[SPARK-1553] Alternating nonnegative least-squares

This pull request includes a nonnegative least-squares solver (NNLS) tailored to the kinds of small-scale problems that come up when training matrix factorisation models by alternating nonnegative least-squares (ANNLS).

The method used for the NNLS subproblems is based on the classical method of projected gradients.  There is a modification where, if the set of active constraints has not changed since the last iteration, a conjugate gradient step is considered and possibly rejected in favour of the gradient; this improves convergence once the optimal face has been located.

The NNLS solver is in `org.apache.spark.mllib.optimization.NNLSbyPCG`.

Author: Tor Myklebust <tmyklebu@gmail.com>

Closes #460 from tmyklebu/annls and squashes the following commits:

79bc4b5 [Tor Myklebust] Merge branch 'master' of https://github.com/apache/spark into annls
199b0bc [Tor Myklebust] Make the ctor private again and use the builder pattern.
7fbabf1 [Tor Myklebust] Cleanup matrix math in NNLSSuite.
65ef7f2 [Tor Myklebust] Make ALS's ctor public and remove a couple of "convenience" wrappers.
2d4f3cb [Tor Myklebust] Cleanup.
0cb4481 [Tor Myklebust] Drop the iteration limit from 40k to max(400,20n).
e2a01d1 [Tor Myklebust] Create a workspace object for NNLS to cut down on memory allocations.
b285106 [Tor Myklebust] Clean up NNLS test cases.
9c820b6 [Tor Myklebust] Tweak variable names.
8a1a436 [Tor Myklebust] Describe the problem and add a reference to Polyak's paper.
5345402 [Tor Myklebust] Style fixes that got eaten.
ac673bd [Tor Myklebust] More safeguards against numerical ridiculousness.
c288b6a [Tor Myklebust] Finish moving the NNLS solver.
9a82fa6 [Tor Myklebust] Fix scalastyle moanings.
33bf4f2 [Tor Myklebust] Fix missing space.
89ea0a8 [Tor Myklebust] Hack ALSSuite to support NNLS testing.
f5dbf4d [Tor Myklebust] Teach ALS how to use the NNLS solver.
6cb563c [Tor Myklebust] Tests for the nonnegative least squares solver.
a68ac10 [Tor Myklebust] A nonnegative least-squares solver.
[SPARK-1958] Calling .collect() on a SchemaRDD should call executeCollect() on the underlying query plan.

In cases like `Limit` and `TakeOrdered`, `executeCollect()` makes optimizations that `execute().collect()` will not.

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

Closes #939 from liancheng/spark-1958 and squashes the following commits:

bdc4a14 [Cheng Lian] Copy rows to present immutable data to users
8250976 [Cheng Lian] Added return type explicitly for public API
192a25c [Cheng Lian] [SPARK-1958] Calling .collect() on a SchemaRDD should call executeCollect() on the underlying query plan.
[SPARK-1995][SQL] system function upper and lower can be supported

I don't know whether it's time to implement system function about string operation in spark sql now.

Author: egraldlo <egraldlo@gmail.com>

Closes #936 from egraldlo/stringoperator and squashes the following commits:

3c6c60a [egraldlo] Add UPPER, LOWER, MAX and MIN into hive parser
ea76d0a [egraldlo] modify the formatting issues
b49f25e [egraldlo] modify the formatting issues
1f0bbb5 [egraldlo] system function upper and lower supported
13d3267 [egraldlo] system function upper and lower supported
Avoid dynamic dispatching when unwrapping Hive data.

This is a follow up of PR #758.

The `unwrapHiveData` function is now composed statically before actual rows are scanned according to the field object inspector to avoid dynamic dispatching cost.

According to the same micro benchmark used in PR #758, this simple change brings slight performance boost: 2.5% for CSV table and 1% for RCFile table.

```
Optimized version:

CSV: 6870 ms, RCFile: 5687 ms
CSV: 6832 ms, RCFile: 5800 ms
CSV: 6822 ms, RCFile: 5679 ms
CSV: 6704 ms, RCFile: 5758 ms
CSV: 6819 ms, RCFile: 5725 ms

Original version:

CSV: 7042 ms, RCFile: 5667 ms
CSV: 6883 ms, RCFile: 5703 ms
CSV: 7115 ms, RCFile: 5665 ms
CSV: 7020 ms, RCFile: 5981 ms
CSV: 6871 ms, RCFile: 5906 ms
```

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

Closes #935 from liancheng/staticUnwrapping and squashes the following commits:

c49c70c [Cheng Lian] Avoid dynamic dispatching when unwrapping Hive data.
[SPARK-1942] Stop clearing spark.driver.port in unit tests

stop resetting spark.driver.port in unit tests (scala, java and python).

Author: Syed Hashmi <shashmi@cloudera.com>
Author: CodingCat <zhunansjtu@gmail.com>

Closes #943 from syedhashmi/master and squashes the following commits:

885f210 [Syed Hashmi] Removing unnecessary file (created by mergetool)
b8bd4b5 [Syed Hashmi] Merge remote-tracking branch 'upstream/master'
b895e59 [Syed Hashmi] Revert "[SPARK-1784] Add a new partitioner"
57b6587 [Syed Hashmi] Revert "[SPARK-1784] Add a balanced partitioner"
1574769 [Syed Hashmi] [SPARK-1942] Stop clearing spark.driver.port in unit tests
4354836 [Syed Hashmi] Revert "SPARK-1686: keep schedule() calling in the main thread"
fd36542 [Syed Hashmi] [SPARK-1784] Add a balanced partitioner
6668015 [CodingCat] SPARK-1686: keep schedule() calling in the main thread
4ca94cc [Syed Hashmi] [SPARK-1784] Add a new partitioner
SPARK-2001 : Remove docs/spark-debugger.md from master

Per discussion in dev list:
"
Seemed like the spark-debugger.md is no longer accurate (see
http://spark.apache.org/docs/latest/spark-debugger.html) and since it
was originally written Spark has evolved that makes the doc obsolete.
There are already work pending for new replay debugging (I could not
find the PR links for it) so I
With version control we could always reinstate the old doc if needed,
but as of today the doc is no longer reflect the current state of
Spark's RDD.
"

Author: Henry Saputra <henry.saputra@gmail.com>

Closes #953 from hsaputra/SPARK-2001-hsaputra and squashes the following commits:

dc324aa [Henry Saputra] SPARK-2001 : Remove docs/spark-debugger.md from master since it is obsolete
[SPARK-1912] fix compress memory issue during reduce

When we need to read a compressed block, we will first create a compress stream instance(LZF or Snappy) and use it to wrap that block.
Let's say a reducer task need to read 1000 local shuffle blocks, it will first prepare to read that 1000 blocks, which means create 1000 compression stream instance to wrap them. But the initialization of compression instance will allocate some memory and when we have many compression instance at the same time, it is a problem.
Actually reducer reads the shuffle blocks one by one, so we can do the compression instance initialization lazily.

Author: Wenchen Fan(Cloud) <cloud0fan@gmail.com>

Closes #860 from cloud-fan/fix-compress and squashes the following commits:

0924a6b [Wenchen Fan(Cloud)] rename 'doWork' into 'getIterator'
07f32c2 [Wenchen Fan(Cloud)] move the LazyProxyIterator to dataDeserialize
d80c426 [Wenchen Fan(Cloud)] remove empty lines in short class
2c8adb2 [Wenchen Fan(Cloud)] add inline comment
8ebff77 [Wenchen Fan(Cloud)] fix compress memory issue during reduce
Add support for Pivotal HD in the Maven build: SPARK-1992

Allow Spark to build against particular Pivotal HD distributions. For example to build Spark against Pivotal HD 2.0.1 one can run:
```
mvn -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0-gphd-3.0.1.0 -DskipTests clean package
```

Author: tzolov <christian.tzolov@gmail.com>

Closes #942 from tzolov/master and squashes the following commits:

bc3e05a [tzolov] Add support for Pivotal HD in the Maven build and SBT build: [SPARK-1992]
[SPARK-1468] Modify the partition function used by partitionBy.

Make partitionBy use a tweaked version of hash as its default partition function
since the python hash function does not consistently assign the same value
to None across python processes.

Associated JIRA at https://issues.apache.org/jira/browse/SPARK-1468

Author: Erik Selin <erik.selin@jadedpixel.com>

Closes #371 from tyro89/consistent_hashing and squashes the following commits:

201c301 [Erik Selin] Make partitionBy use a tweaked version of hash as its default partition function since the python hash function does not consistently assign the same value to None across python processes.
fix java.lang.ClassCastException

get Exception when run：bin/run-example org.apache.spark.examples.sql.RDDRelation
Exception's detail is:
Exception in thread "main" java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Integer
	at scala.runtime.BoxesRunTime.unboxToInt(BoxesRunTime.java:106)
	at org.apache.spark.sql.catalyst.expressions.GenericRow.getInt(Row.scala:145)
	at org.apache.spark.examples.sql.RDDRelation$.main(RDDRelation.scala:49)
	at org.apache.spark.examples.sql.RDDRelation.main(RDDRelation.scala)
change sql("SELECT COUNT(*) FROM records").collect().head.getInt(0) to sql("SELECT COUNT(*) FROM records").collect().head.getLong(0), then the Exception do not occur any more

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #949 from baishuo/master and squashes the following commits:

f4b319f [baishuo(白硕)] fix java.lang.ClassCastException
Synthetic GraphX Benchmark

This PR accomplishes two things:

1. It introduces a Synthetic Benchmark application that generates an arbitrarily large log-normal graph and executes either PageRank or connected components on the graph.  This can be used to profile GraphX system on arbitrary clusters without access to large graph datasets

2. This PR improves the implementation of the log-normal graph generator.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>
Author: Ankur Dave <ankurdave@gmail.com>

Closes #720 from jegonzal/graphx_synth_benchmark and squashes the following commits:

e40812a [Ankur Dave] Exclude all of GraphX from compatibility checks vs. 1.0.0
bccccad [Ankur Dave] Fix long lines
374678a [Ankur Dave] Bugfix and style changes
1bdf39a [Joseph E. Gonzalez] updating options
d943972 [Joseph E. Gonzalez] moving the benchmark application into the examples folder.
f4f839a [Joseph E. Gonzalez] Creating a synthetic benchmark script.
[SPARK-1991] Support custom storage levels for vertices and edges

This PR adds support for specifying custom storage levels for the vertices and edges of a graph. This enables GraphX to handle graphs larger than memory size by specifying MEMORY_AND_DISK and then repartitioning the graph to use many small partitions, each of which does fit in memory. Spark will then automatically load partitions from disk as needed.

The user specifies the desired vertex and edge storage levels when building the graph by passing them to the graph constructor. These are then stored in the `targetStorageLevel` attribute of the VertexRDD and EdgeRDD respectively. Whenever GraphX needs to cache a VertexRDD or EdgeRDD (because it plans to use it more than once, for example), it uses the specified target storage level. Also, when the user calls `Graph#cache()`, the vertices and edges are persisted using their target storage levels.

In order to facilitate propagating the target storage levels across VertexRDD and EdgeRDD operations, we remove raw calls to the constructors and instead introduce the `withPartitionsRDD` and `withTargetStorageLevel` methods.

I tested this change by running PageRank and triangle count on a severely memory-constrained cluster (1 executor with 300 MB of memory, and a 1 GB graph). Before this PR, these algorithms used to fail with OutOfMemoryErrors. With this PR, and using the DISK_ONLY storage level, they succeed.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #946 from ankurdave/SPARK-1991 and squashes the following commits:

ce17d95 [Ankur Dave] Move pickStorageLevel to StorageLevel.fromString
ccaf06f [Ankur Dave] Shadow members in withXYZ() methods rather than using underscores
c34abc0 [Ankur Dave] Exclude all of GraphX from compatibility checks vs. 1.0.0
c5ca068 [Ankur Dave] Revert "Exclude all of GraphX from binary compatibility checks"
34bcefb [Ankur Dave] Exclude all of GraphX from binary compatibility checks
6fdd137 [Ankur Dave] [SPARK-1991] Support custom storage levels for vertices and edges
Fixed a typo

in RowMatrix.scala

Author: DB Tsai <dbtsai@dbtsai.com>

Closes #959 from dbtsai/dbtsai-typo and squashes the following commits:

fab0e0e [DB Tsai] Fixed typo
[SPARK-1161] Add saveAsPickleFile and SparkContext.pickleFile in Python

Author: Kan Zhang <kzhang@apache.org>

Closes #755 from kanzhang/SPARK-1161 and squashes the following commits:

24ed8a2 [Kan Zhang] [SPARK-1161] Fixing doc tests
44e0615 [Kan Zhang] [SPARK-1161] Adding an optional batchSize with default value 10
d929429 [Kan Zhang] [SPARK-1161] Add saveAsObjectFile and SparkContext.objectFile in Python
SPARK-1941: Update streamlib to 2.7.0 and use HyperLogLogPlus instead of HyperLogLog.

I also corrected some errors made in the previous HLL count approximate API, including relativeSD wasn't really a measure for error (and we used it to test error bounds in test results).

Author: Reynold Xin <rxin@apache.org>

Closes #897 from rxin/hll and squashes the following commits:

4d83f41 [Reynold Xin] New error bound and non-randomness.
f154ea0 [Reynold Xin] Added a comment on the value bound for testing.
e367527 [Reynold Xin] One more round of code review.
41e649a [Reynold Xin] Update final mima list.
9e320c8 [Reynold Xin] Incorporate code review feedback.
e110d70 [Reynold Xin] Merge branch 'master' into hll
354deb8 [Reynold Xin] Added comment on the Mima exclude rules.
acaa524 [Reynold Xin] Added the right exclude rules in MimaExcludes.
6555bfe [Reynold Xin] Added a default method and re-arranged MimaExcludes.
1db1522 [Reynold Xin] Excluded util.SerializableHyperLogLog from MIMA check.
9221b27 [Reynold Xin] Merge branch 'master' into hll
88cfe77 [Reynold Xin] Updated documentation and restored the old incorrect API to maintain API compatibility.
1294be6 [Reynold Xin] Updated HLL+.
e7786cb [Reynold Xin] Merge branch 'master' into hll
c0ef0c2 [Reynold Xin] SPARK-1941: Update streamlib to 2.7.0 and use HyperLogLogPlus instead of HyperLogLog.
use env default python in merge_spark_pr.py

A minor change to use env default python instead of fixed `/usr/bin/python`.

Author: Xiangrui Meng <meng@databricks.com>

Closes #965 from mengxr/merge-pr-python and squashes the following commits:

1ae0013 [Xiangrui Meng] use env default python in merge_spark_pr.py
Enable repartitioning of graph over different number of partitions

It is currently very difficult to repartition a graph over a different number of partitions.  This PR adds an additional `partitionBy` function that takes the number of partitions.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #719 from jegonzal/graph_partitioning_options and squashes the following commits:

730b405 [Joseph E. Gonzalez] adding an additional number of partitions option to partitionBy
Update spark-ec2 scripts for 1.0.0 on master

The change was previously committed only to branch-1.0 as part of https://github.com/apache/spark/commit/a34e6fda1d6fb8e769c21db70845f1a6dde968d8

Author: Aaron Davidson <aaron@databricks.com>

This patch had conflicts when merged, resolved by
Committer: Patrick Wendell <pwendell@gmail.com>

Closes #938 from aarondav/sparkec2 and squashes the following commits:

067cc31 [Aaron Davidson] Update spark-ec2 scripts for 1.0.0 on master
SPARK-1806 (addendum) Use non-deprecated methods in Mesos 0.18

The update to Mesos 0.18 caused some deprecation warnings in the build. The change to the non-deprecated version is straightforward as it emulates what the Mesos driver does with the deprecated method anyway (https://github.com/apache/mesos/blob/c5aa1dd22155d79c5a7c33076319299a40fd63b3/src/sched/sched.cpp#L1354)

Author: Sean Owen <sowen@cloudera.com>

Closes #920 from srowen/SPARK-1806 and squashes the following commits:

8d76b6a [Sean Owen] Use non-deprecated methods in Mesos 0.18
[SPARK-1817] RDD.zip() should verify partition sizes for each partition

RDD.zip() will throw an exception if it finds partition sizes are not the same.

Author: Kan Zhang <kzhang@apache.org>

Closes #944 from kanzhang/SPARK-1817 and squashes the following commits:

c073848 [Kan Zhang] [SPARK-1817] Cosmetic updates
524c670 [Kan Zhang] [SPARK-1817] RDD.zip() should verify partition sizes for each partition