JIRA issue [here](https://issues.apache.org/jira/browse/SPARK-1415).

New Hadoop API of `InputFormat` does not provide the `minSplits` parameter, which makes the API incompatible between `HadoopRDD` and `NewHadoopRDD`. The PR is for constructing compatible APIs.

Though `minSplits` is deprecated by New Hadoop API, we think it is better to make APIs compatible here.

**Note** that `minSplits` in `wholeTextFiles` could only be treated as a *suggestion*, the real number of splits may not be greater than `minSplits` due to `isSplitable()=false`.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #376 from yinxusen/hadoop-min-split and squashes the following commits:

76417f6 [Xusen Yin] refine comments
c10af60 [Xusen Yin] refine comments and rewrite new class for wholeTextFile
766d05b [Xusen Yin] refine Java API and comments
4875755 [Xusen Yin] add minSplits for WholeTextFiles

The Spark codebase is a bit fast-and-loose when accessing classloaders and this has caused a few bugs to surface in master.

This patch defines some utility methods for accessing classloaders. This makes the intention when accessing a classloader much more explicit in the code and fixes a few cases where the wrong one was chosen.

case (a) -> We want the classloader that loaded Spark
case (b) -> We want the context class loader, or if not present, we want (a)

This patch provides a better fix for SPARK-1403 (https://issues.apache.org/jira/browse/SPARK-1403) than the current work around, which it reverts. It also fixes a previously unreported bug that the `./spark-submit` script did not work for running with `local` master. It didn't work because the executor classloader did not properly delegate to the context class loader (if it is defined) and in local mode the context class loader is set by the `./spark-submit` script. A unit test is added for that case.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #398 from pwendell/class-loaders and squashes the following commits:

b4a1a58 [Patrick Wendell] Minor clean up
14f1272 [Patrick Wendell] SPARK-1480: Clean up use of classloaders

[SPARK-1403] I investigated why spark 0.9.0 loads fine on mesos while spark 1.0.0 fails. What I found was that in SparkEnv.scala, while creating the SparkEnv object, the current thread's classloader is null. But in 0.9.0, at the same place, it is set to org.apache.spark.repl.ExecutorClassLoader . I saw that https://github.com/apache/spark/commit/7edbea41b43e0dc11a2de156be220db8b7952d01 moved it to it current place. I moved it back and saw that 1.0.0 started working fine on mesos.

I just created a minimal patch that allows me to run spark on mesos correctly. It seems like SecurityManager's creation needs to be taken into account for a correct fix. Also moving the creation of the serializer out of SparkEnv might be a part of the right solution. PTAL.

Author: Bharath Bhushan <manku.timma@outlook.com>

Closes #322 from manku-timma/spark-1403 and squashes the following commits:

606c2b9 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
ec8f870 [Bharath Bhushan] revert the logger change for java 6 compatibility as PR 334 is doing it
728beca [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
044027d [Bharath Bhushan] fix compile error
6f260a4 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
b3a053f [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
04b9662 [Bharath Bhushan] add missing line
4803c19 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
f3c9a14 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
42d3d6a [Bharath Bhushan] used code fragment from @ueshin to fix the problem in a better way
89109d7 [Bharath Bhushan] move the class loader creation back to where it was in 0.9.0

This PR is self-explanatory.

Author: Andrew Or <andrewor14@gmail.com>

Closes #381 from andrewor14/master and squashes the following commits:

3e8dde2 [Andrew Or] Fix comments for #204

When debugging Spark Streaming applications it is necessary to monitor certain metrics that are not shown in the Spark application UI. For example, what is average processing time of batches? What is the scheduling delay? Is the system able to process as fast as it is receiving data? How many records I am receiving through my receivers?

While the StreamingListener interface introduced in the 0.9 provided some of this information, it could only be accessed programmatically. A UI that shows information specific to the streaming applications is necessary for easier debugging. This PR introduces such a UI. It shows various statistics related to the streaming application. Here is a screenshot of the UI running on my local machine.

http://i.imgur.com/1ooDGhm.png

This UI is integrated into the Spark UI running at 4040.

Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Andrew Or <andrewor14@gmail.com>

Closes #290 from tdas/streaming-web-ui and squashes the following commits:

fc73ca5 [Tathagata Das] Merge pull request #9 from andrewor14/ui-refactor
642dd88 [Andrew Or] Merge SparkUISuite.scala into UISuite.scala
eb30517 [Andrew Or] Merge github.com:apache/spark into ui-refactor
f4f4cbe [Tathagata Das] More minor fixes.
34bb364 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
252c566 [Tathagata Das] Merge pull request #8 from andrewor14/ui-refactor
e038b4b [Tathagata Das] Addressed Patrick's comments.
125a054 [Andrew Or] Disable serving static resources with gzip
90feb8d [Andrew Or] Address Patrick's comments
89dae36 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
72fe256 [Tathagata Das] Merge pull request #6 from andrewor14/ui-refactor
2fc09c8 [Tathagata Das] Added binary check exclusions
aa396d4 [Andrew Or] Rename tabs and pages (No more IndexPage.scala)
f8e1053 [Tathagata Das] Added Spark and Streaming UI unit tests.
caa5e05 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
585cd65 [Tathagata Das] Merge pull request #5 from andrewor14/ui-refactor
914b8ff [Tathagata Das] Moved utils functions to UIUtils.
548c98c [Andrew Or] Wide refactoring of WebUI, UITab, and UIPage (see commit message)
6de06b0 [Tathagata Das] Merge remote-tracking branch 'apache/master' into streaming-web-ui
ee6543f [Tathagata Das] Minor changes based on Andrew's comments.
fa760fe [Tathagata Das] Fixed long line.
1c0bcef [Tathagata Das] Refactored streaming UI into two files.
1af239b [Tathagata Das] Changed streaming UI to attach itself as a tab with the Spark UI.
827e81a [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
168fe86 [Tathagata Das] Merge pull request #2 from andrewor14/ui-refactor
3e986f8 [Tathagata Das] Merge remote-tracking branch 'apache/master' into streaming-web-ui
c78c92d [Andrew Or] Remove outdated comment
8f7323b [Andrew Or] End of file new lines, indentation, and imports (minor)
0d61ee8 [Andrew Or] Merge branch 'streaming-web-ui' of github.com:tdas/spark into ui-refactor
9a48fa1 [Andrew Or] Allow adding tabs to SparkUI dynamically + add example
61358e3 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into streaming-web-ui
53be2c5 [Tathagata Das] Minor style updates.
ed25dfc [Andrew Or] Generalize SparkUI header to display tabs dynamically
a37ad4f [Andrew Or] Comments, imports and formatting (minor)
cd000b0 [Andrew Or] Merge github.com:apache/spark into ui-refactor
7d57444 [Andrew Or] Refactoring the UI interface to add flexibility
aef4dd5 [Tathagata Das] Added Apache licenses.
db27bad [Tathagata Das] Added last batch processing time to StreamingUI.
4d86e98 [Tathagata Das] Added basic stats to the StreamingUI and refactored the UI to a Page to make it easier to transition to using SparkUI later.
93f1c69 [Tathagata Das] Added network receiver information to the Streaming UI.
56cc7fb [Tathagata Das] First cut implementation of Streaming UI.

(This is for discussion at this point -- I'm not suggesting this should be committed.)

This is what removing fastutil looks like. Much of it is straightforward, like using `java.io` buffered stream classes, and Guava for murmurhash3.

Uses of the `FastByteArrayOutputStream` were a little trickier. In only one case though do I think the change to use `java.io` actually entails an extra array copy.

The rest is using `OpenHashMap` and `OpenHashSet`.  These are now written in terms of more scala-like operations.

`OpenHashMap` is where I made three non-trivial changes to make it work, and they need review:

- It is no longer private
- The key must be a `ClassTag`
- Unless a lot of other code changes, the key type can't enforce being a supertype of `Null`

It all works and tests pass, and I think there is reason to believe it's OK from a speed perspective.

But what about those last changes?

Author: Sean Owen <sowen@cloudera.com>

Closes #266 from srowen/SPARK-1057-alternate and squashes the following commits:

2601129 [Sean Owen] Fix Map return type error not previously caught
ec65502 [Sean Owen] Updates from matei's review
00bc81e [Sean Owen] Remove use of fastutil and replace with use of java.io, spark.util and Guava classes

update the content of Exception when windowDuration is not multiple of parent.slideDuration

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #390 from baishuo/windowdstream and squashes the following commits:

533c968 [baishuo(白硕)] Update WindowedDStream.scala

As with the new vector system in MLlib, we find that it is good to add some new APIs to precess the `RDD[Vector]`. Beside, the former implementation of `computeStat` is not stable which could loss precision, and has the possibility to cause `Nan` in scientific computing, just as said in the [SPARK-1328](https://spark-project.atlassian.net/browse/SPARK-1328).

APIs contain:

* rowMeans(): RDD[Double]
* rowNorm2(): RDD[Double]
* rowSDs(): RDD[Double]
* colMeans(): Vector
* colMeans(size: Int): Vector
* colNorm2(): Vector
* colNorm2(size: Int): Vector
* colSDs(): Vector
* colSDs(size: Int): Vector
* maxOption((Vector, Vector) => Boolean): Option[Vector]
* minOption((Vector, Vector) => Boolean): Option[Vector]
* rowShrink(): RDD[Vector]
* colShrink(): RDD[Vector]

This is working in process now, and some more APIs will add to `LabeledPoint`. Moreover, the implicit declaration will move from `MLUtils` to `MLContext` later.

Author: Xusen Yin <yinxusen@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #268 from yinxusen/vector-statistics and squashes the following commits:

d61363f [Xusen Yin] rebase to latest master
16ae684 [Xusen Yin] fix minor error and remove useless method
10cf5d3 [Xusen Yin] refine some return type
b064714 [Xusen Yin] remove computeStat in MLUtils
cbbefdb [Xiangrui Meng] update multivariate statistical summary interface and clean tests
4eaf28a [Xusen Yin] merge VectorRDDStatistics into RowMatrix
48ee053 [Xusen Yin] fix minor error
e624f93 [Xusen Yin] fix scala style error
1fba230 [Xusen Yin] merge while loop together
69e1f37 [Xusen Yin] remove lazy eval, and minor memory footprint
548e9de [Xusen Yin] minor revision
86522c4 [Xusen Yin] add comments on functions
dc77e38 [Xusen Yin] test sparse vector RDD
18cf072 [Xusen Yin] change def to lazy val to make sure that the computations in function be evaluated only once
f7a3ca2 [Xusen Yin] fix the corner case of maxmin
967d041 [Xusen Yin] full revision with Aggregator class
138300c [Xusen Yin] add new Aggregator class
1376ff4 [Xusen Yin] rename variables and adjust code
4a5c38d [Xusen Yin] add scala doc, refine code and comments
036b7a5 [Xusen Yin] fix the bug of Nan occur
f6e8e9a [Xusen Yin] add sparse vectors test
4cfbadf [Xusen Yin] fix bug of min max
4e4fbd1 [Xusen Yin] separate seqop and combop out as independent functions
a6d5a2e [Xusen Yin] rewrite for only computing non-zero elements
3980287 [Xusen Yin] rename variables
62a2c3e [Xusen Yin] use axpy and in-place if possible
9a75ebd [Xusen Yin] add case class to wrap return values
d816ac7 [Xusen Yin] remove useless APIs
c4651bb [Xusen Yin] remove row-wise APIs and refine code
1338ea1 [Xusen Yin] all-in-one version test passed
cc65810 [Xusen Yin] add parallel mean and variance
9af2e95 [Xusen Yin] refine the code style
ad6c82d [Xusen Yin] add shrink test
e09d5d2 [Xusen Yin] add scala docs and refine shrink method
8ef3377 [Xusen Yin] pass all tests
28cf060 [Xusen Yin] fix error of column means
54b19ab [Xusen Yin] add new API to shrink RDD[Vector]
8c6c0e1 [Xusen Yin] add basic statistics

Make coalesce test deterministic by setting pre-defined seeds. (Saw random failures in other PRs.)

Author: Xiangrui Meng <meng@databricks.com>

Closes #387 from mengxr/fix-random and squashes the following commits:

59bc16f [Xiangrui Meng] make coalesce test deterministic in RDDSuite

This was causing some errors with pull request tests.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #393 from pwendell/hotfix and squashes the following commits:

6201dd3 [Patrick Wendell] HOTFIX: Ignore python metastore files in RAT checks.

This PR implements a generic version of `AreaUnderCurve` using the `RDD.sliding` implementation from https://github.com/apache/spark/pull/136 . It also contains refactoring of https://github.com/apache/spark/pull/160 for binary classification evaluation.

Author: Xiangrui Meng <meng@databricks.com>

Closes #364 from mengxr/auc and squashes the following commits:

a05941d [Xiangrui Meng] replace TP/FP/TN/FN by their full names
3f42e98 [Xiangrui Meng] add (0, 0), (1, 1) to roc, and (0, 1) to pr
fb4b6d2 [Xiangrui Meng] rename Evaluator to Metrics and add more metrics
b1b7dab [Xiangrui Meng] fix code styles
9dc3518 [Xiangrui Meng] add tests for BinaryClassificationEvaluator
ca31da5 [Xiangrui Meng] remove PredictionAndResponse
3d71525 [Xiangrui Meng] move binary evalution classes to evaluation.binary
8f78958 [Xiangrui Meng] add PredictionAndResponse
dda82d5 [Xiangrui Meng] add confusion matrix
aa7e278 [Xiangrui Meng] add initial version of binary classification evaluator
221ebce [Xiangrui Meng] add a new test to sliding
a920865 [Xiangrui Meng] Merge branch 'sliding' into auc
a9b250a [Xiangrui Meng] move sliding to mllib
cab9a52 [Xiangrui Meng] use last for the last element
db6cb30 [Xiangrui Meng] remove unnecessary toSeq
9916202 [Xiangrui Meng] change RDD.sliding return type to RDD[Seq[T]]
284d991 [Xiangrui Meng] change SlidedRDD to SlidingRDD
c1c6c22 [Xiangrui Meng] add AreaUnderCurve
65461b2 [Xiangrui Meng] Merge branch 'sliding' into auc
5ee6001 [Xiangrui Meng] add TODO
d2a600d [Xiangrui Meng] add sliding to rdd

(a) Deleted an outdated line from the docs
(b) Removed a work around that is no longer necessary given the mesos version bump.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #382 from pwendell/maven-clean and squashes the following commits:

f0447fa [Patrick Wendell] Minor doc clean-up

Author: Thomas Graves <tgraves@apache.org>

Closes #344 from tgravescs/SPARK-1417 and squashes the following commits:

c450b5f [Thomas Graves] fix test
e1c1d7e [Thomas Graves] add missing $ to appUIAddress
e982ddb [Thomas Graves] use appUIHostPort in appUIAddress
0803ec2 [Thomas Graves] Review comment updates - remove extra newline, simplify assert in test
658a8ec [Thomas Graves] Add a appUIHostPort routine
0614208 [Thomas Graves] Fix test
2a6b1b7 [Thomas Graves] SPARK-1417: Spark on Yarn - spark UI link from resourcemanager is broken

1. Adds a separate endpoint for the killing logic that is outside of a page.
2. Narrows the scope of the killingEnabled tracking.
3. Some style improvements.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #386 from pwendell/kill-link and squashes the following commits:

8efe02b [Patrick Wendell] Improvements to task killing in the UI.

Mainly ported from branch-0.9.

Author: Harvey Feng <hyfeng224@gmail.com>

Closes #385 from harveyfeng/0.9.1-ec2 and squashes the following commits:

769ac2f [Harvey Feng] Add Spark v0.9.1 to ec2 launch script and use it as the default

The Mesos backend uses this property when setting up a slave process.  It is similarly set in the Scala repl (org.apache.spark.repl.SparkILoop), but I couldn't find any analogous for pyspark.

Author: Ivan Wick <ivanwick+github@gmail.com>

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

Closes #311 from ivanwick/master and squashes the following commits:

da0c3e4 [Ivan Wick] Set spark.executor.uri from environment variable (needed by Mesos)

Author: Sundeep Narravula <sundeepn@superduel.local>
Author: Sundeep Narravula <sundeepn@dhcpx-204-110.corp.yahoo.com>

Closes #246 from sundeepn/uikilljob and squashes the following commits:

5fdd0e2 [Sundeep Narravula] Fix test string
f6fdff1 [Sundeep Narravula] Format fix; reduced line size to less than 100 chars
d1daeb9 [Sundeep Narravula] Incorporating review comments.
8d97923 [Sundeep Narravula] Ability to kill jobs thru the UI. This behavior can be turned on be settings the following variable: spark.ui.killEnabled=true (default=false) Adding DAGScheduler event StageCancelled and corresponding handlers. Added cancellation reason to handlers.

Author: Michael Armbrust <michael@databricks.com>

Closes #378 from marmbrus/columnPruning and squashes the following commits:

779da56 [Michael Armbrust] More consistent naming.
1a4e9ea [Michael Armbrust] More comments.
2f4e7b9 [Michael Armbrust] Improve column pruning in the optimizer.

stack these together in a commit else they show up chunk by chunk in different commits.

Author: Sandeep <sandeep@techaddict.me>

Closes #380 from techaddict/white_space and squashes the following commits:

b58f294 [Sandeep] Remove Unnecessary Whitespace's

http://stackoverflow.com/questions/9699071/what-is-the-javas-internal-represention-for-string-modified-utf-8-utf-16

Author: Andrew Ash <andrew@andrewash.com>

Closes #384 from ash211/patch-2 and squashes the following commits:

da1b0be [Andrew Ash] Update tuning.md

This reverts commit 12c077d5.

Author: Sandeep <sandeep@techaddict.me>

Closes #356 from techaddict/1428 and squashes the following commits:

3bdf5f6 [Sandeep] SPARK-1428: MLlib should convert non-float64 NumPy arrays to float64 instead of complaining

The new feature of event logging, introduced in #42, allows the user to persist the details of his/her Spark application to storage, and later replay these events to reconstruct an after-the-fact SparkUI.
Currently, however, a persisted UI can only be rendered through the standalone Master. This greatly limits the use case of this new feature as many people also run Spark on Yarn / Mesos.

This PR introduces a new entity called the HistoryServer, which, given a log directory, keeps track of all completed applications independently of a Spark Master. Unlike Master, the HistoryServer needs not be running while the application is still running. It is relatively light-weight in that it only maintains static information of applications and performs no scheduling.

To quickly test it out, generate event logs with ```spark.eventLog.enabled=true``` and run ```sbin/start-history-server.sh <log-dir-path>```. Your HistoryServer awaits on port 18080.

Comments and feedback are most welcome.

---

A few other changes introduced in this PR include refactoring the WebUI interface, which is beginning to have a lot of duplicate code now that we have added more functionality to it. Two new SparkListenerEvents have been introduced (SparkListenerApplicationStart/End) to keep track of application name and start/finish times. This PR also clarifies the semantics of the ReplayListenerBus introduced in #42.

A potential TODO in the future (not part of this PR) is to render live applications in addition to just completed applications. This is useful when applications fail, a condition that our current HistoryServer does not handle unless the user manually signals application completion (by creating the APPLICATION_COMPLETION file). Handling live applications becomes significantly more challenging, however, because it is now necessary to render the same SparkUI multiple times. To avoid reading the entire log every time, which is inefficient, we must handle reading the log from where we previously left off, but this becomes fairly complicated because we must deal with the arbitrary behavior of each input stream.

Author: Andrew Or <andrewor14@gmail.com>

Closes #204 from andrewor14/master and squashes the following commits:

7b7234c [Andrew Or] Finished -> Completed
b158d98 [Andrew Or] Address Patrick's comments
69d1b41 [Andrew Or] Do not block on posting SparkListenerApplicationEnd
19d5dd0 [Andrew Or] Merge github.com:apache/spark
f7f5bf0 [Andrew Or] Make history server's web UI port a Spark configuration
2dfb494 [Andrew Or] Decouple checking for application completion from replaying
d02dbaa [Andrew Or] Expose Spark version and include it in event logs
2282300 [Andrew Or] Add documentation for the HistoryServer
567474a [Andrew Or] Merge github.com:apache/spark
6edf052 [Andrew Or] Merge github.com:apache/spark
19e1fb4 [Andrew Or] Address Thomas' comments
248cb3d [Andrew Or] Limit number of live applications + add configurability
a3598de [Andrew Or] Do not close file system with ReplayBus + fix bind address
bc46fc8 [Andrew Or] Merge github.com:apache/spark
e2f4ff9 [Andrew Or] Merge github.com:apache/spark
050419e [Andrew Or] Merge github.com:apache/spark
81b568b [Andrew Or] Fix strange error messages...
0670743 [Andrew Or] Decouple page rendering from loading files from disk
1b2f391 [Andrew Or] Minor changes
a9eae7e [Andrew Or] Merge branch 'master' of github.com:apache/spark
d5154da [Andrew Or] Styling and comments
5dbfbb4 [Andrew Or] Merge branch 'master' of github.com:apache/spark
60bc6d5 [Andrew Or] First complete implementation of HistoryServer (only for finished apps)
7584418 [Andrew Or] Report application start/end times to HistoryServer
8aac163 [Andrew Or] Add basic application table
c086bd5 [Andrew Or] Add HistoryServer and scripts ++ Refactor WebUI interface

Author: witgo <witgo@qq.com>

Closes #325 from witgo/SPARK-1413 and squashes the following commits:

e57cd8e [witgo] use scala reflection to access and call the SLF4JBridgeHandler  methods
45c8f40 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
5e35d87 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
0d5f819 [witgo] review commit
45e5b70 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
fa69dcf [witgo] Merge branch 'master' into SPARK-1413
3c98dc4 [witgo] Merge branch 'master' into SPARK-1413
38160cb [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
ba09bcd [witgo] remove set the parquet log level
a63d574 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
5231ecd [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
3feb635 [witgo] parquet logger use parent handler
fa00d5d [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
8bb6ffd [witgo] enableLogForwarding note fix
edd9630 [witgo]  move to
f447f50 [witgo] merging master
5ad52bd [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413
76670c1 [witgo] review commit
70f3c64 [witgo] Fix SPARK-1413

This reverts commit 8ca3b2bc.

Spark examples should exit nice using SparkContext.stop() method, rather than System.exit
System.exit can cause issues like in SPARK-1407

Author: Sandeep <sandeep@techaddict.me>

Closes #370 from techaddict/1446 and squashes the following commits:

e9234cf [Sandeep] SPARK-1446: Spark examples should not do a System.exit Spark examples should exit nice using SparkContext.stop() method, rather than System.exit System.exit can cause issues like in SPARK-1407

[SPARK-729](https://spark-project.atlassian.net/browse/SPARK-729) concerns when free variables in closure arguments to transformations are captured.  Currently, it is possible for closures to get the environment in which they are serialized (not the environment in which they are created).  There are a few possible approaches to solving this problem and this PR will discuss some of them.  The approach I took has the advantage of being simple, obviously correct, and minimally-invasive, but it preserves something that has been bothering me about Spark's closure handling, so I'd like to discuss an alternative and get some feedback on whether or not it is worth pursuing.

## What I did

The basic approach I took depends on the work I did for #143, and so this PR is based atop that.  Specifically: #143 modifies `ClosureCleaner.clean` to preemptively determine whether or not closures are serializable immediately upon closure cleaning (rather than waiting for an job involving that closure to be scheduled).  Thus non-serializable closure exceptions will be triggered by the line defining the closure rather than triggered where the closure is used.

Since the easiest way to determine whether or not a closure is serializable is to attempt to serialize it, the code in #143 is creating a serialized closure as part of `ClosureCleaner.clean`.  `clean` currently modifies its argument, but the method in `SparkContext` that wraps it to return a value (a reference to the modified-in-place argument).  This branch modifies `ClosureCleaner.clean` so that it returns a value:  if it is cleaning a serializable closure, it returns the result of deserializing its serialized argument; therefore it is returning a closure with an environment captured at cleaning time.  `SparkContext.clean` then returns the result of `ClosureCleaner.clean`, rather than a reference to its modified-in-place argument.

I've added tests for this behavior (777a1bc).  The pull request as it stands, given the changes in #143, is nearly trivial.  There is some overhead from deserializing the closure, but it is minimal and the benefit of obvious operational correctness (vs. a more sophisticated but harder-to-validate transformation in `ClosureCleaner`) seems pretty important.  I think this is a fine way to solve this problem, but it's not perfect.

## What we might want to do

The thing that has been bothering me about Spark's handling of closures is that it seems like we should be able to statically ensure that cleaning and serialization happen exactly once for a given closure.  If we serialize a closure in order to determine whether or not it is serializable, we should be able to hang on to the generated byte buffer and use it instead of re-serializing the closure later.  By replacing closures with instances of a sum type that encodes whether or not a closure has been cleaned or serialized, we could handle clean, to-be-cleaned, and serialized closures separately with case matches.  Here's a somewhat-concrete sketch (taken from my git stash) of what this might look like:

```scala
package org.apache.spark.util

import java.nio.ByteBuffer
import scala.reflect.ClassManifest

sealed abstract class ClosureBox[T] { def func: T }
final case class RawClosure[T](func: T) extends ClosureBox[T] {}
final case class CleanedClosure[T](func: T) extends ClosureBox[T] {}
final case class SerializedClosure[T](func: T, bytebuf: ByteBuffer) extends ClosureBox[T] {}

object ClosureBoxImplicits {
  implicit def closureBoxFromFunc[T <: AnyRef](fun: T) = new RawClosure[T](fun)
}
```

With these types declared, we'd be able to change `ClosureCleaner.clean` to take a `ClosureBox[T=>U]` (possibly generated by implicit conversion) and return a `ClosureBox[T=>U]` (either a `CleanedClosure[T=>U]` or a `SerializedClosure[T=>U]`, depending on whether or not serializability-checking was enabled) instead of a `T=>U`.  A case match could thus short-circuit cleaning or serializing closures that had already been cleaned or serialized (both in `ClosureCleaner` and in the closure serializer).  Cleaned-and-serialized closures would be represented by a boxed tuple of the original closure and a serialized copy (complete with an environment quiesced at transformation time).  Additional implicit conversions could convert from `ClosureBox` instances to the underlying function type where appropriate.  Tracking this sort of state in the type system seems like the right thing to do to me.

### Why we might not want to do that

_It's pretty invasive._  Every function type used by every `RDD` subclass would have to change to reflect that they expected a `ClosureBox[T=>U]` instead of a `T=>U`.  This obscures what's going on and is not a little ugly.  Although I really like the idea of using the type system to enforce the clean-or-serialize once discipline, it might not be worth adding another layer of types (even if we could hide some of the extra boilerplate with judicious application of implicit conversions).

_It statically guarantees a property whose absence is unlikely to cause any serious problems as it stands._  It appears that all closures are currently dynamically cleaned once and it's not obvious that repeated closure-cleaning is likely to be a problem in the future.  Furthermore, serializing closures is relatively cheap, so doing it once to check for serialization and once again to actually ship them across the wire doesn't seem like a big deal.

Taken together, these seem like a high price to pay for statically guaranteeing that closures are operated upon only once.

## Other possibilities

I felt like the serialize-and-deserialize approach was best due to its obvious simplicity.  But it would be possible to do a more sophisticated transformation within `ClosureCleaner.clean`.  It might also be possible for `clean` to modify its argument in a way so that whether or not a given closure had been cleaned would be apparent upon inspection; this would buy us some of the operational benefits of the `ClosureBox` approach but not the static cleanliness.

I'm interested in any feedback or discussion on whether or not the problems with the type-based approach indeed outweigh the advantage, as well as of approaches to this issue and to closure handling in general.

Author: William Benton <willb@redhat.com>

Closes #189 from willb/spark-729 and squashes the following commits:

f4cafa0 [William Benton] Stylistic changes and cleanups
b3d9c86 [William Benton] Fixed style issues in tests
9b56ce0 [William Benton] Added array-element capture test
97e9d91 [William Benton] Split closure-serializability failure tests
12ef6e3 [William Benton] Skip proactive closure capture for runJob
8ee3ee7 [William Benton] Predictable closure environment capture
12c63a7 [William Benton] Added tests for variable capture in closures
d6e8dd6 [William Benton] Don't check serializability of DStream transforms.
4ecf841 [William Benton] Make proactive serializability checking optional.
d8df3db [William Benton] Adds proactive closure-serializablilty checking
21b4b06 [William Benton] Test cases for SPARK-897.
d5947b3 [William Benton] Ensure assertions in Graph.apply are asserted.

Remove empty line after :: DeveloperApi/Experimental :: in comments to make the original doc show up in the preview of the generated html docs. Thanks @andrewor14 !

Author: Xiangrui Meng <meng@databricks.com>

Closes #373 from mengxr/api and squashes the following commits:

9c35bdc [Xiangrui Meng] remove the empty line after :: DeveloperApi/Experimental ::

Author: Kan Zhang <kzhang@apache.org>

Closes #366 from kanzhang/SPARK-1407 and squashes the following commits:

cd0629f [Kan Zhang] code refactoring and adding test
b073ee6 [Kan Zhang] SPARK-1407 drain event queue before stopping event logger

Annotate developer and experimental APIs in MLlib.

Author: Xiangrui Meng <meng@databricks.com>

Closes #298 from mengxr/api and squashes the following commits:

13390e8 [Xiangrui Meng] Merge branch 'master' into api
dc4cbb3 [Xiangrui Meng] mark distribute matrices experimental
6b9f8e2 [Xiangrui Meng] add Experimental annotation
8773d0d [Xiangrui Meng] add DeveloperApi annotation
da31733 [Xiangrui Meng] update developer and experimental tags
555e0fe [Xiangrui Meng] Merge branch 'master' into api
ef1a717 [Xiangrui Meng] mark some constructors private add default parameters to JavaDoc
00ffbcc [Xiangrui Meng] update tree API annotation
0b674fa [Xiangrui Meng] mark decision tree APIs
86b9e34 [Xiangrui Meng] one pass over APIs of GLMs, NaiveBayes, and ALS
f21d862 [Xiangrui Meng] Merge branch 'master' into api
2b133d6 [Xiangrui Meng] intial annotation of developer and experimental apis

This patch marks some existing classes as private[spark] and adds two types of API annotations:
- `EXPERIMENTAL API` = experimental user-facing module
- `DEVELOPER API - UNSTABLE` = developer-facing API that might change

There is some discussion of the different mechanisms for doing this here:
https://issues.apache.org/jira/browse/SPARK-1081

I was pretty aggressive with marking things private. Keep in mind that if we want to open something up in the future we can, but we can never reduce visibility.

A few notes here:
- In the past we've been inconsistent with the visiblity of the X-RDD classes. This patch marks them private whenever there is an existing function in RDD that can directly creat them (e.g. CoalescedRDD and rdd.coalesce()). One trade-off here is users can't subclass them.
- Noted that compression and serialization formats don't have to be wire compatible across versions.
- Compression codecs and serialization formats are semi-private as users typically don't instantiate them directly.
- Metrics sources are made private - user only interacts with them through Spark's reflection

Author: Patrick Wendell <pwendell@gmail.com>
Author: Andrew Or <andrewor14@gmail.com>

Closes #274 from pwendell/private-apis and squashes the following commits:

44179e4 [Patrick Wendell] Merge remote-tracking branch 'apache-github/master' into private-apis
042c803 [Patrick Wendell] spark.annotations -> spark.annotation
bfe7b52 [Patrick Wendell] Adding experimental for approximate counts
8d0c873 [Patrick Wendell] Warning in SparkEnv
99b223a [Patrick Wendell] Cleaning up annotations
e849f64 [Patrick Wendell] Merge pull request #2 from andrewor14/annotations
982a473 [Andrew Or] Generalize jQuery matching for non Spark-core API docs
a01c076 [Patrick Wendell] Merge pull request #1 from andrewor14/annotations
c1bcb41 [Andrew Or] DeveloperAPI -> DeveloperApi
0d48908 [Andrew Or] Comments and new lines (minor)
f3954e0 [Andrew Or] Add identifier tags in comments to work around scaladocs bug
99192ef [Andrew Or] Dynamically add badges based on annotations
824011b [Andrew Or] Add support for injecting arbitrary JavaScript to API docs
037755c [Patrick Wendell] Some changes after working with andrew or
f7d124f [Patrick Wendell] Small fixes
c318b24 [Patrick Wendell] Use CSS styles
e4c76b9 [Patrick Wendell] Logging
f390b13 [Patrick Wendell] Better visibility for workaround constructors
d6b0afd [Patrick Wendell] Small chang to existing constructor
403ba52 [Patrick Wendell] Style fix
870a7ba [Patrick Wendell] Work around for SI-8479
7fb13b2 [Patrick Wendell] Changes to UnionRDD and EmptyRDD
4a9e90c [Patrick Wendell] EXPERIMENTAL API --> EXPERIMENTAL
c581dce [Patrick Wendell] Changes after building against Shark.
8452309 [Patrick Wendell] Style fixes
1ed27d2 [Patrick Wendell] Formatting and coloring of badges
cd7a465 [Patrick Wendell] Code review feedback
2f706f1 [Patrick Wendell] Don't use floats
542a736 [Patrick Wendell] Small fixes
cf23ec6 [Patrick Wendell] Marking GraphX as alpha
d86818e [Patrick Wendell] Another naming change
5a76ed6 [Patrick Wendell] More visiblity clean-up
42c1f09 [Patrick Wendell] Using better labels
9d48cbf [Patrick Wendell] Initial pass

This is to refactor interfaces for matrices backed by RDDs. It would be better if we have a clear separation of local matrices and those backed by RDDs. Right now, we have

1. `org.apache.spark.mllib.linalg.SparseMatrix`, which is a wrapper over an RDD of matrix entries, i.e., coordinate list format.
2. `org.apache.spark.mllib.linalg.TallSkinnyDenseMatrix`, which is a wrapper over RDD[Array[Double]], i.e. row-oriented format.

We will see naming collision when we introduce local `SparseMatrix`, and the name `TallSkinnyDenseMatrix` is not exact if we switch to `RDD[Vector]` from `RDD[Array[Double]]`. It would be better to have "RDD" in the class name to suggest that operations may trigger jobs.

The proposed names are (all under `org.apache.spark.mllib.linalg.rdd`):

1. `RDDMatrix`: trait for matrices backed by one or more RDDs
2. `CoordinateRDDMatrix`: wrapper of `RDD[(Long, Long, Double)]`
3. `RowRDDMatrix`: wrapper of `RDD[Vector]` whose rows do not have special ordering
4. `IndexedRowRDDMatrix`: wrapper of `RDD[(Long, Vector)]` whose rows are associated with indices

The current code also introduces local matrices.

Author: Xiangrui Meng <meng@databricks.com>

Closes #296 from mengxr/mat and squashes the following commits:

24d8294 [Xiangrui Meng] fix for groupBy returning Iterable
bfc2b26 [Xiangrui Meng] merge master
8e4f1f5 [Xiangrui Meng] Merge branch 'master' into mat
0135193 [Xiangrui Meng] address Reza's comments
03cd7e1 [Xiangrui Meng] add pca/gram to IndexedRowMatrix add toBreeze to DistributedMatrix for test simplify tests
b177ff1 [Xiangrui Meng] address Matei's comments
be119fe [Xiangrui Meng] rename m/n to numRows/numCols for local matrix add tests for matrices
b881506 [Xiangrui Meng] rename SparkPCA/SVD to TallSkinnyPCA/SVD
e7d0d4a [Xiangrui Meng] move IndexedRDDMatrixRow to IndexedRowRDDMatrix
0d1491c [Xiangrui Meng] fix test errors
a85262a [Xiangrui Meng] rename RDDMatrixRow to IndexedRDDMatrixRow
b8b6ac3 [Xiangrui Meng] Remove old code
4cf679c [Xiangrui Meng] port pca to RowRDDMatrix, and add multiply and covariance
7836e2f [Xiangrui Meng] initial refactoring of matrices backed by RDDs

I still need to do a small bit of re-factoring [mostly the one Java file I'll switch it back to a Scala file and use it in both the close loaders], but comments on other things I should do would be great.

Author: Holden Karau <holden@pigscanfly.ca>

Closes #217 from holdenk/spark-939-allow-user-jars-to-take-precedence-over-spark-jars and squashes the following commits:

cf0cac9 [Holden Karau] Fix the executorclassloader
1955232 [Holden Karau] Fix long line in TestUtils
8f89965 [Holden Karau] Fix tests for new class name
7546549 [Holden Karau] CR feedback, merge some of the testutils methods down, rename the classloader
644719f [Holden Karau] User the class generator for the repl class loader tests too
f0b7114 [Holden Karau] Fix the core/src/test/scala/org/apache/spark/executor/ExecutorURLClassLoaderSuite.scala tests
204b199 [Holden Karau] Fix the generated classes
9f68f10 [Holden Karau] Start rewriting the ExecutorURLClassLoaderSuite to not use the hard coded classes
858aba2 [Holden Karau] Remove a bunch of test junk
261aaee [Holden Karau] simplify executorurlclassloader a bit
7a7bf5f [Holden Karau] CR feedback
d4ae848 [Holden Karau] rewrite component into scala
aa95083 [Holden Karau] CR feedback
7752594 [Holden Karau] re-add https comment
a0ef85a [Holden Karau] Fix style issues
125ea7f [Holden Karau] Easier to just remove those files, we don't need them
bb8d179 [Holden Karau] Fix issues with the repl class loader
241b03d [Holden Karau] fix my rat excludes
a343350 [Holden Karau] Update rat-excludes and remove a useless file
d90d217 [Holden Karau] Fix fall back with custom class loader and add a test for it
4919bf9 [Holden Karau] Fix parent calling class loader issue
8a67302 [Holden Karau] Test are good
9e2d236 [Holden Karau] It works comrade
691ee00 [Holden Karau] It works ish
dc4fe44 [Holden Karau] Does not depend on being in my home directory
47046ff [Holden Karau] Remove bad import'
22d83cb [Holden Karau] Add a test suite for the executor url class loader suite
7ef4628 [Holden Karau] Clean up
792d961 [Holden Karau] Almost works
16aecd1 [Holden Karau] Doesn't quite work
8d2241e [Holden Karau] Adda FakeClass for testing ClassLoader precedence options
648b559 [Holden Karau] Both class loaders compile. Now for testing
e1d9f71 [Holden Karau] One loader workers.

This is a patch to address @mateiz 's comment in https://github.com/apache/spark/pull/245

MLUtils#loadLibSVMData uses an anonymous function for the label parser. Java users won't like it. So I make a trait for LabelParser and provide two implementations: binary and multiclass.

Author: Xiangrui Meng <meng@databricks.com>

Closes #345 from mengxr/label-parser and squashes the following commits:

ac44409 [Xiangrui Meng] use singleton objects for label parsers
3b1a7c6 [Xiangrui Meng] add tests for label parsers
c2e571c [Xiangrui Meng] rename LabelParser.apply to LabelParser.parse use extends for singleton
11c94e0 [Xiangrui Meng] add return types
7f8eb36 [Xiangrui Meng] change labelParser from annoymous function to trait

Author: Holden Karau <holden@pigscanfly.ca>

Closes #242 from holdenk/spark-1320-cogroupandgroupshouldpassiterator and squashes the following commits:

f289536 [Holden Karau] Fix bad merge, should have been Iterable rather than Iterator
77048f8 [Holden Karau] Fix merge up to master
d3fe909 [Holden Karau] use toSeq instead
7a092a3 [Holden Karau] switch resultitr to resultiterable
eb06216 [Holden Karau] maybe I should have had a coffee first. use correct import for guava iterables
c5075aa [Holden Karau] If guava 14 had iterables
2d06e10 [Holden Karau] Fix Java 8 cogroup tests for the new API
11e730c [Holden Karau] Fix streaming tests
66b583d [Holden Karau] Fix the core test suite to compile
4ed579b [Holden Karau] Refactor from iterator to iterable
d052c07 [Holden Karau] Python tests now pass with iterator pandas
3bcd81d [Holden Karau] Revert "Try and make pickling list iterators work"
cd1e81c [Holden Karau] Try and make pickling list iterators work
c60233a [Holden Karau] Start investigating moving to iterators for python API like the Java/Scala one. tl;dr: We will have to write our own iterator since the default one doesn't pickle well
88a5cef [Holden Karau] Fix cogroup test in JavaAPISuite for streaming
a5ee714 [Holden Karau] oops, was checking wrong iterator
e687f21 [Holden Karau] Fix groupbykey test in JavaAPISuite of streaming
ec8cc3e [Holden Karau] Fix test issues\!
4b0eeb9 [Holden Karau] Switch cast in PairDStreamFunctions
fa395c9 [Holden Karau] Revert "Add a join based on the problem in SVD"
ec99e32 [Holden Karau] Revert "Revert this but for now put things in list pandas"
b692868 [Holden Karau] Revert
7e533f7 [Holden Karau] Fix the bug
8a5153a [Holden Karau] Revert me, but we have some stuff to debug
b4e86a9 [Holden Karau] Add a join based on the problem in SVD
c4510e2 [Holden Karau] Revert this but for now put things in list pandas
b4e0b1d [Holden Karau] Fix style issues
71e8b9f [Holden Karau] I really need to stop calling size on iterators, it is the path of sadness.
b1ae51a [Holden Karau] Fix some of the types in the streaming JavaAPI suite. Probably still needs more work
37888ec [Holden Karau] core/tests now pass
249abde [Holden Karau] org.apache.spark.rdd.PairRDDFunctionsSuite passes
6698186 [Holden Karau] Revert "I think this might be a bad rabbit hole. Started work to make CoGroupedRDD use iterator and then went crazy"
fe992fe [Holden Karau] hmmm try and fix up basic operation suite
172705c [Holden Karau] Fix Java API suite
caafa63 [Holden Karau] I think this might be a bad rabbit hole. Started work to make CoGroupedRDD use iterator and then went crazy
88b3329 [Holden Karau] Fix groupbykey to actually give back an iterator
4991af6 [Holden Karau] Fix some tests
be50246 [Holden Karau] Calling size on an iterator is not so good if we want to use it after
687ffbc [Holden Karau] This is the it compiles point of replacing Seq with Iterator and JList with JIterator in the groupby and cogroup signatures

Mesos 0.13.0 was released 6 months ago.
Upgrade Mesos dependency to 0.17.0

Author: Sandeep <sandeep@techaddict.me>

Closes #355 from techaddict/mesos_update and squashes the following commits:

f1abeee [Sandeep] SPARK-1433: Upgrade Mesos dependency to 0.17.0 Mesos 0.13.0 was released 6 months ago. Upgrade Mesos dependency to 0.17.0

[I wanted to post this for folks to comment but it depends on (and thus includes the changes in) a currently outstanding PR, #305.  You can look at just the second commit: https://github.com/kayousterhout/spark-1/commit/93f08baf731b9eaf5c9792a5373560526e2bccac to see just the changes relevant to this PR]

Previously, when stages fail or get cancelled, the SparkListener is only notified
indirectly through the SparkListenerJobEnd, where we sometimes pass in a single
stage that failed.  This worked before job cancellation, because jobs would only fail
due to a single stage failure.  However, with job cancellation, multiple running stages
can fail when a job gets cancelled.  Right now, this is not handled correctly, which
results in stages that get stuck in the “Running Stages” window in the UI even
though they’re dead.

This PR changes the SparkListenerStageCompleted event to a SparkListenerStageEnded
event, and uses this event to tell SparkListeners when stages fail in addition to when
they complete successfully.  This change is NOT publicly backward compatible for two
reasons.  First, it changes the SparkListener interface.  We could alternately add a new event,
SparkListenerStageFailed, and keep the existing SparkListenerStageCompleted.  However,
this is less consistent with the listener events for tasks / jobs ending, and will result in some
code duplication for listeners (because failed and completed stages are handled in similar
ways).  Note that I haven’t finished updating the JSON code to correctly handle the new event
because I’m waiting for feedback on whether this is a good or bad idea (hence the “WIP”).

It is also not backwards compatible because it changes the publicly visible JobWaiter.jobFailed()
method to no longer include a stage that caused the failure.  I think this change should definitely
stay, because with cancellation (as described above), a failure isn’t necessarily caused by a
single stage.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #309 from kayousterhout/stage_cancellation and squashes the following commits:

5533ecd [Kay Ousterhout] Fixes in response to Mark's review
320c7c7 [Kay Ousterhout] Notify SparkListeners when stages fail or are cancelled.

This was added to the check for the assembly jar, forgot it for the datanucleus jars.

Author: Aaron Davidson <aaron@databricks.com>

Closes #361 from aarondav/cc and squashes the following commits:

8facc16 [Aaron Davidson] SPARK-1445: compute-classpath should not print error if lib_managed not found

Author: Kan Zhang <kzhang@apache.org>

Closes #318 from kanzhang/SPARK-1348 and squashes the following commits:

e625a5f [Kan Zhang] reverting the changes to startJettyServer()
7a8084e [Kan Zhang] SPARK-1348 binding Master, Worker, and App Web UI to all interfaces

Small nit cleanup to remove extra semicolon and unused import in Yarn's stable ApplicationMaster (it bothers me every time I saw it)

Author: Henry Saputra <hsaputra@apache.org>

Closes #358 from hsaputra/nitcleanup_removesemicolon_import_applicationmaster and squashes the following commits:

bffb685 [Henry Saputra] Remove extra semicolon in import statement and unused import in ApplicationMaster.scala