Fix for class of test suite failures in jenkins

Author: Peter MacKinnon <pmackinn@redhat.com>

Closes #1271 from pdmack/master and squashes the following commits:

cfe59fd [Peter MacKinnon] exclude servlet-api in hadoop-client for sbt
6f39fec [Peter MacKinnon] add exclusion for old servlet-api on hadoop-client in core

This is the only occurrence of this pattern in the examples that needs to be replaced. It only addresses the example change.

Author: Sean Owen <sowen@cloudera.com>

Closes #1250 from srowen/SPARK-2293 and squashes the following commits:

6b1b28c [Sean Owen] Compute prediction-and-label RDD directly rather than by zipping, for efficiency

Author: Reynold Xin <rxin@apache.org>

Closes #1260 from rxin/signalhandler1 and squashes the following commits:

8e73552 [Reynold Xin] Uh add Logging back in ApplicationMaster.
0402ba8 [Reynold Xin] Synchronize SignalLogger.register.
dc70705 [Reynold Xin] Added SignalLogger to YARN ApplicationMaster.
79a21b4 [Reynold Xin] Added license header.
0da052c [Reynold Xin] Added the SignalLogger itself.
e587d2e [Reynold Xin] [SPARK-2318] When exiting on a signal, print the signal name first.

This should go into 1.0.1.

Author: Reynold Xin <rxin@apache.org>

Closes #1264 from rxin/SPARK-2322 and squashes the following commits:

c77c07f [Reynold Xin] Added comment to SparkDriverExecutionException and a test case for accumulator.
5d8d920 [Reynold Xin] [SPARK-2322] Exception in resultHandler could crash DAGScheduler and shutdown SparkContext.

I could settle with this being a debug also if we provided an example of how to turn it on in `log4j.properties`

https://issues.apache.org/jira/browse/SPARK-2077

Author: Andrew Ash <andrew@andrewash.com>

Closes #1017 from ash211/SPARK-2077 and squashes the following commits:

580f680 [Andrew Ash] Drop to debug
0266415 [Andrew Ash] SPARK-2077 Log serializer that actually ends up being used

These commits cause `ClosureCleaner.clean` to attempt to serialize the cleaned closure with the default closure serializer and throw a `SparkException` if doing so fails.  This behavior is enabled by default but can be disabled at individual callsites of `SparkContext.clean`.

Commit 98e01ae8 fixes some no-op assertions in `GraphSuite` that this work exposed; I'm happy to put that in a separate PR if that would be more appropriate.

Author: William Benton <willb@redhat.com>

Closes #143 from willb/spark-897 and squashes the following commits:

bceab8a [William Benton] Commented DStream corner cases for serializability checking.
64d04d2 [William Benton] FailureSuite now checks both messages and causes.
3b3f74a [William Benton] Stylistic and doc cleanups.
b215dea [William Benton] Fixed spurious failures in ImplicitOrderingSuite
be1ecd6 [William Benton] Don't check serializability of DStream transforms.
abe816b [William Benton] Make proactive serializability checking optional.
5bfff24 [William Benton] Adds proactive closure-serializablilty checking
ed2ccf0 [William Benton] Test cases for SPARK-897.

Details can be see in [SPARK-2104](https://issues.apache.org/jira/browse/SPARK-2104). This work is based on Reynold's work, add some unit tests to validate the issue.

@rxin , would you please take a look at this PR, thanks a lot.

Author: jerryshao <saisai.shao@intel.com>

Closes #1245 from jerryshao/SPARK-2104 and squashes the following commits:

c8ee362 [jerryshao] Make field partitions transient
2b41917 [jerryshao] Minor changes
47d763c [jerryshao] Fix task serializing issue when sort with Java non serializable class

This commit adds a new metric in TaskMetrics to record
the input data size and displays this information in the UI.

An earlier version of this commit also added the read time,
which can be useful for diagnosing straggler problems,
but unfortunately that change introduced a significant performance
regression for jobs that don't do much computation. In order to
track read time, we'll need to do sampling.

The screenshots below show the UI with the new "Input" field,
which I added to the stage summary page, the executor summary page,
and the per-stage page.

![image](https://cloud.githubusercontent.com/assets/1108612/3167930/2627f92a-eb77-11e3-861c-98ea5bb7a1a2.png)

![image](https://cloud.githubusercontent.com/assets/1108612/3167936/475a889c-eb77-11e3-9706-f11c48751f17.png)

![image](https://cloud.githubusercontent.com/assets/1108612/3167948/80ebcf12-eb77-11e3-87ed-349fce6a770c.png)

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #962 from kayousterhout/read_metrics and squashes the following commits:

f13b67d [Kay Ousterhout] Correctly format input bytes on executor page
8b70cde [Kay Ousterhout] Added comment about potential inaccuracy of bytesRead
d1016e8 [Kay Ousterhout] Udated SparkListenerSuite test
8461492 [Kay Ousterhout] Miniscule style fix
ae04d99 [Kay Ousterhout] Remove input metrics for parallel collections
719f19d [Kay Ousterhout] Style fixes
bb6ec62 [Kay Ousterhout] Small fixes
869ac7b [Kay Ousterhout] Updated Json tests
44a0301 [Kay Ousterhout] Fixed accidentally added line
4bd0568 [Kay Ousterhout] Added input source, renamed Hdfs to Hadoop.
f27e535 [Kay Ousterhout] Updates based on review comments and to fix rebase
bf41029 [Kay Ousterhout] Updated Json tests to pass
0fc33e0 [Kay Ousterhout] Added explicit backward compatibility test
4e52925 [Kay Ousterhout] Added Json output and associated tests.
365400b [Kay Ousterhout] [SPARK-1683] Track task read metrics.

Author: Reynold Xin <rxin@apache.org>

Closes #1261 from rxin/ui-pre-size and squashes the following commits:

7ab1a69 [Reynold Xin] [SPARK-2320] Reduce exception/code block font size in web ui

Author: Reynold Xin <rxin@apache.org>

Closes #1258 from rxin/mapOutputTracker and squashes the following commits:

a7c95b6 [Reynold Xin] Improve MapOutputTracker error logging.

It should not be the responsibility of the worker subprocess, which
does not intentionally fork, to try and cleanup child processes. Doing
so is complex and interferes with operations such as
platform.system().

If it is desirable to have tighter control over subprocesses, then
namespaces should be used and it should be the manager's resposibility
to handle cleanup.

Author: Matthew Farrellee <matt@redhat.com>

Closes #1247 from mattf/SPARK-1394 and squashes the following commits:

c36f308 [Matthew Farrellee] [SPARK-1394] Remove SIGCHLD handler in worker subprocess

This patch adds the git revision hash (short version) to the RELEASE file. It uses git instead of simply checking for the existence of .git, so as to make sure that this is a functional repository.

Author: Guillaume Ballet <gballet@gmail.com>

Closes #1216 from gballet/master and squashes the following commits:

eabc50f [Guillaume Ballet] Refactored the script to take comments into account.
d93e5e8 [Guillaume Ballet] [SPARK 2233] make-distribution script now lists the git hash tag in the RELEASE file.

Author: Matthew Farrellee <matt@redhat.com>

Closes #1246 from mattf/SPARK-2003 and squashes the following commits:

b12e7ca [Matthew Farrellee] [SPARK-2003] Fix python SparkContext example

The existing docs are highly misleading. For standalone mode, for example, it encourages the user to use standalone-cluster mode, which is not officially supported. The safeguards have been added in Spark submit itself to prevent bad documentation from leading users down the wrong path in the future.

This PR is prompted by countless headaches users of Spark have run into on the mailing list.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1200 from andrewor14/submit-docs and squashes the following commits:

5ea2460 [Andrew Or] Rephrase cluster vs client explanation
c827f32 [Andrew Or] Clarify spark submit messages
9f7ed8f [Andrew Or] Clarify client vs cluster deploy mode + add safeguards

The issue here is that the `StorageTab` listens for updates from the `StorageStatusListener`, but when a block is kicked out of the cache, `StorageStatusListener` removes it from its list. Thus, there is no way for the `StorageTab` to know whether a block has been dropped.

This issue was introduced in #1080, which was itself a bug fix. Here we revert that PR and offer a different fix for the original bug (SPARK-2144).

Author: Andrew Or <andrewor14@gmail.com>

Closes #1249 from andrewor14/storage-ui-fix and squashes the following commits:

af019ce [Andrew Or] Fix SPARK-2307

Author: witgo <witgo@qq.com>

Closes #1135 from witgo/SPARK-2181 and squashes the following commits:

39dad90 [witgo] The keys for sorting the columns of Executor page in SparkUI are incorrect

The following code is very likely to throw an exception:

~~~
val rdd = sc.parallelize(0 until 111, 10).sample(false, 0.1)
rdd.zip(rdd).count()
~~~

because the same random number generator is used in compute partitions.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1229 from mengxr/fix-sample and squashes the following commits:

f1ee3d7 [Xiangrui Meng] fix concurrency issues in random sampler

New UI:

![screen shot 2014-06-26 at 1 43 52 pm](https://cloud.githubusercontent.com/assets/323388/3404643/82b9ddc6-fd73-11e3-96f9-f7592a7aee79.png)

Author: Reynold Xin <rxin@apache.org>

Closes #1236 from rxin/ui-task-attempt and squashes the following commits:

3b645dd [Reynold Xin] Expose attemptId in Stage.
c0474b1 [Reynold Xin] Beefed up unit test.
c404bdd [Reynold Xin] Fix ReplayListenerSuite.
f56be4b [Reynold Xin] Fixed JsonProtocolSuite.
e29e0f7 [Reynold Xin] Minor update.
5e4354a [Reynold Xin] [SPARK-2297][UI] Make task attempt and speculation more explicit in UI.

FetchFailedException used to have a Throwable field, but in reality we never propagate any of the throwable/exceptions back to the driver because Executor explicitly looks for FetchFailedException and then sends FetchFailed as the TaskEndReason.

This pull request removes the throwable and adds a MetadataFetchFailedException that extends FetchFailedException (so now MapOutputTracker throws MetadataFetchFailedException instead).

Author: Reynold Xin <rxin@apache.org>

Closes #1227 from rxin/metadataFetchException and squashes the following commits:

5cb1e0a [Reynold Xin] MetadataFetchFailedException extends FetchFailedException.
8861ee2 [Reynold Xin] Throw MetadataFetchFailedException in MapOutputTracker.

Extract the join keys from equality conditions, that can be evaluated using equi-join.

Author: Cheng Hao <hao.cheng@intel.com>

Closes #1190 from chenghao-intel/extract_join_keys and squashes the following commits:

4a1060a [Cheng Hao] Fix some of the small issues
ceb4924 [Cheng Hao] Remove the redundant pattern of join keys extraction
cec34e8 [Cheng Hao] Update the code style issues
dcc4584 [Cheng Hao] Extract the joinkeys from join condition

Currently all of the commits with 'X' in them cause person X to
receive e-mails every time someone makes a public fork of Spark.

marmbrus who requested this.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #1239 from pwendell/strip and squashes the following commits:

22e5a97 [Patrick Wendell] Strip '@' symbols when merging pull requests.

Fixed a problem in previous file in which some information regarding AWS instance types were wrong. Such information was updated base upon current AWS EC2 data.

Author: Zichuan Ye <jerry@tangentds.com>

Closes #1156 from jerry86/master and squashes the following commits:

ff36e95 [Zichuan Ye] Fixing AWS instance type information based upon current EC2 data

Also added inline doc for each TaskEndReason.

Author: Reynold Xin <rxin@apache.org>

Closes #1225 from rxin/SPARK-2286 and squashes the following commits:

6a7959d [Reynold Xin] Fix unit test failure.
cf9d5eb [Reynold Xin] Merge branch 'master' into SPARK-2286
a61fae1 [Reynold Xin] Move to line above ...
38c7391 [Reynold Xin] [SPARK-2286][UI] Report exception/errors for failed tasks that are not ExceptionFailure.

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

Closes #1235 from ueshin/issues/SPARK-2295 and squashes the following commits:

201c508 [Takuya UESHIN] Make JavaBeans nullability stricter.

spark.worker.instances was added as part of this commit: https://github.com/apache/spark/commit/1617816090e7b20124a512a43860a21232ebf511

My understanding is that SPARK_WORKER_INSTANCES is supported for backwards compatibility,
but spark.worker.instances is never used (SparkSubmit.scala sets spark.executor.instances) so should
not have been added.

@sryza @pwendell @tgravescs LMK if I'm understanding this correctly

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1214 from kayousterhout/yarn_config and squashes the following commits:

3d7c491 [Kay Ousterhout] Remove use of spark.worker.instances

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

Closes #1193 from ueshin/issues/SPARK-2254 and squashes the following commits:

cfd6088 [Takuya UESHIN] Modify ScalaRefection.schemaFor method to return nullability of Scala Type.

Include pyspark/mllib python sources as resources in the mllib.jar.
This way they will be included in the final assembly

Author: Szul, Piotr <Piotr.Szul@csiro.au>

Closes #1223 from piotrszul/branch-1.0 and squashes the following commits:

69d5174 [Szul, Piotr] Removed unsed resource directory src/main/resource from mllib pom
f8c52a0 [Szul, Piotr] [SPARK-2172] PySpark cannot import mllib modules in YARN-client mode Include pyspark/mllib python sources as resources in the jar

(cherry picked from commit fa167194)
Signed-off-by: Reynold Xin <rxin@apache.org>

Previously only tasks failed with ExceptionFailure reason was marked as failure.

Author: Reynold Xin <rxin@apache.org>

Closes #1224 from rxin/SPARK-2284 and squashes the following commits:

be79dbd [Reynold Xin] [SPARK-2284][UI] Mark all failed tasks as failures.

This is a fixed up version of #686 (cc @markhamstra @pwendell).  The last commit (the only one I authored) reflects the changes I made from Mark's original patch.

Author: Mark Hamstra <markhamstra@gmail.com>
Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1219 from kayousterhout/mark-SPARK-1749 and squashes the following commits:

42dfa7e [Kay Ousterhout] Got rid of terrible double-negative name
80b3205 [Kay Ousterhout] Don't notify listeners of job failure if it wasn't successfully cancelled.
d156d33 [Mark Hamstra] Do nothing in no-kill submitTasks
9312baa [Mark Hamstra] code review update
cc353c8 [Mark Hamstra] scalastyle
e61f7f8 [Mark Hamstra] Catch UnsupportedOperationException when DAGScheduler tries to cancel a job on a SchedulerBackend that does not implement killTask

JIRA issue: [SPARK-2283](https://issues.apache.org/jira/browse/SPARK-2283)

If `PruningSuite` is run right after `HiveCompatibilitySuite`, the first test case fails because `srcpart` table is cached in-memory by `HiveCompatibilitySuite`, but column pruning is not implemented for `InMemoryColumnarTableScan` operator yet.

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

Closes #1221 from liancheng/spark-2283 and squashes the following commits:

dc0b663 [Cheng Lian] SPARK-2283: reset test environment before running PruningSuite

This PR is based off Michael's [PR 734](https://github.com/apache/spark/pull/734) and includes a bunch of cleanups.

Moreover, this PR also
- makes `SparkLogicalPlan` take a `tableName: String`, which facilitates testing.
- moves join-related tests to a single file.

Author: Zongheng Yang <zongheng.y@gmail.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #1163 from concretevitamin/auto-broadcast-hash-join and squashes the following commits:

d0f4991 [Zongheng Yang] Fix bug in broadcast hash join & add test to cover it.
af080d7 [Zongheng Yang] Fix in joinIterators()'s next().
440d277 [Zongheng Yang] Fixes to imports; add back requiredChildDistribution (lost when merging)
208d5f6 [Zongheng Yang] Make LeftSemiJoinHash mix in HashJoin.
ad6c7cc [Zongheng Yang] Minor cleanups.
814b3bf [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
a8a093e [Zongheng Yang] Minor cleanups.
6fd8443 [Zongheng Yang] Cut down size estimation related stuff.
a4267be [Zongheng Yang] Add test for broadcast hash join and related necessary refactorings:
0e64b08 [Zongheng Yang] Scalastyle fix.
91461c2 [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
7c7158b [Zongheng Yang] Prototype of auto conversion to broadcast hash join.
0ad122f [Zongheng Yang] Merge branch 'master' into auto-broadcast-hash-join
3e5d77c [Zongheng Yang] WIP: giant and messy WIP.
a92ed0c [Michael Armbrust] Formatting.
76ca434 [Michael Armbrust] A simple strategy that broadcasts tables only when they are found in a configuration hint.
cf6b381 [Michael Armbrust] Split out generic logic for hash joins and create two concrete physical operators: BroadcastHashJoin and ShuffledHashJoin.
a8420ca [Michael Armbrust] Copy records in executeCollect to avoid issues with mutable rows.

The scheduler for Mesos in fine-grained mode launches tasks on the wrong executors. `MesosSchedulerBackend.resourceOffers(SchedulerDriver, List[Offer])` is assuming that `TaskSchedulerImpl.resourceOffers(Seq[WorkerOffer])` is returning task lists in the same order as the offers it was passed, but in the current implementation `TaskSchedulerImpl.resourceOffers` shuffles the offers to avoid assigning the tasks always to the same executors. The result is that the tasks are launched on the wrong executors. The jobs are sometimes able to complete, but most of the time they fail. It seems that as soon as something goes wrong with a task for some reason Spark is not able to recover since it's mistaken as to where the tasks are actually running. Also, it seems that the more the cluster is under load the more likely the job is to fail because there's a higher probability that Spark is trying to launch a task on a slave that doesn't actually have enough resources, again because it's using the wrong offers.

The solution is to not assume that the order in which the tasks are returned is the same as the offers, and simply launch the tasks on the executor decided by `TaskSchedulerImpl.resourceOffers`. What I am not sure about is that I considered slaveId and executorId to be the same, which is true at least in my setup, but I don't know if that is always true.

I tested this on top of the 1.0.0 release and it seems to work fine on our cluster.

Author: Sebastien Rainville <sebastien@hopper.com>

Closes #1140 from sebastienrainville/fine-grained-mode-fix-master and squashes the following commits:

a98b0e0 [Sebastien Rainville] Use a HashMap to retrieve the offer indices
d6ffe54 [Sebastien Rainville] Launch tasks on the proper executors in mesos fine-grained mode

and thus groupBy/cogroup are broken in Java APIs when Kryo is used).

@pwendell this should be merged into 1.0.1.

Thanks @sorenmacbeth for reporting this & helping out with the fix.

Author: Reynold Xin <rxin@apache.org>

Closes #1206 from rxin/kryo-iterable-2270 and squashes the following commits:

09da0aa [Reynold Xin] Updated the comment.
009bf64 [Reynold Xin] [SPARK-2270] Kryo cannot serialize results returned by asJavaIterable (and thus groupBy/cogroup are broken in Java APIs when Kryo is used).

**SPARK-2258.** Worker UI displays zombie processes if the executor throws an exception before a process is launched. This is because we only inform the Worker of the change if the process is already launched, which in this case it isn't.

**SPARK-2266.** We expose "Some(app-id)" on the log page. This is fairly minor.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1213 from andrewor14/fix-worker-ui and squashes the following commits:

c1223fe [Andrew Or] Fix worker UI bugs

This reverts a change introduced in 38702487, which redirected all stderr to the OS pipe instead of directly to the `bin/pyspark` shell output. This causes a simple job to hang in two ways:

1. If the cluster is not configured correctly or does not have enough resources, the job hangs without producing any output, because the relevant warning messages are masked.
2. If the stderr volume is large, this could lead to a deadlock if we redirect everything to the OS pipe. From the [python docs](https://docs.python.org/2/library/subprocess.html):

```
Note Do not use stdout=PIPE or stderr=PIPE with this function as that can deadlock
based on the child process output volume. Use Popen with the communicate() method
when you need pipes.
```

Note that we cannot remove `stdout=PIPE` in a similar way, because we currently use it to communicate the py4j port. However, it should be fine (as it has been for a long time) because we do not produce a ton of traffic through `stdout`.

That commit was not merged in branch-1.0, so this fix is for master only.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1178 from andrewor14/fix-python and squashes the following commits:

e68e870 [Andrew Or] Merge branch 'master' of github.com:apache/spark into fix-python
20849a8 [Andrew Or] Tone down stdout interference message
a09805b [Andrew Or] Return more than 1 line of error message to user
6dfbd1e [Andrew Or] Don't swallow original exception
0d1861f [Andrew Or] Provide more helpful output if stdout is garbled
21c9d7c [Andrew Or] Do not mask stderr from output

https://issues.apache.org/jira/browse/SPARK-2038

to differentiate with SparkConf object and at the same time keep the source level compatibility

Author: CodingCat <zhunansjtu@gmail.com>

Closes #1137 from CodingCat/SPARK-2038 and squashes the following commits:

11abeba [CodingCat] revise the comments
7ee5712 [CodingCat] to keep the source-compatibility
763975f [CodingCat] style fix
d91288d [CodingCat] rename "conf" parameters in the saveAsHadoop functions

The `BigDecimal` branch in `unwrap` matches to `scala.math.BigDecimal` rather than `java.math.BigDecimal`.

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

Closes #1199 from liancheng/javaBigDecimal and squashes the following commits:

e9bb481 [Cheng Lian] Should match java.math.BigDecimal when wnrapping Hive output

JIRA issue: [SPARK-2263](https://issues.apache.org/jira/browse/SPARK-2263)

Map objects were not converted to Hive types before inserting into Hive tables.

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

Closes #1205 from liancheng/spark-2263 and squashes the following commits:

c7a4373 [Cheng Lian] Addressed @concretevitamin's comment
784940b [Cheng Lian] SARPK-2263: support inserting MAP<K, V> to Hive tables

Author: witgo <witgo@qq.com>

Closes #1194 from witgo/SPARK-2248 and squashes the following commits:

6ac950b [witgo] spark.default.parallelism does not apply in local mode