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.

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

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

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

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]

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

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.

This reverts commit 06dc0d2c.

#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"

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.

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

I think it's better to defined hiveQlTable as a val

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

Closes #1569 from baishuo/patch-1 and squashes the following commits:

dc2f895 [baishuo(白硕)] Update HiveMetastoreCatalog.scala
a7b32a2 [baishuo(白硕)] Update HiveMetastoreCatalog.scala

Add genjavadocSettings back to SparkBuild. It requires #1585 .

https://issues.apache.org/jira/browse/SPARK-2682

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

Closes #1584 from yhuai/SPARK-2682 and squashes the following commits:

2e89461 [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2682
54e3b66 [Yin Huai] Add genjavadocSettings back.

JIRA issue:

- Main: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)
- Related: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678)

Cherry picked 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.)

TODO

- [x] Use `spark-submit` to launch the server, the CLI and beeline
- [x] Migration guideline draft for Shark users

----

Hit by a bug in `SparkSubmitArguments` while working on this PR: all application options that are recognized by `SparkSubmitArguments` are stolen as `SparkSubmit` options. For example:

```bash
$ spark-submit --class org.apache.hive.beeline.BeeLine spark-internal --help
```

This actually shows usage information of `SparkSubmit` rather than `BeeLine`.

~~Fixed this bug here since the `spark-internal` related stuff also touches `SparkSubmitArguments` and I'd like to avoid conflict.~~

**UPDATE** The bug mentioned above is now tracked by [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678). Decided to revert changes to this bug since it involves more subtle considerations and worth a separate PR.

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

Closes #1399 from liancheng/thriftserver and squashes the following commits:

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

Renaming `short` to `shortForm` and `long` to `longForm`.

JIRA: https://issues.apache.org/jira/browse/SPARK-2683

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

Closes #1585 from yhuai/SPARK-2683 and squashes the following commits:

5ddb843 [Yin Huai] "short" and "long" are Java keyworks. In order to generate javadoc, renaming "short" to "shortForm" and "long" to "longForm".

Our program needs to receive a large amount of data and run for a long
time.
We set the log level to WARN but "Storing iterator" "received single"
as such message written to the log file. (over yarn)

Author: fireflyc <fireflyc@126.com>

Closes #1372 from fireflyc/fix-replace-stdout-log and squashes the following commits:

e684140 [fireflyc] 'info' modified into the 'debug'
fa22a38 [fireflyc] replace println to log4j

Hive Supports the operator "<=>", which returns same result with EQUAL(=) operator for non-null operands, but returns TRUE if both are NULL, FALSE if one of the them is NULL.

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

Closes #1570 from chenghao-intel/equalns and squashes the following commits:

8d6c789 [Cheng Hao] Remove the test case orc_predicate_pushdown
5b2ca88 [Cheng Hao] Add cases into whitelist
8e66cdd [Cheng Hao] Rename the EqualNSTo ==> EqualNullSafe
7af4b0b [Cheng Hao] Add EqualNS & Unit Tests

Author: Reynold Xin <rxin@apache.org>

Closes #1583 from rxin/closureClean and squashes the following commits:

8982fe6 [Reynold Xin] [SPARK-2529] Clean closures in foreach and foreachPartition.

JIRA: https://issues.apache.org/jira/browse/SPARK-2657

Our current code uses ArrayBuffers for each group of values in groupBy, as well as for the key's elements in CoGroupedRDD. ArrayBuffers have a lot of overhead if there are few values in them, which is likely to happen in cases such as join. In particular, they have a pointer to an Object[] of size 16 by default, which is 24 bytes for the array header + 128 for the pointers in there, plus at least 32 for the ArrayBuffer data structure. This patch replaces the per-group buffers with a CompactBuffer class that can store up to 2 elements more efficiently (in fields of itself) and acts like an ArrayBuffer beyond that. For a key's elements in CoGroupedRDD, we use an Array of CompactBuffers instead of an ArrayBuffer of ArrayBuffers.

There are some changes throughout the code to deal with CoGroupedRDD returning Array instead. We can also decide not to do that but CoGroupedRDD is a `DeveloperAPI` so I think it's okay to change it here.

Author: Matei Zaharia <matei@databricks.com>

Closes #1555 from mateiz/compact-groupby and squashes the following commits:

845a356 [Matei Zaharia] Lower initial size of CompactBuffer's vector to 8
07621a7 [Matei Zaharia] Review comments
0c1cd12 [Matei Zaharia] Don't use varargs in CompactBuffer.apply
bdc8a39 [Matei Zaharia] Small tweak to +=, and typos
f61f040 [Matei Zaharia] Fix line lengths
59da88b0 [Matei Zaharia] Fix line lengths
197cde8 [Matei Zaharia] Make CompactBuffer extend Seq to make its toSeq more efficient
775110f [Matei Zaharia] Change CoGroupedRDD to give (K, Array[Iterable[_]]) to avoid wrappers
9b4c6e8 [Matei Zaharia] Use CompactBuffer in CoGroupedRDD
ed577ab [Matei Zaharia] Use CompactBuffer in groupByKey
10f0de1 [Matei Zaharia] A CompactBuffer that's more memory-efficient than ArrayBuffer for small buffers

exact sample size not supported for now.

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

Closes #1554 from dorx/pystratified and squashes the following commits:

4ba927a [Doris Xin] use rel diff (+- 50%) instead of abs diff (+- 50)
bdc3f8b [Doris Xin] updated unit to check sample holistically
7713c7b [Doris Xin] Python version of stratified sampling

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

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

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.

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

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

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-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.

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

...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

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-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

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.

Author: GuoQiang Li <witgo@qq.com>

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

2b6227f [GuoQiang Li] Fix NPE for JsonProtocol

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

Author: witgo <witgo@qq.com>

Closes #1403 from witgo/hive_compatibility and squashes the following commits:

4e5ecdb [witgo] The default does not run hive compatibility tests

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

Closes #1510 from ScrapCodes/SPARK-2549/fun-in-fun and squashes the following commits:

9458bc5 [Prashant Sharma] Tested by removing an inner function from excludes.
bc03b1c [Prashant Sharma] SPARK-2549 Functions defined inside of other functions trigger failures

[SPARK-2102][SQL][CORE] Add option for kryo registration required and use a resource pool in Spark SQL for Kryo instances.

Author: Ian O Connell <ioconnell@twitter.com>

Closes #1377 from ianoc/feature/SPARK-2102 and squashes the following commits:

5498566 [Ian O Connell] Docs update suggested by Patrick
20e8555 [Ian O Connell] Slight style change
f92c294 [Ian O Connell] Add docs for new KryoSerializer option
f3735c8 [Ian O Connell] Add using a kryo resource pool for the SqlSerializer
4e5c342 [Ian O Connell] Register the SparkConf for kryo, it gets swept into serialization
665805a [Ian O Connell] Add a spark.kryo.registrationRequired option for configuring the Kryo Serializer

Instead of shipping just the name and then looking up the info on the workers, we now ship the whole classname.  Also, I refactored the file as it was getting pretty large to move out the type conversion code to its own file.

Author: Michael Armbrust <michael@databricks.com>

Closes #1552 from marmbrus/fixTempUdfs and squashes the following commits:

b695904 [Michael Armbrust] Make add jar execute with Hive.  Ship the whole function class name since sometimes we cannot lookup temporary functions on the workers.

SPARK-2226:  [SQL] transform HAVING clauses with aggregate expressions that aren't in the aggregation list

This change adds an analyzer rule to
  1. find expressions in `HAVING` clause filters that depend on unresolved attributes,
  2. push these expressions down to the underlying aggregates, and then
  3. project them away above the filter.

It also enables the `HAVING` queries in the Hive compatibility suite.

Author: William Benton <willb@redhat.com>

Closes #1497 from willb/spark-2226 and squashes the following commits:

92c9a93 [William Benton] Removed unnecessary import
f1d4f34 [William Benton] Cleanups missed in prior commit
0e1624f [William Benton] Incorporated suggestions from @marmbrus; thanks!
541d4ee [William Benton] Cleanups from review
5a12647 [William Benton] Explanatory comments and stylistic cleanups.
c7f2b2c [William Benton] Whitelist HAVING queries.
29a26e3 [William Benton] Added rule to handle unresolved attributes in HAVING clauses (SPARK-2226)

Hi mridulm, I just think of this issue of [#1212](https://github.com/apache/spark/pull/1212): I added FakeRackUtil to hold the host -> rack mapping. It should be cleaned up after use so that it won't mess up with test cases others may add later.
Really sorry about this.

Author: Rui Li <rui.li@intel.com>

Closes #1454 from lirui-intel/SPARK-2277-fix-UT and squashes the following commits:

f8ea25c [Rui Li] SPARK-2277: clear host->rack info properly

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

Closes #1491 from ueshin/issues/SPARK-2588 and squashes the following commits:

43d0a46 [Takuya UESHIN] Merge branch 'master' into issues/SPARK-2588
1023ea0 [Takuya UESHIN] Modify tests to use DSLs.
2310bf1 [Takuya UESHIN] Add some more DSLs.