Remove extracon and multiple, fix #291 (#360)

Extra-connection and module duplication functionality was added
to scale model for benchmarking. Over last few years we haven't used
this functionality as it's often easy to just scale the model and BBP
model's are already big. Hence no need to carry the old code.

Author: Nicolas Cornu

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;
 };