diff --git a/benchmark_results/.gitignore b/benchmark_results/.gitignore new file mode 100644 index 0000000..46488db --- /dev/null +++ b/benchmark_results/.gitignore @@ -0,0 +1,5 @@ +output/north +output/random_regular +output/rome +output/scale_free +output/steinlib diff --git a/benchmark_results/benchmark.bash b/benchmark_results/benchmark.bash new file mode 100644 index 0000000..9c89f2c --- /dev/null +++ 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" diff --git a/benchmark_results/dpt_planarizer b/benchmark_results/dpt_planarizer new file mode 120000 index 0000000..7f26706 --- /dev/null +++ b/benchmark_results/dpt_planarizer @@ -0,0 +1 @@ +../../deferred_planarity_test/bin/dpt_planarizer \ No newline at end of file diff --git a/benchmark_results/get_graph_characteristics b/benchmark_results/get_graph_characteristics new file mode 120000 index 0000000..0717435 --- /dev/null +++ b/benchmark_results/get_graph_characteristics @@ -0,0 +1 @@ +../make_planar/bin/get_graph_characteristics \ No newline at end of file diff --git a/benchmark_results/input/north.txt b/benchmark_results/input/north.txt new file mode 100644 index 0000000..b0034cc --- /dev/null +++ b/benchmark_results/input/north.txt @@ -0,0 +1,423 @@ +/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/g.10.19.gml +/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/g.10.20.gml +/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/g.10.22.gml +/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/g.10.25.gml +/home/richard/Projects/06_research/maximum_planar_subgraph/benchmark_data/graph_datasets/north/gml_non_planar/g.10.27.gml 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+/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 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+/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 diff --git a/benchmark_results/north/.gitignore b/benchmark_results/north/.gitignore deleted file mode 100644 index 43a911f..0000000 --- a/benchmark_results/north/.gitignore +++ /dev/null @@ -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 diff --git a/benchmark_results/north/benchmark_north.bash b/benchmark_results/north/benchmark_north.bash deleted file mode 100644 index 651235c..0000000 --- a/benchmark_results/north/benchmark_north.bash +++ /dev/null @@ -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 diff --git a/benchmark_results/ogdf_mps_cactus b/benchmark_results/ogdf_mps_cactus new file mode 120000 index 0000000..fff9564 --- /dev/null +++ b/benchmark_results/ogdf_mps_cactus @@ -0,0 +1 @@ +../make_planar/bin/ogdf_mps_cactus \ No newline at end of file diff --git a/benchmark_results/ogdf_mps_fast b/benchmark_results/ogdf_mps_fast new file mode 120000 index 0000000..f1e7d97 --- /dev/null +++ b/benchmark_results/ogdf_mps_fast @@ -0,0 +1 @@ +../make_planar/bin/ogdf_mps_fast \ No newline at end of file diff --git a/benchmark_results/rome/.gitignore b/benchmark_results/rome/.gitignore deleted file mode 100644 index 093fa52..0000000 --- a/benchmark_results/rome/.gitignore +++ /dev/null @@ -1,6 +0,0 @@ -dpt_planarizer -ogdf_mps_fast -output_rome_dfs.txt -output_rome_fast.txt -rome.txt -rome_result.csv diff --git a/benchmark_results/rome/benchmark_rome.bash b/benchmark_results/rome/benchmark_rome.bash deleted file mode 100644 index ed68323..0000000 --- a/benchmark_results/rome/benchmark_rome.bash +++ /dev/null @@ -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 diff --git a/benchmark_results/run_all.sh b/benchmark_results/run_all.sh new file mode 100644 index 0000000..784ac0a --- /dev/null +++ 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" diff --git a/benchmark_results/steinlib/.gitignore b/benchmark_results/steinlib/.gitignore deleted file mode 100644 index c624765..0000000 --- a/benchmark_results/steinlib/.gitignore +++ /dev/null @@ -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 diff --git a/make_planar/build_script.sh b/make_planar/build_script.sh new file mode 100644 index 0000000..1f1b09b --- /dev/null +++ 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" + diff --git a/make_planar/get_graph_characteristics.cpp b/make_planar/get_graph_characteristics.cpp index d1f2968..e24cbcd 100644 --- 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 - +#include #include 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; diff --git a/make_planar/ogdf_mps_cactus.cpp b/make_planar/ogdf_mps_cactus.cpp index 6f1a24d..87f35f4 100644 --- a/make_planar/ogdf_mps_cactus.cpp +++ b/make_planar/ogdf_mps_cactus.cpp @@ -1,11 +1,13 @@ -#include -#include +/* Maximum Planar Subgraph by cactus + * + */ -// #include +#include #include #include #include - +#include +#include #include 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; } - - NodeArray numbering(G); - computeSTNumbering(G, numbering, nullptr, nullptr, true); - OGDF_ASSERT(num == G.numberOfNodes()); + // -------------------------------- + // 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; - - // separator for planarization - // <--------------> - - // std::cout << "start planarization" << std::endl; List *delEdges = new List; // empty list + auto start = std::chrono::high_resolution_clock::now(); + + // compute a cactus, then compute edge addition PlanarSubgraphCactus psc; ogdf::MaximalPlanarSubgraphSimple mps(psc); mps.call(G, *delEdges); - - std::cout << delEdges->size() << std::endl; + auto end = std::chrono::high_resolution_clock::now(); + auto microseconds = std::chrono::duration_cast(end - start).count(); + double time = static_cast(microseconds) / 1'000'000.0; + // -------------------------------- + // 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; diff --git a/make_planar/ogdf_mps_exact.cpp b/make_planar/ogdf_mps_exact.cpp index 3c2ffed..82d0f6f 100644 --- a/make_planar/ogdf_mps_exact.cpp +++ b/make_planar/ogdf_mps_exact.cpp @@ -1,17 +1,12 @@ -#include +/* Maximum Planar Subgraph by Integer Linear Program (ILP) + * + */ + #include -// #include - -#include -#include -#include #include -#include - +#include #include -#include #include -#include 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 *delEdges = new List; - // separator for planarization - // <--------------> - // PQ implementation to make planar subgraph - std::cout << "start planarization" << std::endl; - List *delEdges = new List; // empty list + auto start = std::chrono::high_resolution_clock::now(); - std::cout << "running maximum" << std::endl; + // perform planarization by ILP ogdf::MaximumPlanarSubgraph mps; mps.call(G, *delEdges); + auto end = std::chrono::high_resolution_clock::now(); + auto microseconds = std::chrono::duration_cast(end - start).count(); + double time = static_cast(microseconds) / 1'000'000.0; + + + // -------------------------------- + // print out result of planarization + // -------------------------------- - std::cout << "Edges removed:" << delEdges->size() << std::endl; - - - // 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; } diff --git a/make_planar/ogdf_mps_fast.cpp b/make_planar/ogdf_mps_fast.cpp index bfbdb2c..f0de955 100644 --- 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 #include - #include -// #include #include #include - +#include +#include #include 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 *delEdges = new List; // empty list + auto start = std::chrono::high_resolution_clock::now(); + PlanarSubgraphFast psf; - // comment out to use default options - // psf.runs(1); ogdf::MaximalPlanarSubgraphSimple mps(psf); mps.call(G, *delEdges); + auto end = std::chrono::high_resolution_clock::now(); + auto microseconds = std::chrono::duration_cast(end - start).count(); + double time = static_cast(microseconds) / 1'000'000.0; + + // -------------------------------- + // print out result of planarization + // -------------------------------- - // print edges removed - std::cout << delEdges->size() << std::endl; - - - // 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;