Support hbase-0.96-1.1 in SparkBuild
overwrote sparkbuild
update pom.xml for hadoop-2.3-cdh50.0 and hbase 0.96.1.1
Merge branch 'master' of https://github.com/apache/spark
Mesos workaround
[SPARK-2523] [SQL] Hadoop table scan bug fixing

In HiveTableScan.scala, ObjectInspector was created for all of the partition based records, which probably causes ClassCastException if the object inspector is not identical among table & partitions.

This is the follow up with:
https://github.com/apache/spark/pull/1408
https://github.com/apache/spark/pull/1390

I've run a micro benchmark in my local with 15000000 records totally, and got the result as below:

With This Patch  |  Partition-Based Table  |  Non-Partition-Based Table
------------ | ------------- | -------------
No  |  1927 ms  |  1885 ms
Yes  | 1541 ms  |  1524 ms

It showed this patch will also improve the performance.

PS:  the benchmark code is also attached. (thanks liancheng )
```
package org.apache.spark.sql.hive

import org.apache.spark.SparkContext
import org.apache.spark.SparkConf
import org.apache.spark.sql._

object HiveTableScanPrepare extends App {
  case class Record(key: String, value: String)

  val sparkContext = new SparkContext(
    new SparkConf()
      .setMaster("local")
      .setAppName(getClass.getSimpleName.stripSuffix("$")))

  val hiveContext = new LocalHiveContext(sparkContext)

  val rdd = sparkContext.parallelize((1 to 3000000).map(i => Record(s"$i", s"val_$i")))

  import hiveContext._

  hql("SHOW TABLES")
  hql("DROP TABLE if exists part_scan_test")
  hql("DROP TABLE if exists scan_test")
  hql("DROP TABLE if exists records")
  rdd.registerAsTable("records")

  hql("""CREATE TABLE part_scan_test (key STRING, value STRING) PARTITIONED BY (part1 string, part2 STRING)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)
  hql("""CREATE TABLE scan_test (key STRING, value STRING)
                 | ROW FORMAT SERDE
                 | 'org.apache.hadoop.hive.serde2.columnar.LazyBinaryColumnarSerDe'
                 | STORED AS RCFILE
               """.stripMargin)

  for (part1 <- 2000 until 2001) {
    for (part2 <- 1 to 5) {
      hql(s"""from records
                 | insert into table part_scan_test PARTITION (part1='$part1', part2='2010-01-$part2')
                 | select key, value
               """.stripMargin)
      hql(s"""from records
                 | insert into table scan_test select key, value
               """.stripMargin)
    }
  }
}

object HiveTableScanTest extends App {
  val sparkContext = new SparkContext(
    new SparkConf()
      .setMaster("local")
      .setAppName(getClass.getSimpleName.stripSuffix("$")))

  val hiveContext = new LocalHiveContext(sparkContext)

  import hiveContext._

  hql("SHOW TABLES")
  val part_scan_test = hql("select key, value from part_scan_test")
  val scan_test = hql("select key, value from scan_test")

  val r_part_scan_test = (0 to 5).map(i => benchmark(part_scan_test))
  val r_scan_test = (0 to 5).map(i => benchmark(scan_test))
  println("Scanning Partition-Based Table")
  r_part_scan_test.foreach(printResult)
  println("Scanning Non-Partition-Based Table")
  r_scan_test.foreach(printResult)

  def printResult(result: (Long, Long)) {
    println(s"Duration: ${result._1} ms Result: ${result._2}")
  }

  def benchmark(srdd: SchemaRDD) = {
    val begin = System.currentTimeMillis()
    val result = srdd.count()
    val end = System.currentTimeMillis()
    ((end - begin), result)
  }
}
```

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

Closes #1439 from chenghao-intel/hadoop_table_scan and squashes the following commits:

888968f [Cheng Hao] Fix issues in code style
27540ba [Cheng Hao] Fix the TableScan Bug while partition serde differs
40a24a7 [Cheng Hao] Add Unit Test
[SPARK-2479][MLlib] Comparing floating-point numbers using relative error in UnitTests

Floating point math is not exact, and most floating-point numbers end up being slightly imprecise due to rounding errors.

Simple values like 0.1 cannot be precisely represented using binary floating point numbers, and the limited precision of floating point numbers means that slight changes in the order of operations or the precision of intermediates can change the result.

That means that comparing two floats to see if they are equal is usually not what we want. As long as this imprecision stays small, it can usually be ignored.

Based on discussion in the community, we have implemented two different APIs for relative tolerance, and absolute tolerance. It makes sense that test writers should know which one they need depending on their circumstances.

Developers also need to explicitly specify the eps, and there is no default value which will sometimes cause confusion.

When comparing against zero using relative tolerance, a exception will be raised to warn users that it's meaningless.

For relative tolerance, users can now write

    assert(23.1 ~== 23.52 relTol 0.02)
    assert(23.1 ~== 22.74 relTol 0.02)
    assert(23.1 ~= 23.52 relTol 0.02)
    assert(23.1 ~= 22.74 relTol 0.02)
    assert(!(23.1 !~= 23.52 relTol 0.02))
    assert(!(23.1 !~= 22.74 relTol 0.02))

    // This will throw exception with the following message.
    // "Did not expect 23.1 and 23.52 to be within 0.02 using relative tolerance."
    assert(23.1 !~== 23.52 relTol 0.02)

    // "Expected 23.1 and 22.34 to be within 0.02 using relative tolerance."
    assert(23.1 ~== 22.34 relTol 0.02)

For absolute error,

    assert(17.8 ~== 17.99 absTol 0.2)
    assert(17.8 ~== 17.61 absTol 0.2)
    assert(17.8 ~= 17.99 absTol 0.2)
    assert(17.8 ~= 17.61 absTol 0.2)
    assert(!(17.8 !~= 17.99 absTol 0.2))
    assert(!(17.8 !~= 17.61 absTol 0.2))

    // This will throw exception with the following message.
    // "Did not expect 17.8 and 17.99 to be within 0.2 using absolute error."
    assert(17.8 !~== 17.99 absTol 0.2)

    // "Expected 17.8 and 17.59 to be within 0.2 using absolute error."
    assert(17.8 ~== 17.59 absTol 0.2)

Authors:
  DB Tsai <dbtsaialpinenow.com>
  Marek Kolodziej <marekalpinenow.com>

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #1425 from dbtsai/SPARK-2479_comparing_floating_point and squashes the following commits:

8c7cbcc [DB Tsai] Alpine Data Labs
[SPARK-2410][SQL] Merging Hive Thrift/JDBC server (with Maven profile fix)

JIRA issue: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)

Another try for #1399 & #1600. Those two PR breaks Jenkins builds because we made a separate profile `hive-thriftserver` in sub-project `assembly`, but the `hive-thriftserver` module is defined outside the `hive-thriftserver` profile. Thus every time a pull request that doesn't touch SQL code will also execute test suites defined in `hive-thriftserver`, but tests fail because related .class files are not included in the assembly jar.

In the most recent commit, module `hive-thriftserver` is moved into its own profile to fix this problem. All previous commits are squashed for clarity.

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

Closes #1620 from liancheng/jdbc-with-maven-fix and squashes the following commits:

629988e [Cheng Lian] Moved hive-thriftserver module definition into its own profile
ec3c7a7 [Cheng Lian] Cherry picked the Hive Thrift server
Use commons-lang3 in SignalLogger rather than commons-lang

Spark only transitively depends on the latter, based on the Hadoop version.

Author: Aaron Davidson <aaron@databricks.com>

Closes #1621 from aarondav/lang3 and squashes the following commits:

93c93bf [Aaron Davidson] Use commons-lang3 in SignalLogger rather than commons-lang
Excess judgment

Author: Yadong Qi <qiyadong2010@gmail.com>

Closes #1629 from watermen/bug-fix2 and squashes the following commits:

59b7237 [Yadong Qi] Update HiveQl.scala
[SPARK-2580] [PySpark] keep silent in worker if JVM close the socket

During rdd.take(n), JVM will close the socket if it had got enough data, the Python worker should keep silent in this case.

In the same time, the worker should not print the trackback into stderr if it send the traceback to JVM successfully.

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

Closes #1625 from davies/error and squashes the following commits:

4fbcc6d [Davies Liu] disable log4j during testing when exception is expected.
cc14202 [Davies Liu] keep silent in worker if JVM close the socket
[SPARK-791] [PySpark] fix pickle itemgetter with cloudpickle

fix the problem with pickle operator.itemgetter with multiple index.

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

Closes #1627 from davies/itemgetter and squashes the following commits:

aabd7fa [Davies Liu] fix pickle itemgetter with cloudpickle
[SPARK-2726] and [SPARK-2727] Remove SortOrder and do in-place sort.

The pull request includes two changes:

1. Removes SortOrder introduced by SPARK-2125. The key ordering already includes the SortOrder information since an Ordering can be reverse. This is similar to Java's Comparator interface. Rarely does an API accept both a Comparator as well as a SortOrder.

2. Replaces the sortWith call in HashShuffleReader with an in-place quick sort.

Author: Reynold Xin <rxin@apache.org>

Closes #1631 from rxin/sortOrder and squashes the following commits:

c9d37e1 [Reynold Xin] [SPARK-2726] and [SPARK-2727] Remove SortOrder and do in-place sort.
[SPARK-2174][MLLIB] treeReduce and treeAggregate

In `reduce` and `aggregate`, the driver node spends linear time on the number of partitions. It becomes a bottleneck when there are many partitions and the data from each partition is big.

SPARK-1485 (#506) tracks the progress of implementing AllReduce on Spark. I did several implementations including butterfly, reduce + broadcast, and treeReduce + broadcast. treeReduce + BT broadcast seems to be right way to go for Spark. Using binary tree may introduce some overhead in communication, because the driver still need to coordinate on data shuffling. In my experiments, n -> sqrt(n) -> 1 gives the best performance in general, which is why I set "depth = 2" in MLlib algorithms. But it certainly needs more testing.

I left `treeReduce` and `treeAggregate` public for easy testing. Some numbers from a test on 32-node m3.2xlarge cluster.

code:

~~~
import breeze.linalg._
import org.apache.log4j._

Logger.getRootLogger.setLevel(Level.OFF)

for (n <- Seq(1, 10, 100, 1000, 10000, 100000, 1000000)) {
  val vv = sc.parallelize(0 until 1024, 1024).map(i => DenseVector.zeros[Double](n))
  var start = System.nanoTime(); vv.treeReduce(_ + _, 2); println((System.nanoTime() - start) / 1e9)
  start = System.nanoTime(); vv.reduce(_ + _); println((System.nanoTime() - start) / 1e9)
}
~~~

out:

| n | treeReduce(,2) | reduce |
|---|---------------------|-----------|
| 10 | 0.215538731 | 0.204206899 |
| 100 | 0.278405907 | 0.205732582 |
| 1000 | 0.208972182 | 0.214298272 |
| 10000 | 0.194792071 | 0.349353687 |
| 100000 | 0.347683285 | 6.086671892 |
| 1000000 | 2.589350682 | 66.572906702 |

CC: @pwendell

This is clearly more scalable than the default implementation. My question is whether we should use this implementation in `reduce` and `aggregate` or put them as separate methods. The concern is that users may use `reduce` and `aggregate` as collect, where having multiple stages doesn't reduce the data size. However, in this case, `collect` is more appropriate.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1110 from mengxr/tree and squashes the following commits:

c6cd267 [Xiangrui Meng] make depth default to 2
b04b96a [Xiangrui Meng] address comments
9bcc5d3 [Xiangrui Meng] add depth for readability
7495681 [Xiangrui Meng] fix compile error
142a857 [Xiangrui Meng] merge master
d58a087 [Xiangrui Meng] move treeReduce and treeAggregate to mllib
8a2a59c [Xiangrui Meng] Merge branch 'master' into tree
be6a88a [Xiangrui Meng] use treeAggregate in mllib
0f94490 [Xiangrui Meng] add docs
eb71c33 [Xiangrui Meng] add treeReduce
fe42a5e [Xiangrui Meng] add treeAggregate
Minor indentation and comment typo fixes.

Author: Aaron Staple <astaple@gmail.com>

Closes #1630 from staple/minor and squashes the following commits:

6f295a2 [Aaron Staple] Fix typos in comment about ExprId.
8566467 [Aaron Staple] Fix off by one column indentation in SqlParser.
[STREAMING] SPARK-1729. Make Flume pull data from source, rather than the current pu...

...sh model

Currently Spark uses Flume's internal Avro Protocol to ingest data from Flume. If the executor running the
receiver fails, it currently has to be restarted on the same node to be able to receive data.

This commit adds a new Sink which can be deployed to a Flume agent. This sink can be polled by a new
DStream that is also included in this commit. This model ensures that data can be pulled into Spark from
Flume even if the receiver is restarted on a new node. This also allows the receiver to receive data on
multiple threads for better performance.

Author: Hari Shreedharan <harishreedharan@gmail.com>
Author: Hari Shreedharan <hshreedharan@apache.org>
Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: harishreedharan <hshreedharan@cloudera.com>

Closes #807 from harishreedharan/master and squashes the following commits:

e7f70a3 [Hari Shreedharan] Merge remote-tracking branch 'asf-git/master'
96cfb6f [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
e48d785 [Hari Shreedharan] Documenting flume-sink being ignored for Mima checks.
5f212ce [Hari Shreedharan] Ignore Spark Sink from mima.
981bf62 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
7a1bc6e [Hari Shreedharan] Fix SparkBuild.scala
a082eb3 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
1f47364 [Hari Shreedharan] Minor fixes.
73d6f6d [Hari Shreedharan] Cleaned up tests a bit. Added some docs in multiple places.
65b76b4 [Hari Shreedharan] Fixing the unit test.
e59cc20 [Hari Shreedharan] Use SparkFlumeEvent instead of the new type. Also, Flume Polling Receiver now uses the store(ArrayBuffer) method.
f3c99d1 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
3572180 [Hari Shreedharan] Adding a license header, making Jenkins happy.
799509f [Hari Shreedharan] Fix a compile issue.
3c5194c [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
d248d22 [harishreedharan] Merge pull request #1 from tdas/flume-polling
10b6214 [Tathagata Das] Changed public API, changed sink package, and added java unit test to make sure Java API is callable from Java.
1edc806 [Hari Shreedharan] SPARK-1729. Update logging in Spark Sink.
8c00289 [Hari Shreedharan] More debug messages
393bd94 [Hari Shreedharan] SPARK-1729. Use LinkedBlockingQueue instead of ArrayBuffer to keep track of connections.
120e2a1 [Hari Shreedharan] SPARK-1729. Some test changes and changes to utils classes.
9fd0da7 [Hari Shreedharan] SPARK-1729. Use foreach instead of map for all Options.
8136aa6 [Hari Shreedharan] Adding TransactionProcessor to map on returning batch of data
86aa274 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
205034d [Hari Shreedharan] Merging master in
4b0c7fc [Hari Shreedharan] FLUME-1729. New Flume-Spark integration.
bda01fc [Hari Shreedharan] FLUME-1729. Flume-Spark integration.
0d69604 [Hari Shreedharan] FLUME-1729. Better Flume-Spark integration.
3c23c18 [Hari Shreedharan] SPARK-1729. New Spark-Flume integration.
70bcc2a [Hari Shreedharan] SPARK-1729. New Flume-Spark integration.
d6fa3aa [Hari Shreedharan] SPARK-1729. New Flume-Spark integration.
e7da512 [Hari Shreedharan] SPARK-1729. Fixing import order
9741683 [Hari Shreedharan] SPARK-1729. Fixes based on review.
c604a3c [Hari Shreedharan] SPARK-1729. Optimize imports.
0f10788 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
87775aa [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
8df37e4 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
03d6c1c [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
08176ad [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
d24d9d4 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
6d6776a [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
[SQL]change some test lists

1. there's no `hook_context.q` but a `hook_context_cs.q` in query folder
2. there's no `compute_stats_table.q` in query folder
3. there's no `having1.q` in query folder
4. `udf_E` and `udf_PI` appear twice in white list

Author: Daoyuan <daoyuan.wang@intel.com>

Closes #1634 from adrian-wang/testcases and squashes the following commits:

d7482ce [Daoyuan] change some test lists
[SPARK-2730][SQL] When retrieving a value from a Map, GetItem evaluates key twice

JIRA: https://issues.apache.org/jira/browse/SPARK-2730

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

Closes #1637 from yhuai/SPARK-2730 and squashes the following commits:

1a9f24e [Yin Huai] Remove unnecessary key evaluation.
[SPARK-2674] [SQL] [PySpark] support datetime type for SchemaRDD

Datetime and time in Python will be converted into java.util.Calendar after serialization, it will be converted into java.sql.Timestamp during inferSchema().

In javaToPython(), Timestamp will be converted into Calendar, then be converted into datetime in Python after pickling.

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

Closes #1601 from davies/date and squashes the following commits:

f0599b0 [Davies Liu] remove tests for sets and tuple in sql, fix list of list
c9d607a [Davies Liu] convert datetype for runtime
709d40d [Davies Liu] remove brackets
96db384 [Davies Liu] support datetime type for SchemaRDD
[SPARK-2082] stratified sampling in PairRDDFunctions that guarantees exact sample size

Implemented stratified sampling that guarantees exact sample size using ScaRSR with two passes over the RDD for sampling without replacement and three passes for sampling with replacement.

Author: Doris Xin <doris.s.xin@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #1025 from dorx/stratified and squashes the following commits:

245439e [Doris Xin] moved minSamplingRate to getUpperBound
eaf5771 [Doris Xin] bug fixes.
17a381b [Doris Xin] fixed a merge issue and a failed unit
ea7d27f [Doris Xin] merge master
b223529 [Xiangrui Meng] use approx bounds for poisson fix poisson mean for waitlisting add unit tests for Java
b3013a4 [Xiangrui Meng] move math3 back to test scope
eecee5f [Doris Xin] Merge branch 'master' into stratified
f4c21f3 [Doris Xin] Reviewer comments
a10e68d [Doris Xin] style fix
a2bf756 [Doris Xin] Merge branch 'master' into stratified
680b677 [Doris Xin] use mapPartitionWithIndex instead
9884a9f [Doris Xin] style fix
bbfb8c9 [Doris Xin] Merge branch 'master' into stratified
ee9d260 [Doris Xin] addressed reviewer comments
6b5b10b [Doris Xin] Merge branch 'master' into stratified
254e03c [Doris Xin] minor fixes and Java API.
4ad516b [Doris Xin] remove unused imports from PairRDDFunctions
bd9dc6e [Doris Xin] unit bug and style violation fixed
1fe1cff [Doris Xin] Changed fractionByKey to a map to enable arg check
944a10c [Doris Xin] [SPARK-2145] Add lower bound on sampling rate
0214a76 [Doris Xin] cleanUp
90d94c0 [Doris Xin] merge master
9e74ab5 [Doris Xin] Separated out most of the logic in sampleByKey
7327611 [Doris Xin] merge master
50581fc [Doris Xin] added a TODO for logging in python
46f6c8c [Doris Xin] fixed the NPE caused by closures being cleaned before being passed into the aggregate function
7e1a481 [Doris Xin] changed the permission on SamplingUtil
1d413ce [Doris Xin] fixed checkstyle issues
9ee94ee [Doris Xin] [SPARK-2082] stratified sampling in PairRDDFunctions that guarantees exact sample size
e3fd6a6 [Doris Xin] Merge branch 'master' into takeSample
7cab53a [Doris Xin] fixed import bug in rdd.py
ffea61a [Doris Xin] SPARK-1939: Refactor takeSample method in RDD
1441977 [Doris Xin] SPARK-1939 Refactor takeSample method in RDD to use ScaSRS