This lets us explicitly include Avro based on a profile for 0.23.X
builds. It makes me sad how convoluted it is to express this logic
in Maven. @tgraves and @sryza curious if this works for you.

I'm also considering just reverting to how it was before. The only
real problem was that Spark advertised a dependency on Avro
even though it only really depends transitively on Avro through
other deps.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #49 from pwendell/avro-build-fix and squashes the following commits:

8d6ee92 [Patrick Wendell] SPARK-1121: Add avro to yarn-alpha profile

(Ported from https://github.com/apache/incubator-spark/pull/650 )

This adds one more change though, to fix the scala version warning introduced by json4s recently.

Author: Sean Owen <sowen@cloudera.com>

Closes #32 from srowen/SPARK-1084.2 and squashes the following commits:

9240abd [Sean Owen] Avoid scala version conflict in scalap induced by json4s dependency
1561cec [Sean Owen] Remove "exclude *" dependencies that are causing Maven warnings, and that are apparently unneeded anyway

This test has been flaky. We can re-enable it after @tdas has a chance to look at it.

Author: Reynold Xin <rxin@apache.org>

Closes #54 from rxin/ratelimit and squashes the following commits:

1a12198 [Reynold Xin] Ignore RateLimitedOutputStreamSuite for now.

Previously, ZooKeeperPersistenceEngine would crash the whole Master process if
there was stored data from a prior Spark version. Now, we just delete these files.

Author: Aaron Davidson <aaron@databricks.com>

Closes #4 from aarondav/zookeeper2 and squashes the following commits:

fa8b40f [Aaron Davidson] SPARK-1137: Make ZK PersistenceEngine not crash for wrong serialVersionUID

This removes some loose ends not caught by the other (incubating -> tlp) patches. @markhamstra this updates the version as you mentioned earlier.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #51 from pwendell/tlp and squashes the following commits:

d553b1b [Patrick Wendell] Remove remaining references to incubation

This update contains a lot of bug fixes and some new perf improvements.
It is also binary compatible with the current 4.0.13.Final

For more information: http://netty.io/news/2014/02/25/4-0-17-Final.html

Author: Binh Nguyen <ngbinh@gmail.com>

Author: Binh Nguyen <ngbinh@gmail.com>

Closes #41 from ngbinh/master and squashes the following commits:

a9498f4 [Binh Nguyen] update io.netty to 4.0.17.Final

This allows developers to pass options (such as -D) to sbt.  I also modified the SparkBuild to ensure spark specific properties are propagated to forked test JVMs.

Author: Michael Armbrust <michael@databricks.com>

Closes #14 from marmbrus/sbtScripts and squashes the following commits:

c008b18 [Michael Armbrust] Merge the old sbt-launch-lib.bash with the new sbt-launcher jar downloading logic.

Ported from https://github.com/apache/incubator-spark/pull/633

In runMiniBatchSGD, the regVal (for 1st iter) should be initialized
as sum of sqrt of weights if it's L2 update; for L1 update, the same logic is followed.

It maybe not be important here for SGD since the updater doesn't take the loss
as parameter to find the new weights. But it will give us the correct history of loss.
However, for LBFGS optimizer we implemented, the correct loss with regVal is crucial to
find the new weights.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #40 from dbtsai/dbtsai-smallRegValFix and squashes the following commits:

77d47da [DB Tsai] In runMiniBatchSGD, the regVal (for 1st iter) should be initialized as sum of sqrt of weights if it's L2 update; for L1 update, the same logic is followed.

Thanks for Diana Carroll to report this issue (https://spark-project.atlassian.net/browse/SPARK-1100)

the current saveAsTextFile/SequenceFile will overwrite the output directory silently if the directory already exists, this behaviour is not desirable because

overwriting the data silently is not user-friendly

if the partition number of two writing operation changed, then the output directory will contain the results generated by two runnings

My fix includes:

add some new APIs with a flag for users to define whether he/she wants to overwrite the directory:
if the flag is set to true, then the output directory is deleted first and then written into the new data to prevent the output directory contains results from multiple rounds of running;

if the flag is set to false, Spark will throw an exception if the output directory already exists

changed JavaAPI part

default behaviour is overwriting

Two questions

should we deprecate the old APIs without such a flag?

I noticed that Spark Streaming also called these APIs, I thought we don't need to change the related part in streaming? @tdas

Author: CodingCat <zhunansjtu@gmail.com>

Closes #11 from CodingCat/SPARK-1100 and squashes the following commits:

6a4e3a3 [CodingCat] code clean
ef2d43f [CodingCat] add new test cases and code clean
ac63136 [CodingCat] checkOutputSpecs not applicable to FSOutputFormat
ec490e8 [CodingCat] prevent Spark from overwriting directory silently and leaving dirty directory

reopen for https://spark-project.atlassian.net/browse/SPARK-1150

Author: CodingCat <zhunansjtu@gmail.com>

Closes #52 from CodingCat/script_fixes and squashes the following commits:

fc05a71 [CodingCat] fix repo location in create script

This reverts commit 9aa09571.

https://spark-project.atlassian.net/browse/SPARK-1150

fix the repo location in create_release script

Author: Mark Grover <mark@apache.org>

Closes #48 from CodingCat/script_fixes and squashes the following commits:

01f4bf7 [Mark Grover] Fixing some nitpicks
d2244d4 [Mark Grover] SPARK-676: Abbreviation in SPARK_MEM but not in SPARK_WORKER_MEMORY

This commit randomizes the order of resource offers to avoid scheduling
all tasks on the same small set of machines.

This is a much simpler solution to SPARK-979 than #7.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #27 from kayousterhout/randomize and squashes the following commits:

435d817 [Kay Ousterhout] [SPARK-979] Randomize order of offers.

Author: Thomas Graves <tgraves@apache.org>

Closes #47 from tgravescs/fix_merge_script and squashes the following commits:

8209ab1 [Thomas Graves] Update dev merge script to use spark.git instead of incubator-spark

This reopens https://github.com/apache/incubator-spark/pull/538 against the new repo

Author: Sandy Ryza <sandy@cloudera.com>

Closes #29 from sryza/sandy-spark-1051 and squashes the following commits:

708ce49 [Sandy Ryza] SPARK-1051. doAs submitting user in YARN

...d long after

This reopens https://github.com/apache/incubator-spark/pull/648 against the new repo.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #28 from sryza/sandy-spark-1032 and squashes the following commits:

5953f50 [Sandy Ryza] SPARK-1032. If Yarn app fails before registering, app master stays around long after

This trait seems to have been created a while ago when there
were multiple implementations; now that there's just one, I think it
makes sense to merge it into the BlockFetcherIterator trait.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #39 from kayousterhout/remove_tracker and squashes the following commits:

8173939 [Kay Ousterhout] Remote BlockFetchTracker.

Author: Reynold Xin <rxin@apache.org>

Closes #2 from rxin/docs and squashes the following commits:

08bbd5f [Reynold Xin] Removed reference to incubation in Spark user docs.

That patch removed the Maven avro declaration but didn't remove the
actual dependency in core. /cc @scrapcodes

Author: Patrick Wendell <pwendell@gmail.com>

Closes #37 from pwendell/master and squashes the following commits:

0ef3008 [Patrick Wendell] [HOTFIX] Patching maven build after #6 (SPARK-1121).

(Ported from https://github.com/apache/incubator-spark/pull/637 )

Author: Sean Owen <sowen@cloudera.com>

Closes #31 from srowen/SPARK-1084.1 and squashes the following commits:

6c4a32c [Sean Owen] Suppress warnings about legitimate unchecked array creations, or change code to avoid it
f35b833 [Sean Owen] Fix two misc javadoc problems
254e8ef [Sean Owen] Fix one new style error introduced in scaladoc warning commit
5b2fce2 [Sean Owen] Fix scaladoc invocation warning, and enable javac warnings properly, with plugin config updates
007762b [Sean Owen] Remove dead scaladoc links
b8ff8cb [Sean Owen] Replace deprecated Ant <tasks> with <target>

For standalone HA mode, A status is useful to identify the current master, already in json format too.

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

Closes #24 from colorant/status and squashes the following commits:

df630b3 [Raymond Liu] Show Master status on UI page

https://spark-project.atlassian.net/browse/SPARK-1089

copied from JIRA, reported by @ash211

"Using the ADD_JARS environment variable with spark-shell used to add the jar to both the shell and the various workers. Now it only adds to the workers and importing a custom class in the shell is broken.
The workaround is to add custom jars to both ADD_JARS and SPARK_CLASSPATH.
We should fix ADD_JARS so it works properly again.
See various threads on the user list:
https://mail-archives.apache.org/mod_mbox/incubator-spark-user/201402.mbox/%3CCAJbo4neMLiTrnm1XbyqomWmp0m+EUcg4yE-txuRGSVKOb5KLeA@mail.gmail.com%3E
(another one that doesn't appear in the archives yet titled "ADD_JARS not working on 0.9")"

The reason of this bug is two-folds

in the current implementation of SparkILoop.scala, the settings.classpath is not set properly when the process() method is invoked

the weird behaviour of Scala 2.10, (I personally thought it is a bug)

if we simply set value of a PathSettings object (like settings.classpath), the isDefault is not set to true (this is a flag showing if the variable is modified), so it makes the PathResolver loads the default CLASSPATH environment variable value to calculated the path (see https://github.com/scala/scala/blob/2.10.x/src/compiler/scala/tools/util/PathResolver.scala#L215)

what we have to do is to manually make this flag set, (https://github.com/CodingCat/incubator-spark/blob/e3991d97ddc33e77645e4559b13bf78b9e68239a/repl/src/main/scala/org/apache/spark/repl/SparkILoop.scala#L884)

Author: CodingCat <zhunansjtu@gmail.com>

Closes #13 from CodingCat/SPARK-1089 and squashes the following commits:

8af81e7 [CodingCat] impose non-null settings
9aa2125 [CodingCat] code cleaning
ce36676 [CodingCat] code cleaning
e045582 [CodingCat] fix the regression problem on ADD_JARS in 0.9

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

Closes #6 from ScrapCodes/SPARK-1121/avro-dep-fix and squashes the following commits:

9b29e34 [Prashant Sharma] Review feedback on PR
46ed2ad [Prashant Sharma] SPARK-1121-Only add avro if the build is for Hadoop 0.23.X and SPARK_YARN is set

If the seed is zero, XORShift generates all zeros, which would create unexpected result.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1129

Author: Xiangrui Meng <meng@databricks.com>

Closes #645 from mengxr/xor and squashes the following commits:

1b086ab [Xiangrui Meng] use MurmurHash3 to set seed in XORShiftRandom
45c6f16 [Xiangrui Meng] minor style change
51f4050 [Xiangrui Meng] use a predefined seed when seed is zero in XORShiftRandom

ClusterScheduler was renamed to TaskSchedulerImpl; this commit
updates comments and tests accordingly.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #9 from kayousterhout/cluster_scheduler_death and squashes the following commits:

d6fd119 [Kay Ousterhout] Remove references to ClusterScheduler.

Author: Jyotiska NK <jyotiska123@gmail.com>

Closes #22 from jyotiska/pyspark_docs and squashes the following commits:

426136c [Jyotiska NK] Updated link for pyspark examples

PR [402](https://github.com/apache/incubator-spark/pull/402) from incubator repo.

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

Closes #19 from ScrapCodes/java-api-completeness and squashes the following commits:

11d0c2b [Prashant Sharma] Integer -> java.lang.Integer
737819a [Prashant Sharma] SPARK-1095 add explicit return types to APIs.
3ddc8bb [Prashant Sharma] Deprected *With functions in scala and added a few missing Java APIs

Author: Reynold Xin <rxin@apache.org>

Closes #1 from rxin/readme and squashes the following commits:

b3a77cd [Reynold Xin] Removed reference to incubation in README.md.

This surroungs the complete worker code in a try/except block so we catch any error that arrives. An example would be the depickling failing for some reason

@JoshRosen

Author: Bouke van der Bijl <boukevanderbijl@gmail.com>

Closes #644 from bouk/catch-depickling-errors and squashes the following commits:

f0f67cc [Bouke van der Bijl] Lol indentation
0e4d504 [Bouke van der Bijl] Surround the complete python worker with the try block

A recent PR that added Java vs Scala tabs for streaming also
inadvertently added some bad code to a document.ready handler, breaking
our other handler that manages scrolling to anchors correctly with the
floating top bar. As a result the section title ended up always being
hidden below the top bar. This removes the unnecessary JavaScript code.

Author: Matei Zaharia <matei@databricks.com>

Closes #3 from mateiz/doc-links and squashes the following commits:

e2a3488 [Matei Zaharia] SPARK-1135: fix broken anchors in docs

The aim of the Json4s project is to provide a common API for
Scala JSON libraries.  It is Apache-licensed, easier for
downstream distributions to package, and mostly API-compatible
with lift-json.  Furthermore, the Jackson-backed implementation
parses faster than lift-json on all but the smallest inputs.

Author: William Benton <willb@redhat.com>

Closes #582 from willb/json4s and squashes the following commits:

7ca62c4 [William Benton] Replace lift-json with json4s-jackson.

It looks this just requires taking out the checks.

I verified that, with the patch, I was able to run spark-shell through yarn without setting the environment variable.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #553 from sryza/sandy-spark-1053 and squashes the following commits:

b037676 [Sandy Ryza] SPARK-1053.  Don't require SPARK_YARN_APP_JAR

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

Closes #611 from colorant/curator and squashes the following commits:

7556aa1 [Raymond Liu] Address review comments
af92e1f [Raymond Liu] Fix coding style
964f3c2 [Raymond Liu] Ignore NodeExists exception
6df2966 [Raymond Liu] Rewrite zookeeper client code with curator

Hi guys,

I'm following Joey and Ankur's suggestions to add collectEdges and pickRandomVertex. I'm also adding the tests for collectEdges and refactoring one method getCycleGraph in GraphOpsSuite.scala.

Thank you,

semih

Author: Semih Salihoglu <semihsalihoglu@gmail.com>

Closes #580 from semihsalihoglu/GraphPrimitives2 and squashes the following commits:

937d3ec [Semih Salihoglu] - Fixed the scalastyle errors.
a69a152 [Semih Salihoglu] - Adding collectEdges and pickRandomVertices. - Adding tests for collectEdges. - Refactoring a getCycle utility function for GraphOpsSuite.scala.
41265a6 [Semih Salihoglu] - Adding collectEdges and pickRandomVertex. - Adding tests for collectEdges. - Recycling a getCycle utility test file.

Author: Andrew Ash <andrew@andrewash.com>

Closes #647 from ash211/doc-tuning and squashes the following commits:

b87de0a [Andrew Ash] Include reference to twitter/chill in tuning docs

[SPARK-1108] This allows us to use, e.g. HBase's TableOutputFormat with PairRDDFunctions.saveAsNewAPIHadoopFile, which otherwise would throw NullPointerException because the output table name hasn't been configured.

Note this bug also affects branch-0.9

Author: Bryn Keller <bryn.keller@intel.com>

Closes #638 from xoltar/SPARK-1108 and squashes the following commits:

7e94e7d [Bryn Keller] Import, comment, and format cleanup per code review
7cbcaa1 [Bryn Keller] For outputformats that are Configurable, call setConf before sending data to them. This allows us to use, e.g. HBase TableOutputFormat, which otherwise would throw NullPointerException because the output table name hasn't been configured

SPARK-1124: Fix infinite retries of reduce stage when a map stage failed

In the previous code, if you had a failing map stage and then tried to run reduce stages on it repeatedly, the first reduce stage would fail correctly, but the later ones would mistakenly believe that all map outputs are available and start failing infinitely with fetch failures from "null". See https://spark-project.atlassian.net/browse/SPARK-1124 for an example.

This PR also cleans up code style slightly where there was a variable named "s" and some weird map manipulation.

our stage instead of using our shuffleID.

In the previous code, if you had a failing map stage and then tried to
run reduce stages on it repeatedly, the first reduce stage would fail
correctly, but the later ones would mistakenly believe that all map
outputs are available and start failing infinitely with fetch failures
from "null".

Prompted by a recent thread on the mailing list, I tried and failed to see if Spark can be made independent of log4j. There are a few cases where control of the underlying logging is pretty useful, and to do that, you have to bind to a specific logger.

Instead I propose some tidying that leaves Spark's use of log4j, but gets rid of warnings and should still enable downstream users to switch. The idea is to pipe everything (except log4j) through SLF4J, and have Spark use SLF4J directly when logging, and where Spark needs to output info (REPL and tests), bind from SLF4J to log4j.

This leaves the same behavior in Spark. It means that downstream users who want to use something except log4j should:

- Exclude dependencies on log4j, slf4j-log4j12 from Spark
- Include dependency on log4j-over-slf4j
- Include dependency on another logger X, and another slf4j-X
- Recreate any log config that Spark does, that is needed, in the other logger's config

That sounds about right.

Here are the key changes:

- Include the jcl-over-slf4j shim everywhere by depending on it in core.
- Exclude dependencies on commons-logging from third-party libraries.
- Include the jul-to-slf4j shim everywhere by depending on it in core.
- Exclude slf4j-* dependencies from third-party libraries to prevent collision or warnings
- Added missing slf4j-log4j12 binding to GraphX, Bagel module tests

And minor/incidental changes:

- Update to SLF4J 1.7.5, which happily matches Hadoop 2’s version and is a recommended update over 1.7.2
- (Remove a duplicate HBase dependency declaration in SparkBuild.scala)
- (Remove a duplicate mockito dependency declaration that was causing warnings and bugging me)

Author: Sean Owen <sowen@cloudera.com>

Closes #570 from srowen/SPARK-1071 and squashes the following commits:

52eac9f [Sean Owen] Add slf4j-over-log4j12 dependency to core (non-test) and remove it from things that depend on core.
77a7fa9 [Sean Owen] SPARK-1071: Tidy logging strategy and use of log4j