Merge branch 'master' into takeSample

.gitignore

@@ -7,7 +7,7 @@
 sbt/*.jar
 .settings
 .cache
-.mima-excludes
+.generated-mima-excludes
 /build/
 work/
 out/

.rat-excludes

@@ -3,6 +3,7 @@ target
 .project
 .classpath
 .mima-excludes
+.generated-mima-excludes
 .rat-excludes
 .*md
 derby.log

core/pom.xml

@@ -263,35 +263,6 @@
     <outputDirectory>target/scala-${scala.binary.version}/classes</outputDirectory>
     <testOutputDirectory>target/scala-${scala.binary.version}/test-classes</testOutputDirectory>
     <plugins>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-antrun-plugin</artifactId>
-        <executions>
-          <execution>
-            <phase>test</phase>
-            <goals>
-              <goal>run</goal>
-            </goals>
-            <configuration>
-              <exportAntProperties>true</exportAntProperties>
-              <target>
-                <property name="spark.classpath" refid="maven.test.classpath" />
-                <property environment="env" />
-                <fail message="Please set the SCALA_HOME (or SCALA_LIBRARY_PATH if scala is on the path) environment variables and retry.">
-                  <condition>
-                    <not>
-                      <or>
-                        <isset property="env.SCALA_HOME" />
-                        <isset property="env.SCALA_LIBRARY_PATH" />
-                      </or>
-                    </not>
-                  </condition>
-                </fail>
-              </target>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
       <plugin>
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>

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

@@ -76,8 +76,8 @@ class SparkContext(config: SparkConf) extends Logging {
    * :: DeveloperApi ::
    * Alternative constructor for setting preferred locations where Spark will create executors.
    *
-   * @param preferredNodeLocationData used in YARN mode to select nodes to launch containers on. Ca
-   * be generated using [[org.apache.spark.scheduler.InputFormatInfo.computePreferredLocations]]
+   * @param preferredNodeLocationData used in YARN mode to select nodes to launch containers on.
+   * Can be generated using [[org.apache.spark.scheduler.InputFormatInfo.computePreferredLocations]]
    * from a list of input files or InputFormats for the application.
    */
   @DeveloperApi

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

@@ -269,6 +269,26 @@ private object SpecialLengths {
 private[spark] object PythonRDD {
   val UTF8 = Charset.forName("UTF-8")
 
+  /**
+   * Adapter for calling SparkContext#runJob from Python.
+   *
+   * This method will return an iterator of an array that contains all elements in the RDD
+   * (effectively a collect()), but allows you to run on a certain subset of partitions,
+   * or to enable local execution.
+   */
+  def runJob(
+      sc: SparkContext,
+      rdd: JavaRDD[Array[Byte]],
+      partitions: JArrayList[Int],
+      allowLocal: Boolean): Iterator[Array[Byte]] = {
+    type ByteArray = Array[Byte]
+    type UnrolledPartition = Array[ByteArray]
+    val allPartitions: Array[UnrolledPartition] =
+      sc.runJob(rdd, (x: Iterator[ByteArray]) => x.toArray, partitions, allowLocal)
+    val flattenedPartition: UnrolledPartition = Array.concat(allPartitions: _*)
+    flattenedPartition.iterator
+  }
+
   def readRDDFromFile(sc: JavaSparkContext, filename: String, parallelism: Int):
   JavaRDD[Array[Byte]] = {
     val file = new DataInputStream(new FileInputStream(filename))

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

@@ -381,16 +381,19 @@ private[spark] class SparkSubmitArguments(args: Seq[String]) {
 object SparkSubmitArguments {
   /** Load properties present in the given file. */
   def getPropertiesFromFile(file: File): Seq[(String, String)] = {
-    require(file.exists(), s"Properties file ${file.getName} does not exist")
+    require(file.exists(), s"Properties file $file does not exist")
+    require(file.isFile(), s"Properties file $file is not a normal file")
     val inputStream = new FileInputStream(file)
-    val properties = new Properties()
     try {
+      val properties = new Properties()
       properties.load(inputStream)
+      properties.stringPropertyNames().toSeq.map(k => (k, properties(k).trim))
     } catch {
       case e: IOException =>
-        val message = s"Failed when loading Spark properties file ${file.getName}"
+        val message = s"Failed when loading Spark properties file $file"
         throw new SparkException(message, e)
+    } finally {
+      inputStream.close()
     }
-    properties.stringPropertyNames().toSeq.map(k => (k, properties(k).trim))
   }
 }

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

@@ -61,17 +61,23 @@ private[spark] class ExecutorRunner(
     // Shutdown hook that kills actors on shutdown.
     shutdownHook = new Thread() {
       override def run() {
-        killProcess()
+        killProcess(Some("Worker shutting down"))
       }
     }
     Runtime.getRuntime.addShutdownHook(shutdownHook)
   }
 
-  private def killProcess() {
+  /**
+   * kill executor process, wait for exit and notify worker to update resource status
+   *
+   * @param message the exception message which caused the executor's death 
+   */
+  private def killProcess(message: Option[String]) {
     if (process != null) {
       logInfo("Killing process!")
       process.destroy()
-      process.waitFor()
+      val exitCode = process.waitFor()
+      worker ! ExecutorStateChanged(appId, execId, state, message, Some(exitCode))
     }
   }
 
@@ -82,7 +88,6 @@ private[spark] class ExecutorRunner(
       workerThread.interrupt()
       workerThread = null
       state = ExecutorState.KILLED
-      worker ! ExecutorStateChanged(appId, execId, state, None, None)
       Runtime.getRuntime.removeShutdownHook(shutdownHook)
     }
   }
@@ -148,14 +153,13 @@ private[spark] class ExecutorRunner(
     } catch {
       case interrupted: InterruptedException => {
         logInfo("Runner thread for executor " + fullId + " interrupted")
-        killProcess()
+        state = ExecutorState.KILLED
+        killProcess(None)
       }
       case e: Exception => {
         logError("Error running executor", e)
-        killProcess()
         state = ExecutorState.FAILED
-        val message = e.getClass + ": " + e.getMessage
-        worker ! ExecutorStateChanged(appId, execId, state, Some(message), None)
+        killProcess(Some(e.toString))
       }
     }
   }

dev/mima

@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+
+#
+# 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.
+#
+
+set -o pipefail
+
+# Go to the Spark project root directory
+FWDIR="$(cd `dirname $0`/..; pwd)"
+cd $FWDIR
+
+./bin/spark-class org.apache.spark.tools.GenerateMIMAIgnore
+echo -e "q\n" | sbt/sbt mima-report-binary-issues | grep -v -e "info.*Resolving"
+ret_val=$?
+
+if [ $ret_val != 0 ]; then
+  echo "NOTE: Exceptions to binary compatibility can be added in project/MimaExcludes.scala"
+fi
+
+exit $ret_val

dev/run-tests

@@ -81,5 +81,4 @@ fi
 echo "========================================================================="
 echo "Detecting binary incompatibilites with MiMa"
 echo "========================================================================="
-./bin/spark-class org.apache.spark.tools.GenerateMIMAIgnore
-echo -e "q\n" | sbt/sbt mima-report-binary-issues | grep -v -e "info.*Resolving" 
+dev/mima

docs/_layouts/global.html

@@ -9,6 +9,11 @@
         <title>{{ page.title }} - Spark {{site.SPARK_VERSION_SHORT}} Documentation</title>
         <meta name="description" content="">
 
+        {% if page.redirect %}
+          <meta http-equiv="refresh" content="0; url={{page.redirect}}">
+          <link rel="canonical" href="{{page.redirect}}" />
+        {% endif %}
+
         <link rel="stylesheet" href="css/bootstrap.min.css">
         <style>
             body {
@@ -61,15 +66,13 @@
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Programming Guides<b class="caret"></b></a>
                             <ul class="dropdown-menu">
                                 <li><a href="quick-start.html">Quick Start</a></li>
-                                <li><a href="scala-programming-guide.html">Spark in Scala</a></li>
-                                <li><a href="java-programming-guide.html">Spark in Java</a></li>
-                                <li><a href="python-programming-guide.html">Spark in Python</a></li>
+                                <li><a href="programming-guide.html">Spark Programming Guide</a></li>
                                 <li class="divider"></li>
                                 <li><a href="streaming-programming-guide.html">Spark Streaming</a></li>
                                 <li><a href="sql-programming-guide.html">Spark SQL</a></li>
                                 <li><a href="mllib-guide.html">MLlib (Machine Learning)</a></li>
-                                <li><a href="bagel-programming-guide.html">Bagel (Pregel on Spark)</a></li>
                                 <li><a href="graphx-programming-guide.html">GraphX (Graph Processing)</a></li>
+                                <li><a href="bagel-programming-guide.html">Bagel (Pregel on Spark)</a></li>
                             </ul>
                         </li>
 
@@ -86,6 +89,8 @@
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Deploying<b class="caret"></b></a>
                             <ul class="dropdown-menu">
                                 <li><a href="cluster-overview.html">Overview</a></li>
+                                <li><a href="submitting-applications.html">Submitting Applications</a></li>
+                                <li class="divider"></li>
                                 <li><a href="ec2-scripts.html">Amazon EC2</a></li>
                                 <li><a href="spark-standalone.html">Standalone Mode</a></li>
                                 <li><a href="running-on-mesos.html">Mesos</a></li>
@@ -99,9 +104,10 @@
                                 <li><a href="configuration.html">Configuration</a></li>
                                 <li><a href="monitoring.html">Monitoring</a></li>
                                 <li><a href="tuning.html">Tuning Guide</a></li>
-                                <li><a href="hadoop-third-party-distributions.html">Running with CDH/HDP</a></li>
-                                <li><a href="hardware-provisioning.html">Hardware Provisioning</a></li>
                                 <li><a href="job-scheduling.html">Job Scheduling</a></li>
+                                <li><a href="security.html">Security</a></li>
+                                <li><a href="hardware-provisioning.html">Hardware Provisioning</a></li>
+                                <li><a href="hadoop-third-party-distributions.html">3<sup>rd</sup>-Party Hadoop Distros</a></li>
                                 <li class="divider"></li>
                                 <li><a href="building-with-maven.html">Building Spark with Maven</a></li>
                                 <li><a href="https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark">Contributing to Spark</a></li>

docs/bagel-programming-guide.md

@@ -21,7 +21,7 @@ To use Bagel in your program, add the following SBT or Maven dependency:
 
 # Programming Model
 
-Bagel operates on a graph represented as a [distributed dataset](scala-programming-guide.html) of (K, V) pairs, where keys are vertex IDs and values are vertices plus their associated state. In each superstep, Bagel runs a user-specified compute function on each vertex that takes as input the current vertex state and a list of messages sent to that vertex during the previous superstep, and returns the new vertex state and a list of outgoing messages.
+Bagel operates on a graph represented as a [distributed dataset](programming-guide.html) of (K, V) pairs, where keys are vertex IDs and values are vertices plus their associated state. In each superstep, Bagel runs a user-specified compute function on each vertex that takes as input the current vertex state and a list of messages sent to that vertex during the previous superstep, and returns the new vertex state and a list of outgoing messages.
 
 For example, we can use Bagel to implement PageRank. Here, vertices represent pages, edges represent links between pages, and messages represent shares of PageRank sent to the pages that a particular page links to.