diff --git a/java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java b/java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java new file mode 100644 --- /dev/null +++ b/java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java @@ -0,0 +1,134 @@ +/* + * Copyright (c) 2022 The Software Heritage developers + * See the AUTHORS file at the top-level directory of this distribution + * License: GNU General Public License version 3, or any later version + * See top-level LICENSE file for more information + */ + +package org.softwareheritage.graph.utils; + +import com.martiansoftware.jsap.*; +import it.unimi.dsi.big.webgraph.LazyLongIterator; +import it.unimi.dsi.big.webgraph.NodeIterator; +import org.softwareheritage.graph.*; + +import java.io.IOException; +import java.util.*; + +/* Lists all nodes nodes of the types given as argument, in topological order, + * from leaves (contents, if selected) to the top (origins, if selected). + * + * This uses a DFS, so nodes are likely to be close to their neighbors. + * + * Some extra information is provided to allow more efficient consumption + * of the output: number of ancestors, successors, and a sample of two ancestors. + * + * Sample invocation: + * + * $ java -cp ~/swh-environment/swh-graph/java/target/swh-graph-*.jar -Xmx1000G -XX:PretenureSizeThreshold=512M -XX:MaxNewSize=4G -XX:+UseLargePages -XX:+UseTransparentHugePages -XX:+UseNUMA -XX:+UseTLAB -XX:+ResizeTLAB org.softwareheritage.graph.utils.TopoSort /dev/shm/swh-graph/default/graph 'rev,rel,snp,ori' \ + * | pv --line-mode --wait \ + * | zstdmt \ + * > /poolswh/softwareheritage/vlorentz/2022-04-25_toposort_rev,rel,snp,ori.txt.zst + */ + +public class TopoSort { + private Subgraph graph; + private Subgraph transposedGraph; + + public static void main(String[] args) throws IOException, ClassNotFoundException { + if (args.length != 2) { + System.err.println("Syntax: java org.softwareheritage.graph.utils.TopoSort "); + System.exit(1); + } + String graphPath = args[0]; + String nodeTypes = args[1]; + + TopoSort toposort = new TopoSort(); + + toposort.load_graph(graphPath, nodeTypes); + toposort.toposortDFS(); + } + + public void load_graph(String graphBasename, String nodeTypes) throws IOException { + System.err.println("Loading graph " + graphBasename + " ..."); + var underlyingGraph = SwhBidirectionalGraph.loadMapped(graphBasename); + System.err.println("Selecting subgraphs."); + graph = new Subgraph(underlyingGraph, new AllowedNodes(nodeTypes)); + transposedGraph = graph.transpose(); + System.err.println("Graph loaded."); + } + + /* Prints nodes in topological order, based on a DFS. */ + public void toposortDFS() { + HashSet visited = new HashSet(); + Stack ready = new Stack<>(); + + /* First, push all leaves to the stack */ + System.err.println("Listing leaves."); + long total_nodes = 0; + NodeIterator nodeIterator = graph.nodeIterator(); + for (long currentNodeId = nodeIterator.nextLong(); nodeIterator + .hasNext(); currentNodeId = nodeIterator.nextLong()) { + total_nodes++; + long firstSuccessor = graph.successors(currentNodeId).nextLong(); + if (firstSuccessor != -1) { + /* The node has ancestor, so it is not a leaf. */ + continue; + } + ready.push(currentNodeId); + if (ready.size() % 10000000 == 0) { + float ready_size_f = ready.size(); + float total_nodes_f = total_nodes; + System.err.printf("Listed %.02f B leaves (out of %.02f B nodes)\n", ready_size_f / 1000000000., + total_nodes_f / 1000000000.); + } + } + System.err.println("Leaves loaded, starting DFS."); + + System.out.format("SWHID,ancestors,successors,sample_ancestor1,sample_ancestor2\n"); + while (!ready.isEmpty()) { + long currentNodeId = ready.pop(); + visited.add(currentNodeId); + + /* Find its successors which are ready */ + LazyLongIterator successors = transposedGraph.successors(currentNodeId); + long successorCount = 0; + for (long successorNodeId; (successorNodeId = successors.nextLong()) != -1;) { + successorCount++; + LazyLongIterator successorAncestors = graph.successors(successorNodeId); + boolean isReady = true; + for (long successorAncestorNodeId; (successorAncestorNodeId = successorAncestors.nextLong()) != -1;) { + if (!visited.contains(successorAncestorNodeId)) { + /* + * This ancestor of the successor is not yet visited, so the ancestor is not ready. + */ + isReady = false; + break; + } + } + if (isReady) { + ready.push(successorNodeId); + } + } + + String[] sampleAncestors = {"", ""}; + long ancestorCount = 0; + LazyLongIterator ancestors = graph.successors(currentNodeId); + for (long ancestorNodeId; (ancestorNodeId = ancestors.nextLong()) != -1;) { + if (ancestorCount < sampleAncestors.length) { + sampleAncestors[(int) ancestorCount] = graph.getSWHID(ancestorNodeId).toString(); + } + ancestorCount++; + } + + /* + * Print the node + * + * TODO: print its depth too? + */ + SWHID currentNodeSWHID = graph.getSWHID(currentNodeId); + System.out.format("%s,%d,%d,%s,%s\n", currentNodeSWHID, ancestorCount, successorCount, sampleAncestors[0], + sampleAncestors[1]); + } + } +} diff --git a/swh/graph/luigi.py b/swh/graph/luigi.py --- a/swh/graph/luigi.py +++ b/swh/graph/luigi.py @@ -73,7 +73,8 @@ # WARNING: do not import unnecessary things here to keep cli startup time under # control -from typing import List +from pathlib import Path +from typing import Dict, List import luigi @@ -427,3 +428,51 @@ def _meta(self): return luigi.LocalTarget(self.local_graph_path / "meta" / "compression.json") + + +class TopoSort(luigi.Task): + """Creates a file that contains all SWHIDs in topological order from a compressed + graph.""" + + local_graph_path = luigi.PathParameter() + topological_order_path = luigi.PathParameter() + graph_name = luigi.Parameter(default="graph") + + def requires(self) -> List[luigi.Task]: + """Returns an instance of :class:`LocalGraph`.""" + return [LocalGraph(local_graph_path=self.local_graph_path)] + + def output(self) -> luigi.Target: + """.csv.zst file that contains the topological order.""" + return luigi.LocalTarget(self.topological_order_path) + + def run(self) -> None: + """Runs org.softwareheritage.graph.utils.TopoSort and compresses""" + import os + import subprocess + + from .config import check_config + + conf: Dict = {} # TODO: configurable + + conf = check_config(conf) + env = { + **os.environ.copy(), + "JAVA_TOOL_OPTIONS": conf["java_tool_options"], + "CLASSPATH": conf["classpath"], + } + + tmp_path = Path(f"{self.topological_order_path}.tmp") + + object_types = "rev,rel,snp,ori" + class_name = "org.softwareheritage.graph.utils.TopoSort" + script = f""" + java {class_name} '{self.local_graph_path}/{self.graph_name}' '{object_types}' \ + | pv --line-mode --wait \ + | zstdmt -19 \ + > '{tmp_path}' + """ + subprocess.run(["bash", "-c", script], env=env, check=True) + + # Atomically write the output file + tmp_path.replace(self.topological_order_path) diff --git a/swh/graph/tests/test_toposort.py b/swh/graph/tests/test_toposort.py new file mode 100644 --- /dev/null +++ b/swh/graph/tests/test_toposort.py @@ -0,0 +1,58 @@ +# Copyright (C) 2022 The Software Heritage developers +# See the AUTHORS file at the top-level directory of this distribution +# License: GNU General Public License version 3, or any later version +# See top-level LICENSE file for more information + +from pathlib import Path +import subprocess + +from swh.graph.luigi import TopoSort + +DATA_DIR = Path(__file__).parents[0] / "dataset" + + +EXPECTED_ROWS = """ +swh:1:rev:0000000000000000000000000000000000000003,0,1,, +swh:1:rev:0000000000000000000000000000000000000009,1,3,swh:1:rev:0000000000000000000000000000000000000003, +swh:1:rel:0000000000000000000000000000000000000010,1,1,swh:1:rev:0000000000000000000000000000000000000009, +swh:1:snp:0000000000000000000000000000000000000020,2,1,swh:1:rev:0000000000000000000000000000000000000009,swh:1:rel:0000000000000000000000000000000000000010 +swh:1:ori:83404f995118bd25774f4ac14422a8f175e7a054,1,0,swh:1:snp:0000000000000000000000000000000000000020, +swh:1:rev:0000000000000000000000000000000000000013,1,1,swh:1:rev:0000000000000000000000000000000000000009, +swh:1:rev:0000000000000000000000000000000000000018,1,1,swh:1:rev:0000000000000000000000000000000000000013, +swh:1:rel:0000000000000000000000000000000000000019,1,0,swh:1:rev:0000000000000000000000000000000000000018, +""" + + +def test_toposort(tmpdir): + tmpdir = Path(tmpdir) + + topological_order_path = tmpdir / "topo_order.csv.zst" + + task = TopoSort( + local_graph_path=DATA_DIR / "compressed", + topological_order_path=topological_order_path, + graph_name="example", + ) + + task.run() + + csv_text = subprocess.check_output(["zstdcat", topological_order_path]).decode() + + lines = csv_text.split("\n") + (header, *rows) = lines + assert header == "SWHID,ancestors,successors,sample_ancestor1,sample_ancestor2" + + # The only possible first line + assert rows[0] == "swh:1:rev:0000000000000000000000000000000000000003,0,1,," + + assert set(rows) == set(EXPECTED_ROWS.split("\n")) + + assert rows.pop() == "", "Missing trailing newline" + + # The only two possible last lines + assert rows[-1] in [ + "swh:1:ori:83404f995118bd25774f4ac14422a8f175e7a054,1,0" + ",swh:1:snp:0000000000000000000000000000000000000020,", + "swh:1:rel:0000000000000000000000000000000000000019,1,0" + ",swh:1:rev:0000000000000000000000000000000000000018,", + ]