Merge pull request nest#2948 from heplesser/fix-examples

Fix bug in reconstruction of connection data structures after disconnect and fix small problems with examples

Author: heplesser

examples/run_examples.sh

@@ -93,11 +93,13 @@ for i in $EXAMPLES; do
     echo "  output_dir: '$output_dir'" >>"$metafile"
     echo "  log: '$logfile'" >>"$metafile"
 
-    export NEST_DATA_PATH=""  # $output_dir"
+    export NEST_DATA_PATH="$output_dir"
     touch .start_example
     sleep 1
     set +e
+    # The following line will not work on macOS. There, `brew install gnu-time` and use the commented-out line below.
     /usr/bin/time -f "$time_format" --quiet sh -c "'$runner' '$example' >'$logfile' 2>&1" |& tee -a "$metafile"
+    # /usr/local/bin/gtime -f "$time_format" --quiet sh -c "'$runner' '$example' >'$logfile' 2>&1" | tee -a "$metafile" 2>&1
     ret=$?
     set -e
 

nestkernel/connection_manager.cpp

@@ -1583,6 +1583,10 @@ nest::ConnectionManager::remove_disabled_connections( const size_t tid )
     {
       continue;
     }
+
+    // Source table and connectors are sorted synchronously. All invalid connections have
+    // been sorted to end of source_table_. We find them there, then remove corresponding
+    // elements from connectors.
     const size_t first_disabled_index = source_table_.remove_disabled_sources( tid, syn_id );
 
     if ( first_disabled_index != invalid_index )

nestkernel/connector_base.h

@@ -392,6 +392,7 @@ class Connector : public ConnectorBase
 
     while ( true )
     {
+      assert( lcid + lcid_offset < C_.size() );
       ConnectionT& conn = C_[ lcid + lcid_offset ];
       const bool is_disabled = conn.is_disabled();
       const bool source_has_more_targets = conn.source_has_more_targets();

nestkernel/simulation_manager.cpp

@@ -811,40 +811,6 @@ nest::SimulationManager::update_()
           gettimeofday( &t_slice_begin_, nullptr );
         }
 
-        if ( kernel().sp_manager.is_structural_plasticity_enabled()
-          and ( std::fmod( Time( Time::step( clock_.get_steps() + from_step_ ) ).get_ms(),
-                  kernel().sp_manager.get_structural_plasticity_update_interval() )
-            == 0 ) )
-        {
-          for ( SparseNodeArray::const_iterator i = kernel().node_manager.get_local_nodes( tid ).begin();
-                i != kernel().node_manager.get_local_nodes( tid ).end();
-                ++i )
-          {
-            Node* node = i->get_node();
-            node->update_synaptic_elements( Time( Time::step( clock_.get_steps() + from_step_ ) ).get_ms() );
-          }
-#pragma omp barrier
-#pragma omp single
-          {
-            kernel().sp_manager.update_structural_plasticity();
-          }
-          // Remove 10% of the vacant elements
-          for ( SparseNodeArray::const_iterator i = kernel().node_manager.get_local_nodes( tid ).begin();
-                i != kernel().node_manager.get_local_nodes( tid ).end();
-                ++i )
-          {
-            Node* node = i->get_node();
-            node->decay_synaptic_elements_vacant();
-          }
-
-          // after structural plasticity has created and deleted
-          // connections, update the connection infrastructure; implies
-          // complete removal of presynaptic part and reconstruction
-          // from postsynaptic data
-          update_connection_infrastructure( tid );
-
-        } // of structural plasticity
-
         // Do not deliver events at beginning of first slice, nothing can be there yet
         // and invalid markers have not been properly set in send buffers.
         if ( slice_ > 0 and from_step_ == 0 )
@@ -989,6 +955,42 @@ nest::SimulationManager::update_()
         } // of if(wfr_is_used)
           // end of preliminary update
 
+        if ( kernel().sp_manager.is_structural_plasticity_enabled()
+          and ( std::fmod( Time( Time::step( clock_.get_steps() + from_step_ ) ).get_ms(),
+                  kernel().sp_manager.get_structural_plasticity_update_interval() )
+            == 0 ) )
+        {
+#pragma omp barrier
+          for ( SparseNodeArray::const_iterator i = kernel().node_manager.get_local_nodes( tid ).begin();
+                i != kernel().node_manager.get_local_nodes( tid ).end();
+                ++i )
+          {
+            Node* node = i->get_node();
+            node->update_synaptic_elements( Time( Time::step( clock_.get_steps() + from_step_ ) ).get_ms() );
+          }
+#pragma omp barrier
+#pragma omp single
+          {
+            kernel().sp_manager.update_structural_plasticity();
+          }
+          // Remove 10% of the vacant elements
+          for ( SparseNodeArray::const_iterator i = kernel().node_manager.get_local_nodes( tid ).begin();
+                i != kernel().node_manager.get_local_nodes( tid ).end();
+                ++i )
+          {
+            Node* node = i->get_node();
+            node->decay_synaptic_elements_vacant();
+          }
+
+          // after structural plasticity has created and deleted
+          // connections, update the connection infrastructure; implies
+          // complete removal of presynaptic part and reconstruction
+          // from postsynaptic data
+          update_connection_infrastructure( tid );
+
+        } // of structural plasticity
+
+
 #ifdef TIMER_DETAILED
 #pragma omp barrier
         if ( tid == 0 )

nestkernel/source_table.cpp

@@ -166,14 +166,14 @@ nest::SourceTable::remove_disabled_sources( const size_t tid, const synindex syn
 {
   if ( sources_[ tid ].size() <= syn_id )
   {
-    return invalid_index;
+    return invalid_index; // no source table entry for this synapse model
   }
 
   BlockVector< Source >& mysources = sources_[ tid ][ syn_id ];
   const size_t max_size = mysources.size();
   if ( max_size == 0 )
   {
-    return invalid_index;
+    return invalid_index; // no connections for this synapse model
   }
 
   // lcid needs to be signed, to allow lcid >= 0 check in while loop
@@ -184,15 +184,14 @@ nest::SourceTable::remove_disabled_sources( const size_t tid, const synindex syn
   {
     --lcid;
   }
-  ++lcid; // lcid marks first disabled source, but the while loop only
-          // exits if lcid points at a not disabled element, hence we
-          // need to increase it by one again
-  mysources.erase( mysources.begin() + lcid, mysources.end() );
-  if ( static_cast< size_t >( lcid ) == max_size )
+  const size_t first_invalid_lcid = static_cast< size_t >( lcid + 1 ); // loop stopped on first valid entry or -1
+  if ( first_invalid_lcid == max_size )
   {
-    return invalid_index;
+    return invalid_index; // all lcids are valid, nothing to remove
   }
-  return static_cast< size_t >( lcid );
+
+  mysources.erase( mysources.begin() + first_invalid_lcid, mysources.end() );
+  return first_invalid_lcid;
 }
 
 void
@@ -458,6 +457,10 @@ nest::SourceTable::collect_compressible_sources( const size_t tid )
         kernel().connection_manager.set_source_has_more_targets( tid, syn_id, lcid - 1, true );
         ++lcid;
       }
+      // Mark last connection in sequence as not having successor. This is essential if connections are
+      // delete, e.g., by structural plasticity, because we do not globally reset the more_targets flag.
+      assert( lcid - 1 < syn_sources.size() );
+      kernel().connection_manager.set_source_has_more_targets( tid, syn_id, lcid - 1, false );
     }
   }
 }

pynest/examples/evaluate_quantal_stp_synapse.py

@@ -84,7 +84,7 @@
 
 # We define the number of trials as well as the number of release sites.
 
-n_sites = 10.0  # number of synaptic release sites
+n_sites = 10  # number of synaptic release sites
 n_trials = 500  # number of measurement trials
 
 # The pre-synaptic neuron is driven by an injected current for a part of each

pynest/examples/pong/README.rst

@@ -5,7 +5,7 @@ the classic game of Pong.
 
 Requirements
 ------------
-- NEST 3.3
+- NEST 3.3 or later
 - NumPy
 - Matplotlib
 
@@ -19,4 +19,4 @@ based on the ``stdp_dopamine_synapse`` and temporal difference learning
 is implemented, see ``networks.py`` for details.
 
 The learning progress and resulting game can be visualized with the
-``generate_gif.py`` script.
+``generate_gif.py`` script.

pynest/examples/store_restore_network.py

@@ -304,8 +304,6 @@ def add_to_plot(self, net, n_max=100, t_min=0, t_max=1000, lbl=""):
 
 
 if __name__ == "__main__":
-    plt.ion()
-
     T_sim = 1000
 
     dplot = DemoPlot()
@@ -370,6 +368,4 @@ def add_to_plot(self, net, n_max=100, t_min=0, t_max=1000, lbl=""):
     nest.Simulate(T_sim)
     dplot.add_to_plot(ein2, lbl="Reloaded simulation (different seed)")
 
-    dplot.fig.savefig("store_restore_network.png")
-
-    input("Press ENTER to close figure!")
+    plt.show()

testsuite/pytests/test_spike_transmission_after_disconnect.py

@@ -0,0 +1,44 @@
+# -*- coding: utf-8 -*-
+#
+# test_spike_transmission_after_disconnect.py
+#
+# This file is part of NEST.
+#
+# Copyright (C) 2004 The NEST Initiative
+#
+# NEST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# NEST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+import nest
+
+
+def test_spike_transmission_after_disconnect():
+    """
+    Confirm that spikes can be transmitted after connections have been removed.
+    """
+
+    n = nest.Create("parrot_neuron", 10)
+    nest.Connect(n, n)
+
+    # Delete 1/3 of connections
+    c = nest.GetConnections()
+    c[::3].disconnect()
+
+    # Add spike generator to drive
+    g = nest.Create("spike_generator", params={"spike_times": [1]})
+    nest.Connect(g, n)
+
+    # Simulate long enough for spikes to be delivered, but not too long
+    # since we otherwise will be buried by exponential growth in number
+    # of spikes.
+    nest.Simulate(3)