Merge branch 'master' into cornu/split_sparse13

cmake/ConfigFileSetting.cmake

@@ -30,7 +30,6 @@ set(HAVE_NAMESPACES "/**/")
 set(HAVE_STTY 0)
 # below two are universal nowadays
 set(IVOS_FABS "::fabs")
-set(HAVE_STL "/**/")
 set(prefix ${CMAKE_INSTALL_PREFIX})
 set(host_cpu ${CMAKE_SYSTEM_PROCESSOR})
 set(exec_prefix ${prefix})
@@ -223,8 +222,6 @@ nrn_check_symbol_exists("vprintf" "" HAVE_VPRINTF)
 nrn_check_cxx_symbol_exists("getpw" "sys/types.h;pwd.h" HAVE_GETPW)
 nrn_check_cxx_symbol_exists("fesetround" "" HAVE_FESETROUND)
 nrn_check_cxx_symbol_exists("feenableexcept" "" HAVE_FEENABLEEXCEPT)
-# not necessary to check as it should be always there
-set(HAVE_SSTREAM /**/)
 
 # =============================================================================
 # Check data types

cmake_nrnconf.h.in

@@ -153,9 +153,6 @@
 /* (Define if this signal exists) */
 #undef HAVE_SIGSEGV
 
-/* define if the compiler has stringstream */
-#undef HAVE_SSTREAM
-
 /* Define to 1 if you have the <stdarg.h> header file. */
 #undef HAVE_STDARG_H
 

share/lib/python/neuron/rxd/initializer.py

@@ -14,16 +14,17 @@ def _do_ion_register():
 
 _init_lock = RLock()
 has_initialized = False
+is_initializing = False
 
 
 def _do_init():
-    global has_initialized, _init_lock
+    global has_initialized, is_initializing, _init_lock
     with _init_lock:
-        if not has_initialized:
+        if not has_initialized and not is_initializing:
             from . import species, region, rxd
 
             if len(species._all_species) > 0:
-                has_initialized = True
+                is_initializing = True
                 # TODO: clean this up so not repetitive; can't do it super cleanly because of the multiple phases of species
                 for obj in region._all_regions:
                     obj = obj()
@@ -55,6 +56,8 @@ def _do_init():
                     if obj is not None:
                         obj._do_init()
                 rxd._init()
+                has_initialized = True
+            is_initializing = False
 
 
 def is_initialized():

share/lib/python/neuron/rxd/rxd.py

@@ -617,8 +617,10 @@ def _update_node_data(force=False, newspecies=False):
                 # TODO: separate compiling reactions -- so the indices can be updated without recompiling
                 _include_flux(True)
                 _setup_units(force=True)
-
-            # end#if
+            else:
+                # don't call _setup_memb_currents if nsegs changed -- because
+                # it is called by change units.
+                _setup_memb_currents()
 
 
 def _matrix_to_rxd_sparse(m):

share/lib/python/neuron/rxdtests/do_test.py

@@ -60,9 +60,14 @@ def collect_data():
             data["data"] = []
             data["record_count"] = 1
         # remove previous record if h.t is the same
-        if data["record_count"] > 1 and h.t == data["data"][-len(local_data)]:
-            data["record_count"] -= 1
-            del data["data"][-len(local_data) :]
+        if data["record_count"] > 1:
+            if len(local_data) > len(data["data"]):
+                # model changed -- reset data collection
+                data["data"] = []
+                data["record_count"] = 1
+            elif h.t == data["data"][-len(local_data)]:
+                data["record_count"] -= 1
+                del data["data"][-len(local_data) :]
         # add new data record
         data["data"].extend(local_data)
         # print correct record length

src/ivoc/ivocmain.cpp

@@ -182,15 +182,6 @@ extern void setneuronhome(const char*) {
 }
 #endif
 
-#if 0
-void penv() {
-	int i;
-	for (i=0; environ[i]; ++i) {
-		printf("%p %s\n", environ[i], environ[i]);
-	}
-}
-#endif
-
 #if DARWIN || defined(__linux__)
 #include "nrnwrap_dlfcn.h"
 #include <string>
@@ -314,16 +305,6 @@ static int nrn_optargint(const char* opt, int* pargc, const char** argv, int dfl
 void nrn_InitializeJavaVM();
 #endif
 
-#if 0  // for debugging
-void prargs(const char* s, int argc, const char** argv) {
-	int i;
-	printf("%s argc=%d\n", s, argc);
-	for (i=0; i < argc; ++i) {
-		printf(" %d |%s|\n", i, argv[i]);
-	}
-}
-#endif
-
 void hoc_nrnmpi_init() {
 #if NRNMPI
     if (!nrnmpi_use) {
@@ -529,14 +510,6 @@ int ivocmain_session(int argc, const char** argv, const char** env, int start_se
 #endif
         // putenv and setenv may invalidate env but we no longer
         // use it so following should not be needed
-#if 0
-#if HAVE_UNISTD_H && !defined(__APPLE__)
-	env = environ;
-#endif
-#if defined(__APPLE__)
-	env = (*_NSGetEnviron());
-#endif
-#endif
     }
 
 #else  // Not unix:

src/ivoc/nrnmain.cpp

@@ -27,12 +27,6 @@ int main(int argc, char** argv, char** env) {
     nrn_noauto_dlopen_nrnmech = 1;
 #endif
 
-#if 0
-printf("argc=%d\n", argc);
-for (int i=0; i < argc; ++i) {
-printf("argv[%d]=|%s|\n", i, argv[i]);
-}
-#endif
 #if NRNMPI
 #if NRNMPI_DYNAMICLOAD
     nrnmpi_stubs();
@@ -80,42 +74,3 @@ printf("argv[%d]=|%s|\n", i, argv[i]);
 #if USENCS
 void nrn2ncs_outputevent(int, double) {}
 #endif
-
-// moving following to src/oc/ockludge.cpp since on
-// Darwin Kernel Version 8.9.1 on apple i686 (and the newest config.guess
-// thinks it is a i386, but that is a different story)
-// including mpi.h gives some errors like:
-// /Users/hines/mpich2-1.0.5p4/instl/include/mpicxx.h:26:2: error: #error
-// SEEK_SET is #defined but must not be for the C++ binding of MPI"
-
-#if 0 && NRNMPI && DARWIN
-// For DARWIN I do not really know the proper way to avoid
-// dyld: lazy symbol binding failed: Symbol not found: _MPI_Init
-// when the MPI functions are all used in the libnrnmpi.dylib
-// but the libmpi.a is statically linked. Therefore I am forcing
-// the linking here by listing all the MPI functions being used.
-#include <mpi.h>
-static void work_around() {
-	MPI_Comm c = MPI_COMM_WORLD;
-	MPI_Init(0, 0);
-	MPI_Comm_rank(c, 0);
-	MPI_Comm_size(c, 0);
-	MPI_Wtime();
-	MPI_Finalize();
-	MPI_Unpack(0, 0, 0, 0, 0, 0, c);
-	MPI_Pack(0, 0, 0, 0, 0, 0, c);
-	MPI_Pack_size(0, 0, c, 0);
-	MPI_Send(0,0,0,0,0,c);
-	MPI_Probe(0, 0, c, 0);
-	MPI_Get_count(0, 0, 0);
-	MPI_Recv(0,0,0,0,0,c,0);
-	MPI_Sendrecv(0,0,0,0,0,0,0,0,0,0,c,0);
-	MPI_Iprobe(0,0,c,0,0);
-	MPI_Get_address(0,0);
-	MPI_Type_create_struct(0,0,0,0,0);
-	MPI_Type_commit(0);
-	MPI_Allgather(0,0,0,0,0,0,c);
-	MPI_Allgatherv(0,0,0,0,0,0,0,c);
-	MPI_Allreduce(0,0,0,0,0,c);
-}
-#endif

src/nrniv/nvector_nrnparallel_ld.cpp

@@ -21,23 +21,11 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-/* for NRNMPI_DYNAMICLOAD */
 #include <nrnmpiuse.h>
-#if NRNMPI_DYNAMICLOAD
-extern "C" void nrnmpi_dbl_allreduce_vec(double* src, double* dest, int cnt, int type);
-extern "C" void nrnmpi_longdbl_allreduce_vec(long double* src,
-                                             long double* dest,
-                                             int cnt,
-                                             int type);
-extern "C" void nrnmpi_long_allreduce_vec(long* src, long* dest, int cnt, int type);
+#include <nrnmpidec.h>
 extern int nrnmpi_numprocs;
-#endif
 
 #include "nvector_nrnparallel_ld.h"
-#if NRNMPI_DYNAMICLOAD
-#else
-extern MPI_Comm nrnmpi_comm;
-#endif
 #include "sundialsmath.h"
 #include "sundialstypes.h"
 
@@ -97,12 +85,7 @@ N_Vector N_VNewEmpty_NrnParallelLD(MPI_Comm comm, long int local_length, long in
 
     /* Compute global length as sum of local lengths */
     n = local_length;
-#if NRNMPI_DYNAMICLOAD
     nrnmpi_long_allreduce_vec(&n, &Nsum, 1, 1);
-#else
-    comm = nrnmpi_comm;
-    MPI_Allreduce(&n, &Nsum, 1, MPI_LONG, MPI_SUM, comm);
-#endif
     if (Nsum != global_length) {
         printf(BAD_N);
         return (NULL);
@@ -428,11 +411,7 @@ void N_VSpace_NrnParallelLD(N_Vector v, long int* lrw, long int* liw) {
     int npes;
 
     comm = NV_COMM_P_LD(v);
-#if NRNMPI_DYNAMICLOAD
     npes = nrnmpi_numprocs;
-#else
-    MPI_Comm_size(comm, &npes);
-#endif
 
     *lrw = NV_GLOBLENGTH_P_LD(v);
     *liw = 2 * npes;
@@ -905,31 +884,9 @@ static realtype VAllReduce_NrnParallelLD(realtype d, int op, MPI_Comm comm) {
      *   min if op = 3.
      * The operation is over all processors in the communicator
      */
-
     realtype out = 0.0;
-
-#if NRNMPI_DYNAMICLOAD
     nrnmpi_dbl_allreduce_vec(&d, &out, 1, op);
-#else
-    switch (op) {
-    case 1:
-        MPI_Allreduce(&d, &out, 1, MPI_DOUBLE, MPI_SUM, comm);
-        break;
-
-    case 2:
-        MPI_Allreduce(&d, &out, 1, MPI_DOUBLE, MPI_MAX, comm);
-        break;
-
-    case 3:
-        MPI_Allreduce(&d, &out, 1, MPI_DOUBLE, MPI_MIN, comm);
-        break;
-
-    default:
-        break;
-    }
-#endif
-
-    return (out);
+    return out;
 }
 
 static realtype VAllReduce_long_NrnParallelLD(realtype d, int op, MPI_Comm comm) {
@@ -942,11 +899,7 @@ static realtype VAllReduce_long_NrnParallelLD(realtype d, int op, MPI_Comm comm)
      */
     assert(op == 1);
     long double ld_in{d}, ld_out{};
-#if NRNMPI_DYNAMICLOAD
     nrnmpi_longdbl_allreduce_vec(&ld_in, &ld_out, 1, op);
-#else
-    MPI_Allreduce(&ld_in, &ld_out, 1, MPI_LONG_DOUBLE, MPI_SUM, comm);
-#endif
     return ld_out;
 }
 

src/nrniv/nvector_nrnparallel_ld.h

@@ -65,13 +65,7 @@ mv temp nvector_nrnparallel_ld.cpp
 
 
 #include <nrnmpiuse.h>
-#if NRNMPI_DYNAMICLOAD
-#define MPI_DOUBLE double
-#define MPI_LONG   long
-#define MPI_Comm   int
-#else
-#include <mpi.h>
-#endif
+#define MPI_Comm int
 
 #include "nvector.h"
 #include "sundialstypes.h"

src/nrnmpi/mpispike.cpp

@@ -643,11 +643,10 @@ double nrnmpi_dbl_allreduce(double x, int type) {
 }
 
 extern "C" void nrnmpi_dbl_allreduce_vec(double* src, double* dest, int cnt, int type) {
-    int i;
     MPI_Op t;
     assert(src != dest);
     if (nrnmpi_numprocs < 2) {
-        for (i = 0; i < cnt; ++i) {
+        for (int i = 0; i < cnt; ++i) {
             dest[i] = src[i];
         }
         return;

src/nrnmpi/nrnmpidec.h

@@ -7,7 +7,7 @@ the prototypes be of the form "type foo(type arg, ...)"
 #define nrnmpidec_h
 #include <nrnmpiuse.h>
 #include <cstdint>
-typedef long double longdbl;
+using longdbl = long double;
 #if NRNMPI
 #include <stdlib.h>
 #include <string>
@@ -22,6 +22,8 @@ typedef struct bbsmpibuf {
     int refcount;
 } bbsmpibuf;
 
+struct NRNMPI_Spike;
+
 // olupton 2022-07-06: dynamic MPI needs to dlopen some of these (slightly
 // redefined) symbol names, so keep C linkage for simplicity
 extern "C" {

src/nrnpython/rxd.cpp

@@ -483,7 +483,6 @@ extern "C" void set_setup_matrices(fptr setup_matrices) {
 
 extern "C" void set_setup_units(fptr setup_units) {
     _setup_units = setup_units;
-    _setup_units();
 }
 
 /* nrn_tree_solve modified from nrnoc/ldifus.c */
@@ -884,7 +883,7 @@ extern "C" void register_rate(int nspecies,
     } else {
         react->vptrs = NULL;
     }
-    react->state_idx = (int***) malloc(nseg * sizeof(double**));
+    react->state_idx = (int***) malloc(nseg * sizeof(int**));
     for (i = 0, idx = 0; i < nseg; i++) {
         react->state_idx[i] = (int**) malloc((nspecies + nparam) * sizeof(int*));
         for (j = 0; j < nspecies + nparam; j++) {

src/oc/nrnmpi.h

@@ -14,10 +14,10 @@ extern int nrnmpi_myid;           /* rank in subworld */
 extern int nrnmpi_numprocs_bbs;   /* number of subworlds */
 extern int nrnmpi_myid_bbs;       /* rank in nrn_bbs_comm of rank 0 of a subworld */
 
-typedef struct {
+struct NRNMPI_Spike {
     int gid;
     double spiketime;
-} NRNMPI_Spike;
+};
 
 #if NRNMPI