SPARK-2481: The environment variables SPARK_HISTORY_OPTS is covered in spark-env.sh

Author: witgo <witgo@qq.com>
Author: GuoQiang Li <witgo@qq.com>

Closes #1341 from witgo/history_env and squashes the following commits:

b4fd9f8 [GuoQiang Li] review commit
0ebe401 [witgo] *-history-server.sh load spark-config.sh
[SPARK-2976] Replace tabs with spaces

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

Closes #1895 from sarutak/SPARK-2976 and squashes the following commits:

1cf7e69 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2976
d1e0666 [Kousuke Saruta] Modified styles
c5e80a4 [Kousuke Saruta] Remove tab from JavaPageRank.java and JavaKinesisWordCountASL.java
c003b36 [Kousuke Saruta] Removed tab from sorttable.js
[Spark-3222] [SQL] Cross join support in HiveQL

We can simple treat cross join as inner join without join conditions.

Author: Daoyuan Wang <daoyuan.wang@intel.com>
Author: adrian-wang <daoyuanwong@gmail.com>

Closes #2124 from adrian-wang/crossjoin and squashes the following commits:

8c9b7c5 [Daoyuan Wang] add a test
7d47bbb [adrian-wang] add cross join support for hql
[SPARK-2886] Use more specific actor system name than "spark"

As of #1777 we log the name of the actor system when it binds to a port. The current name "spark" is super general and does not convey any meaning. For instance, the following line is taken from my driver log after setting `spark.driver.port` to 5001.
```
14/08/13 19:33:29 INFO Remoting: Remoting started; listening on addresses:
[akka.tcp://sparkandrews-mbp:5001]
14/08/13 19:33:29 INFO Remoting: Remoting now listens on addresses:
[akka.tcp://sparkandrews-mbp:5001]
14/08/06 13:40:05 INFO Utils: Successfully started service 'spark' on port 5001.
```
This commit renames this to "sparkDriver" and "sparkExecutor". The goal of this unambitious PR is simply to make the logged information more explicit without introducing any change in functionality.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1810 from andrewor14/service-name and squashes the following commits:

8c459ed [Andrew Or] Use a common variable for driver/executor actor system names
3a92843 [Andrew Or] Change actor name to sparkDriver and sparkExecutor
921363e [Andrew Or] Merge branch 'master' of github.com:apache/spark into service-name
c8c6a62 [Andrew Or] Do not include hyphens in actor name
1c1b42e [Andrew Or] Avoid spaces in akka system name
f644b55 [Andrew Or] Use more specific service name
[SPARK-3131][SQL] Allow user to set parquet compression codec for writing ParquetFile in SQLContext

There are 4 different compression codec available for ```ParquetOutputFormat```

in Spark SQL, it was set as a hard-coded value in ```ParquetRelation.defaultCompression```

original discuss:
https://github.com/apache/spark/pull/195#discussion-diff-11002083

i added a new config property in SQLConf to allow user to change this compression codec, and i used similar short names syntax as described in SPARK-2953 #1873 (https://github.com/apache/spark/pull/1873/files#diff-0)

btw, which codec should we use as default? it was set to GZIP (https://github.com/apache/spark/pull/195/files#diff-4), but i think maybe we should change this to SNAPPY, since SNAPPY is already the default codec for shuffling in spark-core (SPARK-2469, #1415), and parquet-mr supports Snappy codec natively (https://github.com/Parquet/parquet-mr/commit/e440108de57199c12d66801ca93804086e7f7632).

Author: chutium <teng.qiu@gmail.com>

Closes #2039 from chutium/parquet-compression and squashes the following commits:

2f44964 [chutium] [SPARK-3131][SQL] parquet compression default codec set to snappy, also in test suite
e578e21 [chutium] [SPARK-3131][SQL] compression codec config property name and default codec set to snappy
21235dc [chutium] [SPARK-3131][SQL] Allow user to set parquet compression codec for writing ParquetFile in SQLContext
[SPARK-2871] [PySpark] add histgram() API

RDD.histogram(buckets)

        Compute a histogram using the provided buckets. The buckets
        are all open to the right except for the last which is closed.
        e.g. [1,10,20,50] means the buckets are [1,10) [10,20) [20,50],
        which means 1<=x<10, 10<=x<20, 20<=x<=50. And on the input of 1
        and 50 we would have a histogram of 1,0,1.

        If your histogram is evenly spaced (e.g. [0, 10, 20, 30]),
        this can be switched from an O(log n) inseration to O(1) per
        element(where n = # buckets).

        Buckets must be sorted and not contain any duplicates, must be
        at least two elements.

        If `buckets` is a number, it will generates buckets which is
        evenly spaced between the minimum and maximum of the RDD. For
        example, if the min value is 0 and the max is 100, given buckets
        as 2, the resulting buckets will be [0,50) [50,100]. buckets must
        be at least 1 If the RDD contains infinity, NaN throws an exception
        If the elements in RDD do not vary (max == min) always returns
        a single bucket.

        It will return an tuple of buckets and histogram.

        >>> rdd = sc.parallelize(range(51))
        >>> rdd.histogram(2)
        ([0, 25, 50], [25, 26])
        >>> rdd.histogram([0, 5, 25, 50])
        ([0, 5, 25, 50], [5, 20, 26])
        >>> rdd.histogram([0, 15, 30, 45, 60], True)
        ([0, 15, 30, 45, 60], [15, 15, 15, 6])
        >>> rdd = sc.parallelize(["ab", "ac", "b", "bd", "ef"])
        >>> rdd.histogram(("a", "b", "c"))
        (('a', 'b', 'c'), [2, 2])

closes #122, it's duplicated.

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

Closes #2091 from davies/histgram and squashes the following commits:

a322f8a [Davies Liu] fix deprecation of e.message
84e85fa [Davies Liu] remove evenBuckets, add more tests (including str)
d9a0722 [Davies Liu] address comments
0e18a2d [Davies Liu] add histgram() API
[SPARK-2969][SQL] Make ScalaReflection be able to handle ArrayType.containsNull and MapType.valueContainsNull.

Make `ScalaReflection` be able to handle like:

- `Seq[Int]` as `ArrayType(IntegerType, containsNull = false)`
- `Seq[java.lang.Integer]` as `ArrayType(IntegerType, containsNull = true)`
- `Map[Int, Long]` as `MapType(IntegerType, LongType, valueContainsNull = false)`
- `Map[Int, java.lang.Long]` as `MapType(IntegerType, LongType, valueContainsNull = true)`

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

Closes #1889 from ueshin/issues/SPARK-2969 and squashes the following commits:

24f1c5c [Takuya UESHIN] Change the default value of ArrayType.containsNull to true in Python API.
79f5b65 [Takuya UESHIN] Change the default value of ArrayType.containsNull to true in Java API.
7cd1a7a [Takuya UESHIN] Fix json test failures.
2cfb862 [Takuya UESHIN] Change the default value of ArrayType.containsNull to true.
2f38e61 [Takuya UESHIN] Revert the default value of MapTypes.valueContainsNull.
9fa02f5 [Takuya UESHIN] Fix a test failure.
1a9a96b [Takuya UESHIN] Modify ScalaReflection to handle ArrayType.containsNull and MapType.valueContainsNull.
[SPARK-3063][SQL] ExistingRdd should convert Map to catalyst Map.

Currently `ExistingRdd.convertToCatalyst` doesn't convert `Map` value.

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

Closes #1963 from ueshin/issues/SPARK-3063 and squashes the following commits:

3ba41f2 [Takuya UESHIN] Merge branch 'master' into issues/SPARK-3063
4d7bae2 [Takuya UESHIN] Merge branch 'master' into issues/SPARK-3063
9321379 [Takuya UESHIN] Merge branch 'master' into issues/SPARK-3063
d8a900a [Takuya UESHIN] Make ExistingRdd.convertToCatalyst be able to convert Map value.
[SPARK-3226][MLLIB] doc update for native libraries

to mention `-Pnetlib-lgpl` option. atalwalkar

Author: Xiangrui Meng <meng@databricks.com>

Closes #2128 from mengxr/mllib-native and squashes the following commits:

4cbba57 [Xiangrui Meng] update mllib dependencies
[SPARK-2839][MLlib] Stats Toolkit documentation updated

Documentation updated for the Statistics Toolkit of MLlib. mengxr atalwalkar

https://issues.apache.org/jira/browse/SPARK-2839

P.S. Accidentally closed #2123. New commits didn't show up after I reopened the PR. I've opened this instead and closed the old one.

Author: Burak <brkyvz@gmail.com>

Closes #2130 from brkyvz/StatsLib-Docs and squashes the following commits:

a54a855 [Burak] [SPARK-2839][MLlib] Addressed comments
bfc6896 [Burak] [SPARK-2839][MLlib] Added a more specific link to colStats() for pyspark
213fe3f [Burak] [SPARK-2839][MLlib] Modifications made according to review
fec4d9d [Burak] [SPARK-2830][MLlib] Stats Toolkit documentation updated
[SPARK-3194][SQL] Add AttributeSet to fix bugs with invalid comparisons of AttributeReferences

It is common to want to describe sets of attributes that are in various parts of a query plan.  However, the semantics of putting `AttributeReference` objects into a standard Scala `Set` result in subtle bugs when references differ cosmetically.  For example, with case insensitive resolution it is possible to have two references to the same attribute whose names are not equal.

In this PR I introduce a new abstraction, an `AttributeSet`, which performs all comparisons using the globally unique `ExpressionId` instead of case class equality.  (There is already a related class, [`AttributeMap`](https://github.com/marmbrus/spark/blob/inMemStats/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/expressions/AttributeMap.scala#L32))  This new type of set is used to fix a bug in the optimizer where needed attributes were getting projected away underneath join operators.

I also took this opportunity to refactor the expression and query plan base classes.  In all but one instance the logic for computing the `references` of an `Expression` were the same.  Thus, I moved this logic into the base class.

For query plans the semantics of  the `references` method were ill defined (is it the references output? or is it those used by expression evaluation? or what?).  As a result, this method wasn't really used very much.  So, I removed it.

TODO:
 - [x] Finish scala doc for `AttributeSet`
 - [x] Scan the code for other instances of `Set[Attribute]` and refactor them.
 - [x] Finish removing `references` from `QueryPlan`

Author: Michael Armbrust <michael@databricks.com>

Closes #2109 from marmbrus/attributeSets and squashes the following commits:

1c0dae5 [Michael Armbrust] work on serialization bug.
9ba868d [Michael Armbrust] Merge remote-tracking branch 'origin/master' into attributeSets
3ae5288 [Michael Armbrust] review comments
40ce7f6 [Michael Armbrust] style
d577cc7 [Michael Armbrust] Scaladoc
cae5d22 [Michael Armbrust] remove more references implementations
d6e16be [Michael Armbrust] Remove more instances of "def references" and normal sets of attributes.
fc26b49 [Michael Armbrust] Add AttributeSet class, remove references from Expression.
[SPARK-3073] [PySpark] use external sort in sortBy() and sortByKey()

Using external sort to support sort large datasets in reduce stage.

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

Closes #1978 from davies/sort and squashes the following commits:

bbcd9ba [Davies Liu] check spilled bytes in tests
b125d2f [Davies Liu] add test for external sort in rdd
eae0176 [Davies Liu] choose different disks from different processes and instances
1f075ed [Davies Liu] Merge branch 'master' into sort
eb53ca6 [Davies Liu] Merge branch 'master' into sort
644abaf [Davies Liu] add license in LICENSE
19f7873 [Davies Liu] improve tests
55602ee [Davies Liu] use external sort in sortBy() and sortByKey()
[SPARK-3225]Typo in script

use_conf_dir => user_conf_dir in load-spark-env.sh.

Author: WangTao <barneystinson@aliyun.com>

Closes #1926 from WangTaoTheTonic/TypoInScript and squashes the following commits:

0c104ad [WangTao] Typo in script
[SPARK-2964] [SQL] Remove duplicated code from spark-sql and start-thriftserver.sh

Author: Cheng Lian <lian.cs.zju@gmail.com>
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #1886 from sarutak/SPARK-2964 and squashes the following commits:

8ef8751 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2964
26e7c95 [Kousuke Saruta] Revert "Shorten timeout to more reasonable value"
ffb68fa [Kousuke Saruta] Modified spark-sql and start-thriftserver.sh to use bin/utils.sh
8c6f658 [Kousuke Saruta] Merge branch 'spark-3026' of https://github.com/liancheng/spark into SPARK-2964
81b43a8 [Cheng Lian] Shorten timeout to more reasonable value
a89e66d [Cheng Lian] Fixed command line options quotation in scripts
9c894d3 [Cheng Lian] Fixed bin/spark-sql -S option typo
be4736b [Cheng Lian] Report better error message when running JDBC/CLI without hive-thriftserver profile enabled
[Docs] Run tests like in contributing guide

The Contributing to Spark guide [recommends](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark#ContributingtoSpark-AutomatedTesting) running tests by calling `./dev/run-tests`. The README should, too.

`./sbt/sbt test` does not cover Python tests or style tests.

Author: nchammas <nicholas.chammas@gmail.com>

Closes #2149 from nchammas/patch-2 and squashes the following commits:

2b3b132 [nchammas] [Docs] Run tests like in contributing guide
[SPARK-3036][SPARK-3037][SQL] Add MapType/ArrayType containing null value support to Parquet.

JIRA:
- https://issues.apache.org/jira/browse/SPARK-3036
- https://issues.apache.org/jira/browse/SPARK-3037

Currently this uses the following Parquet schema for `MapType` when `valueContainsNull` is `true`:

```
message root {
  optional group a (MAP) {
    repeated group map (MAP_KEY_VALUE) {
      required int32 key;
      optional int32 value;
    }
  }
}
```

for `ArrayType` when `containsNull` is `true`:

```
message root {
  optional group a (LIST) {
    repeated group bag {
      optional int32 array;
    }
  }
}
```

We have to think about compatibilities with older version of Spark or Hive or others I mentioned in the JIRA issues.

Notice:
This PR is based on #1963 and #1889.
Please check them first.

/cc marmbrus, yhuai

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

Closes #2032 from ueshin/issues/SPARK-3036_3037 and squashes the following commits:

4e8e9e7 [Takuya UESHIN] Add ArrayType containing null value support to Parquet.
013c2ca [Takuya UESHIN] Add MapType containing null value support to Parquet.
62989de [Takuya UESHIN] Merge branch 'issues/SPARK-2969' into issues/SPARK-3036_3037
8e38b53 [Takuya UESHIN] Merge branch 'issues/SPARK-3063' into issues/SPARK-3036_3037
[SPARK-3240] Adding known issue for MESOS-1688

When using Mesos with the fine-grained mode, a Spark job can run into a dead lock on low allocatable memory on Mesos slaves. As a work-around 32 MB (= Mesos MIN_MEM) are allocated for each task, to ensure Mesos making new offers after task completion.
From my perspective, it would be better to fix this problem in Mesos by dropping the constraint on memory for offers, but as temporary solution this patch helps to avoid the dead lock on current Mesos versions.
See [[MESOS-1688] No offers if no memory is allocatable](https://issues.apache.org/jira/browse/MESOS-1688) for details for this problem.

Author: Martin Weindel <martin.weindel@gmail.com>

Closes #1860 from MartinWeindel/master and squashes the following commits:

5762030 [Martin Weindel] reverting work-around
a6bf837 [Martin Weindel] added known issue for issue MESOS-1688
d9d2ca6 [Martin Weindel] work around for problem with Mesos offering semantic (see [https://issues.apache.org/jira/browse/MESOS-1688])
Fix unclosed HTML tag in Yarn docs.
Manually close some old pull requests

Closes #530, Closes #223, Closes #738, Closes #546
Manually close old pull requests

Closes #671, Closes #515