SPARK-1124: Fix infinite retries of reduce stage when a map stage failed

In the previous code, if you had a failing map stage and then tried to
run reduce stages on it repeatedly, the first reduce stage would fail
correctly, but the later ones would mistakenly believe that all map
outputs are available and start failing infinitely with fetch failures
from "null".
Fix removal from shuffleToMapStage to search for a key-value pair with
our stage instead of using our shuffleID.
Merge pull request #641 from mateiz/spark-1124-master

SPARK-1124: Fix infinite retries of reduce stage when a map stage failed

In the previous code, if you had a failing map stage and then tried to run reduce stages on it repeatedly, the first reduce stage would fail correctly, but the later ones would mistakenly believe that all map outputs are available and start failing infinitely with fetch failures from "null". See https://spark-project.atlassian.net/browse/SPARK-1124 for an example.

This PR also cleans up code style slightly where there was a variable named "s" and some weird map manipulation.
For outputformats that are Configurable, call setConf before sending data to them.

[SPARK-1108] This allows us to use, e.g. HBase's TableOutputFormat with PairRDDFunctions.saveAsNewAPIHadoopFile, which otherwise would throw NullPointerException because the output table name hasn't been configured.

Note this bug also affects branch-0.9

Author: Bryn Keller <bryn.keller@intel.com>

Closes #638 from xoltar/SPARK-1108 and squashes the following commits:

7e94e7d [Bryn Keller] Import, comment, and format cleanup per code review
7cbcaa1 [Bryn Keller] For outputformats that are Configurable, call setConf before sending data to them. This allows us to use, e.g. HBase TableOutputFormat, which otherwise would throw NullPointerException because the output table name hasn't been configured
Include reference to twitter/chill in tuning docs

Author: Andrew Ash <andrew@andrewash.com>

Closes #647 from ash211/doc-tuning and squashes the following commits:

b87de0a [Andrew Ash] Include reference to twitter/chill in tuning docs
Graph primitives2

Hi guys,

I'm following Joey and Ankur's suggestions to add collectEdges and pickRandomVertex. I'm also adding the tests for collectEdges and refactoring one method getCycleGraph in GraphOpsSuite.scala.

Thank you,

semih

Author: Semih Salihoglu <semihsalihoglu@gmail.com>

Closes #580 from semihsalihoglu/GraphPrimitives2 and squashes the following commits:

937d3ec [Semih Salihoglu] - Fixed the scalastyle errors.
a69a152 [Semih Salihoglu] - Adding collectEdges and pickRandomVertices. - Adding tests for collectEdges. - Refactoring a getCycle utility function for GraphOpsSuite.scala.
41265a6 [Semih Salihoglu] - Adding collectEdges and pickRandomVertex. - Adding tests for collectEdges. - Recycling a getCycle utility test file.
For SPARK-1082, Use Curator for ZK interaction in standalone cluster

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

Closes #611 from colorant/curator and squashes the following commits:

7556aa1 [Raymond Liu] Address review comments
af92e1f [Raymond Liu] Fix coding style
964f3c2 [Raymond Liu] Ignore NodeExists exception
6df2966 [Raymond Liu] Rewrite zookeeper client code with curator
SPARK-1053.  Don't require SPARK_YARN_APP_JAR

It looks this just requires taking out the checks.

I verified that, with the patch, I was able to run spark-shell through yarn without setting the environment variable.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #553 from sryza/sandy-spark-1053 and squashes the following commits:

b037676 [Sandy Ryza] SPARK-1053.  Don't require SPARK_YARN_APP_JAR
SPARK-1078:  Replace lift-json with json4s-jackson.

The aim of the Json4s project is to provide a common API for
Scala JSON libraries.  It is Apache-licensed, easier for
downstream distributions to package, and mostly API-compatible
with lift-json.  Furthermore, the Jackson-backed implementation
parses faster than lift-json on all but the smallest inputs.

Author: William Benton <willb@redhat.com>

Closes #582 from willb/json4s and squashes the following commits:

7ca62c4 [William Benton] Replace lift-json with json4s-jackson.
SPARK-1135: fix broken anchors in docs

A recent PR that added Java vs Scala tabs for streaming also
inadvertently added some bad code to a document.ready handler, breaking
our other handler that manages scrolling to anchors correctly with the
floating top bar. As a result the section title ended up always being
hidden below the top bar. This removes the unnecessary JavaScript code.

Author: Matei Zaharia <matei@databricks.com>

Closes #3 from mateiz/doc-links and squashes the following commits:

e2a3488 [Matei Zaharia] SPARK-1135: fix broken anchors in docs
SPARK-1115: Catch depickling errors

This surroungs the complete worker code in a try/except block so we catch any error that arrives. An example would be the depickling failing for some reason

@JoshRosen

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

Closes #644 from bouk/catch-depickling-errors and squashes the following commits:

f0f67cc [Bouke van der Bijl] Lol indentation
0e4d504 [Bouke van der Bijl] Surround the complete python worker with the try block
Removed reference to incubation in README.md.

Author: Reynold Xin <rxin@apache.org>

Closes #1 from rxin/readme and squashes the following commits:

b3a77cd [Reynold Xin] Removed reference to incubation in README.md.
Deprecated and added a few java api methods for corresponding scala api.

PR [402](https://github.com/apache/incubator-spark/pull/402) from incubator repo.

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

Closes #19 from ScrapCodes/java-api-completeness and squashes the following commits:

11d0c2b [Prashant Sharma] Integer -> java.lang.Integer
737819a [Prashant Sharma] SPARK-1095 add explicit return types to APIs.
3ddc8bb [Prashant Sharma] Deprected *With functions in scala and added a few missing Java APIs
Updated link for pyspark examples in docs

Author: Jyotiska NK <jyotiska123@gmail.com>

Closes #22 from jyotiska/pyspark_docs and squashes the following commits:

426136c [Jyotiska NK] Updated link for pyspark examples
Remove references to ClusterScheduler (SPARK-1140)

ClusterScheduler was renamed to TaskSchedulerImpl; this commit
updates comments and tests accordingly.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #9 from kayousterhout/cluster_scheduler_death and squashes the following commits:

d6fd119 [Kay Ousterhout] Remove references to ClusterScheduler.
SPARK-1129: use a predefined seed when seed is zero in XORShiftRandom

If the seed is zero, XORShift generates all zeros, which would create unexpected result.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1129

Author: Xiangrui Meng <meng@databricks.com>

Closes #645 from mengxr/xor and squashes the following commits:

1b086ab [Xiangrui Meng] use MurmurHash3 to set seed in XORShiftRandom
45c6f16 [Xiangrui Meng] minor style change
51f4050 [Xiangrui Meng] use a predefined seed when seed is zero in XORShiftRandom
SPARK-1121 Only add avro if the build is for Hadoop 0.23.X and SPARK_YARN is set

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

Closes #6 from ScrapCodes/SPARK-1121/avro-dep-fix and squashes the following commits:

9b29e34 [Prashant Sharma] Review feedback on PR
46ed2ad [Prashant Sharma] SPARK-1121-Only add avro if the build is for Hadoop 0.23.X and SPARK_YARN is set
[SPARK-1089] fix the regression problem on ADD_JARS in 0.9

https://spark-project.atlassian.net/browse/SPARK-1089

copied from JIRA, reported by @ash211

"Using the ADD_JARS environment variable with spark-shell used to add the jar to both the shell and the various workers. Now it only adds to the workers and importing a custom class in the shell is broken.
The workaround is to add custom jars to both ADD_JARS and SPARK_CLASSPATH.
We should fix ADD_JARS so it works properly again.
See various threads on the user list:
https://mail-archives.apache.org/mod_mbox/incubator-spark-user/201402.mbox/%3CCAJbo4neMLiTrnm1XbyqomWmp0m+EUcg4yE-txuRGSVKOb5KLeA@mail.gmail.com%3E
(another one that doesn't appear in the archives yet titled "ADD_JARS not working on 0.9")"

The reason of this bug is two-folds

in the current implementation of SparkILoop.scala, the settings.classpath is not set properly when the process() method is invoked

the weird behaviour of Scala 2.10, (I personally thought it is a bug)

if we simply set value of a PathSettings object (like settings.classpath), the isDefault is not set to true (this is a flag showing if the variable is modified), so it makes the PathResolver loads the default CLASSPATH environment variable value to calculated the path (see https://github.com/scala/scala/blob/2.10.x/src/compiler/scala/tools/util/PathResolver.scala#L215)

what we have to do is to manually make this flag set, (https://github.com/CodingCat/incubator-spark/blob/e3991d97ddc33e77645e4559b13bf78b9e68239a/repl/src/main/scala/org/apache/spark/repl/SparkILoop.scala#L884)

Author: CodingCat <zhunansjtu@gmail.com>

Closes #13 from CodingCat/SPARK-1089 and squashes the following commits:

8af81e7 [CodingCat] impose non-null settings
9aa2125 [CodingCat] code cleaning
ce36676 [CodingCat] code cleaning
e045582 [CodingCat] fix the regression problem on ADD_JARS in 0.9
Show Master status on UI page

For standalone HA mode, A status is useful to identify the current master, already in json format too.

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

Closes #24 from colorant/status and squashes the following commits:

df630b3 [Raymond Liu] Show Master status on UI page
SPARK 1084.1 (resubmitted)

(Ported from https://github.com/apache/incubator-spark/pull/637 )

Author: Sean Owen <sowen@cloudera.com>

Closes #31 from srowen/SPARK-1084.1 and squashes the following commits:

6c4a32c [Sean Owen] Suppress warnings about legitimate unchecked array creations, or change code to avoid it
f35b833 [Sean Owen] Fix two misc javadoc problems
254e8ef [Sean Owen] Fix one new style error introduced in scaladoc warning commit
5b2fce2 [Sean Owen] Fix scaladoc invocation warning, and enable javac warnings properly, with plugin config updates
007762b [Sean Owen] Remove dead scaladoc links
b8ff8cb [Sean Owen] Replace deprecated Ant <tasks> with <target>