[SPARK-2140] Updating heap memory calculation for YARN stable and alpha.

Updated pull request, reflecting YARN stable and alpha states. I am getting intermittent test failures on my own test infrastructure. Is that tracked anywhere yet?

Author: Chris Cope <ccope@resilientscience.com>

Closes #2253 from copester/master and squashes the following commits:

5ad89da [Chris Cope] [SPARK-2140] Removing calculateAMMemory functions since they are no longer needed.
52b4e45 [Chris Cope] [SPARK-2140] Updating heap memory calculation for YARN stable and alpha.
[SPARK-3047] [PySpark] add an option to use str in textFileRDD

str is much efficient than unicode (both CPU and memory), it'e better to use str in textFileRDD. In order to keep compatibility, use unicode by default. (Maybe change it in the future).

use_unicode=True:

daviesliudm:~/work/spark$ time python wc.py
(u'./universe/spark/sql/core/target/java/org/apache/spark/sql/execution/ExplainCommand$.java', 7776)

real	2m8.298s
user	0m0.185s
sys	0m0.064s

use_unicode=False

daviesliudm:~/work/spark$ time python wc.py
('./universe/spark/sql/core/target/java/org/apache/spark/sql/execution/ExplainCommand$.java', 7776)

real	1m26.402s
user	0m0.182s
sys	0m0.062s

We can see that it got 32% improvement!

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

Closes #1951 from davies/unicode and squashes the following commits:

8352d57 [Davies Liu] update version number
a286f2f [Davies Liu] rollback loads()
85246e5 [Davies Liu] add docs for use_unicode
a0295e1 [Davies Liu] add an option to use str in textFile()
[SPARK-2917] [SQL] Avoid table creation in logical plan analyzing for CTAS

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

Closes #1846 from chenghao-intel/ctas and squashes the following commits:

56a0578 [Cheng Hao] remove the unused imports
9a57abc [Cheng Hao] Avoid table creation in logical plan analyzing
[SPARK-3390][SQL] sqlContext.jsonRDD fails on a complex structure of JSON array and JSON object nesting

This PR aims to correctly handle JSON arrays in the type of `ArrayType(...(ArrayType(StructType)))`.

JIRA: https://issues.apache.org/jira/browse/SPARK-3390.

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

Closes #2364 from yhuai/SPARK-3390 and squashes the following commits:

46db418 [Yin Huai] Handle JSON arrays in the type of ArrayType(...(ArrayType(StructType))).
[Spark-3490] Disable SparkUI for tests

We currently open many ephemeral ports during the tests, and as a result we occasionally can't bind to new ones. This has caused the `DriverSuite` and the `SparkSubmitSuite` to fail intermittently.

By disabling the `SparkUI` when it's not needed, we already cut down on the number of ports opened significantly, on the order of the number of `SparkContexts` ever created. We must keep it enabled for a few tests for the UI itself, however.

Author: Andrew Or <andrewor14@gmail.com>

Closes #2363 from andrewor14/disable-ui-for-tests and squashes the following commits:

332a7d5 [Andrew Or] No need to set spark.ui.port to 0 anymore
30c93a2 [Andrew Or] Simplify streaming UISuite
a431b84 [Andrew Or] Fix streaming test failures
8f5ae53 [Andrew Or] Fix no new line at the end
29c9b5b [Andrew Or] Disable SparkUI for tests
[SPARK-3429] Don't include the empty string "" as a defaultAclUser

Changes logging from

```
14/09/05 02:01:08 INFO SecurityManager: Changing view acls to: aash,
14/09/05 02:01:08 INFO SecurityManager: Changing modify acls to: aash,
14/09/05 02:01:08 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(aash, ); users with modify permissions: Set(aash, )
```
to
```
14/09/05 02:28:28 INFO SecurityManager: Changing view acls to: aash
14/09/05 02:28:28 INFO SecurityManager: Changing modify acls to: aash
14/09/05 02:28:28 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(aash); users with modify permissions: Set(aash)
```

Note that the first set of logs have a Set of size 2 containing "aash" and the empty string ""

cc tgravescs

Author: Andrew Ash <andrew@andrewash.com>

Closes #2286 from ash211/empty-default-acl and squashes the following commits:

18cc612 [Andrew Ash] Use .isEmpty instead of ==""
cf973a1 [Andrew Ash] Don't include the empty string "" as a defaultAclUser
SPARK-3462 push down filters and projections into Unions

Author: Cody Koeninger <cody.koeninger@mediacrossing.com>

Closes #2345 from koeninger/SPARK-3462 and squashes the following commits:

5c8d24d [Cody Koeninger] SPARK-3462 remove now-unused parameter
0788691 [Cody Koeninger] SPARK-3462 add tests, handle compatible schema with different aliases, per marmbrus feedback
ef47b3b [Cody Koeninger] SPARK-3462 push down filters and projections into Unions
SPARK-2482: Resolve sbt warnings during build

At the same time, import the `scala.language.postfixOps` and ` org.scalatest.time.SpanSugar._` cause `scala.language.postfixOps` doesn't work

Author: witgo <witgo@qq.com>

Closes #1330 from witgo/sbt_warnings3 and squashes the following commits:

179ba61 [witgo] Resolve sbt warnings during build
[SPARK-3465] fix task metrics aggregation in local mode

Before overwrite t.taskMetrics, take a deepcopy of it.

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

Closes #2338 from davies/fix_metric and squashes the following commits:

a5cdb63 [Davies Liu] Merge branch 'master' into fix_metric
7c879e0 [Davies Liu] add more comments
754b5b8 [Davies Liu] copy taskMetrics only when isLocal is true
5ca26dc [Davies Liu] fix task metrics aggregation in local mode
[SPARK-3160] [SPARK-3494] [mllib]  DecisionTree: eliminate pre-allocated nodes, parentImpurities arrays. Memory calc bug fix.

This PR includes some code simplifications and re-organization which will be helpful for implementing random forests.  The main changes are that the nodes and parentImpurities arrays are no longer pre-allocated in the main train() method.

Also added 2 bug fixes:
* maxMemoryUsage calculation
* over-allocation of space for bins in DTStatsAggregator for unordered features.

Relation to RFs:
* Since RFs will be deeper and will therefore be more likely sparse (not full trees), it could be a cost savings to avoid pre-allocating a full tree.
* The associated re-organization also reduces bookkeeping, which will make RFs easier to implement.
* The return code doneTraining may be generalized to include cases such as nodes ready for local training.

Details:

No longer pre-allocate parentImpurities array in main train() method.
* parentImpurities values are now stored in individual nodes (in Node.stats.impurity).
* These were not really needed.  They were used in calculateGainForSplit(), but they can be calculated anyways using parentNodeAgg.

No longer using Node.build since tree structure is constructed on-the-fly.
* Did not eliminate since it is public (Developer) API.  Marked as deprecated.

Eliminated pre-allocated nodes array in main train() method.
* Nodes are constructed and added to the tree structure as needed during training.
* Moved tree construction from main train() method into findBestSplitsPerGroup() since there is no need to keep the (split, gain) array for an entire level of nodes.  Only one element of that array is needed at a time, so we do not the array.

findBestSplits() now returns 2 items:
* rootNode (newly created root node on first iteration, same root node on later iterations)
* doneTraining (indicating if all nodes at that level were leafs)

Updated DecisionTreeSuite.  Notes:
* Improved test "Second level node building with vs. without groups"
** generateOrderedLabeledPoints() modified so that it really does require 2 levels of internal nodes.
* Related update: Added Node.deepCopy (private[tree]), used for test suite

CC: mengxr

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #2341 from jkbradley/dt-spark-3160 and squashes the following commits:

07dd1ee [Joseph K. Bradley] Fixed overflow bug with computing maxMemoryUsage in DecisionTree.  Also fixed bug with over-allocating space in DTStatsAggregator for unordered features.
debe072 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-spark-3160
5c4ac33 [Joseph K. Bradley] Added check in Strategy to make sure minInstancesPerNode >= 1
0dd4d87 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-spark-3160
306120f [Joseph K. Bradley] Fixed typo in DecisionTreeModel.scala doc
eaa1dcf [Joseph K. Bradley] Added topNode doc in DecisionTree and scalastyle fix
d4d7864 [Joseph K. Bradley] Marked Node.build as deprecated
d4dbb99 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-spark-3160
1a8f0ad [Joseph K. Bradley] Eliminated pre-allocated nodes array in main train() method. * Nodes are constructed and added to the tree structure as needed during training.
2ab763b [Joseph K. Bradley] Simplifications to DecisionTree code:
[SPARK-2558][DOCS] Add --queue example to YARN doc

Put original YARN queue spark-submit arg description in
running-on-yarn html table and example command line

Author: Mark G. Whitney <mark@whitneyindustries.com>

Closes #2218 from kramimus/2258-yarndoc and squashes the following commits:

4b5d808 [Mark G. Whitney] remove yarn queue config
f8cda0d [Mark G. Whitney] [SPARK-2558][DOCS] Add spark.yarn.queue description to YARN doc
[PySpark] Add blank line so that Python RDD.top() docstring renders correctly

Author: RJ Nowling <rnowling@gmail.com>

Closes #2370 from rnowling/python_rdd_docstrings and squashes the following commits:

5230574 [RJ Nowling] Add blank line so that Python RDD.top() docstring renders correctly
[SPARK-3481] [SQL] Eliminate the error log in local Hive comparison test

Logically, we should remove the Hive Table/Database first and then reset the Hive configuration, repoint to the new data warehouse directory etc.
Otherwise it raised exceptions like "Database doesn't not exists: default" in the local testing.

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

Closes #2352 from chenghao-intel/test_hive and squashes the following commits:

74fd76b [Cheng Hao] eliminate the error log
MAINTENANCE: Automated closing of pull requests.

This commit exists to close the following pull requests on Github:

Closes #930 (close requested by 'andrewor14')
Closes #867 (close requested by 'marmbrus')
Closes #1829 (close requested by 'marmbrus')
Closes #1131 (close requested by 'JoshRosen')
Closes #1571 (close requested by 'andrewor14')
Closes #2359 (close requested by 'andrewor14')
[SPARK-3427] [GraphX] Avoid active vertex tracking in static PageRank

GraphX's current implementation of static (fixed iteration count) PageRank uses the Pregel API. This unnecessarily tracks active vertices, even though in static PageRank all vertices are always active. Active vertex tracking incurs the following costs:

1. A shuffle per iteration to ship the active sets to the edge partitions.
2. A hash table creation per iteration at each partition to index the active sets for lookup.
3. A hash lookup per edge to check whether the source vertex is active.

I reimplemented static PageRank using the lower-level GraphX API instead of the Pregel API. In benchmarks on a 16-node m2.4xlarge cluster, this provided a 23% speedup (from 514 s to 397 s, mean over 3 trials) for 10 iterations of PageRank on a synthetic graph with 10M vertices and 1.27B edges.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #2308 from ankurdave/SPARK-3427 and squashes the following commits:

449996a [Ankur Dave] Avoid unnecessary active vertex tracking in static PageRank
SPARK-3014. Log a more informative messages in a couple failure scenario...

...s

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1934 from sryza/sandy-spark-3014 and squashes the following commits:

ae19cc1 [Sandy Ryza] SPARK-3014. Log a more informative messages in a couple failure scenarios
[SPARK-3217] Add Guava to classpath when SPARK_PREPEND_CLASSES is set.

When that option is used, the compiled classes from the build directory
are prepended to the classpath. Now that we avoid packaging Guava, that
means we have classes referencing the original Guava location in the app's
classpath, so errors happen.

For that case, add Guava manually to the classpath.

Note: if Spark is compiled with "-Phadoop-provided", it's tricky to
make things work with SPARK_PREPEND_CLASSES, because you need to add
the Hadoop classpath using SPARK_CLASSPATH and that means the older
Hadoop Guava overrides the newer one Spark needs. So someone using
SPARK_PREPEND_CLASSES needs to remember to not use that profile.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2141 from vanzin/SPARK-3217 and squashes the following commits:

b967324 [Marcelo Vanzin] [SPARK-3217] Add Guava to classpath when SPARK_PREPEND_CLASSES is set.
[SPARK-3456] YarnAllocator on alpha can lose container requests to RM

Author: Thomas Graves <tgraves@apache.org>

Closes #2373 from tgravescs/SPARK-3456 and squashes the following commits:

77e9532 [Thomas Graves] [SPARK-3456] YarnAllocator on alpha can lose container requests to RM
[SPARK-3094] [PySpark] compatitable with PyPy

After this patch, we can run PySpark in PyPy (testing with PyPy 2.3.1 in Mac 10.9), for example:

```
PYSPARK_PYTHON=pypy ./bin/spark-submit wordcount.py
```

The performance speed up will depend on work load (from 20% to 3000%). Here are some benchmarks:

 Job | CPython 2.7 | PyPy 2.3.1  | Speed up
 ------- | ------------ | ------------- | -------
 Word Count | 41s   | 15s  | 2.7x
 Sort | 46s |  44s | 1.05x
 Stats | 174s | 3.6s | 48x

Here is the code used for benchmark:

```python
rdd = sc.textFile("text")
def wordcount():
    rdd.flatMap(lambda x:x.split('/'))\
        .map(lambda x:(x,1)).reduceByKey(lambda x,y:x+y).collectAsMap()
def sort():
    rdd.sortBy(lambda x:x, 1).count()
def stats():
    sc.parallelize(range(1024), 20).flatMap(lambda x: xrange(5024)).stats()
```

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

Closes #2144 from davies/pypy and squashes the following commits:

9aed6c5 [Davies Liu] use protocol 2 in CloudPickle
4bc1f04 [Davies Liu] refactor
b20ab3a [Davies Liu] pickle sys.stdout and stderr in portable way
3ca2351 [Davies Liu] Merge branch 'master' into pypy
fae8b19 [Davies Liu] improve attrgetter, add tests
591f830 [Davies Liu] try to run tests with PyPy in run-tests
c8d62ba [Davies Liu] cleanup
f651fd0 [Davies Liu] fix tests using array with PyPy
1b98fb3 [Davies Liu] serialize itemgetter/attrgetter in portable ways
3c1dbfe [Davies Liu] Merge branch 'master' into pypy
42fb5fa [Davies Liu] Merge branch 'master' into pypy
cb2d724 [Davies Liu] fix tests
9986692 [Davies Liu] Merge branch 'master' into pypy
25b4ca7 [Davies Liu] support PyPy
[SPARK-3500] [SQL] use JavaSchemaRDD as SchemaRDD._jschema_rdd

Currently, SchemaRDD._jschema_rdd is SchemaRDD, the Scala API (coalesce(), repartition()) can not been called in Python easily, there is no way to specify the implicit parameter `ord`. The _jrdd is an JavaRDD, so _jschema_rdd should also be JavaSchemaRDD.

In this patch, change _schema_rdd to JavaSchemaRDD, also added an assert for it. If some methods are missing from JavaSchemaRDD, then it's called by _schema_rdd.baseSchemaRDD().xxx().

BTW, Do we need JavaSQLContext?

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

Closes #2369 from davies/fix_schemardd and squashes the following commits:

abee159 [Davies Liu] use JavaSchemaRDD as SchemaRDD._jschema_rdd