Patch to allow PySpark to use existing JVM and Gateway. Changes to PySpark implementation of SparkConf to take existing SparkConf JVM handle. Change to PySpark SparkContext to allow subclass specific context initialization.

Author: Ahir Reddy <ahirreddy@gmail.com>

Closes #622 from ahirreddy/pyspark-existing-jvm and squashes the following commits:

a86f457 [Ahir Reddy] Patch to allow PySpark to use existing JVM and Gateway. Changes to PySpark implementation of SparkConf to take existing SparkConf JVM handle. Change to PySpark SparkContext to allow subclass specific context initialization.

We changed the behavior in 0.9.0 from requiring that mergeCombiners be null when mapSideCombine was false to requiring that mergeCombiners *never* be null, for external sorting. This patch adds a require() to make this behavior change explicitly messaged rather than resulting in a NPE.

Author: Aaron Davidson <aaron@databricks.com>

Closes #623 from aarondav/master and squashes the following commits:

520b80c [Aaron Davidson] Super minor: Add require for mergeCombiners in combineByKey

I'm back with another less trivial suggestion for ALS:

In ALS for implicit feedback, input values are treated as weights on squared-errors in a loss function (or rather, the weight is a simple function of the input r, like c = 1 + alpha*r). The paper on which it's based assumes that the input is positive. Indeed, if the input is negative, it will create a negative weight on squared-errors, which causes things to go haywire. The optimization will try to make the error in a cell as large possible, and the result is silently bogus.

There is a good use case for negative input values though. Implicit feedback is usually collected from signals of positive interaction like a view or like or buy, but equally, can come from "not interested" signals. The natural representation is negative values.

The algorithm can be extended quite simply to provide a sound interpretation of these values: negative values should encourage the factorization to come up with 0 for cells with large negative input values, just as much as positive values encourage it to come up with 1.

The implications for the algorithm are simple:
* the confidence function value must not be negative, and so can become 1 + alpha*|r|
* the matrix P should have a value 1 where the input R is _positive_, not merely where it is non-zero. Actually, that's what the paper already says, it's just that we can't assume P = 1 when a cell in R is specified anymore, since it may be negative

This in turn entails just a few lines of code change in `ALS.scala`:
* `rs(i)` becomes `abs(rs(i))`
* When constructing `userXy(us(i))`, it's implicitly only adding where P is 1. That had been true for any us(i) that is iterated over, before, since these are exactly the ones for which P is 1. But now P is zero where rs(i) <= 0, and should not be added

I think it's a safe change because:
* It doesn't change any existing behavior (unless you're using negative values, in which case results are already borked)
* It's the simplest direct extension of the paper's algorithm
* (I've used it to good effect in production FWIW)

Tests included.

I tweaked minor things en route:
* `ALS.scala` javadoc writes "R = Xt*Y" when the paper and rest of code defines it as "R = X*Yt"
* RMSE in the ALS tests uses a confidence-weighted mean, but the denominator is not actually sum of weights

Excuse my Scala style; I'm sure it needs tweaks.

Author: Sean Owen <sowen@cloudera.com>

Closes #500 from srowen/ALSNegativeImplicitInput and squashes the following commits:

cf902a9 [Sean Owen] Support negative implicit input in ALS
953be1c [Sean Owen] Make weighted RMSE in ALS test actually weighted; adjust comment about R = X*Yt

url of "Collaborative Filtering for Implicit Feedback Datasets"  is invalid now. A new url is provided. http://research.yahoo.com/files/HuKorenVolinsky-ICDM08.pdf

Author: Chen Chao <crazyjvm@gmail.com>

Closes #619 from CrazyJvm/master and squashes the following commits:

a0b54e4 [Chen Chao] change url to IEEE
9e0e9f0 [Chen Chao] correct spell mistale
fcfab5d [Chen Chao] wrap line to to fit within 100 chars
590d56e [Chen Chao] url error

https://spark-project.atlassian.net/browse/SPARK-1105

fix site scala version error

Author: CodingCat <zhunansjtu@gmail.com>

Closes #618 from CodingCat/doc_version and squashes the following commits:

39bb8aa [CodingCat] more fixes
65bedb0 [CodingCat] fix site scala version error in doc

I launched an EC2 cluster without providing a key name and an identity file. The error showed up after two minutes. It would be good to check those options before launch, given the fact that EC2 billing rounds up to hours.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1106

Author: Xiangrui Meng <meng@databricks.com>

Closes #617 from mengxr/ec2 and squashes the following commits:

2dfb316 [Xiangrui Meng] check key name and identity file before launch a cluster

This reverts commit d99773d5.

https://spark-project.atlassian.net/browse/SPARK-1105

fix site scala version error

Author: CodingCat <zhunansjtu@gmail.com>

Closes #616 from CodingCat/doc_version and squashes the following commits:

eafd99a [CodingCat] fix site scala version error in doc

Optimized imports and arranged according to scala style guide @
https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide#SparkCodeStyleGuide-Imports

Author: NirmalReddy <nirmal.reddy@imaginea.com>
Author: NirmalReddy <nirmal_reddy2000@yahoo.com>

Closes #613 from NirmalReddy/opt-imports and squashes the following commits:

578b4f5 [NirmalReddy] imported java.lang.Double as JDouble
a2cbcc5 [NirmalReddy] addressed the comments
776d664 [NirmalReddy] Optimized imports in core

Our usage of fake ClassTags in this manner is probably not healthy, but I'm not sure if there's a better solution available, so I just cleaned up and documented the current one.

Author: Aaron Davidson <aaron@databricks.com>

Closes #604 from aarondav/master and squashes the following commits:

b398e89 [Aaron Davidson] SPARK-1098: Minor cleanup of ClassTag usage in Java API

https://spark-project.atlassian.net/browse/SPARK-1090

spark-shell should print help information about parameters and should allow user to configure exe memory
there is no document about hot to set --cores/-c in spark-shell

and also

users should be able to set executor memory through command line options

In this PR I also check the format of the options passed by the user

Author: CodingCat <zhunansjtu@gmail.com>

Closes #599 from CodingCat/spark_shell_improve and squashes the following commits:

de5aa38 [CodingCat] add parameter to set driver memory
915cbf8 [CodingCat] improvement on spark_shell (help information, configure memory)

Author: Andrew Or <andrewor14@gmail.com>

Closes #536 from andrewor14/streaming-typos and squashes the following commits:

a05faa6 [Andrew Or] Fix broken link and wording
bc2e4bc [Andrew Or] Merge github.com:apache/incubator-spark into streaming-typos
d5515b4 [Andrew Or] TD's comments
767ef12 [Andrew Or] Fix broken links
8f4c731 [Andrew Or] Fix typos in programming guide

Author: Andrew Ash <andrew@andrewash.com>

Closes #608 from ash211/patch-7 and squashes the following commits:

bd85f2a [Andrew Ash] Worker registration logging fix

Author: Punya Biswal <pbiswal@palantir.com>

Closes #600 from punya/subtractByKey-java and squashes the following commits:

e961913 [Punya Biswal] Hide implicit ClassTags from Java API
c5d317b [Punya Biswal] Add subtractByKey to the JavaPairRDD wrapper

Author: Bijay Bisht <bijay.bisht@gmail.com>

Closes #568 from bijaybisht/SPARK-1052 and squashes the following commits:

da70395 [Bijay Bisht] fix for https://spark-project.atlassian.net/browse/SPARK-1052 - comments incorporated
fdb1d94 [Bijay Bisht] fix for https://spark-project.atlassian.net/browse/SPARK-1052



(cherry picked from commit e797c1ab)
Signed-off-by: Aaron Davidson <aaron@databricks.com>

https://spark-project.atlassian.net/browse/SPARK-1092?jql=project%20%3D%20SPARK

print warning information if user set SPARK_MEM to regulate memory usage of executors

----
OUTDATED:

Currently, users will usually set SPARK_MEM to control the memory usage of driver programs, (in spark-class)
91 JAVA_OPTS="$OUR_JAVA_OPTS"
92 JAVA_OPTS="$JAVA_OPTS -Djava.library.path=$SPARK_LIBRARY_PATH"
93 JAVA_OPTS="$JAVA_OPTS -Xms$SPARK_MEM -Xmx$SPARK_MEM"
if they didn't set spark.executor.memory, the value in this environment variable will also affect the memory usage of executors, because the following lines in SparkContext
privatespark val executorMemory = conf.getOption("spark.executor.memory")
.orElse(Option(System.getenv("SPARK_MEM")))
.map(Utils.memoryStringToMb)
.getOrElse(512)
also
since SPARK_MEM has been (proposed to) deprecated in SPARK-929 (https://spark-project.atlassian.net/browse/SPARK-929) and the corresponding PR (https://github.com/apache/incubator-spark/pull/104)
we should remove this line

Author: CodingCat <zhunansjtu@gmail.com>

Closes #602 from CodingCat/clean_spark_mem and squashes the following commits:

302bb28 [CodingCat] print warning information if user use SPARK_MEM to regulate executor memory usage

Author: Andrew Ash <andrew@andrewash.com>

Closes #601 from ash211/typo and squashes the following commits:

9cd43ac [Andrew Ash] Change docs references to metrics.properties, not metrics.conf
3813ff1 [Andrew Ash] Typo: mulitcast -> multicast
873bd2f [Andrew Ash] Typo: Standlone -> Standalone

Update spark_ec2 to use 0.9.0 by default

Backports change from branch-0.9

Author: Shivaram Venkataraman <shivaram@eecs.berkeley.edu>

Closes #598 and squashes the following commits:

f6d3ed0 [Shivaram Venkataraman] Update spark_ec2 to use 0.9.0 by default Backports change from branch-0.9

The number of disks for the c3 instance types taken from here: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/InstanceStorage.html#StorageOnInstanceTypes



Author: Christian Lundgren <christian.lundgren@gameanalytics.com>

Closes #595 from chrisavl/branch-0.9 and squashes the following commits:

c8af5f9 [Christian Lundgren] Add c3 instance types to Spark EC2
(cherry picked from commit 19b4bb2b)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>

#522 got messed after i rewrote the branch hadoop_jar_name. So created a new one.

Author: Bijay Bisht <bijay.bisht@gmail.com>

Closes #584 from bijaybisht/hadoop_jar_name_on_0.9.0 and squashes the following commits:

1b6fb3c [Bijay Bisht] Ported hadoopClient jar for < 1.0.1 fix
(cherry picked from commit 8093de1b)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>

The first line of a git commit message is the line that's used with many git
tools as the most concise textual description of that message.  The most
common use that I see is in the short log, which is a one line per commit
log of recent commits.

This commit moves the line

  Merge pull request #%s from %s.

Lower into the message to reserve the first line of the resulting commit for
the much more important pull request title.

http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html

Author: Andrew Ash <andrew@andrewash.com>

Closes #574 from ash211/gh-pr-merge-title and squashes the following commits:

b240823 [Andrew Ash] More merge_message improvements
d2986db [Andrew Ash] Keep GitHub pull request title as commit summary

SPARK-1088: Create a script for running tests so we can have version specific testing on Jenkins.

@pwendell

Author: Reynold Xin <rxin@apache.org>

Closes #592 and squashes the following commits:

be02359 [Reynold Xin] SPARK-1088: Create a script for running tests so we can have version specific testing on Jenkins.

SPARK-1076: [Fix #578] add @transient to some vals

I'll try to be more careful next time.

Author: Xiangrui Meng <meng@databricks.com>

Closes #591 and squashes the following commits:

2b4f044 [Xiangrui Meng] add @transient to prev in ZippedWithIndexRDD add @transient to seed in PartitionwiseSampledRDD

SPARK-1076: Convert Int to Long to avoid overflow

Patch for PR #578.

Author: Xiangrui Meng <meng@databricks.com>

Closes #589 and squashes the following commits:

98c435e [Xiangrui Meng] cast Int to Long to avoid Int overflow

SPARK-1076: zipWithIndex and zipWithUniqueId to RDD

Assign ranks to an ordered or unordered data set is a common operation. This could be done by first counting records in each partition and then assign ranks in parallel.

The purpose of assigning ranks to an unordered set is usually to get a unique id for each item, e.g., to map feature names to feature indices. In such cases, the assignment could be done without counting records, saving one spark job.

https://spark-project.atlassian.net/browse/SPARK-1076

== update ==
Because assigning ranks is very similar to Scala's zipWithIndex, I changed the method name to zipWithIndex and put the index in the value field.

Author: Xiangrui Meng <meng@databricks.com>

Closes #578 and squashes the following commits:

52a05e1 [Xiangrui Meng] changed assignRanks to zipWithIndex changed assignUniqueIds to zipWithUniqueId minor updates
756881c [Xiangrui Meng] simplified RankedRDD by implementing assignUniqueIds separately moved couting iterator size to Utils do not count items in the last partition and skip counting if there is only one partition
630868c [Xiangrui Meng] newline
21b434b [Xiangrui Meng] add assignRanks and assignUniqueIds to RDD

Minor fix for ZooKeeperPersistenceEngine to use configured working dir

Author: Raymond Liu <raymond.liu@intel.com>

Closes #583 and squashes the following commits:

91b0609 [Raymond Liu] Minor fix for ZooKeeperPersistenceEngine to use configured working dir

SPARK-1072 Use binary search when needed in RangePartioner

Author: Holden Karau <holden@pigscanfly.ca>

Closes #571 and squashes the following commits:

f31a2e1 [Holden Karau] Swith to using CollectionsUtils in Partitioner
4c7a0c3 [Holden Karau] Add CollectionsUtil as suggested by aarondav
7099962 [Holden Karau] Add the binary search to only init once
1bef01d [Holden Karau] CR feedback
a21e097 [Holden Karau] Use binary search if we have more than 1000 elements inside of RangePartitioner

SPARK-1075 Fix doc in the Spark Streaming custom receiver closing bracket in the class constructor

The closing parentheses in the constructor in the first code block example is reversed:
diff --git a/docs/streaming-custom-receivers.md b/docs/streaming-custom-receivers.md
index 4e27d65..3fb540c 100644
— a/docs/streaming-custom-receivers.md
+++ b/docs/streaming-custom-receivers.md
@@ -14,7 +14,7 @@ This starts with implementing NetworkReceiver(api/streaming/index.html#org.apa
The following is a simple socket text-stream receiver.
{% highlight scala %}
class SocketTextStreamReceiver(host: String, port: Int(
+ class SocketTextStreamReceiver(host: String, port: Int)
extends NetworkReceiverString
{
protected lazy val blocksGenerator: BlockGenerator =

Author: Henry Saputra <henry@platfora.com>

Closes #577 and squashes the following commits:

6508341 [Henry Saputra] SPARK-1075 Fix doc in the Spark Streaming custom receiver.

"in the source DStream" rather than "int the source DStream"

"flatMap is a one-to-many DStream operation that creates a new DStream by generating multiple new records from each record int the source DStream."

Author: Chen Chao <crazyjvm@gmail.com>

Closes #579 and squashes the following commits:

4abcae3 [Chen Chao] in the source DStream

This reverts commit b6d40b78.

SPARK-1058, Fix Style Errors and Add Scala Style to Spark Build. Pt 2

Continuation of PR #557

With this all scala style errors are fixed across the code base !!

The reason for creating a separate PR was to not interrupt an already reviewed and ready to merge PR. Hope this gets reviewed soon and merged too.

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

Closes #567 and squashes the following commits:

3b1ec30 [Prashant Sharma] scala style fixes

new MLlib documentation for optimization, regression and classification

new documentation with tex formulas, hopefully improving usability and reproducibility of the offered MLlib methods.
also did some minor changes in the code for consistency. scala tests pass.

this is the rebased branch, i deleted the old PR

jira:
https://spark-project.atlassian.net/browse/MLLIB-19

Author: Martin Jaggi <m.jaggi@gmail.com>

Closes #566 and squashes the following commits:

5f0f31e [Martin Jaggi] line wrap at 100 chars
4e094fb [Martin Jaggi] better description of GradientDescent
1d6965d [Martin Jaggi] remove broken url
ea569c3 [Martin Jaggi] telling what updater actually does
964732b [Martin Jaggi] lambda R() in documentation
a6c6228 [Martin Jaggi] better comments in SGD code for regression
b32224a [Martin Jaggi] new optimization documentation
d5dfef7 [Martin Jaggi] new classification and regression documentation
b07ead6 [Martin Jaggi] correct scaling for MSE loss
ba6158c [Martin Jaggi] use d for the number of features
bab2ed2 [Martin Jaggi] renaming LeastSquaresGradient

[SPARK-1038] Add more fields in JsonProtocol and add tests that verify the JSON itself

This is a PR for SPARK-1038. Two major changes:
1 add some fields to JsonProtocol which is new and important to standalone-related data structures
2 Use Diff in liftweb.json to verity the stringified Json output for detecting someone mod type T to Option[T]

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

Closes #551 and squashes the following commits:

fdf0b4e [qqsun8819] [SPARK-1038] 1. Change code style for more readable according to rxin review 2. change submitdate hard-coded string to a date object toString for more complexiblity
095a26f [qqsun8819] [SPARK-1038] mod according to  review of pwendel, use hard-coded json string for json data validation. Each test use its own json string
0524e41 [qqsun8819] Merge remote-tracking branch 'upstream/master' into json-protocol
d203d5c [qqsun8819] [SPARK-1038] Add more fields in JsonProtocol and add tests that verify the JSON itself

Fixes bug where merges won't close associated pull request.

Previously we added "Closes #XX" in the title. Github will sometimes
linbreak the title in a way that causes this to not work. This patch
instead adds the line in the body.

This also makes the commit format more concise for merge commits.
We might consider just dropping those in the future.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #569 and squashes the following commits:

732eba1 [Patrick Wendell] Fixes bug where merges won't close associated pull request.

SPARK-1058, Fix Style Errors and Add Scala Style to Spark Build.

Author: Patrick Wendell <pwendell@gmail.com>
Author: Prashant Sharma <scrapcodes@gmail.com>

== Merge branch commits ==

commit 1a8bd1c059b842cb95cc246aaea74a79fec684f4
Author: Prashant Sharma <scrapcodes@gmail.com>
Date:   Sun Feb 9 17:39:07 2014 +0530

    scala style fixes

commit f91709887a8e0b608c5c2b282db19b8a44d53a43
Author: Patrick Wendell <pwendell@gmail.com>
Date:   Fri Jan 24 11:22:53 2014 -0800

    Adding scalastyle snapshot

[SPARK-1060] startJettyServer should explicitly use IP information

https://spark-project.atlassian.net/browse/SPARK-1060

In the current implementation, the webserver in Master/Worker is started with

val (srv, bPort) = JettyUtils.startJettyServer("0.0.0.0", port, handlers)

inside startJettyServer:

val server = new Server(currentPort) //here, the Server will take "0.0.0.0" as the hostname, i.e. will always bind to the IP address of the first NIC

this can cause wrong IP binding, e.g. if the host has two NICs, N1 and N2, the user specify the SPARK_LOCAL_IP as the N2's IP address, however, when starting the web server, for the reason stated above, it will always bind to the N1's address

Author: CodingCat <zhunansjtu@gmail.com>

== Merge branch commits ==

commit 6c6d9a8ccc9ec4590678a3b34cb03df19092029d
Author: CodingCat <zhunansjtu@gmail.com>
Date:   Thu Feb 6 14:53:34 2014 -0500

    startJettyServer should explicitly use IP information

Added example Python code for sort

I added an example Python code for sort. Right now, PySpark has limited examples for new people willing to use the project. This example code sorts integers stored in a file. I was able to sort 5 million, 10 million and 25 million integers with this code.

Author: jyotiska <jyotiska123@gmail.com>

== Merge branch commits ==

commit 8ad8faf6c8e02ae1cd68565d98524edf165f54df
Author: jyotiska <jyotiska123@gmail.com>
Date:   Sun Feb 9 11:00:41 2014 +0530

    Added comments in code on collect() method

commit 6f98f1e313f4472a7c2207d36c4f0fbcebc95a8c
Author: jyotiska <jyotiska123@gmail.com>
Date:   Sat Feb 8 13:12:37 2014 +0530

    Updated python example code sort.py

commit 945e39a5d68daa7e5bab0d96cbd35d7c4b04eafb
Author: jyotiska <jyotiska123@gmail.com>
Date:   Sat Feb 8 12:59:09 2014 +0530

    Added example python code for sort

[WIP] SPARK-1067: Default log4j initialization causes errors for those not using log4j

To fix this - we add a check when initializing log4j.

Author: Patrick Wendell <pwendell@gmail.com>

== Merge branch commits ==

commit ffdce513877f64b6eed6d36138c3e0003d392889
Author: Patrick Wendell <pwendell@gmail.com>
Date:   Fri Feb 7 15:22:29 2014 -0800

    Logging fix

SPARK-1066: Add developer scripts to repository.

These are some developer scripts I've been maintaining in a separate public repo. This patch adds them to the Spark repository so they can evolve here and are clearly accessible to all committers.

I may do some small additional clean-up in this PR, but wanted to put them here in case others want to review. There are a few types of scripts here:

1. A tool to merge pull requests.
2. A script for packaging releases.
3. A script for auditing release candidates.

Author: Patrick Wendell <pwendell@gmail.com>

== Merge branch commits ==

commit 5d5d331d01f6fd59c2eb830f652955119b012173
Author: Patrick Wendell <pwendell@gmail.com>
Date:   Sat Feb 8 22:11:47 2014 -0800

    SPARK-1066: Add developer scripts to repository.

Version number to 1.0.0-SNAPSHOT

Since 0.9.0-incubating is done and out the door, we shouldn't be building 0.9.0-incubating-SNAPSHOT anymore.

@pwendell

Author: Mark Hamstra <markhamstra@gmail.com>

== Merge branch commits ==

commit 1b00a8a7c1a7f251b4bb3774b84b9e64758eaa71
Author: Mark Hamstra <markhamstra@gmail.com>
Date:   Wed Feb 5 09:30:32 2014 -0800

    Version number to 1.0.0-SNAPSHOT