[SPARK-2125] Add sort flag and move sort into shuffle implementations

This patch adds a sort flag into ShuffleDependecy and moves sort into hash shuffle implementation.

Moving sort into shuffle implementation can give space for other shuffle implementations (like sort-based shuffle) to better optimize sort through shuffle.

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

Closes #1210 from jerryshao/SPARK-2125 and squashes the following commits:

2feaf7b [jerryshao] revert MimaExcludes
ceddf75 [jerryshao] add MimaExeclude
f674ff4 [jerryshao] Add missing Scope restriction
b9fe0dd [jerryshao] Fix some style issues according to comments
ef6b729 [jerryshao] Change sort flag into Option
3f6eeed [jerryshao] Fix issues related to unit test
2f552a5 [jerryshao] Minor changes about naming and order
c92a281 [jerryshao] Move sort into shuffle implementations
[SPARK-1726] [SPARK-2567] Eliminate zombie stages in UI.

Due to problems with when we update runningStages (in DAGScheduler.scala)
and how we decide to send a SparkListenerStageCompleted message to
SparkListeners, sometimes stages can be shown as "running" in the UI forever
(even after they have failed).  This issue can manifest when stages are
resubmitted with 0 tasks, or when the DAGScheduler catches non-serializable
tasks. The problem also resulted in a (small) memory leak in the DAGScheduler,
where stages can stay in runningStages forever. This commit fixes
that problem and adds a unit test.

Thanks tsudukim for helping to look into this issue!

cc markhamstra rxin

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1566 from kayousterhout/dag_fix and squashes the following commits:

217d74b [Kay Ousterhout] [SPARK-1726] [SPARK-2567] Eliminate zombie stages in UI.
Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

This reverts commit 06dc0d2c6b69c5d59b4d194ced2ac85bfe2e05e2.

#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"
Part of [SPARK-2456] Removed some HashMaps from DAGScheduler by storing information in Stage.

This is part of the scheduler cleanup/refactoring effort to make the scheduler code easier to maintain.

@kayousterhout @markhamstra please take a look ...

Author: Reynold Xin <rxin@apache.org>

Closes #1561 from rxin/dagSchedulerHashMaps and squashes the following commits:

1c44e15 [Reynold Xin] Clear pending tasks in submitMissingTasks.
620a0d1 [Reynold Xin] Use filterKeys.
5b54404 [Reynold Xin] Code review feedback.
c1e9a1c [Reynold Xin] Removed some HashMaps from DAGScheduler by storing information in Stage.
[SPARK-2659][SQL] Fix division semantics for hive

Author: Michael Armbrust <michael@databricks.com>

Closes #1557 from marmbrus/fixDivision and squashes the following commits:

b85077f [Michael Armbrust] Fix unit tests.
af98f29 [Michael Armbrust] Change DIV to long type
0c29ae8 [Michael Armbrust] Fix division semantics for hive
[SPARK-1458] [PySpark] Expose sc.version in Java and PySpark

Author: Josh Rosen <joshrosen@apache.org>

Closes #1596 from JoshRosen/spark-1458 and squashes the following commits:

fdbb0bf [Josh Rosen] Add SparkContext.version to Python & Java [SPARK-1458]
[SPARK-2696] Reduce default value of spark.serializer.objectStreamReset

The current default value of spark.serializer.objectStreamReset is 10,000.
When trying to re-partition (e.g., to 64 partitions) a large file (e.g., 500MB), containing 1MB records, the serializer will cache 10000 x 1MB x 64 ~= 640 GB which will cause out of memory errors.

This patch sets the default value to a more reasonable default value (100).

Author: Hossein <hossein@databricks.com>

Closes #1595 from falaki/objectStreamReset and squashes the following commits:

650a935 [Hossein] Updated documentation
1aa0df8 [Hossein] Reduce default value of spark.serializer.objectStreamReset
[SPARK-2652] [PySpark] Turning some default configs for PySpark

Add several default configs for PySpark, related to serialization in JVM.

spark.serializer = org.apache.spark.serializer.KryoSerializer
spark.serializer.objectStreamReset = 100
spark.rdd.compress = True

This will help to reduce the memory usage during RDD.partitionBy()

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

Closes #1568 from davies/conf and squashes the following commits:

cd316f1 [Davies Liu] remove duplicated line
f71a355 [Davies Liu] rebase to master, add spark.rdd.compress = True
8f63f45 [Davies Liu] Merge branch 'master' into conf
8bc9f08 [Davies Liu] fix unittest
c04a83d [Davies Liu] some default configs for PySpark
[SPARK-2279] Added emptyRDD method to Java API

Added emptyRDD method to Java API with tests.

Author: bpaulin <bob@bobpaulin.com>

Closes #1597 from bobpaulin/SPARK-2279 and squashes the following commits:

5ad57c2 [bpaulin] [SPARK-2279] Added emptyRDD method to Java API
[SPARK-2704] Name threads in ConnectionManager and mark them as daemon.

handleMessageExecutor, handleReadWriteExecutor, and handleConnectExecutor are not marked as daemon and not named. I think there exists some condition in which Spark programs won't terminate because of this.

Stack dump attached in https://issues.apache.org/jira/browse/SPARK-2704

Author: Reynold Xin <rxin@apache.org>

Closes #1604 from rxin/daemon and squashes the following commits:

98d6a6c [Reynold Xin] [SPARK-2704] Name threads in ConnectionManager and mark them as daemon.
[SPARK-2601] [PySpark] Fix Py4J error when transforming pickleFiles

Similar to SPARK-1034, the problem was that Py4J didn’t cope well with the fake ClassTags used in the Java API.  It doesn’t look like there’s any reason why PythonRDD needs to take a ClassTag, since it just ignores the type of the previous RDD, so I removed the type parameter and we no longer pass ClassTags from Python.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1605 from JoshRosen/spark-2601 and squashes the following commits:

b68e118 [Josh Rosen] Fix Py4J error when transforming pickleFiles [SPARK-2601]
SPARK-2680: Lower spark.shuffle.memoryFraction to 0.2 by default

Author: Matei Zaharia <matei@databricks.com>

Closes #1593 from mateiz/spark-2680 and squashes the following commits:

3c949c4 [Matei Zaharia] Lower spark.shuffle.memoryFraction to 0.2 by default
[SPARK-2361][MLLIB] Use broadcast instead of serializing data directly into task closure

We saw task serialization problems with large feature dimension, which could be avoid if we don't serialize data directly into task but use broadcast variables. This PR uses broadcast in both training and prediction and adds tests to make sure the task size is small.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1427 from mengxr/broadcast-new and squashes the following commits:

b9a1228 [Xiangrui Meng] style update
b97c184 [Xiangrui Meng] minimal change to LBFGS
9ebadcc [Xiangrui Meng] add task size test to RowMatrix
9427bf0 [Xiangrui Meng] add task size tests to linear methods
e0a5cf2 [Xiangrui Meng] add task size test to GD
28a8411 [Xiangrui Meng] add test for NaiveBayes
380778c [Xiangrui Meng] update KMeans test
bccab92 [Xiangrui Meng] add task size test to LBFGS
02103ba [Xiangrui Meng] remove print
e73d68e [Xiangrui Meng] update tests for k-means
174cb15 [Xiangrui Meng] use local-cluster for test with a small akka.frameSize
1928a5a [Xiangrui Meng] add test for KMeans task size
e00c2da [Xiangrui Meng] use broadcast in GD, KMeans
010d076 [Xiangrui Meng] modify NaiveBayesModel and GLM to use broadcast
[SPARK-2679] [MLLib] Ser/De for Double

Added a set of serializer/deserializer for Double in _common.py and PythonMLLibAPI in MLLib.

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1581 from dorx/doubleSerDe and squashes the following commits:

86a85b3 [Doris Xin] Merge branch 'master' into doubleSerDe
2bfe7a4 [Doris Xin] Removed magic byte
ad4d0d9 [Doris Xin] removed a space in unit
a9020bc [Doris Xin] units passed
7dad9af [Doris Xin] WIP
SPARK-2684: Update ExternalAppendOnlyMap to take an iterator as input

This will decrease object allocation from the "update" closure used in map.changeValue.

Author: Matei Zaharia <matei@databricks.com>

Closes #1607 from mateiz/spark-2684 and squashes the following commits:

b7d89e6 [Matei Zaharia] Add insertAll for Iterables too, and fix some code style
561fc97 [Matei Zaharia] Update ExternalAppendOnlyMap to take an iterator as input
[SPARK-2705][CORE] Fixed stage description in stage info page

Stage description should be a `String`, but was changed to an `Option[String]` by mistake:

![stage-desc-small](https://cloud.githubusercontent.com/assets/230655/3655611/f6d0b0f6-117b-11e4-83ed-71000dcd5009.png)

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

Closes #1524 from liancheng/fix-stage-desc and squashes the following commits:

3c69327 [Cheng Lian] Fixed stage description object type in Web UI stage table
[SPARK-2410][SQL] Merging Hive Thrift/JDBC server

(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
[SPARK-1777] Prevent OOMs from single partitions

**Problem.** When caching, we currently unroll the entire RDD partition before making sure we have enough free memory. This is a common cause for OOMs especially when (1) the BlockManager has little free space left in memory, and (2) the partition is large.

**Solution.** We maintain a global memory pool of `M` bytes shared across all threads, similar to the way we currently manage memory for shuffle aggregation. Then, while we unroll each partition, periodically check if there is enough space to continue. If not, drop enough RDD blocks to ensure we have at least `M` bytes to work with, then try again. If we still don't have enough space to unroll the partition, give up and drop the block to disk directly if applicable.

**New configurations.**
- `spark.storage.bufferFraction` - the value of `M` as a fraction of the storage memory. (default: 0.2)
- `spark.storage.safetyFraction` - a margin of safety in case size estimation is slightly off. This is the equivalent of the existing `spark.shuffle.safetyFraction`. (default 0.9)

For more detail, see the [design document](https://issues.apache.org/jira/secure/attachment/12651793/spark-1777-design-doc.pdf). Tests pending for performance and memory usage patterns.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1165 from andrewor14/them-rdd-memories and squashes the following commits:

e77f451 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
c7c8832 [Andrew Or] Simplify logic + update a few comments
269d07b [Andrew Or] Very minor changes to tests
6645a8a [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
b7e165c [Andrew Or] Add new tests for unrolling blocks
f12916d [Andrew Or] Slightly clean up tests
71672a7 [Andrew Or] Update unrollSafely tests
369ad07 [Andrew Or] Correct ensureFreeSpace and requestMemory behavior
f4d035c [Andrew Or] Allow one thread to unroll multiple blocks
a66fbd2 [Andrew Or] Rename a few things + update comments
68730b3 [Andrew Or] Fix weird scalatest behavior
e40c60d [Andrew Or] Fix MIMA excludes
ff77aa1 [Andrew Or] Fix tests
1a43c06 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
b9a6eee [Andrew Or] Simplify locking behavior on unrollMemoryMap
ed6cda4 [Andrew Or] Formatting fix (super minor)
f9ff82e [Andrew Or] putValues -> putIterator + putArray
beb368f [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
8448c9b [Andrew Or] Fix tests
a49ba4d [Andrew Or] Do not expose unroll memory check period
69bc0a5 [Andrew Or] Always synchronize on putLock before unrollMemoryMap
3f5a083 [Andrew Or] Simplify signature of ensureFreeSpace
dce55c8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
8288228 [Andrew Or] Synchronize put and unroll properly
4f18a3d [Andrew Or] bufferFraction -> unrollFraction
28edfa3 [Andrew Or] Update a few comments / log messages
728323b [Andrew Or] Do not synchronize every 1000 elements
5ab2329 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
129c441 [Andrew Or] Fix bug: Use toArray rather than array
9a65245 [Andrew Or] Update a few comments + minor control flow changes
57f8d85 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
abeae4f [Andrew Or] Add comment clarifying the MEMORY_AND_DISK case
3dd96aa [Andrew Or] AppendOnlyBuffer -> Vector (+ a few small changes)
f920531 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
0871835 [Andrew Or] Add an effective storage level interface to BlockManager
64e7d4c [Andrew Or] Add/modify a few comments (minor)
8af2f35 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
4f4834e [Andrew Or] Use original storage level for blocks dropped to disk
ecc8c2d [Andrew Or] Fix binary incompatibility
24185ea [Andrew Or] Avoid dropping a block back to disk if reading from disk
2b7ee66 [Andrew Or] Fix bug in SizeTracking*
9b9a273 [Andrew Or] Fix tests
20eb3e5 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
649bdb3 [Andrew Or] Document spark.storage.bufferFraction
a10b0e7 [Andrew Or] Add initial memory request threshold + rename a few things
e9c3cb0 [Andrew Or] cacheMemoryMap -> unrollMemoryMap
198e374 [Andrew Or] Unfold -> unroll
0d50155 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
d9d02a8 [Andrew Or] Remove unused param in unfoldSafely
ec728d8 [Andrew Or] Add tests for safe unfolding of blocks
22b2209 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
078eb83 [Andrew Or] Add check for hasNext in PrimitiveVector.iterator
0871535 [Andrew Or] Fix tests in BlockManagerSuite
d68f31e [Andrew Or] Safely unfold blocks for all memory puts
5961f50 [Andrew Or] Fix tests
195abd7 [Andrew Or] Refactor: move unfold logic to MemoryStore
1e82d00 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
3ce413e [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
d5dd3b4 [Andrew Or] Free buffer memory in finally
ea02eec [Andrew Or] Fix tests
b8e1d9c [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
a8704c1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
e1b8b25 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
87aa75c [Andrew Or] Fix mima excludes again (typo)
11eb921 [Andrew Or] Clarify comment (minor)
50cae44 [Andrew Or] Remove now duplicate mima exclude
7de5ef9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
df47265 [Andrew Or] Fix binary incompatibility
6d05a81 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories
f94f5af [Andrew Or] Update a few comments (minor)
776aec9 [Andrew Or] Prevent OOM if a single RDD partition is too large
bbd3eea [Andrew Or] Fix CacheManagerSuite to use Array
97ea499 [Andrew Or] Change BlockManager interface to use Arrays
c12f093 [Andrew Or] Add SizeTrackingAppendOnlyBuffer and tests
[SPARK-2514] [mllib] Random RDD generator

Utilities for generating random RDDs.

RandomRDD and RandomVectorRDD are created instead of using `sc.parallelize(range:Range)` because `Range` objects in Scala can only have `size <= Int.MaxValue`.

The object `RandomRDDGenerators` can be transformed into a generator class to reduce the number of auxiliary methods for optional arguments.

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1520 from dorx/randomRDD and squashes the following commits:

01121ac [Doris Xin] reviewer comments
6bf27d8 [Doris Xin] Merge branch 'master' into randomRDD
a8ea92d [Doris Xin] Reviewer comments
063ea0b [Doris Xin] Merge branch 'master' into randomRDD
aec68eb [Doris Xin] newline
bc90234 [Doris Xin] units passed.
d56cacb [Doris Xin] impl with RandomRDD
92d6f1c [Doris Xin] solution for Cloneable
df5bcff [Doris Xin] Merge branch 'generator' into randomRDD
f46d928 [Doris Xin] WIP
49ed20d [Doris Xin] alternative poisson distribution generator
7cb0e40 [Doris Xin] fix for data inconsistency
8881444 [Doris Xin] RandomRDDGenerator: initial design
Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

This reverts commit f6ff2a61d00d12481bfb211ae13d6992daacdcc2.