Projected views in katana.local [KAT-2411] (#918)

* Adds iterators to DynamicBitset because I'm sick of not having them. * Cleans up the PropertyGraph::MakeProjectedGraph method to accept type IDs and allow null selection. * Add Graph.project to python to create a projected graph view.
KatanaGraph · Feb 22, 2022 · 95ad4cf · 95ad4cf
1 parent 77b2655
commit 95ad4cf
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Showing 27 changed files with 370 additions and 210 deletions.
diff --git a/libgalois/include/katana/DynamicBitset.h b/libgalois/include/katana/DynamicBitset.h
@@ -34,6 +34,7 @@
 #include <boost/mpl/has_xxx.hpp>
 
 #include "katana/AtomicWrapper.h"
+#include "katana/DynamicBitsetSlow.h"
 #include "katana/Galois.h"
 #include "katana/PODVector.h"
 #include "katana/config.h"
@@ -45,6 +46,7 @@ namespace katana {
 class KATANA_EXPORT DynamicBitset {
 public:  // types
   using TItem = katana::CopyableAtomic<uint64_t>;
+  using iterator = DynamicBitsetIterator<DynamicBitset>;
 
 private:  // variables
   katana::PODVector<TItem> bitvec_;
@@ -92,6 +94,18 @@ class KATANA_EXPORT DynamicBitset {
    */
   auto& get_vec() { return bitvec_; }
 
+  iterator begin() const {
+    iterator bit0{this, 0, 0};
+    if (test(0)) {
+      // If bit 0 is set then we have the right iterator
+      return bit0;
+    }
+    // Otherwise, increment to find the first set bit.
+    return ++bit0;
+  }
+
+  iterator end() const { return {this, bitvec_.size(), 0}; }
+
   /**
    * Resizes the bitset.
    *

diff --git a/libgraph/include/katana/PropertyGraph.h b/libgraph/include/katana/PropertyGraph.h
@@ -279,12 +279,23 @@ class KATANA_EXPORT PropertyGraph {
       const katana::RDGManifest& rdg_manifest,
       const katana::RDGLoadOptions& opts, katana::TxnContext* txn_ctx);
 
-  /// Make a projected graph from a property graph. Shares state with
-  /// the original graph.
-  static std::unique_ptr<PropertyGraph> MakeProjectedGraph(
+  [[deprecated]] static std::unique_ptr<PropertyGraph> MakeProjectedGraph(
       const PropertyGraph& pg, const std::vector<std::string>& node_types,
       const std::vector<std::string>& edge_types);
 
+  /// Make a projected graph from a property graph. Shares state with
+  /// the original graph.
+  static Result<std::unique_ptr<PropertyGraph>> MakeProjectedGraph(
+      const PropertyGraph& pg,
+      std::optional<std::vector<std::string>> node_types,
+      std::optional<std::vector<std::string>> edge_types);
+
+  /// Make a projected graph from a property graph. Shares state with
+  /// the original graph.
+  static Result<std::unique_ptr<PropertyGraph>> MakeProjectedGraph(
+      const PropertyGraph& pg, std::optional<SetOfEntityTypeIDs> node_types,
+      std::optional<SetOfEntityTypeIDs> edge_types);
+
   /// \return A copy of this with the same set of properties. The copy shares no
   ///       state with this.
   Result<std::unique_ptr<PropertyGraph>> Copy(

diff --git a/libgraph/src/PropertyGraph.cpp b/libgraph/src/PropertyGraph.cpp
@@ -351,6 +351,36 @@ std::unique_ptr<katana::PropertyGraph>
 katana::PropertyGraph::MakeProjectedGraph(
     const PropertyGraph& pg, const std::vector<std::string>& node_types,
     const std::vector<std::string>& edge_types) {
+  auto ret = MakeProjectedGraph(
+      pg, node_types.empty() ? std::nullopt : std::make_optional(node_types),
+      edge_types.empty() ? std::nullopt : std::make_optional(edge_types));
+  KATANA_LOG_VASSERT(ret.has_value(), "{}", ret.error());
+  return std::move(ret.value());
+}
+
+katana::Result<std::unique_ptr<katana::PropertyGraph>>
+katana::PropertyGraph::MakeProjectedGraph(
+    const PropertyGraph& pg, std::optional<std::vector<std::string>> node_types,
+    std::optional<std::vector<std::string>> edge_types) {
+  std::optional<SetOfEntityTypeIDs> node_type_ids;
+  if (node_types) {
+    node_type_ids = KATANA_CHECKED(
+        pg.GetNodeTypeManager().GetEntityTypeIDs(node_types.value()));
+  }
+  std::optional<SetOfEntityTypeIDs> edge_type_ids;
+  if (edge_types) {
+    edge_type_ids = KATANA_CHECKED(
+        pg.GetEdgeTypeManager().GetEntityTypeIDs(edge_types.value()));
+  }
+  return MakeProjectedGraph(pg, node_type_ids, edge_type_ids);
+}
+
+/// Make a projected graph from a property graph. Shares state with
+/// the original graph.
+katana::Result<std::unique_ptr<katana::PropertyGraph>>
+katana::PropertyGraph::MakeProjectedGraph(
+    const PropertyGraph& pg, std::optional<SetOfEntityTypeIDs> node_types,
+    std::optional<SetOfEntityTypeIDs> edge_types) {
   const auto& topology = pg.topology();
   if (topology.empty()) {
     return std::make_unique<PropertyGraph>();
@@ -366,7 +396,7 @@ katana::PropertyGraph::MakeProjectedGraph(
   NUMAArray<Node> original_to_projected_nodes_mapping;
   original_to_projected_nodes_mapping.allocateInterleaved(topology.NumNodes());
 
-  if (node_types.empty()) {
+  if (!node_types) {
     num_new_nodes = topology.NumNodes();
     // set all nodes
     katana::do_all(katana::iterate(topology.Nodes()), [&](auto src) {
@@ -378,21 +408,14 @@ katana::PropertyGraph::MakeProjectedGraph(
         original_to_projected_nodes_mapping.begin(),
         original_to_projected_nodes_mapping.end(), Node{0});
 
-    std::set<katana::EntityTypeID> node_entity_type_ids;
-
-    for (auto node_type : node_types) {
-      auto entity_type_id = pg.GetNodeEntityTypeID(node_type);
-      node_entity_type_ids.insert(entity_type_id);
-    }
-
     katana::GAccumulator<uint32_t> accum_num_new_nodes;
 
     katana::do_all(katana::iterate(topology.Nodes()), [&](auto src) {
-      for (auto type : node_entity_type_ids) {
+      for (auto type : node_types.value()) {
         if (pg.DoesNodeHaveType(src, type)) {
           accum_num_new_nodes += 1;
           bitset_nodes.set(src);
-          // this sets the correspondign entry in the array to 1
+          // this sets the corresponding entry in the array to 1
           // will perform a prefix sum on this array later on
           original_to_projected_nodes_mapping[src] = 1;
           return;
@@ -444,7 +467,7 @@ katana::PropertyGraph::MakeProjectedGraph(
   // initializes the edge-index array to all zeros
   katana::ParallelSTL::fill(out_indices.begin(), out_indices.end(), Edge{0});
 
-  if (edge_types.empty()) {
+  if (!edge_types) {
     katana::GAccumulator<uint32_t> accum_num_new_edges;
     // set all edges incident to projected nodes
     katana::do_all(
@@ -464,13 +487,6 @@ katana::PropertyGraph::MakeProjectedGraph(
 
     num_new_edges = accum_num_new_edges.reduce();
   } else {
-    std::set<katana::EntityTypeID> edge_entity_type_ids;
-
-    for (auto edge_type : edge_types) {
-      auto entity_type_id = pg.GetEdgeEntityTypeID(edge_type);
-      edge_entity_type_ids.insert(entity_type_id);
-    }
-
     katana::GAccumulator<uint32_t> accum_num_new_edges;
 
     katana::do_all(
@@ -481,7 +497,7 @@ katana::PropertyGraph::MakeProjectedGraph(
           for (Edge e : topology.OutEdges(old_src)) {
             auto dest = topology.OutEdgeDst(e);
             if (bitset_nodes.test(dest)) {
-              for (auto type : edge_entity_type_ids) {
+              for (auto type : edge_types.value()) {
                 if (pg.DoesEdgeHaveTypeFromTopoIndex(e, type)) {
                   accum_num_new_edges += 1;
                   bitset_edges.set(e);

diff --git a/libgraph/test/projection.cpp b/libgraph/test/projection.cpp
@@ -68,8 +68,14 @@ main(int argc, char** argv) {
   std::vector<std::string> edge_types;
   SplitString(edgeTypes, &edge_types);
 
-  auto pg_view = katana::PropertyGraph::MakeProjectedGraph(
-      full_graph, node_types, edge_types);
+  auto pg_view_res = katana::PropertyGraph::MakeProjectedGraph(
+      full_graph,
+      node_types.empty() ? std::nullopt : std::make_optional(node_types),
+      edge_types.empty() ? std::nullopt : std::make_optional(edge_types));
+  if (!pg_view_res) {
+    KATANA_LOG_FATAL("Failed to construct projection: {}", pg_view_res.error());
+  }
+  auto pg_view = std::move(pg_view_res.value());
 
   katana::analytics::TemporaryPropertyGuard temp_node_property{
       full_graph.NodeMutablePropertyView()};

diff --git a/libgraph/test/transformation-view-optional-topology.cpp b/libgraph/test/transformation-view-optional-topology.cpp
@@ -83,8 +83,13 @@ main(int argc, char** argv) {
   std::vector<std::string> edge_types;
   SplitString(edgeTypes, &edge_types);
 
-  auto pg_view =
-      katana::PropertyGraph::MakeProjectedGraph(pg, node_types, edge_types);
+  auto pg_view_res = katana::PropertyGraph::MakeProjectedGraph(
+      pg, node_types.empty() ? std::nullopt : std::make_optional(node_types),
+      edge_types.empty() ? std::nullopt : std::make_optional(edge_types));
+  if (!pg_view_res) {
+    KATANA_LOG_FATAL("Failed to construct projection: {}", pg_view_res.error());
+  }
+  auto pg_view = std::move(pg_view_res.value());
 
   TestOptionalTopologyGenerationEdgeShuffleTopology(*pg_view);
   TestOptionalTopologyGenerationShuffleTopology(*pg_view);

diff --git a/libkatana_python_native/src/PropertyGraph.cpp b/libkatana_python_native/src/PropertyGraph.cpp
@@ -205,6 +205,46 @@ DefPropertyGraph(py::module& m) {
   katana::DefWithNumba<&PropertyGraph::NumNodes>(cls, "num_nodes");
   katana::DefWithNumba<&PropertyGraph::NumEdges>(cls, "num_edges");
 
+  cls.def(
+      "project",
+      [](PropertyGraph& self, py::object node_types,
+         py::object edge_types) -> Result<std::shared_ptr<PropertyGraph>> {
+        std::optional<katana::SetOfEntityTypeIDs> node_type_ids;
+        if (!node_types.is_none()) {
+          node_type_ids = katana::SetOfEntityTypeIDs();
+          node_type_ids->resize(self.GetNodeTypeManager().GetNumEntityTypes());
+          for (auto& t : node_types) {
+            node_type_ids->set(py::cast<EntityType>(t).type_id);
+          }
+        }
+        std::optional<katana::SetOfEntityTypeIDs> edge_type_ids;
+        if (!edge_types.is_none()) {
+          edge_type_ids = katana::SetOfEntityTypeIDs();
+          edge_type_ids->resize(self.GetEdgeTypeManager().GetNumEntityTypes());
+          for (auto& t : edge_types) {
+            edge_type_ids->set(py::cast<EntityType>(t).type_id);
+          }
+        }
+
+        py::gil_scoped_release
+            guard;  // graph projection may copy or load data.
+        // is_none is safe without the GIL because it is just a pointer compare.
+        return KATANA_CHECKED(PropertyGraph::MakeProjectedGraph(
+            self, node_type_ids, edge_type_ids));
+      },
+      py::arg("node_types") = py::none(), py::arg("edge_types") = py::none(),
+      R"""(
+      Get a projected view of the graph which only contains nodes or edges of
+      specific types.
+
+      :type node_types: Optional[Iterable[EntityType]]
+      :param node_types: A set of node types to include in the projected graph,
+        or ``None`` to keep all nodes.
+      :type edge_types: Optional[Iterable[EntityType]]
+      :param edge_types: A set of edge types to include in the projected graph,
+        or ``None`` to keep all edges on the selected nodes.
+      )""");
+
   // GetLocalNodeID(NodeHandle) -> LocalNodeID  - local node ID
   cls.def(
       "get_local_node_id",

diff --git a/libsupport/include/katana/DynamicBitsetSlow.h b/libsupport/include/katana/DynamicBitsetSlow.h
@@ -14,6 +14,97 @@
 
 namespace katana {
 
+/// An iterator over dynamic bitsets.
+///
+/// Increment is an optimized linear search over the bitset, so iteration is
+/// O(N) where N is the size of the bitset, not O(|S|) where |S| is the number
+/// of set bits in the bit set.
+
+// TODO(amp): This is a template so it can be used for both DynamicBitsetSlow
+//  and DynamicBitset. This can be made a simple class once DynamicBitsetSlow
+//  is removed.
+template <typename DynamicBitsetType>
+class KATANA_EXPORT DynamicBitsetIterator
+    : public std::iterator<
+          std::forward_iterator_tag, uint64_t, int64_t, const uint64_t*,
+          uint64_t> {
+  const DynamicBitsetType* underlying_;
+  uint64_t array_index_;
+  uint8_t bit_offset_;
+
+public:
+  DynamicBitsetIterator(
+      const DynamicBitsetType* underlying, uint64_t array_index,
+      uint8_t bit_offset)
+      : underlying_(underlying),
+        array_index_(array_index),
+        bit_offset_(bit_offset) {}
+
+  DynamicBitsetIterator& operator++() {
+    // Step forward one to the bit we want to examine first.
+    bit_offset_++;
+    if (bit_offset_ > DynamicBitsetType::kNumBitsInUint64) {
+      bit_offset_ = 0;
+      array_index_++;
+    }
+
+    const auto& bitvec = underlying_->get_vec();
+    const size_t size = underlying_->size();
+
+    // Used only to make sure we stop on the last real used bit in cases where
+    // the number of bits is not a multiple of kNumBitsInUint64.
+    uint64_t current_bit_index = **this;
+
+    // The following code is optimized to make the search process fast for
+    // sparse bitsets. It's performance for densely filled bitsets should be
+    // good too.
+
+    // Iterate forward word by word
+    for (; array_index_ < bitvec.size(); array_index_++) {
+      uint64_t word = bitvec[array_index_].load(std::memory_order_relaxed);
+      // For each word we check if it is non-zero (that is it contains a 1 bit)
+      if (word != 0) {
+        // Iterate over the bits in the work
+        uint64_t bit_mask = uint64_t{1} << bit_offset_;
+        for (; bit_offset_ < DynamicBitsetType::kNumBitsInUint64 &&
+               current_bit_index < size;
+             bit_offset_++, current_bit_index++, bit_mask <<= 1) {
+          // Check if the bit is set. If it is we have reached where we need to be
+          if ((word & bit_mask) != 0) {
+            return *this;
+          }
+        }
+        // Reset bit_offset_ here so that we start from our last bit_offset_ and
+        // only reset when we roll over to the next word.
+        bit_offset_ = 0;
+      }
+    }
+    bit_offset_ = 0;
+    array_index_ = bitvec.size();
+    return *this;
+  }
+
+  DynamicBitsetIterator operator++(int) {
+    auto r = *this;
+    ++(*this);
+    return r;
+  }
+
+  reference operator*() const {
+    return array_index_ * DynamicBitsetType::kNumBitsInUint64 + bit_offset_;
+  }
+
+  bool operator==(const DynamicBitsetIterator& other) {
+    return underlying_ == other.underlying_ &&
+           array_index_ == other.array_index_ &&
+           bit_offset_ == other.bit_offset_;
+  }
+
+  bool operator!=(const DynamicBitsetIterator& other) {
+    return !(*this == other);
+  }
+};
+
 //TODO(emcginnis): Remove this class entirely when DynamicBitset is available to libsupport
 /**
  * Concurrent, thread safe, serial implementation of a dynamically allocated bitset
@@ -24,6 +115,8 @@ class KATANA_EXPORT DynamicBitsetSlow {
   size_t num_bits_{0};
 
 public:
+  using iterator = DynamicBitsetIterator<DynamicBitsetSlow>;
+
   static constexpr uint32_t kNumBitsInUint64 = sizeof(uint64_t) * CHAR_BIT;
 
   explicit DynamicBitsetSlow(
@@ -75,6 +168,18 @@ class KATANA_EXPORT DynamicBitsetSlow {
    */
   auto& get_vec() { return bitvec_; }
 
+  iterator begin() const {
+    iterator bit0{this, 0, 0};
+    if (test(0)) {
+      // If bit 0 is set then we have the right iterator
+      return bit0;
+    }
+    // Otherwise, increment to find the first set bit.
+    return ++bit0;
+  }
+
+  iterator end() const { return {this, bitvec_.size(), 0}; }
+
   /**
    * Resizes the bitset.
    *

diff --git a/libsupport/test/CMakeLists.txt b/libsupport/test/CMakeLists.txt
@@ -16,11 +16,12 @@ function(add_unit_test name)
     )
 endfunction()
 
-add_unit_test(arrow)
 add_unit_test(array-from-scalars)
+add_unit_test(arrow)
 add_unit_test(bitmath)
 add_unit_test(cache)
 add_unit_test(disjoint_range_iterator)
+add_unit_test(dynamic-bitset)
 add_unit_test(env)
 add_unit_test(experimental)
 add_unit_test(logging)