIRECTORY(library/mpi)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MPI_C_COMPILE_FLAGS} ") set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MPI_C_COMPILE_FLAGS} ")
include_directories(${MPI_C_INCLUDE_PATH}) include_directories(${MPI_C_INCLUDE_PATH})
@ -979,9 +1004,9 @@ if (MPI_C_FOUND)
set_target_properties(yap-bin PROPERTIES set_target_properties(yap-bin PROPERTIES
LINK_FLAGS "${MPI_C_LINK_FLAGS}") LINK_FLAGS "${MPI_C_LINK_FLAGS}")
endif () endif ()
endif (MPI_C_FOUND) endif (MPI_C_FOUND)
endif(NOT ANDROID) endif(WITH_MPI)
## add_subDIRECTORY(utils) ## add_subDIRECTORY(utils)

12
configure vendored
View File

@ -165,7 +165,7 @@ print_help() {
--mandir=DIR man documentation [DATAROOTDIR/man] --mandir=DIR man documentation [DATAROOTDIR/man]
--docdir=DIR documentation root [DATAROOTDIR/doc/PROJECT_NAME] --docdir=DIR documentation root [DATAROOTDIR/doc/PROJECT_NAME]
--generator=Generator Specify the tool used to send callss --generator=GENERATOR Specify the tool used to send callss
EOF EOF
first=y first=y
@ -220,6 +220,8 @@ EOF
exit 0 exit 0
} }
while [ $# != 0 ]; do while [ $# != 0 ]; do
case "$1" in case "$1" in
"--cmake="*) "--cmake="*)
@ -291,10 +293,10 @@ while [ $# != 0 ]; do
"--docdir") "--docdir")
CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_INSTALL_DOCDIR=$(quote "$2")"; shift;; CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_INSTALL_DOCDIR=$(quote "$2")"; shift;;
"-G="|"--generator="*) "--generator="*)
CMAKE_ARGS+="-G"${1#*=};; CMAKE_ARGS="$CMAKE_ARGS -G ${1#*=}";;
"-G"|"--generator") "-G")
CMAKE_ARGS+="-G$"$2; shift;; CMAKE_ARGS="$CMAKE_ARGS -G $2"; shift;;
"CC="*) "CC="*)
CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_C_COMPILER=$(quote "${1#*=}")";; CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_C_COMPILER=$(quote "${1#*=}")";;

4
os/sysbits.c
View File

@ -769,11 +769,11 @@ static Int real_path(USES_REGS1) {
int lvl = push_text_stack(); int lvl = push_text_stack();
rc0 = myrealpath(cmd PASS_REGS); rc0 = myrealpath(cmd PASS_REGS);
if (!rc0) { if (!rc0) {
pop_text_stack(lvl);
PlIOError(SYSTEM_ERROR_OPERATING_SYSTEM, ARG1, NULL); PlIOError(SYSTEM_ERROR_OPERATING_SYSTEM, ARG1, NULL);
} }
bool out = Yap_unify(MkAtomTerm(Yap_LookupAtom(rc0)), ARG2); bool out = Yap_unify(MkAtomTerm(Yap_LookupAtom(rc0)), ARG2);
pop_output_text_stack(lvl, rc0); pop_text_stack(lvl);
return out; return out;
} }

6
packages/ProbLog/problog_lbdd.yap
View File

@ -24,6 +24,7 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
bind_maplist(MapList, BoundVars), bind_maplist(MapList, BoundVars),
bdd_tree(BDD, bdd(Dir, Tree, _Vars)), bdd_tree(BDD, bdd(Dir, Tree, _Vars)),
bdd_to_probability_sum_product(BDD, BoundVars, Prob), bdd_to_probability_sum_product(BDD, BoundVars, Prob),
bdd_close(BDD),
(problog_flag(verbose, true)-> (problog_flag(verbose, true)->
problog_statistics problog_statistics
; ;
@ -37,7 +38,8 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
problog_kbest_bdd(Goal, K, Prob, ok) :- problog_kbest_bdd(Goal, K, Prob, ok) :-
problog_kbest_to_bdd(Goal, K, BDD, MapList), problog_kbest_to_bdd(Goal, K, BDD, MapList),
bind_maplist(MapList, BoundVars), bind_maplist(MapList, BoundVars),
bdd_to_probability_sum_product(BDD, BoundVars, Prob). bdd_to_probability_sum_product(BDD, BoundVars, Prob),
bdd_close(BDD).
problog_kbest_as_bdd(Goal, K, bdd(Dir, Tree, MapList)) :- problog_kbest_as_bdd(Goal, K, bdd(Dir, Tree, MapList)) :-
problog_kbest_to_bdd(Goal, K, BDD, MapList), problog_kbest_to_bdd(Goal, K, BDD, MapList),
@ -70,6 +72,7 @@ problog_fl_bdd(_,Prob) :-
bind_maplist(MapList, BoundVars), bind_maplist(MapList, BoundVars),
bdd_to_probability_sum_product(BDD, BoundVars, Prob), bdd_to_probability_sum_product(BDD, BoundVars, Prob),
(problog_flag(retain_tables, true) -> retain_tabling; true), (problog_flag(retain_tables, true) -> retain_tabling; true),
bdd_close(BDD),
clear_tabling. clear_tabling.
problog_full_bdd(Goal,_K, _) :- problog_full_bdd(Goal,_K, _) :-
@ -86,6 +89,7 @@ problog_full_bdd(_,Prob) :-
tabled_trie_to_bdd(Trie_Completed_Proofs, BDD, MapList), tabled_trie_to_bdd(Trie_Completed_Proofs, BDD, MapList),
bind_maplist(MapList, BoundVars), bind_maplist(MapList, BoundVars),
bdd_to_probability_sum_product(BDD, BoundVars, Prob), bdd_to_probability_sum_product(BDD, BoundVars, Prob),
bdd_close(BDD),
(problog_flag(retain_tables, true) -> retain_tabling; true), (problog_flag(retain_tables, true) -> retain_tabling; true),
clear_tabling. clear_tabling.

156
packages/ProbLog/problog_lbfgs.yap
View File

@ -431,7 +431,7 @@ do_learning_intern(Iterations,Epsilon) :-
true true
), ),
% update_values, update_values,
( (
last_mse(Last_MSE) last_mse(Last_MSE)
@ -449,16 +449,12 @@ do_learning_intern(Iterations,Epsilon) :-
) )
), ),
(
(problog_flag(rebuild_bdds,BDDFreq),BDDFreq>0,0 =:= CurrentIteration mod BDDFreq)
->
( (
retractall(values_correct), retractall(values_correct),
retractall(query_is_similar(_,_)), retractall(query_is_similar(_,_)),
retractall(query_md5(_,_,_)), retractall(query_md5(_,_,_)),
empty_bdd_directory, empty_bdd_directory,
init_queries init_queries
); true
), ),
@ -491,11 +487,48 @@ init_learning :-
init_learning :- init_learning :-
check_examples, check_examples,
retractall(current_iteration(_)),
assert(current_iteration(0)),
% empty_output_directory, % empty_output_directory,
logger_write_header, logger_write_header,
format_learning(1,'Initializing everything~n',[]), format_learning(1,'Initializing everything~n',[]),
succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
format_learning(3,'~q test examples~n',[TestExampleCount]),
succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
assertz(example_count(TrainingExampleCount)),
format_learning(3,'~q training examples~n',[TrainingExampleCount]),
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% build BDD script for every example
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
once(init_queries),
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% done
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
assertz(current_iteration(-1)),
assertz(learning_initialized),
format_learning(1,'~n',[]).
%========================================================================
%= Updates all values of query_probability/2 and query_gradient/4
%= should be called always before these predicates are accessed
%= if the old values are still valid, nothing happens
%========================================================================
update_values :-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% delete old values
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
retractall(query_probability_intern(_,_)),
retractall(query_gradient_intern(_,_,_,_)).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -503,7 +536,7 @@ init_learning :-
% if yes, switch to problog_exact % if yes, switch to problog_exact
% continuous facts are not supported yet. % continuous facts are not supported yet.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
set_default_gradient_method, set_default_gradient_method :-
( problog_flag(continuous_facts, true ) ( problog_flag(continuous_facts, true )
-> ->
problog_flag(init_method,(_,_,_,_,OldCall)), problog_flag(init_method,(_,_,_,_,OldCall)),
@ -527,31 +560,11 @@ init_learning :-
set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))) set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile)))
); );
true true
), ).
succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
format_learning(3,'~q test examples~n',[TestExampleCount]),
succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
assertz(example_count(TrainingExampleCount)),
format_learning(3,'~q training examples~n',[TrainingExampleCount]),
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% empty_bdd_directory :-
% build BDD script for every example
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
once(init_queries),
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% done
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
assertz(current_iteration(0)),
assertz(learning_initialized),
format_learning(1,'~n',[]).
empty_bdd_directory :-
current_key(_,I), current_key(_,I),
integer(I), integer(I),
recorded(I,bdd(_,_,_),R), recorded(I,bdd(_,_,_),R),
@ -560,21 +573,6 @@ init_learning :-
empty_bdd_directory. empty_bdd_directory.
set_default_gradient_method :-
problog_flag(continuous_facts, true),
!,
% problog_flag(init_method,OldMethod),
format_learning(2,'Theory uses continuous facts.~nWill use problog_exact/3 as initalization method.~2n',[]),
set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
set_default_gradient_method :-
problog_tabled(_), problog_flag(fast_proofs,false),
!,
format_learning(2,'Theory uses tabling.~nWill use problog_exact/3 as initalization method.~2n',[]),
set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
%set_default_gradient_method :-
% problog_flag(init_method,(gene(X,Y),N,Bdd,graph2bdd(X,Y,N,Bdd))),
% !.
set_default_gradient_method.
%======================================================================== %========================================================================
%= This predicate goes over all training and test examples, %= This predicate goes over all training and test examples,
@ -584,6 +582,7 @@ set_default_gradient_method.
init_queries :- init_queries :-
empty_bdd_directory,
format_learning(2,'Build BDDs for examples~n',[]), format_learning(2,'Build BDDs for examples~n',[]),
forall(user:test_example(ID,Query,_Prob,_),init_one_query(ID,Query,test)), forall(user:test_example(ID,Query,_Prob,_),init_one_query(ID,Query,test)),
forall(user:example(ID,Query,_Prob,_),init_one_query(ID,Query,training)). forall(user:example(ID,Query,_Prob,_),init_one_query(ID,Query,training)).
@ -703,28 +702,56 @@ ground_truth_difference :-
%= -Float %= -Float
%======================================================================== %========================================================================
mse_trainingset_only_for_linesearch(MSE, FX) :- mse_trainingset :-
current_iteration(Iteration),
create_training_predictions_file_name(Iteration,File_Name),
open(File_Name, write,Handle),
format_learning(2,'MSE_Training ',[]),
update_values, update_values,
findall(t(LogCurrentProb,SquaredError),
(user:training_example(QueryID,Query,TrueQueryProb,_Type),
once(update_query(QueryID,'+',probability)),
query_probability(QueryID,CurrentProb),
format(Handle,'ex(~q,training,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
example_count(Example_Count),
bb_put(error_train_line_search,0.0),
forall(user:example(QueryID,_Query,QueryProb,Type),
(
once(update_query(QueryID,'.',probability)),
once(update_query_cleanup(QueryID)), once(update_query_cleanup(QueryID)),
SquaredError is (CurrentProb-TrueQueryProb)**2,
LogCurrentProb is log(CurrentProb)
), ),
format_learning(3,' (~8f)~n',[MSE]), All),
retractall(values_correct). maplist(tuple, All, AllLogs, AllSquaredErrors),
sum_list( AllLogs, LLH_Training_Queries),
close(Handle),
length(AllSquaredErrors,Length),
(
Length>0
->
(
sum_list(AllSquaredErrors,SumAllSquaredErrors),
min_list(AllSquaredErrors,MinError),
max_list(AllSquaredErrors,MaxError),
MSE is SumAllSquaredErrors/Length
);(
MSE=0.0,
MinError=0.0,
MaxError=0.0
)
),
logger_set_variable(mse_trainingset,MSE),
logger_set_variable(mse_min_trainingset,MinError),
logger_set_variable(mse_max_trainingset,MaxError),
logger_set_variable(llh_training_queries,LLH_Training_Queries),
format_learning(2,' (~8f)~n',[MSE]).
tuple(t(X,Y),X,Y).
mse_testset :- mse_testset :-
current_iteration(Iteration), current_iteration(Iteration),
create_test_predictions_file_name(Iteration,File_Name), create_test_predictions_file_name(Iteration,File_Name),
open(File_Name,'write',Handle), open(File_Name, write,Handle),
format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
format_learning(2,'MSE_Test ',[]), format_learning(2,'MSE_Test ',[]),
update_values, update_values,
bb_put(llh_test_queries,0.0), bb_put(llh_test_queries,0.0),
@ -808,11 +835,6 @@ save_old_probabilities :-
gradient_descent :- gradient_descent :-
problog_flag(sigmoid_slope,Slope), problog_flag(sigmoid_slope,Slope),
% current_iteration(Iteration), % current_iteration(Iteration),
% create_training_predictions_file_name(Iteration,File_Name),
Handle = user_error,
format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
findall(FactID,tunable_fact(FactID,GroundTruth),L), length(L,N), findall(FactID,tunable_fact(FactID,GroundTruth),L), length(L,N),
% leash(0),trace, % leash(0),trace,
lbfgs_initialize(N,X,0,Solver), lbfgs_initialize(N,X,0,Solver),
@ -839,13 +861,13 @@ user:evaluate(LLH_Training_Queries, X,Grad,N,_,_) :-
N1 is N-1, N1 is N-1,
forall(between(0,N1,I), forall(between(0,N1,I),
(Grad[I] <== 0.0, S <== X[I], sigmoid(S,Slope, P), Probs[I] <== P) (Grad[I] <== 0.0, S <== X[I], sigmoid(S,Slope, P), Probs[I] <== P)
), nl, ),
forall( forall(
full_example(QueryID,QueryProb,BDD), full_example(QueryID,QueryProb,BDD),
compute_grad(QueryID, BDD, QueryProb,Grad, Probs, Slope,LLs) compute_grad(QueryID, BDD, QueryProb,Grad, Probs, Slope,LLs)
), ),
LLH_Training_Queries <== sum(LLs), LLH_Training_QueriesSum <== sum(LLs),
writeln(LLH_Training_Queries). LLH_Training_Queries is LLH_Training_QueriesSum/TrainingExampleCount .
%wrap(X, Grad, GradCount). %wrap(X, Grad, GradCount).
full_example(QueryID,QueryProb,BDD) :- full_example(QueryID,QueryProb,BDD) :-
@ -971,7 +993,7 @@ user:progress(FX,X,_G,X_Norm,G_Norm,Step,_N,Iteration,Ls,0) :-
NextIteration is CurrentIteration+1, NextIteration is CurrentIteration+1,
assertz(current_iteration(NextIteration)), assertz(current_iteration(NextIteration)),
save_model, save_model,
set_problog_flag(mse_trainingset, FX), logger_set_variable(mse_trainingset, FX),
X0 <== X[0], sigmoid(X0,Slope,P0), X0 <== X[0], sigmoid(X0,Slope,P0),
X1 <== X[1], sigmoid(X1,Slope,P1), X1 <== X[1], sigmoid(X1,Slope,P1),
format('~d. Iteration : (x0,x1)=(~4f,~4f) f(X)=~4f |X|=~4f |X\'|=~4f Step=~4f Ls=~4f~n',[Iteration,P0 ,P1,FX,X_Norm,G_Norm,Step,Ls]). format('~d. Iteration : (x0,x1)=(~4f,~4f) f(X)=~4f |X|=~4f |X\'|=~4f Step=~4f Ls=~4f~n',[Iteration,P0 ,P1,FX,X_Norm,G_Norm,Step,Ls]).

3
packages/bdd/cudd.c
View File

@ -863,6 +863,9 @@ static YAP_Bool p_cudd_print_with_names(void) {
static YAP_Bool p_cudd_die(void) { static YAP_Bool p_cudd_die(void) {
DdManager *manager = (DdManager *)YAP_IntOfTerm(YAP_ARG1); DdManager *manager = (DdManager *)YAP_IntOfTerm(YAP_ARG1);
//Cudd_FreeTree(manager);
//cuddFreeTable(manager);
Cudd_CheckZeroRef(manager);
Cudd_Quit(manager); Cudd_Quit(manager);
return TRUE; return TRUE;
} }

4
packages/myddas/mysql/CMakeLists.txt
View File

@ -1,4 +1,6 @@
if (WITH_MYSQL)
set(MYSQL_SOURCES set(MYSQL_SOURCES
myddas_mysql.c myddas_mysql.c
myddas_util.c myddas_util.c
@ -51,3 +53,5 @@
"enable the MYDDAS top-level (REPL) support for MySQL" OFF "enable the MYDDAS top-level (REPL) support for MySQL" OFF
'USE_MYDDAS AND MYSQL_FOUND' OFF) 'USE_MYDDAS AND MYSQL_FOUND' OFF)
#TODO: #TODO:
endif()

27
packages/myddas/odbc/CMakeLists.txt
View File

@ -1,23 +1,24 @@
if (WITH_ODBC)
set( YAPODBC_SOURCES set( YAPODBC_SOURCES
myddas_odbc.c myddas_odbc.c
) )
set(SO_MAJOR 1) set(SO_MAJOR 1)
set(SO_MINOR 0) set(SO_MINOR 0)
set(SO_PATCH 0) set(SO_PATCH 0)
macro_optional_find_package(ODBC ON) macro_optional_find_package(ODBC ON)
if (ODBC_FOUND) if (ODBC_FOUND)
# ODBC_INCLUDE_DIRECTORIES, where to find sql.h # ODBC_INCLUDE_DIRECTORIES, where to find sql.h
# ODBC_LIBRARIES, the libraries to link against to use ODBC # ODBC_LIBRARIES, the libraries to link against to use ODBC
# ODBC_FOUND. If false, you cannot build anything that requires Odbc. # ODBC_FOUND. If false, you cannot build anything that requires Odbc.
add_lib(YAPodbc ${YAPODBC_SOURCES}) add_lib(YAPodbc ${YAPODBC_SOURCES})
target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES}) target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES})
include_directories (${ODBC_INCLUDE_DIRECTORIES} ..) include_directories (${ODBC_INCLUDE_DIRECTORIES} ..)
set_target_properties (YAPodbc PROPERTIES set_target_properties (YAPodbc PROPERTIES
POSITION_INDEPENDENT_CODE ON POSITION_INDEPENDENT_CODE ON
PREFIX "" PREFIX ""
) )
@ -34,6 +35,8 @@ set_target_properties (YAPodbc PROPERTIES
ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR} ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
) )
else() else()
add_definitions (-DMYDDAS_ODBC=0) add_definitions (-DMYDDAS_ODBC=0)
endif (ODBC_FOUND) endif (ODBC_FOUND)
endif()

36
packages/myddas/postgres/CMakeLists.txt
View File

@ -1,19 +1,21 @@
set( YAPPOSTGRES_SOURCES if (WITH_POSTGRES)
set( YAPPOSTGRES_SOURCES
myddas_postgres.c myddas_postgres.c
) )
set(SO_MAJOR 1) set(SO_MAJOR 1)
set(SO_MINOR 0) set(SO_MINOR 0)
set(SO_PATCH 0) set(SO_PATCH 0)
macro_optional_find_package(PostgreSQL ON) macro_optional_find_package(PostgreSQL ON)
if (PostgreSQL_FOUND) if (PostgreSQL_FOUND)
# PostgreSQL_FOUND - Set to true when PostgreSQL is found. # PostgreSQL_FOUND - Set to true when PostgreSQL is found.
# PostgreSQL_INCLUDE_DIRS - Include directories for PostgreSQL # PostgreSQL_INCLUDE_DIRS - Include directories for PostgreSQL
# PostgreSQL_LIBRARY_DIRS - Link directories for PostgreSQL libraries # PostgreSQL_LIBRARY_DIRS - Link directories for PostgreSQL libraries
# PostgreSQL_LIBRARIES - The PostgreSQL libraries. # PostgreSQL_LIBRARIES - The PostgreSQL libraries.
add_lib(YAPpostgres ${YAPPOSTGRES_SOURCES}) add_lib(YAPpostgres ${YAPPOSTGRES_SOURCES})
target_link_libraries(YAPpostgres libYap ${PostgreSQL_LIBRARIES}) target_link_libraries(YAPpostgres libYap ${PostgreSQL_LIBRARIES})
include_directories (${PostgreSQL_INCLUDE_DIRS} ..) include_directories (${PostgreSQL_INCLUDE_DIRS} ..)
@ -22,14 +24,16 @@ if (PostgreSQL_FOUND)
PREFIX "" PREFIX ""
) )
list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1) list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1)
set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE) set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
-DMYDDAS_POSTGRES=1) -DMYDDAS_POSTGRES=1)
install(TARGETS YAPpostgres install(TARGETS YAPpostgres
LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR} LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR} RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR} ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
) )
endif (PostgreSQL_FOUND) endif (PostgreSQL_FOUND)
endif()

44
packages/myddas/sqlite3/CMakeLists.txt
View File

@ -1,49 +1,51 @@
message( " * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" ) if (WITH_SQLITE3)
set (SQLITE_EXTRA message( " * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
set (SQLITE_EXTRA
chinook.db chinook.db
sqlitest.yap) sqlitest.yap)
set( YAPSQLITE3_SOURCES set( YAPSQLITE3_SOURCES
myddas_sqlite3.c myddas_sqlite3.c
src/sqlite3.h src/sqlite3.h
src/sqlite3ext.h src/sqlite3ext.h
) )
#sqlite3 is now in the system #sqlite3 is now in the system
set (SQLITE3_FOUND ON CACHE PRIVATE "") set (SQLITE3_FOUND ON CACHE PRIVATE "")
include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..) include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
if (ANDROID) if (ANDROID)
add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 ) add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 )
endif() endif()
add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 ) add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 )
add_definitions(-DSQLITE_ENABLE_JSON1=1 ) add_definitions(-DSQLITE_ENABLE_JSON1=1 )
add_definitions(-DSQLITE_ENABLE_RBU=1 ) add_definitions(-DSQLITE_ENABLE_RBU=1 )
add_definitions(-DSQLITE_ENABLE_RTREE=1 ) add_definitions(-DSQLITE_ENABLE_RTREE=1 )
add_definitions(-DSQLITE_ENABLE_FTS5=1 ) add_definitions(-DSQLITE_ENABLE_FTS5=1 )
SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 ) SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 )
if (ANDROID ) if (ANDROID )
add_library( YAPsqlite3 OBJECT add_library( YAPsqlite3 OBJECT
${YAPSQLITE3_SOURCES} ) ${YAPSQLITE3_SOURCES} )
else() else()
list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c) list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c)
add_library( YAPsqlite3 SHARED add_library( YAPsqlite3 SHARED
${YAPSQLITE3_SOURCES}) ${YAPSQLITE3_SOURCES})
target_link_libraries(YAPsqlite3 libYap ) target_link_libraries(YAPsqlite3 libYap )
@ -56,13 +58,15 @@ add_library( YAPsqlite3 SHARED
PREFIX "" PREFIX ""
) )
install(TARGETS YAPsqlite3 install(TARGETS YAPsqlite3
RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR} RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR} ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR} LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
) )
endif() endif()
install(FILES ${SQLITE_EXTRA} install(FILES ${SQLITE_EXTRA}
DESTINATION ${libpl} DESTINATION ${libpl}
) )
endif()

6
packages/python/pybips.c
View File

@ -591,7 +591,8 @@ static long get_len_of_range(long lo, long hi, long step) {
} }
#if PY_MAJOR_VERSION >= 3 #if PY_MAJOR_VERSION >= 3
static PyStructSequence_Field pnull[] = { /*
static PyStructSequence_Field pnull[] = {
{"A1", NULL}, {"A2", NULL}, {"A3", NULL}, {"A4", NULL}, {"A5", NULL}, {"A1", NULL}, {"A2", NULL}, {"A3", NULL}, {"A4", NULL}, {"A5", NULL},
{"A6", NULL}, {"A7", NULL}, {"A8", NULL}, {"A9", NULL}, {"A9", NULL}, {"A6", NULL}, {"A7", NULL}, {"A8", NULL}, {"A9", NULL}, {"A9", NULL},
{"A10", NULL}, {"A11", NULL}, {"A12", NULL}, {"A13", NULL}, {"A14", NULL}, {"A10", NULL}, {"A11", NULL}, {"A12", NULL}, {"A13", NULL}, {"A14", NULL},
@ -600,6 +601,7 @@ static PyStructSequence_Field pnull[] = {
{"A24", NULL}, {"A25", NULL}, {"A26", NULL}, {"A27", NULL}, {"A28", NULL}, {"A24", NULL}, {"A25", NULL}, {"A26", NULL}, {"A27", NULL}, {"A28", NULL},
{"A29", NULL}, {"A29", NULL}, {"A30", NULL}, {"A31", NULL}, {"A32", NULL}, {"A29", NULL}, {"A29", NULL}, {"A30", NULL}, {"A31", NULL}, {"A32", NULL},
{NULL, NULL}}; {NULL, NULL}};
*/
static PyObject *structseq_str(PyObject *iobj) { static PyObject *structseq_str(PyObject *iobj) {
@ -763,7 +765,7 @@ PyObject *term_to_nametuple(const char *s, arity_t arity, PyObject *tuple) {
PyStructSequence_Desc *desc = calloc(sizeof(PyStructSequence_Desc), 1); PyStructSequence_Desc *desc = calloc(sizeof(PyStructSequence_Desc), 1);
desc->name = PyMem_Malloc(strlen(s) + 1); desc->name = PyMem_Malloc(strlen(s) + 1);
desc->doc = "YAPTerm"; desc->doc = "YAPTerm";
desc->fields = pnull; desc->fields = NULL;
desc->n_in_sequence = arity; desc->n_in_sequence = arity;
if (PyStructSequence_InitType2(typp, desc) < 0) if (PyStructSequence_InitType2(typp, desc) < 0)
return NULL; return NULL;