BinQ and spike compression fixes (#701)

* Bug fixes with regard to option --spkcompress <nspike>
* After compressed spike exchange, do interthread_enqueue.
* nrn binq must be initialized before core2nrn queue transfer.
* nrncore binq must be initialized before nrn2core queue transfer
* interthread buffer must be enqueued at beginning of psolve.
* Initialization of binq consistent everywhere.
* Avoid Random123 globalindex warning if the index has not changed.
    Release random123 instance when multisend setup no longer needs it.
    Psolve restores a few more arg default values.
* Revert  nrnran123.cu
    Eliminating the warning when Random123 global index does not change, increases the chance of hiding a bug.
* update nmodl submodule
* ntasks=16 for gpu tests as well

Co-authored-by: Alexandru Săvulescu <alexandru.savulescu@epfl.ch>
Co-authored-by: Olli Lupton <oliver.lupton@epfl.ch>
Co-authored-by: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>

Author: 4 people

.gitlab-ci.yml

@@ -49,6 +49,7 @@ spack_setup:
 .gpu_node:
   variables:
     bb5_constraint: volta
+    bb5_ntasks: 16
 .test_neuron:
   extends: [.ctest]
   stage: test_neuron

coreneuron/apps/main1.cpp

@@ -472,6 +472,7 @@ static void* load_dynamic_mpi(const std::string& libname) {
 extern "C" void mk_mech_init(int argc, char** argv) {
     // reset all parameters to their default values
     corenrn_param.reset();
+
     // read command line parameters and parameter config files
     corenrn_param.parse(argc, argv);
 

coreneuron/io/core2nrn_data_return.cpp

@@ -170,6 +170,14 @@ static void core2nrn_corepointer(int tid, NrnThreadMembList* tml) {
  */
 static void core2nrn_tqueue(NrnThread&);
 
+/** @brief Callback to clear NEURON thread queues.
+    In particular need to initialize bin queues to the current time before
+    transferring events.
+ */
+extern "C" {
+void (*core2nrn_clear_queues_)(double t);
+}
+
 /** @brief All activated WATCH statements need activation on NEURON side.
  */
 // vector in unpermuted Memb_list index order of vector of
@@ -200,6 +208,9 @@ void core2nrn_data_return() {
     if (!nrn2core_type_return_) {
         return;
     }
+
+    (*core2nrn_clear_queues_)(nrn_threads[0]._t);  // all threads at same time
+
     for (int tid = 0; tid < nrn_nthread; ++tid) {
         size_t n = 0;
         double* data = nullptr;

coreneuron/io/nrn2core_data_init.cpp

@@ -51,6 +51,8 @@ void direct_mode_initialize() {
     dt2thread(-1.);
     nrn_thread_table_check();
 
+    clear_event_queue();
+
     // Reproduce present NEURON WATCH activation
     // Start from nothing active.
     watch_activate_clear();

coreneuron/io/nrn_setup.cpp

@@ -180,7 +180,7 @@ void nrn_read_filesdat(int& ngrp, int*& grp, const char* filesdat) {
     FILE* fp = fopen(filesdat, "r");
 
     if (!fp) {
-        nrn_fatal_error("No input file with nrnthreads, exiting...");
+        nrn_fatal_error("No input file ( %s ) with nrnthreads, exiting...", filesdat);
     }
 
     char version[256];
@@ -710,6 +710,9 @@ void nrn_cleanup_ion_map() {
 
 void nrn_cleanup() {
     clear_event_queue();  // delete left-over TQItem
+    for (auto psi: gid2in) {
+        delete psi.second;
+    }
     gid2in.clear();
     gid2out.clear();
 

coreneuron/mpi/lib/mpispike.cpp

@@ -24,7 +24,7 @@ extern MPI_Comm nrnmpi_comm;
 
 static int np;
 static int* displs{nullptr};
-static int* byteovfl; /* for the compressed transfer method */
+static int* byteovfl{nullptr}; /* for the compressed transfer method */
 static MPI_Datatype spike_type;
 
 static void* emalloc(size_t size) {
@@ -175,7 +175,7 @@ The allgather sends the first part of the buf and the allgatherv buffer
 sends any overflow.
 */
 int nrnmpi_spike_exchange_compressed_impl(int localgid_size,
-                                          unsigned char* spfixin_ovfl,
+                                          unsigned char*& spfixin_ovfl,
                                           int send_nspike,
                                           int* nin,
                                           int ovfl_capacity,
@@ -187,9 +187,10 @@ int nrnmpi_spike_exchange_compressed_impl(int localgid_size,
         np = nrnmpi_numprocs_;
         displs = (int*) emalloc(np * sizeof(int));
         displs[0] = 0;
+    }
+    if (!byteovfl) {
         byteovfl = (int*) emalloc(np * sizeof(int));
     }
-
     MPI_Allgather(
         spikeout_fixed, ag_send_size, MPI_BYTE, spikein_fixed, ag_send_size, MPI_BYTE, nrnmpi_comm);
     int novfl = 0;

coreneuron/mpi/lib/nrnmpi.cpp

@@ -35,6 +35,12 @@ static void nrn_fatal_error(const char* msg) {
 }
 
 nrnmpi_init_ret_t nrnmpi_init_impl(int* pargc, char*** pargv, bool is_quiet) {
+    // Execute at most once per launch. Avoid memory leak.
+    static bool executed = false;
+    if (executed) {
+        return {nrnmpi_numprocs_, nrnmpi_myid_};
+    }
+
     nrnmpi_under_nrncontrol_ = true;
 
     if (!nrnmpi_initialized_impl()) {
@@ -62,6 +68,7 @@ nrnmpi_init_ret_t nrnmpi_init_impl(int* pargc, char*** pargv, bool is_quiet) {
 #endif
     }
 
+    executed = true;
     return {nrnmpi_numprocs_, nrnmpi_myid_};
 }
 

coreneuron/mpi/nrnmpidec.h

@@ -37,7 +37,7 @@ extern mpi_function<cnrn_make_integral_constant_t(nrnmpi_write_file_impl)> nrnmp
 extern "C" int nrnmpi_spike_exchange_impl(int* nin, NRNMPI_Spike* spikeout, int icapacity, NRNMPI_Spike** spikein, int& ovfl, int nout, NRNMPI_Spikebuf* spbufout, NRNMPI_Spikebuf* spbufin);
 extern mpi_function<cnrn_make_integral_constant_t(nrnmpi_spike_exchange_impl)>
     nrnmpi_spike_exchange;
-extern "C" int nrnmpi_spike_exchange_compressed_impl(int, unsigned char*, int, int*, int, unsigned char*, int, unsigned char*, int& ovfl);
+extern "C" int nrnmpi_spike_exchange_compressed_impl(int, unsigned char*&, int, int*, int, unsigned char*, int, unsigned char*, int& ovfl);
 extern mpi_function<cnrn_make_integral_constant_t(nrnmpi_spike_exchange_compressed_impl)>
     nrnmpi_spike_exchange_compressed;
 extern "C" int nrnmpi_int_allmax_impl(int i);

coreneuron/network/multisend_setup.cpp

@@ -224,7 +224,7 @@ void TarList::alloc() {
 
 // for two phase
 
-static nrnran123_State* ranstate;
+static nrnran123_State* ranstate{nullptr};
 
 static void random_init(int i) {
     if (!ranstate) {
@@ -236,6 +236,14 @@ static unsigned int get_random() {
     return nrnran123_ipick(ranstate);
 }
 
+// Avoid warnings if the global index is changed on subsequent psolve.
+static void random_delete() {
+    if (ranstate) {
+        nrnran123_deletestream(ranstate);
+        ranstate = nullptr;
+    }
+}
+
 static int iran(int i1, int i2) {
     // discrete uniform random integer from i2 to i2 inclusive. Must
     // work if i1 == i2
@@ -575,6 +583,7 @@ static std::vector<int> setup_target_lists(bool use_phase2) {
                 phase2organize(tl);
             }
         }
+        random_delete();
     }
 
     // For clarity, use the all2allv_int style of information flow

coreneuron/network/netcvode.cpp

@@ -135,6 +135,10 @@ void NetCvodeThreadData::interthread_send(double td, DiscreteEvent* db, NrnThrea
     inter_thread_events_.emplace_back(InterThreadEvent{db, td});
 }
 
+void interthread_enqueue(NrnThread* nt) {
+    net_cvode_instance->p[nt->id].enqueue(net_cvode_instance, nt);
+}
+
 void NetCvodeThreadData::enqueue(NetCvode* nc, NrnThread* nt) {
     std::lock_guard<OMP_Mutex> lock(mut);
     for (const auto& ite: inter_thread_events_) {
@@ -229,14 +233,14 @@ void NetCvode::clear_events() {
         d.unreffed_event_cnt_ = 0;
         d.inter_thread_events_.clear();
         d.tqe_->nshift_ = -1;
-        d.tqe_->shift_bin(nrn_threads->_t);
+        d.tqe_->shift_bin(nrn_threads->_t - 0.5 * nrn_threads->_dt);
     }
 }
 
 void NetCvode::init_events() {
     for (int i = 0; i < nrn_nthread; ++i) {
         p[i].tqe_->nshift_ = -1;
-        p[i].tqe_->shift_bin(nrn_threads->_t);
+        p[i].tqe_->shift_bin(nrn_threads->_t - 0.5 * nrn_threads->_dt);
     }
 
     for (int tid = 0; tid < nrn_nthread; ++tid) {  // can be done in parallel