[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
[SPARK-2844][SQL] Correctly set JVM HiveContext if it is passed into Python HiveContext constructor

https://issues.apache.org/jira/browse/SPARK-2844

Author: Ahir Reddy <ahirreddy@gmail.com>

Closes #1768 from ahirreddy/python-hive-context-fix and squashes the following commits:

7972d3b [Ahir Reddy] Correctly set JVM HiveContext if it is passed into Python HiveContext constructor
[SPARK-2590][SQL] Added option to handle incremental collection, disabled by default

JIRA issue: [SPARK-2590](https://issues.apache.org/jira/browse/SPARK-2590)

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

Closes #1853 from liancheng/inc-collect-option and squashes the following commits:

cb3ea45 [Cheng Lian] Moved incremental collection option to Thrift server
43ce3aa [Cheng Lian] Changed incremental collect option name
623abde [Cheng Lian] Added option to handle incremental collection, disabled by default
[sql]use SparkSQLEnv.stop() in ShutdownHook

Author: wangfei <wangfei1@huawei.com>

Closes #1852 from scwf/patch-3 and squashes the following commits:

ae28c29 [wangfei] use SparkSQLEnv.stop() in ShutdownHook
[SQL] A tiny refactoring in HiveContext#analyze

I should use `EliminateAnalysisOperators` in  `analyze` instead of manually pattern matching.

Author: Yin Huai <huaiyin.thu@gmail.com>

Closes #1881 from yhuai/useEliminateAnalysisOperators and squashes the following commits:

f3e1e7f [Yin Huai] Use EliminateAnalysisOperators.
[SPARK-2965][SQL] Fix HashOuterJoin output nullabilities.

Output attributes of opposite side of `OuterJoin` should be nullable.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #1887 from ueshin/issues/SPARK-2965 and squashes the following commits:

bcb2d37 [Takuya UESHIN] Fix HashOuterJoin output nullabilities.
[SPARK-2968][SQL] Fix nullabilities of Explode.

Output nullabilities of `Explode` could be detemined by `ArrayType.containsNull` or `MapType.valueContainsNull`.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #1888 from ueshin/issues/SPARK-2968 and squashes the following commits:

d128c95 [Takuya UESHIN] Fix nullability of Explode.
[SPARK-2650][SQL] Build column buffers in smaller batches

Author: Michael Armbrust <michael@databricks.com>

Closes #1880 from marmbrus/columnBatches and squashes the following commits:

0649987 [Michael Armbrust] add test
4756fad [Michael Armbrust] fix compilation
2314532 [Michael Armbrust] Build column buffers in smaller batches
[SQL] [SPARK-2826] Reduce the memory copy while building the hashmap for HashOuterJoin

This is a follow up for #1147 , this PR will improve the performance about 10% - 15% in my local tests.
```
Before:
LeftOuterJoin: took 16750 ms ([3000000] records)
LeftOuterJoin: took 15179 ms ([3000000] records)
RightOuterJoin: took 15515 ms ([3000000] records)
RightOuterJoin: took 15276 ms ([3000000] records)
FullOuterJoin: took 19150 ms ([6000000] records)
FullOuterJoin: took 18935 ms ([6000000] records)

After:
LeftOuterJoin: took 15218 ms ([3000000] records)
LeftOuterJoin: took 13503 ms ([3000000] records)
RightOuterJoin: took 13663 ms ([3000000] records)
RightOuterJoin: took 14025 ms ([3000000] records)
FullOuterJoin: took 16624 ms ([6000000] records)
FullOuterJoin: took 16578 ms ([6000000] records)
```

Besides the performance improvement, I also do some clean up as suggested in #1147

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

Closes #1765 from chenghao-intel/hash_outer_join_fixing and squashes the following commits:

ab1f9e0 [Cheng Hao] Reduce the memory copy while building the hashmap
[SPARK-2923][MLLIB] Implement some basic BLAS routines

Having some basic BLAS operations implemented in MLlib can help simplify the current implementation and improve some performance.

Tested on my local machine:

~~~
bin/spark-submit --class org.apache.spark.examples.mllib.BinaryClassification \
examples/target/scala-*/spark-examples-*.jar --algorithm LR --regType L2 \
--regParam 1.0 --numIterations 1000 ~/share/data/rcv1.binary/rcv1_train.binary
~~~

1. before: ~1m
2. after: ~30s

CC: jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #1849 from mengxr/ml-blas and squashes the following commits:

ba583a2 [Xiangrui Meng] exclude Vector.copy
a4d7d2f [Xiangrui Meng] Merge branch 'master' into ml-blas
6edeab9 [Xiangrui Meng] address comments
940bdeb [Xiangrui Meng] rename MLlibBLAS to BLAS
c2a38bc [Xiangrui Meng] enhance dot tests
4cfaac4 [Xiangrui Meng] add apache header
48d01d2 [Xiangrui Meng] add tests for zeros and copy
3b882b1 [Xiangrui Meng] use blas.scal in gradient
735eb23 [Xiangrui Meng] remove d from BLAS routines
d2d7d3c [Xiangrui Meng] update gradient and lbfgs
7f78186 [Xiangrui Meng] add zeros to Vectors; add dscal and dcopy to BLAS
14e6645 [Xiangrui Meng] add ddot
cbb8273 [Xiangrui Meng] add daxpy test
07db0bb [Xiangrui Meng] Merge branch 'master' into ml-blas
e8c326d [Xiangrui Meng] axpy
[MLlib] Correctly set vectorSize and alpha

mengxr
Correctly set vectorSize and alpha in Word2Vec training.

Author: Liquan Pei <liquanpei@gmail.com>

Closes #1900 from Ishiihara/Word2Vec-bugfix and squashes the following commits:

85f64f2 [Liquan Pei] correctly set vectorSize and alpha
fix flaky tests

Python 2.6 does not handle float error well as 2.7+

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

Closes #1910 from davies/fix_test and squashes the following commits:

7e51200 [Davies Liu] fix flaky tests
SPARK-2830 [MLlib]: re-organize mllib documentation

As per discussions with Xiangrui, I've reorganized and edited the mllib documentation.

Author: Ameet Talwalkar <atalwalkar@gmail.com>

Closes #1908 from atalwalkar/master and squashes the following commits:

fe6938a [Ameet Talwalkar] made xiangruis suggested changes
840028b [Ameet Talwalkar] made xiangruis suggested changes
7ec366a [Ameet Talwalkar] reorganize and edit mllib documentation
[SPARK-2953] Allow using short names for io compression codecs

Instead of requiring "org.apache.spark.io.LZ4CompressionCodec", it is easier for users if Spark just accepts "lz4", "lzf", "snappy".

Author: Reynold Xin <rxin@apache.org>

Closes #1873 from rxin/compressionCodecShortForm and squashes the following commits:

9f50962 [Reynold Xin] Specify short-form compression codec names first.
63f78ee [Reynold Xin] Updated configuration documentation.
47b3848 [Reynold Xin] [SPARK-2953] Allow using short names for io compression codecs
Use transferTo when copy merge files in ExternalSorter

Since this is a file to file copy, using transferTo should be faster.

Author: Raymond Liu <raymond.liu@intel.com>

Closes #1884 from colorant/externalSorter and squashes the following commits:

6e42f3c [Raymond Liu] More code into copyStream
bfb496b [Raymond Liu] Use transferTo when copy merge files in ExternalSorter
[SPARK-1777 (partial)] bugfix: make size of requested memory correctly

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #1892 from liyezhang556520/lazy_memory_request and squashes the following commits:

335ab61 [Zhang, Liye] [SPARK-1777 (partial)] bugfix: make size of requested memory correctly
[SPARK-2993] [MLLib] colStats (wrapper around MultivariateStatisticalSummary) in Statistics

For both Scala and Python.

The ser/de util functions were moved out of `PythonMLLibAPI` and into their own object to avoid creating the `PythonMLLibAPI` object inside of `MultivariateStatisticalSummarySerialized`, which is then referenced inside of a method in `PythonMLLibAPI`.

`MultivariateStatisticalSummarySerialized` was created to serialize the `Vector` fields in `MultivariateStatisticalSummary`.

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

Closes #1911 from dorx/colStats and squashes the following commits:

77b9924 [Doris Xin] developerAPI tag
de9cbbe [Doris Xin] reviewer comments and moved more ser/de
459faba [Doris Xin] colStats in Statistics for both Scala and Python
[SPARK-2963] [SQL] There no documentation about building to use HiveServer and CLI for SparkSQL

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #1885 from sarutak/SPARK-2963 and squashes the following commits:

ed53329 [Kousuke Saruta] Modified description and notaton of proper noun
07c59fc [Kousuke Saruta] Added a description about how to build to use HiveServer and CLI for SparkSQL to building-with-maven.md
6e6645a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2963
c88fa93 [Kousuke Saruta] Added a description about building to use HiveServer and CLI for SparkSQL
[SPARK-3013] [SQL] [PySpark] convert array into list

because Pyrolite does not support array from Python 2.6

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

Closes #1928 from davies/fix_array and squashes the following commits:

858e6c5 [Davies Liu] convert array into list
[SPARK-2983] [PySpark] improve performance of sortByKey()

1. skip partitionBy() when numOfPartition is 1
2. use bisect_left (O(lg(N))) instread of loop (O(N)) in
rangePartitioner

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

Closes #1898 from davies/sort and squashes the following commits:

0a9608b [Davies Liu] Merge branch 'master' into sort
1cf9565 [Davies Liu] improve performance of sortByKey()