Extend CoreNEURON POINTER transfer to any RANGE variable in a NRN_THREAD

cmake/NeuronTestHelper.cmake

@@ -389,7 +389,7 @@ function(nrn_add_test)
     ${test_names}
     PROPERTIES
       ENVIRONMENT
-      "${NRN_TEST_ENV};PATH=${nrnivmodl_working_directory}/${CMAKE_HOST_SYSTEM_PROCESSOR}:$ENV{PATH};CORENEURONLIB=${nrnivmodl_working_directory}/${CMAKE_HOST_SYSTEM_PROCESSOR}/libcorenrnmech${CMAKE_SHARED_LIBRARY_SUFFIX}"
+      "${NRN_TEST_ENV};PATH=${nrnivmodl_working_directory}/${CMAKE_HOST_SYSTEM_PROCESSOR}:${PROJECT_BINARY_DIR}/bin:$ENV{PATH};CORENEURONLIB=${nrnivmodl_working_directory}/${CMAKE_HOST_SYSTEM_PROCESSOR}/libcorenrnmech${CMAKE_SHARED_LIBRARY_SUFFIX}"
   )
 
   # Construct an expression containing the names of the test output files that will be passed to the

src/nrncvode/netcvode.cpp

@@ -5752,14 +5752,14 @@ int& n_trajec, int*& types, int*& indices, double**& pvars, double**& varrays) {
           }
         }
       }
-      if (n_trajec == 0) { // if errors reduced to 0, clean up
-        assert(n_pr == 0);
-        if (types) { delete [] types; types = NULL; }
-        if (indices) { delete [] indices; indices = NULL; }
-        if (vpr) { delete [] vpr; vpr = NULL; }
-        if (varrays) { delete [] varrays; varrays = NULL; }
-        if (pvars) { delete [] pvars; pvars = NULL; }
-      }
+    }
+    if (n_trajec == 0) { // if errors reduced to 0, clean up
+      assert(n_pr == 0);
+      if (types) { delete [] types; types = NULL; }
+      if (indices) { delete [] indices; indices = NULL; }
+      if (vpr) { delete [] vpr; vpr = NULL; }
+      if (varrays) { delete [] varrays; varrays = NULL; }
+      if (pvars) { delete [] pvars; pvars = NULL; }
     }
 #if 0
     printf("nrnthread_get_trajectory_requests tid=%d bsize=%d n_pr=%d n_trajec=%d\n", tid, bsize, n_pr, n_trajec);

src/nrniv/nrncore_write/callbacks/nrncore_callbacks.cpp

@@ -8,6 +8,7 @@
 #include "nrncvode.h"
 #include "nrniv_mf.h"
 #include "hocdec.h"
+#include "nrncore_write/utils/nrncore_utils.h"
 #include "nrncore_write/data/cell_group.h"
 #include "nrncore_write/io/nrncore_io.h"
 #include "parse.hpp"
@@ -323,7 +324,7 @@ int nrnthread_dat2_2(int tid, int*& v_parent_index, double*& a, double*& b,
 }
 
 int nrnthread_dat2_mech(int tid, size_t i, int dsz_inst, int*& nodeindices,
-                               double*& data, int*& pdata) {
+                               double*& data, int*& pdata, std::vector<int>& pointer2type) {
 
     if (tid >= nrn_nthread) { return 0; }
     CellGroup& cg = cellgroups_[tid];
@@ -367,7 +368,7 @@ int nrnthread_dat2_mech(int tid, size_t i, int dsz_inst, int*& nodeindices,
     sz = bbcore_dparam_size[type]; // nrn_prop_dparam_size off by 1 if cvode_ieq.
     if (sz) {
         int* pdata1;
-        pdata1 = datum2int(type, ml, nt, cg, cg.datumindices[dsz_inst], vdata_offset);
+        pdata1 = datum2int(type, ml, nt, cg, cg.datumindices[dsz_inst], vdata_offset, pointer2type);
         if (copy) {
             int nn = n*sz;
             for (int i=0; i < nn; ++i) {
@@ -498,25 +499,38 @@ int core2nrn_corepointer_mech(int tid, int type,
     return 1;
 }
 
-int* datum2int(int type, Memb_list* ml, NrnThread& nt, CellGroup& cg, DatumIndices& di, int ml_vdata_offset) {
+int* datum2int(int type, Memb_list* ml, NrnThread& nt, CellGroup& cg, DatumIndices& di, int ml_vdata_offset, std::vector<int>& pointer2type) {
     int isart = nrn_is_artificial_[di.type];
     int sz = bbcore_dparam_size[type];
     int* pdata = new int[ml->nodecount * sz];
+    int* semantics = memb_func[type].dparam_semantics;
     for (int i=0; i < ml->nodecount; ++i) {
         int ioff = i*sz;
         for (int j = 0; j < sz; ++j) {
             int jj = ioff + j;
             int etype = di.ion_type[jj];
             int eindex = di.ion_index[jj];
-            if (etype == -1) {
+            int seman = semantics[j];
+            // Would probably be more clear if use seman for as many as
+            // possible of the cases
+            // below and within each case deal with etype appropriately.
+            // ion_type and ion_index have become misnomers as they no longer
+            // refer to ions specificially but the mechanism type where the
+            // range variable lives (and otherwise is generally the same as
+            // seman). And ion_index refers to the index of the range variable
+            // within the mechanism (or voltage, area, etc.)
+            if (seman == -5) { // POINTER to range variable (e.g. voltage)
+                pdata[jj] = eindex;
+                pointer2type.push_back(etype);
+            }else if (etype == -1) {
                 if (isart) {
                     pdata[jj] = -1; // maybe save this space eventually. but not many of these in bb models
                 }else{
                     pdata[jj] = eindex;
                 }
             }else if (etype == -9) {
                 pdata[jj] = eindex;
-            }else if (etype > 0 && etype < 1000){//ion pointer and also POINTER
+            }else if (etype > 0 && etype < 1000){//ion pointer
                 pdata[jj] = eindex;
             }else if (etype > 1000 && etype < 2000) { //ionstyle can be explicit instead of pointer to int*
                 pdata[jj] = eindex;
@@ -531,9 +545,6 @@ int* datum2int(int type, Memb_list* ml, NrnThread& nt, CellGroup& cg, DatumIndic
             }else if (etype == -7) { // bbcorepointer
                 pdata[jj] = ml_vdata_offset + eindex;
                 //printf("etype %d jj=%d eindex=%d pdata=%d\n", etype, jj, eindex, pdata[jj]);
-            }else if (etype == -5) { // POINTER to voltage
-                pdata[jj] = eindex;
-                //printf("etype %d\n", etype);
             }else{ //uninterpreted
                 assert(eindex != -3); // avoided if last
                 pdata[jj] = 0;

src/nrniv/nrncore_write/callbacks/nrncore_callbacks.h

@@ -44,7 +44,7 @@ int nrnthread_dat2_1(int tid, int& ngid, int& n_real_gid, int& nnode, int& ndiam
 int nrnthread_dat2_2(int tid, int*& v_parent_index, double*& a, double*& b,
                      double*& area, double*& v, double*& diamvec);
 int nrnthread_dat2_mech(int tid, size_t i, int dsz_inst, int*& nodeindices,
-                        double*& data, int*& pdata);
+                        double*& data, int*& pdata, std::vector<int>& pointer2type);
 int nrnthread_dat2_3(int tid, int nweight, int*& output_vindex, double*& output_threshold,
                      int*& netcon_pnttype, int*& netcon_pntindex, double*& weights, double*& delays);
 int nrnthread_dat2_corepointer(int tid, int& n);
@@ -55,7 +55,7 @@ int nrnthread_dat2_vecplay_inst(int tid, int i, int& vptype, int& mtype,
                                 int& ix, int& sz, double*& yvec, double*& tvec,
                                 int& last_index, int& discon_index, int& ubound_index);
 
-int* datum2int(int type, Memb_list* ml, NrnThread& nt, CellGroup& cg, DatumIndices& di, int ml_vdata_offset);
+int* datum2int(int type, Memb_list* ml, NrnThread& nt, CellGroup& cg, DatumIndices& di, int ml_vdata_offset, std::vector<int>& pointer2type);
 }
 
 extern "C" {

src/nrniv/nrncore_write/data/cell_group.cpp

@@ -1,4 +1,5 @@
 #include "cell_group.h"
+#include "nrncore_write/utils/nrncore_utils.h"
 #include "nrnran123.h" // globalindex written to globals.dat
 #include "section.h"
 #include "parse.hpp"
@@ -161,7 +162,7 @@ CellGroup* CellGroup::mk_cellgroups(CellGroup* cgs) {
 }
 
 void CellGroup::datumtransform(CellGroup* cgs) {
-    // ions, area, and POINTER to v.
+    // ions, area, and POINTER to v or mechanism data.
     for (int ith=0; ith < nrn_nthread; ++ith) {
         NrnThread& nt = nrn_threads[ith];
         CellGroup& cg = cgs[ith];

src/nrniv/nrncore_write/data/cell_group.h

@@ -12,8 +12,6 @@ class PreSyn;
 class NetCon;
 class NrnThread;
 
-extern "C" int nrn_dblpntr2nrncore(double*, NrnThread&, int& type, int& etype);
-
 typedef std::pair < int, Memb_list* > MlWithArtItem;
 typedef std::vector < MlWithArtItem > MlWithArt;
 typedef std::map<double*, int> PVoid2Int;

src/nrniv/nrncore_write/data/datum_indices.h

@@ -12,8 +12,8 @@ class DatumIndices {
     virtual ~DatumIndices();
     int type;
     // ordering as though pdata[i][j] was pdata[0][i*sz+j]
-    int* ion_type; // -1 -2 -3 -4 -5 means area,iontype,cvodeieq,netsend,pointer
-    int* ion_index; // or index into _actual_area
+    int* ion_type; // negative codes semantics, positive codes mechanism type
+    int* ion_index; // index of range variable relative to beginning of that type
 };
 
 #endif //NRN_DATUM_INDICES_H

src/nrniv/nrncore_write/io/nrncore_io.cpp

@@ -22,7 +22,7 @@ extern NetCvode* net_cvode_instance;
 extern void (*nrnthread_v_transfer_)(NrnThread*);
 
 int chkpnt;
-const char *bbcore_write_version = "1.4"; // Generalize *_gap.dat to allow transfer of any range variable
+const char *bbcore_write_version = "1.5"; // Generalize POINTER to allow pointing to any RANGE variable
 
 /// create directory with given path
 void create_dir_path(const std::string& path) {
@@ -183,7 +183,8 @@ void write_nrnthread(const char* path, NrnThread& nt, CellGroup& cg) {
     for (size_t i = 0; i < mla.size(); ++i) {
         int type = mla[i].first;
         int *nodeindices=NULL, *pdata=NULL; double* data=NULL;
-        nrnthread_dat2_mech(nt.id, i, dsz_inst, nodeindices, data, pdata);
+        std::vector<int> pointer2type;
+        nrnthread_dat2_mech(nt.id, i, dsz_inst, nodeindices, data, pdata, pointer2type);
         Memb_list* ml = mla[i].second;
         int n = ml->nodecount;
         int sz = nrn_prop_param_size_[type];
@@ -199,6 +200,11 @@ void write_nrnthread(const char* path, NrnThread& nt, CellGroup& cg) {
             ++dsz_inst;
             writeint(pdata, n * sz);
             delete [] pdata;
+            sz = pointer2type.size();
+            fprintf(f, "%d npointer\n", int(sz));
+            if (sz > 0) {
+                writeint(pointer2type.data(), sz);
+            }
         }
     }
 

test/CMakeLists.txt

@@ -229,7 +229,7 @@ if(NRN_ENABLE_PYTHON AND PYTEST_FOUND)
     NAME coreneuron_modtests
     # This get used in 4 tests so make it the default and override in other tests.
     SCRIPT_PATTERNS test/coreneuron/test_spikes.py
-    MODFILE_PATTERNS test/coreneuron/mod/*.mod test/pynrn/unitstest.mod test/gjtests/natrans.mod)
+    MODFILE_PATTERNS test/coreneuron/mod/*.mod test/coreneuron/mod/axial.inc test/pynrn/unitstest.mod test/gjtests/natrans.mod)
   # In GPU builds run all of the tests on both CPU and GPU
   set(coreneuron_modtests_gpu_env CORENRN_ENABLE_GPU=true)
   foreach(processor cpu gpu)
@@ -294,6 +294,13 @@ if(NRN_ENABLE_PYTHON AND PYTEST_FOUND)
       SCRIPT_PATTERNS test/coreneuron/test_netmove.py
       COMMAND ${processor_env} COVERAGE_FILE=.coverage.coreneuron_test_netmove_py
               ${modtests_launch_py} test/coreneuron/test_netmove.py)
+    nrn_add_test(
+      GROUP coreneuron_modtests
+      NAME test_pointer_py_${processor}
+      REQUIRES coreneuron ${processor}
+      SCRIPT_PATTERNS test/coreneuron/test_pointer.py
+      COMMAND ${processor_env} COVERAGE_FILE=.coverage.coreneuron_test_pointer_py
+              ${modtests_launch_py} test/coreneuron/test_pointer.py)
     nrn_add_test(
       GROUP coreneuron_modtests
       NAME test_watchrange_py_${processor}

test/coreneuron/mod/axial.inc

@@ -0,0 +1,52 @@
+: Axial current and derivative with respect to x
+: INCLUDE in density and point process
+
+NEURON {
+    THREADSAFE
+    RANGE ri, ia, im
+    POINTER pv, pia, pim
+}
+
+UNITS {
+  (mv) = (millivolt)
+  (nA) = (nanoamp)
+  (MOhm) = (megohm)
+}
+
+PARAMETER {
+    ri (MOhm) : center of compartment to center of parent compartment
+}
+
+ASSIGNED {
+    v (mV)
+    ia (nA)
+    im (nA) : im - i_membrane_ = electode_currents
+    pv (mV) : parent v
+    pia (nA) : parent ia 
+    pim (nA) : parent im
+}
+
+AFTER INITIAL {
+    im = 0 : pia not ready yet
+    if (ri > 0) {
+        ia = (pv - v) / ri
+    }
+}
+
+AFTER SOLVE {
+    if (ri > 0) {
+        ia = (pv - v) / ri
+        im = ia : contribution from parent side
+    }
+}
+
+COMMENT
+Need to explictly duplicate in axial.mod and axial_pp.mod since
+a test of coreneuron checkpoint requires calculating iaSum and
+nmodl does not currently allow multiple BEFORE STEP in same mod file
+BEFORE STEP {
+    if (ri > 0) {
+        pim = pim - ia : child contributions
+    }
+}
+ENDCOMMENT

test/coreneuron/mod/axial.mod

@@ -0,0 +1,14 @@
+NEURON {
+    SUFFIX axial
+}
+
+INCLUDE "axial.inc"
+
+: get rid of following when nmodl allows multiple BEFORE STEP in same
+:mod file
+BEFORE STEP {
+    if (ri > 0) {
+        pim = pim - ia : child contributions
+    }
+}
+

test/coreneuron/mod/axial_pp.mod

@@ -0,0 +1,36 @@
+NEURON {
+    POINT_PROCESS AxialPP
+    RANGE iaSum
+}
+
+INCLUDE "axial.inc"
+
+
+: Just for testing coreneuron file mode checkpoint by integrating
+: abs(ia) and using that to generate spikes (which are automatically
+: output).
+
+ASSIGNED {
+  iaSum (nA)
+}
+
+INITIAL {
+  iaSum = 0
+  net_send(0, 1)
+}
+
+BEFORE STEP {
+  if (ri > 0) {
+    pim = pim - ia : child contributions
+    iaSum = iaSum + fabs(ia)
+  }
+}
+
+NET_RECEIVE(w) {
+  if (flag == 1) {
+    WATCH (iaSum > .5) 2
+  } else if (flag == 2) {
+    iaSum = 0
+    net_event(t)
+  }
+}