[SPARK-1545] [mllib] Add Random Forests

This PR adds RandomForest to MLlib.  The implementation is basic, and future performance optimizations will be important.  (Note: RFs = Random Forests.)

# Overview

## RandomForest
* trains multiple trees at once to reduce the number of passes over the data
* allows feature subsets at each node
* uses a queue of nodes instead of fixed groups for each level

This implementation is based an implementation by manishamde and the [Alpine Labs Sequoia Forest](https://github.com/AlpineNow/SparkML2) by codedeft (in particular, the TreePoint, BaggedPoint, and node queue implementations).  Thank you for your inputs!

## Testing

Correctness: This has been tested for correctness with the test suites and with DecisionTreeRunner on example datasets.

Performance: This has been performance tested using [this branch of spark-perf](https://github.com/jkbradley/spark-perf/tree/rfs).  Results below.

### Regression tests for DecisionTree

Summary: For training 1 tree, there are small regressions, especially from feature subsampling.

In the table below, each row is a single (random) dataset.  The 2 different sets of result columns are for 2 different RF implementations:
* (numTrees): This is from an earlier commit, after implementing RandomForest to train multiple trees at once.  It does not include any code for feature subsampling.
* (feature subsets): This is from this current PR's code, after implementing feature subsampling.
These tests were to identify regressions in DecisionTree, so they are training 1 tree with all of the features (i.e., no feature subsampling).

These were run on an EC2 cluster with 15 workers, training 1 tree with maxDepth = 5 (= 6 levels).  Speedup values < 1 indicate slowdowns from the old DecisionTree implementation.

numInstances | numFeatures | runtime (sec) | speedup | runtime (sec) | speedup
---- | ---- | ---- | ---- | ---- | ----
 | | (numTrees) | (numTrees) | (feature subsets) | (feature subsets)
20000 | 100 | 4.051 | 1.044433473 | 4.478 | 0.9448414471
20000 | 500 | 8.472 | 1.104461756 | 9.315 | 1.004508857
20000 | 1500 | 19.354 | 1.05854087 | 20.863 | 0.9819776638
20000 | 3500 | 43.674 | 1.072033704 | 45.887 | 1.020332556
200000 | 100 | 4.196 | 1.171830315 | 4.848 | 1.014232673
200000 | 500 | 8.926 | 1.082791844 | 9.771 | 0.989151571
200000 | 1500 | 20.58 | 1.068415938 | 22.134 | 0.9934038131
200000 | 3500 | 48.043 | 1.075203464 | 52.249 | 0.9886505005
2000000 | 100 | 4.944 | 1.01355178 | 5.796 | 0.8645617667
2000000 | 500 | 11.11 | 1.016831683 | 12.482 | 0.9050632911
2000000 | 1500 | 31.144 | 1.017852556 | 35.274 | 0.8986789136
2000000 | 3500 | 79.981 | 1.085382778 | 101.105 | 0.8586123337
20000000 | 100 | 8.304 | 0.9270231214 | 9.073 | 0.8484514494
20000000 | 500 | 28.174 | 1.083268262 | 34.236 | 0.8914592826
20000000 | 1500 | 143.97 | 0.9579634646 | 159.275 | 0.8659111599

### Tests for forests

I have run other tests with numTrees=10 and with sqrt(numFeatures), and those indicate that multi-model training and feature subsets can speed up training for forests, especially when training deeper trees.

# Details on specific classes

## Changes to DecisionTree
* Main train() method is now in RandomForest.
* findBestSplits() is no longer needed.  (It split levels into groups, but we now use a queue of nodes.)
* Many small changes to support RFs.  (Note: These methods should be moved to RandomForest.scala in a later PR, but are in DecisionTree.scala to make code comparison easier.)

## RandomForest
* Main train() method is from old DecisionTree.
* selectNodesToSplit: Note that it selects nodes and feature subsets jointly to track memory usage.

## RandomForestModel
* Stores an Array[DecisionTreeModel]
* Prediction:
 * For classification, most common label.  For regression, mean.
 * We could support other methods later.

## examples/.../DecisionTreeRunner
* This now takes numTrees and featureSubsetStrategy, to support RFs.

## DTStatsAggregator
* 2 types of functionality (w/ and w/o subsampling features): These require different indexing methods.  (We could treat both as subsampling, but this is less efficient
  DTStatsAggregator is now abstract, and 2 child classes implement these 2 types of functionality.

## impurities
* These now take instance weights.

## Node
* Some vals changed to vars.
 * This is unfortunately a public API change (DeveloperApi).  This could be avoided by creating a LearningNode struct, but would be awkward.

## RandomForestSuite
Please let me know if there are missing tests!

## BaggedPoint
This wraps TreePoint and holds bootstrap weights/counts.

# Design decisions

* BaggedPoint: BaggedPoint is separate from TreePoint since it may be useful for other bagging algorithms later on.

* RandomForest public API: What options should be easily supported by the train* methods?  Should ALL options be in the Java-friendly constructors?  Should there be a constructor taking Strategy?

* Feature subsampling options: What options should be supported?  scikit-learn supports the same options, except for "onethird."  One option would be to allow users to specific fractions ("0.1"): the current options could be supported, and any unrecognized values would be parsed as Doubles in [0,1].

* Splits and bins are computed before bootstrapping, so all trees use the same discretization.

* One queue, instead of one queue per tree.

CC: mengxr manishamde codedeft chouqin  Please let me know if you have suggestions---thanks!

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>
Author: qiping.lqp <qiping.lqp@alibaba-inc.com>
Author: chouqin <liqiping1991@gmail.com>

Closes #2435 from jkbradley/rfs-new and squashes the following commits:

c694174 [Joseph K. Bradley] Fixed typo
cc59d78 [Joseph K. Bradley] fixed imports
e25909f [Joseph K. Bradley] Simplified node group maps.  Specifically, created NodeIndexInfo to store node index in agg and feature subsets, and no longer create extra maps in findBestSplits
fbe9a1e [Joseph K. Bradley] Changed default featureSubsetStrategy to be sqrt for classification, onethird for regression.  Updated docs with references.
ef7c293 [Joseph K. Bradley] Updates based on code review.  Most substantial changes: * Simplified DTStatsAggregator * Made RandomForestModel.trees public * Added test for regression to RandomForestSuite
593b13c [Joseph K. Bradley] Fixed bug in metadata for computing log2(num features).  Now it checks >= 1.
a1a08df [Joseph K. Bradley] Removed old comments
866e766 [Joseph K. Bradley] Changed RandomForestSuite randomized tests to use multiple fixed random seeds.
ff8bb96 [Joseph K. Bradley] removed usage of null from RandomForest and replaced with Option
bf1a4c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into rfs-new
6b79c07 [Joseph K. Bradley] Added RandomForestSuite, and fixed small bugs, style issues.
d7753d4 [Joseph K. Bradley] Added numTrees and featureSubsetStrategy to DecisionTreeRunner (to support RandomForest).  Fixed bugs so that RandomForest now runs.
746d43c [Joseph K. Bradley] Implemented feature subsampling.  Tested DecisionTree but not RandomForest.
6309d1d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into rfs-new.  Added RandomForestModel.toString
b7ae594 [Joseph K. Bradley] Updated docs.  Small fix for bug which does not cause errors: No longer allocate unused child nodes for leaf nodes.
121c74e [Joseph K. Bradley] Basic random forests are implemented.  Random features per node not yet implemented.  Test suite not implemented.
325d18a [Joseph K. Bradley] Merge branch 'chouqin-dt-preprune' into rfs-new
4ef9bf1 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into rfs-new
61b2e72 [Joseph K. Bradley] Added max of 10GB for maxMemoryInMB in Strategy.
a95e7c8 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into chouqin-dt-preprune
6da8571 [Joseph K. Bradley] RFs partly implemented, not done yet
eddd1eb [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into rfs-new
5c4ac33 [Joseph K. Bradley] Added check in Strategy to make sure minInstancesPerNode >= 1
0dd4d87 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-spark-3160
95c479d [Joseph K. Bradley] * Fixed typo in tree suite test "do not choose split that does not satisfy min instance per node requirements" * small style fixes
e2628b6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into chouqin-dt-preprune
19b01af [Joseph K. Bradley] Merge remote-tracking branch 'chouqin/dt-preprune' into chouqin-dt-preprune
f1d11d1 [chouqin] fix typo
c7ebaf1 [chouqin] fix typo
39f9b60 [chouqin] change edge `minInstancesPerNode` to 2 and add one more test
c6e2dfc [Joseph K. Bradley] Added minInstancesPerNode and minInfoGain parameters to DecisionTreeRunner.scala and to Python API in tree.py
306120f [Joseph K. Bradley] Fixed typo in DecisionTreeModel.scala doc
eaa1dcf [Joseph K. Bradley] Added topNode doc in DecisionTree and scalastyle fix
d4d7864 [Joseph K. Bradley] Marked Node.build as deprecated
d4dbb99 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-spark-3160
1a8f0ad [Joseph K. Bradley] Eliminated pre-allocated nodes array in main train() method. * Nodes are constructed and added to the tree structure as needed during training.
0278a11 [chouqin] remove `noSplit` and set `Predict` private to tree
d593ec7 [chouqin] fix docs and change minInstancesPerNode to 1
2ab763b [Joseph K. Bradley] Simplifications to DecisionTree code:
efcc736 [qiping.lqp] fix bug
10b8012 [qiping.lqp] fix style
6728fad [qiping.lqp] minor fix: remove empty lines
bb465ca [qiping.lqp] Merge branch 'master' of https://github.com/apache/spark into dt-preprune
cadd569 [qiping.lqp] add api docs
46b891f [qiping.lqp] fix bug
e72c7e4 [qiping.lqp] add comments
845c6fa [qiping.lqp] fix style
f195e83 [qiping.lqp] fix style
987cbf4 [qiping.lqp] fix bug
ff34845 [qiping.lqp] separate calculation of predict of node from calculation of info gain
ac42378 [qiping.lqp] add min info gain and min instances per node parameters in decision tree
[EC2] Cleanup Python parens and disk dict

Minor fixes:
* Remove unnecessary parens (Python style)
* Sort `disks_by_instance` dict and remove duplicate `t1.micro` key

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2571 from nchammas/ec2-polish and squashes the following commits:

9d203d5 [Nicholas Chammas] paren and dict cleanup
[CORE] Bugfix: LogErr format in DAGScheduler.scala

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #2572 from liyezhang556520/DAGLogErr and squashes the following commits:

5be2491 [Zhang, Liye] Bugfix: LogErr format in DAGScheduler.scala
[EC2] Sort long, manually-inputted dictionaries

Similar to the work done in #2571, this PR just sorts the remaining manually-inputted dicts in the EC2 script so they are easier to maintain.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2578 from nchammas/ec2-dict-sort and squashes the following commits:

f55c692 [Nicholas Chammas] sort long dictionaries
[MLlib] [SPARK-2885] DIMSUM: All-pairs similarity

# All-pairs similarity via DIMSUM
Compute all pairs of similar vectors using brute force approach, and also DIMSUM sampling approach.

Laying down some notation: we are looking for all pairs of similar columns in an m x n RowMatrix whose entries are denoted a_ij, with the i’th row denoted r_i and the j’th column denoted c_j. There is an oversampling parameter labeled ɣ that should be set to 4 log(n)/s to get provably correct results (with high probability), where s is the similarity threshold.

The algorithm is stated with a Map and Reduce, with proofs of correctness and efficiency in published papers [1] [2]. The reducer is simply the summation reducer. The mapper is more interesting, and is also the heart of the scheme. As an exercise, you should try to see why in expectation, the map-reduce below outputs cosine similarities.

![dimsumv2](https://cloud.githubusercontent.com/assets/3220351/3807272/d1d9514e-1c62-11e4-9f12-3cfdb1d78b3a.png)

[1] Bosagh-Zadeh, Reza and Carlsson, Gunnar (2013), Dimension Independent Matrix Square using MapReduce, arXiv:1304.1467 http://arxiv.org/abs/1304.1467

[2] Bosagh-Zadeh, Reza and Goel, Ashish (2012), Dimension Independent Similarity Computation, arXiv:1206.2082 http://arxiv.org/abs/1206.2082

# Testing

Tests for all invocations included.

Added L1 and L2 norm computation to MultivariateStatisticalSummary since it was needed. Added tests for both of them.

Author: Reza Zadeh <rizlar@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #1778 from rezazadeh/dimsumv2 and squashes the following commits:

404c64c [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2
4eb71c6 [Reza Zadeh] Add excludes for normL1 and normL2
ee8bd65 [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2
976ddd4 [Reza Zadeh] Broadcast colMags. Avoid div by zero.
3467cff [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2
aea0247 [Reza Zadeh] Allow large thresholds to promote sparsity
9fe17c0 [Xiangrui Meng] organize imports
2196ba5 [Xiangrui Meng] Merge branch 'rezazadeh-dimsumv2' into dimsumv2
254ca08 [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2
f2947e4 [Xiangrui Meng] some optimization
3c4cf41 [Xiangrui Meng] Merge branch 'master' into rezazadeh-dimsumv2
0e4eda4 [Reza Zadeh] Use partition index for RNG
251bb9c [Reza Zadeh] Documentation
25e9d0d [Reza Zadeh] Line length for style
fb296f6 [Reza Zadeh] renamed to normL1 and normL2
3764983 [Reza Zadeh] Documentation
e9c6791 [Reza Zadeh] New interface and documentation
613f261 [Reza Zadeh] Column magnitude summary
75a0b51 [Reza Zadeh] Use Ints instead of Longs in the shuffle
0f12ade [Reza Zadeh] Style changes
eb1dc20 [Reza Zadeh] Use Double.PositiveInfinity instead of Double.Max
f56a882 [Reza Zadeh] Remove changes to MultivariateOnlineSummarizer
dbc55ba [Reza Zadeh] Make colMagnitudes a method in RowMatrix
41e8ece [Reza Zadeh] style changes
139c8e1 [Reza Zadeh] Syntax changes
029aa9c [Reza Zadeh] javadoc and new test
75edb25 [Reza Zadeh] All tests passing!
05e59b8 [Reza Zadeh] Add test
502ce52 [Reza Zadeh] new interface
654c4fb [Reza Zadeh] default methods
3726ca9 [Reza Zadeh] Remove MatrixAlgebra
6bebabb [Reza Zadeh] remove changes to MatrixSuite
5b8cd7d [Reza Zadeh] Initial files
[SPARK-3032][Shuffle] Fix key comparison integer overflow introduced sorting exception

Previous key comparison in `ExternalSorter` will get wrong sorting result or exception when key comparison overflows, details can be seen in [SPARK-3032](https://issues.apache.org/jira/browse/SPARK-3032). Here fix this and add a unit test to prove it.

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

Closes #2514 from jerryshao/SPARK-3032 and squashes the following commits:

6f3c302 [jerryshao] Improve the unit test according to comments
01911e6 [jerryshao] Change the test to show the contract violate exception
83acb38 [jerryshao] Minor changes according to comments
fa2a08f [jerryshao] Fix key comparison integer overflow introduced sorting exception
Add more debug message for ManagedBuffer

This is to help debug the error reported at http://apache-spark-user-list.1001560.n3.nabble.com/SQL-queries-fail-in-1-2-0-SNAPSHOT-td15327.html

Author: Reynold Xin <rxin@apache.org>

Closes #2580 from rxin/buffer-debug and squashes the following commits:

5814292 [Reynold Xin] Logging close() in case close() fails.
323dfec [Reynold Xin] Add more debug message.
[SPARK-3007][SQL]Add Dynamic Partition support to Spark Sql hive

a new PR base on new master.  changes are the same as https://github.com/apache/spark/pull/1919

Author: baishuo(白硕) <vc_java@hotmail.com>
Author: baishuo <vc_java@hotmail.com>
Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2226 from baishuo/patch-3007 and squashes the following commits:

e69ce88 [Cheng Lian] Adds tests to verify dynamic partitioning folder layout
b20a3dc [Cheng Lian] Addresses @yhuai's comments
096bbbc [baishuo(白硕)] Merge pull request #1 from liancheng/refactor-dp
1093c20 [Cheng Lian] Adds more tests
5004542 [Cheng Lian] Minor refactoring
fae9eff [Cheng Lian] Refactors InsertIntoHiveTable to a Command
528e84c [Cheng Lian] Fixes typo in test name, regenerated golden answer files
c464b26 [Cheng Lian] Refactors dynamic partitioning support
5033928 [baishuo] pass check style
2201c75 [baishuo] use HiveConf.DEFAULTPARTITIONNAME to replace hive.exec.default.partition.name
b47c9bf [baishuo] modify according micheal's advice
c3ab36d [baishuo] modify for some bad indentation
7ce2d9f [baishuo] modify code to pass scala style checks
37c1c43 [baishuo] delete a empty else branch
66e33fc [baishuo] do a little modify
88d0110 [baishuo] update file after test
a3961d9 [baishuo(白硕)] Update Cast.scala
f7467d0 [baishuo(白硕)] Update InsertIntoHiveTable.scala
c1a59dd [baishuo(白硕)] Update Cast.scala
0e18496 [baishuo(白硕)] Update HiveQuerySuite.scala
60f70aa [baishuo(白硕)] Update InsertIntoHiveTable.scala
0a50db9 [baishuo(白硕)] Update HiveCompatibilitySuite.scala
491c7d0 [baishuo(白硕)] Update InsertIntoHiveTable.scala
a2374a8 [baishuo(白硕)] Update InsertIntoHiveTable.scala
701a814 [baishuo(白硕)] Update SparkHadoopWriter.scala
dc24c41 [baishuo(白硕)] Update HiveQl.scala
[graphX] GraphOps: random pick vertex bug

When `numVertices > 50`, probability is set to 0. This would cause infinite loop.

Author: yingjieMiao <yingjie@42go.com>

Closes #2553 from yingjieMiao/graphx and squashes the following commits:

6adf3c8 [yingjieMiao] [graphX] GraphOps: random pick vertex bug
Fixed the condition in StronglyConnectedComponents Issue: SPARK-3635

Author: oded <oded@HP-DV6.c4internal.c4-security.com>

Closes #2486 from odedz/master and squashes the following commits:

dd7890a [oded] Fixed the condition in StronglyConnectedComponents Issue: SPARK-3635
Minor cleanup of code.

Author: Reynold Xin <rxin@apache.org>

Closes #2581 from rxin/minor-cleanup and squashes the following commits:

736a91b [Reynold Xin] Minor cleanup of code.
[SPARK-3613] Record only average block size in MapStatus for large stages

This changes the way we send MapStatus from executors back to driver for large stages (>2000 tasks). For large stages, we no longer send one byte per block. Instead, we just send the average block size.

This makes large jobs (tens of thousands of tasks) much more reliable since the driver no longer sends huge amount of data.

Author: Reynold Xin <rxin@apache.org>

Closes #2470 from rxin/mapstatus and squashes the following commits:

822ff54 [Reynold Xin] Code review feedback.
3b86f56 [Reynold Xin] Added MimaExclude.
f89d182 [Reynold Xin] Fixed a bug in MapStatus
6a0401c [Reynold Xin] [SPARK-3613] Record only average block size in MapStatus for large stages.
[SPARK-3709] Executors don't always report broadcast block removal properly back to the driver

The problem was that the 2nd argument in RemoveBroadcast is not tellMaster! It is "removeFromDriver". Basically when removeFromDriver is not true, we don't report broadcast block removal back to the driver, and then other executors mistakenly think that the executor would still have the block, and try to fetch from it.

cc @tdas

Author: Reynold Xin <rxin@apache.org>

Closes #2588 from rxin/debug and squashes the following commits:

6dab2e3 [Reynold Xin] Don't log random messages.
f430686 [Reynold Xin] Always report broadcast removal back to master.
2a13f70 [Reynold Xin] iii
[SPARK-3734] DriverRunner should not read SPARK_HOME from submitter's environment

When using spark-submit in `cluster` mode to submit a job to a Spark Standalone
cluster, if the JAVA_HOME environment variable was set on the submitting
machine then DriverRunner would attempt to use the submitter's JAVA_HOME to
launch the driver process (instead of the worker's JAVA_HOME), causing the
driver to fail unless the submitter and worker had the same Java location.

This commit fixes this by reading JAVA_HOME from sys.env instead of
command.environment.

Author: Josh Rosen <joshrosen@apache.org>

Closes #2586 from JoshRosen/SPARK-3734 and squashes the following commits:

e9513d9 [Josh Rosen] [SPARK-3734] DriverRunner should not read SPARK_HOME from submitter's environment.
Revert "[SPARK-3007][SQL]Add Dynamic Partition support to Spark Sql hive"

This reverts commit 0bbe7faeffa17577ae8a33dfcd8c4c783db5c909.
HOTFIX: Ignore flaky tests in YARN
[SPARK-3356] [DOCS] Document when RDD elements' ordering within partitions is nondeterministic

As suggested by mateiz , and because it came up on the mailing list again last week, this attempts to document that ordering of elements is not guaranteed across RDD evaluations in groupBy, zip, and partition-wise RDD methods. Suggestions welcome about the wording, or other methods that need a note.

Author: Sean Owen <sowen@cloudera.com>

Closes #2508 from srowen/SPARK-3356 and squashes the following commits:

b7c96fd [Sean Owen] Undo change to programming guide
ad4aeec [Sean Owen] Don't mention ordering in partition-wise methods, reword description of ordering for zip methods per review, and add similar note to programming guide, which mentions groupByKey (but not zip methods)
fce943b [Sean Owen] Note that ordering of elements is not guaranteed across RDD evaluations in groupBy, zip, and partition-wise RDD methods
SPARK-3745 - fix check-license to properly download and check jar

for details, see: https://issues.apache.org/jira/browse/SPARK-3745

Author: shane knapp <incomplete@gmail.com>

Closes #2596 from shaneknapp/SPARK-3745 and squashes the following commits:

c95eea9 [shane knapp] SPARK-3745 - fix check-license to properly download and check jar
[Build] Post commit hash with timeout messages

[By request](https://github.com/apache/spark/pull/2588#issuecomment-57266871), and because it also makes sense.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2597 from nchammas/timeout-commit-hash and squashes the following commits:

3d90714 [Nicholas Chammas] Revert "testing: making timeout 1 minute"
2353c95 [Nicholas Chammas] testing: making timeout 1 minute
e3a477e [Nicholas Chammas] post commit hash with timeout
SPARK-3744 [STREAMING] FlumeStreamSuite will fail during port contention

Since it looked quite easy, I took the liberty of making a quick PR that just uses `Utils.startServiceOnPort` to fix this. It works locally for me.

Author: Sean Owen <sowen@cloudera.com>

Closes #2601 from srowen/SPARK-3744 and squashes the following commits:

ddc9319 [Sean Owen] Avoid port contention in tests by retrying several ports for Flume stream