[SPARK-2702][Core] Upgrade Tachyon dependency to 0.5.0

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
SPARK-2632, SPARK-2576. Fixed by only importing what is necessary during class definition.

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.
SPARK-2738. Remove redundant imports in BlockManagerSuite

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
[SPARK-2670] FetchFailedException should be thrown when local fetch has failed

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
SPARK-983. Support external sorting in sortByKey()

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()
SPARK-2134: Report metrics before application finishes

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
[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
[SPARK-2103][Streaming] Change to ClassTag for KafkaInputDStream and fix reflection issue

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-2768 [MLLIB] Add product, user recommend method to MatrixFactorizationModel

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
[SPARK-1997] update breeze to version 0.8.1

`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
[HOTFIX] downgrade breeze version to 0.7

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
SPARK-2099. Report progress while task is running.

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.
[SPARK-2179][SQL] A minor refactoring Java data type APIs (2179 follow-up).

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.
[SQL][SPARK-2212]Hash Outer Join

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
[SPARK-2729] [SQL] Forgot to match Timestamp type in ColumnBuilder

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
[SPARK-2767] [SQL] SparkSQL CLI doens't output error message if query failed.

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
[SQL] Documentation: Explain cacheTable command

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
[SPARK-695] In DAGScheduler's getPreferredLocs, track set of visited partitions.

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.
[SPARK-2490] Change recursive visiting on RDD dependencies to iterative approach

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.
SPARK-1612: Fix potential resource leaks

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