Merge pull request #607 from UWB-Biocomputing/release-0.9.2

Release 0.9.2

Author: stiber

.github/workflows/tests.yml

@@ -25,7 +25,7 @@ jobs:
       run: cmake ..
     - id: build
       name: build
-      run: make
+      run: make -j
     - name: run unit tests
       run: ./tests    
 
@@ -70,6 +70,14 @@ jobs:
       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
 
+    - id: ts911
+      name: run test-small-911
+      if: always() && steps.build.conclusion == 'success'
+      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
+
     - id: tm
       name: run test-medium
       if: always() && steps.build.conclusion == 'success'

.gitignore

@@ -27,6 +27,7 @@
 *.lib
 
 # Generated Files
+__pycache__/
 build/.cmake
 build/bin
 build/Simulator
@@ -88,3 +89,5 @@ build/Output/Results/*.xml
 build/Output/Results/*.h5
 Testing/RegressionTesting/TestOutput/*.xml
 Testing/RegressionTesting/TestOutput/*.h5
+Testing/UnitTesting/TestOutput/*.xml
+Testing/UnitTesting/TestOutput/*.h5

CMakeLists.txt

@@ -343,20 +343,22 @@ endif()
 # included in the executable.
 add_executable(tests
         Testing/RunTests.cpp
-        Testing/Core/OperationManagerTests.cpp
-        Testing/Core/EdgeIndexMapTests.cpp
-        Testing/Core/FunctionNodeTests.cpp
-        Testing/Core/SimulatorTests.cpp
-        Testing/Core/OperationManagerTestingClass.h
-        Testing/Core/VerticesFactoryTests.cpp
-        Testing/Core/ConnectionsFactoryTests.cpp
-        Testing/Core/EdgesFactoryTests.cpp
-        Testing/Core/LayoutFactoryTests.cpp
-        Testing/Core/RecorderFactoryTests.cpp
-        Testing/Core/InputManagerTests.cpp
-        Testing/Core/RNGFactoryTests.cpp
+        Testing/UnitTesting/OperationManagerTests.cpp
+        Testing/UnitTesting/EdgeIndexMapTests.cpp
+        Testing/UnitTesting/FunctionNodeTests.cpp
+        Testing/UnitTesting/SimulatorTests.cpp
+        Testing/UnitTesting/OperationManagerTestingClass.h
+        Testing/UnitTesting/VerticesFactoryTests.cpp
+        Testing/UnitTesting/ConnectionsFactoryTests.cpp
+        Testing/UnitTesting/EdgesFactoryTests.cpp
+        Testing/UnitTesting/LayoutFactoryTests.cpp
+        Testing/UnitTesting/RecorderFactoryTests.cpp
+        Testing/UnitTesting/InputManagerTests.cpp
+        Testing/UnitTesting/RNGFactoryTests.cpp
         Testing/Utils/ParameterManagerTests.cpp
-        Testing/Utils/CircularBufferTests.cpp)
+        Testing/Utils/CircularBufferTests.cpp
+#        Testing/UnitTesting/XmlRecorderTests.cpp)
+        )
 
 # Links the Googletest framework with the testing executable
 target_link_libraries(tests gtest gtest_main)
@@ -366,7 +368,7 @@ target_link_libraries(tests combinedLib)
 
 add_executable(serialTest
         Testing/RunTests.cpp
-        Testing/Core/SerializationTests.cpp)
+        Testing/UnitTesting/SerializationTests.cpp)
 
 # Links the Googletest framework with the serialTest executable
 target_link_libraries(serialTest gtest gtest_main)
@@ -376,14 +378,24 @@ target_link_libraries(serialTest combinedLib)
 
 add_executable(deserialTest
         Testing/RunTests.cpp
-        Testing/Core/DeserializationTests.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 serialFileAccessTest executable
+target_link_libraries(serialFileAccessTest gtest gtest_main)
+
+# Link the combined library into the 'serialFileAccessTest' executable.
+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)
 unset(PERFORMANCE_METRICS CACHE)

Simulator/Connections/Connections.cpp

@@ -89,8 +89,7 @@ bool Connections::updateConnections(AllVertices &vertices)
 }
 
 #if defined(USE_GPU)
-void Connections::updateSynapsesWeights(const int numVertices, AllVertices &vertices,
-                                        AllEdges &synapses,
+void Connections::updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
                                         AllSpikingNeuronsDeviceProperties *allVerticesDevice,
                                         AllSpikingSynapsesDeviceProperties *allEdgesDevice,
                                         Layout &layout)
@@ -121,13 +120,12 @@ void Connections::createSynapsesFromWeights()
          // 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];
-            BGFLOAT *sumPoint = &(vertices.summationMap_[i]);
             int srcVertex = edges_->sourceVertexIndex_[iEdg];
             int destVertex = edges_->destVertexIndex_[iEdg];
             edgeType type = layout.edgType(srcVertex, destVertex);
             edges_->edgeCounts_[i]++;
-            edges_->createEdge(iEdg, srcVertex, destVertex, sumPoint,
-                               Simulator::getInstance().getDeltaT(), type);
+            edges_->createEdge(iEdg, srcVertex, destVertex, Simulator::getInstance().getDeltaT(),
+                               type);
             edges_->W_[iEdg] = theW;
          }
       }

Simulator/Connections/Connections.h

@@ -85,8 +85,7 @@ class Connections {
    ///  @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(const int numVertices, AllVertices &vertices,
-                                      AllEdges &synapses,
+   virtual void updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
                                       AllSpikingNeuronsDeviceProperties *allVerticesDevice,
                                       AllSpikingSynapsesDeviceProperties *allEdgesDevice,
                                       Layout &layout);

Simulator/Connections/NG911/Connections911.cpp

@@ -3,12 +3,11 @@
 *
 * @ingroup Simulator/Connections/NG911
 * 
-* @brief The model of the static network
-*
+* @brief This class manages the Connections of the NG911 network
 */
 
 #include "Connections911.h"
-#include "All911Vertices.h"
+#include "All911Edges.h"
 #include "GraphManager.h"
 #include "Layout911.h"
 #include "ParameterManager.h"
@@ -31,13 +30,11 @@ void Connections911::setup()
       size_t srcV = gm.source(*it);
       size_t destV = gm.target(*it);
       edgeType type = layout.edgType(srcV, destV);
-      BGFLOAT *sumPoint = &vertices.summationMap_[destV];
 
       BGFLOAT dist = layout.dist_(srcV, destV);
       LOG4CPLUS_DEBUG(edgeLogger_, "Source: " << srcV << " Dest: " << destV << " Dist: " << dist);
 
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, type, srcV, destV, sumPoint, Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg = edges_->addEdge(type, srcV, destV, Simulator::getInstance().getDeltaT());
       added++;
    }
 
@@ -46,7 +43,6 @@ void Connections911::setup()
 
 void Connections911::loadParameters()
 {
-   ParameterManager::getInstance().getIntByXpath("//connsPerVertex/text()", connsPerVertex_);
    ParameterManager::getInstance().getIntByXpath("//psapsToErase/text()", psapsToErase_);
    ParameterManager::getInstance().getIntByXpath("//respsToErase/text()", respsToErase_);
 }
@@ -55,20 +51,18 @@ void Connections911::loadParameters()
 ///  Registered to OperationManager as Operation::printParameters
 void Connections911::printParameters() const
 {
-   LOG4CPLUS_DEBUG(fileLogger_, "CONNECTIONS PARAMETERS"
-                                   << endl
-                                   << "\tConnections Type: Connections911" << endl
-                                   << "\tConnections per vertex: " << connsPerVertex_ << endl
-                                   << "\tPSAPs to erase: " << psapsToErase_ << endl
-                                   << "\tRESPs to erase: " << respsToErase_ << endl
-                                   << endl);
+   LOG4CPLUS_DEBUG(fileLogger_,
+                   "CONNECTIONS PARAMETERS"
+                      << endl
+                      << "\tConnections Type: Connections911" << endl
+                      << "\tMaximum Connections per vertex: " << edges_->maxEdgesPerVertex_ << endl
+                      << "\tPSAPs to erase: " << psapsToErase_ << endl
+                      << "\tRESPs to erase: " << respsToErase_ << endl
+                      << endl);
 }
 
 #if !defined(USE_GPU)
 ///  Update the connections status in every epoch.
-///
-///  @param  vertices  The Vertex list to search from.
-///  @return true if successful, false otherwise.
 bool Connections911::updateConnections(AllVertices &vertices)
 {
    // Only run on the first epoch
@@ -94,11 +88,54 @@ bool Connections911::updateConnections(AllVertices &vertices)
    return true;
 }
 
+
+/// Finds the outgoing edge from the given vertex to the Responder closest to
+/// the emergency call location
+BGSIZE Connections911::getEdgeToClosestResponder(const Call &call, BGSIZE vertexIdx)
+{
+   All911Edges &edges911 = dynamic_cast<All911Edges &>(*edges_);
+
+   vertexType requiredType;
+   if (call.type == "Law")
+      requiredType = LAW;
+   else if (call.type == "EMS")
+      requiredType = EMS;
+   else if (call.type == "Fire")
+      requiredType = FIRE;
+
+   // loop over the outgoing edges looking for the responder with the shortest
+   // Euclidean distance to the call's location.
+   BGSIZE startOutEdg = synapseIndexMap_->outgoingEdgeBegin_[vertexIdx];
+   BGSIZE outEdgCount = synapseIndexMap_->outgoingEdgeCount_[vertexIdx];
+   Layout911 &layout911
+      = dynamic_cast<Layout911 &>(Simulator::getInstance().getModel().getLayout());
+
+   BGSIZE resp, respEdge;
+   double minDistance = numeric_limits<double>::max();
+   for (BGSIZE eIdxMap = startOutEdg; eIdxMap < startOutEdg + outEdgCount; ++eIdxMap) {
+      BGSIZE outEdg = synapseIndexMap_->outgoingEdgeIndexMap_[eIdxMap];
+      assert(edges911.inUse_[outEdg]);   // Edge must be in use
+
+      BGSIZE dstVertex = edges911.destVertexIndex_[outEdg];
+      if (layout911.vertexTypeMap_[dstVertex] == requiredType) {
+         double distance = layout911.getDistance(dstVertex, call.x, call.y);
+
+         if (distance < minDistance) {
+            minDistance = distance;
+            resp = dstVertex;
+            respEdge = outEdg;
+         }
+      }
+   }
+
+   // We must have found the closest responder of the right type
+   assert(minDistance < numeric_limits<double>::max());
+   assert(layout911.vertexTypeMap_[resp] == requiredType);
+   return respEdge;
+}
+
+
 ///  Randomly delete 1 PSAP and rewire all the edges around it.
-///
-///  @param  vertices  The Vertex list to search from.
-///  @param  layout   Layout information of the vertex network.
-///  @return true if successful, false otherwise.
 bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
 {
    int numVertices = Simulator::getInstance().getTotalVertices();
@@ -157,7 +194,8 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
          }
 
          // Identify all psap-less responders
-         if (layout.vertexTypeMap_[destVertex] == RESP) {
+         if (layout.vertexTypeMap_[destVertex] == LAW || layout.vertexTypeMap_[destVertex] == FIRE
+             || layout.vertexTypeMap_[destVertex] == EMS) {
             respsToReroute.push_back(destVertex);
          }
       }
@@ -191,10 +229,8 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       }
 
       // Insert Caller to PSAP edge
-      BGFLOAT *sumPoint = &vertices.summationMap_[closestPSAP];
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, CP, srcVertex, closestPSAP, sumPoint,
-                      Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg
+         = edges_->addEdge(CP, srcVertex, closestPSAP, Simulator::getInstance().getDeltaT());
 
       // Record added edge
       ChangedEdge addedEdge;
@@ -221,10 +257,8 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       }
 
       // Insert PSAP to Responder edge
-      BGFLOAT *sumPoint = &vertices.summationMap_[destVertex];
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, PR, closestPSAP, destVertex, sumPoint,
-                      Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg
+         = edges_->addEdge(PR, closestPSAP, destVertex, Simulator::getInstance().getDeltaT());
 
       // Record added edge
       ChangedEdge addedEdge;
@@ -238,10 +272,6 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
 }
 
 ///  Randomly delete 1 RESP.
-///
-///  @param  vertices  The Vertex list to search from.
-///  @param  layout   Layout information of the vertex network.
-///  @return true if successful, false otherwise.
 bool Connections911::eraseRESP(AllVertices &vertices, Layout &layout)
 {
    int numVertices = Simulator::getInstance().getTotalVertices();
@@ -251,7 +281,8 @@ bool Connections911::eraseRESP(AllVertices &vertices, Layout &layout)
 
    // Find all resps
    for (int i = 0; i < numVertices; i++) {
-      if (layout.vertexTypeMap_[i] == RESP) {
+      if (layout.vertexTypeMap_[i] == LAW || layout.vertexTypeMap_[i] == FIRE
+          || layout.vertexTypeMap_[i] == EMS) {
          resps.push_back(i);
       }
    }
@@ -300,7 +331,8 @@ bool Connections911::eraseRESP(AllVertices &vertices, Layout &layout)
    return changesMade;
 }
 
-///  @return xml representation of a single edge
+
+///  Returns an xml representation of a single edge
 string Connections911::ChangedEdge::toString()
 {
    stringstream os;
@@ -322,6 +354,9 @@ string Connections911::ChangedEdge::toString()
       case RP:
          type_s = "RP";
          break;
+      case RC:
+         type_s = "RC";
+         break;
       default:
          type_s = "ETYPE_UNDEF";
    }
@@ -334,8 +369,6 @@ string Connections911::ChangedEdge::toString()
 }
 
 ///  Returns the complete list of all deleted or added edges as a string.
-///  @param added    true returns the list of added edges, false = erased
-///  @return xml representation of all deleted or added edges
 string Connections911::changedEdgesToXML(bool added)
 {
    stringstream os;
@@ -360,7 +393,6 @@ string Connections911::changedEdgesToXML(bool added)
 }
 
 ///  Returns the complete list of deleted vertices as a string.
-///  @return xml representation of all deleted vertices
 string Connections911::erasedVerticesToXML()
 {
    stringstream os;