SPY-302 pick up dropped backports

core/src/main/scala/org/apache/spark/api/python/PythonRDD.scala

@@ -218,7 +218,6 @@ private[spark] object PythonRDD {
       }
     } catch {
       case eof: EOFException => {}
-      case e: Throwable => throw e
     }
     JavaRDD.fromRDD(sc.sc.parallelize(objs, parallelism))
   }

core/src/main/scala/org/apache/spark/api/python/PythonWorkerFactory.scala

@@ -58,13 +58,11 @@ private[spark] class PythonWorkerFactory(pythonExec: String, envVars: Map[String
       try {
         new Socket(daemonHost, daemonPort)
       } catch {
-        case exc: SocketException => {
+        case exc: SocketException => 
           logWarning("Python daemon unexpectedly quit, attempting to restart")
           stopDaemon()
           startDaemon()
           new Socket(daemonHost, daemonPort)
-        }
-        case e: Throwable => throw e
       }
     }
   }

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

@@ -89,7 +89,7 @@ object SparkHadoopUtil {
           .newInstance()
           .asInstanceOf[SparkHadoopUtil]
       } catch {
-       case th: Throwable => throw new SparkException("Unable to load YARN support", th)
+       case e: Exception => throw new SparkException("Unable to load YARN support", e)
       }
     } else {
       new SparkHadoopUtil

core/src/main/scala/org/apache/spark/deploy/client/AppClient.scala

@@ -31,6 +31,8 @@ import org.apache.spark.deploy.{ApplicationDescription, ExecutorState}
 import org.apache.spark.deploy.DeployMessages._
 import org.apache.spark.deploy.master.Master
 import org.apache.spark.util.AkkaUtils
+import org.apache.spark.util.Utils
+
 
 /**
  * Interface allowing applications to speak with a Spark deploy cluster. Takes a master URL,
@@ -88,14 +90,16 @@ private[spark] class AppClient(
       var retries = 0
       registrationRetryTimer = Some {
         context.system.scheduler.schedule(REGISTRATION_TIMEOUT, REGISTRATION_TIMEOUT) {
-          retries += 1
-          if (registered) {
-            registrationRetryTimer.foreach(_.cancel())
-          } else if (retries >= REGISTRATION_RETRIES) {
-            logError("All masters are unresponsive! Giving up.")
-            markDead()
-          } else {
-            tryRegisterAllMasters()
+          Utils.tryOrExit {
+            retries += 1
+            if (registered) {
+              registrationRetryTimer.foreach(_.cancel())
+            } else if (retries >= REGISTRATION_RETRIES) {
+              logError("All masters are unresponsive! Giving up.")
+              markDead()
+            } else {
+              tryRegisterAllMasters()
+            }
           }
         }
       }

core/src/main/scala/org/apache/spark/deploy/worker/Worker.scala

@@ -163,14 +163,16 @@ private[spark] class Worker(
     var retries = 0
     registrationRetryTimer = Some {
       context.system.scheduler.schedule(REGISTRATION_TIMEOUT, REGISTRATION_TIMEOUT) {
-        retries += 1
-        if (registered) {
-          registrationRetryTimer.foreach(_.cancel())
-        } else if (retries >= REGISTRATION_RETRIES) {
-          logError("All masters are unresponsive! Giving up.")
-          System.exit(1)
-        } else {
-          tryRegisterAllMasters()
+        Utils.tryOrExit {
+          retries += 1
+          if (registered) {
+            registrationRetryTimer.foreach(_.cancel())
+          } else if (retries >= REGISTRATION_RETRIES) {
+            logError("All masters are unresponsive! Giving up.")
+            System.exit(1)
+          } else {
+            tryRegisterAllMasters()
+          }
         }
       }
     }

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

@@ -78,28 +78,7 @@ private[spark] class Executor(
     // Setup an uncaught exception handler for non-local mode.
     // Make any thread terminations due to uncaught exceptions kill the entire
     // executor process to avoid surprising stalls.
-    Thread.setDefaultUncaughtExceptionHandler(
-      new Thread.UncaughtExceptionHandler {
-        override def uncaughtException(thread: Thread, exception: Throwable) {
-          try {
-            logError("Uncaught exception in thread " + thread, exception)
-
-            // We may have been called from a shutdown hook. If so, we must not call System.exit().
-            // (If we do, we will deadlock.)
-            if (!Utils.inShutdown()) {
-              if (exception.isInstanceOf[OutOfMemoryError]) {
-                System.exit(ExecutorExitCode.OOM)
-              } else {
-                System.exit(ExecutorExitCode.UNCAUGHT_EXCEPTION)
-              }
-            }
-          } catch {
-            case oom: OutOfMemoryError => Runtime.getRuntime.halt(ExecutorExitCode.OOM)
-            case t: Throwable => Runtime.getRuntime.halt(ExecutorExitCode.UNCAUGHT_EXCEPTION_TWICE)
-          }
-        }
-      }
-    )
+    Thread.setDefaultUncaughtExceptionHandler(ExecutorUncaughtExceptionHandler)
   }
 
   val executorSource = new ExecutorSource(this, executorId)
@@ -257,6 +236,11 @@ private[spark] class Executor(
         }
 
         case t: Throwable => {
+          // Attempt to exit cleanly by informing the driver of our failure.
+          // If anything goes wrong (or this was a fatal exception), we will delegate to
+          // the default uncaught exception handler, which will terminate the Executor.
+          logError("Exception in task ID " + taskId, t)
+
           val serviceTime = (System.currentTimeMillis() - taskStart).toInt
           val metrics = attemptedTask.flatMap(t => t.metrics)
           for (m <- metrics) {
@@ -266,11 +250,11 @@ private[spark] class Executor(
           val reason = ExceptionFailure(t.getClass.getName, t.toString, t.getStackTrace, metrics)
           execBackend.statusUpdate(taskId, TaskState.FAILED, ser.serialize(reason))
 
-          // TODO: Should we exit the whole executor here? On the one hand, the failed task may
-          // 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)
+          // Don't forcibly exit unless the exception was inherently fatal, to avoid
+          // stopping other tasks unnecessarily.
+          if (Utils.isFatalError(t)) {
+            ExecutorUncaughtExceptionHandler.uncaughtException(t)
+          }
         }
       } finally {
         // TODO: Unregister shuffle memory only for ResultTask

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

@@ -0,0 +1,53 @@
+/*
+ * 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.executor
+
+import org.apache.spark.Logging
+import org.apache.spark.util.Utils
+
+/**
+ * The default uncaught exception handler for Executors terminates the whole process, to avoid
+ * getting into a bad state indefinitely. Since Executors are relatively lightweight, it's better
+ * to fail fast when things go wrong.
+ */
+private[spark] object ExecutorUncaughtExceptionHandler
+  extends Thread.UncaughtExceptionHandler with Logging {
+
+  override def uncaughtException(thread: Thread, exception: Throwable) {
+    try {
+      logError("Uncaught exception in thread " + thread, exception)
+
+      // We may have been called from a shutdown hook. If so, we must not call System.exit().
+      // (If we do, we will deadlock.)
+      if (!Utils.inShutdown()) {
+        if (exception.isInstanceOf[OutOfMemoryError]) {
+          System.exit(ExecutorExitCode.OOM)
+        } else {
+          System.exit(ExecutorExitCode.UNCAUGHT_EXCEPTION)
+        }
+      }
+    } catch {
+      case oom: OutOfMemoryError => Runtime.getRuntime.halt(ExecutorExitCode.OOM)
+      case t: Throwable => Runtime.getRuntime.halt(ExecutorExitCode.UNCAUGHT_EXCEPTION_TWICE)
+    }
+  }
+
+  def uncaughtException(exception: Throwable) {
+    uncaughtException(Thread.currentThread(), exception)
+  }
+}

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

@@ -133,7 +133,7 @@ private[spark] class BlockManager(
     BlockManagerWorker.startBlockManagerWorker(this)
     if (!BlockManager.getDisableHeartBeatsForTesting(conf)) {
       heartBeatTask = actorSystem.scheduler.schedule(0.seconds, heartBeatFrequency.milliseconds) {
-        heartBeat()
+        Utils.tryOrExit { heartBeat() }
       }
     }
   }
@@ -842,8 +842,26 @@ private[spark] class BlockManager(
       bytes: ByteBuffer,
       serializer: Serializer = defaultSerializer): Iterator[Any] = {
     bytes.rewind()
-    val stream = wrapForCompression(blockId, new ByteBufferInputStream(bytes, true))
-    serializer.newInstance().deserializeStream(stream).asIterator
+
+    def getIterator = {
+      val stream = wrapForCompression(blockId, new ByteBufferInputStream(bytes, true))
+      serializer.newInstance().deserializeStream(stream).asIterator
+    }
+
+    if (blockId.isShuffle) {
+      // Reducer may need to read many local shuffle blocks and will wrap them into Iterators
+      // at the beginning. The wrapping will cost some memory (compression instance
+      // initialization, etc.). Reducer read shuffle blocks one by one so we could do the
+      // wrapping lazily to save memory.
+      class LazyProxyIterator(f: => Iterator[Any]) extends Iterator[Any] {
+        lazy val proxy = f
+        override def hasNext: Boolean = proxy.hasNext
+        override def next(): Any = proxy.next()
+      }
+      new LazyProxyIterator(getIterator)
+    } else {
+      getIterator
+    }
   }
 
   def stop() {

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

@@ -134,14 +134,14 @@ private[spark] class DiskBlockManager(shuffleManager: ShuffleBlockManager, rootD
   private def addShutdownHook() {
     localDirs.foreach(localDir => Utils.registerShutdownDeleteDir(localDir))
     Runtime.getRuntime.addShutdownHook(new Thread("delete Spark local dirs") {
-      override def run() {
+      override def run(): Unit = Utils.logUncaughtExceptions {
         logDebug("Shutdown hook called")
         localDirs.foreach { localDir =>
           try {
             if (!Utils.hasRootAsShutdownDeleteDir(localDir)) Utils.deleteRecursively(localDir)
           } catch {
-            case t: Throwable =>
-              logError("Exception while deleting local spark dir: " + localDir, t)
+            case e: Exception =>
+              logError("Exception while deleting local spark dir: " + localDir, e)
           }
         }
 

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

@@ -19,6 +19,7 @@ package org.apache.spark.util
 
 import java.io._
 import java.net.{InetAddress, URL, URI, NetworkInterface, Inet4Address}
+import java.nio.ByteBuffer
 import java.util.{Locale, Random, UUID}
 import java.util.concurrent.{ConcurrentHashMap, Executors, ThreadPoolExecutor}
 
@@ -27,19 +28,16 @@ import scala.collection.Map
 import scala.collection.mutable.ArrayBuffer
 import scala.io.Source
 import scala.reflect.ClassTag
+import scala.util.control.{ControlThrowable, NonFatal}
 
 import com.google.common.io.Files
 import com.google.common.util.concurrent.ThreadFactoryBuilder
 
-import org.apache.hadoop.conf.Configuration
-import org.apache.hadoop.fs.{Path, FileSystem, FileUtil}
-import org.apache.hadoop.io._
-
-import org.apache.spark.serializer.{DeserializationStream, SerializationStream, SerializerInstance}
+import org.apache.hadoop.fs.{FileSystem, FileUtil, Path}
+import org.apache.spark.{Logging, SparkConf, SparkException}
 import org.apache.spark.deploy.SparkHadoopUtil
-import java.nio.ByteBuffer
-import org.apache.spark.{SparkConf, SparkException, Logging}
-
+import org.apache.spark.executor.ExecutorUncaughtExceptionHandler
+import org.apache.spark.serializer.{DeserializationStream, SerializationStream, SerializerInstance}
 
 /**
  * Various utility methods used by Spark.
@@ -621,6 +619,18 @@ private[spark] object Utils extends Logging {
     output.toString
   }
 
+  /**
+   * Execute a block of code that evaluates to Unit, forwarding any uncaught exceptions to the
+   * default UncaughtExceptionHandler
+   */
+  def tryOrExit(block: => Unit) {
+    try {
+      block
+    } catch {
+      case t: Throwable => ExecutorUncaughtExceptionHandler.uncaughtException(t)
+    }
+  }
+
   /**
    * A regular expression to match classes of the "core" Spark API that we want to skip when
    * finding the call site of a method.
@@ -833,4 +843,28 @@ private[spark] object Utils extends Logging {
     System.currentTimeMillis - start
   }
 
+  /** 
+   * Executes the given block, printing and re-throwing any uncaught exceptions.
+   * This is particularly useful for wrapping code that runs in a thread, to ensure
+   * that exceptions are printed, and to avoid having to catch Throwable.
+   */
+  def logUncaughtExceptions[T](f: => T): T = {
+    try {
+      f
+    } catch {
+      case t: Throwable =>
+        logError(s"Uncaught exception in thread ${Thread.currentThread().getName}", t)
+        throw t
+    }
+  }
+
+  /** Returns true if the given exception was fatal. See docs for scala.util.control.NonFatal. */
+  def isFatalError(e: Throwable): Boolean = {
+    e match {
+      case NonFatal(_) | _: InterruptedException | _: NotImplementedError | _: ControlThrowable =>
+        false
+      case _ =>
+        true
+    }
+  }
 }

ec2/spark-ec2

@@ -19,4 +19,4 @@
 #
 
 cd "`dirname $0`"
-PYTHONPATH="./third_party/boto-2.4.1.zip/boto-2.4.1:$PYTHONPATH" python ./spark_ec2.py $@
+PYTHONPATH="./third_party/boto-2.4.1.zip/boto-2.4.1:$PYTHONPATH" python ./spark_ec2.py "$@"

ec2/spark_ec2.py

@@ -629,9 +629,23 @@ def ssh(host, opts, command):
       time.sleep(30)
       tries = tries + 1
 
+# Backported from Python 2.7 for compatiblity with 2.6 (See SPARK-1990)
+def _check_output(*popenargs, **kwargs):
+    if 'stdout' in kwargs:
+        raise ValueError('stdout argument not allowed, it will be overridden.')
+    process = subprocess.Popen(stdout=subprocess.PIPE, *popenargs, **kwargs)
+    output, unused_err = process.communicate()
+    retcode = process.poll()
+    if retcode:
+        cmd = kwargs.get("args")
+        if cmd is None:
+            cmd = popenargs[0]
+        raise subprocess.CalledProcessError(retcode, cmd, output=output)
+    return output
+
 
 def ssh_read(host, opts, command):
-  return subprocess.check_output(
+  return _check_output(
       ssh_command(opts) + ['%s@%s' % (opts.user, host), stringify_command(command)])