[SPARK-4003] [SQL] add 3 types for java SQL context

In JavaSqlContext, we need to let java program use big decimal, timestamp, date types.

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #2850 from adrian-wang/javacontext and squashes the following commits:

4c4292c [Daoyuan Wang] change underlying type of JavaSchemaRDD as scala
bb0508f [Daoyuan Wang] add test cases
3c58b0d [Daoyuan Wang] add 3 types for java SQL context
[SPARK-3822] Executor scaling mechanism for Yarn

This is part of a broader effort to enable dynamic scaling of executors ([SPARK-3174](https://issues.apache.org/jira/browse/SPARK-3174)). This is intended to work alongside SPARK-3795 (#2746), SPARK-3796 and SPARK-3797, but is functionally independently of these other issues.

The logic is built on top of PraveenSeluka's changes at #2798. This is different from the changes there in a few major ways: (1) the mechanism is implemented within the existing scheduler backend framework rather than in new `Actor` classes. This also introduces a parent abstract class `YarnSchedulerBackend` to encapsulate common logic to communicate with the Yarn `ApplicationMaster`. (2) The interface of requesting executors exposed to the `SparkContext` is the same, but the communication between the scheduler backend and the AM uses total number executors desired instead of an incremental number. This is discussed in #2746 and explained in the comments in the code.

I have tested this significantly on a stable Yarn cluster.

------------
A remaining task for this issue is to tone down the error messages emitted when an executor is removed.
Currently, `SparkContext` and its components react as if the executor has failed, resulting in many scary error messages and eventual timeouts. While it's not strictly necessary to fix this as of the first-cut implementation of this mechanism, it would be good to add logic to distinguish this case. I prefer to address this in a separate PR. I have filed a separate JIRA for this task at SPARK-4134.

Author: Andrew Or <andrew@databricks.com>
Author: Andrew Or <andrewor14@gmail.com>

Closes #2840 from andrewor14/yarn-scaling-mechanism and squashes the following commits:

485863e [Andrew Or] Minor log message changes
4920be8 [Andrew Or] Clarify that public API is only for Yarn mode for now
1c57804 [Andrew Or] Reword a few comments + other review comments
6321140 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism
02836c0 [Andrew Or] Limit scope of synchronization
4e2ed7f [Andrew Or] Fix bug: keep track of removed executors properly
73ade46 [Andrew Or] Wording changes (minor)
2a7a6da [Andrew Or] Add `sc.killExecutor` as a shorthand (minor)
665f229 [Andrew Or] Mima excludes
79aa2df [Andrew Or] Simplify the request interface by asking for a total
04f625b [Andrew Or] Fix race condition that causes over-allocation of executors
f4783f8 [Andrew Or] Change the semantics of requesting executors
005a124 [Andrew Or] Fix tests
4628b16 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism
db4a679 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism
572f5c5 [Andrew Or] Unused import (minor)
f30261c [Andrew Or] Kill multiple executors rather than one at a time
de260d9 [Andrew Or] Simplify by skipping useless null check
9c52542 [Andrew Or] Simplify by skipping the TaskSchedulerImpl
97dd1a8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism
d987b3e [Andrew Or] Move addWebUIFilters to Yarn scheduler backend
7b76d0a [Andrew Or] Expose mechanism in SparkContext as developer API
47466cd [Andrew Or] Refactor common Yarn scheduler backend logic
c4dfaac [Andrew Or] Avoid thrashing when removing executors
53e8145 [Andrew Or] Start yarn actor early to listen for AM registration message
bbee669 [Andrew Or] Add mechanism in yarn client mode
[SPARK-4097] Fix the race condition of 'thread'

There is a chance that `thread` is null when calling `thread.interrupt()`.

```Scala
  override def cancel(): Unit = this.synchronized {
    _cancelled = true
    if (thread != null) {
      thread.interrupt()
    }
  }
```
Should put `thread = null` into a `synchronized` block to fix the race condition.

Author: zsxwing <zsxwing@gmail.com>

Closes #2957 from zsxwing/SPARK-4097 and squashes the following commits:

edf0aee [zsxwing] Add comments to explain the lock
c5cfeca [zsxwing] Fix the race condition of 'thread'
[SPARK-3795] Heuristics for dynamically scaling executors

This is part of a bigger effort to provide elastic scaling of executors within a Spark application ([SPARK-3174](https://issues.apache.org/jira/browse/SPARK-3174)). This PR does not provide any functionality by itself; it is a skeleton that is missing a mechanism to be added later in [SPARK-3822](https://issues.apache.org/jira/browse/SPARK-3822).

Comments and feedback are most welcome. For those of you reviewing this in detail, I highly recommend doing it through your favorite IDE instead of through the diff here.

Author: Andrew Or <andrewor14@gmail.com>
Author: Andrew Or <andrew@databricks.com>

Closes #2746 from andrewor14/scaling-heuristics and squashes the following commits:

8a4fdaa [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
e045df8 [Andrew Or] Add warning message (minor)
dfa31ec [Andrew Or] Fix tests
c0becc4 [Andrew Or] Merging with SPARK-3822
4784f93 [Andrew Or] Reword an awkward log message
181f27f [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
c79e907 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
4672b90 [Andrew Or] It's nano time.
a6a30f2 [Andrew Or] Do not allow min/max executors of 0
c60ec33 [Andrew Or] Rewrite test logic with clocks
b00b680 [Andrew Or] Fix style
c3caa65 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
7f9da14 [Andrew Or] Factor out logic to verify bounds on # executors (minor)
f279019 [Andrew Or] Add time mocking tests for polling loop
685e347 [Andrew Or] Factor out clock in polling loop to facilitate testing
3cea7f7 [Andrew Or] Use PrivateMethodTester to keep original class private
3156d81 [Andrew Or] Update comments and exception messages
92f36f9 [Andrew Or] Address minor review comments
abdea61 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
2aefd09 [Andrew Or] Correct listener behavior
9fe6e44 [Andrew Or] Rename variables and configs + update comments and log messages
149cc32 [Andrew Or] Fix style
254c958 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
5ff829b [Andrew Or] Add tests for ExecutorAllocationManager
19c6c4b [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
5896515 [Andrew Or] Move ExecutorAllocationManager out of scheduler package
9ca8945 [Andrew Or] Rewrite callbacks through the listener interface
5e336b9 [Andrew Or] Remove code from backend to avoid conflict with SPARK-3822
092d1fd [Andrew Or] Remove timeout logic for pending requests
1309fab [Andrew Or] Request executors by specifying the number pending
8bc0e9d [Andrew Or] Add logic to expire pending requests after timeouts
b750ee1 [Andrew Or] Express timers in terms of expiration times + remove retry logic
7f8dd47 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
9d516cc [Andrew Or] Bug fix: Actually trigger the add timer / add retry timer
44f1832 [Andrew Or] Rename configs to include time units
eaae7ef [Andrew Or] Address various review comments
6f8be6c [Andrew Or] Beef up comments on what each of the timers mean
baaa403 [Andrew Or] Simplify variable names (minor)
42beec8 [Andrew Or] Reset whether the add threshold is crossed on cancellation
9bcc0bc [Andrew Or] ExecutorScalingManager -> ExecutorAllocationManager
2784398 [Andrew Or] Merge branch 'master' of github.com:apache/spark into scaling-heuristics
5a97d9e [Andrew Or] Log retry attempts in INFO + clean up logging
2f55c9f [Andrew Or] Do not keep requesting executors even after max attempts
0acd1cb [Andrew Or] Rewrite timer logic with polling
b3c7d44 [Andrew Or] Start the retry timer for adding executors at the right time
9b5f2ea [Andrew Or] Wording changes in comments and log messages
c2203a5 [Andrew Or] Simplify code to access the scheduler backend
e519d08 [Andrew Or] Simplify initialization code
2cc87a7 [Andrew Or] Add retry logic for removing executors
d0b34a6 [Andrew Or] Add retry logic for adding executors
9cc4649 [Andrew Or] Simplifying synchronization logic
67c03c7 [Andrew Or] Correct semantics of adding executors + update comments
6c48ab0 [Andrew Or] Update synchronization comment
8901900 [Andrew Or] Simplify remove policy + change the semantics of add policy
1cc8444 [Andrew Or] Minor wording change
ae5b64a [Andrew Or] Add synchronization
20ec6b9 [Andrew Or] First cut implementation of removing executors dynamically
4077ae2 [Andrew Or] Minor code re-organization
6f1fa66 [Andrew Or] First cut implementation of adding executors dynamically
b2e6dcc [Andrew Or] Add skeleton interface for requesting / killing executors
[SPARK-4053][Streaming] Made the ReceiverSuite test more reliable, by fixing block generator throttling

In the unit test that checked whether blocks generated by throttled block generator had expected number of records, the thresholds are too tight, which sometimes led to the test failing.
This PR fixes it by relaxing the thresholds and the time intervals for testing.

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

Closes #2900 from tdas/receiver-suite-flakiness and squashes the following commits:

28508a2 [Tathagata Das] Made the ReceiverSuite test more reliable
[SPARK-1720][SPARK-1719] use LD_LIBRARY_PATH instead of -Djava.library.path

- [X] Standalone
- [X] YARN
- [X] Mesos
- [X]  Mac OS X
- [X] Linux
- [ ]  Windows

This is another implementation about #1031

Author: GuoQiang Li <witgo@qq.com>

Closes #2711 from witgo/SPARK-1719 and squashes the following commits:

c7b26f6 [GuoQiang Li] review commits
4488e41 [GuoQiang Li] Refactoring CommandUtils
a444094 [GuoQiang Li] review commits
40c0b4a [GuoQiang Li] Add buildLocalCommand method
c1a0ddd [GuoQiang Li] fix comments
156ce88 [GuoQiang Li] review commit
38aa377 [GuoQiang Li] Refactor CommandUtils.scala
4269e00 [GuoQiang Li] Refactor SparkSubmitDriverBootstrapper.scala
7a1d634 [GuoQiang Li] use LD_LIBRARY_PATH instead of -Djava.library.path
[SPARK-4102] Remove unused ShuffleReader.stop() method.

This method is not implemented by the only subclass
(HashShuffleReader), nor is it ever called. While the
use of Scala's fancy "???" was pretty exciting, the method's
existence can only lead to confusion and it therefore should
be deleted.

mateiz was there a reason for adding this that I'm
missing?

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #2966 from kayousterhout/SPARK-4102 and squashes the following commits:

532c564 [Kay Ousterhout] Added back commented-out method, as per Matei's request
904655e [Kay Ousterhout] [SPARK-4102] Remove unused ShuffleReader.stop() method.
[SPARK-4130][MLlib] Fixing libSVM parser bug with extra whitespace

This simple patch filters out extra whitespace entries.

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

Closes #2996 from jegonzal/loadLibSVM and squashes the following commits:

e0227ab [Joey] improving readability
e028e84 [Joseph E. Gonzalez] fixing whitespace bug in loadLibSVMFile when parsing libSVM files
SPARK-4111 [MLlib] add regression metrics

Add RegressionMetrics.scala as regression metrics used for evaluation and corresponding test case RegressionMetricsSuite.scala.

Author: Yanbo Liang <yanbohappy@gmail.com>
Author: liangyanbo <liangyanbo@meituan.com>

Closes #2978 from yanbohappy/regression_metrics and squashes the following commits:

730d0a9 [Yanbo Liang] more clearly annotation
3d0bec1 [Yanbo Liang] rename and keep code style
a8ad3e3 [Yanbo Liang] simplify code for keeping style
d454909 [Yanbo Liang] rename parameter and function names, delete unused columns, add reference
2e56282 [liangyanbo] rename r2_score() and remove unused column
43bb12b [liangyanbo] add regression metrics
Modified UserDefinedType to store Java class of user type so that registerUDT takes only the udt argument.

Mid-process adding Java support for UDTs.
Merge remote-tracking branch 'upstream/master' into sql-udt