dmlc--dgl
bbebde4660
* 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>
1036 行
31 KiB
C++
1036 行
31 KiB
C++
/*!
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* Copyright (c) 2018 by Contributors
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* \file dgl/immutable_graph.h
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* \brief DGL immutable graph index class.
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*/
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#ifndef DGL_IMMUTABLE_GRAPH_H_
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#define DGL_IMMUTABLE_GRAPH_H_
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#include <vector>
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#include <string>
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#include <cstdint>
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#include <utility>
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#include <tuple>
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#include <algorithm>
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#include <memory>
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#include "runtime/ndarray.h"
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#include "graph_interface.h"
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#include "lazy.h"
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#include "base_heterograph.h"
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namespace dgl {
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class CSR;
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class COO;
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typedef std::shared_ptr<CSR> CSRPtr;
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typedef std::shared_ptr<COO> COOPtr;
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class ImmutableGraph;
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typedef std::shared_ptr<ImmutableGraph> ImmutableGraphPtr;
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/*!
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* \brief Graph class stored using CSR structure.
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*/
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class CSR : public GraphInterface {
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public:
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// Create a csr graph that has the given number of verts and edges.
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CSR(int64_t num_vertices, int64_t num_edges);
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// Create a csr graph whose memory is stored in the shared memory
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// that has the given number of verts and edges.
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CSR(const std::string &shared_mem_name,
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int64_t num_vertices, int64_t num_edges);
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// Create a csr graph that shares the given indptr and indices.
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CSR(IdArray indptr, IdArray indices, IdArray edge_ids);
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// Create a csr graph by data iterator
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template <typename IndptrIter, typename IndicesIter, typename EdgeIdIter>
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CSR(int64_t num_vertices, int64_t num_edges,
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IndptrIter indptr_begin, IndicesIter indices_begin, EdgeIdIter edge_ids_begin);
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// Create a csr graph whose memory is stored in the shared memory
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// and the structure is given by the indptr and indcies.
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CSR(IdArray indptr, IdArray indices, IdArray edge_ids,
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const std::string &shared_mem_name);
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void AddVertices(uint64_t num_vertices) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void AddEdge(dgl_id_t src, dgl_id_t dst) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void AddEdges(IdArray src_ids, IdArray dst_ids) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void Clear() override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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DLContext Context() const override {
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return adj_.indptr->ctx;
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}
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uint8_t NumBits() const override {
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return adj_.indices->dtype.bits;
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}
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bool IsMultigraph() const override;
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bool IsReadonly() const override {
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return true;
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}
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uint64_t NumVertices() const override {
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return adj_.indptr->shape[0] - 1;
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}
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uint64_t NumEdges() const override {
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return adj_.indices->shape[0];
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}
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BoolArray HasVertices(IdArray vids) const override {
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LOG(FATAL) << "Not enabled for CSR graph";
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return {};
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}
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bool HasEdgeBetween(dgl_id_t src, dgl_id_t dst) const override;
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BoolArray HasEdgesBetween(IdArray src_ids, IdArray dst_ids) const override;
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IdArray Predecessors(dgl_id_t vid, uint64_t radius = 1) const override {
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LOG(FATAL) << "CSR graph does not support efficient predecessor query."
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<< " Please use successors on the reverse CSR graph.";
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return {};
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}
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IdArray Successors(dgl_id_t vid, uint64_t radius = 1) const override;
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IdArray EdgeId(dgl_id_t src, dgl_id_t dst) const override;
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EdgeArray EdgeIds(IdArray src, IdArray dst) const override;
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std::pair<dgl_id_t, dgl_id_t> FindEdge(dgl_id_t eid) const override {
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LOG(FATAL) << "CSR graph does not support efficient FindEdge."
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<< " Please use COO graph.";
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return {};
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}
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EdgeArray FindEdges(IdArray eids) const override {
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LOG(FATAL) << "CSR graph does not support efficient FindEdges."
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<< " Please use COO graph.";
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return {};
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}
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EdgeArray InEdges(dgl_id_t vid) const override {
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LOG(FATAL) << "CSR graph does not support efficient inedges query."
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<< " Please use outedges on the reverse CSR graph.";
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return {};
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}
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EdgeArray InEdges(IdArray vids) const override {
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LOG(FATAL) << "CSR graph does not support efficient inedges query."
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<< " Please use outedges on the reverse CSR graph.";
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return {};
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}
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EdgeArray OutEdges(dgl_id_t vid) const override;
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EdgeArray OutEdges(IdArray vids) const override;
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EdgeArray Edges(const std::string &order = "") const override;
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uint64_t InDegree(dgl_id_t vid) const override {
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LOG(FATAL) << "CSR graph does not support efficient indegree query."
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<< " Please use outdegree on the reverse CSR graph.";
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return 0;
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}
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DegreeArray InDegrees(IdArray vids) const override {
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LOG(FATAL) << "CSR graph does not support efficient indegree query."
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<< " Please use outdegree on the reverse CSR graph.";
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return {};
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}
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uint64_t OutDegree(dgl_id_t vid) const override {
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return aten::CSRGetRowNNZ(adj_, vid);
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}
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DegreeArray OutDegrees(IdArray vids) const override;
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Subgraph VertexSubgraph(IdArray vids) const override;
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Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override {
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LOG(FATAL) << "CSR graph does not support efficient EdgeSubgraph."
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<< " Please use COO graph instead.";
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return {};
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}
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DGLIdIters SuccVec(dgl_id_t vid) const override;
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DGLIdIters OutEdgeVec(dgl_id_t vid) const override;
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DGLIdIters PredVec(dgl_id_t vid) const override {
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LOG(FATAL) << "CSR graph does not support efficient PredVec."
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<< " Please use SuccVec on the reverse CSR graph.";
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return DGLIdIters(nullptr, nullptr);
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}
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DGLIdIters InEdgeVec(dgl_id_t vid) const override {
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LOG(FATAL) << "CSR graph does not support efficient InEdgeVec."
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<< " Please use OutEdgeVec on the reverse CSR graph.";
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return DGLIdIters(nullptr, nullptr);
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}
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std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
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CHECK(!transpose && fmt == "csr") << "Not valid adj format request.";
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return {adj_.indptr, adj_.indices, adj_.data};
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}
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/*! \brief Indicate whether this uses shared memory. */
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bool IsSharedMem() const {
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return !shared_mem_name_.empty();
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}
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/*! \brief Return the reverse of this CSR graph (i.e, a CSC graph) */
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CSRPtr Transpose() const;
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/*! \brief Convert this CSR to COO */
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COOPtr ToCOO() const;
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/*!
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* \return the csr matrix that represents this graph.
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* \note The csr matrix shares the storage with this graph.
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* The data field of the CSR matrix stores the edge ids.
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*/
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aten::CSRMatrix ToCSRMatrix() const {
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return adj_;
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}
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/*!
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* \brief Copy the data to another context.
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* \param ctx The target context.
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* \return The graph under another context.
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*/
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CSR CopyTo(const DLContext& ctx) const;
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/*!
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* \brief Copy data to shared memory.
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* \param name The name of the shared memory.
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* \return The graph in the shared memory
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*/
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CSR CopyToSharedMem(const std::string &name) const;
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/*!
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* \brief Convert the graph to use the given number of bits for storage.
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* \param bits The new number of integer bits (32 or 64).
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* \return The graph with new bit size storage.
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*/
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CSR AsNumBits(uint8_t bits) const;
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// member getters
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IdArray indptr() const { return adj_.indptr; }
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IdArray indices() const { return adj_.indices; }
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IdArray edge_ids() const { return adj_.data; }
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/*! \return Load CSR from stream */
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bool Load(dmlc::Stream *fs);
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/*! \return Save CSR to stream */
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void Save(dmlc::Stream* fs) const;
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void SortCSR() override {
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if (adj_.sorted)
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return;
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aten::CSRSort_(&adj_);
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}
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private:
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friend class Serializer;
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/*! \brief private default constructor */
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CSR() {adj_.sorted = false;}
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// The internal CSR adjacency matrix.
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// The data field stores edge ids.
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aten::CSRMatrix adj_;
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// The name of the shared memory to store data.
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// If it's empty, data isn't stored in shared memory.
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std::string shared_mem_name_;
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};
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class COO : public GraphInterface {
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public:
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// Create a coo graph that shares the given src and dst
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COO(int64_t num_vertices, IdArray src, IdArray dst,
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bool row_sorted = false, bool col_sorted = false);
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// TODO(da): add constructor for creating COO from shared memory
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void AddVertices(uint64_t num_vertices) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void AddEdge(dgl_id_t src, dgl_id_t dst) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void AddEdges(IdArray src_ids, IdArray dst_ids) override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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void Clear() override {
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LOG(FATAL) << "CSR graph does not allow mutation.";
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}
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DLContext Context() const override {
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return adj_.row->ctx;
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}
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uint8_t NumBits() const override {
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return adj_.row->dtype.bits;
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}
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bool IsMultigraph() const override;
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bool IsReadonly() const override {
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return true;
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}
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uint64_t NumVertices() const override {
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return adj_.num_rows;
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}
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uint64_t NumEdges() const override {
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return adj_.row->shape[0];
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}
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bool HasVertex(dgl_id_t vid) const override {
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return vid < NumVertices();
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}
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BoolArray HasVertices(IdArray vids) const override {
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LOG(FATAL) << "Not enabled for COO graph";
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return {};
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}
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bool HasEdgeBetween(dgl_id_t src, dgl_id_t dst) const override {
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LOG(FATAL) << "COO graph does not support efficient HasEdgeBetween."
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<< " Please use CSR graph or AdjList graph instead.";
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return false;
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}
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BoolArray HasEdgesBetween(IdArray src_ids, IdArray dst_ids) const override {
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LOG(FATAL) << "COO graph does not support efficient HasEdgeBetween."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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IdArray Predecessors(dgl_id_t vid, uint64_t radius = 1) const override {
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LOG(FATAL) << "COO graph does not support efficient Predecessors."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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IdArray Successors(dgl_id_t vid, uint64_t radius = 1) const override {
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LOG(FATAL) << "COO graph does not support efficient Successors."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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IdArray EdgeId(dgl_id_t src, dgl_id_t dst) const override {
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LOG(FATAL) << "COO graph does not support efficient EdgeId."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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EdgeArray EdgeIds(IdArray src, IdArray dst) const override {
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LOG(FATAL) << "COO graph does not support efficient EdgeId."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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std::pair<dgl_id_t, dgl_id_t> FindEdge(dgl_id_t eid) const override;
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EdgeArray FindEdges(IdArray eids) const override;
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EdgeArray InEdges(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient InEdges."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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EdgeArray InEdges(IdArray vids) const override {
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LOG(FATAL) << "COO graph does not support efficient InEdges."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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EdgeArray OutEdges(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient OutEdges."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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EdgeArray OutEdges(IdArray vids) const override {
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LOG(FATAL) << "COO graph does not support efficient OutEdges."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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EdgeArray Edges(const std::string &order = "") const override;
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uint64_t InDegree(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient InDegree."
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<< " Please use CSR graph or AdjList graph instead.";
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return 0;
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}
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DegreeArray InDegrees(IdArray vids) const override {
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LOG(FATAL) << "COO graph does not support efficient InDegrees."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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uint64_t OutDegree(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient OutDegree."
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<< " Please use CSR graph or AdjList graph instead.";
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return 0;
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}
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DegreeArray OutDegrees(IdArray vids) const override {
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LOG(FATAL) << "COO graph does not support efficient OutDegrees."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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Subgraph VertexSubgraph(IdArray vids) const override {
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LOG(FATAL) << "COO graph does not support efficient VertexSubgraph."
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<< " Please use CSR graph or AdjList graph instead.";
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return {};
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}
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Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
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DGLIdIters SuccVec(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient SuccVec."
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<< " Please use CSR graph or AdjList graph instead.";
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return DGLIdIters(nullptr, nullptr);
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}
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DGLIdIters OutEdgeVec(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient OutEdgeVec."
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<< " Please use CSR graph or AdjList graph instead.";
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return DGLIdIters(nullptr, nullptr);
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}
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DGLIdIters PredVec(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient PredVec."
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<< " Please use CSR graph or AdjList graph instead.";
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return DGLIdIters(nullptr, nullptr);
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}
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DGLIdIters InEdgeVec(dgl_id_t vid) const override {
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LOG(FATAL) << "COO graph does not support efficient InEdgeVec."
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<< " Please use CSR graph or AdjList graph instead.";
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return DGLIdIters(nullptr, nullptr);
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}
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std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
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CHECK(fmt == "coo") << "Not valid adj format request.";
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if (transpose) {
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return {aten::HStack(adj_.col, adj_.row)};
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} else {
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return {aten::HStack(adj_.row, adj_.col)};
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}
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}
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/*! \brief Return the transpose of this COO */
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COOPtr Transpose() const {
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return COOPtr(new COO(adj_.num_rows, adj_.col, adj_.row));
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}
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/*! \brief Convert this COO to CSR */
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CSRPtr ToCSR() const;
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/*!
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* \brief Get the coo matrix that represents this graph.
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* \note The coo matrix shares the storage with this graph.
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* The data field of the coo matrix is none.
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*/
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aten::COOMatrix ToCOOMatrix() const {
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return adj_;
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}
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/*!
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* \brief Copy the data to another context.
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* \param ctx The target context.
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* \return The graph under another context.
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*/
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COO CopyTo(const DLContext& ctx) const;
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/*!
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* \brief Copy data to shared memory.
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* \param name The name of the shared memory.
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* \return The graph in the shared memory
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*/
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COO CopyToSharedMem(const std::string &name) const;
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/*!
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* \brief Convert the graph to use the given number of bits for storage.
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* \param bits The new number of integer bits (32 or 64).
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* \return The graph with new bit size storage.
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*/
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COO AsNumBits(uint8_t bits) const;
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/*! \brief Indicate whether this uses shared memory. */
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bool IsSharedMem() const {
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return false;
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}
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// member getters
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IdArray src() const { return adj_.row; }
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IdArray dst() const { return adj_.col; }
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private:
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/* !\brief private default constructor */
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COO() {}
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// The internal COO adjacency matrix.
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// The data field is empty
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aten::COOMatrix adj_;
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};
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/*!
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* \brief DGL immutable graph index class.
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*
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* DGL's graph is directed. Vertices are integers enumerated from zero.
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*/
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class ImmutableGraph: public GraphInterface {
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public:
|
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/*! \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++);
|
|
}
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}
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} // namespace dgl
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namespace dmlc {
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DMLC_DECLARE_TRAITS(has_saveload, dgl::CSR, true);
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DMLC_DECLARE_TRAITS(has_saveload, dgl::ImmutableGraph, true);
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} // namespace dmlc
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#endif // DGL_IMMUTABLE_GRAPH_H_
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