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nv-dlasalle bbebde4660 [Performance] Track sorted status of COO from creation (#2645)
* Add row/col sorted flags

* improve sorting paths

* Remove print statement

* Keep track of sorted matrices

* Remove sort check in to_block

* Improve CPU sorted COO->CSR

* Handle the zero edge case

* Remove omp default clause to work with MSVC

* Update comments on sorted COO->CSR cpu implementatoin

* Expose sorted to python interface

* Make check_sorted default to false for dgl.graph()

* remove check sorted; add utests

* remove check_sorted flag

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-04-16 10:30:07 +08:00

1036 行
31 KiB
C++

/*!
* Copyright (c) 2018 by Contributors
* \file dgl/immutable_graph.h
* \brief DGL immutable graph index class.
*/
#ifndef DGL_IMMUTABLE_GRAPH_H_
#define DGL_IMMUTABLE_GRAPH_H_
#include <vector>
#include <string>
#include <cstdint>
#include <utility>
#include <tuple>
#include <algorithm>
#include <memory>
#include "runtime/ndarray.h"
#include "graph_interface.h"
#include "lazy.h"
#include "base_heterograph.h"
namespace dgl {
class CSR;
class COO;
typedef std::shared_ptr<CSR> CSRPtr;
typedef std::shared_ptr<COO> COOPtr;
class ImmutableGraph;
typedef std::shared_ptr<ImmutableGraph> ImmutableGraphPtr;
/*!
* \brief Graph class stored using CSR structure.
*/
class CSR : public GraphInterface {
public:
// Create a csr graph that has the given number of verts and edges.
CSR(int64_t num_vertices, int64_t num_edges);
// Create a csr graph whose memory is stored in the shared memory
// that has the given number of verts and edges.
CSR(const std::string &shared_mem_name,
int64_t num_vertices, int64_t num_edges);
// Create a csr graph that shares the given indptr and indices.
CSR(IdArray indptr, IdArray indices, IdArray edge_ids);
// Create a csr graph by data iterator
template <typename IndptrIter, typename IndicesIter, typename EdgeIdIter>
CSR(int64_t num_vertices, int64_t num_edges,
IndptrIter indptr_begin, IndicesIter indices_begin, EdgeIdIter edge_ids_begin);
// Create a csr graph whose memory is stored in the shared memory
// and the structure is given by the indptr and indcies.
CSR(IdArray indptr, IdArray indices, IdArray edge_ids,
const std::string &shared_mem_name);
void AddVertices(uint64_t num_vertices) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void AddEdge(dgl_id_t src, dgl_id_t dst) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void AddEdges(IdArray src_ids, IdArray dst_ids) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void Clear() override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
DLContext Context() const override {
return adj_.indptr->ctx;
}
uint8_t NumBits() const override {
return adj_.indices->dtype.bits;
}
bool IsMultigraph() const override;
bool IsReadonly() const override {
return true;
}
uint64_t NumVertices() const override {
return adj_.indptr->shape[0] - 1;
}
uint64_t NumEdges() const override {
return adj_.indices->shape[0];
}
BoolArray HasVertices(IdArray vids) const override {
LOG(FATAL) << "Not enabled for CSR graph";
return {};
}
bool HasEdgeBetween(dgl_id_t src, dgl_id_t dst) const override;
BoolArray HasEdgesBetween(IdArray src_ids, IdArray dst_ids) const override;
IdArray Predecessors(dgl_id_t vid, uint64_t radius = 1) const override {
LOG(FATAL) << "CSR graph does not support efficient predecessor query."
<< " Please use successors on the reverse CSR graph.";
return {};
}
IdArray Successors(dgl_id_t vid, uint64_t radius = 1) const override;
IdArray EdgeId(dgl_id_t src, dgl_id_t dst) const override;
EdgeArray EdgeIds(IdArray src, IdArray dst) const override;
std::pair<dgl_id_t, dgl_id_t> FindEdge(dgl_id_t eid) const override {
LOG(FATAL) << "CSR graph does not support efficient FindEdge."
<< " Please use COO graph.";
return {};
}
EdgeArray FindEdges(IdArray eids) const override {
LOG(FATAL) << "CSR graph does not support efficient FindEdges."
<< " Please use COO graph.";
return {};
}
EdgeArray InEdges(dgl_id_t vid) const override {
LOG(FATAL) << "CSR graph does not support efficient inedges query."
<< " Please use outedges on the reverse CSR graph.";
return {};
}
EdgeArray InEdges(IdArray vids) const override {
LOG(FATAL) << "CSR graph does not support efficient inedges query."
<< " Please use outedges on the reverse CSR graph.";
return {};
}
EdgeArray OutEdges(dgl_id_t vid) const override;
EdgeArray OutEdges(IdArray vids) const override;
EdgeArray Edges(const std::string &order = "") const override;
uint64_t InDegree(dgl_id_t vid) const override {
LOG(FATAL) << "CSR graph does not support efficient indegree query."
<< " Please use outdegree on the reverse CSR graph.";
return 0;
}
DegreeArray InDegrees(IdArray vids) const override {
LOG(FATAL) << "CSR graph does not support efficient indegree query."
<< " Please use outdegree on the reverse CSR graph.";
return {};
}
uint64_t OutDegree(dgl_id_t vid) const override {
return aten::CSRGetRowNNZ(adj_, vid);
}
DegreeArray OutDegrees(IdArray vids) const override;
Subgraph VertexSubgraph(IdArray vids) const override;
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override {
LOG(FATAL) << "CSR graph does not support efficient EdgeSubgraph."
<< " Please use COO graph instead.";
return {};
}
DGLIdIters SuccVec(dgl_id_t vid) const override;
DGLIdIters OutEdgeVec(dgl_id_t vid) const override;
DGLIdIters PredVec(dgl_id_t vid) const override {
LOG(FATAL) << "CSR graph does not support efficient PredVec."
<< " Please use SuccVec on the reverse CSR graph.";
return DGLIdIters(nullptr, nullptr);
}
DGLIdIters InEdgeVec(dgl_id_t vid) const override {
LOG(FATAL) << "CSR graph does not support efficient InEdgeVec."
<< " Please use OutEdgeVec on the reverse CSR graph.";
return DGLIdIters(nullptr, nullptr);
}
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
CHECK(!transpose && fmt == "csr") << "Not valid adj format request.";
return {adj_.indptr, adj_.indices, adj_.data};
}
/*! \brief Indicate whether this uses shared memory. */
bool IsSharedMem() const {
return !shared_mem_name_.empty();
}
/*! \brief Return the reverse of this CSR graph (i.e, a CSC graph) */
CSRPtr Transpose() const;
/*! \brief Convert this CSR to COO */
COOPtr ToCOO() const;
/*!
* \return the csr matrix that represents this graph.
* \note The csr matrix shares the storage with this graph.
* The data field of the CSR matrix stores the edge ids.
*/
aten::CSRMatrix ToCSRMatrix() const {
return adj_;
}
/*!
* \brief Copy the data to another context.
* \param ctx The target context.
* \return The graph under another context.
*/
CSR CopyTo(const DLContext& ctx) const;
/*!
* \brief Copy data to shared memory.
* \param name The name of the shared memory.
* \return The graph in the shared memory
*/
CSR CopyToSharedMem(const std::string &name) const;
/*!
* \brief Convert the graph to use the given number of bits for storage.
* \param bits The new number of integer bits (32 or 64).
* \return The graph with new bit size storage.
*/
CSR AsNumBits(uint8_t bits) const;
// member getters
IdArray indptr() const { return adj_.indptr; }
IdArray indices() const { return adj_.indices; }
IdArray edge_ids() const { return adj_.data; }
/*! \return Load CSR from stream */
bool Load(dmlc::Stream *fs);
/*! \return Save CSR to stream */
void Save(dmlc::Stream* fs) const;
void SortCSR() override {
if (adj_.sorted)
return;
aten::CSRSort_(&adj_);
}
private:
friend class Serializer;
/*! \brief private default constructor */
CSR() {adj_.sorted = false;}
// The internal CSR adjacency matrix.
// The data field stores edge ids.
aten::CSRMatrix adj_;
// The name of the shared memory to store data.
// If it's empty, data isn't stored in shared memory.
std::string shared_mem_name_;
};
class COO : public GraphInterface {
public:
// Create a coo graph that shares the given src and dst
COO(int64_t num_vertices, IdArray src, IdArray dst,
bool row_sorted = false, bool col_sorted = false);
// TODO(da): add constructor for creating COO from shared memory
void AddVertices(uint64_t num_vertices) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void AddEdge(dgl_id_t src, dgl_id_t dst) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void AddEdges(IdArray src_ids, IdArray dst_ids) override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
void Clear() override {
LOG(FATAL) << "CSR graph does not allow mutation.";
}
DLContext Context() const override {
return adj_.row->ctx;
}
uint8_t NumBits() const override {
return adj_.row->dtype.bits;
}
bool IsMultigraph() const override;
bool IsReadonly() const override {
return true;
}
uint64_t NumVertices() const override {
return adj_.num_rows;
}
uint64_t NumEdges() const override {
return adj_.row->shape[0];
}
bool HasVertex(dgl_id_t vid) const override {
return vid < NumVertices();
}
BoolArray HasVertices(IdArray vids) const override {
LOG(FATAL) << "Not enabled for COO graph";
return {};
}
bool HasEdgeBetween(dgl_id_t src, dgl_id_t dst) const override {
LOG(FATAL) << "COO graph does not support efficient HasEdgeBetween."
<< " Please use CSR graph or AdjList graph instead.";
return false;
}
BoolArray HasEdgesBetween(IdArray src_ids, IdArray dst_ids) const override {
LOG(FATAL) << "COO graph does not support efficient HasEdgeBetween."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
IdArray Predecessors(dgl_id_t vid, uint64_t radius = 1) const override {
LOG(FATAL) << "COO graph does not support efficient Predecessors."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
IdArray Successors(dgl_id_t vid, uint64_t radius = 1) const override {
LOG(FATAL) << "COO graph does not support efficient Successors."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
IdArray EdgeId(dgl_id_t src, dgl_id_t dst) const override {
LOG(FATAL) << "COO graph does not support efficient EdgeId."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
EdgeArray EdgeIds(IdArray src, IdArray dst) const override {
LOG(FATAL) << "COO graph does not support efficient EdgeId."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
std::pair<dgl_id_t, dgl_id_t> FindEdge(dgl_id_t eid) const override;
EdgeArray FindEdges(IdArray eids) const override;
EdgeArray InEdges(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient InEdges."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
EdgeArray InEdges(IdArray vids) const override {
LOG(FATAL) << "COO graph does not support efficient InEdges."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
EdgeArray OutEdges(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient OutEdges."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
EdgeArray OutEdges(IdArray vids) const override {
LOG(FATAL) << "COO graph does not support efficient OutEdges."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
EdgeArray Edges(const std::string &order = "") const override;
uint64_t InDegree(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient InDegree."
<< " Please use CSR graph or AdjList graph instead.";
return 0;
}
DegreeArray InDegrees(IdArray vids) const override {
LOG(FATAL) << "COO graph does not support efficient InDegrees."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
uint64_t OutDegree(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient OutDegree."
<< " Please use CSR graph or AdjList graph instead.";
return 0;
}
DegreeArray OutDegrees(IdArray vids) const override {
LOG(FATAL) << "COO graph does not support efficient OutDegrees."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
Subgraph VertexSubgraph(IdArray vids) const override {
LOG(FATAL) << "COO graph does not support efficient VertexSubgraph."
<< " Please use CSR graph or AdjList graph instead.";
return {};
}
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
DGLIdIters SuccVec(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient SuccVec."
<< " Please use CSR graph or AdjList graph instead.";
return DGLIdIters(nullptr, nullptr);
}
DGLIdIters OutEdgeVec(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient OutEdgeVec."
<< " Please use CSR graph or AdjList graph instead.";
return DGLIdIters(nullptr, nullptr);
}
DGLIdIters PredVec(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient PredVec."
<< " Please use CSR graph or AdjList graph instead.";
return DGLIdIters(nullptr, nullptr);
}
DGLIdIters InEdgeVec(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient InEdgeVec."
<< " Please use CSR graph or AdjList graph instead.";
return DGLIdIters(nullptr, nullptr);
}
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
CHECK(fmt == "coo") << "Not valid adj format request.";
if (transpose) {
return {aten::HStack(adj_.col, adj_.row)};
} else {
return {aten::HStack(adj_.row, adj_.col)};
}
}
/*! \brief Return the transpose of this COO */
COOPtr Transpose() const {
return COOPtr(new COO(adj_.num_rows, adj_.col, adj_.row));
}
/*! \brief Convert this COO to CSR */
CSRPtr ToCSR() const;
/*!
* \brief Get the coo matrix that represents this graph.
* \note The coo matrix shares the storage with this graph.
* The data field of the coo matrix is none.
*/
aten::COOMatrix ToCOOMatrix() const {
return adj_;
}
/*!
* \brief Copy the data to another context.
* \param ctx The target context.
* \return The graph under another context.
*/
COO CopyTo(const DLContext& ctx) const;
/*!
* \brief Copy data to shared memory.
* \param name The name of the shared memory.
* \return The graph in the shared memory
*/
COO CopyToSharedMem(const std::string &name) const;
/*!
* \brief Convert the graph to use the given number of bits for storage.
* \param bits The new number of integer bits (32 or 64).
* \return The graph with new bit size storage.
*/
COO AsNumBits(uint8_t bits) const;
/*! \brief Indicate whether this uses shared memory. */
bool IsSharedMem() const {
return false;
}
// member getters
IdArray src() const { return adj_.row; }
IdArray dst() const { return adj_.col; }
private:
/* !\brief private default constructor */
COO() {}
// The internal COO adjacency matrix.
// The data field is empty
aten::COOMatrix adj_;
};
/*!
* \brief DGL immutable graph index class.
*
* DGL's graph is directed. Vertices are integers enumerated from zero.
*/
class ImmutableGraph: public GraphInterface {
public:
/*! \brief Construct an immutable graph from the COO format. */
explicit ImmutableGraph(COOPtr coo): coo_(coo) { }
/*!
* \brief Construct an immutable graph from the CSR format.
*
* For a single graph, we need two CSRs, one stores the in-edges of vertices and
* the other stores the out-edges of vertices. These two CSRs stores the same edges.
* The reason we need both is that some operators are faster on in-edge CSR and
* the other operators are faster on out-edge CSR.
*
* However, not both CSRs are required. Technically, one CSR contains all information.
* Thus, when we construct a temporary graphs (e.g., the sampled subgraphs), we only
* construct one of the CSRs that runs fast for some operations we expect and construct
* the other CSR on demand.
*/
ImmutableGraph(CSRPtr in_csr, CSRPtr out_csr)
: in_csr_(in_csr), out_csr_(out_csr) {
CHECK(in_csr_ || out_csr_) << "Both CSR are missing.";
}
/*! \brief Construct an immutable graph from one CSR. */
explicit ImmutableGraph(CSRPtr csr): out_csr_(csr) { }
/*! \brief default copy constructor */
ImmutableGraph(const ImmutableGraph& other) = default;
#ifndef _MSC_VER
/*! \brief default move constructor */
ImmutableGraph(ImmutableGraph&& other) = default;
#else
ImmutableGraph(ImmutableGraph&& other) {
this->in_csr_ = other.in_csr_;
this->out_csr_ = other.out_csr_;
this->coo_ = other.coo_;
other.in_csr_ = nullptr;
other.out_csr_ = nullptr;
other.coo_ = nullptr;
}
#endif // _MSC_VER
/*! \brief default assign constructor */
ImmutableGraph& operator=(const ImmutableGraph& other) = default;
/*! \brief default destructor */
~ImmutableGraph() = default;
void AddVertices(uint64_t num_vertices) override {
LOG(FATAL) << "AddVertices isn't supported in ImmutableGraph";
}
void AddEdge(dgl_id_t src, dgl_id_t dst) override {
LOG(FATAL) << "AddEdge isn't supported in ImmutableGraph";
}
void AddEdges(IdArray src_ids, IdArray dst_ids) override {
LOG(FATAL) << "AddEdges isn't supported in ImmutableGraph";
}
void Clear() override {
LOG(FATAL) << "Clear isn't supported in ImmutableGraph";
}
DLContext Context() const override {
return AnyGraph()->Context();
}
uint8_t NumBits() const override {
return AnyGraph()->NumBits();
}
/*!
* \note not const since we have caches
* \return whether the graph is a multigraph
*/
bool IsMultigraph() const override {
return AnyGraph()->IsMultigraph();
}
/*!
* \return whether the graph is read-only
*/
bool IsReadonly() const override {
return true;
}
/*! \return the number of vertices in the graph.*/
uint64_t NumVertices() const override {
return AnyGraph()->NumVertices();
}
/*! \return the number of edges in the graph.*/
uint64_t NumEdges() const override {
return AnyGraph()->NumEdges();
}
/*! \return true if the given vertex is in the graph.*/
bool HasVertex(dgl_id_t vid) const override {
return vid < NumVertices();
}
BoolArray HasVertices(IdArray vids) const override;
/*! \return true if the given edge is in the graph.*/
bool HasEdgeBetween(dgl_id_t src, dgl_id_t dst) const override {
if (in_csr_) {
return in_csr_->HasEdgeBetween(dst, src);
} else {
return GetOutCSR()->HasEdgeBetween(src, dst);
}
}
BoolArray HasEdgesBetween(IdArray src, IdArray dst) const override {
if (in_csr_) {
return in_csr_->HasEdgesBetween(dst, src);
} else {
return GetOutCSR()->HasEdgesBetween(src, dst);
}
}
/*!
* \brief Find the predecessors of a vertex.
* \param vid The vertex id.
* \param radius The radius of the neighborhood. Default is immediate neighbor (radius=1).
* \return the predecessor id array.
*/
IdArray Predecessors(dgl_id_t vid, uint64_t radius = 1) const override {
return GetInCSR()->Successors(vid, radius);
}
/*!
* \brief Find the successors of a vertex.
* \param vid The vertex id.
* \param radius The radius of the neighborhood. Default is immediate neighbor (radius=1).
* \return the successor id array.
*/
IdArray Successors(dgl_id_t vid, uint64_t radius = 1) const override {
return GetOutCSR()->Successors(vid, radius);
}
/*!
* \brief Get all edge ids between the two given endpoints
* \note Edges are associated with an integer id start from zero.
* The id is assigned when the edge is being added to the graph.
* \param src The source vertex.
* \param dst The destination vertex.
* \return the edge id array.
*/
IdArray EdgeId(dgl_id_t src, dgl_id_t dst) const override {
if (in_csr_) {
return in_csr_->EdgeId(dst, src);
} else {
return GetOutCSR()->EdgeId(src, dst);
}
}
/*!
* \brief Get all edge ids between the given endpoint pairs.
* \note Edges are associated with an integer id start from zero.
* The id is assigned when the edge is being added to the graph.
* If duplicate pairs exist, the returned edge IDs will also duplicate.
* The order of returned edge IDs will follow the order of src-dst pairs
* first, and ties are broken by the order of edge ID.
* \return EdgeArray containing all edges between all pairs.
*/
EdgeArray EdgeIds(IdArray src, IdArray dst) const override {
if (in_csr_) {
EdgeArray edges = in_csr_->EdgeIds(dst, src);
return EdgeArray{edges.dst, edges.src, edges.id};
} else {
return GetOutCSR()->EdgeIds(src, dst);
}
}
/*!
* \brief Find the edge ID and return the pair of endpoints
* \param eid The edge ID
* \return a pair whose first element is the source and the second the destination.
*/
std::pair<dgl_id_t, dgl_id_t> FindEdge(dgl_id_t eid) const override {
return GetCOO()->FindEdge(eid);
}
/*!
* \brief Find the edge IDs and return their source and target node IDs.
* \param eids The edge ID array.
* \return EdgeArray containing all edges with id in eid. The order is preserved.
*/
EdgeArray FindEdges(IdArray eids) const override {
return GetCOO()->FindEdges(eids);
}
/*!
* \brief Get the in edges of the vertex.
* \note The returned dst id array is filled with vid.
* \param vid The vertex id.
* \return the edges
*/
EdgeArray InEdges(dgl_id_t vid) const override {
const EdgeArray& ret = GetInCSR()->OutEdges(vid);
return {ret.dst, ret.src, ret.id};
}
/*!
* \brief Get the in edges of the vertices.
* \param vids The vertex id array.
* \return the id arrays of the two endpoints of the edges.
*/
EdgeArray InEdges(IdArray vids) const override {
const EdgeArray& ret = GetInCSR()->OutEdges(vids);
return {ret.dst, ret.src, ret.id};
}
/*!
* \brief Get the out edges of the vertex.
* \note The returned src id array is filled with vid.
* \param vid The vertex id.
* \return the id arrays of the two endpoints of the edges.
*/
EdgeArray OutEdges(dgl_id_t vid) const override {
return GetOutCSR()->OutEdges(vid);
}
/*!
* \brief Get the out edges of the vertices.
* \param vids The vertex id array.
* \return the id arrays of the two endpoints of the edges.
*/
EdgeArray OutEdges(IdArray vids) const override {
return GetOutCSR()->OutEdges(vids);
}
/*!
* \brief Get all the edges in the graph.
* \note If sorted is true, the returned edges list is sorted by their src and
* dst ids. Otherwise, they are in their edge id order.
* \param sorted Whether the returned edge list is sorted by their src and dst ids
* \return the id arrays of the two endpoints of the edges.
*/
EdgeArray Edges(const std::string &order = "") const override;
/*!
* \brief Get the in degree of the given vertex.
* \param vid The vertex id.
* \return the in degree
*/
uint64_t InDegree(dgl_id_t vid) const override {
return GetInCSR()->OutDegree(vid);
}
/*!
* \brief Get the in degrees of the given vertices.
* \param vid The vertex id array.
* \return the in degree array
*/
DegreeArray InDegrees(IdArray vids) const override {
return GetInCSR()->OutDegrees(vids);
}
/*!
* \brief Get the out degree of the given vertex.
* \param vid The vertex id.
* \return the out degree
*/
uint64_t OutDegree(dgl_id_t vid) const override {
return GetOutCSR()->OutDegree(vid);
}
/*!
* \brief Get the out degrees of the given vertices.
* \param vid The vertex id array.
* \return the out degree array
*/
DegreeArray OutDegrees(IdArray vids) const override {
return GetOutCSR()->OutDegrees(vids);
}
/*!
* \brief Construct the induced subgraph of the given vertices.
*
* The induced subgraph is a subgraph formed by specifying a set of vertices V' and then
* selecting all of the edges from the original graph that connect two vertices in V'.
*
* Vertices and edges in the original graph will be "reindexed" to local index. The local
* index of the vertices preserve the order of the given id array, while the local index
* of the edges preserve the index order in the original graph. Vertices not in the
* original graph are ignored.
*
* The result subgraph is read-only.
*
* \param vids The vertices in the subgraph.
* \return the induced subgraph
*/
Subgraph VertexSubgraph(IdArray vids) const override;
/*!
* \brief Construct the induced edge subgraph of the given edges.
*
* The induced edges subgraph is a subgraph formed by specifying a set of edges E' and then
* selecting all of the nodes from the original graph that are endpoints in E'.
*
* Vertices and edges in the original graph will be "reindexed" to local index. The local
* index of the edges preserve the order of the given id array, while the local index
* of the vertices preserve the index order in the original graph. Edges not in the
* original graph are ignored.
*
* The result subgraph is read-only.
*
* \param eids The edges in the subgraph.
* \return the induced edge subgraph
*/
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
/*!
* \brief Return the successor vector
* \param vid The vertex id.
* \return the successor vector
*/
DGLIdIters SuccVec(dgl_id_t vid) const override {
return GetOutCSR()->SuccVec(vid);
}
/*!
* \brief Return the out edge id vector
* \param vid The vertex id.
* \return the out edge id vector
*/
DGLIdIters OutEdgeVec(dgl_id_t vid) const override {
return GetOutCSR()->OutEdgeVec(vid);
}
/*!
* \brief Return the predecessor vector
* \param vid The vertex id.
* \return the predecessor vector
*/
DGLIdIters PredVec(dgl_id_t vid) const override {
return GetInCSR()->SuccVec(vid);
}
/*!
* \brief Return the in edge id vector
* \param vid The vertex id.
* \return the in edge id vector
*/
DGLIdIters InEdgeVec(dgl_id_t vid) const override {
return GetInCSR()->OutEdgeVec(vid);
}
/*!
* \brief Get the adjacency matrix of the graph.
*
* By default, a row of returned adjacency matrix represents the destination
* of an edge and the column represents the source.
* \param transpose A flag to transpose the returned adjacency matrix.
* \param fmt the format of the returned adjacency matrix.
* \return a vector of three IdArray.
*/
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override;
/* !\brief Return in csr. If not exist, transpose the other one.*/
CSRPtr GetInCSR() const;
/* !\brief Return out csr. If not exist, transpose the other one.*/
CSRPtr GetOutCSR() const;
/* !\brief Return coo. If not exist, create from csr.*/
COOPtr GetCOO() const;
/*! \brief Create an immutable graph from CSR. */
static ImmutableGraphPtr CreateFromCSR(
IdArray indptr, IdArray indices, IdArray edge_ids, const std::string &edge_dir);
static ImmutableGraphPtr CreateFromCSR(const std::string &shared_mem_name);
/*! \brief Create an immutable graph from COO. */
static ImmutableGraphPtr CreateFromCOO(
int64_t num_vertices, IdArray src, IdArray dst,
bool row_osrted = false, bool col_sorted = false);
/*!
* \brief Convert the given graph to an immutable graph.
*
* If the graph is already an immutable graph. The result graph will share
* the storage with the given one.
*
* \param graph The input graph.
* \return an immutable graph object.
*/
static ImmutableGraphPtr ToImmutable(GraphPtr graph);
/*!
* \brief Copy the data to another context.
* \param ctx The target context.
* \return The graph under another context.
*/
static ImmutableGraphPtr CopyTo(ImmutableGraphPtr g, const DLContext& ctx);
/*!
* \brief Copy data to shared memory.
* \param name The name of the shared memory.
* \return The graph in the shared memory
*/
static ImmutableGraphPtr CopyToSharedMem(ImmutableGraphPtr g, const std::string &name);
/*!
* \brief Convert the graph to use the given number of bits for storage.
* \param bits The new number of integer bits (32 or 64).
* \return The graph with new bit size storage.
*/
static ImmutableGraphPtr AsNumBits(ImmutableGraphPtr g, uint8_t bits);
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
ImmutableGraphPtr Reverse() const;
/*! \return Load ImmutableGraph from stream, using out csr */
bool Load(dmlc::Stream *fs);
/*! \return Save ImmutableGraph to stream, using out csr */
void Save(dmlc::Stream* fs) const;
void SortCSR() override {
GetInCSR()->SortCSR();
GetOutCSR()->SortCSR();
}
bool HasInCSR() const {
return in_csr_ != NULL;
}
bool HasOutCSR() const {
return out_csr_ != NULL;
}
/*! \brief Cast this graph to a heterograph */
HeteroGraphPtr AsHeteroGraph() const;
protected:
friend class Serializer;
friend class UnitGraph;
/* !\brief internal default constructor */
ImmutableGraph() {}
/* !\brief internal constructor for all the members */
ImmutableGraph(CSRPtr in_csr, CSRPtr out_csr, COOPtr coo)
: in_csr_(in_csr), out_csr_(out_csr), coo_(coo) {
CHECK(AnyGraph()) << "At least one graph structure should exist.";
}
ImmutableGraph(CSRPtr in_csr, CSRPtr out_csr, const std::string shared_mem_name)
: in_csr_(in_csr), out_csr_(out_csr) {
CHECK(in_csr_ || out_csr_) << "Both CSR are missing.";
this->shared_mem_name_ = shared_mem_name;
}
/* !\brief return pointer to any available graph structure */
GraphPtr AnyGraph() const {
if (in_csr_) {
return in_csr_;
} else if (out_csr_) {
return out_csr_;
} else {
return coo_;
}
}
// Store the in csr (i.e, the reverse csr)
CSRPtr in_csr_;
// Store the out csr (i.e, the normal csr)
CSRPtr out_csr_;
// Store the edge list indexed by edge id (COO)
COOPtr coo_;
// The name of shared memory for this graph.
// If it's empty, the graph isn't stored in shared memory.
std::string shared_mem_name_;
// We serialize the metadata of the graph index here for shared memory.
NDArray serialized_shared_meta_;
};
// inline implementations
template <typename IndptrIter, typename IndicesIter, typename EdgeIdIter>
CSR::CSR(int64_t num_vertices, int64_t num_edges,
IndptrIter indptr_begin, IndicesIter indices_begin, EdgeIdIter edge_ids_begin) {
// TODO(minjie): this should be changed to a device-agnostic implementation
// in the future
adj_.num_rows = num_vertices;
adj_.num_cols = num_vertices;
adj_.indptr = aten::NewIdArray(num_vertices + 1);
adj_.indices = aten::NewIdArray(num_edges);
adj_.data = aten::NewIdArray(num_edges);
dgl_id_t* indptr_data = static_cast<dgl_id_t*>(adj_.indptr->data);
dgl_id_t* indices_data = static_cast<dgl_id_t*>(adj_.indices->data);
dgl_id_t* edge_ids_data = static_cast<dgl_id_t*>(adj_.data->data);
for (int64_t i = 0; i < num_vertices + 1; ++i)
*(indptr_data++) = *(indptr_begin++);
for (int64_t i = 0; i < num_edges; ++i) {
*(indices_data++) = *(indices_begin++);
*(edge_ids_data++) = *(edge_ids_begin++);
}
}
} // namespace dgl
namespace dmlc {
DMLC_DECLARE_TRAITS(has_saveload, dgl::CSR, true);
DMLC_DECLARE_TRAITS(has_saveload, dgl::ImmutableGraph, true);
} // namespace dmlc
#endif // DGL_IMMUTABLE_GRAPH_H_