In memory model transfer between neuron and coreneuron

coreneuron/nrniv/global_vars.cpp

@@ -9,6 +9,10 @@
 #include "coreneuron/nrniv/nrniv_decl.h"
 #include "coreneuron/nrnoc/membfunc.h"
 #include "coreneuron/nrniv/nrn_assert.h"
+#include "coreneuron/nrniv/nrn2core_direct.h"
+
+void* (*nrn2core_get_global_dbl_item_)(void*, const char*& name, int& size, double*& val);
+int (*nrn2core_get_global_int_item_)(const char* name);
 
 using namespace std;
 namespace coreneuron {
@@ -37,69 +41,99 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
     (*n2v)["dt"] = PSD(0, &dt);
     (*n2v)["t"] = PSD(0, &t);
 
-    string fname = string(path) + string("/globals.dat");
-    FILE* f = fopen(fname.c_str(), "r");
-    if (!f) {
-        printf("ignore: could not open %s\n", fname.c_str());
-        delete n2v;
-        n2v = NULL;
-        return;
-    }
-
-    char line[256];
-    char name[256];
-    double val;
-    int n;
-
-    fscanf(f, "%s\n", line);
-    check_bbcore_write_version(line);
+    if (corenrn_embedded) {  // CoreNEURON embedded, get info direct from NEURON
 
-    for (;;) {
-        nrn_assert(fgets(line, 256, f) != NULL);
-        N2V::iterator it;
-        if (sscanf(line, "%s %lf", name, &val) == 2) {
-            if (strcmp(name, "0") == 0) {
-                break;
-            }
+        const char* name;
+        int size;
+        double* val = NULL;
+        for (void* p = NULL; (p = (*nrn2core_get_global_dbl_item_)(p, name, size, val)) != NULL;) {
+            N2V::iterator it;
             it = n2v->find(name);
             if (it != n2v->end()) {
-                nrn_assert(it->second.first == 0);
-                *(it->second.second) = val;
-            }
-        } else if (sscanf(line, "%[^[][%d]\n", name, &n) == 2) {
-            if (strcmp(name, "0") == 0) {
-                break;
+                if (size == 0) {
+                    nrn_assert(it->second.first == 0);
+                    *(it->second.second) = val[0];
+                } else {
+                    nrn_assert(it->second.first == (size_t)size);
+                    double* pval = it->second.second;
+                    for (int i = 0; i < size; ++i) {
+                        pval[i] = val[i];
+                    }
+                }
             }
-            it = n2v->find(name);
-            if (it != n2v->end()) {
-                nrn_assert(it->second.first == (size_t)n);
-                double* pval = it->second.second;
-                for (int i = 0; i < n; ++i) {
-                    nrn_assert(fgets(line, 256, f) != NULL);
-                    nrn_assert(sscanf(line, "%lf\n", &val) == 1);
-                    pval[i] = val;
+            delete[] val;
+        }
+        secondorder = (*nrn2core_get_global_int_item_)("secondorder");
+        nrnran123_set_globalindex((*nrn2core_get_global_int_item_)("Random123_global_index"));
+
+    } else {  // get the info from the globals.dat file
+
+        string fname = string(path) + string("/globals.dat");
+        FILE* f = fopen(fname.c_str(), "r");
+        if (!f) {
+            printf("ignore: could not open %s\n", fname.c_str());
+            delete n2v;
+            n2v = NULL;
+            return;
+        }
+
+        char line[256];
+        char name[256];
+        double val;
+        int n;
+
+        fscanf(f, "%s\n", line);
+        check_bbcore_write_version(line);
+
+        for (;;) {
+            nrn_assert(fgets(line, 256, f) != NULL);
+            N2V::iterator it;
+            if (sscanf(line, "%s %lf", name, &val) == 2) {
+                if (strcmp(name, "0") == 0) {
+                    break;
+                }
+                it = n2v->find(name);
+                if (it != n2v->end()) {
+                    nrn_assert(it->second.first == 0);
+                    *(it->second.second) = val;
                 }
+            } else if (sscanf(line, "%[^[][%d]\n", name, &n) == 2) {
+                if (strcmp(name, "0") == 0) {
+                    break;
+                }
+                it = n2v->find(name);
+                if (it != n2v->end()) {
+                    nrn_assert(it->second.first == (size_t)n);
+                    double* pval = it->second.second;
+                    for (int i = 0; i < n; ++i) {
+                        nrn_assert(fgets(line, 256, f) != NULL);
+                        nrn_assert(sscanf(line, "%lf\n", &val) == 1);
+                        pval[i] = val;
+                    }
+                }
+            } else {
+                nrn_assert(0);
             }
-        } else {
-            nrn_assert(0);
         }
-    }
 
-    while (fgets(line, 256, f)) {
-        if (sscanf(line, "%s %d", name, &n) == 2) {
-            if (strcmp(name, "secondorder") == 0) {
-                secondorder = n;
-            } else if ( strcmp(name, "Random123_globalindex") == 0) {
-                nrnran123_set_globalindex((uint32_t)n);
+        while (fgets(line, 256, f)) {
+            if (sscanf(line, "%s %d", name, &n) == 2) {
+                if (strcmp(name, "secondorder") == 0) {
+                    secondorder = n;
+                } else if (strcmp(name, "Random123_globalindex") == 0) {
+                    nrnran123_set_globalindex((uint32_t)n);
+                }
             }
         }
-    }
 
-    fclose(f);
-    // overwrite global.dat config if seed is specified on Command line
-    if (cli_global_seed) {
-      nrnran123_set_globalindex((uint32_t)cli_global_seed_value);
+        fclose(f);
+
+        // overwrite global.dat config if seed is specified on Command line
+        if (cli_global_seed) {
+            nrnran123_set_globalindex((uint32_t)cli_global_seed_value);
+        }
     }
+
 #if 0
   for (N2V::iterator i = n2v->begin(); i != n2v->end(); ++i) {
     printf("%s %ld %p\n", i->first.c_str(), i->second.first, i->second.second);
@@ -109,4 +143,5 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
     delete n2v;
     n2v = NULL;
 }
+
 }  // namespace coreneuron

coreneuron/nrniv/main1.cpp

@@ -41,6 +41,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrnoc/nrnoc_decl.h"
 #include "coreneuron/nrnmpi/nrnmpi.h"
 #include "coreneuron/nrniv/nrniv_decl.h"
+#include "coreneuron/nrniv/nrnmutdec.h"
 #include "coreneuron/nrniv/output_spikes.h"
 #include "coreneuron/nrniv/nrn_checkpoint.h"
 #include "coreneuron/utils/endianness.h"
@@ -54,9 +55,86 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrniv/partrans.h"
 #include "coreneuron/nrniv/multisend.h"
 #include "coreneuron/utils/file_utils.h"
+#include "coreneuron/nrniv/nrn2core_direct.h"
 #include <string.h>
 #include <climits>
 
+extern "C" {
+const char* corenrn_version() {
+    return coreneuron::bbcore_write_version;
+}
+
+/**
+ * If "export OMP_NUM_THREADS=n" is not set then omp by default sets
+ * the number of threads equal to the number of cores on this node.
+ * If there are a number of mpi processes on this node as well, things
+ * can go very slowly as there are so many more threads than cores.
+ * Assume the NEURON users pc.nthread() is well chosen if
+ * OMP_NUM_THREADS is not set.
+ */
+void set_openmp_threads(int nthread) {
+#if defined(_OPENMP)
+    if (!getenv("OMP_NUM_THREADS")) {
+        omp_set_num_threads(nthread);
+    }
+#endif
+}
+
+/**
+ * Convert char* containing arguments from neuron to char* argv[] for
+ * coreneuron command line argument parser.
+ */
+char* prepare_args(int& argc, char**& argv, int use_mpi, const char* arg) {
+    // first construct all arguments as string
+    std::string args(arg);
+    args.insert(0, " coreneuron ");
+    if (use_mpi) {
+        args.append(" -mpi ");
+    }
+
+    // we can't modify string with strtok, make copy
+    char* first = strdup(args.c_str());
+    const char* sep = " ";
+
+    // first count the no of argument
+    char* token = strtok(first, sep);
+    argc = 0;
+    while (token) {
+        token = strtok(NULL, sep);
+        argc++;
+    }
+    free(first);
+
+    // now build char*argv
+    argv = new char*[argc];
+    first = strdup(args.c_str());
+    token = strtok(first, sep);
+    for (int i = 0; token; i++) {
+        argv[i] = token;
+        token = strtok(NULL, sep);
+    }
+
+    // return actual data to be freed
+    return first;
+}
+
+int corenrn_embedded_run(int nthread, int have_gaps, int use_mpi, const char* arg) {
+    corenrn_embedded = 1;
+    corenrn_embedded_nthread = nthread;
+    coreneuron::nrn_have_gaps = have_gaps;
+
+    set_openmp_threads(nthread);
+    int argc = 0;
+    char** argv;
+    char* new_arg = prepare_args(argc, argv, use_mpi, arg);
+    solve_core(argc, argv);
+    free(new_arg);
+    delete[] argv;
+
+    return corenrn_embedded;
+}
+}
+
 #if 0
 #include <fenv.h>
 #define NRN_FEEXCEPT (FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW)
@@ -120,7 +198,8 @@ void nrn_init_and_load_data(int argc,
     mk_mech(nrnopt_get_str("--datpath").c_str());
 
     // read the global variable names and set their values from globals.dat
-    set_globals(nrnopt_get_str("--datpath").c_str(), nrnopt_get_flag("--seed"), nrnopt_get_int("--seed"));
+    set_globals(nrnopt_get_str("--datpath").c_str(), nrnopt_get_flag("--seed"),
+                nrnopt_get_int("--seed"));
 
     report_mem_usage("After mk_mech");
 
@@ -285,7 +364,6 @@ extern "C" int solve_core(int argc, char** argv) {
             reports_needs_finalize = configs.size();
         }
     }
-
     // initializationa and loading functions moved to separate
     nrn_init_and_load_data(argc, argv, configs.size() > 0);
     std::string checkpoint_path = nrnopt_get_str("--checkpoint");
@@ -329,7 +407,7 @@ extern "C" int solve_core(int argc, char** argv) {
 
         // register all reports into reportinglib
         double min_report_dt = INT_MAX;
-        for (int i = 0; i < configs.size(); i++) {
+        for (size_t i = 0; i < configs.size(); i++) {
             register_report(dt, tstop, delay, configs[i]);
             if (configs[i].report_dt < min_report_dt) {
                 min_report_dt = configs[i].report_dt;