HostAPI directed graph iteration and access via index.

This necessitated updating Edge/Vertex classes to internally track via index rather than ID.
This removed redundant index lookups from every accessor, so will have negligbly improved performance.

EdgeMap and VertexMap are now franken datastructures, which have attributes of both maps and arrays.
This is great for usability, but has the potential to confuse users that don't read documentation.

Tests extended in C & Python to cover this.

Closes #1237

include/flamegpu/simulation/detail/CUDAEnvironmentDirectedGraphBuffers.cuh

@@ -146,6 +146,14 @@ class CUDAEnvironmentDirectedGraphBuffers {
      * Returns the number of edges the graph is currently allocated to hold
      */
     size_type getEdgeCount() const { return edge_count; }
+    /**
+     * Returns the number of vertices that have been assigned IDs
+     */
+    size_type getReadyVertexCount() const { return static_cast<size_type>(h_vertex_index_map.size()); }
+    /**
+     * Returns the number of edges that have been assigned valid source/destination vertex pairs
+     */
+    size_type getReadyEdgeCount() const { return static_cast<size_type>(h_edge_index_map.size()); }
     /**
      * Attempt to assign the provided vertex_id with an index inside h_vertex_index_map
      * @param vertex_id The ID of the vertex to be created
@@ -265,17 +273,59 @@ class CUDAEnvironmentDirectedGraphBuffers {
     * @param src_vertex_id The ID that has been assigned to the source vertex of the edge
     * @param dest_vertex_id The ID that has been assigned to the destination vertex of the edge
     *
-    * @throws exception::IDCollision If the ID is already assigned to a different vertex
+    * @throws exception::IDCollision If the ID source/dest pair is already assigned to a different edge
     */
     void setEdgeSourceDestination(unsigned int edge_index, id_t src_vertex_id, id_t dest_vertex_id);
     /**
+    * Updates the edge ID buffer
+    * Updates the internal host map of src:dest->index
+    *
+    * @param edge_index The index of the edge
+    * @param src_vertex_id The ID that has been assigned to the source vertex of the edge
+    *
+    * @throws exception::IDCollision If the ID source/dest pair is already assigned to a different edge
+    */
+    void setEdgeSource(unsigned int edge_index, id_t src_vertex_id);
+    /**
+    * Updates the edge ID buffer
+    * Updates the internal host map of src:dest->index
+    *
+    * @param edge_index The index of the edge
+    * @param dest_vertex_id The ID that has been assigned to the destination vertex of the edge
+    *
+    * @throws exception::IDCollision If the ID source/dest pair is already assigned to a different edge
+    */
+    void setEdgeDestination(unsigned int edge_index, id_t dest_vertex_id);
+    /**
     * Returns the index of the edge with the given source and destination vertices
     * @param src_vertex_id The ID that has been assigned to the source vertex of the edge
     * @param dest_vertex_id The ID that has been assigned to the destination vertex of the edge
     *
     * @throws exception::InvalidID If the ID is not in use
     */
     unsigned int getEdgeIndex(id_t src_vertex_id, id_t dest_vertex_id) const;
+    /**
+    * Returns the source vertex id of the edge with the given index
+    * @param edge_index The index of the edge
+     * @param stream CUDA stream to be used if data must be copied back from device
+    *
+    * @note ID_NOT_SET may be returned, if edge source is not yet set.
+    *
+    * @see getDestinationVertexID(unsigned int)
+    * @throws exception::OutOfBoundsException If the index exceeds the number of edges
+    */
+    id_t getSourceVertexID(unsigned int edge_index, cudaStream_t stream) const;
+    /**
+    * Returns the destination vertex id of the edge with the given index
+    * @param edge_index The index of the edge
+     * @param stream CUDA stream to be used if data must be copied back from device
+    *
+    * @note ID_NOT_SET may be returned, if edge source is not yet set.
+    *
+    * @see getSourceVertexID(unsigned int)
+    * @throws exception::OutOfBoundsException If the index exceeds the number of edges
+    */
+    id_t getDestinationVertexID(unsigned int edge_index, cudaStream_t stream) const;
 #ifdef FLAMEGPU_VISUALISATION
     void setVisualisation(std::shared_ptr<visualiser::ModelVisData> &_visualisation) const {
         this->visualisation = _visualisation;

src/flamegpu/runtime/environment/HostEnvironmentDirectedGraph.cu

@@ -107,24 +107,29 @@ VertexMap HostEnvironmentDirectedGraph::vertices() {
 VertexMap::VertexMap(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream)
     : directed_graph(std::move(_directed_graph))
     , stream(_stream) { }
+size_type VertexMap::size() const {
+    return directed_graph->getReadyVertexCount();
+}
+size_type VertexMap::allocated_size() const {
+    return directed_graph->getVertexCount();
+}
+Vertex VertexMap::atIndex(unsigned int index) {
+    return Vertex{ directed_graph, stream, index, true };
+}
 Vertex VertexMap::operator[](id_t vertex_id) {
     // Attempt to create vertex in id_map if it doesn't already exist
     directed_graph->createIfNotExistVertex(vertex_id, stream);
     // Return
     return Vertex{directed_graph, stream, vertex_id};
 }
 
-Vertex::Vertex(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream, id_t _vertex_id)
+Vertex::Vertex(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream, id_t _vertex_id, bool is_index)
     : directed_graph(std::move(_directed_graph))
     , stream(_stream)
-    , vertex_id(_vertex_id) { }
+    , vertex_index(is_index ? _vertex_id : directed_graph->getVertexIndex(_vertex_id)) { }
 void Vertex::setID(id_t vertex_identifier) {
-    // Get index
-    const unsigned int vertex_index = directed_graph->getVertexIndex(vertex_id);
     // Update ID
     directed_graph->setVertexID(vertex_index, vertex_identifier, stream);
-    // Update local copy of ID
-    vertex_id = vertex_identifier;
 }
 id_t Vertex::getID() const {
     return getProperty<id_t>(ID_VARIABLE_NAME);
@@ -142,6 +147,16 @@ EdgeMap HostEnvironmentDirectedGraph::edges() {
 EdgeMap::EdgeMap(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream)
     : directed_graph(std::move(_directed_graph))
     , stream(_stream) { }
+
+size_type EdgeMap::size() const {
+    return directed_graph->getReadyEdgeCount();
+}
+size_type EdgeMap::allocated_size() const {
+    return directed_graph->getEdgeCount();
+}
+Edge EdgeMap::atIndex(unsigned int index) {
+    return Edge{ directed_graph, stream, index };
+}
 Edge EdgeMap::operator[](SrcDestPair source_dest_vertex_ids) {
     // Attempt to create edge in id_map if it doesn't already exist
     directed_graph->createIfNotExistEdge(source_dest_vertex_ids.first, source_dest_vertex_ids.second, stream);
@@ -152,31 +167,24 @@ Edge EdgeMap::operator[](SrcDestPair source_dest_vertex_ids) {
 Edge::Edge(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream, id_t _source_vertex_id, id_t _dest_vertex_id)
     : directed_graph(std::move(_directed_graph))
     , stream(_stream)
-    , source_vertex_id(_source_vertex_id)
-    , destination_vertex_id(_dest_vertex_id) { }
+    , edge_index(directed_graph->getEdgeIndex(_source_vertex_id, _dest_vertex_id)) { }
+
+Edge::Edge(std::shared_ptr<detail::CUDAEnvironmentDirectedGraphBuffers> _directed_graph, const cudaStream_t _stream, unsigned int _edge_index)
+    : directed_graph(std::move(_directed_graph))
+    , stream(_stream)
+    , edge_index(_edge_index)
+    { }
 void Edge::setSourceVertexID(id_t _source_vertex_id) {
-    // Get index
-    const unsigned int edge_index = directed_graph->getEdgeIndex(source_vertex_id, destination_vertex_id);
     // Update ID
-    directed_graph->setEdgeSourceDestination(edge_index, _source_vertex_id, destination_vertex_id);
-    // Update local copy of ID
-    source_vertex_id = _source_vertex_id;
+    directed_graph->setEdgeSource(edge_index, _source_vertex_id);
 }
 void Edge::setDestinationVertexID(id_t _dest_vertex_id) {
-    // Get index
-    const unsigned int edge_index = directed_graph->getEdgeIndex(source_vertex_id, destination_vertex_id);
     // Update ID
-    directed_graph->setEdgeSourceDestination(edge_index, source_vertex_id, _dest_vertex_id);
-    // Update local copy of ID
-    destination_vertex_id = _dest_vertex_id;
+    directed_graph->setEdgeDestination(edge_index, _dest_vertex_id);
 }
 void Edge::setSourceDestinationVertexID(id_t _source_vertex_id, id_t _dest_vertex_id) {
-    // Get index
-    const unsigned int edge_index = directed_graph->getEdgeIndex(source_vertex_id, destination_vertex_id);
     // Update ID
     directed_graph->setEdgeSourceDestination(edge_index, _source_vertex_id, _dest_vertex_id);
-    // Update local copy of ID
-    destination_vertex_id = _dest_vertex_id;
 }
 id_t Edge::getSourceVertexID() const {
     return getProperty<id_t, 2>(GRAPH_SOURCE_DEST_VARIABLE_NAME, 1);

src/flamegpu/simulation/detail/CUDAEnvironmentDirectedGraphBuffers.cu

@@ -411,15 +411,17 @@ void CUDAEnvironmentDirectedGraphBuffers::syncDevice_async(detail::CUDAScatter&
         }
     }
     if (requires_rebuild && vertex_count && edge_count) {
+        if (edge_count != h_edge_index_map.size()) {
+            THROW exception::IDNotSet("Unable to build graph, only %u/%u edges have been assigned both a source and destination, in CUDAEnvironmentDirectedGraphBuffers::syncDevice_async()", edge_count, static_cast<unsigned int>(h_edge_index_map.size()));
+        } else if (vertex_count != h_vertex_index_map.size()) {
+            THROW exception::IDNotSet("Unable to build graph, only %u/%u vertices have been assigned an ID, in CUDAEnvironmentDirectedGraphBuffers::syncDevice_async()", vertex_count, static_cast<unsigned int>(h_vertex_index_map.size()));
+        }
         // Construct the vertex ID : index map
         {
             if (vertex_id_min == std::numeric_limits<unsigned int>::max() || vertex_id_max == std::numeric_limits<unsigned int>::min()) {
                 THROW flamegpu::exception::IDOutOfBounds("No IDs have been set, in CUDAEnvironmentDirectedGraphBuffers::syncDevice_async()");
             }
             const unsigned int ID_RANGE = 1 + vertex_id_max - vertex_id_min;
-            if (ID_RANGE < vertex_count) {
-                THROW flamegpu::exception::IDNotSet("Not all vertices have been assigned a unique ID, in CUDAEnvironmentDirectedGraphBuffers::syncDevice_async()");
-            }
             if (d_vertex_index_map) {
                 gpuErrchk(flamegpu::detail::cuda::cudaFree(d_vertex_index_map));
             }
@@ -625,7 +627,7 @@ void CUDAEnvironmentDirectedGraphBuffers::setVertexID(unsigned int vertex_index,
         h_vertex_index_map.erase(static_cast<id_t*>(vb.h_ptr)[vertex_index]);
     }
 
-    // Add new vertex ID to host map (validate it's not already in us)
+    // Add new vertex ID to host map (validate it's not already in use)
     const auto find = h_vertex_index_map.find(vertex_id);
     if (find != h_vertex_index_map.end()) {
         THROW exception::IDCollision("ID collision, %u has already been assigned to vertex at index %u, "
@@ -688,13 +690,118 @@ void CUDAEnvironmentDirectedGraphBuffers::setEdgeSourceDestination(unsigned int
     // Require rebuild before use
     markForRebuild();
 }
+void CUDAEnvironmentDirectedGraphBuffers::setEdgeSource(unsigned int edge_index, id_t src_vertex_id) {
+    if (edge_index >= edge_count) {
+        THROW exception::OutOfBoundsException("Edge index exceeds bounds %u >= %u, "
+            "in CUDAEnvironmentDirectedGraphBuffers::setEdgeSource()\n", edge_index, edge_count);
+    } else if (src_vertex_id == ID_NOT_SET) {
+        THROW exception::IDOutOfBounds("Source vertex ID of %u is not valid, "
+            "in CUDAEnvironmentDirectedGraphBuffers::setEdgeSource()\n", ID_NOT_SET);
+    }
+    // Purge old edge src/dest from host map
+    auto& eb = edge_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    // Don't need to update buffer, src_dest is not stored as ID on device
+    id_t& edge_dest = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 0];
+    id_t& edge_src = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 1];
+
+    // Remove old edge from src map if it's complete
+    if (edge_src != ID_NOT_SET && edge_dest != ID_NOT_SET) {
+        h_edge_index_map.erase({edge_src, edge_dest});
+    }
+
+    // Update edge's src dest in buffer
+    edge_src = src_vertex_id;
+    eb.ready = Buffer::Host;
+
+    // Add new edge ID to host map if it's complete
+    if (edge_src != ID_NOT_SET && edge_dest != ID_NOT_SET) {
+        // validate it's not already in use
+        const auto find = h_edge_index_map.find({ edge_src, edge_dest });
+        if (find != h_edge_index_map.end()) {
+            THROW exception::IDCollision("Edge collision, an edge has already been assigned source %u dest %u at index %u, "
+                "in CUDAEnvironmentDirectedGraphBuffers::setEdgeSource()\n", src_vertex_id, edge_dest, find->second);
+        }
+        h_edge_index_map.emplace(std::pair{src_vertex_id, edge_dest }, edge_index);
+    }
+
+    // Require rebuild before use
+    markForRebuild();
+}
+void CUDAEnvironmentDirectedGraphBuffers::setEdgeDestination(unsigned int edge_index, id_t dest_vertex_id) {
+    if (edge_index >= edge_count) {
+        THROW exception::OutOfBoundsException("Edge index exceeds bounds %u >= %u, "
+            "in CUDAEnvironmentDirectedGraphBuffers::setEdgeDestination()\n", edge_index, edge_count);
+    } else if (dest_vertex_id == ID_NOT_SET) {
+        THROW exception::IDOutOfBounds("Destination vertex ID of %u is not valid, "
+            "in CUDAEnvironmentDirectedGraphBuffers::setEdgeDestination()\n", ID_NOT_SET);
+    }
+    // Purge old edge src/dest from host map
+    auto& eb = edge_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    // Don't need to update buffer, src_dest is not stored as ID on device
+    id_t& edge_dest = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 0];
+    id_t& edge_src = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 1];
+
+    // Update edge's src dest in buffer
+    if (edge_src != ID_NOT_SET && edge_dest != ID_NOT_SET) {
+        h_edge_index_map.erase({edge_src, edge_dest});
+    }
+
+    // Update edge's src dest in buffer
+    edge_dest = dest_vertex_id;
+    eb.ready = Buffer::Host;
+
+    // Add new edge ID to host map if it's complete
+    if (edge_src != ID_NOT_SET && edge_dest != ID_NOT_SET) {
+        // validate it's not already in use
+        const auto find = h_edge_index_map.find({ edge_src, edge_dest });
+        if (find != h_edge_index_map.end()) {
+            THROW exception::IDCollision("Edge collision, an edge has already been assigned source %u dest %u at index %u, "
+                "in CUDAEnvironmentDirectedGraphBuffers::setEdgeDestination()\n", edge_src, edge_dest, find->second);
+        }
+        h_edge_index_map.emplace(std::pair{ edge_src, edge_dest }, edge_index);
+    }
+
+    // Require rebuild before use
+    markForRebuild();
+}
 unsigned int CUDAEnvironmentDirectedGraphBuffers::getEdgeIndex(id_t src_vertex_id, id_t dest_vertex_id) const {
     const auto find = h_edge_index_map.find({src_vertex_id, dest_vertex_id});
     if (find == h_edge_index_map.end()) {
         THROW exception::InvalidID("No edge found with source %u, dest %u, in CUDAEnvironmentDirectedGraphBuffers::getEdgeIndex()\n", src_vertex_id, dest_vertex_id);
     }
     return find->second;
 }
+id_t CUDAEnvironmentDirectedGraphBuffers::getSourceVertexID(unsigned int edge_index, cudaStream_t stream) const {
+    if (edge_index >= edge_count) {
+        THROW exception::OutOfBoundsException("Edge index exceeds bounds %u >= %u, "
+            "in CUDAEnvironmentDirectedGraphBuffers::getSourceVertexID()\n", edge_index, edge_count);
+    }
+    // Purge old edge src/dest from host map
+    auto& eb = edge_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    eb.updateHostBuffer(edge_count, stream);
+    const unsigned int vertex_index = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 1];
+    if (vertex_index == ID_NOT_SET)
+        return vertex_index;
+    auto& vb = vertex_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    vb.updateHostBuffer(vertex_count, stream);
+    return static_cast<id_t*>(vb.h_ptr)[vertex_index];
+}
+id_t CUDAEnvironmentDirectedGraphBuffers::getDestinationVertexID(unsigned int edge_index, cudaStream_t stream) const {
+    if (edge_index >= edge_count) {
+        THROW exception::OutOfBoundsException("Edge index exceeds bounds %u >= %u, "
+            "in CUDAEnvironmentDirectedGraphBuffers::getDestinationVertexID()\n", edge_index, edge_count);
+    }
+    // Purge old edge src/dest from host map
+    auto& eb = edge_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    eb.updateHostBuffer(edge_count, stream);
+    // Don't need to update buffer, src_dest is not stored as ID on device
+    const unsigned int vertex_index = static_cast<id_t*>(eb.h_ptr)[edge_index * 2 + 0];
+    if (vertex_index == ID_NOT_SET)
+        return vertex_index;
+    auto& vb = vertex_buffers.at(GRAPH_SOURCE_DEST_VARIABLE_NAME);
+    vb.updateHostBuffer(vertex_count, stream);
+    return static_cast<id_t*>(vb.h_ptr)[vertex_index];
+}
 
 unsigned int CUDAEnvironmentDirectedGraphBuffers::createIfNotExistVertex(id_t vertex_id, const cudaStream_t stream) {
     if (vertex_id == ID_NOT_SET) {

swig/python/flamegpu.i

@@ -656,6 +656,13 @@ class ModelVis;
 %ignore flamegpu::DeviceEnvironmentDirectedGraph;
 %ignore flamegpu::EnvironmentDirectedGraphData;
 %ignore flamegpu::CUDAEnvironmentDirectedGraphBuffers;
+// Disable functions which use C++ iterators/type_index
+%ignore flamegpu::HostEnvironmentDirectedGraph::VertexMap::Iterator;
+%ignore flamegpu::HostEnvironmentDirectedGraph::VertexMap::begin;
+%ignore flamegpu::HostEnvironmentDirectedGraph::VertexMap::end;
+%ignore flamegpu::HostEnvironmentDirectedGraph::EdgeMap::Iterator;
+%ignore flamegpu::HostEnvironmentDirectedGraph::EdgeMap::begin;
+%ignore flamegpu::HostEnvironmentDirectedGraph::EdgeMap::end;
 %include "flamegpu/model/EnvironmentDirectedGraphDescription.cuh"
 %feature("flatnested");     // flat nested on to maps and children are included
 %include "flamegpu/runtime/environment/HostEnvironmentDirectedGraph.cuh"
@@ -840,11 +847,28 @@ namespace std {
     SWIG_fail;
   }
 }
+// Add custom python code for an iterator class, needed when swigifying iterables.
+%pythoncode %{
+class FLAMEGPUGraphMapIterator(object):
+
+    def __init__(self, pointerToVector):
+        self.pointerToVector = pointerToVector
+        self.index = -1
+
+    def __next__(self):
+        self.index += 1
+        if self.index < self.pointerToVector.allocated_size():
+            return self.pointerToVector.atIndex(self.index)
+        else:
+            raise StopIteration
+%}
 // Extend VertexMap/EdgeMap so they can be accessed like a dictionary
 %extend flamegpu::HostEnvironmentDirectedGraph::VertexMap {
     %pythoncode {
         def __len__(self):
             return self.size()
+        def __iter__(self):
+            return FLAMEGPUGraphMapIterator(self)
     }
     flamegpu::HostEnvironmentDirectedGraph::VertexMap::Vertex flamegpu::HostEnvironmentDirectedGraph::VertexMap::__getitem__(const unsigned int vertex_id) {
         return $self->operator[](vertex_id);
@@ -857,6 +881,8 @@ namespace std {
             return self.get_item(int(src), int(dest))
         def __len__(self):
             return self.size()
+        def __iter__(self):
+            return FLAMEGPUGraphMapIterator(self)
     }
     flamegpu::HostEnvironmentDirectedGraph::EdgeMap::Edge flamegpu::HostEnvironmentDirectedGraph::EdgeMap::get_item(const unsigned int src, const unsigned int dest) {
         return $self->operator[]({src, dest});