[SPARK-2014] Make PySpark store RDDs in MEMORY_ONLY_SER with compression by default

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

Closes #1051 from ScrapCodes/SPARK-2014/pyspark-cache and squashes the following commits:

f192df7 [Prashant Sharma] Code Review
2a2f43f [Prashant Sharma] [SPARK-2014] Make PySpark store RDDs in MEMORY_ONLY_SER with compression by default
[SPARK-2538] [PySpark] Hash based disk spilling aggregation

During aggregation in Python worker, if the memory usage is above spark.executor.memory, it will do disk spilling aggregation.

It will split the aggregation into multiple stage, in each stage, it will partition the aggregated data by hash and dump them into disks. After all the data are aggregated, it will merge all the stages together (partition by partition).

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

Closes #1460 from davies/spill and squashes the following commits:

cad91bf [Davies Liu] call gc.collect() after data.clear() to release memory as much as possible.
37d71f7 [Davies Liu] balance the partitions
902f036 [Davies Liu] add shuffle.py into run-tests
dcf03a9 [Davies Liu] fix memory_info() of psutil
67e6eba [Davies Liu] comment for MAX_TOTAL_PARTITIONS
f6bd5d6 [Davies Liu] rollback next_limit() again, the performance difference is huge:
e74b785 [Davies Liu] fix code style and change next_limit to memory_limit
400be01 [Davies Liu] address all the comments
6178844 [Davies Liu] refactor and improve docs
fdd0a49 [Davies Liu] add long doc string for ExternalMerger
1a97ce4 [Davies Liu] limit used memory and size of objects in partitionBy()
e6cc7f9 [Davies Liu] Merge branch 'master' into spill
3652583 [Davies Liu] address comments
e78a0a0 [Davies Liu] fix style
24cec6a [Davies Liu] get local directory by SPARK_LOCAL_DIR
57ee7ef [Davies Liu] update docs
286aaff [Davies Liu] let spilled aggregation in Python configurable
e9a40f6 [Davies Liu] recursive merger
6edbd1f [Davies Liu] Hash based disk spilling aggregation
[SPARK-2656] Python version of stratified sampling

exact sample size not supported for now.

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

Closes #1554 from dorx/pystratified and squashes the following commits:

4ba927a [Doris Xin] use rel diff (+- 50%) instead of abs diff (+- 50)
bdc3f8b [Doris Xin] updated unit to check sample holistically
7713c7b [Doris Xin] Python version of stratified sampling
SPARK-2657 Use more compact data structures than ArrayBuffer in groupBy & cogroup

JIRA: https://issues.apache.org/jira/browse/SPARK-2657

Our current code uses ArrayBuffers for each group of values in groupBy, as well as for the key's elements in CoGroupedRDD. ArrayBuffers have a lot of overhead if there are few values in them, which is likely to happen in cases such as join. In particular, they have a pointer to an Object[] of size 16 by default, which is 24 bytes for the array header + 128 for the pointers in there, plus at least 32 for the ArrayBuffer data structure. This patch replaces the per-group buffers with a CompactBuffer class that can store up to 2 elements more efficiently (in fields of itself) and acts like an ArrayBuffer beyond that. For a key's elements in CoGroupedRDD, we use an Array of CompactBuffers instead of an ArrayBuffer of ArrayBuffers.

There are some changes throughout the code to deal with CoGroupedRDD returning Array instead. We can also decide not to do that but CoGroupedRDD is a `DeveloperAPI` so I think it's okay to change it here.

Author: Matei Zaharia <matei@databricks.com>

Closes #1555 from mateiz/compact-groupby and squashes the following commits:

845a356 [Matei Zaharia] Lower initial size of CompactBuffer's vector to 8
07621a7 [Matei Zaharia] Review comments
0c1cd12 [Matei Zaharia] Don't use varargs in CompactBuffer.apply
bdc8a39 [Matei Zaharia] Small tweak to +=, and typos
f61f040 [Matei Zaharia] Fix line lengths
59da88b0 [Matei Zaharia] Fix line lengths
197cde8 [Matei Zaharia] Make CompactBuffer extend Seq to make its toSeq more efficient
775110f [Matei Zaharia] Change CoGroupedRDD to give (K, Array[Iterable[_]]) to avoid wrappers
9b4c6e8 [Matei Zaharia] Use CompactBuffer in CoGroupedRDD
ed577ab [Matei Zaharia] Use CompactBuffer in groupByKey
10f0de1 [Matei Zaharia] A CompactBuffer that's more memory-efficient than ArrayBuffer for small buffers
[SPARK-2529] Clean closures in foreach and foreachPartition.

Author: Reynold Xin <rxin@apache.org>

Closes #1583 from rxin/closureClean and squashes the following commits:

8982fe6 [Reynold Xin] [SPARK-2529] Clean closures in foreach and foreachPartition.
[SPARK-2665] [SQL] Add EqualNS & Unit Tests

Hive Supports the operator "<=>", which returns same result with EQUAL(=) operator for non-null operands, but returns TRUE if both are NULL, FALSE if one of the them is NULL.

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

Closes #1570 from chenghao-intel/equalns and squashes the following commits:

8d6c789 [Cheng Hao] Remove the test case orc_predicate_pushdown
5b2ca88 [Cheng Hao] Add cases into whitelist
8e66cdd [Cheng Hao] Rename the EqualNSTo ==> EqualNullSafe
7af4b0b [Cheng Hao] Add EqualNS & Unit Tests
replace println to log4j

Our program needs to receive a large amount of data and run for a long
time.
We set the log level to WARN but "Storing iterator" "received single"
as such message written to the log file. (over yarn)

Author: fireflyc <fireflyc@126.com>

Closes #1372 from fireflyc/fix-replace-stdout-log and squashes the following commits:

e684140 [fireflyc] 'info' modified into the 'debug'
fa22a38 [fireflyc] replace println to log4j
[SPARK-2683] unidoc failed because org.apache.spark.util.CallSite uses Java keywords as value names

Renaming `short` to `shortForm` and `long` to `longForm`.

JIRA: https://issues.apache.org/jira/browse/SPARK-2683

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

Closes #1585 from yhuai/SPARK-2683 and squashes the following commits:

5ddb843 [Yin Huai] "short" and "long" are Java keyworks. In order to generate javadoc, renaming "short" to "shortForm" and "long" to "longForm".
Fixed SPARK-2678
Merge branch 'spark-submit-args' into thriftserver

Conflicts:
	core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala
Uses random port for HiveThriftServer2 to avoid collision with parallel builds