ALS implicit: added missing parameter alpha in doc string

Author: Felix Maximilian Möller <felixmaximilian.moeller@immobilienscout24.de>

Closes #3343 from felixmaximilian/fix-documentation and squashes the following commits:

43dcdfb [Felix Maximilian Möller] Removed the information about the switch implicitPrefs. The parameter implicitPrefs cannot be set in this context because it is inherent true when calling the trainImplicit method.
7d172ba [Felix Maximilian Möller] added missing parameter alpha in doc string.
[SPARK-4435] [MLlib] [PySpark] improve classification

This PR add setThrehold() and clearThreshold() for LogisticRegressionModel and SVMModel, also support RDD of vector in LogisticRegressionModel.predict(), SVNModel.predict() and NaiveBayes.predict()

Author: Davies Liu <davies@databricks.com>

Closes #3305 from davies/setThreshold and squashes the following commits:

d0b835f [Davies Liu] Merge branch 'master' of github.com:apache/spark into setThreshold
e4acd76 [Davies Liu] address comments
2231a5f [Davies Liu] bugfix
7bd9009 [Davies Liu] address comments
0b0a8a7 [Davies Liu] address comments
c1e5573 [Davies Liu] improve classification
[SPARK-4396] allow lookup by index in Python's Rating

In PySpark, ALS can take an RDD of (user, product, rating) tuples as input. However, model.predict outputs an RDD of Rating. So on the input side, users can use r[0], r[1], r[2], while on the output side, users have to use r.user, r.product, r.rating. We should allow lookup by index in Rating by making Rating a namedtuple.

davies

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Author: Xiangrui Meng <meng@databricks.com>

Closes #3261 from mengxr/SPARK-4396 and squashes the following commits:

543aef0 [Xiangrui Meng] use named tuple to implement ALS
0b61bae [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-4396
d3bd7d4 [Xiangrui Meng] allow lookup by index in Python's Rating
[SQL] Support partitioned parquet tables that have the key in both the directory and the file

Author: Michael Armbrust <michael@databricks.com>

Closes #3272 from marmbrus/keyInPartitionedTable and squashes the following commits:

447f08c [Michael Armbrust] Support partitioned parquet tables that have the key in both the directory and the file
[SPARK-4075][SPARK-4434] Fix the URI validation logic for Application Jar name.

This PR adds a regression test for SPARK-4434.

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

Closes #3326 from sarutak/add-triple-slash-testcase and squashes the following commits:

82bc9cc [Kousuke Saruta] Fixed wrong grammar in comment
9149027 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into add-triple-slash-testcase
c1c80ca [Kousuke Saruta] Fixed style
4f30210 [Kousuke Saruta] Modified comments
9e09da2 [Kousuke Saruta] Fixed URI validation for jar file
d4b99ef [Kousuke Saruta] [SPARK-4075] [Deploy] Jar url validation is not enough for Jar file
ac79906 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into add-triple-slash-testcase
6d4f47e [Kousuke Saruta] Added a test case as a regression check for SPARK-4434
[SPARK-4404] remove sys.exit() in shutdown hook

If SparkSubmit die first, then bootstrapper will be blocked by shutdown hook. sys.exit() in a shutdown hook will cause some kind of dead lock.

cc andrewor14

Author: Davies Liu <davies@databricks.com>

Closes #3289 from davies/fix_bootstraper and squashes the following commits:

ea5cdd1 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_bootstraper
e04b690 [Davies Liu] remove sys.exit in hook
4d11366 [Davies Liu] remove shutdown hook if subprocess die fist
[SPARK-4017] show progress bar in console

The progress bar will look like this:

![1___spark_job__85_250_finished__4_are_running___java_](https://cloud.githubusercontent.com/assets/40902/4854813/a02f44ac-6099-11e4-9060-7c73a73151d6.png)

In the right corner, the numbers are: finished tasks, running tasks, total tasks.

After the stage has finished, it will disappear.

The progress bar is only showed if logging level is WARN or higher (but progress in title is still showed), it can be turned off by spark.driver.showConsoleProgress.

Author: Davies Liu <davies@databricks.com>

Closes #3029 from davies/progress and squashes the following commits:

95336d5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
fc49ac8 [Davies Liu] address commentse
2e90f75 [Davies Liu] show multiple stages in same time
0081bcc [Davies Liu] address comments
38c42f1 [Davies Liu] fix tests
ab87958 [Davies Liu] disable progress bar during tests
30ac852 [Davies Liu] re-implement progress bar
b3f34e5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
6fd30ff [Davies Liu] show progress bar if no task finished in 500ms
e4e7344 [Davies Liu] refactor
e1f524d [Davies Liu] revert unnecessary change
a60477c [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
5cae3f2 [Davies Liu] fix style
ea49fe0 [Davies Liu] address comments
bc53d99 [Davies Liu] refactor
e6bb189 [Davies Liu] fix logging in sparkshell
7e7d4e7 [Davies Liu] address commments
5df26bb [Davies Liu] fix style
9e42208 [Davies Liu] show progress bar in console and title
[SPARK-4463] Add (de)select all button for add'l metrics.

This commit removes the behavior where when a user clicks
"Show additional metrics" on the stage page, all of the additional
metrics are automatically selected; now, collapsing and expanding
the additional metrics has no effect on which options are selected.
Instead, there's a "(De)select All" box at the top; checking this box
checks all additional metrics (and similarly, unchecking it unchecks
all additional metrics).

This commit is intended to be backported to 1.2, so that the additional
metrics behavior is not confusing to users.

Now when a user clicks the "Show additional metrics" menu, this is what
it looks like:
![image](https://cloud.githubusercontent.com/assets/1108612/5094347/1541ead6-6f15-11e4-8e8c-25a65ddbdfb2.png)

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #3331 from kayousterhout/SPARK-4463 and squashes the following commits:

9e17cea [Kay Ousterhout] Added italics
b731230 [Kay Ousterhout] [SPARK-4463] Add (de)select all button for add'l metrics.
[SPARK-4306] [MLlib] Python API for LogisticRegressionWithLBFGS

```
class LogisticRegressionWithLBFGS
 |  train(cls, data, iterations=100, initialWeights=None, corrections=10, tolerance=0.0001, regParam=0.01, intercept=False)
 |      Train a logistic regression model on the given data.
 |
 |      :param data:           The training data, an RDD of LabeledPoint.
 |      :param iterations:     The number of iterations (default: 100).
 |      :param initialWeights: The initial weights (default: None).
 |      :param regParam:       The regularizer parameter (default: 0.01).
 |      :param regType:        The type of regularizer used for training
 |                             our model.
 |                             :Allowed values:
 |                               - "l1" for using L1 regularization
 |                               - "l2" for using L2 regularization
 |                               - None for no regularization
 |                               (default: "l2")
 |      :param intercept:      Boolean parameter which indicates the use
 |                             or not of the augmented representation for
 |                             training data (i.e. whether bias features
 |                             are activated or not).
 |      :param corrections:    The number of corrections used in the LBFGS update (default: 10).
 |      :param tolerance:      The convergence tolerance of iterations for L-BFGS (default: 1e-4).
 |
 |      >>> data = [
 |      ...     LabeledPoint(0.0, [0.0, 1.0]),
 |      ...     LabeledPoint(1.0, [1.0, 0.0]),
 |      ... ]
 |      >>> lrm = LogisticRegressionWithLBFGS.train(sc.parallelize(data))
 |      >>> lrm.predict([1.0, 0.0])
 |      1
 |      >>> lrm.predict([0.0, 1.0])
 |      0
 |      >>> lrm.predict(sc.parallelize([[1.0, 0.0], [0.0, 1.0]])).collect()
 |      [1, 0]
```

Author: Davies Liu <davies@databricks.com>

Closes #3307 from davies/lbfgs and squashes the following commits:

34bd986 [Davies Liu] Merge branch 'master' of http://git-wip-us.apache.org/repos/asf/spark into lbfgs
5a945a6 [Davies Liu] address comments
941061b [Davies Liu] Merge branch 'master' of github.com:apache/spark into lbfgs
03e5543 [Davies Liu] add it to docs
ed2f9a8 [Davies Liu] add regType
76cd1b6 [Davies Liu] reorder arguments
4429a74 [Davies Liu] Update classification.py
9252783 [Davies Liu] python api for LogisticRegressionWithLBFGS
[SPARK-3721] [PySpark] broadcast objects larger than 2G

This patch will bring support for broadcasting objects larger than 2G.

pickle, zlib, FrameSerializer and Array[Byte] all can not support objects larger than 2G, so this patch introduce LargeObjectSerializer to serialize broadcast objects, the object will be serialized and compressed into small chunks, it also change the type of Broadcast[Array[Byte]]] into Broadcast[Array[Array[Byte]]]].

Testing for support broadcast objects larger than 2G is slow and memory hungry, so this is tested manually, could be added into SparkPerf.

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

Closes #2659 from davies/huge and squashes the following commits:

7b57a14 [Davies Liu] add more tests for broadcast
28acff9 [Davies Liu] Merge branch 'master' of github.com:apache/spark into huge
a2f6a02 [Davies Liu] bug fix
4820613 [Davies Liu] Merge branch 'master' of github.com:apache/spark into huge
5875c73 [Davies Liu] address comments
10a349b [Davies Liu] address comments
0c33016 [Davies Liu] Merge branch 'master' of github.com:apache/spark into huge
6182c8f [Davies Liu] Merge branch 'master' into huge
d94b68f [Davies Liu] Merge branch 'master' of github.com:apache/spark into huge
2514848 [Davies Liu] address comments
fda395b [Davies Liu] Merge branch 'master' of github.com:apache/spark into huge
1c2d928 [Davies Liu] fix scala style
091b107 [Davies Liu] broadcast objects larger than 2G
[SPARK-4433] fix a racing condition in zipWithIndex

Spark hangs with the following code:

~~~
sc.parallelize(1 to 10).zipWithIndex.repartition(10).count()
~~~

This is because ZippedWithIndexRDD triggers a job in getPartitions and it causes a deadlock in DAGScheduler.getPreferredLocs (synced). The fix is to compute `startIndices` during construction.

This should be applied to branch-1.0, branch-1.1, and branch-1.2.

pwendell

Author: Xiangrui Meng <meng@databricks.com>

Closes #3291 from mengxr/SPARK-4433 and squashes the following commits:

c284d9f [Xiangrui Meng] fix a racing condition in zipWithIndex
[SPARK-4327] [PySpark] Python API for RDD.randomSplit()

```
pyspark.RDD.randomSplit(self, weights, seed=None)
    Randomly splits this RDD with the provided weights.

    :param weights: weights for splits, will be normalized if they don't sum to 1
    :param seed: random seed
    :return: split RDDs in an list

    >>> rdd = sc.parallelize(range(10), 1)
    >>> rdd1, rdd2, rdd3 = rdd.randomSplit([0.4, 0.6, 1.0], 11)
    >>> rdd1.collect()
    [3, 6]
    >>> rdd2.collect()
    [0, 5, 7]
    >>> rdd3.collect()
    [1, 2, 4, 8, 9]
```

Author: Davies Liu <davies@databricks.com>

Closes #3193 from davies/randomSplit and squashes the following commits:

78bf997 [Davies Liu] fix tests, do not use numpy in randomSplit, no performance gain
f5fdf63 [Davies Liu] fix bug with int in weights
4dfa2cd [Davies Liu] refactor
f866bcf [Davies Liu] remove unneeded change
c7a2007 [Davies Liu] switch to python implementation
95a48ac [Davies Liu] Merge branch 'master' of github.com:apache/spark into randomSplit
0d9b256 [Davies Liu] refactor
1715ee3 [Davies Liu] address comments
41fce54 [Davies Liu] randomSplit()
[SPARK-4468][SQL] Fixes Parquet filter creation for inequality predicates with literals on the left hand side

For expressions like `10 < someVar`, we should create an `Operators.Gt` filter, but right now an `Operators.Lt` is created. This issue affects all inequality predicates with literals on the left hand side.

(This bug existed before #3317 and affects branch-1.1. #3338 was opened to backport this to branch-1.1.)

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Author: Cheng Lian <lian@databricks.com>

Closes #3334 from liancheng/fix-parquet-comp-filter and squashes the following commits:

0130897 [Cheng Lian] Fixes Parquet comparison filter generation
Bumping version to 1.3.0-SNAPSHOT.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #3277 from vanzin/version-1.3 and squashes the following commits:

7c3c396 [Marcelo Vanzin] Added temp repo to sbt build.
5f404ff [Marcelo Vanzin] Add another exclusion.
19457e7 [Marcelo Vanzin] Update old version to 1.2, add temporary 1.2 repo.
3c8d705 [Marcelo Vanzin] Workaround for MIMA checks.
e940810 [Marcelo Vanzin] Bumping version to 1.3.0-SNAPSHOT.
[SPARK-4441] Close Tachyon client when TachyonBlockManager is shutdown

Currently Tachyon client is not closed when TachyonBlockManager is shut down. which causes some resources in Tachyon not reclaimed

Author: Mingfei <mingfei.shi@intel.com>

Closes #3299 from shimingfei/closeClient and squashes the following commits:

0913fbd [Mingfei] close Tachyon client when TachyonBlockManager is shutdown
[Spark-4432]close InStream after the block is accessed

InStream is not closed after data is read from Tachyon. which makes the blocks in Tachyon locked after accessed.

Author: Mingfei <mingfei.shi@intel.com>

Closes #3290 from shimingfei/lockFix and squashes the following commits:

fffe345 [Mingfei] close InStream after the block is accessed
MAINTENANCE: Automated closing of pull requests.

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

Closes #2777 (close requested by 'ankurdave')
Closes #2947 (close requested by 'nchammas')
Closes #3141 (close requested by 'tdas')
Closes #2989 (close requested by 'pwendell')
SPARK-4455 Exclude dependency on hbase-annotations module

pwendell
Please take a look

Author: tedyu <yuzhihong@gmail.com>

Closes #3286 from tedyu/master and squashes the following commits:

e61e610 [tedyu] SPARK-4455 Exclude dependency on hbase-annotations module
7e3a57a [tedyu] Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/spark
2f28b08 [tedyu] Exclude dependency on hbase-annotations module
[SPARK-4467] fix elements read count for ExtrenalSorter

the elementsRead variable should be reset to 0 after each spilling

Author: Tianshuo Deng <tdeng@twitter.com>

Closes #3302 from tsdeng/fix_external_sorter_record_count and squashes the following commits:

7b56ca0 [Tianshuo Deng] fix method signature
782c7de [Tianshuo Deng] make elementsRead private, fix comment
bb7ff28 [Tianshuo Deng] update elemetsRead through addElementsRead method
74ca246 [Tianshuo Deng] fix elements read count
Merge branch 'master' of github.com:apache/spark into avoid-small-spills

Conflicts:
	core/src/main/scala/org/apache/spark/util/collection/Spillable.scala