Fixes for multi-execution in-memory transfer with NEURON (#349)

  - global ion maps were deleted at the end of every run
  - in case of in-memory execution mechanisms are registered
    only once and hence ions map is created only one
  - this is why ions shouldnt not be deleted if we are doing
    embedded run with neuron

coreneuron/io/nrn_setup.cpp

@@ -985,11 +985,34 @@ inline void mech_layout(FileHandler& F, T* data, int cnt, int sz, int layout) {
     }
 }
 
+/**
+ * Cleanup global ion map created during mechanism registration
+ *
+ * In case of coreneuron standalone execution nrn_ion_global_map
+ * can be deleted at the end of execution. But in case embedded
+ * run via neuron, mechanisms are registered only once i.e. during
+ * first call to coreneuron. This is why we call cleanup only in
+ * case of standalone coreneuron execution via nrniv-core or
+ * special-core.
+ *
+ * @todo coreneuron should have finalise callback which can be
+ * called from NEURON for final memory cleanup including global
+ * state like registered mechanisms and ions map.
+ */
+void nrn_cleanup_ion_map() {
+    for (int i = 0; i < nrn_ion_global_map_size; i++) {
+        free_memory(nrn_ion_global_map[i]);
+    }
+    free_memory(nrn_ion_global_map);
+    nrn_ion_global_map = nullptr;
+    nrn_ion_global_map_size = 0;
+}
+
 /* nrn_threads_free() presumes all NrnThread and NrnThreadMembList data is
  * allocated with malloc(). This is not the case here, so let's try and fix
  * things up first. */
 
-void nrn_cleanup(bool clean_ion_global_map) {
+void nrn_cleanup() {
     clear_event_queue();  // delete left-over TQItem
     gid2in.clear();
     gid2out.clear();
@@ -1000,15 +1023,6 @@ void nrn_cleanup(bool clean_ion_global_map) {
         nrnthread_chkpnt = nullptr;
     }
 
-    // clean ions global maps
-    if (clean_ion_global_map) {
-        for (int i = 0; i < nrn_ion_global_map_size; i++)
-            free_memory(nrn_ion_global_map[i]);
-        free_memory(nrn_ion_global_map);
-        nrn_ion_global_map = nullptr;
-        nrn_ion_global_map_size = 0;
-    }
-
     // clean NrnThreads
     for (int it = 0; it < nrn_nthread; ++it) {
         NrnThread* nt = nrn_threads + it;

coreneuron/mechanism/mech/enginemech.cpp

@@ -28,6 +28,8 @@ void modl_reg() {
 extern bool nrn_have_gaps;
 extern bool nrn_use_fast_imem;
 
+/// function defined in coreneuron library
+extern void nrn_cleanup_ion_map();
 }  // namespace coreneuron
 
 /** Initialize mechanisms and run simulation using CoreNEURON
@@ -37,7 +39,9 @@ extern bool nrn_use_fast_imem;
 int solve_core(int argc, char** argv) {
     mk_mech_init(argc, argv);
     coreneuron::modl_reg();
-    return run_solve_core(argc, argv);
+    int ret = run_solve_core(argc, argv);
+    coreneuron::nrn_cleanup_ion_map();
+    return ret;
 }
 
 extern "C" {

coreneuron/nrniv/nrniv_decl.h

@@ -67,7 +67,8 @@ extern double* stdindex2ptr(int mtype, int index, NrnThread&);
 extern void delete_trajectory_requests(NrnThread&);
 extern int nrn_setup_multiple;
 extern int nrn_setup_extracon;
-extern void nrn_cleanup(bool clean_ion_global_map = true);
+extern void nrn_cleanup();
+extern void nrn_cleanup_ion_map();
 extern void BBS_netpar_solve(double);
 extern void nrn_mkPatternStim(const char* filename);
 extern int nrn_extra_thread0_vdata;

tests/jenkins/neuron_direct.py

@@ -27,10 +27,12 @@
 tvstd = tv.cl()
 i_memstd = i_mem.cl()
 
-#h.CoreNeuronRun[0].run()
 pc = h.ParallelContext()
 h.stdinit()
 pc.nrncore_run("-e %g"%h.tstop, 0)
+# running second time for testing multiple executions
+h.stdinit()
+pc.nrncore_run("-e %g"%h.tstop, 0)
 
 if not bool(tv.eq(tvstd)):
     print("Voltage times are different")