More CDH 5.1.0
[SPARK-2852][MLLIB] Separate model from IDF/StandardScaler algorithms

This is part of SPARK-2828:

1. separate IDF model from IDF algorithm (which generates a model)
2. separate StandardScaler model from StandardScaler

CC: dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #1814 from mengxr/feature-api-update and squashes the following commits:

40d863b [Xiangrui Meng] move mean and variance to model
48a0fff [Xiangrui Meng] separate Model from StandardScaler algorithm
89f3486 [Xiangrui Meng] update IDF to separate Model from Algorithm

(cherry picked from commit b9e9e53773a618e4322b845c40deae22f2ba52ac)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
SPARK-2905 Fixed path sbin => bin

Author: Oleg Danilov <oleg.danilov@wandisco.com>

Closes #1835 from dosoft/SPARK-2905 and squashes the following commits:

4df423c [Oleg Danilov] SPARK-2905 Fixed path sbin => bin
(cherry picked from commit 80ec5bad1311651fe56e1d5178090dc63753233b)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
SPARK-2899 Doc generation is back to working in new SBT Build.

The reason for this bug was introduciton of OldDeps project. It had to be excluded to prevent unidocs from trying to put it on "docs compile" classpath.

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

Closes #1830 from ScrapCodes/doc-fix and squashes the following commits:

e5d52e6 [Prashant Sharma] SPARK-2899 Doc generation is back to working in new SBT Build.
(cherry picked from commit 32096c2aed9978cfb9a904b4f56bb61800d17e9e)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
SPARK-2787: Make sort-based shuffle write files directly when there's no sorting/aggregation and # partitions is small

As described in https://issues.apache.org/jira/browse/SPARK-2787, right now sort-based shuffle is more expensive than hash-based for map operations that do no partial aggregation or sorting, such as groupByKey. This is because it has to serialize each data item twice (once when spilling to intermediate files, and then again when merging these files object-by-object). This patch adds a code path to just write separate files directly if the # of output partitions is small, and concatenate them at the end to produce a sorted file.

On the unit test side, I added some tests that force or don't force this bypass path to be used, and checked that our tests for other features (e.g. all the operations) cover both cases.

Author: Matei Zaharia <matei@databricks.com>

Closes #1799 from mateiz/SPARK-2787 and squashes the following commits:

88cf26a [Matei Zaharia] Fix rebase
10233af [Matei Zaharia] Review comments
398cb95 [Matei Zaharia] Fix looking up shuffle manager in conf
ca3efd9 [Matei Zaharia] Add docs for shuffle manager properties, and allow short names for them
d0ae3c5 [Matei Zaharia] Fix some comments
90d084f [Matei Zaharia] Add code path to bypass merge-sort in ExternalSorter, and tests
31e5d7c [Matei Zaharia] Move existing logic for writing partitioned files into ExternalSorter

(cherry picked from commit 6906b69cf568015f20c7d7c77cbcba650e5431a9)
Signed-off-by: Reynold Xin <rxin@apache.org>
SPARK-2565. Update ShuffleReadMetrics as blocks are fetched

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1507 from sryza/sandy-spark-2565 and squashes the following commits:

74dad41 [Sandy Ryza] SPARK-2565. Update ShuffleReadMetrics as blocks are fetched
(cherry picked from commit 4c51098f320f164eb66f92ff0f26b0b595a58f38)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-2904] Remove non-used local variable in SparkSubmitArguments

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

Closes #1834 from sarutak/SPARK-2904 and squashes the following commits:

38e7d45 [Kousuke Saruta] Removed non-used variable in SparkSubmitArguments
(cherry picked from commit 9de6a42bb34ea8963225ce90f1a45adcfee38b58)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-2888] [SQL] Fix addColumnMetadataToConf in HiveTableScan

JIRA: https://issues.apache.org/jira/browse/SPARK-2888

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1817 from yhuai/fixAddColumnMetadataToConf and squashes the following commits:

fba728c [Yin Huai] Fix addColumnMetadataToConf.

(cherry picked from commit 9016af3f2729101027e33593e094332f05f48d92)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2908] [SQL] JsonRDD.nullTypeToStringType does not convert all NullType to StringType

JIRA: https://issues.apache.org/jira/browse/SPARK-2908

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1840 from yhuai/SPARK-2908 and squashes the following commits:

86e833e [Yin Huai] Update test.
cb11759 [Yin Huai] nullTypeToStringType should check columns with the type of array of structs.

(cherry picked from commit 0489cee6b24ca34f1adab03a75d157e04a9e06b7)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2877] [SQL] MetastoreRelation should use SparkClassLoader when creating the tableDesc

JIRA: https://issues.apache.org/jira/browse/SPARK-2877

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1806 from yhuai/SPARK-2877 and squashes the following commits:

4142bcb [Yin Huai] Use Spark's classloader.

(cherry picked from commit c874723fa844b49f057bb2434a12228b2f717e99)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2919] [SQL] Basic support for analyze command in HiveQl

The command we will support is
```
ANALYZE TABLE tablename COMPUTE STATISTICS noscan
```
Other cases shown in https://cwiki.apache.org/confluence/display/Hive/StatsDev#StatsDev-ExistingTables will still be treated as Hive native commands.

JIRA: https://issues.apache.org/jira/browse/SPARK-2919

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1848 from yhuai/sqlAnalyze and squashes the following commits:

0b79d36 [Yin Huai] Typo and format.
c59d94b [Yin Huai] Support "ANALYZE TABLE tableName COMPUTE STATISTICS noscan".

(cherry picked from commit 45d8f4deab50ae069ecde2201bd486d464a4501e)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2700] [SQL] Hidden files (such as .impala_insert_staging) should be filtered out by sqlContext.parquetFile

Author: chutium <teng.qiu@gmail.com>

Closes #1691 from chutium/SPARK-2700 and squashes the following commits:

b76ae8c [chutium] [SPARK-2700] [SQL] fixed styling issue
d75a8bd [chutium] [SPARK-2700] [SQL] Hidden files (such as .impala_insert_staging) should be filtered out by sqlContext.parquetFile

(cherry picked from commit b7c89a7f0ca73153dce36e0f01b81a3947ee1189)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[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

(cherry picked from commit 74d6f62264babfc6045c21545552f0a2e6958155)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[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"

(cherry picked from commit ec79063fad44751a6689f5e58d47886babeaecff)
Signed-off-by: Reynold Xin <rxin@apache.org>
[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
(cherry picked from commit 28dbae85aaf6842e22cd7465cb11cb34d58fc56d)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[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
(cherry picked from commit b431e6747f410aaf9624585920adc1f303159861)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[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

(cherry picked from commit 5b6585de6b939837d5bdc4b1a44634301949add6)
Signed-off-by: Reynold Xin <rxin@apache.org>
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.

(cherry picked from commit 482c5afbf6f3f12ac23851300a33249b26ddff3c)
Signed-off-by: Reynold Xin <rxin@apache.org>