remove outdated runtime Information scala home

Author: witgo <witgo@qq.com>

Closes #728 from witgo/scala_home and squashes the following commits:

cdfd8be [witgo] Merge branch 'master' of https://github.com/apache/spark into scala_home
fac094a [witgo] remove outdated runtime Information scala home
SPARK-1770: Load balance elements when repartitioning.

This patch adds better balancing when performing a repartition of an
RDD. Previously the elements in the RDD were hash partitioned, meaning
if the RDD was skewed certain partitions would end up being very large.

This commit adds load balancing of elements across the repartitioned
RDD splits. The load balancing is not perfect: a given output partition
can have up to N more elements than the average if there are N input
partitions. However, some randomization is used to minimize the
probabiliy that this happens.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #727 from pwendell/load-balance and squashes the following commits:

f9da752 [Patrick Wendell] Response to Matei's feedback
acfa46a [Patrick Wendell] SPARK-1770: Load balance elements when repartitioning.
SPARK-1652: Set driver memory correctly in spark-submit.

The previous check didn't account for the fact that the default
deploy mode is "client" unless otherwise specified. Also, this
sets the more narrowly defined SPARK_DRIVER_MEMORY instead of setting
SPARK_MEM.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #730 from pwendell/spark-submit and squashes the following commits:

430b98f [Patrick Wendell] Feedback from Aaron
e788edf [Patrick Wendell] Changes based on Aaron's feedback
f508146 [Patrick Wendell] SPARK-1652: Set driver memory correctly in spark-submit.
Fix error in 2d Graph Partitioner

Their was a minor bug in which negative partition ids could be generated when constructing a 2D partitioning of a graph.  This could lead to an inefficient 2D partition for large vertex id values.

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

Closes #709 from jegonzal/fix_2d_partitioning and squashes the following commits:

937c562 [Joseph E. Gonzalez] fixing bug in 2d partitioning algorithm where negative partition ids could be generated.
SPARK-1786: Edge Partition Serialization

This appears to address the issue with edge partition serialization.  The solution appears to be just registering the `PrimitiveKeyOpenHashMap`.  However I noticed that we appear to have forked that code in GraphX but retained the same name (which is confusing).  I also renamed our local copy to `GraphXPrimitiveKeyOpenHashMap`.  We should consider dropping that and using the one in Spark if possible.

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

Closes #724 from jegonzal/edge_partition_serialization and squashes the following commits:

b0a525a [Ankur Dave] Disable reference tracking to fix serialization test
bb7f548 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
67dac22 [Joseph E. Gonzalez] Making EdgePartition serializable.
Revert "SPARK-1786: Edge Partition Serialization"

This reverts commit a6b02fb7486356493474c7f42bb714c9cce215ca.
SPARK-1772 Stop catching Throwable, let Executors die

The main issue this patch fixes is [SPARK-1772](https://issues.apache.org/jira/browse/SPARK-1772), in which Executors may not die when fatal exceptions (e.g., OOM) are thrown. This patch causes Executors to delegate to the ExecutorUncaughtExceptionHandler when a fatal exception is thrown.

This patch also continues the fight in the neverending war against `case t: Throwable =>`, by only catching Exceptions in many places, and adding a wrapper for Threads and Runnables to make sure any uncaught exceptions are at least printed to the logs.

It also turns out that it is unlikely that the IndestructibleActorSystem actually works, given testing ([here](https://gist.github.com/aarondav/ca1f0cdcd50727f89c0d)). The uncaughtExceptionHandler is not called from the places that we expected it would be.
[SPARK-1620](https://issues.apache.org/jira/browse/SPARK-1620) deals with part of this issue, but refactoring our Actor Systems to ensure that exceptions are dealt with properly is a much bigger change, outside the scope of this PR.

Author: Aaron Davidson <aaron@databricks.com>

Closes #715 from aarondav/throwable and squashes the following commits:

f9b9bfe [Aaron Davidson] Remove other redundant 'throw e'
e937a0a [Aaron Davidson] Address Prashant and Matei's comments
1867867 [Aaron Davidson] [RFC] SPARK-1772 Stop catching Throwable, let Executors die
SPARK-1806: Upgrade Mesos dependency to 0.18.1

Enabled Mesos (0.18.1) dependency with shaded protobuf

Why is this needed?
Avoids any protobuf version collision between Mesos and any other
dependency in Spark e.g. Hadoop HDFS 2.2+ or 1.0.4.

Ticket: https://issues.apache.org/jira/browse/SPARK-1806

* Should close https://issues.apache.org/jira/browse/SPARK-1433

Author berngp

Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>

Closes #741 from berngp/feature/SPARK-1806 and squashes the following commits:

5d70646 [Bernardo Gomez Palacio] SPARK-1806: Upgrade Mesos dependency to 0.18.1
SPARK-1786: Reopening PR 724

Addressing issue in MimaBuild.scala.

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

Closes #742 from jegonzal/edge_partition_serialization and squashes the following commits:

8ba6e0d [Ankur Dave] Add concatenation operators to MimaBuild.scala
cb2ed3a [Joseph E. Gonzalez] addressing missing exclusion in MimaBuild.scala
5d27824 [Ankur Dave] Disable reference tracking to fix serialization test
c0a9ae5 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
a4a3faa [Joseph E. Gonzalez] Making EdgePartition serializable.
BUILD: Include Hive with default packages when creating a release
SPARK-1798. Tests should clean up temp files

Three issues related to temp files that tests generate – these should be touched up for hygiene but are not urgent.

Modules have a log4j.properties which directs the unit-test.log output file to a directory like `[module]/target/unit-test.log`. But this ends up creating `[module]/[module]/target/unit-test.log` instead of former.

The `work/` directory is not deleted by "mvn clean", in the parent and in modules. Neither is the `checkpoint/` directory created under the various external modules.

Many tests create a temp directory, which is not usually deleted. This can be largely resolved by calling `deleteOnExit()` at creation and trying to call `Utils.deleteRecursively` consistently to clean up, sometimes in an `@After` method.

_If anyone seconds the motion, I can create a more significant change that introduces a new test trait along the lines of `LocalSparkContext`, which provides management of temp directories for subclasses to take advantage of._

Author: Sean Owen <sowen@cloudera.com>

Closes #732 from srowen/SPARK-1798 and squashes the following commits:

5af578e [Sean Owen] Try to consistently delete test temp dirs and files, and set deleteOnExit() for each
b21b356 [Sean Owen] Remove work/ and checkpoint/ dirs with mvn clean
bdd0f41 [Sean Owen] Remove duplicate module dir in log4j.properties output path for tests
SPARK-1802. Audit dependency graph when Spark is built with -Phive

This initial commit resolves the conflicts in the Hive profiles as noted in https://issues.apache.org/jira/browse/SPARK-1802 .

Most of the fix was to note that Hive drags in Avro, and so if the hive module depends on Spark's version of the `avro-*` dependencies, it will pull in our exclusions as needed too. But I found we need to copy some exclusions between the two Avro dependencies to get this right. And then had to squash some commons-logging intrusions.

This turned up another annoying find, that `hive-exec` is basically an "assembly" artifact that _also_ packages all of its transitive dependencies. This means the final assembly shows lots of collisions between itself and its dependencies, and even other project dependencies. I have a TODO to examine whether that is going to be a deal-breaker or not.

In the meantime I'm going to tack on a second commit to this PR that will also fix some similar, last collisions in the YARN profile.

Author: Sean Owen <sowen@cloudera.com>

Closes #744 from srowen/SPARK-1802 and squashes the following commits:

a856604 [Sean Owen] Resolve JAR version conflicts specific to Hive profile
Rename testExecutorEnvs --> executorEnvs.

This was changed, but in fact, it's used for things other than tests.
So I've changed it back.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #747 from pwendell/executor-env and squashes the following commits:

36a60a5 [Patrick Wendell] Rename testExecutorEnvs --> executorEnvs.
SPARK-1623: Use File objects instead of String's in HTTPBroadcast

This seems strictly better, and I think it's justified only the grounds of
clean-up. It might also fix issues with path conversions, but I haven't
yet isolated any instance of that happening.

/cc @srowen @tdas

Author: Patrick Wendell <pwendell@gmail.com>

Closes #749 from pwendell/broadcast-cleanup and squashes the following commits:

d6d54f2 [Patrick Wendell] SPARK-1623: Use File objects instead of string's in HTTPBroadcast
SPARK-1802. (Addendium) Audit dependency graph when Spark is built with -Pyarn

Following on a few more items from SPARK-1802 --

The first commit touches up a few similar problems remaining with the YARN profile. I think this is worth cherry-picking.

The second commit is more of the same for hadoop-client, although the fix is a little more complex. It may or may not be worth bothering with.

Author: Sean Owen <sowen@cloudera.com>

Closes #746 from srowen/SPARK-1802.2 and squashes the following commits:

52aeb41 [Sean Owen] Add more commons-logging, servlet excludes to avoid conflicts in assembly when building for YARN
[SPARK-1736] Spark submit for Windows

Tested on Windows 7.

Author: Andrew Or <andrewor14@gmail.com>

Closes #745 from andrewor14/windows-submit and squashes the following commits:

c0b58fb [Andrew Or] Allow spaces in parameters
162e54d [Andrew Or] Merge branch 'master' of github.com:apache/spark into windows-submit
91597ce [Andrew Or] Make spark-shell.cmd use spark-submit.cmd
af6fd29 [Andrew Or] Add spark submit for Windows
Adding hadoop-2.2 profile to the build
[SQL] Make Hive Metastore conversion functions publicly visible.

I need this to be public for the implementation of SharkServer2.  However, I think this functionality is generally useful and should be pretty stable.

Author: Michael Armbrust <michael@databricks.com>

Closes #750 from marmbrus/metastoreTypes and squashes the following commits:

f51b62e [Michael Armbrust] Make Hive Metastore conversion functions publicly visible.
Typo: resond -> respond

Author: Andrew Ash <andrew@andrewash.com>

Closes #743 from ash211/patch-4 and squashes the following commits:

c959f3b [Andrew Ash] Typo: resond -> respond
L-BFGS Documentation

Documentation for L-BFGS, and an example of training binary L2 logistic regression using L-BFGS.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #702 from dbtsai/dbtsai-lbfgs-doc and squashes the following commits:

0712215 [DB Tsai] Update
38fdfa1 [DB Tsai] Removed extra empty line
5745b64 [DB Tsai] Update again
e9e418e [DB Tsai] Update
7381521 [DB Tsai] L-BFGS Documentation