Merge branch 'development' of https://github.com/UWB-Biocomputing/Graphitti into issue-581-serialization-documentation

Author: Divya Kamath

.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

CMakeLists.txt

@@ -363,7 +363,8 @@ add_executable(tests
 	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)

Contributors.md

@@ -74,6 +74,8 @@ Andrzej Dawiec
 
 ChengHao Hsu
 
+Zaina Shaikh
+
 <!-- ---------------------------------------------------------------------------------- -->
 # Graduate
 

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;
-         }
-      }
-   }
-}

Simulator/Connections/Connections.h

@@ -73,9 +73,6 @@ class Connections {
    ///  @return true if successful, false otherwise.
    virtual bool updateConnections(AllVertices &vertices);
 
-   ///  Creates synapses from synapse weights saved in the serialization file.
-   void createSynapsesFromWeights();
-
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive, std::uint32_t const version);
 
@@ -115,6 +112,6 @@ CEREAL_CLASS_VERSION(Connections, 1);
 ///  Cereal serialization method
 template <class Archive> void Connections::serialize(Archive &archive, std::uint32_t const version)
 {
-   archive(cereal::make_nvp("edges_", edges_),
-           cereal::make_nvp("synapseIndexMap_", synapseIndexMap_));
+   archive(cereal::make_nvp("edges", edges_),
+           cereal::make_nvp("synapseIndexMap", synapseIndexMap_));
 }

Simulator/Connections/Neuro/ConnGrowth.cpp

@@ -46,7 +46,7 @@
 #include "ParseParamError.h"
 
 #ifdef USE_HDF5
-   #include "Hdf5GrowthRecorder.h"
+   #include "Hdf5Recorder.h"
 #endif
 
 ConnGrowth::ConnGrowth()
@@ -67,10 +67,15 @@ void ConnGrowth::setup()
    W_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices, numVertices, 0);
    radii_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices, growthParams_.startRadius);
    rates_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices, 0);
+   delta_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices, numVertices);
    area_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices, numVertices, 0);
    outgrowth_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices);
    deltaR_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices);
 
+   // Initialize connection frontier distance change matrix with the current distances
+   Layout &layout = Simulator::getInstance().getModel().getLayout();
+   delta_ = layout.dist_;
+
    // Register VertorMatrix radii_ for Recording if need
    // Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
    // string variableName = "radii";
@@ -128,6 +133,9 @@ bool ConnGrowth::updateConnections(AllVertices &vertices)
    // Update Connections data
    updateConns(vertices);
 
+   // Updata the distance between forntiers of vertices
+   updateFrontiers();
+
    // Update the areas of overlap in between vertices
    updateOverlap();
 
@@ -161,10 +169,22 @@ void ConnGrowth::updateConns(AllVertices &vertices)
    radii_ += deltaR_;
 }
 
+/// Update the distance between frontiers of vertices.
+void ConnGrowth::updateFrontiers()
+{
+   LOG4CPLUS_INFO(fileLogger_, "Updating distance between frontiers...");
+   // Update distance between frontiers
+   Layout &layout = Simulator::getInstance().getModel().getLayout();
+   int numVertices = Simulator::getInstance().getTotalVertices();
+   for (int unit = 0; unit < numVertices - 1; unit++) {
+      for (int i = unit + 1; i < numVertices; i++) {
+         delta_(unit, i) = layout.dist_(unit, i) - (radii_[unit] + radii_[i]);
+         delta_(i, unit) = delta_(unit, i);
+      }
+   }
+}
+
 ///  Update the areas of overlap in between Neurons.
-///
-///  @param  numVertices  Number of vertices to update.
-///  @param  layout      Layout information of the neural network.
 void ConnGrowth::updateOverlap()
 {
    int numVertices = Simulator::getInstance().getTotalVertices();
@@ -173,14 +193,11 @@ void ConnGrowth::updateOverlap()
    LOG4CPLUS_INFO(fileLogger_, "Computing areas of overlap");
 
    // Compute areas of overlap; this is only done for overlapping units
-   for (int i = 0; i < numVertices - 1; i++) {
-      for (int j = i + 1; j < numVertices; j++) {
+   for (int i = 0; i < numVertices; i++) {
+      for (int j = 0; j < numVertices; j++) {
          area_(i, j) = 0.0;
 
-         // Calculate the distance between neuron frontiers
-         BGFLOAT frontierDelta = layout.dist_(j, i) - (radii_[j] + radii_[i]);
-
-         if (frontierDelta < 0) {
+         if (delta_(i, j) < 0) {
             BGFLOAT lenAB = layout.dist_(i, j);
             BGFLOAT r1 = radii_[i];
             BGFLOAT r2 = radii_[j];

Simulator/Connections/Neuro/ConnGrowth.h

@@ -143,6 +143,9 @@ class ConnGrowth : public Connections {
    ///  @param  neurons  The Neuron list to search from.
    void updateConns(AllVertices &neurons);
 
+   /// Update the distance between frontiers of Neurons.
+   void updateFrontiers();
+
    ///  Update the areas of overlap in between Neurons.
    void updateOverlap();
 
@@ -182,6 +185,9 @@ class ConnGrowth : public Connections {
    /// spiking rate
    VectorMatrix rates_;
 
+   /// distance between connection frontiers
+   CompleteMatrix delta_;
+
    /// areas of overlap
    CompleteMatrix area_;
 
@@ -198,8 +204,8 @@ CEREAL_REGISTER_TYPE(ConnGrowth);   // to enable polymorphism
 template <class Archive> void ConnGrowth::serialize(Archive &archive)
 {
    archive(cereal::base_class<Connections>(this), cereal::make_nvp("radiiSize", radiiSize_),
-           cereal::make_nvp("growthParams_", growthParams_), cereal::make_nvp("W_", W_),
-           cereal::make_nvp("radii_", radii_), cereal::make_nvp("rates_", rates_),
-           cereal::make_nvp("area_", area_), cereal::make_nvp("outgrowth_", outgrowth_),
-           cereal::make_nvp("deltaR_", deltaR_));
+           cereal::make_nvp("growthParams", growthParams_), cereal::make_nvp("W", W_),
+           cereal::make_nvp("radii", radii_), cereal::make_nvp("rates", rates_),
+           cereal::make_nvp("delta", delta_), cereal::make_nvp("area", area_),
+           cereal::make_nvp("outgrowth", outgrowth_), cereal::make_nvp("deltaR", deltaR_));
 }

Simulator/Connections/Neuro/ConnStatic.h

@@ -137,12 +137,12 @@ CEREAL_REGISTER_TYPE(ConnStatic);
 template <class Archive> void ConnStatic::serialize(Archive &archive)
 {
    archive(cereal::base_class<Connections>(this),
-           cereal::make_nvp("sourceVertexIndexCurrentEpoch_", sourceVertexIndexCurrentEpoch_),
-           cereal::make_nvp("destVertexIndexCurrentEpoch_", destVertexIndexCurrentEpoch_),
-           cereal::make_nvp("WCurrentEpoch_", WCurrentEpoch_),
-           cereal::make_nvp("radiiSize_", radiiSize_),
-           cereal::make_nvp("connsPerVertex_", connsPerVertex_),
-           cereal::make_nvp("threshConnsRadius_", threshConnsRadius_),
-           cereal::make_nvp("rewiringProbability_", rewiringProbability_),
-           cereal::make_nvp("excWeight_", excWeight_), cereal::make_nvp("inhWeight_", inhWeight_));
-}
+           cereal::make_nvp("sourceVertexIndexCurrentEpoch", sourceVertexIndexCurrentEpoch_),
+           cereal::make_nvp("destVertexIndexCurrentEpoch", destVertexIndexCurrentEpoch_),
+           cereal::make_nvp("WCurrentEpoch", WCurrentEpoch_),
+           cereal::make_nvp("radiiSize", radiiSize_),
+           cereal::make_nvp("connsPerVertex", connsPerVertex_),
+           cereal::make_nvp("threshConnsRadius", threshConnsRadius_),
+           cereal::make_nvp("rewiringProbability", rewiringProbability_),
+           cereal::make_nvp("excWeight", excWeight_), cereal::make_nvp("inhWeight", inhWeight_));
+}

Simulator/Core/Core.cpp

@@ -184,12 +184,15 @@ int Core::runSimulation(string executableName, string cmdLineArguments)
       LOG4CPLUS_TRACE(consoleLogger, "Deserializing state from file.");
 
       // Deserialization
-      if (!serializer.deserializeSynapses()) {
+      if (!serializer.deserialize()) {
          LOG4CPLUS_FATAL(consoleLogger, "Failed while deserializing objects");
          return -1;
       }
    }
 
+   // Helper function for recorder to register spike history variables for all neurons.
+   simulator.getModel().getLayout().getVertices().registerHistoryVariables();
+
    // Run simulation
    LOG4CPLUS_TRACE(consoleLogger, "Starting Simulation");
    simulator.simulate();
@@ -211,7 +214,7 @@ int Core::runSimulation(string executableName, string cmdLineArguments)
    // Serializes internal state for the current simulation
    if (!simulator.getSerializationFileName().empty()) {
       LOG4CPLUS_TRACE(consoleLogger, "Serializing current state");
-      serializer.serializeSynapses();
+      serializer.serialize();
    }
 
    // Tell simulation to clean-up and run any post-simulation logic.

Simulator/Core/EdgeIndexMap.h

@@ -111,12 +111,12 @@ struct EdgeIndexMapDevice {
 ///  Cereal serialization method
 template <class Archive> void EdgeIndexMap::serialize(Archive &archive)
 {
-   archive(cereal::make_nvp("outgoingEdgeIndexMap_", outgoingEdgeIndexMap_),
-           cereal::make_nvp("outgoingEdgeBegin_", outgoingEdgeBegin_),
-           cereal::make_nvp("outgoingEdgeCount_", outgoingEdgeCount_),
-           cereal::make_nvp("incomingEdgeIndexMap_", incomingEdgeIndexMap_),
-           cereal::make_nvp("incomingEdgeBegin_", incomingEdgeBegin_),
-           cereal::make_nvp("incomingEdgeCount_", incomingEdgeCount_),
-           cereal::make_nvp("numOfVertices_", numOfVertices_),
-           cereal::make_nvp("numOfEdges_", numOfEdges_));
+   archive(cereal::make_nvp("outgoingEdgeIndexMap", outgoingEdgeIndexMap_),
+           cereal::make_nvp("outgoingEdgeBegin", outgoingEdgeBegin_),
+           cereal::make_nvp("outgoingEdgeCount", outgoingEdgeCount_),
+           cereal::make_nvp("incomingEdgeIndexMap", incomingEdgeIndexMap_),
+           cereal::make_nvp("incomingEdgeBegin", incomingEdgeBegin_),
+           cereal::make_nvp("incomingEdgeCount", incomingEdgeCount_),
+           cereal::make_nvp("numOfVertices", numOfVertices_),
+           cereal::make_nvp("numOfEdges", numOfEdges_));
 }