SPARK-1553 added alternating nonnegative least squares to MLLib, however it's not possible to access it via the python API.  This pull request resolves that.

Author: Michelangelo D'Agostino <mdagostino@civisanalytics.com>

Closes #3095 from mdagost/python_nmf and squashes the following commits:

a6743ad [Michelangelo D'Agostino] Use setters instead of static methods in PythonMLLibAPI.  Remove the new static methods I added.  Set seed in tests.  Change ratings to ratingsRDD in both train and trainImplicit for consistency.
7cffd39 [Michelangelo D'Agostino] Swapped nonnegative and seed in a few more places.
3fdc851 [Michelangelo D'Agostino] Moved seed to the end of the python parameter list.
bdcc154 [Michelangelo D'Agostino] Change seed type to java.lang.Long so that it can handle null.
cedf043 [Michelangelo D'Agostino] Added in ability to set the seed from python and made that play nice with the nonnegative changes.  Also made the python ALS tests more exact.
a72fdc9 [Michelangelo D'Agostino] Expose nonnegative ALS in the python API.

This PR fix sortBy()/sortByKey() on empty RDD.

This should be back ported into 1.1/1.2

Author: Davies Liu <davies@databricks.com>

Closes #3162 from davies/fix_sort and squashes the following commits:

84f64b7 [Davies Liu] add tests
52995b5 [Davies Liu] fix sortByKey() on empty RDD

This commit exists to close the following pull requests on Github:

Closes #3016 (close requested by 'andrewor14')
Closes #2798 (close requested by 'andrewor14')
Closes #2864 (close requested by 'andrewor14')
Closes #3154 (close requested by 'JoshRosen')
Closes #3156 (close requested by 'JoshRosen')
Closes #214 (close requested by 'kayousterhout')
Closes #2584 (close requested by 'andrewor14')

数组下标越界

Author: xiao321 <1042460381@qq.com>

Closes #3153 from xiao321/patch-1 and squashes the following commits:

0ed17b5 [xiao321] Update JavaCustomReceiver.java

select * from src, get the wrong result set as follows:
```
...
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 309  | val_309  |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
| 97   | val_97   |
...

```

Author: wangfei <wangfei1@huawei.com>

Closes #3149 from scwf/SPARK-4292 and squashes the following commits:

1574a43 [wangfei] using result.collect
8b2d845 [wangfei] adding test
f64eddf [wangfei] result set iter bug

When doing an insert into hive table with partitions the folders written to the file system are in a random order instead of the order defined in table creation. Seems that the loadPartition method in Hive.java has a Map<String,String> parameter but expects to be called with a map that has a defined ordering such as LinkedHashMap. Working on a test but having intillij problems

Author: Matthew Taylor <matthew.t@tbfe.net>

Closes #3076 from tbfenet/partition_dir_order_problem and squashes the following commits:

f1b9a52 [Matthew Taylor] Comment format fix
bca709f [Matthew Taylor] review changes
0e50f6b [Matthew Taylor] test fix
99f1a31 [Matthew Taylor] partition ordering fix
369e618 [Matthew Taylor] partition ordering fix

`Cast` from `DateType` to `DecimalType` throws `NullPointerException`.

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

Closes #3134 from ueshin/issues/SPARK-4270 and squashes the following commits:

7394e4b [Takuya UESHIN] Fix Cast from DateType to DecimalType.

Currently, the data "unwrap" only support couple of primitive types, not all, it will not cause exception, but may get some performance in table scanning for the type like binary, date, timestamp, decimal etc.

Author: Cheng Hao <hao.cheng@intel.com>

Closes #3136 from chenghao-intel/table_reader and squashes the following commits:

fffb729 [Cheng Hao] fix bug for retrieving the timestamp object
e9c97a4 [Cheng Hao] Add more unwrapper functions for primitive type in TableReader

Following description is quoted from JIRA:

When I issue a hql query against a HiveContext where my predicate uses a column of string type with one of LT, LTE, GT, or GTE operator, I get the following error:
scala.MatchError: StringType (of class org.apache.spark.sql.catalyst.types.StringType$)
Looking at the code in org.apache.spark.sql.parquet.ParquetFilters, StringType is absent from the corresponding functions for creating these filters.
To reproduce, in a Hive 0.13.1 shell, I created the following table (at a specified DB):

    create table sparkbug (
    id int,
    event string
    ) stored as parquet;

Insert some sample data:

    insert into table sparkbug select 1, '2011-06-18' from <some table> limit 1;
    insert into table sparkbug select 2, '2012-01-01' from <some table> limit 1;

Launch a spark shell and create a HiveContext to the metastore where the table above is located.

    import org.apache.spark.sql._
    import org.apache.spark.sql.SQLContext
    import org.apache.spark.sql.hive.HiveContext
    val hc = new HiveContext(sc)
    hc.setConf("spark.sql.shuffle.partitions", "10")
    hc.setConf("spark.sql.hive.convertMetastoreParquet", "true")
    hc.setConf("spark.sql.parquet.compression.codec", "snappy")
    import hc._
    hc.hql("select * from <db>.sparkbug where event >= '2011-12-01'")

A scala.MatchError will appear in the output.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3083 from sarutak/SPARK-4213 and squashes the following commits:

4ab6e56 [Kousuke Saruta] WIP
b6890c6 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-4213
9a1fae7 [Kousuke Saruta] Fixed ParquetFilters so that compare Strings

'DOUBLE' should be moved before 'ELSE' according to the ordering convension

Author: Jacky Li <jacky.likun@gmail.com>

Closes #3080 from jackylk/patch-5 and squashes the following commits:

3c11df7 [Jacky Li] [SQL] Modify keyword val location according to ordering

Author: Michael Armbrust <michael@databricks.com>

Closes #3096 from marmbrus/reflectionContext and squashes the following commits:

adc221f [Michael Armbrust] Support ScalaReflection of schema in different universes

This PR resorts to `SparkContext.version` rather than META-INF/MANIFEST.MF in the assembly jar to inspect Spark version. Currently, when built with Maven, the MANIFEST.MF file in the assembly jar is incorrectly replaced by Guava 15.0 MANIFEST.MF, probably because of the assembly/shading tricks.

Another related PR is #3103, which tries to fix the MANIFEST issue.

Author: Cheng Lian <lian@databricks.com>

Closes #3105 from liancheng/spark-4225 and squashes the following commits:

d9585e1 [Cheng Lian] Resorts to SparkContext.version to inspect Spark version

Author: wangfei <wangfei1@huawei.com>

Closes #3127 from scwf/patch-9 and squashes the following commits:

e39a560 [wangfei] now support dynamic partitioning

This PR elimiantes the network package's usage of the Java serializer and replaces it with Encodable, which is a lightweight binary protocol. Each message is preceded by a type id, which will allow us to change messages (by only adding new ones), or to change the format entirely by switching to a special id (such as -1).

This protocol has the advantage over Java that we can guarantee that messages will remain compatible across compiled versions and JVMs, though it does not provide a clean way to do schema migration. In the future, it may be good to use a more heavy-weight serialization format like protobuf, thrift, or avro, but these all add several dependencies which are unnecessary at the present time.

Additionally this unifies the RPC messages of NettyBlockTransferService and ExternalShuffleClient.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3146 from aarondav/free and squashes the following commits:

ed1102a [Aaron Davidson] Remove some unused imports
b8e2a49 [Aaron Davidson] Add appId to test
538f2a3 [Aaron Davidson] [SPARK-4187] [Core] Switch to binary protocol for external shuffle service messages

[SPARK-4204][Core][WebUI] Change Utils.exceptionString to contain the inner exceptions and make the error information in Web UI more friendly

This PR fixed `Utils.exceptionString` to output the full exception information. However, the stack trace may become very huge, so I also updated the Web UI to collapse the error information by default (display the first line and clicking `+detail` will display the full info).

Here are the screenshots:

Stages:
![stages](https://cloud.githubusercontent.com/assets/1000778/4882441/66d8cc68-6356-11e4-8346-6318677d9470.png)

Details for one stage:
![stage](https://cloud.githubusercontent.com/assets/1000778/4882513/1311043c-6357-11e4-8804-ca14240a9145.png)

The full information in the gray text field is:
```Java
org.apache.spark.shuffle.FetchFailedException: Connection reset by peer
	at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$.org$apache$spark$shuffle$hash$BlockStoreShuffleFetcher$$unpackBlock$1(BlockStoreShuffleFetcher.scala:67)
	at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$$anonfun$3.apply(BlockStoreShuffleFetcher.scala:83)
	at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$$anonfun$3.apply(BlockStoreShuffleFetcher.scala:83)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
	at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:30)
	at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
	at org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:129)
	at org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$5.apply(CoGroupedRDD.scala:160)
	at org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$5.apply(CoGroupedRDD.scala:159)
	at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
	at org.apache.spark.rdd.CoGroupedRDD.compute(CoGroupedRDD.scala:159)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
	at org.apache.spark.rdd.MappedValuesRDD.compute(MappedValuesRDD.scala:31)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
	at org.apache.spark.rdd.FlatMappedValuesRDD.compute(FlatMappedValuesRDD.scala:31)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
	at org.apache.spark.scheduler.Task.run(Task.scala:56)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:189)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.IOException: Connection reset by peer
	at sun.nio.ch.FileDispatcher.read0(Native Method)
	at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:21)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:198)
	at sun.nio.ch.IOUtil.read(IOUtil.java:166)
	at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:245)
	at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:311)
	at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)
	at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:225)
	at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)
	at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
	at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
	at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
	at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
	... 1 more
```

/cc aarondav

Author: zsxwing <zsxwing@gmail.com>

Closes #3073 from zsxwing/SPARK-4204 and squashes the following commits:

176d1e3 [zsxwing] Add comments to explain the stack trace difference
ca509d3 [zsxwing] Add fullStackTrace to the constructor of ExceptionFailure
a07057b [zsxwing] Core style fix
dfb0032 [zsxwing] Backward compatibility for old history server
1e50f71 [zsxwing] Update as per review and increase the max height of the stack trace details
94f2566 [zsxwing] Change Utils.exceptionString to contain the inner exceptions and make the error information in Web UI more friendly

This relies on a hook from whoever is hosting the shuffle service to invoke removeApplication() when the application is completed. Once invoked, we will clean up all the executors' shuffle directories we know about.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3126 from aarondav/cleanup and squashes the following commits:

33a64a9 [Aaron Davidson] Missing brace
e6e428f [Aaron Davidson] Address comments
16a0d27 [Aaron Davidson] Cleanup
e4df3e7 [Aaron Davidson] [SPARK-4236] Cleanup removed applications' files in shuffle service

This adds a RetryingBlockFetcher to the NettyBlockTransferService which is wrapped around our typical OneForOneBlockFetcher, adding retry logic in the event of an IOException.

This sort of retry allows us to avoid marking an entire executor as failed due to garbage collection or high network load.

TODO:
- [x] unit tests
- [x] put in ExternalShuffleClient too

Author: Aaron Davidson <aaron@databricks.com>

Closes #3101 from aarondav/retry and squashes the following commits:

72a2a32 [Aaron Davidson] Add that we should remove the condition around the retry thingy
c7fd107 [Aaron Davidson] Fix unit tests
e80e4c2 [Aaron Davidson] Address initial comments
6f594cd [Aaron Davidson] Fix unit test
05ff43c [Aaron Davidson] Add to external shuffle client and add unit test
66e5a24 [Aaron Davidson] [SPARK-4238] [Core] Perform network-level retry of shuffle file fetches

Author: Aaron Davidson <aaron@databricks.com>

Closes #3142 from aarondav/worker and squashes the following commits:

3780bd7 [Aaron Davidson] Address comments
2dcdfc1 [Aaron Davidson] Add private[worker]
47f49d3 [Aaron Davidson] NettyBlockTransferService shouldn't care about app ids (it's only b/t executors)
258417c [Aaron Davidson] [SPARK-4277] Support external shuffle service on executor

I did not realize there was a `network.util.JavaUtils` when I wrote this code. This PR moves the `ByteBuffer` string conversion to the appropriate place. I tested the changes on a stable yarn cluster.

Author: Andrew Or <andrew@databricks.com>

Closes #3144 from andrewor14/yarn-shuffle-util and squashes the following commits:

b6c08bf [Andrew Or] Remove unused import
94e205c [Andrew Or] Use netty Unpooled
85202a5 [Andrew Or] Use guava Charsets
057135b [Andrew Or] Reword comment
adf186d [Andrew Or] Move byte buffer String conversion logic to JavaUtils

This was added by me in https://github.com/apache/spark/commit/61a5cced049a8056292ba94f23fa7bd040f50685. The real fix will be added in [SPARK-4281](https://issues.apache.org/jira/browse/SPARK-4281).

Author: Andrew Or <andrew@databricks.com>

Closes #3145 from andrewor14/fix-make-distribution and squashes the following commits:

c78be61 [Andrew Or] Hot fix make distribution

at first srcIds is not initialized and are all 0. so we use edgeArray(0).srcId to currSrcId

Author: lianhuiwang <lianhuiwang09@gmail.com>

Closes #3138 from lianhuiwang/SPARK-4249 and squashes the following commits:

3f4e503 [lianhuiwang] fix a problem of EdgePartitionBuilder in Graphx

Author: Aaron Davidson <aaron@databricks.com>

Closes #3128 from aarondav/compiter and squashes the following commits:

698e4be [Aaron Davidson] [SPARK-4264] Completion iterator should only invoke callback once

add binaryFiles() and binaryRecords() in Python
```
binaryFiles(self, path, minPartitions=None):
    :: Developer API ::

    Read a directory of binary files from HDFS, a local file system
    (available on all nodes), or any Hadoop-supported file system URI
    as a byte array. Each file is read as a single record and returned
    in a key-value pair, where the key is the path of each file, the
    value is the content of each file.

    Note: Small files are preferred, large file is also allowable, but
    may cause bad performance.

binaryRecords(self, path, recordLength):
    Load data from a flat binary file, assuming each record is a set of numbers
    with the specified numerical format (see ByteBuffer), and the number of
    bytes per record is constant.

    :param path: Directory to the input data files
    :param recordLength: The length at which to split the records
```

Author: Davies Liu <davies@databricks.com>

Closes #3078 from davies/binary and squashes the following commits:

cd0bdbd [Davies Liu] Merge branch 'master' of github.com:apache/spark into binary
3aa349b [Davies Liu] add experimental notes
24e84b6 [Davies Liu] Merge branch 'master' of github.com:apache/spark into binary
5ceaa8a [Davies Liu] Merge branch 'master' of github.com:apache/spark into binary
1900085 [Davies Liu] bugfix
bb22442 [Davies Liu] add binaryFiles and binaryRecords in Python

This commit stripes table rows after hiding some rows, to
ensure that rows are correct striped to alternate white
and grey even when rows are hidden by default.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #3117 from kayousterhout/striping and squashes the following commits:

be6e10a [Kay Ousterhout] [SPARK-4255] Fix incorrect table striping

This issue was uncovered after [this discussion](https://issues.apache.org/jira/browse/SPARK-3398?focusedCommentId=14187471&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-14187471).

Don't change the working directory on the user. This breaks relative paths the user may pass in, e.g., for the SSH identity file.

```
./ec2/spark-ec2 -i ../my.pem
```

This patch will preserve the user's current working directory and allow calls like the one above to work.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2988 from nchammas/spark-ec2-cwd and squashes the following commits:

f3850b5 [Nicholas Chammas] pep8 fix
fbc20c7 [Nicholas Chammas] revert to old commenting style
752f958 [Nicholas Chammas] specify deploy.generic path absolutely
bcdf6a5 [Nicholas Chammas] fix typo
77871a2 [Nicholas Chammas] add clarifying comment
ce071fc [Nicholas Chammas] don't change working dir

 marmbrus

Author: Xiangrui Meng <meng@databricks.com>

Closes #3125 from mengxr/SPARK-4262 and squashes the following commits:

307695e [Xiangrui Meng] add .schemaRDD to JavaSchemaRDD

Changed code so it does not try to serialize Params.
CC: mengxr 	debasish83 srowen

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3116 from jkbradley/als-bugfix and squashes the following commits:

e575bd8 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into als-bugfix
9401b16 [Joseph K. Bradley] changed implicitPrefs so it is not serialized to fix MovieLensALS example bug

Mesos offers may not contain all resources, and Spark needs to check to
ensure they are present and sufficient.  Spark may throw an erroneous
exception when resources aren't present.

Author: Brenden Matthews <brenden@diddyinc.com>

Closes #3024 from brndnmtthws/fix-mesos-resource-misuse and squashes the following commits:

e5f9580 [Brenden Matthews] [SPARK-4158] Fix for missing resources.

...n mesos cluster mode

- change master newer

Author: Jongyoul Lee <jongyoul@gmail.com>

Closes #3034 from jongyoul/SPARK-3223 and squashes the following commits:

42b2ed3 [Jongyoul Lee] SPARK-3223 runAsSparkUser cannot change HDFS write permission properly in mesos cluster mode - change master newer

This is a minor docs update which helps to clarify the way local[n] is used for streaming apps.

Author: jay@apache.org <jayunit100>

Closes #2964 from jayunit100/SPARK-4040 and squashes the following commits:

35b5a5e [jay@apache.org] SPARK-4040: Update documentation to exemplify use of local (n) value.

This creates a new module `network/yarn` that depends on `network/shuffle` recently created in #3001. This PR introduces a custom Yarn auxiliary service that runs the external shuffle service. As of the changes here this shuffle service is required for using dynamic allocation with Spark.

This is still WIP mainly because it doesn't handle security yet. I have tested this on a stable Yarn cluster.

Author: Andrew Or <andrew@databricks.com>

Closes #3082 from andrewor14/yarn-shuffle-service and squashes the following commits:

ef3ddae [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
0ee67a2 [Andrew Or] Minor wording suggestions
1c66046 [Andrew Or] Remove unused provided dependencies
0eb6233 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
6489db5 [Andrew Or] Try catch at the right places
7b71d8f [Andrew Or] Add detailed java docs + reword a few comments
d1124e4 [Andrew Or] Add security to shuffle service (INCOMPLETE)
5f8a96f [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
9b6e058 [Andrew Or] Address various feedback
f48b20c [Andrew Or] Fix tests again
f39daa6 [Andrew Or] Do not make network-yarn an assembly module
761f58a [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
15a5b37 [Andrew Or] Fix build for Hadoop 1.x
baff916 [Andrew Or] Fix tests
5bf9b7e [Andrew Or] Address a few minor comments
5b419b8 [Andrew Or] Add missing license header
804e7ff [Andrew Or] Include the Yarn shuffle service jar in the distribution
cd076a4 [Andrew Or] Require external shuffle service for dynamic allocation
ea764e0 [Andrew Or] Connect to Yarn shuffle service only if it's enabled
1bf5109 [Andrew Or] Use the shuffle service port specified through hadoop config
b4b1f0c [Andrew Or] 4 tabs -> 2 tabs
43dcb96 [Andrew Or] First cut integration of shuffle service with Yarn aux service
b54a0c4 [Andrew Or] Initial skeleton for Yarn shuffle service

replaces the existing read() call with readFully().

Author: industrial-sloth <industrial-sloth@users.noreply.github.com>

Closes #3093 from industrial-sloth/branch-1.2-fixedLenRecRdr and squashes the following commits:

a245c8a [industrial-sloth] use readFully in FixedLengthBinaryRecordReader

(cherry picked from commit 6844e7a8)
Signed-off-by: Matei Zaharia <matei@databricks.com>

This commit fixes the scheduler delay in the UI (which previously
included things that are not scheduler delay, like time to
deserialize the task and serialize the result), and also
adds information about time to deserialize tasks to the optional
additional metrics.  Time to deserialize the task can be large relative
to task time for short jobs, and understanding when it is high can help
developers realize that they should try to reduce closure size (e.g, by including
less data in the task description).

cc shivaram etrain

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #2832 from kayousterhout/SPARK-3983 and squashes the following commits:

0c1398e [Kay Ousterhout] Fixed ordering
531575d [Kay Ousterhout] Removed executor launch time
1f13afe [Kay Ousterhout] Minor spacing fixes
335be4b [Kay Ousterhout] Made metrics hideable
5bc3cba [Kay Ousterhout] [SPARK-3984] [SPARK-3983] Improve UI task metrics.

Does three things: (1) Adds SASL to ExternalShuffleClient, (2) puts SecurityManager in BlockManager's constructor, and (3) adds unit test.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3108 from aarondav/sasl-client and squashes the following commits:

48b622d [Aaron Davidson] Screw it, let's just get LimitedInputStream
3543b70 [Aaron Davidson] Back out of pom change due to unknown test issue?
b58518a [Aaron Davidson] ByteStreams.limit() not available :(
cbe451a [Aaron Davidson] Address comments
2bf2908 [Aaron Davidson] [SPARK-4242] [Core] Add SASL to external shuffle service

### Summary

* Made it easier to construct default Strategy and BoostingStrategy and to set parameters using simple types.
* Added Scala and Java examples for GradientBoostedTrees
* small cleanups and fixes

### Details

GradientBoosting bug fixes (“bug” = bad default options)
* Force boostingStrategy.weakLearnerParams.algo = Regression
* Force boostingStrategy.weakLearnerParams.impurity = impurity.Variance
* Only persist data if not yet persisted (since it causes an error if persisted twice)

BoostingStrategy
* numEstimators: renamed to numIterations
* removed subsamplingRate (duplicated by Strategy)
* removed categoricalFeaturesInfo since it belongs with the weak learner params (since boosting can be oblivious to feature type)
* Changed algo to var (not val) and added BeanProperty, with overload taking String argument
* Added assertValid() method
* Updated defaultParams() method and eliminated defaultWeakLearnerParams() since that belongs in Strategy

Strategy (for DecisionTree)
* Changed algo to var (not val) and added BeanProperty, with overload taking String argument
* Added setCategoricalFeaturesInfo method taking Java Map.
* Cleaned up assertValid
* Changed val’s to def’s since parameters can now be changed.

CC: manishamde mengxr codedeft

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3094 from jkbradley/gbt-api and squashes the following commits:

7a27e22 [Joseph K. Bradley] scalastyle fix
52013d5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into gbt-api
e9b8410 [Joseph K. Bradley] Summary of changes

[SPARK-4029][Streaming] Update streaming driver to reliably save and recover received block metadata on driver failures

As part of the initiative of preventing data loss on driver failure, this JIRA tracks the sub task of modifying the streaming driver to reliably save received block metadata, and recover them on driver restart.

This was solved by introducing a `ReceivedBlockTracker` that takes all the responsibility of managing the metadata of received blocks (i.e. `ReceivedBlockInfo`, and any actions on them (e.g, allocating blocks to batches, etc.). All actions to block info get written out to a write ahead log (using `WriteAheadLogManager`). On recovery, all the actions are replaying to recreate the pre-failure state of the `ReceivedBlockTracker`, which include the batch-to-block allocations and the unallocated blocks.

Furthermore, the `ReceiverInputDStream` was modified to create `WriteAheadLogBackedBlockRDD`s when file segment info is present in the `ReceivedBlockInfo`. After recovery of all the block info (through recovery `ReceivedBlockTracker`), the `WriteAheadLogBackedBlockRDD`s gets recreated with the recovered info, and jobs submitted. The data of the blocks gets pulled from the write ahead logs, thanks to the segment info present in the `ReceivedBlockInfo`.

This is still a WIP. Things that are missing here are.

- *End-to-end integration tests:* Unit tests that tests the driver recovery, by killing and restarting the streaming context, and verifying all the input data gets processed. This has been implemented but not included in this PR yet. A sneak peek of that DriverFailureSuite can be found in this PR (on my personal repo): https://github.com/tdas/spark/pull/25 I can either include it in this PR, or submit that as a separate PR after this gets in.

- *WAL cleanup:* Cleaning up the received data write ahead log, by calling `ReceivedBlockHandler.cleanupOldBlocks`. This is being worked on.

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

Closes #3026 from tdas/driver-ha-rbt and squashes the following commits:

a8009ed [Tathagata Das] Added comment
1d704bb [Tathagata Das] Enabled storing recovered WAL-backed blocks to BM
2ee2484 [Tathagata Das] More minor changes based on PR
47fc1e3 [Tathagata Das] Addressed PR comments.
9a7e3e4 [Tathagata Das] Refactored ReceivedBlockTracker API a bit to make things a little cleaner for users of the tracker.
af63655 [Tathagata Das] Minor changes.
fce2b21 [Tathagata Das] Removed commented lines
59496d3 [Tathagata Das] Changed class names, made allocation more explicit and added cleanup
19aec7d [Tathagata Das] Fixed casting bug.
f66d277 [Tathagata Das] Fix line lengths.
cda62ee [Tathagata Das] Added license
25611d6 [Tathagata Das] Minor changes before submitting PR
7ae0a7fb [Tathagata Das] Transferred changes from driver-ha-working branch

```
pyspark.mllib.stat.StatisticschiSqTest(observed, expected=None)
    :: Experimental ::

    If `observed` is Vector, conduct Pearson's chi-squared goodness
    of fit test of the observed data against the expected distribution,
    or againt the uniform distribution (by default), with each category
    having an expected frequency of `1 / len(observed)`.
    (Note: `observed` cannot contain negative values)

    If `observed` is matrix, conduct Pearson's independence test on the
    input contingency matrix, which cannot contain negative entries or
    columns or rows that sum up to 0.

    If `observed` is an RDD of LabeledPoint, conduct Pearson's independence
    test for every feature against the label across the input RDD.
    For each feature, the (feature, label) pairs are converted into a
    contingency matrix for which the chi-squared statistic is computed.
    All label and feature values must be categorical.

    :param observed: it could be a vector containing the observed categorical
                     counts/relative frequencies, or the contingency matrix
                     (containing either counts or relative frequencies),
                     or an RDD of LabeledPoint containing the labeled dataset
                     with categorical features. Real-valued features will be
                     treated as categorical for each distinct value.
    :param expected: Vector containing the expected categorical counts/relative
                     frequencies. `expected` is rescaled if the `expected` sum
                     differs from the `observed` sum.
    :return: ChiSquaredTest object containing the test statistic, degrees
             of freedom, p-value, the method used, and the null hypothesis.
```

Author: Davies Liu <davies@databricks.com>

Closes #3091 from davies/his and squashes the following commits:

145d16c [Davies Liu] address comments
0ab0764 [Davies Liu] fix float
5097d54 [Davies Liu] add Hypothesis test Python API

Author: Michael Armbrust <michael@databricks.com>

Closes #3097 from marmbrus/asString and squashes the following commits:

6430520 [Michael Armbrust] Add String option for DSL AS

Also lays the groundwork for supporting it inside the external shuffle service.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3087 from aarondav/sasl and squashes the following commits:

3481718 [Aaron Davidson] Delete rogue println
44f8410 [Aaron Davidson] Delete documentation - muahaha!
eb9f065 [Aaron Davidson] Improve documentation and add end-to-end test at Spark-level
a6b95f1 [Aaron Davidson] Address comments
785bbde [Aaron Davidson] Cleanup
79973cb [Aaron Davidson] Remove unused file
151b3c5 [Aaron Davidson] Add docs, timeout config, better failure handling
f6177d7 [Aaron Davidson] Cleanup SASL state upon connection termination
7b42adb [Aaron Davidson] Add unit tests
8191bcb [Aaron Davidson] [SPARK-2938] Support SASL authentication in NettyBlockTransferService

Author: Niklas Wilcke <1wilcke@informatik.uni-hamburg.de>

Closes #2907 from numbnut/master and squashes the following commits:

7f7c767 [Niklas Wilcke] [Spark-4060] [MLlib] exposing special rdd functions to the public, #2907