Remove extracon and multiple, fix #291

coreneuron/apps/corenrn_parameters.cpp

@@ -89,10 +89,6 @@ corenrn_parameters::corenrn_parameters(){
         ->check(CLI::Range(0., 1e9));
     sub_config -> add_option("-l, --celsius", this->celsius, "Temperature in degC. The default value is set in defaults.dat or else is 34.0.", true)
         ->check(CLI::Range(-1000., 1000.));
-    sub_config -> add_option("-x, --extracon", this->extracon, "Number of extra random connections in each thread to other duplicate models.")
-        ->check(CLI::Range(0, 10'000'000));
-    sub_config -> add_option("-z, --multiple", this->multiple, "Model duplication factor. Model size is normal size * multiple")
-        ->check(CLI::Range(1, 10'000'000));
     sub_config -> add_option("--mindelay", this->mindelay, "Maximum integration interval (likely reduced by minimum NetCon delay).", true)
         ->check(CLI::Range(0., 1e9));
     sub_config -> add_option("--report-buffer-size", this->report_buff_size, "Size in MB of the report buffer.")
@@ -162,8 +158,6 @@ std::ostream& operator<<(std::ostream& os, const corenrn_parameters& corenrn_par
         << "--prcellgid=" << corenrn_param.prcellgid << std::endl
         << "--forwardskip=" << corenrn_param.forwardskip << std::endl
         << "--celsius=" << corenrn_param.celsius << std::endl
-        << "--extracon=" << corenrn_param.extracon << std::endl
-        << "--multiple=" << corenrn_param.multiple << std::endl
         << "--mindelay=" << corenrn_param.mindelay << std::endl
         << "--report-buffer-size=" << corenrn_param.report_buff_size << std::endl
         << std::endl

coreneuron/apps/corenrn_parameters.hpp

@@ -75,8 +75,6 @@ struct corenrn_parameters {
     unsigned spkcompress=0;        /// Spike Compression
     unsigned cell_interleave_permute=0; /// Cell interleaving permutation
     unsigned nwarp=0;              /// Number of warps to balance for cell_interleave_permute == 2
-    unsigned multiple=1;           /// Model duplication factor
-    unsigned extracon=0;           /// Number of extra random connections in each thread to other duplicate models.
     unsigned report_buff_size=report_buff_size_default; ///Size in MB of the report buffer.
     int seed=-1;                   /// Initialization seed for random number generator (int)
 

coreneuron/apps/main1.cpp

@@ -242,9 +242,6 @@ void nrn_init_and_load_data(int argc,
         use_solve_interleave = true;
     }
 
-    // pass by flag so existing tests do not need a changed nrn_setup prototype.
-    nrn_setup_multiple = corenrn_param.multiple;
-    nrn_setup_extracon = corenrn_param.extracon;
     // multisend options
     use_multisend_ = corenrn_param.multisend ? 1 : 0;
     n_multisend_interval = corenrn_param.ms_subint;
@@ -478,15 +475,10 @@ extern "C" int run_solve_core(int argc, char** argv) {
     }
 
     if (!corenrn_param.reportfilepath.empty()) {
-        if (corenrn_param.multiple > 1) {
-            if (nrnmpi_myid == 0)
-                printf("\n WARNING! : Can't enable reports with model duplications feature! \n");
-        } else {
-            configs = create_report_configurations(corenrn_param.reportfilepath.c_str(),
-                                                   corenrn_param.outpath.c_str(),
-                                                   spikes_population_name);
-            reports_needs_finalize = configs.size();
-        }
+        configs = create_report_configurations(corenrn_param.reportfilepath.c_str(),
+                                               corenrn_param.outpath.c_str(),
+                                               spikes_population_name);
+        reports_needs_finalize = configs.size();
     }
 
     // initializationa and loading functions moved to separate

coreneuron/io/nrn_checkpoint.cpp

@@ -372,7 +372,7 @@ static void write_phase2(NrnThread& nt, FileHandlerWrap& fh) {
         }
     }
 
-    int nnetcon = nt.n_netcon - nrn_setup_extracon;
+    int nnetcon = nt.n_netcon;
 
     int* output_vindex = new int[nt.n_presyn];
     double* output_threshold = new double[nt.ncell];

coreneuron/io/nrn_setup.cpp

@@ -161,33 +161,6 @@ int (*nrn2core_all_spike_vectors_return_)(std::vector<double>& spikevec, std::ve
 // stored in the nt.presyns array and nt.netcons array respectively
 namespace coreneuron {
 extern corenrn_parameters corenrn_param;
-int nrn_setup_multiple = 1; /* default */
-int nrn_setup_extracon = 0; /* default */
-
-// nrn_setup_extracon extra connections per NrnThread.
-// i.e. nrn_setup_extracon * nrn_setup_multiple * nrn_nthread
-// extra connections on this process.
-// The targets of the connections on a NrnThread are randomly selected
-// (with replacement) from the set of ProbAMPANMDA_EMS on the thread.
-// (This synapse type is not strictly appropriate to be used as
-// a generalized synapse with multiple input streams since some of its
-// range variables store quantities that should be stream specific
-// and therefore should be stored in the NetCon weight vector. But it
-// might be good enough for our purposes. In any case, we'd like to avoid
-// creating new POINT_PROCESS instances with all the extra complexities
-// involved in adjusting the data arrays.)
-// The nrn_setup_extracon value is used to allocate the appropriae
-// amount of extra space for NrnThread.netcons and NrnThread.weights
-//
-// The most difficult problem is to augment the rank wide inputpresyn_ list.
-// We wish to randomly choose source gids for the extracon NetCons from the
-// set of gids not in "multiple" instance of the model the NrnThread is a
-// member of. We need to take into account the possibilty of multiple
-// NrnThread in multiple "multiple" instances having extra NetCon with the
-// same source gid. That some of the source gids may be already be
-// associated with already existing PreSyn on this rank is a minor wrinkle.
-// This is done between phase1 and phase2 during the call to
-// determine_inputpresyn().
 
 #ifdef _OPENMP
 static OMP_Mutex mut;
@@ -208,17 +181,12 @@ std::vector<NetCon*> netcon_in_presyn_order_;
 std::vector<int*> netcon_srcgid;
 
 /* read files.dat file and distribute cellgroups to all mpi ranks */
-void nrn_read_filesdat(int& ngrp, int*& grp, int multiple, int*& imult, const char* filesdat) {
+void nrn_read_filesdat(int& ngrp, int*& grp, const char* filesdat) {
     patstimtype = nrn_get_mechtype("PatternStim");
     if (corenrn_embedded) {
         ngrp = corenrn_embedded_nthread;
-        nrn_assert(multiple == 1);
         grp = new int[ngrp + 1];
-        imult = new int[ngrp + 1];
         (*nrn2core_group_ids_)(grp);
-        for (int i = 0; i <= ngrp; ++i) {
-            imult[i] = 0;
-        }
         return;
     }
 
@@ -251,25 +219,17 @@ void nrn_read_filesdat(int& ngrp, int*& grp, int multiple, int*& imult, const ch
     }
 
     ngrp = 0;
-    grp = new int[iNumFiles * multiple / nrnmpi_numprocs + 1];
-    imult = new int[iNumFiles * multiple / nrnmpi_numprocs + 1];
+    grp = new int[iNumFiles / nrnmpi_numprocs + 1];
 
     // irerate over gids in files.dat
-    for (int iNum = 0; iNum < iNumFiles * multiple; ++iNum) {
+    for (int iNum = 0; iNum < iNumFiles; ++iNum) {
         int iFile;
 
         nrn_assert(fscanf(fp, "%d\n", &iFile) == 1);
         if ((iNum % nrnmpi_numprocs) == nrnmpi_myid) {
             grp[ngrp] = iFile;
-            imult[ngrp] = iNum / iNumFiles;
             ngrp++;
         }
-        if ((iNum + 1) % iNumFiles == 0) {
-            // re-read file for each multiple (skipping the two header lines)
-            rewind(fp);
-            nrn_assert(fscanf(fp, "%*s\n") == 0);
-            nrn_assert(fscanf(fp, "%*d\n") == 0);
-        }
     }
 
     fclose(fp);
@@ -448,11 +408,9 @@ void nrn_setup(const char* filesdat,
 
     int ngroup;
     int* gidgroups;
-    int* imult;
-    nrn_read_filesdat(ngroup, gidgroups, nrn_setup_multiple, imult, filesdat);
+    nrn_read_filesdat(ngroup, gidgroups, filesdat);
     UserParams userParams(ngroup,
                           gidgroups,
-                          imult,
                           datpath,
                           strlen(restore_path) == 0 ? datpath : restore_path);
 
@@ -497,7 +455,6 @@ void nrn_setup(const char* filesdat,
 
     // gap junctions
     if (nrn_have_gaps) {
-        assert(nrn_setup_multiple == 1);
         nrn_partrans::transfer_thread_data_ = new nrn_partrans::TransferThreadData[nrn_nthread];
         nrn_partrans::setup_info_ = new nrn_partrans::SetupInfo[userParams.ngroup];
         if (!corenrn_embedded) {
@@ -522,9 +479,9 @@ void nrn_setup(const char* filesdat,
             NrnThread& nt = *n;
             {
 #ifdef _OPENMP
-                p1.populate(nt, 0, mut);
+                p1.populate(nt, mut);
 #else
-                p1.populate(nt, 0);
+                p1.populate(nt);
 #endif
             }
         });
@@ -565,7 +522,6 @@ void nrn_setup(const char* filesdat,
 
     model_size();
     delete[] userParams.gidgroups;
-    delete[] userParams.imult;
 
     if (nrnmpi_myid == 0 && !corenrn_param.is_quiet()) {
         printf(" Setup Done   : %.2lf seconds \n", nrn_wtime() - time);
@@ -593,7 +549,6 @@ void setup_ThreadData(NrnThread& nt) {
 }
 
 void read_phasegap(NrnThread& nt, UserParams& userParams) {
-    nrn_assert(userParams.imult[nt.id] == 0);
     nrn_partrans::SetupInfo& si = nrn_partrans::setup_info_[nt.id];
     si.ntar = 0;
     si.nsrc = 0;
@@ -903,9 +858,9 @@ void read_phase1(NrnThread& nt, UserParams& userParams) {
 
     { // Protect gid2in, gid2out and neg_gid2out
 #ifdef _OPENMP
-        p1.populate(nt, userParams.imult[nt.id], mut);
+        p1.populate(nt, mut);
 #else
-        p1.populate(nt, userParams.imult[nt.id]);
+        p1.populate(nt);
 #endif
     }
 }

coreneuron/io/output_spikes.hpp

@@ -29,6 +29,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #ifndef output_spikes_h
 #define output_spikes_h
 
+#include <string>
 #include <vector>
 #include <utility>
 namespace coreneuron {

coreneuron/io/phase1.cpp

@@ -43,93 +43,19 @@ void Phase1::read_direct(int thread_id) {
     delete[] netcon_srcgid;
 }
 
-void Phase1::shift_gids(int imult) {
-    // maxgid is the maxgid to have the different multiple in the same gid space.
-    int maxgid = 0x7fffffff / nrn_setup_multiple;
-    // this value is the beginning of the new cluster of gids.
-    // the correct cluster is choose with imult.
-    int offset_gids = imult * maxgid;  // offset for each gid
-
-    // offset the (non-negative) gids according to multiple
-    // make sure everything fits into gid space.
-    for (auto& gid: this->output_gids) {
-        if (gid >= 0) {
-            nrn_assert(gid < maxgid);
-            gid += offset_gids;
-        }
-    }
-
-    for (auto& srcgid: this->netcon_srcgids) {
-        if (srcgid >= 0) {
-            nrn_assert(srcgid < maxgid);
-            srcgid += offset_gids;
-        }
-    }
-}
-
-void Phase1::add_extracon(NrnThread& nt, int imult) {
-    int maxgid = 0x7fffffff / nrn_setup_multiple;
-    if (nrn_setup_extracon <= 0) {
-        return;
-    }
-
-    // very simplistic
-    // Use this threads positive source gids - zz in nt.netcon order as the
-    // source gids for extracon.
-    // The edge cases are:
-    // The 0th duplicate uses uses source gids for the last duplicate.
-    // If there are fewer positive source gids than extracon, then keep
-    // rotating through the nt.netcon .
-    // If there are no positive source gids, use a source gid of -1.
-    // Would not be difficult to modify so that random positive source was
-    // used, and/or random connect to another duplicate.
-    // Note that we increment the nt.n_netcon at the end of this function.
-    int sidoffset = 0;  // how much to increment the corresponding positive gid
-    // like ring connectivity
-    if (imult > 0) {
-        sidoffset = -maxgid;
-    } else if (nrn_setup_multiple > 1) {
-        sidoffset = (nrn_setup_multiple - 1) * maxgid;
-    }
-    // set up the extracon srcgid_
-    int* nc_srcgid = netcon_srcgid[nt.id];
-    int j = 0;  // rotate through the n_netcon netcon_srcgid
-    for (int i = 0; i < nrn_setup_extracon; ++i) {
-        int sid = -1;
-        for (int k = 0; k < nt.n_netcon; ++k) {
-            // potentially rotate j through the entire n_netcon but no further
-            sid = nc_srcgid[j];
-            j = (j + 1) % nt.n_netcon;
-            if (sid >= 0) {
-                break;
-            }
-        }
-        if (sid < 0) {  // only connect to real cells.
-            sid = -1;
-        } else {
-            sid += sidoffset;
-        }
-        nc_srcgid[nt.n_netcon + i] = sid;
-    }
-    // finally increment the n_netcon
-    nt.n_netcon += nrn_setup_extracon;
-}
-
 #ifdef _OPENMP
-void Phase1::populate(NrnThread& nt, int imult, OMP_Mutex& mut) {
+void Phase1::populate(NrnThread& nt, OMP_Mutex& mut) {
 #else
-void Phase1::populate(NrnThread& nt, int imult) {
+void Phase1::populate(NrnThread& nt) {
 #endif
     nt.n_presyn = this->output_gids.size();
     nt.n_netcon = this->netcon_srcgids.size();
 
-    shift_gids(imult);
-
-    netcon_srcgid[nt.id] = new int[nt.n_netcon + nrn_setup_extracon];
+    netcon_srcgid[nt.id] = new int[nt.n_netcon];
     std::copy(this->netcon_srcgids.begin(), this->netcon_srcgids.end(),
               netcon_srcgid[nt.id]);
 
-    nt.netcons = new NetCon[nt.n_netcon + nrn_setup_extracon];
+    nt.netcons = new NetCon[nt.n_netcon];
     nt.presyns_helper = (PreSynHelper*)ecalloc_align(nt.n_presyn, sizeof(PreSynHelper));
 
     nt.presyns = new PreSyn[nt.n_presyn];
@@ -177,8 +103,6 @@ void Phase1::populate(NrnThread& nt, int imult) {
 
         ++ps;
     }
-
-    add_extracon(nt, imult);
 }
 
 }  // namespace coreneuron

coreneuron/io/phase1.hpp

@@ -14,15 +14,12 @@ class Phase1 {
     void read_file(FileHandler& F);
     void read_direct(int thread_id);
 #ifdef _OPENMP
-    void populate(NrnThread& nt, int imult, OMP_Mutex& mut);
+    void populate(NrnThread& nt, OMP_Mutex& mut);
 #else
-    void populate(NrnThread& nt, int imult);
+    void populate(NrnThread& nt);
 #endif
 
     private:
-    void shift_gids(int imult);
-    void add_extracon(NrnThread& nt, int imult);
-
     std::vector<int> output_gids;
     std::vector<int> netcon_srcgids;
 };