Address SPARK-1717

I tested the change locally with Spark 0.9.1, but I can't test with 1.0.0 because there was no AMI for it at the time. It's a trivial fix, so it shouldn't cause any problems.

Author: msiddalingaiah <madhu@madhu.com>

Closes #641 from msiddalingaiah/master and squashes the following commits:

a4f7404 [msiddalingaiah] Address SPARK-1717
Updated doc for spark.closure.serializer to indicate only Java serializer work.

See discussion from http://apache-spark-developers-list.1001551.n3.nabble.com/bug-using-kryo-as-closure-serializer-td6473.html

Author: Reynold Xin <rxin@apache.org>

Closes #642 from rxin/docs-ser and squashes the following commits:

a507db5 [Reynold Xin] Use "Java" instead of default.
5eb8cdd [Reynold Xin] Updated doc for spark.closure.serializer to indicate only the default serializer work.
SPARK-1556. jets3t dep doesn't update properly with newer Hadoop versions

See related discussion at https://github.com/apache/spark/pull/468

This PR may still overstep what you have in mind, but let me put it on the table to start. Besides fixing the issue, it has one substantive change, and that is to manage Hadoop-specific things only in Hadoop-related profiles. This does _not_ remove `yarn.version`.

- Moves the YARN and Hadoop profiles together in pom.xml. Sorry that this makes the diff a little hard to grok but the changes are only as follows.
- Removes `hadoop.major.version`
- Introduce `hadoop-2.2` and `hadoop-2.3` profiles to control Hadoop-specific changes:
  - like the protobuf version issue - this was only 'solved' now by enabling YARN for 2.2+, which is really an orthogonal issue
  - like the jets3t version issue now
- Hadoop profiles set an appropriate default `hadoop.version`, that can be overridden
- _(YARN profiles in the parent now only exist to add the sub-module)_
- Fixes the jets3t dependency issue
 - and makes it a runtime dependency
 - and centralizes config of this guy in the parent pom
- Updates build docs
- Updates SBT build too
  - and fixes a regex problem along the way

Author: Sean Owen <sowen@cloudera.com>

Closes #629 from srowen/SPARK-1556 and squashes the following commits:

c3fa967 [Sean Owen] Fix hadoop-2.4 profile typo in doc
a2105fd [Sean Owen] Add hadoop-2.4 profile and don't set hadoop.version in profiles
274f4f9 [Sean Owen] Make jets3t a runtime dependency, and bring its exclusion up into parent config
bbed826 [Sean Owen] Use jets3t 0.9.0 for Hadoop 2.3+ (and correct similar regex issue in SBT build)
f21f356 [Sean Owen] Build changes to set up for jets3t fix
SPARK-1721: Reset the thread classLoader in the Mesos Executor

This is because Mesos calls it with a different environment or something, the result is that the Spark jar is missing and it can't load classes.

This fixes http://apache-spark-user-list.1001560.n3.nabble.com/java-lang-ClassNotFoundException-spark-on-mesos-td3510.html

I have no idea whether this is the right fix, I can only confirm that it fixes the issue for us.

The `registered` method is called from mesos (https://github.com/apache/mesos/blob/765ff9bc2ac5a12d4362f8235b572a37d646390a/src/java/jni/org_apache_mesos_MesosExecutorDriver.cpp)

I am unsure which commit caused this regression

Author: Bouke van der Bijl <boukevanderbijl@gmail.com>

Closes #620 from bouk/mesos-classloader-fix and squashes the following commits:

c13eae0 [Bouke van der Bijl] Use getContextOrSparkClassLoader in SparkEnv and CompressionCodec
[SPARK-1504], [SPARK-1505], [SPARK-1558] Updated Spark Streaming guide

- SPARK-1558: Updated custom receiver guide to match it with the new API
- SPARK-1504: Added deployment and monitoring subsection to streaming
- SPARK-1505: Added migration guide for migrating from 0.9.x and below to Spark 1.0
- Updated various Java streaming examples to use JavaReceiverInputDStream to highlight the API change.
- Removed the requirement for cleaner ttl from streaming guide

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #652 from tdas/doc-fix and squashes the following commits:

cb4f4b7 [Tathagata Das] Possible fix for flaky graceful shutdown test.
ab71f7f [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into doc-fix
8d6ff9b [Tathagata Das] Addded migration guide to Spark Streaming.
7d171df [Tathagata Das] Added reference to JavaReceiverInputStream in examples and streaming guide.
49edd7c [Tathagata Das] Change java doc links to use Java docs.
11528d7 [Tathagata Das] Updated links on index page.
ff80970 [Tathagata Das] More updates to streaming guide.
4dc42e9 [Tathagata Das] Added monitoring and other documentation in the streaming guide.
14c6564 [Tathagata Das] Updated custom receiver guide.
[SPARK-1681] Include datanucleus jars in Spark Hive distribution

This copies the datanucleus jars over from `lib_managed` into `dist/lib`, if any. The `CLASSPATH` must also be updated to reflect this change.

Author: Andrew Or <andrewor14@gmail.com>

Closes #610 from andrewor14/hive-distribution and squashes the following commits:

a4bc96f [Andrew Or] Rename search path in jar error check
fa205e1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into hive-distribution
7855f58 [Andrew Or] Have jar command respect JAVA_HOME + check for jar errors both cases
c16bbfd [Andrew Or] Merge branch 'master' of github.com:apache/spark into hive-distribution
32f6826 [Andrew Or] Leave the double colons
940a1bb [Andrew Or] Add back 2>/dev/null
58357cc [Andrew Or] Include datanucleus jars in Spark distribution built with Hive support
SPARK-1728. JavaRDDLike.mapPartitionsWithIndex requires ClassTag

Author: Sandy Ryza <sandy@cloudera.com>

Closes #657 from sryza/sandy-spark-1728 and squashes the following commits:

4751443 [Sandy Ryza] SPARK-1728. JavaRDDLike.mapPartitionsWithIndex requires ClassTag
Expose SparkListeners and relevant classes as DeveloperApi

Hopefully this can go into 1.0, as a few people on the user list have asked for this.

Author: Andrew Or <andrewor14@gmail.com>

Closes #648 from andrewor14/expose-listeners and squashes the following commits:

e45e1ef [Andrew Or] Add missing colons (minor)
350d643 [Andrew Or] Expose SparkListeners and relevant classes as DeveloperApi
[SPARK-1594][MLLIB] Cleaning up MLlib APIs and guide

Final pass before the v1.0 release.

* Remove `VectorRDDs`
* Move `BinaryClassificationMetrics` from `evaluation.binary` to `evaluation`
* Change default value of `addIntercept` to false and allow to add intercept in Ridge and Lasso.
* Clean `DecisionTree` package doc and test suite.
* Mark model constructors `private[spark]`
* Rename `loadLibSVMData` to `loadLibSVMFile` and hide `LabelParser` from users.
* Add `saveAsLibSVMFile`.
* Add `appendBias` to `MLUtils`.

Author: Xiangrui Meng <meng@databricks.com>

Closes #524 from mengxr/mllib-cleaning and squashes the following commits:

295dc8b [Xiangrui Meng] update loadLibSVMFile doc
1977ac1 [Xiangrui Meng] fix doc of appendBias
649fcf0 [Xiangrui Meng] rename loadLibSVMData to loadLibSVMFile; hide LabelParser from user APIs
54b812c [Xiangrui Meng] add appendBias
a71e7d0 [Xiangrui Meng] add saveAsLibSVMFile
d976295 [Xiangrui Meng] Merge branch 'master' into mllib-cleaning
b7e5cec [Xiangrui Meng] remove some experimental annotations and make model constructors private[mllib]
9b02b93 [Xiangrui Meng] minor code style update
a593ddc [Xiangrui Meng] fix python tests
fc28c18 [Xiangrui Meng] mark more classes experimental
f6cbbff [Xiangrui Meng] fix Java tests
0af70b0 [Xiangrui Meng] minor
6e139ef [Xiangrui Meng] Merge branch 'master' into mllib-cleaning
94e6dce [Xiangrui Meng] move BinaryLabelCounter and BinaryConfusionMatrixImpl to evaluation.binary
df34907 [Xiangrui Meng] clean DecisionTreeSuite to use LocalSparkContext
c81807f [Xiangrui Meng] set the default value of AddIntercept to false
03389c0 [Xiangrui Meng] allow to add intercept in Ridge and Lasso
c66c56f [Xiangrui Meng] move tree md to package object doc
a2695df [Xiangrui Meng] update guide for BinaryClassificationMetrics
9194f4c [Xiangrui Meng] move BinaryClassificationMetrics one level up
1c1a0e3 [Xiangrui Meng] remove VectorRDDs because it only contains one function that is not necessary for us to maintain
[SPARK-1678][SPARK-1679] In-memory compression bug fix and made compression configurable, disabled by default

In-memory compression is now configurable in `SparkConf` by the `spark.sql.inMemoryCompression.enabled` property, and is disabled by default.

To help code review, the bug fix is in [the first commit](https://github.com/liancheng/spark/commit/d537a367edf0bf24d0b925cc58b21d805ccbc11f), compression configuration is in [the second one](https://github.com/liancheng/spark/commit/4ce09aa8aa820bbbbbaa0f3f084a6cff1d4e6195).

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

Closes #608 from liancheng/spark-1678 and squashes the following commits:

66c3a8d [Cheng Lian] Renamed in-memory compression configuration key
f8fb3a0 [Cheng Lian] Added assertion for testing .hasNext of various decoder
4ce09aa [Cheng Lian] Made in-memory compression configurable via SparkConf
d537a36 [Cheng Lian] Fixed SPARK-1678
[SPARK-1735] Add the missing special profiles to make-distribution.sh

73b0cbcc241cca3d318ff74340e80b02f884acbd introduced a few special profiles that are not covered in the `make-distribution.sh`. This affects hadoop versions 2.2.x, 2.3.x, and 2.4.x. Without these special profiles, a java version error for protobufs is thrown at run time.

I took the opportunity to rewrite the way we construct the maven command. Previously, the only hadoop version that triggered the `yarn-alpha` profile was 0.23.x, which was inconsistent with the [docs](https://github.com/apache/spark/blob/master/docs/building-with-maven.md). This is now generalized to hadoop versions from 0.23.x to 2.1.x.

Author: Andrew Or <andrewor14@gmail.com>

Closes #660 from andrewor14/hadoop-distribution and squashes the following commits:

6740126 [Andrew Or] Generalize the yarn profile to hadoop versions 2.2+
88f192d [Andrew Or] Add the required special profiles to make-distribution.sh
[SQL] SPARK-1732 - Support for null primitive values.

I also removed a println that I bumped into.

Author: Michael Armbrust <michael@databricks.com>

Closes #658 from marmbrus/nullPrimitives and squashes the following commits:

a3ec4f3 [Michael Armbrust] Remove println.
695606b [Michael Armbrust] Support for null primatives from using scala and java reflection.
Update OpenHashSet.scala

Modify wrong comment of function addWithoutResize.

Author: ArcherShao <ArcherShao@users.noreply.github.com>

Closes #667 from ArcherShao/patch-3 and squashes the following commits:

a607358 [ArcherShao] Update OpenHashSet.scala
SPARK-1474: Spark on yarn assembly doesn't include AmIpFilter

We use org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter in spark on yarn but are not included it in the assembly jar.

I tested this on yarn cluster by removing the yarn jars from the classpath and spark runs fine now.

Author: Thomas Graves <tgraves@apache.org>

Closes #406 from tgravescs/SPARK-1474 and squashes the following commits:

1548bf9 [Thomas Graves] SPARK-1474: Spark on yarn assembly doesn't include org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter
Fix two download suggestions in the docs:

1) On the quick start page provide a direct link to the downloads (suggested by @pbailis).
2) On the index page, don't suggest users always have to build Spark, since many won't.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #662 from pwendell/quick-start and squashes the following commits:

0622f27 [Patrick Wendell] Fix two download suggestions in the docs:
[SPARK-1685] Cancel retryTimer on restart of Worker or AppClient

See https://issues.apache.org/jira/browse/SPARK-1685 for a more complete description, but in essence: If the Worker or AppClient actor restarts before successfully registering with Master, multiple retryTimers will be running, which will lead to less than the full number of registration retries being attempted before the new actor is forced to give up.

Author: Mark Hamstra <markhamstra@gmail.com>

Closes #602 from markhamstra/SPARK-1685 and squashes the following commits:

11cc088 [Mark Hamstra] retryTimer -> registrationRetryTimer
69c348c [Mark Hamstra] Cancel retryTimer on restart of Worker or AppClient
SPARK-1734: spark-submit throws an exception: Exception in thread "main"...

... java.lang.ClassNotFoundException: org.apache.spark.broadcast.TorrentBroadcastFactory

Author: witgo <witgo@qq.com>

Closes #665 from witgo/SPARK-1734 and squashes the following commits:

cacf238 [witgo] SPARK-1734: spark-submit throws an exception: Exception in thread "main" java.lang.ClassNotFoundException: org.apache.spark.broadcast.TorrentBroadcastFactory
[SPARK-1549] Add Python support to spark-submit

This PR updates spark-submit to allow submitting Python scripts (currently only with deploy-mode=client, but that's all that was supported before) and updates the PySpark code to properly find various paths, etc. One significant change is that we assume we can always find the Python files either from the Spark assembly JAR (which will happen with the Maven assembly build in make-distribution.sh) or from SPARK_HOME (which will exist in local mode even if you use sbt assembly, and should be enough for testing). This means we no longer need a weird hack to modify the environment for YARN.

This patch also updates the Python worker manager to run python with -u, which means unbuffered output (send it to our logs right away instead of waiting a while after stuff was written); this should simplify debugging.

In addition, it fixes https://issues.apache.org/jira/browse/SPARK-1709, setting the main class from a JAR's Main-Class attribute if not specified by the user, and fixes a few help strings and style issues in spark-submit.

In the future we may want to make the `pyspark` shell use spark-submit as well, but it seems unnecessary for 1.0.

Author: Matei Zaharia <matei@databricks.com>

Closes #664 from mateiz/py-submit and squashes the following commits:

15e9669 [Matei Zaharia] Fix some uses of path.separator property
051278c [Matei Zaharia] Small style fixes
0afe886 [Matei Zaharia] Add license headers
4650412 [Matei Zaharia] Add pyFiles to PYTHONPATH in executors, remove old YARN stuff, add tests
15f8e1e [Matei Zaharia] Set PYTHONPATH in PythonWorkerFactory in case it wasn't set from outside
47c0655 [Matei Zaharia] More work to make spark-submit work with Python:
d4375bd [Matei Zaharia] Clean up description of spark-submit args a bit and add Python ones
SPARK-1737: Warn rather than fail when Java 7+ is used to create distributions

Also moves a few lines of code around in make-distribution.sh.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #669 from pwendell/make-distribution and squashes the following commits:

8bfac49 [Patrick Wendell] Small fix
46918ec [Patrick Wendell] SPARK-1737: Warn rather than fail when Java 7+ is used to create distributions.
SPARK-1637: Clean up examples for 1.0

- [x] Move all of them into subpackages of org.apache.spark.examples (right now some are in org.apache.spark.streaming.examples, for instance, and others are in org.apache.spark.examples.mllib)
- [x] Move Python examples into examples/src/main/python
- [x] Update docs to reflect these changes

Author: Sandeep <sandeep@techaddict.me>

This patch had conflicts when merged, resolved by
Committer: Matei Zaharia <matei@databricks.com>

Closes #571 from techaddict/SPARK-1637 and squashes the following commits:

47ef86c [Sandeep] Changes based on Discussions on PR, removing use of RawTextHelper from examples
8ed2d3f [Sandeep] Docs Updated for changes, Change for java examples
5f96121 [Sandeep] Move Python examples into examples/src/main/python
0a8dd77 [Sandeep] Move all Scala Examples to org.apache.spark.examples (some are in org.apache.spark.streaming.examples, for instance, and others are in org.apache.spark.examples.mllib)