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From tjungb...@apache.org
Subject svn commit: r1448523 [4/4] - in /hama/trunk: ./ core/src/main/java/org/apache/hama/ core/src/main/java/org/apache/hama/bsp/ core/src/main/java/org/apache/hama/bsp/ft/ core/src/main/java/org/apache/hama/bsp/message/compress/ core/src/main/java/org/apach...
Date Thu, 21 Feb 2013 06:38:36 GMT
Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/PageRank.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/PageRank.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/PageRank.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/PageRank.java Thu Feb 21 06:38:33 2013
@@ -17,8 +17,6 @@
  */
 package org.apache.hama.examples;
 
-import java.io.DataInput;
-import java.io.DataOutput;
 import java.io.IOException;
 import java.util.Iterator;
 
@@ -101,29 +99,6 @@ public class PageRank {
           / numEdges));
     }
 
-    @Override
-    public void readState(DataInput in) throws IOException {
-    }
-
-    @Override
-    public void writeState(DataOutput out) throws IOException {
-    }
-
-    @Override
-    public Text createVertexIDObject() {
-      return new Text();
-    }
-
-    @Override
-    public NullWritable createEdgeCostObject() {
-      return NullWritable.get();
-    }
-
-    @Override
-    public DoubleWritable createVertexValue() {
-      return new DoubleWritable();
-    }
-
   }
 
   public static class DanglingNodeAggregator
@@ -172,7 +147,7 @@ public class PageRank {
       throws IOException {
     GraphJob pageJob = new GraphJob(conf, PageRank.class);
     pageJob.setJobName("Pagerank");
-    
+
     pageJob.setVertexClass(PageRankVertex.class);
     pageJob.setInputPath(new Path(args[0]));
     pageJob.setOutputPath(new Path(args[1]));
@@ -192,7 +167,7 @@ public class PageRank {
 
     // Vertex reader
     pageJob.setVertexInputReaderClass(PagerankSeqReader.class);
-    
+
     pageJob.setVertexIDClass(Text.class);
     pageJob.setVertexValueClass(DoubleWritable.class);
     pageJob.setEdgeValueClass(NullWritable.class);

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/SSSP.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/SSSP.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/SSSP.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/SSSP.java Thu Feb 21 06:38:33 2013
@@ -17,8 +17,6 @@
  */
 package org.apache.hama.examples;
 
-import java.io.DataInput;
-import java.io.DataOutput;
 import java.io.IOException;
 import java.util.Iterator;
 
@@ -73,28 +71,6 @@ public class SSSP {
       }
     }
 
-    @Override
-    public void readState(DataInput in) throws IOException {}
-
-    @Override
-    public void writeState(DataOutput out) throws IOException {}
-
-    @Override
-    public Text createVertexIDObject() {
-      return new Text();
-    }
-
-    @Override
-    public IntWritable createEdgeCostObject() {
-      return new IntWritable();
-    }
-
-    @Override
-    public IntWritable createVertexValue() {
-      return new IntWritable();
-    }
-
-    
   }
 
   public static class MinIntCombiner extends Combiner<IntWritable> {

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/SpMV.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/SpMV.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/SpMV.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/SpMV.java Thu Feb 21 06:38:33 2013
@@ -152,7 +152,7 @@ public class SpMV {
      */
     bsp.setInputFormat(SequenceFileInputFormat.class);
     bsp.setInputKeyClass(IntWritable.class);
-    bsp.setInputValueClass(SparseVectorWritable.class); 
+    bsp.setInputValueClass(SparseVectorWritable.class);
     bsp.setOutputKeyClass(IntWritable.class);
     bsp.setOutputValueClass(DoubleWritable.class);
     bsp.setOutputFormat(SequenceFileOutputFormat.class);

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/util/DenseVectorWritable.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/util/DenseVectorWritable.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/util/DenseVectorWritable.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/util/DenseVectorWritable.java Thu Feb 21 06:38:33 2013
@@ -25,9 +25,9 @@ import org.apache.hadoop.io.Writable;
 
 /**
  * This class represents dense vector. It will improve memory consumption up to
- * two times in comparison to SparseVectorWritable in case of vectors
- * which sparsity is close to 1. Internally represents vector values as array.
- * Can be used in SpMV for representation of input and output vector.
+ * two times in comparison to SparseVectorWritable in case of vectors which
+ * sparsity is close to 1. Internally represents vector values as array. Can be
+ * used in SpMV for representation of input and output vector.
  */
 public class DenseVectorWritable implements Writable {
 
@@ -78,9 +78,9 @@ public class DenseVectorWritable impleme
   @Override
   public String toString() {
     StringBuilder st = new StringBuilder();
-    st.append(" "+getSize()+" "+getSize());
-    for (int i = 0; i < getSize(); i++) 
-      st.append(" "+i+" "+values[i]);
+    st.append(" " + getSize() + " " + getSize());
+    for (int i = 0; i < getSize(); i++)
+      st.append(" " + i + " " + values[i]);
     return st.toString();
   }
 

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/util/Generator.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/util/Generator.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/util/Generator.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/util/Generator.java Thu Feb 21 06:38:33 2013
@@ -30,12 +30,12 @@ public class Generator {
 
     String[] newArgs = new String[args.length - 1];
     System.arraycopy(args, 1, newArgs, 0, args.length - 1);
-    
+
     if (args[0].equals("symmetric")) {
       SymmetricMatrixGen.main(newArgs);
-    } else if(args[0].equals("square")) {
+    } else if (args[0].equals("square")) {
       System.out.println("Not implemented yet.");
-      //SquareMatrixGen.main(newArgs);
+      // SquareMatrixGen.main(newArgs);
     }
   }
 }

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SparseVectorWritable.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SparseVectorWritable.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SparseVectorWritable.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SparseVectorWritable.java Thu Feb 21 06:38:33 2013
@@ -28,8 +28,8 @@ import org.apache.hadoop.io.Writable;
 /**
  * This class represents sparse vector. It will give improvement in memory
  * consumption in case of vectors which sparsity is close to zero. Can be used
- * in SpMV for representing input matrix rows efficiently. Internally
- * represents values as list of indeces and list of values.
+ * in SpMV for representing input matrix rows efficiently. Internally represents
+ * values as list of indeces and list of values.
  */
 public class SparseVectorWritable implements Writable {
 
@@ -41,10 +41,10 @@ public class SparseVectorWritable implem
     indeces = new ArrayList<Integer>();
     values = new ArrayList<Double>();
   }
-  
-  public void clear(){
+
+  public void clear() {
     indeces = new ArrayList<Integer>();
-    values = new ArrayList<Double>();    
+    values = new ArrayList<Double>();
   }
 
   public void addCell(int index, double value) {
@@ -96,10 +96,10 @@ public class SparseVectorWritable implem
   @Override
   public String toString() {
     StringBuilder st = new StringBuilder();
-    st.append(" "+getSize()+" "+indeces.size());
-    for (int i = 0; i < indeces.size(); i++) 
-      st.append(" "+indeces.get(i)+" "+values.get(i));
+    st.append(" " + getSize() + " " + indeces.size());
+    for (int i = 0; i < indeces.size(); i++)
+      st.append(" " + indeces.get(i) + " " + values.get(i));
     return st.toString();
   }
 
-}
\ No newline at end of file
+}

Modified: hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SymmetricMatrixGen.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SymmetricMatrixGen.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SymmetricMatrixGen.java (original)
+++ hama/trunk/examples/src/main/java/org/apache/hama/examples/util/SymmetricMatrixGen.java Thu Feb 21 06:38:33 2013
@@ -82,12 +82,12 @@ public class SymmetricMatrixGen {
           boolean nonZero = new Random().nextInt(density) == 0;
           if (nonZero && !edges.contains(j) && i != j) {
             edges.add(j);
-            
+
             // allocate remainders to the last task
             int peerIndex = j / interval;
-            if(peerIndex == peer.getNumPeers())
+            if (peerIndex == peer.getNumPeers())
               peerIndex = peerIndex - 1;
-            
+
             peer.send(peer.getPeerName(peerIndex), new Text(j + "," + i));
           }
         }

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/CombineExampleTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/CombineExampleTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/CombineExampleTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/CombineExampleTest.java Thu Feb 21 06:38:33 2013
@@ -17,10 +17,10 @@
  */
 package org.apache.hama.examples;
 
-import org.junit.Test;
-
 import static org.junit.Assert.fail;
 
+import org.junit.Test;
+
 /**
  * Testcase for {@link org.apache.hama.examples.CombineExample}
  */

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/LinearRegressionTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/LinearRegressionTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/LinearRegressionTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/LinearRegressionTest.java Thu Feb 21 06:38:33 2013
@@ -25,7 +25,8 @@ import org.junit.Test;
 public class LinearRegressionTest {
   @Test
   public void testCorrectGDWithLinearRegressionExecution() throws Exception {
-    GradientDescentExample.main(new String[]{"src/test/resources/linear_regression_sample.txt", "linear"});
+    GradientDescentExample.main(new String[] {
+        "src/test/resources/linear_regression_sample.txt", "linear" });
   }
 
 }

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/LogisticRegressionTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/LogisticRegressionTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/LogisticRegressionTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/LogisticRegressionTest.java Thu Feb 21 06:38:33 2013
@@ -20,12 +20,14 @@ package org.apache.hama.examples;
 import org.junit.Test;
 
 /**
- * Testcase for {@link GradientDescentExample} execution for 'logistic regression'
+ * Testcase for {@link GradientDescentExample} execution for 'logistic
+ * regression'
  */
 public class LogisticRegressionTest {
 
   @Test
   public void testCorrectGDWithLogisticRegressionExecution() throws Exception {
-    GradientDescentExample.main(new String[]{"src/test/resources/logistic_regression_sample.txt", "logistic"});
+    GradientDescentExample.main(new String[] {
+        "src/test/resources/logistic_regression_sample.txt", "logistic" });
   }
 }

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/MindistSearchTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/MindistSearchTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/MindistSearchTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/MindistSearchTest.java Thu Feb 21 06:38:33 2013
@@ -29,13 +29,15 @@ import org.apache.hadoop.conf.Configurat
 import org.apache.hadoop.fs.FileStatus;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
 import org.apache.hama.HamaConfiguration;
+import org.apache.hama.bsp.SequenceFileInputFormat;
 import org.apache.hama.examples.MindistSearch.MinTextCombiner;
-import org.apache.hama.examples.MindistSearch.MindistSearchVertex;
-import org.apache.hama.graph.Edge;
+import org.apache.hama.graph.GraphJob;
+
+import com.google.common.base.Optional;
 
 public class MindistSearchTest extends TestCase {
 
@@ -60,7 +62,12 @@ public class MindistSearchTest extends T
   public void testMindistSearch() throws Exception {
     generateTestData();
     try {
-      MindistSearch.main(new String[] { INPUT, OUTPUT, "30", "3" });
+      GraphJob job = MindistSearch.getJob(INPUT, OUTPUT, Optional.of(3),
+          Optional.of(30));
+      job.setInputFormat(SequenceFileInputFormat.class);
+      job.setInputKeyClass(LongWritable.class);
+      job.setInputValueClass(Text.class);
+      assertTrue(job.waitForCompletion(true));
 
       verifyResult();
     } finally {
@@ -99,18 +106,10 @@ public class MindistSearchTest extends T
   private void generateTestData() {
     try {
       SequenceFile.Writer writer = SequenceFile.createWriter(fs, conf,
-          new Path(INPUT), MindistSearchVertex.class, NullWritable.class);
+          new Path(INPUT), LongWritable.class, Text.class);
 
       for (int i = 0; i < input.length; i++) {
-        String[] x = input[i].split("\t");
-        Text key = new Text(x[0]);
-        MindistSearchVertex vertex = new MindistSearchVertex();
-        vertex.setVertexID(key);
-        for (int j = 1; j < x.length; j++) {
-          vertex.addEdge(new Edge<Text, NullWritable>(new Text(x[j]),
-              NullWritable.get()));
-        }
-        writer.append(vertex, NullWritable.get());
+        writer.append(new LongWritable(i), new Text(input[i]));
       }
 
       writer.close();

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/PiEstimatorTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/PiEstimatorTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/PiEstimatorTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/PiEstimatorTest.java Thu Feb 21 06:38:33 2013
@@ -17,10 +17,10 @@
  */
 package org.apache.hama.examples;
 
-import org.junit.Test;
-
 import static org.junit.Assert.fail;
 
+import org.junit.Test;
+
 /**
  * Testcase for {@link PiEstimator}
  */

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/RandBenchTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/RandBenchTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/RandBenchTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/RandBenchTest.java Thu Feb 21 06:38:33 2013
@@ -17,10 +17,10 @@
  */
 package org.apache.hama.examples;
 
-import org.junit.Test;
-
 import static org.junit.Assert.fail;
 
+import org.junit.Test;
+
 /**
  * Testcase for {@link org.apache.hama.examples.RandBench}
  */

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/SSSPTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/SSSPTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/SSSPTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/SSSPTest.java Thu Feb 21 06:38:33 2013
@@ -37,17 +37,9 @@ import org.apache.hama.HamaConfiguration
  * Testcase for {@link ShortestPaths}
  */
 public class SSSPTest extends TestCase {
-  String[] input = new String[] { 
-      "1:85\t2:217\t4:173", 
-      "0:85\t5:80",
-      "0:217\t6:186\t7:103", 
-      "7:183", 
-      "0:173\t9:502", 
-      "1:80\t8:250", 
-      "2:186",
-      "3:183\t9:167\t2:103", 
-      "5:250\t9:84", 
-      "4:502\t7:167\t8:84" };
+  String[] input = new String[] { "1:85\t2:217\t4:173", "0:85\t5:80",
+      "0:217\t6:186\t7:103", "7:183", "0:173\t9:502", "1:80\t8:250", "2:186",
+      "3:183\t9:167\t2:103", "5:250\t9:84", "4:502\t7:167\t8:84" };
 
   private static String INPUT = "/tmp/sssp-tmp.seq";
   private static String TEXT_INPUT = "/tmp/sssp.txt";

Modified: hama/trunk/examples/src/test/java/org/apache/hama/examples/SymmetricMatrixGenTest.java
URL: http://svn.apache.org/viewvc/hama/trunk/examples/src/test/java/org/apache/hama/examples/SymmetricMatrixGenTest.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/examples/src/test/java/org/apache/hama/examples/SymmetricMatrixGenTest.java (original)
+++ hama/trunk/examples/src/test/java/org/apache/hama/examples/SymmetricMatrixGenTest.java Thu Feb 21 06:38:33 2013
@@ -31,16 +31,14 @@ import org.apache.hama.examples.util.Sym
 import org.junit.Test;
 
 public class SymmetricMatrixGenTest {
-  protected static Log LOG = LogFactory
-      .getLog(SymmetricMatrixGenTest.class);
+  protected static Log LOG = LogFactory.getLog(SymmetricMatrixGenTest.class);
   private static String TEST_OUTPUT = "/tmp/test";
 
   @Test
   public void testGraphGenerator() throws Exception {
     Configuration conf = new Configuration();
 
-    SymmetricMatrixGen
-        .main(new String[] { "20", "10", TEST_OUTPUT, "3" });
+    SymmetricMatrixGen.main(new String[] { "20", "10", TEST_OUTPUT, "3" });
     FileSystem fs = FileSystem.get(conf);
 
     FileStatus[] globStatus = fs.globStatus(new Path(TEST_OUTPUT + "/part-*"));

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/AbstractAggregator.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/AbstractAggregator.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/AbstractAggregator.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/AbstractAggregator.java Thu Feb 21 06:38:33 2013
@@ -87,7 +87,7 @@ public abstract class AbstractAggregator
   public IntWritable getTimesAggregated() {
     return new IntWritable(timesAggregated);
   }
-  
+
   @Override
   public String toString() {
     return "VAL=" + getValue();

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/AggregationRunner.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/AggregationRunner.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/AggregationRunner.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/AggregationRunner.java Thu Feb 21 06:38:33 2013
@@ -24,6 +24,7 @@ import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.util.ReflectionUtils;
 import org.apache.hama.bsp.BSPPeer;
 import org.apache.hama.bsp.sync.SyncException;
@@ -35,7 +36,7 @@ import com.google.common.base.Preconditi
  * configured.
  * 
  */
-public final class AggregationRunner<V extends Writable, E extends Writable, M extends Writable> {
+public final class AggregationRunner<V extends WritableComparable<V>, E extends Writable, M extends Writable> {
 
   // multiple aggregator arrays
   private Aggregator<M, Vertex<V, E, M>>[] aggregators;

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/Edge.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/Edge.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/Edge.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/Edge.java Thu Feb 21 06:38:33 2013
@@ -19,11 +19,12 @@ package org.apache.hama.graph;
 
 import org.apache.hadoop.io.NullWritable;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 
 /**
  * The edge class
  */
-public final class Edge<VERTEX_ID extends Writable, EDGE_VALUE_TYPE extends Writable> {
+public final class Edge<VERTEX_ID extends WritableComparable<? super VERTEX_ID>, EDGE_VALUE_TYPE extends Writable> {
   private final VERTEX_ID destinationVertexID;
   private final EDGE_VALUE_TYPE cost;
 

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJob.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJob.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJob.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJob.java Thu Feb 21 06:38:33 2013
@@ -42,6 +42,7 @@ public class GraphJob extends BSPJob {
 
   public final static String AGGREGATOR_CLASS_ATTR = "hama.graph.aggregator.class";
   public final static String VERTEX_MESSAGE_COMBINER_CLASS_ATTR = "hama.vertex.message.combiner.class";
+
   /**
    * Creates a new Graph Job with the given configuration and an exampleClass.
    * The exampleClass is used to determine the user's jar to distribute in the
@@ -169,6 +170,13 @@ public class GraphJob extends BSPJob {
         .checkArgument(this.getConfiguration()
             .get(VERTEX_EDGE_VALUE_CLASS_ATTR) != null,
             "Please provide an edge value class, if you don't need one, use NullWritable!");
+
+    Preconditions
+        .checkArgument(
+            this.getConfiguration().get(
+                Constants.RUNTIME_PARTITION_RECORDCONVERTER) != null,
+            "Please provide a converter class for your vertex by using GraphJob#setVertexInputReaderClass!");
+
     super.submit();
   }
 

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobMessage.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobMessage.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobMessage.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobMessage.java Thu Feb 21 06:38:33 2013
@@ -26,6 +26,7 @@ import java.util.List;
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.util.ReflectionUtils;
 
 /**
@@ -41,13 +42,6 @@ public final class GraphJobMessage imple
   public static final int PARTITION_FLAG = 0x08;
   public static final int VERTICES_SIZE_FLAG = 0x10;
 
-  // staticly defined because it is process-wide information, therefore in caps
-  // considered as a constant
-  public static Class<?> VERTEX_CLASS;
-  public static Class<? extends Writable> VERTEX_ID_CLASS;
-  public static Class<? extends Writable> VERTEX_VALUE_CLASS;
-  public static Class<? extends Writable> EDGE_VALUE_CLASS;
-
   // default flag to -1 "unknown"
   private int flag = -1;
   private MapWritable map;
@@ -127,45 +121,49 @@ public final class GraphJobMessage imple
   public void readFields(DataInput in) throws IOException {
     flag = in.readByte();
     if (isVertexMessage()) {
-      vertexId = ReflectionUtils.newInstance(VERTEX_ID_CLASS, null);
+      vertexId = GraphJobRunner.createVertexIDObject();
       vertexId.readFields(in);
-      vertexValue = ReflectionUtils.newInstance(VERTEX_VALUE_CLASS, null);
+      vertexValue = GraphJobRunner.createVertexValue();
       vertexValue.readFields(in);
     } else if (isMapMessage()) {
       map = new MapWritable();
       map.readFields(in);
     } else if (isPartitioningMessage()) {
-      Vertex<Writable, Writable, Writable> vertex = GraphJobRunner
-          .newVertexInstance(VERTEX_CLASS, null);
-      Writable vertexId = ReflectionUtils.newInstance(VERTEX_ID_CLASS, null);
+      Vertex<WritableComparable<Writable>, Writable, Writable> vertex = GraphJobRunner
+          .newVertexInstance(GraphJobRunner.VERTEX_CLASS);
+      WritableComparable<Writable> vertexId = GraphJobRunner
+          .createVertexIDObject();
       vertexId.readFields(in);
       vertex.setVertexID(vertexId);
       if (in.readBoolean()) {
-        Writable vertexValue = ReflectionUtils.newInstance(VERTEX_VALUE_CLASS,
-            null);
+        Writable vertexValue = GraphJobRunner.createVertexValue();
         vertexValue.readFields(in);
         vertex.setValue(vertexValue);
       }
       int size = in.readInt();
-      vertex.setEdges(new ArrayList<Edge<Writable, Writable>>(size));
+      vertex
+          .setEdges(new ArrayList<Edge<WritableComparable<Writable>, Writable>>(
+              size));
       for (int i = 0; i < size; i++) {
-        Writable edgeVertexID = ReflectionUtils.newInstance(VERTEX_ID_CLASS,
-            null);
+        WritableComparable<Writable> edgeVertexID = GraphJobRunner
+            .createVertexIDObject();
         edgeVertexID.readFields(in);
         Writable edgeValue = null;
         if (in.readBoolean()) {
-          edgeValue = ReflectionUtils.newInstance(EDGE_VALUE_CLASS, null);
+          edgeValue = GraphJobRunner.createEdgeCostObject();
           edgeValue.readFields(in);
         }
         vertex.getEdges().add(
-            new Edge<Writable, Writable>(edgeVertexID, edgeValue));
+            new Edge<WritableComparable<Writable>, Writable>(edgeVertexID,
+                edgeValue));
       }
       this.vertex = vertex;
     } else if (isVerticesSizeMessage()) {
       vertices_size = new IntWritable();
       vertices_size.readFields(in);
     } else {
-      vertexId = ReflectionUtils.newInstance(VERTEX_ID_CLASS, null);
+      vertexId = ReflectionUtils.newInstance(GraphJobRunner.VERTEX_ID_CLASS,
+          null);
       vertexId.readFields(in);
     }
   }

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java Thu Feb 21 06:38:33 2013
@@ -32,7 +32,7 @@ import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.util.ReflectionUtils;
+import org.apache.hadoop.io.WritableComparable;
 import org.apache.hama.bsp.BSP;
 import org.apache.hama.bsp.BSPPeer;
 import org.apache.hama.bsp.Combiner;
@@ -40,6 +40,7 @@ import org.apache.hama.bsp.HashPartition
 import org.apache.hama.bsp.Partitioner;
 import org.apache.hama.bsp.sync.SyncException;
 import org.apache.hama.util.KeyValuePair;
+import org.apache.hama.util.ReflectionUtils;
 
 /**
  * Fully generic graph job runner.
@@ -48,7 +49,7 @@ import org.apache.hama.util.KeyValuePair
  * @param <E> the value type of an edge.
  * @param <M> the value type of a vertex.
  */
-public final class GraphJobRunner<V extends Writable, E extends Writable, M extends Writable>
+public final class GraphJobRunner<V extends WritableComparable<V>, E extends Writable, M extends Writable>
     extends BSP<Writable, Writable, Writable, Writable, GraphJobMessage> {
 
   public static enum GraphJobCounter {
@@ -63,14 +64,19 @@ public final class GraphJobRunner<V exte
   public static final String S_FLAG_AGGREGATOR_INCREMENT = "hama.2";
   public static final Text FLAG_MESSAGE_COUNTS = new Text(S_FLAG_MESSAGE_COUNTS);
 
-  public static final String MESSAGE_COMBINER_CLASS = "hama.vertex.message.combiner.class";
-  public static final String GRAPH_REPAIR = "hama.graph.repair";
-  public static final String VERTEX_CLASS = "hama.graph.vertex.class";
+  public static final String MESSAGE_COMBINER_CLASS_KEY = "hama.vertex.message.combiner.class";
+  public static final String VERTEX_CLASS_KEY = "hama.graph.vertex.class";
 
   private Configuration conf;
   private Combiner<M> combiner;
   private Partitioner<V, M> partitioner;
 
+  public static Class<?> VERTEX_CLASS;
+  public static Class<? extends WritableComparable<?>> VERTEX_ID_CLASS;
+  public static Class<? extends Writable> VERTEX_VALUE_CLASS;
+  public static Class<? extends Writable> EDGE_VALUE_CLASS;
+  public static Class<Vertex<?, ?, ?>> vertexClass;
+
   private VerticesInfo<V, E, M> vertices;
   private boolean updated = true;
   private int globalUpdateCounts = 0;
@@ -80,8 +86,6 @@ public final class GraphJobRunner<V exte
   private int maxIteration = -1;
   private long iteration;
 
-  private Class<Vertex<V, E, M>> vertexClass;
-
   private AggregationRunner<V, E, M> aggregationRunner;
 
   private BSPPeer<Writable, Writable, Writable, Writable, GraphJobMessage> peer;
@@ -109,7 +113,8 @@ public final class GraphJobRunner<V exte
     // we do supersteps while we still have updates and have not reached our
     // maximum iterations yet
     while (updated && !((maxIteration > 0) && iteration > maxIteration)) {
-      // reset the global update counter from our master in every superstep
+      // reset the global update counter from our master in every
+      // superstep
       globalUpdateCounts = 0;
       peer.sync();
 
@@ -229,33 +234,20 @@ public final class GraphJobRunner<V exte
     maxIteration = peer.getConfiguration().getInt("hama.graph.max.iteration",
         -1);
 
-      Class<V> vertexIdClass = (Class<V>) conf.getClass(GraphJob.VERTEX_ID_CLASS_ATTR,
-              Text.class, Writable.class);
-      Class<M> vertexValueClass = (Class<M>) conf.getClass(
-              GraphJob.VERTEX_VALUE_CLASS_ATTR, IntWritable.class, Writable.class);
-      Class<E> edgeValueClass = (Class<E>) conf.getClass(
-              GraphJob.VERTEX_EDGE_VALUE_CLASS_ATTR, IntWritable.class,
-              Writable.class);
-    vertexClass = (Class<Vertex<V, E, M>>) conf.getClass(
-        "hama.graph.vertex.class", Vertex.class);
+    initClasses(conf);
 
-    // set the classes statically, so we can save memory per message
-    GraphJobMessage.VERTEX_ID_CLASS = vertexIdClass;
-    GraphJobMessage.VERTEX_VALUE_CLASS = vertexValueClass;
-    GraphJobMessage.VERTEX_CLASS = vertexClass;
-    GraphJobMessage.EDGE_VALUE_CLASS = edgeValueClass;
-
-    partitioner = (Partitioner<V, M>) ReflectionUtils.newInstance(
-        conf.getClass("bsp.input.partitioner.class", HashPartitioner.class),
-        conf);
+    partitioner = (Partitioner<V, M>) org.apache.hadoop.util.ReflectionUtils
+        .newInstance(
+            conf.getClass("bsp.input.partitioner.class", HashPartitioner.class),
+            conf);
 
-    if (!conf.getClass(MESSAGE_COMBINER_CLASS, Combiner.class).equals(
+    if (!conf.getClass(MESSAGE_COMBINER_CLASS_KEY, Combiner.class).equals(
         Combiner.class)) {
-      LOG.debug("Combiner class: " + conf.get(MESSAGE_COMBINER_CLASS));
+      LOG.debug("Combiner class: " + conf.get(MESSAGE_COMBINER_CLASS_KEY));
 
-      combiner = (Combiner<M>) ReflectionUtils.newInstance(
-          conf.getClass("hama.vertex.message.combiner.class", Combiner.class),
-          conf);
+      combiner = (Combiner<M>) org.apache.hadoop.util.ReflectionUtils
+          .newInstance(conf.getClass("hama.vertex.message.combiner.class",
+              Combiner.class), conf);
     }
 
     aggregationRunner = new AggregationRunner<V, E, M>();
@@ -264,6 +256,26 @@ public final class GraphJobRunner<V exte
     vertices = new VerticesInfo<V, E, M>();
   }
 
+  @SuppressWarnings("unchecked")
+  public static <V extends WritableComparable<V>, E extends Writable, M extends Writable> void initClasses(
+      Configuration conf) {
+    Class<V> vertexIdClass = (Class<V>) conf.getClass(
+        GraphJob.VERTEX_ID_CLASS_ATTR, Text.class, Writable.class);
+    Class<M> vertexValueClass = (Class<M>) conf.getClass(
+        GraphJob.VERTEX_VALUE_CLASS_ATTR, IntWritable.class, Writable.class);
+    Class<E> edgeValueClass = (Class<E>) conf.getClass(
+        GraphJob.VERTEX_EDGE_VALUE_CLASS_ATTR, IntWritable.class,
+        Writable.class);
+    vertexClass = (Class<Vertex<?, ?, ?>>) conf.getClass(
+        "hama.graph.vertex.class", Vertex.class);
+
+    // set the classes statically, so we can save memory per message
+    VERTEX_ID_CLASS = vertexIdClass;
+    VERTEX_VALUE_CLASS = vertexValueClass;
+    VERTEX_CLASS = vertexClass;
+    EDGE_VALUE_CLASS = edgeValueClass;
+  }
+
   /**
    * Loads vertices into memory of each peer.
    */
@@ -271,8 +283,6 @@ public final class GraphJobRunner<V exte
   private void loadVertices(
       BSPPeer<Writable, Writable, Writable, Writable, GraphJobMessage> peer)
       throws IOException, SyncException, InterruptedException {
-    final boolean repairNeeded = conf.getBoolean(GRAPH_REPAIR, false);
-
     final boolean selfReference = conf.getBoolean("hama.graph.self.ref", false);
 
     if (LOG.isDebugEnabled())
@@ -289,70 +299,13 @@ public final class GraphJobRunner<V exte
       }
     }
 
-    LOG.info(vertices.size() + " vertices are loaded into " + peer.getPeerName());
-
-    /*
-     * If the user want to repair the graph, it should traverse through that
-     * local chunk of adjancency list and message the corresponding peer to
-     * check whether that vertex exists. In real-life this may be dead-ending
-     * vertices, since we have no information about outgoing edges. Mainly this
-     * procedure is to prevent NullPointerExceptions from happening.
-     */
-    if (repairNeeded) {
-      if (LOG.isDebugEnabled())
-        LOG.debug("Starting repair of this graph!");
-      repair(peer, selfReference);
-    }
+    LOG.info(vertices.size() + " vertices are loaded into "
+        + peer.getPeerName());
 
     if (LOG.isDebugEnabled())
       LOG.debug("Starting Vertex processing!");
   }
 
-  @SuppressWarnings("unchecked")
-  private void repair(
-      BSPPeer<Writable, Writable, Writable, Writable, GraphJobMessage> peer,
-      boolean selfReference) throws IOException, SyncException,
-      InterruptedException {
-
-    Map<V, Vertex<V, E, M>> tmp = new HashMap<V, Vertex<V, E, M>>();
-
-    for (Vertex<V, E, M> v : vertices) {
-      for (Edge<V, E> e : v.getEdges()) {
-        peer.send(v.getDestinationPeerName(e),
-            new GraphJobMessage(e.getDestinationVertexID()));
-      }
-    }
-
-    peer.sync();
-    GraphJobMessage msg;
-    while ((msg = peer.getCurrentMessage()) != null) {
-      V vertexName = (V) msg.getVertexId();
-
-      Vertex<V, E, M> newVertex = newVertexInstance(vertexClass, conf);
-      newVertex.setVertexID(vertexName);
-      newVertex.runner = this;
-      if (selfReference) {
-        newVertex.setEdges(Collections.singletonList(new Edge<V, E>(newVertex
-            .getVertexID(), null)));
-      } else {
-        newVertex.setEdges(new ArrayList<Edge<V, E>>(0));
-      }
-      newVertex.setup(conf);
-      tmp.put(vertexName, newVertex);
-    }
-
-    for (Vertex<V, E, M> e : vertices) {
-      if (tmp.containsKey((e.getVertexID()))) {
-        tmp.remove(e.getVertexID());
-      }
-    }
-
-    for (Vertex<V, E, M> v : tmp.values()) {
-      vertices.addVertex(v);
-    }
-    tmp.clear();
-  }
-
   /**
    * Counts vertices globally by sending the count of vertices in the map to the
    * other peers.
@@ -505,10 +458,36 @@ public final class GraphJobRunner<V exte
   /**
    * @return a new vertex instance
    */
-  public static <V extends Writable, E extends Writable, M extends Writable> Vertex<V, E, M> newVertexInstance(
-      Class<?> vertexClass, Configuration conf) {
-    return (Vertex<V, E, M>) ReflectionUtils.newInstance(
-        vertexClass, conf);
+  @SuppressWarnings({ "unchecked" })
+  public static <V extends WritableComparable<? super V>, E extends Writable, M extends Writable> Vertex<V, E, M> newVertexInstance(
+      Class<?> vertexClass) {
+    return (Vertex<V, E, M>) ReflectionUtils.newInstance(vertexClass);
+  }
+
+  // following new instances don't need conf injects.
+
+  /**
+   * @return a new vertex id object.
+   */
+  @SuppressWarnings("unchecked")
+  public static <X extends Writable> X createVertexIDObject() {
+    return (X) ReflectionUtils.newInstance(VERTEX_ID_CLASS);
+  }
+
+  /**
+   * @return a new vertex value object.
+   */
+  @SuppressWarnings("unchecked")
+  public static <X extends Writable> X createVertexValue() {
+    return (X) ReflectionUtils.newInstance(VERTEX_VALUE_CLASS);
+  }
+
+  /**
+   * @return a new edge cost object.
+   */
+  @SuppressWarnings("unchecked")
+  public static <X extends Writable> X createEdgeCostObject() {
+    return (X) ReflectionUtils.newInstance(EDGE_VALUE_CLASS);
   }
 
 }

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/Vertex.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/Vertex.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/Vertex.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/Vertex.java Thu Feb 21 06:38:33 2013
@@ -20,12 +20,13 @@ package org.apache.hama.graph;
 import java.io.DataInput;
 import java.io.DataOutput;
 import java.io.IOException;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 import org.apache.hama.bsp.BSPPeer;
 import org.apache.hama.bsp.Partitioner;
 
@@ -45,7 +46,7 @@ import org.apache.hama.bsp.Partitioner;
  * @param <E> Edge cost object type
  * @param <M> Vertex value object type
  */
-public abstract class Vertex<V extends Writable, E extends Writable, M extends Writable>
+public abstract class Vertex<V extends WritableComparable<? super V>, E extends Writable, M extends Writable>
     implements VertexInterface<V, E, M>, Writable {
 
   GraphJobRunner<?, ?, ?> runner;
@@ -92,7 +93,7 @@ public abstract class Vertex<V extends W
         getPartitioner().getPartition(vertexId, value,
             runner.getPeer().getNumPeers()));
   }
-  
+
   @Override
   public void sendMessageToNeighbors(M msg) throws IOException {
     final List<Edge<V, E>> outEdges = this.getEdges();
@@ -121,7 +122,7 @@ public abstract class Vertex<V extends W
 
   public void addEdge(Edge<V, E> edge) {
     if (edges == null) {
-      this.edges = new LinkedList<Edge<V, E>>();
+      this.edges = new ArrayList<Edge<V, E>>();
     }
     this.edges.add(edge);
   }
@@ -243,26 +244,26 @@ public abstract class Vertex<V extends W
   public void readFields(DataInput in) throws IOException {
     if (in.readBoolean()) {
       if (vertexID == null) {
-        vertexID = createVertexIDObject();
+        vertexID = GraphJobRunner.createVertexIDObject();
       }
       vertexID.readFields(in);
     }
     if (in.readBoolean()) {
       if (this.value == null) {
-        value = createVertexValue();
+        value = GraphJobRunner.createVertexValue();
       }
       value.readFields(in);
     }
-    this.edges = new LinkedList<Edge<V, E>>();
+    this.edges = new ArrayList<Edge<V, E>>();
     if (in.readBoolean()) {
       int num = in.readInt();
       if (num > 0) {
         for (int i = 0; i < num; ++i) {
-          V vertex = createVertexIDObject();
+          V vertex = GraphJobRunner.createVertexIDObject();
           vertex.readFields(in);
           E edgeCost = null;
           if (in.readBoolean()) {
-            edgeCost = this.createEdgeCostObject();
+            edgeCost = GraphJobRunner.createEdgeCostObject();
             edgeCost.readFields(in);
           }
           Edge<V, E> edge = new Edge<V, E>(vertex, edgeCost);
@@ -310,49 +311,23 @@ public abstract class Vertex<V extends W
   }
 
   /**
-   * Create the vertex id object. This function is used by the framework to
-   * construct the vertex id object.
-   * 
-   * @return instance of V
-   */
-  public abstract V createVertexIDObject();
-
-  /**
-   * Create the Edge cost object. This function is used by the framework to
-   * construct the edge cost object
-   * 
-   * @return instance of E
-   */
-  public abstract E createEdgeCostObject();
-
-  /**
-   * Create the vertex value object. This function is used by the framework to
-   * construct the vertex value object.
-   * 
-   * @return
-   */
-  public abstract M createVertexValue();
-
-  /**
    * Read the state of the vertex from the input stream. The framework would
    * have already constructed and loaded the vertex-id, edges and voteToHalt
    * state. This function is essential if there is any more properties of vertex
    * to be read from.
-   * 
-   * @param in
-   * @throws IOException
    */
-  public abstract void readState(DataInput in) throws IOException;
+  public void readState(DataInput in) throws IOException {
+
+  }
 
   /**
    * Writes the state of vertex to the output stream. The framework writes the
    * vertex and edge information to the output stream. This function could be
    * used to save the state variable of the vertex added in the implementation
    * of object.
-   * 
-   * @param out
-   * @throws IOException
    */
-  public abstract void writeState(DataOutput out) throws IOException;
+  public void writeState(DataOutput out) throws IOException {
+
+  }
 
 }

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInputReader.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInputReader.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInputReader.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInputReader.java Thu Feb 21 06:38:33 2013
@@ -22,6 +22,7 @@ import org.apache.commons.logging.LogFac
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.io.NullWritable;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 import org.apache.hama.bsp.BSPPeer;
 import org.apache.hama.bsp.Partitioner;
 import org.apache.hama.bsp.PartitioningRunner.RecordConverter;
@@ -29,12 +30,25 @@ import org.apache.hama.util.KeyValuePair
 
 /**
  * A reader to read Hama's input files and parses a vertex out of it.
+ * 
+ * 
+ * @param <KEYIN> the input format's KEYIN type.
+ * @param <VALUEIN> the input format's VALUE_IN type.
+ * @param <V> the vertex id type.
+ * @param <E> the Edge cost object type.
+ * @param <M> the Vertex value/message object type.
  */
-public abstract class VertexInputReader<KEYIN extends Writable, VALUEIN extends Writable, V extends Writable, E extends Writable, M extends Writable>
+public abstract class VertexInputReader<KEYIN extends Writable, VALUEIN extends Writable, V extends WritableComparable<? super V>, E extends Writable, M extends Writable>
     implements RecordConverter {
 
   private static final Log LOG = LogFactory.getLog(VertexInputReader.class);
 
+  @Override
+  public void setup(Configuration conf) {
+    // initialize the usual vertex structures for read/write methods
+    GraphJobRunner.initClasses(conf);
+  }
+
   private final KeyValuePair<Writable, Writable> outputRecord = new KeyValuePair<Writable, Writable>();
 
   /**
@@ -52,8 +66,7 @@ public abstract class VertexInputReader<
     Class<Vertex<V, E, M>> vertexClass = (Class<Vertex<V, E, M>>) conf
         .getClass(GraphJob.VERTEX_CLASS_ATTR, Vertex.class);
     boolean vertexCreation;
-    Vertex<V, E, M> vertex = GraphJobRunner
-        .newVertexInstance(vertexClass, conf);
+    Vertex<V, E, M> vertex = GraphJobRunner.newVertexInstance(vertexClass);
     try {
       vertexCreation = parseVertex((KEYIN) inputRecord.getKey(),
           (VALUEIN) inputRecord.getValue(), vertex);
@@ -72,10 +85,9 @@ public abstract class VertexInputReader<
   @SuppressWarnings("unchecked")
   @Override
   public int getPartitionId(KeyValuePair<Writable, Writable> inputRecord,
-      @SuppressWarnings("rawtypes")
-      Partitioner partitioner, Configuration conf,
-      @SuppressWarnings("rawtypes")
-      BSPPeer peer, int numTasks) {
+      @SuppressWarnings("rawtypes") Partitioner partitioner,
+      Configuration conf, @SuppressWarnings("rawtypes") BSPPeer peer,
+      int numTasks) {
     Vertex<V, E, M> vertex = (Vertex<V, E, M>) outputRecord.getKey();
     return Math.abs(partitioner.getPartition(vertex.getVertexID(),
         vertex.getValue(), numTasks));

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInterface.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInterface.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInterface.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/VertexInterface.java Thu Feb 21 06:38:33 2013
@@ -23,6 +23,7 @@ import java.util.List;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 
 /**
  * The vertex interface.
@@ -33,7 +34,7 @@ import org.apache.hadoop.io.Writable;
  *          edge.
  * @param <M> the type used for messaging, usually the value of a vertex.
  */
-public interface VertexInterface<V extends Writable, E extends Writable, M extends Writable> {
+public interface VertexInterface<V extends WritableComparable<? super V>, E extends Writable, M extends Writable> {
 
   /**
    * Used to setup a vertex.

Modified: hama/trunk/graph/src/main/java/org/apache/hama/graph/VerticesInfo.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/main/java/org/apache/hama/graph/VerticesInfo.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/main/java/org/apache/hama/graph/VerticesInfo.java (original)
+++ hama/trunk/graph/src/main/java/org/apache/hama/graph/VerticesInfo.java Thu Feb 21 06:38:33 2013
@@ -24,6 +24,7 @@ import java.util.Iterator;
 import java.util.List;
 
 import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
 
 /**
  * VerticesInfo encapsulates the storage of vertices in a BSP Task.
@@ -32,10 +33,11 @@ import org.apache.hadoop.io.Writable;
  * @param <E> Edge cost object type
  * @param <M> Vertex value object type
  */
-public class VerticesInfo<V extends Writable, E extends Writable, M extends Writable>
+public class VerticesInfo<V extends WritableComparable<V>, E extends Writable, M extends Writable>
     implements Iterable<Vertex<V, E, M>> {
 
-  private final List<Vertex<V, E, M>> vertices = new ArrayList<Vertex<V, E, M>>(100);
+  private final List<Vertex<V, E, M>> vertices = new ArrayList<Vertex<V, E, M>>(
+      100);
 
   public void addVertex(Vertex<V, E, M> vertex) {
     int i = 0;

Modified: hama/trunk/graph/src/test/java/org/apache/hama/graph/TestSubmitGraphJob.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/test/java/org/apache/hama/graph/TestSubmitGraphJob.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/test/java/org/apache/hama/graph/TestSubmitGraphJob.java (original)
+++ hama/trunk/graph/src/test/java/org/apache/hama/graph/TestSubmitGraphJob.java Thu Feb 21 06:38:33 2013
@@ -25,6 +25,7 @@ import org.apache.hadoop.io.DoubleWritab
 import org.apache.hadoop.io.NullWritable;
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
 import org.apache.hama.Constants;
 import org.apache.hama.bsp.BSPJobClient;
 import org.apache.hama.bsp.ClusterStatus;
@@ -32,8 +33,9 @@ import org.apache.hama.bsp.HashPartition
 import org.apache.hama.bsp.SequenceFileInputFormat;
 import org.apache.hama.bsp.SequenceFileOutputFormat;
 import org.apache.hama.bsp.TestBSPMasterGroomServer;
+import org.apache.hama.bsp.TextArrayWritable;
 import org.apache.hama.graph.example.PageRank;
-import org.apache.hama.graph.example.PageRank.PageRankVertex;
+import org.apache.hama.graph.example.PageRank.PagerankSeqReader;
 
 public class TestSubmitGraphJob extends TestBSPMasterGroomServer {
 
@@ -53,11 +55,6 @@ public class TestSubmitGraphJob extends 
 
     generateTestData();
 
-    // Set multi-step partitioning interval to 30 bytes
-    configuration.setInt("hama.graph.multi.step.partitioning.interval", 30);
-
-    configuration.setBoolean(Constants.ENABLE_RUNTIME_PARTITIONING, false);
-
     GraphJob bsp = new GraphJob(configuration, PageRank.class);
     bsp.setInputPath(new Path("/tmp/pagerank/real-tmp.seq"));
     bsp.setOutputPath(new Path(OUTPUT));
@@ -70,16 +67,20 @@ public class TestSubmitGraphJob extends 
     bsp.setVertexClass(PageRank.PageRankVertex.class);
     // set the defaults
     bsp.setMaxIteration(30);
-    bsp.set("hama.pagerank.alpha", "0.85");
-    bsp.set("hama.graph.repair", "true");
+    // FIXME why is the sum correct when 1-ALPHA instead of ALPHA itself?
+    bsp.set("hama.pagerank.alpha", "0.25");
+
     bsp.setAggregatorClass(AverageAggregator.class,
         PageRank.DanglingNodeAggregator.class);
 
     bsp.setInputFormat(SequenceFileInputFormat.class);
-    
+    bsp.setInputKeyClass(Text.class);
+    bsp.setInputValueClass(TextArrayWritable.class);
+
     bsp.setVertexIDClass(Text.class);
     bsp.setVertexValueClass(DoubleWritable.class);
     bsp.setEdgeValueClass(NullWritable.class);
+    bsp.setVertexInputReaderClass(PagerankSeqReader.class);
 
     bsp.setPartitioner(HashPartitioner.class);
     bsp.setOutputFormat(SequenceFileOutputFormat.class);
@@ -115,46 +116,29 @@ public class TestSubmitGraphJob extends 
       reader.close();
     }
     LOG.info("Sum is: " + sum);
-    assertTrue(sum > 0.9d && sum <= 1.1d);
+    assertTrue("Sum was: " + sum, sum > 0.9d && sum <= 1.1d);
   }
 
-
   private void generateTestData() {
     try {
       SequenceFile.Writer writer1 = SequenceFile.createWriter(fs, getConf(),
-          new Path(INPUT+"/part0"), PageRankVertex.class, NullWritable.class);
+          new Path(INPUT + "/part0"), Text.class, TextArrayWritable.class);
 
-      for (int i = 0; i < input.length/2; i++) {
+      for (int i = 0; i < input.length; i++) {
         String[] x = input[i].split("\t");
 
-        PageRankVertex vertex = new PageRankVertex();
-        vertex.setVertexID(new Text(x[0]));
+        Text vertex = new Text(x[0]);
+        TextArrayWritable arr = new TextArrayWritable();
+        Writable[] values = new Writable[x.length - 1];
         for (int j = 1; j < x.length; j++) {
-          vertex.addEdge(new Edge<Text, NullWritable>(new Text(x[j]),
-              NullWritable.get()));
+          values[j - 1] = new Text(x[j]);
         }
-        writer1.append(vertex, NullWritable.get());
+        arr.set(values);
+        writer1.append(vertex, arr);
       }
 
       writer1.close();
-      
-      SequenceFile.Writer writer2 = SequenceFile.createWriter(fs, getConf(),
-          new Path(INPUT+"/part1"), PageRankVertex.class, NullWritable.class);
-
-      for (int i = 0; i < input.length/2 + 1; i++) {
-        String[] x = input[i].split("\t");
-
-        PageRankVertex vertex = new PageRankVertex();
-        vertex.setVertexID(new Text(x[0]));
-        for (int j = 1; j < x.length; j++) {
-          vertex.addEdge(new Edge<Text, NullWritable>(new Text(x[j]),
-              NullWritable.get()));
-        }
-        writer2.append(vertex, NullWritable.get());
-      }
 
-      writer2.close();
-      
     } catch (IOException e) {
       e.printStackTrace();
     }

Modified: hama/trunk/graph/src/test/java/org/apache/hama/graph/example/PageRank.java
URL: http://svn.apache.org/viewvc/hama/trunk/graph/src/test/java/org/apache/hama/graph/example/PageRank.java?rev=1448523&r1=1448522&r2=1448523&view=diff
==============================================================================
--- hama/trunk/graph/src/test/java/org/apache/hama/graph/example/PageRank.java (original)
+++ hama/trunk/graph/src/test/java/org/apache/hama/graph/example/PageRank.java Thu Feb 21 06:38:33 2013
@@ -17,22 +17,30 @@
  */
 package org.apache.hama.graph.example;
 
-import java.io.DataInput;
-import java.io.DataOutput;
 import java.io.IOException;
 import java.util.Iterator;
 
 import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.DoubleWritable;
-import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.NullWritable;
 import org.apache.hadoop.io.Text;
-import org.apache.hama.bsp.PartitioningRunner.RecordConverter;
+import org.apache.hadoop.io.Writable;
+import org.apache.hama.HamaConfiguration;
+import org.apache.hama.bsp.HashPartitioner;
+import org.apache.hama.bsp.SequenceFileInputFormat;
+import org.apache.hama.bsp.TextArrayWritable;
+import org.apache.hama.bsp.TextOutputFormat;
 import org.apache.hama.graph.AbstractAggregator;
+import org.apache.hama.graph.AverageAggregator;
 import org.apache.hama.graph.Edge;
+import org.apache.hama.graph.GraphJob;
 import org.apache.hama.graph.Vertex;
 import org.apache.hama.graph.VertexInputReader;
 
+/**
+ * Real pagerank with dangling node contribution.
+ */
 public class PageRank {
 
   public static class PageRankVertex extends
@@ -91,56 +99,6 @@ public class PageRank {
           / numEdges));
     }
 
-    @Override
-    public Text createVertexIDObject() {
-      return new Text();
-    }
-
-    @Override
-    public NullWritable createEdgeCostObject() {
-      return NullWritable.get();
-    }
-
-    @Override
-    public DoubleWritable createVertexValue() {
-      return new DoubleWritable();
-    }
-
-    @Override
-    public void readState(DataInput in) throws IOException {}
-
-    @Override
-    public void writeState(DataOutput out) throws IOException {}
-
-  }
-
-  public static class PagerankTextReader extends
-      VertexInputReader<LongWritable, Text, Text, NullWritable, DoubleWritable>
-      implements RecordConverter {
-
-    /**
-     * The text file essentially should look like: <br/>
-     * VERTEX_ID\t(n-tab separated VERTEX_IDs)<br/>
-     * E.G:<br/>
-     * 1\t2\t3\t4<br/>
-     * 2\t3\t1<br/>
-     * etc.
-     */
-    @Override
-    public boolean parseVertex(LongWritable key, Text value,
-        Vertex<Text, NullWritable, DoubleWritable> vertex) {
-      String[] split = value.toString().split("\t");
-      for (int i = 0; i < split.length; i++) {
-        if (i == 0) {
-          vertex.setVertexID(new Text(split[i]));
-        } else {
-          vertex
-              .addEdge(new Edge<Text, NullWritable>(new Text(split[i]), null));
-        }
-      }
-      return true;
-    }
-
   }
 
   public static class DanglingNodeAggregator
@@ -168,4 +126,78 @@ public class PageRank {
 
   }
 
+  public static class PagerankSeqReader
+      extends
+      VertexInputReader<Text, TextArrayWritable, Text, NullWritable, DoubleWritable> {
+    @Override
+    public boolean parseVertex(Text key, TextArrayWritable value,
+        Vertex<Text, NullWritable, DoubleWritable> vertex) throws Exception {
+      vertex.setVertexID(key);
+
+      for (Writable v : value.get()) {
+        vertex.addEdge(new Edge<Text, NullWritable>((Text) v, null));
+      }
+
+      return true;
+    }
+  }
+
+  @SuppressWarnings("unchecked")
+  public static GraphJob createJob(String[] args, HamaConfiguration conf)
+      throws IOException {
+    GraphJob pageJob = new GraphJob(conf, PageRank.class);
+    pageJob.setJobName("Pagerank");
+
+    pageJob.setVertexClass(PageRankVertex.class);
+    pageJob.setInputPath(new Path(args[0]));
+    pageJob.setOutputPath(new Path(args[1]));
+
+    // set the defaults
+    pageJob.setMaxIteration(30);
+    pageJob.set("hama.pagerank.alpha", "0.85");
+    pageJob.set("hama.graph.max.convergence.error", "0.001");
+
+    if (args.length == 3) {
+      pageJob.setNumBspTask(Integer.parseInt(args[2]));
+    }
+
+    // error, dangling node probability sum
+    pageJob.setAggregatorClass(AverageAggregator.class,
+        DanglingNodeAggregator.class);
+
+    // Vertex reader
+    pageJob.setVertexInputReaderClass(PagerankSeqReader.class);
+
+    pageJob.setVertexIDClass(Text.class);
+    pageJob.setVertexValueClass(DoubleWritable.class);
+    pageJob.setEdgeValueClass(NullWritable.class);
+
+    pageJob.setInputFormat(SequenceFileInputFormat.class);
+
+    pageJob.setPartitioner(HashPartitioner.class);
+    pageJob.setOutputFormat(TextOutputFormat.class);
+    pageJob.setOutputKeyClass(Text.class);
+    pageJob.setOutputValueClass(DoubleWritable.class);
+    return pageJob;
+  }
+
+  private static void printUsage() {
+    System.out.println("Usage: <input> <output> [tasks]");
+    System.exit(-1);
+  }
+
+  public static void main(String[] args) throws IOException,
+      InterruptedException, ClassNotFoundException {
+    if (args.length < 2)
+      printUsage();
+
+    HamaConfiguration conf = new HamaConfiguration(new Configuration());
+    GraphJob pageJob = createJob(args, conf);
+
+    long startTime = System.currentTimeMillis();
+    if (pageJob.waitForCompletion(true)) {
+      System.out.println("Job Finished in "
+          + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
+    }
+  }
 }



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