Re: RuntimeException Gelly API: Memory ran out. Compaction failed.

[Mihail Vieru]

And the correct SSSPUnweighted attached.

On 17.03.2015 01:23, Mihail Vieru wrote:

Hi,

I'm getting the following RuntimeException for an adaptation of the SingleSourceShortestPaths example using the Gelly API (see attachment). It's been adapted for unweighted graphs having vertices with Long values.

As an input graph I'm using the social network graph (~200MB unpacked) from here: https://snap.stanford.edu/data/higgs-twitter.html

For the small SSSPDataUnweighted graph (also attached) it terminates and computes the distances correctly.

03/16/2015 17:18:23 IterationHead(WorksetIteration (Vertex-centric iteration (org.apache.flink.graph.library.SingleSourceShortestPathsUnweighted$VertexDistanceUpdater@dca6fe4 | org.apache.flink.graph.library.SingleSourceShortestPathsUnweighted$MinDistanceMessenger@6577e8ce)))(2/4) switched to FAILED java.lang.RuntimeException: Memory ran out. Compaction failed. numPartitions: 32 minPartition: 5 maxPartition: 8 number of overflow segments: 176 bucketSize: 217 Overall memory: 20316160 Partition memory: 7208960 Message: Index: 8, Size: 7 at org.apache.flink.runtime.operators.hash.CompactingHashTable.insert(CompactingHashTable.java:390) at org.apache.flink.runtime.operators.hash.CompactingHashTable.buildTable(CompactingHashTable.java:337) at org.apache.flink.runtime.iterative.task.IterationHeadPactTask.readInitialSolutionSet(IterationHeadPactTask.java:216) at org.apache.flink.runtime.iterative.task.IterationHeadPactTask.run(IterationHeadPactTask.java:278) at org.apache.flink.runtime.operators.RegularPactTask.invoke(RegularPactTask.java:362) at org.apache.flink.runtime.execution.RuntimeEnvironment.run(RuntimeEnvironment.java:205)

    at java.lang.Thread.run(Thread.java:745)


Best,
Mihail

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package org.apache.flink.graph.library;

import org.apache.flink.api.common.functions.MapFunction;
import org.apache.flink.graph.Edge;
import org.apache.flink.graph.Graph;
import org.apache.flink.graph.GraphAlgorithm;
import org.apache.flink.graph.Vertex;
import org.apache.flink.graph.spargel.MessageIterator;
import org.apache.flink.graph.spargel.MessagingFunction;
import org.apache.flink.graph.spargel.VertexCentricIteration;
import org.apache.flink.graph.spargel.VertexUpdateFunction;
import org.apache.flink.types.NullValue;

import java.io.Serializable;

@SuppressWarnings("serial")
public class SingleSourceShortestPathsUnweighted<K extends Comparable<K> & Serializable>
		implements GraphAlgorithm<K, Long, NullValue> {

	private final K srcVertexId;
	private final Integer maxIterations;

	public SingleSourceShortestPathsUnweighted(K srcVertexId, Integer maxIterations) {
		this.srcVertexId = srcVertexId;
		this.maxIterations = maxIterations;
	}

	@Override
	public Graph<K, Long, NullValue> run(Graph<K, Long, NullValue> input) {

		Graph<K, Long, NullValue> mappedInput = input.mapVertices(new InitVerticesMapper<K>(srcVertexId));

		VertexCentricIteration<K, Long, Long, NullValue> iteration = mappedInput.createVertexCentricIteration(
				new VertexDistanceUpdater<K>(), new MinDistanceMessenger<K>(), maxIterations);

		return mappedInput.runVertexCentricIteration(iteration);
	}

	public static final class InitVerticesMapper<K extends Comparable<K> & Serializable>
			implements MapFunction<Vertex<K, Long>, Long> {

		private K srcVertexId;

		public InitVerticesMapper(K srcId) {
			this.srcVertexId = srcId;
		}

		public Long map(Vertex<K, Long> value) {
			if (value.f0.equals(srcVertexId)) {
				return 0L;
			} else {
				return 999999999999L;
				//return Long.MAX_VALUE;	// 9223372036854775807L => type overflow
			}
		}
	}

	/**
	 * Function that updates the value of a vertex by picking the minimum
	 * distance from all incoming messages.
	 * 
	 * @param <K>
	 */
	public static final class VertexDistanceUpdater<K extends Comparable<K> & Serializable>
			extends VertexUpdateFunction<K, Long, Long> {

		@Override
		public void updateVertex(K vertexKey, Long vertexValue,
				MessageIterator<Long> inMessages) {

			Long minDistance = 999999999999L;
			//Long minDistance = Long.MAX_VALUE;	// 9223372036854775807L => type overflow

			for (Long msg : inMessages) {
				if (msg < minDistance) {
					minDistance = msg;
				}
			}

			if (vertexValue > minDistance) {
				setNewVertexValue(minDistance);
			}
		}
	}

	/**
	 * Distributes the minimum distance associated with a given vertex among all
	 * the target vertices summed up with the edge's value.
	 * 
	 * @param <K>
	 */
	public static final class MinDistanceMessenger<K extends Comparable<K> & Serializable>
			extends MessagingFunction<K, Long, Long, NullValue> {

		@Override
		public void sendMessages(K vertexKey, Long newDistance)
				throws Exception {
			for (Edge<K, NullValue> edge : getOutgoingEdges()) {
				sendMessageTo(edge.getTarget(), newDistance + 1L); // NullValue => 1L (Long) on edges
				//sendMessageTo(edge.getTarget(), newDistance + edge.getValue());
			}
		}
	}
}