Use numpy directly for matrix multiply.

Using matrix multiply to compute XtX and XtY yields a 5-20x speedup depending on problem size.

For example - the following takes 19s locally after this change vs. 5m21s before the change. (16x speedup).
bin/pyspark examples/src/main/python/als.py local[8] 1000 1000 50 10 10

Author: Evan Sparks <evan.sparks@gmail.com>

Closes #687 from etrain/patch-1 and squashes the following commits:

e094dbc [Evan Sparks] Touching only diaganols on update.
d1ab9b6 [Evan Sparks] Use numpy directly for matrix multiply.
[SQL] Improve SparkSQL Aggregates

* Add native min/max (was using hive before).
* Handle nulls correctly in Avg and Sum.

Author: Michael Armbrust <michael@databricks.com>

Closes #683 from marmbrus/aggFixes and squashes the following commits:

64fe30b [Michael Armbrust] Improve SparkSQL Aggregates * Add native min/max (was using hive before). * Handle nulls correctly in Avg and Sum.
SPARK-1565, update examples to be used with spark-submit script.

Commit for initial feedback, basically I am curious if we should prompt user for providing args esp. when its mandatory. And can we skip if they are not ?

Also few other things that did not work like
`bin/spark-submit examples/target/scala-2.10/spark-examples-1.0.0-SNAPSHOT-hadoop1.0.4.jar --class org.apache.spark.examples.SparkALS --arg 100 500 10 5 2`

Not all the args get passed properly, may be I have messed up something will try to sort it out hopefully.

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

Closes #552 from ScrapCodes/SPARK-1565/update-examples and squashes the following commits:

669dd23 [Prashant Sharma] Review comments
2727e70 [Prashant Sharma] SPARK-1565, update examples to be used with spark-submit script.
[SPARK-1745] Move interrupted flag from TaskContext constructor (minor)

It makes little sense to start a TaskContext that is interrupted. Indeed, I searched for all use cases of it and didn't find a single instance in which `interrupted` is true on construction.

This was inspired by reviewing #640, which adds an additional `@volatile var completed` that is similar. These are not the most urgent changes, but I wanted to push them out before I forget.

Author: Andrew Or <andrewor14@gmail.com>

Closes #675 from andrewor14/task-context and squashes the following commits:

9575e02 [Andrew Or] Add space
69455d1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into task-context
c471490 [Andrew Or] Oops, removed one flag too many. Adding it back.
85311f8 [Andrew Or] Move interrupted flag from TaskContext constructor
Fixing typo in als.py

XtY should be Xty.

Author: Evan Sparks <evan.sparks@gmail.com>

Closes #696 from etrain/patch-2 and squashes the following commits:

634cb8d [Evan Sparks] Fixing typo in als.py
[SPARK-1754] [SQL] Add missing arithmetic DSL operations.

Add missing arithmetic DSL operations: `unary_-`, `%`.

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

Closes #689 from ueshin/issues/SPARK-1754 and squashes the following commits:

a09ef69 [Takuya UESHIN] Add also missing ! (not) operation.
f73ae2c [Takuya UESHIN] Remove redundant tests.
5b3f087 [Takuya UESHIN] Add tests relating DSL operations.
e09c5b8 [Takuya UESHIN] Add missing arithmetic DSL operations.
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
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
[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