[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
Add Python includes to path before depickling broadcast values

This fixes https://issues.apache.org/jira/browse/SPARK-1731 by adding the Python includes to the PYTHONPATH before depickling the broadcast values

@airhorns

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

Closes #656 from bouk/python-includes-before-broadcast and squashes the following commits:

7b0dfe4 [Bouke van der Bijl] Add Python includes to path before depickling broadcast values
[SPARK-1690] Tolerating empty elements when saving Python RDD to text files

Tolerate empty strings in PythonRDD

Author: Kan Zhang <kzhang@apache.org>

Closes #644 from kanzhang/SPARK-1690 and squashes the following commits:

c62ad33 [Kan Zhang] Adding Python doctest
473ec4b [Kan Zhang] [SPARK-1690] Tolerating empty elements when saving Python RDD to text files
Unify GraphImpl RDDs + other graph load optimizations

This PR makes the following changes, primarily in e4fbd329aef85fe2c38b0167255d2a712893d683:

1. *Unify RDDs to avoid zipPartitions.* A graph used to be four RDDs: vertices, edges, routing table, and triplet view. This commit merges them down to two: vertices (with routing table), and edges (with replicated vertices).

2. *Avoid duplicate shuffle in graph building.* We used to do two shuffles when building a graph: one to extract routing information from the edges and move it to the vertices, and another to find nonexistent vertices referred to by edges. With this commit, the latter is done as a side effect of the former.

3. *Avoid no-op shuffle when joins are fully eliminated.* This is a side effect of unifying the edges and the triplet view.

4. *Join elimination for mapTriplets.*

5. *Ship only the needed vertex attributes when upgrading the triplet view.* If the triplet view already contains source attributes, and we now need both attributes, only ship destination attributes rather than re-shipping both. This is done in `ReplicatedVertexView#upgrade`.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #497 from ankurdave/unify-rdds and squashes the following commits:

332ab43 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds
4933e2e [Ankur Dave] Exclude RoutingTable from binary compatibility check
5ba8789 [Ankur Dave] Add GraphX upgrade guide from Spark 0.9.1
13ac845 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds
a04765c [Ankur Dave] Remove unnecessary toOps call
57202e8 [Ankur Dave] Replace case with pair parameter
75af062 [Ankur Dave] Add explicit return types
04d3ae5 [Ankur Dave] Convert implicit parameter to context bound
c88b269 [Ankur Dave] Revert upgradeIterator to if-in-a-loop
0d3584c [Ankur Dave] EdgePartition.size should be val
2a928b2 [Ankur Dave] Set locality wait
10b3596 [Ankur Dave] Clean up public API
ae36110 [Ankur Dave] Fix style errors
e4fbd32 [Ankur Dave] Unify GraphImpl RDDs + other graph load optimizations
d6d60e2 [Ankur Dave] In GraphLoader, coalesce to minEdgePartitions
62c7b78 [Ankur Dave] In Analytics, take PageRank numIter
d64e8d4 [Ankur Dave] Log current Pregel iteration
SPARK-1789. Multiple versions of Netty dependencies cause FlumeStreamSuite failure

TL;DR is there is a bit of JAR hell trouble with Netty, that can be mostly resolved and will resolve a test failure.

I hit the error described at http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-startup-time-out-td1753.html while running FlumeStreamingSuite, and have for a short while (is it just me?)

velvia notes:
"I have found a workaround.  If you add akka 2.2.4 to your dependencies, then everything works, probably because akka 2.2.4 brings in newer version of Jetty."

There are at least 3 versions of Netty in play in the build:

- the new Flume 1.4.0 dependency brings in io.netty:netty:3.4.0.Final, and that is the immediate problem
- the custom version of akka 2.2.3 depends on io.netty:netty:3.6.6.
- but, Spark Core directly uses io.netty:netty-all:4.0.17.Final

The POMs try to exclude other versions of netty, but are excluding org.jboss.netty:netty, when in fact older versions of io.netty:netty (not netty-all) are also an issue.

The org.jboss.netty:netty excludes are largely unnecessary. I replaced many of them with io.netty:netty exclusions until everything agreed on io.netty:netty-all:4.0.17.Final.

But this didn't work, since Akka 2.2.3 doesn't work with Netty 4.x. Down-grading to 3.6.6.Final across the board made some Spark code not compile.

If the build *keeps* io.netty:netty:3.6.6.Final as well, everything seems to work. Part of the reason seems to be that Netty 3.x used the old `org.jboss.netty` packages. This is less than ideal, but is no worse than the current situation.

So this PR resolves the issue and improves the JAR hell, even if it leaves the existing theoretical Netty 3-vs-4 conflict:

- Remove org.jboss.netty excludes where possible, for clarity; they're not needed except with Hadoop artifacts
- Add io.netty:netty excludes where needed -- except, let akka keep its io.netty:netty
- Change a bit of test code that actually depended on Netty 3.x, to use 4.x equivalent
- Update SBT build accordingly

A better change would be to update Akka far enough such that it agrees on Netty 4.x, but I don't know if that's feasible.

Author: Sean Owen <sowen@cloudera.com>

Closes #723 from srowen/SPARK-1789 and squashes the following commits:

43661b7 [Sean Owen] Update and add Netty excludes to prevent some JAR conflicts that cause test issues
[SPARK-1774] Respect SparkSubmit --jars on YARN (client)

SparkSubmit ignores `--jars` for YARN client. This is a bug.

This PR also automatically adds the application jar to `spark.jar`. Previously, when running as yarn-client, you must specify the jar additionally through `--files` (because `--jars` didn't work). Now you don't have to explicitly specify it through either.

Tested on a YARN cluster.

Author: Andrew Or <andrewor14@gmail.com>

Closes #710 from andrewor14/yarn-jars and squashes the following commits:

35d1928 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-jars
c27bf6c [Andrew Or] For yarn-cluster and python, do not add primaryResource to spark.jar
c92c5bf [Andrew Or] Minor cleanups
269f9f3 [Andrew Or] Fix format
013d840 [Andrew Or] Fix tests
1407474 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-jars
3bb75e8 [Andrew Or] Allow SparkSubmit --jars to take effect in yarn-client mode
Enabled incremental build that comes with sbt 0.13.2

More info at. https://github.com/sbt/sbt/issues/1010

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

Closes #525 from ScrapCodes/sbt-inc-opt and squashes the following commits:

ba8fa42 [Prashant Sharma] Enabled incremental build that comes with sbt 0.13.2