[SPARK-1997][MLLIB] update breeze to 0.9

0.9 dependences (this version doesn't depend on scalalogging and I excluded commons-math3 from its transitive dependencies):
~~~
+-org.scalanlp:breeze_2.10:0.9 [S]
  +-com.github.fommil.netlib:core:1.1.2
  +-com.github.rwl:jtransforms:2.4.0
  +-net.sf.opencsv:opencsv:2.3
  +-net.sourceforge.f2j:arpack_combined_all:0.1
  +-org.scalanlp:breeze-macros_2.10:0.3.1 [S]
  | +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
  |
  +-org.slf4j:slf4j-api:1.7.5
  +-org.spire-math:spire_2.10:0.7.4 [S]
    +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
    |
    +-org.spire-math:spire-macros_2.10:0.7.4 [S]
      +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
~~~

Closes #1749

CC: witgo avati

Author: Xiangrui Meng <meng@databricks.com>

Closes #1857 from mengxr/breeze-0.9 and squashes the following commits:

7fc16b6 [Xiangrui Meng] don't know why but exclude a private method for mima
dcc502e [Xiangrui Meng] update breeze to 0.9
[SPARK-2897][SPARK-2920]TorrentBroadcast does use the serializer class specified in the spark option "spark.serializer"

Author: GuoQiang Li <witgo@qq.com>

Closes #1836 from witgo/SPARK-2897 and squashes the following commits:

23cdc5b [GuoQiang Li] review commit
ada4fba [GuoQiang Li] TorrentBroadcast does not support broadcast compression
fb91792 [GuoQiang Li] org.apache.spark.broadcast.TorrentBroadcast does use the serializer class specified in the spark option "spark.serializer"
[Web UI]Make decision order of Worker's WebUI port consistent with Master's

The decision order of Worker's WebUI port is "--webui-port", SPARK_WORKER_WEBUI_POR, 8081(default), spark.worker.ui.port. But in Master, the order is "--webui-port", spark.master.ui.port, SPARK_MASTER_WEBUI_PORT and 8080(default).

So we change the order in Worker's to keep it consistent with Master.

Author: WangTao <barneystinson@aliyun.com>

Closes #1838 from WangTaoTheTonic/reOrder and squashes the following commits:

460f4d4 [WangTao] Make decision order of Worker's WebUI consistent with Master's
[SPARK-2911] apply parent[T](j) to clarify UnionRDD code

References to dependencies(j) for actually obtaining RDD parents are less common than I originally estimated.   It does clarify UnionRDD (also will clarify some of my other PRs)

Use of firstParent[T] is ubiquitous, but not as sure that benefits from being replaced with parent(0)[T].

Author: Erik Erlandson <eerlands@redhat.com>

Closes #1858 from erikerlandson/spark-2911-pr2 and squashes the following commits:

7ffea74 [Erik Erlandson] [SPARK-2911] apply parent[T](j) to clarify UnionRDD code
[SPARK-2635] Fix race condition at SchedulerBackend.isReady in standalone mode

In SPARK-1946(PR #900), configuration <code>spark.scheduler.minRegisteredExecutorsRatio</code> was introduced. However, in standalone mode, there is a race condition where isReady() can return true because totalExpectedExecutors has not been correctly set.

Because expected executors is uncertain in standalone mode, the PR try to use CPU cores(<code>--total-executor-cores</code>) as expected resources to judge whether SchedulerBackend is ready.

Author: li-zhihui <zhihui.li@intel.com>
Author: Li Zhihui <zhihui.li@intel.com>

Closes #1525 from li-zhihui/fixre4s and squashes the following commits:

e9a630b [Li Zhihui] Rename variable totalExecutors and clean codes
abf4860 [Li Zhihui] Push down variable totalExpectedResources to children classes
ca54bd9 [li-zhihui] Format log with String interpolation
88c7dc6 [li-zhihui] Few codes and docs refactor
41cf47e [li-zhihui] Fix race condition at SchedulerBackend.isReady in standalone mode
[SPARK-2861] Fix Doc comment of histogram method

Tested and ready to merge.

Author: Chandan Kumar <chandan.kumar@imaginea.com>

Closes #1786 from nrchandan/spark-2861 and squashes the following commits:

cb0bc1e [Chandan Kumar] [SPARK-2861] Fix a typo in the histogram doc comment
6a2a71b [Chandan Kumar] SPARK-2861. Fix Doc comment of histogram method
[SPARK-1766] sorted functions to meet pedantic requirements

Pedantry is underrated

Author: Chris Cope <ccope@resilientscience.com>

Closes #1859 from copester/master and squashes the following commits:

0fb4499 [Chris Cope] [SPARK-1766] sorted functions to meet pedantic requirements
[SPARK-2894] spark-shell doesn't accept flags

As sryza reported, spark-shell doesn't accept any flags.
The root cause is wrong usage of spark-submit in spark-shell and it come to the surface by #1801

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1715, Closes #1864, and Closes #1861

Closes #1825 from sarutak/SPARK-2894 and squashes the following commits:

47f3510 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2894
2c899ed [Kousuke Saruta] Removed useless code from java_gateway.py
98287ed [Kousuke Saruta] Removed useless code from java_gateway.py
513ad2e [Kousuke Saruta] Modified util.sh to enable to use option including white spaces
28a374e [Kousuke Saruta] Modified java_gateway.py to recognize arguments
5afc584 [Cheng Lian] Filter out spark-submit options when starting Python gateway
e630d19 [Cheng Lian] Fixing pyspark and spark-shell CLI options
Updated Spark SQL README to include the hive-thriftserver module

Author: Reynold Xin <rxin@apache.org>

Closes #1867 from rxin/sql-readme and squashes the following commits:

42a5307 [Reynold Xin] Updated Spark SQL README to include the hive-thriftserver module
Turn UpdateBlockInfo into case class.

This helps us log UpdateBlockInfo properly once #1870 is merged.

Author: Reynold Xin <rxin@apache.org>

Closes #1872 from rxin/UpdateBlockInfo and squashes the following commits:

0cee1c2 [Reynold Xin] Turn UpdateBlockInfo into case class.
Remove extra semicolon in Task.scala

Author: GuoQiang Li <witgo@qq.com>

Closes #1876 from witgo/remove_semicolon_in_Task_scala and squashes the following commits:

c6ea732 [GuoQiang Li] Remove extra semicolon in Task.scala
[SPARK-2950] Add gc time and shuffle write time to JobLogger

The JobLogger is very useful for performing offline performance profiling of Spark jobs. GC Time and Shuffle Write time are available in TaskMetrics but are currently missed from the JobLogger output. This patch adds these two fields.

~~Since this is a small change, I didn't create a JIRA. Let me know if I should do that.~~

cc kayousterhout

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #1869 from shivaram/job-logger and squashes the following commits:

1b709fc [Shivaram Venkataraman] Add a space before GC_TIME
c418105 [Shivaram Venkataraman] Add gc time and shuffle write time to JobLogger
[SPARK-2898] [PySpark] fix bugs in deamon.py

1. do not use signal handler for SIGCHILD, it's easy to cause deadlock
2. handle EINTR during accept()
3. pass errno into JVM
4. handle EAGAIN during fork()

Now, it can pass 50k tasks tests in 180 seconds.

Author: Davies Liu <davies.liu@gmail.com>

Closes #1842 from davies/qa and squashes the following commits:

f0ea451 [Davies Liu] fix lint
03a2e8c [Davies Liu] cleanup dead children every seconds
32cb829 [Davies Liu] fix lint
0cd0817 [Davies Liu] fix bugs in deamon.py
[SPARK-2937] Separate out samplyByKeyExact as its own API in PairRDDFunction

To enable Python consistency and `Experimental` label of the `sampleByKeyExact` API.

Author: Doris Xin <doris.s.xin@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #1866 from dorx/stratified and squashes the following commits:

0ad97b2 [Doris Xin] reviewer comments.
2948aae [Doris Xin] remove unrelated changes
e990325 [Doris Xin] Merge branch 'master' into stratified
555a3f9 [Doris Xin] separate out sampleByKeyExact as its own API
616e55c [Doris Xin] merge master
245439e [Doris Xin] moved minSamplingRate to getUpperBound
eaf5771 [Doris Xin] bug fixes.
17a381b [Doris Xin] fixed a merge issue and a failed unit
ea7d27f [Doris Xin] merge master
b223529 [Xiangrui Meng] use approx bounds for poisson fix poisson mean for waitlisting add unit tests for Java
b3013a4 [Xiangrui Meng] move math3 back to test scope
eecee5f [Doris Xin] Merge branch 'master' into stratified
f4c21f3 [Doris Xin] Reviewer comments
a10e68d [Doris Xin] style fix
a2bf756 [Doris Xin] Merge branch 'master' into stratified
680b677 [Doris Xin] use mapPartitionWithIndex instead
9884a9f [Doris Xin] style fix
bbfb8c9 [Doris Xin] Merge branch 'master' into stratified
ee9d260 [Doris Xin] addressed reviewer comments
6b5b10b [Doris Xin] Merge branch 'master' into stratified
254e03c [Doris Xin] minor fixes and Java API.
4ad516b [Doris Xin] remove unused imports from PairRDDFunctions
bd9dc6e [Doris Xin] unit bug and style violation fixed
1fe1cff [Doris Xin] Changed fractionByKey to a map to enable arg check
944a10c [Doris Xin] [SPARK-2145] Add lower bound on sampling rate
0214a76 [Doris Xin] cleanUp
90d94c0 [Doris Xin] merge master
9e74ab5 [Doris Xin] Separated out most of the logic in sampleByKey
7327611 [Doris Xin] merge master
50581fc [Doris Xin] added a TODO for logging in python
46f6c8c [Doris Xin] fixed the NPE caused by closures being cleaned before being passed into the aggregate function
7e1a481 [Doris Xin] changed the permission on SamplingUtil
1d413ce [Doris Xin] fixed checkstyle issues
9ee94ee [Doris Xin] [SPARK-2082] stratified sampling in PairRDDFunctions that guarantees exact sample size
e3fd6a6 [Doris Xin] Merge branch 'master' into takeSample
7cab53a [Doris Xin] fixed import bug in rdd.py
ffea61a [Doris Xin] SPARK-1939: Refactor takeSample method in RDD
1441977 [Doris Xin] SPARK-1939 Refactor takeSample method in RDD to use ScaSRS
[SPARK-2936] Migrate Netty network module from Java to Scala

The Netty network module was originally written when Scala 2.9.x had a bug that prevents a pure Scala implementation, and a subset of the files were done in Java. We have since upgraded to Scala 2.10, and can migrate all Java files now to Scala.

https://github.com/netty/netty/issues/781

https://github.com/mesos/spark/pull/522

Author: Reynold Xin <rxin@apache.org>

Closes #1865 from rxin/netty and squashes the following commits:

332422f [Reynold Xin] Code review feedback
ca9eeee [Reynold Xin] Minor update.
7f1434b [Reynold Xin] [SPARK-2936] Migrate Netty network module from Java to Scala
[PySpark] [SPARK-2954] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 Fixes

- Modify python/run-tests to test with Python 2.6
- Use unittest2 when running on Python 2.6.
- Fix issue with namedtuple.
- Skip TestOutputFormat.test_newhadoop on Python 2.6 until SPARK-2951 is fixed.
- Fix MLlib _deserialize_double on Python 2.6.

Closes #1868.  Closes #1042.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1874 from JoshRosen/python2.6 and squashes the following commits:

983d259 [Josh Rosen] [SPARK-2954] Fix MLlib _deserialize_double on Python 2.6.
5d18fd7 [Josh Rosen] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 fixes
[SPARK-2952] Enable logging actor messages at DEBUG level

Example messages:
```
14/08/09 21:37:01 DEBUG BlockManagerMasterActor: [actor] received message RegisterBlockManager(BlockManagerId(0, rxin-mbp, 58092, 0),278302556,Actor[akka.tcp://spark@rxin-mbp:58088/user/BlockManagerActor1#-63596539]) from Actor[akka.tcp://spark@rxin-mbp:58088/temp/$c]

14/08/09 21:37:01 DEBUG BlockManagerMasterActor: [actor] handled message (0.279 ms) RegisterBlockManager(BlockManagerId(0, rxin-mbp, 58092, 0),278302556,Actor[akka.tcp://spark@rxin-mbp:58088/user/BlockManagerActor1#-63596539]) from Actor[akka.tcp://spark@rxin-mbp:58088/temp/$c]
```

cc @mengxr @tdas @pwendell

Author: Reynold Xin <rxin@apache.org>

Closes #1870 from rxin/actorLogging and squashes the following commits:

c531ee5 [Reynold Xin] Added license header for ActorLogReceive.
f6b1ebe [Reynold Xin] [SPARK-2952] Enable logging actor messages at DEBUG level
[SPARK-2931] In TaskSetManager, reset currentLocalityIndex after recomputing locality levels

This addresses SPARK-2931, a bug where getAllowedLocalityLevel() could throw ArrayIndexOutOfBoundsException.  The fix here is to reset currentLocalityIndex after recomputing the locality levels.

Thanks to kayousterhout, mridulm, and lirui-intel for helping me to debug this.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1896 from JoshRosen/SPARK-2931 and squashes the following commits:

48b60b5 [Josh Rosen] Move FakeRackUtil.cleanUp() info beforeEach().
6fec474 [Josh Rosen] Set currentLocalityIndex after recomputing locality levels.
9384897 [Josh Rosen] Update SPARK-2931 test to reflect changes in 63bdb1f41b4895e3a9444f7938094438a94d3007.
9ecd455 [Josh Rosen] Apply @mridulm's patch for reproducing SPARK-2931.
[SPARK-2515][mllib] Chi Squared test

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1733 from dorx/chisquare and squashes the following commits:

cafb3a7 [Doris Xin] fixed p-value for extreme case.
d286783 [Doris Xin] Merge branch 'master' into chisquare
e95e485 [Doris Xin] reviewer comments.
7dde711 [Doris Xin] ChiSqTestResult renaming and changed to Class
80d03e2 [Doris Xin] Reviewer comments.
c39eeb5 [Doris Xin] units passed with updated API
e90d90a [Doris Xin] Merge branch 'master' into chisquare
7eea80b [Doris Xin] WIP
d64c2fb [Doris Xin] Merge branch 'master' into chisquare
5686082 [Doris Xin] facelift
bc7eb2e [Doris Xin] unit passed; still need docs and some refactoring
50703a5 [Doris Xin] merge master
4e4e361 [Doris Xin] WIP
e6b83f3 [Doris Xin] reviewer comments
3d61582 [Doris Xin] input names
706d436 [Doris Xin] Added API for RDD[Vector]
6598379 [Doris Xin] API and code structure.
ff17423 [Doris Xin] WIP
[SPARK-2934][MLlib] Adding LogisticRegressionWithLBFGS Interface

for training with LBFGS Optimizer which will converge faster than SGD.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #1862 from dbtsai/dbtsai-lbfgs-lor and squashes the following commits:

aa84b81 [DB Tsai] small change
f852bcd [DB Tsai] Remove duplicate method
f119fdc [DB Tsai] Formatting
97776aa [DB Tsai] address more feedback
85b4a91 [DB Tsai] address feedback
3cf50c2 [DB Tsai] LogisticRegressionWithLBFGS interface