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

R/log4j.properties

@@ -19,7 +19,7 @@
 log4j.rootCategory=INFO, file
 log4j.appender.file=org.apache.log4j.FileAppender
 log4j.appender.file.append=true
-log4j.appender.file.file=R-unit-tests.log
+log4j.appender.file.file=R/target/unit-tests.log
 log4j.appender.file.layout=org.apache.log4j.PatternLayout
 log4j.appender.file.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss.SSS} %t %p %c{1}: %m%n
 

build/mvn

@@ -69,11 +69,14 @@ install_app() {
 
 # Install maven under the build/ folder
 install_mvn() {
+  local MVN_VERSION="3.3.3"
+
   install_app \
-    "http://archive.apache.org/dist/maven/maven-3/3.2.5/binaries" \
-    "apache-maven-3.2.5-bin.tar.gz" \
-    "apache-maven-3.2.5/bin/mvn"
-  MVN_BIN="${_DIR}/apache-maven-3.2.5/bin/mvn"
+    "http://archive.apache.org/dist/maven/maven-3/${MVN_VERSION}/binaries" \
+    "apache-maven-${MVN_VERSION}-bin.tar.gz" \
+    "apache-maven-${MVN_VERSION}/bin/mvn"
+
+  MVN_BIN="${_DIR}/apache-maven-${MVN_VERSION}/bin/mvn"
 }
 
 # Install zinc under the build/ folder
@@ -105,28 +108,16 @@ install_scala() {
   SCALA_LIBRARY="$(cd "$(dirname ${scala_bin})/../lib" && pwd)/scala-library.jar"
 }
 
-# Determines if a given application is already installed. If not, will attempt
-# to install
-## Arg1 - application name
-## Arg2 - Alternate path to local install under build/ dir
-check_and_install_app() {
-  # create the local environment variable in uppercase
-  local app_bin="`echo $1 | awk '{print toupper(\$0)}'`_BIN"
-  # some black magic to set the generated app variable (i.e. MVN_BIN) into the
-  # environment
-  eval "${app_bin}=`which $1 2>/dev/null`"
-
-  if [ -z "`which $1 2>/dev/null`" ]; then
-    install_$1
-  fi
-}
-
 # Setup healthy defaults for the Zinc port if none were provided from
 # the environment
 ZINC_PORT=${ZINC_PORT:-"3030"}
 
-# Check and install all applications necessary to build Spark
-check_and_install_app "mvn"
+# Install Maven if necessary
+MVN_BIN="$(command -v mvn)"
+
+if [ ! "$MVN_BIN" ]; then
+  install_mvn
+fi
 
 # Install the proper version of Scala and Zinc for the build
 install_zinc

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

@@ -192,7 +192,7 @@ private[spark] class SecurityManager(sparkConf: SparkConf)
   // key used to store the spark secret in the Hadoop UGI
   private val sparkSecretLookupKey = "sparkCookie"
 
-  private val authOn = sparkConf.getBoolean("spark.authenticate", false)
+  private val authOn = sparkConf.getBoolean(SecurityManager.SPARK_AUTH_CONF, false)
   // keep spark.ui.acls.enable for backwards compatibility with 1.0
   private var aclsOn =
     sparkConf.getBoolean("spark.acls.enable", sparkConf.getBoolean("spark.ui.acls.enable", false))
@@ -365,10 +365,12 @@ private[spark] class SecurityManager(sparkConf: SparkConf)
       cookie
     } else {
       // user must have set spark.authenticate.secret config
-      sparkConf.getOption("spark.authenticate.secret") match {
+      // For Master/Worker, auth secret is in conf; for Executors, it is in env variable
+      sys.env.get(SecurityManager.ENV_AUTH_SECRET)
+        .orElse(sparkConf.getOption(SecurityManager.SPARK_AUTH_SECRET_CONF)) match {
         case Some(value) => value
         case None => throw new Exception("Error: a secret key must be specified via the " +
-          "spark.authenticate.secret config")
+          SecurityManager.SPARK_AUTH_SECRET_CONF + " config")
       }
     }
     sCookie
@@ -449,3 +451,12 @@ private[spark] class SecurityManager(sparkConf: SparkConf)
   override def getSaslUser(appId: String): String = getSaslUser()
   override def getSecretKey(appId: String): String = getSecretKey()
 }
+
+private[spark] object SecurityManager {
+
+  val SPARK_AUTH_CONF: String = "spark.authenticate"
+  val SPARK_AUTH_SECRET_CONF: String = "spark.authenticate.secret"
+  // This is used to set auth secret to an executor's env variable. It should have the same
+  // value as SPARK_AUTH_SECERET_CONF set in SparkConf
+  val ENV_AUTH_SECRET = "_SPARK_AUTH_SECRET"
+}

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

@@ -557,7 +557,7 @@ private[spark] object SparkConf extends Logging {
   def isExecutorStartupConf(name: String): Boolean = {
     isAkkaConf(name) ||
     name.startsWith("spark.akka") ||
-    name.startsWith("spark.auth") ||
+    (name.startsWith("spark.auth") && name != SecurityManager.SPARK_AUTH_SECRET_CONF) ||
     name.startsWith("spark.ssl") ||
     isSparkPortConf(name)
   }

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

@@ -35,7 +35,8 @@ import org.apache.ivy.core.resolve.ResolveOptions
 import org.apache.ivy.core.retrieve.RetrieveOptions
 import org.apache.ivy.core.settings.IvySettings
 import org.apache.ivy.plugins.matcher.GlobPatternMatcher
-import org.apache.ivy.plugins.resolver.{ChainResolver, IBiblioResolver}
+import org.apache.ivy.plugins.repository.file.FileRepository
+import org.apache.ivy.plugins.resolver.{FileSystemResolver, ChainResolver, IBiblioResolver}
 import org.apache.spark.SPARK_VERSION
 import org.apache.spark.deploy.rest._
 import org.apache.spark.util.{ChildFirstURLClassLoader, MutableURLClassLoader, Utils}
@@ -735,8 +736,14 @@ private[spark] object SparkSubmitUtils {
   }
 
   /** Path of the local Maven cache. */
-  private[spark] def m2Path: File = new File(System.getProperty("user.home"),
-    ".m2" + File.separator + "repository" + File.separator)
+  private[spark] def m2Path: File = {
+    if (Utils.isTesting) {
+      // test builds delete the maven cache, and this can cause flakiness
+      new File("dummy", ".m2" + File.separator + "repository")
+    } else {
+      new File(System.getProperty("user.home"), ".m2" + File.separator + "repository")
+    }
+  }
 
   /**
    * Extracts maven coordinates from a comma-delimited string
@@ -756,12 +763,13 @@ private[spark] object SparkSubmitUtils {
     localM2.setName("local-m2-cache")
     cr.add(localM2)
 
-    val localIvy = new IBiblioResolver
-    localIvy.setRoot(new File(ivySettings.getDefaultIvyUserDir,
-      "local" + File.separator).toURI.toString)
+    val localIvy = new FileSystemResolver
+    val localIvyRoot = new File(ivySettings.getDefaultIvyUserDir, "local")
+    localIvy.setLocal(true)
+    localIvy.setRepository(new FileRepository(localIvyRoot))
     val ivyPattern = Seq("[organisation]", "[module]", "[revision]", "[type]s",
       "[artifact](-[classifier]).[ext]").mkString(File.separator)
-    localIvy.setPattern(ivyPattern)
+    localIvy.addIvyPattern(localIvyRoot.getAbsolutePath + File.separator + ivyPattern)
     localIvy.setName("local-ivy-cache")
     cr.add(localIvy)
 

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

@@ -160,7 +160,7 @@ private[history] class FsHistoryProvider(conf: SparkConf, clock: Clock)
           replayBus.addListener(appListener)
           val appInfo = replay(fs.getFileStatus(new Path(logDir, attempt.logPath)), replayBus)
 
-          ui.setAppName(s"${appInfo.name} ($appId)")
+          appInfo.foreach { app => ui.setAppName(s"${app.name} ($appId)") }
 
           val uiAclsEnabled = conf.getBoolean("spark.history.ui.acls.enable", false)
           ui.getSecurityManager.setAcls(uiAclsEnabled)
@@ -282,8 +282,12 @@ private[history] class FsHistoryProvider(conf: SparkConf, clock: Clock)
     val newAttempts = logs.flatMap { fileStatus =>
       try {
         val res = replay(fileStatus, bus)
-        logInfo(s"Application log ${res.logPath} loaded successfully.")
-        Some(res)
+        res match {
+          case Some(r) => logDebug(s"Application log ${r.logPath} loaded successfully.")
+          case None => logWarning(s"Failed to load application log ${fileStatus.getPath}. " +
+            "The application may have not started.")
+        }
+        res
       } catch {
         case e: Exception =>
           logError(
@@ -429,9 +433,11 @@ private[history] class FsHistoryProvider(conf: SparkConf, clock: Clock)
 
   /**
    * Replays the events in the specified log file and returns information about the associated
-   * application.
+   * application. Return `None` if the application ID cannot be located.
    */
-  private def replay(eventLog: FileStatus, bus: ReplayListenerBus): FsApplicationAttemptInfo = {
+  private def replay(
+      eventLog: FileStatus,
+      bus: ReplayListenerBus): Option[FsApplicationAttemptInfo] = {
     val logPath = eventLog.getPath()
     logInfo(s"Replaying log path: $logPath")
     val logInput =
@@ -445,16 +451,18 @@ private[history] class FsHistoryProvider(conf: SparkConf, clock: Clock)
       val appCompleted = isApplicationCompleted(eventLog)
       bus.addListener(appListener)
       bus.replay(logInput, logPath.toString, !appCompleted)
-      new FsApplicationAttemptInfo(
-        logPath.getName(),
-        appListener.appName.getOrElse(NOT_STARTED),
-        appListener.appId.getOrElse(logPath.getName()),
-        appListener.appAttemptId,
-        appListener.startTime.getOrElse(-1L),
-        appListener.endTime.getOrElse(-1L),
-        getModificationTime(eventLog).get,
-        appListener.sparkUser.getOrElse(NOT_STARTED),
-        appCompleted)
+      appListener.appId.map { appId =>
+        new FsApplicationAttemptInfo(
+          logPath.getName(),
+          appListener.appName.getOrElse(NOT_STARTED),
+          appId,
+          appListener.appAttemptId,
+          appListener.startTime.getOrElse(-1L),
+          appListener.endTime.getOrElse(-1L),
+          getModificationTime(eventLog).get,
+          appListener.sparkUser.getOrElse(NOT_STARTED),
+          appCompleted)
+      }
     } finally {
       logInput.close()
     }

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

@@ -24,6 +24,7 @@ import scala.collection.JavaConversions._
 import scala.collection.Map
 
 import org.apache.spark.Logging
+import org.apache.spark.SecurityManager
 import org.apache.spark.deploy.Command
 import org.apache.spark.launcher.WorkerCommandBuilder
 import org.apache.spark.util.Utils
@@ -40,12 +41,14 @@ object CommandUtils extends Logging {
    */
   def buildProcessBuilder(
       command: Command,
+      securityMgr: SecurityManager,
       memory: Int,
       sparkHome: String,
       substituteArguments: String => String,
       classPaths: Seq[String] = Seq[String](),
       env: Map[String, String] = sys.env): ProcessBuilder = {
-    val localCommand = buildLocalCommand(command, substituteArguments, classPaths, env)
+    val localCommand = buildLocalCommand(
+      command, securityMgr, substituteArguments, classPaths, env)
     val commandSeq = buildCommandSeq(localCommand, memory, sparkHome)
     val builder = new ProcessBuilder(commandSeq: _*)
     val environment = builder.environment()
@@ -69,27 +72,34 @@ object CommandUtils extends Logging {
    */
   private def buildLocalCommand(
       command: Command,
+      securityMgr: SecurityManager,
       substituteArguments: String => String,
       classPath: Seq[String] = Seq[String](),
       env: Map[String, String]): Command = {
     val libraryPathName = Utils.libraryPathEnvName
     val libraryPathEntries = command.libraryPathEntries
     val cmdLibraryPath = command.environment.get(libraryPathName)
 
-    val newEnvironment = if (libraryPathEntries.nonEmpty && libraryPathName.nonEmpty) {
+    var newEnvironment = if (libraryPathEntries.nonEmpty && libraryPathName.nonEmpty) {
       val libraryPaths = libraryPathEntries ++ cmdLibraryPath ++ env.get(libraryPathName)
       command.environment + ((libraryPathName, libraryPaths.mkString(File.pathSeparator)))
     } else {
       command.environment
     }
 
+    // set auth secret to env variable if needed
+    if (securityMgr.isAuthenticationEnabled) {
+      newEnvironment += (SecurityManager.ENV_AUTH_SECRET -> securityMgr.getSecretKey)
+    }
+
     Command(
       command.mainClass,
       command.arguments.map(substituteArguments),
       newEnvironment,
       command.classPathEntries ++ classPath,
       Seq[String](), // library path already captured in environment variable
-      command.javaOpts)
+      // filter out auth secret from java options
+      command.javaOpts.filterNot(_.startsWith("-D" + SecurityManager.SPARK_AUTH_SECRET_CONF)))
   }
 
   /** Spawn a thread that will redirect a given stream to a file */

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

@@ -85,8 +85,8 @@ private[deploy] class DriverRunner(
           }
 
           // TODO: If we add ability to submit multiple jars they should also be added here
-          val builder = CommandUtils.buildProcessBuilder(driverDesc.command, driverDesc.mem,
-            sparkHome.getAbsolutePath, substituteVariables)
+          val builder = CommandUtils.buildProcessBuilder(driverDesc.command, securityManager,
+            driverDesc.mem, sparkHome.getAbsolutePath, substituteVariables)
           launchDriver(builder, driverDir, driverDesc.supervise)
         }
         catch {

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

@@ -25,7 +25,7 @@ import akka.actor.ActorRef
 import com.google.common.base.Charsets.UTF_8
 import com.google.common.io.Files
 
-import org.apache.spark.{SparkConf, Logging}
+import org.apache.spark.{SecurityManager, SparkConf, Logging}
 import org.apache.spark.deploy.{ApplicationDescription, ExecutorState}
 import org.apache.spark.deploy.DeployMessages.ExecutorStateChanged
 import org.apache.spark.util.Utils
@@ -125,8 +125,8 @@ private[deploy] class ExecutorRunner(
   private def fetchAndRunExecutor() {
     try {
       // Launch the process
-      val builder = CommandUtils.buildProcessBuilder(appDesc.command, memory,
-        sparkHome.getAbsolutePath, substituteVariables)
+      val builder = CommandUtils.buildProcessBuilder(appDesc.command, new SecurityManager(conf),
+        memory, sparkHome.getAbsolutePath, substituteVariables)
       val command = builder.command()
       logInfo("Launch command: " + command.mkString("\"", "\" \"", "\""))
 

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

@@ -83,8 +83,10 @@ private[spark] class BlockManager(
   private var externalBlockStoreInitialized = false
   private[spark] val memoryStore = new MemoryStore(this, maxMemory)
   private[spark] val diskStore = new DiskStore(this, diskBlockManager)
-  private[spark] lazy val externalBlockStore: ExternalBlockStore =
+  private[spark] lazy val externalBlockStore: ExternalBlockStore = {
+    externalBlockStoreInitialized = true
     new ExternalBlockStore(this, executorId)
+  }
 
   private[spark]
   val externalShuffleServiceEnabled = conf.getBoolean("spark.shuffle.service.enabled", false)

core/src/main/scala/org/apache/spark/ui/UIUtils.scala

@@ -362,7 +362,7 @@ private[spark] object UIUtils extends Logging {
               { g.incomingEdges.map { e => <div class="incoming-edge">{e.fromId},{e.toId}</div> } }
               { g.outgoingEdges.map { e => <div class="outgoing-edge">{e.fromId},{e.toId}</div> } }
               {
-                g.rootCluster.getAllNodes.filter(_.cached).map { n =>
+                g.rootCluster.getCachedNodes.map { n =>
                   <div class="cached-rdd">{n.id}</div>
                 }
               }

core/src/main/scala/org/apache/spark/ui/scope/RDDOperationGraph.scala

@@ -66,9 +66,9 @@ private[ui] class RDDOperationCluster(val id: String, private var _name: String)
     _childClusters += childCluster
   }
 
-  /** Return all the nodes container in this cluster, including ones nested in other clusters. */
-  def getAllNodes: Seq[RDDOperationNode] = {
-    _childNodes ++ _childClusters.flatMap(_.childNodes)
+  /** Return all the nodes which are cached. */
+  def getCachedNodes: Seq[RDDOperationNode] = {
+    _childNodes.filter(_.cached) ++ _childClusters.flatMap(_.getCachedNodes)
   }
 }