Merge pull request #583 from colorant/zookeeper.

Minor fix for ZooKeeperPersistenceEngine to use configured working dir

Author: Raymond Liu <raymond.liu@intel.com>

Closes #583 and squashes the following commits:

91b0609 [Raymond Liu] Minor fix for ZooKeeperPersistenceEngine to use configured working dir
Merge pull request #578 from mengxr/rank.

SPARK-1076: zipWithIndex and zipWithUniqueId to RDD

Assign ranks to an ordered or unordered data set is a common operation. This could be done by first counting records in each partition and then assign ranks in parallel.

The purpose of assigning ranks to an unordered set is usually to get a unique id for each item, e.g., to map feature names to feature indices. In such cases, the assignment could be done without counting records, saving one spark job.

https://spark-project.atlassian.net/browse/SPARK-1076

== update ==
Because assigning ranks is very similar to Scala's zipWithIndex, I changed the method name to zipWithIndex and put the index in the value field.

Author: Xiangrui Meng <meng@databricks.com>

Closes #578 and squashes the following commits:

52a05e1 [Xiangrui Meng] changed assignRanks to zipWithIndex changed assignUniqueIds to zipWithUniqueId minor updates
756881c [Xiangrui Meng] simplified RankedRDD by implementing assignUniqueIds separately moved couting iterator size to Utils do not count items in the last partition and skip counting if there is only one partition
630868c [Xiangrui Meng] newline
21b434b [Xiangrui Meng] add assignRanks and assignUniqueIds to RDD
Merge pull request #589 from mengxr/index.

SPARK-1076: Convert Int to Long to avoid overflow

Patch for PR #578.

Author: Xiangrui Meng <meng@databricks.com>

Closes #589 and squashes the following commits:

98c435e [Xiangrui Meng] cast Int to Long to avoid Int overflow
Merge pull request #591 from mengxr/transient-new.

SPARK-1076: [Fix #578] add @transient to some vals

I'll try to be more careful next time.

Author: Xiangrui Meng <meng@databricks.com>

Closes #591 and squashes the following commits:

2b4f044 [Xiangrui Meng] add @transient to prev in ZippedWithIndexRDD add @transient to seed in PartitionwiseSampledRDD
Merge pull request #592 from rxin/test.

SPARK-1088: Create a script for running tests so we can have version specific testing on Jenkins.

@pwendell

Author: Reynold Xin <rxin@apache.org>

Closes #592 and squashes the following commits:

be02359 [Reynold Xin] SPARK-1088: Create a script for running tests so we can have version specific testing on Jenkins.
SPARK-1073 Keep GitHub pull request title as commit summary

The first line of a git commit message is the line that's used with many git
tools as the most concise textual description of that message.  The most
common use that I see is in the short log, which is a one line per commit
log of recent commits.

This commit moves the line

  Merge pull request #%s from %s.

Lower into the message to reserve the first line of the resulting commit for
the much more important pull request title.

http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html

Author: Andrew Ash <andrew@andrewash.com>

Closes #574 from ash211/gh-pr-merge-title and squashes the following commits:

b240823 [Andrew Ash] More merge_message improvements
d2986db [Andrew Ash] Keep GitHub pull request title as commit summary
Ported hadoopClient jar for < 1.0.1 fix

#522 got messed after i rewrote the branch hadoop_jar_name. So created a new one.

Author: Bijay Bisht <bijay.bisht@gmail.com>

Closes #584 from bijaybisht/hadoop_jar_name_on_0.9.0 and squashes the following commits:

1b6fb3c [Bijay Bisht] Ported hadoopClient jar for < 1.0.1 fix
(cherry picked from commit 8093de1bb319e86dcf0d6d8d97b043a2bc1aa8f2)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
Add c3 instance types to Spark EC2

The number of disks for the c3 instance types taken from here: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/InstanceStorage.html#StorageOnInstanceTypes

Author: Christian Lundgren <christian.lundgren@gameanalytics.com>

Closes #595 from chrisavl/branch-0.9 and squashes the following commits:

c8af5f9 [Christian Lundgren] Add c3 instance types to Spark EC2
(cherry picked from commit 19b4bb2b444f1dbc4592bf3d58b17652e0ae6d6b)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
Merge pull request #598 from shivaram/master.

Update spark_ec2 to use 0.9.0 by default

Backports change from branch-0.9

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

Closes #598 and squashes the following commits:

f6d3ed0 [Shivaram Venkataraman] Update spark_ec2 to use 0.9.0 by default Backports change from branch-0.9
Typo: Standlone -> Standalone

Author: Andrew Ash <andrew@andrewash.com>

Closes #601 from ash211/typo and squashes the following commits:

9cd43ac [Andrew Ash] Change docs references to metrics.properties, not metrics.conf
3813ff1 [Andrew Ash] Typo: mulitcast -> multicast
873bd2f [Andrew Ash] Typo: Standlone -> Standalone
[SPARK-1092] print warning information if user use SPARK_MEM to regulate executor memory usage

https://spark-project.atlassian.net/browse/SPARK-1092?jql=project%20%3D%20SPARK

print warning information if user set SPARK_MEM to regulate memory usage of executors

----
OUTDATED:

Currently, users will usually set SPARK_MEM to control the memory usage of driver programs, (in spark-class)
91 JAVA_OPTS="$OUR_JAVA_OPTS"
92 JAVA_OPTS="$JAVA_OPTS -Djava.library.path=$SPARK_LIBRARY_PATH"
93 JAVA_OPTS="$JAVA_OPTS -Xms$SPARK_MEM -Xmx$SPARK_MEM"
if they didn't set spark.executor.memory, the value in this environment variable will also affect the memory usage of executors, because the following lines in SparkContext
privatespark val executorMemory = conf.getOption("spark.executor.memory")
.orElse(Option(System.getenv("SPARK_MEM")))
.map(Utils.memoryStringToMb)
.getOrElse(512)
also
since SPARK_MEM has been (proposed to) deprecated in SPARK-929 (https://spark-project.atlassian.net/browse/SPARK-929) and the corresponding PR (https://github.com/apache/incubator-spark/pull/104)
we should remove this line

Author: CodingCat <zhunansjtu@gmail.com>

Closes #602 from CodingCat/clean_spark_mem and squashes the following commits:

302bb28 [CodingCat] print warning information if user use SPARK_MEM to regulate executor memory usage
fix for https://spark-project.atlassian.net/browse/SPARK-1052

Author: Bijay Bisht <bijay.bisht@gmail.com>

Closes #568 from bijaybisht/SPARK-1052 and squashes the following commits:

da70395 [Bijay Bisht] fix for https://spark-project.atlassian.net/browse/SPARK-1052 - comments incorporated
fdb1d94 [Bijay Bisht] fix for https://spark-project.atlassian.net/browse/SPARK-1052

(cherry picked from commit e797c1abd9692f1b7ec290e4c83d31fd106e6b05)
Signed-off-by: Aaron Davidson <aaron@databricks.com>
Add subtractByKey to the JavaPairRDD wrapper

Author: Punya Biswal <pbiswal@palantir.com>

Closes #600 from punya/subtractByKey-java and squashes the following commits:

e961913 [Punya Biswal] Hide implicit ClassTags from Java API
c5d317b [Punya Biswal] Add subtractByKey to the JavaPairRDD wrapper
Worker registration logging fix

Author: Andrew Ash <andrew@andrewash.com>

Closes #608 from ash211/patch-7 and squashes the following commits:

bd85f2a [Andrew Ash] Worker registration logging fix
Fix typos in Spark Streaming programming guide

Author: Andrew Or <andrewor14@gmail.com>

Closes #536 from andrewor14/streaming-typos and squashes the following commits:

a05faa6 [Andrew Or] Fix broken link and wording
bc2e4bc [Andrew Or] Merge github.com:apache/incubator-spark into streaming-typos
d5515b4 [Andrew Or] TD's comments
767ef12 [Andrew Or] Fix broken links
8f4c731 [Andrew Or] Fix typos in programming guide
[SPARK-1090] improvement on spark_shell (help information, configure memory)

https://spark-project.atlassian.net/browse/SPARK-1090

spark-shell should print help information about parameters and should allow user to configure exe memory
there is no document about hot to set --cores/-c in spark-shell

and also

users should be able to set executor memory through command line options

In this PR I also check the format of the options passed by the user

Author: CodingCat <zhunansjtu@gmail.com>

Closes #599 from CodingCat/spark_shell_improve and squashes the following commits:

de5aa38 [CodingCat] add parameter to set driver memory
915cbf8 [CodingCat] improvement on spark_shell (help information, configure memory)
SPARK-1098: Minor cleanup of ClassTag usage in Java API

Our usage of fake ClassTags in this manner is probably not healthy, but I'm not sure if there's a better solution available, so I just cleaned up and documented the current one.

Author: Aaron Davidson <aaron@databricks.com>

Closes #604 from aarondav/master and squashes the following commits:

b398e89 [Aaron Davidson] SPARK-1098: Minor cleanup of ClassTag usage in Java API
Merge branch 'master' of https://github.com/apache/incubator-spark into csd-1.0