Add a config (spark.yarn.access.namenodes) to allow applications running on yarn to access other secure HDFS cluster.  User just specifies the namenodes of the other clusters and we get Tokens for those and ship them with the spark application.

Author: Thomas Graves <tgraves@apache.org>

Closes #1159 from tgravescs/spark-1528 and squashes the following commits:

ddbcd16 [Thomas Graves] review comments
0ac8501 [Thomas Graves] SPARK-1528 - add support for accessing remote HDFS

This PR is a updated version of (https://github.com/apache/spark/pull/557) to actually test sending and receiving data through Kafka, and fix previous flaky issues.

@tdas, would you mind reviewing this PR? Thanks a lot.

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

Closes #1751 from jerryshao/kafka-unit-test and squashes the following commits:

b6a505f [jerryshao] code refactor according to comments
5222330 [jerryshao] Change JavaKafkaStreamSuite to better test it
5525f10 [jerryshao] Fix flaky issue of Kafka real unit test
4559310 [jerryshao] Minor changes for Kafka unit test
860f649 [jerryshao] Minor style changes, and tests ignored due to flakiness
796d4ca [jerryshao] Add real Kafka streaming test

Author: Reynold Xin <rxin@apache.org>

Closes #1780 from rxin/kryo-init-size and squashes the following commits:

551b935 [Reynold Xin] [SPARK-2856] Decrease initial buffer size for Kryo to 64KB.

Author: wangfei <scnbwf@yeah.net>
Author: wangfei <wangfei1@huawei.com>

Closes #714 from scwf/memoryFraction and squashes the following commits:

6e385b9 [wangfei] Update SparkConf.scala
da6ee59 [wangfei] add configs
829a195 [wangfei] add indent
717c0ca [wangfei] updated to make more concise
fc45476 [wangfei] validate memoryfraction in sparkconf
2e79b3d [wangfei] && => ||
43621bd [wangfei] && => ||
cf38bcf [wangfei] throw IllegalArgumentException
14d18ac [wangfei] throw IllegalArgumentException
dff1f0f [wangfei] Update BlockManager.scala
764965f [wangfei] Update ExternalAppendOnlyMap.scala
a59d76b [wangfei] Throw exception when memoryFracton is out of range
7b899c2 [wangfei] 【SPARK-1779】

`master.ui.port` and `worker.ui.port` were never picked up by SparkConf, simply because they are not prefixed with "spark." Unfortunately, this is also currently the documented way of setting these values.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1779 from andrewor14/master-worker-port and squashes the following commits:

8475e95 [Andrew Or] Update docs to reflect changes in configs
4db3d5d [Andrew Or] Stop using configs that don't actually work

This tracks memory properly if there are multiple spilling collections in the same task (which was a problem before), and also implements an algorithm that lets each thread grow up to 1 / 2N of the memory pool (where N is the number of threads) before spilling, which avoids an inefficiency with small spills we had before (some threads would spill many times at 0-1 MB because the pool was allocated elsewhere).

Author: Matei Zaharia <matei@databricks.com>

Closes #1707 from mateiz/spark-2711 and squashes the following commits:

debf75b [Matei Zaharia] Review comments
24f28f3 [Matei Zaharia] Small rename
c8f3a8b [Matei Zaharia] Update ShuffleMemoryManager to be able to partially grant requests
315e3a5 [Matei Zaharia] Some review comments
b810120 [Matei Zaharia] Create central manager to track memory for all spilling collections

Replaces this with an O(1) operation that does not have to shift over
the whole tail of the array into the gap produced by the element removed.

Author: Matei Zaharia <matei@databricks.com>

Closes #1773 from mateiz/SPARK-2685 and squashes the following commits:

1ea028a [Matei Zaharia] Update comments in StreamBuffer and EAOM, and reuse ArrayBuffers
eb1abfd [Matei Zaharia] Update ExternalAppendOnlyMap to avoid buffer.remove()

Author: Reynold Xin <rxin@apache.org>

Closes #1772 from rxin/accumulator-dagscheduler and squashes the following commits:

6a58520 [Reynold Xin] [SPARK-2323] Exception in accumulator update should not crash DAGScheduler & SparkContext.

serializer is imported multiple times during doctests, so it's better to make _hijack_namedtuple() safe to be called multiple times.

Author: Davies Liu <davies.liu@gmail.com>

Closes #1771 from davies/fix and squashes the following commits:

1a9e336 [Davies Liu] fix unit tests

All these changes are from mridulm's work in #1609, but extracted here to fix this specific issue and make it easier to merge not 1.1. This particular set of changes is to make sure that we read exactly the right range of bytes from each spill file in EAOM: some serializers can write bytes after the last object (e.g. the TC_RESET flag in Java serialization) and that would confuse the previous code into reading it as part of the next batch. There are also improvements to cleanup to make sure files are closed.

In addition to bringing in the changes to ExternalAppendOnlyMap, I also copied them to the corresponding code in ExternalSorter and updated its test suite to test for the same issues.

Author: Matei Zaharia <matei@databricks.com>

Closes #1722 from mateiz/spark-2792 and squashes the following commits:

5d4bfb5 [Matei Zaharia] Make objectStreamReset counter count the last object written too
18fe865 [Matei Zaharia] Update docs on objectStreamReset
576ee83 [Matei Zaharia] Allow objectStreamReset to be 0
0374217 [Matei Zaharia] Remove super paranoid code to close file handles
bda37bb [Matei Zaharia] Implement Mridul's ExternalAppendOnlyMap fixes in ExternalSorter too
0d6dad7 [Matei Zaharia] Added Mridul's test changes for ExternalAppendOnlyMap
9a78e4b [Matei Zaharia] Add @mridulm's fixes to ExternalAppendOnlyMap for batch sizes

Add an hook to replace original namedtuple with an pickable one, then namedtuple could be used in RDDs.

PS: pyspark should be import BEFORE "from collections import namedtuple"

Author: Davies Liu <davies.liu@gmail.com>

Closes #1623 from davies/namedtuple and squashes the following commits:

045dad8 [Davies Liu] remove unrelated code changes
4132f32 [Davies Liu] address comment
55b1c1a [Davies Liu] fix tests
61f86eb [Davies Liu] replace all the reference of namedtuple to new hacked one
98df6c6 [Davies Liu] Merge branch 'master' of github.com:apache/spark into namedtuple
f7b1bde [Davies Liu] add hack for CloudPickleSerializer
0c5c849 [Davies Liu] Merge branch 'master' of github.com:apache/spark into namedtuple
21991e6 [Davies Liu] hack namedtuple in __main__ module, make it picklable.
93b03b8 [Davies Liu] pickable namedtuple

This is a pull request regarding SPARK-2510 at https://issues.apache.org/jira/browse/SPARK-2510. Word2Vec creates vector representation of words in a text corpus. The algorithm first constructs a vocabulary from the corpus and then learns vector representation of words in the vocabulary. The vector representation can be used as features in natural language processing and machine learning algorithms.

To make our implementation more scalable, we train each partition separately and merge the model of each partition after each iteration. To make the model more accurate, multiple iterations may be needed.

To investigate the vector representations is to find the closest words for a query word. For example, the top 20 closest words to "china" are for 1 partition and 1 iteration :

taiwan 0.8077646146334014
korea 0.740913304563621
japan 0.7240667798885471
republic 0.7107151279078352
thailand 0.6953217332072862
tibet 0.6916782118129544
mongolia 0.6800858715972612
macau 0.6794925677480378
singapore 0.6594048695593799
manchuria 0.658989931844148
laos 0.6512978726001666
nepal 0.6380792327845325
mainland 0.6365469459587788
myanmar 0.6358614338840394
macedonia 0.6322366180313249
xinjiang 0.6285291551708028
russia 0.6279951236068411
india 0.6272874944023487
shanghai 0.6234544135576999
macao 0.6220588462925876

The result with 10 partitions and 5 iterations is:
taiwan 0.8310495079388313
india 0.7737171315919039
japan 0.756777901233668
korea 0.7429767187102452
indonesia 0.7407557427278356
pakistan 0.712883426985585
mainland 0.7053379963140822
thailand 0.696298191073948
mongolia 0.693690656871415
laos 0.6913069680735292
macau 0.6903427690029617
republic 0.6766381604813666
malaysia 0.676460699141784
singapore 0.6728790997360923
malaya 0.672345232966194
manchuria 0.6703732292753156
macedonia 0.6637955686322028
myanmar 0.6589462882439646
kazakhstan 0.657017801081494
cambodia 0.6542383836451932

Author: Liquan Pei <lpei@gopivotal.com>
Author: Xiangrui Meng <meng@databricks.com>
Author: Liquan Pei <liquanpei@gmail.com>

Closes #1719 from Ishiihara/master and squashes the following commits:

2ba9483 [Liquan Pei] minor fix for Word2Vec test
e248441 [Liquan Pei] minor style change
26a948d [Liquan Pei] Merge pull request #1 from mengxr/Ishiihara-master
c14da41 [Xiangrui Meng] fix styles
384c771 [Xiangrui Meng] remove minCount and window from constructor change model to use float instead of double
e93e726 [Liquan Pei] use treeAggregate instead of aggregate
1a8fb41 [Liquan Pei] use weighted sum in combOp
7efbb6f [Liquan Pei] use broadcast version of vocab in aggregate
6bcc8be [Liquan Pei] add multiple iteration support
720b5a3 [Liquan Pei] Add test for Word2Vec algorithm, minor fixes
2e92b59 [Liquan Pei] modify according to feedback
57dc50d [Liquan Pei] code formatting
e4a04d3 [Liquan Pei] minor fix
0aafb1b [Liquan Pei] Add comments, minor fixes
8d6befe [Liquan Pei] initial commit

SPARK-2272 [MLlib] Feature scaling which standardizes the range of independent variables or features of data

Feature scaling is a method used to standardize the range of independent variables or features of data. In data processing, it is generally performed during the data preprocessing step.

In this work, a trait called `VectorTransformer` is defined for generic transformation on a vector. It contains one method to be implemented, `transform` which applies transformation on a vector.

There are two implementations of `VectorTransformer` now, and they all can be easily extended with PMML transformation support.

1) `StandardScaler` - Standardizes features by removing the mean and scaling to unit variance using column summary statistics on the samples in the training set.

2) `Normalizer` - Normalizes samples individually to unit L^n norm

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #1207 from dbtsai/dbtsai-feature-scaling and squashes the following commits:

78c15d3 [DB Tsai] Alpine Data Labs

Any time you use the directory name (`FWDIR`) it needs to be surrounded
in quotes. If you're also using wildcards, you can safely put the quotes
around just `$FWDIR`.

Author: Sarah Gerweck <sarah.a180@gmail.com>

Closes #1756 from sarahgerweck/folderSpaces and squashes the following commits:

732629d [Sarah Gerweck] Fix some bugs with spaces in directory name.

Needed for Scala 2.11 compiler-interface

Signed-off-by: Anand Avati <avatiredhat.com>

Author: Anand Avati <avati@redhat.com>

Closes #1711 from avati/SPARK-1812-scala-maven-plugin and squashes the following commits:

9a22fc8 [Anand Avati] SPARK-1812: upgrade to scala-maven-plugin 3.2.0

Kill only the python worker related to cancelled tasks.

The daemon will start a background thread to monitor all the opened sockets for all workers. If the socket is closed by JVM, this thread will kill the worker.

When an task is cancelled, the socket to worker will be closed, then the worker will be killed by deamon.

Author: Davies Liu <davies.liu@gmail.com>

Closes #1643 from davies/kill and squashes the following commits:

8ffe9f3 [Davies Liu] kill worker by deamon, because runtime.exec() is too heavy
46ca150 [Davies Liu] address comment
acd751c [Davies Liu] kill the worker when task is canceled

JIRA: https://issues.apache.org/jira/browse/SPARK-2783

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

Closes #1741 from yhuai/analyzeTable and squashes the following commits:

7bb5f02 [Yin Huai] Use sql instead of hql.
4d09325 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
e3ebcd4 [Yin Huai] Renaming.
c170f4e [Yin Huai] Do not use getContentSummary.
62393b6 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
db233a6 [Yin Huai] Trying to debug jenkins...
fee84f0 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
f0501f3 [Yin Huai] Fix compilation error.
24ad391 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
8918140 [Yin Huai] Wording.
23df227 [Yin Huai] Add a simple analyze method to get the size of a table and update the "totalSize" property of this table in the Hive metastore.

JIRA issue: [SPARK-2814](https://issues.apache.org/jira/browse/SPARK-2814)

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

Closes #1753 from liancheng/spark-2814 and squashes the following commits:

c74a3b2 [Cheng Lian] Fixed SPARK-2814

Many users have reported being confused by the distinction between the `sql` and `hql` methods.  Specifically, many users think that `sql(...)` cannot be used to read hive tables.  In this PR I introduce a new configuration option `spark.sql.dialect` that picks which dialect with be used for parsing.  For SQLContext this must be set to `sql`.  In `HiveContext` it defaults to `hiveql` but can also be set to `sql`.

The `hql` and `hiveql` methods continue to act the same but are now marked as deprecated.

**This is a possibly breaking change for some users unless they set the dialect manually, though this is unlikely.**

For example: `hiveContex.sql("SELECT 1")` will now throw a parsing exception by default.

Author: Michael Armbrust <michael@databricks.com>

Closes #1746 from marmbrus/sqlLanguageConf and squashes the following commits:

ad375cc [Michael Armbrust] Merge remote-tracking branch 'apache/master' into sqlLanguageConf
20c43f8 [Michael Armbrust] override function instead of just setting the value
7e4ae93 [Michael Armbrust] Deprecate hql() method in favor of a config option, 'spark.sql.dialect'

Bug fix: Before, when an RDD was created in Java and passed to DecisionTree.train(), the fake class tag caused problems.
* Fix: DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java.

Other improvements to Decision Trees for easy-of-use with Java:
* impurity classes: Added instance() methods to help with Java interface.
* Strategy: Added Java-friendly constructor
--> Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently.  I suspect we will redo the API before the other options are included.

CC: mengxr

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1740 from jkbradley/dt-java-new and squashes the following commits:

0805dc6 [Joseph K. Bradley] Changed Strategy to use JavaConverters instead of JavaConversions
519b1b7 [Joseph K. Bradley] * Organized imports in JavaDecisionTreeSuite.java * Using JavaConverters instead of JavaConversions in DecisionTreeSuite.scala
f7b5ca1 [Joseph K. Bradley] Improvements to make it easier to run DecisionTree from Java. * DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java. * impurity classes: Added instance() methods to help with Java interface. * Strategy: Added Java-friendly constructor ** Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently.  I suspect we will redo the API before the other options are included.
d78ada6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-java
320853f [Joseph K. Bradley] Added JavaDecisionTreeSuite, partly written
13a585e [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-java
f1a8283 [Joseph K. Bradley] Added old JavaDecisionTreeSuite, to be updated later
225822f [Joseph K. Bradley] Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature.

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

Closes #1186 from douglaz/spark_ec2_user_data and squashes the following commits:

94a36f9 [Allan Douglas R. de Oliveira] Added user data option to EC2 script

Per request by Reynold adding small note about proper sequencing of build then test.

Author: Stephen Boesch <javadba@gmail.com>

Closes #1615 from javadba/docs and squashes the following commits:

6c3183e [Stephen Boesch] Moved updated testing blurb per PWendell
5764757 [Stephen Boesch] SPARK-2712 - Add a small note to maven doc that mvn package must happen before test

Minor fixes on top of #1679.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1736 from andrewor14/amend-#1679 and squashes the following commits:

3b46f5e [Andrew Or] Minor fixes

The JIRA concerned removing jquery, and this does not remove jquery. While it is distributed by Spark it should have an accompanying line in LICENSE, very technically, as per http://www.apache.org/dev/licensing-howto.html

Author: Sean Owen <srowen@gmail.com>

Closes #1748 from srowen/SPARK-2414 and squashes the following commits:

2fdb03c [Sean Owen] Add LICENSE entry for jquery

As per https://issues.apache.org/jira/browse/SPARK-2602 , this may be resolved for Java 6 with the java.awt.headless system property, which never hurt anyone running a command line app. I tested it and seemed to get rid of focus stealing.

Author: Sean Owen <srowen@gmail.com>

Closes #1747 from srowen/SPARK-2602 and squashes the following commits:

b141018 [Sean Owen] Set java.awt.headless during tests

There have been user complaints that the difference between `registerAsTable` and `saveAsTable` is too subtle.  This PR addresses this by renaming `registerAsTable` to `registerTempTable`, which more clearly reflects what is happening.  `registerAsTable` remains, but will cause a deprecation warning.

Author: Michael Armbrust <michael@databricks.com>

Closes #1743 from marmbrus/registerTempTable and squashes the following commits:

d031348 [Michael Armbrust] Merge remote-tracking branch 'apache/master' into registerTempTable
4dff086 [Michael Armbrust] Fix .java files too
89a2f12 [Michael Armbrust] Merge remote-tracking branch 'apache/master' into registerTempTable
0b7b71e [Michael Armbrust] Rename registerAsTable to registerTempTable

The cause is explained in https://issues.apache.org/jira/browse/SPARK-2797.

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

Closes #1745 from yhuai/SPARK-2797 and squashes the following commits:

7b1627d [Yin Huai] The unpersist method of the Scala RDD cannot be called without the input parameter (blocking) from PySpark.

This is a follow up of #1636.

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

Closes #1738 from liancheng/test-for-spark-2729 and squashes the following commits:

b13692a [Cheng Lian] Added test case for SPARK-2729

Author: Michael Armbrust <michael@databricks.com>

Closes #1742 from marmbrus/asserts and squashes the following commits:

5182d54 [Michael Armbrust] Remove assertions that throw when users try unsupported Hive commands.

This patch adds the ability to register lambda functions written in Python, Java or Scala as UDFs for use in SQL or HiveQL.

Scala:
```scala
registerFunction("strLenScala", (_: String).length)
sql("SELECT strLenScala('test')")
```
Python:
```python
sqlCtx.registerFunction("strLenPython", lambda x: len(x), IntegerType())
sqlCtx.sql("SELECT strLenPython('test')")
```
Java:
```java
sqlContext.registerFunction("stringLengthJava", new UDF1<String, Integer>() {
  Override
  public Integer call(String str) throws Exception {
    return str.length();
  }
}, DataType.IntegerType);

sqlContext.sql("SELECT stringLengthJava('test')");
```

Author: Michael Armbrust <michael@databricks.com>

Closes #1063 from marmbrus/udfs and squashes the following commits:

9eda0fe [Michael Armbrust] newline
747c05e [Michael Armbrust] Add some scala UDF tests.
d92727d [Michael Armbrust] Merge remote-tracking branch 'apache/master' into udfs
005d684 [Michael Armbrust] Fix naming and formatting.
d14dac8 [Michael Armbrust] Fix last line of autogened java files.
8135c48 [Michael Armbrust] Move UDF unit tests to pyspark.
40b0ffd [Michael Armbrust] Merge remote-tracking branch 'apache/master' into udfs
6a36890 [Michael Armbrust] Switch logging so that SQLContext can be serializable.
7a83101 [Michael Armbrust] Drop toString
795fd15 [Michael Armbrust] Try to avoid capturing SQLContext.
e54fb45 [Michael Armbrust] Docs and tests.
437cbe3 [Michael Armbrust] Update use of dataTypes, fix some python tests, address review comments.
01517d6 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udfs
8e6c932 [Michael Armbrust] WIP
3f96a52 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udfs
6237c8d [Michael Armbrust] WIP
2766f0b [Michael Armbrust] Move udfs support to SQL from hive. Add support for Java UDFs.
0f7d50c [Michael Armbrust] Draft of native Spark SQL UDFs for Scala and Python.

This also Closes #1701.

Author: GuoQiang Li <witgo@qq.com>

Closes #1208 from witgo/SPARK-1470 and squashes the following commits:

422646b [GuoQiang Li] Remove scalalogging-slf4j dependency

Author: Chris Fregly <chris@fregly.com>

Closes #1434 from cfregly/master and squashes the following commits:

4774581 [Chris Fregly] updated docs, renamed retry to retryRandom to be more clear, removed retries around store() method
0393795 [Chris Fregly] moved Kinesis examples out of examples/ and back into extras/kinesis-asl
691a6be [Chris Fregly] fixed tests and formatting, fixed a bug with JavaKinesisWordCount during union of streams
0e1c67b [Chris Fregly] Merge remote-tracking branch 'upstream/master'
74e5c7c [Chris Fregly] updated per TD's feedback.  simplified examples, updated docs
e33cbeb [Chris Fregly] Merge remote-tracking branch 'upstream/master'
bf614e9 [Chris Fregly] per matei's feedback:  moved the kinesis examples into the examples/ dir
d17ca6d [Chris Fregly] per TD's feedback:  updated docs, simplified the KinesisUtils api
912640c [Chris Fregly] changed the foundKinesis class to be a publically-avail class
db3eefd [Chris Fregly] Merge remote-tracking branch 'upstream/master'
21de67f [Chris Fregly] Merge remote-tracking branch 'upstream/master'
6c39561 [Chris Fregly] parameterized the versions of the aws java sdk and kinesis client
338997e [Chris Fregly] improve build docs for kinesis
828f8ae [Chris Fregly] more cleanup
e7c8978 [Chris Fregly] Merge remote-tracking branch 'upstream/master'
cd68c0d [Chris Fregly] fixed typos and backward compatibility
d18e680 [Chris Fregly] Merge remote-tracking branch 'upstream/master'
b3b0ff1 [Chris Fregly] [SPARK-1981] Add AWS Kinesis streaming support

I think we will not generate the plan triggering this bug at this moment. But, let me explain it...

Right now, we are using `left.outputPartitioning` as the `outputPartitioning` of a `BroadcastHashJoin`. We may have a wrong physical plan for cases like...
```sql
SELECT l.key, count(*)
FROM (SELECT key, count(*) as cnt
      FROM src
      GROUP BY key) l // This is buildPlan
JOIN r // This is the streamedPlan
ON (l.cnt = r.value)
GROUP BY l.key
```
Let's say we have a `BroadcastHashJoin` on `l` and `r`. For this case, we will pick `l`'s `outputPartitioning` for the `outputPartitioning`of the `BroadcastHashJoin` on `l` and `r`. Also, because the last `GROUP BY` is using `l.key` as the key, we will not introduce an `Exchange` for this aggregation. However, `r`'s outputPartitioning may not match the required distribution of the last `GROUP BY` and we fail to group data correctly.

JIRA is being reindexed. I will create a JIRA ticket once it is back online.

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

Closes #1735 from yhuai/BroadcastHashJoin and squashes the following commits:

96d9cb3 [Yin Huai] Set outputPartitioning correctly.

Added experimental Python API for Decision Trees.

API:
* class DecisionTreeModel
** predict() for single examples and RDDs, taking both feature vectors and LabeledPoints
** numNodes()
** depth()
** __str__()
* class DecisionTree
** trainClassifier()
** trainRegressor()
** train()

Examples and testing:
* Added example testing classification and regression with batch prediction: examples/src/main/python/mllib/tree.py
* Have also tested example usage in doc of python/pyspark/mllib/tree.py which tests single-example prediction with dense and sparse vectors

Also: Small bug fix in python/pyspark/mllib/_common.py: In _linear_predictor_typecheck, changed check for RDD to use isinstance() instead of type() in order to catch RDD subclasses.

CC mengxr manishamde

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1727 from jkbradley/decisiontree-python-new and squashes the following commits:

3744488 [Joseph K. Bradley] Renamed test tree.py to decision_tree_runner.py Small updates based on github review.
6b86a9d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
affceb9 [Joseph K. Bradley] * Fixed bug in doc tests in pyspark/mllib/util.py caused by change in loadLibSVMFile behavior.  (It used to threshold labels at 0 to make them 0/1, but it now leaves them as they are.) * Fixed small bug in loadLibSVMFile: If a data file had no features, then loadLibSVMFile would create a single all-zero feature.
67a29bc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
cf46ad7 [Joseph K. Bradley] Python DecisionTreeModel * predict(empty RDD) returns an empty RDD instead of an error. * Removed support for calling predict() on LabeledPoint and RDD[LabeledPoint] * predict() does not cache serialized RDD any more.
aa29873 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
bf21be4 [Joseph K. Bradley] removed old run() func from DecisionTree
fa10ea7 [Joseph K. Bradley] Small style update
7968692 [Joseph K. Bradley] small braces typo fix
e34c263 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4801b40 [Joseph K. Bradley] Small style update to DecisionTreeSuite
db0eab2 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix2' into decisiontree-python-new
6873fa9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
225822f [Joseph K. Bradley] Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature.
93953f1 [Joseph K. Bradley] Likely done with Python API.
6df89a9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4562c08 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
665ba78 [Joseph K. Bradley] Small updates towards Python DecisionTree API
188cb0d [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
6622247 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
b8fac57 [Joseph K. Bradley] Finished Python DecisionTree API and example but need to test a bit more.
2b20c61 [Joseph K. Bradley] Small doc and style updates
1b29c13 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
584449a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals
8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type.
376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1
e06e423 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
bab3f19 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them.
52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
f5a036c [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification.  Caused problems in past, but fixed now.
8e227ea [Joseph K. Bradley] Changed Strategy so it only requires numClassesForClassification >= 2 for classification
cd1d933 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features.
8a758db [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
5fe44ed [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
2283df8 [Joseph K. Bradley] 2 bug fixes.
73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail.  Will describe bug in next commit.
f825352 [Joseph K. Bradley] Wrote Python API and example for DecisionTree.  Also added toString, depth, and numNodes methods to DecisionTreeModel.

`spark.test.home` was introduced in #1734. This is fine for SBT but is failing maven tests. Either way it shouldn't throw an NPE.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1739 from andrewor14/fix-spark-test-home and squashes the following commits:

ce2624c [Andrew Or] Do not throw NPE if spark.test.home is not set

This commit exists to close the following pull requests on Github:

Closes #706 (close requested by 'pwendell')
Closes #453 (close requested by 'pwendell')
Closes #557 (close requested by 'tdas')
Closes #495 (close requested by 'tdas')
Closes #1232 (close requested by 'pwendell')
Closes #82 (close requested by 'pwendell')
Closes #600 (close requested by 'pwendell')
Closes #473 (close requested by 'pwendell')
Closes #351 (close requested by 'pwendell')

This has been failing on master. One possible cause is that the port
gets contended if multiple test runs happen concurrently and they
hit this test at the same time. Since this test takes a long time
(60 seconds) that's very plausible. This patch randomizes the port
used in this test to avoid contention.

We needed to add an explicit dependency on scalatest since this
module will not get it from spark core like others do.

For Scala 2.11 compatibility.

Without the explicit type specification, withNullability
return type is inferred to be Attribute, and thus calling
at() on the returned object fails in these tests:

[ERROR] /Users/avati/work/spark/sql/catalyst/src/test/scala/org/apache/spark/sql/catalyst/expressions/ExpressionEvaluationSuite.scala:370: value at is not a
[ERROR]     val c4_notNull = 'a.boolean.notNull.at(3)
[ERROR]                                         ^
[ERROR] /Users/avati/work/spark/sql/catalyst/src/test/scala/org/apache/spark/sql/catalyst/expressions/ExpressionEvaluationSuite.scala:371: value at is not a
[ERROR]     val c5_notNull = 'a.boolean.notNull.at(4)
[ERROR]                                         ^
[ERROR] /Users/avati/work/spark/sql/catalyst/src/test/scala/org/apache/spark/sql/catalyst/expressions/ExpressionEvaluationSuite.scala:372: value at is not a
[ERROR]     val c6_notNull = 'a.boolean.notNull.at(5)
[ERROR]                                         ^
[ERROR] /Users/avati/work/spark/sql/catalyst/src/test/scala/org/apache/spark/sql/catalyst/expressions/ExpressionEvaluationSuite.scala:558: value at is not a
[ERROR]     val s_notNull = 'a.string.notNull.at(0)

Signed-off-by: Anand Avati <avatiredhat.com>

Author: Anand Avati <avati@redhat.com>

Closes #1709 from avati/SPARK-1812-notnull and squashes the following commits:

0470eb3 [Anand Avati] SPARK-1812: sql/catalyst - Provide explicit type information

When standalone Workers launch executors, they inherit the Spark home set by the driver. This means if the worker machines do not share the same directory structure as the driver node, the Workers will attempt to run scripts (e.g. bin/compute-classpath.sh) that do not exist locally and fail. This is a common scenario if the driver is launched from outside of the cluster.

The solution is to simply not pass the driver's Spark home to the Workers. This PR further makes an attempt to avoid overloading the usages of `spark.home`, which is now only used for setting executor Spark home on Mesos and in python.

This is based on top of #1392 and originally reported by YanTangZhai. Tested on standalone cluster.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1734 from andrewor14/spark-home-reprise and squashes the following commits:

f71f391 [Andrew Or] Revert changes in python
1c2532c [Andrew Or] Merge branch 'master' of github.com:apache/spark into spark-home-reprise
188fc5d [Andrew Or] Avoid using spark.home where possible
09272b7 [Andrew Or] Always use Worker's working directory as spark home