iFub algorithm

src/main/java/ml/grafos/okapi/iFub/LongLongEdgesListInputFormat.java

@@ -0,0 +1,51 @@
+package ml.grafos.okapi.iFub;
+
+import java.io.IOException;
+import java.util.regex.Pattern;
+
+import org.apache.giraph.io.EdgeReader;
+import org.apache.giraph.io.formats.TextEdgeInputFormat;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapreduce.InputSplit;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+public class LongLongEdgesListInputFormat extends
+			TextEdgeInputFormat<LongWritable, NullWritable> {
+		/** Splitter for endpoints */
+		private static final Pattern SEPARATOR = Pattern.compile("[\001\t ]");
+
+		@Override
+		public EdgeReader<LongWritable, NullWritable> createEdgeReader(
+				InputSplit split, TaskAttemptContext context)
+				throws IOException {
+			return new LongLongEdgesReader();
+		}
+
+		public class LongLongEdgesReader extends
+				TextEdgeReaderFromEachLineProcessed<String[]> {
+			@Override
+			protected String[] preprocessLine(Text line) throws IOException {
+				return SEPARATOR.split(line.toString());
+			}
+
+			@Override
+			protected LongWritable getSourceVertexId(String[] endpoints)
+					throws IOException {
+				return new LongWritable(Long.parseLong(endpoints[0]));
+			}
+
+			@Override
+			protected LongWritable getTargetVertexId(String[] endpoints)
+					throws IOException {
+				return new LongWritable(Long.parseLong(endpoints[1]));
+			}
+
+			@Override
+			protected NullWritable getValue(String[] endpoints) throws IOException {
+
+				return NullWritable.get();
+			}
+		}
+	}

src/main/java/ml/grafos/okapi/iFub/MaxDegreeComputation.java

@@ -0,0 +1,47 @@
+/**	
+ * Inria Sophia Antipolis - Team COATI - 2015 
+ * @author Flavian Jacquot
+ * 
+ */
+package ml.grafos.okapi.iFub;
+
+import java.io.IOException;
+
+import org.apache.giraph.graph.BasicComputation;
+import org.apache.giraph.graph.Vertex;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.log4j.Logger;
+/*
+ * This class simply aggregate the degrees with a maxLong aggregator
+ * and aggregate the id of vertices with maximum degree.
+ */
+public class MaxDegreeComputation extends BasicComputation<LongWritable, iFubVertexValue, NullWritable, IntWritable>{
+private Logger LOG = Logger.getLogger(MaxDegreeComputation.class);
+	int maxDegree=1;
+	boolean sourceFound = false;
+	@Override
+		public void preSuperstep() {
+			super.preSuperstep();
+			maxDegree=(int)((LongWritable)getAggregatedValue(iFubMasterCompute.MAX_DEGREE)).get();
+		}
+
+	@Override
+	public void compute(
+			Vertex<LongWritable, iFubVertexValue, NullWritable> vertex,
+			Iterable<IntWritable> messages) throws IOException {
+		if(getSuperstep()==0)
+			aggregate(iFubMasterCompute.MAX_DEGREE, new LongWritable(vertex.getNumEdges()));
+		else
+		{
+			if(vertex.getNumEdges()==maxDegree&&!sourceFound)
+			{
+				sourceFound=true;
+				LOG.info("Source FOUND ! "+vertex.getId());
+				aggregate(iFubMasterCompute.SOURCE_ID, new LongWritable(vertex.getId().get()));
+			}
+		}
+	}
+
+}

src/main/java/ml/grafos/okapi/iFub/README

@@ -0,0 +1,27 @@
+Inria Sophia Antipolis - Team COATI - 2015 - Flavian Jacquot
+
+This folder contains an implementation of the iFub algorithm : an exact algorithm to compute the diameter of undirected graphs.
+It's described in an article at http://www.sciencedirect.com/science/article/pii/S0304397512008687
+
+I've tried it on several graphs from http://snap.stanford.edu/data/ :
+com-amazon 	~1M edges
+com-Friendster	~2B edges
+
+In this folder you can found formats to make an undirected graph.
+The master compute iFubMasterCompute must be declared in the giraph job command with -mc :
+
+Example :
+
+COMPUTE_CLASS="ml.graphos.okapi.iFub.iFubBFSCompute -mc ml.graphos.okapi.iFub.iFubMasterCompute"
+EIF=ml.graphos.okapi.iFub.iFubInputToUndirected
+EIP=data/com-amazon.ungraph.txt
+VOF=org.apache.giraph.io.formats.IdWithValueTextOutputFormat
+OP=output/FS30G.UN.txt
+WORKER=8
+
+$HADOOP_HOME/bin/hadoop jar $GIRAPH_JAR org.apache.giraph.GiraphRunner $COMPUTE_CLASS -eif $EIF -eip $EIP -vof $VOF -op $OP -w $WORKER
+
+The result is printed as a counter in the job trace.
+The number of BFS is also printed.
+
+For any question you can contact me at tki1.50@gmail.com

src/main/java/ml/grafos/okapi/iFub/README~

@@ -0,0 +1,22 @@
+Inria Sophia Antipolis - Team COATI - 2015 - Flavian Jacquot
+
+This folder contains an implementation of the iFub algorithm : an exact algorithm to compute the diameter of undirected graphs.
+It's described in an article at http://www.sciencedirect.com/science/article/pii/S0304397512008687
+
+I've tried it on several graphs from http://snap.stanford.edu/data/ :
+com-amazon 	~1M edges
+com-Friendster	~2B edges
+
+In this folder you can found formats to make an undirected graph.
+The master compute iFubMasterCompute must be declared in the giraph job command with -mc :
+
+Example :
+
+COMPUTE_CLASS="ml.graphos.okapi.iFub.iFubBFSCompute -mc ml.graphos.okapi.iFub.iFubMasterCompute"
+EIF=ml.graphos.okapi.iFub.iFubInputToUndirected
+EIP=data/com-amazon.ungraph.txt
+VOF=org.apache.giraph.io.formats.IdWithValueTextOutputFormat
+OP=output/FS30G.UN.txt
+WORKER=8
+
+$HADOOP_HOME/bin/hadoop jar $GIRAPH_JAR org.apache.giraph.GiraphRunner $COMPUTE_CLASS -eif $EIF -eip $EIP -vof $VOF -op $OP -w $WORKER

src/main/java/ml/grafos/okapi/iFub/ToUndirected.java

@@ -0,0 +1,34 @@
+package ml.grafos.okapi.iFub;
+
+import java.io.IOException;
+
+import org.apache.giraph.edge.EdgeFactory;
+import org.apache.giraph.graph.BasicComputation;
+import org.apache.giraph.graph.Vertex;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+
+public class ToUndirected extends BasicComputation<LongWritable, NullWritable, NullWritable, LongWritable>{
+
+	@Override
+	public void compute(Vertex<LongWritable, NullWritable, NullWritable> vertex, Iterable<LongWritable> inbox) throws IOException {
+		// TODO Auto-generated method stub
+		if(getSuperstep()==0)
+		{
+			sendMessageToAllEdges(vertex, vertex.getId());
+		}
+		else if(getSuperstep()==1)
+		{
+			for(LongWritable sourceId : inbox)
+			{
+				if(vertex.getEdgeValue(sourceId)==null)
+				{
+					vertex.addEdge(EdgeFactory.create(sourceId));
+				}
+			}
+		}
+		vertex.voteToHalt();
+
+	}
+
+}

src/main/java/ml/grafos/okapi/iFub/iFubAssignLayer.java

@@ -0,0 +1,27 @@
+/**	
+ * Inria Sophia Antipolis - Team COATI - 2015 
+ * @author Flavian Jacquot
+ * 
+ */
+package ml.grafos.okapi.iFub;
+/*
+ * This class is used to assign the layer of every vertex and reset the source flag
+ */
+import java.io.IOException;
+
+import org.apache.giraph.graph.BasicComputation;
+import org.apache.giraph.graph.Vertex;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+
+public class iFubAssignLayer extends BasicComputation<LongWritable, iFubVertexValue, NullWritable, IntWritable> {
+
+
+	@Override
+	public void compute(Vertex<LongWritable, iFubVertexValue, NullWritable> vertex, Iterable<IntWritable> arg1) throws IOException {
+		vertex.getValue().setLayer(vertex.getValue().getDistance());
+		vertex.getValue().setSource(false);
+	}
+
+}

src/main/java/ml/grafos/okapi/iFub/iFubBFSCompute.java

@@ -0,0 +1,79 @@
+/**	
+ * Inria Sophia Antipolis - Team COATI - 2015 
+ * @author Flavian Jacquot
+ * 
+ */
+package ml.grafos.okapi.iFub;
+
+import java.io.IOException;
+
+import org.apache.giraph.edge.Edge;
+import org.apache.giraph.graph.BasicComputation;
+import org.apache.giraph.graph.Vertex;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+/*
+ * This class is a version of BFS used in iFub.
+ * There is a cache for the sourceID and the current BFS step=distance from source
+ * The method propagateDistance update the aggregators for the iFub Algorithm
+ */
+public class iFubBFSCompute extends BasicComputation<LongWritable, iFubVertexValue, NullWritable, IntWritable>{
+	private long Source_ID;
+	private long bfsStep;
+
+	private boolean isSource(
+			Vertex<LongWritable, iFubVertexValue, NullWritable> vertex) {
+		return vertex.getId().get() == Source_ID;
+	}
+	@Override
+	public void preSuperstep() {
+		// TODO Auto-generated method stub
+		super.preSuperstep();
+		this.bfsStep = ((LongWritable)getAggregatedValue(iFubMasterCompute.BFS_STEP)).get();
+		if(bfsStep==0)
+			this.Source_ID = ((LongWritable)getAggregatedValue(iFubMasterCompute.SOURCE_ID)).get();
+	}
+	@Override
+	public void compute(
+			Vertex<LongWritable, iFubVertexValue, NullWritable> vertex,
+			Iterable<IntWritable> messages) throws IOException {
+
+		if (bfsStep==0) {
+			if(vertex.getValue()==null)
+			{
+				vertex.setValue(new iFubVertexValue());
+			}
+
+			vertex.getValue().setDistance(Long.MAX_VALUE);
+			if (isSource(vertex)) {
+				vertex.getValue().setSource(true);
+				propagateDistance(vertex);
+			}
+
+		}
+		else
+		{
+			if (messages.iterator().hasNext()
+					&& vertex.getValue().getDistance() == Long.MAX_VALUE) {
+				propagateDistance(vertex);
+			}
+		}
+	}
+
+	private void propagateDistance(
+			Vertex<LongWritable, iFubVertexValue, NullWritable> vertex)
+			throws IOException {
+		aggregate(iFubMasterCompute.NUM_ACTIVE_VERTEX, new LongWritable(1));
+
+		aggregate(iFubMasterCompute.LOWER_B,new LongWritable(bfsStep));
+		vertex.getValue().setDistance(bfsStep);
+		sendMessageToAllEdges(vertex, new IntWritable(0));
+		for(Edge<LongWritable,NullWritable> arrete : vertex.getEdges())
+		{
+			sendMessage(arrete.getTargetVertexId(), new IntWritable(1));
+		}
+	}
+
+
+}

src/main/java/ml/grafos/okapi/iFub/iFubInputToUndirected.java

@@ -0,0 +1,54 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**	
+ * Inria Sophia Antipolis - Team COATI - 2015 
+ * @author Flavian Jacquot
+ * 
+ */
+package ml.grafos.okapi.iFub;
+
+import org.apache.giraph.io.EdgeReader;
+import org.apache.giraph.io.ReverseEdgeDuplicator;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapreduce.InputSplit;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+import cutGraph.LongLongEdgesListInputFormat;
+
+import java.io.IOException;
+
+/**
+ * Simple text-based {@link org.apache.giraph.io.EdgeInputFormat} for
+ * unweighted graphs with long ids.
+ *
+ * Each line consists of: source_vertex target_vertex
+ *
+ * This version also creates the reverse edges.
+ */
+public class iFubInputToUndirected
+    extends LongLongEdgesListInputFormat {
+  @Override
+  public EdgeReader<LongWritable, NullWritable> createEdgeReader(
+      InputSplit split, TaskAttemptContext context) throws IOException {
+    EdgeReader<LongWritable, NullWritable> edgeReader =
+        super.createEdgeReader(split, context);
+    edgeReader.setConf(getConf());
+    return new ReverseEdgeDuplicator<LongWritable, NullWritable>(edgeReader);
+  }
+}