In client mode, if yarn was shut down with spark application running, the application will hang up after several retries(default: 30) because the exception throwed by YarnClientImpl could not be caught by upper level, we should exit in case that user can not be aware that.

The exception we wanna catch is [here](https://github.com/apache/hadoop/blob/branch-2.7.0/hadoop-common-project/hadoop-common/src/main/java/org/apache/hadoop/io/retry/RetryInvocationHandler.java#L122), and I try to fix it refer to [MR](https://github.com/apache/hadoop/blob/branch-2.7.0/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-jobclient/src/main/java/org/apache/hadoop/mapred/ClientServiceDelegate.java#L320).

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #6717 from WangTaoTheTonic/SPARK-8273 and squashes the following commits:

28752d6 [WangTaoTheTonic] catch the throwed exception

SPARK_JAVA_OPTS was missed in reconstructing the launcher part, we should add it back so process launched by spark-class could read it properly. And so does `SPARK_DRIVER_MEMORY`.

The missing part is [here](https://github.com/apache/spark/blob/1c30afdf94b27e1ad65df0735575306e65d148a1/bin/spark-class#L97).

Author: WangTaoTheTonic <wangtao111@huawei.com>
Author: Tao Wang <wangtao111@huawei.com>

Closes #6741 from WangTaoTheTonic/SPARK-8290 and squashes the following commits:

bd89f0f [Tao Wang] make sure the memory setting is right too
e313520 [WangTaoTheTonic] spark class command builder need read SPARK_JAVA_OPTS

1. Add `log4j-defaults-repl.properties` that has log level WARN.
2. When logging is initialized, check whether inside the REPL. If so, use `log4j-defaults-repl.properties`.
3. Print the following information if using `log4j-defaults-repl.properties`:
```
Using Spark's repl log4j profile: org/apache/spark/log4j-defaults-repl.properties
To adjust logging level use sc.setLogLevel("INFO")
```

Author: zsxwing <zsxwing@gmail.com>

Closes #6734 from zsxwing/log4j-repl and squashes the following commits:

3835eff [zsxwing] Change default log level to WARN in the REPL

The root cause of SPARK-7527 is `createNullValue` returns an incompatible value `Byte(0)` for `char` and `boolean`.

This PR fixes it and corrects the class name of the main class, and also adds an unit test to demonstrate it.

Author: zsxwing <zsxwing@gmail.com>

Closes #6735 from zsxwing/SPARK-7527 and squashes the following commits:

bbdb271 [zsxwing] Use pattern match in createNullValue
b0a0e7e [zsxwing] Remove the noisy in the test output
903e269 [zsxwing] Remove the code for Utils.isInInterpreter == false
5f92dc1 [zsxwing] Fix createNullValue to return the correct null values and REPL mode detection

IBM Java has an extra method when we do getStackTrace(): this is "getStackTraceImpl", a native method. This causes two tests to fail within "DStreamScopeSuite" when running with IBM Java. Instead of "map" or "filter" being the method names found, "getStackTrace" is returned. This commit addresses such an issue by using dropWhile. Given that our current method is withScope, we look for the next method that isn't ours: we don't care about methods that come before us in the stack trace: e.g. getStackTrace (regardless of how many levels this might go).

IBM:
java.lang.Thread.getStackTraceImpl(Native Method)
java.lang.Thread.getStackTrace(Thread.java:1117)
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:104)

Oracle:
PRINTING STACKTRACE!!!
java.lang.Thread.getStackTrace(Thread.java:1552)
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:106)

I've tested this with Oracle and IBM Java, no side effects for other tests introduced.

Author: Adam Roberts <aroberts@uk.ibm.com>
Author: a-roberts <aroberts@uk.ibm.com>

Closes #6740 from a-roberts/RDDScopeStackCrawlFix and squashes the following commits:

13ce390 [Adam Roberts] Ensure consistency with String equality checking
a4fc0e0 [a-roberts] Update RDDOperationScope.scala

Read number of threads for RBackend from configuration.

[SPARK-8282] #comment Linking with JIRA

Author: Hossein <hossein@databricks.com>

Closes #6730 from falaki/SPARK-8282 and squashes the following commits:

33b3d98 [Hossein] Documented new config parameter
70f2a9c [Hossein] Fixing import
ec44225 [Hossein] Read number of threads for RBackend from configuration

The bug description is a little misleading: the actual issue is that
.py files are not handled correctly when distributed by YARN. They're
added to "spark.submit.pyFiles", which, when processed by context.py,
explicitly whitelists certain extensions (see PACKAGE_EXTENSIONS),
and that does not include .py files.

On top of that, archives were not handled at all! They made it to the
driver's python path, but never made it to executors, since the mechanism
used to propagate their location (spark.submit.pyFiles) only works on
the driver side.

So, instead, ignore "spark.submit.pyFiles" and just build PYTHONPATH
correctly for both driver and executors. Individual .py files are
placed in a subdirectory of the container's local dir in the cluster,
which is then added to the python path. Archives are added directly.

The change, as a side effect, ends up solving the symptom described
in the bug. The issue was not that the files were not being distributed,
but that they were never made visible to the python application
running under Spark.

Also included is a proper unit test for running python on YARN, which
broke in several different ways with the previous code.

A short walk around of the changes:
- SparkSubmit does not try to be smart about how YARN handles python
  files anymore. It just passes down the configs to the YARN client
  code.
- The YARN client distributes python files and archives differently,
  placing the files in a subdirectory.
- The YARN client now sets PYTHONPATH for the processes it launches;
  to properly handle different locations, it uses YARN's support for
  embedding env variables, so to avoid YARN expanding those at the
  wrong time, SparkConf is now propagated to the AM using a conf file
  instead of command line options.
- Because the Client initialization code is a maze of implicit
  dependencies, some code needed to be moved around to make sure
  all needed state was available when the code ran.
- The pyspark tests in YarnClusterSuite now actually distribute and try
  to use both a python file and an archive containing a different python
  module. Also added a yarn-client tests for completeness.
- I cleaned up some of the code around distributing files to YARN, to
  avoid adding more copied & pasted code to handle the new files being
  distributed.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #6360 from vanzin/SPARK-5479 and squashes the following commits:

bcaf7e6 [Marcelo Vanzin] Feedback.
c47501f [Marcelo Vanzin] Fix yarn-client mode.
46b1d0c [Marcelo Vanzin] Merge branch 'master' into SPARK-5479
c743778 [Marcelo Vanzin] Only pyspark cares about python archives.
c8e5a82 [Marcelo Vanzin] Actually run pyspark in client mode.
705571d [Marcelo Vanzin] Move some code to the YARN module.
1dd4d0c [Marcelo Vanzin] Review feedback.
71ee736 [Marcelo Vanzin] Merge branch 'master' into SPARK-5479
220358b [Marcelo Vanzin] Scalastyle.
cdbb990 [Marcelo Vanzin] Merge branch 'master' into SPARK-5479
7fe3cd4 [Marcelo Vanzin] No need to distribute primary file to executors.
09045f1 [Marcelo Vanzin] Style.
943cbf4 [Marcelo Vanzin] [SPARK-5479] [yarn] Handle --py-files correctly in YARN.

Author: Cheng Lian <lian@databricks.com>

Closes #6749 from liancheng/java-sample-fix and squashes the following commits:

5b44585 [Cheng Lian] Fixes a minor Java example error in SQL programming guide

Changed ```SparkEnv.actorSystem``` to be a function such that we can use the deprecated flag with it and added a deprecated message.

Author: Ilya Ganelin <ilya.ganelin@capitalone.com>

Closes #6731 from ilganeli/SPARK-7996 and squashes the following commits:

be43817 [Ilya Ganelin] Restored to val
9ed89e7 [Ilya Ganelin] Added a version info for deprecation
9610b08 [Ilya Ganelin] Converted actorSystem to function and added deprecated flag

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #6716 from adrian-wang/epi and squashes the following commits:

e2e8dbd [Daoyuan Wang] move tests
11b351c [Daoyuan Wang] add tests and remove pu
db331c9 [Daoyuan Wang] py style
599ddd8 [Daoyuan Wang] add py
e6783ef [Daoyuan Wang] register function
82d426e [Daoyuan Wang] add function entry
dbf3ab5 [Daoyuan Wang] add PI and E

This is a followup to #6712.

Author: Reynold Xin <rxin@databricks.com>

Closes #6739 from rxin/6712-followup and squashes the following commits:

fd9acfb [Reynold Xin] [SPARK-7886] Added unit test for HAVING aggregate pushdown.

This builds on #6710 and also uses FunctionRegistry for function lookup in HiveContext.

Author: Reynold Xin <rxin@databricks.com>

Closes #6712 from rxin/udf-registry-hive and squashes the following commits:

f4c2df0 [Reynold Xin] Fixed style violation.
0bd4127 [Reynold Xin] Fixed Python UDFs.
f9a0378 [Reynold Xin] Disable one more test.
5609494 [Reynold Xin] Disable some failing tests.
4efea20 [Reynold Xin] Don't check children resolved for UDF resolution.
2ebe549 [Reynold Xin] Removed more hardcoded functions.
aadce78 [Reynold Xin] [SPARK-7886] Use FunctionRegistry for built-in expressions in HiveContext.

Just replaced mutable.HashMap to ConcurrentHashMap

Author: navis.ryu <navis@apache.org>

Closes #6699 from navis/SPARK-7792 and squashes the following commits:

f03654a [navis.ryu] [SPARK-7792] [SQL] HiveContext registerTempTable not thread safe

This provides preliminary documentation pointing out how to use the
Hadoop free builds. I am hoping over time this list can grow to
include most of the popular Hadoop distributions.

Getting more people using these builds will help us long term reduce
the number of binaries we build.

Author: Patrick Wendell <patrick@databricks.com>

Closes #6729 from pwendell/hadoop-provided and squashes the following commits:

1113b76 [Patrick Wendell] [SPARK-6511] [Documentation] Explain how to use Hadoop provided builds

Just as a safeguard against DOM rewriting.

Author: Andrew Or <andrew@databricks.com>

Closes #6732 from andrewor14/dag-viz-trim and squashes the following commits:

7e9bacb [Andrew Or] [MINOR] [UI] DAG visualization: trim whitespace from input

There is a mistake in the URLs of the Scala section of FP-Growth in the MLlib Frequent Pattern Mining documentation. The URL points to https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/fpm/FPGrowth.html which is the Java's API, the link should point to the Scala API https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.fpm.FPGrowth

There's another mistake in the FP-GrowthModel in the same section, the link points, again, to the Java's API https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/fpm/FPGrowthModel.html, the link should point to the Scala API https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.fpm.FPGrowthModel

Author: FavioVazquez <favio.vazquezp@gmail.com>

Closes #6722 from FavioVazquez/fix-wrog-urls-mllib-fpgrowth and squashes the following commits:

e1ca54d [FavioVazquez] - Fixed wrong URLs in MLlib Frequent Pattern Mining, FP-Growth Scala section
ad882a3 [FavioVazquez] Merge remote-tracking branch 'upstream/master'
f27a20b [FavioVazquez] Merge remote-tracking branch 'upstream/master'
9af7074 [FavioVazquez] Merge remote-tracking branch 'upstream/master'
edab1ef [FavioVazquez] Merge remote-tracking branch 'upstream/master'
b2e2f8c [FavioVazquez] Merge remote-tracking branch 'upstream/master'

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #6720 from MechCoder/empty_model_check and squashes the following commits:

3a07de5 [MechCoder] Remove construct to get weights in StreamingLinearAlgorithm

I noticed there is a duplicated description about WAL.

```
To ensure zero-data loss, you have to additionally enable Write Ahead Logs in Spark Streaming. To ensure zero data loss, enable the Write Ahead Logs (introduced in Spark 1.2).
```

Let's remove the duplication.

I don't file this issue in JIRA because it's minor.

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

Closes #6719 from sarutak/remove-multiple-description and squashes the following commits:

cc9bb21 [Kousuke Saruta] Removed duplicated description about WAL

This patch switches to using FunctionRegistry for built-in expressions. It is based on #6463, but with some work to simplify it along with unit tests.

TODOs for future pull requests:
- Use static registration so we don't need to register all functions every time we start a new SQLContext
- Switch to using this in HiveContext

Author: Reynold Xin <rxin@databricks.com>
Author: Santiago M. Mola <santi@mola.io>

Closes #6710 from rxin/udf-registry and squashes the following commits:

6930822 [Reynold Xin] Fixed Python test.
b802c9a [Reynold Xin] Made UDF case insensitive.
e60d815 [Reynold Xin] Made UDF case insensitive.
852f9c0 [Reynold Xin] Fixed style violation.
e76a3c1 [Reynold Xin] Fixed parser.
52ddaba [Reynold Xin] Fixed compilation.
ee7854f [Reynold Xin] Improved error reporting.
ff906f2 [Reynold Xin] More robust constructor calling.
77b46f1 [Reynold Xin] Simplified the code.
2a2a149 [Reynold Xin] Merge pull request #6463 from smola/SPARK-7886
8616924 [Santiago M. Mola] [SPARK-7886] Add built-in expressions to FunctionRegistry.

Update to Netty 4.0.28-Final

Author: Sean Owen <sowen@cloudera.com>

Closes #6701 from srowen/SPARK-8101 and squashes the following commits:

f3b6369 [Sean Owen] Update to Netty 4.0.28-Final

JIRA: https://issues.apache.org/jira/browse/SPARK-7990

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

Closes #6616 from viirya/multi_keys_equi_join and squashes the following commits:

cd5c888 [Liang-Chi Hsieh] Import reduce in python3.
c43722c [Liang-Chi Hsieh] For comments.
0400e89 [Liang-Chi Hsieh] Fix scala style.
cc90015 [Liang-Chi Hsieh] Add methods to facilitate equi-join on multiple joining keys.

Author: hqzizania <qian.huang@intel.com>

Closes #6190 from hqzizania/R and squashes the following commits:

1641f9e [hqzizania] fixes and add test units
bb3411a [hqzizania] Convert NAs to null type in SparkR DataFrames

This makes the constructor callable in Python. dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #6709 from mengxr/SPARK-8168 and squashes the following commits:

f871de4 [Xiangrui Meng] Add Python friendly constructor to PipelineModel

This was caused by this commit: f2713478

This patch does not attempt to fix the root cause of why the `VisibleForTesting` annotation causes a NPE in the shell. We should find a way to fix that separately.

Author: Andrew Or <andrew@databricks.com>

Closes #6711 from andrewor14/fix-spark-shell and squashes the following commits:

bf62ecc [Andrew Or] Prevent NPE in spark-shell

Use DoubleType instead to be more stable and robust.

Author: Reynold Xin <rxin@databricks.com>

Closes #6692 from rxin/SPARK-8148 and squashes the following commits:

6742ecc [Reynold Xin] [SPARK-8148] Do not use FloatType in partition column inference.

We already have a rule to do type coercion for fixed decimal and unlimited decimal in `WidenTypes`, so we don't need to handle them in `DecimalPrecision`.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #6698 from cloud-fan/fix and squashes the following commits:

413ad4a [Wenchen Fan] remove duplicated cases

For Hadoop 1.x, `TaskAttemptContext` constructor clones the `Configuration` argument, thus configurations done in `HadoopFsRelation.prepareForWriteJob()` are not populated to *driver* side `TaskAttemptContext` (executor side configurations are properly populated). Currently this should only affect Parquet output committer class configuration.

Author: Cheng Lian <lian@databricks.com>

Closes #6669 from liancheng/spark-8121 and squashes the following commits:

73819e8 [Cheng Lian] Minor logging fix
fce089c [Cheng Lian] Adds more logging
b6f78a6 [Cheng Lian] Fixes compilation error introduced while rebasing
963a1aa [Cheng Lian] Addresses @yhuai's comment
c3a0b1a [Cheng Lian] Fixes InsertIntoHadoopFsRelation job initialization

1. explicitly import implicit conversion support.
2. use .nonEmpty instead of .size > 0
3. use val instead of var
4. comment indention

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #6700 from adrian-wang/shimsimprove and squashes the following commits:

d22e108 [Daoyuan Wang] several fix for HiveShim

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #6434 from adrian-wang/joinerr and squashes the following commits:

ee1b64f [Daoyuan Wang] break line
f7c53e9 [Daoyuan Wang] to IllegalArgumentException
f8dea2d [Daoyuan Wang] sys.err to IllegalStateException
be82259 [Daoyuan Wang] change new exception to sys.err

Return null if catch EOFException, just like function "asKeyValueIterator" in this class

Author: Mingfei <mingfei.shi@intel.com>

Closes #6703 from shimingfei/returnNull and squashes the following commits:

205deec [Mingfei] return null if catch EOFException

1. Prevent creating a map of data to find numFeatures
2. If model is empty, then initialize with a zero vector of numFeature

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #6684 from MechCoder/spark-8140 and squashes the following commits:

7fbf5f9 [MechCoder] [SPARK-8140] Remove empty model check in StreamingLinearAlgorithm And other minor cosmits

Even with all the efforts to cleanup the temp directories created by
unit tests, Spark leaves a lot of garbage in /tmp after a test run.
This change overrides java.io.tmpdir to place those files under the
build directory instead.

After an sbt full unit test run, I was left with > 400 MB of temp
files. Since they're now under the build dir, it's much easier to
clean them up.

Also make a slight change to a unit test to make it not pollute the
source directory with test data.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #6674 from vanzin/SPARK-8126 and squashes the following commits:

0f8ad41 [Marcelo Vanzin] Make sure tmp dir exists when tests run.
643e916 [Marcelo Vanzin] [MINOR] [BUILD] Use custom temp directory during build.

JIRA: https://issues.apache.org/jira/browse/SPARK-7939

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

Closes #6503 from viirya/disable_partition_type_inference and squashes the following commits:

3e90470 [Liang-Chi Hsieh] Default to enable type inference and update docs.
455edb1 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into disable_partition_type_inference
9a57933 [Liang-Chi Hsieh] Add conf to enable/disable partition column type inference.

As I have tested, if we cancel or kill the app then the final status may be undefined, killed or succeeded, so clean up staging directory when appMaster exit at any final application status.

Author: linweizhong <linweizhong@huawei.com>

Closes #6409 from Sephiroth-Lin/SPARK-7705 and squashes the following commits:

3a5a0a5 [linweizhong] Update
83dc274 [linweizhong] Update
923d44d [linweizhong] Update
0dd7c2d [linweizhong] Update
b76a102 [linweizhong] Update code style
7846b69 [linweizhong] Update
bd6cf0d [linweizhong] Refactor
aed9f18 [linweizhong] Clean up stagingDir when launch app on yarn
95595c3 [linweizhong] Cleanup of .sparkStaging directory when AppMaster exit at any final application status

this is a follow up of #3621

/cc liancheng pwendell

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #6639 from adrian-wang/kryodoc and squashes the following commits:

3c4b1cf [Daoyuan Wang] [DOC] kryo default setting in SQL Thrift server

From my perspective as a code reviewer, I find them more confusing than using String directly.

Author: Reynold Xin <rxin@databricks.com>

Closes #6694 from rxin/SPARK-8154 and squashes the following commits:

4e5056c [Reynold Xin] [SPARK-8154][SQL] Remove Term/Code type aliases in code generation.

Also moved a few files in expressions package around to match test suites.

Author: Reynold Xin <rxin@databricks.com>

Closes #6693 from rxin/expr-refactoring and squashes the following commits:

857599f [Reynold Xin] Fixed style violation.
c0eb74b [Reynold Xin] Fixed compilation.
b3a40f8 [Reynold Xin] Refactored expression test suites.

This PR move codegen implementation of expressions into Expression class itself, make it easy to manage.

It introduces two APIs in Expression:
```
def gen(ctx: CodeGenContext): GeneratedExpressionCode
def genCode(ctx: CodeGenContext, ev: GeneratedExpressionCode): Code
```

gen(ctx) will call genSource(ctx, ev) to generate Java source code for the current expression. A expression needs to override genSource().

Here are the types:
```
type Term String
type Code String

/**
 * Java source for evaluating an [[Expression]] given a [[Row]] of input.
 */
case class GeneratedExpressionCode(var code: Code,
                               nullTerm: Term,
                               primitiveTerm: Term,
                               objectTerm: Term)
/**
 * A context for codegen, which is used to bookkeeping the expressions those are not supported
 * by codegen, then they are evaluated directly. The unsupported expression is appended at the
 * end of `references`, the position of it is kept in the code, used to access and evaluate it.
 */
class CodeGenContext {
  /**
   * Holding all the expressions those do not support codegen, will be evaluated directly.
   */
  val references: Seq[Expression] = new mutable.ArrayBuffer[Expression]()
}
```

This is basically #6660, but fixed style violation and compilation failure.

Author: Davies Liu <davies@databricks.com>
Author: Reynold Xin <rxin@databricks.com>

Closes #6690 from rxin/codegen and squashes the following commits:

e1368c2 [Reynold Xin] Fixed tests.
73db80e [Reynold Xin] Fixed compilation failure.
19d6435 [Reynold Xin] Fixed style violation.
9adaeaf [Davies Liu] address comments
f42c732 [Davies Liu] improve coverage and tests
bad6828 [Davies Liu] address comments
e03edaa [Davies Liu] consts fold
86fac2c [Davies Liu] fix style
02262c9 [Davies Liu] address comments
b5d3617 [Davies Liu] Merge pull request #5 from rxin/codegen
48c454f [Reynold Xin] Some code gen update.
2344bc0 [Davies Liu] fix test
12ff88a [Davies Liu] fix build
c5fb514 [Davies Liu] rename
8c6d82d [Davies Liu] update docs
b145047 [Davies Liu] fix style
e57959d [Davies Liu] add type alias
3ff25f8 [Davies Liu] refactor
593d617 [Davies Liu] pushing codegen into Expression

see if requiring producer acks eliminates the need for waitUntilLeaderOffset calls in tests

Author: cody koeninger <cody@koeninger.org>

Closes #5921 from koeninger/kafka-0.8.2-test-cleanup and squashes the following commits:

1e89dc8 [cody koeninger] Merge branch 'master' into kafka-0.8.2-test-cleanup
4662828 [cody koeninger] [Streaming][Kafka] filter mima issue for removal of method from private test class
af1e083 [cody koeninger] Merge branch 'master' into kafka-0.8.2-test-cleanup
4298ac2 [cody koeninger] [Streaming][Kafka] update comment to trigger jenkins attempt
1274afb [cody koeninger] [Streaming][Kafka] see if requiring producer acks eliminates the need for waitUntilLeaderOffset calls in tests

Update build to use Java 7, and remove some comments and special-case support for Java 6.

Author: Sean Owen <sowen@cloudera.com>

Closes #6265 from srowen/SPARK-7733 and squashes the following commits:

59bda4e [Sean Owen] Update build to use Java 7, and remove some comments and special-case support for Java 6