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From surajsme...@apache.org
Subject svn commit: r1369566 - in /hama/branches/HAMA-505-branch: ./ conf/ core/ core/src/main/java/org/apache/hama/bsp/ core/src/main/java/org/apache/hama/util/ dist/ examples/ graph/ graph/src/main/java/org/apache/hama/graph/ ml/ ml/src/main/java/org/apache/...
Date Sun, 05 Aug 2012 12:32:59 GMT
Author: surajsmenon
Date: Sun Aug  5 12:32:58 2012
New Revision: 1369566

URL: http://svn.apache.org/viewvc?rev=1369566&view=rev
Log:
Merged the trunk changes to branch HAMA-505-branch

Added:
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/
      - copied from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DenseDoubleMatrix.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DenseDoubleMatrix.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DenseDoubleVector.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DenseDoubleVector.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DoubleDoubleVectorFunction.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DoubleDoubleVectorFunction.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DoubleMatrix.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DoubleMatrix.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DoubleVector.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DoubleVector.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/DoubleVectorFunction.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/DoubleVectorFunction.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/math/Tuple.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/math/Tuple.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/writable/
      - copied from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/writable/
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/writable/MatrixWritable.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/writable/MatrixWritable.java
    hama/branches/HAMA-505-branch/ml/src/main/java/org/apache/hama/ml/writable/VectorWritable.java
      - copied unchanged from r1369557, hama/trunk/ml/src/main/java/org/apache/hama/ml/writable/VectorWritable.java
Modified:
    hama/branches/HAMA-505-branch/   (props changed)
    hama/branches/HAMA-505-branch/CHANGES.txt
    hama/branches/HAMA-505-branch/conf/hama-default.xml
    hama/branches/HAMA-505-branch/core/pom.xml
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/BSPTask.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/LocalBSPRunner.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPNetUtils.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPServletUtil.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/Bytes.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/ClusterUtil.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/RandomVariable.java
    hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/VersionInfo.java
    hama/branches/HAMA-505-branch/dist/pom.xml
    hama/branches/HAMA-505-branch/examples/pom.xml
    hama/branches/HAMA-505-branch/graph/pom.xml
    hama/branches/HAMA-505-branch/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java
    hama/branches/HAMA-505-branch/ml/pom.xml
    hama/branches/HAMA-505-branch/pom.xml
    hama/branches/HAMA-505-branch/src/site/resources/css/site.css
    hama/branches/HAMA-505-branch/src/site/site.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/downloads.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/getting_started_with_hama.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/hama_bsp_tutorial.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/hama_graph_tutorial.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/hama_on_clouds.xml
    hama/branches/HAMA-505-branch/src/site/xdoc/index.xml
    hama/branches/HAMA-505-branch/yarn/pom.xml

Propchange: hama/branches/HAMA-505-branch/
------------------------------------------------------------------------------
    svn:mergeinfo = /hama/trunk:1353353-1369557

Modified: hama/branches/HAMA-505-branch/CHANGES.txt
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/CHANGES.txt?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/CHANGES.txt (original)
+++ hama/branches/HAMA-505-branch/CHANGES.txt Sun Aug  5 12:32:58 2012
@@ -1,5 +1,15 @@
 Hama Change Log
 
+Release 0.6 (unreleased changes)
+
+  NEW FEATURES
+
+  BUG FIXES
+
+   HAMA-608: LocalRunner should honor the configured queues (tjungblut)
+
+  IMPROVEMENTS
+
 Release 0.5 - April 10, 2012 
 
   NEW FEATURES

Modified: hama/branches/HAMA-505-branch/conf/hama-default.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/conf/hama-default.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/conf/hama-default.xml (original)
+++ hama/branches/HAMA-505-branch/conf/hama-default.xml Sun Aug  5 12:32:58 2012
@@ -135,7 +135,11 @@
     <value>1</value>
     <description>If bsp.checkpoint.enabled is set to true, the checkpointing is initiated on the valueth synchronization process of BSP tasks.</description>
   </property>
-
+  <property>
+    <name>bsp.groomserver.pingperiod</name>
+    <value>10000</value>
+    <description>The default timeout period for checking groom server health.</description>
+  </property>
   
   <!--
   Beginning of properties that are directly mapped from ZooKeeper's zoo.cfg.

Modified: hama/branches/HAMA-505-branch/core/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/pom.xml (original)
+++ hama/branches/HAMA-505-branch/core/pom.xml Sun Aug  5 12:32:58 2012
@@ -15,20 +15,19 @@
    limitations under the License.
 -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-core</artifactId>
   <name>core</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <dependencies>
@@ -197,11 +196,9 @@
             </goals>
             <configuration>
               <target>
-                <mkdir
-                  dir="${project.build.directory}/generated-sources/java" />
+                <mkdir dir="${project.build.directory}/generated-sources/java" />
                 <exec executable="sh">
-                  <arg
-                    line="${basedir}/dev-support/saveVersion.sh ${project.version} ${project.build.directory}/generated-sources/annotations" />
+                  <arg line="${basedir}/dev-support/saveVersion.sh ${project.version} ${project.build.directory}/generated-sources/annotations" />
                 </exec>
               </target>
             </configuration>

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/BSPTask.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/BSPTask.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/BSPTask.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/BSPTask.java Sun Aug  5 12:32:58 2012
@@ -121,7 +121,6 @@ public final class BSPTask extends Task 
       if (pingPeriod > 0) {
         pingService.scheduleWithFixedDelay(new PingGroomServer(umbilical,
             taskId), 0, pingPeriod, TimeUnit.MILLISECONDS);
-        LOG.error("Started pinging to groom");
       }
     } catch (Exception e) {
       LOG.error("Error scheduling ping service", e);

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/LocalBSPRunner.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/LocalBSPRunner.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/LocalBSPRunner.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/bsp/LocalBSPRunner.java Sun Aug  5 12:32:58 2012
@@ -20,17 +20,13 @@ package org.apache.hama.bsp;
 import java.io.DataInputStream;
 import java.io.IOException;
 import java.net.InetSocketAddress;
-import java.util.HashMap;
-import java.util.Iterator;
 import java.util.LinkedList;
-import java.util.Map.Entry;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.CyclicBarrier;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
-import java.util.concurrent.LinkedBlockingDeque;
 import java.util.concurrent.ThreadPoolExecutor;
 
 import org.apache.commons.logging.Log;
@@ -45,11 +41,9 @@ import org.apache.hama.Constants;
 import org.apache.hama.HamaConfiguration;
 import org.apache.hama.bsp.BSPJobClient.RawSplit;
 import org.apache.hama.bsp.BSPMaster.State;
-import org.apache.hama.bsp.message.MemoryQueue;
-import org.apache.hama.bsp.message.MessageEventListener;
+import org.apache.hama.bsp.message.AbstractMessageManager;
 import org.apache.hama.bsp.message.MessageManager;
 import org.apache.hama.bsp.message.MessageManagerFactory;
-import org.apache.hama.bsp.message.MessageQueue;
 import org.apache.hama.bsp.sync.BSPPeerSyncClient;
 import org.apache.hama.bsp.sync.SyncClient;
 import org.apache.hama.bsp.sync.SyncEvent;
@@ -58,7 +52,6 @@ import org.apache.hama.bsp.sync.SyncExce
 import org.apache.hama.bsp.sync.SyncServiceFactory;
 import org.apache.hama.ipc.BSPPeerProtocol;
 import org.apache.hama.ipc.JobSubmissionProtocol;
-import org.apache.hama.util.BSPNetUtils;
 
 /**
  * A multithreaded local BSP runner that can be used for debugging and local
@@ -72,7 +65,7 @@ public class LocalBSPRunner implements J
   private volatile ThreadPoolExecutor threadPool;
 
   @SuppressWarnings("rawtypes")
-  private static final LinkedList<Future<BSPPeerImpl>> futureList = new LinkedList<Future<BSPPeerImpl>>();
+  private static final LinkedList<Future<BSPPeerImpl>> FUTURE_LIST = new LinkedList<Future<BSPPeerImpl>>();
 
   private String jobFile;
   private String jobName;
@@ -156,7 +149,7 @@ public class LocalBSPRunner implements J
     peerNames = new String[numBspTask];
     for (int i = 0; i < numBspTask; i++) {
       peerNames[i] = "local:" + i;
-      futureList.add(threadPool.submit(new BSPRunner(new Configuration(conf),
+      FUTURE_LIST.add(threadPool.submit(new BSPRunner(new Configuration(conf),
           job, i, splits)));
       globalCounters.incrCounter(JobInProgress.JobCounter.LAUNCHED_TASKS, 1L);
     }
@@ -306,7 +299,7 @@ public class LocalBSPRunner implements J
     @Override
     public void run() {
       boolean success = true;
-      for (Future<BSPPeerImpl> future : futureList) {
+      for (Future<BSPPeerImpl> future : FUTURE_LIST) {
         try {
           BSPPeerImpl bspPeerImpl = future.get();
           currentJobStatus.getCounter().incrAllCounters(
@@ -331,53 +324,17 @@ public class LocalBSPRunner implements J
 
   }
 
-  public static class LocalMessageManager<M extends Writable> implements
-      MessageManager<M> {
+  public static class LocalMessageManager<M extends Writable> extends
+      AbstractMessageManager<M> {
 
     @SuppressWarnings("rawtypes")
-    private static final ConcurrentHashMap<InetSocketAddress, LocalMessageManager> managerMap = new ConcurrentHashMap<InetSocketAddress, LocalBSPRunner.LocalMessageManager>();
-
-    private final HashMap<InetSocketAddress, MessageQueue<M>> localOutgoingMessages = new HashMap<InetSocketAddress, MessageQueue<M>>();
-    private static final ConcurrentHashMap<String, InetSocketAddress> socketCache = new ConcurrentHashMap<String, InetSocketAddress>();
-    private final LinkedBlockingDeque<M> localIncomingMessages = new LinkedBlockingDeque<M>();
-
-    private BSPPeer<?, ?, ?, ?, M> peer;
+    private static final ConcurrentHashMap<InetSocketAddress, LocalMessageManager> MANAGER_MAP = new ConcurrentHashMap<InetSocketAddress, LocalBSPRunner.LocalMessageManager>();
 
     @Override
     public void init(TaskAttemptID attemptId, BSPPeer<?, ?, ?, ?, M> peer,
         Configuration conf, InetSocketAddress peerAddress) {
-      this.peer = peer;
-      managerMap.put(peerAddress, this);
-    }
-
-    @Override
-    public void close() {
-
-    }
-
-    @Override
-    public M getCurrentMessage() throws IOException {
-      if (localIncomingMessages.isEmpty()) {
-        return null;
-      } else {
-        return localIncomingMessages.pop();
-      }
-    }
-
-    @Override
-    public void send(String peerName, M msg) throws IOException {
-      InetSocketAddress inetSocketAddress = socketCache.get(peerName);
-      if (inetSocketAddress == null) {
-        inetSocketAddress = BSPNetUtils.getAddress(peerName);
-        socketCache.put(peerName, inetSocketAddress);
-      }
-      MessageQueue<M> msgs = localOutgoingMessages.get(inetSocketAddress);
-      if (msgs == null) {
-        msgs = new MemoryQueue<M>();
-      }
-      msgs.add(msg);
-      peer.incrementCounter(BSPPeerImpl.PeerCounter.TOTAL_MESSAGES_SENT, 1L);
-      localOutgoingMessages.put(inetSocketAddress, msgs);
+      super.init(attemptId, peer, conf, peerAddress);
+      MANAGER_MAP.put(peerAddress, this);
     }
 
     @SuppressWarnings("unchecked")
@@ -385,54 +342,11 @@ public class LocalBSPRunner implements J
     public void transfer(InetSocketAddress addr, BSPMessageBundle<M> bundle)
         throws IOException {
       for (M value : bundle.getMessages()) {
-        managerMap.get(addr).localIncomingMessages.add(value);
+        MANAGER_MAP.get(addr).localQueueForNextIteration.add(value);
         peer.incrementCounter(BSPPeerImpl.PeerCounter.TOTAL_MESSAGES_RECEIVED,
             1L);
       }
     }
-
-    @Override
-    public Iterator<Entry<InetSocketAddress, MessageQueue<M>>> getMessageIterator() {
-      return localOutgoingMessages.entrySet().iterator();
-    }
-
-    @Override
-    public void clearOutgoingQueues() {
-      localOutgoingMessages.clear();
-    }
-
-    @Override
-    public int getNumCurrentMessages() {
-      return localIncomingMessages.size();
-    }
-
-    @Override
-    public void finishSendPhase() throws IOException {
-    }
-
-    @Override
-    public void loopBackMessages(BSPMessageBundle<? extends Writable> bundle) {
-      for (Writable value : bundle.getMessages()) {
-        loopBackMessage(value);
-      }
-      
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public void loopBackMessage(Writable message) {
-      localIncomingMessages.add((M)message);
-      peer.incrementCounter(BSPPeerImpl.PeerCounter.TOTAL_MESSAGES_RECEIVED,
-          1L);
-    }
-
-    @Override
-    public void registerListener(MessageEventListener<M> listener)
-        throws IOException {
-    }
-    
-    
-
   }
 
   public static class LocalUmbilical implements BSPPeerProtocol {
@@ -550,13 +464,9 @@ public class LocalBSPRunner implements J
     }
 
     @Override
-    public void close() throws IOException {
+    public void close() {
       barrier = null;
     }
-    @Override
-    public boolean getInformation(String key, Writable writableVal) {
-      return false;
-    }
 
     @Override
     public String constructKey(BSPJobID jobId, String... args) {
@@ -570,20 +480,18 @@ public class LocalBSPRunner implements J
     }
 
     @Override
-    public boolean addKey(String key, boolean permanent,
-        SyncEventListener listener) {
+    public boolean getInformation(String key, Writable valueHolder) {
       return false;
     }
 
     @Override
-    public boolean hasKey(String key) {
+    public boolean addKey(String key, boolean permanent,
+        SyncEventListener listener) {
       return false;
     }
 
     @Override
-    public boolean registerListener(String key,
-        SyncEvent event,
-        SyncEventListener listener) {
+    public boolean hasKey(String key) {
       return false;
     }
 
@@ -593,11 +501,15 @@ public class LocalBSPRunner implements J
     }
 
     @Override
-    public boolean remove(String key, SyncEventListener listener) {
+    public boolean registerListener(String key, SyncEvent event,
+        SyncEventListener listener) {
       return false;
     }
 
-	
+    @Override
+    public boolean remove(String key, SyncEventListener listener) {
+      return false;
+    }
   }
 
   @Override

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPNetUtils.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPNetUtils.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPNetUtils.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPNetUtils.java Sun Aug  5 12:32:58 2012
@@ -17,17 +17,13 @@
  */
 package org.apache.hama.util;
 
-import java.io.IOException;
-import java.net.DatagramSocket;
-import java.net.InetAddress;
-import java.net.InetSocketAddress;
-import java.net.ServerSocket;
-import java.net.UnknownHostException;
-import java.util.NoSuchElementException;
-
 import org.apache.hama.Constants;
 import org.apache.mina.util.AvailablePortFinder;
 
+import java.io.IOException;
+import java.net.*;
+import java.util.NoSuchElementException;
+
 /**
  * NetUtils for our needs.
  */
@@ -37,7 +33,7 @@ public class BSPNetUtils {
   /**
    * Gets the canonical hostname of this machine.
    * 
-   * @return
+   * @return String representing host canonical host name
    * @throws UnknownHostException
    */
   public static String getCanonicalHostname() throws UnknownHostException {
@@ -71,8 +67,8 @@ public class BSPNetUtils {
    * Gets a new InetSocketAddress from the given peerName. peerName must contain
    * a colon to distinct between host and port.
    * 
-   * @param peerName
-   * @return
+   * @param peerName the name as a String of the BSP peer to get the address from
+   * @return the InetSocketAddress of the given BSP peer
    */
   public static InetSocketAddress getAddress(String peerName) {
     String[] peerAddrParts = peerName.split(":");

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPServletUtil.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPServletUtil.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPServletUtil.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/BSPServletUtil.java Sun Aug  5 12:32:58 2012
@@ -17,17 +17,17 @@
  */
 package org.apache.hama.util;
 
-import java.io.IOException;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.Map.Entry;
-
 import org.apache.hadoop.util.ServletUtil;
 import org.apache.hama.bsp.BSPMaster;
 import org.apache.hama.bsp.ClusterStatus;
 import org.apache.hama.bsp.GroomServerStatus;
 import org.apache.hama.bsp.JobStatus;
 
+import java.io.IOException;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Map.Entry;
+
 public class BSPServletUtil extends ServletUtil {
 
   public static final String HTML_TAIL = "<hr />\n"
@@ -103,7 +103,7 @@ public class BSPServletUtil extends Serv
     for (Entry<String, GroomServerStatus> entry : status
         .getActiveGroomServerStatus().entrySet()) {
       sb.append("<tr><td>");
-      sb.append("<a href='http://" + entry.getKey() + "'>");
+      sb.append("<a href='http://").append(entry.getKey()).append("'>");
       sb.append(entry.getKey()).append("</a></td><td>");
       sb.append(entry.getValue().getGroomHostName()).append("</td>").append(
           "<td>").append(entry.getValue().getMaxTasks()).append("</td><td>");

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/Bytes.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/Bytes.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/Bytes.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/Bytes.java Sun Aug  5 12:32:58 2012
@@ -17,6 +17,13 @@
  */
 package org.apache.hama.util;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.io.RawComparator;
+import org.apache.hadoop.io.WritableComparator;
+import org.apache.hadoop.io.WritableUtils;
+import org.apache.hama.Constants;
+
 import java.io.DataInput;
 import java.io.DataOutput;
 import java.io.IOException;
@@ -25,13 +32,6 @@ import java.math.BigInteger;
 import java.nio.ByteBuffer;
 import java.util.Comparator;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.hadoop.io.RawComparator;
-import org.apache.hadoop.io.WritableComparator;
-import org.apache.hadoop.io.WritableUtils;
-import org.apache.hama.Constants;
-
 /**
  * Utility class that handles byte arrays, conversions to/from other types,
  * comparisons, hash code generation, manufacturing keys for HashMaps or
@@ -892,10 +892,7 @@ public class Bytes {
   public static boolean equals(final byte[] left, final byte[] right) {
     // Could use Arrays.equals?
     // noinspection SimplifiableConditionalExpression
-    if (left == null && right == null) {
-      return true;
-    }
-    return (!(left == null || right == null || (left.length != right.length)) && compareTo(left, right) == 0);
+    return left == null && right == null || (!(left == null || right == null || (left.length != right.length)) && compareTo(left, right) == 0);
   }
 
   /**

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/ClusterUtil.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/ClusterUtil.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/ClusterUtil.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/ClusterUtil.java Sun Aug  5 12:32:58 2012
@@ -17,9 +17,6 @@
  */
 package org.apache.hama.util;
 
-import java.io.IOException;
-import java.util.List;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
@@ -27,6 +24,9 @@ import org.apache.hama.HamaConfiguration
 import org.apache.hama.bsp.BSPMaster;
 import org.apache.hama.bsp.GroomServer;
 
+import java.io.IOException;
+import java.util.List;
+
 public class ClusterUtil {
   private static final Log LOG = LogFactory.getLog(ClusterUtil.class);
   
@@ -86,9 +86,9 @@ public class ClusterUtil {
 
   /**
    * Start the cluster.
-   * @param m
-   * @param conf 
-   * @param groomservers
+   * @param m the BSP master
+   * @param conf cluster configuration to be used
+   * @param groomservers list of threads holding groom servers
    * @return Address to use contacting master.
    * @throws InterruptedException 
    * @throws IOException 

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/RandomVariable.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/RandomVariable.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/RandomVariable.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/RandomVariable.java Sun Aug  5 12:32:58 2012
@@ -31,8 +31,7 @@ public class RandomVariable {
    * @return a double between 0 and 1.
    */
   public static double rand() {
-    double x = Math.random();
-    return x;
+    return Math.random();
   }
 
   /**
@@ -44,8 +43,7 @@ public class RandomVariable {
    */
   public static int randInt(int i0, int i1) {
     double x = rand();
-    int i = i0 + (int) Math.floor((i1 - i0 + 1) * x);
-    return i;
+    return i0 + (int) Math.floor((i1 - i0 + 1) * x);
   }
   
   /**
@@ -74,8 +72,7 @@ public class RandomVariable {
    * @return a double.
    */
   public static double uniform(double min, double max) {
-    double x = min + (max - min) * rand();
-    return x;
+    return min + (max - min) * rand();
   }
 
   /**
@@ -109,9 +106,8 @@ public class RandomVariable {
    * @return a double.
    */
   public static double normal(double mu, double sigma) {
-    double x = mu + sigma * Math.cos(2 * Math.PI * rand())
+    return mu + sigma * Math.cos(2 * Math.PI * rand())
         * Math.sqrt(-2 * Math.log(rand()));
-    return x;
   }
 
   /**
@@ -137,9 +133,8 @@ public class RandomVariable {
    * @return a double.
    */
   public static double logNormal(double mu, double sigma) {
-    double x = mu + sigma * Math.cos(2 * Math.PI * rand())
+    return mu + sigma * Math.cos(2 * Math.PI * rand())
         * Math.sqrt(-2 * Math.log(rand()));
-    return x;
   }
 
   /**
@@ -150,8 +145,7 @@ public class RandomVariable {
    * @return a double.
    */
   public static double exponential(double lambda) {
-    double x = -1 / lambda * Math.log(rand());
-    return x;
+    return -1 / lambda * Math.log(rand());
   }
 
   /**
@@ -162,9 +156,8 @@ public class RandomVariable {
    * @return a double.
    */
   public static double triangular(double min, double max) {
-    double x = min / 2 + (max - min) * rand() / 2 + min / 2 + (max - min)
+    return min / 2 + (max - min) * rand() / 2 + min / 2 + (max - min)
         * rand() / 2;
-    return x;
   }
 
   /**
@@ -177,10 +170,9 @@ public class RandomVariable {
    */
   public static double triangular(double min, double med, double max) {
     double y = rand();
-    double x = (y < ((med - min) / (max - min))) ? (min + Math.sqrt(y
+    return (y < ((med - min) / (max - min))) ? (min + Math.sqrt(y
         * (max - min) * (med - min))) : (max - Math.sqrt((1 - y) * (max - min)
         * (max - med)));
-    return x;
   }
 
   /**
@@ -209,8 +201,7 @@ public class RandomVariable {
    * @return a double.
    */
   public static double cauchy(double mu, double sigma) {
-    double x = sigma * Math.tan(Math.PI * (rand() - 0.5)) + mu;
-    return x;
+    return sigma * Math.tan(Math.PI * (rand() - 0.5)) + mu;
   }
 
   /**
@@ -221,7 +212,6 @@ public class RandomVariable {
    * @return a double.
    */
   public static double weibull(double lambda, double c) {
-    double x = Math.pow(-Math.log(1 - rand()), 1 / c) / lambda;
-    return x;
+    return Math.pow(-Math.log(1 - rand()), 1 / c) / lambda;
   }
 }

Modified: hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/VersionInfo.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/VersionInfo.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/VersionInfo.java (original)
+++ hama/branches/HAMA-505-branch/core/src/main/java/org/apache/hama/util/VersionInfo.java Sun Aug  5 12:32:58 2012
@@ -40,7 +40,7 @@ public class VersionInfo {
 
   /**
    * Get the meta-data for the Hama package.
-   * @return
+   * @return the current package
    */
   static Package getPackage() {
     return myPackage;

Modified: hama/branches/HAMA-505-branch/dist/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/dist/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/dist/pom.xml (original)
+++ hama/branches/HAMA-505-branch/dist/pom.xml Sun Aug  5 12:32:58 2012
@@ -14,15 +14,13 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
   
   <artifactId>hama-dist</artifactId>

Modified: hama/branches/HAMA-505-branch/examples/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/examples/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/examples/pom.xml (original)
+++ hama/branches/HAMA-505-branch/examples/pom.xml Sun Aug  5 12:32:58 2012
@@ -15,20 +15,19 @@
    limitations under the License.
 -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-examples</artifactId>
   <name>examples</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <dependencies>

Modified: hama/branches/HAMA-505-branch/graph/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/graph/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/graph/pom.xml (original)
+++ hama/branches/HAMA-505-branch/graph/pom.xml Sun Aug  5 12:32:58 2012
@@ -15,20 +15,19 @@
    limitations under the License.
 -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-graph</artifactId>
   <name>graph</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <dependencies>
@@ -40,9 +39,9 @@
     <dependency>
       <groupId>org.apache.hama</groupId>
       <artifactId>hama-core</artifactId>
+      <version>${project.version}</version>
       <type>test-jar</type>
       <scope>test</scope>
-      <version>${project.version}</version>
     </dependency>
   </dependencies>
   <build>

Modified: hama/branches/HAMA-505-branch/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java (original)
+++ hama/branches/HAMA-505-branch/graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java Sun Aug  5 12:32:58 2012
@@ -391,16 +391,16 @@ public final class GraphJobRunner<V exte
     Vertex<V, E, M> vertex = newVertexInstance(vertexClass, conf);
     vertex.setPeer(peer);
     vertex.runner = this;
-    while (true) {
-      KeyValuePair<Writable, Writable> next = peer.readNext();
-      if (next == null) {
-        break;
-      }
+    
+    KeyValuePair<Writable, Writable> next = null;
+    int lines = 0;
+    while ((next = peer.readNext()) != null) {
       boolean vertexFinished = reader.parseVertex(next.getKey(),
           next.getValue(), vertex);
       if (!vertexFinished) {
         continue;
       }
+      
       if (vertex.getEdges() == null) {
         vertex.setEdges(new ArrayList<Edge<V, E>>(0));
       }
@@ -420,12 +420,26 @@ public final class GraphJobRunner<V exte
         }
         peer.send(peer.getPeerName(partition), new GraphJobMessage(vertex));
       } else {
+        // FIXME need to set destination names
         vertex.setup(conf);
         vertices.put(vertex.getVertexID(), vertex);
       }
       vertex = newVertexInstance(vertexClass, conf);
       vertex.setPeer(peer);
       vertex.runner = this;
+      
+      lines++;
+      if((lines % 100000) == 0) {
+        peer.sync();
+        GraphJobMessage msg = null;
+        while ((msg = peer.getCurrentMessage()) != null) {
+          Vertex<V, E, M> messagedVertex = (Vertex<V, E, M>) msg.getVertex();
+          messagedVertex.setPeer(peer);
+          messagedVertex.runner = this;
+          messagedVertex.setup(conf);
+          vertices.put(messagedVertex.getVertexID(), messagedVertex);
+        }
+      }
     }
 
     if (runtimePartitioning) {
@@ -440,6 +454,8 @@ public final class GraphJobRunner<V exte
       }
     }
 
+    LOG.info("Loading finished at " + peer.getSuperstepCount() + " steps.");
+    
     /*
      * If the user want to repair the graph, it should traverse through that
      * local chunk of adjancency list and message the corresponding peer to

Modified: hama/branches/HAMA-505-branch/ml/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/ml/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/ml/pom.xml (original)
+++ hama/branches/HAMA-505-branch/ml/pom.xml Sun Aug  5 12:32:58 2012
@@ -15,20 +15,19 @@
    limitations under the License.
 -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-ml</artifactId>
   <name>machine learning</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <dependencies>

Modified: hama/branches/HAMA-505-branch/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/pom.xml (original)
+++ hama/branches/HAMA-505-branch/pom.xml Sun Aug  5 12:32:58 2012
@@ -15,8 +15,7 @@
    limitations under the License.
 -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache</groupId>
@@ -28,7 +27,7 @@
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-parent</artifactId>
   <name>Apache Hama parent POM</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <url>http://hama.apache.org</url>
   <packaging>pom</packaging>
   <prerequisites>
@@ -277,7 +276,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-site-plugin</artifactId>
-        <version>2.1.1</version>
+        <version>3.1</version>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>

Modified: hama/branches/HAMA-505-branch/src/site/resources/css/site.css
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/resources/css/site.css?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/resources/css/site.css (original)
+++ hama/branches/HAMA-505-branch/src/site/resources/css/site.css Sun Aug  5 12:32:58 2012
@@ -36,7 +36,7 @@ h2, h3, h4, h5 {
 
 h5 {
   font-size: 15px;
-  margin-top: -0.8em;
+  margin-top: -0.1em;
 }
 
 table {
@@ -56,11 +56,17 @@ ul {
  background: #edf7f4;
  background-color: #edf7f4;
 }
+
+pre {
+ width: 95%;
+ margin: 20px 20px 20px 20px;
+}
+
 .green a:link, .green a:active, .green a:visited { color: #0a4d39; }
 .green a:hover { color: #888800; }
 .green h3 {
   margin-bottom:-5px;
-  margin-top:-2px;
+  margin-top:5px;
   padding: 0px 0px 0px 0px;
   border: 0px;
   color: #74240f;
@@ -90,3 +96,15 @@ ul {
   padding-left: 1em;
   list-style-position: inside;
 }
+
+#leftColumn li.none{
+  text-indent:-1em;
+  margin-left:-1em;
+}
+
+#leftColumn h3 {
+  font-size: 16px;
+  margin-left:-0.7em;
+}
+
+body.topBarDisabled{padding-top:0px;}
\ No newline at end of file

Modified: hama/branches/HAMA-505-branch/src/site/site.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/site.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/site.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/site.xml Sun Aug  5 12:32:58 2012
@@ -27,16 +27,16 @@
 
   <skin>
     <groupId>org.apache.maven.skins</groupId>
-    <artifactId>maven-default-skin</artifactId>
-    <version>1.0</version>
+    <artifactId>maven-fluido-skin</artifactId>
+    <version>1.2.2</version>
   </skin>
 
   <body>
     <links position="left">
-      <item name="Wiki" href="https://wiki.apache.org/hama" />
+      <item name="Wiki" href="http://wiki.apache.org/hama" />
       <item name="Blog" href="http://blogs.apache.org/hama/" />
-      <item name="JIRA" href="https://issues.apache.org/jira/browse/HAMA" />
-      <item name="SVN" href="https://svn.apache.org/repos/asf/hama/" />
+      <item name="JIRA" href="http://issues.apache.org/jira/browse/HAMA" />
+      <item name="SVN" href="http://svn.apache.org/repos/asf/hama/" />
       <item name="Twitter" href="http://twitter.com/apachehama" />
     </links>
 
@@ -62,8 +62,8 @@
     <menu name="Documentation">
       <item name="Getting Started" href="getting_started_with_hama.html" />
       <item name="Hama on Clouds" href="hama_on_clouds.html" />
-      <item name="Hama BSP tutorial" href="hama_bsp_tutorial.html" />
-      <item name="Hama Graph tutorial" href="hama_graph_tutorial.html" />
+      <item name="BSP tutorial" href="hama_bsp_tutorial.html" />
+      <item name="Graph tutorial" href="hama_graph_tutorial.html" />
       <item name="Benchmarks" href="http://wiki.apache.org/hama/Benchmarks" />
       <item name="Presentations" href="http://wiki.apache.org/hama/Presentations" />
       <item name="Research Papers" href="http://wiki.apache.org/hama/Articles" />
@@ -72,13 +72,26 @@
 
     <menu name="Related Projects">
       <item name="Hadoop" href="http://hadoop.apache.org/" />
-      <item name="Whirr" href="https://whirr.apache.org/" />
-      <item name="Bigtop" href="https://incubator.apache.org/bigtop/" />
+      <item name="Whirr" href="http://whirr.apache.org/" />
+      <item name="Bigtop" href="http://incubator.apache.org/bigtop/" />
       <item name="Mahout" href="http://mahout.apache.org/" />
     </menu>
     
     <menu name="Art works">
       <item name="Artwork and Clothing" href="artwork.html" />
     </menu>
+
+    <menu name="ASF">
+      <item name="How Apache Works" href="http://www.apache.org/foundation/how-it-works.html"/>
+      <item name="Foundation" href="http://www.apache.org/foundation/"/>
+      <item name="Sponsoring Apache" href="http://www.apache.org/foundation/sponsorship.html"/>
+      <item name="Thanks" href="http://www.apache.org/foundation/thanks.html"/>
+    </menu>
+    <footer>
+      <div class="row span16">Apache Hama, Apache, the Apache feather logo, and
+          the Apache Hama project logos are trademarks of The Apache Software
+          Foundation. All other marks mentioned may be trademarks or registered
+          trademarks of their respective owners.</div>
+    </footer>
   </body>
 </project>

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/downloads.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/downloads.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/downloads.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/downloads.xml Sun Aug  5 12:32:58 2012
@@ -42,10 +42,10 @@ xsi:schemaLocation="http://maven.apache.
     which is located within each download directory.
     <br/><br/>
     Always use the signature files to verify the authenticity of the distribution, e.g.,
-    <pre class="green">  % pgpk -a KEYS
+    <pre>  % pgpk -a KEYS
   % pgpv hama-x.x.x.tar.gz.asc</pre>
     or,
-    <pre class="green">  % gpg --import KEYS
+    <pre>  % gpg --import KEYS
   % gpg --verify hama-x.x.x.tar.gz.asc</pre>
     We offer MD5 hashes as an alternative to validate the integrity of the downloaded files.
     A unix program called md5 or md5sum is included in many unix distributions.

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/getting_started_with_hama.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/getting_started_with_hama.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/getting_started_with_hama.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/getting_started_with_hama.xml Sun Aug  5 12:32:58 2012
@@ -62,7 +62,7 @@ xsi:schemaLocation="http://maven.apache.
     <ul><li>BSPMaster and Zookeeper settings - Figure out where to run your HDFS namenode and BSPMaster. Set the variable bsp.master.address to the BSPMaster's intended host:port. Set the variable fs.default.name to the HDFS Namenode's intended host:port.</li></ul>
     <p>Here's an example of a hama-site.xml file:</p>
 
-<pre class="green">
+<pre>
   &lt;?xml version="1.0"?&gt;
   &lt;?xml-stylesheet type="text/xsl" href="configuration.xsl"?&gt;
   &lt;configuration&gt;
@@ -99,7 +99,7 @@ xsi:schemaLocation="http://maven.apache.
 
 <p>If you are managing your own ZooKeeper, you have to specify the port number as below:</p>
 
-<pre class="green">
+<pre>
   &lt;property&gt;
     &lt;name&gt;hama.zookeeper.property.clientPort&lt;/name&gt;
     &lt;value&gt;2181&lt;/value&gt;
@@ -111,16 +111,16 @@ xsi:schemaLocation="http://maven.apache.
     <p>NOTE: Skip this step if you're in Local Mode.
     <br/>Run the command:</p>
     
-  <pre class="green">
+  <pre>
   % $HAMA_HOME/bin/start-bspd.sh</pre>
     <p>This will startup a BSPMaster, GroomServers and Zookeeper on your machine.</p>
     <p>Run the command:</p>
-  <pre class="green">
+  <pre>
   % $HAMA_HOME/bin/stop-bspd.sh</pre>
 
     <p>to stop all the daemons running on your cluster.</p>
     <subsection name="Execute Hama Examples"></subsection>
-  <pre class="green">
+  <pre>
   % $HAMA_HOME/bin/hama jar hama-examples-x.x.x.jar [args]</pre>
     </body>
 </document>

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/hama_bsp_tutorial.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/hama_bsp_tutorial.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/hama_bsp_tutorial.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/hama_bsp_tutorial.xml Sun Aug  5 12:32:58 2012
@@ -40,7 +40,7 @@ xsi:schemaLocation="http://maven.apache.
     <br/>
     The extending class must override the bsp() method, which is declared like this:
     </p>
-    <pre class="green">
+    <pre>
   public abstract void bsp(BSPPeer&lt;K1, V1, K2, V2, M extends Writable&gt; peer) throws IOException, 
     SyncException, InterruptedException;</pre>
     
@@ -56,7 +56,7 @@ xsi:schemaLocation="http://maven.apache.
     <br/><br/>
     After your own BSP is created, you will need to configure a <b>BSPJob</b> and submit it to Hama cluster to execute a job.
     The BSP job configuration and submission interfaces is almost the same as the MapReduce job configuration:</p>
-    <pre class="green">
+    <pre>
   HamaConfiguration conf = new HamaConfiguration();
   BSPJob job = new BSPJob(conf, MyBSP.class);
   job.setJobName("My BSP program");
@@ -68,9 +68,9 @@ xsi:schemaLocation="http://maven.apache.
     <p>See the below section for more detailed description of BSP user interfaces.</p>
     
     <subsection name="User Interfaces"></subsection>
-    <h5>Inputs and Outputs</h5>
+    <h4>Inputs and Outputs</h4>
     <p>When setting up a BSPJob, you can provide a Input/OutputFormat and Paths like this:</p>
-    <pre class="green">
+    <pre>
   job.setInputPath(new Path("/tmp/sequence.dat");
   job.setInputFormat(org.apache.hama.bsp.SequenceFileInputFormat.class);
   or,
@@ -87,7 +87,7 @@ xsi:schemaLocation="http://maven.apache.
     <p>Then, you can read the input and write the output from the methods in BSP class which has "BSPPeer" which contains an communication, counters, and IO interfaces as parameter.
     In this case we read a normal text file:</p>
 
-    <pre class="green">
+    <pre>
  @Override
   public final void bsp(
       BSPPeer&lt;LongWritable, Text, Text, LongWritable, Text&gt; peer)
@@ -108,7 +108,7 @@ xsi:schemaLocation="http://maven.apache.
     There is also a function which allows you to re-read the input from the beginning.
     This snippet reads the input five times:
     </p>
-    <pre class="green">
+    <pre>
   for(int i = 0; i &lt; 5; i++){
     LongWritable key = new LongWritable();
     Text value = new Text();
@@ -119,7 +119,7 @@ xsi:schemaLocation="http://maven.apache.
     peer.reopenInput()
   }</pre>
   
-    <h5>Communication</h5>
+    <h4>Communication</h4>
     <p>Hama BSP provides simple but powerful communication APIs for many purposes. 
     We tried to follow the standard library of BSP world as much as possible. 
     The following table describes all the methods you can use:</p>
@@ -137,7 +137,7 @@ xsi:schemaLocation="http://maven.apache.
 
     <p>The send() and all the other functions are very flexible. Here is an example that sends a message to all peers:</p>
     
-    <pre class="green">
+    <pre>
   @Override
   public void bsp(
       BSPPeer&lt;NullWritable, NullWritable, Text, DoubleWritable, Text&gt; peer)
@@ -150,7 +150,7 @@ xsi:schemaLocation="http://maven.apache.
     peer.sync();
   }</pre>
     
-    <h5>Synchronization</h5>
+    <h4>Synchronization</h4>
 
     <p>When all the processes have entered the barrier via the sync() method, 
     the Hama proceeds to the next superstep. 
@@ -162,7 +162,7 @@ xsi:schemaLocation="http://maven.apache.
     For example, the sync() method also can be called in a for loop 
     so that you can use to program the iterative methods sequentially:</p>
     
-    <pre class="green">
+    <pre>
   @Override
   public void bsp(
       BSPPeer&lt;NullWritable, NullWritable, Text, DoubleWritable, Text&gt; peer)
@@ -191,7 +191,7 @@ xsi:schemaLocation="http://maven.apache.
 
     <subsection name="Example: Pi Calculation"></subsection>
     <p>Here is an BSP-based Pi Calculation example and submit it to Hama cluster:</p>
-    <pre class="green">
+    <pre>
   private static Path TMP_OUTPUT = new Path("/tmp/pi-" + System.currentTimeMillis());
 
   public static class MyEstimator extends

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/hama_graph_tutorial.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/hama_graph_tutorial.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/hama_graph_tutorial.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/hama_graph_tutorial.xml Sun Aug  5 12:32:58 2012
@@ -30,7 +30,7 @@ xsi:schemaLocation="http://maven.apache.
     <subsection name="Vertex API"></subsection>    
 
     <p>Writing a Hama graph application involves subclassing the predefined Vertex class. Its template arguments define three value types, associated with vertices, edges, and messages.</p>
-    <pre class="green">
+    <pre>
   public abstract class Vertex&lt;V extends Writable, E extends Writable, M extends Writable&gt;
       implements VertexInterface&lt;V, E, M&gt; {
 
@@ -48,7 +48,7 @@ In this example, the algorithm described
 From Superstep 1 to 30, each vertex sums up the values arriving on all its messages and sets its tentative page rank to (1 - 0.85) / numOfVertices + (0.85 * sum).
    </p>
 
-    <pre class="green">
+    <pre>
   public static class PageRankVertex extends
       Vertex&lt;Text, NullWritable, DoubleWritable&gt; {
 

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/hama_on_clouds.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/hama_on_clouds.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/hama_on_clouds.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/hama_on_clouds.xml Sun Aug  5 12:32:58 2012
@@ -27,7 +27,7 @@ xsi:schemaLocation="http://maven.apache.
     
     <subsection name="Deploy a Hama cluster on EC2"></subsection>
     <p>The following commands install Whirr and start a 5 node Hama cluster on Amazon EC2 in 5 minutes or less.
-    <pre class="green">
+    <pre>
   % curl -O http://www.apache.org/dist/whirr/whirr-0.x.0/whirr-0.x.0.tar.gz
   % tar zxf whirr-0.x.0.tar.gz; cd whirr-0.x.0
 
@@ -38,7 +38,7 @@ xsi:schemaLocation="http://maven.apache.
   % bin/whirr launch-cluster --config recipes/hama-ec2.properties --private-key-file ~/.ssh/id_rsa_whirr</pre>
     </p>
     <subsection name="Execute Hama Examples"></subsection>
-    <pre class="green">
+    <pre>
   % cd /usr/local/hama-0.x.0
   % bin/hama jar hama-examples-x.x.x.jar [args]</pre>
     </body>

Modified: hama/branches/HAMA-505-branch/src/site/xdoc/index.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/src/site/xdoc/index.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/src/site/xdoc/index.xml (original)
+++ hama/branches/HAMA-505-branch/src/site/xdoc/index.xml Sun Aug  5 12:32:58 2012
@@ -26,8 +26,7 @@ xsi:schemaLocation="http://maven.apache.
       <p>
       <strong>Apache Hama</strong> is a pure BSP (Bulk Synchronous Parallel) computing framework on top of HDFS (Hadoop Distributed File System) for massive scientific computations 
       such as matrix, graph and network algorithms.</p>
-      <table class="green" width="100%" cellspacing="0" cellpadding="5" border="1"> 
-      <tr><td> 
+      <div class="green">
           <h3 align="center">Recent News</h3>
           <ul>
             <li>June 31, 2012: release 0.5.0 available [<a href="downloads.html">downloads</a>]</li>
@@ -37,7 +36,7 @@ xsi:schemaLocation="http://maven.apache.
             <li>June 2, 2011: release 0.2.0 available</li>
             <li>Apr 30, 2010: Introduced in the <a href="http://www.bsp-worldwide.org/bspww3000.html">BSP Worldwide</a></li>
           </ul>
-      </td></tr></table>
+      </div>
     <subsection name="Why Hama and BSP?"></subsection>
     <p>Today, many practical data processing applications require a more flexible programming abstraction model that is compatible to run on highly scalable and massive data systems (e.g., HDFS, HBase, etc). A message passing paradigm beyond Map-Reduce framework would increase its flexibility in its communication capability. Bulk Synchronous Parallel (BSP) model fills the bill appropriately. Some of its significant advantages over MapReduce and MPI are:</p>
     <ul>

Modified: hama/branches/HAMA-505-branch/yarn/pom.xml
URL: http://svn.apache.org/viewvc/hama/branches/HAMA-505-branch/yarn/pom.xml?rev=1369566&r1=1369565&r2=1369566&view=diff
==============================================================================
--- hama/branches/HAMA-505-branch/yarn/pom.xml (original)
+++ hama/branches/HAMA-505-branch/yarn/pom.xml Sun Aug  5 12:32:58 2012
@@ -14,20 +14,19 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <parent>
     <groupId>org.apache.hama</groupId>
     <artifactId>hama-parent</artifactId>
-    <version>0.5.0-SNAPSHOT</version>
+    <version>0.6.0-SNAPSHOT</version>
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.apache.hama</groupId>
   <artifactId>hama-yarn</artifactId>
   <name>yarn</name>
-  <version>0.5.0-SNAPSHOT</version>
+  <version>0.6.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <dependencies>



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