Issue 716 regression testing for growth and stdp simulation

.github/workflows/tests.yml

@@ -101,3 +101,23 @@ jobs:
         run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-medium-connected-long.xml
       - name: verify test-medium-connected-long
         run: ../Testing/RegressionTesting/compare_matrices ../Testing/RegressionTesting/GoodOutput/Cpu/test-medium-connected-long-out.xml ../Testing/RegressionTesting/TestOutput/test-medium-connected-long-out.xml
+
+      # Growth-to-STDP integration: serialize a grown network, then deserialize it as the
+      # input for an STDP simulation and verify the STDP output. This is a sequential,
+      # dependent pipeline (the STDP run consumes the growth run's checkpoint), so it cannot
+      # be part of the parallel single-simulation tests above.
+      # The unit tests below check that the import mechanism itself behaves (the STDP run keeps
+      # its own classes and receives every grown edge); the regression run after them checks that
+      # the resulting simulation output has not changed.
+      - id: gs_unit
+        name: run growth-to-STDP unit tests
+        run: ./run_growth_stdp_test.sh
+
+      - id: gs_source
+        name: run growth source for growth-to-STDP
+        run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-growth-stdp-source.xml -s ../Testing/RegressionTesting/TestOutput/test-growth-stdp-checkpoint.xml
+      - id: gs_stdp
+        name: run STDP from grown network
+        run: ./cgraphitti -c ../Testing/RegressionTesting/configfiles/test-growth-stdp.xml -d ../Testing/RegressionTesting/TestOutput/test-growth-stdp-checkpoint.xml
+      - name: verify growth-to-STDP
+        run: ../Testing/RegressionTesting/compare_matrices ../Testing/RegressionTesting/GoodOutput/Cpu/test-growth-stdp-out.xml ../Testing/RegressionTesting/TestOutput/test-growth-stdp-out.xml

.gitignore

@@ -47,6 +47,8 @@ serialFullTest
 serialFirstHalfTest
 serialSecondHalfTest
 serialFileAccessTest
+growthStdpSourceTest
+growthStdpImportTest
 core 
 # core is generated by GDB during debugging 
 

CMakeLists.txt

@@ -535,6 +535,30 @@ target_link_libraries(serialFirstHalfTest combinedLib)
 target_link_libraries(serialSecondHalfTest stdc++fs)
 target_link_libraries(serialSecondHalfTest combinedLib)
 
+#------- GROWTH-TO-STDP INTEGRATION TESTS --------------------
+# Like the serialization tests above, each of these runs a simulation from start to finish and so
+# needs its own executable. growthStdpImportTest consumes the checkpoint written by
+# growthStdpSourceTest, so they must run in that order; run_growth_stdp_test.sh sequences them.
+
+add_executable(growthStdpSourceTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/GrowthToStdpSourceTest.cpp)
+
+add_executable(growthStdpImportTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/GrowthToStdpImportTest.cpp)
+
+# Links the Googletest framework to each of the growth-to-STDP test executables.
+target_link_libraries(growthStdpSourceTest gtest gtest_main)
+target_link_libraries(growthStdpImportTest gtest gtest_main)
+
+# Link the combined library and filesystem support to the respective test executables.
+target_link_libraries(growthStdpSourceTest stdc++fs)
+target_link_libraries(growthStdpSourceTest combinedLib)
+
+target_link_libraries(growthStdpImportTest stdc++fs)
+target_link_libraries(growthStdpImportTest combinedLib)
+
 # commenting out serialFileAccessTest until issue-754 is resolved
 # add_executable(serialFileAccessTest
 #        Testing/RunTests.cpp

Simulator/Core/Model.cpp

@@ -172,6 +172,12 @@ Connections &Model::getConnections() const
    return *connections_;
 }
 
+/// Replaces the Connections subgraph with a new instance, taking ownership.
+void Model::setConnections(unique_ptr<Connections> connections)
+{
+   connections_ = std::move(connections);
+}
+
 /// Get the Layout class object.
 /// @return Pointer to the Layout class object.
 Layout &Model::getLayout() const

Simulator/Core/Model.h

@@ -42,6 +42,13 @@ class Model {
    /// Returns reference to Connections
    Connections &getConnections() const;
 
+   /// Replaces the Connections subgraph with a new instance, taking ownership.
+   ///
+   /// Used when deserializing a growth checkpoint into a different (e.g. STDP) model:
+   /// after the checkpoint is loaded, the grown topology is imported into a freshly
+   /// constructed Connections object and installed here. See Serializer::deserialize().
+   void setConnections(unique_ptr<Connections> connections);
+
    /// Returns reference to Layout
    Layout &getLayout() const;
 

Simulator/Core/Serializer.cpp

@@ -24,9 +24,14 @@
  */
 
 #include "Serializer.h"
+#include "AllEdges.h"
 #include "ConnGrowth.h"
+#include "Connections.h"
+#include "Factory.h"
 #include "GPUModel.h"
+#include "Model.h"
 #include "OperationManager.h"
+#include "ParameterManager.h"
 #include <fstream>
 
 // About CEREAL_XML_STRING_VALUE
@@ -36,6 +41,67 @@
 #include <cereal/archives/binary.hpp>
 #include <cereal/archives/xml.hpp>
 
+namespace {
+
+   /// Imports the grown network topology from a deserialized ConnGrowth checkpoint into a
+   /// freshly constructed Connections object of the type requested by the current run's
+   /// configuration file (for example ConnStatic with AllSTDPSynapses).
+   ///
+   /// This enables the output network of a growth simulation to be used as the starting
+   /// point ("input") for a subsequent STDP simulation: only the edge source, destination,
+   /// weight, and type are carried over. The restored vertices/layout and global simulation
+   /// state (RNG, simulation step) are left untouched.
+   ///
+   /// @param connectionClassName  Connections class named in the current configuration file.
+   void importGrowthTopology(const string &connectionClassName)
+   {
+      Simulator &simulator = Simulator::getInstance();
+      Model &model = simulator.getModel();
+
+      // Edges grown during the checkpointed growth simulation (still owned by the model).
+      AllEdges &grownEdges = model.getConnections().getEdges();
+
+      // Build the Connections/Edges objects requested by the current configuration file.
+      unique_ptr<Connections> importedConnections
+         = Factory<Connections>::getInstance().createType(connectionClassName);
+      if (importedConnections == nullptr) {
+         throw runtime_error("Deserialization topology import: unknown Connections class '"
+                             + connectionClassName + "'");
+      }
+
+      AllEdges &importedEdges = importedConnections->getEdges();
+      importedEdges.setupEdges();
+      // Populate per-edge parameters (e.g. STDP constants) from the configuration file so that
+      // addEdge()/createEdge() initialize the new edges with the correct values.
+      importedEdges.loadParameters();
+
+      BGFLOAT deltaT = simulator.getDeltaT();
+      BGSIZE importedCount = 0;
+      for (BGSIZE iEdg = 0; iEdg < grownEdges.inUse_.size(); iEdg++) {
+         if (grownEdges.inUse_[iEdg] == 0) {
+            continue;
+         }
+         int srcVertex = grownEdges.sourceVertexIndex_[iEdg];
+         int destVertex = grownEdges.destVertexIndex_[iEdg];
+         edgeType type = grownEdges.type_[iEdg];
+         BGSIZE newEdg = importedEdges.addEdge(type, srcVertex, destVertex, deltaT);
+         importedEdges.W_[newEdg] = grownEdges.W_[iEdg];
+         ++importedCount;
+      }
+
+      // Install the new connection subgraph (destroys the checkpoint's ConnGrowth) and rebuild
+      // its edge index map from the imported edges.
+      model.setConnections(std::move(importedConnections));
+      model.getConnections().createEdgeIndexMap();
+
+      log4cplus::Logger consoleLogger = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("console"));
+      LOG4CPLUS_INFO(consoleLogger, "Imported " << importedCount << " grown edges into a "
+                                                << connectionClassName
+                                                << " network for the current simulation.");
+   }
+
+}   // namespace
+
 /// Deserializes all member variables of the
 /// Connections, Layout, Edges, Vertices, and associated helper classes.
 ///
@@ -66,6 +132,18 @@ bool Serializer::deserialize()
       return false;
    }
 
+   // If a growth checkpoint is being loaded into a non-growth (e.g. STDP) configuration,
+   // carry over only the grown topology rather than resuming the growth model. This is what
+   // enables using a growth simulation's output network as the input for an STDP simulation.
+   string connectionClassName;
+   ParameterManager::getInstance().getStringByXpath("//ConnectionsParams/@class",
+                                                    connectionClassName);
+   bool checkpointIsGrowth
+      = dynamic_cast<ConnGrowth *>(&simulator.getModel().getConnections()) != nullptr;
+   if (checkpointIsGrowth && connectionClassName != "ConnGrowth") {
+      importGrowthTopology(connectionClassName);
+   }
+
    // Deserialization rebuilds Connections/Layout subgraphs (and nested edges_/vertices_
    // unique_ptrs). Constructors register OperationManager callbacks via std::bind(this, ...),
    // but destroyed objects leave stale entries that segfault on the next executeOperation().

Testing/RegressionTesting/GoodOutput/Cpu/test-growth-stdp-out.xml

@@ -0,0 +1,37 @@
+<?xml version="1.0" standalone="no"?>
+<Matrix name="x_Location" type="complete" rows="1" columns="100" multiplier="1.0">
+   0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 
+</Matrix>
+<Matrix name="y_Location" type="complete" rows="1" columns="100" multiplier="1.0">
+   0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 
+</Matrix>
+<Matrix name="vertexTypeMap" type="complete" rows="1" columns="100" multiplier="1.0">
+   2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 1 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 1 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 1 2 2 2 1 2 2 2 2 2 2 2 
+</Matrix>
+<Matrix name="Neuron_7" type="complete" rows="1" columns="6" multiplier="1.0">
+   102695 104216 126232 162426 188819 190770 
+</Matrix>
+<Matrix name="Neuron_11" type="complete" rows="1" columns="6" multiplier="1.0">
+   100007 116938 135037 151070 172143 185912 
+</Matrix>
+<Matrix name="Neuron_14" type="complete" rows="1" columns="13" multiplier="1.0">
+   100749 109075 116463 118598 122407 138333 140142 141758 148424 151342 168901 183717 191945 
+</Matrix>
+<Matrix name="Neuron_41" type="complete" rows="1" columns="9" multiplier="1.0">
+   102754 108353 110406 125856 162410 173350 179751 182987 186910 
+</Matrix>
+<Matrix name="Neuron_44" type="complete" rows="1" columns="17" multiplier="1.0">
+   109677 114613 117544 119338 132427 138054 143270 150357 158933 164963 173002 174424 183694 186887 189155 190274 194910 
+</Matrix>
+<Matrix name="Neuron_67" type="complete" rows="1" columns="25" multiplier="1.0">
+   107554 115269 116826 120492 122455 130386 132229 134708 141253 147423 149068 156490 158588 163903 167668 169617 171811 174424 175946 178047 179248 184349 186009 187713 195563 
+</Matrix>
+<Matrix name="Neuron_71" type="complete" rows="1" columns="3" multiplier="1.0">
+   190761 193391 199116 
+</Matrix>
+<Matrix name="Neuron_74" type="complete" rows="1" columns="25" multiplier="1.0">
+   103180 105295 116474 118786 123459 130782 132936 134262 137969 149350 152549 153678 155363 161192 162146 167142 170557 172113 174395 187966 189555 192201 195336 198036 199650 
+</Matrix>
+<Matrix name="Neuron_97" type="complete" rows="1" columns="26" multiplier="1.0">
+   109044 111981 113415 116004 117654 127890 129016 129973 132523 139506 144408 145703 150069 154906 155673 158397 161765 163873 165357 169303 170739 172134 180880 187211 189009 192370 
+</Matrix>

Testing/RegressionTesting/configfiles/test-growth-stdp-source.xml

@@ -0,0 +1,114 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Growth simulation that produces the input network for the growth-to-STDP regression
+     test. Run with `-s` to serialize the grown network; the resulting checkpoint is then
+     deserialized by test-growth-stdp.xml. The start radius is large enough that neighboring
+     neurons on the grid overlap and edges are grown within a single short epoch, keeping the
+     regression fast while still exercising a non-trivial grown topology. -->
+<BGSimParams>
+  <SimInfoParams name="SimInfoParams">
+    <graphmlFile name="graphmlFile">../configfiles/graphs/test-small.graphml</graphmlFile>
+    <SimParams name="SimParams">
+      <epochDuration name="epochDuration">10.0</epochDuration>
+      <numEpochs name="numEpochs">1</numEpochs>
+    </SimParams>
+    <SimConfig name="SimConfig">
+      <maxFiringRate name="maxFiringRate">200</maxFiringRate>
+      <maxEdgesPerVertex name="maxEdgesPerVertex">200</maxEdgesPerVertex>
+    </SimConfig>
+    <RNGConfig name="RNGConfig">
+      <InitRNGSeed name="InitRNGSeed">1</InitRNGSeed>
+      <NoiseRNGSeed class="Norm" name="NoiseRNGSeed">1</NoiseRNGSeed>
+    </RNGConfig>
+  </SimInfoParams>
+
+  <ModelParams>
+    <VerticesParams class="AllLIFNeurons" name="VerticesParams">
+      <Iinject name="Iinject">
+        <min name="min">13.5e-09</min>
+        <max name="max">13.5e-09</max>
+      </Iinject>
+      <Inoise name="Inoise">
+        <min name="min">1.0e-09</min>
+        <max name="max">1.5e-09</max>
+      </Inoise>
+      <Vthresh name="Vthresh">
+        <min name="min">15.0e-03</min>
+        <max name="max">15.0e-03</max>
+      </Vthresh>
+      <Vresting name="Vresting">
+        <min name="min">0.0</min>
+        <max name="max">0.0</max>
+      </Vresting>
+      <Vreset name="Vreset">
+        <min name="min">13.5e-03</min>
+        <max name="max">13.5e-03</max>
+      </Vreset>
+      <Vinit name="Vinit">
+        <min name="min">13.0e-03</min>
+        <max name="max">13.0e-03</max>
+      </Vinit>
+      <starter_vthresh name="starter_vthresh">
+        <min name="min">13.565e-3</min>
+        <max name="max">13.655e-3</max>
+      </starter_vthresh>
+      <starter_vreset name="starter_vreset">
+        <min name="min">13.0e-3</min>
+        <max name="max">13.0e-3</max>
+      </starter_vreset>
+    </VerticesParams>
+
+    <EdgesParams class="AllDSSynapses" name="EdgesParams">
+      <tau name="tau">
+        <ii name="ii">6e-3</ii>
+        <ie name="ie">6e-3</ie>
+        <ei name="ei">3e-3</ei>
+        <ee name="ee">3e-3</ee>
+      </tau>
+      <delay name="delay">
+        <ii name="ii">0.8e-3</ii>
+        <ie name="ie">0.8e-3</ie>
+        <ei name="ei">0.8e-3</ei>
+        <ee name="ee">1.5e-3</ee>
+      </delay>
+      <U name="U">
+        <ii name="ii">0.32</ii>
+        <ie name="ie">0.25</ie>
+        <ei name="ei">0.05</ei>
+        <ee name="ee">0.5</ee>
+      </U>
+      <D name="D">
+        <ii name="ii">0.144</ii>
+        <ie name="ie">0.7</ie>
+        <ei name="ei">0.125</ei>
+        <ee name="ee">1.1</ee>
+      </D>
+      <F name="F">
+        <ii name="ii">0.06</ii>
+        <ie name="ie">0.02</ie>
+        <ei name="ei">1.2</ei>
+        <ee name="ee">0.05</ee>
+      </F>
+    </EdgesParams>
+
+    <ConnectionsParams class="ConnGrowth" name="ConnectionsParams">
+      <!-- Growth parameters -->
+      <GrowthParams name="GrowthParams">
+        <epsilon name="epsilon">0.60</epsilon>
+        <beta name="beta">0.10</beta>
+        <rho name="rho">0.0001</rho>
+        <targetRate name="targetRate">1.0</targetRate>
+        <minRadius name="minRadius">0.1</minRadius>
+        <startRadius name="startRadius">0.6</startRadius>
+      </GrowthParams>
+    </ConnectionsParams>
+
+    <LayoutParams class="LayoutNeuro" name="LayoutParams">
+    </LayoutParams>
+
+    <RecorderParams class="XmlRecorder" name="RecorderParams">
+      <RecorderFiles name="RecorderFiles">
+        <resultFileName name="resultFileName">../Testing/RegressionTesting/TestOutput/test-growth-stdp-source-out.xml</resultFileName>
+      </RecorderFiles>
+    </RecorderParams>
+  </ModelParams>
+</BGSimParams>