[SPARK-2124] Move aggregation into shuffle implementations

This PR is a sub-task of SPARK-2044 to move the execution of aggregation into shuffle implementations.

I leave `CoGoupedRDD` and `SubtractedRDD` unchanged because they have their implementations of aggregation. I'm not sure is it suitable to change these two RDDs.

Also I do not move sort related code of `OrderedRDDFunctions` into shuffle, this will be solved in another sub-task.

Author: jerryshao <saisai.shao@intel.com>

Closes #1064 from jerryshao/SPARK-2124 and squashes the following commits:

4a05a40 [jerryshao] Modify according to comments
1f7dcc8 [jerryshao] Style changes
50a2fd6 [jerryshao] Fix test suite issue after moving aggregator to Shuffle reader and writer
1a96190 [jerryshao] Code modification related to the ShuffledRDD
308f635 [jerryshao] initial works of move combiner to ShuffleManager's reader and writer
[SPARK-2252] Fix MathJax for HTTPs.

Found out about this from the Hacker News link to GraphX which was using HTTPs.

@mengxr

Author: Reynold Xin <rxin@apache.org>

Closes #1189 from rxin/mllib-doc and squashes the following commits:

5328be0 [Reynold Xin] [SPARK-2252] Fix MathJax for HTTPs.
SPARK-1937: fix issue with task locality

Don't check executor/host availability when creating a TaskSetManager. Because the executors may haven't been registered when the TaskSetManager is created, in which case all tasks will be considered "has no preferred locations", and thus losing data locality in later scheduling.

Author: Rui Li <rui.li@intel.com>
Author: lirui-intel <rui.li@intel.com>

Closes #892 from lirui-intel/delaySchedule and squashes the following commits:

8444d7c [Rui Li] fix code style
fafd57f [Rui Li] keep locality constraints within the valid levels
18f9e05 [Rui Li] restrict allowed locality
5b3fb2f [Rui Li] refine UT
99f843e [Rui Li] add unit test and fix bug
fff4123 [Rui Li] fix computing valid locality levels
685ed3d [Rui Li] remove delay shedule for pendingTasksWithNoPrefs
7b0177a [Rui Li] remove redundant code
c7b93b5 [Rui Li] revise patch
3d7da02 [lirui-intel] Update TaskSchedulerImpl.scala
cab4c71 [Rui Li] revised patch
539a578 [Rui Li] fix code style
cf0d6ac [Rui Li] fix code style
3dfae86 [Rui Li] re-compute pending tasks when new host is added
a225ac2 [Rui Li] SPARK-1937: fix issue with task locality
HOTFIX: Disabling tests per SPARK-2264
Fix broken Json tests.

The assertJsonStringEquals method was missing an "assert" so
did not actually check that the strings were equal. This commit
adds the missing assert and fixes subsequently revealed problems
with the JsonProtocolSuite.

@andrewor14 I changed some of the test functionality to match what it
looks like you intended based on the expected strings -- let me know if
anything here looks wrong.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1198 from kayousterhout/json_test_fix and squashes the following commits:

77f858f [Kay Ousterhout] Fix broken Json tests.
[SPARK-2264][SQL] Fix failing CachedTableSuite

Author: Michael Armbrust <michael@databricks.com>

Closes #1201 from marmbrus/fixCacheTests and squashes the following commits:

9d87ed1 [Michael Armbrust] Use analyzer (which runs to fixed point) instead of manually removing analysis operators.
[SPARK-1112, 2156] Bootstrap to fetch the driver's Spark properties.

This is an alternative solution to #1124 . Before launching the executor backend, we first fetch driver's spark properties and use it to overwrite executor's spark properties. This should be better than #1124.

@pwendell Are there spark properties that might be different on the driver and on the executors?

Author: Xiangrui Meng <meng@databricks.com>

Closes #1132 from mengxr/akka-bootstrap and squashes the following commits:

77ff32d [Xiangrui Meng] organize imports
68e1dfb [Xiangrui Meng] use timeout from AkkaUtils; remove props from RegisteredExecutor
46d332d [Xiangrui Meng] fix a test
7947c18 [Xiangrui Meng] increase slack size for akka
4ab696a [Xiangrui Meng] bootstrap to retrieve driver spark conf
[SQL]Add base row updating methods for JoinedRow

This will be helpful in join operators.

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

Closes #1187 from chenghao-intel/joinedRow and squashes the following commits:

87c19e3 [Cheng Hao] Add base row set methods for JoinedRow
Autodetect JAVA_HOME on RPM-based systems

Author: Matthew Farrellee <matt@redhat.com>

Closes #1185 from mattf/master-1 and squashes the following commits:

42150fc [Matthew Farrellee] Autodetect JAVA_HOME on RPM-based systems
Fix possible null pointer in acumulator toString

Author: Michael Armbrust <michael@databricks.com>

Closes #1204 from marmbrus/nullPointerToString and squashes the following commits:

35b5fce [Michael Armbrust] Fix possible null pointer in acumulator toString
SPARK-2248: spark.default.parallelism does not apply in local mode

Author: witgo <witgo@qq.com>

Closes #1194 from witgo/SPARK-2248 and squashes the following commits:

6ac950b [witgo] spark.default.parallelism does not apply in local mode
[SPARK-2263][SQL] Support inserting MAP<K, V> to Hive tables

JIRA issue: [SPARK-2263](https://issues.apache.org/jira/browse/SPARK-2263)

Map objects were not converted to Hive types before inserting into Hive tables.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1205 from liancheng/spark-2263 and squashes the following commits:

c7a4373 [Cheng Lian] Addressed @concretevitamin's comment
784940b [Cheng Lian] SARPK-2263: support inserting MAP<K, V> to Hive tables
[BUGFIX][SQL] Should match java.math.BigDecimal when wnrapping Hive output

The `BigDecimal` branch in `unwrap` matches to `scala.math.BigDecimal` rather than `java.math.BigDecimal`.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1199 from liancheng/javaBigDecimal and squashes the following commits:

e9bb481 [Cheng Lian] Should match java.math.BigDecimal when wnrapping Hive output
SPARK-2038: rename "conf" parameters in the saveAsHadoop functions with source-compatibility

https://issues.apache.org/jira/browse/SPARK-2038

to differentiate with SparkConf object and at the same time keep the source level compatibility

Author: CodingCat <zhunansjtu@gmail.com>

Closes #1137 from CodingCat/SPARK-2038 and squashes the following commits:

11abeba [CodingCat] revise the comments
7ee5712 [CodingCat] to keep the source-compatibility
763975f [CodingCat] style fix
d91288d [CodingCat] rename "conf" parameters in the saveAsHadoop functions
Replace doc reference to Shark with Spark SQL.
[SPARK-2242] HOTFIX: pyspark shell hangs on simple job

This reverts a change introduced in 3870248740d83b0292ccca88a494ce19783847f0, which redirected all stderr to the OS pipe instead of directly to the `bin/pyspark` shell output. This causes a simple job to hang in two ways:

1. If the cluster is not configured correctly or does not have enough resources, the job hangs without producing any output, because the relevant warning messages are masked.
2. If the stderr volume is large, this could lead to a deadlock if we redirect everything to the OS pipe. From the [python docs](https://docs.python.org/2/library/subprocess.html):

```
Note Do not use stdout=PIPE or stderr=PIPE with this function as that can deadlock
based on the child process output volume. Use Popen with the communicate() method
when you need pipes.
```

Note that we cannot remove `stdout=PIPE` in a similar way, because we currently use it to communicate the py4j port. However, it should be fine (as it has been for a long time) because we do not produce a ton of traffic through `stdout`.

That commit was not merged in branch-1.0, so this fix is for master only.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1178 from andrewor14/fix-python and squashes the following commits:

e68e870 [Andrew Or] Merge branch 'master' of github.com:apache/spark into fix-python
20849a8 [Andrew Or] Tone down stdout interference message
a09805b [Andrew Or] Return more than 1 line of error message to user
6dfbd1e [Andrew Or] Don't swallow original exception
0d1861f [Andrew Or] Provide more helpful output if stdout is garbled
21c9d7c [Andrew Or] Do not mask stderr from output
[SPARK-2258 / 2266] Fix a few worker UI bugs

**SPARK-2258.** Worker UI displays zombie processes if the executor throws an exception before a process is launched. This is because we only inform the Worker of the change if the process is already launched, which in this case it isn't.

**SPARK-2266.** We expose "Some(app-id)" on the log page. This is fairly minor.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1213 from andrewor14/fix-worker-ui and squashes the following commits:

c1223fe [Andrew Or] Fix worker UI bugs
[SPARK-2270] Kryo cannot serialize results returned by asJavaIterable

and thus groupBy/cogroup are broken in Java APIs when Kryo is used).

@pwendell this should be merged into 1.0.1.

Thanks @sorenmacbeth for reporting this & helping out with the fix.

Author: Reynold Xin <rxin@apache.org>

Closes #1206 from rxin/kryo-iterable-2270 and squashes the following commits:

09da0aa [Reynold Xin] Updated the comment.
009bf64 [Reynold Xin] [SPARK-2270] Kryo cannot serialize results returned by asJavaIterable (and thus groupBy/cogroup are broken in Java APIs when Kryo is used).
[SPARK-2204] Launch tasks on the proper executors in mesos fine-grained mode

The scheduler for Mesos in fine-grained mode launches tasks on the wrong executors. `MesosSchedulerBackend.resourceOffers(SchedulerDriver, List[Offer])` is assuming that `TaskSchedulerImpl.resourceOffers(Seq[WorkerOffer])` is returning task lists in the same order as the offers it was passed, but in the current implementation `TaskSchedulerImpl.resourceOffers` shuffles the offers to avoid assigning the tasks always to the same executors. The result is that the tasks are launched on the wrong executors. The jobs are sometimes able to complete, but most of the time they fail. It seems that as soon as something goes wrong with a task for some reason Spark is not able to recover since it's mistaken as to where the tasks are actually running. Also, it seems that the more the cluster is under load the more likely the job is to fail because there's a higher probability that Spark is trying to launch a task on a slave that doesn't actually have enough resources, again because it's using the wrong offers.

The solution is to not assume that the order in which the tasks are returned is the same as the offers, and simply launch the tasks on the executor decided by `TaskSchedulerImpl.resourceOffers`. What I am not sure about is that I considered slaveId and executorId to be the same, which is true at least in my setup, but I don't know if that is always true.

I tested this on top of the 1.0.0 release and it seems to work fine on our cluster.

Author: Sebastien Rainville <sebastien@hopper.com>

Closes #1140 from sebastienrainville/fine-grained-mode-fix-master and squashes the following commits:

a98b0e0 [Sebastien Rainville] Use a HashMap to retrieve the offer indices
d6ffe54 [Sebastien Rainville] Launch tasks on the proper executors in mesos fine-grained mode
[SQL] SPARK-1800 Add broadcast hash join operator & associated hints.

This PR is based off Michael's [PR 734](https://github.com/apache/spark/pull/734) and includes a bunch of cleanups.

Moreover, this PR also
- makes `SparkLogicalPlan` take a `tableName: String`, which facilitates testing.
- moves join-related tests to a single file.

Author: Zongheng Yang <zongheng.y@gmail.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #1163 from concretevitamin/auto-broadcast-hash-join and squashes the following commits:

d0f4991 [Zongheng Yang] Fix bug in broadcast hash join & add test to cover it.
af080d7 [Zongheng Yang] Fix in joinIterators()'s next().
440d277 [Zongheng Yang] Fixes to imports; add back requiredChildDistribution (lost when merging)
208d5f6 [Zongheng Yang] Make LeftSemiJoinHash mix in HashJoin.
ad6c7cc [Zongheng Yang] Minor cleanups.
814b3bf [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
a8a093e [Zongheng Yang] Minor cleanups.
6fd8443 [Zongheng Yang] Cut down size estimation related stuff.
a4267be [Zongheng Yang] Add test for broadcast hash join and related necessary refactorings:
0e64b08 [Zongheng Yang] Scalastyle fix.
91461c2 [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
7c7158b [Zongheng Yang] Prototype of auto conversion to broadcast hash join.
0ad122f [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
3e5d77c [Zongheng Yang] WIP: giant and messy WIP.
a92ed0c [Michael Armbrust] Formatting.
76ca434 [Michael Armbrust] A simple strategy that broadcasts tables only when they are found in a configuration hint.
cf6b381 [Michael Armbrust] Split out generic logic for hash joins and create two concrete physical operators: BroadcastHashJoin and ShuffledHashJoin.
a8420ca [Michael Armbrust] Copy records in executeCollect to avoid issues with mutable rows.