Fix issue with progress bar not showing in gap junction simulations (#254)

* Fixes issue with progressbar not instantiated when running sim with nrn_fixed_step_minimal
  - Moved block of code calling nrn_fixed_step_minimal from netcvode to fadvance_core
  - Added instantiation and update of progressbar for it
  - Update progressbar every 5 steps

Author: iomaganaris

coreneuron/network/netcvode.cpp

@@ -576,26 +576,12 @@ void SelfEvent::pr(const char* s, double tt, NetCvode*) {
 }
 
 void ncs2nrn_integrate(double tstop) {
-    double ts;
-    int n = (int)((tstop - nrn_threads->_t) / dt + 1e-9);
+    int total_sim_steps = static_cast<int>((tstop - nrn_threads->_t) / dt + 1e-9);
 
-    if (n > 3 && !nrn_have_gaps) {
-        nrn_fixed_step_group_minimal(n);
+    if (total_sim_steps > 3 && !nrn_have_gaps) {
+        nrn_fixed_step_group_minimal(total_sim_steps);
     } else {
-#if NRNMPI
-        ts = tstop - dt;
-        nrn_assert(nrn_threads->_t <= tstop);
-        // It may very well be the case that we do not advance at all
-        while (nrn_threads->_t <= ts) {
-#else
-        ts = tstop - .5 * dt;
-        while (nrn_threads->_t < ts) {
-#endif
-            nrn_fixed_step_minimal();
-
-            if (stoprun)
-                break;
-        }
+        nrn_fixed_single_steps_minimal(total_sim_steps, tstop);
     }
 
     // handle all the pending flag=1 self events

coreneuron/sim/fadvance_core.cpp

@@ -108,11 +108,36 @@ void finalize_progress_bar() {
     }
 }
 
-void nrn_fixed_step_group_minimal(int n) {
-    static int step = 0;
+void nrn_fixed_single_steps_minimal(int total_sim_steps, double tstop) {
+    const int progressbar_update_interval = 5;
+    static int current_steps = 0;
+    initialize_progress_bar(total_sim_steps);
+#if NRNMPI
+    double updated_tstop = tstop - dt;
+    nrn_assert(nrn_threads->_t <= tstop);
+    // It may very well be the case that we do not advance at all
+    while (nrn_threads->_t <= updated_tstop) {
+#else
+    double updated_tstop = tstop - .5 * dt;
+    while (nrn_threads->_t < updated_tstop) {
+#endif
+        nrn_fixed_step_minimal();
+        if (stoprun) {
+            break;
+        }
+        current_steps++;
+        if (!(current_steps % progressbar_update_interval)) {
+            update_progress_bar(current_steps, nrn_threads[0]._t);
+        }
+    }
+    finalize_progress_bar();
+}
+
+void nrn_fixed_step_group_minimal(int total_sim_steps) {
+    static int current_steps = 0;
     dt2thread(dt);
     nrn_thread_table_check();
-    step_group_n = n;
+    step_group_n = total_sim_steps;
     step_group_begin = 0;
     step_group_end = 0;
     initialize_progress_bar(step_group_n);
@@ -129,7 +154,7 @@ void nrn_fixed_step_group_minimal(int n) {
         if (stoprun) {
             break;
         }
-        step++;
+        current_steps++;
         step_group_begin = step_group_end;
         update_progress_bar(step_group_end, nrn_threads[0]._t);
     }

coreneuron/sim/multicore.hpp

@@ -170,7 +170,8 @@ extern void nrn_solve_minimal(NrnThread*);
 extern void nrncore2nrn_send_init();
 extern void* setup_tree_matrix_minimal(NrnThread*);
 extern void nrncore2nrn_send_values(NrnThread*);
-extern void nrn_fixed_step_group_minimal(int n);
+extern void nrn_fixed_step_group_minimal(int total_sim_steps);
+extern void nrn_fixed_single_steps_minimal(int total_sim_steps, double tstop);
 extern void nrn_fixed_step_minimal(void);
 extern void nrn_finitialize(int setv, double v);
 extern void nrn_mk_table_check(void);

extra/instrumentation.tau

@@ -37,6 +37,7 @@ BEGIN_INCLUDE_LIST
  void coreneuron::nrn_finitialize(int, double)
  void coreneuron::nrn_fixed_step_group(int)
  void coreneuron::nrn_fixed_step_group_minimal(int)
+ void coreneuron::nrn_fixed_single_steps_minimal(int, double)
  void coreneuron::nrn_flush_reports(double)
  void coreneuron::nrn_lhs(coreneuron::NrnThread *)
  void coreneuron::nrn_multithread_job(void *(*)(coreneuron::NrnThread *))