Replace RoutingTableMessage with pair

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
SPARK-2662: Fix NPE for JsonProtocol

Author: GuoQiang Li <witgo@qq.com>

Closes #1511 from witgo/JsonProtocol and squashes the following commits:

2b6227f [GuoQiang Li] Fix NPE for JsonProtocol
[SPARK-2658][SQL] Add rule for true = 1.

Author: Michael Armbrust <michael@databricks.com>

Closes #1556 from marmbrus/fixBooleanEqualsOne and squashes the following commits:

ad8edd4 [Michael Armbrust] Add rule for true = 1 and false = 0.
SPARK-2310. Support arbitrary Spark properties on the command line with ...

...spark-submit

The PR allows invocations like
  spark-submit --class org.MyClass --spark.shuffle.spill false myjar.jar

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1253 from sryza/sandy-spark-2310 and squashes the following commits:

1dc9855 [Sandy Ryza] More doc and cleanup
00edfb9 [Sandy Ryza] Review comments
91b244a [Sandy Ryza] Change format to --conf PROP=VALUE
8fabe77 [Sandy Ryza] SPARK-2310. Support arbitrary Spark properties on the command line with spark-submit
[SPARK-2661][bagel]unpersist old processed rdd

Unpersist useless rdd during bagel iteration to make full use of memory.

Author: Daoyuan <daoyuan.wang@intel.com>

Closes #1519 from adrian-wang/bagelunpersist and squashes the following commits:

182c9dd [Daoyuan] rename var nextUseless to lastRDD
87fd3a4 [Daoyuan] bagel unpersist old processed rdd
SPARK-2150: Provide direct link to finished application UI in yarn resou...

...rce manager UI

Use the event logger directory to provide a direct link to finished
application UI in yarn resourcemanager UI.

Author: Rahul Singhal <rahul.singhal@guavus.com>

Closes #1094 from rahulsinghaliitd/SPARK-2150 and squashes the following commits:

95f230c [Rahul Singhal] SPARK-2150: Provide direct link to finished application UI in yarn resource manager UI
[Build] SPARK-2619: Configurable filemode for the spark/bin folder in debian package

Add  a `<deb.bin.filemode>744</deb.bin.filemode>` property to the `assembly/pom.xml` that defaults to `744`.
Use this property for ../bin folder <filemode>.

This patch doesn't change the current default modes but allows one override the modes at build time:
`-Ddeb.bin.filemode=<new mode>`

Author: tzolov <christian.tzolov@gmail.com>

Closes #1531 from tzolov/SPARK-2619 and squashes the following commits:

6d95343 [tzolov] [Build] SPARK-2619: Configurable filemode for the spark/bin folder in the .deb package
[SPARK-2603][SQL] Remove unnecessary toMap and toList in converting Java collections to Scala collections JsonRDD.scala

In JsonRDD.scalafy, we are using toMap/toList to convert a Java Map/List to a Scala one. These two operations are pretty expensive because they read elements from a Java Map/List and then load to a Scala Map/List. We can use Scala wrappers to wrap those Java collections instead of using toMap/toList.

I did a quick test to see the performance. I had a 2.9GB cached RDD[String] storing one JSON object per record (twitter dataset). My simple test program is attached below.
```scala
val sqlContext = new org.apache.spark.sql.SQLContext(sc)
import sqlContext._

val jsonData = sc.textFile("...")
jsonData.cache.count

val jsonSchemaRDD = sqlContext.jsonRDD(jsonData)
jsonSchemaRDD.registerAsTable("jt")

sqlContext.sql("select count(*) from jt").collect
```
Stages for the schema inference and the table scan both had 48 tasks. These tasks were executed sequentially. For the current implementation, scanning the JSON dataset will materialize values of all fields of a record. The inferred schema of the dataset can be accessed at https://gist.github.com/yhuai/05fe8a57c638c6666f8d.

From the result, there was no significant difference on running `jsonRDD`. For the simple aggregation query, results are attached below.
```
Original:
Run 1: 26.1s
Run 2: 27.03s
Run 3: 27.035s

With this change:
Run 1: 21.086s
Run 2: 21.035s
Run 3: 21.029s
```

JIRA: https://issues.apache.org/jira/browse/SPARK-2603

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1504 from yhuai/removeToMapToList and squashes the following commits:

6831b77 [Yin Huai] Fix failed tests.
09b9bca [Yin Huai] Merge remote-tracking branch 'upstream/master' into removeToMapToList
d1abdb8 [Yin Huai] Remove unnecessary toMap and toList.
[SPARK-2479 (partial)][MLLIB] fix binary metrics unit tests

Allow small errors in comparison.

@dbtsai , this unit test blocks https://github.com/apache/spark/pull/1562 . I may need to merge this one first. We can change it to use the tools in https://github.com/apache/spark/pull/1425 after that PR gets merged.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1576 from mengxr/fix-binary-metrics-unit-tests and squashes the following commits:

5076a7f [Xiangrui Meng] fix binary metrics unit tests
[SPARK-2037]: yarn client mode doesn't support spark.yarn.max.executor.failures

Author: GuoQiang Li <witgo@qq.com>

Closes #1180 from witgo/SPARK-2037 and squashes the following commits:

3d52411 [GuoQiang Li] review commit
7058f4d [GuoQiang Li] Correctly stop SparkContext
6d0561f [GuoQiang Li] Fix: yarn client mode doesn't support spark.yarn.max.executor.failures
SPARK-2250: show stage RDDs in UI

Author: Neville Li <neville@spotify.com>

Closes #1188 from nevillelyh/neville/ui and squashes the following commits:

d3ac425 [Neville Li] SPARK-2250: show persisted RDD in stage UI
f075db9 [Neville Li] SPARK-2035: show call stack even when description is available
[SPARK-2464][Streaming] Fixed Twitter stream stopping bug

Stopping the Twitter Receiver would call twitter4j's TwitterStream.shutdown, which in turn causes an Exception to be thrown to the listener. This exception caused the Receiver to be restarted. This patch check whether the receiver was stopped or not, and accordingly restarts on exception.

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

Closes #1577 from tdas/twitter-stop and squashes the following commits:

011b525 [Tathagata Das] Fixed Twitter stream stopping bug.
[SPARK-2014] Make PySpark store RDDs in MEMORY_ONLY_SER with compression by default

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

Closes #1051 from ScrapCodes/SPARK-2014/pyspark-cache and squashes the following commits:

f192df7 [Prashant Sharma] Code Review
2a2f43f [Prashant Sharma] [SPARK-2014] Make PySpark store RDDs in MEMORY_ONLY_SER with compression by default
[SPARK-2538] [PySpark] Hash based disk spilling aggregation

During aggregation in Python worker, if the memory usage is above spark.executor.memory, it will do disk spilling aggregation.

It will split the aggregation into multiple stage, in each stage, it will partition the aggregated data by hash and dump them into disks. After all the data are aggregated, it will merge all the stages together (partition by partition).

Author: Davies Liu <davies.liu@gmail.com>

Closes #1460 from davies/spill and squashes the following commits:

cad91bf [Davies Liu] call gc.collect() after data.clear() to release memory as much as possible.
37d71f7 [Davies Liu] balance the partitions
902f036 [Davies Liu] add shuffle.py into run-tests
dcf03a9 [Davies Liu] fix memory_info() of psutil
67e6eba [Davies Liu] comment for MAX_TOTAL_PARTITIONS
f6bd5d6 [Davies Liu] rollback next_limit() again, the performance difference is huge:
e74b785 [Davies Liu] fix code style and change next_limit to memory_limit
400be01 [Davies Liu] address all the comments
6178844 [Davies Liu] refactor and improve docs
fdd0a49 [Davies Liu] add long doc string for ExternalMerger
1a97ce4 [Davies Liu] limit used memory and size of objects in partitionBy()
e6cc7f9 [Davies Liu] Merge branch 'master' into spill
3652583 [Davies Liu] address comments
e78a0a0 [Davies Liu] fix style
24cec6a [Davies Liu] get local directory by SPARK_LOCAL_DIR
57ee7ef [Davies Liu] update docs
286aaff [Davies Liu] let spilled aggregation in Python configurable
e9a40f6 [Davies Liu] recursive merger
6edbd1f [Davies Liu] Hash based disk spilling aggregation