Merge github.com:apache/spark into cleanup

Author: andrewor14

core/src/main/scala/org/apache/spark/SparkEnv.scala

@@ -81,7 +81,7 @@ class SparkEnv private[spark] (
     // Unfortunately Akka's awaitTermination doesn't actually wait for the Netty server to shut
     // down, but let's call it anyway in case it gets fixed in a later release
     // UPDATE: In Akka 2.1.x, this hangs if there are remote actors, so we can't call it.
-    //actorSystem.awaitTermination()
+    // actorSystem.awaitTermination()
   }
 
   private[spark]

core/src/main/scala/org/apache/spark/deploy/LocalSparkCluster.scala

@@ -66,9 +66,9 @@ class LocalSparkCluster(numWorkers: Int, coresPerWorker: Int, memoryPerWorker: I
     // TODO: In Akka 2.1.x, ActorSystem.awaitTermination hangs when you have remote actors!
     //       This is unfortunate, but for now we just comment it out.
     workerActorSystems.foreach(_.shutdown())
-    //workerActorSystems.foreach(_.awaitTermination())
+    // workerActorSystems.foreach(_.awaitTermination())
     masterActorSystems.foreach(_.shutdown())
-    //masterActorSystems.foreach(_.awaitTermination())
+    // masterActorSystems.foreach(_.awaitTermination())
     masterActorSystems.clear()
     workerActorSystems.clear()
   }

core/src/main/scala/org/apache/spark/deploy/master/LeaderElectionAgent.scala

@@ -30,7 +30,7 @@ import org.apache.spark.deploy.master.MasterMessages.ElectedLeader
  * [[org.apache.spark.deploy.master.MasterMessages.RevokedLeadership RevokedLeadership]]
  */
 private[spark] trait LeaderElectionAgent extends Actor {
-  //TODO: LeaderElectionAgent does not necessary to be an Actor anymore, need refactoring.
+  // TODO: LeaderElectionAgent does not necessary to be an Actor anymore, need refactoring.
   val masterActor: ActorRef
 }
 

core/src/main/scala/org/apache/spark/executor/Executor.scala

@@ -112,11 +112,10 @@ private[spark] class Executor(
     }
   }
 
-  // Create our ClassLoader and set it on this thread
+  // Create our ClassLoader
   // do this after SparkEnv creation so can access the SecurityManager
   private val urlClassLoader = createClassLoader()
   private val replClassLoader = addReplClassLoaderIfNeeded(urlClassLoader)
-  Thread.currentThread.setContextClassLoader(replClassLoader)
 
   // Akka's message frame size. If task result is bigger than this, we use the block manager
   // to send the result back.
@@ -276,7 +275,6 @@ private[spark] class Executor(
           // have left some weird state around depending on when the exception was thrown, but on
           // the other hand, maybe we could detect that when future tasks fail and exit then.
           logError("Exception in task ID " + taskId, t)
-          //System.exit(1)
         }
       } finally {
         // TODO: Unregister shuffle memory only for ResultTask
@@ -294,7 +292,7 @@ private[spark] class Executor(
    * created by the interpreter to the search path
    */
   private def createClassLoader(): ExecutorURLClassLoader = {
-    val loader = this.getClass.getClassLoader
+    val loader = Thread.currentThread().getContextClassLoader
 
     // For each of the jars in the jarSet, add them to the class loader.
     // We assume each of the files has already been fetched.

core/src/main/scala/org/apache/spark/metrics/MetricsConfig.scala

@@ -42,7 +42,7 @@ private[spark] class MetricsConfig(val configFile: Option[String]) extends Loggi
   }
 
   def initialize() {
-    //Add default properties in case there's no properties file
+    // Add default properties in case there's no properties file
     setDefaultProperties(properties)
 
     // If spark.metrics.conf is not set, try to get file in class path

core/src/main/scala/org/apache/spark/network/Connection.scala

@@ -48,7 +48,7 @@ abstract class Connection(val channel: SocketChannel, val selector: Selector,
   channel.socket.setTcpNoDelay(true)
   channel.socket.setReuseAddress(true)
   channel.socket.setKeepAlive(true)
-  /*channel.socket.setReceiveBufferSize(32768) */
+  /* channel.socket.setReceiveBufferSize(32768) */
 
   @volatile private var closed = false
   var onCloseCallback: Connection => Unit = null
@@ -206,12 +206,12 @@ class SendingConnection(val address: InetSocketAddress, selector_ : Selector,
 
   private class Outbox {
     val messages = new Queue[Message]()
-    val defaultChunkSize = 65536  //32768 //16384
+    val defaultChunkSize = 65536
     var nextMessageToBeUsed = 0
 
     def addMessage(message: Message) {
       messages.synchronized{
-        /*messages += message*/
+        /* messages += message*/
         messages.enqueue(message)
         logDebug("Added [" + message + "] to outbox for sending to " +
           "[" + getRemoteConnectionManagerId() + "]")
@@ -221,8 +221,8 @@ class SendingConnection(val address: InetSocketAddress, selector_ : Selector,
     def getChunk(): Option[MessageChunk] = {
       messages.synchronized {
         while (!messages.isEmpty) {
-          /*nextMessageToBeUsed = nextMessageToBeUsed % messages.size */
-          /*val message = messages(nextMessageToBeUsed)*/
+          /* nextMessageToBeUsed = nextMessageToBeUsed % messages.size */
+          /* val message = messages(nextMessageToBeUsed)*/
           val message = messages.dequeue
           val chunk = message.getChunkForSending(defaultChunkSize)
           if (chunk.isDefined) {
@@ -262,7 +262,7 @@ class SendingConnection(val address: InetSocketAddress, selector_ : Selector,
 
   val currentBuffers = new ArrayBuffer[ByteBuffer]()
 
-  /*channel.socket.setSendBufferSize(256 * 1024)*/
+  /* channel.socket.setSendBufferSize(256 * 1024)*/
 
   override def getRemoteAddress() = address
 
@@ -355,7 +355,7 @@ class SendingConnection(val address: InetSocketAddress, selector_ : Selector,
               }
               case None => {
                 // changeConnectionKeyInterest(0)
-                /*key.interestOps(0)*/
+                /* key.interestOps(0)*/
                 return false
               }
             }
@@ -540,10 +540,10 @@ private[spark] class ReceivingConnection(
           return false
         }
 
-        /*logDebug("Read " + bytesRead + " bytes for the buffer")*/
+        /* logDebug("Read " + bytesRead + " bytes for the buffer")*/
 
         if (currentChunk.buffer.remaining == 0) {
-          /*println("Filled buffer at " + System.currentTimeMillis)*/
+          /* println("Filled buffer at " + System.currentTimeMillis)*/
           val bufferMessage = inbox.getMessageForChunk(currentChunk).get
           if (bufferMessage.isCompletelyReceived) {
             bufferMessage.flip

core/src/main/scala/org/apache/spark/network/ConnectionManager.scala

@@ -504,7 +504,7 @@ private[spark] class ConnectionManager(port: Int, conf: SparkConf,
       }
     }
     handleMessageExecutor.execute(runnable)
-    /*handleMessage(connection, message)*/
+    /* handleMessage(connection, message)*/
   }
 
   private def handleClientAuthentication(
@@ -732,7 +732,7 @@ private[spark] class ConnectionManager(port: Int, conf: SparkConf,
     logTrace("Sending Security [" + message + "] to [" + connManagerId + "]")
     val connection = connectionsById.getOrElseUpdate(connManagerId, startNewConnection())
 
-    //send security message until going connection has been authenticated
+    // send security message until going connection has been authenticated
     connection.send(message)
 
     wakeupSelector()
@@ -858,14 +858,14 @@ private[spark] object ConnectionManager {
       None
     })
 
-    /*testSequentialSending(manager)*/
-    /*System.gc()*/
+    /* testSequentialSending(manager)*/
+    /* System.gc()*/
 
-    /*testParallelSending(manager)*/
-    /*System.gc()*/
+    /* testParallelSending(manager)*/
+    /* System.gc()*/
 
-    /*testParallelDecreasingSending(manager)*/
-    /*System.gc()*/
+    /* testParallelDecreasingSending(manager)*/
+    /* System.gc()*/
 
     testContinuousSending(manager)
     System.gc()
@@ -947,7 +947,7 @@ private[spark] object ConnectionManager {
     val ms = finishTime - startTime
     val tput = mb * 1000.0 / ms
     println("--------------------------")
-    /*println("Started at " + startTime + ", finished at " + finishTime) */
+    /* println("Started at " + startTime + ", finished at " + finishTime) */
     println("Sent " + mb + " MB in " + ms + " ms (" + tput + " MB/s)")
     println("--------------------------")
     println()

core/src/main/scala/org/apache/spark/network/ConnectionManagerTest.scala

@@ -47,8 +47,8 @@ private[spark] object ConnectionManagerTest extends Logging{
     val slaves = slavesFile.mkString.split("\n")
     slavesFile.close()
 
-    /*println("Slaves")*/
-    /*slaves.foreach(println)*/
+    /* println("Slaves")*/
+    /* slaves.foreach(println)*/
     val tasknum = if (args.length > 2) args(2).toInt else slaves.length
     val size = ( if (args.length > 3) (args(3).toInt) else 10 ) * 1024 * 1024 
     val count = if (args.length > 4) args(4).toInt else 3

core/src/main/scala/org/apache/spark/network/ReceiverTest.scala

@@ -27,7 +27,7 @@ private[spark] object ReceiverTest {
     println("Started connection manager with id = " + manager.id)
 
     manager.onReceiveMessage((msg: Message, id: ConnectionManagerId) => {
-      /*println("Received [" + msg + "] from [" + id + "] at " + System.currentTimeMillis)*/
+      /* println("Received [" + msg + "] from [" + id + "] at " + System.currentTimeMillis)*/
       val buffer = ByteBuffer.wrap("response".getBytes)
       Some(Message.createBufferMessage(buffer, msg.id))
     })

core/src/main/scala/org/apache/spark/network/SenderTest.scala

@@ -50,7 +50,7 @@ private[spark] object SenderTest {
     (0 until count).foreach(i => {
       val dataMessage = Message.createBufferMessage(buffer.duplicate)
       val startTime = System.currentTimeMillis
-      /*println("Started timer at " + startTime)*/
+      /* println("Started timer at " + startTime)*/
       val responseStr = manager.sendMessageReliablySync(targetConnectionManagerId, dataMessage)
         .map { response =>
           val buffer = response.asInstanceOf[BufferMessage].buffers(0)

core/src/main/scala/org/apache/spark/network/netty/FileHeader.scala

@@ -32,7 +32,7 @@ private[spark] class FileHeader (
     buf.writeInt(fileLen)
     buf.writeInt(blockId.name.length)
     blockId.name.foreach((x: Char) => buf.writeByte(x))
-    //padding the rest of header
+    // padding the rest of header
     if (FileHeader.HEADER_SIZE - buf.readableBytes > 0 ) {
       buf.writeZero(FileHeader.HEADER_SIZE - buf.readableBytes)
     } else {

core/src/main/scala/org/apache/spark/scheduler/DAGScheduler.scala

@@ -753,7 +753,7 @@ class DAGScheduler(
     val properties = if (stageIdToActiveJob.contains(jobId)) {
       stageIdToActiveJob(stage.jobId).properties
     } else {
-      //this stage will be assigned to "default" pool
+      // this stage will be assigned to "default" pool
       null
     }
 

core/src/main/scala/org/apache/spark/scheduler/cluster/CoarseGrainedSchedulerBackend.scala

@@ -172,7 +172,7 @@ class CoarseGrainedSchedulerBackend(scheduler: TaskSchedulerImpl, actorSystem: A
         properties += ((key, value))
       }
     }
-    //TODO (prashant) send conf instead of properties
+    // TODO (prashant) send conf instead of properties
     driverActor = actorSystem.actorOf(
       Props(new DriverActor(properties)), name = CoarseGrainedSchedulerBackend.ACTOR_NAME)
   }

core/src/main/scala/org/apache/spark/storage/BlockFetcherIterator.scala

@@ -284,7 +284,7 @@ object BlockFetcherIterator {
               }
             } catch {
               case x: InterruptedException => logInfo("Copier Interrupted")
-              //case _ => throw new SparkException("Exception Throw in Shuffle Copier")
+              // case _ => throw new SparkException("Exception Throw in Shuffle Copier")
             }
           }
         }

core/src/main/scala/org/apache/spark/util/ClosureCleaner.scala

@@ -112,7 +112,7 @@ private[spark] object ClosureCleaner extends Logging {
       accessedFields(cls) = Set[String]()
     for (cls <- func.getClass :: innerClasses)
       getClassReader(cls).accept(new FieldAccessFinder(accessedFields), 0)
-    //logInfo("accessedFields: " + accessedFields)
+    // logInfo("accessedFields: " + accessedFields)
 
     val inInterpreter = {
       try {
@@ -139,21 +139,21 @@ private[spark] object ClosureCleaner extends Logging {
         val field = cls.getDeclaredField(fieldName)
         field.setAccessible(true)
         val value = field.get(obj)
-        //logInfo("1: Setting " + fieldName + " on " + cls + " to " + value);
+        // logInfo("1: Setting " + fieldName + " on " + cls + " to " + value);
         field.set(outer, value)
       }
     }
 
     if (outer != null) {
-      //logInfo("2: Setting $outer on " + func.getClass + " to " + outer);
+      // logInfo("2: Setting $outer on " + func.getClass + " to " + outer);
       val field = func.getClass.getDeclaredField("$outer")
       field.setAccessible(true)
       field.set(func, outer)
     }
   }
 
   private def instantiateClass(cls: Class[_], outer: AnyRef, inInterpreter: Boolean): AnyRef = {
-    //logInfo("Creating a " + cls + " with outer = " + outer)
+    // logInfo("Creating a " + cls + " with outer = " + outer)
     if (!inInterpreter) {
       // This is a bona fide closure class, whose constructor has no effects
       // other than to set its fields, so use its constructor
@@ -170,7 +170,7 @@ private[spark] object ClosureCleaner extends Logging {
       val newCtor = rf.newConstructorForSerialization(cls, parentCtor)
       val obj = newCtor.newInstance().asInstanceOf[AnyRef]
       if (outer != null) {
-        //logInfo("3: Setting $outer on " + cls + " to " + outer);
+        // logInfo("3: Setting $outer on " + cls + " to " + outer);
         val field = cls.getDeclaredField("$outer")
         field.setAccessible(true)
         field.set(obj, outer)

core/src/main/scala/org/apache/spark/util/IndestructibleActorSystem.scala

@@ -49,7 +49,7 @@ private[akka] class IndestructibleActorSystemImpl(
         if (isFatalError(cause) && !settings.JvmExitOnFatalError) {
           log.error(cause, "Uncaught fatal error from thread [{}] not shutting down " +
             "ActorSystem [{}] tolerating and continuing.... ", thread.getName, name)
-          //shutdown()                 //TODO make it configurable
+          // shutdown()                 //TODO make it configurable
         } else {
           fallbackHandler.uncaughtException(thread, cause)
         }

core/src/main/scala/org/apache/spark/util/MutablePair.scala

@@ -24,8 +24,8 @@ package org.apache.spark.util
  * @param  _1   Element 1 of this MutablePair
  * @param  _2   Element 2 of this MutablePair
  */
-case class MutablePair[@specialized(Int, Long, Double, Char, Boolean/*, AnyRef*/) T1,
-                       @specialized(Int, Long, Double, Char, Boolean/*, AnyRef*/) T2]
+case class MutablePair[@specialized(Int, Long, Double, Char, Boolean/* , AnyRef*/) T1,
+                       @specialized(Int, Long, Double, Char, Boolean/* , AnyRef*/) T2]
   (var _1: T1, var _2: T2)
   extends Product2[T1, T2]
 {

core/src/main/scala/org/apache/spark/util/collection/BitSet.scala

@@ -88,6 +88,45 @@ class BitSet(numBits: Int) extends Serializable {
     newBS
   }
 
+  /**
+   * Compute the symmetric difference by performing bit-wise XOR of the two sets returning the
+   * result.
+   */
+  def ^(other: BitSet): BitSet = {
+    val newBS = new BitSet(math.max(capacity, other.capacity))
+    val smaller = math.min(numWords, other.numWords)
+    var ind = 0
+    while (ind < smaller) {
+      newBS.words(ind) = words(ind) ^ other.words(ind)
+      ind += 1
+    }
+    if (ind < numWords) {
+      Array.copy( words, ind, newBS.words, ind, numWords - ind )
+    }
+    if (ind < other.numWords) {
+      Array.copy( other.words, ind, newBS.words, ind, other.numWords - ind )
+    }
+    newBS
+  }
+
+  /**
+   * Compute the difference of the two sets by performing bit-wise AND-NOT returning the
+   * result.
+   */
+  def andNot(other: BitSet): BitSet = {
+    val newBS = new BitSet(capacity)
+    val smaller = math.min(numWords, other.numWords)
+    var ind = 0
+    while (ind < smaller) {
+      newBS.words(ind) = words(ind) & ~other.words(ind)
+      ind += 1
+    }
+    if (ind < numWords) {
+      Array.copy( words, ind, newBS.words, ind, numWords - ind )
+    }
+    newBS
+  }
+
   /**
    * Sets the bit at the specified index to true.
    * @param index the bit index

core/src/test/scala/org/apache/spark/AccumulatorSuite.scala

@@ -66,7 +66,7 @@ class AccumulatorSuite extends FunSuite with ShouldMatchers with LocalSparkConte
 
   test ("add value to collection accumulators") {
     val maxI = 1000
-    for (nThreads <- List(1, 10)) { //test single & multi-threaded
+    for (nThreads <- List(1, 10)) { // test single & multi-threaded
       sc = new SparkContext("local[" + nThreads + "]", "test")
       val acc: Accumulable[mutable.Set[Any], Any] = sc.accumulable(new mutable.HashSet[Any]())
       val d = sc.parallelize(1 to maxI)
@@ -83,7 +83,7 @@ class AccumulatorSuite extends FunSuite with ShouldMatchers with LocalSparkConte
 
   test ("value not readable in tasks") {
     val maxI = 1000
-    for (nThreads <- List(1, 10)) { //test single & multi-threaded
+    for (nThreads <- List(1, 10)) { // test single & multi-threaded
       sc = new SparkContext("local[" + nThreads + "]", "test")
       val acc: Accumulable[mutable.Set[Any], Any] = sc.accumulable(new mutable.HashSet[Any]())
       val d = sc.parallelize(1 to maxI)
@@ -124,7 +124,7 @@ class AccumulatorSuite extends FunSuite with ShouldMatchers with LocalSparkConte
 
   test ("localValue readable in tasks") {
     val maxI = 1000
-    for (nThreads <- List(1, 10)) { //test single & multi-threaded
+    for (nThreads <- List(1, 10)) { // test single & multi-threaded
       sc = new SparkContext("local[" + nThreads + "]", "test")
       val acc: Accumulable[mutable.Set[Any], Any] = sc.accumulable(new mutable.HashSet[Any]())
       val groupedInts = (1 to (maxI/20)).map {x => (20 * (x - 1) to 20 * x).toSet}

core/src/test/scala/org/apache/spark/CheckpointSuite.scala

@@ -432,7 +432,6 @@ object CheckpointSuite {
   // This is a custom cogroup function that does not use mapValues like
   // the PairRDDFunctions.cogroup()
   def cogroup[K, V](first: RDD[(K, V)], second: RDD[(K, V)], part: Partitioner) = {
-    //println("First = " + first + ", second = " + second)
     new CoGroupedRDD[K](
       Seq(first.asInstanceOf[RDD[(K, _)]], second.asInstanceOf[RDD[(K, _)]]),
       part