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

assembly/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent_2.10</artifactId>
-    <version>1.3.0-SNAPSHOT</version>
+    <version>1.4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

bagel/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent_2.10</artifactId>
-    <version>1.3.0-SNAPSHOT</version>
+    <version>1.4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

core/pom.xml

@@ -21,7 +21,7 @@
   <parent>
     <groupId>org.apache.spark</groupId>
     <artifactId>spark-parent_2.10</artifactId>
-    <version>1.3.0-SNAPSHOT</version>
+    <version>1.4.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
@@ -275,7 +275,7 @@
     <dependency>
       <groupId>org.tachyonproject</groupId>
       <artifactId>tachyon-client</artifactId>
-      <version>0.5.0</version>
+      <version>0.6.1</version>
       <exclusions>
         <exclusion>
           <groupId>org.apache.hadoop</groupId>

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

@@ -27,6 +27,8 @@ private[spark] object TaskState extends Enumeration {
 
   type TaskState = Value
 
+  def isFailed(state: TaskState) = (LOST == state) || (FAILED == state)
+
   def isFinished(state: TaskState) = FINISHED_STATES.contains(state)
 
   def toMesos(state: TaskState): MesosTaskState = state match {

core/src/main/scala/org/apache/spark/api/java/JavaRDD.scala

@@ -101,12 +101,23 @@ class JavaRDD[T](val rdd: RDD[T])(implicit val classTag: ClassTag[T])
 
   /**
    * Return a sampled subset of this RDD.
+   * 
+   * @param withReplacement can elements be sampled multiple times (replaced when sampled out)
+   * @param fraction expected size of the sample as a fraction of this RDD's size
+   *  without replacement: probability that each element is chosen; fraction must be [0, 1]
+   *  with replacement: expected number of times each element is chosen; fraction must be >= 0
    */
   def sample(withReplacement: Boolean, fraction: Double): JavaRDD[T] =
     sample(withReplacement, fraction, Utils.random.nextLong)
 
   /**
    * Return a sampled subset of this RDD.
+   * 
+   * @param withReplacement can elements be sampled multiple times (replaced when sampled out)
+   * @param fraction expected size of the sample as a fraction of this RDD's size
+   *  without replacement: probability that each element is chosen; fraction must be [0, 1]
+   *  with replacement: expected number of times each element is chosen; fraction must be >= 0
+   * @param seed seed for the random number generator
    */
   def sample(withReplacement: Boolean, fraction: Double, seed: Long): JavaRDD[T] =
     wrapRDD(rdd.sample(withReplacement, fraction, seed))

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

@@ -33,6 +33,7 @@ import org.json4s.jackson.JsonMethods
 
 import org.apache.spark.{Logging, SparkConf, SparkContext}
 import org.apache.spark.deploy.master.{RecoveryState, SparkCuratorUtil}
+import org.apache.spark.util.Utils
 
 /**
  * This suite tests the fault tolerance of the Spark standalone scheduler, mainly the Master.
@@ -405,8 +406,7 @@ private object SparkDocker {
 
   private def startNode(dockerCmd: ProcessBuilder) : (String, DockerId, File) = {
     val ipPromise = promise[String]()
-    val outFile = File.createTempFile("fault-tolerance-test", "")
-    outFile.deleteOnExit()
+    val outFile = File.createTempFile("fault-tolerance-test", "", Utils.createTempDir())
     val outStream: FileWriter = new FileWriter(outFile)
     def findIpAndLog(line: String): Unit = {
       if (line.startsWith("CONTAINER_IP=")) {

core/src/main/scala/org/apache/spark/deploy/history/FsHistoryProvider.scala

@@ -233,7 +233,8 @@ private[history] class FsHistoryProvider(conf: SparkConf) extends ApplicationHis
       } catch {
         case e: Exception =>
           logError(
-            s"Exception encountered when attempting to load application log ${fileStatus.getPath}")
+            s"Exception encountered when attempting to load application log ${fileStatus.getPath}",
+            e)
           None
       }
     }.toSeq.sortWith(compareAppInfo)

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

@@ -43,5 +43,5 @@ package org.apache
 
 package object spark {
   // For package docs only
-  val SPARK_VERSION = "1.3.0-SNAPSHOT"
+  val SPARK_VERSION = "1.4.0-SNAPSHOT"
 }

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

@@ -377,6 +377,12 @@ abstract class RDD[T: ClassTag](
 
   /**
    * Return a sampled subset of this RDD.
+   * 
+   * @param withReplacement can elements be sampled multiple times (replaced when sampled out)
+   * @param fraction expected size of the sample as a fraction of this RDD's size
+   *  without replacement: probability that each element is chosen; fraction must be [0, 1]
+   *  with replacement: expected number of times each element is chosen; fraction must be >= 0
+   * @param seed seed for the random number generator
    */
   def sample(withReplacement: Boolean,
       fraction: Double,

core/src/main/scala/org/apache/spark/scheduler/cluster/mesos/CoarseMesosSchedulerBackend.scala

@@ -277,7 +277,7 @@ private[spark] class CoarseMesosSchedulerBackend(
           coresByTaskId -= taskId
         }
         // If it was a failure, mark the slave as failed for blacklisting purposes
-        if (state == MesosTaskState.TASK_FAILED || state == MesosTaskState.TASK_LOST) {
+        if (TaskState.isFailed(TaskState.fromMesos(state))) {
           failuresBySlaveId(slaveId) = failuresBySlaveId.getOrElse(slaveId, 0) + 1
           if (failuresBySlaveId(slaveId) >= MAX_SLAVE_FAILURES) {
             logInfo("Blacklisting Mesos slave " + slaveId + " due to too many failures; " +

core/src/main/scala/org/apache/spark/scheduler/cluster/mesos/MemoryUtils.scala

@@ -21,15 +21,11 @@ import org.apache.spark.SparkContext
 
 private[spark] object MemoryUtils {
   // These defaults copied from YARN
-  val OVERHEAD_FRACTION = 1.10
+  val OVERHEAD_FRACTION = 0.10
   val OVERHEAD_MINIMUM = 384
 
   def calculateTotalMemory(sc: SparkContext) = {
-    math.max(
-      sc.conf.getOption("spark.mesos.executor.memoryOverhead")
-        .getOrElse(OVERHEAD_MINIMUM.toString)
-        .toInt + sc.executorMemory,
-        OVERHEAD_FRACTION * sc.executorMemory
-    )
+    sc.conf.getInt("spark.mesos.executor.memoryOverhead",
+      math.max(OVERHEAD_FRACTION * sc.executorMemory, OVERHEAD_MINIMUM).toInt) + sc.executorMemory
   }
 }

core/src/main/scala/org/apache/spark/scheduler/cluster/mesos/MesosSchedulerBackend.scala

@@ -318,7 +318,8 @@ private[spark] class MesosSchedulerBackend(
       val tid = status.getTaskId.getValue.toLong
       val state = TaskState.fromMesos(status.getState)
       synchronized {
-        if (status.getState == MesosTaskState.TASK_LOST && taskIdToSlaveId.contains(tid)) {
+        if (TaskState.isFailed(TaskState.fromMesos(status.getState))
+          && taskIdToSlaveId.contains(tid)) {
           // We lost the executor on this slave, so remember that it's gone
           removeExecutor(taskIdToSlaveId(tid), "Lost executor")
         }

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

@@ -20,8 +20,8 @@ package org.apache.spark.storage
 import java.text.SimpleDateFormat
 import java.util.{Date, Random}
 
-import tachyon.client.TachyonFS
-import tachyon.client.TachyonFile
+import tachyon.TachyonURI
+import tachyon.client.{TachyonFile, TachyonFS}
 
 import org.apache.spark.Logging
 import org.apache.spark.executor.ExecutorExitCode
@@ -40,7 +40,7 @@ private[spark] class TachyonBlockManager(
     val master: String)
   extends Logging {
 
-  val client = if (master != null && master != "") TachyonFS.get(master) else null
+  val client = if (master != null && master != "") TachyonFS.get(new TachyonURI(master)) else null
 
   if (client == null) {
     logError("Failed to connect to the Tachyon as the master address is not configured")
@@ -60,11 +60,11 @@ private[spark] class TachyonBlockManager(
   addShutdownHook()
 
   def removeFile(file: TachyonFile): Boolean = {
-    client.delete(file.getPath(), false)
+    client.delete(new TachyonURI(file.getPath()), false)
   }
 
   def fileExists(file: TachyonFile): Boolean = {
-    client.exist(file.getPath())
+    client.exist(new TachyonURI(file.getPath()))
   }
 
   def getFile(filename: String): TachyonFile = {
@@ -81,15 +81,15 @@ private[spark] class TachyonBlockManager(
         if (old != null) {
           old
         } else {
-          val path = tachyonDirs(dirId) + "/" + "%02x".format(subDirId)
+          val path = new TachyonURI(s"${tachyonDirs(dirId)}/${"%02x".format(subDirId)}")
           client.mkdir(path)
           val newDir = client.getFile(path)
           subDirs(dirId)(subDirId) = newDir
           newDir
         }
       }
     }
-    val filePath = subDir + "/" + filename
+    val filePath = new TachyonURI(s"$subDir/$filename")
     if(!client.exist(filePath)) {
       client.createFile(filePath)
     }
@@ -101,7 +101,7 @@ private[spark] class TachyonBlockManager(
 
   // TODO: Some of the logic here could be consolidated/de-duplicated with that in the DiskStore.
   private def createTachyonDirs(): Array[TachyonFile] = {
-    logDebug("Creating tachyon directories at root dirs '" + rootDirs + "'")
+    logDebug(s"Creating tachyon directories at root dirs '$rootDirs'")
     val dateFormat = new SimpleDateFormat("yyyyMMddHHmmss")
     rootDirs.split(",").map { rootDir =>
       var foundLocalDir = false
@@ -113,22 +113,21 @@ private[spark] class TachyonBlockManager(
         tries += 1
         try {
           tachyonDirId = "%s-%04x".format(dateFormat.format(new Date), rand.nextInt(65536))
-          val path = rootDir + "/" + "spark-tachyon-" + tachyonDirId
+          val path = new TachyonURI(s"$rootDir/spark-tachyon-$tachyonDirId")
           if (!client.exist(path)) {
             foundLocalDir = client.mkdir(path)
             tachyonDir = client.getFile(path)
           }
         } catch {
           case e: Exception =>
-            logWarning("Attempt " + tries + " to create tachyon dir " + tachyonDir + " failed", e)
+            logWarning(s"Attempt $tries to create tachyon dir $tachyonDir failed", e)
         }
       }
       if (!foundLocalDir) {
-        logError("Failed " + MAX_DIR_CREATION_ATTEMPTS + " attempts to create tachyon dir in " +
-          rootDir)
+        logError(s"Failed $MAX_DIR_CREATION_ATTEMPTS attempts to create tachyon dir in $rootDir")
         System.exit(ExecutorExitCode.TACHYON_STORE_FAILED_TO_CREATE_DIR)
       }
-      logInfo("Created tachyon directory at " + tachyonDir)
+      logInfo(s"Created tachyon directory at $tachyonDir")
       tachyonDir
     }
   }
@@ -145,7 +144,7 @@ private[spark] class TachyonBlockManager(
             }
           } catch {
             case e: Exception =>
-              logError("Exception while deleting tachyon spark dir: " + tachyonDir, e)
+              logError(s"Exception while deleting tachyon spark dir: $tachyonDir", e)
           }
         }
         client.close()

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

@@ -42,6 +42,8 @@ import org.apache.hadoop.security.UserGroupInformation
 import org.apache.log4j.PropertyConfigurator
 import org.eclipse.jetty.util.MultiException
 import org.json4s._
+
+import tachyon.TachyonURI
 import tachyon.client.{TachyonFS, TachyonFile}
 
 import org.apache.spark._
@@ -288,7 +290,7 @@ private[spark] object Utils extends Logging {
       } catch { case e: SecurityException => dir = null; }
     }
 
-    dir
+    dir.getCanonicalFile
   }
 
   /**
@@ -970,7 +972,7 @@ private[spark] object Utils extends Logging {
    * Delete a file or directory and its contents recursively.
    */
   def deleteRecursively(dir: TachyonFile, client: TachyonFS) {
-    if (!client.delete(dir.getPath(), true)) {
+    if (!client.delete(new TachyonURI(dir.getPath()), true)) {
       throw new IOException("Failed to delete the tachyon dir: " + dir)
     }
   }

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

@@ -33,8 +33,7 @@ class CheckpointSuite extends FunSuite with LocalSparkContext with Logging {
 
   override def beforeEach() {
     super.beforeEach()
-    checkpointDir = File.createTempFile("temp", "")
-    checkpointDir.deleteOnExit()
+    checkpointDir = File.createTempFile("temp", "", Utils.createTempDir())
     checkpointDir.delete()
     sc = new SparkContext("local", "test")
     sc.setCheckpointDir(checkpointDir.toString)

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

@@ -21,6 +21,8 @@ import java.io.File
 
 import org.scalatest.FunSuite
 
+import org.apache.spark.util.Utils
+
 class SecurityManagerSuite extends FunSuite {
 
   test("set security with conf") {
@@ -160,8 +162,7 @@ class SecurityManagerSuite extends FunSuite {
   }
 
   test("ssl off setup") {
-    val file = File.createTempFile("SSLOptionsSuite", "conf")
-    file.deleteOnExit()
+    val file = File.createTempFile("SSLOptionsSuite", "conf", Utils.createTempDir())
 
     System.setProperty("spark.ssl.configFile", file.getAbsolutePath)
     val conf = new SparkConf()

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

@@ -79,13 +79,14 @@ class SparkContextSuite extends FunSuite with LocalSparkContext {
     val byteArray2 = converter.convert(bytesWritable)
     assert(byteArray2.length === 0)
   }
-  
+
   test("addFile works") {
-    val file1 = File.createTempFile("someprefix1", "somesuffix1")
+    val dir = Utils.createTempDir()
+
+    val file1 = File.createTempFile("someprefix1", "somesuffix1", dir)
     val absolutePath1 = file1.getAbsolutePath
 
-    val pluto = Utils.createTempDir()
-    val file2 = File.createTempFile("someprefix2", "somesuffix2", pluto)
+    val file2 = File.createTempFile("someprefix2", "somesuffix2", dir)
     val relativePath = file2.getParent + "/../" + file2.getParentFile.getName + "/" + file2.getName
     val absolutePath2 = file2.getAbsolutePath
 
@@ -129,7 +130,7 @@ class SparkContextSuite extends FunSuite with LocalSparkContext {
       sc.stop()
     }
   }
-  
+
   test("addFile recursive works") {
     val pluto = Utils.createTempDir()
     val neptune = Utils.createTempDir(pluto.getAbsolutePath)

core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala

@@ -402,8 +402,10 @@ class SparkSubmitSuite extends FunSuite with Matchers with ResetSystemProperties
     val archives = "file:/archive1,archive2" // spark.yarn.dist.archives
     val pyFiles = "py-file1,py-file2" // spark.submit.pyFiles
 
+    val tmpDir = Utils.createTempDir()
+
     // Test jars and files
-    val f1 = File.createTempFile("test-submit-jars-files", "")
+    val f1 = File.createTempFile("test-submit-jars-files", "", tmpDir)
     val writer1 = new PrintWriter(f1)
     writer1.println("spark.jars " + jars)
     writer1.println("spark.files " + files)
@@ -420,7 +422,7 @@ class SparkSubmitSuite extends FunSuite with Matchers with ResetSystemProperties
     sysProps("spark.files") should be(Utils.resolveURIs(files))
 
     // Test files and archives (Yarn)
-    val f2 = File.createTempFile("test-submit-files-archives", "")
+    val f2 = File.createTempFile("test-submit-files-archives", "", tmpDir)
     val writer2 = new PrintWriter(f2)
     writer2.println("spark.yarn.dist.files " + files)
     writer2.println("spark.yarn.dist.archives " + archives)
@@ -437,7 +439,7 @@ class SparkSubmitSuite extends FunSuite with Matchers with ResetSystemProperties
     sysProps2("spark.yarn.dist.archives") should be(Utils.resolveURIs(archives))
 
     // Test python files
-    val f3 = File.createTempFile("test-submit-python-files", "")
+    val f3 = File.createTempFile("test-submit-python-files", "", tmpDir)
     val writer3 = new PrintWriter(f3)
     writer3.println("spark.submit.pyFiles " + pyFiles)
     writer3.close()

core/src/test/scala/org/apache/spark/rdd/PipedRDDSuite.scala

@@ -22,14 +22,16 @@ import java.io.File
 import org.apache.hadoop.fs.Path
 import org.apache.hadoop.io.{LongWritable, Text}
 import org.apache.hadoop.mapred.{FileSplit, JobConf, TextInputFormat}
-import org.apache.spark._
 import org.scalatest.FunSuite
 
 import scala.collection.Map
 import scala.language.postfixOps
 import scala.sys.process._
 import scala.util.Try
 
+import org.apache.spark._
+import org.apache.spark.util.Utils
+
 class PipedRDDSuite extends FunSuite with SharedSparkContext {
 
   test("basic pipe") {
@@ -141,7 +143,7 @@ class PipedRDDSuite extends FunSuite with SharedSparkContext {
       // make sure symlinks were created
       assert(pipedLs.length > 0)
       // clean up top level tasks directory
-      new File("tasks").delete()
+      Utils.deleteRecursively(new File("tasks"))
     } else {
       assert(true)
     }