Just a Scala version increment

Author: Mark Hamstra <markhamstra@gmail.com>

Closes #259 from markhamstra/scala-2.10.4 and squashes the following commits:

fbec547 [Mark Hamstra] [SPARK-1342] Bumped Scala version to 2.10.4

This doesn't yet support different databases in Hive (though you can probably workaround this by calling `USE <dbname>`).  However, given the time constraints for 1.0 I think its probably worth including this now and extending the functionality in the next release.

Author: Michael Armbrust <michael@databricks.com>

Closes #282 from marmbrus/cacheTables and squashes the following commits:

83785db [Michael Armbrust] Support for caching and uncaching tables in a SQLContext.

If a previously persisted RDD is re-used, its information disappears from the Storage page.

This is because the tasks associated with re-using the RDD do not report the RDD's blocks as updated (which is correct). On stage submit, however, we overwrite any existing information regarding that RDD with a fresh one, whether or not the information for the RDD already exists.

Author: Andrew Or <andrewor14@gmail.com>

Closes #281 from andrewor14/ui-storage-fix and squashes the following commits:

408585a [Andrew Or] Fix storage UI bug

Previous version was 7.6.8v20121106. The only difference between Jetty 7 and Jetty 8 is that the former uses Servlet API 2.5, while the latter uses Servlet API 3.0.

Author: Andrew Or <andrewor14@gmail.com>

Closes #280 from andrewor14/jetty-upgrade and squashes the following commits:

dd57104 [Andrew Or] Merge github.com:apache/spark into jetty-upgrade
e75fa85 [Andrew Or] Upgrade Jetty to 8.1.14v20131031

Author: Sandy Ryza <sandy@cloudera.com>

Closes #279 from sryza/sandy-spark-1376 and squashes the following commits:

d8aebfa [Sandy Ryza] SPARK-1376. In the yarn-cluster submitter, rename "args" option to "arg"

This test needs to be fixed. It currently depends on Thread.sleep() having exact-timing
semantics, which is not a valid assumption.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #277 from pwendell/rate-limited-stream and squashes the following commits:

6c0ff81 [Patrick Wendell] SPARK-1365: Fix RateLimitedOutputStream test

Before we were materializing everything in memory.  This also uses the projection interface so will be easier to plug in code gen (its ported from that branch).

@rxin @liancheng

Author: Michael Armbrust <michael@databricks.com>

Closes #250 from marmbrus/hashJoin and squashes the following commits:

1ad873e [Michael Armbrust] Change hasNext logic back to the correct version.
8e6f2a2 [Michael Armbrust] Review comments.
1e9fb63 [Michael Armbrust] style
bc0cb84 [Michael Armbrust] Rewrite join implementation to allow streaming of one relation.

1. Better error messages when required arguments are missing.
2. Support for unit testing cases where presented arguments are invalid.
3. Bug fix: Only use environment varaibles when they are set (otherwise will cause NPE).
4. A verbose mode to aid debugging.
5. Visibility of several variables is set to private.
6. Deprecation warning for existing scripts.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #271 from pwendell/spark-submit and squashes the following commits:

9146def [Patrick Wendell] SPARK-1352: Improve robustness of spark-submit script

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

Closes #261 from ScrapCodes/comment-style-check2 and squashes the following commits:

6cde61e [Prashant Sharma] comment style space before ending */ check.

Fix attribute unresolved when query with table name as a qualifier in SQLContext with SimplCatelog, details please see [SPARK-1354](https://issues.apache.org/jira/browse/SPARK-1354?jql=project%20%3D%20SPARK).

Author: jerryshao <saisai.shao@intel.com>

Closes #272 from jerryshao/qualifier-fix and squashes the following commits:

7950170 [jerryshao] Add tableName as a qualifier for SimpleCatelogy

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

Closes #262 from ScrapCodes/SPARK-1336/ReduceVerbosity and squashes the following commits:

87dfa54 [Prashant Sharma] Further reduction in noise and made pyspark tests to fail fast.
811170f [Prashant Sharma] Reducing the ouput of run-tests script.

@AndreSchumacher, please take a look.

https://spark-project.atlassian.net/browse/SPARK-1354

Author: Michael Armbrust <michael@databricks.com>

Closes #269 from marmbrus/parquetJoin and squashes the following commits:

4081e77 [Michael Armbrust] Create new instances of Parquet relation when multiple copies are in a single plan.

Author: Michael Armbrust <michael@databricks.com>

Closes #142 from marmbrus/kryoErrors and squashes the following commits:

9c72d1f [Michael Armbrust] Make the test more future proof.
78f5a42 [Michael Armbrust] Don't swallow all kryo errors, only those that indicate we are out of data.

Enrich the Spark Shell functionality to support the following options.

```
Usage: spark-shell [OPTIONS]

OPTIONS:
    -h  --help              : Print this help information.
    -c  --cores             : The maximum number of cores to be used by the Spark Shell.
    -em --executor-memory   : The memory used by each executor of the Spark Shell, the number
                              is followed by m for megabytes or g for gigabytes, e.g. "1g".
    -dm --driver-memory     : The memory used by the Spark Shell, the number is followed
                              by m for megabytes or g for gigabytes, e.g. "1g".
    -m  --master            : A full string that describes the Spark Master, defaults to "local"
                              e.g. "spark://localhost:7077".
    --log-conf              : Enables logging of the supplied SparkConf as INFO at start of the
                              Spark Context.

e.g.
    spark-shell -m spark://localhost:7077 -c 4 -dm 512m -em 2g
```

**Note**: this commit reflects the changes applied to _master_ based on [5d98cfc1].

[ticket: SPARK-1186] : Enrich the Spark Shell to support additional arguments.
                        https://spark-project.atlassian.net/browse/SPARK-1186

Author      : bernardo.gomezpalcio@gmail.com

Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>

Closes #116 from berngp/feature/enrich-spark-shell and squashes the following commits:

c5f455f [Bernardo Gomez Palacio] [SPARK-1186] : Enrich the Spark Shell to support additional arguments.

This PR includes:
1) Unify the unit test for expression evaluation
2) Add implementation of RLike & Like

Author: Cheng Hao <hao.cheng@intel.com>

Closes #224 from chenghao-intel/string_expression and squashes the following commits:

84f72e9 [Cheng Hao] fix bug in RLike/Like & Simplify the unit test
aeeb1d7 [Cheng Hao] Simplify the implementation/unit test of RLike/Like
319edb7 [Cheng Hao] change to spark code style
91cfd33 [Cheng Hao] add implementation for rlike/like
2c8929e [Cheng Hao] Update the unit test for expression evaluation

This is a starting version of the spark-app script for running compiled binaries against Spark.  It still needs tests and some polish.  The only testing I've done so far has been using it to launch jobs in yarn-standalone mode against a pseudo-distributed cluster.

This leaves out the changes required for launching python scripts.  I think it might be best to save those for another JIRA/PR (while keeping to the design so that they won't require backwards-incompatible changes).

Author: Sandy Ryza <sandy@cloudera.com>

Closes #86 from sryza/sandy-spark-1126 and squashes the following commits:

d428d85 [Sandy Ryza] Commenting, doc, and import fixes from Patrick's comments
e7315c6 [Sandy Ryza] Fix failing tests
34de899 [Sandy Ryza] Change --more-jars to --jars and fix docs
299ddca [Sandy Ryza] Fix scalastyle
a94c627 [Sandy Ryza] Add newline at end of SparkSubmit
04bc4e2 [Sandy Ryza] SPARK-1126. spark-submit script

...sql pom files

Author: Thomas Graves <tgraves@apache.org>

Closes #263 from tgravescs/SPARK-1345 and squashes the following commits:

b43a2a0 [Thomas Graves] SPARK-1345 adding missing dependency on avro for hadoop 0.23 to the new sql pom files

Author: Nick Lanham <nick@afternight.org>

Closes #264 from nicklan/make-distribution-fixes and squashes the following commits:

172b981 [Nick Lanham] fix path for jar, make sed actually work on OSX

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

Closes #124 from ScrapCodes/SPARK-1096/scalastyle-comment-check and squashes the following commits:

214135a [Prashant Sharma] Review feedback.
5eba88c [Prashant Sharma] Fixed style checks for ///+ comments.
e54b2f8 [Prashant Sharma] improved message, work around.
83e7144 [Prashant Sharma] removed dependency on scalastyle in plugin, since scalastyle sbt plugin already depends on the right version. Incase we update the plugin we will have to adjust our spark-style project to depend on right scalastyle version.
810a1d6 [Prashant Sharma] SPARK-1096, a space after comment style checker.
ba33193 [Prashant Sharma] scala style as a project

I don't have access to an OSX machine, so if someone could test this that would be great.

Author: Nick Lanham <nick@afternight.org>

Closes #258 from nicklan/osx-sed-fix and squashes the following commits:

a6f158f [Nick Lanham] Also make mktemp work on OSX
558fd6e [Nick Lanham] Make sed do -i '' on OSX

...r.

Constructor of `org.apache.spark.executor.Executor` should not set context class loader of current thread, which is backend Actor's thread.

Run the following code in local-mode REPL.

```
scala> case class Foo(i: Int)
scala> val ret = sc.parallelize((1 to 100).map(Foo), 10).collect
```

This causes errors as follows:

```
ERROR actor.OneForOneStrategy: [L$line5.$read$$iwC$$iwC$$iwC$$iwC$Foo;
java.lang.ArrayStoreException: [L$line5.$read$$iwC$$iwC$$iwC$$iwC$Foo;
     at scala.runtime.ScalaRunTime$.array_update(ScalaRunTime.scala:88)
     at org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:870)
     at org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:870)
     at org.apache.spark.scheduler.JobWaiter.taskSucceeded(JobWaiter.scala:56)
     at org.apache.spark.scheduler.DAGScheduler.handleTaskCompletion(DAGScheduler.scala:859)
     at org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:616)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$start$1$$anon$2$$anonfun$receive$1.applyOrElse(DAGScheduler.scala:207)
     at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
     at akka.actor.ActorCell.invoke(ActorCell.scala:456)
     at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
     at akka.dispatch.Mailbox.run(Mailbox.scala:219)
     at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
     at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
     at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
     at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
     at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
```

This is because the class loaders to deserialize result `Foo` instances might be different from backend Actor's, and the Actor's class loader should be the same as Driver's.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #15 from ueshin/wip/wrongcontextclassloader and squashes the following commits:

d79e8c0 [Takuya UESHIN] Change a parent class loader of ExecutorURLClassLoader.
c6c09b6 [Takuya UESHIN] Add a test to collect objects of class defined in repl.
43e0feb [Takuya UESHIN] Prevent ContextClassLoader of Actor from becoming ClassLoader of Executor.

Symmetric difference (xor) in particular is useful for computing some distance metrics (e.g. Hamming). Unit tests added.

Author: Petko Nikolov <nikolov@soundcloud.com>

Closes #172 from petko-nikolov/bitset-imprv and squashes the following commits:

451f28b [Petko Nikolov] fixed style mistakes
5beba18 [Petko Nikolov] rm outer loop in andNot test
0e61035 [Petko Nikolov] conform to spark style; rm redundant asserts; more unit tests added; use arraycopy instead of loop
d53cdb9 [Petko Nikolov] rm incidentally added space
4e1df43 [Petko Nikolov] adding xor and and-not to BitSet; unit tests added

I am observing build failures when the Maven build reaches tests in the new SQL components. (I'm on Java 7 / OSX 10.9). The failure is the usual complaint from scala, that it's out of permgen space, or that JIT out of code cache space.

I see that various build scripts increase these both for SBT. This change simply adds these settings to scalatest's arguments. Works for me and seems a bit more consistent.

(I also snuck in cures for new build warnings from new scaladoc. Felt too trivial for a new PR, although it's separate. Just something I also saw while examining the build output.)

Author: Sean Owen <sowen@cloudera.com>

Closes #253 from srowen/SPARK-1335 and squashes the following commits:

c0f2d31 [Sean Owen] Appease scalastyle with a newline at the end of the file
a02679c [Sean Owen] Fix scaladoc errors due to missing links, which are generating build warnings, from some recent doc changes. We apparently can't generate links outside the module.
b2c6a09 [Sean Owen] Add perm gen, code cache settings to scalatest, mirroring SBT settings elsewhere, which allows tests to complete in at least one environment where they are failing. (Also removed a duplicate -Xms setting elsewhere.)

remove the extra echo which prevents spark-class from working.  Note that I did not update the comment above it, which is also wrong because I'm not sure what it should do.

Should hive only be included if explicitly built with sbt hive/assembly or should sbt assembly build it?

Author: Thomas Graves <tgraves@apache.org>

Closes #241 from tgravescs/SPARK-1330 and squashes the following commits:

b10d708 [Thomas Graves] SPARK-1330 removed extra echo from comput_classpath.sh

This PR amortizes the cost of downloading all the jars and compiling core across more test cases.  In one anecdotal run this change takes the cumulative time down from ~80 minutes to ~40 minutes.

Author: Michael Armbrust <michael@databricks.com>

Closes #255 from marmbrus/travis and squashes the following commits:

506b22d [Michael Armbrust] Cut down the granularity of travis tests so we can amortize the cost of compilation.

GLM needs to check addIntercept for intercept and weights. The current implementation always uses the first weight as intercept. Added a test for training without adding intercept.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1327

Author: Xiangrui Meng <meng@databricks.com>

Closes #236 from mengxr/glm and squashes the following commits:

bcac1ac [Xiangrui Meng] add two tests to ensure {Lasso, Ridge}.setIntercept will throw an exceptions
a104072 [Xiangrui Meng] remove protected to be compatible with 0.9
0e57aa4 [Xiangrui Meng] update Lasso and RidgeRegression to parse the weights correctly from GLM mark createModel protected mark predictPoint protected
d7f629f [Xiangrui Meng] fix a bug in GLM when intercept is not used

This is just a slight variation on https://github.com/apache/spark/pull/234 and alternative suggestion for SPARK-1325. `scala-actors` is not necessary. `SparkBuild.scala` should be updated to reflect the direct dependency on `scala-reflect` and `scala-compiler`. And the `repl` build, which has the same dependencies, should also be consistent between Maven / SBT.

Author: Sean Owen <sowen@cloudera.com>
Author: witgo <witgo@qq.com>

Closes #240 from srowen/SPARK-1325 and squashes the following commits:

25bd7db [Sean Owen] Add necessary dependencies scala-reflect and scala-compiler to tools. Update repl dependencies, which are similar, to be consistent between Maven / SBT in this regard too.

Excluded those that are self-evident and the cases that are discussed in the mailing list.

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

Closes #168 from NirmalReddy/Spark-1095 and squashes the following commits:

ac54b29 [NirmalReddy] import misplaced
8c5ff3e [NirmalReddy] Changed syntax of unit returning methods
02d0778 [NirmalReddy] fixed explicit types in all the other packages
1c17773 [NirmalReddy] fixed explicit types in core package

/cc @aarondav and @andrewor14

Author: Patrick Wendell <pwendell@gmail.com>

Closes #231 from pwendell/ui-binding and squashes the following commits:

e8025f8 [Patrick Wendell] SPARK-1324: SparkUI Should Not Bind to SPARK_PUBLIC_DNS

Author: Michael Armbrust <michael@databricks.com>

Closes #243 from marmbrus/mapSer and squashes the following commits:

54045f7 [Michael Armbrust] Add a custom serializer for maps since they do not have a no-arg constructor.

Add golden answer for aforementioned test.

Also, fix golden test generation from sbt/sbt by setting the classpath correctly.

Author: Michael Armbrust <michael@databricks.com>

Closes #244 from marmbrus/partTest and squashes the following commits:

37a33c9 [Michael Armbrust] Un-ignore a test that is now passing, add golden answer for aforementioned test.  Fix golden test generation from sbt/sbt.

According to discussions in comments of PR #208, this PR unifies package definition format in Spark SQL.

Some broken links in ScalaDoc and typos detected along the way are also fixed.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #225 from liancheng/packageDefinition and squashes the following commits:

75c47b3 [Cheng Lian] Fixed file line length
4f87968 [Cheng Lian] Unified package definition format in Spark SQL

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

Closes #235 from ScrapCodes/SPARK-1322/top-rev-sort and squashes the following commits:

f316266 [Prashant Sharma] Minor change in comment.
58e58c6 [Prashant Sharma] SPARK-1322, top in pyspark should sort result in descending order.

SPARK-1321 Use Guava's top k implementation rather than our BoundedPriorityQueue based implementation

Also updated the documentation for top and takeOrdered.

On my simple test of sorting 100 million (Int, Int) tuples using Spark, Guava's top k implementation (in Ordering) is much faster than the BoundedPriorityQueue implementation for roughly sorted input (10 - 20X faster), and still faster for purely random input (2 - 5X).

Author: Reynold Xin <rxin@apache.org>

Closes #229 from rxin/takeOrdered and squashes the following commits:

0d11844 [Reynold Xin] Use Guava's top k implementation rather than our BoundedPriorityQueue based implementation. Also updated the documentation for top and takeOrdered.

This is not intended to replace Jenkins immediately, and Jenkins will remain the CI of reference for merging pull requests in the near term.  Long term, it is possible that Travis will give us better integration with github, so we are investigating its use.

Author: Michael Armbrust <michael@databricks.com>

Closes #230 from marmbrus/travis and squashes the following commits:

93f9a32 [Michael Armbrust] Add Apache license to .travis.yml
d7c0e78 [Michael Armbrust] Initial experimentation with Travis CI configuration

This is an update on https://github.com/apache/spark/pull/180, which changes the solution from blacklisting "Option.scala" to avoiding the Option code path while generating the call path.

Also includes a unit test to prevent this issue in the future, and some minor refactoring.

Thanks @witgo for reporting this issue and working on the initial solution!

Author: witgo <witgo@qq.com>
Author: Aaron Davidson <aaron@databricks.com>

Closes #222 from aarondav/180 and squashes the following commits:

f74aad1 [Aaron Davidson] Avoid Option while generating call site & add unit tests
d2b4980 [witgo] Modify the position of the filter
1bc22d7 [witgo] Fix Stage.name return "apply at Option.scala:120"

Move CPUS_PER_TASK to TaskSchedulerImpl as the value is a constant and use it in both Mesos and CoarseGrained scheduler backends.

Thanks @kayousterhout for the design discussion

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

Closes #219 from shivaram/multi-cpus and squashes the following commits:

5c7d685 [Shivaram Venkataraman] Don't pass availableCpus to TaskSetManager
260e4d5 [Shivaram Venkataraman] Add a check for non-zero CPUs in TaskSetManager
73fcf6f [Shivaram Venkataraman] Add documentation for spark.task.cpus
647bc45 [Shivaram Venkataraman] Fix scheduler to account for tasks using > 1 CPUs. Move CPUS_PER_TASK to TaskSchedulerImpl as the value is a constant and use it in both Mesos and CoarseGrained scheduler backends.

(This follows from a side point on SPARK-1133, in discussion of the PR: https://github.com/apache/spark/pull/164 )

Commons IO is barely used in the project, and can easily be replaced with equivalent calls to Guava or the existing Spark `Utils.scala` class.

Removing a dependency feels good, and this one in particular can get a little problematic since Hadoop uses it too.

Author: Sean Owen <sowen@cloudera.com>

Closes #226 from srowen/SPARK-1316 and squashes the following commits:

21efef3 [Sean Owen] Remove use of Commons IO

Author: Michael Armbrust <michael@databricks.com>

Closes #220 from marmbrus/moreTests and squashes the following commits:

223ec35 [Michael Armbrust] Blacklist machine specific test
9c966cc [Michael Armbrust] add more hive compatability tests to whitelist

Various spark scripts load spark-env.sh. This can cause growth of any variables that may be appended to (SPARK_CLASSPATH, SPARK_REPL_OPTS) and it makes the precedence order for options specified in spark-env.sh less clear.

One use-case for the latter is that we want to set options from the command-line of spark-shell, but these options will be overridden by subsequent loading of spark-env.sh. If we were to load the spark-env.sh first and then set our command-line options, we could guarantee correct precedence order.

Note that we use SPARK_CONF_DIR if available to support the sbin/ scripts, which always set this variable from sbin/spark-config.sh. Otherwise, we default to the ../conf/ as usual.

Author: Aaron Davidson <aaron@databricks.com>

Closes #184 from aarondav/idem and squashes the following commits:

e291f91 [Aaron Davidson] Use "private" variables in load-spark-env.sh
8da8360 [Aaron Davidson] Add .sh extension to load-spark-env.sh
93a2471 [Aaron Davidson] SPARK-1286: Make usage of spark-env.sh idempotent