autotools cpp update: linux

src/memacs/redef.h

@@ -13,8 +13,7 @@ redef.h,v
 */
 
 /*Publics by module*/
-
-#define exit emacs_exit
+#define exit(int) emacs_exit(int)
 
 /*ANSI size = 250*/
 #define ansibeep emacs_ansibeep

src/nrnmpi/Makefile.am

@@ -1,11 +1,12 @@
 lib_LTLIBRARIES = libnrnmpi.la
 
 nsrc=$(top_srcdir)/src
-includes = -I$(nsrc)/oc -I@MUSIC_INCDIR@ -I$(nsrc)/ivos
+includes = -I$(nsrc)/oc @NRN_REALTIME_INCLUDE@ -I@MUSIC_INCDIR@ -I$(nsrc)/ivos
 AM_CPPFLAGS = $(includes)
 
 libnrnmpi_la_SOURCES = nrnmpi.cpp bbsmpipack.cpp mpispike.cpp nrnrt.cpp
 
+CXX = @MPICCnrnmpi@
 
 if BUILD_NRNMPI_DYNAMIC
 

src/nrnmpi/nrnmpi_impl.h

@@ -11,11 +11,11 @@ extern void* hoc_Emalloc(size_t size);
 extern void hoc_malchk();
 extern void* hoc_Erealloc(void* buf, size_t size);
 
+extern MPI_Comm nrnmpi_world_comm;
+extern MPI_Comm nrnmpi_comm;
+
 #if defined(__cplusplus)
 }
 #endif
 
-extern MPI_Comm nrnmpi_world_comm;
-extern MPI_Comm nrnmpi_comm;
-
 #endif

src/nrnoc/Makefile.am

@@ -34,6 +34,8 @@ libnrnoc_la_SOURCES = $(MODFILES_C) cabcode.cpp capac.cpp clamp.cpp eion.cpp
     seclist.cpp method3.cpp hocprax.cpp secref.cpp ldifus.cpp hocusr.cpp nrnversion.cpp \
     nrnversion.h nrntimeout.cpp passive0.cpp
 
+libnrnoc_la_LIBADD = -lpthread
+
 ##
 ## The list of .c files which are actually built during the build procedure.
 ## These files should not be packaged in a distribution.

src/nrnoc/nrnnoiv.cpp

@@ -68,7 +68,7 @@ extern "C" double nrn_random_pick(void *r) { return 0.; }
 
 extern "C" int nrn_random_isran123(void *r, uint32_t *id1, uint32_t *id2, uint32_t *id3) { return 0.; }
 
-void hoc_new_opoint() {}
+void hoc_new_opoint(int) {}
 
 int special_pnt_call(Object *ob, Symbol *sym, int narg) { return 0; }
 
@@ -100,25 +100,25 @@ void nrn_fihexec(int i)
 {
 }
 
-void nrn_deliver_events(double tt)
+void nrn_deliver_events(NrnThread*)
 {
 }
 
 void nrn_record_init() {}
 
 void nrn_play_init() {}
 
-void fixed_record_continuous() {}
+void fixed_record_continuous(NrnThread*) {}
 
-void fixed_play_continuous() {}
+void fixed_play_continuous(NrnThread*) {}
 
 void nrniv_recalc_ptrs() {}
 
 void nrn_recalc_ptrvector() {}
 
 void nrn_extra_scatter_gather(int direction, int tid) {}
 
-void nrn_update_ion_pointer(int type, Datum *d, int i, int j) {}
+extern "C" void nrn_update_ion_pointer(int type, Datum *d, int i, int j) {}
 
 void nrn_update_ps2nt() {}
 
@@ -135,7 +135,7 @@ extern "C" void net_event() { hoc_execerror("net_event only available in nrniv",
 
 extern "C" void net_send() { hoc_execerror("net_send only available in nrniv", (char *) 0); }
 
-void artcell_net_send() { hoc_execerror("net_send only available in nrniv", (char *) 0); }
+extern "C" void artcell_net_send() { hoc_execerror("net_send only available in nrniv", (char *) 0); }
 
 extern "C" void net_move() { hoc_execerror("net_move only available in nrniv", (char *) 0); }
 
@@ -147,7 +147,7 @@ void nrn_use_daspk(int i)
 
 #if CVODE
 
-void cvode_fadvance(double t)
+extern "C" void cvode_fadvance(double t)
 {
 }
 
@@ -163,7 +163,7 @@ extern "C" void clear_event_queue() {}
 
 void init_net_events() {}
 
-void deliver_net_events() {}
+void deliver_net_events(NrnThread*) {}
 
 void hoc_reg_singlechan() {}
 
@@ -194,11 +194,11 @@ void nrn_daq_scanstart() {}
 
 void nrn_multisplit_ptr_update() {}
 
-void nrn_multisplit_bksub() { assert(0); }
+void nrn_multisplit_bksub(NrnThread*) { assert(0); }
 
-void nrn_multisplit_reduce_solve() { assert(0); }
+void nrn_multisplit_reduce_solve(NrnThread*) { assert(0); }
 
-void nrn_multisplit_triang() { assert(0); }
+void nrn_multisplit_triang(NrnThread*) { assert(0); }
 
 #if 1 || PARANEURON
 
@@ -208,6 +208,8 @@ double *nrn_classicalNodeB(Node *n) { return (double *) 0; }
 
 #endif
 
+extern "C" {
+
 void *nrn_pool_create(long count, int itemsize) {
     assert(0);
     return nullptr;
@@ -222,6 +224,8 @@ void *nrn_pool_alloc(void *pool) {
     return nullptr;
 }
 
+}
+
 #if NRN_MUSIC
 void nrnmusic_init(int* parg, char*** pargv){}      
 void nrnmusic_terminate(){}

src/nrnpython/rxdmath.cpp

@@ -4,29 +4,29 @@
  * names and arguments match the wrappers used in rxdmath.py
  */
 
-double factorial(const double x)
+extern "C" double factorial(const double x)
 {
 	return tgamma(x+1.);
 }
 
 
-double degrees(const double radians)
+extern "C" double degrees(const double radians)
 {
     return radians * (180. / M_PI);
 }
 
-void radians(const double degrees, double *radians)
+extern "C" void radians(const double degrees, double *radians)
 {
     *radians = degrees * (M_PI / 180.);
 }
 
 
-double log1p(const double x)
+extern "C" double log1p(const double x)
 {
 	return log(x+1.);
 }
 
-double vtrap(const double x, const double y)
+extern "C" double vtrap(const double x, const double y)
 {
     if(fabs(x/y) < 1e-6)
     {

src/oc/code.cpp

@@ -308,21 +308,23 @@ static void frame_objauto_recover_on_err(Frame *ff) { /* only on error */
            Here, stkp is the last+1 localobj slot pair on the stack.
         */
         Datum *stkp = f->argn + 2 + sp->u.u_proc->nauto * 2;
-        for (i = sp->u.u_proc->nobjauto; i > 0; --i) {
-            Object *ob = stkp[-2 * i].obj;
-            hoc_obj_unref(ob);
-            /* Note that these AUTOOBJECT stack locations have an itemtype that
-               are left over from the previous stack usage of that location.
-               Regardless of that itemtype (e.g. OBJECTTMP), these did NOT
-               increment tobj_count so we need to guarantee that the subsequent
-               stack_obtmp_recover_on_err does not inadvertently free it again
-               by setting the itemtype to a non OBJECTTMP value.  I hope this is
-               the only place where stack space was used in which no item type
-               was specified.
-               We are doing this here which happens rarely to avoid having to
-               set them when the stack obj pointers are zeroed.
-            */
-            stkp[-2 * i + 1].i = 0;
+        if(sp->u.u_proc != 0) {
+            for (i = sp->u.u_proc->nobjauto; i > 0; --i) {
+                Object *ob = stkp[-2 * i].obj;
+                hoc_obj_unref(ob);
+                /* Note that these AUTOOBJECT stack locations have an itemtype that
+                   are left over from the previous stack usage of that location.
+                   Regardless of that itemtype (e.g. OBJECTTMP), these did NOT
+                   increment tobj_count so we need to guarantee that the subsequent
+                   stack_obtmp_recover_on_err does not inadvertently free it again
+                   by setting the itemtype to a non OBJECTTMP value.  I hope this is
+                   the only place where stack space was used in which no item type
+                   was specified.
+                   We are doing this here which happens rarely to avoid having to
+                   set them when the stack obj pointers are zeroed.
+                */
+                stkp[-2 * i + 1].i = 0;
+            }
         }
     }
 }

src/oc/hocmodl.h

@@ -1,7 +1,7 @@
 extern void hoc_model(), hoc_initmodel(), hoc_terminal(), hoc_prconst();
 extern int *hoc_pindepindex;
 
-static VoidFunc function[] = {
+static VoidFunc functions[] = {
 "model", hoc_model,
 "initmodel", hoc_initmodel,
 "terminal", hoc_terminal,

src/oc/hocusr.cpp

@@ -44,7 +44,7 @@ void nrn_load_name_check(const char *name) {
 
 static void arayinstal(Symbol *sp, int nsub, int sub1, int sub2, int sub3);
 
-void hoc_spinit(void)    /* install user variables and functions */
+extern "C" void hoc_spinit(void)    /* install user variables and functions */
 {
     int i;
     Symbol *s;

src/oc/mk_hocusr_h.py

@@ -59,7 +59,7 @@ def process(type, names):
 
 print('''
 /* Functions */
-static VoidFunc function[] = {
+static VoidFunc functions[] = {
 ''')
 
 for i in voidfun:

src/oc/ocnoiv.cpp

@@ -59,6 +59,12 @@ const char* path_prefix_to_libnrniv() { return NULL; }
 #endif
 
 #if !defined(SOME_IV)
+#if defined(__cplusplus)
+class IvocVect;
+#else
+#define IvocVect void
+#endif
+extern "C" {
 /*ARGSUSED*/
 int ivoc_list_look(Object* ob, Object* oblook, char* path, int depth)
 {
@@ -76,41 +82,38 @@ void hoc_template_notify(Object* ob, int create) {}
 #endif
 
 /*ARGSUSED*/
-int hoc_readcheckpoint(char* f) { return 0; }
-
-/*ARGSUSED*/
-extern "C" int vector_arg_px(int i, double** p) {
+extern int vector_arg_px(int i, double** p) {
 	hoc_execerror("implemented in ivoc library", "vector_arg_px");
 	return 0;
 }
-int vector_capacity(void* v) {return 0;}
-extern "C" void install_vector_method(const char* name, Pfrd_vp f) {}
-extern "C" int vector_instance_px(void* vv, double** px){return 0;}
-void vector_resize(void* v, void* n) {
+int vector_capacity(IvocVect* v) {return 0;}
+void install_vector_method(const char* name, Pfrd_vp f) {}
+ int vector_instance_px(void* vv, double** px){return 0;}
+void vector_resize(IvocVect* v, int n) {
 	hoc_execerror("implemented in ivoc library", "vector_resize");
 }
-void vector_append(void* vv, double x) {}
-void vector_delete(void* v) {}
+void vector_append(IvocVect* vv, double x) {}
+void vector_delete(IvocVect* v) {}
+
+IvocVect *vector_arg(int i) { return nullptr; }
+IvocVect *vector_new2(IvocVect *v) { return nullptr; }
+Object **vector_pobj(IvocVect *v) { return (Object **) 0; }
+double *vector_vec(IvocVect *v) {
+    hoc_execerror("implemented in ivoc library", "vector_vec");
+    return (double *) 0;
+}
 
+Object *ivoc_list_item(Object *list, int item) {
+    hoc_execerror("implemented in ivoc library", "ivoc_list_item");
+    return nullptr;
+}
+int ivoc_list_count(Object *list) { return 0; }
 #if defined(__cplusplus)
-class IvocVect;
-#else
-#define IvocVect void
-#endif
-
-IvocVect* vector_arg(int i) { return nullptr;}
-IvocVect* vector_new2(void* v) { return nullptr;}
-Object** vector_pobj(void* v) { return (Object**)0;}
-double* vector_vec(void* v) {
-	hoc_execerror("implemented in ivoc library", "vector_vec");
-	return (double*)0;
 }
+#endif
+/*ARGSUSED*/
+int hoc_readcheckpoint(char* f) { return 0; }
 
-extern "C" Object* ivoc_list_item(Object* list, int item) {
-	hoc_execerror("implemented in ivoc library", "ivoc_list_item");
-	return nullptr;
-}
-int ivoc_list_count(Object* list) { return 0; }
 void bbs_done(void){}
 
 Symbol* ivoc_alias_lookup(const char* name, Object* ob) {return (Symbol*)0;}

src/oc/spinit.cpp

@@ -31,6 +31,6 @@ spinit.cpp,v
 */
 
 
-void hoc_spinit(void)	/* Dummy special init */
+extern "C" void hoc_spinit(void)	/* Dummy special init */
 {
 }