[Pass] Check in infershape, move indexedgraph to graph.h (#15)

nnvm/include/nnvm/graph.h

@@ -18,6 +18,8 @@
 
 namespace nnvm {
 
+class IndexedGraph;
+
 /*!
  * \brief Symbolic computation graph.
  *  This is the intermediate representation for optimization pass.
@@ -32,6 +34,145 @@ class Graph {
    *  and can be shared across multiple Instance of graph
    */
   std::unordered_map<std::string, std::shared_ptr<const any> > attrs;
+  /*!
+   * \brief Get the attribute from attrs.
+   * \param attr_name the name of the attribute
+   * \return the reference to corresponding attribute
+   * \tparam T the type of the attribute.
+   */
+  template<typename T>
+  inline const T& GetAttr(const std::string& attr_name);
+  /*!
+   * \brief get a indexed graph of current graph, if not exist, create it on demand
+   * \return The indexed graph.
+   * \sa IndexedGraph
+   */
+  const IndexedGraph& indexed_graph();
+
+ private:
+  // internal structure of indexed graph
+  std::shared_ptr<const IndexedGraph> indexed_graph_;
+};
+
+/*!
+ * \brief Auxililary data structure to index a graph.
+ *  It maps Nodes in the graph to consecutive integers node_id.
+ *  It also maps IndexedGraph::NodeEntry to consecutive integer entry_id.
+ *  This allows storing properties of Node and NodeEntry into
+ *  compact vector and quickly access them without resorting to hashmap.
+ *
+ *  The node_id and entry_rptr are the same as the JSON graph produced by SaveJSON Pass.
+ */
+class IndexedGraph {
+ public:
+  /*! \brief represents a data in the graph */
+  struct NodeEntry {
+    /*! \brief the source node id in the computation graph */
+    uint32_t node_id;
+    /*! \brief index of output from the source. */
+    uint32_t index;
+    /*!
+     * \brief compare equality
+     * \param other the other entry to compare
+     * \return whether two entries equals to each other
+     */
+    inline bool operator==(const NodeEntry& other) const {
+      return node_id == other.node_id && index == other.index;
+    }
+  };
+  /*! \brief Node data structure in IndexedGraph */
+  struct Node {
+    /*! \brief pointer to the source node */
+    const nnvm::Node* source;
+    /*! \brief inputs to the node */
+    array_view<NodeEntry> inputs;
+    /*! \brief control flow dependencies to the node */
+    array_view<uint32_t> control_deps;
+  };
+  /*! \return number of nodes in the graph */
+  inline size_t num_nodes() const {
+    return nodes_.size();
+  }
+  /*! \return total number of NodeEntry in the graph */
+  inline size_t num_node_entries() const {
+    return entry_rptr_.back();
+  }
+  /*!
+   * \brief Get a unique entry id between 0 to num_node_entries()
+   *  for a given IndexedGraph::NodeEntry
+   * \param node_id The node index
+   * \param index the output index
+   * \return the unique index.
+   */
+  inline uint32_t entry_id(uint32_t node_id, uint32_t index) const {
+    return entry_rptr_[node_id] + index;
+  }
+  /*!
+   * \brief Get a unique entry id between 0 to num_node_entries()
+   *  for a given IndexedGraph::NodeEntry
+   * \param e The entry to query for index.
+   * \return the unique index.
+   */
+  inline uint32_t entry_id(const NodeEntry& e) const {
+    return entry_rptr_[e.node_id] + e.index;
+  }
+  /*!
+   * \brief Get a unique entry id between 0 to num_node_entries()
+   *  for a given NodeEntry.
+   * \param e The entry to query for index.
+   * \return the unique index.
+   */
+  inline uint32_t entry_id(const nnvm::NodeEntry& e) const {
+    return entry_rptr_[node_id(e.node.get())] + e.index;
+  }
+  /*!
+   * \brief Get the corresponding node id for a given Node in the IndexedGraph.
+   * \param node The Node to query for index.
+   * \return the node index.
+   */
+  inline uint32_t node_id(const nnvm::Node* node) const {
+    return node2index_.at(node);
+  }
+  /*!
+   * \brief Get the corresponding Node structure for a given node_id.
+   * \param node_id The node id
+   * \return const reference to the corresponding IndexedGraph::Node
+   */
+  inline const Node& operator[](uint32_t node_id) const {
+    return nodes_[node_id];
+  }
+  /*!
+   * \brief Get the corresponding Node structure
+   * \param node The pointer to the Node structure
+   * \return const reference to the corresponding IndexedGraph::Node
+   */
+  inline const Node& operator[](const nnvm::Node* node) const {
+    return nodes_[node_id(node)];
+  }
+  /*! \return list of argument nodes */
+  inline const std::vector<uint32_t>& arg_nodes() const {
+    return arg_nodes_;
+  }
+
+ private:
+  friend class Graph;
+  /*!
+   * \brief Constructor an IndexedGraph from normal Graph
+   * \param other The source graph.
+   */
+  explicit IndexedGraph(const Graph& other);
+  // node pointers in CSR structure.
+  std::vector<Node> nodes_;
+  // index to argument nodes
+  std::vector<uint32_t> arg_nodes_;
+  // mapping from node to index.
+  std::unordered_map<const nnvm::Node*, uint32_t> node2index_;
+  // CSR pointer of node entries
+  std::vector<size_t> entry_rptr_;
+  // space to store input entries of each
+  std::vector<NodeEntry> input_entries_;
+  // control flow dependencies
+  std::vector<uint32_t> control_deps_;
 };
 
 /*!
@@ -45,6 +186,14 @@ template<typename FVisit>
 inline void DFSVisit(const std::vector<NodeEntry>& heads, FVisit fvisit);
 
 // inline function implementations
+template<typename T>
+inline const T& Graph::GetAttr(const std::string& attr_name) {
+  auto it = attrs.find(attr_name);
+  CHECK(it != attrs.end())
+      << "Cannot find attribute " << attr_name << " in the graph";
+  return nnvm::get<T>(*it->second);
+}
+
 template <typename GNode, typename HashType,
            typename FVisit, typename HashFunc,
           typename InDegree, typename GetInput>

nnvm/include/nnvm/graph_attr_types.h

@@ -7,120 +7,37 @@
 #define NNVM_GRAPH_ATTR_TYPES_H_
 
 #include <vector>
-#include <unordered_map>
-#include "./graph.h"
+#include <string>
+#include "./tuple.h"
 
 namespace nnvm {
 
 /*!
- * \brief Auxililary data structure to index a graph.
- *  It maps Nodes in the graph to consecutive integers node_id.
- *  It also maps IndexedGraph::NodeEntry to consecutive integer entry_id.
- *  This allows storing properties of Node and NodeEntry into
- *  compact vector and quickly access them without resorting to hashmap.
+ * \brief The result holder of JSON serializer
+ *
+ * \note Stored under ret.attrs["json"], provided by Pass "SaveJSON"
+
+ * \code
+ *  Graph ret = ApplyPass(src_graph, {"SaveJSON"});
+ *  const JSONString& json = ret.GetAttr<JSONString>("shape");
+ * \endcode
  */
-struct IndexedGraph {
- public:
-  /*! \brief represents a data in the graph */
-  struct NodeEntry {
-    /*! \brief the source node id in the computation graph */
-    uint32_t node_id;
-    /*! \brief index of output from the source. */
-    uint32_t index;
-    /*!
-     * \brief compare equality
-     * \param other the other entry to compare
-     * \return whether two entries equals to each other
-     */
-    inline bool operator==(const NodeEntry& other) const {
-      return node_id == other.node_id && index == other.index;
-    }
-  };
-  /*! \brief Node data structure in IndexedGraph */
-  struct Node {
-    /*! \brief pointer to the source node */
-    const nnvm::Node* source;
-    /*! \brief inputs to the node */
-    array_view<NodeEntry> inputs;
-    /*! \brief control flow dependencies to the node */
-    array_view<uint32_t> control_deps;
-  };
-  /*! \return number of nodes in the graph */
-  inline size_t num_nodes() const {
-    return nodes_.size();
-  }
-  /*! \return total number of NodeEntry in the graph */
-  inline size_t num_node_entries() const {
-    return entry_rptr_.back();
-  }
-  /*!
-   * \brief Get a unique entry id between 0 to num_node_entries()
-   *  for a given IndexedGraph::NodeEntry
-   * \param e The entry to query for index.
-   * \return the unique index.
-   */
-  inline uint32_t entry_id(const NodeEntry& e) const {
-    return entry_rptr_[e.node_id] + e.index;
-  }
-  /*!
-   * \brief Get a unique entry id between 0 to num_node_entries()
-   *  for a given NodeEntry.
-   * \param e The entry to query for index.
-   * \return the unique index.
-   */
-  inline uint32_t entry_id(const nnvm::NodeEntry& e) const {
-    return entry_rptr_[node_id(e.node.get())] + e.index;
-  }
-  /*!
-   * \brief Get the corresponding node id for a given Node in the IndexedGraph.
-   * \param node The Node to query for index.
-   * \return the node index.
-   */
-  inline uint32_t node_id(const nnvm::Node* node) const {
-    return node2index_.at(node);
-  }
-  /*!
-   * \brief Get the corresponding Node structure for a given node_id.
-   * \param node_id The node id
-   * \return const reference to the corresponding IndexedGraph::Node
-   */
-  inline const Node& operator[](uint32_t node_id) const {
-    return nodes_[node_id];
-  }
-  /*!
-   * \brief Get the corresponding Node structure
-   * \param node The pointer to the Node structure
-   * \return const reference to the corresponding IndexedGraph::Node
-   */
-  inline const Node& operator[](const nnvm::Node* node) const {
-    return nodes_[node_id(node)];
-  }
-  /*! \return list of argument nodes */
-  inline const std::vector<uint32_t>& arg_nodes() const {
-    return arg_nodes_;
-  }
-  /*!
-   * \brief Constructor an IndexedGraph from normal Graph
-   * \param other The source graph.
-   */
-  explicit IndexedGraph(const Graph& other);
-  // disallow copy assign
-  IndexedGraph(const IndexedGraph& other) = delete;
+using JSONString = std::string;
 
- private:
-  // node pointers in CSR structure.
-  std::vector<Node> nodes_;
-  // index to argument nodes
-  std::vector<uint32_t> arg_nodes_;
-  // mapping from node to index.
-  std::unordered_map<const nnvm::Node*, uint32_t> node2index_;
-  // CSR pointer of node entries
-  std::vector<size_t> entry_rptr_;
-  // space to store input entries of each
-  std::vector<NodeEntry> input_entries_;
-  // control flow dependencies
-  std::vector<uint32_t> control_deps_;
-};
+/*!
+ * \brief The result holder of shape of each NodeEntry in the graph.
+ * \note Stored under graph.attrs["shape"], provided by Pass "InferShape"
+ *
+ * \code
+ *  Graph g = ApplyPass(src_graph, {"InferShape"});
+ *  const ShapeVector& shapes = g.GetAttr<ShapeVector>("shape");
+ *  // get shape by entry id
+ *  TShape entry_shape = shapes[g.indexed_graph().entry_id(my_entry)];
+ * \endcode
+ *
+ * \sa FInferShape
+ */
+using ShapeVector = std::vector<TShape>;
 
 }  // namespace nnvm
 

nnvm/include/nnvm/op_attr_types.h

@@ -9,6 +9,8 @@
 #include <vector>
 #include <string>
 #include <functional>
+#include "./base.h"
+#include "./tuple.h"
 
 namespace nnvm {
 
@@ -39,6 +41,7 @@ using FListOutputNames = std::function<std::vector<std::string> (const NodeAttrs
 
 /*!
  * \brief Check whether operator will mutate k-th input.
+ * \param attrs The attributes of the node.
  * \param index The input index
  * \return Whether this operator will mutate index-th input.
  *
@@ -47,6 +50,26 @@ using FListOutputNames = std::function<std::vector<std::string> (const NodeAttrs
  */
 using FMutateInput = std::function<bool (const NodeAttrs& attrs, uint32_t index)>;
 
+/*!
+ * \brief Shape inference function.
+ *  Update the shapes given the input shape information.
+ *  TShape.ndim() == 0 means the shape is still unknown.
+ *
+ * \param attrs The attributes of the node.
+ * \param in_shapes Array of shapes from the inputs.
+ * \param out_shapes Array of shapes from the outputs.
+ *
+ * \return Whether all the shapes are known.
+ *
+ * \note Register under "FInferShape",
+ *  by default do not update any shapes.
+ *
+ *  FInferShape is needed by shape inference
+ */
+using FInferShape = std::function<bool (const NodeAttrs& attrs,
+                                        array_view<TShape*> in_shapes,
+                                        array_view<TShape*> out_shapes)>;
+
 }  // namespace nnvm
 
 #endif  // NNVM_OP_ATTR_TYPES_H_

nnvm/include/nnvm/tuple.h

@@ -10,6 +10,7 @@
 #include <type_traits>
 #include <algorithm>
 #include <iostream>
+#include "./base.h"
 
 namespace nnvm {
 
@@ -179,7 +180,23 @@ class Tuple {
   inline const ValueType& operator[](index_t i) const {
     return begin()[i];
   }
-
+  /*!
+   * \brief Save Tuple to JSON.
+   * \param writer JSONWriter
+   */
+  inline void Save(dmlc::JSONWriter* writer) const {
+    std::vector<ValueType> tmp(begin(), end());
+    writer->Write(tmp);
+  }
+  /*!
+   * \brief Load Tuple from JSON.
+   * \param reader JSONReader
+   */
+  inline void Load(dmlc::JSONReader* reader) {
+    std::vector<ValueType> tmp;
+    reader->Read(&tmp);
+    this->assign(tmp.begin(), tmp.end());
+  }
   /*!
    * \brief allow output string of tuple to ostream
    * \param os the output stream
@@ -287,6 +304,8 @@ class TShape : public Tuple<index_t> {
  public:
   // inheritate other constructors from Tuple
   using Tuple<index_t>::Tuple;
+  /*! \brief default constructor */
+  TShape() = default;
   /*!
    * \brief copy constructor of TShape
    * \param s source shape.

nnvm/src/core/graph_attr_types.cc → nnvm/src/core/graph.cc

@@ -3,11 +3,18 @@
  * \file graph_attr_types.cc
  * \brief Graph node data structure.
  */
-#include <nnvm/graph_attr_types.h>
+#include <nnvm/graph.h>
 #include <limits>
 
 namespace nnvm {
 
+const IndexedGraph& Graph::indexed_graph() {
+  if (indexed_graph_ == nullptr) {
+    indexed_graph_.reset(new IndexedGraph(*this));
+  }
+  return *indexed_graph_;
+}
+
 // implement constructor from graph
 IndexedGraph::IndexedGraph(const Graph &g) {
   entry_rptr_.push_back(0);

nnvm/src/example/operator.cc

 // Copyright (c) 2016 by Contributors
 // This is an example on how we can register operator information to NNVM
 
+#include <nnvm/base.h>
 #include <nnvm/op.h>
 #include <nnvm/op_attr_types.h>
+#include <nnvm/graph_attr_types.h>
 #include <utility>
 
+namespace myproject {
+
 using nnvm::FListInputNames;
 using nnvm::FMutateInput;
+using nnvm::FInferShape;
 using nnvm::NodeAttrs;
+using nnvm::TShape;
+using nnvm::array_view;
+
+// simply return the shape as same
+inline bool SameShape(const NodeAttrs& attrs,
+                      array_view<TShape*> ishape,
+                      array_view<TShape*> oshape) {
+  if (ishape.size() == 0 || ishape[0]->ndim() == 0) return false;
+  for (TShape* pshape : oshape) {
+    *pshape = *ishape[0];
+  }
+  for (TShape* pshape : ishape) {
+    *pshape = *ishape[0];
+  }
+  return true;
+}
 
 NNVM_REGISTER_OP(add)
 .describe("add two data together")
-.set_num_inputs(2);
+.set_num_inputs(2)
+.attr<FInferShape>("FInferShape", SameShape);
 
 NNVM_REGISTER_OP(__add_symbol__)
 .describe("Alias of add")
@@ -20,7 +42,8 @@ NNVM_REGISTER_OP(__add_symbol__)
 NNVM_REGISTER_OP(exp)
 .describe("take exponmential")
 .set_num_inputs(1)
-.attr("inplace_pair", std::make_pair(0, 0));
+.attr("inplace_pair", std::make_pair(0, 0))
+.attr<FInferShape>("FInferShape", SameShape);
 
 
 NNVM_REGISTER_OP(conv2d)
@@ -39,3 +62,5 @@ NNVM_REGISTER_OP(assign)
 .attr<FMutateInput>("FMutateInput", [](const NodeAttrs& attrs, uint32_t index) {
     return index == 0;
   });
+
+}  // namespace myproject

nnvm/src/pass/infer_shape.cc

+/*!
+ *  Copyright (c) 2016 by Contributors
+ * \file infer_shape.cc
+ * \brief Inference the shapes given
+ */
+#include <nnvm/pass.h>
+#include <nnvm/op_attr_types.h>
+#include <nnvm/graph_attr_types.h>
+
+namespace nnvm {
+namespace pass {
+
+Graph InferShape(const Graph& src) {
+  Graph ret = src;
+  const IndexedGraph& idx = ret.indexed_graph();
+  static auto& finfer_shape = Op::GetAttr<FInferShape>("FInferShape");
+  // reshape shape vector
+  ShapeVector rshape(idx.num_node_entries());
+  // temp space for shape inference.
+  std::vector<TShape*> ishape, oshape;
+  // number of completed nodes
+  size_t num_known = 0;
+  for (uint32_t nid = 0; nid < idx.num_nodes(); ++nid) {
+    const auto& inode = idx[nid];
+    if (inode.source->is_variable()) continue;
+    ishape.resize(inode.inputs.size());
+    for (uint32_t i = 0; i < ishape.size(); ++i) {
+      ishape[i] = &rshape[idx.entry_id(inode.inputs[i])];
+    }
+    oshape.resize(inode.source->num_outputs());
+    for (uint32_t i = 0; i < oshape.size(); ++i) {
+      oshape[i] = &rshape[idx.entry_id(nid, i)];
+    }
+    if (finfer_shape.count(inode.source->op)) {
+      num_known +=
+          finfer_shape[inode.source->op](inode.source->attrs, ishape, oshape);
+    }
+  }
+  // set the shapes
+  ret.attrs["shape"] = std::make_shared<any>(std::move(rshape));
+  // number of nodes who knows the shape.
+  ret.attrs["shape_num_known_nodes"] = std::make_shared<any>(num_known);
+  return ret;
+}
+
+}  // namespace pass
+}  // namespace nnvm

nnvm/src/pass/order_mutation.cc

@@ -9,6 +9,7 @@
 #include <nnvm/op_attr_types.h>
 
 namespace nnvm {
+namespace pass {
 
 template<typename T>
 inline T get_with_default(const std::unordered_map<Node*, T> &map,
@@ -139,4 +140,5 @@ NNVM_REGISTER_PASS(OrderMutation)
 .set_body(OrderMutation)
 .set_change_graph(true);
 
+}  // namespace pass
 }  // namespace nnvm

nnvm/src/pass/saveload_json.cc

@@ -120,6 +120,7 @@ struct JSONNode {
 struct JSONGraph {
   std::vector<JSONNode> nodes;
   std::vector<uint32_t> arg_nodes;
+  std::vector<uint32_t> node_row_ptr;
   std::vector<JSONNode::Entry> heads;
   std::unordered_map<std::string, std::shared_ptr<const any> > attrs;
 
@@ -127,6 +128,7 @@ struct JSONGraph {
     writer->BeginObject();
     writer->WriteObjectKeyValue("nodes", nodes);
     writer->WriteObjectKeyValue("arg_nodes", arg_nodes);
+    writer->WriteObjectKeyValue("node_row_ptr", node_row_ptr);
     writer->WriteObjectKeyValue("heads", heads);
     if (attrs.size() != 0) {
       writer->WriteObjectKeyValue("attrs", attrs);
@@ -140,6 +142,7 @@ struct JSONGraph {
     helper.DeclareField("nodes", &nodes);
     helper.DeclareField("arg_nodes", &arg_nodes);
     helper.DeclareField("heads", &heads);
+    helper.DeclareOptionalField("node_row_ptr", &node_row_ptr);
     helper.DeclareOptionalField("attrs", &attrs);
     helper.ReadAllFields(reader);
   }
@@ -188,6 +191,7 @@ Graph LoadJSON(const Graph& src) {
 Graph SaveJSON(const Graph& src) {
   JSONGraph jgraph;
   std::unordered_map<Node*, uint32_t> node2index;
+  jgraph.node_row_ptr.push_back(0);
   DFSVisit(src.outputs, [&node2index, &jgraph](const NodePtr& n) {
       uint32_t nid = static_cast<uint32_t>(jgraph.nodes.size());
       node2index[n.get()] = nid;
@@ -204,6 +208,8 @@ Graph SaveJSON(const Graph& src) {
       for (const NodePtr& c : n->control_deps) {
         jnode.control_deps.push_back(node2index.at(c.get()));
       }
+      jgraph.node_row_ptr.push_back(
+          jgraph.node_row_ptr.back() + n->num_outputs());
       jgraph.nodes.emplace_back(std::move(jnode));
     });