diff --git a/java/src/main/java/org/softwareheritage/graph/experiments/topology/ConnectedComponents.java b/java/src/main/java/org/softwareheritage/graph/experiments/topology/ConnectedComponents.java index 43fd11b..c1f5b75 100644 --- a/java/src/main/java/org/softwareheritage/graph/experiments/topology/ConnectedComponents.java +++ b/java/src/main/java/org/softwareheritage/graph/experiments/topology/ConnectedComponents.java @@ -1,193 +1,199 @@ package org.softwareheritage.graph.experiments.topology; import com.google.common.primitives.Longs; import com.martiansoftware.jsap.*; import it.unimi.dsi.big.webgraph.LazyLongIterator; import it.unimi.dsi.bits.LongArrayBitVector; import it.unimi.dsi.fastutil.Arrays; import it.unimi.dsi.io.ByteDiskQueue; import it.unimi.dsi.logging.ProgressLogger; import org.softwareheritage.graph.AllowedNodes; import org.softwareheritage.graph.Graph; +import org.softwareheritage.graph.Node; import org.softwareheritage.graph.Subgraph; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.io.PrintWriter; import java.util.*; public class ConnectedComponents { private Subgraph graph; private void load_graph(String graphBasename, String nodeTypes) throws IOException { System.err.println("Loading graph " + graphBasename + " ..."); var underlyingGraph = Graph.loadMapped(graphBasename); var underlyingGraphSym = underlyingGraph.symmetrize(); graph = new Subgraph(underlyingGraphSym, new AllowedNodes(nodeTypes)); System.err.println("Graph loaded."); } private static JSAPResult parse_args(String[] args) { JSAPResult config = null; try { SimpleJSAP jsap = new SimpleJSAP(ConnectedComponents.class.getName(), "", new Parameter[]{ new FlaggedOption("graphPath", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'g', "graph", "Basename of the compressed graph"), new FlaggedOption("outdir", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'o', "outdir", "Directory where to put the results"), + new Switch("byOrigins", JSAP.NO_SHORTFLAG, "by-origins", + "Compute size of components by number of origins"), new FlaggedOption("nodeTypes", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'n', "nodetypes", "Allowed node types (comma-separated)"),}); config = jsap.parse(args); if (jsap.messagePrinted()) { System.exit(1); } } catch (JSAPException e) { e.printStackTrace(); } return config; } - private HashMap /* ArrayList> */ compute(ProgressLogger pl) throws IOException { + private HashMap /* ArrayList> */ compute(ProgressLogger pl, boolean byOrigin) throws IOException { final long n = graph.numNodes(); final long maxN = graph.maxNodeNumber(); // Allow enough memory to behave like in-memory queue int bufferSize = (int) Math.min(Arrays.MAX_ARRAY_SIZE & ~0x7, 8L * maxN); // Use a disk based queue to store BFS frontier final File queueFile = File.createTempFile(ConnectedComponents.class.getSimpleName(), "queue"); final ByteDiskQueue queue = ByteDiskQueue.createNew(queueFile, bufferSize, true); final byte[] byteBuf = new byte[Long.BYTES]; // WARNING: no 64-bit version of this data-structure, but it can support // indices up to 2^37 LongArrayBitVector visited = LongArrayBitVector.ofLength(maxN); pl.expectedUpdates = n; pl.itemsName = "nodes"; pl.start("Starting connected components visit..."); // ArrayList> components = new ArrayList<>(); HashMap componentDistribution = new HashMap<>(); var it = graph.nodeIterator(); while (it.hasNext()) { long i = it.nextLong(); if (visited.getBoolean(i)) continue; // ArrayList component = new ArrayList<>(); long componentNodes = 0; queue.enqueue(Longs.toByteArray(i)); visited.set(i); while (!queue.isEmpty()) { queue.dequeue(byteBuf); final long currentNode = Longs.fromByteArray(byteBuf); // component.add(currentNode); - componentNodes += 1; + + if (!byOrigin || graph.getNodeType(currentNode) == Node.Type.ORI) + componentNodes += 1; final LazyLongIterator iterator = graph.successors(currentNode); long succ; while ((succ = iterator.nextLong()) != -1) { if (visited.getBoolean(succ)) continue; visited.set(succ); queue.enqueue(Longs.toByteArray(succ)); } pl.update(); } /* * if (component.size() > 0) { components.add(component); } */ if (componentNodes > 0) componentDistribution.merge(componentNodes, 1L, Long::sum); } pl.done(); // return components; return componentDistribution; } private static void printDistribution(ArrayList> components, Formatter out) { TreeMap distribution = new TreeMap<>(); for (ArrayList component : components) { distribution.merge((long) component.size(), 1L, Long::sum); } for (Map.Entry entry : distribution.entrySet()) { out.format("%d %d\n", entry.getKey(), entry.getValue()); } out.close(); } private static void printLargestComponent(ArrayList> components, Formatter out) { int indexLargest = 0; for (int i = 1; i < components.size(); ++i) { if (components.get(i).size() > components.get(indexLargest).size()) indexLargest = i; } ArrayList component = components.get(indexLargest); for (Long node : component) { out.format("%d\n", node); } out.close(); } private static void printAllComponents(ArrayList> components, Formatter out) { for (int i = 1; i < components.size(); ++i) { ArrayList component = components.get(i); for (Long node : component) { out.format("%d ", node); } out.format("\n"); } out.close(); } public static void main(String[] args) { JSAPResult config = parse_args(args); String graphPath = config.getString("graphPath"); String outdirPath = config.getString("outdir"); String nodeTypes = config.getString("nodeTypes"); + boolean byOrigin = config.getBoolean("byOrigins"); ConnectedComponents connectedComponents = new ConnectedComponents(); try { connectedComponents.load_graph(graphPath, nodeTypes); } catch (IOException e) { System.out.println("Could not load graph: " + e); System.exit(2); } ProgressLogger logger = new ProgressLogger(); // noinspection ResultOfMethodCallIgnored new File(outdirPath).mkdirs(); try { // ArrayList> components = connectedComponents.compute(logger); // components.sort(Comparator.comparing(ArrayList::size).reversed()); // printDistribution(components, new Formatter(outdirPath + "/distribution.txt")); // printLargestComponent(components, new Formatter(outdirPath + "/largest_component.txt")); // printAllComponents(components, new Formatter(outdirPath + "/all_components.txt")); - HashMap componentDistribution = connectedComponents.compute(logger); + HashMap componentDistribution = connectedComponents.compute(logger, byOrigin); PrintWriter f = new PrintWriter(new FileWriter(outdirPath + "/distribution.txt")); TreeMap sortedDistribution = new TreeMap<>(componentDistribution); for (Map.Entry entry : sortedDistribution.entrySet()) { f.println(entry.getKey() + " " + entry.getValue()); } f.close(); } catch (IOException e) { e.printStackTrace(); } logger.done(); } }