Exemplo n.º 1
0
void ORD::buildGraph() {
    Graph::GraphCreatorFile creator(this->filename);
    Graph::GraphUtil util;
    Graph::GraphProperties properties;
    
    int wr;
    int size;
    MPI_Comm_size(comm, &size);
    MPI_Comm_rank(comm, &wr);

    G = creator.create_weighted_mutable_graph();
    properties.make_canonical(G);
    char compname[512];
    if (!properties.is_connected(G))
    {
        Graph::GraphReaderWriterFactory factory;
        Graph::VertexWeightedGraph *H;

        // Since we are going to proceed with processing largest
        // component , set a mark as not original and write largest
        // component into a file.
        this->set_original(false);

        vector<list<int> *> members;
        int comp;
        comp = util.find_all_components(G, &members);

        DEBUG("found %d components\n", comp);
        int i = 0;
        int gsize = 0;
        int index = 0;
        for (int j = 0; j < comp; j++)
        {
            i = members[j]->size();
            if (i > gsize)
            {
                gsize = i;
                index = j;
                sprintf(compname, "%s_%d_comp", filename.c_str(), gsize);
                DEBUG("new larger comp : %d\n", gsize);
            }
        }

        this->set_filename(compname);
        H = creator.create_component(G, members[index], true);
        delete G;
        G = H;

        // Change the label into 1-base DIMACS format
        int j = 0;
        int gs = G->get_num_nodes();
        Graph::Node *n;
        for (int i = 0 ; i < gs; i++)
        {
            n = G->get_node(i);
            n->set_label(i+1);
        }

    }
}
Exemplo n.º 2
0
TEST_F(GraphCreatorFileTest, testCreateComponent)
{
	Graph::WeightedMutableGraph *wmg;
	Graph::WeightedMutableGraph *wmg_sub;
	Graph::GraphUtil util;

	creator->set_file_name("../data/1et.64.txt");
	creator->set_graph_type("DIMACS");

	wmg = creator->create_weighted_mutable_graph();

	list<int> f;
	list<int>::iterator it;
	list<int>::iterator jt;
	list<int>::iterator kt;
	util.find_component(wmg, 25, &f);

	wmg_sub = creator->create_component(wmg, &f, true);

	EXPECT_EQ(f.size(), wmg_sub->get_num_nodes())
		;

	vector<Graph::Node> wmg_nodes = wmg->get_nodes();
	vector<Graph::Node> wmg_sub_nodes = wmg_sub->get_nodes();
	int i = 0;
	int j = 0;
	int n = wmg_sub->get_num_nodes();

	it = f.begin();
	for (i = 0; i < n; i++)
	{
		EXPECT_EQ(wmg_nodes[*it].get_label(), wmg_sub_nodes[i].get_label())
			;
		EXPECT_EQ(wmg_nodes[*it].get_degree(), wmg_sub_nodes[i].get_degree())
			;
		list<int> wmg_nbrs = wmg_nodes[*it].get_nbrs();
		list<int> wmg_sub_nbrs = wmg_sub_nodes[i].get_nbrs();
		wmg_nbrs.sort();
		wmg_sub_nbrs.sort();

		for (jt = wmg_nbrs.begin(), kt = wmg_sub_nbrs.begin(); jt
                 != wmg_nbrs.end(); ++jt, ++kt)
		{
			ASSERT_EQ(wmg_nodes[*jt].get_label(), wmg_sub_nodes[*kt].get_label())
				;
		}
		++it;
	}

}
Exemplo n.º 3
0
TEST_F(GraphCreatorFileTest, testCreateRecAllComponents)
{
	Graph::GraphUtil util;
	Graph::WeightedMutableGraph *wmg;

	creator->set_file_name("../data/1et.64.txt");
	creator->set_graph_type("DIMACS");
	wmg = creator->create_weighted_mutable_graph();

	vector<list<int> *> members;
	int x = util.find_all_components(wmg, &members);
	EXPECT_EQ(x, members.size())
		;
	list<Graph::WeightedMutableGraph *> cmembers;
	cmembers = creator->create_rec_all_components(wmg, true);

	EXPECT_EQ(cmembers.size(), members.size())
		;

	int wmg_size = 0;
	int mem_size = members[3]->size();
	list<Graph::WeightedMutableGraph *>::iterator giter;
	Graph::WeightedMutableGraph cmg;
	vector<Graph::Node> nodes;

	for (giter = cmembers.begin(); giter != cmembers.end(); ++giter)
	{
		if (mem_size == (*giter)->get_num_nodes())
		{
			nodes = (*giter)->get_nodes();
			break;
		}
	}

	list<int>::iterator it;
	int i = 0;
	for (it = members[3]->begin(); it != members[3]->end(); ++it)
	{
		EXPECT_EQ((*it), nodes[i].get_label() - 1);
		i++;
	}
}
Exemplo n.º 4
0
int main(int argc, char **argv){
    string infile;
    string outfilename;
    string outprefix;
    string apspinputfilename;
    string lcc_apspinputfilename;
    ofstream outfile;
    ofstream timing_file;
    bool record_timings = false;
    bool file_append = false;
    bool run_largest_cc = true;
    string intype ("edge");
    std::map<string, bool> req_methods;
    std::map<string, bool> val_methods;
    ORB_t t1, t2;
    int spectrum_spread = 0;
    create_map(allowed_methods, val_methods);
    parse_options(argc, argv, infile, intype, outfilename, outprefix, req_methods, record_timings, file_append, run_largest_cc, &spectrum_spread, apspinputfilename, lcc_apspinputfilename);
    if(outfilename.length() == 0){
        if(outprefix.length() != 0){
            outfilename = outprefix + ".stats";
        }
        else {
            outfilename = "graph-stats.txt";
        }
    }
    if(outprefix.length() == 0){
        outprefix = infile;
    }

    // we'd like higher precision when printing values
    std::cout.precision(10);
    #ifdef MPI_VERSION
    MPI_Init(&argc, &argv);
    int myrank;
    MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
    if(myrank == 0){
    #endif
    cout << "done parsing options" << endl;
    cout << "Input  file: " << infile << endl;
    cout << "Input  type: " << intype << endl;
    cout << "Output file: " << outfilename << endl;
    cout << "Appending  : ";
    cout << std::boolalpha << file_append << endl;
    cout << "Methods    :";
    for(map<string, bool>::iterator it = req_methods.begin(); it != req_methods.end(); ++it){
        cout << " " << it->first;
        if(val_methods[it->first] != true){
            cerr << "Error: " << it->first << " is not a valid method! " << endl;
        }
    }
    cout << endl;
    cout << "Calibrating timers" << endl;
    #ifdef MPI_VERSION
} // main

    #endif
    ORB_calibrate();

    // let's do some calculations

    Graph::Graph *g = new(Graph::Graph);
    Graph::GraphReader gr;
    Graph::GraphProperties gp;
    Graph::GraphUtil gu;

    #ifdef MPI_VERSION
    //int myrank;
    //MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
    if(myrank == 0){
    #endif

    // Set up output streams
    if(file_append == false){
        outfile.open(outfilename.c_str());
    }
    else {
        outfile.open(outfilename.c_str(), ios_base::out | ios_base::app);
    }
    if(!outfile.is_open()){
        cerr << "Error opening " << outfilename << " for writing, exiting" << endl;
        exit(1);
    }

    #ifdef MPI_VERSION
}
    #endif

    // Read in the graph and start recording things to output streams
    cout << "Reading graph" << endl;
    ORB_read(t1);
    if(gr.read_graph(g, infile, intype, false) == -1){
        exit(1);
    }
    ORB_read(t2);

    if(outfile.tellp() == 0){
        outfile << "filename " << infile << endl;
        outfile << "input_num_nodes " << g->get_num_nodes() << endl;
        outfile << "input_num_edges " << g->get_num_edges() << endl;
    }

    if(record_timings){
        string of = outfilename + ".timings";

        #ifdef MPI_VERSION
        if(0 == myrank){
        #endif
        if(file_append == false){
            timing_file.open(of.c_str());
        }
        else {
            timing_file.open(of.c_str(), ios_base::out | ios_base::app);
        }
        if(!timing_file.is_open()){
            cerr << "Error opening " << timing_file << " for writing, exiting" << endl;
            exit(1);
        }
        if(false == file_append){
            outfile << "timing_file " << of << endl;
        }
        #ifdef MPI_VERSION
    }
        #endif
    }

    print_time(timing_file, "Time(read_graph)", t1, t2);

    if(apspinputfilename.length() != 0){
        cout << "Reading APSP matrix from " << apspinputfilename << endl;
        vector< vector<int> > *apsp_dists = new vector< vector<int> >;
        ORB_read(t1);
        read_apsp_matrix(apspinputfilename, *apsp_dists);
        ORB_read(t2);
        print_time(timing_file, "Time(read_apsp_matrix)", t1, t2);
        g->set_shortest_path_dist(apsp_dists);
    }

    outfile.precision(16);
    vector<int> components;
    ORB_read(t1);
    gu.label_all_components(g, &components);
    ORB_read(t2);
    print_time(timing_file, "Time(label_all_components)", t1, t2);
    bool is_connected = gp.is_connected(g);
    cout << "Connected components: " << g->get_num_connected_components() << endl;
    //cout << "Graph is connected: " << std::boolalpha << is_connected << endl;

    run_all_methods(g, outfile, timing_file, outprefix, req_methods, file_append, spectrum_spread);
    outfile.close();
    timing_file.close();

    // some algorithms only make sense to run on a connected graph/component
    if(not is_connected and run_largest_cc){  // run everything against the other algorithms
        cout << "Graph is not connected, re-running stats on largest connected component" << endl;
        outfilename = outprefix + ".largest_component.stats";
        if(file_append == false){
            outfile.open(outfilename.c_str());
        }
        else {
            outfile.open(outfilename.c_str(), ios_base::out | ios_base::app);
        }
        if(!outfile.is_open()){
            cerr << "Error opening " << outfilename << " for writing, exiting" << endl;
            exit(1);
        }

        // get the largest component
        Graph::Graph *largest_component = gu.get_largest_component_graph(g);
        cerr << "Deleting g" << endl;
        delete(g);  // delete g here to save on memory
        cerr << "g deleted" << endl;
        if(outfile.tellp() == 0){
            #ifdef MPI_VERSION
            if(0 == myrank){
            #endif
            outfile << "largest_component_from " << infile << endl;
            outfile << "input_num_nodes " << largest_component->get_num_nodes() << endl;
            outfile << "input_num_edges " << largest_component->get_num_edges() << endl;
            #ifdef MPI_VERSION
        }
            #endif
        }
        if(record_timings){
            string of = outfilename + ".timings";
            if(file_append == false){
                timing_file.open(of.c_str());
                #ifdef MPI_VERSION
                if(0 == myrank){
                #endif
                outfile << "timing_file " << of << endl;
                #ifdef MPI_VERSION
            }
                #endif
            }
            else {
                timing_file.open(of.c_str(), ios_base::out | ios_base::app);
            }

            if(!timing_file.is_open()){
                cerr << "Error opening " << timing_file << " for writing, exiting" << endl;
                exit(1);
            }
        }
        if(lcc_apspinputfilename.length() != 0){
            cout << "Reading LCC APSP matrix from " << lcc_apspinputfilename << endl;
            vector< vector<int> > *apsp_dists = new vector< vector<int> >;
            ORB_read(t1);
            read_apsp_matrix(lcc_apspinputfilename, *apsp_dists);
            ORB_read(t2);
            print_time(timing_file, "Time(read_apsp_matrix)", t1, t2);
            largest_component->set_shortest_path_dist(apsp_dists);
        }

        outprefix = outprefix + ".largest_component";

        outfile.precision(16);
        cerr << "Running methods on largest component" << endl;
        run_all_methods(largest_component, outfile, timing_file, outprefix, req_methods, file_append, spectrum_spread);
        outfile.close();
        timing_file.close();
    }

    #ifdef MPI_VERSION
    MPI_Finalize();
    #endif

    exit(0);
} // main
Exemplo n.º 5
0
void run_all_methods(Graph::Graph *g, ofstream &outfile, ofstream &timing_file, string outprefix, std::map<string, bool> req_methods,  bool &file_append, int spectrum_spread){
    Graph::GraphReader gr;
    Graph::GraphProperties gp;
    Graph::GraphUtil gu;
    ORB_t t1, t2;

    double global_cc, avg_cc, assortativity;

    vector<double> local_cc, freq_ecc, norm_hops, eigen_spectrum;
    float edge_density, avg_degree, eff_diam;
    vector<int> deg_dist, ecc;
    int degeneracy, diam;
    vector<int> k_cores;
    vector<list<int> *> components;
    double avg_path_length;
    int xmin;
    double prob, lambda, alpha, KS, max_delta;
    vector<vector<double> > delta;
    vector<double> betweenness;

    Graph::Graph *largest_component;

    vector< vector<int> > shortest_path_distances;

    cout << "Simplifying graph" << endl;
    ORB_read(t1);
    gp.make_simple(g);
    ORB_read(t2);
    print_time(timing_file, "Time(make_simple)", t1, t2);
    int num_components = g->get_num_connected_components();
    if(false == file_append){
        outfile << "connected_components " << num_components << endl;
        outfile << "net_num_nodes " << g->get_num_nodes() << endl;
        outfile << "net_num_edges " << g->get_num_edges() << endl;
    }

    if(req_methods["edge_density"] == true){
        cout << "Calculating edge density" << endl;
        ORB_read(t1);
        gp.edge_density(g, edge_density);
        ORB_read(t2);
        print_time(timing_file, "Time(edge_density)", t1, t2);
        outfile << "edge_density " << edge_density << endl;
    }
    if(req_methods["avg_degree"] == true){
        cout << "Calculating average degree" << endl;
        ORB_read(t1);
        gp.avg_degree(g, avg_degree);
        ORB_read(t2);
        print_time(timing_file, "Time(average_degree)", t1, t2);
        outfile << "avg_degree " << avg_degree << endl;
    }
    if(req_methods["degree_dist"] == true){
        cout << "Calculating degree distribution" << endl;
        ORB_read(t1);
        gp.deg_dist(g, deg_dist);
        ORB_read(t2);
        print_time(timing_file, "Time(degree_distribution)", t1, t2);
        string of = outprefix + ".deg_dist";
        write_degree_distribution(of, deg_dist);
        outfile << "degree_distribution " <<  of << endl;
    }
    if(num_components != 1){
        if(req_methods["component_sizes"] == true){
            cout << "Calculating component sizes" << endl;
            ORB_read(t1);
            gu.find_all_components(g, &components);
            ORB_read(t2);
            print_time(timing_file, "Time(component_sizes)", t1, t2);
            string of = outprefix + ".component_sizes";
            write_components(of, components);
            outfile << "component_sizes " << of << endl;
        }
    }

    if(req_methods["assortativity"] == true){
        cout << "Calculating degree assortativity" << endl;
        ORB_read(t1);
        gp.deg_assortativity(g, assortativity);
        ORB_read(t2);
        print_time(timing_file, "Time(assortativity)", t1, t2);
        outfile << "assortativity " <<  assortativity << endl;
    }
    if((req_methods["degeneracy"] == true) || (req_methods["k_cores"] == true)){
        cout << "Calculating k_cores and degeneracy" << endl;
        ORB_read(t1);
        degeneracy = gu.find_kcore(g, &k_cores);
        ORB_read(t2);
        print_time(timing_file, "Time(find_kcore)", t1, t2);
        outfile << "degeneracy " << degeneracy << endl;
        if(req_methods["k_cores"] == true){
            string of = outprefix + ".kcores";
            outfile << "kcore file " << of << endl;
            write_kcores(of, k_cores);
        }
    }

    if((req_methods["global_cc"] == true) || (req_methods["local_ccs"] == true) || (req_methods["avg_cc"] == true)){
        cout << "Calculating clustering coefficients" << endl;
        ORB_read(t1);
        gp.clustering_coefficients(g, global_cc, avg_cc, local_cc);
        ORB_read(t2);
        print_time(timing_file, "Time(clustering_coeffecients)", t1, t2);
        if(req_methods["global_cc"] == true){
            outfile << "global_clustering_coefficient " << global_cc << endl;
        }
        if(req_methods["avg_cc"] == true){
            outfile << "average_clustering_coefficient " << avg_cc << endl;
        }
        if(req_methods["local_ccs"] == true){
            string of = outprefix + ".local_ccs";
            outfile << "local_ccs file " << of << endl;
            write_local_ccs(of, local_cc);
        }
    }
    if(req_methods["shortest_paths"] == true){
        cout << "Calculating shortest paths" << endl;
        ORB_read(t1);
        gp.paths_dijkstra_all(g, shortest_path_distances);
        ORB_read(t2);
        print_time(timing_file, "Time(shortest_paths_dijkstra)", t1, t2);
    }

    #ifdef HAS_BOOST
    if((req_methods["shortest_paths_boost"] == true)){
        cout << "Creating BOOST representation of g" << endl;
        ORB_read(t1);
        gu.populate_boost(g);
        ORB_read(t2);
        print_time(timing_file, "Time(populate_boost)", t1, t2);
        cout << "Calculating shortest paths (boost)" << endl;
        ORB_read(t1);
        gp.paths_dijkstra_boost_all(g, shortest_path_distances);
        ORB_read(t2);
        print_time(timing_file, "Time(shortest_paths_dijkstra_boost)", t1, t2);
    }
    if(req_methods["betweenness"]){
        /* cout << "Creating BOOST representation of g" << endl;
           ORB_read(t1);
           gu.populate_boost(g);
           ORB_read(t2);
           print_time(timing_file, "Time(populate_boost)", t1, t2);
         */cout << "Calculating betweeneess centrality" << endl;
        ORB_read(t1);
        gp.betweenness_centrality(g, betweenness);
        ORB_read(t2);
        print_time(timing_file, "Time(betweenness_centrality)",t1,t2);
        string of = outprefix + ".betweenness";
        outfile << "betweenness_file " << of << endl;
        write_betweenness(of, g->get_betweenness_ref());
    }
    #else // ifdef HAS_BOOST
    cerr << "Error: BOOST support was not compiled, cannot run shortest_paths_boost or betweenness" << endl;
    #endif // ifdef HAS_BOOST

    if(num_components == 1){
        if(req_methods["eccentricity"] == true){
            cout << "Calculating eccentricities" << endl;
            ORB_read(t1);
            gp.eccentricity(g, ecc);
            ORB_read(t2);
            print_time(timing_file, "Time(eccentricity)",t1,t2);
            string of = outprefix + ".eccentricity";
            outfile << "eccentricity_file " << of << endl;
            write_eccentricity(of, ecc);
        }
        if(req_methods["eccentricity_dist"] == true){
            cout << "Calculating distribution of eccentricities" << endl;
            ORB_read(t1);
            gp.eccentricity_dist(g, ecc, freq_ecc);
            ORB_read(t2);
            print_time(timing_file, "Time(eccentricity distribution)",t1,t2);
            string of = outprefix + ".eccentricity_dist";
            outfile << "eccentricity_dist_file " << of << endl;
            write_eccentricity_distribution(of, freq_ecc);
        }
    }
    else {
        cout << "Graph is disconnected - not calculating eccentricities" << endl;
    }

    if(req_methods["expansion"] == true){
        cout << "Calculating normalized expansion (distance distribution) - no self loops allowed" << endl;
        ORB_read(t1);
        gp.expansion(g, norm_hops);
        ORB_read(t2);
        print_time(timing_file, "Time(expansion)",t1,t2);
        string of = outprefix + ".expansion";
        outfile << "expansion_file " << of << endl;
        write_expansion(of, norm_hops);
    }
    if(req_methods["avg_shortest_path"] == true){
        cout << "Calculating average shortest path length" << endl;
        ORB_read(t1);
        gp.avg_path_length(g, avg_path_length);
        ORB_read(t2);
        print_time(timing_file, "Time(avg_path_length)", t1, t2);
        outfile << "avg_path_length " << avg_path_length << endl;
    }
    if((req_methods["apsp_output"] == true)){
        string of = outprefix + ".apsp";
        ORB_read(t1);
        write_apsp_matrix(of, shortest_path_distances);
        ORB_read(t2);
        print_time(timing_file, "Time(write_apsp_matrix)", t1, t2);
    }

    #ifdef HAS_PETSC
    if(req_methods["eigen_spectrum"] == true){
        //If petsc/slepc are present, initalize those.
        //If MPI support is added in the future, init MPI before Petsc. Petsc will do it's own MPI
        //init if MPI isn't already inited.
        #ifdef HAS_SLEPC
        SlepcInitializeNoArguments();
        #elif HAVE_PETSC
        PetscInitializeNoArguments();
        #endif
        if(spectrum_spread == 0){
            spectrum_spread = 3;
        }

        cout << "Calculating adjacency matrix eigen spectrum\n";
        ORB_read(t1);
        gp.eigen_spectrum(g, eigen_spectrum, spectrum_spread);
        ORB_read(t2);
        print_time(timing_file, "Time(eigen spectrum)",t1,t2);

        #ifdef MPI_VERSION
        int myrank;
        MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
        if(myrank == 0){
        #endif
        outfile << "eigen_spectrum ";
        if(eigen_spectrum.size() > 0){
            outfile << eigen_spectrum[0];
        }
        for(int idx = 1; idx < eigen_spectrum.size(); idx++){
            outfile << ", " << eigen_spectrum[idx];
        }
        outfile << "\n";
        #ifdef MPI_VERSION
    }
        #endif
    }
    #endif // ifdef HAS_PETSC

    if(num_components == 1){
        if(req_methods["delta_hyperbolicity"] == true){
            cout << "Calculating delta hyperbolicity" << endl;
            ORB_read(t1);
            gp.delta_hyperbolicity(g, max_delta, delta);
            ORB_read(t2);

            print_time(timing_file, "Time(delta_hyperbolicity)", t1, t2);
            //outfile << "delta_hyperbolicity " << max_delta << endl;
            //for(int idx = 0; idx < delta.size(); idx++){
            //    for(int jdx = 0; jdx < delta[idx].size(); jdx++){
            //        outfile << delta[idx][jdx] << " ";
            //    }
            //    outfile << endl;
            //}
            string of = outprefix + ".delta_hyp";
            write_delta_hyperbolicity(of, delta);
            outfile << "max_delta_hyperbolicity " << max_delta;
        }
    }
    else {
        cout << "Graph is disconnected - not calculating delta hyperbolicity" << endl;
    }
    if(req_methods["diameter"] == true){
        cout << "Calculating diameter" << endl;
        ORB_read(t1);
        gp.diameter(g, diam);
        ORB_read(t2);
        print_time(timing_file, "Time(diameter)", t1, t2);
        outfile << "diameter " << diam << endl;
    }
    if(req_methods["effective_diameter"] == true){
        cout << "Calculating effective diameter" << endl;
        ORB_read(t1);
        gp.effective_diameter(g, eff_diam);
        ORB_read(t2);
        print_time(timing_file, "Time(effective_diameter)", t1, t2);
        outfile << "effective_diameter " << eff_diam << endl;
    }

    outfile.close();

    #ifdef HAS_SLEPC
    SlepcFinalize();
    #elif HAVE_PETSC
    PetscFinalize();
    #endif
} // run_all_methods