Merge PoseyDevelopment into SharedDevelopment (#798)

* [issue-745] Refactor where summation is calculated (#777)

* Refactor model class to generalize the summation logic method and move implementation into neuron class

* Implement new AllVertices method in 911 class

* Fix last compile errors

* Clean up commented out code

* Resolve code format failure

* Remove dynamic cast of vertices so model with work with non-neuron models

* Add override keyword to integrateVertexInputs declaration

* Fix formatting issue

* [issue-785] Remove neuro items from gpu model (#789)

* Rename edge index map device variable name

* Rename method names to remove neuro context

* Rename variables both in method signature and implementation

* Fix formatting

* Remove neuro from GPU model and generalize what we can

* Remove summation point operation as it's now done in the neuro vertices base class

* Revert formatting that breaks code style

* Clean up comments, variable names, and includes

* Move edge sum index into all spiking synapses and rename neuro GPU methods in both edges and vertices

* Fix style violation

* Make corresponding updates to documentation

* Re add serialize method to documentation

* Fix const representation

* Add All911Edges to connections documentation

* Update diagram images

Author: NicolasJPosey

Simulator/Connections/Connections.cpp

@@ -89,17 +89,16 @@ bool Connections::updateConnections(AllVertices &vertices)
 }
 
 #if defined(USE_GPU)
-void Connections::updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
-                                        AllSpikingNeuronsDeviceProperties *allVerticesDevice,
-                                        AllSpikingSynapsesDeviceProperties *allEdgesDevice,
-                                        Layout &layout)
+void Connections::updateEdgesWeights(int numVertices, AllVertices &vertices, AllEdges &edges,
+                                     AllVerticesDeviceProperties *allVerticesDevice,
+                                     AllEdgesDeviceProperties *allEdgesDevice, Layout &layout)
 {
 }
 #else
 
-///  Update the weight of the Synapses in the simulation.
+///  Update the weight of the edges in the simulation.
 ///  Note: Platform Dependent.
-void Connections::updateSynapsesWeights()
+void Connections::updateEdgesWeights()
 {
 }
 #endif   // !USE_GPU

Simulator/Connections/Connections.h

@@ -24,8 +24,6 @@
 #pragma once
 
 #include "AllEdges.h"
-#include "AllSpikingNeurons.h"
-#include "AllSpikingSynapses.h"
 #include "AllVertices.h"
 #include "EdgeIndexMap.h"
 #include "Layout.h"
@@ -69,7 +67,7 @@ class Connections {
 
    ///  Update the connections status in every epoch.
    ///
-   ///  @param  neurons  The Neuron list to search from.
+   ///  @param  vertices  The vertex list to search from.
    ///  @return true if successful, false otherwise.
    virtual bool updateConnections(AllVertices &vertices);
 
@@ -78,35 +76,36 @@ class Connections {
 
 #if defined(USE_GPU)
 public:
-   ///  Update the weight of the Synapses in the simulation.
+   ///  Update the weight of the edges in the simulation.
    ///  Note: Platform Dependent.
    ///
    ///  @param  numVertices          number of vertices to update.
-   ///  @param  neurons             the Neuron list to search from.
-   ///  @param  synapses            the Synapse list to search from.
+   ///  @param  vertices             the vertex list to search from.
+   ///  @param  edges                the edge list to search from.
    ///  @param  allVerticesDevice    GPU address of the allVertices struct on device memory.
-   ///  @param  allEdgesDevice   GPU address of the allEdges struct on device memory.
-   ///  @param  layout              Layout information of the neural network.
-   virtual void updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
-                                      AllSpikingNeuronsDeviceProperties *allVerticesDevice,
-                                      AllSpikingSynapsesDeviceProperties *allEdgesDevice,
-                                      Layout &layout);
+   ///  @param  allEdgesDevice       GPU address of the allEdges struct on device memory.
+   ///  @param  layout               Layout information of the graph network.
+   virtual void updateEdgesWeights(int numVertices, AllVertices &vertices, AllEdges &edges,
+                                   AllVerticesDeviceProperties *allVerticesDevice,
+                                   AllEdgesDeviceProperties *allEdgesDevice, Layout &layout);
 #else
 public:
-   ///  Update the weight of the Synapses in the simulation.
+   ///  Update the weight of the edges in the simulation.
    ///  Note: Platform Dependent.
-   virtual void updateSynapsesWeights();
+   virtual void updateEdgesWeights();
 
 #endif   // USE_GPU
 
 protected:
    unique_ptr<AllEdges> edges_;
+   ///  TODO: Rename to edgeIndexMap_ since this is a base class
    unique_ptr<EdgeIndexMap> synapseIndexMap_;
 
    log4cplus::Logger fileLogger_;
    log4cplus::Logger edgeLogger_;
 };
 
+///  TODO: Rename to synapseIndexMap since this is a base class
 ///  Cereal serialization method
 template <class Archive> void Connections::serialize(Archive &archive)
 {

Simulator/Connections/Neuro/ConnGrowth.cpp

@@ -240,7 +240,7 @@ void ConnGrowth::updateOverlap()
 ///  To be clear, iterates through all source and destination neurons
 ///  and updates their synaptic strengths from the weight matrix.
 ///  Note: Platform Dependent.
-void ConnGrowth::updateSynapsesWeights()
+void ConnGrowth::updateEdgesWeights()
 {
    int numVertices = Simulator::getInstance().getTotalVertices();
    AllNeuroEdges &synapses = dynamic_cast<AllNeuroEdges &>(*edges_);

Simulator/Connections/Neuro/ConnGrowth.h

@@ -103,9 +103,9 @@ class ConnGrowth : public Connections {
 
    ///  Update the connections status in every epoch.
    ///
-   ///  @param  neurons  The Neuron list to search from.
+   ///  @param  vertices  The vertex list to search from.
    ///  @return true if successful, false otherwise.
-   virtual bool updateConnections(AllVertices &neurons) override;
+   virtual bool updateConnections(AllVertices &vertices) override;
 
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
@@ -121,20 +121,20 @@ class ConnGrowth : public Connections {
    ///
    ///  @param  numVertices          The number of vertices to update.
    ///  @param  vertices             The AllVertices object.
-   ///  @param  synapses             The AllEdges object.
+   ///  @param  edges                The AllEdges object.
    ///  @param  allVerticesDevice    GPU address of the AllVertices struct in device memory.
    ///  @param  allEdgesDevice       GPU address of the AllEdges struct in device memory.
    ///  @param  layout               The Layout object.
-   virtual void updateSynapsesWeights(int numVertices, AllVertices &neurons, AllEdges &synapses,
-                                      AllSpikingNeuronsDeviceProperties *allVerticesDevice,
-                                      AllSpikingSynapsesDeviceProperties *allEdgesDevice,
-                                      Layout &layout) override;
+   virtual void updateEdgesWeights(int numVertices, AllVertices &vertices, AllEdges &edges,
+                                   AllVerticesDeviceProperties *allVerticesDevice,
+                                   AllEdgesDeviceProperties *allEdgesDevice,
+                                   Layout &layout) override;
 #else
    ///  Update the weights of the Synapses in the simulation. To be clear,
    ///  iterates through all source and destination neurons and updates their
    ///  synaptic strengths from the weight matrix.
    ///  Note: Platform Dependent.
-   virtual void updateSynapsesWeights() override;
+   virtual void updateEdgesWeights() override;
 
 #endif
 private:

Simulator/Connections/Neuro/ConnGrowth_d.cpp

@@ -7,6 +7,7 @@
  * @brief Update the weights of the Synapses in the simulation.
  */
 
+#include "AllSpikingNeurons.h"
 #include "AllSpikingSynapses.h"
 #include "AllSynapsesDeviceFuncs.h"
 #include "Book.h"
@@ -21,15 +22,14 @@
  *
  *  @param  numVertices         The number of vertices to update.
  *  @param  vertices            The AllVertices object.
- *  @param  synapses            The AllEdges object.
+ *  @param  edges               The AllEdges object.
  *  @param  allVerticesDevice   GPU address to the AllVertices struct in device memory.
  *  @param  allEdgesDevice      GPU address to the AllEdges struct in device memory.
  *  @param  layout              The Layout object.
  */
-void ConnGrowth::updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
-                                       AllSpikingNeuronsDeviceProperties *allVerticesDevice,
-                                       AllSpikingSynapsesDeviceProperties *allEdgesDevice,
-                                       Layout &layout)
+void ConnGrowth::updateEdgesWeights(int numVertices, AllVertices &vertices, AllEdges &edges,
+                                    AllVerticesDeviceProperties *allVerticesDevice,
+                                    AllEdgesDeviceProperties *allEdgesDevice, Layout &layout)
 {
    Simulator &simulator = Simulator::getInstance();
    // For now, we just set the weights to equal the areas. We will later
@@ -66,7 +66,8 @@ void ConnGrowth::updateSynapsesWeights(int numVertices, AllVertices &vertices, A
    blocksPerGrid = (simulator.getTotalVertices() + threadsPerBlock - 1) / threadsPerBlock;
    updateSynapsesWeightsDevice<<<blocksPerGrid, threadsPerBlock>>>(
       simulator.getTotalVertices(), deltaT, W_d, simulator.getMaxEdgesPerVertex(),
-      allVerticesDevice, allEdgesDevice, neuronTypeMapD);
+      (AllSpikingNeuronsDeviceProperties *)allVerticesDevice,
+      (AllSpikingSynapsesDeviceProperties *)allEdgesDevice, neuronTypeMapD);
 
    // free memories
    HANDLE_ERROR(cudaFree(W_d));
@@ -75,7 +76,7 @@ void ConnGrowth::updateSynapsesWeights(int numVertices, AllVertices &vertices, A
    HANDLE_ERROR(cudaFree(neuronTypeMapD));
 
    // copy device synapse count to host memory
-   synapses.copyDeviceEdgeCountsToHost(allEdgesDevice);
+   edges.copyDeviceEdgeCountsToHost(allEdgesDevice);
    // copy device synapse summation coordinate to host memory
-   synapses.copyDeviceEdgeSumIdxToHost(allEdgesDevice);
+   dynamic_cast<AllSpikingSynapses &>(edges).copyDeviceEdgeSumIdxToHost(allEdgesDevice);
 }

Simulator/Core/CPUModel.cpp

@@ -7,7 +7,6 @@
  */
 
 #include "CPUModel.h"
-#include "AllDSSynapses.h"
 #include "Simulator.h"
 
 #if !defined(USE_GPU)
@@ -23,30 +22,34 @@ void CPUModel::advance()
 {
    // ToDo: look at pointer v no pointer in params - to change
    // dereferencing the ptr, lose late binding -- look into changing!
-   layout_->getVertices().advanceVertices(connections_->getEdges(),
-                                          connections_->getEdgeIndexMap());
-   connections_->getEdges().advanceEdges(layout_->getVertices(), connections_->getEdgeIndexMap());
+   AllVertices &vertices = layout_->getVertices();
+   AllEdges &edges = connections_->getEdges();
+   EdgeIndexMap &edgeIndexMap = connections_->getEdgeIndexMap();
+
+   vertices.advanceVertices(edges, edgeIndexMap);
+   edges.advanceEdges(vertices, edgeIndexMap);
+   vertices.integrateVertexInputs(edges, edgeIndexMap);
 }
 
-/// Update the connection of all the Neurons and Synapses of the simulation.
+/// Update the connection of all the vertices and edges of the simulation.
 void CPUModel::updateConnections()
 {
    // Update Connections data
    if (connections_->updateConnections(layout_->getVertices())) {
-      connections_->updateSynapsesWeights();
-      // create synapse inverse map
+      connections_->updateEdgesWeights();
+      // create edge inverse map
       connections_->createEdgeIndexMap();
    }
 }
 
-/// Copy GPU Synapse data to CPU. (Inheritance, no implem)
+/// Copy GPU edge data to CPU. (Inheritance, no implem)
 void CPUModel::copyGPUtoCPU()
 {
    LOG4CPLUS_WARN(fileLogger_, "ERROR: CPUModel::copyGPUtoCPU() was called." << endl);
    exit(EXIT_FAILURE);
 }
 
-/// Copy CPU Synapse data to GPU. (Inheritance, no implem, GPUModel has implem)
+/// Copy CPU edge data to GPU. (Inheritance, no implem, GPUModel has implem)
 void CPUModel::copyCPUtoGPU()
 {
    LOG4CPLUS_WARN(fileLogger_, "ERROR: CPUModel::copyCPUtoGPU() was called." << endl);

Simulator/Core/CPUModel.h

@@ -6,28 +6,14 @@
  * @brief Implementation of Model for execution on CPU (single core).
  * 
  * The Model class maintains and manages classes of objects that make up
- * essential components of the spiking neural network.
- *    -# AllVertices: A class to define a list of particular type of neurons.
- *    -# AllEdges: A class to define a list of particular type of synapses.
- *    -# Connections: A class to define connections of the neural network.
- *    -# Layout: A class to define neurons' layout information in the network.
+ * essential components of the graph network.
+ *    -# AllVertices: A class to define a list of particular type of vertices.
+ *    -# AllEdges: A class to define a list of particular type of edges.
+ *    -# Connections: A class to define connections of the graph network.
+ *    -# Layout: A class to define vertices' layout information in the network.
  *
- * The network is composed of 3 superimposed 2-d arrays: neurons, synapses, and
- * summation points.
- *
- * Synapses in the synapse map are located at the coordinates of the neuron
- * from which they receive output.  Each synapse stores a pointer into a
- * summation point.
- *
- * If, during an advance cycle, a neuron \f$A\f$ at coordinates \f$x,y\f$ fires, every synapse
- * which receives output is notified of the spike. Those synapses then hold
- * the spike until their delay period is completed.  At a later advance cycle, once the delay
- * period has been completed, the synapses apply their PSRs (Post-Synaptic-Response) to
- * the summation points.
- *
- * Finally, on the next advance cycle, each neuron \f$B\f$ adds the value stored
- * in their corresponding summation points to their \f$V_m\f$ and resets the summation points to
- * zero.
+ * Edges in the edge map are located at the coordinates of the vertex
+ * from which they receive output.
  *
  * The model runs on a single thread.
  *
@@ -54,13 +40,13 @@ class CPUModel : public Model {
    /// Advances network state one simulation step.
    virtual void advance() override;
 
-   /// Modifies connections between neurons based on current state of the network and behavior
+   /// Modifies connections between vertices based on current state of the network and behavior
    /// over the past epoch. Should be called once every epoch.
    virtual void updateConnections() override;
 
-   /// Copy GPU Synapse data to CPU.
+   /// Copy GPU edge data to CPU.
    virtual void copyGPUtoCPU() override;
 
-   /// Copy CPU Synapse data to GPU.
+   /// Copy CPU edge data to GPU.
    virtual void copyCPUtoGPU() override;
 };