Merge branch 'master' into hines/contour-test

share/lib/python/neuron/coreneuron.py

@@ -41,12 +41,17 @@ class coreneuron(object):
     Attributes
     ----------
     cell_permute
+    model_path
     enable
     file_mode
     gpu
     prcellstate
+    sim_config
     verbose
     warp_balance
+    save_path
+    restore_path
+    skip_write_model_to_disk
 
     Examples
     --------
@@ -72,6 +77,11 @@ def __init__(self):
         self._verbose = 2  # INFO
         self._prcellstate = -1
         self._model_stats = False
+        self._sim_config = None
+        self._model_path = None
+        self._save_path = None
+        self._restore_path = None
+        self._skip_write_model_to_disk = False
 
     def __call__(self, **kwargs):
         """
@@ -211,6 +221,57 @@ def model_stats(self):
     def model_stats(self, value):
         self._model_stats = bool(value)
 
+    @property
+    def sim_config(self):
+        """Simulation config file."""
+        return self._sim_config
+
+    @sim_config.setter
+    def sim_config(self, value):
+        self._sim_config = str(value)
+
+    @property
+    def model_path(self):
+        """Data path of the model."""
+        return self._model_path
+
+    @sim_config.setter
+    def model_path(self, value):
+        self._model_path = str(value)
+
+    @property
+    def save_path(self):
+        """Data path for save."""
+        return self._save_path
+
+    @sim_config.setter
+    def save_path(self, value):
+        self._save_path = str(value)
+
+    @property
+    def restore_path(self):
+        """Data path for restore."""
+        return self._restore_path
+
+    @sim_config.setter
+    def restore_path(self, value):
+        self._restore_path = str(value)
+
+    @property
+    def skip_write_model_to_disk(self):
+        """Set internal flag to only simulate the model with CoreNEURON.
+        Avoids writing the coreneuron input data to the data_path in
+        CoreNEURON embedded mode when launched thourgh the NEURON Python
+        API. The coreneuron input data should already be there by calling
+        prior to pc.psolve() pc.nrncore_write() and CoreNEURON uses them
+        for launching the simulation.
+        """
+        return self._skip_write_model_to_disk
+
+    @sim_config.setter
+    def skip_write_model_to_disk(self, value):
+        self._skip_write_model_to_disk = value
+
     def nrncore_arg(self, tstop):
         """
         Return str that can be used for pc.nrncore_run(str)
@@ -234,7 +295,12 @@ def nrncore_arg(self, tstop):
             if self._num_gpus:
                 arg += " --num-gpus %d" % self._num_gpus
         if self._file_mode:
-            arg += " --datpath %s" % CORENRN_DATA_DIR
+            if self._model_path is not None:
+                arg += " --datpath %s" % self._model_path
+            else:
+                arg += " --datpath %s" % CORENRN_DATA_DIR
+            if self._skip_write_model_to_disk:
+                arg += " --skip-write-model-to-disk"
         arg += " --tstop %g" % tstop
         arg += " --cell-permute %d" % self.cell_permute
         if self._warp_balance > 0:
@@ -244,6 +310,12 @@ def nrncore_arg(self, tstop):
         arg += " --verbose %d" % self.verbose
         if self._model_stats:
             arg += " --model-stats"
+        if self._save_path:
+            arg += " --checkpoint %s" % self._save_path
+        if self._restore_path:
+            arg += " --restore %s" % self._restore_path
+        if self._sim_config:
+            arg += " --read-config %s" % self._sim_config
 
         # args derived from current NEURON settings.
         pc = h.ParallelContext()

src/coreneuron/apps/main1.cpp

@@ -621,7 +621,7 @@ extern "C" int run_solve_core(int argc, char** argv) {
     }
 
     // copy weights back to NEURON NetCon
-    if (nrn2core_all_weights_return_) {
+    if (nrn2core_all_weights_return_ && corenrn_embedded) {
         // first update weights from gpu
         update_weights_from_gpu(nrn_threads, nrn_nthread);
 
@@ -635,7 +635,9 @@ extern "C" int run_solve_core(int argc, char** argv) {
         (*nrn2core_all_weights_return_)(weights);
     }
 
-    core2nrn_data_return();
+    if (corenrn_embedded) {
+        core2nrn_data_return();
+    }
 
     {
         Instrumentor::phase p("checkpoint");

src/coreneuron/mechanism/mech/enginemech.cpp

@@ -18,6 +18,7 @@
 #include <cstdlib>
 #include <coreneuron/engine.h>
 #include <string>
+#include <iostream>
 
 namespace coreneuron {
 
@@ -107,32 +108,42 @@ int corenrn_embedded_run(int nthread,
                          int use_fast_imem,
                          const char* mpi_lib,
                          const char* nrn_arg) {
+    bool corenrn_skip_write_model_to_disk = false;
+    const std::string corenrn_skip_write_model_to_disk_arg{"--skip-write-model-to-disk"};
+    // If "only_simulate_str" exists in "nrn_arg" then avoid transferring any data between NEURON
+    // and CoreNEURON Instead run the CoreNEURON simulation only with the coredat files provided
+    // "only_simulate_str" is an internal string and shouldn't be made public to the CoreNEURON CLI
+    // options so it is removed from "nrn_arg" first construct all arguments as string
+    std::string filtered_nrn_arg{nrn_arg};
+    const auto ind =
+        static_cast<std::string>(filtered_nrn_arg).find(corenrn_skip_write_model_to_disk_arg);
+    if (ind != std::string::npos) {
+        corenrn_skip_write_model_to_disk = true;
+        filtered_nrn_arg.erase(ind, corenrn_skip_write_model_to_disk_arg.size());
+    }
     // set coreneuron's internal variable based on neuron arguments
-    corenrn_embedded = true;
+    corenrn_embedded = !corenrn_skip_write_model_to_disk;
     corenrn_embedded_nthread = nthread;
     coreneuron::nrn_have_gaps = have_gaps != 0;
     coreneuron::nrn_use_fast_imem = use_fast_imem != 0;
 
     // set number of openmp threads
     set_openmp_threads(nthread);
 
-    // first construct all arguments as string
-    std::string args(nrn_arg);
-
-    args.insert(0, " coreneuron ");
-    args.append(" --skip-mpi-finalize ");
+    filtered_nrn_arg.insert(0, " coreneuron ");
+    filtered_nrn_arg.append(" --skip-mpi-finalize ");
 
     if (use_mpi) {
-        args.append(" --mpi ");
+        filtered_nrn_arg.append(" --mpi ");
     }
 
-    add_mpi_library_arg(mpi_lib, args);
+    add_mpi_library_arg(mpi_lib, filtered_nrn_arg);
 
     // pre-process argumnets from neuron and prepare new for coreneuron
     int argc;
     char** argv;
 
-    char* new_arg = prepare_args(argc, argv, args);
+    char* new_arg = prepare_args(argc, argv, filtered_nrn_arg);
 
     // initialize internal arguments
     mk_mech_init(argc, argv);

src/ivoc/matrix.cpp

@@ -48,14 +48,13 @@ Matrix* matrix_arg(int i) {
     return (Matrix*) (ob->u.this_pointer);
 }
 
-Object** Matrix::temp_objvar() {
-    Matrix* m = (Matrix*) this;
+static Object** temp_objvar(Matrix* m) {
     Object** po;
     if (m->obj_) {
         po = hoc_temp_objptr(m->obj_);
     } else {
         po = hoc_temp_objvar(nrn_matrix_sym, (void*) m);
-        obj_ = *po;
+        m->obj_ = *po;
     }
     return po;
 }
@@ -189,7 +188,7 @@ static double m_scanf(void* v) {
 static Object** m_resize(void* v) {
     Matrix* m = (Matrix*) v;
     m->resize((int) (chkarg(1, 1., 1e9) + EPS), (int) (chkarg(2, 1., 1e9) + EPS));
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_mulv(void* v) {
@@ -265,7 +264,7 @@ static Object** m_add(void* v) {
         out = matrix_arg(2);
     }
     m->add(matrix_arg(1), out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_bcopy(void* v) {
@@ -287,7 +286,7 @@ static Object** m_bcopy(void* v) {
     }
     out = get_out_mat(m, m0, n0, i);
     m->bcopy(out, i0, j0, m0, n0, i1, j1);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_mulm(void* v) {
@@ -305,22 +304,22 @@ static Object** m_mulm(void* v) {
     out->resize(m->nrow(), in->ncol());
     check_domain(m->ncol(), in->nrow());
     m->mulm(in, out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_c(void* v) {
     Matrix* m = (Matrix*) v;
     Matrix* out = get_out_mat(m, 1);
     m->copy(out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_transpose(void* v) {
     Matrix* m = (Matrix*) v;
     Matrix* out = get_out_mat(m, 1);
     out->resize(m->ncol(), m->nrow());
     m->transpose(out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_symmeig(void* v) {
@@ -375,7 +374,7 @@ static Object** m_muls(void* v) {
     //		out->resize(...
     //	}
     m->muls(*getarg(1), out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_getrow(void* v) {
@@ -444,7 +443,7 @@ static Object** m_setrow(void* v) {
 #endif
         m->setrow(k, in);
     }
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_setcol(void* v) {
@@ -461,7 +460,7 @@ static Object** m_setcol(void* v) {
 #endif
         m->setcol(k, in);
     }
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_setdiag(void* v) {
@@ -478,7 +477,7 @@ static Object** m_setdiag(void* v) {
 #endif
         m->setdiag(k, in);
     }
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_getdiag(void* v) {
@@ -510,35 +509,35 @@ static Object** m_getdiag(void* v) {
 static Object** m_zero(void* v) {
     Matrix* m = (Matrix*) v;
     m->zero();
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_ident(void* v) {
     Matrix* m = (Matrix*) v;
     m->ident();
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_exp(void* v) {
     Matrix* m = (Matrix*) v;
     Matrix* out = get_out_mat(m, 1, "exponentiation");
     m->exp(out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_pow(void* v) {
     Matrix* m = (Matrix*) v;
     int k = (int) chkarg(1, 0., 100.);
     Matrix* out = get_out_mat(m, 2, "raising to a power");
     m->pow(k, out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static Object** m_inverse(void* v) {
     Matrix* m = (Matrix*) v;
     Matrix* out = get_out_mat(m, 1);
     m->inverse(out);
-    return out->temp_objvar();
+    return temp_objvar(out);
 }
 
 static double m_det(void* v) {
@@ -619,7 +618,7 @@ static Object** m_set(void* v) {
             *(m->mep(i, j)) = *getarg(++k);
         }
     }
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Object** m_to_vector(void* v) {
@@ -657,7 +656,7 @@ static Object** m_from_vector(void* v) {
         for (i = 0; i < nrow; ++i) {
             *(m->mep(i, j)) = ve[k++];
         }
-    return m->temp_objvar();
+    return temp_objvar(m);
 }
 
 static Member_func m_members[] = {

src/ivoc/ocmatrix.cpp

@@ -41,7 +41,6 @@ static void Vect2VEC(Vect* v1, VEC& v2) {
 }
 
 OcMatrix::OcMatrix(int type) {
-    obj_ = nullptr;
     type_ = type;
 }
 OcMatrix::~OcMatrix() {}

src/ivoc/ocmatrix.h

@@ -139,13 +139,12 @@ class OcMatrix {
     }
 
     void unimp();
-    Object** temp_objvar();
 
   protected:
     OcMatrix(int type);
 
   public:
-    Object* obj_;
+    Object* obj_{};
 
   private:
     int type_;

src/neuron/container/node.hpp

@@ -249,7 +249,7 @@ struct handle_interface: handle_base<Identifier> {
                       << " v=" << handle.v() << " area=" << handle.area() << " a=" << handle.a()
                       << " b=" << handle.b() << " d=" << handle.d() << '}';
         } else {
-            os << "Node{null}";
+            return os << "Node{null}";
         }
     }
 };