Merge pull request #869 from UWB-Biocomputing/SharedDevelopment

Release for summer 2025

Author: stiber

.github/workflows/tests.yml

@@ -76,7 +76,7 @@ jobs:
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-small-911.xml
     - name: verify test-small-911
       if: always() && steps.tt.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-small-911-out.xml ../Testing/RegressionTesting/GoodOutput/test-small-911-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-small-911-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-small-911-out.xml
 
     - id: tm
       name: run test-medium

.gitignore

@@ -41,11 +41,16 @@ ThirdParty/log4cplus-2.0.7/src/liblog4cplus.so.2.0.7
 graphitti
 ggraphitti
 cgraphitti
+compare_matrices
 tests
-serialTest
-deserialTest
+serialFullTest
+serialFirstHalfTest
+serialSecondHalfTest
 serialFileAccessTest
-#recorderTest
+core 
+# core is generated by GDB during debugging 
+
+# Recorder Test
 *.exe
 *.out
 *.app
@@ -93,3 +98,6 @@ Testing/RegressionTesting/TestOutput/*.xml
 Testing/RegressionTesting/TestOutput/*.h5
 Testing/UnitTesting/TestOutput/*.xml
 Testing/UnitTesting/TestOutput/*.h5
+
+# Machine Specific build script
+build.sh

CMakeLists.txt

@@ -78,6 +78,15 @@ ChengHao Hsu
 
 Zaina Shaikh
 
+Rimjhim Sudhesh
+
+## 2025
+Andrew Madison
+
+Padmanabh Patil
+
+Lawrence Scott
+
 <!-- ---------------------------------------------------------------------------------- -->
 # Graduate
 

Contributors.md

@@ -38,12 +38,16 @@ Connections::Connections()
 
    // Register loadParameters function with Operation Manager
    function<void()> loadParamsFunc = bind(&Connections::loadParameters, this);
-   opsManager.registerOperation(Operations::op::loadParameters, loadParamsFunc);
+   opsManager.registerOperation(Operations::loadParameters, loadParamsFunc);
 
    // Register registerGraphProperties as Operations registerGraphProperties
    function<void()> regGraphPropsFunc = bind(&Connections::registerGraphProperties, this);
    opsManager.registerOperation(Operations::registerGraphProperties, regGraphPropsFunc);
 
+   // Register registerHistoryVariables function as a registerHistoryVariables operation in the OperationManager
+   function<void()> registerHistoryVarsFunc = bind(&Connections::registerHistoryVariables, this);
+   opsManager.registerOperation(Operations::registerHistoryVariables, registerHistoryVarsFunc);
+
    // Get a copy of the file logger to use log4cplus macros
    fileLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("file"));
    edgeLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("edge"));
@@ -81,25 +85,23 @@ void Connections::createEdgeIndexMap()
 
 ///  Update the connections status in every epoch.
 ///
-///  @param  vertices  The vertex list to search from.
 ///  @return true if successful, false otherwise.
-bool Connections::updateConnections(AllVertices &vertices)
+bool Connections::updateConnections()
 {
    return false;
 }
 
 #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.cpp

@@ -24,8 +24,6 @@
 #pragma once
 
 #include "AllEdges.h"
-#include "AllSpikingNeurons.h"
-#include "AllSpikingSynapses.h"
 #include "AllVertices.h"
 #include "EdgeIndexMap.h"
 #include "Layout.h"
@@ -67,46 +65,49 @@ class Connections {
    ///  Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const = 0;
 
+   /// Registers history variables for recording during simulation
+   virtual void registerHistoryVariables() = 0;
+
    ///  Update the connections status in every epoch.
    ///
-   ///  @param  neurons  The Neuron list to search from.
    ///  @return true if successful, false otherwise.
-   virtual bool updateConnections(AllVertices &vertices);
+   virtual bool updateConnections();
 
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
 
 #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)
 {