Return all spikes vectors to NEURON (#354)

* Return all spikes vectors to NEURON
* don't write out.dat if NEURON gets spike vectors

Author: alexsavulescu

coreneuron/io/nrn2core_direct.h

@@ -106,6 +106,9 @@ extern void (*nrn2core_trajectory_values_)(int tid, int n_pr, void** vpr, double
 
 /* Filled the Vector data arrays and send back the sizes at end of run */
 extern void (*nrn2core_trajectory_return_)(int tid, int n_pr, int vecsz, void** vpr, double t);
+
+/* send all spikes vectors to NEURON */  
+extern int (*nrn2core_all_spike_vectors_return_)(std::vector<double>& spikevec, std::vector<int>& gidvec);
 }
 
 #endif /* nrn2core_direct_h */

coreneuron/io/nrn_setup.cpp

@@ -146,6 +146,8 @@ void (*nrn2core_trajectory_values_)(int tid, int n_pr, void** vpr, double t);
 
 void (*nrn2core_trajectory_return_)(int tid, int n_pr, int vecsz, void** vpr, double t);
 
+int (*nrn2core_all_spike_vectors_return_)(std::vector<double>& spikevec, std::vector<int>& gidvec);
+
 // file format defined in cooperation with nrncore/src/nrniv/nrnbbcore_write.cpp
 // single integers are ascii one per line. arrays are binary int or double
 // Note that regardless of the gid contents of a group, since all gids are

coreneuron/io/output_spikes.cpp

@@ -36,6 +36,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 
 #include "coreneuron/nrnconf.h"
 #include "coreneuron/nrniv/nrniv_decl.h"
+#include "coreneuron/io/nrn2core_direct.h"
 #include "coreneuron/io/output_spikes.hpp"
 #include "coreneuron/mpi/nrnmpi.h"
 #include "coreneuron/utils/nrnmutdec.h"
@@ -46,6 +47,18 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "bbp/sonata/reports.h"
 #endif  // ENABLE_SONATA_REPORTS
 
+/**
+ * @brief Return all spike vectors to NEURON
+ *
+ * @param spiketvec - vector of spikes at the end of CORENEURON simulation
+ * @param spikegidvec - vector of gids at the end of CORENEURON simulation
+ * @return true if we are in embedded_run and NEURON has successfully retrieved the vectors
+ */
+static bool all_spikes_return(std::vector<double>& spiketvec, std::vector<int>& spikegidvec) {
+    return corenrn_embedded && nrn2core_all_spike_vectors_return_ &&
+            (*nrn2core_all_spike_vectors_return_)(spiketvec, spikegidvec);
+}
+
 namespace coreneuron {
 
 /// --> Coreneuron as SpikeBuffer class
@@ -168,6 +181,7 @@ void output_spikes_parallel(const char* outpath, const std::string& population_n
     sonata_write_spikes(population_name.data(), spikevec_time.data(), spikevec_time.size(), spikevec_gid.data(),
                         spikevec_gid.size(), outpath);
 #endif  // ENABLE_SONATA_REPORTS
+
     sort_spikes(spikevec_time, spikevec_gid);
     nrnmpi_barrier();
 
@@ -226,6 +240,7 @@ void output_spikes_parallel(const char* outpath, const std::string& population_n
 #endif
 
 void output_spikes_serial(const char* outpath) {
+
     std::stringstream ss;
     ss << outpath << "/out.dat";
     std::string fname = ss.str();
@@ -252,6 +267,9 @@ void output_spikes_serial(const char* outpath) {
 }
 
 void output_spikes(const char* outpath, const std::string& population_name) {
+    // try to transfer spikes to NEURON. If successfull, don't write out.dat
+    if (all_spikes_return(spikevec_time, spikevec_gid))
+        return;
 #if NRNMPI
     if (nrnmpi_initialized()) {
         output_spikes_parallel(outpath, population_name);