Merge pull request #718 from UWB-Biocomputing/release-v1.0

Release v1.0

Author: stiber

.github/workflows/tests.yml

@@ -36,39 +36,39 @@ jobs:
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-tiny.xml
     - name: verify test-tiny
       if: always() && steps.tt.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-tiny-out.xml ../Testing/RegressionTesting/GoodOutput/test-tiny-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-tiny-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-tiny-out.xml
 
     - id: ts
       name: run test-small
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-small.xml
     - name: verify test-small
       if: always() && steps.ts.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-small-out.xml ../Testing/RegressionTesting/GoodOutput/test-small-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-small-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-small-out.xml
 
     - id: tsc
       name: run test-small-connected
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-small-connected.xml
     - name: verify test-small-connected
       if: always() && steps.tsc.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-small-connected-out.xml ../Testing/RegressionTesting/GoodOutput/test-small-connected-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-small-connected-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-small-connected-out.xml
 
     - id: tsl
       name: run test-small-long
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-small-long.xml
     - name: verify test-small-long
       if: always() && steps.tsl.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-small-long-out.xml ../Testing/RegressionTesting/GoodOutput/test-small-long-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-small-long-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-small-long-out.xml
 
     - id: tscl
       name: run test-small-connected-long
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-small-connected-long.xml
     - name: verify test-small-connected-long
       if: always() && steps.tscl.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-small-connected-long-out.xml ../Testing/RegressionTesting/GoodOutput/test-small-connected-long-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-small-connected-long-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-small-connected-long-out.xml
 
     - id: ts911
       name: run test-small-911
@@ -84,28 +84,28 @@ jobs:
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-medium.xml
     - name: verify test-medium
       if: always() && steps.tm.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-out.xml ../Testing/RegressionTesting/GoodOutput/test-medium-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-medium-out.xml
 
     - id: tmc
       name: run test-medium-connected
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-medium-connected.xml
     - name: verify test-medium-connected
       if: always() && steps.tmc.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-connected-out.xml ../Testing/RegressionTesting/GoodOutput/test-medium-connected-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-connected-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-medium-connected-out.xml
 
     - id: tml
       name: run test-medium-long
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-medium-long.xml
     - name: verify test-medium-long
       if: always() && steps.tml.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-long-out.xml ../Testing/RegressionTesting/GoodOutput/test-medium-long-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-long-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-medium-long-out.xml
 
     - id: tmcl
       name: run test-medium-connected-long
       if: always() && steps.build.conclusion == 'success'
       run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-medium-connected-long.xml
     - name: verify test-medium-connected-long
       if: always() && steps.tmcl.conclusion == 'success'
-      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-connected-long-out.xml ../Testing/RegressionTesting/GoodOutput/test-medium-connected-long-out.xml
+      run: diff ../Testing/RegressionTesting/TestOutput/test-medium-connected-long-out.xml ../Testing/RegressionTesting/GoodOutput/Cpu/test-medium-connected-long-out.xml

.gitignore

@@ -44,6 +44,8 @@ cgraphitti
 tests
 serialTest
 deserialTest
+serialFileAccessTest
+#recorderTest
 *.exe
 *.out
 *.app

CMakeLists.txt

@@ -1,47 +1,49 @@
 cmake_minimum_required(VERSION 3.12)
 
 ############################################################################################
-# CONDITIONAL FLAG (to run simulation on CPU or GPU)
-# 
-# For GPU:                      For CPU:
-# set(ENABLE_CUDA YES)       set(ENABLE_CUDA NO)                       
+#CONDITIONAL FLAG(to run simulation on CPU or GPU)
 #
-# You can also pass this flag when running cmake from the command line like this:
+#For GPU : For CPU:
+#set(ENABLE_CUDA YES) set(ENABLE_CUDA NO)
 #
-#       cmake .. -D ENABLE_CUDA=YES
+#You can also pass this flag when running cmake from the command line like this:
 #
-# "YES"/GPU choice only available if CUDA library is installed and the GPU is CUDA capable.
+#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()
 
-# CONDITIONAL FLAG to turn on the performance metrics 
+#CONDITIONAL FLAG to turn on the performance metrics 
 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" 
+#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)
 endif()
 
-# Creates the Graphitti project with the correct languages, depending on if using GPU or not
-# If using CUDA, also verify the CUDA package and set the required CUDA variables
+#Creates the Graphitti project with the correct languages, depending on if using GPU or not
+#If using CUDA, also verify the CUDA package and set the required CUDA variables
 if(ENABLE_CUDA)	
         message("\n----Generating Makefile for Graphitti GPU version----")
         project(Graphitti LANGUAGES CXX CUDA C)
-        # Verify CUDA package is present
+#Verify CUDA package is present
         find_Package(CUDA REQUIRED)
-        # Set the USE_GPU preprocessor macro so that GPU code will be compiled.
+#Set the USE_GPU preprocessor macro so that GPU code will be compiled.
         add_compile_definitions(USE_GPU)
-        # Specify the CUDA architecture/gencode that will be targeted
+#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)
@@ -51,11 +53,11 @@ else()
         project(Graphitti LANGUAGES CXX C)
 endif()
 
-# Setting the base version to C++ 11
+#Setting the base version to C++ 11
 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 YES) for debugging, no optimization
+#set(DEBUG_MODE NO) for production code, -O3 optimization enabled
 set(DEBUG_MODE NO)
 
 if(PERFORMANCE_METRICS)
@@ -70,7 +72,8 @@ if(GPROF)
         set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -pg")
 endif()
 
-# HDF5 Support, finds HDF5 package for C and C++ and links the hdf5 libraries to the executable later in the file.
+#HDF5 Support, finds HDF5 package for C and C++ and links the hdf5 libraries to the executable     \
+#                  later in the file.
 find_package(HDF5 COMPONENTS C CXX)
 if (HDF5_FOUND)
         message("-- HDF5 version ${HDF5_VERSION} located. HDF5 recorders are available.")
@@ -81,20 +84,20 @@ else()
         message("-- HDF5 library was not located. Please only use XML recorders.")
 endif()
 
-# Find boost graph library
+#Find boost graph library
 find_package(Boost REQUIRED COMPONENTS graph)
 
-# Get git commit ID
-# Change to "git rev-parse --short HEAD" for short commit ID
+#Get git commit ID
+#Change to "git rev-parse --short HEAD" for short commit ID
 execute_process(
         COMMAND
         git rev-parse HEAD
         OUTPUT_VARIABLE        GIT_COMMIT_ID )
 
-# GIT_COMMIT_ID has trailing whitespaces
+#GIT_COMMIT_ID has trailing whitespaces
 string(REGEX REPLACE "\n$" "" GIT_COMMIT_ID "${GIT_COMMIT_ID}")
 
-# Save GIT_COMMIT_ID to config.h, which is included in Core.cpp
+#Save GIT_COMMIT_ID to config.h, which is included in Core.cpp
 configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/config.h.in
                 ${CMAKE_BINARY_DIR}/config.h
                 @ONLY )
@@ -103,13 +106,14 @@ set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
 #set(CMAKE_VERBOSE_MAKEFILE TRUE)
 
-# Setting the location of the executable to be in the top-level directory. This helps when using file paths during
-# runtime.
+#Setting the location of the executable to be in the top                                           \
+#  - level directory.This helps when using file paths during
+#runtime.
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
-# Set extra warning flags
+#Set extra warning flags
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
 
 if (NOT DEBUG_MODE)
@@ -121,11 +125,11 @@ endif()
 add_compile_definitions(TIXML_USE_STL)
 message("-- Setting Compile Definition: TIMXL_USE_STL")
 
-# Used to define file paths for #include definitions. For example, you can write:
+#Used to define file paths for #include definitions.For example, you can write:
 # #include "Simulator.h"
-# rather than:
+#rather than:
 # #include "Simulator/Core/Simulator.h"
-# if the file path "Simulator/Core" is in the following statement.
+#if the file path "Simulator/Core" is in the following statement.
 include_directories(
         ../Graphitti
         Simulator
@@ -171,11 +175,12 @@ if(ENABLE_CUDA)
         set_source_files_properties(${cuda_sources} PROPERTIES LANGUAGE CUDA)
 endif()
 
-# Collect source files and create libraries
-# Libraries containing .cpp files compiled as CUDA .cu files should be created as STATIC to ensure proper linking
+   #Collect source files and create libraries
+   #Libraries containing.cpp files compiled as CUDA.cu files should be created as STATIC to ensure \
+   #proper linking
 
 
-# Create Connections library
+   #Create Connections library
 file(GLOB_RECURSE Connections_Source Simulator/Connections/*.cpp Simulator/Connections/*.h)
 
 if(ENABLE_CUDA)
@@ -285,8 +290,8 @@ include_directories(Testing/lib/GoogleTest/googletest-master/googletest/include)
 
 # Set CUDA_SEPERABLE_COMPILATION to ON for all libraries that contain .cpp files with device functions compiled as CUDA files
 if(ENABLE_CUDA)
-        set_property(TARGET Edges PROPERTY CUDA_STANDARD 11)
-        set_property(TARGET Vertices PROPERTY CUDA_STANDARD 11)
+        set_property(TARGET Edges PROPERTY CUDA_STANDARD 17)
+        set_property(TARGET Vertices PROPERTY CUDA_STANDARD 17)
         # Enables CUDA code in these libraries to be compiled into separate object files and then linked together
         set_property(TARGET Edges PROPERTY CUDA_SEPARABLE_COMPILATION ON)
         set_property(TARGET Vertices PROPERTY CUDA_SEPARABLE_COMPILATION ON)
@@ -355,36 +360,47 @@ add_executable(tests
         Testing/UnitTesting/RecorderFactoryTests.cpp
         Testing/UnitTesting/InputManagerTests.cpp
         Testing/UnitTesting/RNGFactoryTests.cpp
+	Testing/UnitTesting/GraphManagerTests.cpp
         Testing/Utils/ParameterManagerTests.cpp
         Testing/Utils/CircularBufferTests.cpp
-#        Testing/UnitTesting/XmlRecorderTests.cpp)
-        )
+        Testing/UnitTesting/XmlRecorderTests.cpp
+        Testing/UnitTesting/Hdf5RecorderTests.cpp)
 
 # Links the Googletest framework with the testing executable
 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)
+# add_executable(serialTest
+#         Testing/RunTests.cpp
+#         Testing/UnitTesting/SerializationTests.cpp)
 
-# Links the Googletest framework with the serialTest executable
-target_link_libraries(serialTest gtest gtest_main)
+# # Links the Googletest framework with the serialTest executable
+# target_link_libraries(serialTest gtest gtest_main)
 
-# Link the combined library into the 'serialTest' executable.
-target_link_libraries(serialTest combinedLib)
+# # Link the combined library into the 'serialTest' executable.
+# target_link_libraries(serialTest combinedLib)
 
-add_executable(deserialTest
-        Testing/RunTests.cpp
-        Testing/UnitTesting/DeserializationTests.cpp)
+# add_executable(deserialTest
+#         Testing/RunTests.cpp
+#         Testing/UnitTesting/DeserializationTests.cpp)
+
+# # Links the Googletest framework with the deserialTest executable
+# target_link_libraries(deserialTest gtest gtest_main)
+
+# # Link the combined library into the 'deserialTest' executable.
+# target_link_libraries(deserialTest combinedLib)
+
+# add_executable(serialFileAccessTest
+#         Testing/RunTests.cpp
+#         Testing/UnitTesting/SerializationFileAccessTest.cpp)
 
-# Links the Googletest framework with the deserialTest executable
-target_link_libraries(deserialTest gtest gtest_main)
+# # Links the Googletest framework with the serialFileAccessTest executable
+# target_link_libraries(serialFileAccessTest gtest gtest_main)
 
-# Link the combined library into the 'deserialTest' executable.
-target_link_libraries(deserialTest combinedLib)
+# # Link the combined library into the 'serialFileAccessTest' executable.
+# target_link_libraries(serialFileAccessTest combinedLib)
 
 add_executable(serialFileAccessTest
         Testing/RunTests.cpp

Contributors.md

@@ -74,6 +74,10 @@ Andrzej Dawiec
 
 Jasleen Kaur Saini
 
+ChengHao Hsu
+
+Zaina Shaikh
+
 <!-- ---------------------------------------------------------------------------------- -->
 # Graduate
 
@@ -112,8 +116,10 @@ Victoria Jo Salvatore
 Divya Kamath    
 
 ## 2024
+Vanessa Arndorfer
+
+Xiang Li
+
 Jardi Martinez
 
 Nicholas Posey
-
-Xiang Li  

Simulator/Connections/Connections.cpp

@@ -103,31 +103,3 @@ void Connections::updateSynapsesWeights()
 {
 }
 #endif   // !USE_GPU
-
-///  Creates synapses from synapse weights saved in the serialization file.
-void Connections::createSynapsesFromWeights()
-{
-   int numVertices = Simulator::getInstance().getTotalVertices();
-   Layout &layout = Simulator::getInstance().getModel().getLayout();
-   AllVertices &vertices = layout.getVertices();
-
-   // for each neuron
-   for (int i = 0; i < numVertices; i++) {
-      // for each synapse in the vertex
-      for (BGSIZE synapseIndex = 0; synapseIndex < Simulator::getInstance().getMaxEdgesPerVertex();
-           synapseIndex++) {
-         BGSIZE iEdg = Simulator::getInstance().getMaxEdgesPerVertex() * i + synapseIndex;
-         // if the synapse weight is not zero (which means there is a connection), create the synapse
-         if (edges_->W_[iEdg] != 0.0) {
-            BGFLOAT theW = edges_->W_[iEdg];
-            int srcVertex = edges_->sourceVertexIndex_[iEdg];
-            int destVertex = edges_->destVertexIndex_[iEdg];
-            edgeType type = layout.edgType(srcVertex, destVertex);
-            edges_->edgeCounts_[i]++;
-            edges_->createEdge(iEdg, srcVertex, destVertex, Simulator::getInstance().getDeltaT(),
-                               type);
-            edges_->W_[iEdg] = theW;
-         }
-      }
-   }
-}