Rebuild routing table after Graph.reverse

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

(cherry picked from commit 235a47ce14b3c7523e79ce671355dea7ee06f4b7)
Signed-off-by: Reynold Xin <rxin@apache.org>
SPARK-1329: Create pid2vid with correct number of partitions

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

(cherry picked from commit 17d323455a9c8b640f149be4a81139ed638765b5)
Signed-off-by: Reynold Xin <rxin@apache.org>
remove unnecessary brace and semicolon in 'putBlockInfo.synchronize'  block

delete semicolon

Author: Chen Chao <crazyjvm@gmail.com>

Closes #411 from CrazyJvm/patch-5 and squashes the following commits:

72333a3 [Chen Chao] remove unnecessary brace
de5d9a7 [Chen Chao] style fix

(cherry picked from commit 016a87764a7eb1092b6489e5f411d9e67c56e027)
Signed-off-by: Reynold Xin <rxin@apache.org>
Fixing a race condition in event listener unit test

Author: Kan Zhang <kzhang@apache.org>

Closes #401 from kanzhang/fix-1475 and squashes the following commits:

c6058bd [Kan Zhang] Fixing a race condition in event listener unit test

(cherry picked from commit 38877ccf394a50bfd37c8433d4aafaa91683d3b8)
Signed-off-by: Reynold Xin <rxin@apache.org>
misleading task number of groupByKey

"By default, this uses only 8 parallel tasks to do the grouping." is a big misleading. Please refer to https://github.com/apache/spark/pull/389

detail is as following code :

  def defaultPartitioner(rdd: RDD[_], others: RDD[_]*): Partitioner = {
    val bySize = (Seq(rdd) ++ others).sortBy(_.partitions.size).reverse
    for (r <- bySize if r.partitioner.isDefined) {
      return r.partitioner.get
    }
    if (rdd.context.conf.contains("spark.default.parallelism")) {
      new HashPartitioner(rdd.context.defaultParallelism)
    } else {
      new HashPartitioner(bySize.head.partitions.size)
    }
  }

Author: Chen Chao <crazyjvm@gmail.com>

Closes #403 from CrazyJvm/patch-4 and squashes the following commits:

42f6c9e [Chen Chao] fix format
829a995 [Chen Chao] fix format
1568336 [Chen Chao] misleading task number of groupByKey

(cherry picked from commit 9c40b9ead0d17ad836b3507c701198645c33d878)
Signed-off-by: Reynold Xin <rxin@apache.org>
Update ReducedWindowedDStream.scala

change  _slideDuration  to   _windowDuration

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

Closes #425 from baishuo/master and squashes the following commits:

6f09ea1 [baishuo(白硕)] Update ReducedWindowedDStream.scala

(cherry picked from commit 07b7ad30808ea73a375be8a86e96199d704d1422)
Signed-off-by: Reynold Xin <rxin@apache.org>
Include stack trace for exceptions thrown by user code.

It is very confusing when your code throws an exception, but the only stack trace show is in the DAGScheduler.  This is a simple patch to include the stack trace for the actual failure in the error message.  Suggestions on formatting welcome.

Before:
```
scala> sc.parallelize(1 :: Nil).map(_ => sys.error("Ahh!")).collect()
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0.0:3 failed 1 times (most recent failure: Exception failure in TID 3 on host localhost: java.lang.RuntimeException: Ahh!)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1055)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1039)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1037)
...
```

After:
```
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0.0:3 failed 1 times, most recent failure: Exception failure in TID 3 on host localhost: java.lang.RuntimeException: Ahh!
        scala.sys.package$.error(package.scala:27)
        $iwC$$iwC$$iwC$$iwC$$anonfun$1.apply(<console>:13)
        $iwC$$iwC$$iwC$$iwC$$anonfun$1.apply(<console>:13)
        scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        scala.collection.Iterator$class.foreach(Iterator.scala:727)
        scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        scala.collection.AbstractIterator.to(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        org.apache.spark.rdd.RDD$$anonfun$6.apply(RDD.scala:676)
        org.apache.spark.rdd.RDD$$anonfun$6.apply(RDD.scala:676)
        org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1048)
        org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1048)
        org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:110)
        org.apache.spark.scheduler.Task.run(Task.scala:50)
        org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$1.apply$mcV$sp(Executor.scala:211)
        org.apache.spark.deploy.SparkHadoopUtil.runAsUser(SparkHadoopUtil.scala:46)
        org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:176)
        java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        java.lang.Thread.run(Thread.java:744)
Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1055)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1039)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1037)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$abortStage(DAGScheduler.scala:1037)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:614)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:614)
	at scala.Option.foreach(Option.scala:236)
	at org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:614)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$start$1$$anon$2$$anonfun$receive$1.applyOrElse(DAGScheduler.scala:143)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
	at akka.actor.ActorCell.invoke(ActorCell.scala:456)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
	at akka.dispatch.Mailbox.run(Mailbox.scala:219)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
	at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
```

Author: Michael Armbrust <michael@databricks.com>

Closes #409 from marmbrus/stacktraces and squashes the following commits:

3e4eb65 [Michael Armbrust] indent. include header for driver stack trace.
018b06b [Michael Armbrust] Include stack trace for exceptions in user code.

(cherry picked from commit d4916a8eeb747e748b9fba380e9c9503ed11faed)
Signed-off-by: Reynold Xin <rxin@apache.org>
SPARK-1462: Examples of ML algorithms are using deprecated APIs

This will also fix SPARK-1464: Update MLLib Examples to Use Breeze.

Author: Sandeep <sandeep@techaddict.me>

Closes #416 from techaddict/1462 and squashes the following commits:

a43638e [Sandeep] Some Style Changes
3ce69c3 [Sandeep] Fix Ordering and Naming of Imports in Examples
6c7e543 [Sandeep] SPARK-1462: Examples of ML algorithms are using deprecated APIs

(cherry picked from commit 6ad4c5498d7fd241912044f893aa8a21b7c4d24b)
Signed-off-by: Matei Zaharia <matei@databricks.com>
[python alternative] pyspark require Python2, failing if system default is Py3 from shell.py

Python alternative for https://github.com/apache/spark/pull/392; managed from shell.py

Author: AbhishekKr <abhikumar163@gmail.com>

Closes #399 from abhishekkr/pyspark_shell and squashes the following commits:

134bdc9 [AbhishekKr] pyspark require Python2, failing if system default is Py3 from shell.py

(cherry picked from commit bb76eae1b50e4bf18360220110f7d0a4bee672ec)
Signed-off-by: Reynold Xin <rxin@apache.org>