[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.

(cherry picked from commit 6b5584ef1c605cd30f25dbe7099ab32aea1746fb)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[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

(cherry picked from commit adbd5c1636669fc474ab02b54cd1ced353f68712)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[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

(cherry picked from commit 1208f72ac78960fe5060187761479b2a9a417c1b)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[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.

(cherry picked from commit c4787a3690a9ed3b8b2c6c294fc4a6915436b6f7)
Signed-off-by: Reynold Xin <rxin@apache.org>
[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

(cherry picked from commit faeb9c0e1440f4af888be0dfc5de7b57efc92b00)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[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

(cherry picked from commit 73b3089b8d2901dab11bb1ef6f46c29625b677fe)
Signed-off-by: Reynold Xin <rxin@apache.org>
[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

(cherry picked from commit 727cb25bcc29481d6b744abef1ca091e64b5f91f)
Signed-off-by: Michael Armbrust <michael@databricks.com>
Fix unclosed HTML tag in Yarn docs.
[SPARK-3224] FetchFailed reduce stages should only show up once in failed stages (in UI)

This is a HOTFIX for 1.1.

Author: Reynold Xin <rxin@apache.org>
Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #2127 from rxin/SPARK-3224 and squashes the following commits:

effb1ce [Reynold Xin] Move log message.
49282b3 [Reynold Xin] Kay's feedback.
3f01847 [Reynold Xin] Merge pull request #2 from kayousterhout/SPARK-3224
796d282 [Kay Ousterhout] Added unit test for SPARK-3224
3d3d356 [Reynold Xin] Remove map output loc even for repeated FetchFaileds.
1dd3eb5 [Reynold Xin] [SPARK-3224] FetchFailed reduce stages should only show up once in the failed stages UI.
(cherry picked from commit bf719056b71d55e1194554661dfa194ed03d364d)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-3167] Handle special driver configs in Windows (Branch 1.1)

This is an effort to bring the Windows scripts up to speed after recent splashing changes in #1845.

Author: Andrew Or <andrewor14@gmail.com>

Closes #2156 from andrewor14/windows-config-branch-1.1 and squashes the following commits:

00b9dfe [Andrew Or] [SPARK-3167] Handle special driver configs in Windows
HOTFIX: Minor typo in conf template
[SPARK-3139] Made ContextCleaner to not block on shuffles

As a workaround for SPARK-3015, the ContextCleaner was made "blocking", that is, it cleaned items one-by-one. But shuffles can take a long time to be deleted. Given that the RC for 1.1 is imminent, this PR makes a narrow change in the context cleaner - not wait for shuffle cleanups to complete. Also it changes the error messages on failure to delete to be milder warnings, as exceptions in the delete code path for one item does not really stop the actual functioning of the system.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #2143 from tdas/cleaner-shuffle-fix and squashes the following commits:

9c84202 [Tathagata Das] Restoring default blocking behavior in ContextCleanerSuite, and added docs to identify that spark.cleaner.referenceTracking.blocking does not control shuffle.
2181329 [Tathagata Das] Mark shuffle cleanup as non-blocking.
e337cc2 [Tathagata Das] Changed semantics based on PR comments.
387b578 [Tathagata Das] Made ContextCleaner to not block on shuffles
(cherry picked from commit 3e2864e40472b32e6a7eec5ba3bc83562d2a1a62)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-3237][SQL] Fix parquet filters with UDFs

Author: Michael Armbrust <michael@databricks.com>

Closes #2153 from marmbrus/parquetFilters and squashes the following commits:

712731a [Michael Armbrust] Use closure serializer for sending filters.
1e83f80 [Michael Armbrust] Clean udf functions.

(cherry picked from commit e1139dd60e0692e8adb1337c1f605165ce4b8895)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2830][MLLIB] doc update for 1.1

1. renamed mllib-basics to mllib-data-types
1. renamed mllib-stats to mllib-statistics
1. moved random data generation to the bottom of mllib-stats
1. updated toc accordingly

atalwalkar

Author: Xiangrui Meng <meng@databricks.com>

Closes #2151 from mengxr/mllib-doc-1.1 and squashes the following commits:

0bd79f3 [Xiangrui Meng] add mllib-data-types
b64a5d7 [Xiangrui Meng] update the content list of basis statistics in mllib-guide
f625cc2 [Xiangrui Meng] move mllib-basics to mllib-data-types
4d69250 [Xiangrui Meng] move random data generation to the bottom of statistics
e64f3ce [Xiangrui Meng] move mllib-stats.md to mllib-statistics.md

(cherry picked from commit 43dfc84f883822ea27b6e312d4353bf301c2e7ef)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[SPARK-3227] [mllib] Added migration guide for v1.0 to v1.1

The only updates are in DecisionTree.

CC: mengxr

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #2146 from jkbradley/mllib-migration and squashes the following commits:

5a1f487 [Joseph K. Bradley] small edit to doc
411d6d9 [Joseph K. Bradley] Added migration guide for v1.0 to v1.1.  The only updates are in DecisionTree.

(cherry picked from commit 171a41cb034f4ea80f6a3c91a6872970de16a14a)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[SPARK-3154][STREAMING] Make FlumePollingInputDStream shutdown cleaner.

Currently lot of errors get thrown from Avro IPC layer when the dstream
or sink is shutdown. This PR cleans it up. Some refactoring is done in the
receiver code to put all of the RPC code into a single Try and just recover
from that. The sink code has also been cleaned up.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #2065 from harishreedharan/clean-flume-shutdown and squashes the following commits:

f93a07c [Hari Shreedharan] Formatting fixes.
d7427cc [Hari Shreedharan] More fixes!
a0a8852 [Hari Shreedharan] Fix race condition, hopefully! Minor other changes.
4c9ed02 [Hari Shreedharan] Remove unneeded list in Callback handler. Other misc changes.
8fee36f [Hari Shreedharan] Scala-library is required, else maven build fails. Also catch InterruptedException in TxnProcessor.
445e700 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into clean-flume-shutdown
87232e0 [Hari Shreedharan] Refactor Flume Input Stream. Clean up code, better error handling.
9001d26 [Hari Shreedharan] Change log level to debug in TransactionProcessor#shutdown method
e7b8d82 [Hari Shreedharan] Incorporate review feedback
598efa7 [Hari Shreedharan] Clean up some exception handling code
e1027c6 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into clean-flume-shutdown
ed608c8 [Hari Shreedharan] [SPARK-3154][STREAMING] Make FlumePollingInputDStream shutdown cleaner.

(cherry picked from commit 6f671d04fa98f97fd48c5e749b9f47dd4a8b4f44)
Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>
[SPARK-3170][CORE][BUG]:RDD info loss in "StorageTab" and "ExecutorTab"

compeleted stage only need to remove its own partitions that are no longer cached. However, "StorageTab" may lost some rdds which are cached actually. Not only in "StorageTab", "ExectutorTab" may also lose some rdd info which have been overwritten by last rdd in a same task.
1. "StorageTab": when multiple stages run simultaneously, completed stage will remove rdd info which belong to other stages that are still running.
2. "ExectutorTab": taskcontext may lose some "updatedBlocks" info of  rdds  in a dependency chain. Like the following example:
         val r1 = sc.paralize(..).cache()
         val r2 = r1.map(...).cache()
         val n = r2.count()

When count the r2, r1 and r2 will be cached finally. So in CacheManager.getOrCompute, the taskcontext should contain "updatedBlocks" of r1 and r2. Currently, the "updatedBlocks" only contain the info of r2.

Author: uncleGen <hustyugm@gmail.com>

Closes #2131 from uncleGen/master_ui_fix and squashes the following commits:

a6a8a0b [uncleGen] fix some coding style
3a1bc15 [uncleGen] fix some error in unit test
56ea488 [uncleGen] there's some line too long
c82ba82 [uncleGen] Bug Fix: RDD info loss in "StorageTab" and "ExecutorTab"

(cherry picked from commit d8298c46b7bf566d1cd2f7ea9b1b2b2722dcfb17)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
[SPARK-3239] [PySpark] randomize the dirs for each process

This can avoid the IO contention during spilling, when you have multiple disks.

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

Closes #2152 from davies/randomize and squashes the following commits:

a4863c4 [Davies Liu] randomize the dirs for each process
[SPARK-2608][Core] Fixed command line option passing issue over Mesos via SPARK_EXECUTOR_OPTS

This is another try after #2145 to fix [SPARK-2608](https://issues.apache.org/jira/browse/SPARK-2608).

### Basic Idea

The basic idea is to pass `extraJavaOpts` and `extraLibraryPath` together via environment variable `SPARK_EXECUTOR_OPTS`. This variable is recognized by `spark-class` and not used anywhere else. In this way, we still launch Mesos executors with `spark-class`/`spark-executor`, but avoids the executor side Spark home issue.

### Known Issue

Quoted string with spaces is not allowed in either `extraJavaOpts` or `extraLibraryPath` when using Spark over Mesos. The reason is that Mesos passes the whole command line as a single string argument to `sh -c` to start the executor, and this makes shell string escaping non-trivial to handle. This should be fixed in a later release.

### Background

Classes in package `org.apache.spark.deploy` shouldn't be used as they assume Spark is deployed in standalone mode, and give wrong executor side Spark home directory. Please refer to comments in #2145 for more details.

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

Closes #2161 from liancheng/mesos-fix-with-env-var and squashes the following commits:

ba59190 [Cheng Lian] Added fine grained Mesos executor support
1174076 [Cheng Lian] Draft fix for CoarseMesosSchedulerBackend
SPARK-3259 - User data should be given to the master

Author: Allan Douglas R. de Oliveira <allan@chaordicsystems.com>

Closes #2162 from douglaz/user_data_master and squashes the following commits:

10d15f6 [Allan Douglas R. de Oliveira] Give user data also to the master
(cherry picked from commit 5ac4093c9fa29a11e38f884eebb3f5db087de76f)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>