(This is a replacement of #1399, trying to fix potential `HiveThriftServer2` port collision between parallel builds. Please refer to [these comments](https://github.com/apache/spark/pull/1399#issuecomment-50212572) for details.)

JIRA issue: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)

Merging the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.

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

Closes #1600 from liancheng/jdbc and squashes the following commits:

ac4618b [Cheng Lian] Uses random port for HiveThriftServer2 to avoid collision with parallel builds
090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

This reverts commit 06dc0d2c.

#1399 is making Jenkins fail.  We should investigate and put this back after its passing tests.

Author: Michael Armbrust <michael@databricks.com>

Closes #1594 from marmbrus/revertJDBC and squashes the following commits:

59748da [Michael Armbrust] Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

JIRA issue:

- Main: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)
- Related: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678)

Cherry picked the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

(Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.)

TODO

- [x] Use `spark-submit` to launch the server, the CLI and beeline
- [x] Migration guideline draft for Shark users

----

Hit by a bug in `SparkSubmitArguments` while working on this PR: all application options that are recognized by `SparkSubmitArguments` are stolen as `SparkSubmit` options. For example:

```bash
$ spark-submit --class org.apache.hive.beeline.BeeLine spark-internal --help
```

This actually shows usage information of `SparkSubmit` rather than `BeeLine`.

~~Fixed this bug here since the `spark-internal` related stuff also touches `SparkSubmitArguments` and I'd like to avoid conflict.~~

**UPDATE** The bug mentioned above is now tracked by [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678). Decided to revert changes to this bug since it involves more subtle considerations and worth a separate PR.

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

Closes #1399 from liancheng/thriftserver and squashes the following commits:

090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

RoutingTableMessage was used to construct routing tables to enable
joining VertexRDDs with partitioned edges. It stored three elements: the
destination vertex ID, the source edge partition, and a byte specifying
the position in which the edge partition referenced the vertex to enable
join elimination.

However, this was incompatible with sort-based shuffle (SPARK-2045). It
was also slightly wasteful, because partition IDs are usually much
smaller than 2^32, though this was mitigated by a custom serializer that
used variable-length encoding.

This commit replaces RoutingTableMessage with a pair of (VertexId, Int)
where the Int encodes both the source partition ID (in the lower 30
bits) and the position (in the top 2 bits).

Author: Ankur Dave <ankurdave@gmail.com>

Closes #1553 from ankurdave/remove-RoutingTableMessage and squashes the following commits:

697e17b [Ankur Dave] Replace RoutingTableMessage with pair

MessageToPartition was used in `Graph#partitionBy`. Unlike a Tuple2, it marked the key as transient to avoid sending it over the network. However, it was incompatible with sort-based shuffle (SPARK-2045) and represented only a minor optimization: for partitionBy, it improved performance by 6.3% (30.4 s to 28.5 s) and reduced communication by 5.6% (114.2 MB to 107.8 MB).

Author: Ankur Dave <ankurdave@gmail.com>

Closes #1537 from ankurdave/remove-MessageToPartition and squashes the following commits:

f9d0054 [Ankur Dave] Remove MessageToPartition
ab71364 [Ankur Dave] Remove unused VertexBroadcastMsg

fix examples

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1523 from CrazyJvm/graphx-example and squashes the following commits:

663457a [CrazyJvm] outDegrees does not take parameters
7cfff1d [CrazyJvm] fix example for joinVertices

VertexPartition and ShippableVertexPartition are contained in RDDs but are not marked Serializable, leading to NotSerializableExceptions when using Java serialization.

The fix is simply to mark them as Serializable. This PR does that and adds a test for serializing them using Java and Kryo serialization.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #1376 from ankurdave/SPARK-2455 and squashes the following commits:

ed4a51b [Ankur Dave] Make (Shippable)VertexPartition serializable
1fd42c5 [Ankur Dave] Add failing tests for Java serialization

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1368 from CrazyJvm/graph-comment-1 and squashes the following commits:

d47f3c5 [CrazyJvm] fix style
e190d6f [CrazyJvm] fix Graph partitionStrategy comment

Patch introduces the new way of working also retaining the existing ways of doing things.

For example build instruction for yarn in maven is
`mvn -Pyarn -PHadoop2.2 clean package -DskipTests`
in sbt it can become
`MAVEN_PROFILES="yarn, hadoop-2.2" sbt/sbt clean assembly`
Also supports
`sbt/sbt -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0 clean assembly`

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #772 from ScrapCodes/sbt-maven and squashes the following commits:

a8ac951 [Prashant Sharma] Updated sbt version.
62b09bb [Prashant Sharma] Improvements.
fa6221d [Prashant Sharma] Excluding sql from mima
4b8875e [Prashant Sharma] Sbt assembly no longer builds tools by default.
72651ca [Prashant Sharma] Addresses code reivew comments.
acab73d [Prashant Sharma] Revert "Small fix to run-examples script."
ac4312c [Prashant Sharma] Revert "minor fix"
6af91ac [Prashant Sharma] Ported oldDeps back. + fixes issues with prev commit.
65cf06c [Prashant Sharma] Servelet API jars mess up with the other servlet jars on the class path.
446768e [Prashant Sharma] minor fix
89b9777 [Prashant Sharma] Merge conflicts
d0a02f2 [Prashant Sharma] Bumped up pom versions, Since the build now depends on pom it is better updated there. + general cleanups.
dccc8ac [Prashant Sharma] updated mima to check against 1.0
a49c61b [Prashant Sharma] Fix for tools jar
a2f5ae1 [Prashant Sharma] Fixes a bug in dependencies.
cf88758 [Prashant Sharma] cleanup
9439ea3 [Prashant Sharma] Small fix to run-examples script.
96cea1f [Prashant Sharma] SPARK-1776 Have Spark's SBT build read dependencies from Maven.
36efa62 [Patrick Wendell] Set project name in pom files and added eclipse/intellij plugins.
4973dbd [Patrick Wendell] Example build using pom reader.

This PR is a sub-task of SPARK-2044 to move the execution of aggregation into shuffle implementations.

I leave `CoGoupedRDD` and `SubtractedRDD` unchanged because they have their implementations of aggregation. I'm not sure is it suitable to change these two RDDs.

Also I do not move sort related code of `OrderedRDDFunctions` into shuffle, this will be solved in another sub-task.

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

Closes #1064 from jerryshao/SPARK-2124 and squashes the following commits:

4a05a40 [jerryshao] Modify according to comments
1f7dcc8 [jerryshao] Style changes
50a2fd6 [jerryshao] Fix test suite issue after moving aggregator to Shuffle reader and writer
1a96190 [jerryshao] Code modification related to the ShuffledRDD
308f635 [jerryshao] initial works of move combiner to ShuffleManager's reader and writer

In GraphImpl, mapVertices and outerJoinVertices use a more efficient implementation when the map function conserves vertex attribute types. This is implemented by comparing the ClassTags of the old and new vertex attribute types. However, ClassTags store erased types, so the comparison will return a false positive for types with different type parameters, such as Option[Int] and Option[Double].

This PR resolves the problem by requesting that the compiler generate evidence of equality between the old and new vertex attribute types, and providing a default value for the evidence parameter if the two types are not equal. The methods can then check the value of the evidence parameter to see whether the types are equal.

It also adds a test called "mapVertices changing type with same erased type" that failed before the PR and succeeds now.

Callers of mapVertices and outerJoinVertices can no longer use a wildcard for a graph's VD type. To avoid "Error occurred in an application involving default arguments," they must bind VD to a type parameter, as this PR does for ShortestPaths and LabelPropagation.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #967 from ankurdave/SPARK-1552 and squashes the following commits:

68a4fff [Ankur Dave] Undo conserve naming
7388705 [Ankur Dave] Remove unnecessary ClassTag for VD parameters
a704e5f [Ankur Dave] Use type equality constraint with default argument
29a5ab7 [Ankur Dave] Add failing test
f458c83 [Ankur Dave] Revert "[SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices"
16d6af8 [Ankur Dave] [SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices

Due to a bug introduced by apache/spark#497, Pregel does not unpersist replicated vertices from previous iterations. As a result, they stay cached until memory is full, wasting GC time.

This PR corrects the problem by unpersisting both the edges and the replicated vertices of previous iterations. This is safe because the edges and replicated vertices of the current iteration are cached by the call to `g.cache()` and then materialized by the call to `messages.count()`. Therefore no unmaterialized RDDs depend on `prevG.edges`. I verified that no recomputation occurs by running PageRank with a custom patch to Spark that warns when a partition is recomputed.

Thanks to Tim Weninger for reporting this bug.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #972 from ankurdave/SPARK-2025 and squashes the following commits:

13d5b07 [Ankur Dave] Unpersist edges of previous graph in Pregel

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #974 from ueshin/issues/SPARK-2029 and squashes the following commits:

e19e8f4 [Takuya UESHIN] Bump version number to 1.1.0-SNAPSHOT.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #970 from ankurdave/SPARK-1991_docfix and squashes the following commits:

6d07343 [Ankur Dave] Minor: Fix documentation error from apache/spark#946

It is currently very difficult to repartition a graph over a different number of partitions.  This PR adds an additional `partitionBy` function that takes the number of partitions.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #719 from jegonzal/graph_partitioning_options and squashes the following commits:

730b405 [Joseph E. Gonzalez] adding an additional number of partitions option to partitionBy

This PR adds support for specifying custom storage levels for the vertices and edges of a graph. This enables GraphX to handle graphs larger than memory size by specifying MEMORY_AND_DISK and then repartitioning the graph to use many small partitions, each of which does fit in memory. Spark will then automatically load partitions from disk as needed.

The user specifies the desired vertex and edge storage levels when building the graph by passing them to the graph constructor. These are then stored in the `targetStorageLevel` attribute of the VertexRDD and EdgeRDD respectively. Whenever GraphX needs to cache a VertexRDD or EdgeRDD (because it plans to use it more than once, for example), it uses the specified target storage level. Also, when the user calls `Graph#cache()`, the vertices and edges are persisted using their target storage levels.

In order to facilitate propagating the target storage levels across VertexRDD and EdgeRDD operations, we remove raw calls to the constructors and instead introduce the `withPartitionsRDD` and `withTargetStorageLevel` methods.

I tested this change by running PageRank and triangle count on a severely memory-constrained cluster (1 executor with 300 MB of memory, and a 1 GB graph). Before this PR, these algorithms used to fail with OutOfMemoryErrors. With this PR, and using the DISK_ONLY storage level, they succeed.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #946 from ankurdave/SPARK-1991 and squashes the following commits:

ce17d95 [Ankur Dave] Move pickStorageLevel to StorageLevel.fromString
ccaf06f [Ankur Dave] Shadow members in withXYZ() methods rather than using underscores
c34abc0 [Ankur Dave] Exclude all of GraphX from compatibility checks vs. 1.0.0
c5ca068 [Ankur Dave] Revert "Exclude all of GraphX from binary compatibility checks"
34bcefb [Ankur Dave] Exclude all of GraphX from binary compatibility checks
6fdd137 [Ankur Dave] [SPARK-1991] Support custom storage levels for vertices and edges

This PR accomplishes two things:

1. It introduces a Synthetic Benchmark application that generates an arbitrarily large log-normal graph and executes either PageRank or connected components on the graph.  This can be used to profile GraphX system on arbitrary clusters without access to large graph datasets

2. This PR improves the implementation of the log-normal graph generator.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>
Author: Ankur Dave <ankurdave@gmail.com>

Closes #720 from jegonzal/graphx_synth_benchmark and squashes the following commits:

e40812a [Ankur Dave] Exclude all of GraphX from compatibility checks vs. 1.0.0
bccccad [Ankur Dave] Fix long lines
374678a [Ankur Dave] Bugfix and style changes
1bdf39a [Joseph E. Gonzalez] updating options
d943972 [Joseph E. Gonzalez] moving the benchmark application into the examples folder.
f4f839a [Joseph E. Gonzalez] Creating a synthetic benchmark script.

stop resetting spark.driver.port in unit tests (scala, java and python).

Author: Syed Hashmi <shashmi@cloudera.com>
Author: CodingCat <zhunansjtu@gmail.com>

Closes #943 from syedhashmi/master and squashes the following commits:

885f210 [Syed Hashmi] Removing unnecessary file (created by mergetool)
b8bd4b5 [Syed Hashmi] Merge remote-tracking branch 'upstream/master'
b895e59 [Syed Hashmi] Revert "[SPARK-1784] Add a new partitioner"
57b6587 [Syed Hashmi] Revert "[SPARK-1784] Add a balanced partitioner"
1574769 [Syed Hashmi] [SPARK-1942] Stop clearing spark.driver.port in unit tests
4354836 [Syed Hashmi] Revert "SPARK-1686: keep schedule() calling in the main thread"
fd36542 [Syed Hashmi] [SPARK-1784] Add a balanced partitioner
6668015 [CodingCat] SPARK-1686: keep schedule() calling in the main thread
4ca94cc [Syed Hashmi] [SPARK-1784] Add a new partitioner

This is a modified version of apache/spark#10.

Author: Ankur Dave <ankurdave@gmail.com>
Author: Andres Perez <andres@tresata.com>

Closes #933 from ankurdave/shortestpaths and squashes the following commits:

03a103c [Ankur Dave] Style fixes
7a1ff48 [Ankur Dave] Improve ShortestPaths documentation
d75c8fc [Ankur Dave] Remove unnecessary VD type param, and pass through ED
d983fb4 [Ankur Dave] Fix style errors
60ed8e6 [Andres Perez] Add Shortest-path computations to graphx.lib with unit tests.

A straightforward implementation of LPA algorithm for detecting graph communities using the Pregel framework.  Amongst the growing literature on community detection algorithms in networks, LPA is perhaps the most elementary, and despite its flaws it remains a nice and simple approach.

Author: Ankur Dave <ankurdave@gmail.com>
Author: haroldsultan <haroldsultan@gmail.com>
Author: Harold Sultan <haroldsultan@gmail.com>

Closes #905 from haroldsultan/master and squashes the following commits:

327aee0 [haroldsultan] Merge pull request #2 from ankurdave/label-propagation
227a4d0 [Ankur Dave] Untabify
0ac574c [haroldsultan] Merge pull request #1 from ankurdave/label-propagation
0e24303 [Ankur Dave] Add LabelPropagationSuite
84aa061 [Ankur Dave] LabelPropagation: Fix compile errors and style; rename from LPA
9830342 [Harold Sultan] initial version of LPA

905173df introduced a bug in partitionBy where, after repartitioning the edges, it reuses the VertexRDD without updating the routing tables to reflect the new edge layout. Subsequent accesses of the triplets contain nulls for many vertex properties.

This commit adds a test for this bug and fixes it by introducing `VertexRDD#withEdges` and calling it in `partitionBy`.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #885 from ankurdave/SPARK-1931 and squashes the following commits:

3930cdd [Ankur Dave] Note how to set up VertexRDD for efficient joins
9bdbaa4 [Ankur Dave] [SPARK-1931] Reconstruct routing tables in Graph.partitionBy

Author: Zhen Peng <zhenpeng01@baidu.com>

Closes #769 from zhpengg/bugfix-graphx-edge-compare and squashes the following commits:

8a978ff [Zhen Peng] add ut for graphx Edge.lexicographicOrdering.compare
413c258 [Zhen Peng] there maybe a overflow for two Long's substraction

Fixes a misplaced comment from #785.

@pwendell

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #788 from ScrapCodes/patch-1 and squashes the following commits:

3ef6a69 [Prashant Sharma] Update package-info.java
67d9461 [Prashant Sharma] Update package-info.java

This is a few changes based on the original patch by @scrapcodes.

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #785 from pwendell/package-docs and squashes the following commits:

c32b731 [Patrick Wendell] Changes based on Prashant's patch
c0463d3 [Prashant Sharma] added eof new line
ce8bf73 [Prashant Sharma] Added eof new line to all files.
4c35f2e [Prashant Sharma] SPARK-1563 Add package-info.java and package.scala files for all packages that appear in docs

Three issues related to temp files that tests generate – these should be touched up for hygiene but are not urgent.

Modules have a log4j.properties which directs the unit-test.log output file to a directory like `[module]/target/unit-test.log`. But this ends up creating `[module]/[module]/target/unit-test.log` instead of former.

The `work/` directory is not deleted by "mvn clean", in the parent and in modules. Neither is the `checkpoint/` directory created under the various external modules.

Many tests create a temp directory, which is not usually deleted. This can be largely resolved by calling `deleteOnExit()` at creation and trying to call `Utils.deleteRecursively` consistently to clean up, sometimes in an `@After` method.

_If anyone seconds the motion, I can create a more significant change that introduces a new test trait along the lines of `LocalSparkContext`, which provides management of temp directories for subclasses to take advantage of._

Author: Sean Owen <sowen@cloudera.com>

Closes #732 from srowen/SPARK-1798 and squashes the following commits:

5af578e [Sean Owen] Try to consistently delete test temp dirs and files, and set deleteOnExit() for each
b21b356 [Sean Owen] Remove work/ and checkpoint/ dirs with mvn clean
bdd0f41 [Sean Owen] Remove duplicate module dir in log4j.properties output path for tests

Addressing issue in MimaBuild.scala.

Author: Ankur Dave <ankurdave@gmail.com>
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #742 from jegonzal/edge_partition_serialization and squashes the following commits:

8ba6e0d [Ankur Dave] Add concatenation operators to MimaBuild.scala
cb2ed3a [Joseph E. Gonzalez] addressing missing exclusion in MimaBuild.scala
5d27824 [Ankur Dave] Disable reference tracking to fix serialization test
c0a9ae5 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
a4a3faa [Joseph E. Gonzalez] Making EdgePartition serializable.

This reverts commit a6b02fb7.

This appears to address the issue with edge partition serialization.  The solution appears to be just registering the `PrimitiveKeyOpenHashMap`.  However I noticed that we appear to have forked that code in GraphX but retained the same name (which is confusing).  I also renamed our local copy to `GraphXPrimitiveKeyOpenHashMap`.  We should consider dropping that and using the one in Spark if possible.

Author: Ankur Dave <ankurdave@gmail.com>
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #724 from jegonzal/edge_partition_serialization and squashes the following commits:

b0a525a [Ankur Dave] Disable reference tracking to fix serialization test
bb7f548 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
67dac22 [Joseph E. Gonzalez] Making EdgePartition serializable.

Their was a minor bug in which negative partition ids could be generated when constructing a 2D partitioning of a graph.  This could lead to an inefficient 2D partition for large vertex id values.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #709 from jegonzal/fix_2d_partitioning and squashes the following commits:

937c562 [Joseph E. Gonzalez] fixing bug in 2d partitioning algorithm where negative partition ids could be generated.

This PR makes the following changes, primarily in e4fbd329aef85fe2c38b0167255d2a712893d683:

1. *Unify RDDs to avoid zipPartitions.* A graph used to be four RDDs: vertices, edges, routing table, and triplet view. This commit merges them down to two: vertices (with routing table), and edges (with replicated vertices).

2. *Avoid duplicate shuffle in graph building.* We used to do two shuffles when building a graph: one to extract routing information from the edges and move it to the vertices, and another to find nonexistent vertices referred to by edges. With this commit, the latter is done as a side effect of the former.

3. *Avoid no-op shuffle when joins are fully eliminated.* This is a side effect of unifying the edges and the triplet view.

4. *Join elimination for mapTriplets.*

5. *Ship only the needed vertex attributes when upgrading the triplet view.* If the triplet view already contains source attributes, and we now need both attributes, only ship destination attributes rather than re-shipping both. This is done in `ReplicatedVertexView#upgrade`.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #497 from ankurdave/unify-rdds and squashes the following commits:

332ab43 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds
4933e2e [Ankur Dave] Exclude RoutingTable from binary compatibility check
5ba8789 [Ankur Dave] Add GraphX upgrade guide from Spark 0.9.1
13ac845 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds
a04765c [Ankur Dave] Remove unnecessary toOps call
57202e8 [Ankur Dave] Replace case with pair parameter
75af062 [Ankur Dave] Add explicit return types
04d3ae5 [Ankur Dave] Convert implicit parameter to context bound
c88b269 [Ankur Dave] Revert upgradeIterator to if-in-a-loop
0d3584c [Ankur Dave] EdgePartition.size should be val
2a928b2 [Ankur Dave] Set locality wait
10b3596 [Ankur Dave] Clean up public API
ae36110 [Ankur Dave] Fix style errors
e4fbd32 [Ankur Dave] Unify GraphImpl RDDs + other graph load optimizations
d6d60e2 [Ankur Dave] In GraphLoader, coalesce to minEdgePartitions
62c7b78 [Ankur Dave] In Analytics, take PageRank numIter
d64e8d4 [Ankur Dave] Log current Pregel iteration

This pull request contains a rebased patch from @heathermiller (https://github.com/heathermiller/spark/pull/1) to add ClassTags on Serializer and types that depend on it (Broadcast and AccumulableCollection). Putting these in the public API signatures now will allow us to use Scala Pickling for serialization down the line without breaking binary compatibility.

One question remaining is whether we also want them on Accumulator -- Accumulator is passed as part of a bigger Task or TaskResult object via the closure serializer so it doesn't seem super useful to add the ClassTag there. Broadcast and AccumulableCollection in contrast were being serialized directly.

CC @rxin, @pwendell, @heathermiller

Author: Matei Zaharia <matei@databricks.com>

Closes #700 from mateiz/spark-1708 and squashes the following commits:

1a3d8b0 [Matei Zaharia] Use fake ClassTag in Java
3b449ed [Matei Zaharia] test fix
2209a27 [Matei Zaharia] Code style fixes
9d48830 [Matei Zaharia] Add a ClassTag on Serializer and things that depend on it

Commit for initial feedback, basically I am curious if we should prompt user for providing args esp. when its mandatory. And can we skip if they are not ?

Also few other things that did not work like
`bin/spark-submit examples/target/scala-2.10/spark-examples-1.0.0-SNAPSHOT-hadoop1.0.4.jar --class org.apache.spark.examples.SparkALS --arg 100 500 10 5 2`

Not all the args get passed properly, may be I have messed up something will try to sort it out hopefully.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #552 from ScrapCodes/SPARK-1565/update-examples and squashes the following commits:

669dd23 [Prashant Sharma] Review comments
2727e70 [Prashant Sharma] SPARK-1565, update examples to be used with spark-submit script.

... that do not change schema

Author: Kan Zhang <kzhang@apache.org>

Closes #448 from kanzhang/SPARK-1460 and squashes the following commits:

111e388 [Kan Zhang] silence MiMa errors in EdgeRDD and VertexRDD
91dc787 [Kan Zhang] Taking into account newly added Ordering param
79ed52a [Kan Zhang] [SPARK-1460] Returning SchemaRDD on Set operations that do not change schema

1, Fix SPARK-1441: compile spark core error with hadoop 0.23.x
2, Fix SPARK-1491: maven hadoop-provided profile fails to build
3, Fix org.scala-lang: * ,org.apache.avro:* inconsistent versions dependency
4, A modified on the sql/catalyst/pom.xml,sql/hive/pom.xml,sql/core/pom.xml (Four spaces formatted into two spaces)

Author: witgo <witgo@qq.com>

Closes #480 from witgo/format_pom and squashes the following commits:

03f652f [witgo] review commit
b452680 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
bee920d [witgo] revert fix SPARK-1629: Spark Core missing commons-lang dependence
7382a07 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
6902c91 [witgo] fix SPARK-1629: Spark Core missing commons-lang dependence
0da4bc3 [witgo] merge master
d1718ed [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
e345919 [witgo] add avro dependency to yarn-alpha
77fad08 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
62d0862 [witgo] Fix org.scala-lang: * inconsistent versions dependency
1a162d7 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
934f24d [witgo] review commit
cf46edc [witgo] exclude jruby
06e7328 [witgo] Merge branch 'SparkBuild' into format_pom
99464d2 [witgo] fix maven hadoop-provided profile fails to build
0c6c1fc [witgo] Fix compile spark core error with hadoop 0.23.x
6851bec [witgo] Maintain consistent SparkBuild.scala, pom.xml

Any comments are welcome

Author: Sandeep <sandeep@techaddict.me>

Closes #531 from techaddict/stylefix-1 and squashes the following commits:

7492730 [Sandeep] Pass 4
98b2428 [Sandeep] fix rxin suggestions
b5e2e6f [Sandeep] Pass 3
05932d7 [Sandeep] fix if else styling 2
08690e5 [Sandeep] fix if else styling

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`

Each vertex partition is co-located with a pid2vid array created in RoutingTable.scala. This array maps edge partition IDs to the list of vertices in the current vertex partition that are mentioned by edges in that partition. Therefore the pid2vid array should have one entry per edge partition.

GraphX currently creates one entry per *vertex* partition, which is a bug that leads to an ArrayIndexOutOfBoundsException when there are more edge partitions than vertex partitions. This commit fixes the bug and adds a test for this case.

Resolves SPARK-1329. Thanks to Daniel Darabos for reporting this bug.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #368 from ankurdave/fix-pid2vid-size and squashes the following commits:

5a5c52a [Ankur Dave] SPARK-1329: Create pid2vid with correct number of partitions

GraphImpl.reverse used to reverse edges in each partition of the edge RDD but preserve the routing table and replicated vertex view, since reversing should not affect partitioning.

However, the old routing table would then have incorrect information for srcAttrOnly and dstAttrOnly. These RDDs should be switched.

A simple fix is for Graph.reverse to rebuild the routing table and replicated vertex view.

Thanks to Bogdan Ghidireac for reporting this issue on the [mailing list](http://apache-spark-user-list.1001560.n3.nabble.com/graph-reverse-amp-Pregel-API-td4338.html).

Author: Ankur Dave <ankurdave@gmail.com>

Closes #431 from ankurdave/fix-reverse-bug and squashes the following commits:

75d63cb [Ankur Dave] Rebuild routing table after Graph.reverse

The Graph.apply test in GraphSuite had some assertions in a closure in
a graph transformation. As a consequence, these assertions never
actually executed.  Furthermore, these closures had a reference to
(non-serializable) test harness classes because they called assert(),
which could be a problem if we proactively check closure serializability
in the future.

This commit simply changes the Graph.apply test to collect the graph
triplets so it can assert about each triplet from a map method.

Author: William Benton <willb@redhat.com>

Closes #415 from willb/graphsuite-nop-fix and squashes the following commits:

0b63658 [William Benton] Ensure assertions in Graph.apply are asserted.

For your consideration: scalac currently notes a number of feature warnings during compilation:

```
[warn] there were 65 feature warning(s); re-run with -feature for details
```

Warnings are like:

```
[warn] /Users/srowen/Documents/spark/core/src/main/scala/org/apache/spark/SparkContext.scala:1261: implicit conversion method rddToPairRDDFunctions should be enabled
[warn] by making the implicit value scala.language.implicitConversions visible.
[warn] This can be achieved by adding the import clause 'import scala.language.implicitConversions'
[warn] or by setting the compiler option -language:implicitConversions.
[warn] See the Scala docs for value scala.language.implicitConversions for a discussion
[warn] why the feature should be explicitly enabled.
[warn]   implicit def rddToPairRDDFunctions[K: ClassTag, V: ClassTag](rdd: RDD[(K, V)]) =
[warn]                ^
```

scalac is suggesting that it's just best practice to explicitly enable certain language features by importing them where used.

This PR simply adds the imports it suggests (and squashes one other Java warning along the way). This leaves just deprecation warnings in the build.

Author: Sean Owen <sowen@cloudera.com>

Closes #404 from srowen/SPARK-1488 and squashes the following commits:

8598980 [Sean Owen] Quiet scalac warnings about language features by explicitly importing language features.
39bc831 [Sean Owen] Enable -feature in scalac to emit language feature warnings