rebase with upstream

LICENSE

@@ -250,11 +250,11 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
         (Interpreter classes (all .scala files in repl/src/main/scala
         except for Main.Scala, SparkHelper.scala and ExecutorClassLoader.scala),
         and for SerializableMapWrapper in JavaUtils.scala)
-     (BSD-like) Scala Actors library (org.scala-lang:scala-actors:2.10.4 - http://www.scala-lang.org/)
-     (BSD-like) Scala Compiler (org.scala-lang:scala-compiler:2.10.4 - http://www.scala-lang.org/)
-     (BSD-like) Scala Compiler (org.scala-lang:scala-reflect:2.10.4 - http://www.scala-lang.org/)
-     (BSD-like) Scala Library (org.scala-lang:scala-library:2.10.4 - http://www.scala-lang.org/)
-     (BSD-like) Scalap (org.scala-lang:scalap:2.10.4 - http://www.scala-lang.org/)
+     (BSD-like) Scala Actors library (org.scala-lang:scala-actors:2.10.5 - http://www.scala-lang.org/)
+     (BSD-like) Scala Compiler (org.scala-lang:scala-compiler:2.10.5 - http://www.scala-lang.org/)
+     (BSD-like) Scala Compiler (org.scala-lang:scala-reflect:2.10.5 - http://www.scala-lang.org/)
+     (BSD-like) Scala Library (org.scala-lang:scala-library:2.10.5 - http://www.scala-lang.org/)
+     (BSD-like) Scalap (org.scala-lang:scalap:2.10.5 - http://www.scala-lang.org/)
      (BSD-style) scalacheck (org.scalacheck:scalacheck_2.10:1.10.0 - http://www.scalacheck.org)
      (BSD-style) spire (org.spire-math:spire_2.10:0.7.1 - http://spire-math.org)
      (BSD-style) spire-macros (org.spire-math:spire-macros_2.10:0.7.1 - http://spire-math.org)

core/src/main/java/org/apache/spark/shuffle/sort/UnsafeShuffleWriter.java

@@ -254,8 +254,8 @@ private long[] mergeSpills(SpillInfo[] spills) throws IOException {
     final CompressionCodec compressionCodec = CompressionCodec$.MODULE$.createCodec(sparkConf);
     final boolean fastMergeEnabled =
       sparkConf.getBoolean("spark.shuffle.unsafe.fastMergeEnabled", true);
-    final boolean fastMergeIsSupported =
-      !compressionEnabled || compressionCodec instanceof LZFCompressionCodec;
+    final boolean fastMergeIsSupported = !compressionEnabled ||
+      CompressionCodec$.MODULE$.supportsConcatenationOfSerializedStreams(compressionCodec);
     try {
       if (spills.length == 0) {
         new FileOutputStream(outputFile).close(); // Create an empty file

core/src/main/java/org/apache/spark/unsafe/map/BytesToBytesMap.java

@@ -35,7 +35,6 @@
 import org.apache.spark.unsafe.Platform;
 import org.apache.spark.unsafe.array.ByteArrayMethods;
 import org.apache.spark.unsafe.array.LongArray;
-import org.apache.spark.unsafe.bitset.BitSet;
 import org.apache.spark.unsafe.hash.Murmur3_x86_32;
 import org.apache.spark.unsafe.memory.MemoryBlock;
 import org.apache.spark.unsafe.memory.MemoryLocation;
@@ -123,12 +122,6 @@ public final class BytesToBytesMap extends MemoryConsumer {
    */
   private boolean canGrowArray = true;
 
-  /**
-   * A {@link BitSet} used to track location of the map where the key is set.
-   * Size of the bitset should be half of the size of the long array.
-   */
-  @Nullable private BitSet bitset;
-
   private final double loadFactor;
 
   /**
@@ -427,7 +420,6 @@ public Location lookup(Object keyBase, long keyOffset, int keyLength) {
    * This is a thread-safe version of `lookup`, could be used by multiple threads.
    */
   public void safeLookup(Object keyBase, long keyOffset, int keyLength, Location loc) {
-    assert(bitset != null);
     assert(longArray != null);
 
     if (enablePerfMetrics) {
@@ -440,7 +432,7 @@ public void safeLookup(Object keyBase, long keyOffset, int keyLength, Location l
       if (enablePerfMetrics) {
         numProbes++;
       }
-      if (!bitset.isSet(pos)) {
+      if (longArray.get(pos * 2) == 0) {
         // This is a new key.
         loc.with(pos, hashcode, false);
         return;
@@ -644,7 +636,6 @@ public boolean putNewKey(Object keyBase, long keyOffset, int keyLength,
       assert (!isDefined) : "Can only set value once for a key";
       assert (keyLength % 8 == 0);
       assert (valueLength % 8 == 0);
-      assert(bitset != null);
       assert(longArray != null);
 
       if (numElements == MAX_CAPACITY || !canGrowArray) {
@@ -678,7 +669,6 @@ public boolean putNewKey(Object keyBase, long keyOffset, int keyLength,
       Platform.putInt(base, offset, Platform.getInt(base, offset) + 1);
       pageCursor += recordLength;
       numElements++;
-      bitset.set(pos);
       final long storedKeyAddress = taskMemoryManager.encodePageNumberAndOffset(
         currentPage, recordOffset);
       longArray.set(pos * 2, storedKeyAddress);
@@ -734,7 +724,6 @@ private void allocate(int capacity) {
     assert (capacity <= MAX_CAPACITY);
     acquireMemory(capacity * 16);
     longArray = new LongArray(MemoryBlock.fromLongArray(new long[capacity * 2]));
-    bitset = new BitSet(MemoryBlock.fromLongArray(new long[capacity / 64]));
 
     this.growthThreshold = (int) (capacity * loadFactor);
     this.mask = capacity - 1;
@@ -749,7 +738,6 @@ public void freeArray() {
       long used = longArray.memoryBlock().size();
       longArray = null;
       releaseMemory(used);
-      bitset = null;
     }
   }
 
@@ -795,9 +783,7 @@ public long getTotalMemoryConsumption() {
     for (MemoryBlock dataPage : dataPages) {
       totalDataPagesSize += dataPage.size();
     }
-    return totalDataPagesSize +
-      ((bitset != null) ? bitset.memoryBlock().size() : 0L) +
-      ((longArray != null) ? longArray.memoryBlock().size() : 0L);
+    return totalDataPagesSize + ((longArray != null) ? longArray.memoryBlock().size() : 0L);
   }
 
   private void updatePeakMemoryUsed() {
@@ -852,7 +838,6 @@ public int getNumDataPages() {
    */
   @VisibleForTesting
   void growAndRehash() {
-    assert(bitset != null);
     assert(longArray != null);
 
     long resizeStartTime = -1;
@@ -861,39 +846,26 @@ void growAndRehash() {
     }
     // Store references to the old data structures to be used when we re-hash
     final LongArray oldLongArray = longArray;
-    final BitSet oldBitSet = bitset;
-    final int oldCapacity = (int) oldBitSet.capacity();
+    final int oldCapacity = (int) oldLongArray.size() / 2;
 
     // Allocate the new data structures
-    try {
-      allocate(Math.min(growthStrategy.nextCapacity(oldCapacity), MAX_CAPACITY));
-    } catch (OutOfMemoryError oom) {
-      longArray = oldLongArray;
-      bitset = oldBitSet;
-      throw oom;
-    }
+    allocate(Math.min(growthStrategy.nextCapacity(oldCapacity), MAX_CAPACITY));
 
     // Re-mask (we don't recompute the hashcode because we stored all 32 bits of it)
-    for (int pos = oldBitSet.nextSetBit(0); pos >= 0; pos = oldBitSet.nextSetBit(pos + 1)) {
-      final long keyPointer = oldLongArray.get(pos * 2);
-      final int hashcode = (int) oldLongArray.get(pos * 2 + 1);
+    for (int i = 0; i < oldLongArray.size(); i += 2) {
+      final long keyPointer = oldLongArray.get(i);
+      if (keyPointer == 0) {
+        continue;
+      }
+      final int hashcode = (int) oldLongArray.get(i + 1);
       int newPos = hashcode & mask;
       int step = 1;
-      boolean keepGoing = true;
-
-      // No need to check for equality here when we insert so this has one less if branch than
-      // the similar code path in addWithoutResize.
-      while (keepGoing) {
-        if (!bitset.isSet(newPos)) {
-          bitset.set(newPos);
-          longArray.set(newPos * 2, keyPointer);
-          longArray.set(newPos * 2 + 1, hashcode);
-          keepGoing = false;
-        } else {
-          newPos = (newPos + step) & mask;
-          step++;
-        }
+      while (longArray.get(newPos * 2) != 0) {
+        newPos = (newPos + step) & mask;
+        step++;
       }
+      longArray.set(newPos * 2, keyPointer);
+      longArray.set(newPos * 2 + 1, hashcode);
     }
     releaseMemory(oldLongArray.memoryBlock().size());
 

core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java

@@ -157,11 +157,14 @@ public void closeCurrentPage() {
    */
   @Override
   public long spill(long size, MemoryConsumer trigger) throws IOException {
+    assert(inMemSorter != null);
     if (trigger != this) {
       if (readingIterator != null) {
         return readingIterator.spill();
+      } else {
+
       }
-      return 0L;
+      return 0L; // this should throw exception
     }
 
     if (inMemSorter == null || inMemSorter.numRecords() <= 0) {

core/src/main/scala/org/apache/spark/io/CompressionCodec.scala

@@ -47,6 +47,11 @@ trait CompressionCodec {
 private[spark] object CompressionCodec {
 
   private val configKey = "spark.io.compression.codec"
+
+  private[spark] def supportsConcatenationOfSerializedStreams(codec: CompressionCodec): Boolean = {
+    codec.isInstanceOf[SnappyCompressionCodec] || codec.isInstanceOf[LZFCompressionCodec]
+  }
+
   private val shortCompressionCodecNames = Map(
     "lz4" -> classOf[LZ4CompressionCodec].getName,
     "lzf" -> classOf[LZFCompressionCodec].getName,

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

@@ -947,7 +947,13 @@ class DAGScheduler(
     // serializable. If tasks are not serializable, a SparkListenerStageCompleted event
     // will be posted, which should always come after a corresponding SparkListenerStageSubmitted
     // event.
-    outputCommitCoordinator.stageStart(stage.id)
+    stage match {
+      case s: ShuffleMapStage =>
+        outputCommitCoordinator.stageStart(stage = s.id, maxPartitionId = s.numPartitions - 1)
+      case s: ResultStage =>
+        outputCommitCoordinator.stageStart(
+          stage = s.id, maxPartitionId = s.rdd.partitions.length - 1)
+    }
     val taskIdToLocations: Map[Int, Seq[TaskLocation]] = try {
       stage match {
         case s: ShuffleMapStage =>

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

@@ -47,6 +47,8 @@ private[spark] class OutputCommitCoordinator(conf: SparkConf, isDriver: Boolean)
   private type PartitionId = Int
   private type TaskAttemptNumber = Int
 
+  private val NO_AUTHORIZED_COMMITTER: TaskAttemptNumber = -1
+
   /**
    * Map from active stages's id => partition id => task attempt with exclusive lock on committing
    * output for that partition.
@@ -56,9 +58,7 @@ private[spark] class OutputCommitCoordinator(conf: SparkConf, isDriver: Boolean)
    *
    * Access to this map should be guarded by synchronizing on the OutputCommitCoordinator instance.
    */
-  private val authorizedCommittersByStage: CommittersByStageMap = mutable.Map()
-  private type CommittersByStageMap =
-    mutable.Map[StageId, mutable.Map[PartitionId, TaskAttemptNumber]]
+  private val authorizedCommittersByStage = mutable.Map[StageId, Array[TaskAttemptNumber]]()
 
   /**
    * Returns whether the OutputCommitCoordinator's internal data structures are all empty.
@@ -95,9 +95,21 @@ private[spark] class OutputCommitCoordinator(conf: SparkConf, isDriver: Boolean)
     }
   }
 
-  // Called by DAGScheduler
-  private[scheduler] def stageStart(stage: StageId): Unit = synchronized {
-    authorizedCommittersByStage(stage) = mutable.HashMap[PartitionId, TaskAttemptNumber]()
+  /**
+   * Called by the DAGScheduler when a stage starts.
+   *
+   * @param stage the stage id.
+   * @param maxPartitionId the maximum partition id that could appear in this stage's tasks (i.e.
+   *                       the maximum possible value of `context.partitionId`).
+   */
+  private[scheduler] def stageStart(
+      stage: StageId,
+      maxPartitionId: Int): Unit = {
+    val arr = new Array[TaskAttemptNumber](maxPartitionId + 1)
+    java.util.Arrays.fill(arr, NO_AUTHORIZED_COMMITTER)
+    synchronized {
+      authorizedCommittersByStage(stage) = arr
+    }
   }
 
   // Called by DAGScheduler
@@ -122,10 +134,10 @@ private[spark] class OutputCommitCoordinator(conf: SparkConf, isDriver: Boolean)
         logInfo(s"Task was denied committing, stage: $stage, partition: $partition, " +
           s"attempt: $attemptNumber")
       case otherReason =>
-        if (authorizedCommitters.get(partition).exists(_ == attemptNumber)) {
+        if (authorizedCommitters(partition) == attemptNumber) {
           logDebug(s"Authorized committer (attemptNumber=$attemptNumber, stage=$stage, " +
             s"partition=$partition) failed; clearing lock")
-          authorizedCommitters.remove(partition)
+          authorizedCommitters(partition) = NO_AUTHORIZED_COMMITTER
         }
     }
   }
@@ -145,16 +157,16 @@ private[spark] class OutputCommitCoordinator(conf: SparkConf, isDriver: Boolean)
       attemptNumber: TaskAttemptNumber): Boolean = synchronized {
     authorizedCommittersByStage.get(stage) match {
       case Some(authorizedCommitters) =>
-        authorizedCommitters.get(partition) match {
-          case Some(existingCommitter) =>
-            logDebug(s"Denying attemptNumber=$attemptNumber to commit for stage=$stage, " +
-              s"partition=$partition; existingCommitter = $existingCommitter")
-            false
-          case None =>
+        authorizedCommitters(partition) match {
+          case NO_AUTHORIZED_COMMITTER =>
             logDebug(s"Authorizing attemptNumber=$attemptNumber to commit for stage=$stage, " +
               s"partition=$partition")
             authorizedCommitters(partition) = attemptNumber
             true
+          case existingCommitter =>
+            logDebug(s"Denying attemptNumber=$attemptNumber to commit for stage=$stage, " +
+              s"partition=$partition; existingCommitter = $existingCommitter")
+            false
         }
       case None =>
         logDebug(s"Stage $stage has completed, so not allowing attempt number $attemptNumber of" +

core/src/test/scala/org/apache/spark/io/CompressionCodecSuite.scala

@@ -100,12 +100,10 @@ class CompressionCodecSuite extends SparkFunSuite {
     testCodec(codec)
   }
 
-  test("snappy does not support concatenation of serialized streams") {
+  test("snappy supports concatenation of serialized streams") {
     val codec = CompressionCodec.createCodec(conf, classOf[SnappyCompressionCodec].getName)
     assert(codec.getClass === classOf[SnappyCompressionCodec])
-    intercept[Exception] {
-      testConcatenationOfSerializedStreams(codec)
-    }
+    testConcatenationOfSerializedStreams(codec)
   }
 
   test("bad compression codec") {

core/src/test/scala/org/apache/spark/scheduler/OutputCommitCoordinatorSuite.scala

@@ -171,7 +171,7 @@ class OutputCommitCoordinatorSuite extends SparkFunSuite with BeforeAndAfter {
     val partition: Int = 2
     val authorizedCommitter: Int = 3
     val nonAuthorizedCommitter: Int = 100
-    outputCommitCoordinator.stageStart(stage)
+    outputCommitCoordinator.stageStart(stage, maxPartitionId = 2)
 
     assert(outputCommitCoordinator.canCommit(stage, partition, authorizedCommitter))
     assert(!outputCommitCoordinator.canCommit(stage, partition, nonAuthorizedCommitter))

dev/audit-release/README.md

@@ -4,7 +4,7 @@ run them locally by setting appropriate environment variables.
 
 ```
 $ cd sbt_app_core
-$ SCALA_VERSION=2.10.4 \
+$ SCALA_VERSION=2.10.5 \
   SPARK_VERSION=1.0.0-SNAPSHOT \
   SPARK_RELEASE_REPOSITORY=file:///home/patrick/.ivy2/local \
   sbt run

dev/audit-release/audit_release.py

@@ -35,7 +35,7 @@
 RELEASE_KEY = "XXXXXXXX" # Your 8-digit hex
 RELEASE_REPOSITORY = "https://repository.apache.org/content/repositories/orgapachespark-1033"
 RELEASE_VERSION = "1.1.1"
-SCALA_VERSION = "2.10.4"
+SCALA_VERSION = "2.10.5"
 SCALA_BINARY_VERSION = "2.10"
 
 # Do not set these

docker/spark-test/base/Dockerfile

@@ -25,7 +25,7 @@ RUN apt-get update && \
     apt-get install -y less openjdk-7-jre-headless net-tools vim-tiny sudo openssh-server && \
     rm -rf /var/lib/apt/lists/*
 
-ENV SCALA_VERSION 2.10.4
+ENV SCALA_VERSION 2.10.5
 ENV CDH_VERSION cdh4
 ENV SCALA_HOME /opt/scala-$SCALA_VERSION
 ENV SPARK_HOME /opt/spark

docs/_config.yml

@@ -17,7 +17,7 @@ include:
 SPARK_VERSION: 1.6.0-SNAPSHOT
 SPARK_VERSION_SHORT: 1.6.0
 SCALA_BINARY_VERSION: "2.10"
-SCALA_VERSION: "2.10.4"
+SCALA_VERSION: "2.10.5"
 MESOS_VERSION: 0.21.0
 SPARK_ISSUE_TRACKER_URL: https://issues.apache.org/jira/browse/SPARK
 SPARK_GITHUB_URL: https://github.com/apache/spark

mllib/src/main/scala/org/apache/spark/mllib/api/python/PrefixSpanModelWrapper.scala

@@ -0,0 +1,32 @@
+/*
+ * 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.
+ */
+
+package org.apache.spark.mllib.api.python
+
+import org.apache.spark.mllib.fpm.PrefixSpanModel
+import org.apache.spark.rdd.RDD
+
+/**
+ * A Wrapper of PrefixSpanModel to provide helper method for Python
+ */
+private[python] class PrefixSpanModelWrapper(model: PrefixSpanModel[Any])
+  extends PrefixSpanModel(model.freqSequences) {
+
+  def getFreqSequences: RDD[Array[Any]] = {
+    SerDe.fromTuple2RDD(model.freqSequences.map(x => (x.javaSequence, x.freq)))
+  }
+}