[SPARK-2521] Broadcast RDD object (instead of sending it along with every task)

This is a resubmission of #1452. It was reverted because it broke the build.

Currently (as of Spark 1.0.1), Spark sends RDD object (which contains closures) using Akka along with the task itself to the executors. This is inefficient because all tasks in the same stage use the same RDD object, but we have to send RDD object multiple times to the executors. This is especially bad when a closure references some variable that is very large. The current design led to users having to explicitly broadcast large variables.

The patch uses broadcast to send RDD objects and the closures to executors, and use Akka to only send a reference to the broadcast RDD/closure along with the partition specific information for the task. For those of you who know more about the internals, Spark already relies on broadcast to send the Hadoop JobConf every time it uses the Hadoop input, because the JobConf is large.

The user-facing impact of the change include:

1. Users won't need to decide what to broadcast anymore, unless they would want to use a large object multiple times in different operations
2. Task size will get smaller, resulting in faster scheduling and higher task dispatch throughput.

In addition, the change will simplify some internals of Spark, eliminating the need to maintain task caches and the complex logic to broadcast JobConf (which also led to a deadlock recently).

A simple way to test this:
```scala
val a = new Array[Byte](1000*1000); scala.util.Random.nextBytes(a);
sc.parallelize(1 to 1000, 1000).map { x => a; x }.groupBy { x => a; x }.count
```

Numbers on 3 r3.8xlarge instances on EC2
```
master branch: 5.648436068 s, 4.715361895 s, 5.360161877 s
with this change: 3.416348793 s, 1.477846558 s, 1.553432156 s
```

Author: Reynold Xin <rxin@apache.org>

Closes #1498 from rxin/broadcast-task and squashes the following commits:

f7364db [Reynold Xin] Code review feedback.
f8535dc [Reynold Xin] Fixed the style violation.
252238d [Reynold Xin] Serialize the final task closure as well as ShuffleDependency in taskBinary.
111007d [Reynold Xin] Fix broadcast tests.
797c247 [Reynold Xin] Properly send SparkListenerStageSubmitted and SparkListenerStageCompleted.
bab1d8b [Reynold Xin] Check for NotSerializableException in submitMissingTasks.
cf38450 [Reynold Xin] Use TorrentBroadcastFactory.
991c002 [Reynold Xin] Use HttpBroadcast.
de779f8 [Reynold Xin] Fix TaskContextSuite.
cc152fc [Reynold Xin] Don't cache the RDD broadcast variable.
d256b45 [Reynold Xin] Fixed unit test failures. One more to go.
cae0af3 [Reynold Xin] [SPARK-2521] Broadcast RDD object (instead of sending it along with every task).
[SPARK-2747] git diff --dirstat can miss sql changes and not run Hive tests

dev/run-tests use "git diff --dirstat master" to check whether sql is changed. However, --dirstat won't show sql if sql's change is negligible (e.g. 1k loc change in core, and only 1 loc change in hive).

We should use "git diff --name-only master" instead.

Author: Reynold Xin <rxin@apache.org>

Closes #1656 from rxin/hiveTest and squashes the following commits:

f5eab9f [Reynold Xin] [SPARK-2747] git diff --dirstat can miss sql changes and not run Hive tests.
Avoid numerical instability

This avoids basically doing 1 - 1, for example:

```python
>>> from math import exp
>>> margin = -40
>>> 1 - 1 / (1 + exp(margin))
0.0
>>> exp(margin) / (1 + exp(margin))
4.248354255291589e-18
>>>
```

Author: Naftali Harris <naftaliharris@gmail.com>

Closes #1652 from naftaliharris/patch-2 and squashes the following commits:

0d55a9f [Naftali Harris] Avoid numerical instability
[SPARK-2544][MLLIB] Improve ALS algorithm resource usage

Author: GuoQiang Li <witgo@qq.com>
Author: witgo <witgo@qq.com>

Closes #929 from witgo/improve_als and squashes the following commits:

ea25033 [GuoQiang Li] checkpoint products 3,6,9 ...
154dccf [GuoQiang Li] checkpoint products only
c5779ff [witgo] Improve ALS algorithm resource usage
[SPARK-2746] Set SBT_MAVEN_PROFILES only when it is not set explicitly by the user.

Author: Reynold Xin <rxin@apache.org>

Closes #1655 from rxin/SBT_MAVEN_PROFILES and squashes the following commits:

b268c4b [Reynold Xin] [SPARK-2746] Set SBT_MAVEN_PROFILES only when it is not set explicitly by the user.
Wrap FWDIR in quotes.
Wrap FWDIR in quotes in dev/check-license.
More wrapping FWDIR in quotes.
[SQL] Fix compiling of catalyst docs.

Author: Michael Armbrust <michael@databricks.com>

Closes #1653 from marmbrus/fixDocs and squashes the following commits:

0aa1feb [Michael Armbrust] Fix compiling of catalyst docs.
dev/check-license wrap folders in quotes.
[SPARK-2024] Add saveAsSequenceFile to PySpark

JIRA issue: https://issues.apache.org/jira/browse/SPARK-2024

This PR is a followup to #455 and adds capabilities for saving PySpark RDDs using SequenceFile or any Hadoop OutputFormats.

* Added RDD methods ```saveAsSequenceFile```, ```saveAsHadoopFile``` and ```saveAsHadoopDataset```, for both old and new MapReduce APIs.

* Default converter for converting common data types to Writables. Users may specify custom converters to convert to desired data types.

* No out-of-box support for reading/writing arrays, since ArrayWritable itself doesn't have a no-arg constructor for creating an empty instance upon reading. Users need to provide ArrayWritable subtypes. Custom converters for converting arrays to suitable ArrayWritable subtypes are also needed when writing. When reading, the default converter will convert any custom ArrayWritable subtypes to ```Object[]``` and they get pickled to Python tuples.

* Added HBase and Cassandra output examples to show how custom output formats and converters can be used.

cc MLnick mateiz ahirreddy pwendell

Author: Kan Zhang <kzhang@apache.org>

Closes #1338 from kanzhang/SPARK-2024 and squashes the following commits:

c01e3ef [Kan Zhang] [SPARK-2024] code formatting
6591e37 [Kan Zhang] [SPARK-2024] renaming pickled -> pickledRDD
d998ad6 [Kan Zhang] [SPARK-2024] refectoring to get method params below 10
57a7a5e [Kan Zhang] [SPARK-2024] correcting typo
75ca5bd [Kan Zhang] [SPARK-2024] Better type checking for batch serialized RDD
0bdec55 [Kan Zhang] [SPARK-2024] Refactoring newly added tests
9f39ff4 [Kan Zhang] [SPARK-2024] Adding 2 saveAsHadoopDataset tests
0c134f3 [Kan Zhang] [SPARK-2024] Test refactoring and adding couple unbatched cases
7a176df [Kan Zhang] [SPARK-2024] Add saveAsSequenceFile to PySpark
Wrap JAR_DL in dev/check-license.
Set AMPLAB_JENKINS_BUILD_PROFILE.
Properly pass SBT_MAVEN_PROFILES into sbt.
SPARK-2749 [BUILD]. Spark SQL Java tests aren't compiling in Jenkins' Maven builds; missing junit:junit dep

The Maven-based builds in the build matrix have been failing for a few days:

https://amplab.cs.berkeley.edu/jenkins/view/Spark/

On inspection, it looks like the Spark SQL Java tests don't compile:

https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/hadoop.version=1.0.4,label=centos/244/consoleFull

I confirmed it by repeating the command vs master:

`mvn -Dhadoop.version=1.0.4 -Dlabel=centos -DskipTests clean package`

The problem is that this module doesn't depend on JUnit. In fact, none of the modules do, but `com.novocode:junit-interface` (the SBT-JUnit bridge) pulls it in, in most places. However this module doesn't depend on `com.novocode:junit-interface`

Adding the `junit:junit` dependency fixes the compile problem. In fact, the other modules with Java tests should probably depend on it explicitly instead of happening to get it via `com.novocode:junit-interface`, since that is a bit SBT/Scala-specific (and I am not even sure it's needed).

Author: Sean Owen <srowen@gmail.com>

Closes #1660 from srowen/SPARK-2749 and squashes the following commits:

858ff7c [Sean Owen] Add explicit junit dep to other modules with Java tests for robustness
9636794 [Sean Owen] Add junit dep so that Spark SQL Java tests compile
SPARK-2741 - Publish version of spark assembly which does not contain Hive

Provide a version of the Spark tarball which does not package Hive. This is meant for HIve + Spark users.

Author: Brock Noland <brock@apache.org>

Closes #1667 from brockn/master and squashes the following commits:

5beafb2 [Brock Noland] SPARK-2741 - Publish version of spark assembly which does not contain Hive
[SPARK-2734][SQL] Remove tables from cache when DROP TABLE is run.

Author: Michael Armbrust <michael@databricks.com>

Closes #1650 from marmbrus/dropCached and squashes the following commits:

e6ab80b [Michael Armbrust] Support if exists.
83426c6 [Michael Armbrust] Remove tables from cache when DROP TABLE is run.
SPARK-2341 [MLLIB] loadLibSVMFile doesn't handle regression datasets

Per discussion at https://issues.apache.org/jira/browse/SPARK-2341 , this is a look at deprecating the multiclass parameter. Thoughts welcome of course.

Author: Sean Owen <srowen@gmail.com>

Closes #1663 from srowen/SPARK-2341 and squashes the following commits:

8a3abd7 [Sean Owen] Suppress MIMA error for removed package private classes
18a8c8e [Sean Owen] Updates from review
83d0092 [Sean Owen] Deprecated methods with multiclass, and instead always parse target as a double (ie. multiclass = true)
Update DecisionTreeRunner.scala

Author: strat0sphere <stratos.dimopoulos@gmail.com>

Closes #1676 from strat0sphere/patch-1 and squashes the following commits:

044d2fa [strat0sphere] Update DecisionTreeRunner.scala
SPARK-2045 Sort-based shuffle

This adds a new ShuffleManager based on sorting, as described in https://issues.apache.org/jira/browse/SPARK-2045. The bulk of the code is in an ExternalSorter class that is similar to ExternalAppendOnlyMap, but sorts key-value pairs by partition ID and can be used to create a single sorted file with a map task's output. (Longer-term I think this can take on the remaining functionality in ExternalAppendOnlyMap and replace it so we don't have code duplication.)

The main TODOs still left are:
- [x] enabling ExternalSorter to merge across spilled files
  - [x] with an Ordering
  - [x] without an Ordering, using the keys' hash codes
- [x] adding more tests (e.g. a version of our shuffle suite that runs on this)
- [x] rebasing on top of the size-tracking refactoring in #1165 when that is merged
- [x] disabling spilling if spark.shuffle.spill is set to false

Despite this though, this seems to work pretty well (running successfully in cases where the hash shuffle would OOM, such as 1000 reduce tasks on executors with only 1G memory), and it seems to be comparable in speed or faster than hash-based shuffle (it will create much fewer files for the OS to keep track of). So I'm posting it to get some early feedback.

After these TODOs are done, I'd also like to enable ExternalSorter to sort data within each partition by a key as well, which will allow us to use it to implement external spilling in reduce tasks in `sortByKey`.

Author: Matei Zaharia <matei@databricks.com>

Closes #1499 from mateiz/sort-based-shuffle and squashes the following commits:

bd841f9 [Matei Zaharia] Various review comments
d1c137fd [Matei Zaharia] Various review comments
a611159 [Matei Zaharia] Compile fixes due to rebase
62c56c8 [Matei Zaharia] Fix ShuffledRDD sometimes not returning Tuple2s.
f617432 [Matei Zaharia] Fix a failing test (seems to be due to change in SizeTracker logic)
9464d5f [Matei Zaharia] Simplify code and fix conflicts after latest rebase
0174149 [Matei Zaharia] Add cleanup behavior and cleanup tests for sort-based shuffle
eb4ee0d [Matei Zaharia] Remove customizable element type in ShuffledRDD
fa2e8db [Matei Zaharia] Allow nextBatchStream to be called after we're done looking at all streams
a34b352 [Matei Zaharia] Fix tracking of indices within a partition in SpillReader, and add test
03e1006 [Matei Zaharia] Add a SortShuffleSuite that runs ShuffleSuite with sort-based shuffle
3c7ff1f [Matei Zaharia] Obey the spark.shuffle.spill setting in ExternalSorter
ad65fbd [Matei Zaharia] Rebase on top of Aaron's Sorter change, and use Sorter in our buffer
44d2a93 [Matei Zaharia] Use estimateSize instead of atGrowThreshold to test collection sizes
5686f71 [Matei Zaharia] Optimize merging phase for in-memory only data:
5461cbb [Matei Zaharia] Review comments and more tests (e.g. tests with 1 element per partition)
e9ad356 [Matei Zaharia] Update ContextCleanerSuite to make sure shuffle cleanup tests use hash shuffle (since they were written for it)
c72362a [Matei Zaharia] Added bug fix and test for when iterators are empty
de1fb40 [Matei Zaharia] Make trait SizeTrackingCollection private[spark]
4988d16 [Matei Zaharia] tweak
c1b7572 [Matei Zaharia] Small optimization
ba7db7f [Matei Zaharia] Handle null keys in hash-based comparator, and add tests for collisions
ef4e397 [Matei Zaharia] Support for partial aggregation even without an Ordering
4b7a5ce [Matei Zaharia] More tests, and ability to sort data if a total ordering is given
e1f84be [Matei Zaharia] Fix disk block manager test
5a40a1c [Matei Zaharia] More tests
614f1b4 [Matei Zaharia] Add spill metrics to map tasks
cc52caf [Matei Zaharia] Add more error handling and tests for error cases
bbf359d [Matei Zaharia] More work
3a56341 [Matei Zaharia] More partial work towards sort-based shuffle
7a0895d [Matei Zaharia] Some more partial work towards sort-based shuffle
b615476 [Matei Zaharia] Scaffolding for sort-based shuffle