Fix for [SPARK-13002](https://issues.apache.org/jira/browse/SPARK-13002) about the initial number of executors when running with dynamic allocation on Mesos.
Instead of fixing it just for the Mesos case, made the change in `ExecutorAllocationManager`. It is already driving the number of executors running on Mesos, only no the initial value.

The `None` and `Some(0)` are internal details on the computation of resources to reserved, in the Mesos backend scheduler. `executorLimitOption` has to be initialized correctly, otherwise the Mesos backend scheduler will, either, create to many executors at launch, or not create any executors and not be able to recover from this state.

Removed the 'special case' description in the doc. It was not totally accurate, and is not needed anymore.

This doesn't fix the same problem visible with Spark standalone. There is no straightforward way to send the initial value in standalone mode.

Somebody knowing this part of the yarn support should review this change.

Author: Luc Bourlier <luc.bourlier@typesafe.com>

Closes #11047 from skyluc/issue/initial-dyn-alloc-2.

Author: Bill Chambers <bill@databricks.com>

Closes #11094 from anabranch/dynamic-docs.

https://issues.apache.org/jira/browse/SPARK-12939

Now we will catch `ObjectOperator` in `Analyzer` and resolve the `fromRowExpression/deserializer` inside it.  Also update the `MapGroups` and `CoGroup` to pass in `dataAttributes`, so that we can correctly resolve value deserializer(the `child.output` contains both groupking key and values, which may mess things up if they have same-name attribtues). End-to-end tests are added.

follow-ups:

* remove encoders from typed aggregate expression.
* completely remove resolve/bind in `ExpressionEncoder`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10852 from cloud-fan/bug.

A follow up PR for #11062 because it didn't rename the test suite.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #11096 from zsxwing/rename.

This patch adds option function for boolean, long, and double types. This makes it slightly easier for Spark users to specify options without turning them into strings. Using the JSON data source as an example.

Before this patch:
```scala
sqlContext.read.option("primitivesAsString", "true").json("/path/to/json")
```

After this patch:
Before this patch:
```scala
sqlContext.read.option("primitivesAsString", true).json("/path/to/json")
```

Author: Reynold Xin <rxin@databricks.com>

Closes #11072 from rxin/SPARK-13187.

Another trivial deprecation fix for Scala 2.11

Author: Jakob Odersky <jakob@odersky.com>

Closes #11089 from jodersky/SPARK-13208.

JIRA: https://issues.apache.org/jira/browse/SPARK-12850

This PR is to support bucket pruning when the predicates are `EqualTo`, `EqualNullSafe`, `IsNull`, `In`, and `InSet`.

Like HIVE, in this PR, the bucket pruning works when the bucketing key has one and only one column.

So far, I do not find a way to verify how many buckets are actually scanned. However, I did verify it when doing the debug. Could you provide a suggestion how to do it properly? Thank you! cloud-fan yhuai rxin marmbrus

BTW, we can add more cases to support complex predicate including `Or` and `And`. Please let me know if I should do it in this PR.

Maybe we also need to add test cases to verify if bucket pruning works well for each data type.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #10942 from gatorsmile/pruningBuckets.

Author: Raafat Akkad <raafat.akkad@gmail.com>

Closes #10959 from RaafatAkkad/master.

[SPARK-13195][STREAMING] Fix NoSuchElementException when a state is not set but timeoutThreshold is defined

Check the state Existence before calling get.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #11081 from zsxwing/SPARK-13195.

This patch incorporates review feedback from #11069, which is already merged.

Author: Andrew Or <andrew@databricks.com>

Closes #11080 from andrewor14/catalog-follow-ups.

The config already describes time and accepts a general format
that is not restricted to ms. This commit renames the internal
config to use a format that's consistent in Spark.

Spark SQL should collapse adjacent `Repartition` operators and only keep the last one.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #11064 from JoshRosen/collapse-repartition.

This commit exists to close the following pull requests on Github:

Closes #7971 (requested by yhuai)
Closes #8539 (requested by srowen)
Closes #8746 (requested by yhuai)
Closes #9288 (requested by andrewor14)
Closes #9321 (requested by andrewor14)
Closes #9935 (requested by JoshRosen)
Closes #10442 (requested by andrewor14)
Closes #10585 (requested by srowen)
Closes #10785 (requested by srowen)
Closes #10832 (requested by andrewor14)
Closes #10941 (requested by marmbrus)
Closes #11024 (requested by andrewor14)

These were ignored because they are incorrectly written; they don't actually trigger stage retries, which is what the tests are testing. These tests are now rewritten to induce stage retries through fetch failures.

Note: there were 2 tests before and now there's only 1. What happened? It turns out that the case where we only resubmit a subset of of the original missing partitions is very difficult to simulate in tests without potentially introducing flakiness. This is because the `DAGScheduler` removes all map outputs associated with a given executor when this happens, and we will need multiple executors to trigger this case, and sometimes the scheduler still removes map outputs from all executors.

Author: Andrew Or <andrew@databricks.com>

Closes #10969 from andrewor14/unignore-accum-test.

Currently the Master would always set an application's initial executor limit to infinity. If the user specified `spark.dynamicAllocation.initialExecutors`, the config would not take effect. This is similar to #11047 but for standalone mode.

Author: Andrew Or <andrew@databricks.com>

Closes #11054 from andrewor14/standalone-da-initial.

Building with scala 2.11 results in the warning trait SynchronizedBuffer in package mutable is deprecated: Synchronization via traits is deprecated as it is inherently unreliable. Consider java.util.concurrent.ConcurrentLinkedQueue as an alternative. Investigation shows we are already using ConcurrentLinkedQueue in other locations so switch our uses of SynchronizedBuffer to ConcurrentLinkedQueue.

Author: Holden Karau <holden@us.ibm.com>

Closes #11059 from holdenk/SPARK-13164-replace-deprecated-synchronized-buffer-in-core.

In the current implementation the mesos coarse scheduler does not wait for the mesos tasks to complete before ending the driver. This causes a race where the task has to finish cleaning up before the mesos driver terminates it with a SIGINT (and SIGKILL after 3 seconds if the SIGINT doesn't work).

This PR causes the mesos coarse scheduler to wait for the mesos tasks to finish (with a timeout defined by `spark.mesos.coarse.shutdown.ms`)

This PR also fixes a regression caused by [SPARK-10987] whereby submitting a shutdown causes a race between the local shutdown procedure and the notification of the scheduler driver disconnection. If the scheduler driver disconnection wins the race, the coarse executor incorrectly exits with status 1 (instead of the proper status 0)

With this patch the mesos coarse scheduler terminates properly, the executors clean up, and the tasks are reported as `FINISHED` in the Mesos console (as opposed to `KILLED` in < 1.6 or `FAILED` in 1.6 and later)

Author: Charles Allen <charles@allen-net.com>

Closes #10319 from drcrallen/SPARK-12330.

This is a small addendum to #10762 to make the code more robust again future changes.

Author: Reynold Xin <rxin@databricks.com>

Closes #11070 from rxin/SPARK-12828-natural-join.

JIRA: https://issues.apache.org/jira/browse/SPARK-13113

As we shift bits right, looks like the bitwise AND operation is unnecessary.

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #11002 from viirya/improve-decodepagenumber.

minor fix for api link in ml onevsrest

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #11068 from hhbyyh/onevsrestDoc.

Jira:
https://issues.apache.org/jira/browse/SPARK-12828

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

Closes #10762 from adrian-wang/naturaljoin.

This is a step towards consolidating `SQLContext` and `HiveContext`.

This patch extends the existing Catalog API added in #10982 to include methods for handling table partitions. In particular, a partition is identified by `PartitionSpec`, which is just a `Map[String, String]`. The Catalog is still not used by anything yet, but its API is now more or less complete and an implementation is fully tested.

About 200 lines are test code.

Author: Andrew Or <andrew@databricks.com>

Closes #11069 from andrewor14/catalog.

Make an internal non-deprecated version of incBytesRead and incRecordsRead so we don't have unecessary deprecation warnings in our build.

Right now incBytesRead and incRecordsRead are marked as deprecated and for internal use only. We should make private[spark] versions which are not deprecated and switch to those internally so as to not clutter up the warning messages when building.

cc andrewor14 who did the initial deprecation

Author: Holden Karau <holden@us.ibm.com>

Closes #11056 from holdenk/SPARK-13152-fix-task-metrics-deprecation-warnings.

Best time is stabler than average time, also added a column for nano seconds per row (which could be used to estimate contributions of each components in a query).

Having best time and average time together for more information (we can see kind of variance).

rate, time per row and relative are all calculated using best time.

The result looks like this:
```
Intel(R) Core(TM) i7-4558U CPU  2.80GHz
rang/filter/sum:                    Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
-------------------------------------------------------------------------------------------
rang/filter/sum codegen=false          14332 / 16646         36.0          27.8       1.0X
rang/filter/sum codegen=true              845 /  940        620.0           1.6      17.0X
```

Author: Davies Liu <davies@databricks.com>

Closes #11018 from davies/gen_bench.

They seem redundant and we can simply use DataFrameReader/Writer. The new usage looks like:

```scala
val df = sqlContext.read.stream("...")
val handle = df.write.stream("...")
handle.stop()
```

Author: Reynold Xin <rxin@databricks.com>

Closes #11062 from rxin/SPARK-13166.

Added a Cores column in the Executors UI

Author: Alex Bozarth <ajbozart@us.ibm.com>

Closes #11039 from ajbozarth/spark3611.

The ```SparkSqlLexer``` currently swallows characters which have not been defined in the grammar. This causes problems with SQL commands, such as: ```add jar file:///tmp/ab/TestUDTF.jar```. In this example the `````` is swallowed.

This PR adds an extra Lexer rule to handle such input, and makes a tiny modification to the ```ASTNode```.

cc davies liancheng

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #11052 from hvanhovell/SPARK-13157.

A row from stream side could match multiple rows on build side, the loop for these matched rows should not be interrupted when emitting a row, so we buffer the output rows in a linked list, check the termination condition on producer loop (for example, Range or Aggregate).

Author: Davies Liu <davies@databricks.com>

Closes #10989 from davies/gen_join.

I have clearly prefix the two 'Duration' columns in 'Details of Batch' Streaming tab as 'Output Op Duration' and 'Job Duration'

Author: Mario Briggs <mario.briggs@in.ibm.com>
Author: mariobriggs <mariobriggs@in.ibm.com>

Closes #11022 from mariobriggs/spark-12739.

Based on the semantics of a query, we can derive a number of data constraints on output of each (logical or physical) operator. For instance, if a filter defines `‘a > 10`, we know that the output data of this filter satisfies 2 constraints:

1. `‘a > 10`
2. `isNotNull(‘a)`

This PR proposes a possible way of keeping track of these constraints and propagating them in the logical plan, which can then help us build more advanced optimizations (such as pruning redundant filters, optimizing joins, among others). We define constraints as a set of (implicitly conjunctive) expressions. For e.g., if a filter operator has constraints = `Set(‘a > 10, ‘b < 100)`, it’s implied that the outputs satisfy both individual constraints (i.e., `‘a > 10` AND `‘b < 100`).

Design Document: https://docs.google.com/a/databricks.com/document/d/1WQRgDurUBV9Y6CWOBS75PQIqJwT-6WftVa18xzm7nCo/edit?usp=sharing

Author: Sameer Agarwal <sameer@databricks.com>

Closes #10844 from sameeragarwal/constraints.

1. try to avoid the suffix (unique id)
2. remove the comment if there is no code generated.
3. re-arrange the order of functions
4. trop the new line for inlined blocks.

Author: Davies Liu <davies@databricks.com>

Closes #11032 from davies/better_suffix.

`rpcEnv.awaitTermination()` was not added in #10854 because some Streaming Python tests hung forever.

This patch fixed the hung issue and added rpcEnv.awaitTermination() back to SparkEnv.

Previously, Streaming Kafka Python tests shutdowns the zookeeper server before stopping StreamingContext. Then when stopping StreamingContext, KafkaReceiver may be hung due to https://issues.apache.org/jira/browse/KAFKA-601, hence, some thread of RpcEnv's Dispatcher cannot exit and rpcEnv.awaitTermination is hung.The patch just changed the shutdown order to fix it.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #11031 from zsxwing/awaitTermination.

Fixed the bug in linear regression train for the case when the target variable is constant. The two cases for `fitIntercept=true` or `fitIntercept=false` should be treated differently.

Author: Imran Younus <iyounus@us.ibm.com>

Closes #10702 from iyounus/SPARK-12732_bug_fix_in_linear_regression_train.

This PR add spilling support for generated TungstenAggregate.

If spilling happened, it's not that bad to do the iterator based sort-merge-aggregate (not generated).

The changes will be covered by TungstenAggregationQueryWithControlledFallbackSuite

Author: Davies Liu <davies@databricks.com>

Closes #10998 from davies/gen_spilling.

https://issues.apache.org/jira/browse/SPARK-13122

A race condition can occur in MemoryStore's unrollSafely() method if two threads that
return the same value for currentTaskAttemptId() execute this method concurrently. This
change makes the operation of reading the initial amount of unroll memory used, performing
the unroll, and updating the associated memory maps atomic in order to avoid this race
condition.

Initial proposed fix wraps all of unrollSafely() in a memoryManager.synchronized { } block. A cleaner approach might be introduce a mechanism that synchronizes based on task attempt ID. An alternative option might be to track unroll/pending unroll memory based on block ID rather than task attempt ID.

Author: Adam Budde <budde@amazon.com>

Closes #11012 from budde/master.

This patch implements support for more types when doing the vectorized decode. There are
a few more types remaining but they should be very straightforward after this. This code
has a few copy and paste pieces but they are difficult to eliminate due to performance
considerations.

Specifically, this patch adds support for:
  - String, Long, Byte types
  - Dictionary encoding for those types.

Author: Nong Li <nong@databricks.com>

Closes #10908 from nongli/spark-12992.

when we generate map, we first randomly pick a length, then create a seq of key value pair with the expected length, and finally call `toMap`. However, `toMap` will remove all duplicated keys, which makes the actual map size much less than we expected.

This PR fixes this problem by put keys in a set first, to guarantee we have enough keys to build a map with expected length.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10930 from cloud-fan/random-generator.

Author: Davies Liu <davies@databricks.com>

Closes #11037 from davies/disable_flaky.

The example will throw error like
<console>:20: error: not found: value StructType

Need to add this line:
import org.apache.spark.sql.types._

Author: Kevin (Sangwoo) Kim <sangwookim.me@gmail.com>

Closes #10141 from swkimme/patch-1.