EC2 configurable workers

Added option to configure number of worker instances and to set SPARK_MASTER_OPTS

Depends on: https://github.com/mesos/spark-ec2/pull/46

Author: Allan Douglas R. de Oliveira <allan@chaordicsystems.com>

Closes #612 from douglaz/ec2_configurable_workers and squashes the following commits:

d6c5d65 [Allan Douglas R. de Oliveira] Added master opts parameter
6c34671 [Allan Douglas R. de Oliveira] Use number of worker instances as string on template
ba528b9 [Allan Douglas R. de Oliveira] Added SPARK_WORKER_INSTANCES parameter
[SQL] Better logging when applying rules.

Author: Michael Armbrust <michael@databricks.com>

Closes #616 from marmbrus/ruleLogging and squashes the following commits:

39c09fe [Michael Armbrust] Fix off by one error.
5af3537 [Michael Armbrust] Better logging when applying rules.
Whitelist Hive Tests

This is ready when Jenkins is.

Author: Michael Armbrust <michael@databricks.com>

Closes #596 from marmbrus/moreTests and squashes the following commits:

85be703 [Michael Armbrust] Blacklist MR required tests.
35bc311 [Michael Armbrust] Add hive golden answers.
ede98fd [Michael Armbrust] More hive gitignore
da096ea [Michael Armbrust] update whitelist
The default version of yarn is equal to the hadoop version

This is a part of [PR 590](https://github.com/apache/spark/pull/590)

Author: witgo <witgo@qq.com>

Closes #626 from witgo/yarn_version and squashes the following commits:

c390631 [witgo] restore  the yarn dependency declarations
f8a4ad8 [witgo] revert remove the dependency of avro in yarn-alpha
2df6cf5 [witgo] review commit
a1d876a [witgo] review commit
20e7e3e [witgo] review commit
c76763b [witgo] The default value of yarn.version is equal to hadoop.version
SPARK-1658: Correctly identify if maven is installed and working

The current test is checking the exit code of "tail" rather than "mvn".
This new check will make sure that mvn is installed and was able to
execute the "version command".

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

Closes #580 from rahulsinghaliitd/SPARK-1658 and squashes the following commits:

83c0313 [Rahul Singhal] SPARK-1658: Correctly identify if maven is installed and working
bf821b9 [Rahul Singhal] SPARK-1658: Correctly identify if maven is installed and working
SPARK-1663. (Addendum) Fix signature of one version of JavaPairRDDStream.reduceByKeyAndWindow()

It appears that one of these methods doesn't use `org.apache.spark.api.java.function.Function2` like all the others, but uses Scala's `Function2`.

Author: Sean Owen <sowen@cloudera.com>

Closes #633 from srowen/SPARK-1663.2 and squashes the following commits:

1e0232d [Sean Owen] Fix signature of one version of reduceByKeyAndWindow to use Java API Function2, as apparently intended
SPARK-1703 Warn users if Spark is run on JRE6 but compiled with JDK7.

This add some guards and good warning messages if users hit this issue. /cc @aarondav with whom I discussed parts of the design.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #627 from pwendell/jdk6 and squashes the following commits:

a38a958 [Patrick Wendell] Code review feedback
94e9f84 [Patrick Wendell] SPARK-1703 Warn users if Spark is run on JRE6 but compiled with JDK7.
SPARK-1629. Addendum: Depend on commons lang3 (already used by tachyon) as it's used in ReplSuite, and return to use lang3 utility in Utils.scala

For consideration. This was proposed in related discussion: https://github.com/apache/spark/pull/569

Author: Sean Owen <sowen@cloudera.com>

Closes #635 from srowen/SPARK-1629.2 and squashes the following commits:

a442b98 [Sean Owen] Depend on commons lang3 (already used by tachyon) as it's used in ReplSuite, and return to use lang3 utility in Utils.scala
SPARK-1693: Most of the tests throw a java.lang.SecurityException when s...

...park built for hadoop 2.3.0 , 2.4.0

Author: witgo <witgo@qq.com>

Closes #628 from witgo/SPARK-1693_new and squashes the following commits:

e3af968 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1693_new
dc63905 [witgo] SPARK-1693: Most of the tests throw a java.lang.SecurityException when spark built for hadoop 2.3.0 , 2.4.0
EC2 script should exit with non-zero code on UsageError

This is specially import because some ssh errors are raised as UsageError, preventing an automated usage of the script from detecting the failure.

Author: Allan Douglas R. de Oliveira <allan@chaordicsystems.com>

Closes #638 from douglaz/ec2_exit_code_fix and squashes the following commits:

5915e6d [Allan Douglas R. de Oliveira] EC2 script should exit with non-zero code on UsageError
SPARK-1710: spark-submit should print better errors than "InvocationTargetException"

Catching the InvocationTargetException, printing getTargetException.

Author: Sandeep <sandeep@techaddict.me>

Closes #630 from techaddict/SPARK-1710 and squashes the following commits:

834d79b [Sandeep] changes from srowen  suggestions
109d604 [Sandeep] SPARK-1710: spark-submit should print better errors than "InvocationTargetException"
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