SPARK-2741 - Publish version of spark assembly which does not contain Hive

Provide a version of the Spark tarball which does not package Hive. This is meant for HIve + Spark users.

Author: Brock Noland <brock@apache.org>

Closes #1667 from brockn/master and squashes the following commits:

5beafb2 [Brock Noland] SPARK-2741 - Publish version of spark assembly which does not contain Hive
[SPARK-2734][SQL] Remove tables from cache when DROP TABLE is run.

Author: Michael Armbrust <michael@databricks.com>

Closes #1650 from marmbrus/dropCached and squashes the following commits:

e6ab80b [Michael Armbrust] Support if exists.
83426c6 [Michael Armbrust] Remove tables from cache when DROP TABLE is run.
SPARK-2341 [MLLIB] loadLibSVMFile doesn't handle regression datasets

Per discussion at https://issues.apache.org/jira/browse/SPARK-2341 , this is a look at deprecating the multiclass parameter. Thoughts welcome of course.

Author: Sean Owen <srowen@gmail.com>

Closes #1663 from srowen/SPARK-2341 and squashes the following commits:

8a3abd7 [Sean Owen] Suppress MIMA error for removed package private classes
18a8c8e [Sean Owen] Updates from review
83d0092 [Sean Owen] Deprecated methods with multiclass, and instead always parse target as a double (ie. multiclass = true)
Update DecisionTreeRunner.scala

Author: strat0sphere <stratos.dimopoulos@gmail.com>

Closes #1676 from strat0sphere/patch-1 and squashes the following commits:

044d2fa [strat0sphere] Update DecisionTreeRunner.scala
SPARK-2045 Sort-based shuffle

This adds a new ShuffleManager based on sorting, as described in https://issues.apache.org/jira/browse/SPARK-2045. The bulk of the code is in an ExternalSorter class that is similar to ExternalAppendOnlyMap, but sorts key-value pairs by partition ID and can be used to create a single sorted file with a map task's output. (Longer-term I think this can take on the remaining functionality in ExternalAppendOnlyMap and replace it so we don't have code duplication.)

The main TODOs still left are:
- [x] enabling ExternalSorter to merge across spilled files
  - [x] with an Ordering
  - [x] without an Ordering, using the keys' hash codes
- [x] adding more tests (e.g. a version of our shuffle suite that runs on this)
- [x] rebasing on top of the size-tracking refactoring in #1165 when that is merged
- [x] disabling spilling if spark.shuffle.spill is set to false

Despite this though, this seems to work pretty well (running successfully in cases where the hash shuffle would OOM, such as 1000 reduce tasks on executors with only 1G memory), and it seems to be comparable in speed or faster than hash-based shuffle (it will create much fewer files for the OS to keep track of). So I'm posting it to get some early feedback.

After these TODOs are done, I'd also like to enable ExternalSorter to sort data within each partition by a key as well, which will allow us to use it to implement external spilling in reduce tasks in `sortByKey`.

Author: Matei Zaharia <matei@databricks.com>

Closes #1499 from mateiz/sort-based-shuffle and squashes the following commits:

bd841f9 [Matei Zaharia] Various review comments
d1c137fd [Matei Zaharia] Various review comments
a611159 [Matei Zaharia] Compile fixes due to rebase
62c56c8 [Matei Zaharia] Fix ShuffledRDD sometimes not returning Tuple2s.
f617432 [Matei Zaharia] Fix a failing test (seems to be due to change in SizeTracker logic)
9464d5f [Matei Zaharia] Simplify code and fix conflicts after latest rebase
0174149 [Matei Zaharia] Add cleanup behavior and cleanup tests for sort-based shuffle
eb4ee0d [Matei Zaharia] Remove customizable element type in ShuffledRDD
fa2e8db [Matei Zaharia] Allow nextBatchStream to be called after we're done looking at all streams
a34b352 [Matei Zaharia] Fix tracking of indices within a partition in SpillReader, and add test
03e1006 [Matei Zaharia] Add a SortShuffleSuite that runs ShuffleSuite with sort-based shuffle
3c7ff1f [Matei Zaharia] Obey the spark.shuffle.spill setting in ExternalSorter
ad65fbd [Matei Zaharia] Rebase on top of Aaron's Sorter change, and use Sorter in our buffer
44d2a93 [Matei Zaharia] Use estimateSize instead of atGrowThreshold to test collection sizes
5686f71 [Matei Zaharia] Optimize merging phase for in-memory only data:
5461cbb [Matei Zaharia] Review comments and more tests (e.g. tests with 1 element per partition)
e9ad356 [Matei Zaharia] Update ContextCleanerSuite to make sure shuffle cleanup tests use hash shuffle (since they were written for it)
c72362a [Matei Zaharia] Added bug fix and test for when iterators are empty
de1fb40 [Matei Zaharia] Make trait SizeTrackingCollection private[spark]
4988d16 [Matei Zaharia] tweak
c1b7572 [Matei Zaharia] Small optimization
ba7db7f [Matei Zaharia] Handle null keys in hash-based comparator, and add tests for collisions
ef4e397 [Matei Zaharia] Support for partial aggregation even without an Ordering
4b7a5ce [Matei Zaharia] More tests, and ability to sort data if a total ordering is given
e1f84be [Matei Zaharia] Fix disk block manager test
5a40a1c [Matei Zaharia] More tests
614f1b4 [Matei Zaharia] Add spill metrics to map tasks
cc52caf [Matei Zaharia] Add more error handling and tests for error cases
bbf359d [Matei Zaharia] More work
3a56341 [Matei Zaharia] More partial work towards sort-based shuffle
7a0895d [Matei Zaharia] Some more partial work towards sort-based shuffle
b615476 [Matei Zaharia] Scaffolding for sort-based shuffle
[SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDs

Author: Reynold Xin <rxin@apache.org>

Closes #1675 from rxin/unionrdd and squashes the following commits:

941d316 [Reynold Xin] Clear RDDs for checkpointing.
c9f05f2 [Reynold Xin] [SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDs
Required AM memory is "amMem", not "args.amMemory"

"ERROR yarn.Client: Required AM memory (1024) is above the max threshold (1048) of this cluster" appears if this code is not changed. obviously, 1024 is less than 1048, so change this

Author: derek ma <maji3@asiainfo-linkage.com>

Closes #1494 from maji2014/master and squashes the following commits:

b0f6640 [derek ma] Required AM memory is "amMem", not "args.amMemory"
[SPARK-2340] Resolve event logging and History Server paths properly

We resolve relative paths to the local `file:/` system for `--jars` and `--files` in spark submit (#853). We should do the same for the history server.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1280 from andrewor14/hist-serv-fix and squashes the following commits:

13ff406 [Andrew Or] Merge branch 'master' of github.com:apache/spark into hist-serv-fix
b393e17 [Andrew Or] Strip trailing "/" from logging directory
622a471 [Andrew Or] Fix test in EventLoggingListenerSuite
0e20f71 [Andrew Or] Shift responsibility of resolving paths up one level
b037c0c [Andrew Or] Use resolved paths for everything in history server
c7e36ee [Andrew Or] Resolve paths for event logging too
40e3933 [Andrew Or] Resolve history server file paths
[SPARK-2737] Add retag() method for changing RDDs' ClassTags.

The Java API's use of fake ClassTags doesn't seem to cause any problems for Java users, but it can lead to issues when passing JavaRDDs' underlying RDDs to Scala code (e.g. in the MLlib Java API wrapper code). If we call collect() on a Scala RDD with an incorrect ClassTag, this causes ClassCastExceptions when we try to allocate an array of the wrong type (for example, see SPARK-2197).

There are a few possible fixes here. An API-breaking fix would be to completely remove the fake ClassTags and require Java API users to pass java.lang.Class instances to all parallelize() calls and add returnClass fields to all Function implementations. This would be extremely verbose.

Instead, this patch adds internal APIs to "repair" a Scala RDD with an incorrect ClassTag by wrapping it and overriding its ClassTag. This should be okay for cases where the Scala code that calls collect() knows what type of array should be allocated, which is the case in the MLlib wrappers.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1639 from JoshRosen/SPARK-2737 and squashes the following commits:

572b4c8 [Josh Rosen] Replace newRDD[T] with mapPartitions().
469d941 [Josh Rosen] Preserve partitioner in retag().
af78816 [Josh Rosen] Allow retag() to get classTag implicitly.
d1d54e6 [Josh Rosen] [SPARK-2737] Add retag() method for changing RDDs' ClassTags.
[SPARK-2497] Included checks for module symbols too.

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

Closes #1463 from ScrapCodes/SPARK-2497/mima-exclude-all and squashes the following commits:

72077b1 [Prashant Sharma] Check separately for module symbols.
cd96192 [Prashant Sharma] SPARK-2497 Produce "member excludes" irrespective of the fact that class itself is excluded or not.
automatically set master according to `spark.master` in `spark-defaults....

automatically set master according to `spark.master` in `spark-defaults.conf`

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1644 from CrazyJvm/standalone-guide and squashes the following commits:

bb12b95 [CrazyJvm] automatically set master according to `spark.master` in `spark-defaults.conf`
Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
[SPARK-2762] SparkILoop leaks memory in multi-repl configurations

This pull request is a small refactor so that a partial function (hence a closure) is not created. Instead, a regular function is used. The behavior of the code is not changed.

Author: Timothy Hunter <timhunter@databricks.com>

Closes #1674 from thunterdb/closure_issue and squashes the following commits:

e1e664d [Timothy Hunter] simplify closure
* Updated Strategy to check numClassesForClassification only if algo=Classification.
* Updates based on comments:
** DecisionTreeRunner
*** Made dataFormat arg default to libsvm
** Small cleanups
** tree.Node: Made recursive helper methods private, and renamed them.
Updated meaning of maxDepth by 1 to fit scikit-learn and rpart.
* In code, replaced usages of maxDepth <-- maxDepth + 1
* In params, replace settings of maxDepth <-- maxDepth - 1
In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type.
Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix