[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
[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.
[SPARK-3167] Handle special driver configs in Windows

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 #2129 from andrewor14/windows-config and squashes the following commits:

881a8f0 [Andrew Or] Add reference to Windows taskkill
92e6047 [Andrew Or] Update a few comments (minor)
22b1acd [Andrew Or] Fix style again (minor)
afcffea [Andrew Or] Fix style (minor)
72004c2 [Andrew Or] Actually respect --driver-java-options
803218b [Andrew Or] Actually respect SPARK_*_CLASSPATH
eeb34a0 [Andrew Or] Update outdated comment (minor)
35caecc [Andrew Or] In Windows, actually kill Java processes on exit
f97daa2 [Andrew Or] Fix Windows spark shell stdin issue
83ebe60 [Andrew Or] Parse special driver configs in Windows (broken)
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
[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.
[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
[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.
[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.
[SPARK-2933] [yarn] Refactor and cleanup Yarn AM code.

This change modifies the Yarn module so that all the logic related
to running the ApplicationMaster is localized. Instead of, previously,
4 different classes with mostly identical code, now we have:

- A single, shared ApplicationMaster class, which can operate both in
  client and cluster mode, and substitutes the old ApplicationMaster
  (for cluster mode) and ExecutorLauncher (for client mode).

The benefit here is that all different execution modes for all supported
yarn versions use the same shared code for monitoring executor allocation,
setting up configuration, and monitoring the process's lifecycle.

- A new YarnRMClient interface, which defines basic RM functionality needed
  by the ApplicationMaster. This interface has concrete implementations for
  each supported Yarn version.

- A new YarnAllocator interface, which just abstracts the existing interface
  of the YarnAllocationHandler class. This is to avoid having to touch the
  allocator code too much in this change, although it might benefit from a
  similar effort in the future.

The end result is much easier to understand code, with much less duplication,
making it much easier to fix bugs, add features, and test everything knowing
that all supported versions will behave the same.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2020 from vanzin/SPARK-2933 and squashes the following commits:

3bbf3e7 [Marcelo Vanzin] Merge branch 'master' into SPARK-2933
ff389ed [Marcelo Vanzin] Do not interrupt reporter thread from within itself.
3a8ed37 [Marcelo Vanzin] Remote stale comment.
0f5142c [Marcelo Vanzin] Review feedback.
41f8c8a [Marcelo Vanzin] Fix app status reporting.
c0794be [Marcelo Vanzin] Correctly clean up staging directory.
92770cc [Marcelo Vanzin] Merge branch 'master' into SPARK-2933
ecaf332 [Marcelo Vanzin] Small fix to shutdown code.
f02d3f8 [Marcelo Vanzin] Merge branch 'master' into SPARK-2933
f581122 [Marcelo Vanzin] Review feedback.
557fdeb [Marcelo Vanzin] Cleanup a couple more constants.
be6068d [Marcelo Vanzin] Restore shutdown hook to clean up staging dir.
5150993 [Marcelo Vanzin] Some more cleanup.
b6289ab [Marcelo Vanzin] Move cluster/client code to separate methods.
ecb23cd [Marcelo Vanzin] More trivial cleanup.
34f1e63 [Marcelo Vanzin] Fix some questionable error handling.
5657c7d [Marcelo Vanzin] Finish app if SparkContext initialization times out.
0e4be3d [Marcelo Vanzin] Keep "ExecutorLauncher" as the main class for client-mode AM.
91beabb [Marcelo Vanzin] Fix UI filter registration.
8c72239 [Marcelo Vanzin] Trivial cleanups.
99a52d5 [Marcelo Vanzin] Changes to the yarn-alpha project to use common AM code.
848ca6d [Marcelo Vanzin] [SPARK-2933] [yarn] Refactor and cleanup Yarn AM code.
[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"