Merge branch 'master' of github.com:apache/spark into R5

Author: Davies Liu

R/pkg/R/RDD.R

@@ -85,7 +85,7 @@ setMethod("initialize", "PipelinedRDD", function(.Object, prev, func, jrdd_val)
 
   if (!inherits(prev, "PipelinedRDD") || !isPipelinable(prev)) {
     # This transformation is the first in its stage:
-    .Object@func <- func
+    .Object@func <- cleanClosure(func)
     .Object@prev_jrdd <- getJRDD(prev)
     .Object@env$prev_serializedMode <- prev@env$serializedMode
     # NOTE: We use prev_serializedMode to track the serialization mode of prev_JRDD
@@ -94,7 +94,7 @@ setMethod("initialize", "PipelinedRDD", function(.Object, prev, func, jrdd_val)
     pipelinedFunc <- function(split, iterator) {
       func(split, prev@func(split, iterator))
     }
-    .Object@func <- pipelinedFunc
+    .Object@func <- cleanClosure(pipelinedFunc)
     .Object@prev_jrdd <- prev@prev_jrdd # maintain the pipeline
     # Get the serialization mode of the parent RDD
     .Object@env$prev_serializedMode <- prev@env$prev_serializedMode
@@ -144,17 +144,13 @@ setMethod("getJRDD", signature(rdd = "PipelinedRDD"),
               return(rdd@env$jrdd_val)
             }
 
-            computeFunc <- function(split, part) {
-              rdd@func(split, part)
-            }
-
             packageNamesArr <- serialize(.sparkREnv[[".packages"]],
                                          connection = NULL)
 
             broadcastArr <- lapply(ls(.broadcastNames),
                                    function(name) { get(name, .broadcastNames) })
 
-            serializedFuncArr <- serialize(computeFunc, connection = NULL)
+            serializedFuncArr <- serialize(rdd@func, connection = NULL)
 
             prev_jrdd <- rdd@prev_jrdd
 
@@ -279,7 +275,7 @@ setMethod("unpersist",
 #' @examples
 #'\dontrun{
 #' sc <- sparkR.init()
-#' setCheckpointDir(sc, "checkpoints")
+#' setCheckpointDir(sc, "checkpoint")
 #' rdd <- parallelize(sc, 1:10, 2L)
 #' checkpoint(rdd)
 #'}
@@ -551,11 +547,7 @@ setMethod("mapPartitions",
 setMethod("lapplyPartitionsWithIndex",
           signature(X = "RDD", FUN = "function"),
           function(X, FUN) {
-            FUN <- cleanClosure(FUN)
-            closureCapturingFunc <- function(split, part) {
-              FUN(split, part)
-            }
-            PipelinedRDD(X, closureCapturingFunc)
+            PipelinedRDD(X, FUN)
           })
 
 #' @rdname lapplyPartitionsWithIndex

R/pkg/R/context.R

@@ -216,7 +216,7 @@ broadcast <- function(sc, object) {
 #' @examples
 #'\dontrun{
 #' sc <- sparkR.init()
-#' setCheckpointDir(sc, "~/checkpoints")
+#' setCheckpointDir(sc, "~/checkpoint")
 #' rdd <- parallelize(sc, 1:2, 2L)
 #' checkpoint(rdd)
 #'}

R/pkg/R/pairRDD.R

@@ -694,10 +694,6 @@ setMethod("cogroup",
             for (i in 1:rddsLen) {
               rdds[[i]] <- lapply(rdds[[i]],
                                   function(x) { list(x[[1]], list(i, x[[2]])) })
-              # TODO(hao): As issue [SparkR-142] mentions, the right value of i
-              # will not be captured into UDF if getJRDD is not invoked.
-              # It should be resolved together with that issue.
-              getJRDD(rdds[[i]])  # Capture the closure.
             }
             union.rdd <- Reduce(unionRDD, rdds)
             group.func <- function(vlist) {

R/pkg/inst/tests/test_binaryFile.R

@@ -27,7 +27,7 @@ test_that("saveAsObjectFile()/objectFile() following textFile() works", {
   fileName2 <- tempfile(pattern="spark-test", fileext=".tmp")
   writeLines(mockFile, fileName1)
 
-  rdd <- textFile(sc, fileName1)
+  rdd <- textFile(sc, fileName1, 1)
   saveAsObjectFile(rdd, fileName2)
   rdd <- objectFile(sc, fileName2)
   expect_equal(collect(rdd), as.list(mockFile))
@@ -40,7 +40,7 @@ test_that("saveAsObjectFile()/objectFile() works on a parallelized list", {
   fileName <- tempfile(pattern="spark-test", fileext=".tmp")
 
   l <- list(1, 2, 3)
-  rdd <- parallelize(sc, l)
+  rdd <- parallelize(sc, l, 1)
   saveAsObjectFile(rdd, fileName)
   rdd <- objectFile(sc, fileName)
   expect_equal(collect(rdd), l)

R/pkg/inst/tests/test_rdd.R

@@ -141,7 +141,8 @@ test_that("PipelinedRDD support actions: cache(), persist(), unpersist(), checkp
   unpersist(rdd2)
   expect_false(rdd2@env$isCached)
 
-  setCheckpointDir(sc, "checkpoints")
+  tempDir <- tempfile(pattern = "checkpoint")
+  setCheckpointDir(sc, tempDir)
   checkpoint(rdd2)
   expect_true(rdd2@env$isCheckpointed)
 
@@ -152,7 +153,7 @@ test_that("PipelinedRDD support actions: cache(), persist(), unpersist(), checkp
   # make sure the data is collectable
   collect(rdd2)
 
-  unlink("checkpoints")
+  unlink(tempDir)
 })
 
 test_that("reduce on RDD", {

R/pkg/inst/tests/test_textFile.R

@@ -81,7 +81,7 @@ test_that("textFile() followed by a saveAsTextFile() returns the same content",
   fileName2 <- tempfile(pattern="spark-test", fileext=".tmp")
   writeLines(mockFile, fileName1)
 
-  rdd <- textFile(sc, fileName1)
+  rdd <- textFile(sc, fileName1, 1L)
   saveAsTextFile(rdd, fileName2)
   rdd <- textFile(sc, fileName2)
   expect_equal(collect(rdd), as.list(mockFile))
@@ -93,7 +93,7 @@ test_that("textFile() followed by a saveAsTextFile() returns the same content",
 test_that("saveAsTextFile() on a parallelized list works as expected", {
   fileName <- tempfile(pattern="spark-test", fileext=".tmp")
   l <- list(1, 2, 3)
-  rdd <- parallelize(sc, l)
+  rdd <- parallelize(sc, l, 1L)
   saveAsTextFile(rdd, fileName)
   rdd <- textFile(sc, fileName)
   expect_equal(collect(rdd), lapply(l, function(x) {toString(x)}))

bagel/src/test/resources/log4j.properties

@@ -24,4 +24,4 @@ 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
 
 # Ignore messages below warning level from Jetty, because it's a bit verbose
-log4j.logger.org.eclipse.jetty=WARN
+log4j.logger.org.spark-project.jetty=WARN

bin/load-spark-env.sh

@@ -20,6 +20,7 @@
 # This script loads spark-env.sh if it exists, and ensures it is only loaded once.
 # spark-env.sh is loaded from SPARK_CONF_DIR if set, or within the current directory's
 # conf/ subdirectory.
+FWDIR="$(cd "`dirname "$0"`"/..; pwd)"
 
 if [ -z "$SPARK_ENV_LOADED" ]; then
   export SPARK_ENV_LOADED=1
@@ -41,8 +42,8 @@ fi
 
 if [ -z "$SPARK_SCALA_VERSION" ]; then
 
-    ASSEMBLY_DIR2="$SPARK_HOME/assembly/target/scala-2.11"
-    ASSEMBLY_DIR1="$SPARK_HOME/assembly/target/scala-2.10"
+    ASSEMBLY_DIR2="$FWDIR/assembly/target/scala-2.11"
+    ASSEMBLY_DIR1="$FWDIR/assembly/target/scala-2.10"
 
     if [[ -d "$ASSEMBLY_DIR2" && -d "$ASSEMBLY_DIR1" ]]; then
         echo -e "Presence of build for both scala versions(SCALA 2.10 and SCALA 2.11) detected." 1>&2

conf/log4j.properties.template

@@ -6,7 +6,7 @@ log4j.appender.console.layout=org.apache.log4j.PatternLayout
 log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{1}: %m%n
 
 # Settings to quiet third party logs that are too verbose
-log4j.logger.org.eclipse.jetty=WARN
-log4j.logger.org.eclipse.jetty.util.component.AbstractLifeCycle=ERROR
+log4j.logger.org.spark-project.jetty=WARN
+log4j.logger.org.spark-project.jetty.util.component.AbstractLifeCycle=ERROR
 log4j.logger.org.apache.spark.repl.SparkIMain$exprTyper=INFO
 log4j.logger.org.apache.spark.repl.SparkILoop$SparkILoopInterpreter=INFO

core/src/main/resources/org/apache/spark/log4j-defaults.properties

@@ -6,7 +6,7 @@ log4j.appender.console.layout=org.apache.log4j.PatternLayout
 log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{1}: %m%n
 
 # Settings to quiet third party logs that are too verbose
-log4j.logger.org.eclipse.jetty=WARN
-log4j.logger.org.eclipse.jetty.util.component.AbstractLifeCycle=ERROR
+log4j.logger.org.spark-project.jetty=WARN
+log4j.logger.org.spark-project.jetty.util.component.AbstractLifeCycle=ERROR
 log4j.logger.org.apache.spark.repl.SparkIMain$exprTyper=INFO
 log4j.logger.org.apache.spark.repl.SparkILoop$SparkILoopInterpreter=INFO

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

@@ -22,7 +22,7 @@ import java.lang.ref.{ReferenceQueue, WeakReference}
 import scala.collection.mutable.{ArrayBuffer, SynchronizedBuffer}
 
 import org.apache.spark.broadcast.Broadcast
-import org.apache.spark.rdd.RDD
+import org.apache.spark.rdd.{RDDCheckpointData, RDD}
 import org.apache.spark.util.Utils
 
 /**
@@ -33,6 +33,7 @@ private case class CleanRDD(rddId: Int) extends CleanupTask
 private case class CleanShuffle(shuffleId: Int) extends CleanupTask
 private case class CleanBroadcast(broadcastId: Long) extends CleanupTask
 private case class CleanAccum(accId: Long) extends CleanupTask
+private case class CleanCheckpoint(rddId: Int) extends CleanupTask
 
 /**
  * A WeakReference associated with a CleanupTask.
@@ -94,12 +95,12 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   @volatile private var stopped = false
 
   /** Attach a listener object to get information of when objects are cleaned. */
-  def attachListener(listener: CleanerListener) {
+  def attachListener(listener: CleanerListener): Unit = {
     listeners += listener
   }
 
   /** Start the cleaner. */
-  def start() {
+  def start(): Unit = {
     cleaningThread.setDaemon(true)
     cleaningThread.setName("Spark Context Cleaner")
     cleaningThread.start()
@@ -108,7 +109,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   /**
    * Stop the cleaning thread and wait until the thread has finished running its current task.
    */
-  def stop() {
+  def stop(): Unit = {
     stopped = true
     // Interrupt the cleaning thread, but wait until the current task has finished before
     // doing so. This guards against the race condition where a cleaning thread may
@@ -121,7 +122,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Register a RDD for cleanup when it is garbage collected. */
-  def registerRDDForCleanup(rdd: RDD[_]) {
+  def registerRDDForCleanup(rdd: RDD[_]): Unit = {
     registerForCleanup(rdd, CleanRDD(rdd.id))
   }
 
@@ -130,17 +131,22 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Register a ShuffleDependency for cleanup when it is garbage collected. */
-  def registerShuffleForCleanup(shuffleDependency: ShuffleDependency[_, _, _]) {
+  def registerShuffleForCleanup(shuffleDependency: ShuffleDependency[_, _, _]): Unit = {
     registerForCleanup(shuffleDependency, CleanShuffle(shuffleDependency.shuffleId))
   }
 
   /** Register a Broadcast for cleanup when it is garbage collected. */
-  def registerBroadcastForCleanup[T](broadcast: Broadcast[T]) {
+  def registerBroadcastForCleanup[T](broadcast: Broadcast[T]): Unit = {
     registerForCleanup(broadcast, CleanBroadcast(broadcast.id))
   }
 
+  /** Register a RDDCheckpointData for cleanup when it is garbage collected. */
+  def registerRDDCheckpointDataForCleanup[T](rdd: RDD[_], parentId: Int): Unit = {
+    registerForCleanup(rdd, CleanCheckpoint(parentId))
+  }
+
   /** Register an object for cleanup. */
-  private def registerForCleanup(objectForCleanup: AnyRef, task: CleanupTask) {
+  private def registerForCleanup(objectForCleanup: AnyRef, task: CleanupTask): Unit = {
     referenceBuffer += new CleanupTaskWeakReference(task, objectForCleanup, referenceQueue)
   }
 
@@ -164,6 +170,8 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
                 doCleanupBroadcast(broadcastId, blocking = blockOnCleanupTasks)
               case CleanAccum(accId) =>
                 doCleanupAccum(accId, blocking = blockOnCleanupTasks)
+              case CleanCheckpoint(rddId) =>
+                doCleanCheckpoint(rddId)
             }
           }
         }
@@ -175,7 +183,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Perform RDD cleanup. */
-  def doCleanupRDD(rddId: Int, blocking: Boolean) {
+  def doCleanupRDD(rddId: Int, blocking: Boolean): Unit = {
     try {
       logDebug("Cleaning RDD " + rddId)
       sc.unpersistRDD(rddId, blocking)
@@ -187,7 +195,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Perform shuffle cleanup, asynchronously. */
-  def doCleanupShuffle(shuffleId: Int, blocking: Boolean) {
+  def doCleanupShuffle(shuffleId: Int, blocking: Boolean): Unit = {
     try {
       logDebug("Cleaning shuffle " + shuffleId)
       mapOutputTrackerMaster.unregisterShuffle(shuffleId)
@@ -200,7 +208,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Perform broadcast cleanup. */
-  def doCleanupBroadcast(broadcastId: Long, blocking: Boolean) {
+  def doCleanupBroadcast(broadcastId: Long, blocking: Boolean): Unit = {
     try {
       logDebug(s"Cleaning broadcast $broadcastId")
       broadcastManager.unbroadcast(broadcastId, true, blocking)
@@ -212,7 +220,7 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
   }
 
   /** Perform accumulator cleanup. */
-  def doCleanupAccum(accId: Long, blocking: Boolean) {
+  def doCleanupAccum(accId: Long, blocking: Boolean): Unit = {
     try {
       logDebug("Cleaning accumulator " + accId)
       Accumulators.remove(accId)
@@ -223,6 +231,18 @@ private[spark] class ContextCleaner(sc: SparkContext) extends Logging {
     }
   }
 
+  /** Perform checkpoint cleanup. */
+  def doCleanCheckpoint(rddId: Int): Unit = {
+    try {
+      logDebug("Cleaning rdd checkpoint data " + rddId)
+      RDDCheckpointData.clearRDDCheckpointData(sc, rddId)
+      logInfo("Cleaned rdd checkpoint data " + rddId)
+    }
+    catch {
+      case e: Exception => logError("Error cleaning rdd checkpoint data " + rddId, e)
+    }
+  }
+
   private def blockManagerMaster = sc.env.blockManager.master
   private def broadcastManager = sc.env.broadcastManager
   private def mapOutputTrackerMaster = sc.env.mapOutputTracker.asInstanceOf[MapOutputTrackerMaster]