[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eeb34a0 [Andrew Or] Update outdated comment (minor)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"
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
[SPARK-3118][SQL]add "SHOW TBLPROPERTIES tblname;" and "SHOW COLUMNS (FROM|IN) table_name [(FROM|IN) db_name]" support

JIRA issue: [SPARK-3118] https://issues.apache.org/jira/browse/SPARK-3118

eg:
> SHOW TBLPROPERTIES test;
SHOW TBLPROPERTIES test;
numPartitions	0
numFiles	1
transient_lastDdlTime	1407923642
numRows	0
totalSize	82
rawDataSize	0

eg:
> SHOW COLUMNS  in test;
SHOW COLUMNS  in test;
OK
Time taken: 0.304 seconds
id
stid
bo

Author: u0jing <u9jing@gmail.com>

Closes #2034 from u0jing/spark-3118 and squashes the following commits:

b231d87 [u0jing] add golden answer files
35f4885 [u0jing] add 'show columns' and 'show tblproperties' support
[SPARK-3197] [SQL] Reduce the Expression tree object creations for aggregation function (min/max)

Aggregation function min/max in catalyst will create expression tree for each single row, however, the expression tree creation is quite expensive in a multithreading env currently. Hence we got a very bad performance for the min/max.
Here is the benchmark that I've done in my local.

Master | Previous Result (ms) | Current Result (ms)
------------ | ------------- | -------------
local | 3645 | 3416
local[6] | 3602 | 1002

The Benchmark source code.
```
case class Record(key: Int, value: Int)

object TestHive2 extends HiveContext(new SparkContext("local[6]", "TestSQLContext", new SparkConf()))

object DataPrepare extends App {
  import TestHive2._

  val rdd = sparkContext.parallelize((1 to 10000000).map(i => Record(i % 3000, i)), 12)

  runSqlHive("SHOW TABLES")
  runSqlHive("DROP TABLE if exists a")
  runSqlHive("DROP TABLE if exists result")
  rdd.registerAsTable("records")

  runSqlHive("""CREATE TABLE a (key INT, value INT)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)
  runSqlHive("""CREATE TABLE result (key INT, value INT)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)

  hql(s"""from records
             | insert into table a
             | select key, value
           """.stripMargin)
}

object PerformanceTest extends App {
  import TestHive2._

  hql("SHOW TABLES")
  hql("set spark.sql.shuffle.partitions=12")

  val cmd = "select min(value), max(value) from a group by key"

  val results = ("Result1", benchmark(cmd)) ::
                ("Result2", benchmark(cmd)) ::
                ("Result3", benchmark(cmd)) :: Nil
  results.foreach { case (prompt, result) => {
      println(s"$prompt: took ${result._1} ms (${result._2} records)")
    }
  }

  def benchmark(cmd: String) = {
    val begin = System.currentTimeMillis()
    val count = hql(cmd).count
    val end = System.currentTimeMillis()
    ((end - begin), count)
  }
}
```

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

Closes #2113 from chenghao-intel/aggregation_expression_optimization and squashes the following commits:

db40395 [Cheng Hao] remove the transient and add val for the expression property
d56167d [Cheng Hao] Reduce the Expressions creation
[SPARK-3256] Added support for :cp <jar> that was broken in Scala 2.10.x for REPL

As seen with [SI-6502](https://issues.scala-lang.org/browse/SI-6502) of Scala, the _:cp_ command was broken in Scala 2.10.x. As the Spark shell is a friendly wrapper on top of the Scala REPL, it is also affected by this problem.

My solution was to alter the internal classpath and invalidate any new entries. I also had to add the ability to add new entries to the parent classloader of the interpreter (SparkIMain's global).

The advantage of this versus wiping the interpreter and replaying all of the commands is that you don't have to worry about rerunning heavy Spark-related commands (going to the cluster) or potentially reloading data that might have changed. Instead, you get to work from where you left off.

Until this is fixed upstream for 2.10.x, I had to use reflection to alter the internal compiler classpath.

The solution now looks like this:
![screen shot 2014-08-13 at 3 46 02 pm](https://cloud.githubusercontent.com/assets/2481802/3912625/f02b1440-232c-11e4-9bf6-bafb3e352d14.png)

Author: Chip Senkbeil <rcsenkbe@us.ibm.com>

Closes #1929 from rcsenkbeil/FixReplClasspathSupport and squashes the following commits:

f420cbf [Chip Senkbeil] Added SparkContext.addJar calls to support executing code on remote clusters
a826795 [Chip Senkbeil] Updated AddUrlsToClasspath to use 'new Run' suggestion over hackish compiler error
2ff1d86 [Chip Senkbeil] Added compilation failure on symbols hack to get Scala classes to load correctly
a220639 [Chip Senkbeil] Added support for :cp <jar> that was broken in Scala 2.10.x for REPL
[SPARK-3138][SQL] sqlContext.parquetFile should be able to take a single file as parameter

```if (!fs.getFileStatus(path).isDir) throw Exception``` make no sense after this commit #1370

be careful if someone is working on SPARK-2551, make sure the new change passes test case ```test("Read a parquet file instead of a directory")```

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

Closes #2044 from chutium/parquet-singlefile and squashes the following commits:

4ae477f [chutium] [SPARK-3138][SQL] sqlContext.parquetFile should be able to take a single file as parameter
[SPARK-2871] [PySpark] add RDD.lookup(key)

RDD.lookup(key)

        Return the list of values in the RDD for key `key`. This operation
        is done efficiently if the RDD has a known partitioner by only
        searching the partition that the key maps to.

        >>> l = range(1000)
        >>> rdd = sc.parallelize(zip(l, l), 10)
        >>> rdd.lookup(42)  # slow
        [42]
        >>> sorted = rdd.sortByKey()
        >>> sorted.lookup(42)  # fast
        [42]

It also clean up the code in RDD.py, and fix several bugs (related to preservesPartitioning).

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

Closes #2093 from davies/lookup and squashes the following commits:

1789cd4 [Davies Liu] `f` in foreach could be generator or not.
2871b80 [Davies Liu] Merge branch 'master' into lookup
c6390ea [Davies Liu] address all comments
0f1bce8 [Davies Liu] add test case for lookup()
be0e8ba [Davies Liu] fix preservesPartitioning
eb1305d [Davies Liu] add RDD.lookup(key)
Spark-3213 Fixes issue with spark-ec2 not detecting slaves created with "Launch More like this"

... copy the spark_cluster_tag from a spot instance requests over to the instances.

Author: Vida Ha <vida@databricks.com>

Closes #2163 from vidaha/vida/spark-3213 and squashes the following commits:

5070a70 [Vida Ha] Spark-3214 Fix issue with spark-ec2 not detecting slaves created with 'Launch More Like This' and using Spot Requests
[SPARK-3243] Don't use stale spark-driver.* system properties

If we set both `spark.driver.extraClassPath` and `--driver-class-path`, then the latter correctly overrides the former. However, the value of the system property `spark.driver.extraClassPath` still uses the former, which is actually not added to the class path. This may cause some confusion...

Of course, this also affects other options (i.e. java options, library path, memory...).

Author: Andrew Or <andrewor14@gmail.com>

Closes #2154 from andrewor14/driver-submit-configs-fix and squashes the following commits:

17ec6fc [Andrew Or] Fix tests
0140836 [Andrew Or] Don't forget spark.driver.memory
e39d20f [Andrew Or] Also set spark.driver.extra* configs in client mode
[SPARK-3252][SQL] Add missing condition for test

According to the text message, both relations should be tested. So add the missing condition.

Author: viirya <viirya@gmail.com>

Closes #2159 from viirya/fix_test and squashes the following commits:

b1c0f52 [viirya] add missing condition.
[SQL] [SPARK-3236] Reading Parquet tables from Metastore mangles location

Currently we do `relation.hiveQlTable.getDataLocation.getPath`, which returns the path-part of the URI (e.g., "s3n://my-bucket/my-path" => "/my-path"). We should do `relation.hiveQlTable.getDataLocation.toString` instead, as a URI's toString returns a faithful representation of the full URI, which can later be passed into a Hadoop Path.

Author: Aaron Davidson <aaron@databricks.com>

Closes #2150 from aarondav/parquet-location and squashes the following commits:

459f72c [Aaron Davidson] [SQL] [SPARK-3236] Reading Parquet tables from Metastore mangles location