SPARK-2685. Update ExternalAppendOnlyMap to avoid buffer.remove()

Replaces this with an O(1) operation that does not have to shift over
the whole tail of the array into the gap produced by the element removed.

Author: Matei Zaharia <matei@databricks.com>

Closes #1773 from mateiz/SPARK-2685 and squashes the following commits:

1ea028a [Matei Zaharia] Update comments in StreamBuffer and EAOM, and reuse ArrayBuffers
eb1abfd [Matei Zaharia] Update ExternalAppendOnlyMap to avoid buffer.remove()
SPARK-2711. Create a ShuffleMemoryManager to track memory for all spilling collections

This tracks memory properly if there are multiple spilling collections in the same task (which was a problem before), and also implements an algorithm that lets each thread grow up to 1 / 2N of the memory pool (where N is the number of threads) before spilling, which avoids an inefficiency with small spills we had before (some threads would spill many times at 0-1 MB because the pool was allocated elsewhere).

Author: Matei Zaharia <matei@databricks.com>

Closes #1707 from mateiz/spark-2711 and squashes the following commits:

debf75b [Matei Zaharia] Review comments
24f28f3 [Matei Zaharia] Small rename
c8f3a8b [Matei Zaharia] Update ShuffleMemoryManager to be able to partially grant requests
315e3a5 [Matei Zaharia] Some review comments
b810120 [Matei Zaharia] Create central manager to track memory for all spilling collections
[SPARK-2857] Correct properties to set Master / Worker ports

`master.ui.port` and `worker.ui.port` were never picked up by SparkConf, simply because they are not prefixed with "spark." Unfortunately, this is also currently the documented way of setting these values.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1779 from andrewor14/master-worker-port and squashes the following commits:

8475e95 [Andrew Or] Update docs to reflect changes in configs
4db3d5d [Andrew Or] Stop using configs that don't actually work
[SPARK-1779] Throw an exception if memory fractions are not between 0 and 1

Author: wangfei <scnbwf@yeah.net>
Author: wangfei <wangfei1@huawei.com>

Closes #714 from scwf/memoryFraction and squashes the following commits:

6e385b9 [wangfei] Update SparkConf.scala
da6ee59 [wangfei] add configs
829a195 [wangfei] add indent
717c0ca [wangfei] updated to make more concise
fc45476 [wangfei] validate memoryfraction in sparkconf
2e79b3d [wangfei] && => ||
43621bd [wangfei] && => ||
cf38bcf [wangfei] throw IllegalArgumentException
14d18ac [wangfei] throw IllegalArgumentException
dff1f0f [wangfei] Update BlockManager.scala
764965f [wangfei] Update ExternalAppendOnlyMap.scala
a59d76b [wangfei] Throw exception when memoryFracton is out of range
7b899c2 [wangfei] 【SPARK-1779】
[SPARK-2856] Decrease initial buffer size for Kryo to 64KB.

Author: Reynold Xin <rxin@apache.org>

Closes #1780 from rxin/kryo-init-size and squashes the following commits:

551b935 [Reynold Xin] [SPARK-2856] Decrease initial buffer size for Kryo to 64KB.
[SPARK-1022][Streaming] Add Kafka real unit test

This PR is a updated version of (https://github.com/apache/spark/pull/557) to actually test sending and receiving data through Kafka, and fix previous flaky issues.

@tdas, would you mind reviewing this PR? Thanks a lot.

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

Closes #1751 from jerryshao/kafka-unit-test and squashes the following commits:

b6a505f [jerryshao] code refactor according to comments
5222330 [jerryshao] Change JavaKafkaStreamSuite to better test it
5525f10 [jerryshao] Fix flaky issue of Kafka real unit test
4559310 [jerryshao] Minor changes for Kafka unit test
860f649 [jerryshao] Minor style changes, and tests ignored due to flakiness
796d4ca [jerryshao] Add real Kafka streaming test
SPARK-1528 - spark on yarn, add support for accessing remote HDFS

Add a config (spark.yarn.access.namenodes) to allow applications running on yarn to access other secure HDFS cluster.  User just specifies the namenodes of the other clusters and we get Tokens for those and ship them with the spark application.

Author: Thomas Graves <tgraves@apache.org>

Closes #1159 from tgravescs/spark-1528 and squashes the following commits:

ddbcd16 [Thomas Graves] review comments
0ac8501 [Thomas Graves] SPARK-1528 - add support for accessing remote HDFS
SPARK-1890 and SPARK-1891- add admin and modify acls

It was easier to combine these 2 jira since they touch many of the same places.  This pr adds the following:

- adds modify acls
- adds admin acls (list of admins/users that get added to both view and modify acls)
- modify Kill button on UI to take modify acls into account
- changes config name of spark.ui.acls.enable to spark.acls.enable since I choose poorly in original name. We keep backwards compatibility so people can still use spark.ui.acls.enable. The acls should apply to any web ui as well as any CLI interfaces.
- send view and modify acls information on to YARN so that YARN interfaces can use (yarn cli for killing applications for example).

Author: Thomas Graves <tgraves@apache.org>

Closes #1196 from tgravescs/SPARK-1890 and squashes the following commits:

8292eb1 [Thomas Graves] review comments
b92ec89 [Thomas Graves] remove unneeded variable from applistener
4c765f4 [Thomas Graves] Add in admin acls
72eb0ac [Thomas Graves] Add modify acls
[SPARK-2860][SQL] Fix coercion of CASE WHEN.

Author: Michael Armbrust <michael@databricks.com>

Closes #1785 from marmbrus/caseNull and squashes the following commits:

126006d [Michael Armbrust] better error message
2fe357f [Michael Armbrust] Fix coercion of CASE WHEN.
[SPARK-2859] Update url of Kryo project in related docs

JIRA Issue: https://issues.apache.org/jira/browse/SPARK-2859

Kryo project has been migrated from googlecode to github, hence we need to update its URL in related docs such as tuning.md.

Author: Guancheng (G.C.) Chen <chenguancheng@gmail.com>

Closes #1782 from gchen/kryo-docs and squashes the following commits:

b62543c [Guancheng (G.C.) Chen] update url of Kryo project
SPARK-2380: Support displaying accumulator values in the web UI

This patch adds support for giving accumulators user-visible names and displaying accumulator values in the web UI. This allows users to create custom counters that can display in the UI. The current approach displays both the accumulator deltas caused by each task and a "current" value of the accumulator totals for each stage, which gets update as tasks finish.

Currently in Spark developers have been extending the `TaskMetrics` functionality to provide custom instrumentation for RDD's. This provides a potentially nicer alternative of going through the existing accumulator framework (actually `TaskMetrics` and accumulators are on an awkward collision course as we add more features to the former). The current patch demo's how we can use the feature to provide instrumentation for RDD input sizes. The nice thing about going through accumulators is that users can read the current value of the data being tracked in their programs. This could be useful to e.g. decide to short-circuit a Spark stage depending on how things are going.

![counters](https://cloud.githubusercontent.com/assets/320616/3488815/6ee7bc34-0505-11e4-84ce-e36d9886e2cf.png)

Author: Patrick Wendell <pwendell@gmail.com>

Closes #1309 from pwendell/metrics and squashes the following commits:

8815308 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into HEAD
93fbe0f [Patrick Wendell] Other minor fixes
cc43f68 [Patrick Wendell] Updating unit tests
c991b1b [Patrick Wendell] Moving some code into the Accumulators class
9a9ba3c [Patrick Wendell] More merge fixes
c5ace9e [Patrick Wendell] More merge conflicts
1da15e3 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into metrics
9860c55 [Patrick Wendell] Potential solution to posting listener events
0bb0e33 [Patrick Wendell] Remove "display" variable and assume display = name.isDefined
0ec4ac7 [Patrick Wendell] Java API's
e95bf69 [Patrick Wendell] Stash
be97261 [Patrick Wendell] Style fix
8407308 [Patrick Wendell] Removing examples in Hadoop and RDD class
64d405f [Patrick Wendell] Adding missing file
5d8b156 [Patrick Wendell] Changes based on Kay's review.
9f18bad [Patrick Wendell] Minor style changes and tests
7a63abc [Patrick Wendell] Adding Json serialization and responding to Reynold's feedback
ad85076 [Patrick Wendell] Example of using named accumulators for custom RDD metrics.
0b72660 [Patrick Wendell] Initial WIP example of supporing globally named accumulators.
SPARK-1680: use configs for specifying environment variables on YARN

Note that this also documents spark.executorEnv.*  which to me means its public.  If we don't want that please speak up.

Author: Thomas Graves <tgraves@apache.org>

Closes #1512 from tgravescs/SPARK-1680 and squashes the following commits:

11525df [Thomas Graves] more doc changes
553bad0 [Thomas Graves] fix documentation
152bf7c [Thomas Graves] fix docs
5382326 [Thomas Graves] try fix docs
32f86a4 [Thomas Graves] use configs for specifying environment variables on YARN
[SPARK-2864][MLLIB] fix random seed in word2vec; move model to local

It also moves the model to local in order to map `RDD[String]` to `RDD[Vector]`.

Ishiihara

Author: Xiangrui Meng <meng@databricks.com>

Closes #1790 from mengxr/word2vec-fix and squashes the following commits:

a87146c [Xiangrui Meng] add setters and make a default constructor
e5c923b [Xiangrui Meng] fix random seed in word2vec; move model to local
[SPARK-2503] Lower shuffle output buffer (spark.shuffle.file.buffer.kb) to 32KB.

This can substantially reduce memory usage during shuffle.

Author: Reynold Xin <rxin@apache.org>

Closes #1781 from rxin/SPARK-2503-spark.shuffle.file.buffer.kb and squashes the following commits:

104b8d8 [Reynold Xin] [SPARK-2503] Lower shuffle output buffer (spark.shuffle.file.buffer.kb) to 32KB.
[SPARK-2550][MLLIB][APACHE SPARK] Support regularization and intercept in pyspark's linear methods

Related to Jira Issue: [SPARK-2550](https://issues.apache.org/jira/browse/SPARK-2550?jql=project%20%3D%20SPARK%20AND%20resolution%20%3D%20Unresolved%20AND%20priority%20%3D%20Major%20ORDER%20BY%20key%20DESC)

Author: Michael Giannakopoulos <miccagiann@gmail.com>

Closes #1775 from miccagiann/linearMethodsReg and squashes the following commits:

cb774c3 [Michael Giannakopoulos] MiniBatchFraction added in related PythonMLLibAPI java stubs.
81fcbc6 [Michael Giannakopoulos] Fixing a typo-error.
8ad263e [Michael Giannakopoulos] Adding regularizer type and intercept parameters to LogisticRegressionWithSGD and SVMWithSGD.
SPARK-2869 - Fix tiny bug in JdbcRdd for closing jdbc connection

I inquired on  dev mailing list about the motivation for checking the jdbc statement instead of the connection in the close() logic of JdbcRDD. Ted Yu believes there essentially is none-  it is a simple cut and paste issue. So here is the tiny fix to patch it.

Author: Stephen Boesch <javadba>
Author: Stephen Boesch <javadba@gmail.com>

Closes #1792 from javadba/closejdbc and squashes the following commits:

363be4f [Stephen Boesch] SPARK-2869 - Fix tiny bug in JdbcRdd for closing jdbc connection (reformat with braces)
6518d36 [Stephen Boesch] SPARK-2689 Fix tiny bug in JdbcRdd for closing jdbc connection
3fb23ed [Stephen Boesch] SPARK-2689 Fix potential leak of connection/PreparedStatement in case of error in JdbcRDD
095b2c9 [Stephen Boesch] Fix tiny bug (likely copy and paste error) in closing jdbc connection
[sql] rename project name in pom.xml of hive-thriftserver module

module spark-hive-thriftserver_2.10 and spark-hive_2.10 both named "Spark Project Hive" in pom.xml, so rename spark-hive-thriftserver_2.10 project name to "Spark Project Hive Thrift Server"

Author: wangfei <wangfei1@huawei.com>

Closes #1789 from scwf/patch-1 and squashes the following commits:

ca1f5e9 [wangfei] [sql] rename module name of hive-thriftserver
[SPARK-2650][SQL] Try to partially fix SPARK-2650 by adjusting initial buffer size and reducing memory allocation

JIRA issue: [SPARK-2650](https://issues.apache.org/jira/browse/SPARK-2650)

Please refer to [comments](https://issues.apache.org/jira/browse/SPARK-2650?focusedCommentId=14084397&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-14084397) of SPARK-2650 for some other details.

This PR adjusts the initial in-memory columnar buffer size to 1MB, same as the default value of Shark's `shark.column.partitionSize.mb` property when running in local mode. Will add Shark style partition size estimation in another PR.

Also, before this PR, `NullableColumnBuilder` copies the whole buffer to add the null positions section, and then `CompressibleColumnBuilder` copies and compresses the buffer again, even if compression is disabled (`PassThrough` compression scheme is used to disable compression). In this PR the first buffer copy is eliminated to reduce memory consumption.

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

Closes #1769 from liancheng/spark-2650 and squashes the following commits:

88a042e [Cheng Lian] Fixed method visibility and removed dead code
001f2e5 [Cheng Lian] Try fixing SPARK-2650 by adjusting initial buffer size and reducing memory allocation
[SPARK-2854][SQL] Finalize _acceptable_types in pyspark.sql

This PR aims to finalize accepted data value types in Python RDDs provided to Python `applySchema`.

JIRA: https://issues.apache.org/jira/browse/SPARK-2854

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

Closes #1793 from yhuai/SPARK-2854 and squashes the following commits:

32f0708 [Yin Huai] LongType only accepts long values.
c2b23dd [Yin Huai] Do data type conversions based on the specified Spark SQL data type.
[SPARK-2866][SQL] Support attributes in ORDER BY that aren't in SELECT

Minor refactoring to allow resolution either using a nodes input or output.

Author: Michael Armbrust <michael@databricks.com>

Closes #1795 from marmbrus/ordering and squashes the following commits:

237f580 [Michael Armbrust] style
74d833b [Michael Armbrust] newline
705d963 [Michael Armbrust] Add a rule for resolving ORDER BY expressions that reference attributes not present in the SELECT clause.
82cabda [Michael Armbrust] Generalize attribute resolution.