Feat: changed benchmark procedure to use parallel

Feat: include time and filename in ogdf_mps
Feat: added graph generation for barabasi-albert and regular
2024-05-08 16:03:40 +09:00 · 2024-05-07 11:38:31 +09:00
29 changed files with 10283 additions and 207 deletions
--- a/benchmark_results/.gitignore
+++ b/benchmark_results/.gitignore
@ -0,0 +1,5 @@
+output/north
+output/random_regular
+output/rome
+output/scale_free
+output/steinlib
--- a/benchmark_results/benchmark.bash
+++ b/benchmark_results/benchmark.bash
@ -0,0 +1,11 @@
+#!/bin/bash
+
+FILE_LIST=$1
+
+PROGRAM=$2
+
+ARGS=$3
+
+THREADS=11
+
+cat  $FILE_LIST | parallel -k --jobs $THREADS "./$PROGRAM {} $ARGS"
--- a/benchmark_results/dpt_planarizer
+++ b/benchmark_results/dpt_planarizer
@ -0,0 +1 @@
+../../deferred_planarity_test/bin/dpt_planarizer
--- a/benchmark_results/get_graph_characteristics
+++ b/benchmark_results/get_graph_characteristics
@ -0,0 +1 @@
+../make_planar/bin/get_graph_characteristics
--- a/benchmark_results/input/north.txt
+++ b/benchmark_results/input/north.txt
@ -0,0 +1,423 @@
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+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-85.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-86.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-88.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-91.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-92.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-94.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-95.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-96.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-98.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp3-99.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-11.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-13.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-14.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-15.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-16.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-17.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-18.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-19.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-21.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-22.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-23.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-24.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-25.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-26.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-27.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-28.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-29.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-30.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-31.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-32.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-33.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-34.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-35.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-36.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-37.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-38.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-39.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-40.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-41.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-42.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-43.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-44.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-45.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-46.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-47.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-48.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-49.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-50.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-51.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-52.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-53.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-54.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-55.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-56.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-58.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-59.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-60.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-61.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-62.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-63.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-64.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-66.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-67.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-68.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-69.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-70.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-71.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-72.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-73.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-74.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-75.gml
+/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/steinlib/gml_non_planar/wrp4-76.gml
--- a/benchmark_results/north/.gitignore
+++ b/benchmark_results/north/.gitignore
@ -1,7 +0,0 @@
-dpt_planarizer
-north.txt
-north_result.csv
-north_subset.txt
-ogdf_mps_fast
-output_north_dfs.txt
-output_north_fast.txt
--- a/benchmark_results/north/benchmark_north.bash
+++ b/benchmark_results/north/benchmark_north.bash
@ -1,33 +0,0 @@
-#!/bin/bash
-
-FILE_LIST=$1
-
-PROGRAM=$2
-
-
-# Check if file_list.txt exists
-if [ ! -f $FILE_LIST ]; then
-    echo "input file not found!"
-    exit 1
-fi
-
-INPUT_PATH=/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/
-
-# Read file paths from file_list.txt
-while IFS= read -r INPUT_FILE; do
-    # Extract filename stem
-    filename=$(basename -- "$INPUT_FILE")
-    filename_stem="${filename%.*}"
-    
-    
-    # Run your program and capture its output
-    if [ "$PROGRAM" == "ogdf_mps_fast" ]; then
-        # do something if strings are equal
-        ./$PROGRAM "$INPUT_PATH$INPUT_FILE"
-    elif [ "$PROGRAM" == "dpt_planarizer" ]; then
-        # do something if strings are not equal
-        ./$PROGRAM "$INPUT_PATH$INPUT_FILE" 1000
-    fi
-
-
-done < $FILE_LIST
--- a/benchmark_results/ogdf_mps_cactus
+++ b/benchmark_results/ogdf_mps_cactus
@ -0,0 +1 @@
+../make_planar/bin/ogdf_mps_cactus
--- a/benchmark_results/ogdf_mps_fast
+++ b/benchmark_results/ogdf_mps_fast
@ -0,0 +1 @@
+../make_planar/bin/ogdf_mps_fast
--- a/benchmark_results/rome/.gitignore
+++ b/benchmark_results/rome/.gitignore
@ -1,6 +0,0 @@
-dpt_planarizer
-ogdf_mps_fast
-output_rome_dfs.txt
-output_rome_fast.txt
-rome.txt
-rome_result.csv
--- a/benchmark_results/rome/benchmark_rome.bash
+++ b/benchmark_results/rome/benchmark_rome.bash
@ -1,33 +0,0 @@
-#!/bin/bash
-
-FILE_LIST=$1
-
-PROGRAM=$2
-
-
-# Check if file_list.txt exists
-if [ ! -f $FILE_LIST ]; then
-    echo "input file not found!"
-    exit 1
-fi
-
-INPUT_PATH=/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/rome/gml_non_planar/
-
-# Read file paths from file_list.txt
-while IFS= read -r INPUT_FILE; do
-    # Extract filename stem
-    filename=$(basename -- "$INPUT_FILE")
-    filename_stem="${filename%.*}"
-    
-    
-    # Run your program and capture its output
-    if [ "$PROGRAM" == "ogdf_mps_fast" ]; then
-        # do something if strings are equal
-        ./$PROGRAM "$INPUT_PATH$INPUT_FILE"
-    elif [ "$PROGRAM" == "dpt_planarizer" ]; then
-        # do something if strings are not equal
-        ./$PROGRAM "$INPUT_PATH$INPUT_FILE" 1000
-    fi
-
-
-done < $FILE_LIST
--- a/benchmark_results/run_all.sh
+++ b/benchmark_results/run_all.sh
@ -0,0 +1,33 @@
+#!/bin/bash
+
+NUM_CYCLES=1000
+
+TYPE=$1
+
+start_time=$(date +%s.%N)
+echo "running $TYPE: dfs"
+bash benchmark.bash input/$TYPE.txt dpt_planarizer $NUM_CYCLES > output/$TYPE/dfs.csv
+end_time=$(date +%s.%N)
+elapsed_time=$(echo "$end_time - $start_time" | bc)
+echo "Elapsed time: $elapsed_time seconds"
+echo ""
+
+echo "running $TYPE: cactus"
+start_time=$(date +%s.%N)
+bash benchmark.bash input/$TYPE.txt ogdf_mps_cactus > output/$TYPE/cactus.csv
+end_time=$(date +%s.%N)
+elapsed_time=$(echo "$end_time - $start_time" | bc)
+echo "Elapsed time: $elapsed_time seconds"
+echo ""
+
+echo "running $TYPE: fast"
+start_time=$(date +%s.%N)
+bash benchmark.bash input/$TYPE.txt ogdf_mps_fast > output/$TYPE/fast.csv
+end_time=$(date +%s.%N)
+elapsed_time=$(echo "$end_time - $start_time" | bc)
+echo "Elapsed time: $elapsed_time seconds"
+echo ""
+
+echo "getting propreties..."
+bash benchmark.bash input/$TYPE.txt get_graph_characteristics > output/$TYPE/graph_properties.csv 
+echo "done"
--- a/benchmark_results/steinlib/.gitignore
+++ b/benchmark_results/steinlib/.gitignore
@ -1,9 +0,0 @@
-benchmark_steinlib.bash
-dpt_planarizer
-dpt_planarizer_random
-dpt_planarizer_wilson
-get_graph_char
-ogdf_mps_cactus
-ogdf_mps_fast
-output_steinlib_*
-steinlib.txt
--- a/make_graphs/make_random_biconnected_graph.cpp
+++ b/make_graphs/make_random_biconnected_graph.cpp
--- a/make_graphs/make_regular_graph.cpp
+++ b/make_graphs/make_regular_graph.cpp
@ -0,0 +1,27 @@
+#include <ogdf/basic/basic.h>
+#include <ogdf/basic/Graph.h>
+#include <ogdf/fileformats/GraphIO.h>
+#include <ogdf/basic/graph_generators.h>
+
+using namespace ogdf;
+
+int main(int argc, char **argv) {
+    int nodeCount = std::stoi(argv[1]);
+    int edgeCount = std::stoi(argv[2]);
+    int copies = std::stoi(argv[3]);
+    int seed = std::stoi(argv[4]);
+    std::string outputFolder = argv[5];
+
+    setSeed(seed);
+    for (int i = 0; i < copies; i++) {
+        Graph G;
+        randomRegularGraph(G, nodeCount, edgeCount);
+
+        std::stringstream ss;
+        ss << outputFolder << "/graphn" << nodeCount << "e" << edgeCount << "s"
+        << seed << "i" << i << ".gml";
+        std::string s = ss.str();
+        GraphIO::write(G, s, GraphIO::writeGML);
+    }
+
+}
--- a/make_graphs/make_scale_free_graph.cpp
+++ b/make_graphs/make_scale_free_graph.cpp
@ -0,0 +1,27 @@
+#include <ogdf/basic/basic.h>
+#include <ogdf/basic/Graph.h>
+#include <ogdf/fileformats/GraphIO.h>
+#include <ogdf/basic/graph_generators.h>
+
+using namespace ogdf;
+
+int main(int argc, char **argv) {
+    int nodeCount = std::stoi(argv[1]);
+    int edgeCount = std::stoi(argv[2]);
+    int copies = std::stoi(argv[3]);
+    int seed = std::stoi(argv[4]);
+    std::string outputFolder = argv[5];
+
+    setSeed(seed);
+    for (int i = 0; i < copies; i++) {
+        Graph G;
+        preferentialAttachmentGraph(G, nodeCount, edgeCount);
+
+        std::stringstream ss;
+        ss << outputFolder << "/graphn" << nodeCount << "e" << edgeCount << "s"
+        << seed << "i" << i << ".gml";
+        std::string s = ss.str();
+        GraphIO::write(G, s, GraphIO::writeGML);
+    }
+
+}
--- a/make_planar/build_script.sh
+++ b/make_planar/build_script.sh
@ -0,0 +1,18 @@
+#!/bin/bash
+
+g++ ogdf_mps_cactus.cpp -lOGDF -lCOIN -o bin/ogdf_mps_cactus -O3 -march=native -Wall
+
+echo "built ogdf_mps_cactus"
+
+g++ ogdf_mps_fast.cpp -lOGDF -lCOIN -o bin/ogdf_mps_fast -O3 -march=native -Wall
+
+echo "built ogdf_mps_fast"
+
+g++ ogdf_mps_exact.cpp -lOGDF -lCOIN -o bin/ogdf_mps_exact -O3 -march=native -Wall
+
+echo "built ogdf_mps_exact"
+
+g++ get_graph_characteristics.cpp -lOGDF -lCOIN -o bin/get_graph_characteristics -O3 -march=native -Wall
+
+echo "built get_graph_characteristics"
+
--- a/make_planar/get_graph_characteristics.cpp
+++ b/make_planar/get_graph_characteristics.cpp
@ -1,8 +1,8 @@
-/* This code converts GraphML to gml
+/*  get number of nodes and edge of graph
 * 
 */
 #include <ogdf/fileformats/GraphIO.h>
-
+#include <filesystem>
 #include <iostream>

 using namespace ogdf;
@ -18,8 +18,8 @@ int main(int argc, char* argv[])
        std::cerr << "Could not read input.gml" << std::endl;
        return 1;
    }
-
-    std::cout <<  G.numberOfNodes() << ", " << G.numberOfEdges() << std::endl;
+    string filename = std::filesystem::path(input_file).stem();
+    std::cout <<  filename << ", " << G.numberOfNodes() << ", " << G.numberOfEdges() << std::endl;
    

    return 0;
--- a/make_planar/ogdf_mps_cactus.cpp
+++ b/make_planar/ogdf_mps_cactus.cpp
@ -1,11 +1,13 @@
-#include <ogdf/basic/STNumbering.h>
-#include <ogdf/fileformats/GraphIO.h>
+/*  Maximum Planar Subgraph by cactus 
+ * 
+ */

-// #include <ogdf/planarity/PlanarSubgraphBoyerMyrvold.h>
+#include <ogdf/fileformats/GraphIO.h>
 #include <ogdf/planarity/MaximumPlanarSubgraph.h>
 #include <ogdf/planarity/PlanarSubgraphCactus.h>
 #include <ogdf/planarity/MaximalPlanarSubgraphSimple.h>
-
+#include <filesystem>
+#include <chrono>
 #include <iostream>

 using namespace ogdf;
@ -14,54 +16,38 @@ using namespace ogdf;
 int main(int argc, char* argv[]) 
 {

-    string inputFile = argv[1];
+    string input_file = argv[1];
    Graph G;

-    if (!GraphIO::read(G, inputFile, GraphIO::readGML)) {
+    if (!GraphIO::read(G, input_file, GraphIO::readGML)) {
        std::cerr << "Could not read input.gml" << std::endl;
        return 1;
    }
        
+    // --------------------------------
+    // planarize 
+    // --------------------------------

-    NodeArray<int> numbering(G);
-    computeSTNumbering(G, numbering, nullptr, nullptr, true);
-    OGDF_ASSERT(num == G.numberOfNodes());
-
-    // print after input
-    // graphPrinter(G);
-    // std::cout << "G Planarity: " << ogdf::isPlanar(G) << std::endl;
-    // std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    // std::cout << "Original number of edges: " << G.numberOfEdges() << std::endl;
-
-    // separator for planarization
-    // <-------------->
-
-    // std::cout << "start planarization" << std::endl;
    List<edge> *delEdges = new List<edge>; // empty list

+    auto start = std::chrono::high_resolution_clock::now();
+
+    // compute a cactus, then compute edge addition
    PlanarSubgraphCactus<int> psc;
    ogdf::MaximalPlanarSubgraphSimple<int> mps(psc);
    mps.call(G, *delEdges);

+    auto end = std::chrono::high_resolution_clock::now();
+    auto microseconds = std::chrono::duration_cast<std::chrono::microseconds>(end - start).count();
+    double time = static_cast<double>(microseconds) / 1'000'000.0;

-    std::cout << delEdges->size() << std::endl;
+    // --------------------------------
+    // print out result of planarization
+    // --------------------------------

-
-    // delete removed edges
-    //for (edge e: *delEdges) {
-    //    // print removed edges
-    //    // std::cout << e->adjSource() << std::endl;
-    //    G.delEdge(e);
-    //}
-
-
-    // write processed graph to new gml file
-    // GraphIO::write(G, "output.gml", GraphIO::writeGML);
-    
-
-    // std::cout << ogdf::isPlanar(G) << std::endl;
-    // std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    // std::cout << "Subgraph number of edges: " << G.numberOfEdges() << std::endl;
+    int removed_edges =  delEdges->size();
+    string filename = std::filesystem::path(input_file).stem();
+    std::cout << filename << ", " << removed_edges << ", " << time << std::endl;


    return 0;
--- a/make_planar/ogdf_mps_exact.cpp
+++ b/make_planar/ogdf_mps_exact.cpp
@ -1,17 +1,12 @@
-#include <ogdf/basic/STNumbering.h>
+/*  Maximum Planar Subgraph by Integer Linear Program (ILP)
+ * 
+ */
+
 #include <ogdf/fileformats/GraphIO.h>
-// #include <ogdf/basic/extended_graph_alg.h>
-
-#include <ogdf/planarity/PlanarSubgraphFast.h>
-#include <ogdf/planarity/PlanarSubgraphBoyerMyrvold.h>
-#include <ogdf/planarity/PlanarSubgraphPC.h>
 #include <ogdf/planarity/MaximumPlanarSubgraph.h>
-#include <ogdf/planarity/MaximalPlanarSubgraphSimple.h>
-
+#include <filesystem>
 #include <iostream>
-#include <map>
 #include <chrono>
-#include <getopt.h>

 using namespace ogdf;

@ -19,52 +14,40 @@ using namespace ogdf;
 int main(int argc, char* argv[]) 
 {

-    string inputFile = argv[1];
+    string input_file = argv[1];
    Graph G;

-    if (!GraphIO::read(G, inputFile, GraphIO::readGML)) {
+    if (!GraphIO::read(G, input_file, GraphIO::readGML)) {
        std::cerr << "Could not read input.gml" << std::endl;
        return 1;
    }

+    // --------------------------------
+    // planarize 
+    // --------------------------------

-    // print after input
-    // graphPrinter(G);
-    std::cout << "G Planarity: " << ogdf::isPlanar(G) << std::endl;
-    std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    std::cout << "Original number of edges: " << G.numberOfEdges() << std::endl;
+    // store the deleted edges to be used to delete edges from G
+    List<edge> *delEdges = new List<edge>; 

-    // separator for planarization
-    // <-------------->

-    // PQ implementation to make planar subgraph
-    std::cout << "start planarization" << std::endl;
-    List<edge> *delEdges = new List<edge>; // empty list
+    auto start = std::chrono::high_resolution_clock::now();

-    std::cout << "running maximum" << std::endl;
+    // perform planarization by ILP
    ogdf::MaximumPlanarSubgraph<int> mps;
    mps.call(G, *delEdges);

-    
-    std::cout << "Edges removed:" << delEdges->size() << std::endl;
+    auto end = std::chrono::high_resolution_clock::now();
+    auto microseconds = std::chrono::duration_cast<std::chrono::microseconds>(end - start).count();
+    double time = static_cast<double>(microseconds) / 1'000'000.0;


-    // delete removed edges
-    for (edge e: *delEdges) {
-        // print removed edges
-        // std::cout << e->adjSource() << std::endl;
-        G.delEdge(e);
-    }
-
-
-    // write processed graph to new gml file
-    // GraphIO::write(G, "output.gml", GraphIO::writeGML);
-    
-
-    std::cout << "G planarity: " << ogdf::isPlanar(G) << std::endl;
-    std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    std::cout << "Subgraph number of edges: " << G.numberOfEdges() << std::endl;
+    // --------------------------------
+    // print out result of planarization
+    // --------------------------------
    
+    int removed_edges =  delEdges->size();
+    string filename = std::filesystem::path(input_file).stem();
+    std::cout << filename << ", " << removed_edges << ", " << time << std::endl;

    return 0;
 }
--- a/make_planar/ogdf_mps_fast.cpp
+++ b/make_planar/ogdf_mps_fast.cpp
@ -1,14 +1,14 @@
-/* 
+/*  Maximum Planar Subgraph by PQ tree-based planarity test
 * 
 */
+
 #include <ogdf/basic/STNumbering.h>
 #include <ogdf/fileformats/GraphIO.h>
-
 #include <ogdf/planarity/PlanarSubgraphFast.h>
-// #include <ogdf/planarity/PlanarSubgraphBoyerMyrvold.h>
 #include <ogdf/planarity/MaximumPlanarSubgraph.h>
 #include <ogdf/planarity/MaximalPlanarSubgraphSimple.h>
-
+#include <filesystem>
+#include <chrono>
 #include <iostream>

 using namespace ogdf;
@ -17,10 +17,10 @@ using namespace ogdf;
 int main(int argc, char* argv[]) 
 {

-    string inputFile = argv[1];
+    string input_file = argv[1];
    Graph G;

-    if (!GraphIO::read(G, inputFile, GraphIO::readGML)) {
+    if (!GraphIO::read(G, input_file, GraphIO::readGML)) {
        std::cerr << "Could not read input.gml" << std::endl;
        return 1;
    }
@ -30,44 +30,29 @@ int main(int argc, char* argv[])
    computeSTNumbering(G, numbering, nullptr, nullptr, true);
    OGDF_ASSERT(num == G.numberOfNodes());

-    // print after input
-    // graphPrinter(G);
-    // std::cout << "G Planarity: " << ogdf::isPlanar(G) << std::endl;
-    // std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    // std::cout << "Original number of edges: " << G.numberOfEdges() << std::endl;
+    // --------------------------------
+    // planarize 
+    // --------------------------------

-    // separator for planarization
-    // <-------------->
-
-    // PQ implementation to make planar subgraph
    List<edge> *delEdges = new List<edge>; // empty list

+    auto start = std::chrono::high_resolution_clock::now();
+
    PlanarSubgraphFast<int> psf;
-    // comment out to use default options
-    // psf.runs(1); 
    ogdf::MaximalPlanarSubgraphSimple<int> mps(psf);
    mps.call(G, *delEdges);

+    auto end = std::chrono::high_resolution_clock::now();
+    auto microseconds = std::chrono::duration_cast<std::chrono::microseconds>(end - start).count();
+    double time = static_cast<double>(microseconds) / 1'000'000.0;

-	// print edges removed
-    std::cout <<  delEdges->size() << std::endl;
+    // --------------------------------
+    // print out result of planarization
+    // --------------------------------
    
-
-    // delete removed edges
-    // for (edge e: *delEdges) {
-    //     // print removed edges
-    //     // std::cout << e->adjSource() << std::endl;
-    //     G.delEdge(e);
-    // }
-
-
-    // write processed graph to new gml file
-    // GraphIO::write(G, "output.gml", GraphIO::writeGML);
-    
-
-    // std::cout << "G planarity: " << ogdf::isPlanar(G) << std::endl;
-    // std::cout << "Original number of nodes: " << G.numberOfNodes() << std::endl;
-    // std::cout << "Subgraph number of edges: " << G.numberOfEdges() << std::endl;
+    int removed_edges =  delEdges->size();
+    string filename = std::filesystem::path(input_file).stem();
+    std::cout << filename << ", " << removed_edges << ", " << time << std::endl;


    return 0;
--- a/synthetic_data/barabasi/.gitignore
+++ b/synthetic_data/barabasi/.gitignore
@ -0,0 +1,2 @@
+100*
+make_scale_free_graph
--- a/synthetic_data/barabasi/generate_graphs.bash
+++ b/synthetic_data/barabasi/generate_graphs.bash
@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Define the parameters
+num_node_range=(100 1000 10000)
+edge_multiplier_range=(2 3 5 10 20)
+copies=20
+seed=41
+
+max_jobs=2
+running_jobs=0
+
+# Loop through different parameters
+for num_node in "${num_node_range[@]}"; do
+	for edge_multiplier in "${edge_multiplier_range[@]}"; do
+		num_edge=$((num_node * edge_multiplier))
+		output_folder="${num_node}n${num_edge}e"
+		mkdir -p $output_folder
+
+		# Run the program with the parameters
+		echo "run with $num_node nodes and $num_edge edges output to $output_folder"
+		./make_scale_free_graph $num_node $num_edge $copies $seed $output_folder &
+
+		((running_jobs++))
+
+		if ((running_jobs >= max_jobs)); then
+			wait
+			running_jobs=0
+		fi
+	done
+done
--- a/synthetic_data/regular/.gitignore
+++ b/synthetic_data/regular/.gitignore
@ -0,0 +1,2 @@
+100*
+make_regular_graph
--- a/synthetic_data/regular/generate_graphs.bash
+++ b/synthetic_data/regular/generate_graphs.bash
@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Define the parameters
+num_node_range=(100 1000 10000)
+edge_multiplier_range=(2 3 5 10 20)
+copies=20
+seed=41
+
+max_jobs=2
+running_jobs=0
+
+# Loop through different parameters
+for num_node in "${num_node_range[@]}"; do
+	for edge_multiplier in "${edge_multiplier_range[@]}"; do
+		num_edge=$((num_node * edge_multiplier))
+		output_folder="${num_node}n${num_edge}e"
+		mkdir -p $output_folder
+
+		# Run the program with the parameters
+		echo "run with $num_node nodes and $num_edge edges output to $output_folder"
+		./make_regular_graph $num_node $num_edge $copies $seed $output_folder &
+
+		((running_jobs++))
+
+		if ((running_jobs >= max_jobs)); then
+			wait
+			running_jobs=0
+		fi
+	done
+done
Author	SHA1	Message	Date
Richard Wong	39b3570e11	Feat: changed benchmark procedure to use parallel Feat: include time and filename in ogdf_mps	2024-05-08 16:03:40 +09:00
Richard Wong	7b875ba141	Feat: added graph generation for barabasi-albert and regular	2024-05-07 11:38:31 +09:00
				`@ -0,0 +1 @@`
				`../../deferred_planarity_test/bin/dpt_planarizer`
				`@ -0,0 +1 @@`
				`../make_planar/bin/get_graph_characteristics`