SPARK-1102: Create a saveAsNewAPIHadoopDataset method

https://spark-project.atlassian.net/browse/SPARK-1102

Create a saveAsNewAPIHadoopDataset method

By @mateiz: "Right now RDDs can only be saved as files using the new Hadoop API, not as "datasets" with no filename and just a JobConf. See http://codeforhire.com/2014/02/18/using-spark-with-mongodb/ for an example of how you have to give a bogus filename. For the old Hadoop API, we have saveAsHadoopDataset."

Author: CodingCat <zhunansjtu@gmail.com>

Closes #12 from CodingCat/SPARK-1102 and squashes the following commits:

6ba0c83 [CodingCat] add test cases for saveAsHadoopDataSet (new&old API)
a8d11ba [CodingCat] style fix.........
95a6929 [CodingCat] code clean
7643c88 [CodingCat] change the parameter type back to Configuration
a8583ee [CodingCat] Create a saveAsNewAPIHadoopDataset method
Update copyright year in NOTICE to 2014

Author: Matei Zaharia <matei@databricks.com>

Closes #174 from mateiz/update-notice and squashes the following commits:

47fc1a5 [Matei Zaharia] Update copyright year in NOTICE to 2014
[SPARK-1260]: faster construction of features with intercept

The current implementation uses `Array(1.0, features: _*)` to construct a new array with intercept. This is not efficient for big arrays because `Array.apply` uses a for loop that iterates over the arguments. `Array.+:` is a better choice here.

Also, I don't see a reason to set initial weights to ones. So I set them to zeros.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1260

Author: Xiangrui Meng <meng@databricks.com>

Closes #161 from mengxr/sgd and squashes the following commits:

b5cfc53 [Xiangrui Meng] set default weights to zeros
a1439c2 [Xiangrui Meng] faster construction of features with intercept
[SPARK-1266] persist factors in implicit ALS

In implicit ALS computation, the user or product factor is used twice in each iteration. Caching can certainly help accelerate the computation. I saw the running time decreased by ~70% for implicit ALS on the movielens data.

I also made the following changes:

1. Change `YtYb` type from `Broadcast[Option[DoubleMatrix]]` to `Option[Broadcast[DoubleMatrix]]`, so we don't need to broadcast None in explicit computation.

2. Mark methods `computeYtY`, `unblockFactors`, `updateBlock`, and `updateFeatures private`. Users do not need those methods.

3. Materialize the final matrix factors before returning the model. It allows us to clean up other cached RDDs before returning the model. I do not have a better solution here, so I use `RDD.count()`.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1266

Author: Xiangrui Meng <meng@databricks.com>

Closes #165 from mengxr/als and squashes the following commits:

c9676a6 [Xiangrui Meng] add a comment about the last products.persist
d3a88aa [Xiangrui Meng] change implicitPrefs match to if ... else ...
63862d6 [Xiangrui Meng] persist factors in implicit ALS
Fix SPARK-1256: Master web UI and Worker web UI returns a 404 error

Author: witgo <witgo@qq.com>

Closes #150 from witgo/SPARK-1256 and squashes the following commits:

08044a2 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1256
c99b030 [witgo] Fix SPARK-1256
Bundle tachyon:  SPARK-1269

This should all work as expected with the current version of the tachyon tarball (0.4.1)

Author: Nick Lanham <nick@afternight.org>

Closes #137 from nicklan/bundle-tachyon and squashes the following commits:

2eee15b [Nick Lanham] Put back in exec, start tachyon first
738ba23 [Nick Lanham] Move tachyon out of sbin
f2f9bc6 [Nick Lanham] More checks for tachyon script
111e8e1 [Nick Lanham] Only try tachyon operations if tachyon script exists
0561574 [Nick Lanham] Copy over web resources so web interface can run
4dc9809 [Nick Lanham] Update to tachyon 0.4.1
0a1a20c [Nick Lanham] Add scripts using tachyon tarball
bugfix: Wrong "Duration" in "Active Stages" in stages page

If a stage which has completed once loss parts of data, it will be resubmitted. At this time, it appears that stage.completionTime > stage.submissionTime.

Author: shiyun.wxm <shiyun.wxm@taobao.com>

Closes #170 from BlackNiuza/duration_problem and squashes the following commits:

a86d261 [shiyun.wxm] tow space indent
c0d7b24 [shiyun.wxm] change the style
3b072e1 [shiyun.wxm] fix scala style
f20701e [shiyun.wxm] bugfix: "Duration" in "Active Stages" in stages page
SPARK-1203 fix saving to hdfs from yarn

Author: Thomas Graves <tgraves@apache.org>

Closes #173 from tgravescs/SPARK-1203 and squashes the following commits:

4fd5ded [Thomas Graves] adding import
964e3f7 [Thomas Graves] SPARK-1203 fix saving to hdfs from yarn
Bugfixes/improvements to scheduler

Move the PR#517 of apache-incubator-spark to the apache-spark

Author: Mridul Muralidharan <mridul@gmail.com>

Closes #159 from mridulm/master and squashes the following commits:

5ff59c2 [Mridul Muralidharan] Change property in suite also
167fad8 [Mridul Muralidharan] Address review comments
9bda70e [Mridul Muralidharan] Address review comments, akwats add to failedExecutors
270d841 [Mridul Muralidharan] Address review comments
fa5d9f1 [Mridul Muralidharan] Bugfixes/improvements to scheduler : PR #517
[SPARK-1132] Persisting Web UI through refactoring the SparkListener interface

The fleeting nature of the Spark Web UI has long been a problem reported by many users: The existing Web UI disappears as soon as the associated application terminates. This is because SparkUI is tightly coupled with SparkContext, and cannot be instantiated independently from it. To solve this, some state must be saved to persistent storage while the application is still running.

The approach taken by this PR involves persisting the UI state through SparkListenerEvents. This requires a major refactor of the SparkListener interface because existing events (1) maintain deep references, making de/serialization is difficult, and (2) do not encode all the information displayed on the UI. In this design, each existing listener for the UI (e.g. ExecutorsListener) maintains state that can be fully constructed from SparkListenerEvents. This state is then supplied to the parent UI (e.g. ExecutorsUI), which renders the associated page(s) on demand.

This PR introduces two important classes: the **EventLoggingListener**, and the **ReplayListenerBus**. In a live application, SparkUI registers an EventLoggingListener with the SparkContext in addition to the existing listeners. Over the course of the application, this listener serializes and logs all events to persisted storage. Then, after the application has finished, the SparkUI can be revived by replaying all the logged events to the existing UI listeners through the ReplayListenerBus.

This feature is currently integrated with the Master Web UI, which optionally rebuilds a SparkUI from event logs as soon as the corresponding application finishes.

More details can be found in the commit messages, comments within the code, and the [design doc](https://spark-project.atlassian.net/secure/attachment/12900/PersistingSparkWebUI.pdf). Comments and feedback are most welcome.

Author: Andrew Or <andrewor14@gmail.com>
Author: andrewor14 <andrewor14@gmail.com>

Closes #42 from andrewor14/master and squashes the following commits:

e5f14fa [Andrew Or] Merge github.com:apache/spark
a1c5cd9 [Andrew Or] Merge github.com:apache/spark
b8ba817 [Andrew Or] Remove UI from map when removing application in Master
83af656 [Andrew Or] Scraps and pieces (no functionality change)
222adcd [Andrew Or] Merge github.com:apache/spark
124429f [Andrew Or] Clarify LiveListenerBus behavior + Add tests for new behavior
f80bd31 [Andrew Or] Simplify static handler and BlockManager status update logic
9e14f97 [Andrew Or] Moved around functionality + renamed classes per Patrick
6740e49 [Andrew Or] Fix comment nits
650eb12 [Andrew Or] Add unit tests + Fix bugs found through tests
45fd84c [Andrew Or] Remove now deprecated test
c5c2c8f [Andrew Or] Remove list of (TaskInfo, TaskMetrics) from StageInfo
3456090 [Andrew Or] Address Patrick's comments
bf80e3d [Andrew Or] Imports, comments, and code formatting, once again (minor)
ac69ec8 [Andrew Or] Fix test fail
d801d11 [Andrew Or] Merge github.com:apache/spark (major)
dc93915 [Andrew Or] Imports, comments, and code formatting (minor)
77ba283 [Andrew Or] Address Kay's and Patrick's comments
b6eaea7 [Andrew Or] Treating SparkUI as a handler of MasterUI
d59da5f [Andrew Or] Avoid logging all the blocks on each executor
d6e3b4a [Andrew Or] Merge github.com:apache/spark
ca258a4 [Andrew Or] Master UI - add support for reading compressed event logs
176e68e [Andrew Or] Fix deprecated message for JavaSparkContext (minor)
4f69c4a [Andrew Or] Master UI - Rebuild SparkUI on application finish
291b2be [Andrew Or] Correct directory in log message "INFO: Logging events to <dir>"
1ba3407 [Andrew Or] Add a few configurable options to event logging
e375431 [Andrew Or] Add new constructors for SparkUI
18b256d [Andrew Or] Refactor out event logging and replaying logic from UI
bb4c503 [Andrew Or] Use a more mnemonic path for logging
aef411c [Andrew Or] Fix bug: storage status was not reflected on UI in the local case
03eda0b [Andrew Or] Fix HDFS flush behavior
36b3e5d [Andrew Or] Add HDFS support for event logging
cceff2b [andrewor14] Fix 100 char format fail
2fee310 [Andrew Or] Address Patrick's comments
2981d61 [Andrew Or] Move SparkListenerBus out of DAGScheduler + Clean up
5d2cec1 [Andrew Or] JobLogger: ID -> Id
0503e4b [Andrew Or] Fix PySpark tests + remove sc.clearFiles/clearJars
4d2fb0c [Andrew Or] Fix format fail
faa113e [Andrew Or] General clean up
d47585f [Andrew Or] Clean up FileLogger
472fd8a [Andrew Or] Fix a couple of tests
996d7a2 [Andrew Or] Reflect RDD unpersist on UI
7b2f811 [Andrew Or] Guard against TaskMetrics NPE + Fix tests
d1f4285 [Andrew Or] Migrate from lift-json to json4s-jackson
28019ca [Andrew Or] Merge github.com:apache/spark
bbe3501 [Andrew Or] Embed storage status and RDD info in Task events
6631c02 [Andrew Or] More formatting changes, this time mainly for Json DSL
70e7e7a [Andrew Or] Formatting changes
e9e1c6d [Andrew Or] Move all JSON de/serialization logic to JsonProtocol
d646df6 [Andrew Or] Completely decouple SparkUI from SparkContext
6814da0 [Andrew Or] Explicitly register each UI listener rather than through some magic
64d2ce1 [Andrew Or] Fix BlockManagerUI bug by introducing new event
4273013 [Andrew Or] Add a gateway SparkListener to simplify event logging
904c729 [Andrew Or] Fix another major bug
5ac906d [Andrew Or] Mostly naming, formatting, and code style changes
3fd584e [Andrew Or] Fix two major bugs
f3fc13b [Andrew Or] General refactor
4dfcd22 [Andrew Or] Merge git://git.apache.org/incubator-spark into persist-ui
b3976b0 [Andrew Or] Add functionality of reconstructing a persisted UI from SparkContext
8add36b [Andrew Or] JobProgressUI: Add JSON functionality
d859efc [Andrew Or] BlockManagerUI: Add JSON functionality
c4cd480 [Andrew Or] Also deserialize new events
8a2ebe6 [Andrew Or] Fix bugs for EnvironmentUI and ExecutorsUI
de8a1cd [Andrew Or] Serialize events both to and from JSON (rather than just to)
bf0b2e9 [Andrew Or] ExecutorUI: Serialize events rather than arbitary executor information
bb222b9 [Andrew Or] ExecutorUI: render completely from JSON
dcbd312 [Andrew Or] Add JSON Serializability for all SparkListenerEvent's
10ed49d [Andrew Or] Merge github.com:apache/incubator-spark into persist-ui
8e09306 [Andrew Or] Use JSON for ExecutorsUI
e3ae35f [Andrew Or] Merge github.com:apache/incubator-spark
3ddeb7e [Andrew Or] Also privatize fields
090544a [Andrew Or] Privatize methods
13920c9 [Andrew Or] Update docs
bd5a1d7 [Andrew Or] Typo: phyiscal -> physical
287ef44 [Andrew Or] Avoid reading the entire batch into memory; also simplify streaming logic
3df7005 [Andrew Or] Merge branch 'master' of github.com:andrewor14/incubator-spark
a531d2e [Andrew Or] Relax assumptions on compressors and serializers when batching
164489d [Andrew Or] Relax assumptions on compressors and serializers when batching
Added doctest for map function in rdd.py

Doctest added for map in rdd.py

Author: Jyotiska NK <jyotiska123@gmail.com>

Closes #177 from jyotiska/pyspark_rdd_map_doctest and squashes the following commits:

a38527f [Jyotiska NK] Added doctest for map function in rdd.py
SPARK-1099:Spark's local mode should probably respect spark.cores.max by default

This is for JIRA:https://spark-project.atlassian.net/browse/SPARK-1099
And this is what I do in this patch (also commented in the JIRA) @aarondav

 This is really a behavioral change, so I do this with great caution, and welcome any review advice:

1 I change the "MASTER=local" pattern of create LocalBackEnd . In the past, we passed 1 core to it . now it use a default cores
The reason here is that when someone use spark-shell to start local mode , Repl will use this "MASTER=local" pattern as default.
So if one also specify cores in the spark-shell command line, it will all go in here. So here pass 1 core is not suitalbe reponding to our change here.
2 In the LocalBackEnd , the "totalCores" variable are fetched following a different rule(in the past it just take in a userd passed cores, like 1 in "MASTER=local" pattern, 2 in "MASTER=local[2]" pattern"
rules:
a The second argument of LocalBackEnd 's constructor indicating cores have a default value which is Int.MaxValue. If user didn't pass it , its first default value is Int.MaxValue
b In getMaxCores, we first compare the former value to Int.MaxValue. if it's not equal, we think that user has passed their desired value, so just use it
c. If b is not satified, we then get cores from spark.cores.max, and we get real logical cores from Runtime. And if cores specified by spark.cores.max is bigger than logical cores, we use logical cores, otherwise we use spark.cores.max
3 In SparkContextSchedulerCreationSuite 's test("local") case, assertion is modified from 1 to logical cores, because "MASTER=local" pattern use default vaules.

Author: qqsun8819 <jin.oyj@alibaba-inc.com>

Closes #110 from qqsun8819/local-cores and squashes the following commits:

731aefa [qqsun8819] 1 LocalBackend not change 2 In SparkContext do some process to the cores and pass it to original LocalBackend constructor
78b9c60 [qqsun8819] 1 SparkContext MASTER=local pattern use default cores instead of 1 to construct LocalBackEnd , for use of spark-shell and cores specified in cmd line 2 some test case change from local to local[1]. 3 SparkContextSchedulerCreationSuite test spark.cores.max config in local pattern
6ae1ee8 [qqsun8819] Add a static function in LocalBackEnd to let it use spark.cores.max specified cores when no cores are passed to it
Revert "SPARK-1099:Spark's local mode should probably respect spark.cores.max by default"

This reverts commit 16789317a34c1974f7b35960f06a7b51d8e0f29f. Jenkins was not run for this PR.
Principal Component Analysis

# Principal Component Analysis

Computes the top k principal component coefficients for the m-by-n data matrix X. Rows of X correspond to observations and columns correspond to variables. The coefficient matrix is n-by-k. Each column of the coefficients return matrix contains coefficients for one principal component, and the columns are in descending order of component variance. This function centers the data and uses the singular value decomposition (SVD) algorithm.

## Testing
Tests included:
 * All principal components
 * Only top k principal components
 * Dense SVD tests
 * Dense/sparse matrix tests

The results are tested against MATLAB's pca: http://www.mathworks.com/help/stats/pca.html

## Documentation
Added to mllib-guide.md

## Example Usage
Added to examples directory under SparkPCA.scala

Author: Reza Zadeh <rizlar@gmail.com>

Closes #88 from rezazadeh/sparkpca and squashes the following commits:

e298700 [Reza Zadeh] reformat using IDE
3f23271 [Reza Zadeh] documentation and cleanup
b025ab2 [Reza Zadeh] documentation
e2667d4 [Reza Zadeh] assertMatrixApproximatelyEquals
3787bb4 [Reza Zadeh] stylin
c6ecc1f [Reza Zadeh] docs
aa2bbcb [Reza Zadeh] rename sparseToTallSkinnyDense
56975b0 [Reza Zadeh] docs
2df9bde [Reza Zadeh] docs update
8fb0015 [Reza Zadeh] rcond documentation
dbf7797 [Reza Zadeh] correct argument number
a9f1f62 [Reza Zadeh] documentation
4ce6caa [Reza Zadeh] style changes
9a56a02 [Reza Zadeh] use rcond relative to larget svalue
120f796 [Reza Zadeh] housekeeping
156ff78 [Reza Zadeh] string comprehension
2e1cf43 [Reza Zadeh] rename rcond
ea223a6 [Reza Zadeh] many style changes
f4002d7 [Reza Zadeh] more docs
bd53c7a [Reza Zadeh] proper accumulator
a8b5ecf [Reza Zadeh] Don't use for loops
0dc7980 [Reza Zadeh] filter zeros in sparse
6115610 [Reza Zadeh] More documentation
36d51e8 [Reza Zadeh] use JBLAS for UVS^-1 computation
bc4599f [Reza Zadeh] configurable rcond
86f7515 [Reza Zadeh] compute per parition, use while
09726b3 [Reza Zadeh] more style changes
4195e69 [Reza Zadeh] private, accumulator
17002be [Reza Zadeh] style changes
4ba7471 [Reza Zadeh] style change
f4982e6 [Reza Zadeh] Use dense matrix in example
2828d28 [Reza Zadeh] optimizations: normalize once, use inplace ops
72c9fa1 [Reza Zadeh] rename DenseMatrix to TallSkinnyDenseMatrix, lean
f807be9 [Reza Zadeh] fix typo
2d7ccde [Reza Zadeh] Array interface for dense svd and pca
cd290fa [Reza Zadeh] provide RDD[Array[Double]] support
398d123 [Reza Zadeh] style change
55abbfa [Reza Zadeh] docs fix
ef29644 [Reza Zadeh] bad chnage undo
472566e [Reza Zadeh] all files from old pr
555168f [Reza Zadeh] initial files