[SPARK-4242] [Core] Add SASL to external shuffle service

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
[SPARK-3984] [SPARK-3983] Fix incorrect scheduler delay and display task deserialization time in UI

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.
SPARK-4222 [CORE] use readFully in FixedLengthBinaryRecordReader

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 6844e7a8219ac78790a422ffd5054924e7d2bea1)
Signed-off-by: Matei Zaharia <matei@databricks.com>
[SPARK-3797] Run external shuffle service in Yarn NM

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
SPARK-4040. Update documentation to exemplify use of local (n) value, fo...

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.
SPARK-3223 runAsSparkUser cannot change HDFS write permission properly i...

...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
[SPARK-4158] Fix for missing resources.

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.
[SPARK-4254] [mllib] MovieLensALS bug fix

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
[SPARK-4262][SQL] add .schemaRDD to JavaSchemaRDD

 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
[SPARK-4137] [EC2] Don't change working dir on user

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
[SPARK-4255] Fix incorrect table striping

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
[SPARK-4186] add binaryFiles and binaryRecords in Python

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
[SPARK-4264] Completion iterator should only invoke callback once

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
[SPARK-4249][GraphX]fix a problem of EdgePartitionBuilder in Graphx

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
[HOT FIX] Make distribution fails

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
[SPARK-3797] Minor addendum to Yarn shuffle service

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
[SPARK-4277] Support external shuffle service on Standalone Worker

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
[SPARK-4188] [Core] Perform network-level retry of shuffle file fetches

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
[SPARK-4236] Cleanup removed applications' files in shuffle service

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
[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