Merge ssh://xato/home/vsc/yap

.configure-custom.sh

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

C/c_interface.c

@@ -1811,27 +1811,6 @@ X_API bool YAP_RetryGoal(YAP_dogoalinfo *dgi) {
   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) {
   CACHE_REGS
   choiceptr myB, handler;

C/fli_absmi_insts.h

@@ -623,6 +623,10 @@
 
       BOp(undef_p, e);
       /* save S for module name */
+      if (LOCAL_DoingUndefp) {
+	PREG=FAILCODE;
+	JMPNext();
+      }
         LOCAL_DoingUndefp = true;
 	saveregs();
       undef_goal(PASS_REGS1);

C/text.c

@@ -59,54 +59,6 @@ typedef struct TextBuffer_manager {
 } text_buffer_t;
 
 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 insert_block(struct mblock *o) {
   int lvl = o->lvl;
@@ -138,6 +90,68 @@ void release_block(struct mblock *o) {
     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) {
   int lvl = LOCAL_TextBuffer->lvl;
   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;
   unsigned char *buf;
   int i, j;
-  // int lvl = push_text_stack();
+
+  int lvl = push_text_stack();
   bufv = Malloc(tot * sizeof(unsigned char *));
   if (!bufv) {
-    // pop_text_stack(lvl);
+     pop_text_stack(lvl);
     return NULL;
   }
   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);
 
     if (!nbuf) {
-      // pop_text_stack(lvl);
+       pop_text_stack(lvl);
       return NULL;
     }
     //      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);
   }
   bool rc = write_Text(buf, out PASS_REGS);
-  // pop_text_stack( lvl );
+   pop_text_stack( lvl );
 
   return rc;
 }

CMakeLists.txt

@@ -67,7 +67,62 @@ if (POLICY CMP0068)
   cmake_policy(SET CMP0068 NEW)
 endif ()
 
+## options: compilation flags
 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_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
@@ -232,7 +287,6 @@ if (APPLE)
 
     set(PATH $ENV{PATH})
 
-    option(WITH_BREW "brew" ON)
     if (WITH_MACPORTS)
       # Add MacPorts
       # Detect if the "port" command is valid on this system; if so, return full path
@@ -252,7 +306,6 @@ IF (${DETECT_MACPORTS} EQUAL 0)
       ENDIF()
     ENDIF()
 
-    option(WITH_BREW "brew" ON)
 
     if (WITH_BREW)
       EXECUTE_PROCESS(COMMAND brew --prefix RESULT_VARIABLE DETECT_BREW OUTPUT_VARIABLE BREW_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
@@ -344,7 +397,6 @@ if (GMP_FOUND)
 
 endif (GMP_FOUND)
 
-    option(WITH_READLINE "use readline or libedit" ON)
 
 if (WITH_READLINE)
   include(FindReadline)
@@ -500,7 +552,6 @@ endif ()
 # set_property( DIRECTORY APPEND_STRING PROPERTY -fsanitize=memory;-fsanitize-memory-track-origins=2)
 if (HAVE_GCC)
   # replace instructions codes by the address of their code
-    option(WITH_THREADED_CODE "threaded code" ON)
   if (WITH_THREADED_CODE)
     set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS THREADED_CODE=1)
   endif (WITH_THREADED_CODE)
@@ -509,8 +560,6 @@ endif (HAVE_GCC)
 #
 #option (YAP_SWI_IO ON)
 
-OPTION(WITH_CALL_TRACER
-        "support for procedure-call tracing" ON)
 #TODO:
 if (WITH_CALL_TRACER)
   list(APPEND YAP_SYSTEM_OPTIONS "call_tracer " ${YAP_SYSTEM_OPTIONS})
@@ -523,11 +572,13 @@ include_directories(utf8proc packages/myddas packages/myddas/sqlite3/src )
 
 set_property(SOURCE ${LIBYAP_SOURCES} APPEND PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1)
 
-add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
 
+IF (WITH_MYDDAS)
   if (ANDROID)
   else()
 
+    add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
+
     if (MYSQL_FOUND)
       add_definitions(= -DMYDDAS_MYSQL=1)
     endif ()
@@ -539,9 +590,9 @@ endif ()
     if (MYSQL_POSTGRES)
       add_definitions(= -DMYDDAS_POSTGRES=1)
     endif ()
-endif()
+  endif(ANDROID)
+endif(WITH_MYDDAS)
 
-OPTION(WITH_SWIG " Enable SWIG interfaces to foreign languages" ON)
 
 IF (WITH_SWIG)
   find_host_package(SWIG)
@@ -551,15 +602,11 @@ IF (WITH_SWIG)
 ENDIF (WITH_SWIG)
 
 
-option(WITH_PYTHON
-        "Allow Python->YAP  and YAP->Python" ON)
 
 IF (WITH_PYTHON)
   include(python )
 ENDIF (WITH_PYTHON)
 
-option(WITH_R
-        "Use R Interface" ON)
 
 IF (WITH_R)
   find_host_package(LibR)
@@ -733,26 +780,24 @@ if (NOT WIN32)
 endif ()
 
 
-option(WITH_JIT
-        "just in Time Clause Compilation" OFF)
 if (WITH_JIT)
   add_subDIRECTORY(JIT)
 endif (WITH_JIT)
 
+
+if (WITH_XML2 OR WITH_RAPTOR)
+
   add_subDIRECTORY(packages/raptor)
 
+endif()
+
+
+if (WITH_XML)
+
   add_subDIRECTORY(packages/xml)
 
+endif ()
 
-OPTION(WITH_CLPBN " Enable the CLPBN and PFL probabilistic languages" ON)
-
-OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON)
-
-OPTION(WITH_HORUS " Enable the CLPBN and PFL probabilistic languages" ON)
-
-find_host_package(Doxygen)
-
-option(WITH_DOCS "Create and install the HTML based API documentation (requires Doxygen)" ${DOXYGEN_FOUND})
 
 IF (WITH_CLPBN)
   add_subDIRECTORY(packages/CLPBN)
@@ -762,39 +807,29 @@ IF (WITH_CPLINT)
   add_subDIRECTORY(packages/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)
   get_target_property(YAP_SOURCES libYap SOURCES)
 
   add_subDIRECTORY(docs)
+
+
+  find_host_package(Doxygen)
+
 ENDIF (WITH_DOCS)
 
 # add_subDIRECTORY (packages/cuda)
 
-option(WITH_GECODE
-        "interface gecode constraint solver" ON)
 if (WITH_GECODE)
   add_subDIRECTORY(packages/gecode)
 endif ()
 
-option(WITH_LBFGS
-        "interface  with lbfgs" ON)
-
 if (WITH_LBFGS)
   add_subDIRECTORY(packages/yap-lbfgs)
 endif ()
 
 
 
-option(WITH_JAVA "Try to use Java (currently Java 6,7,8)" ON)
 
 if (WITH_JAVA)
   #detect java setup, as it is shared between different installations.
@@ -857,18 +892,35 @@ endif (JNI_FOUND)
 
 
   endif (Java_Development_FOUND)
-endif(WITH_JAVA)
 
   add_subDIRECTORY(packages/jpl)
 
+endif(WITH_JAVA)
+
+if (WITH_CUDD)
+
   add_subDIRECTORY(packages/bdd)
 
+endif()
+
+if (WITH_PROBLOG)
+
   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
 # option (USE_MAXPERFORMANCE
@@ -886,28 +938,9 @@ add_subDIRECTORY(packages/clpqr)
 # option (USE_CYGWIN
 #   "use cygwin library in WIN32" OFF)
 
-option(WITH_PRISM
-        "use PRISM system in YAP" ON)
 #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
 # OPTION(WIN64
 #   "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
-        "NOT WITH_YAPOR_THOR; NOT WITH_SYSTEM_MMAP" OFF)
-
-if (NOT ANDROID)
 
   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)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MPI_C_COMPILE_FLAGS} ")
     include_directories(${MPI_C_INCLUDE_PATH})
@@ -981,7 +1006,7 @@ if (MPI_C_FOUND)
     endif ()
   endif (MPI_C_FOUND)
 
-endif(NOT ANDROID)
+endif(WITH_MPI)
 
 ##   add_subDIRECTORY(utils)
 

CXX/yapi.cpp

@@ -977,7 +977,7 @@ PredEntry *YAPPredicate::getPred(Term &t, Term &m, CELL *&out) {
   } else {
     ap = RepPredProp(PredPropByFunc(f, m));
     if (out)
-      memmove(out, RepAppl(t) + 1, ap->ArityOfPE * sizeof(CELL));
+      memmove(out, (const CELL *)RepAppl(t) + 1, ap->ArityOfPE * sizeof(CELL));
     else
       out = RepAppl(t) + 1;
   }

CXX/yapt.hh

@@ -525,8 +525,9 @@ public:
       mk(t);
     }
   }
+  /// type check for unbound
   bool unbound() { return IsUnboundVar(VarOfTerm(gt())); }
-  inline bool isVar() { return true; }       /// type check for unbound
+  inline bool isVar() { return true; }      
   inline bool isAtom() { return false; }     ///  type check for atom
   inline bool isInteger() { return false; }  /// type check for integer
   inline bool isFloat() { return false; }    /// type check for floating-point

configure

@@ -165,7 +165,7 @@ print_help() {
   --mandir=DIR            man documentation [DATAROOTDIR/man]
   --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
 
     first=y
@@ -220,6 +220,8 @@ EOF
     exit 0
 }
 
+
+
 while [ $# != 0 ]; do
     case "$1" in
         "--cmake="*)
@@ -291,10 +293,10 @@ while [ $# != 0 ]; do
         "--docdir")
             CMAKE_ARGS="$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="*)
             CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_C_COMPILER=$(quote "${1#*=}")";;

library/lists.yap

@@ -57,7 +57,7 @@
     with the `use_module(library(lists))` command.
 */
 
-:- include(pl/bootlists).
+%:- include(pl/bootlists).
 
 /** @pred list_concat(+ _Lists_,? _List_)
 

os/sysbits.c

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

packages/ProbLog/problog_lbdd.yap

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

packages/ProbLog/problog_lbfgs.yap

@@ -431,7 +431,7 @@ do_learning_intern(Iterations,Epsilon) :-
 	 true
 	),
 
-%	update_values,
+	update_values,
 
 	(
 	 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(query_is_similar(_,_)),
 	  retractall(query_md5(_,_,_)),
 	  empty_bdd_directory,
 	  init_queries
-	 ); true
 	),
 
 
@@ -491,11 +487,48 @@ init_learning :-
 init_learning :-
 	check_examples,
 
+	retractall(current_iteration(_)),
+	assert(current_iteration(0)),
 %	empty_output_directory,
 	logger_write_header,
-
 	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
         % continuous facts are not supported yet.
         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
-	set_default_gradient_method,
+set_default_gradient_method :-
 	(	problog_flag(continuous_facts, true )
 	->
 	 problog_flag(init_method,(_,_,_,_,OldCall)),
@@ -527,30 +560,10 @@ init_learning :-
 	   set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile)))
 	  );
 	  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]),
   
 
 
-	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	% 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),
 	integer(I),
@@ -560,21 +573,6 @@ init_learning :-
 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,
@@ -584,6 +582,7 @@ set_default_gradient_method.
 
 
 init_queries :-
+    empty_bdd_directory,
 	format_learning(2,'Build BDDs for examples~n',[]),
 	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)).
@@ -703,41 +702,56 @@ ground_truth_difference :-
 %= -Float
 %========================================================================
 
-mse_trainingset_only_for_linesearch(MSE) :-
+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,
-
+	findall(t(LogCurrentProb,SquaredError),
-	example_count(Example_Count),
+		(user:training_example(QueryID,Query,TrueQueryProb,_Type),
-
+		 once(update_query(QueryID,'+',probability)),
-	bb_put(error_train_line_search,0.0),
-	forall(user:example(QueryID,_Query,QueryProb,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]),
+
 		 once(update_query_cleanup(QueryID)),
+		  SquaredError is (CurrentProb-TrueQueryProb)**2,
+		 LogCurrentProb is log(CurrentProb)
+		),
+		All),
+	maplist(tuple, All, AllLogs, AllSquaredErrors),
+	sum_list( AllLogs, LLH_Training_Queries),
+        close(Handle),
+
+	length(AllSquaredErrors,Length),
+
 	(
-		 (Type == '='; (Type == '<', CurrentProb>QueryProb); (Type=='>',CurrentProb<QueryProb))
+	 Length>0
 	->
 	 (
-		  bb_get(error_train_line_search,Old_Error),
+	  sum_list(AllSquaredErrors,SumAllSquaredErrors),
-		  New_Error is Old_Error + (CurrentProb-QueryProb)**2,
+	  min_list(AllSquaredErrors,MinError),
-		  bb_put(error_train_line_search,New_Error)
+	  max_list(AllSquaredErrors,MaxError),
-		 );true
+	  MSE is SumAllSquaredErrors/Length
-		)
+	 );(
+	    MSE=0.0,
+	    MinError=0.0,
+	    MaxError=0.0
 	   )
 	),
-	bb_delete(error_train_line_search,Error),
+
-	MSE is Error/Example_Count,
+	logger_set_variable(mse_trainingset,MSE),
-	format_learning(3,' (~8f)~n',[MSE]),
+	logger_set_variable(mse_min_trainingset,MinError),
-	retractall(values_correct).
+	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 :-
 	current_iteration(Iteration),
 	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 ',[]),
 	update_values,
 	bb_put(llh_test_queries,0.0),
@@ -821,11 +835,6 @@ save_old_probabilities :-
 gradient_descent :-
     problog_flag(sigmoid_slope,Slope),
 %	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),
 %	leash(0),trace,
 	lbfgs_initialize(N,X,0,Solver),
@@ -852,13 +861,13 @@ user:evaluate(LLH_Training_Queries, X,Grad,N,_,_) :-
     N1 is N-1,    
     forall(between(0,N1,I),
 	   (Grad[I] <== 0.0, S <== X[I], sigmoid(S,Slope, P), Probs[I] <== P)
-	  ), nl,
+	  ),
     forall( 
 	full_example(QueryID,QueryProb,BDD),	   
 	   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).
 
 full_example(QueryID,QueryProb,BDD) :-
@@ -984,7 +993,7 @@ user:progress(FX,X,_G,X_Norm,G_Norm,Step,_N,Iteration,Ls,0) :-
     NextIteration is CurrentIteration+1,
     assertz(current_iteration(NextIteration)),
     save_model,
-    set_problog_flag(mse_trainset, FX),
+    logger_set_variable(mse_trainingset, FX),
     X0 <== X[0], sigmoid(X0,Slope,P0),
     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]).

packages/bdd/cudd.c

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

packages/jpl/src/c/jpl.c

@@ -640,7 +640,7 @@ static JNIEnv*
 jni_env(void) /* economically gets a JNIEnv pointer, valid for this thread */
 { JNIEnv	*env;
 
-  switch( (*jvm)->GetEnv(jvm, (void**)&env, JNI_VERSION_1_8) )
+  switch( (*jvm)->GetEnv(jvm, (void**)&env, JNI_VERSION_1_4) )
   { case JNI_OK:
       return env;
     case JNI_EDETACHED:
@@ -5675,7 +5675,7 @@ static foreign_t
 	int			i;
 	term_t		head;
 	term_t		list;
-	char		*s;
+	char		*s = NULL;
 
 	if ( jvm_dia == NULL )  /* presumably, JVM is already started, so default options cannot now be set */
 		{

packages/myddas/mysql/CMakeLists.txt

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

packages/myddas/odbc/CMakeLists.txt

@@ -1,3 +1,4 @@
+if (WITH_ODBC)
   
   set( YAPODBC_SOURCES
     myddas_odbc.c
@@ -37,3 +38,5 @@ set_target_properties (YAPodbc PROPERTIES
   else()
     add_definitions (-DMYDDAS_ODBC=0)
   endif (ODBC_FOUND)
+
+endif()

packages/myddas/postgres/CMakeLists.txt

@@ -1,4 +1,6 @@
 
+if (WITH_POSTGRES)
+
   set( YAPPOSTGRES_SOURCES
     myddas_postgres.c
     )
@@ -33,3 +35,5 @@ install(TARGETS  YAPpostgres
       ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
       )
   endif (PostgreSQL_FOUND)
+
+endif()

packages/myddas/sqlite3/CMakeLists.txt

@@ -1,3 +1,5 @@
+if (WITH_SQLITE3)
+
   message( "   * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
 
   set (SQLITE_EXTRA
@@ -66,3 +68,5 @@ endif()
   install(FILES ${SQLITE_EXTRA}
     DESTINATION ${libpl}
     )
+
+endif()

packages/python/pybips.c

@@ -591,6 +591,7 @@ static long get_len_of_range(long lo, long hi, long step) {
 }
 
 #if PY_MAJOR_VERSION >= 3
+/*
  static PyStructSequence_Field pnull[] = {
     {"A1", NULL},  {"A2", NULL},  {"A3", NULL},  {"A4", NULL},  {"A5", NULL},
     {"A6", NULL},  {"A7", NULL},  {"A8", NULL},  {"A9", NULL},  {"A9", NULL},
@@ -600,6 +601,7 @@ static PyStructSequence_Field pnull[] = {
     {"A24", NULL}, {"A25", NULL}, {"A26", NULL}, {"A27", NULL}, {"A28", NULL},
     {"A29", NULL}, {"A29", NULL}, {"A30", NULL}, {"A31", NULL}, {"A32", NULL},
     {NULL, NULL}};
+*/
  
 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);
       desc->name = PyMem_Malloc(strlen(s) + 1);
       desc->doc = "YAPTerm";
-      desc->fields = pnull;
+      desc->fields = NULL;
       desc->n_in_sequence = arity;
       if (PyStructSequence_InitType2(typp, desc) < 0)
         return NULL;

pl/listing.yap

@@ -166,7 +166,7 @@ listing(Stream, [MV|MVs]) :- !,
     ->
       format( Stream, ':- dynamic ~q/~d.~n', [N,Ar])
     ;
-\      format( Stream, ':- dynamic ~q:~q/~d.~n', [M,N,Ar])
+      format( Stream, ':- dynamic ~q:~q/~d.~n', [M,N,Ar])
      ),
      fail.
 '$list_clauses'(Stream, M, Pred) :-

pl/protect.yap

@@ -49,6 +49,7 @@ prolog:'$protect' :-
     sub_atom(Name,0,1,_, '$'),
     functor(P,Name,Arity),
 %    '$hide_predicate'(P,M),
+    '$stash_predicate'(P,M),
     fail.
 prolog:'$protect' :-
     current_atom(Name),