[SPARK-1506][MLLIB] Documentation improvements for MLlib 1.0

Preview: http://54.82.240.23:4000/mllib-guide.html

Table of contents:

* Basics
  * Data types
  * Summary statistics
* Classification and regression
  * linear support vector machine (SVM)
  * logistic regression
  * linear linear squares, Lasso, and ridge regression
  * decision tree
  * naive Bayes
* Collaborative Filtering
  * alternating least squares (ALS)
* Clustering
  * k-means
* Dimensionality reduction
  * singular value decomposition (SVD)
  * principal component analysis (PCA)
* Optimization
  * stochastic gradient descent
  * limited-memory BFGS (L-BFGS)

Author: Xiangrui Meng <meng@databricks.com>

Closes #422 from mengxr/mllib-doc and squashes the following commits:

944e3a9 [Xiangrui Meng] merge master
f9fda28 [Xiangrui Meng] minor
9474065 [Xiangrui Meng] add alpha to ALS examples
928e630 [Xiangrui Meng] initialization_mode -> initializationMode
5bbff49 [Xiangrui Meng] add imports to labeled point examples
c17440d [Xiangrui Meng] fix python nb example
28f40dc [Xiangrui Meng] remove localhost:4000
369a4d3 [Xiangrui Meng] Merge branch 'master' into mllib-doc
7dc95cc [Xiangrui Meng] update linear methods
053ad8a [Xiangrui Meng] add links to go back to the main page
abbbf7e [Xiangrui Meng] update ALS argument names
648283e [Xiangrui Meng] level down statistics
14e2287 [Xiangrui Meng] add sample libsvm data and use it in guide
8cd2441 [Xiangrui Meng] minor updates
186ab07 [Xiangrui Meng] update section names
6568d65 [Xiangrui Meng] update toc, level up lr and svm
162ee12 [Xiangrui Meng] rename section names
5c1e1b1 [Xiangrui Meng] minor
8aeaba1 [Xiangrui Meng] wrap long lines
6ce6a6f [Xiangrui Meng] add summary statistics to toc
5760045 [Xiangrui Meng] claim beta
cc604bf [Xiangrui Meng] remove classification and regression
92747b3 [Xiangrui Meng] make section titles consistent
e605dd6 [Xiangrui Meng] add LIBSVM loader
f639674 [Xiangrui Meng] add python section to migration guide
c82ffb4 [Xiangrui Meng] clean optimization
31660eb [Xiangrui Meng] update linear algebra and stat
0a40837 [Xiangrui Meng] first pass over linear methods
1fc8271 [Xiangrui Meng] update toc
906ed0a [Xiangrui Meng] add a python example to naive bayes
5f0a700 [Xiangrui Meng] update collaborative filtering
656d416 [Xiangrui Meng] update mllib-clustering
86e143a [Xiangrui Meng] remove data types section from main page
8d1a128 [Xiangrui Meng] move part of linear algebra to data types and add Java/Python examples
d1b5cbf [Xiangrui Meng] merge master
72e4804 [Xiangrui Meng] one pass over tree guide
64f8995 [Xiangrui Meng] move decision tree guide to a separate file
9fca001 [Xiangrui Meng] add first version of linear algebra guide
53c9552 [Xiangrui Meng] update dependencies
f316ec2 [Xiangrui Meng] add migration guide
f399f6c [Xiangrui Meng] move linear-algebra to dimensionality-reduction
182460f [Xiangrui Meng] add guide for naive Bayes
137fd1d [Xiangrui Meng] re-organize toc
a61e434 [Xiangrui Meng] update mllib's toc
[Fix #204] Eliminate delay between binding and log checking

**Bug**: In the existing history server, there is a `spark.history.updateInterval` seconds delay before application logs show up on the UI.

**Cause**: This is because the following events happen in this order: (1) The background thread that checks for logs starts, but realizes the server has not yet bound and so waits for N seconds, (2) server binds, (3) N seconds later the background thread finds that the server has finally bound to a port, and so finally checks for application logs.

**Fix**: This PR forces the log checking thread to start immediately after binding. It also documents two relevant environment variables that are currently missing.

Author: Andrew Or <andrewor14@gmail.com>

Closes #441 from andrewor14/history-server-fix and squashes the following commits:

b2eb46e [Andrew Or] Document SPARK_PUBLIC_DNS and SPARK_HISTORY_OPTS for the history server
e8d1fbc [Andrew Or] Eliminate delay between binding and checking for logs
Fix compilation on Hadoop 2.4.x.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #483 from vanzin/yarn-2.4 and squashes the following commits:

0fc57d8 [Marcelo Vanzin] Fix compilation on Hadoop 2.4.x.
[SPARK-1570] Fix classloading in JavaSQLContext.applySchema

I think I hit a class loading issue when running JavaSparkSQL example using spark-submit in local mode.

Author: Kan Zhang <kzhang@apache.org>

Closes #484 from kanzhang/SPARK-1570 and squashes the following commits:

feaaeba [Kan Zhang] [SPARK-1570] Fix classloading in JavaSQLContext.applySchema
Assorted clean-up for Spark-on-YARN.

In particular when the HADOOP_CONF_DIR is not not specified.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #488 from pwendell/hadoop-cleanup and squashes the following commits:

fe95f13 [Patrick Wendell] Changes based on Andrew's feeback
18d09c1 [Patrick Wendell] Review comments from Andrew
17929cc [Patrick Wendell] Assorted clean-up for Spark-on-YARN.
[Spark-1538] Fix SparkUI incorrectly hiding persisted RDDs

**Bug**: After the following command `sc.parallelize(1 to 1000).persist.map(_ + 1).count()` is run, the the persisted RDD is missing from the storage tab of the SparkUI.

**Cause**: The command creates two RDDs in one stage, a `ParallelCollectionRDD` and a `MappedRDD`. However, the existing StageInfo only keeps the RDDInfo of the last RDD associated with the stage (`MappedRDD`), and so all RDD information regarding the first RDD (`ParallelCollectionRDD`) is discarded. In this case, we persist the first RDD,  but the StorageTab doesn't know about this RDD because it is not encoded in the StageInfo.

**Fix**: Record information of all RDDs in StageInfo, instead of just the last RDD (i.e. `stage.rdd`). Since stage boundaries are marked by shuffle dependencies, the solution is to traverse the last RDD's dependency tree, visiting only ancestor RDDs related through a sequence of narrow dependencies.

---

This PR also moves RDDInfo to its own file, includes a few style fixes, and adds a unit test for constructing StageInfos.

Author: Andrew Or <andrewor14@gmail.com>

Closes #469 from andrewor14/storage-ui-fix and squashes the following commits:

07fc7f0 [Andrew Or] Add back comment that was accidentally removed (minor)
5d799fe [Andrew Or] Add comment to justify testing of getNarrowAncestors with cycles
9d0e2b8 [Andrew Or] Hide details of getNarrowAncestors from outsiders
d2bac8a [Andrew Or] Deal with cycles in RDD dependency graph + add extensive tests
2acb177 [Andrew Or] Move getNarrowAncestors to RDD.scala
bfe83f0 [Andrew Or] Backtrace RDD dependency tree to find all RDDs that belong to a Stage
[streaming][SPARK-1578] Removed requirement for TTL in StreamingContext.

Since shuffles and RDDs that are out of context are automatically cleaned by Spark core (using ContextCleaner) there is no need for setting the cleaner TTL while creating a StreamingContext.

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

Closes #491 from tdas/ttl-fix and squashes the following commits:

cf01dc7 [Tathagata Das] Removed requirement for TTL in StreamingContext.
[FIX: SPARK-1376] use --arg instead of --args in SparkSubmit to avoid warning messages

Even if users use `--arg`, `SparkSubmit` still uses `--args` for child args internally, which triggers a warning message that may confuse users:

~~~
--args is deprecated. Use --arg instead.
~~~

@sryza Does it look good to you?

Author: Xiangrui Meng <meng@databricks.com>

Closes #485 from mengxr/submit-arg and squashes the following commits:

5e1b9fe [Xiangrui Meng] update test
cebbeb7 [Xiangrui Meng] use --arg instead of --args in SparkSubmit to avoid warning messages
SPARK-1562 Fix visibility / annotation of Spark SQL APIs

Author: Michael Armbrust <michael@databricks.com>

Closes #489 from marmbrus/sqlDocFixes and squashes the following commits:

acee4f3 [Michael Armbrust] Fix visibility / annotation of Spark SQL APIs
SPARK-1494 Don't initialize classes loaded by MIMA excludes.

[WIP]  Just seeing how Jenkins likes this...

Author: Michael Armbrust <michael@databricks.com>

Closes #494 from marmbrus/mima and squashes the following commits:

6eec616 [Michael Armbrust] Force hive tests to run.
acaf682 [Michael Armbrust] Don't initialize loaded classes.
[SQL] SPARK-1571 Mistake in java example code

Author: Michael Armbrust <michael@databricks.com>

Closes #496 from marmbrus/javaBeanBug and squashes the following commits:

644fedd [Michael Armbrust] Bean methods must be public.
SPARK-1119 and other build improvements

1. Makes assembly and examples jar naming consistent in maven/sbt.
2. Updates make-distribution.sh to use Maven and fixes some bugs.
3. Updates the create-release script to call make-distribution script.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #502 from pwendell/make-distribution and squashes the following commits:

1a97f0d [Patrick Wendell] SPARK-1119 and other build improvements
SPARK-1583: Fix a bug that using java.util.HashMap by mistake

JIRA: https://issues.apache.org/jira/browse/SPARK-1583

Does anyone know why using `java.util.HashMap` rather than `mutable.HashMap`? Some methods of `java.util.HashMap` are not generics and compiler can not help us find similar problems.

Author: zsxwing <zsxwing@gmail.com>

Closes #500 from zsxwing/SPARK-1583 and squashes the following commits:

7bfd74d [zsxwing] SPARK-1583: Fix a bug that using java.util.HashMap by mistake
SPARK-1572 Don't kill Executor if PythonRDD fails while computing parent

Previously, the behavior was that if the parent RDD threw any exception other than IOException or FileNotFoundException (which is quite possible for Hadoop input sources), the entire Executor would crash, because the default thread a uncaught exception handler calls System.exit().

This patch avoids two related issues:

  1. Always catch exceptions in this reader thread.
  2. Don't mask readerException when Python throws an EOFError
     after worker.shutdownOutput() is called.

Author: Aaron Davidson <aaron@databricks.com>

Closes #486 from aarondav/pyspark and squashes the following commits:

fbb11e9 [Aaron Davidson] Make sure FileNotFoundExceptions are handled same as before
b9acb3e [Aaron Davidson] SPARK-1572 Don't kill Executor if PythonRDD fails while computing parent
Honor default fs name when initializing event logger.

This is related to SPARK-1459 / PR #375. Without this fix,
FileLogger.createLogDir() may try to create the log dir on
HDFS, while createWriter() will try to open the log file on
the local file system, leading to interesting errors and
confusion.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #450 from vanzin/event-file-2 and squashes the following commits:

592cdb3 [Marcelo Vanzin] Honor default fs name when initializing event logger.
SPARK-1582 Invoke Thread.interrupt() when cancelling jobs

Sometimes executor threads are blocked waiting for IO or monitors, and the current implementation of job cancellation may never recover these threads. By simply invoking Thread.interrupt() during cancellation, we can often safely unblock the threads and use them for subsequent work.

Note that this feature must remain optional for now because of a bug in HDFS where Thread.interrupt() may cause nodes to be marked as permanently dead (as the InterruptedException is reinterpreted as an IOException during communication with some node).

Author: Aaron Davidson <aaron@databricks.com>

Closes #498 from aarondav/cancel and squashes the following commits:

e52b829 [Aaron Davidson] Don't use job.properties when null
82f78bb [Aaron Davidson] Update DAGSchedulerSuite
b67f472 [Aaron Davidson] Add comment on why interruptOnCancel is in setJobGroup
4cb9fd6 [Aaron Davidson] SPARK-1582 Invoke Thread.interrupt() when cancelling jobs
[SPARK-1540] Add an optional Ordering parameter to PairRDDFunctions.

In https://issues.apache.org/jira/browse/SPARK-1540 we'd like to look at Spark's API to see if we can take advantage of Comparable keys in more places, which will make external spilling more efficient. This PR is a first step towards that that shows how to pass an Ordering when available and still continue functioning otherwise. It does this using a new implicit parameter with a default value of null.

The API is currently only in Scala -- in Java we'd have to add new versions of mapToPair and such that take a Comparator, or a new method to add a "type hint" to an RDD. We can address those later though.

Unfortunately requiring all keys to be Comparable would not work without requiring RDDs in general to contain only Comparable types. The reason is that methods such as distinct() and intersection() do a shuffle, but should be usable on RDDs of any type. So ordering will have to remain an optimization for the types that can be ordered. I think this isn't a horrible outcome though because one of the nice things about Spark's API is that it works on objects of *any* type, without requiring you to specify a schema or implement Writable or stuff like that.

Author: Matei Zaharia <matei@databricks.com>

This patch had conflicts when merged, resolved by
Committer: Reynold Xin <rxin@apache.org>

Closes #487 from mateiz/ordered-keys and squashes the following commits:

bd565f6 [Matei Zaharia] Pass an Ordering to only one version of groupBy because the Scala language spec doesn't allow having an optional parameter on all of them (this was only compiling in Scala 2.10 due to a bug).
4629965 [Matei Zaharia] Add tests for other versions of groupBy
3beae85 [Matei Zaharia] Added a test for implicit orderings
80b7a3b [Matei Zaharia] Add an optional Ordering parameter to PairRDDFunctions.
[Hot Fix #469] Fix flaky test in SparkListenerSuite

The two modified tests may fail if the race condition does not bid in our favor...

Author: Andrew Or <andrewor14@gmail.com>

Closes #516 from andrewor14/stage-info-test-fix and squashes the following commits:

b4b6100 [Andrew Or] Add/replace missing waitUntilEmpty() calls to listener bus
Update Java api for setJobGroup with interruptOnCancel

Also adds a unit test.

Author: Aaron Davidson <aaron@databricks.com>

Closes #522 from aarondav/cancel2 and squashes the following commits:

565c253 [Aaron Davidson] Update Java api for setJobGroup with interruptOnCancel
65b33d8 [Aaron Davidson] Add unit test for Thread interruption on cancellation
Mark all fields of EdgePartition, Graph, and GraphOps transient

These classes are only serializable to work around closure capture, so their fields should all be marked `@transient` to avoid wasteful serialization.

This PR supersedes apache/spark#519 and fixes the same bug.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #520 from ankurdave/graphx-transient and squashes the following commits:

6431760 [Ankur Dave] Mark all fields of EdgePartition, Graph, and GraphOps `@transient`