All changes from this PR are by mridulm and are drawn from his work in #1609. This patch is intended to fix all major issues related to shuffle file consolidation that mridulm found, while minimizing changes to the code, with the hope that it may be more easily merged into 1.1.

This patch is **not** intended as a replacement for #1609, which provides many additional benefits, including fixes to ExternalAppendOnlyMap, improvements to DiskBlockObjectWriter's API, and several new unit tests.

If it is feasible to merge #1609 for the 1.1 deadline, that is a preferable option.

Author: Aaron Davidson <aaron@databricks.com>

Closes #1678 from aarondav/consol and squashes the following commits:

53b3f6d [Aaron Davidson] Correct behavior when writing unopened file
701d045 [Aaron Davidson] Rebase with sort-based shuffle
9160149 [Aaron Davidson] SPARK-2532: Minimal shuffle consolidation fixes

Author: joyyoj <sunshch@gmail.com>

Closes #1694 from joyyoj/SPARK-2379 and squashes the following commits:

d73790d [joyyoj] SPARK-2379 Fix the bug that streaming's receiver may fall into a dead loop
22e7821 [joyyoj] Merge remote-tracking branch 'apache/master'
3f4a602 [joyyoj] Merge remote-tracking branch 'remotes/apache/master'
f4660c5 [joyyoj] [SPARK-1998] SparkFlumeEvent with body bigger than 1020 bytes are not read properly

JIRA: https://issues.apache.org/jira/browse/SPARK-1612

Move the "close" statements into a "finally" block.

Author: zsxwing <zsxwing@gmail.com>

Closes #535 from zsxwing/SPARK-1612 and squashes the following commits:

ae52f50 [zsxwing] Update to follow the code style
549ba13 [zsxwing] SPARK-1612: Fix potential resource leaks

When performing some transformations on RDDs after many iterations, the dependencies of RDDs could be very long. It can easily cause StackOverflowError when recursively visiting these dependencies in Spark core. For example:

    var rdd = sc.makeRDD(Array(1))
    for (i <- 1 to 1000) {
      rdd = rdd.coalesce(1).cache()
      rdd.collect()
    }

This PR changes recursive visiting on rdd's dependencies to iterative approach to avoid StackOverflowError.

In addition to the recursive visiting, since the Java serializer has a known [bug](http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4152790) that causes StackOverflowError too when serializing/deserializing a large graph of objects. So applying this PR only solves part of the problem. Using KryoSerializer to replace Java serializer might be helpful. However, since KryoSerializer is not supported for `spark.closure.serializer` now, I can not test if KryoSerializer can solve Java serializer's problem completely.

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #1418 from viirya/remove_recursive_visit and squashes the following commits:

6b2c615 [Liang-Chi Hsieh] change function name; comply with code style.
5f072a7 [Liang-Chi Hsieh] add comments to explain Stack usage.
8742dbb [Liang-Chi Hsieh] comply with code style.
900538b [Liang-Chi Hsieh] change recursive visiting on rdd's dependencies to iterative approach to avoid stackoverflowerror.

getPreferredLocs traverses a dependency graph of partitions using depth first search.  Given a complex dependency graph, the old implementation may explore a set of paths in the graph that is exponential in the number of nodes.  By maintaining a set of visited nodes the new implementation avoids revisiting nodes, preventing exponential blowup.

Some comment and whitespace cleanups are also included.

Author: Aaron Staple <aaron.staple@gmail.com>

Closes #1362 from staple/SPARK-695 and squashes the following commits:

ecea0f3 [Aaron Staple] address review comments
751c661 [Aaron Staple] [SPARK-695] Add a unit test.
5adf326 [Aaron Staple] Replace getPreferredLocsInternal's HashMap argument with a simpler HashSet.
58e37d0 [Aaron Staple] Replace comment documenting NarrowDependency.
6751ced [Aaron Staple] Revert "Remove unused variable."
04c7097 [Aaron Staple] Fix indentation.
0030884 [Aaron Staple] Remove unused variable.
33f67c6 [Aaron Staple] Clarify comment.
4e42b46 [Aaron Staple] Remove apparently incorrect comment describing NarrowDependency.
65c2d3d [Aaron Staple] [SPARK-695] In DAGScheduler's getPreferredLocs, track set of visited partitions.

add the `cacheTable` specification

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1681 from CrazyJvm/sql-programming-guide-cache and squashes the following commits:

0a231e0 [CrazyJvm] grammar fixes
a04020e [CrazyJvm] modify title to Cached tables
18b6594 [CrazyJvm] fix format
2cbbf58 [CrazyJvm] add cacheTable guide

Author: Cheng Hao <hao.cheng@intel.com>

Closes #1686 from chenghao-intel/spark_sql_cli and squashes the following commits:

eb664cc [Cheng Hao] Output detailed failure message in console
93b0382 [Cheng Hao] Fix Bug of no output in cli if exception thrown internally

just a match forgot, found after SPARK-2710 , TimestampType can be used by a SchemaRDD generated from JDBC ResultSet

Author: chutium <teng.qiu@gmail.com>

Closes #1636 from chutium/SPARK-2729 and squashes the following commits:

71af77a [chutium] [SPARK-2729] [SQL] added Timestamp in NullableColumnAccessorSuite
39cf9f8 [chutium] [SPARK-2729] add Timestamp Type into ColumnBuilder TestSuite, ref. #1636
ab6ff97 [chutium] [SPARK-2729] Forgot to match Timestamp type in ColumnBuilder

This patch is to support the hash based outer join. Currently, outer join for big relations are resort to `BoradcastNestedLoopJoin`, which is super slow. This PR will create 2 hash tables for both relations in the same partition, which greatly reduce the table scans.

Here is the testing code that I used:
```
package org.apache.spark.sql.hive

import org.apache.spark.SparkContext
import org.apache.spark.SparkConf
import org.apache.spark.sql._

case class Record(key: String, value: String)

object JoinTablePrepare extends App {
  import TestHive2._

  val rdd = sparkContext.parallelize((1 to 3000000).map(i => Record(s"${i % 828193}", s"val_$i")))

  runSqlHive("SHOW TABLES")
  runSqlHive("DROP TABLE if exists a")
  runSqlHive("DROP TABLE if exists b")
  runSqlHive("DROP TABLE if exists result")
  rdd.registerAsTable("records")

  runSqlHive("""CREATE TABLE a (key STRING, value STRING)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)
  runSqlHive("""CREATE TABLE b (key STRING, value STRING)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)
  runSqlHive("""CREATE TABLE result (key STRING, value STRING)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)

  hql(s"""from records
             | insert into table a
             | select key, value
           """.stripMargin)
  hql(s"""from records
             | insert into table b select key + 100000, value
           """.stripMargin)
}

object JoinTablePerformanceTest extends App {
  import TestHive2._

  hql("SHOW TABLES")
  hql("set spark.sql.shuffle.partitions=20")

  val leftOuterJoin = "insert overwrite table result select a.key, b.value from a left outer join b on a.key=b.key"
  val rightOuterJoin = "insert overwrite table result select a.key, b.value from a right outer join b on a.key=b.key"
  val fullOuterJoin = "insert overwrite table result select a.key, b.value from a full outer join b on a.key=b.key"

  val results = ("LeftOuterJoin", benchmark(leftOuterJoin)) :: ("LeftOuterJoin", benchmark(leftOuterJoin)) ::
                ("RightOuterJoin", benchmark(rightOuterJoin)) :: ("RightOuterJoin", benchmark(rightOuterJoin)) ::
                ("FullOuterJoin", benchmark(fullOuterJoin)) :: ("FullOuterJoin", benchmark(fullOuterJoin)) :: Nil
  val explains = hql(s"explain $leftOuterJoin").collect ++ hql(s"explain $rightOuterJoin").collect ++ hql(s"explain $fullOuterJoin").collect
  println(explains.mkString(",\n"))
  results.foreach { case (prompt, result) => {
      println(s"$prompt: took ${result._1} ms (${result._2} records)")
    }
  }

  def benchmark(cmd: String) = {
    val begin = System.currentTimeMillis()
    val result = hql(cmd)
    val end = System.currentTimeMillis()
    val count = hql("select count(1) from result").collect.mkString("")
    ((end - begin), count)
  }
}
```
And the result as shown below:
```
[Physical execution plan:],
[InsertIntoHiveTable (MetastoreRelation default, result, None), Map(), true],
[ Project [key#95,value#98]],
[  HashOuterJoin [key#95], [key#97], LeftOuter, None],
[   Exchange (HashPartitioning [key#95], 20)],
[    HiveTableScan [key#95], (MetastoreRelation default, a, None), None],
[   Exchange (HashPartitioning [key#97], 20)],
[    HiveTableScan [key#97,value#98], (MetastoreRelation default, b, None), None],
[Physical execution plan:],
[InsertIntoHiveTable (MetastoreRelation default, result, None), Map(), true],
[ Project [key#102,value#105]],
[  HashOuterJoin [key#102], [key#104], RightOuter, None],
[   Exchange (HashPartitioning [key#102], 20)],
[    HiveTableScan [key#102], (MetastoreRelation default, a, None), None],
[   Exchange (HashPartitioning [key#104], 20)],
[    HiveTableScan [key#104,value#105], (MetastoreRelation default, b, None), None],
[Physical execution plan:],
[InsertIntoHiveTable (MetastoreRelation default, result, None), Map(), true],
[ Project [key#109,value#112]],
[  HashOuterJoin [key#109], [key#111], FullOuter, None],
[   Exchange (HashPartitioning [key#109], 20)],
[    HiveTableScan [key#109], (MetastoreRelation default, a, None), None],
[   Exchange (HashPartitioning [key#111], 20)],
[    HiveTableScan [key#111,value#112], (MetastoreRelation default, b, None), None]
LeftOuterJoin: took 16072 ms ([3000000] records)
LeftOuterJoin: took 14394 ms ([3000000] records)
RightOuterJoin: took 14802 ms ([3000000] records)
RightOuterJoin: took 14747 ms ([3000000] records)
FullOuterJoin: took 17715 ms ([6000000] records)
FullOuterJoin: took 17629 ms ([6000000] records)
```

Without this PR, the benchmark will run seems never end.

Author: Cheng Hao <hao.cheng@intel.com>

Closes #1147 from chenghao-intel/hash_based_outer_join and squashes the following commits:

65c599e [Cheng Hao] Fix issues with the community comments
72b1394 [Cheng Hao] Fix bug of stale value in joinedRow
55baef7 [Cheng Hao] Add HashOuterJoin

It is a follow-up PR of SPARK-2179 (https://issues.apache.org/jira/browse/SPARK-2179). It makes package names of data type APIs more consistent across languages (Scala: `org.apache.spark.sql`, Java: `org.apache.spark.sql.api.java`, Python: `pyspark.sql`).

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1712 from yhuai/javaDataType and squashes the following commits:

62eb705 [Yin Huai] Move package-info.
add4bcb [Yin Huai] Make the package names of data type classes consistent across languages by moving all Java data type classes to package sql.api.java.

This is a sketch of a patch that allows the UI to show metrics for tasks that have not yet completed.  It adds a heartbeat every 2 seconds from the executors to the driver, reporting metrics for all of the executor's tasks.

It still needs unit tests, polish, and cluster testing, but I wanted to put it up to get feedback on the approach.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1056 from sryza/sandy-spark-2099 and squashes the following commits:

93b9fdb [Sandy Ryza] Up heartbeat interval to 10 seconds and other tidying
132aec7 [Sandy Ryza] Heartbeat and HeartbeatResponse are already Serializable as case classes
38dffde [Sandy Ryza] Additional review feedback and restore test that was removed in BlockManagerSuite
51fa396 [Sandy Ryza] Remove hostname race, add better comments about threading, and some stylistic improvements
3084f10 [Sandy Ryza] Make TaskUIData a case class again
3bda974 [Sandy Ryza] Stylistic fixes
0dae734 [Sandy Ryza] SPARK-2099. Report progress while task is running.

breeze-0.8.1 causes dependency issues, as discussed in #940 .

Author: Xiangrui Meng <meng@databricks.com>

Closes #1718 from mengxr/revert-breeze and squashes the following commits:

99c4681 [Xiangrui Meng] downgrade breeze version to 0.7

`breeze 0.8.1`  dependent on  `scala-logging-slf4j 2.1.1` The relevant code on #1369

Author: witgo <witgo@qq.com>

Closes #940 from witgo/breeze-8.0.1 and squashes the following commits:

65cc65e [witgo] update breeze  to version 0.8.1

Right now, `MatrixFactorizationModel` can only predict a score for one or more `(user,product)` tuples. As a comment in the file notes, it would be more useful to expose a recommend method, that computes top N scoring products for a user (or vice versa – users for a product).

(This also corrects some long lines in the Java ALS test suite.)

As you can see, it's a little messy to access the class from Java. Should there be a Java-friendly wrapper for it? with a pointer about where that should go, I could add that.

Author: Sean Owen <srowen@gmail.com>

Closes #1687 from srowen/SPARK-2768 and squashes the following commits:

b349675 [Sean Owen] Additional review changes
c9edb04 [Sean Owen] Updates from code review
7bc35f9 [Sean Owen] Add recommend methods to MatrixFactorizationModel

This PR updates previous Manifest for KafkaInputDStream's Decoder to ClassTag, also fix the problem addressed in [SPARK-2103](https://issues.apache.org/jira/browse/SPARK-2103).

Previous Java interface cannot actually get the type of Decoder, so when using this Manifest to reconstruct the decode object will meet reflection exception.

Also for other two Java interfaces, ClassTag[String] is useless because calling Scala API will get the right implicit ClassTag.

Current Kafka unit test cannot actually verify the interface. I've tested these interfaces in my local and distribute settings.

Author: jerryshao <saisai.shao@intel.com>

Closes #1508 from jerryshao/SPARK-2103 and squashes the following commits:

e90c37b [jerryshao] Add Mima excludes
7529810 [jerryshao] Change Manifest to ClassTag for KafkaInputDStream's Decoder and fix Decoder construct issue when using Java API

[Spark 2557] fix LOCAL_N_REGEX in createTaskScheduler and make local-n and local-n-failures consistent

[SPARK-2557](https://issues.apache.org/jira/browse/SPARK-2557)

Author: Ye Xianjin <advancedxy@gmail.com>

Closes #1464 from advancedxy/SPARK-2557 and squashes the following commits:

d844d67 [Ye Xianjin] add local-*-n-failures, bad-local-n, bad-local-n-failures test case
3bbc668 [Ye Xianjin] fix LOCAL_N_REGEX regular expression and make local_n_failures accept * as all cores on the computer

Author: Rahul Singhal <rahul.singhal@guavus.com>

Closes #1076 from rahulsinghaliitd/SPARK-2134 and squashes the following commits:

15f18b6 [Rahul Singhal] SPARK-2134: Report metrics before application finishes

This patch simply uses the ExternalSorter class from sort-based shuffle.

Closes #931 and Closes #1090

Author: Matei Zaharia <matei@databricks.com>

Closes #1677 from mateiz/spark-983 and squashes the following commits:

96b3fda [Matei Zaharia] SPARK-983. Support external sorting in sortByKey()

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #1578 from sarutak/SPARK-2670 and squashes the following commits:

85c8938 [Kousuke Saruta] Removed useless results.put for fail fast
e8713cc [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2670
d353984 [Kousuke Saruta] Refined assertion messages in BlockFetcherIteratorSuite.scala
03bcb02 [Kousuke Saruta] Merge branch 'SPARK-2670' of github.com:sarutak/spark into SPARK-2670
5d05855 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2670
4fca130 [Kousuke Saruta] Added test cases for BasicBlockFetcherIterator
b7b8250 [Kousuke Saruta] Modified BasicBlockFetchIterator to fail fast when local fetch error has been occurred
a3a9be1 [Kousuke Saruta] Modified BlockFetcherIterator for SPARK-2670
460dc01 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2670
e310c0b [Kousuke Saruta] Modified BlockFetcherIterator to handle local fetch failure as fatch fail

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1642 from sryza/sandy-spark-2738 and squashes the following commits:

a923e4e [Sandy Ryza] SPARK-2738. Remove redundant imports in BlockManagerSuite

Without this patch, it imports everything available in the scope.

```scala

scala> val a = 10l
val a = 10l
a: Long = 10

scala> import a._
import a._
import a._

scala> case class A(a: Int) // show
case class A(a: Int) // show
class $read extends Serializable {
  def <init>() = {
    super.<init>;
    ()
  };
  class $iwC extends Serializable {
    def <init>() = {
      super.<init>;
      ()
    };
    class $iwC extends Serializable {
      def <init>() = {
        super.<init>;
        ()
      };
      import org.apache.spark.SparkContext._;
      class $iwC extends Serializable {
        def <init>() = {
          super.<init>;
          ()
        };
        val $VAL5 = $line5.$read.INSTANCE;
        import $VAL5.$iw.$iw.$iw.$iw.a;
        class $iwC extends Serializable {
          def <init>() = {
            super.<init>;
            ()
          };
          import a._;
          class $iwC extends Serializable {
            def <init>() = {
              super.<init>;
              ()
            };
            class $iwC extends Serializable {
              def <init>() = {
                super.<init>;
                ()
              };
              case class A extends scala.Product with scala.Serializable {
                <caseaccessor> <paramaccessor> val a: Int = _;
                def <init>(a: Int) = {
                  super.<init>;
                  ()
                }
              }
            };
            val $iw = new $iwC.<init>
          };
          val $iw = new $iwC.<init>
        };
        val $iw = new $iwC.<init>
      };
      val $iw = new $iwC.<init>
    };
    val $iw = new $iwC.<init>
  };
  val $iw = new $iwC.<init>
}
object $read extends scala.AnyRef {
  def <init>() = {
    super.<init>;
    ()
  };
  val INSTANCE = new $read.<init>
}
defined class A
```

With this patch, it just imports  only the necessary.

```scala

scala> val a = 10l
val a = 10l
a: Long = 10

scala> import a._
import a._
import a._

scala> case class A(a: Int) // show
case class A(a: Int) // show
class $read extends Serializable {
  def <init>() = {
    super.<init>;
    ()
  };
  class $iwC extends Serializable {
    def <init>() = {
      super.<init>;
      ()
    };
    class $iwC extends Serializable {
      def <init>() = {
        super.<init>;
        ()
      };
      case class A extends scala.Product with scala.Serializable {
        <caseaccessor> <paramaccessor> val a: Int = _;
        def <init>(a: Int) = {
          super.<init>;
          ()
        }
      }
    };
    val $iw = new $iwC.<init>
  };
  val $iw = new $iwC.<init>
}
object $read extends scala.AnyRef {
  def <init>() = {
    super.<init>;
    ()
  };
  val INSTANCE = new $read.<init>
}
defined class A

scala>

```

This patch also adds a `:fallback` mode on being enabled it will restore the spark-shell's 1.0.0 behaviour.

Author: Prashant Sharma <scrapcodes@gmail.com>
Author: Yin Huai <huai@cse.ohio-state.edu>
Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #1635 from ScrapCodes/repl-fix-necessary-imports and squashes the following commits:

b1968d2 [Prashant Sharma] Added toschemaRDD to test case.
0b712bb [Yin Huai] Add a REPL test to test importing a method.
02ad8ff [Yin Huai] Add a REPL test for importing SQLContext.createSchemaRDD.
ed6d0c7 [Prashant Sharma] Added a fallback mode, incase users run into issues while using repl.
b63d3b2 [Prashant Sharma] SPARK-2632, SPARK-2576. Fixed by only importing what is necessary during class definition.

Author: Haoyuan Li <haoyuan@cs.berkeley.edu>

Closes #1651 from haoyuan/upgrade-tachyon and squashes the following commits:

6f3f98f [Haoyuan Li] upgrade tachyon to 0.5.0

getRanks computes the wrong rank when numPartition >= size in the input RDDs before this patch. added units to address this bug.

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1710 from dorx/correlationBug and squashes the following commits:

733def4 [Doris Xin] bugs and reviewer comments.
31db920 [Doris Xin] revert unnecessary change
043ff83 [Doris Xin] bug fix for spearman corner case

Now the factors are persisted in memory only. If they get kicked off by later jobs, we might have to start the computation from very beginning. A better solution is changing the storage level to `MEMORY_AND_DISK`.

srowen

Author: Xiangrui Meng <meng@databricks.com>

Closes #1700 from mengxr/als-level and squashes the following commits:

c103d76 [Xiangrui Meng] change ALS factors storage level to MEMORY_AND_DISK

Author: GuoQiang Li <witgo@qq.com>

Closes #1683 from witgo/SPARK-2766 and squashes the following commits:

d0db00c [GuoQiang Li] ScalaReflectionSuite  throw an llegalArgumentException in JDK 6

[SPARK-2779] [SQL] asInstanceOf[Map[...]] should use scala.collection.Map instead of scala.collection.immutable.Map

Since we let users create Rows. It makes sense to accept mutable Maps as values of MapType columns.

JIRA: https://issues.apache.org/jira/browse/SPARK-2779

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1705 from yhuai/SPARK-2779 and squashes the following commits:

00d72fd [Yin Huai] Use scala.collection.Map.

(1) Inconsistent aggregate (agg) indexing for unordered features.
(2) Fixed gain calculations for edge cases.
(3) One-off error in choosing thresholds for continuous features for small datasets.
(4) (not a bug) Changed meaning of tree depth by 1 to fit scikit-learn and rpart. (Depth 1 used to mean 1 leaf node; depth 0 now means 1 leaf node.)

Other updates, to help with tests:
* Updated DecisionTreeRunner to print more info.
* Added utility functions to DecisionTreeModel: toString, depth, numNodes
* Improved internal DecisionTree documentation

Bug fix details:

(1) Indexing was inconsistent for aggregate calculations for unordered features (in multiclass classification with categorical features, where the features had few enough values such that they could be considered unordered, i.e., isSpaceSufficientForAllCategoricalSplits=true).

* updateBinForUnorderedFeature indexed agg as (node, feature, featureValue, binIndex), where
** featureValue was from arr (so it was a feature value)
** binIndex was in [0,…, 2^(maxFeatureValue-1)-1)
* The rest of the code indexed agg as (node, feature, binIndex, label).
* Corrected this bug by changing updateBinForUnorderedFeature to use the second indexing pattern.

Unit tests in DecisionTreeSuite
* Updated a few tests to train a model and test its training accuracy, which catches the indexing bug from updateBinForUnorderedFeature() discussed above.
* Added new test (“stump with categorical variables for multiclass classification, with just enough bins”) to test bin extremes.

(2) Bug fix: calculateGainForSplit (for classification):
* It used to return dummy prediction values when either the right or left children had 0 weight.  These were incorrect for multiclass classification.  It has been corrected.

Updated impurities to allow for count = 0.  This was related to the above bug fix for calculateGainForSplit (for classification).

Small updates to documentation and coding style.

(3) Bug fix: Off-by-1 when finding thresholds for splits for continuous features.

* Exhibited bug in new test in DecisionTreeSuite: “stump with 1 continuous variable for binary classification, to check off-by-1 error”
* Description: When finding thresholds for possible splits for continuous features in DecisionTree.findSplitsBins, the thresholds were set according to individual training examples’ feature values.
* Fix: The threshold is set to be the average of 2 consecutive (sorted) examples’ feature values.  E.g.: If the old code set the threshold using example i, the new code sets the threshold using exam
* Note: In 4 DecisionTreeSuite tests with all labels identical, removed check of threshold since it is somewhat arbitrary.

CC: mengxr manishamde  Please let me know if I missed something!

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1673 from jkbradley/decisiontree-bugfix and squashes the following commits:

2b20c61 [Joseph K. Bradley] Small doc and style updates
dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals
8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type.
376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1
59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them.
52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification.  Caused problems in past, but fixed now.
8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features.
2283df8 [Joseph K. Bradley] 2 bug fixes.
73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail.  Will describe bug in next commit.

RandomRDDGenerators but without support for randomRDD and randomVectorRDD, which take in arbitrary DistributionGenerator.

`randomRDD.py` is named to avoid collision with the built-in Python `random` package.

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1628 from dorx/pythonRDD and squashes the following commits:

55c6de8 [Doris Xin] review comments. all python units passed.
f831d9b [Doris Xin] moved default args logic into PythonMLLibAPI
2d73917 [Doris Xin] fix for linalg.py
8663e6a [Doris Xin] reverting back to a single python file for random
f47c481 [Doris Xin] docs update
687aac0 [Doris Xin] add RandomRDDGenerators.py to run-tests
4338f40 [Doris Xin] renamed randomRDD to rand and import as random
29d205e [Doris Xin] created mllib.random package
bd2df13 [Doris Xin] typos
07ddff2 [Doris Xin] units passed.
23b2ecd [Doris Xin] WIP

This PR resolves the following two tickets:

- [SPARK-2531](https://issues.apache.org/jira/browse/SPARK-2531): BNLJ currently assumes the build side is the right relation. This patch refactors some of its logic to take into account a BuildSide properly.
- [SPARK-2436](https://issues.apache.org/jira/browse/SPARK-2436): building on top of the above, we simply use the physical size statistics (if available) of both relations, and make the smaller relation the build side in the planner.

Author: Zongheng Yang <zongheng.y@gmail.com>

Closes #1448 from concretevitamin/bnlj-buildSide and squashes the following commits:

1780351 [Zongheng Yang] Use size estimation to decide optimal build side of BNLJ.
68e6c5b [Zongheng Yang] Consolidate two adjacent pattern matchings.
96d312a [Zongheng Yang] Use a while loop instead of collection methods chaining.
4bc525e [Zongheng Yang] Make BroadcastNestedLoopJoin take a BuildSide.

Prior to this change, every PySpark task completion opened a new socket to the accumulator server, passed its updates through, and then quit. I'm not entirely sure why PySpark always sends accumulator updates, but regardless this causes a very rapid buildup of ephemeral TCP connections that remain in the TCP_WAIT state for around a minute before being cleaned up.

Rather than trying to allow these sockets to be cleaned up faster, this patch simply reuses the connection between tasks completions (since they're fed updates in a single-threaded manner by the DAGScheduler anyway).

The only tricky part here was making sure that the AccumulatorServer was able to shutdown in a timely manner (i.e., stop polling for new data), and this was accomplished via minor feats of magic.

I have confirmed that this patch eliminates the buildup of ephemeral sockets due to the accumulator updates. However, I did note that there were still significant sockets being created against the PySpark daemon port, but my machine was not able to create enough sockets fast enough to fail. This may not be the last time we've seen this issue, though.

Author: Aaron Davidson <aaron@databricks.com>

Closes #1503 from aarondav/accum and squashes the following commits:

b3e12f7 [Aaron Davidson] SPARK-2282: Reuse Socket for sending accumulator updates to Pyspark

It should be more convenient if user can specify ascending and numPartitions when calling sortByKey.

Author: Rui Li <rui.li@intel.com>

Closes #1645 from lirui-intel/spark-2740 and squashes the following commits:

fb5d52e [Rui Li] SPARK-2740: allow user to specify ascending and numPartitions for sortByKey

Fix several awkward wordings and grammatical issues in the following
documents:

*   docs/monitoring.md

*   docs/streaming-programming-guide.md

Author: kballou <kballou@devnulllabs.io>

Closes #1662 from kennyballou/grammar_fixes and squashes the following commits:

e1b8ad6 [kballou] Docs: monitoring, streaming programming guide

This commit fixes a couple of issues in the merge_spark_pr.py developer script:

- Allow recovery from failed cherry-picks.
- Fix detection of pull requests that have already been merged.

Both of these fixes are useful when backporting changes.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1668 from JoshRosen/pr-script-improvements and squashes the following commits:

ff4f33a [Josh Rosen] Default SPARK_HOME to cwd(); detect missing JIRA credentials.
ed5bc57 [Josh Rosen] Improvements for backporting using merge_spark_pr:

This PR tries to resolve the broken Jenkins maven test issue introduced by #1439. Now, we create a single query test to run both the setup work and the test query.

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1669 from yhuai/SPARK-2523-fixTest and squashes the following commits:

358af1a [Yin Huai] Make partition_based_table_scan_with_different_serde run atomically.

This is roughly the TF-IDF implementation used in the Databricks Cloud Demo: http://databricks.com/cloud/ .

Both `HashingTF` and `IDF` are implemented as transformers, similar to scikit-learn.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1671 from mengxr/tfidf and squashes the following commits:

7d65888 [Xiangrui Meng] use JavaConverters._
5fe9ec4 [Xiangrui Meng] fix unit test
6e214ec [Xiangrui Meng] add apache header
cfd9aed [Xiangrui Meng] add Java-friendly methods move classes to mllib.feature
3814440 [Xiangrui Meng] add HashingTF and IDF

The logging code that handles log4j initialization leads to an stack overflow error when used with log4j 2.x, which has just been released. This occurs even a downstream project has correctly adjusted SLF4J bindings, and that is the right thing to do for log4j 2.x, since it is effectively a separate project from 1.x.

Here is the relevant bit of Logging.scala:

```
  private def initializeLogging() {
    // If Log4j is being used, but is not initialized, load a default properties file
    val binder = StaticLoggerBinder.getSingleton
    val usingLog4j = binder.getLoggerFactoryClassStr.endsWith("Log4jLoggerFactory")
    val log4jInitialized = LogManager.getRootLogger.getAllAppenders.hasMoreElements
    if (!log4jInitialized && usingLog4j) {
      val defaultLogProps = "org/apache/spark/log4j-defaults.properties"
      Option(Utils.getSparkClassLoader.getResource(defaultLogProps)) match {
        case Some(url) =>
          PropertyConfigurator.configure(url)
          log.info(s"Using Spark's default log4j profile: $defaultLogProps")
        case None =>
          System.err.println(s"Spark was unable to load $defaultLogProps")
      }
    }
    Logging.initialized = true

    // Force a call into slf4j to initialize it. Avoids this happening from mutliple threads
    // and triggering this: http://mailman.qos.ch/pipermail/slf4j-dev/2010-April/002956.html
    log
  }
```

The first minor issue is that there is a call to a logger inside this method, which is initializing logging. In this situation, it ends up causing the initialization to be called recursively until the stack overflow. It would be slightly tidier to log this only after Logging.initialized = true. Or not at all. But it's not the root problem, or else, it would not work at all now.

The calls to log4j classes here always reference log4j 1.2 no matter what. For example, there is not getAllAppenders in log4j 2.x. That's fine. Really, "usingLog4j" means "using log4j 1.2" and "log4jInitialized" means "log4j 1.2 is initialized".

usingLog4j should be false for log4j 2.x, because the initialization only matters for log4j 1.2. But, it's true, and that's the real issue. And log4jInitialized is always false, since calls to the log4j 1.2 API are stubs and no-ops in this setup, where the caller has swapped in log4j 2.x. Hence the loop.

This is fixed, I believe, if "usingLog4j" can be false for log4j 2.x. The SLF4J static binding class has the same name for both versions, unfortunately, which causes the issue. However they're in different packages. For example, if the test included "... and begins with org.slf4j", it should work, as the SLF4J binding for log4j 2.x is provided by log4j 2.x at the moment, and is in package org.apache.logging.slf4j.

Of course, I assume that SLF4J will eventually offer its own binding. I hope to goodness they at least name the binding class differently, or else this will again not work. But then some other check can probably be made.

Author: Sean Owen <srowen@gmail.com>

Closes #1547 from srowen/SPARK-2646 and squashes the following commits:

92a9898 [Sean Owen] System.out -> System.err
94be4c7 [Sean Owen] Add back log message as System.out, with informational comment
a7f8876 [Sean Owen] Updates from review
6f3c1d3 [Sean Owen] Remove log statement in logging initialization, and distinguish log4j 1.2 from 2.0, to avoid stack overflow in initialization

The test compile error is fixed, but the build still fails because of one scalastyle error.

https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/lastFailedBuild/hadoop.version=1.0.4,label=centos/console

Author: Sean Owen <srowen@gmail.com>

Closes #1690 from srowen/SPARK-2749 and squashes the following commits:

1c9e7a6 [Sean Owen] Also: fix scalastyle error by wrapping a long line

...ags

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1665 from sryza/sandy-spark-2664 and squashes the following commits:

0518c63 [Sandy Ryza] SPARK-2664. Deal with `--conf` options in spark-submit that relate to flags

This allows users to gain access to the InputSplit which backs each partition.

An alternative solution would have been to have a .withInputSplit() method which returns a new RDD[(InputSplit, (K, V))], but this is confusing because you could not cache this RDD or shuffle it, as InputSplit is not inherently serializable.

Author: Aaron Davidson <aaron@databricks.com>

Closes #973 from aarondav/hadoop and squashes the following commits:

9c9112b [Aaron Davidson] Add JavaAPISuite test
9942cd7 [Aaron Davidson] Add Java API
1284a3a [Aaron Davidson] SPARK-2028: Expose mapPartitionsWithInputSplit in HadoopRDD

LocalHiveContext is redundant with HiveContext.  The only difference is it creates `./metastore` instead of `./metastore_db`.

Author: Michael Armbrust <michael@databricks.com>

Closes #1641 from marmbrus/localHiveContext and squashes the following commits:

e5ec497 [Michael Armbrust] Add deprecation version
626e056 [Michael Armbrust] Don't remove from imports yet
905cc5f [Michael Armbrust] Merge remote-tracking branch 'apache/master' into localHiveContext
1c2727e [Michael Armbrust] Deprecate LocalHiveContext