Merge pull request #2601 from med-ayssar/remove-nodeCollection-from-n…

…ode-class

Remove NodeCollection pointer from Node class

nestkernel/node.h

@@ -38,7 +38,6 @@
 #include "nest_names.h"
 #include "nest_time.h"
 #include "nest_types.h"
-#include "node_collection.h"
 #include "secondary_event.h"
 
 // Includes from sli:
@@ -202,10 +201,6 @@ class Node
    */
   size_t get_node_id() const;
 
-  /**
-   * Return lockpointer to the NodeCollection that created this node.
-   */
-  NodeCollectionPTR get_nc() const;
 
   /**
    * Return model ID of the node.
@@ -879,11 +874,6 @@ class Node
 private:
   void set_node_id_( size_t ); //!< Set global node id
 
-  /**
-   * Set the original NodeCollection of this node.
-   */
-  void set_nc_( NodeCollectionPTR );
-
   /** Return a new dictionary datum .
    *
    * This function is called by get_status_base() and returns a new
@@ -958,8 +948,6 @@ class Node
   bool frozen_;        //!< node shall not be updated if true
   bool initialized_;   //!< state and buffers have been initialized
   bool node_uses_wfr_; //!< node uses waveform relaxation method
-
-  NodeCollectionPTR nc_ptr_; //!< Original NodeCollection of this node, used to extract node-specific metadata
 };
 
 inline bool
@@ -1028,11 +1016,6 @@ Node::get_node_id() const
   return node_id_;
 }
 
-inline NodeCollectionPTR
-Node::get_nc() const
-{
-  return nc_ptr_;
-}
 
 inline void
 Node::set_node_id_( size_t i )
@@ -1041,12 +1024,6 @@ Node::set_node_id_( size_t i )
 }
 
 
-inline void
-Node::set_nc_( NodeCollectionPTR nc_ptr )
-{
-  nc_ptr_ = nc_ptr;
-}
-
 inline int
 Node::get_model_id() const
 {

nestkernel/node_collection.h

@@ -395,6 +395,17 @@ class NodeCollection
    */
   virtual bool has_proxies() const = 0;
 
+  /**
+   * return the first stored ID (i.e, ID at index zero) inside the NodeCollection
+   */
+  size_t get_first() const;
+
+  /**
+   * return the last stored ID inside the NodeCollection
+   */
+  size_t get_last() const;
+
+
 private:
   unsigned long fingerprint_; //!< Unique identity of the kernel that created the NodeCollection
   static NodeCollectionPTR create_();
@@ -667,6 +678,20 @@ NodeCollection::set_metadata( NodeCollectionMetadataPTR )
   throw KernelException( "Cannot set Metadata on this type of NodeCollection." );
 }
 
+inline size_t
+NodeCollection::get_first() const
+{
+  return ( *begin() ).node_id;
+}
+
+inline size_t
+NodeCollection::get_last() const
+{
+  size_t offset = size() - 1;
+  return ( *( begin() + offset ) ).node_id;
+}
+
+
 inline nc_const_iterator&
 nc_const_iterator::operator+=( const size_t n )
 {

nestkernel/node_manager.cpp

@@ -23,6 +23,7 @@
 #include "node_manager.h"
 
 // C++ includes:
+#include <algorithm>
 #include <set>
 
 // Includes from libnestutil:
@@ -47,6 +48,7 @@ namespace nest
 
 NodeManager::NodeManager()
   : local_nodes_( 1 )
+  , node_collection_container_()
   , wfr_nodes_vec_()
   , wfr_is_used_( false )
   , wfr_network_size_( 0 ) // zero to force update
@@ -61,6 +63,7 @@ NodeManager::~NodeManager()
 {
   // We must destruct nodes here, since devices may need to close files.
   destruct_nodes_();
+  clear_node_collection_container();
 }
 
 void
@@ -79,6 +82,7 @@ void
 NodeManager::finalize()
 {
   destruct_nodes_();
+  clear_node_collection_container();
 }
 
 void
@@ -135,18 +139,19 @@ NodeManager::add_node( size_t model_id, long n )
     .swap( exceptions_raised_ );
 
   auto nc_ptr = NodeCollectionPTR( new NodeCollectionPrimitive( min_node_id, max_node_id, model_id ) );
+  append_node_collection_( nc_ptr );
 
   if ( model->has_proxies() )
   {
-    add_neurons_( *model, min_node_id, max_node_id, nc_ptr );
+    add_neurons_( *model, min_node_id, max_node_id );
   }
   else if ( not model->one_node_per_process() )
   {
-    add_devices_( *model, min_node_id, max_node_id, nc_ptr );
+    add_devices_( *model, min_node_id, max_node_id );
   }
   else
   {
-    add_music_nodes_( *model, min_node_id, max_node_id, nc_ptr );
+    add_music_nodes_( *model, min_node_id, max_node_id );
   }
 
   // check if any exceptions have been raised
@@ -181,9 +186,8 @@ NodeManager::add_node( size_t model_id, long n )
   return nc_ptr;
 }
 
-
 void
-NodeManager::add_neurons_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr )
+NodeManager::add_neurons_( Model& model, size_t min_node_id, size_t max_node_id )
 {
   const size_t num_vps = kernel().vp_manager.get_num_virtual_processes();
   // Upper limit for number of neurons per thread; in practice, either
@@ -210,7 +214,6 @@ NodeManager::add_neurons_( Model& model, size_t min_node_id, size_t max_node_id,
       {
         Node* node = model.create( t );
         node->set_node_id_( node_id );
-        node->set_nc_( nc_ptr );
         node->set_model_id( model.get_model_id() );
         node->set_thread( t );
         node->set_vp( vp );
@@ -231,7 +234,7 @@ NodeManager::add_neurons_( Model& model, size_t min_node_id, size_t max_node_id,
 }
 
 void
-NodeManager::add_devices_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr )
+NodeManager::add_devices_( Model& model, size_t min_node_id, size_t max_node_id )
 {
   const size_t n_per_thread = max_node_id - min_node_id + 1;
 
@@ -249,7 +252,6 @@ NodeManager::add_devices_( Model& model, size_t min_node_id, size_t max_node_id,
 
         Node* node = model.create( t );
         node->set_node_id_( node_id );
-        node->set_nc_( nc_ptr );
         node->set_model_id( model.get_model_id() );
         node->set_thread( t );
         node->set_vp( kernel().vp_manager.thread_to_vp( t ) );
@@ -270,7 +272,7 @@ NodeManager::add_devices_( Model& model, size_t min_node_id, size_t max_node_id,
 }
 
 void
-NodeManager::add_music_nodes_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr )
+NodeManager::add_music_nodes_( Model& model, size_t min_node_id, size_t max_node_id )
 {
 #pragma omp parallel
   {
@@ -286,7 +288,6 @@ NodeManager::add_music_nodes_( Model& model, size_t min_node_id, size_t max_node
 
           Node* node = model.create( 0 );
           node->set_node_id_( node_id );
-          node->set_nc_( nc_ptr );
           node->set_model_id( model.get_model_id() );
           node->set_thread( 0 );
           node->set_vp( kernel().vp_manager.thread_to_vp( 0 ) );
@@ -307,6 +308,37 @@ NodeManager::add_music_nodes_( Model& model, size_t min_node_id, size_t max_node
   } // omp parallel
 }
 
+NodeCollectionPTR
+NodeManager::node_id_to_node_collection( const size_t node_id ) const
+{
+  // find the largest ID in node_collection_last_ that is still smaller than node_id
+  auto it = std::lower_bound( node_collection_last_.begin(), node_collection_last_.end(), node_id );
+
+  // compute the position of the nodeCollection based on the position of the ID found above
+  size_t pos = it - node_collection_last_.begin();
+  return node_collection_container_.at( pos );
+}
+
+NodeCollectionPTR
+NodeManager::node_id_to_node_collection( Node* node ) const
+{
+  return node_id_to_node_collection( node->get_node_id() );
+}
+
+void
+NodeManager::append_node_collection_( NodeCollectionPTR ncp )
+{
+  node_collection_container_.push_back( ncp );
+  node_collection_last_.push_back( ncp->get_last() );
+}
+
+void
+NodeManager::clear_node_collection_container()
+{
+  node_collection_container_.clear();
+  node_collection_last_.clear();
+}
+
 NodeCollectionPTR
 NodeManager::get_nodes( const DictionaryDatum& params, const bool local_only )
 {

nestkernel/node_manager.h

@@ -242,6 +242,20 @@ class NodeManager : public ManagerInterface
   bool have_nodes_changed() const;
   void set_have_nodes_changed( const bool changed );
 
+  /**
+   * @brief Map the node ID to its original primitive NodeCollection object.
+   * @param node_id  The node ID
+   * @return The primitive NodeCollection object containing the node ID that falls in [first, last)
+   */
+  NodeCollectionPTR node_id_to_node_collection( const size_t node_id ) const;
+
+  /**
+   * @brief Map the node to its original primitive NodeCollection object.
+   * @param node  Node instance
+   * @return The primitive NodeCollection object containing the node with node ID  falls in [first, last)
+   */
+  NodeCollectionPTR node_id_to_node_collection( Node* node ) const;
+
 private:
   /**
    * Initialize the network data structures.
@@ -280,7 +294,7 @@ class NodeManager : public ManagerInterface
    * @param min_node_id node ID of first neuron to create.
    * @param max_node_id node ID of last neuron to create (inclusive).
    */
-  void add_neurons_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr );
+  void add_neurons_( Model& model, size_t min_node_id, size_t max_node_id );
 
   /**
    * Add device nodes.
@@ -291,7 +305,7 @@ class NodeManager : public ManagerInterface
    * @param min_node_id node ID of first neuron to create.
    * @param max_node_id node ID of last neuron to create (inclusive).
    */
-  void add_devices_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr );
+  void add_devices_( Model& model, size_t min_node_id, size_t max_node_id );
 
   /**
    * Add MUSIC nodes.
@@ -303,7 +317,15 @@ class NodeManager : public ManagerInterface
    * @param min_node_id node ID of first neuron to create.
    * @param max_node_id node ID of last neuron to create (inclusive).
    */
-  void add_music_nodes_( Model& model, size_t min_node_id, size_t max_node_id, NodeCollectionPTR nc_ptr );
+  void add_music_nodes_( Model& model, size_t min_node_id, size_t max_node_id );
+
+  /**
+   * @brief Append the NodeCollection instance into the NodeManager::nodeCollection_container.
+   * @param ncp  The NodeCollection instance.
+   */
+  void append_node_collection_( NodeCollectionPTR ncp );
+
+  void clear_node_collection_container();
 
 private:
   /**
@@ -312,6 +334,14 @@ class NodeManager : public ManagerInterface
    */
   std::vector< SparseNodeArray > local_nodes_;
 
+  std::vector< NodeCollectionPTR > node_collection_container_; //!< a vector of the original/primitive NodeCollection
+
+  std::vector< size_t >
+    node_collection_last_; //!< Store the ID of the last element in each NodeCollection instance.
+                           //!<  Mainly, the node_collection_last_ must be the same size as node_collection_container,
+                           //!< where each  element at position i in the nodeCollection_last_ is the last node ID
+                           //!< stored in the node_collection_container_ at position i.
+
   std::vector< std::vector< Node* > > wfr_nodes_vec_; //!< Nodelists for unfrozen nodes that
                                                       //!< use the waveform relaxation method
   bool wfr_is_used_;                                  //!< there is at least one node that uses

nestkernel/parameter.cpp

@@ -137,7 +137,7 @@ NodePosParameter::get_node_pos_( Node* node ) const
   {
     throw KernelException( "NodePosParameter: not node" );
   }
-  NodeCollectionPTR nc = node->get_nc();
+  NodeCollectionPTR nc = kernel().node_manager.node_id_to_node_collection( node );
   if ( not nc.get() )
   {
     throw KernelException( "NodePosParameter: not nc" );

nestkernel/spatial.cpp

@@ -110,14 +110,12 @@ get_position( NodeCollectionPTR layer_nc )
 std::vector< double >
 get_position( const size_t node_id )
 {
-  Node* node = kernel().node_manager.get_node_or_proxy( node_id );
-
   if ( not kernel().node_manager.is_local_node_id( node_id ) )
   {
     throw KernelException( "GetPosition is currently implemented for local nodes only." );
   }
 
-  NodeCollectionPTR nc = node->get_nc();
+  NodeCollectionPTR nc = kernel().node_manager.node_id_to_node_collection( node_id );
   NodeCollectionMetadataPTR meta = nc->get_metadata();
 
   if ( not meta )
@@ -341,9 +339,8 @@ distance( const ArrayDatum conns )
       throw KernelException( "Distance is currently implemented for local nodes only." );
     }
 
-    Node* trgt_node = kernel().node_manager.get_node_or_proxy( trgt );
 
-    NodeCollectionPTR trgt_nc = trgt_node->get_nc();
+    NodeCollectionPTR trgt_nc = kernel().node_manager.node_id_to_node_collection( trgt );
     NodeCollectionMetadataPTR meta = trgt_nc->get_metadata();
 
     // distance is NaN if source, target is not spatially distributed