Merge branch 'SharedDevelopment' into PatilDevelopment

Author: Padmanabh Patil

.gitignore

@@ -42,10 +42,14 @@ graphitti
 ggraphitti
 cgraphitti
 tests
-serialTest
-deserialTest
+serialFullTest
+serialFirstHalfTest
+serialSecondHalfTest
 serialFileAccessTest
-#recorderTest
+core 
+# core is generated by GDB during debugging 
+
+# Recorder Test
 *.exe
 *.out
 *.app

CMakeLists.txt

@@ -53,7 +53,7 @@ else()
         project(Graphitti LANGUAGES CXX C)
 endif()
 
-#Setting the base version to C++ 11
+#Setting the base version to C++ 17
 set(CMAKE_CXX_STANDARD 17)
 
 #set(DEBUG_MODE YES) for debugging, no optimization
@@ -161,18 +161,24 @@ include_directories(
 
 if(ENABLE_CUDA)
 
-        set(cuda_sources Simulator/Edges/Neuro/AllSynapsesDeviceFuncs_d.cpp 
-        Simulator/Vertices/Neuro/AllVerticesDeviceFuncs_d.cpp 
-        Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp 
-        Simulator/Edges/Neuro/AllSTDPSynapses_d.cpp 
-        Simulator/Edges/Neuro/AllDSSynapses_d.cpp 
-        Simulator/Edges/Neuro/AllDynamicSTDPSynapses_d.cpp 
-        Simulator/Vertices/Neuro/AllLIFNeurons_d.cpp 
-        Simulator/Vertices/Neuro/AllIZHNeurons_d.cpp 
-        Simulator/Vertices/Neuro/AllIFNeurons_d.cpp 
-        Simulator/Vertices/Neuro/AllSpikingNeurons_d.cpp 
+        set(cuda_ConnectionsSources 
         Simulator/Connections/Neuro/ConnGrowth_d.cpp )
-        set_source_files_properties(${cuda_sources} PROPERTIES LANGUAGE CUDA)
+        set_source_files_properties(${cuda_ConnectionsSources} PROPERTIES LANGUAGE CUDA)
+
+        set(cuda_EdgesSources Simulator/Edges/Neuro/AllSynapsesDeviceFuncs_d.cpp
+        Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp
+        Simulator/Edges/Neuro/AllSTDPSynapses_d.cpp
+        Simulator/Edges/Neuro/AllDSSynapses_d.cpp
+        Simulator/Edges/Neuro/AllDynamicSTDPSynapses_d.cpp)
+        set_source_files_properties(${cuda_EdgesSources} PROPERTIES LANGUAGE CUDA)
+
+        set(cuda_VerticesSources 
+        Simulator/Vertices/Neuro/AllVerticesDeviceFuncs_d.cpp
+        Simulator/Vertices/Neuro/AllLIFNeurons_d.cpp
+        Simulator/Vertices/Neuro/AllIZHNeurons_d.cpp
+        Simulator/Vertices/Neuro/AllIFNeurons_d.cpp
+        Simulator/Vertices/Neuro/AllSpikingNeurons_d.cpp)
+        set_source_files_properties(${cuda_VerticesSources} PROPERTIES LANGUAGE CUDA)
 endif()
 
    #Collect source files and create libraries
@@ -184,7 +190,7 @@ endif()
 file(GLOB_RECURSE Connections_Source Simulator/Connections/*.cpp Simulator/Connections/*.h)
 
 if(ENABLE_CUDA)
-        add_library(Connections STATIC ${Connections_Source} ${cuda_sources})
+        add_library(Connections STATIC ${Connections_Source} ${cuda_ConnectionsSources})
 else()
         list(REMOVE_ITEM Connections_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Connections/Neuro/ConnGrowth_d.cpp")
         add_library(Connections STATIC ${Connections_Source})
@@ -195,7 +201,7 @@ endif()
 file(GLOB_RECURSE Vertices_Source Simulator/Vertices/*.cpp Simulator/Vertices/*.h)
 
 if(ENABLE_CUDA)
-        add_library(Vertices SHARED ${Vertices_Source} ${cuda_sources})
+        add_library(Vertices STATIC ${Vertices_Source} ${cuda_VerticesSources})
 else()
         list(REMOVE_ITEM Vertices_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Vertices/Neuro/AllVerticesDeviceFuncs.h")
         list(REMOVE_ITEM Vertices_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Vertices/Neuro/AllVerticesDeviceFuncs_d.cpp")
@@ -212,7 +218,7 @@ endif()
 # Create Edges library
 file(GLOB_RECURSE Edges_Source Simulator/Edges/*.cpp Simulator/Edges/*.h)
 if(ENABLE_CUDA)
-        add_library(Edges SHARED ${Edges_Source} ${cuda_sources})
+        add_library(Edges STATIC ${Edges_Source} ${cuda_EdgesSources})
 else()
         list(REMOVE_ITEM Edges_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Edges/Neuro/AllSynapsesDeviceFuncs.h")
         list(REMOVE_ITEM Edges_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Edges/Neuro/AllSynapsesDeviceFuncs_d.cpp")
@@ -373,45 +379,48 @@ target_link_libraries(tests gtest gtest_main)
 # Link the combined library into the 'tests' executable.
 target_link_libraries(tests combinedLib)
 
-# add_executable(serialTest
-#         Testing/RunTests.cpp
-#         Testing/UnitTesting/SerializationTests.cpp)
+#------- SERIALIZATION TESTS --------------------
+# Serialization tests must be executed separately, as each test requires the 
+# simulation to run from start to finish. Running multiple simulations with 
+# the same singleton instance results in a segmentation fault (SEG FAULT).
 
-# # Links the Googletest framework with the serialTest executable
-# target_link_libraries(serialTest gtest gtest_main)
+add_executable(serialFullTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/SerializationFullTest.cpp)
 
-# # Link the combined library into the 'serialTest' executable.
-# target_link_libraries(serialTest combinedLib)
+add_executable(serialFirstHalfTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/SerializationFirstHalfTest.cpp)
 
-# add_executable(deserialTest
-#         Testing/RunTests.cpp
-#         Testing/UnitTesting/DeserializationTests.cpp)
+add_executable(serialSecondHalfTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/SerializationSecondHalfTest.cpp)
 
-# # Links the Googletest framework with the deserialTest executable
-# target_link_libraries(deserialTest gtest gtest_main)
+# Link the GoogleTest framework to each of the serial test executables.
+target_link_libraries(serialFullTest gtest gtest_main)
+target_link_libraries(serialFirstHalfTest gtest gtest_main)
+target_link_libraries(serialSecondHalfTest gtest gtest_main)
 
-# # Link the combined library into the 'deserialTest' executable.
-# target_link_libraries(deserialTest combinedLib)
+# Link the combined library and filesystem support to the respective serial test executables.
+target_link_libraries(serialFullTest stdc++fs)
+target_link_libraries(serialFullTest combinedLib)
 
-# add_executable(serialFileAccessTest
-#         Testing/RunTests.cpp
-#         Testing/UnitTesting/SerializationFileAccessTest.cpp)
+target_link_libraries(serialFirstHalfTest stdc++fs)
+target_link_libraries(serialFirstHalfTest combinedLib)
 
-# # Links the Googletest framework with the serialFileAccessTest executable
-# target_link_libraries(serialFileAccessTest gtest gtest_main)
+target_link_libraries(serialSecondHalfTest stdc++fs)
+target_link_libraries(serialSecondHalfTest combinedLib)
 
-# # Link the combined library into the 'serialFileAccessTest' executable.
-# target_link_libraries(serialFileAccessTest combinedLib)
-
-add_executable(serialFileAccessTest
-        Testing/RunTests.cpp
-        Testing/UnitTesting/SerializationFileAccessTest.cpp)
+# commenting out serialFileAccessTest until issue-754 is resolved
+# add_executable(serialFileAccessTest
+#        Testing/RunTests.cpp
+#        Testing/UnitTesting/SerializationFileAccessTest.cpp)
 
 # Links the Googletest framework with the serialFileAccessTest executable
-target_link_libraries(serialFileAccessTest gtest gtest_main)
+# target_link_libraries(serialFileAccessTest gtest gtest_main)
 
 # Link the combined library into the 'serialFileAccessTest' executable.
-target_link_libraries(serialFileAccessTest combinedLib)
+# target_link_libraries(serialFileAccessTest combinedLib)
 
 # Clear ENABLE_CUDA, PERFORMANCE_METRICS and GPROF from the cache so it's reset for subsequent builds
 unset(ENABLE_CUDA CACHE)

Contributors.md

@@ -78,6 +78,9 @@ ChengHao Hsu
 
 Zaina Shaikh
 
+## 2025
+Andrew Madison
+
 <!-- ---------------------------------------------------------------------------------- -->
 # Graduate
 

Simulator/Connections/Connections.cpp

@@ -38,7 +38,7 @@ 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);
@@ -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)
 {