Merge pull request #533 from andrewor14/master. Closes #533.

External spilling - generalize batching logic

The existing implementation consists of a hack for Kryo specifically and only works for LZF compression. Introducing an intermediate batch-level stream takes care of pre-fetching and other arbitrary behavior of higher level streams in a more general way.

Author: Andrew Or <andrewor14@gmail.com>

== Merge branch commits ==

commit 3ddeb7ef89a0af2b685fb5d071aa0f71c975cc82
Author: Andrew Or <andrewor14@gmail.com>
Date:   Wed Feb 5 12:09:32 2014 -0800

    Also privatize fields

commit 090544a87a0767effd0c835a53952f72fc8d24f0
Author: Andrew Or <andrewor14@gmail.com>
Date:   Wed Feb 5 10:58:23 2014 -0800

    Privatize methods

commit 13920c918efe22e66a1760b14beceb17a61fd8cc
Author: Andrew Or <andrewor14@gmail.com>
Date:   Tue Feb 4 16:34:15 2014 -0800

    Update docs

commit bd5a1d7350467ed3dc19c2de9b2c9f531f0e6aa3
Author: Andrew Or <andrewor14@gmail.com>
Date:   Tue Feb 4 13:44:24 2014 -0800

    Typo: phyiscal -> physical

commit 287ef44e593ad72f7434b759be3170d9ee2723d2
Author: Andrew Or <andrewor14@gmail.com>
Date:   Tue Feb 4 13:38:32 2014 -0800

    Avoid reading the entire batch into memory; also simplify streaming logic

    Additionally, address formatting comments.

commit 3df700509955f7074821e9aab1e74cb53c58b5a5
Merge: a531d2e 164489d
Author: Andrew Or <andrewor14@gmail.com>
Date:   Mon Feb 3 18:27:49 2014 -0800

    Merge branch 'master' of github.com:andrewor14/incubator-spark

commit a531d2e347acdcecf2d0ab72cd4f965ab5e145d8
Author: Andrew Or <andrewor14@gmail.com>
Date:   Mon Feb 3 18:18:04 2014 -0800

    Relax assumptions on compressors and serializers when batching

    This commit introduces an intermediate layer of an input stream on the batch level.
    This guards against interference from higher level streams (i.e. compression and
    deserialization streams), especially pre-fetching, without specifically targeting
    particular libraries (Kryo) and forcing shuffle spill compression to use LZF.

commit 164489d6f176bdecfa9dabec2dfce5504d1ee8af
Author: Andrew Or <andrewor14@gmail.com>
Date:   Mon Feb 3 18:18:04 2014 -0800

    Relax assumptions on compressors and serializers when batching

    This commit introduces an intermediate layer of an input stream on the batch level.
    This guards against interference from higher level streams (i.e. compression and
    deserialization streams), especially pre-fetching, without specifically targeting
    particular libraries (Kryo) and forcing shuffle spill compression to use LZF.
Merge pull request #506 from ash211/intersection. Closes #506.

SPARK-1062 Add rdd.intersection(otherRdd) method

Author: Andrew Ash <andrew@andrewash.com>

== Merge branch commits ==

commit 5d9982b171b9572649e9828f37ef0b43f0242912
Author: Andrew Ash <andrew@andrewash.com>
Date:   Thu Feb 6 18:11:45 2014 -0800

    Minor fixes

    - style: (v,null) => (v, null)
    - mention the shuffle in Javadoc

commit b86d02f14e810902719cef893cf6bfa18ff9acb0
Author: Andrew Ash <andrew@andrewash.com>
Date:   Sun Feb 2 13:17:40 2014 -0800

    Overload .intersection() for numPartitions and custom Partitioner

commit bcaa34911fcc6bb5bc5e4f9fe46d1df73cb71c09
Author: Andrew Ash <andrew@andrewash.com>
Date:   Sun Feb 2 13:05:40 2014 -0800

    Better naming of parameters in intersection's filter

commit b10a6af2d793ec6e9a06c798007fac3f6b860d89
Author: Andrew Ash <andrew@andrewash.com>
Date:   Sat Jan 25 23:06:26 2014 -0800

    Follow spark code format conventions of tab => 2 spaces

commit 965256e4304cca514bb36a1a36087711dec535ec
Author: Andrew Ash <andrew@andrewash.com>
Date:   Fri Jan 24 00:28:01 2014 -0800

    Add rdd.intersection(otherRdd) method
Merge pull request #552 from martinjaggi/master. Closes #552.

tex formulas in the documentation

using mathjax.
and spliting the MLlib documentation by techniques

see jira
https://spark-project.atlassian.net/browse/MLLIB-19
and
https://github.com/shivaram/spark/compare/mathjax

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

== Merge branch commits ==

commit 0364bfabbfc347f917216057a20c39b631842481
Author: Martin Jaggi <m.jaggi@gmail.com>
Date:   Fri Feb 7 03:19:38 2014 +0100

    minor polishing, as suggested by @pwendell

commit dcd2142c164b2f602bf472bb152ad55bae82d31a
Author: Martin Jaggi <m.jaggi@gmail.com>
Date:   Thu Feb 6 18:04:26 2014 +0100

    enabling inline latex formulas with $.$

    same mathjax configuration as used in math.stackexchange.com

    sample usage in the linear algebra (SVD) documentation

commit bbafafd2b497a5acaa03a140bb9de1fbb7d67ffa
Author: Martin Jaggi <m.jaggi@gmail.com>
Date:   Thu Feb 6 17:31:29 2014 +0100

    split MLlib documentation by techniques

    and linked from the main mllib-guide.md site

commit d1c5212b93c67436543c2d8ddbbf610fdf0a26eb
Author: Martin Jaggi <m.jaggi@gmail.com>
Date:   Thu Feb 6 16:59:43 2014 +0100

    enable mathjax formula in the .md documentation files

    code by @shivaram

commit d73948db0d9bc36296054e79fec5b1a657b4eab4
Author: Martin Jaggi <m.jaggi@gmail.com>
Date:   Thu Feb 6 16:57:23 2014 +0100

    minor update on how to compile the documentation
Merge pull request #454 from jey/atomic-sbt-download. Closes #454.

Make sbt download an atomic operation

Modifies the `sbt/sbt` script to gracefully recover when a previous invocation died in the middle of downloading the SBT jar.

Author: Jey Kottalam <jey@cs.berkeley.edu>

== Merge branch commits ==

commit 6c600eb434a2f3e7d70b67831aeebde9b5c0f43b
Author: Jey Kottalam <jey@cs.berkeley.edu>
Date:   Fri Jan 17 10:43:54 2014 -0800

    Make sbt download an atomic operation
Merge pull request #561 from Qiuzhuang/master. Closes #561.

Kill drivers in postStop() for Worker.

 JIRA SPARK-1068:https://spark-project.atlassian.net/browse/SPARK-1068

Author: Qiuzhuang Lian <Qiuzhuang.Lian@gmail.com>

== Merge branch commits ==

commit 9c19ce63637eee9369edd235979288d3d9fc9105
Author: Qiuzhuang Lian <Qiuzhuang.Lian@gmail.com>
Date:   Sat Feb 8 16:07:39 2014 +0800

    Kill drivers in postStop() for Worker.
     JIRA SPARK-1068:https://spark-project.atlassian.net/browse/SPARK-1068
Merge pull request #542 from markhamstra/versionBump. Closes #542.

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
Merge pull request #565 from pwendell/dev-scripts. Closes #565.

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.
Merge pull request #560 from pwendell/logging. Closes #560.

[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
Merge pull request #562 from jyotiska/master. Closes #562.

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
Merge pull request #556 from CodingCat/JettyUtil. Closes #556.

[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
Merge pull request #557 from ScrapCodes/style. Closes #557.

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
Merge pull request #569 from pwendell/merge-fixes.

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.
Merge pull request #551 from qqsun8819/json-protocol.

[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
Merge pull request #566 from martinjaggi/copy-MLlib-d.

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
Merge pull request #567 from ScrapCodes/style2.

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
Revert "Merge pull request #560 from pwendell/logging. Closes #560."

This reverts commit b6d40b782327188a25ded5b22790552121e5271f.
Merge pull request #579 from CrazyJvm/patch-1.

"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
Merge pull request #577 from hsaputra/fix_simple_streaming_doc.

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.
Merge pull request #571 from holdenk/switchtobinarysearch.

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
Merge pull request #583 from colorant/zookeeper.

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