Merge remote-tracking branch 'upstream/master' into ldaonline

Author: hhbyyh

LICENSE

@@ -814,6 +814,7 @@ BSD-style licenses
 The following components are provided under a BSD-style license. See project link for details.
 
      (BSD 3 Clause) core (com.github.fommil.netlib:core:1.1.2 - https://github.com/fommil/netlib-java/core)
+     (BSD 3 Clause) JPMML-Model (org.jpmml:pmml-model:1.1.15 - https://github.com/jpmml/jpmml-model)
      (BSD 3-clause style license) jblas (org.jblas:jblas:1.2.3 - http://jblas.org/)
      (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
      (BSD License) Javolution (javolution:javolution:5.5.1 - http://javolution.org)

assembly/pom.xml

@@ -194,7 +194,6 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-assembly-plugin</artifactId>
-            <version>2.4</version>
             <executions>
               <execution>
                 <id>dist</id>

bin/spark-class2.cmd

@@ -61,7 +61,10 @@ if not "x%JAVA_HOME%"=="x" set RUNNER=%JAVA_HOME%\bin\java
 
 rem The launcher library prints the command to be executed in a single line suitable for being
 rem executed by the batch interpreter. So read all the output of the launcher into a variable.
-for /f "tokens=*" %%i in ('cmd /C ""%RUNNER%" -cp %LAUNCH_CLASSPATH% org.apache.spark.launcher.Main %*"') do (
+set LAUNCHER_OUTPUT=%temp%\spark-class-launcher-output-%RANDOM%.txt
+"%RUNNER%" -cp %LAUNCH_CLASSPATH% org.apache.spark.launcher.Main %* > %LAUNCHER_OUTPUT%
+for /f "tokens=*" %%i in (%LAUNCHER_OUTPUT%) do (
   set SPARK_CMD=%%i
 )
+del %LAUNCHER_OUTPUT%
 %SPARK_CMD%

conf/spark-env.sh.template

@@ -3,7 +3,7 @@
 # This file is sourced when running various Spark programs.
 # Copy it as spark-env.sh and edit that to configure Spark for your site.
 
-# Options read when launching programs locally with 
+# Options read when launching programs locally with
 # ./bin/run-example or ./bin/spark-submit
 # - HADOOP_CONF_DIR, to point Spark towards Hadoop configuration files
 # - SPARK_LOCAL_IP, to set the IP address Spark binds to on this node
@@ -39,6 +39,7 @@
 # - SPARK_WORKER_DIR, to set the working directory of worker processes
 # - SPARK_WORKER_OPTS, to set config properties only for the worker (e.g. "-Dx=y")
 # - SPARK_HISTORY_OPTS, to set config properties only for the history server (e.g. "-Dx=y")
+# - SPARK_SHUFFLE_OPTS, to set config properties only for the external shuffle service (e.g. "-Dx=y")
 # - SPARK_DAEMON_JAVA_OPTS, to set config properties for all daemons (e.g. "-Dx=y")
 # - SPARK_PUBLIC_DNS, to set the public dns name of the master or workers
 

core/pom.xml

@@ -95,6 +95,11 @@
       <artifactId>spark-network-shuffle_${scala.binary.version}</artifactId>
       <version>${project.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.apache.spark</groupId>
+      <artifactId>spark-unsafe_${scala.binary.version}</artifactId>
+      <version>${project.version}</version>
+    </dependency>
     <dependency>
       <groupId>net.java.dev.jets3t</groupId>
       <artifactId>jets3t</artifactId>
@@ -478,7 +483,6 @@
           <plugin>
             <groupId>org.codehaus.mojo</groupId>
             <artifactId>exec-maven-plugin</artifactId>
-            <version>1.3.2</version>
             <executions>
               <execution>
                 <id>sparkr-pkg</id>

core/src/main/java/org/apache/spark/api/java/function/Function0.java

@@ -0,0 +1,27 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.spark.api.java.function;
+
+import java.io.Serializable;
+
+/**
+ * A zero-argument function that returns an R.
+ */
+public interface Function0<R> extends Serializable {
+  public R call() throws Exception;
+}

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

@@ -76,13 +76,15 @@ private[spark] class HeartbeatReceiver(sc: SparkContext)
 
   private var timeoutCheckingTask: ScheduledFuture[_] = null
 
-  private val timeoutCheckingThread =
-    ThreadUtils.newDaemonSingleThreadScheduledExecutor("heartbeat-timeout-checking-thread")
+  // "eventLoopThread" is used to run some pretty fast actions. The actions running in it should not
+  // block the thread for a long time.
+  private val eventLoopThread =
+    ThreadUtils.newDaemonSingleThreadScheduledExecutor("heartbeat-receiver-event-loop-thread")
 
   private val killExecutorThread = ThreadUtils.newDaemonSingleThreadExecutor("kill-executor-thread")
 
   override def onStart(): Unit = {
-    timeoutCheckingTask = timeoutCheckingThread.scheduleAtFixedRate(new Runnable {
+    timeoutCheckingTask = eventLoopThread.scheduleAtFixedRate(new Runnable {
       override def run(): Unit = Utils.tryLogNonFatalError {
         Option(self).foreach(_.send(ExpireDeadHosts))
       }
@@ -99,11 +101,15 @@ private[spark] class HeartbeatReceiver(sc: SparkContext)
   override def receiveAndReply(context: RpcCallContext): PartialFunction[Any, Unit] = {
     case heartbeat @ Heartbeat(executorId, taskMetrics, blockManagerId) =>
       if (scheduler != null) {
-        val unknownExecutor = !scheduler.executorHeartbeatReceived(
-          executorId, taskMetrics, blockManagerId)
-        val response = HeartbeatResponse(reregisterBlockManager = unknownExecutor)
         executorLastSeen(executorId) = System.currentTimeMillis()
-        context.reply(response)
+        eventLoopThread.submit(new Runnable {
+          override def run(): Unit = Utils.tryLogNonFatalError {
+            val unknownExecutor = !scheduler.executorHeartbeatReceived(
+              executorId, taskMetrics, blockManagerId)
+            val response = HeartbeatResponse(reregisterBlockManager = unknownExecutor)
+            context.reply(response)
+          }
+        })
       } else {
         // Because Executor will sleep several seconds before sending the first "Heartbeat", this
         // case rarely happens. However, if it really happens, log it and ask the executor to
@@ -125,7 +131,9 @@ private[spark] class HeartbeatReceiver(sc: SparkContext)
         if (sc.supportDynamicAllocation) {
           // Asynchronously kill the executor to avoid blocking the current thread
           killExecutorThread.submit(new Runnable {
-            override def run(): Unit = sc.killExecutor(executorId)
+            override def run(): Unit = Utils.tryLogNonFatalError {
+              sc.killExecutor(executorId)
+            }
           })
         }
         executorLastSeen.remove(executorId)
@@ -137,7 +145,7 @@ private[spark] class HeartbeatReceiver(sc: SparkContext)
     if (timeoutCheckingTask != null) {
       timeoutCheckingTask.cancel(true)
     }
-    timeoutCheckingThread.shutdownNow()
+    eventLoopThread.shutdownNow()
     killExecutorThread.shutdownNow()
   }
 }

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

@@ -106,7 +106,7 @@ private[spark] abstract class MapOutputTracker(conf: SparkConf) extends Logging
    */
   protected def askTracker[T: ClassTag](message: Any): T = {
     try {
-      trackerEndpoint.askWithReply[T](message)
+      trackerEndpoint.askWithRetry[T](message)
     } catch {
       case e: Exception =>
         logError("Error communicating with MapOutputTracker", e)

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

@@ -211,7 +211,74 @@ class SparkConf(loadDefaults: Boolean) extends Cloneable with Logging {
     Utils.timeStringAsMs(get(key, defaultValue))
   }
 
+  /**
+   * Get a size parameter as bytes; throws a NoSuchElementException if it's not set. If no
+   * suffix is provided then bytes are assumed.
+   * @throws NoSuchElementException
+   */
+  def getSizeAsBytes(key: String): Long = {
+    Utils.byteStringAsBytes(get(key))
+  }
+
+  /**
+   * Get a size parameter as bytes, falling back to a default if not set. If no
+   * suffix is provided then bytes are assumed.
+   */
+  def getSizeAsBytes(key: String, defaultValue: String): Long = {
+    Utils.byteStringAsBytes(get(key, defaultValue))
+  }
+  
+  /**
+   * Get a size parameter as Kibibytes; throws a NoSuchElementException if it's not set. If no
+   * suffix is provided then Kibibytes are assumed.
+   * @throws NoSuchElementException
+   */
+  def getSizeAsKb(key: String): Long = {
+    Utils.byteStringAsKb(get(key))
+  }
+
+  /**
+   * Get a size parameter as Kibibytes, falling back to a default if not set. If no
+   * suffix is provided then Kibibytes are assumed.
+   */
+  def getSizeAsKb(key: String, defaultValue: String): Long = {
+    Utils.byteStringAsKb(get(key, defaultValue))
+  }
+  
+  /**
+   * Get a size parameter as Mebibytes; throws a NoSuchElementException if it's not set. If no
+   * suffix is provided then Mebibytes are assumed.
+   * @throws NoSuchElementException
+   */
+  def getSizeAsMb(key: String): Long = {
+    Utils.byteStringAsMb(get(key))
+  }
+
+  /**
+   * Get a size parameter as Mebibytes, falling back to a default if not set. If no
+   * suffix is provided then Mebibytes are assumed.
+   */
+  def getSizeAsMb(key: String, defaultValue: String): Long = {
+    Utils.byteStringAsMb(get(key, defaultValue))
+  }
+  
+  /**
+   * Get a size parameter as Gibibytes; throws a NoSuchElementException if it's not set. If no
+   * suffix is provided then Gibibytes are assumed.
+   * @throws NoSuchElementException
+   */
+  def getSizeAsGb(key: String): Long = {
+    Utils.byteStringAsGb(get(key))
+  }
 
+  /**
+   * Get a size parameter as Gibibytes, falling back to a default if not set. If no
+   * suffix is provided then Gibibytes are assumed.
+   */
+  def getSizeAsGb(key: String, defaultValue: String): Long = {
+    Utils.byteStringAsGb(get(key, defaultValue))
+  }
+  
   /** Get a parameter as an Option */
   def getOption(key: String): Option[String] = {
     Option(settings.get(key)).orElse(getDeprecatedConfig(key, this))
@@ -407,7 +474,13 @@ private[spark] object SparkConf extends Logging {
         "The spark.cache.class property is no longer being used! Specify storage levels using " +
         "the RDD.persist() method instead."),
       DeprecatedConfig("spark.yarn.user.classpath.first", "1.3",
-        "Please use spark.{driver,executor}.userClassPathFirst instead."))
+        "Please use spark.{driver,executor}.userClassPathFirst instead."),
+      DeprecatedConfig("spark.kryoserializer.buffer.mb", "1.4",
+        "Please use spark.kryoserializer.buffer instead. The default value for " +
+          "spark.kryoserializer.buffer.mb was previously specified as '0.064'. Fractional values " +
+          "are no longer accepted. To specify the equivalent now, one may use '64k'.")
+    )
+    
     Map(configs.map { cfg => (cfg.key -> cfg) }:_*)
   }
 
@@ -432,6 +505,21 @@ private[spark] object SparkConf extends Logging {
       AlternateConfig("spark.yarn.applicationMaster.waitTries", "1.3",
         // Translate old value to a duration, with 10s wait time per try.
         translation = s => s"${s.toLong * 10}s")),
+    "spark.reducer.maxSizeInFlight" -> Seq(
+      AlternateConfig("spark.reducer.maxMbInFlight", "1.4")),
+    "spark.kryoserializer.buffer" ->
+        Seq(AlternateConfig("spark.kryoserializer.buffer.mb", "1.4", 
+          translation = s => s"${s.toDouble * 1000}k")),
+    "spark.kryoserializer.buffer.max" -> Seq(
+      AlternateConfig("spark.kryoserializer.buffer.max.mb", "1.4")),
+    "spark.shuffle.file.buffer" -> Seq(
+      AlternateConfig("spark.shuffle.file.buffer.kb", "1.4")),
+    "spark.executor.logs.rolling.maxSize" -> Seq(
+      AlternateConfig("spark.executor.logs.rolling.size.maxBytes", "1.4")),
+    "spark.io.compression.snappy.blockSize" -> Seq(
+      AlternateConfig("spark.io.compression.snappy.block.size", "1.4")),
+    "spark.io.compression.lz4.blockSize" -> Seq(
+      AlternateConfig("spark.io.compression.lz4.block.size", "1.4")),
     "spark.rpc.numRetries" -> Seq(
       AlternateConfig("spark.akka.num.retries", "1.4")),
     "spark.rpc.retry.wait" -> Seq(

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

@@ -555,7 +555,7 @@ class SparkContext(config: SparkConf) extends Logging with ExecutorAllocationCli
           SparkEnv.executorActorSystemName,
           RpcAddress(host, port),
           ExecutorEndpoint.EXECUTOR_ENDPOINT_NAME)
-        Some(endpointRef.askWithReply[Array[ThreadStackTrace]](TriggerThreadDump))
+        Some(endpointRef.askWithRetry[Array[ThreadStackTrace]](TriggerThreadDump))
       }
     } catch {
       case e: Exception =>
@@ -713,7 +713,9 @@ class SparkContext(config: SparkConf) extends Logging with ExecutorAllocationCli
   RDD[(String, String)] = {
     assertNotStopped()
     val job = new NewHadoopJob(hadoopConfiguration)
-    NewFileInputFormat.addInputPath(job, new Path(path))
+    // Use setInputPaths so that wholeTextFiles aligns with hadoopFile/textFile in taking
+    // comma separated files as input. (see SPARK-7155)
+    NewFileInputFormat.setInputPaths(job, path)
     val updateConf = job.getConfiguration
     new WholeTextFileRDD(
       this,
@@ -759,7 +761,9 @@ class SparkContext(config: SparkConf) extends Logging with ExecutorAllocationCli
       RDD[(String, PortableDataStream)] = {
     assertNotStopped()
     val job = new NewHadoopJob(hadoopConfiguration)
-    NewFileInputFormat.addInputPath(job, new Path(path))
+    // Use setInputPaths so that binaryFiles aligns with hadoopFile/textFile in taking
+    // comma separated files as input. (see SPARK-7155)
+    NewFileInputFormat.setInputPaths(job, path)
     val updateConf = job.getConfiguration
     new BinaryFileRDD(
       this,
@@ -935,7 +939,9 @@ class SparkContext(config: SparkConf) extends Logging with ExecutorAllocationCli
     // The call to new NewHadoopJob automatically adds security credentials to conf,
     // so we don't need to explicitly add them ourselves
     val job = new NewHadoopJob(conf)
-    NewFileInputFormat.addInputPath(job, new Path(path))
+    // Use setInputPaths so that newAPIHadoopFile aligns with hadoopFile/textFile in taking
+    // comma separated files as input. (see SPARK-7155)
+    NewFileInputFormat.setInputPaths(job, path)
     val updatedConf = job.getConfiguration
     new NewHadoopRDD(this, fClass, kClass, vClass, updatedConf).setName(path)
   }
@@ -1396,6 +1402,11 @@ class SparkContext(config: SparkConf) extends Logging with ExecutorAllocationCli
    * Register an RDD to be persisted in memory and/or disk storage
    */
   private[spark] def persistRDD(rdd: RDD[_]) {
+    _executorAllocationManager.foreach { _ =>
+      logWarning(
+        s"Dynamic allocation currently does not support cached RDDs. Cached data for RDD " +
+        s"${rdd.id} will be lost when executors are removed.")
+    }
     persistentRdds(rdd.id) = rdd
   }
 

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

@@ -40,6 +40,7 @@ import org.apache.spark.scheduler.OutputCommitCoordinator.OutputCommitCoordinato
 import org.apache.spark.serializer.Serializer
 import org.apache.spark.shuffle.{ShuffleMemoryManager, ShuffleManager}
 import org.apache.spark.storage._
+import org.apache.spark.unsafe.memory.{ExecutorMemoryManager, MemoryAllocator}
 import org.apache.spark.util.{RpcUtils, Utils}
 
 /**
@@ -69,6 +70,7 @@ class SparkEnv (
     val sparkFilesDir: String,
     val metricsSystem: MetricsSystem,
     val shuffleMemoryManager: ShuffleMemoryManager,
+    val executorMemoryManager: ExecutorMemoryManager,
     val outputCommitCoordinator: OutputCommitCoordinator,
     val conf: SparkConf) extends Logging {
 
@@ -382,6 +384,15 @@ object SparkEnv extends Logging {
       new OutputCommitCoordinatorEndpoint(rpcEnv, outputCommitCoordinator))
     outputCommitCoordinator.coordinatorRef = Some(outputCommitCoordinatorRef)
 
+    val executorMemoryManager: ExecutorMemoryManager = {
+      val allocator = if (conf.getBoolean("spark.unsafe.offHeap", false)) {
+        MemoryAllocator.UNSAFE
+      } else {
+        MemoryAllocator.HEAP
+      }
+      new ExecutorMemoryManager(allocator)
+    }
+
     val envInstance = new SparkEnv(
       executorId,
       rpcEnv,
@@ -398,6 +409,7 @@ object SparkEnv extends Logging {
       sparkFilesDir,
       metricsSystem,
       shuffleMemoryManager,
+      executorMemoryManager,
       outputCommitCoordinator,
       conf)
 

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

@@ -21,6 +21,7 @@ import java.io.Serializable
 
 import org.apache.spark.annotation.DeveloperApi
 import org.apache.spark.executor.TaskMetrics
+import org.apache.spark.unsafe.memory.TaskMemoryManager
 import org.apache.spark.util.TaskCompletionListener
 
 
@@ -133,4 +134,9 @@ abstract class TaskContext extends Serializable {
   /** ::DeveloperApi:: */
   @DeveloperApi
   def taskMetrics(): TaskMetrics
+
+  /**
+   * Returns the manager for this task's managed memory.
+   */
+  private[spark] def taskMemoryManager(): TaskMemoryManager
 }