[SPARK-2529] Clean closures in foreach and foreachPartition.

Author: Reynold Xin <rxin@apache.org>

Closes #1583 from rxin/closureClean and squashes the following commits:

8982fe6 [Reynold Xin] [SPARK-2529] Clean closures in foreach and foreachPartition.
[SPARK-2665] [SQL] Add EqualNS & Unit Tests

Hive Supports the operator "<=>", which returns same result with EQUAL(=) operator for non-null operands, but returns TRUE if both are NULL, FALSE if one of the them is NULL.

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

Closes #1570 from chenghao-intel/equalns and squashes the following commits:

8d6c789 [Cheng Hao] Remove the test case orc_predicate_pushdown
5b2ca88 [Cheng Hao] Add cases into whitelist
8e66cdd [Cheng Hao] Rename the EqualNSTo ==> EqualNullSafe
7af4b0b [Cheng Hao] Add EqualNS & Unit Tests
replace println to log4j

Our program needs to receive a large amount of data and run for a long
time.
We set the log level to WARN but "Storing iterator" "received single"
as such message written to the log file. (over yarn)

Author: fireflyc <fireflyc@126.com>

Closes #1372 from fireflyc/fix-replace-stdout-log and squashes the following commits:

e684140 [fireflyc] 'info' modified into the 'debug'
fa22a38 [fireflyc] replace println to log4j
[SPARK-2683] unidoc failed because org.apache.spark.util.CallSite uses Java keywords as value names

Renaming `short` to `shortForm` and `long` to `longForm`.

JIRA: https://issues.apache.org/jira/browse/SPARK-2683

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

Closes #1585 from yhuai/SPARK-2683 and squashes the following commits:

5ddb843 [Yin Huai] "short" and "long" are Java keyworks. In order to generate javadoc, renaming "short" to "shortForm" and "long" to "longForm".
[SPARK-2410][SQL] Merging Hive Thrift/JDBC server

JIRA issue:

- Main: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)
- Related: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678)

Cherry picked the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

(Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.)

TODO

- [x] Use `spark-submit` to launch the server, the CLI and beeline
- [x] Migration guideline draft for Shark users

----

Hit by a bug in `SparkSubmitArguments` while working on this PR: all application options that are recognized by `SparkSubmitArguments` are stolen as `SparkSubmit` options. For example:

```bash
$ spark-submit --class org.apache.hive.beeline.BeeLine spark-internal --help
```

This actually shows usage information of `SparkSubmit` rather than `BeeLine`.

~~Fixed this bug here since the `spark-internal` related stuff also touches `SparkSubmitArguments` and I'd like to avoid conflict.~~

**UPDATE** The bug mentioned above is now tracked by [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678). Decided to revert changes to this bug since it involves more subtle considerations and worth a separate PR.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1399 from liancheng/thriftserver and squashes the following commits:

090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server
[SPARK-2682] Javadoc generated from Scala source code is not in javadoc's index

Add genjavadocSettings back to SparkBuild. It requires #1585 .

https://issues.apache.org/jira/browse/SPARK-2682

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

Closes #1584 from yhuai/SPARK-2682 and squashes the following commits:

2e89461 [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2682
54e3b66 [Yin Huai] Add genjavadocSettings back.
[SQL]Update HiveMetastoreCatalog.scala

I think it's better to defined hiveQlTable as a val

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #1569 from baishuo/patch-1 and squashes the following commits:

dc2f895 [baishuo(白硕)] Update HiveMetastoreCatalog.scala
a7b32a2 [baishuo(白硕)] Update HiveMetastoreCatalog.scala
[SPARK-2125] Add sort flag and move sort into shuffle implementations

This patch adds a sort flag into ShuffleDependecy and moves sort into hash shuffle implementation.

Moving sort into shuffle implementation can give space for other shuffle implementations (like sort-based shuffle) to better optimize sort through shuffle.

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

Closes #1210 from jerryshao/SPARK-2125 and squashes the following commits:

2feaf7b [jerryshao] revert MimaExcludes
ceddf75 [jerryshao] add MimaExeclude
f674ff4 [jerryshao] Add missing Scope restriction
b9fe0dd [jerryshao] Fix some style issues according to comments
ef6b729 [jerryshao] Change sort flag into Option
3f6eeed [jerryshao] Fix issues related to unit test
2f552a5 [jerryshao] Minor changes about naming and order
c92a281 [jerryshao] Move sort into shuffle implementations
[SPARK-1726] [SPARK-2567] Eliminate zombie stages in UI.

Due to problems with when we update runningStages (in DAGScheduler.scala)
and how we decide to send a SparkListenerStageCompleted message to
SparkListeners, sometimes stages can be shown as "running" in the UI forever
(even after they have failed).  This issue can manifest when stages are
resubmitted with 0 tasks, or when the DAGScheduler catches non-serializable
tasks. The problem also resulted in a (small) memory leak in the DAGScheduler,
where stages can stay in runningStages forever. This commit fixes
that problem and adds a unit test.

Thanks tsudukim for helping to look into this issue!

cc markhamstra rxin

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1566 from kayousterhout/dag_fix and squashes the following commits:

217d74b [Kay Ousterhout] [SPARK-1726] [SPARK-2567] Eliminate zombie stages in UI.
Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

This reverts commit 06dc0d2c6b69c5d59b4d194ced2ac85bfe2e05e2.

#1399 is making Jenkins fail.  We should investigate and put this back after its passing tests.

Author: Michael Armbrust <michael@databricks.com>

Closes #1594 from marmbrus/revertJDBC and squashes the following commits:

59748da [Michael Armbrust] Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"
SPARK-1812: core - upgrade to akka 2.3.4

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: sql/catalyst - upgrade to scala-logging-slf4j 2.1.2

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: core - upgrade to json4s 3.2.10

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: core - upgrade to unofficial chill 1.2 (tv.cntt)

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: mllib - upgrade to breeze 0.8.1

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: core - Fix overloaded methods with default arguments

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: streaming - Fix overloaded methods with default arguments

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: try { } without catch { } warning

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: Fix @transient annotation errors

- convert to @transient val when unsure
- remove @transient annotation elsewhere

Signed-off-by: Anand Avati <avati@redhat.com>
SPARK-1812: update all artifactId to spark-${module}_2.11

Signed-off-by: Anand Avati <avati@redhat.com>