SPARK-3568 [mllib] add ranking metrics

Add common metrics for ranking algorithms (http://www-nlp.stanford.edu/IR-book/), including:
 - Mean Average Precision
 - Precisionn: top-n precision
 - Discounted cumulative gain (DCG) and NDCG

The following methods and the corresponding tests are implemented:

```
class RankingMetrics[T](predictionAndLabels: RDD[(Array[T], Array[T])]) {
  /* Returns the precsionk for each query */
  lazy val precAtK: RDD[Array[Double]]

  /**
   * param k the position to compute the truncated precision
   * return the average precision at the first k ranking positions
   */
  def precision(k: Int): Double

  /* Returns the average precision for each query */
  lazy val avePrec: RDD[Double]

  /*Returns the mean average precision (MAP) of all the queries*/
  lazy val meanAvePrec: Double

  /*Returns the normalized discounted cumulative gain for each query */
  lazy val ndcgAtK: RDD[Array[Double]]

  /**
   * param k the position to compute the truncated ndcg
   * return the average ndcg at the first k ranking positions
   */
  def ndcg(k: Int): Double
}
```

Author: coderxiang <shuoxiangpub@gmail.com>

Closes #2667 from coderxiang/rankingmetrics and squashes the following commits:

d881097 [coderxiang] update doc
14d9cd9 [coderxiang] remove unexpected files
d7fb93f [coderxiang] style change and remove ignored files
f113ee1 [coderxiang] modify doc for displaying superscript and subscript
f626896 [coderxiang] improve doc and remove unnecessary computation while labSet is empty
be6645e [coderxiang] set the precision of empty labset to 0.0
d64c120 [coderxiang] add logWarning for empty ground truth set
dfae292 [coderxiang] handle empty labSet for map. add test
62047c4 [coderxiang] style change and add documentation
f66612d [coderxiang] add additional test of precisionAt
b794cb2 [coderxiang] move private members precAtK, ndcgAtK into public methods. style change
77c9e5d [coderxiang] set precAtK and ndcgAtK as private member. Improve documentation
5f87bce [coderxiang] add API to calculate precision and ndcg at each ranking position
b7851cc [coderxiang] Use generic type to represent IDs
e443fee [coderxiang] change style and use alternative builtin methods
3a5a6ff [coderxiang] add ranking metrics
[SQL]redundant methods for broadcast

redundant methods for broadcast in ```TableReader```

Author: wangfei <wangfei1@huawei.com>

Closes #2862 from scwf/TableReader and squashes the following commits:

414cc24 [wangfei] unnecessary methods for broadcast
SPARK-1813. Add a utility to SparkConf that makes using Kryo really easy

Author: Sandy Ryza <sandy@cloudera.com>

Closes #789 from sryza/sandy-spark-1813 and squashes the following commits:

48b05e9 [Sandy Ryza] Simplify
b824932 [Sandy Ryza] Allow both spark.kryo.classesToRegister and spark.kryo.registrator at the same time
6a15bb7 [Sandy Ryza] Small fix
a2278c0 [Sandy Ryza] Respond to review comments
6ef592e [Sandy Ryza] SPARK-1813. Add a utility to SparkConf that makes using Kryo really easy
Update JavaCustomReceiver.java

Changed the usage string to correctly reflect the file name.

Author: Karthik <karthik.gomadam@gmail.com>

Closes #2699 from namelessnerd/patch-1 and squashes the following commits:

8570e33 [Karthik] Update JavaCustomReceiver.java
use isRunningLocally rather than runningLocally

runningLocally is deprecated now

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #2879 from CrazyJvm/runningLocally and squashes the following commits:

bec0b3e [CrazyJvm] use isRunningLocally rather than runningLocally
Fix for sampling error in NumPy v1.9 [SPARK-3995][PYSPARK]

Change maximum value for default seed during RDD sampling so that it is strictly less than 2 ** 32. This prevents a bug in the most recent version of NumPy, which cannot accept random seeds above this bound.

Adds an extra test that uses the default seed (instead of setting it manually, as in the docstrings).

mengxr

Author: freeman <the.freeman.lab@gmail.com>

Closes #2889 from freeman-lab/pyspark-sampling and squashes the following commits:

dc385ef [freeman] Change maximum value for default seed
[SPARK-3426] Fix sort-based shuffle error when spark.shuffle.compress and spark.shuffle.spill.compress settings are different

This PR fixes SPARK-3426, an issue where sort-based shuffle crashes if the
`spark.shuffle.spill.compress` and `spark.shuffle.compress` settings have
different values.

The problem is that sort-based shuffle's read and write paths use different
settings for determining whether to apply compression.  ExternalSorter writes
runs to files using `TempBlockId` ids, which causes
`spark.shuffle.spill.compress` to be used for enabling compression, but these
spilled files end up being shuffled over the network and read as shuffle files
using `ShuffleBlockId` by BlockStoreShuffleFetcher, which causes
`spark.shuffle.compress` to be used for enabling decompression.  As a result,
this leads to errors when these settings disagree.

Based on the discussions in #2247 and #2178, it sounds like we don't want to
remove the `spark.shuffle.spill.compress` setting.  Therefore, I've tried to
come up with a fix where `spark.shuffle.spill.compress` is used to compress
data that's read and written locally and `spark.shuffle.compress` is used to
compress any data that will be fetched / read as shuffle blocks.

To do this, I split `TempBlockId` into two new id types, `TempLocalBlockId` and
`TempShuffleBlockId`, which map to `spark.shuffle.spill.compress` and
`spark.shuffle.compress`, respectively.  ExternalAppendOnlyMap also used temp
blocks for spilling data.  It looks like ExternalSorter was designed to be
a generic sorter but its configuration already happens to be tied to sort-based
shuffle, so I think it's fine if we use `spark.shuffle.compress` to compress
its spills; we can move the compression configuration to the constructor in
a later commit if we find that ExternalSorter is being used in other contexts
where we want different configuration options to control compression.  To
summarize:

**Before:**

|       | ExternalAppendOnlyMap        | ExternalSorter               |
|-------|------------------------------|------------------------------|
| Read  | spark.shuffle.spill.compress | spark.shuffle.compress       |
| Write | spark.shuffle.spill.compress | spark.shuffle.spill.compress |

**After:**

|       | ExternalAppendOnlyMap        | ExternalSorter         |
|-------|------------------------------|------------------------|
| Read  | spark.shuffle.spill.compress | spark.shuffle.compress |
| Write | spark.shuffle.spill.compress | spark.shuffle.compress |

Thanks to andrewor14 for debugging this with me!

Author: Josh Rosen <joshrosen@databricks.com>

Closes #2890 from JoshRosen/SPARK-3426 and squashes the following commits:

1921cf6 [Josh Rosen] Minor edit for clarity.
c8dd8f2 [Josh Rosen] Add comment explaining use of createTempShuffleBlock().
2c687b9 [Josh Rosen] Fix SPARK-3426.
91e7e40 [Josh Rosen] Combine tests into single test of all combinations
76ca65e [Josh Rosen] Add regression test for SPARK-3426.
[SPARK-3877][YARN] Throw an exception when application is not successful so that the exit code wil be set to 1

When an yarn application fails (yarn-cluster mode), the exit code of spark-submit is still 0. It's hard for people to write some automatic scripts to run spark jobs in yarn because the failure can not be detected in these scripts.

This PR added a status checking after `monitorApplication`. If an application is not successful, `run()` will throw an `SparkException`, so that Client.scala will exit with code 1. Therefore, people can use the exit code of `spark-submit` to write some automatic scripts.

Author: zsxwing <zsxwing@gmail.com>

Closes #2732 from zsxwing/SPARK-3877 and squashes the following commits:

1f89fa5 [zsxwing] Fix the unit test
a0498e1 [zsxwing] Update the docs and the error message
e1cb9ef [zsxwing] Fix the hacky way of calling Client
ff16fec [zsxwing] Remove System.exit in Client.scala and add a test
6a2c103 [zsxwing] [SPARK-3877] Throw an exception when application is not successful so that the exit code wil be set to 1
[SPARK-3812] [BUILD] Adapt maven build to publish effective pom.

I have tried maven help plugin first but that published all projects in top level pom. So I was left with no choice but to roll my own trivial plugin. This patch basically installs an effective pom after maven install is finished.

The problem it fixes is described as follows:
If you install using maven
` mvn install -DskipTests -Dhadoop.version=2.2.0 -Phadoop-2.2 `
Then without this patch the published pom(s) will have hadoop version as 1.0.4. This can be a problem at some point.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #2673 from ScrapCodes/build-changes-effective-pom and squashes the following commits:

aa7b91d [Prashant Sharma] used an unused dep.
0300dac [Prashant Sharma] improved comment messages..
28f891e [Prashant Sharma] Added a useless dependency, so that we can shade it. And realized fake shading works for us.
553d96b [Prashant Sharma] Shaded some unused class of an unused dep, to generate effective pom(s)
[BUILD] Fixed resolver for scalastyle plugin and upgrade sbt version.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #2877 from ScrapCodes/scalastyle-fix and squashes the following commits:

a17b9fe [Prashant Sharma] [BUILD] Fixed resolver for scalastyle plugin.
[SPARK-4055][MLlib] Inconsistent spelling 'MLlib' and 'MLLib'

Thare are some inconsistent spellings 'MLlib' and 'MLLib' in some documents and source codes.

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

Closes #2903 from sarutak/SPARK-4055 and squashes the following commits:

b031640 [Kousuke Saruta] Fixed inconsistent spelling "MLlib and MLLib"
[SPARK-4006] In long running contexts, we encountered the situation of double registe...

...r without a remove in between. The cause for that is unknown, and assumed a temp network issue.

However, since the second register is with a BlockManagerId on a different port, blockManagerInfo.contains() returns false, while blockManagerIdByExecutor returns Some. This inconsistency is caught in a conditional statement that does System.exit(1), which is a huge robustness issue for us.

The fix - simply remove the old id from both maps during register when this happens. We are mimicking the behavior of expireDeadHosts(), by doing local cleanup of the maps before trying to add new ones.

Also - added some logging for register and unregister.

This is just like https://github.com/apache/spark/pull/2854 except it's on master

Author: Tal Sliwowicz <tal.s@taboola.com>

Closes #2886 from tsliwowicz/master-block-mgr-removal and squashes the following commits:

094d508 [Tal Sliwowicz] some more white space change undone
41a2217 [Tal Sliwowicz] some more whitspaces change undone
7bcfc3d [Tal Sliwowicz] whitspaces fix
df9d98f [Tal Sliwowicz] Code review comments fixed
f48bce9 [Tal Sliwowicz] In long running contexts, we encountered the situation of double register without a remove in between. The cause for that is unknown, and assumed a temp network issue.
specify unidocGenjavadocVersion of 0.8

Fixes an issue with being too strict generating javadoc causing errors.

Author: Holden Karau <holden@pigscanfly.ca>

Closes #2893 from holdenk/SPARK-3359-sbtunidoc-java8 and squashes the following commits:

9379a70 [Holden Karau] specify unidocGenjavadocVersion of 0.8
Revert "[SPARK-3812] [BUILD] Adapt maven build to publish effective pom."

This reverts commit c5882c663e054adcd3ecd9f11e91a1929dbc14a3.

I am reverting this becuase it appears to cause the maven tests
to hang.
[SPARK-4019] [SPARK-3740] Fix MapStatus compression bug that could lead to empty results or Snappy errors

This commit fixes a bug in MapStatus that could cause jobs to wrongly return
empty results if those jobs contained stages with more than 2000 partitions
where most of those partitions were empty.

For jobs with > 2000 partitions, MapStatus uses HighlyCompressedMapStatus,
which only stores the average size of blocks.  If the average block size is
zero, then this will cause all blocks to be reported as empty, causing
BlockFetcherIterator to mistakenly skip them.

For example, this would return an empty result:

    sc.makeRDD(0 until 10, 1000).repartition(2001).collect()

This can also lead to deserialization errors (e.g. Snappy decoding errors)
for jobs with > 2000 partitions where the average block size is non-zero but
there is at least one empty block.  In this case, the BlockFetcher attempts to
fetch empty blocks and fails when trying to deserialize them.

The root problem here is that MapStatus has a (previously undocumented)
correctness property that was violated by HighlyCompressedMapStatus:

    If a block is non-empty, then getSizeForBlock must be non-zero.

I fixed this by modifying HighlyCompressedMapStatus to store the average size
of _non-empty_ blocks and to use a compressed bitmap to track which blocks are
empty.

I also removed a test which was broken as originally written: it attempted
to check that HighlyCompressedMapStatus's size estimation error was < 10%,
but this was broken because HighlyCompressedMapStatus is only used for map
statuses with > 2000 partitions, but the test only created 50.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #2866 from JoshRosen/spark-4019 and squashes the following commits:

fc8b490 [Josh Rosen] Roll back hashset change, which didn't improve performance.
5faa0a4 [Josh Rosen] Incorporate review feedback
c8b8cae [Josh Rosen] Two performance fixes:
3b892dd [Josh Rosen] Address Reynold's review comments
ba2e71c [Josh Rosen] Add missing newline
609407d [Josh Rosen] Use Roaring Bitmap to track non-empty blocks.
c23897a [Josh Rosen] Use sets when comparing collect() results
91276a3 [Josh Rosen] [SPARK-4019] Fix MapStatus compression bug that could lead to empty results.
[SPARK-3993] [PySpark] fix bug while reuse worker after take()

After take(), maybe there are some garbage left in the socket, then next task assigned to this worker will hang because of corrupted data.

We should make sure the socket is clean before reuse it, write END_OF_STREAM at the end, and check it after read out all result from python.

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

Closes #2838 from davies/fix_reuse and squashes the following commits:

8872914 [Davies Liu] fix tests
660875b [Davies Liu] fix bug while reuse worker after take()
[SPARK-4000][BUILD] Sends archived unit tests logs to Jenkins master

This PR sends archived unit tests logs to the build history directory in Jenkins master, so that we can serve it via HTTP later to help debugging Jenkins build failures.

pwendell JoshRosen Please help review, thanks!

Author: Cheng Lian <lian@databricks.com>

Closes #2845 from liancheng/log-archive and squashes the following commits:

ac8d9d4 [Cheng Lian] Includes build number in messages posted to GitHub
68c7010 [Cheng Lian] Logs backup should be implemented in dev/run-tests-jenkins
4b912f7 [Cheng Lian] Sends archived unit tests logs to Jenkins master
SPARK-3812 Build changes to publish effective pom.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #2921 from ScrapCodes/build-changes-effective-pom and squashes the following commits:

8841491 [Prashant Sharma] Fixed broken maven build.
aa7b91d [Prashant Sharma] used an unused dep.
0300dac [Prashant Sharma] improved comment messages..
28f891e [Prashant Sharma] Added a useless dependency, so that we can shade it. And realized fake shading works for us.
553d96b [Prashant Sharma] Shaded some unused class of an unused dep, to generate effective pom(s)
[SPARK-2652] [PySpark] donot use KyroSerializer as default serializer

KyroSerializer can not serialize customized class without registered explicitly, use it as default serializer in PySpark will introduce some regression in MLlib.

cc mengxr

Author: Davies Liu <davies@databricks.com>

Closes #2916 from davies/revert and squashes the following commits:

43eb6d3 [Davies Liu] donot use KyroSerializer as default serializer