Merge branch 'SharedDevelopment' into LawrenceDevelopment

Author: lscott-uw

.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

@@ -97,3 +97,6 @@ Testing/RegressionTesting/TestOutput/*.xml
 Testing/RegressionTesting/TestOutput/*.h5
 Testing/UnitTesting/TestOutput/*.xml
 Testing/UnitTesting/TestOutput/*.h5
+
+# Machine Specific build script
+build.sh

CMakeLists.txt

@@ -8,11 +8,10 @@ cmake_minimum_required(VERSION 3.12)
 #
 #You can also pass this flag when running cmake from the command line like this:
 #
-#cmake..- D ENABLE_CUDA = YES
+#cmake -D ENABLE_CUDA=YES ..
 #
 #"YES" / GPU choice only available if CUDA library is installed and the GPU is CUDA capable.
 ############################################################################################
-
 if(NOT ENABLE_CUDA)
         set(ENABLE_CUDA NO)
 endif()
@@ -22,17 +21,24 @@ if(NOT PERFORMANCE_METRICS)
         set(PERFORMANCE_METRICS NO)
 endif()
 
-#CONDITIONAL FLAG to turn on the Gprof profiler(                                                   \
-#   Gprof is a performance analysis tool for Unix applications)
-#Steps to run Gprof
-#Step 01 : set(GPROF YES) below
-#Step 02 : Compile and run the simulation on CPU or GPU as usual
-#Step 03 : Run the generated gmon.out file from the build directory and save the output in an txt  \
-#      file to improve readability                                                                  \
-#If using CPU - "~/Graphitti/build$ gprof cgraphitti gmon.out > analysis_test.txt"
-#If using GPU - "~/Graphitti/build$ gprof ggraphitti gmon.out > analysis_test.txt" 
-if(NOT GPROF)
-        set(GPROF NO)
+############################################################################################
+#CONDITIONAL FLAG to change target architecture for the GPU simulator from the default
+#
+#You can pass this flag when running cmake from the command line like this, setting TARGET_ARCH \
+#       to your desired architecture:                                                            \
+#
+#cmake -D ENABLE_CUDA=YES -D TARGET_ARCH=70 ..
+#
+#"YES" / GPU choice only available if CUDA library is installed and the GPU is CUDA capable.
+#If no TARGET_ARCH is passed in then it will default to 37 which is the kepler architecture
+############################################################################################
+if(NOT DEFINED TARGET_ARCH)
+        set(TARGET_ARCH 37)
+endif()
+
+#CONDITIONAL FLAG to turn on the validation mode
+if(NOT VALIDATION_MODE)
+        set(VALIDATION_MODE NO)
 endif()
 
 #Creates the Graphitti project with the correct languages, depending on if using GPU or not
@@ -46,31 +52,112 @@ if(ENABLE_CUDA)
         add_compile_definitions(USE_GPU)
 #Specify the CUDA architecture / gencode that will be targeted
         ### Set gencode and architecture variables to the correct values for your specific NVIDIA hardware
-        set(CMAKE_CUDA_ARCHITECTURES 37)        
-        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_37,code=sm_37)
+        set(CMAKE_CUDA_ARCHITECTURES ${TARGET_ARCH})
+        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_${TARGET_ARCH},code=sm_${TARGET_ARCH})        
+        message(STATUS "Using CUDA architecture: ${TARGET_ARCH}")
 
 else()
         message("\n----Generating Makefile for Graphitti CPU version----")
         project(Graphitti LANGUAGES CXX C)
 endif()
 
+# -----------------------------------------------------------------------------
+# Build Type Configuration
+#
+# CMake support for different build types controling optimization, debugging and profiling:
+#
+#   - Debug         : No optimizations (`-O0`), includes debug symbols (`-g`).
+#   - Release       : Optimized build (`-O3`), removes debug symbols.
+#   - RelWithDebInfo: Optimized (`-O2`) but keeps debug symbols (`-g`) for profiling.
+#   - Profiling     : Custom build type (defined in this project) that enables:
+#                     - CPU profiling via `-pg` (GPROF)
+#                     - CUDA profiling via `-lineinfo` (for Nsight Compute)
+#
+# Selecting a Build Type:
+#   - By default, CMake does NOT set a build type for single-config generators.
+#   - If no build type is specified, this script defaults to "Release" for performance.
+#   - You can explicitly set the build type when configuring CMake:
+#
+#       cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug      # Debug mode
+#       cmake -S . -B build -DCMAKE_BUILD_TYPE=Release    # Release mode
+#       cmake -S . -B build -DCMAKE_BUILD_TYPE=Profiling  # Profiling mode 
+#       
+#       If you don't want to pass in the build type flag, you can edit this file and add...
+#               set(CMAKE_BUILD_TYPE "Debug") or whichever build type you want
+# -----------------------------------------------------------------------------
+set(CMAKE_CONFIGURATION_TYPES "Debug;Release;RelWithDebInfo;Profiling" CACHE STRING "Supported build types" FORCE)
+
+# Ensure single-config generators use a valid default
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the build type." FORCE)
+endif()
+
+# Set flags for all build types
+set(CMAKE_CXX_FLAGS_DEBUG "-g -O0")
+# We should consider using the -DNDEBUG flag for release code, it disables assert() calls and is higher performance
+set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
+
+# Define a custom build type: "Profiling"
+set(CMAKE_CXX_FLAGS_PROFILING "-pg -O2")
+set(CMAKE_EXE_LINKER_FLAGS_PROFILING "-pg")
+set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -pg")
+
+# Apply the correct flags based on the selected build type
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_DEBUG}")
+    if(ENABLE_CUDA)
+        set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -g -G")   
+    endif()
+elseif(CMAKE_BUILD_TYPE STREQUAL "Release")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_RELEASE}")
+    if(ENABLE_CUDA)
+        set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -O3")
+    endif()
+elseif(CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_RELWITHDEBINFO}")
+elseif(CMAKE_BUILD_TYPE STREQUAL "Profiling")
+    message(STATUS "Profiling build enabled: Adding -pg (GPROF)")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_PROFILING}")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS_PROFILING}")
+    if(ENABLE_CUDA)
+        set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -lineinfo")   
+#       set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -lineinfo -Xptxas=-v")   
+    endif()
+endif()
+
+
+#   Gprof is a performance analysis tool for Unix applications)
+#Steps to run Gprof
+#Step 01 : set build configuration to Profiling  ...   -DCMAKE_BUILD_TYPE=Profiling
+#Step 02 : Compile and run the simulation on CPU or GPU as usual
+#Step 03 : Run the generated gmon.out file from the build directory and save the output in an txt  \
+#      file to improve readability                                                                  \
+#If using CPU - "~/Graphitti/build$ gprof cgraphitti gmon.out > analysis_test.txt"
+#If using GPU - "~/Graphitti/build$ gprof ggraphitti gmon.out > analysis_test.txt" 
+
+
+# Print build type for verification
+message(STATUS "Build Type: ${CMAKE_BUILD_TYPE}")
+message(STATUS "CMAKE_CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
+
+message(STATUS "ENABLE_CUDA: ${ENABLE_CUDA}")
+if(ENABLE_CUDA)
+        message(STATUS "CMAKE_CUDA_FLAGS: ${CMAKE_CUDA_FLAGS}")
+endif()
+
+
 #Setting the base version to C++ 17
 set(CMAKE_CXX_STANDARD 17)
 
-#set(DEBUG_MODE YES) for debugging, no optimization
-#set(DEBUG_MODE NO) for production code, -O3 optimization enabled
-set(DEBUG_MODE NO)
-
 if(PERFORMANCE_METRICS)
         message("-- Setting PEREFORMANCE_METRICS: ON")
         add_definitions(-DPERFORMANCE_METRICS)
 endif()
 
-if(GPROF)
-        message("-- Setting GPROF: ON")
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pg")
-        set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -pg")
+if(VALIDATION_MODE)
+        message("-- Setting VALIDATION_MODE: ON")
+        add_definitions(-DVALIDATION_MODE)
 endif()
 
 #HDF5 Support, finds HDF5 package for C and C++ and links the hdf5 libraries to the executable     \
@@ -117,11 +204,6 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 #Set extra warning flags
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
 
-if (NOT DEBUG_MODE)
-        message("-- Setting Optimization flag: O3")
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
-endif()
-
 #define TIXML_USE_STL as a preproccersser macro to use the C++ standard library with TinyXML
 add_compile_definitions(TIXML_USE_STL)
 message("-- Setting Compile Definition: TIMXL_USE_STL")
@@ -283,9 +365,33 @@ add_library(RNG STATIC ${RNG_Source})
 
 
 # Create Utils library
-file(GLOB Utils_Source  Simulator/Utils/*.cpp Simulator/Utils/*.h)
+file(GLOB Utils_Source Simulator/Utils/*.cpp Simulator/Utils/*.h)
 list(REMOVE_ITEM Utils_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Utils/Factory.cpp")
-add_library(Utils  ${Utils_Source})
+
+if(CMAKE_BUILD_TYPE STREQUAL "Profiling")
+        if(ENABLE_CUDA)
+# Find NVTX Library
+                find_library(NVTX_LIBRARY nvToolsExt)
+                if(NVTX_LIBRARY)
+                        message(STATUS "Found NVTX: ${NVTX_LIBRARY} included in Profiling")
+                        add_compile_definitions(ENABLE_NVTX) 
+                else()
+                        message(STATUS "NVTX library not found! Not included in Profiling.")
+                        list(REMOVE_ITEM Utils_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Utils/NvtxHelper.cpp")
+                endif()
+        endif()
+
+else()
+        list(REMOVE_ITEM Utils_Source "${CMAKE_CURRENT_SOURCE_DIR}/Simulator/Utils/NvtxHelper.cpp")
+endif()
+
+# Always create the Utils library (even if NVTX and CUDA are missing)
+add_library(Utils ${Utils_Source})
+
+# Only link NVTX if it was found
+if(NVTX_LIBRARY)
+        target_link_libraries(Utils PRIVATE ${NVTX_LIBRARY})
+endif()
 
 
 # Used to locate and run other CMakeLists.txt files from Third Party resources for further compilation of the project.
@@ -353,6 +459,15 @@ endif()
 # ------ TESTS EXECUTABLE ------
 # Add the file that contains main (RunTests.cpp) and all test files. GoogleTest will only recognize them if they are
 # included in the executable.
+target_compile_options(gtest PRIVATE -Wno-error=maybe-uninitialized)
+target_compile_options(gtest_main PRIVATE -Wno-error=maybe-uninitialized)
+
+if(ENABLE_CUDA)
+    set(cuda_TestSources
+        Testing/UnitTesting/DeviceVectorTests.cpp)
+    set_source_files_properties(${cuda_TestSources} PROPERTIES LANGUAGE CUDA)
+endif()
+
 add_executable(tests
         Testing/RunTests.cpp
         Testing/UnitTesting/OperationManagerTests.cpp
@@ -372,7 +487,8 @@ add_executable(tests
         Testing/Utils/CircularBufferTests.cpp
         Testing/UnitTesting/EventBufferTests.cpp
         Testing/UnitTesting/XmlRecorderTests.cpp
-        Testing/UnitTesting/Hdf5RecorderTests.cpp)
+        Testing/UnitTesting/Hdf5RecorderTests.cpp
+        Testing/UnitTesting/DeviceVectorTests.cpp)
 
 # Links the Googletest framework with the testing executable
 target_link_libraries(tests gtest gtest_main)
@@ -427,3 +543,7 @@ target_link_libraries(serialSecondHalfTest combinedLib)
 unset(ENABLE_CUDA CACHE)
 unset(PERFORMANCE_METRICS CACHE)
 unset(GPROF CACHE)
+unset(CMAKE_BUILD_TYPE CACHE)
+unset(NVTX_LIBRARY CACHE)
+unset(TARGET_ARCH CACHE)
+unset(VALIDATION_MODE CACHE)

Contributors.md

@@ -78,9 +78,13 @@ ChengHao Hsu
 
 Zaina Shaikh
 
+Rimjhim Sudhesh
+
 ## 2025
 Andrew Madison
 
+Padmanabh Patil
+
 <!-- ---------------------------------------------------------------------------------- -->
 # 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)
 {