merge master

assembly/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

bagel/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

core/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

core/src/main/scala/org/apache/spark/rdd/PairRDDFunctions.scala

@@ -737,7 +737,8 @@ class PairRDDFunctions[K, V](self: RDD[(K, V)])
     val outfmt = job.getOutputFormatClass
     val jobFormat = outfmt.newInstance
 
-    if (jobFormat.isInstanceOf[NewFileOutputFormat[_, _]]) {
+    if (self.conf.getBoolean("spark.hadoop.validateOutputSpecs", true) &&
+      jobFormat.isInstanceOf[NewFileOutputFormat[_, _]]) {
       // FileOutputFormat ignores the filesystem parameter
       jobFormat.checkOutputSpecs(job)
     }
@@ -803,7 +804,8 @@ class PairRDDFunctions[K, V](self: RDD[(K, V)])
     logDebug("Saving as hadoop file of type (" + keyClass.getSimpleName + ", " +
       valueClass.getSimpleName + ")")
 
-    if (outputFormatInstance.isInstanceOf[FileOutputFormat[_, _]]) {
+    if (self.conf.getBoolean("spark.hadoop.validateOutputSpecs", true) &&
+      outputFormatInstance.isInstanceOf[FileOutputFormat[_, _]]) {
       // FileOutputFormat ignores the filesystem parameter
       val ignoredFs = FileSystem.get(conf)
       conf.getOutputFormat.checkOutputSpecs(ignoredFs, conf)

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

@@ -38,7 +38,7 @@ import org.apache.spark.executor.TaskMetrics
 import org.apache.spark.partial.{ApproximateActionListener, ApproximateEvaluator, PartialResult}
 import org.apache.spark.rdd.RDD
 import org.apache.spark.storage.{BlockId, BlockManager, BlockManagerMaster, RDDBlockId}
-import org.apache.spark.util.Utils
+import org.apache.spark.util.{SystemClock, Clock, Utils}
 
 /**
  * The high-level scheduling layer that implements stage-oriented scheduling. It computes a DAG of
@@ -61,7 +61,8 @@ class DAGScheduler(
     listenerBus: LiveListenerBus,
     mapOutputTracker: MapOutputTrackerMaster,
     blockManagerMaster: BlockManagerMaster,
-    env: SparkEnv)
+    env: SparkEnv,
+    clock: Clock = SystemClock)
   extends Logging {
 
   import DAGScheduler._
@@ -781,7 +782,7 @@ class DAGScheduler(
       logDebug("New pending tasks: " + myPending)
       taskScheduler.submitTasks(
         new TaskSet(tasks.toArray, stage.id, stage.newAttemptId(), stage.jobId, properties))
-      stageToInfos(stage).submissionTime = Some(System.currentTimeMillis())
+      stageToInfos(stage).submissionTime = Some(clock.getTime())
     } else {
       logDebug("Stage " + stage + " is actually done; %b %d %d".format(
         stage.isAvailable, stage.numAvailableOutputs, stage.numPartitions))
@@ -807,11 +808,11 @@ class DAGScheduler(
 
     def markStageAsFinished(stage: Stage) = {
       val serviceTime = stageToInfos(stage).submissionTime match {
-        case Some(t) => "%.03f".format((System.currentTimeMillis() - t) / 1000.0)
+        case Some(t) => "%.03f".format((clock.getTime() - t) / 1000.0)
         case _ => "Unknown"
       }
       logInfo("%s (%s) finished in %s s".format(stage, stage.name, serviceTime))
-      stageToInfos(stage).completionTime = Some(System.currentTimeMillis())
+      stageToInfos(stage).completionTime = Some(clock.getTime())
       listenerBus.post(SparkListenerStageCompleted(stageToInfos(stage)))
       runningStages -= stage
     }
@@ -1015,7 +1016,7 @@ class DAGScheduler(
       return
     }
     val dependentStages = resultStageToJob.keys.filter(x => stageDependsOn(x, failedStage)).toSeq
-    stageToInfos(failedStage).completionTime = Some(System.currentTimeMillis())
+    stageToInfos(failedStage).completionTime = Some(clock.getTime())
     for (resultStage <- dependentStages) {
       val job = resultStageToJob(resultStage)
       failJobAndIndependentStages(job, s"Job aborted due to stage failure: $reason",

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

@@ -20,6 +20,7 @@ package org.apache.spark.util.collection
 import java.io.{InputStream, BufferedInputStream, FileInputStream, File, Serializable, EOFException}
 import java.util.Comparator
 
+import scala.collection.BufferedIterator
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer
 
@@ -231,7 +232,7 @@ class ExternalAppendOnlyMap[K, V, C](
     // Input streams are derived both from the in-memory map and spilled maps on disk
     // The in-memory map is sorted in place, while the spilled maps are already in sorted order
     private val sortedMap = currentMap.destructiveSortedIterator(comparator)
-    private val inputStreams = Seq(sortedMap) ++ spilledMaps
+    private val inputStreams = (Seq(sortedMap) ++ spilledMaps).map(it => it.buffered)
 
     inputStreams.foreach { it =>
       val kcPairs = getMorePairs(it)
@@ -246,13 +247,13 @@ class ExternalAppendOnlyMap[K, V, C](
      * In the event of key hash collisions, this ensures no pairs are hidden from being merged.
      * Assume the given iterator is in sorted order.
      */
-    private def getMorePairs(it: Iterator[(K, C)]): ArrayBuffer[(K, C)] = {
+    private def getMorePairs(it: BufferedIterator[(K, C)]): ArrayBuffer[(K, C)] = {
       val kcPairs = new ArrayBuffer[(K, C)]
       if (it.hasNext) {
         var kc = it.next()
         kcPairs += kc
         val minHash = kc._1.hashCode()
-        while (it.hasNext && kc._1.hashCode() == minHash) {
+        while (it.hasNext && it.head._1.hashCode() == minHash) {
           kc = it.next()
           kcPairs += kc
         }
@@ -325,7 +326,8 @@ class ExternalAppendOnlyMap[K, V, C](
      *
      * StreamBuffers are ordered by the minimum key hash found across all of their own pairs.
      */
-    private case class StreamBuffer(iterator: Iterator[(K, C)], pairs: ArrayBuffer[(K, C)])
+    private class StreamBuffer(
+        val iterator: BufferedIterator[(K, C)], val pairs: ArrayBuffer[(K, C)])
       extends Comparable[StreamBuffer] {
 
       def isEmpty = pairs.length == 0

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

@@ -230,6 +230,17 @@ class FileSuite extends FunSuite with LocalSparkContext {
     }
   }
 
+  test ("allow user to disable the output directory existence checking (old Hadoop API") {
+    val sf = new SparkConf()
+    sf.setAppName("test").setMaster("local").set("spark.hadoop.validateOutputSpecs", "false")
+    sc = new SparkContext(sf)
+    val randomRDD = sc.parallelize(Array((1, "a"), (1, "a"), (2, "b"), (3, "c")), 1)
+    randomRDD.saveAsTextFile(tempDir.getPath + "/output")
+    assert(new File(tempDir.getPath + "/output/part-00000").exists() === true)
+    randomRDD.saveAsTextFile(tempDir.getPath + "/output")
+    assert(new File(tempDir.getPath + "/output/part-00000").exists() === true)
+  }
+
   test ("prevent user from overwriting the empty directory (new Hadoop API)") {
     sc = new SparkContext("local", "test")
     val randomRDD = sc.parallelize(Array(("key1", "a"), ("key2", "a"), ("key3", "b"), ("key4", "c")), 1)
@@ -248,6 +259,17 @@ class FileSuite extends FunSuite with LocalSparkContext {
     }
   }
 
+  test ("allow user to disable the output directory existence checking (new Hadoop API") {
+    val sf = new SparkConf()
+    sf.setAppName("test").setMaster("local").set("spark.hadoop.validateOutputSpecs", "false")
+    sc = new SparkContext(sf)
+    val randomRDD = sc.parallelize(Array(("key1", "a"), ("key2", "a"), ("key3", "b"), ("key4", "c")), 1)
+    randomRDD.saveAsNewAPIHadoopFile[NewTextOutputFormat[String, String]](tempDir.getPath + "/output")
+    assert(new File(tempDir.getPath + "/output/part-r-00000").exists() === true)
+    randomRDD.saveAsNewAPIHadoopFile[NewTextOutputFormat[String, String]](tempDir.getPath + "/output")
+    assert(new File(tempDir.getPath + "/output/part-r-00000").exists() === true)
+  }
+
   test ("save Hadoop Dataset through old Hadoop API") {
     sc = new SparkContext("local", "test")
     val randomRDD = sc.parallelize(Array(("key1", "a"), ("key2", "a"), ("key3", "b"), ("key4", "c")), 1)

core/src/test/scala/org/apache/spark/util/collection/ExternalAppendOnlyMapSuite.scala

@@ -277,6 +277,11 @@ class ExternalAppendOnlyMapSuite extends FunSuite with LocalSparkContext {
       ("pomatoes", "eructation")      // 568647356
     )
 
+    collisionPairs.foreach { case (w1, w2) =>
+      // String.hashCode is documented to use a specific algorithm, but check just in case
+      assert(w1.hashCode === w2.hashCode)
+    }
+
     (1 to 100000).map(_.toString).foreach { i => map.insert(i, i) }
     collisionPairs.foreach { case (w1, w2) =>
       map.insert(w1, w2)
@@ -296,7 +301,32 @@ class ExternalAppendOnlyMapSuite extends FunSuite with LocalSparkContext {
       assert(kv._2.equals(expectedValue))
       count += 1
     }
-    assert(count == 100000 + collisionPairs.size * 2)
+    assert(count === 100000 + collisionPairs.size * 2)
+  }
+
+  test("spilling with many hash collisions") {
+    val conf = new SparkConf(true)
+    conf.set("spark.shuffle.memoryFraction", "0.0001")
+    sc = new SparkContext("local-cluster[1,1,512]", "test", conf)
+
+    val map = new ExternalAppendOnlyMap[FixedHashObject, Int, Int](_ => 1, _ + _, _ + _)
+
+    // Insert 10 copies each of lots of objects whose hash codes are either 0 or 1. This causes
+    // problems if the map fails to group together the objects with the same code (SPARK-2043).
+    for (i <- 1 to 10) {
+      for (j <- 1 to 10000) {
+        map.insert(FixedHashObject(j, j % 2), 1)
+      }
+    }
+
+    val it = map.iterator
+    var count = 0
+    while (it.hasNext) {
+      val kv = it.next()
+      assert(kv._2 === 10)
+      count += 1
+    }
+    assert(count === 10000)
   }
 
   test("spilling with hash collisions using the Int.MaxValue key") {
@@ -317,3 +347,10 @@ class ExternalAppendOnlyMapSuite extends FunSuite with LocalSparkContext {
     }
   }
 }
+
+/**
+ * A dummy class that always returns the same hash code, to easily test hash collisions
+ */
+case class FixedHashObject(val v: Int, val h: Int) extends Serializable {
+  override def hashCode(): Int = h
+}

dev/mima

@@ -31,4 +31,5 @@ if [ $ret_val != 0 ]; then
   echo "NOTE: Exceptions to binary compatibility can be added in project/MimaExcludes.scala"
 fi
 
+rm -f .generated-mima-excludes
 exit $ret_val

docs/configuration.md

@@ -487,6 +487,14 @@ Apart from these, the following properties are also available, and may be useful
     this duration will be cleared as well.
   </td>
 </tr>
+<tr>
+    <td>spark.hadoop.validateOutputSpecs</td>
+    <td>true</td>
+    <td>If set to true, validates the output specification (e.g. checking if the output directory already exists) 
+    used in saveAsHadoopFile and other variants. This can be disabled to silence exceptions due to pre-existing 
+    output directories. We recommend that users do not disable this except if trying to achieve compatibility with 
+    previous versions of Spark. Simply use Hadoop's FileSystem API to delete output directories by hand.</td>
+</tr>
 </table>
 
 #### Networking

examples/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

external/flume/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

external/kafka/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

external/mqtt/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

external/twitter/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

external/zeromq/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

extras/java8-tests/pom.xml

@@ -20,7 +20,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

extras/spark-ganglia-lgpl/pom.xml

@@ -20,7 +20,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
 

graphx/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala

@@ -150,6 +150,7 @@ object Pregel extends Logging {
       oldMessages.unpersist(blocking=false)
       newVerts.unpersist(blocking=false)
       prevG.unpersistVertices(blocking=false)
+      prevG.edges.unpersist(blocking=false)
       // count the iteration
       i += 1
     }

mllib/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
@@ -51,6 +51,8 @@
       <artifactId>breeze_${scala.binary.version}</artifactId>
       <version>0.7</version>
       <exclusions>
+        <!-- This is included as a compile-scoped dependency by jtransforms, which is
+             a dependency of breeze. -->
         <exclusion>
           <groupId>junit</groupId>
           <artifactId>junit</artifactId>

pom.xml

@@ -26,7 +26,7 @@
   </parent>
   <groupId>org.apache.spark</groupId>
   <artifactId>spark-parent</artifactId>
-  <version>1.0.0-SNAPSHOT</version>
+  <version>1.1.0-SNAPSHOT</version>
   <packaging>pom</packaging>
   <name>Spark Project Parent POM</name>
   <url>http://spark.apache.org/</url>

project/SparkBuild.scala

@@ -322,9 +322,8 @@ object SparkBuild extends Build {
   val excludeFastutil = ExclusionRule(organization = "it.unimi.dsi")
   val excludeJruby = ExclusionRule(organization = "org.jruby")
   val excludeThrift = ExclusionRule(organization = "org.apache.thrift")
-  val excludeJunit = ExclusionRule(organization = "junit")
-  val excludeCommonsLang = ExclusionRule(organization = "commons-lang")
   val excludeServletApi = ExclusionRule(organization = "javax.servlet", artifact = "servlet-api")
+  val excludeJUnit = ExclusionRule(organization = "junit")
 
   def sparkPreviousArtifact(id: String, organization: String = "org.apache.spark",
       version: String = "1.0.0", crossVersion: String = "2.10"): Option[sbt.ModuleID] = {
@@ -469,7 +468,7 @@ object SparkBuild extends Build {
     previousArtifact := sparkPreviousArtifact("spark-mllib"),
     libraryDependencies ++= Seq(
       "org.jblas" % "jblas" % jblasVersion,
-      "org.scalanlp" %% "breeze" % "0.7" excludeAll(excludeJunit)
+      "org.scalanlp" %% "breeze" % "0.7" excludeAll(excludeJUnit)
     )
   )
 

project/plugins.sbt

@@ -4,7 +4,7 @@ resolvers += Resolver.url("artifactory", url("http://scalasbt.artifactoryonline.
 
 resolvers += "Typesafe Repository" at "http://repo.typesafe.com/typesafe/releases/"
 
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.10.2")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.11.2")
 
 addSbtPlugin("com.typesafe.sbteclipse" % "sbteclipse-plugin" % "2.2.0")