From f47a7bb999fe01d053465b81552631542780a4ee Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Mon, 17 Dec 2012 16:25:27 +0000
Subject: [PATCH 01/12] add debugging hooks to gc

---
 C/heapgc.c | 33 ++++++++++++++++++++++++++++++---
 H/heapgc.h |  4 +++-
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/C/heapgc.c b/C/heapgc.c
index 2f4617664..31b453dba 100644
--- a/C/heapgc.c
+++ b/C/heapgc.c
@@ -410,8 +410,15 @@ push_registers(Int num_regs, yamop *nextop USES_REGS)
     al = al->NextAE;
   }
   while (gl) {
-    check_pr_trail(TR PASS_REGS);
-    TrailTerm(TR++) = gl->global;
+    Term t = gl->global;
+    if (!IsUnboundVar(&gl->global) &&
+	!IsAtomTerm(t) &&
+	!IsIntTerm(t)
+	) {
+      check_pr_trail(TR PASS_REGS);
+      //fprintf(stderr,"in=%s %p\n", gl->AtomOfGE->StrOfAE, gl->global);
+      TrailTerm(TR++) = t;
+    }
     gl = gl->NextGE;
   }
   while (sal) {
@@ -504,7 +511,14 @@ pop_registers(Int num_regs, yamop *nextop USES_REGS)
     al = al->NextAE;
   }
   while (gl) {
-    gl->global = TrailTerm(ptr++);
+    Term t = gl->global;
+    if (!IsUnboundVar(&gl->global) &&
+	!IsAtomTerm(t) &&
+	!IsIntTerm(t)
+	) {
+      //fprintf(stderr,"out=%s %p\n", gl->AtomOfGE->StrOfAE, gl->global);
+      gl->global = TrailTerm(ptr++);
+    }
     gl = gl->NextGE;
   }
   sal = LOCAL_StaticArrays;
@@ -1150,6 +1164,7 @@ mark_variable(CELL_PTR current USES_REGS)
     POP_CONTINUATION();
   }
   if (current >= H0 && current < H) {
+    //fprintf(stderr,"%p M\n", current);
     LOCAL_total_marked++;
     if (current < LOCAL_HGEN) {
       LOCAL_total_oldies++;
@@ -1165,6 +1180,7 @@ mark_variable(CELL_PTR current USES_REGS)
     if (IN_BETWEEN(LOCAL_GlobalBase,current,H) && GlobalIsAttVar(current) && current==next) {
       if (next < H0) POP_CONTINUATION();
       if (!UNMARKED_MARK(next-1,local_bp)) {
+	//fprintf(stderr,"%p M\n", next-1);
 	LOCAL_total_marked++;
 	if (next-1 < LOCAL_HGEN) {
 	  LOCAL_total_oldies++;
@@ -1207,6 +1223,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	    UNMARK(current);
 	    *current = cnext;
 	    if (current >= H0 && current < H) {
+	      //fprintf(stderr,"%p M\n", current-1);
 	      LOCAL_total_marked--;
 	      if (current < LOCAL_HGEN) {
 		LOCAL_total_oldies--;
@@ -1231,6 +1248,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	*current = UNMARK_CELL(cnext);
 	UNMARK(current);
 	if (current >= H0 && current < H ) {
+	  //fprintf(stderr,"%p M\n", current);
 	  LOCAL_total_marked--;
 	  if (current < LOCAL_HGEN) {
 	    LOCAL_total_oldies--;
@@ -1278,6 +1296,7 @@ mark_variable(CELL_PTR current USES_REGS)
       /* speedup for strings */
       if (IsAtomOrIntTerm(*next)) {
 	if (!UNMARKED_MARK(next,local_bp)) {
+	  //fprintf(stderr,"%p M\n", next);
 	  LOCAL_total_marked++;
 	  if (next < LOCAL_HGEN) {
 	    LOCAL_total_oldies++;
@@ -1337,6 +1356,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	  DEBUG_printf0("%p 1\n", next);
 	  DEBUG_printf0("%p 3\n", next);
 	}
+	//fprintf(stderr,"%p M 3\n", next);
 	LOCAL_total_marked += 3;
 	PUSH_POINTER(next PASS_REGS);
 	PUSH_POINTER(next+2 PASS_REGS);
@@ -1352,6 +1372,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	    DEBUG_printf0("%p 1\n", next);
 	    DEBUG_printf1("%p %ld\n", next, (long int)(sz+1));
 	  }
+	  //fprintf(stderr,"%p M %d\n", next,1+sz);
 	  LOCAL_total_marked += 1+sz;
 	  PUSH_POINTER(next+sz PASS_REGS);
 	  MARK(next+sz);
@@ -1390,6 +1411,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	    DEBUG_printf0("%p 1\n", next);
 	    DEBUG_printf1("%p %ld\n", next, (long int)(sz+2));
 	  }
+	  //fprintf(stderr,"%p M %d\n", next,2+sz);
 	  LOCAL_total_marked += 2+sz;
 	  PUSH_POINTER(next PASS_REGS);
 	  sz++;
@@ -1411,6 +1433,7 @@ mark_variable(CELL_PTR current USES_REGS)
 #endif
     arity = ArityOfFunctor((Functor)(cnext));
     MARK(next);
+    //fprintf(stderr,"%p M\n", next);
     ++LOCAL_total_marked;
     if (next < LOCAL_HGEN) {
       ++LOCAL_total_oldies;
@@ -1422,6 +1445,7 @@ mark_variable(CELL_PTR current USES_REGS)
     /* speedup for leaves */
     while (arity && IsAtomOrIntTerm(*next)) {
       if (!UNMARKED_MARK(next,local_bp)) {
+	//fprintf(stderr,"%p M\n", next);
 	LOCAL_total_marked++;
 	if (next < LOCAL_HGEN) {
 	  LOCAL_total_oldies++;
@@ -1695,6 +1719,7 @@ mark_trail(tr_fr_ptr trail_ptr, tr_fr_ptr trail_base, CELL *gc_H, choiceptr gc_B
 	     The ideal solution would be to unbind all variables. The current solution is to
 	     remark it as an attributed variable */
 	  if (IN_BETWEEN(LOCAL_GlobalBase,hp,H) && GlobalIsAttVar(hp) && !UNMARKED_MARK(hp-1,LOCAL_bp)) {
+	    //fprintf(stderr,"%p M\n", hp);
 	    LOCAL_total_marked++;
 	    PUSH_POINTER(hp-1 PASS_REGS);
 	    if (hp-1 < LOCAL_HGEN) {
@@ -3367,6 +3392,7 @@ compact_heap( USES_REGS1 )
 	ptr++;
 	MARK(ptr);
 #ifdef DEBUG
+	//fprintf(stderr,"%p U %d\n", ptr, nofcells);
 	found_marked+=nofcells;
 #endif
 	/* first swap the tag so that it will be seen by the next step */
@@ -3381,6 +3407,7 @@ compact_heap( USES_REGS1 )
 	DEBUG_printf20("%p 1\n", current);
       }
 #ifdef DEBUG
+      //  fprintf(stderr,"%p U\n", current);
       found_marked++;
 #endif /* DEBUG */
       update_relocation_chain(current, dest PASS_REGS);
diff --git a/H/heapgc.h b/H/heapgc.h
index 79d5d97ca..caada250d 100644
--- a/H/heapgc.h
+++ b/H/heapgc.h
@@ -111,7 +111,9 @@ UNMARKED_MARK__(CELL* ptr, char *bp USES_REGS)
 static inline void
 MARK__(CELL* ptr USES_REGS)
 {
-  mcell(ptr) = mcell(ptr) | MARK_BIT;
+  Int pos = ptr - (CELL *)LOCAL_GlobalBase;
+  char t = LOCAL_bp[pos];
+  LOCAL_bp[pos] = t | MARK_BIT;
 }
 
 static inline void

From 06cf32688522106b9ce9c9b3be0e7c7c4037c1b7 Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Mon, 17 Dec 2012 16:27:15 +0000
Subject: [PATCH 02/12] avoi calls to inityaamregs.

---
 C/c_interface.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/C/c_interface.c b/C/c_interface.c
index d3338a2da..775a4992a 100644
--- a/C/c_interface.c
+++ b/C/c_interface.c
@@ -3190,7 +3190,7 @@ YAP_Init(YAP_init_args *yap_init)
       /* first, initialise the saved state */
       Term t_goal = MkAtomTerm(AtomInitProlog);
       YAP_RunGoalOnce(t_goal);
-      Yap_InitYaamRegs( 0 );
+      //      Yap_InitYaamRegs( 0 );
       /* reset stacks */
       return YAP_BOOT_FROM_SAVED_CODE;
     } else {
@@ -3314,7 +3314,7 @@ YAP_Reset(void)
     }
   }
   /* reinitialise the engine */
-  Yap_InitYaamRegs( worker_id );
+  //  Yap_InitYaamRegs( worker_id );
   GLOBAL_Initialised = TRUE;
 
   RECOVER_MACHINE_REGS();

From 4d9d22530fc6c56d81056ec2c6cbe95c1eea5b31 Mon Sep 17 00:00:00 2001
From: "U-vsc-PC\\vsc" <vsc@vsc-PC.(none)>
Date: Wed, 19 Dec 2012 00:48:43 +0000
Subject: [PATCH 03/12] fix compilation on sequential win32

---
 C/sysbits.c | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/C/sysbits.c b/C/sysbits.c
index e46dd7399..497ed2a07 100755
--- a/C/sysbits.c
+++ b/C/sysbits.c
@@ -466,7 +466,7 @@ static clock_t TimesStartOfTimes, Times_last_time;
 
 /* store user time in this variable */
 static void
-InitTime (int)
+InitTime (int wid)
 {
   HANDLE hProcess = GetCurrentProcess();
   FILETIME CreationTime, ExitTime, KernelTime, UserTime;
@@ -476,8 +476,9 @@ InitTime (int)
     t = clock ();
     Times_last_time = TimesStartOfTimes = t;
   } else {
+#if THREADS
     (*REMOTE_ThreadHandle(wid).last_timep).dwLowDateTime = 
-      UserTime.dwLowDateTime;
+      UserTime.dwLowDateTime;pp
     (*REMOTE_ThreadHandle(wid).last_timep).dwHighDateTime =
       UserTime.dwHighDateTime;
     (*REMOTE_ThreadHandle(wid).start_of_timesp).dwLowDateTime =
@@ -488,10 +489,28 @@ InitTime (int)
       KernelTime.dwLowDateTime;
     (*REMOTE_ThreadHandle(wid).last_time_sysp).dwHighDateTime = 
       KernelTime.dwHighDateTime;
-    (*REMOTE_ThreadHandle(wid).start_of_times_sysp).dwLowDateTime =
+    (*REMOTE_ThreadHandle(wid).start_of_times_sysp).dwLowDateTime =
       KernelTime.dwLowDateTime;
     (*REMOTE_ThreadHandle(wid).start_of_times_sysp).dwHighDateTime = 
       KernelTime.dwHighDateTime;
+#else
+    last_time.dwLowDateTime = 
+      UserTime.dwLowDateTime;
+    last_time.dwHighDateTime =
+      UserTime.dwHighDateTime;
+    StartOfTimes.dwLowDateTime =
+      UserTime.dwLowDateTime;
+    StartOfTimes.dwHighDateTime = 
+      UserTime.dwHighDateTime;
+    last_time_sys.dwLowDateTime =
+      KernelTime.dwLowDateTime;
+    last_time_sys.dwHighDateTime = 
+      KernelTime.dwHighDateTime;
+    StartOfTimes_sys.dwLowDateTime =
+      KernelTime.dwLowDateTime;
+    StartOfTimes_sys.dwHighDateTime = 
+      KernelTime.dwHighDateTime;
+#endif
   }
 }
 

From a7307f3faaa1215398e06c0e5dd373f63a85451b Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Wed, 19 Dec 2012 00:52:29 +0000
Subject: [PATCH 04/12] add  SWI PL_uninstantiatin_error

---
 include/SWI-Prolog.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/SWI-Prolog.h b/include/SWI-Prolog.h
index a88e8c450..79a8ca0d9 100755
--- a/include/SWI-Prolog.h
+++ b/include/SWI-Prolog.h
@@ -706,6 +706,7 @@ PL_EXPORT(int) 		PL_get_list_ex(term_t l, term_t h, term_t t);
 PL_EXPORT(int) 		PL_get_nil_ex(term_t l);
 
 PL_EXPORT(int)		PL_instantiation_error(term_t culprit);
+PL_EXPORT(int)		PL_uninstantiation_error(term_t culprit);
 PL_EXPORT(int)		PL_representation_error(const char *resource);
 PL_EXPORT(int)		PL_type_error(const char *expected, term_t culprit);
 PL_EXPORT(int)		PL_domain_error(const char *expected, term_t culprit);

From fe4218be19be7d9a3c7bb5e47c0f20d5f22fdea5 Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:12:30 +0000
Subject: [PATCH 05/12] improve java support

---
 configure.in | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/configure.in b/configure.in
index db505b1ef..cc03e2acd 100755
--- a/configure.in
+++ b/configure.in
@@ -863,7 +863,6 @@ elif test -e "$srcdir"/packages/python/Makefile.in ; then
    PYTHONHOME=`$PYTHON -c'import sys; print sys.prefix'`
    PYTHONVERSION=`"$PYTHON" -c "import sys; print sys.version[[:3]]"`
    PYTHON_LIBS="-L $PYTHONHOME/lib -lpython$PYTHONVERSION"
-   LIBS="$LIBS $PYTHON_LIBS"
    PYTHON_INCLUDES="-I $PYTHONHOME/include/python$PYTHONVERSION"
 else
     PYTHON_TARGET="dummy"
@@ -1110,11 +1109,7 @@ elif test -e "$srcdir"/packages/jpl/Makefile.in; then
 	JAVA_HOME="$yap_cv_java"
 	case "$target_os" in
 	    *cygwin*|*mingw*)
-	       if test $threads = yes; then
-	         JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib -lpthread"
-               else
-	         JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib"
-               fi
+	       JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib"
 	       JPLCFLAGS="-I\"$JAVA_HOME\"/include -I\"$JAVA_HOME\"/include/win32"
 	       	  ;;
 	       *darwin*)
@@ -1475,8 +1470,6 @@ dnl Linux has both elf and a.out, in this case we found elf
 	;;
 esac
 
-EXTRA_LIBS_FOR_SWIDLLS="$EXTRA_LIBS_FOR_DLLS"
-
 if test "$dynamic_loading" = "yes"
 then 
   YAPLIB_CFLAGS="$SHLIB_CFLAGS"
@@ -1813,7 +1806,6 @@ AC_SUBST(SHLIB_CXX_LD)
 AC_SUBST(YAPLIB_LD)
 AC_SUBST(YAPLIB_CFLAGS)
 AC_SUBST(EXTRA_LIBS_FOR_DLLS)
-AC_SUBST(EXTRA_LIBS_FOR_SWIDLLS)
 dnl objects in YAP library
 AC_SUBST(YAPLIB)
 AC_SUBST(DYNYAPLIB)
@@ -2256,6 +2248,9 @@ AC_CHECK_TYPES(ssize_t, [], [],
 #include <sys/socket.h>
 ])
 
+EXTRA_LIBS_FOR_SWIDLLS="$EXTRA_LIBS_FOR_DLLS $CLIB_PTHREADS"
+AC_SUBST(EXTRA_LIBS_FOR_SWIDLLS)
+
 dnl tszet and timezone trouble
 
 AC_MSG_CHECKING("variable timezone in tzset")

From a309f47794a5cc03ffd1a0e88dcf7dc575f5e879 Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:13:20 +0000
Subject: [PATCH 06/12] MT support in win32

---
 C/sysbits.c | 8 ++++++--
 H/Yap.h     | 7 ++++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/C/sysbits.c b/C/sysbits.c
index 497ed2a07..4725607c6 100755
--- a/C/sysbits.c
+++ b/C/sysbits.c
@@ -477,8 +477,12 @@ InitTime (int wid)
     Times_last_time = TimesStartOfTimes = t;
   } else {
 #if THREADS
+    REMOTE_ThreadHandle(wid).start_of_timesp = (struct _FILETIME *)malloc(sizeof(FILETIME));
+    REMOTE_ThreadHandle(wid).last_timep = (struct _FILETIME *)malloc(sizeof(FILETIME));
+    REMOTE_ThreadHandle(wid).start_of_times_sysp = (struct _FILETIME *)malloc(sizeof(FILETIME));
+    REMOTE_ThreadHandle(wid).last_time_sysp = (struct _FILETIME *)malloc(sizeof(FILETIME));
     (*REMOTE_ThreadHandle(wid).last_timep).dwLowDateTime = 
-      UserTime.dwLowDateTime;pp
+      UserTime.dwLowDateTime;
     (*REMOTE_ThreadHandle(wid).last_timep).dwHighDateTime =
       UserTime.dwHighDateTime;
     (*REMOTE_ThreadHandle(wid).start_of_timesp).dwLowDateTime =
@@ -1494,8 +1498,8 @@ STATIC_PROTO (void my_signal, (int, void (*)(int)));
 static RETSIGTYPE
 HandleMatherr(int sig)
 {
-#if HAVE_FETESTEXCEPT
   CACHE_REGS
+#if HAVE_FETESTEXCEPT
   /* This should work in Linux, but it doesn't seem to. */
   
   int raised = fetestexcept(FE_ALL_EXCEPT);
diff --git a/H/Yap.h b/H/Yap.h
index 910a8b8ef..a77e3d4c1 100755
--- a/H/Yap.h
+++ b/H/Yap.h
@@ -746,11 +746,16 @@ typedef struct thandle {
 #endif
   pthread_mutex_t tlock;
   pthread_mutex_t tlock_status;
-#if HAVE_GETRUSAGE||defined(_WIN32)
+#if HAVE_GETRUSAGE
   struct timeval *start_of_timesp;
   struct timeval *last_timep;
   struct timeval *start_of_times_sysp;
   struct timeval *last_time_sysp;
+#elif _WIN32
+  struct _FILETIME *start_of_timesp;
+  struct _FILETIME *last_timep;
+  struct _FILETIME *start_of_times_sysp;
+  struct _FILETIME *last_time_sysp;
 #endif
 } yap_thandle;
 #endif /* THREADS */

From cb37e7714a56641a7b882819f0d2bf056281e253 Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:13:51 +0000
Subject: [PATCH 07/12] fix warnings

---
 C/adtdefs.c | 2 --
 C/amasm.c   | 1 -
 C/dbase.c   | 1 -
 C/gprof.c   | 2 +-
 C/index.c   | 1 -
 C/qlyr.c    | 2 --
 C/qlyw.c    | 2 --
 7 files changed, 1 insertion(+), 10 deletions(-)
 mode change 100644 => 100755 C/adtdefs.c
 mode change 100644 => 100755 C/amasm.c
 mode change 100644 => 100755 C/dbase.c
 mode change 100644 => 100755 C/gprof.c
 mode change 100644 => 100755 C/index.c
 mode change 100644 => 100755 C/qlyr.c
 mode change 100644 => 100755 C/qlyw.c

diff --git a/C/adtdefs.c b/C/adtdefs.c
old mode 100644
new mode 100755
index 9ec4c8fab..30f404c9f
--- a/C/adtdefs.c
+++ b/C/adtdefs.c
@@ -771,7 +771,6 @@ ExpandPredHash(void)
 Prop
 Yap_NewPredPropByFunctor(FunctorEntry *fe, Term cur_mod)
 {
-  CACHE_REGS
   PredEntry *p = (PredEntry *) Yap_AllocAtomSpace(sizeof(*p));
 
   if (p == NULL) {
@@ -907,7 +906,6 @@ Yap_NewThreadPred(PredEntry *ap USES_REGS)
 Prop
 Yap_NewPredPropByAtom(AtomEntry *ae, Term cur_mod)
 {
-  CACHE_REGS
   Prop p0;
   PredEntry *p = (PredEntry *) Yap_AllocAtomSpace(sizeof(*p));
 
diff --git a/C/amasm.c b/C/amasm.c
old mode 100644
new mode 100755
index e160d7f8d..62223ed11
--- a/C/amasm.c
+++ b/C/amasm.c
@@ -2050,7 +2050,6 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
     yamop *newcp;
     /* emit a special instruction and then a label for backpatching */
     if (pass_no) {
-      CACHE_REGS
       UInt size = (UInt)NEXTOP((yamop *)NULL,OtaLl);
       if ((newcp = (yamop *)Yap_AllocCodeSpace(size)) == NULL) {
 	/* OOOPS, got in trouble, must do a longjmp and recover space */
diff --git a/C/dbase.c b/C/dbase.c
old mode 100644
new mode 100755
index 90fc7cb4d..69cf50f9c
--- a/C/dbase.c
+++ b/C/dbase.c
@@ -1887,7 +1887,6 @@ Yap_new_ludbe(Term t, PredEntry *pe, UInt nargs)
 static LogUpdClause *
 record_lu(PredEntry *pe, Term t, int position)
 {
-  CACHE_REGS
   LogUpdClause *cl;
   
   if ((cl = new_lu_db_entry(t, pe)) == NULL) {
diff --git a/C/gprof.c b/C/gprof.c
old mode 100644
new mode 100755
index 80352eb9e..19642cded
--- a/C/gprof.c
+++ b/C/gprof.c
@@ -1177,8 +1177,8 @@ static Int profres0( USES_REGS1 ) {
 void
 Yap_InitLowProf(void)
 {
-  CACHE_REGS
 #if LOW_PROF
+  CACHE_REGS
   LOCAL_ProfCalls = 0;
   LOCAL_ProfilerOn = FALSE;
 
diff --git a/C/index.c b/C/index.c
old mode 100644
new mode 100755
index 8e2c717b2..b7b65e7f8
--- a/C/index.c
+++ b/C/index.c
@@ -1888,7 +1888,6 @@ emit_single_switch_case(ClauseDef *min, struct intermediates *cint, int first, i
 static UInt
 suspend_indexing(ClauseDef *min, ClauseDef *max, PredEntry *ap, struct intermediates *cint)
 {
-  CACHE_REGS
   UInt tcls = ap->cs.p_code.NOfClauses;
   UInt cls = (max-min)+1;
 
diff --git a/C/qlyr.c b/C/qlyr.c
old mode 100644
new mode 100755
index a0a802ae3..5c473b718
--- a/C/qlyr.c
+++ b/C/qlyr.c
@@ -961,7 +961,6 @@ read_ops(IOSTREAM *stream)  {
 
 static void
 read_module(IOSTREAM *stream) {
-  CACHE_REGS
   qlf_tag_t x;
 
   InitHash();
@@ -1045,7 +1044,6 @@ p_read_program( USES_REGS1 )
 int 
 Yap_Restore(char *s, char *lib_dir)
 {
-  CACHE_REGS
   IOSTREAM *stream  = Yap_OpenRestore(s, lib_dir);
   if (!stream) 
     return -1;
diff --git a/C/qlyw.c b/C/qlyw.c
old mode 100644
new mode 100755
index b00b923fb..0bde3d2e6
--- a/C/qlyw.c
+++ b/C/qlyw.c
@@ -765,7 +765,6 @@ save_ops(IOSTREAM *stream, Term mod) {
 
 static size_t
 save_module(IOSTREAM *stream, Term mod) {
-  CACHE_REGS
   PredEntry *ap = Yap_ModulePred(mod);
   InitHash();
   ModuleAdjust(mod);
@@ -803,7 +802,6 @@ save_header(IOSTREAM *stream)
 
 static size_t
 save_program(IOSTREAM *stream) {
-  CACHE_REGS
   ModEntry *me = CurrentModules;
 
   InitHash();

From 4098b9b964ce6a4a562da34691739b0aa58a3f84 Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:15:01 +0000
Subject: [PATCH 08/12] fix compilation MT in win32

---
 packages/prism/src/c/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 mode change 100644 => 100755 packages/prism/src/c/Makefile.in

diff --git a/packages/prism/src/c/Makefile.in b/packages/prism/src/c/Makefile.in
old mode 100644
new mode 100755
index b3d80ef7b..70268027a
--- a/packages/prism/src/c/Makefile.in
+++ b/packages/prism/src/c/Makefile.in
@@ -71,7 +71,7 @@ mp/%.o: $(srcdir)/mp/%.c
 	$(CC) -c $(CFLAGS) $< -o $@
 
 @DO_SECOND_LD@prism.@SO@: $(OBJS)
-@DO_SECOND_LD@	@SHLIB_LD@ $(LDFLAGS) -o $@ $(OBJS)  @EXTRA_LIBS_FOR_DLLS@
+@DO_SECOND_LD@	@SHLIB_LD@ $(LDFLAGS) -o $@ $(OBJS)  @EXTRA_LIBS_FOR_DLLS@ @CLIB_PTHREADS@
 
 all: $(TARGETS)
 

From ebb239b2335fd0c517216a4ec4c63217b9ca6c5c Mon Sep 17 00:00:00 2001
From: Vitor Santos Costa <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:15:26 +0000
Subject: [PATCH 09/12] uninst error

---
 os/pl-error.c | 5 +++++
 1 file changed, 5 insertions(+)
 mode change 100644 => 100755 os/pl-error.c

diff --git a/os/pl-error.c b/os/pl-error.c
old mode 100644
new mode 100755
index f3eb2f63b..8587a9198
--- a/os/pl-error.c
+++ b/os/pl-error.c
@@ -204,6 +204,11 @@ PL_instantiation_error(term_t actual)
 { return PL_error(NULL, 0, NULL, ERR_INSTANTIATION);
 }
 
+int
+PL_uninstantiation_error(term_t actual)
+{ return PL_error(NULL, 0, NULL, ERR_UNINSTANTIATION, 0, actual);
+}
+
 int
 PL_representation_error(const char *resource)
 { atom_t r = PL_new_atom(resource);

From 0ac9f6f4367bdfc7901bd88820a87895149ee750 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADtor=20Santos=20Costa?= <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:17:23 +0000
Subject: [PATCH 10/12] propagate changes

---
 configure | 251 ++++++++++++++++++++++++++++--------------------------
 1 file changed, 128 insertions(+), 123 deletions(-)

diff --git a/configure b/configure
index 509f2e2a8..40c53d5e3 100755
--- a/configure
+++ b/configure
@@ -1,11 +1,9 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68.
+# Generated by GNU Autoconf 2.69.
 #
 #
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
 #
 #
 # This configure script is free software; the Free Software Foundation
@@ -134,6 +132,31 @@ export LANGUAGE
 # CDPATH.
 (unset CDPATH) >/dev/null 2>&1 && unset CDPATH
 
+# Use a proper internal environment variable to ensure we don't fall
+  # into an infinite loop, continuously re-executing ourselves.
+  if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
+    _as_can_reexec=no; export _as_can_reexec;
+    # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+  *v*x* | *x*v* ) as_opts=-vx ;;
+  *v* ) as_opts=-v ;;
+  *x* ) as_opts=-x ;;
+  * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+as_fn_exit 255
+  fi
+  # We don't want this to propagate to other subprocesses.
+          { _as_can_reexec=; unset _as_can_reexec;}
 if test "x$CONFIG_SHELL" = x; then
   as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
   emulate sh
@@ -167,7 +190,8 @@ if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
 else
   exitcode=1; echo positional parameters were not saved.
 fi
-test x\$exitcode = x0 || exit 1"
+test x\$exitcode = x0 || exit 1
+test -x / || exit 1"
   as_suggested="  as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
   as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
   eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
@@ -212,21 +236,25 @@ IFS=$as_save_IFS
 
 
       if test "x$CONFIG_SHELL" != x; then :
-  # We cannot yet assume a decent shell, so we have to provide a
-	# neutralization value for shells without unset; and this also
-	# works around shells that cannot unset nonexistent variables.
-	# Preserve -v and -x to the replacement shell.
-	BASH_ENV=/dev/null
-	ENV=/dev/null
-	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-	export CONFIG_SHELL
-	case $- in # ((((
-	  *v*x* | *x*v* ) as_opts=-vx ;;
-	  *v* ) as_opts=-v ;;
-	  *x* ) as_opts=-x ;;
-	  * ) as_opts= ;;
-	esac
-	exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+  export CONFIG_SHELL
+             # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+  *v*x* | *x*v* ) as_opts=-vx ;;
+  *v* ) as_opts=-v ;;
+  *x* ) as_opts=-x ;;
+  * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
 fi
 
     if test x$as_have_required = xno; then :
@@ -328,6 +356,14 @@ $as_echo X"$as_dir" |
 
 
 } # as_fn_mkdir_p
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+  test -f "$1" && test -x "$1"
+} # as_fn_executable_p
 # as_fn_append VAR VALUE
 # ----------------------
 # Append the text in VALUE to the end of the definition contained in VAR. Take
@@ -449,6 +485,10 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits
   chmod +x "$as_me.lineno" ||
     { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
 
+  # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
+  # already done that, so ensure we don't try to do so again and fall
+  # in an infinite loop.  This has already happened in practice.
+  _as_can_reexec=no; export _as_can_reexec
   # Don't try to exec as it changes $[0], causing all sort of problems
   # (the dirname of $[0] is not the place where we might find the
   # original and so on.  Autoconf is especially sensitive to this).
@@ -483,16 +523,16 @@ if (echo >conf$$.file) 2>/dev/null; then
     # ... but there are two gotchas:
     # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
-    # In both cases, we have to default to `cp -p'.
+    # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp -p'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp -p'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp -p'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -504,28 +544,8 @@ else
   as_mkdir_p=false
 fi
 
-if test -x / >/dev/null 2>&1; then
-  as_test_x='test -x'
-else
-  if ls -dL / >/dev/null 2>&1; then
-    as_ls_L_option=L
-  else
-    as_ls_L_option=
-  fi
-  as_test_x='
-    eval sh -c '\''
-      if test -d "$1"; then
-	test -d "$1/.";
-      else
-	case $1 in #(
-	-*)set "./$1";;
-	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
-	???[sx]*):;;*)false;;esac;fi
-    '\'' sh
-  '
-fi
-as_executable_p=$as_test_x
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
 
 # Sed expression to map a string onto a valid CPP name.
 as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -617,6 +637,7 @@ ZLIB_TARGETS
 ZLIBS
 MAILDROP_CFLAGS
 RFC2045CHARSET
+EXTRA_LIBS_FOR_SWIDLLS
 CLIB_CRYPTLIBS
 CLIB_NETLIBS
 CLIB_PLTARGETS
@@ -686,7 +707,6 @@ YAP_EXTRAS
 SONAMEFLAG
 DYNYAPLIB
 YAPLIB
-EXTRA_LIBS_FOR_SWIDLLS
 EXTRA_LIBS_FOR_DLLS
 YAPLIB_CFLAGS
 YAPLIB_LD
@@ -1315,8 +1335,6 @@ target=$target_alias
 if test "x$host_alias" != x; then
   if test "x$build_alias" = x; then
     cross_compiling=maybe
-    $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
-    If a cross compiler is detected then cross compile mode will be used" >&2
   elif test "x$build_alias" != "x$host_alias"; then
     cross_compiling=yes
   fi
@@ -1607,9 +1625,9 @@ test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
 configure
-generated by GNU Autoconf 2.68
+generated by GNU Autoconf 2.69
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.
 _ACEOF
@@ -1920,7 +1938,7 @@ $as_echo "$ac_try_echo"; } >&5
 	 test ! -s conftest.err
        } && test -s conftest$ac_exeext && {
 	 test "$cross_compiling" = yes ||
-	 $as_test_x conftest$ac_exeext
+	 test -x conftest$ac_exeext
        }; then :
   ac_retval=0
 else
@@ -2023,7 +2041,8 @@ int
 main ()
 {
 static int test_array [1 - 2 * !(($2) >= 0)];
-test_array [0] = 0
+test_array [0] = 0;
+return test_array [0];
 
   ;
   return 0;
@@ -2039,7 +2058,8 @@ int
 main ()
 {
 static int test_array [1 - 2 * !(($2) <= $ac_mid)];
-test_array [0] = 0
+test_array [0] = 0;
+return test_array [0];
 
   ;
   return 0;
@@ -2065,7 +2085,8 @@ int
 main ()
 {
 static int test_array [1 - 2 * !(($2) < 0)];
-test_array [0] = 0
+test_array [0] = 0;
+return test_array [0];
 
   ;
   return 0;
@@ -2081,7 +2102,8 @@ int
 main ()
 {
 static int test_array [1 - 2 * !(($2) >= $ac_mid)];
-test_array [0] = 0
+test_array [0] = 0;
+return test_array [0];
 
   ;
   return 0;
@@ -2115,7 +2137,8 @@ int
 main ()
 {
 static int test_array [1 - 2 * !(($2) <= $ac_mid)];
-test_array [0] = 0
+test_array [0] = 0;
+return test_array [0];
 
   ;
   return 0;
@@ -2299,7 +2322,7 @@ This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
 It was created by $as_me, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
 
@@ -2675,7 +2698,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="${ac_tool_prefix}gcc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2715,7 +2738,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CC="gcc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2768,7 +2791,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="${ac_tool_prefix}cc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2809,7 +2832,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
        ac_prog_rejected=yes
        continue
@@ -2867,7 +2890,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2911,7 +2934,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CC="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3357,8 +3380,7 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 #include <stdarg.h>
 #include <stdio.h>
-#include <sys/types.h>
-#include <sys/stat.h>
+struct stat;
 /* Most of the following tests are stolen from RCS 5.7's src/conf.sh.  */
 struct buf { int x; };
 FILE * (*rcsopen) (struct buf *, struct stat *, int);
@@ -3471,7 +3493,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3515,7 +3537,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CXX="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3718,7 +3740,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_AWK="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -4068,7 +4090,7 @@ do
     for ac_prog in grep ggrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+      as_fn_executable_p "$ac_path_GREP" || continue
 # Check for GNU ac_path_GREP and select it if it is found.
   # Check for GNU $ac_path_GREP
 case `"$ac_path_GREP" --version 2>&1` in
@@ -4134,7 +4156,7 @@ do
     for ac_prog in egrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+      as_fn_executable_p "$ac_path_EGREP" || continue
 # Check for GNU ac_path_EGREP and select it if it is found.
   # Check for GNU $ac_path_EGREP
 case `"$ac_path_EGREP" --version 2>&1` in
@@ -5256,7 +5278,7 @@ case $as_dir/ in #((
     # by default.
     for ac_prog in ginstall scoinst install; do
       for ac_exec_ext in '' $ac_executable_extensions; do
-	if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+	if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
 	  if test $ac_prog = install &&
 	    grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
 	    # AIX install.  It has an incompatible calling convention.
@@ -5329,7 +5351,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5369,7 +5391,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_RANLIB="ranlib"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5421,7 +5443,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_INDENT="${ac_tool_prefix}indent"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5461,7 +5483,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_INDENT="indent"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5513,7 +5535,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_AR="${ac_tool_prefix}ar"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5553,7 +5575,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_AR="ar"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5605,7 +5627,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_MPI_CC="${ac_tool_prefix}mpicc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5645,7 +5667,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_MPI_CC="mpicc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5699,7 +5721,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_path_INSTALL_INFO="$as_dir/$ac_word$ac_exec_ext"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5740,7 +5762,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_path_SHELL="$as_dir/$ac_word$ac_exec_ext"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6730,7 +6752,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_REXE="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6851,7 +6873,7 @@ do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_PYTHON="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6882,7 +6904,6 @@ test -n "$PYTHON" || PYTHON=""none""
    PYTHONHOME=`$PYTHON -c'import sys; print sys.prefix'`
    PYTHONVERSION=`"$PYTHON" -c "import sys; print sys.version[:3]"`
    PYTHON_LIBS="-L $PYTHONHOME/lib -lpython$PYTHONVERSION"
-   LIBS="$LIBS $PYTHON_LIBS"
    PYTHON_INCLUDES="-I $PYTHONHOME/include/python$PYTHONVERSION"
 else
     PYTHON_TARGET="dummy"
@@ -7658,11 +7679,7 @@ elif test -e "$srcdir"/packages/jpl/Makefile.in; then
 	JAVA_HOME="$yap_cv_java"
 	case "$target_os" in
 	    *cygwin*|*mingw*)
-	       if test $threads = yes; then
-	         JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib -lpthread"
-               else
-	         JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib"
-               fi
+	       JAVALIBS="\"$JAVA_HOME\"/lib/jvm.lib"
 	       JPLCFLAGS="-I\"$JAVA_HOME\"/include -I\"$JAVA_HOME\"/include/win32"
 	       	  ;;
 	       *darwin*)
@@ -8425,8 +8442,6 @@ fi
 	;;
 esac
 
-EXTRA_LIBS_FOR_SWIDLLS="$EXTRA_LIBS_FOR_DLLS"
-
 if test "$dynamic_loading" = "yes"
 then
   YAPLIB_CFLAGS="$SHLIB_CFLAGS"
@@ -9702,7 +9717,6 @@ CMDEXT=sh
 
 
 
-
 
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gcc threaded code" >&5
@@ -10806,6 +10820,9 @@ _ACEOF
 fi
 
 
+EXTRA_LIBS_FOR_SWIDLLS="$EXTRA_LIBS_FOR_DLLS $CLIB_PTHREADS"
+
+
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking \"variable timezone in tzset\"" >&5
 $as_echo_n "checking \"variable timezone in tzset\"... " >&6; }
@@ -11832,16 +11849,16 @@ if (echo >conf$$.file) 2>/dev/null; then
     # ... but there are two gotchas:
     # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
-    # In both cases, we have to default to `cp -p'.
+    # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp -p'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp -p'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp -p'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -11901,28 +11918,16 @@ else
   as_mkdir_p=false
 fi
 
-if test -x / >/dev/null 2>&1; then
-  as_test_x='test -x'
-else
-  if ls -dL / >/dev/null 2>&1; then
-    as_ls_L_option=L
-  else
-    as_ls_L_option=
-  fi
-  as_test_x='
-    eval sh -c '\''
-      if test -d "$1"; then
-	test -d "$1/.";
-      else
-	case $1 in #(
-	-*)set "./$1";;
-	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
-	???[sx]*):;;*)false;;esac;fi
-    '\'' sh
-  '
-fi
-as_executable_p=$as_test_x
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+  test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
 
 # Sed expression to map a string onto a valid CPP name.
 as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -11944,7 +11949,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # values after options handling.
 ac_log="
 This file was extended by $as_me, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -12006,10 +12011,10 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
 config.status
-configured by $0, generated by GNU Autoconf 2.68,
+configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
@@ -12099,7 +12104,7 @@ fi
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 if \$ac_cs_recheck; then
-  set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+  set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
   shift
   \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
   CONFIG_SHELL='$SHELL'

From 14b67dc76db1fe0f44642b83749785c7e90fa91b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADtor=20Santos=20Costa?= <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:33:20 +0000
Subject: [PATCH 11/12] fix threads

---
 C/adtdefs.c | 18 ++++++++++++------
 C/amasm.c   |  5 ++++-
 C/dbase.c   | 11 +++++++----
 C/exec.c    |  2 +-
 C/index.c   |  5 ++++-
 5 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/C/adtdefs.c b/C/adtdefs.c
index 30f404c9f..922001d91 100755
--- a/C/adtdefs.c
+++ b/C/adtdefs.c
@@ -851,9 +851,12 @@ Yap_NewPredPropByFunctor(FunctorEntry *fe, Term cur_mod)
   }
   p->FunctorOfPred = fe;
   WRITE_UNLOCK(fe->FRWLock);
-  Yap_inform_profiler_of_clause(&(p->OpcodeOfPred), &(p->OpcodeOfPred)+1, p, GPROF_NEW_PRED_FUNC);
-  if (!(p->PredFlags & (CPredFlag|AsmPredFlag))) {
-    Yap_inform_profiler_of_clause(&(p->cs.p_code.ExpandCode), &(p->cs.p_code.ExpandCode)+1, p, GPROF_NEW_PRED_FUNC);
+  {
+    CACHE_REGS
+    Yap_inform_profiler_of_clause(&(p->OpcodeOfPred), &(p->OpcodeOfPred)+1, p, GPROF_NEW_PRED_FUNC);
+    if (!(p->PredFlags & (CPredFlag|AsmPredFlag))) {
+      Yap_inform_profiler_of_clause(&(p->cs.p_code.ExpandCode), &(p->cs.p_code.ExpandCode)+1, p, GPROF_NEW_PRED_FUNC);
+    }
   }
   return AbsPredProp(p);
 }
@@ -962,9 +965,12 @@ Yap_NewPredPropByAtom(AtomEntry *ae, Term cur_mod)
   p0 = AbsPredProp(p);
   p->FunctorOfPred = (Functor)AbsAtom(ae);
   WRITE_UNLOCK(ae->ARWLock);
-  Yap_inform_profiler_of_clause(&(p->OpcodeOfPred), &(p->OpcodeOfPred)+1, p, GPROF_NEW_PRED_ATOM);
-  if (!(p->PredFlags & (CPredFlag|AsmPredFlag))) {
-    Yap_inform_profiler_of_clause(&(p->cs.p_code.ExpandCode), &(p->cs.p_code.ExpandCode)+1, p, GPROF_NEW_PRED_ATOM);
+  {
+    CACHE_REGS
+    Yap_inform_profiler_of_clause(&(p->OpcodeOfPred), &(p->OpcodeOfPred)+1, p, GPROF_NEW_PRED_ATOM);
+    if (!(p->PredFlags & (CPredFlag|AsmPredFlag))) {
+      Yap_inform_profiler_of_clause(&(p->cs.p_code.ExpandCode), &(p->cs.p_code.ExpandCode)+1, p, GPROF_NEW_PRED_ATOM);
+    }
   }
   return p0;
 }
diff --git a/C/amasm.c b/C/amasm.c
index 62223ed11..7bd09e56c 100755
--- a/C/amasm.c
+++ b/C/amasm.c
@@ -2056,7 +2056,10 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
 	save_machine_regs();
 	siglongjmp(cip->CompilerBotch,2);
       }
-      Yap_inform_profiler_of_clause(newcp, (char *)(newcp)+size, ap, GPROF_INDEX); 
+      {
+        CACHE_REGS
+        Yap_inform_profiler_of_clause(newcp, (char *)(newcp)+size, ap, GPROF_INDEX); 
+      }
       Yap_LUIndexSpace_CP += size;
 #ifdef DEBUG
       Yap_NewCps++;
diff --git a/C/dbase.c b/C/dbase.c
index 69cf50f9c..99438d338 100755
--- a/C/dbase.c
+++ b/C/dbase.c
@@ -1892,7 +1892,10 @@ record_lu(PredEntry *pe, Term t, int position)
   if ((cl = new_lu_db_entry(t, pe)) == NULL) {
     return NULL;
   }
-  Yap_inform_profiler_of_clause(cl, (char *)cl+cl->ClSize, pe, GPROF_NEW_LU_CLAUSE); 
+  {
+    CACHE_REGS
+    Yap_inform_profiler_of_clause(cl, (char *)cl+cl->ClSize, pe, GPROF_NEW_LU_CLAUSE); 
+  }
   Yap_add_logupd_clause(pe, cl, (position == MkFirst ? 2 : 0));
   return cl;
 }
@@ -4429,7 +4432,7 @@ p_increase_reference_counter( USES_REGS1 )
   cl = (LogUpdClause *)DBRefOfTerm(t1);
   PELOCK(67,cl->ClPred);
   cl->ClRefCount++;
-  UNLOCK(cl->ClPred);
+  UNLOCK(cl->ClPred->PELock);
   return TRUE;
 }
 
@@ -4452,10 +4455,10 @@ p_decrease_reference_counter( USES_REGS1 )
   PELOCK(67,cl->ClPred);
   if (cl->ClRefCount) {
     cl->ClRefCount--;
-    UNLOCK(cl->ClPred);
+    UNLOCK(cl->ClPred->PELock);
     return TRUE;
   }
-  UNLOCK(cl->ClPred);
+  UNLOCK(cl->ClPred->PELock);
   return FALSE;
 }
 
diff --git a/C/exec.c b/C/exec.c
index c4c8628d0..6befeace0 100644
--- a/C/exec.c
+++ b/C/exec.c
@@ -1736,7 +1736,7 @@ Yap_InitYaamRegs( int myworker_id )
   Yap_ResetExceptionTerm ( myworker_id );
   Yap_PutValue (AtomBreak, MkIntTerm (0));
   TR = (tr_fr_ptr)REMOTE_TrailBase(myworker_id);
-  H = H0 = ((CELL *) REMOTE_GlobalBase(myworker_id))+1;
+  H = H0 = ((CELL *) REMOTE_GlobalBase(myworker_id))+1; // +1: hack to ensure the gc does not try to mark mistakenly
   LCL0 = ASP = (CELL *) REMOTE_LocalBase(myworker_id);
   CurrentTrailTop = (tr_fr_ptr)(REMOTE_TrailTop(myworker_id)-MinTrailGap);
   /* notice that an initial choice-point and environment
diff --git a/C/index.c b/C/index.c
index b7b65e7f8..252d56409 100755
--- a/C/index.c
+++ b/C/index.c
@@ -1923,7 +1923,10 @@ suspend_indexing(ClauseDef *min, ClauseDef *max, PredEntry *ap, struct intermedi
     } else {
       Yap_IndexSpace_EXT += sz;
     }
-    Yap_inform_profiler_of_clause(ncode, (CODEADDR)ncode+sz, ap, GPROF_NEW_EXPAND_BLOCK); 
+    {
+      CACHE_REGS
+      Yap_inform_profiler_of_clause(ncode, (CODEADDR)ncode+sz, ap, GPROF_NEW_EXPAND_BLOCK); 
+    }
     /* create an expand_block */
     ncode->opc = Yap_opcode(_expand_clauses);
     ncode->u.sssllp.p = ap;

From 3565a01f1eb3ddabfb3be4a8f59a6f687499a651 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADtor=20Santos=20Costa?= <vsc@dcc.fc.up.pt>
Date: Thu, 20 Dec 2012 21:41:06 +0000
Subject: [PATCH 12/12] upstream

---
 packages/real | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/real b/packages/real
index 29a8436d8..4452ed66c 160000
--- a/packages/real
+++ b/packages/real
@@ -1 +1 @@
-Subproject commit 29a8436d86886cf932a790a013cfcf10240c68c8
+Subproject commit 4452ed66c995b13258d74144d64a9d9425f22e77