SPARK-1428: MLlib should convert non-float64 NumPy arrays to float64 instead of complaining

Author: Sandeep <sandeep@techaddict.me>

Closes #356 from techaddict/1428 and squashes the following commits:

3bdf5f6 [Sandeep] SPARK-1428: MLlib should convert non-float64 NumPy arrays to float64 instead of complaining
Revert "SPARK-1433: Upgrade Mesos dependency to 0.17.0"

This reverts commit 12c077d5aa0b76a808a55db625c9677a52bd43f9.
Update tuning.md

http://stackoverflow.com/questions/9699071/what-is-the-javas-internal-represention-for-string-modified-utf-8-utf-16

Author: Andrew Ash <andrew@andrewash.com>

Closes #384 from ash211/patch-2 and squashes the following commits:

da1b0be [Andrew Ash] Update tuning.md
Remove Unnecessary Whitespace's

stack these together in a commit else they show up chunk by chunk in different commits.

Author: Sandeep <sandeep@techaddict.me>

Closes #380 from techaddict/white_space and squashes the following commits:

b58f294 [Sandeep] Remove Unnecessary Whitespace's
[SQL] Improve column pruning in the optimizer.

Author: Michael Armbrust <michael@databricks.com>

Closes #378 from marmbrus/columnPruning and squashes the following commits:

779da56 [Michael Armbrust] More consistent naming.
1a4e9ea [Michael Armbrust] More comments.
2f4e7b9 [Michael Armbrust] Improve column pruning in the optimizer.
SPARK-1202 - Add a "cancel" button in the UI for stages

Author: Sundeep Narravula <sundeepn@superduel.local>
Author: Sundeep Narravula <sundeepn@dhcpx-204-110.corp.yahoo.com>

Closes #246 from sundeepn/uikilljob and squashes the following commits:

5fdd0e2 [Sundeep Narravula] Fix test string
f6fdff1 [Sundeep Narravula] Format fix; reduced line size to less than 100 chars
d1daeb9 [Sundeep Narravula] Incorporating review comments.
8d97923 [Sundeep Narravula] Ability to kill jobs thru the UI. This behavior can be turned on be settings the following variable: spark.ui.killEnabled=true (default=false) Adding DAGScheduler event StageCancelled and corresponding handlers. Added cancellation reason to handlers.
Set spark.executor.uri from environment variable (needed by Mesos)

The Mesos backend uses this property when setting up a slave process.  It is similarly set in the Scala repl (org.apache.spark.repl.SparkILoop), but I couldn't find any analogous for pyspark.

Author: Ivan Wick <ivanwick+github@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Matei Zaharia <matei@databricks.com>

Closes #311 from ivanwick/master and squashes the following commits:

da0c3e4 [Ivan Wick] Set spark.executor.uri from environment variable (needed by Mesos)
Add Spark v0.9.1 to ec2 launch script and use it as the default

Mainly ported from branch-0.9.

Author: Harvey Feng <hyfeng224@gmail.com>

Closes #385 from harveyfeng/0.9.1-ec2 and squashes the following commits:

769ac2f [Harvey Feng] Add Spark v0.9.1 to ec2 launch script and use it as the default
SPARK-1202: Improvements to task killing in the UI.

1. Adds a separate endpoint for the killing logic that is outside of a page.
2. Narrows the scope of the killingEnabled tracking.
3. Some style improvements.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #386 from pwendell/kill-link and squashes the following commits:

8efe02b [Patrick Wendell] Improvements to task killing in the UI.
SPARK-1417: Spark on Yarn - spark UI link from resourcemanager is broken

Author: Thomas Graves <tgraves@apache.org>

Closes #344 from tgravescs/SPARK-1417 and squashes the following commits:

c450b5f [Thomas Graves] fix test
e1c1d7e [Thomas Graves] add missing $ to appUIAddress
e982ddb [Thomas Graves] use appUIHostPort in appUIAddress
0803ec2 [Thomas Graves] Review comment updates - remove extra newline, simplify assert in test
658a8ec [Thomas Graves] Add a appUIHostPort routine
0614208 [Thomas Graves] Fix test
2a6b1b7 [Thomas Graves] SPARK-1417: Spark on Yarn - spark UI link from resourcemanager is broken
Some clean up in build/docs

(a) Deleted an outdated line from the docs
(b) Removed a work around that is no longer necessary given the mesos version bump.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #382 from pwendell/maven-clean and squashes the following commits:

f0447fa [Patrick Wendell] Minor doc clean-up
[SPARK-1225, 1241] [MLLIB] Add AreaUnderCurve and BinaryClassificationMetrics

This PR implements a generic version of `AreaUnderCurve` using the `RDD.sliding` implementation from https://github.com/apache/spark/pull/136 . It also contains refactoring of https://github.com/apache/spark/pull/160 for binary classification evaluation.

Author: Xiangrui Meng <meng@databricks.com>

Closes #364 from mengxr/auc and squashes the following commits:

a05941d [Xiangrui Meng] replace TP/FP/TN/FN by their full names
3f42e98 [Xiangrui Meng] add (0, 0), (1, 1) to roc, and (0, 1) to pr
fb4b6d2 [Xiangrui Meng] rename Evaluator to Metrics and add more metrics
b1b7dab [Xiangrui Meng] fix code styles
9dc3518 [Xiangrui Meng] add tests for BinaryClassificationEvaluator
ca31da5 [Xiangrui Meng] remove PredictionAndResponse
3d71525 [Xiangrui Meng] move binary evalution classes to evaluation.binary
8f78958 [Xiangrui Meng] add PredictionAndResponse
dda82d5 [Xiangrui Meng] add confusion matrix
aa7e278 [Xiangrui Meng] add initial version of binary classification evaluator
221ebce [Xiangrui Meng] add a new test to sliding
a920865 [Xiangrui Meng] Merge branch 'sliding' into auc
a9b250a [Xiangrui Meng] move sliding to mllib
cab9a52 [Xiangrui Meng] use last for the last element
db6cb30 [Xiangrui Meng] remove unnecessary toSeq
9916202 [Xiangrui Meng] change RDD.sliding return type to RDD[Seq[T]]
284d991 [Xiangrui Meng] change SlidedRDD to SlidingRDD
c1c6c22 [Xiangrui Meng] add AreaUnderCurve
65461b2 [Xiangrui Meng] Merge branch 'sliding' into auc
5ee6001 [Xiangrui Meng] add TODO
d2a600d [Xiangrui Meng] add sliding to rdd
HOTFIX: Ignore python metastore files in RAT checks.

This was causing some errors with pull request tests.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #393 from pwendell/hotfix and squashes the following commits:

6201dd3 [Patrick Wendell] HOTFIX: Ignore python metastore files in RAT checks.
[FIX] make coalesce test deterministic in RDDSuite

Make coalesce test deterministic by setting pre-defined seeds. (Saw random failures in other PRs.)

Author: Xiangrui Meng <meng@databricks.com>

Closes #387 from mengxr/fix-random and squashes the following commits:

59bc16f [Xiangrui Meng] make coalesce test deterministic in RDDSuite
[WIP] [SPARK-1328] Add vector statistics

As with the new vector system in MLlib, we find that it is good to add some new APIs to precess the `RDD[Vector]`. Beside, the former implementation of `computeStat` is not stable which could loss precision, and has the possibility to cause `Nan` in scientific computing, just as said in the [SPARK-1328](https://spark-project.atlassian.net/browse/SPARK-1328).

APIs contain:

* rowMeans(): RDD[Double]
* rowNorm2(): RDD[Double]
* rowSDs(): RDD[Double]
* colMeans(): Vector
* colMeans(size: Int): Vector
* colNorm2(): Vector
* colNorm2(size: Int): Vector
* colSDs(): Vector
* colSDs(size: Int): Vector
* maxOption((Vector, Vector) => Boolean): Option[Vector]
* minOption((Vector, Vector) => Boolean): Option[Vector]
* rowShrink(): RDD[Vector]
* colShrink(): RDD[Vector]

This is working in process now, and some more APIs will add to `LabeledPoint`. Moreover, the implicit declaration will move from `MLUtils` to `MLContext` later.

Author: Xusen Yin <yinxusen@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #268 from yinxusen/vector-statistics and squashes the following commits:

d61363f [Xusen Yin] rebase to latest master
16ae684 [Xusen Yin] fix minor error and remove useless method
10cf5d3 [Xusen Yin] refine some return type
b064714 [Xusen Yin] remove computeStat in MLUtils
cbbefdb [Xiangrui Meng] update multivariate statistical summary interface and clean tests
4eaf28a [Xusen Yin] merge VectorRDDStatistics into RowMatrix
48ee053 [Xusen Yin] fix minor error
e624f93 [Xusen Yin] fix scala style error
1fba230 [Xusen Yin] merge while loop together
69e1f37 [Xusen Yin] remove lazy eval, and minor memory footprint
548e9de [Xusen Yin] minor revision
86522c4 [Xusen Yin] add comments on functions
dc77e38 [Xusen Yin] test sparse vector RDD
18cf072 [Xusen Yin] change def to lazy val to make sure that the computations in function be evaluated only once
f7a3ca2 [Xusen Yin] fix the corner case of maxmin
967d041 [Xusen Yin] full revision with Aggregator class
138300c [Xusen Yin] add new Aggregator class
1376ff4 [Xusen Yin] rename variables and adjust code
4a5c38d [Xusen Yin] add scala doc, refine code and comments
036b7a5 [Xusen Yin] fix the bug of Nan occur
f6e8e9a [Xusen Yin] add sparse vectors test
4cfbadf [Xusen Yin] fix bug of min max
4e4fbd1 [Xusen Yin] separate seqop and combop out as independent functions
a6d5a2e [Xusen Yin] rewrite for only computing non-zero elements
3980287 [Xusen Yin] rename variables
62a2c3e [Xusen Yin] use axpy and in-place if possible
9a75ebd [Xusen Yin] add case class to wrap return values
d816ac7 [Xusen Yin] remove useless APIs
c4651bb [Xusen Yin] remove row-wise APIs and refine code
1338ea1 [Xusen Yin] all-in-one version test passed
cc65810 [Xusen Yin] add parallel mean and variance
9af2e95 [Xusen Yin] refine the code style
ad6c82d [Xusen Yin] add shrink test
e09d5d2 [Xusen Yin] add scala docs and refine shrink method
8ef3377 [Xusen Yin] pass all tests
28cf060 [Xusen Yin] fix error of column means
54b19ab [Xusen Yin] add new API to shrink RDD[Vector]
8c6c0e1 [Xusen Yin] add basic statistics
Update WindowedDStream.scala

update the content of Exception when windowDuration is not multiple of parent.slideDuration

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #390 from baishuo/windowdstream and squashes the following commits:

533c968 [baishuo(白硕)] Update WindowedDStream.scala
SPARK-1057 (alternative) Remove fastutil

(This is for discussion at this point -- I'm not suggesting this should be committed.)

This is what removing fastutil looks like. Much of it is straightforward, like using `java.io` buffered stream classes, and Guava for murmurhash3.

Uses of the `FastByteArrayOutputStream` were a little trickier. In only one case though do I think the change to use `java.io` actually entails an extra array copy.

The rest is using `OpenHashMap` and `OpenHashSet`.  These are now written in terms of more scala-like operations.

`OpenHashMap` is where I made three non-trivial changes to make it work, and they need review:

- It is no longer private
- The key must be a `ClassTag`
- Unless a lot of other code changes, the key type can't enforce being a supertype of `Null`

It all works and tests pass, and I think there is reason to believe it's OK from a speed perspective.

But what about those last changes?

Author: Sean Owen <sowen@cloudera.com>

Closes #266 from srowen/SPARK-1057-alternate and squashes the following commits:

2601129 [Sean Owen] Fix Map return type error not previously caught
ec65502 [Sean Owen] Updates from matei's review
00bc81e [Sean Owen] Remove use of fastutil and replace with use of java.io, spark.util and Guava classes
[SPARK-1386] Web UI for Spark Streaming

When debugging Spark Streaming applications it is necessary to monitor certain metrics that are not shown in the Spark application UI. For example, what is average processing time of batches? What is the scheduling delay? Is the system able to process as fast as it is receiving data? How many records I am receiving through my receivers?

While the StreamingListener interface introduced in the 0.9 provided some of this information, it could only be accessed programmatically. A UI that shows information specific to the streaming applications is necessary for easier debugging. This PR introduces such a UI. It shows various statistics related to the streaming application. Here is a screenshot of the UI running on my local machine.

http://i.imgur.com/1ooDGhm.png

This UI is integrated into the Spark UI running at 4040.

Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Andrew Or <andrewor14@gmail.com>

Closes #290 from tdas/streaming-web-ui and squashes the following commits:

fc73ca5 [Tathagata Das] Merge pull request #9 from andrewor14/ui-refactor
642dd88 [Andrew Or] Merge SparkUISuite.scala into UISuite.scala
eb30517 [Andrew Or] Merge github.com:apache/spark into ui-refactor
f4f4cbe [Tathagata Das] More minor fixes.
34bb364 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
252c566 [Tathagata Das] Merge pull request #8 from andrewor14/ui-refactor
e038b4b [Tathagata Das] Addressed Patrick's comments.
125a054 [Andrew Or] Disable serving static resources with gzip
90feb8d [Andrew Or] Address Patrick's comments
89dae36 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
72fe256 [Tathagata Das] Merge pull request #6 from andrewor14/ui-refactor
2fc09c8 [Tathagata Das] Added binary check exclusions
aa396d4 [Andrew Or] Rename tabs and pages (No more IndexPage.scala)
f8e1053 [Tathagata Das] Added Spark and Streaming UI unit tests.
caa5e05 [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
585cd65 [Tathagata Das] Merge pull request #5 from andrewor14/ui-refactor
914b8ff [Tathagata Das] Moved utils functions to UIUtils.
548c98c [Andrew Or] Wide refactoring of WebUI, UITab, and UIPage (see commit message)
6de06b0 [Tathagata Das] Merge remote-tracking branch 'apache/master' into streaming-web-ui
ee6543f [Tathagata Das] Minor changes based on Andrew's comments.
fa760fe [Tathagata Das] Fixed long line.
1c0bcef [Tathagata Das] Refactored streaming UI into two files.
1af239b [Tathagata Das] Changed streaming UI to attach itself as a tab with the Spark UI.
827e81a [Tathagata Das] Merge branch 'streaming-web-ui' of github.com:tdas/spark into streaming-web-ui
168fe86 [Tathagata Das] Merge pull request #2 from andrewor14/ui-refactor
3e986f8 [Tathagata Das] Merge remote-tracking branch 'apache/master' into streaming-web-ui
c78c92d [Andrew Or] Remove outdated comment
8f7323b [Andrew Or] End of file new lines, indentation, and imports (minor)
0d61ee8 [Andrew Or] Merge branch 'streaming-web-ui' of github.com:tdas/spark into ui-refactor
9a48fa1 [Andrew Or] Allow adding tabs to SparkUI dynamically + add example
61358e3 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into streaming-web-ui
53be2c5 [Tathagata Das] Minor style updates.
ed25dfc [Andrew Or] Generalize SparkUI header to display tabs dynamically
a37ad4f [Andrew Or] Comments, imports and formatting (minor)
cd000b0 [Andrew Or] Merge github.com:apache/spark into ui-refactor
7d57444 [Andrew Or] Refactoring the UI interface to add flexibility
aef4dd5 [Tathagata Das] Added Apache licenses.
db27bad [Tathagata Das] Added last batch processing time to StreamingUI.
4d86e98 [Tathagata Das] Added basic stats to the StreamingUI and refactored the UI to a Page to make it easier to transition to using SparkUI later.
93f1c69 [Tathagata Das] Added network receiver information to the Streaming UI.
56cc7fb [Tathagata Das] First cut implementation of Streaming UI.
[Fix #204] Update out-dated comments

This PR is self-explanatory.

Author: Andrew Or <andrewor14@gmail.com>

Closes #381 from andrewor14/master and squashes the following commits:

3e8dde2 [Andrew Or] Fix comments for #204
[SPARK-1403] Move the class loader creation back to where it was in 0.9.0

[SPARK-1403] I investigated why spark 0.9.0 loads fine on mesos while spark 1.0.0 fails. What I found was that in SparkEnv.scala, while creating the SparkEnv object, the current thread's classloader is null. But in 0.9.0, at the same place, it is set to org.apache.spark.repl.ExecutorClassLoader . I saw that https://github.com/apache/spark/commit/7edbea41b43e0dc11a2de156be220db8b7952d01 moved it to it current place. I moved it back and saw that 1.0.0 started working fine on mesos.

I just created a minimal patch that allows me to run spark on mesos correctly. It seems like SecurityManager's creation needs to be taken into account for a correct fix. Also moving the creation of the serializer out of SparkEnv might be a part of the right solution. PTAL.

Author: Bharath Bhushan <manku.timma@outlook.com>

Closes #322 from manku-timma/spark-1403 and squashes the following commits:

606c2b9 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
ec8f870 [Bharath Bhushan] revert the logger change for java 6 compatibility as PR 334 is doing it
728beca [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
044027d [Bharath Bhushan] fix compile error
6f260a4 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
b3a053f [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
04b9662 [Bharath Bhushan] add missing line
4803c19 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
f3c9a14 [Bharath Bhushan] Merge remote-tracking branch 'upstream/master' into spark-1403
42d3d6a [Bharath Bhushan] used code fragment from @ueshin to fix the problem in a better way
89109d7 [Bharath Bhushan] move the class loader creation back to where it was in 0.9.0