[SPARK-4196][SPARK-4602][Streaming] Fix serialization issue in PairDStreamFunctions.saveAsNewAPIHadoopFiles

Solves two JIRAs in one shot
- Makes the ForechDStream created by saveAsNewAPIHadoopFiles serializable for checkpoints
- Makes the default configuration object used saveAsNewAPIHadoopFiles be the Spark's hadoop configuration

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

Closes #3457 from tdas/savefiles-fix and squashes the following commits:

bb4729a [Tathagata Das] Same treatment for saveAsHadoopFiles
b382ea9 [Tathagata Das] Fix serialization issue in PairDStreamFunctions.saveAsNewAPIHadoopFiles.
[SPARK-4592] Avoid duplicate worker registrations in standalone mode

**Summary.** On failover, the Master may receive duplicate registrations from the same worker, causing the worker to exit. This is caused by this commit https://github.com/apache/spark/commit/4afe9a4852ebeb4cc77322a14225cd3dec165f3f, which adds logic for the worker to re-register with the master in case of failures. However, the following race condition may occur:

(1) Master A fails and Worker attempts to reconnect to all masters
(2) Master B takes over and notifies Worker
(3) Worker responds by registering with Master B
(4) Meanwhile, Worker's previous reconnection attempt reaches Master B, causing the same Worker to register with Master B twice

**Fix.** Instead of attempting to register with all known masters, the worker should re-register with only the one that it has been communicating with. This is safe because the fact that a failover has occurred means the old master must have died. Then, when the worker is finally notified of a new master, it gives up on the old one in favor of the new one.

**Caveat.** Even this fix is subject to more obscure race conditions. For instance, if Master B fails and Master A recovers immediately, then Master A may still observe duplicate worker registrations. However, this and other potential race conditions summarized in [SPARK-4592](https://issues.apache.org/jira/browse/SPARK-4592), are much, much less likely than the one described above, which is deterministically reproducible.

Author: Andrew Or <andrew@databricks.com>

Closes #3447 from andrewor14/standalone-failover and squashes the following commits:

0d9716c [Andrew Or] Move re-registration logic to actor for thread-safety
79286dc [Andrew Or] Preserve old behavior for initial retries
83b321c [Andrew Or] Tweak wording
1fce6a9 [Andrew Or] Active master actor could be null in the beginning
b6f269e [Andrew Or] Avoid duplicate worker registrations
[SPARK-4546] Improve HistoryServer first time user experience

The documentation points the user to run the following
```
sbin/start-history-server.sh
```
The first thing this does is throw an exception that complains a log directory is not specified. The exception message itself does not say anything about what to set. Instead we should have a default and a landing page with a better message. The new default log directory is `file:/tmp/spark-events`.

This is what it looks like as of this PR:

![after](https://issues.apache.org/jira/secure/attachment/12682985/after.png)

Author: Andrew Or <andrew@databricks.com>

Closes #3411 from andrewor14/minor-history-improvements and squashes the following commits:

f33d6b3 [Andrew Or] Point user to set config if default log dir does not exist
fc4c17a [Andrew Or] Improve HistoryServer UX
Fix SPARK-4471: blockManagerIdFromJson function throws exception while B...

Fix [SPARK-4471](https://issues.apache.org/jira/browse/SPARK-4471): blockManagerIdFromJson function throws exception while BlockManagerId be null in MetadataFetchFailedException

Author: hushan[胡珊] <hushan@xiaomi.com>

Closes #3340 from suyanNone/fix-blockmanagerId-jnothing-2 and squashes the following commits:

159f9a3 [hushan[胡珊]] Refine test code for blockmanager is null
4380d73 [hushan[胡珊]] remove useless blank line
3ccf651 [hushan[胡珊]] Fix SPARK-4471: blockManagerIdFromJson function throws exception while metadata fetch failed
[Spark-4509] Revert EC2 tag-based cluster membership patch

This PR reverts changes related to tag-based cluster membership. As discussed in SPARK-3332, we didn't figure out a safe strategy to use tags to determine cluster membership, because tagging is not atomic. The following changes are reverted:

SPARK-2333: 94053a7b766788bb62e2dbbf352ccbcc75f71fc0
SPARK-3213: 7faf755ae4f0cf510048e432340260a6e609066d
SPARK-3608: 78d4220fa0bf2f9ee663e34bbf3544a5313b02f0.

I tested launch, login, and destroy. It is easy to check the diff by comparing it to Josh's patch for branch-1.1:

https://github.com/apache/spark/pull/2225/files

JoshRosen I sent the PR to master. It might be easier for us to keep master and branch-1.2 the same at this time. We can always re-apply the patch once we figure out a stable solution.

Author: Xiangrui Meng <meng@databricks.com>

Closes #3453 from mengxr/SPARK-4509 and squashes the following commits:

f0b708b [Xiangrui Meng] revert 94053a7b766788bb62e2dbbf352ccbcc75f71fc0
4298ea5 [Xiangrui Meng] revert 7faf755ae4f0cf510048e432340260a6e609066d
35963a1 [Xiangrui Meng] Revert "SPARK-3608 Break if the instance tag naming succeeds"
[SPARK-4583] [mllib] LogLoss for GradientBoostedTrees fix + doc updates

Currently, the LogLoss used by GradientBoostedTrees has 2 issues:
* the gradient (and therefore loss) does not match that used by Friedman (1999)
* the error computation uses 0/1 accuracy, not log loss

This PR updates LogLoss.
It also adds some doc for boosting and forests.

I tested it on sample data and made sure the log loss is monotonically decreasing with each boosting iteration.

CC: mengxr manishamde codedeft

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3439 from jkbradley/gbt-loss-fix and squashes the following commits:

cfec17e [Joseph K. Bradley] removed forgotten temp comments
a27eb6d [Joseph K. Bradley] corrections to last log loss commit
ed5da2c [Joseph K. Bradley] updated LogLoss (boosting) for numerical stability
5e52bff [Joseph K. Bradley] * Removed the 1/2 from SquaredError.  This also required updating the test suite since it effectively doubles the gradient and loss. * Added doc for developers within RandomForest. * Small cleanup in test suite (generating data only once)
e57897a [Joseph K. Bradley] Fixed LogLoss for GradientBoostedTrees, and updated doc for losses, forests, and boosting
[HOTFIX]: Adding back without-hive dist
[SPARK-4604][MLLIB] make MatrixFactorizationModel public

User could construct an MF model directly. I added a note about the performance.

Author: Xiangrui Meng <meng@databricks.com>

Closes #3459 from mengxr/SPARK-4604 and squashes the following commits:

f64bcd3 [Xiangrui Meng] organize imports
ed08214 [Xiangrui Meng] check preconditions and unit tests
a624c12 [Xiangrui Meng] make MatrixFactorizationModel public
[SPARK-4516] Cap default number of Netty threads at 8

In practice, only 2-4 cores should be required to transfer roughly 10 Gb/s, and each core that we use will have an initial overhead of roughly 32 MB of off-heap memory, which comes at a premium.

Thus, this value should still retain maximum throughput and reduce wasted off-heap memory allocation. It can be overridden by setting the number of serverThreads and clientThreads manually in Spark's configuration.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3469 from aarondav/fewer-pools2 and squashes the following commits:

087c59f [Aaron Davidson] [SPARK-4516] Cap default number of Netty threads at 8
[SPARK-4516] Avoid allocating Netty PooledByteBufAllocators unnecessarily

Turns out we are allocating an allocator pool for every TransportClient (which means that the number increases with the number of nodes in the cluster), when really we should just reuse one for all clients.

This patch, as expected, greatly decreases off-heap memory allocation, and appears to make allocation only proportional to the number of cores.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3465 from aarondav/fewer-pools and squashes the following commits:

36c49da [Aaron Davidson] [SPARK-4516] Avoid allocating unnecessarily Netty PooledByteBufAllocators
[SPARK-4612] Reduce task latency and increase scheduling throughput by making configuration initialization lazy

https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/executor/Executor.scala#L337 creates a configuration object for every task that is launched, even if there is no new dependent file/JAR to update. This is a heavy-weight creation that should be avoided if there is no new file/JAR to update. This PR makes that creation lazy. Quick local test in spark-perf scheduling throughput tests gives the following numbers in a local standalone scheduler mode.
1 job with 10000 tasks: before 7.8395 seconds, after 2.6415 seconds = 3x increase in task scheduling throughput

pwendell JoshRosen

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

Closes #3463 from tdas/lazy-config and squashes the following commits:

c791c1e [Tathagata Das] Reduce task latency by making configuration initialization lazy
Removing confusing TripletFields

After additional discussion with rxin, I think having all the possible `TripletField` options is confusing.  This pull request reduces the triplet fields to:

```java
  /**
   * None of the triplet fields are exposed.
   */
  public static final TripletFields None = new TripletFields(false, false, false);

  /**
   * Expose only the edge field and not the source or destination field.
   */
  public static final TripletFields EdgeOnly = new TripletFields(false, false, true);

  /**
   * Expose the source and edge fields but not the destination field. (Same as Src)
   */
  public static final TripletFields Src = new TripletFields(true, false, true);

  /**
   * Expose the destination and edge fields but not the source field. (Same as Dst)
   */
  public static final TripletFields Dst = new TripletFields(false, true, true);

  /**
   * Expose all the fields (source, edge, and destination).
   */
  public static final TripletFields All = new TripletFields(true, true, true);
```

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #3472 from jegonzal/SimplifyTripletFields and squashes the following commits:

91796b5 [Joseph E. Gonzalez] removing confusing triplet fields
[SPARK-4614][MLLIB] Slight API changes in Matrix and Matrices

Before we have a full picture of the operators we want to add, it might be safer to hide `Matrix.transposeMultiply` in 1.2.0. Another update we want to change is `Matrix.randn` and `Matrix.rand`, both of which should take a `Random` implementation. Otherwise, it is very likely to produce inconsistent RDDs. I also added some unit tests for matrix factory methods. All APIs are new in 1.2, so there is no incompatible changes.

brkyvz

Author: Xiangrui Meng <meng@databricks.com>

Closes #3468 from mengxr/SPARK-4614 and squashes the following commits:

3b0e4e2 [Xiangrui Meng] add mima excludes
6bfd8a4 [Xiangrui Meng] hide transposeMultiply; add rng to rand and randn; add unit tests
[SPARK-732][SPARK-3628][CORE][RESUBMIT] eliminate duplicate update on accmulator

https://issues.apache.org/jira/browse/SPARK-3628

In current implementation, the accumulator will be updated for every successfully finished task, even the task is from a resubmitted stage, which makes the accumulator counter-intuitive

In this patch, I changed the way for the DAGScheduler to update the accumulator,

DAGScheduler maintains a HashTable, mapping the stage id to the received <accumulator_id , value> pairs. Only when the stage becomes independent, (no job needs it any more), we accumulate the values of the <accumulator_id , value> pairs, when a task finished, we check if the HashTable has contained such stageId, it saves the accumulator_id, value only when the task is the first finished task of a new stage or the stage is running for the first attempt...

Author: CodingCat <zhunansjtu@gmail.com>

Closes #2524 from CodingCat/SPARK-732-1 and squashes the following commits:

701a1e8 [CodingCat] roll back change on Accumulator.scala
1433e6f [CodingCat] make MIMA happy
b233737 [CodingCat] address Matei's comments
02261b8 [CodingCat] rollback  some changes
6b0aff9 [CodingCat] update document
2b2e8cf [CodingCat] updateAccumulator
83b75f8 [CodingCat] style fix
84570d2 [CodingCat] re-enable  the bad accumulator guard
1e9e14d [CodingCat] add NPE guard
21b6840 [CodingCat] simplify the patch
88d1f03 [CodingCat] fix rebase error
f74266b [CodingCat] add test case for resubmitted result stage
5cf586f [CodingCat] de-duplicate on task level
138f9b3 [CodingCat] make MIMA happy
67593d2 [CodingCat] make if allowing duplicate update as an option of accumulator
[Release] Automate generation of contributors list

This commit provides a script that computes the contributors list
by linking the github commits with JIRA issues. Automatically
translating github usernames remains a TODO at this point.
SPARK-4170 [CORE] Closure problems when running Scala app that "extends App"

Warn against subclassing scala.App, and remove one instance of this in examples

Author: Sean Owen <sowen@cloudera.com>

Closes #3497 from srowen/SPARK-4170 and squashes the following commits:

4a6131f [Sean Owen] Restore multiline string formatting
a8ca895 [Sean Owen] Warn against subclassing scala.App, and remove one instance of this in examples
[SPARK-4626] Kill a task only if the executorId is (still) registered with the scheduler

Author: roxchkplusony <roxchkplusony@gmail.com>

Closes #3483 from roxchkplusony/bugfix/4626 and squashes the following commits:

aba9184 [roxchkplusony] replace warning message per review
5e7fdea [roxchkplusony] [SPARK-4626] Kill a task only if the executorId is (still) registered with the scheduler
[SPARK-4613][Core] Java API for JdbcRDD

This PR introduces a set of Java APIs for using `JdbcRDD`:

1. Trait (interface) `JdbcRDD.ConnectionFactory`: equivalent to the `getConnection: () => Connection` parameter in `JdbcRDD` constructor.
2. Two overloaded versions of `Jdbc.create`: used to create `JavaRDD` that wraps a `JdbcRDD`.

<!-- Reviewable:start -->
[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/3478)
<!-- Reviewable:end -->

Author: Cheng Lian <lian@databricks.com>

Closes #3478 from liancheng/japi-jdbc-rdd and squashes the following commits:

9a54625 [Cheng Lian] Only shutdowns a single DB rather than the whole Derby driver
d4cedc5 [Cheng Lian] Moves Java JdbcRDD test case to a separate test suite
ffcdf2e [Cheng Lian] Java API for JdbcRDD
Replace Scala.util.Sorting.quickSort with Sorter(TimSort) in Spark