diogo/yap-6.3
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Merge /home/vsc/yap

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This commit is contained in:
Vítor Santos Costa 2018-10-19 17:12:51 +01:00
commit fbcd45bdfe
19 changed files with 779 additions and 696 deletions
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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
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@ -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;
} }

1
packages/jpl/CMakeLists.txt
View File

@ -1,3 +1,4 @@
#CHECK: JavaLibs #CHECK: JavaLibs
set (JPL_SOURCES set (JPL_SOURCES

17
packages/jpl/src/c/CMakeLists.txt
View File

@ -4,16 +4,25 @@ add_lib(jplYap jpl.h jpl.c hacks.h)
include_directories (${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2} ${JAVA_AWT_PATH} ) include_directories (${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2} ${JAVA_AWT_PATH} )
if (APPLE) if (APPLE)
get_filename_component ( JAVA_AWT_DIR ${JAVA_AWT_LIBRARY} DIRECTORY) set(CMAKE_MACOSX_RPATH 1)
find_library (JLI jli ${JAVA_AWT_DIR}/jli) get_filename_component ( JAVA_AWT_DIR ${JAVA_AWT_LIBRARY} DIRECTORY)
get_filename_component ( JAVA_JNI_DIR ${JAVA_JVM_LIBRARY} DIRECTORY)
find_library (JLI jli ${JAVA_AWT_DIR}/jli)
find_library (JAL JavaApplicationLauncher FRAMEWORK ONLY PATH /System/Library/PrivateFrameworks)
find_library (JL JavaLaunching FRAMEWORK ONLY PATH /System/Library/PrivateFrameworks)
SET(CMAKE_INSTALL_RPATH "${JAVA_AWT_DIR}/jli")
target_link_libraries(jplYap libYap ${JL} ${JAL} -L${JAVA_AWT_DIR}/jli -ljli )
else()
target_link_libraries(jplYap libYap ${JAVA_JVM_LIBRARY})
endif() endif()
target_link_libraries(jplYap libYap ${JLI} ${JNI_LIBRARIES})
set_target_properties(jplYap PROPERTIES set_target_properties(jplYap PROPERTIES
OUTPUT_NAME jpl OUTPUT_NAME jpl
INSTALL_RPATH_USE_LINK_PATH TRUE
) )
# set(YAP_SYSTEM_OPTIONS "jpl " ${YAP_SYSTEM_OPTIONS} PARENT_SCOPE) # set(YAP_SYSTEM_OPTIONS "jpl " ${YAP_SYSTEM_OPTIONS} PARENT_SCOPE)

2
packages/jpl/test_jpl.pl
View File

@ -1,4 +1,4 @@
:- module(test_jpl, f:- module(test_jpl,
[ run_tests/0, [ run_tests/0,
run_tests/1 run_tests/1
]). ]).

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;

24
packages/python/yap_kernel/yap_ipython/yapi.py
View File

@ -6,14 +6,14 @@ from traitlets import Bool
from yap4py.yapi import * from yap4py.yapi import *
from yap_ipython.core.completer import Completer from IPython.core.completer import Completer
# import yap_ipython.core # import IPython.core
from traitlets import Instance from traitlets import Instance
from yap_ipython.core.inputsplitter import * from IPython.core.inputsplitter import *
from yap_ipython.core.inputtransformer import * from IPython.core.inputtransformer import *
from yap_ipython.core.interactiveshell import * from IPython.core.interactiveshell import *
from ipython_genutils.py3compat import builtin_mod from ipython_genutils.py3compat import builtin_mod
from yap_ipython.core import interactiveshell from IPython.core import interactiveshell
from collections import namedtuple from collections import namedtuple
import traceback import traceback
@ -198,11 +198,11 @@ class YAPInputSplitter(InputSplitter):
self.reset() self.reset()
def push(self, lines): def push(self, lines):
"""Push one or more lines of yap_ipython input. """Push one or more lines of IPython input.
This stores the given lines and returns a status code indicating This stores the given lines and returns a status code indicating
whether the code forms a complete Python block or not, after processing whether the code forms a complete Python block or not, after processing
all input lines for special yap_ipython syntax. all input lines for special IPython syntax.
Any exceptions generated in compilation are swallowed, but if an Any exceptions generated in compilation are swallowed, but if an
exception was produced, the method returns True. exception was produced, the method returns True.
@ -488,7 +488,7 @@ class YAPCompleter(Completer):
If ``IPCompleter.debug`` is :any:`True` will yield a ``--jedi/ipython--`` If ``IPCompleter.debug`` is :any:`True` will yield a ``--jedi/ipython--``
fake Completion token to distinguish completion returned by Jedi fake Completion token to distinguish completion returned by Jedi
and usual yap_ipython completion. and usual IPython completion.
.. note:: .. note::
@ -507,7 +507,7 @@ class YAPCompleter(Completer):
class YAPRun: class YAPRun(InteractiveShell):
"""An enhanced, interactive shell for YAP.""" """An enhanced, interactive shell for YAP."""
def __init__(self, shell): def __init__(self, shell):
@ -602,10 +602,11 @@ class YAPRun:
return self.result return self.result
def _yrun_cell(self, raw_cell, store_history=True, silent=False, def _yrun_cell(self, raw_cell, store_history=True, silent=False,
shell_futures=True): shell_futures=True):
"""Run a complete IPython cell. """Run a complete IPython cell.
-
Parameters Parameters
---------- ----------
raw_cell : str raw_cell : str
@ -727,6 +728,7 @@ class YAPRun:
self.result.result = False self.result.result = False
has_raised = False has_raised = False
try: try:
builtin_mod.input = self.shell.sys_raw_input
self.yapeng.mgoal(streams(True),"user", True) self.yapeng.mgoal(streams(True),"user", True)
if cell.strip('\n \t'): if cell.strip('\n \t'):
#create a Trace object, telling it what to ignore, and whether to #create a Trace object, telling it what to ignore, and whether to