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
Modify a typo in monitoring.md

As I mentioned in SPARK-1765, there is a word 'JXM' in monitoring.md.
I think it's typo for 'JMX'.

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

Closes #698 from sarutak/SPARK-1765 and squashes the following commits:

bae9843 [Kousuke Saruta] modified a typoe in monitoring.md
SPARK-1757 Failing test for saving null primitives with .saveAsParquetFile()

https://issues.apache.org/jira/browse/SPARK-1757

The first test succeeds, but the second test fails with exception:

```
[info] - save and load case class RDD with Nones as parquet *** FAILED *** (14 milliseconds)
[info]   java.lang.RuntimeException: Unsupported datatype StructType(List())
[info]   at scala.sys.package$.error(package.scala:27)
[info]   at org.apache.spark.sql.parquet.ParquetTypesConverter$.fromDataType(ParquetRelation.scala:201)
[info]   at org.apache.spark.sql.parquet.ParquetTypesConverter$$anonfun$1.apply(ParquetRelation.scala:235)
[info]   at org.apache.spark.sql.parquet.ParquetTypesConverter$$anonfun$1.apply(ParquetRelation.scala:235)
[info]   at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
[info]   at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
[info]   at scala.collection.immutable.List.foreach(List.scala:318)
[info]   at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
[info]   at scala.collection.AbstractTraversable.map(Traversable.scala:105)
[info]   at org.apache.spark.sql.parquet.ParquetTypesConverter$.convertFromAttributes(ParquetRelation.scala:234)
[info]   at org.apache.spark.sql.parquet.ParquetTypesConverter$.writeMetaData(ParquetRelation.scala:267)
[info]   at org.apache.spark.sql.parquet.ParquetRelation$.createEmpty(ParquetRelation.scala:143)
[info]   at org.apache.spark.sql.parquet.ParquetRelation$.create(ParquetRelation.scala:122)
[info]   at org.apache.spark.sql.execution.SparkStrategies$ParquetOperations$.apply(SparkStrategies.scala:139)
[info]   at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
[info]   at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
[info]   at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
[info]   at org.apache.spark.sql.catalyst.planning.QueryPlanner.apply(QueryPlanner.scala:59)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan$lzycompute(SQLContext.scala:264)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan(SQLContext.scala:264)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan$lzycompute(SQLContext.scala:265)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan(SQLContext.scala:265)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.toRdd$lzycompute(SQLContext.scala:268)
[info]   at org.apache.spark.sql.SQLContext$QueryExecution.toRdd(SQLContext.scala:268)
[info]   at org.apache.spark.sql.SchemaRDDLike$class.saveAsParquetFile(SchemaRDDLike.scala:66)
[info]   at org.apache.spark.sql.SchemaRDD.saveAsParquetFile(SchemaRDD.scala:98)
```

Author: Andrew Ash <andrew@andrewash.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #690 from ash211/rdd-parquet-save and squashes the following commits:

747a0b9 [Andrew Ash] Merge pull request #1 from marmbrus/pr/690
54bd00e [Michael Armbrust] Need to put Option first since Option <: Seq.
8f3f281 [Andrew Ash] SPARK-1757 Add failing test for saving SparkSQL Schemas with Option[?] fields as parquet
[SPARK-1780] Non-existent SPARK_DAEMON_OPTS is lurking around

What they really mean is SPARK_DAEMON_***JAVA***_OPTS

Author: Andrew Or <andrewor14@gmail.com>

Closes #751 from andrewor14/spark-daemon-opts and squashes the following commits:

70c41f9 [Andrew Or] SPARK_DAEMON_OPTS -> SPARK_DAEMON_JAVA_OPTS
[SPARK-1753 / 1773 / 1814] Update outdated docs for spark-submit, YARN, standalone etc.

YARN
- SparkPi was updated to not take in master as an argument; we should update the docs to reflect that.
- The default YARN build guide should be in maven, not sbt.
- This PR also adds a paragraph on steps to debug a YARN application.

Standalone
- Emphasize spark-submit more. Right now it's one small paragraph preceding the legacy way of launching through `org.apache.spark.deploy.Client`.
- The way we set configurations / environment variables according to the old docs is outdated. This needs to reflect changes introduced by the Spark configuration changes we made.

In general, this PR also adds a little more documentation on the new spark-shell, spark-submit, spark-defaults.conf etc here and there.

Author: Andrew Or <andrewor14@gmail.com>

Closes #701 from andrewor14/yarn-docs and squashes the following commits:

e2c2312 [Andrew Or] Merge in changes in #752 (SPARK-1814)
25cfe7b [Andrew Or] Merge in the warning from SPARK-1753
a8c39c5 [Andrew Or] Minor changes
336bbd9 [Andrew Or] Tabs -> spaces
4d9d8f7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
041017a [Andrew Or] Abstract Spark submit documentation to cluster-overview.html
3cc0649 [Andrew Or] Detail how to set configurations + remove legacy instructions
5b7140a [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
85a51fc [Andrew Or] Update run-example, spark-shell, configuration etc.
c10e8c7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
381fe32 [Andrew Or] Update docs for standalone mode
757c184 [Andrew Or] Add a note about the requirements for the debugging trick
f8ca990 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
924f04c [Andrew Or] Revert addition of --deploy-mode
d5fe17b [Andrew Or] Update the YARN docs
SPARK-1815. SparkContext should not be marked DeveloperApi

Author: Sandy Ryza <sandy@cloudera.com>

Closes #753 from sryza/sandy-spark-1815 and squashes the following commits:

957a8ac [Sandy Ryza] SPARK-1815. SparkContext should not be marked DeveloperApi