MLlib documentation fix

Fixed the documentation for that `loadLibSVMData` is changed to `loadLibSVMFile`.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #703 from dbtsai/dbtsai-docfix and squashes the following commits:

71dd508 [DB Tsai] loadLibSVMData is changed to loadLibSVMFile
[SPARK-1157][MLlib] Bug fix: lossHistory should exclude rejection steps, and remove miniBatch

Getting the lossHistory from Breeze's API which already excludes the rejection steps in line search. Also, remove the miniBatch in LBFGS since those quasi-Newton methods approximate the inverse of Hessian. It doesn't make sense if the gradients are computed from a varying objective.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #582 from dbtsai/dbtsai-lbfgs-bug and squashes the following commits:

9cc6cf9 [DB Tsai] Removed the miniBatch in LBFGS.
1ba6a33 [DB Tsai] Formatting the code.
d72c679 [DB Tsai] Using Breeze's states to get the loss.
Bug fix of sparse vector conversion

Fixed a small bug caused by the inconsistency of index/data array size and vector length.

Author: Funes <tianshaocun@gmail.com>
Author: funes <tianshaocun@gmail.com>

Closes #661 from funes/bugfix and squashes the following commits:

edb2b9d [funes] remove unused import
75dced3 [Funes] update test case
d129a66 [Funes] Add test for sparse breeze by vector builder
64e7198 [Funes] Copy data only when necessary
b85806c [Funes] Bug fix of sparse vector conversion
Include the sbin/spark-config.sh in spark-executor

This is needed because broadcast values are broken on pyspark on Mesos, it tries to import pyspark but can't, as the PYTHONPATH is not set due to changes in ff5be9a4

https://issues.apache.org/jira/browse/SPARK-1725

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

Closes #651 from bouk/include-spark-config-in-mesos-executor and squashes the following commits:

b2f1295 [Bouke van der Bijl] Inline PYTHONPATH in spark-executor
eedbbcc [Bouke van der Bijl] Include the sbin/spark-config.sh in spark-executor
[SPARK-1755] Respect SparkSubmit --name on YARN

Right now, SparkSubmit ignores the `--name` flag for both yarn-client and yarn-cluster. This is a bug.

In client mode, SparkSubmit treats `--name` as a [cluster config](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala#L170) and does not propagate this to SparkContext.

In cluster mode, SparkSubmit passes this flag to `org.apache.spark.deploy.yarn.Client`, which only uses it for the [YARN ResourceManager](https://github.com/apache/spark/blob/master/yarn/stable/src/main/scala/org/apache/spark/deploy/yarn/Client.scala#L80), but does not propagate this to SparkContext.

This PR ensures that `spark.app.name` is always set if SparkSubmit receives the `--name` flag, which is what the usage promises. This makes it possible for applications to start a SparkContext with an empty conf `val sc = new SparkContext(new SparkConf)`, and inherit the app name from SparkSubmit.

Tested both modes on a YARN cluster.

Author: Andrew Or <andrewor14@gmail.com>

Closes #699 from andrewor14/yarn-app-name and squashes the following commits:

98f6a79 [Andrew Or] Fix tests
dea932f [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-app-name
c86d9ca [Andrew Or] Respect SparkSubmit --name on YARN
[SPARK-1631] Correctly set the Yarn app name when launching the AM.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #539 from vanzin/yarn-app-name and squashes the following commits:

7d1ca4f [Marcelo Vanzin] [SPARK-1631] Correctly set the Yarn app name when launching the AM.
SPARK-1565 (Addendum): Replace `run-example` with `spark-submit`.

Gives a nicely formatted message to the user when `run-example` is run to
tell them to use `spark-submit`.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #704 from pwendell/examples and squashes the following commits:

1996ee8 [Patrick Wendell] Feedback form Andrew
3eb7803 [Patrick Wendell] Suggestions from TD
2474668 [Patrick Wendell] SPARK-1565 (Addendum): Replace `run-example` with `spark-submit`.
SPARK-1775: Unneeded lock in ShuffleMapTask.deserializeInfo

This was used in the past to have a cache of deserialized ShuffleMapTasks, but that's been removed, so there's no need for a lock. It slows down Spark when task descriptions are large, e.g. due to large lineage graphs or local variables.

Author: Sandeep <sandeep@techaddict.me>

Closes #707 from techaddict/SPARK-1775 and squashes the following commits:

18d8ebf [Sandeep] SPARK-1775: Unneeded lock in ShuffleMapTask.deserializeInfo This was used in the past to have a cache of deserialized ShuffleMapTasks, but that's been removed, so there's no need for a lock. It slows down Spark when task descriptions are large, e.g. due to large lineage graphs or local variables.
MINOR: Removing dead code.

Meant to do this when patching up the last merge.
Converted bang to ask to avoid scary warning when a block is removed

Removing a block through the blockmanager gave a scary warning messages in the driver.
```
2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true
2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true
2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true
```

This is because the [BlockManagerSlaveActor](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/storage/BlockManagerSlaveActor.scala#L44) would send back an acknowledgement ("true"). But the BlockManagerMasterActor would have sent the RemoveBlock message as a send, not as ask(), so would reject the receiver "true" as a unknown message.
@pwendell

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #708 from tdas/bm-fix and squashes the following commits:

ed4ef15 [Tathagata Das] Converted bang to ask to avoid scary warning when a block is removed.
[SPARK-1760]: fix building spark with maven documentation

Author: witgo <witgo@qq.com>

Closes #712 from witgo/building-with-maven and squashes the following commits:

215523b [witgo] fix building spark with maven documentation
Merge branch 'master' of git://github.com/apache/spark into wip/build-refactoring
SPARK-1770: Revert accidental(?) fix

Looks like this change was accidentally committed here: https://github.com/apache/spark/commit/06b15baab25951d124bbe6b64906f4139e037deb
but the change does not show up in the PR itself (#704).

Other than not intending to go in with that PR, this also broke the test JavaAPISuite.repartition.

Author: Aaron Davidson <aaron@databricks.com>

Closes #716 from aarondav/shufflerand and squashes the following commits:

b1cf70b [Aaron Davidson] SPARK-1770: Revert accidental(?) fix
SPARK-1686: keep schedule() calling in the main thread

https://issues.apache.org/jira/browse/SPARK-1686

moved from original JIRA (by @markhamstra):

In deploy.master.Master, the completeRecovery method is the last thing to be called when a standalone Master is recovering from failure. It is responsible for resetting some state, relaunching drivers, and eventually resuming its scheduling duties.

There are currently four places in Master.scala where completeRecovery is called. Three of them are from within the actor's receive method, and aren't problems. The last starts from within receive when the ElectedLeader message is received, but the actual completeRecovery() call is made from the Akka scheduler. That means that it will execute on a different scheduler thread, and Master itself will end up running (i.e., schedule() ) from that Akka scheduler thread.

In this PR, I added a new master message TriggerSchedule to trigger the "local" call of schedule() in the scheduler thread

Author: CodingCat <zhunansjtu@gmail.com>

Closes #639 from CodingCat/SPARK-1686 and squashes the following commits:

81bb4ca [CodingCat] rename variable
69e0a2a [CodingCat] style fix
36a2ac0 [CodingCat] address Aaron's comments
ec9b7bb [CodingCat] address the comments
02b37ca [CodingCat] keep schedule() calling in the main thread
Merge branch 'master' of git://github.com/apache/spark into wip/build-refactoring
[SPARK-1644] The org.datanucleus:* should not be packaged into spark-assembly-*.jar

Author: witgo <witgo@qq.com>

Closes #688 from witgo/SPARK-1644 and squashes the following commits:

56ad6ac [witgo] review commit
87c03e4 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1644
6ffa7e4 [witgo] review commit
a597414 [witgo] The org.datanucleus:* should not be packaged into spark-assembly-*.jar
[SQL] Upgrade parquet library.

I think we are hitting this issue in some perf tests: https://github.com/Parquet/parquet-mr/commit/6aed5288fd4a1398063a5a219b2ae4a9f71b02cf

Credit to @aarondav !

Author: Michael Armbrust <michael@databricks.com>

Closes #684 from marmbrus/upgradeParquet and squashes the following commits:

e10a619 [Michael Armbrust] Upgrade parquet library.
[SPARK-1778] [SQL] Add 'limit' transformation to SchemaRDD.

Add `limit` transformation to `SchemaRDD`.

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

Closes #711 from ueshin/issues/SPARK-1778 and squashes the following commits:

33169df [Takuya UESHIN] Add 'limit' transformation to SchemaRDD.
SPARK-1708. Add a ClassTag on Serializer and things that depend on it

This pull request contains a rebased patch from @heathermiller (https://github.com/heathermiller/spark/pull/1) to add ClassTags on Serializer and types that depend on it (Broadcast and AccumulableCollection). Putting these in the public API signatures now will allow us to use Scala Pickling for serialization down the line without breaking binary compatibility.

One question remaining is whether we also want them on Accumulator -- Accumulator is passed as part of a bigger Task or TaskResult object via the closure serializer so it doesn't seem super useful to add the ClassTag there. Broadcast and AccumulableCollection in contrast were being serialized directly.

CC @rxin, @pwendell, @heathermiller

Author: Matei Zaharia <matei@databricks.com>

Closes #700 from mateiz/spark-1708 and squashes the following commits:

1a3d8b0 [Matei Zaharia] Use fake ClassTag in Java
3b449ed [Matei Zaharia] test fix
2209a27 [Matei Zaharia] Code style fixes
9d48830 [Matei Zaharia] Add a ClassTag on Serializer and things that depend on it
fix broken in link in python docs

Author: Andy Konwinski <andykonwinski@gmail.com>

Closes #650 from andyk/python-docs-link-fix and squashes the following commits:

a1f9d51 [Andy Konwinski] fix broken in link in python docs