SPARK-4532: Fix bug in detection of Hive in Spark 1.2

Because the Hive profile is no longer defined in the root pom,
we need to check specifically in the sql/hive pom when we
perform the check in make-distribtion.sh.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #3398 from pwendell/make-distribution and squashes the following commits:

8a58279 [Patrick Wendell] Fix bug in detection of Hive in Spark 1.2
[SPARK-4531] [MLlib] cache serialized java object

The Pyrolite is pretty slow (comparing to the adhoc serializer in 1.1), it cause much performance regression in 1.2, because we cache the serialized Python object in JVM, deserialize them into Java object in each step.

This PR change to cache the deserialized JavaRDD instead of PythonRDD to avoid the deserialization of Pyrolite. It should have similar memory usage as before, but much faster.

Author: Davies Liu <davies@databricks.com>

Closes #3397 from davies/cache and squashes the following commits:

7f6e6ce [Davies Liu] Update -> Updater
4b52edd [Davies Liu] using named argument
63b984e [Davies Liu] fix
7da0332 [Davies Liu] add unpersist()
dff33e1 [Davies Liu] address comments
c2bdfc2 [Davies Liu] refactor
d572f00 [Davies Liu] Merge branch 'master' into cache
f1063e1 [Davies Liu] cache serialized java object
[SPARK-4431][MLlib] Implement efficient foreachActive for dense and sparse vector

Previously, we were using Breeze's activeIterator to access the non-zero elements
in dense/sparse vector. Due to the overhead, we switched back to native `while loop`
in #SPARK-4129.

However, #SPARK-4129 requires de-reference the dv.values/sv.values in
each access to the value, which is very expensive. Also, in MultivariateOnlineSummarizer,
we're using Breeze's dense vector to store the partial stats, and this is very expensive compared
with using primitive scala array.

In this PR, efficient foreachActive is implemented to unify the code path for dense and sparse
vector operation which makes codebase easier to maintain. Breeze dense vector is replaced
by primitive array to reduce the overhead further.

Benchmarking with mnist8m dataset on single JVM
with first 200 samples loaded in memory, and repeating 5000 times.

Before change:
Sparse Vector - 30.02
Dense Vector - 38.27

With this PR:
Sparse Vector - 6.29
Dense Vector - 11.72

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3288 from dbtsai/activeIterator and squashes the following commits:

844b0e6 [DB Tsai] formating
03dd693 [DB Tsai] futher performance tunning.
1907ae1 [DB Tsai] address feedback
98448bb [DB Tsai] Made the override final, and had a local copy of variables which made the accessing a single step operation.
c0cbd5a [DB Tsai] fix a bug
6441f92 [DB Tsai] Finished SPARK-4431
[SPARK-4377] Fixed serialization issue by switching to akka provided serializer.

... - there is no way around this for deserializing actorRef(s).

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

Closes #3402 from ScrapCodes/SPARK-4377/troubleDeserializing and squashes the following commits:

77233fd [Prashant Sharma] Style fixes
9b35c6e [Prashant Sharma] Scalastyle fixes
29880da [Prashant Sharma] [SPARK-4377] Fixed serialization issue by switching to akka provided serializer - there is no way around this for deserializing actorRef(s).
SPARK-4457. Document how to build for Hadoop versions greater than 2.4

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3322 from sryza/sandy-spark-4457 and squashes the following commits:

5e72b77 [Sandy Ryza] Feedback
0cf05c1 [Sandy Ryza] Caveat
be8084b [Sandy Ryza] SPARK-4457. Document how to build for Hadoop versions greater than 2.4
[SPARK-4479][SQL] Avoids unnecessary defensive copies when sort based shuffle is on

This PR is a workaround for SPARK-4479. Two changes are introduced: when merge sort is bypassed in `ExternalSorter`,

1. also bypass RDD elements buffering as buffering is the reason that `MutableRow` backed row objects must be copied, and
2. avoids defensive copies in `Exchange` operator

<!-- Reviewable:start -->
[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/3422)
<!-- Reviewable:end -->

Author: Cheng Lian <lian@databricks.com>

Closes #3422 from liancheng/avoids-defensive-copies and squashes the following commits:

591f2e9 [Cheng Lian] Passes all shuffle suites
0c3c91e [Cheng Lian] Fixes shuffle write metrics when merge sort is bypassed
ed5df3c [Cheng Lian] Fixes styling changes
f75089b [Cheng Lian] Avoids unnecessary defensive copies when sort based shuffle is on
[SQL] Fix comment in HiveShim

This file is for Hive 0.13.1 I think.

Author: Daniel Darabos <darabos.daniel@gmail.com>

Closes #3432 from darabos/patch-2 and squashes the following commits:

4fd22ed [Daniel Darabos] Fix comment. This file is for Hive 0.13.1.
[SQL] Fix path in HiveFromSpark

It require us to run ```HiveFromSpark``` in specified dir because ```HiveFromSpark``` use relative path, this leads to ```run-example``` error(http://apache-spark-developers-list.1001551.n3.nabble.com/src-main-resources-kv1-txt-not-found-in-example-of-HiveFromSpark-td9100.html).

Author: scwf <wangfei1@huawei.com>

Closes #3415 from scwf/HiveFromSpark and squashes the following commits:

ed3d6c9 [scwf] revert no need change
b00e20c [scwf] fix path usring spark_home
dbd321b [scwf] fix path in hivefromspark
[SPARK-4487][SQL] Fix attribute reference resolution error when using ORDER BY.

When we use ORDER BY clause, at first, attributes referenced by projection are resolved (1).
And then, attributes referenced at ORDER BY clause are resolved (2).
 But when resolving attributes referenced at ORDER BY clause, the resolution result generated in (1) is discarded so for example, following query fails.

    SELECT c1 + c2 FROM mytable ORDER BY c1;

The query above fails because when resolving the attribute reference 'c1', the resolution result of 'c2' is discarded.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3363 from sarutak/SPARK-4487 and squashes the following commits:

fd314f3 [Kousuke Saruta] Fixed attribute resolution logic in Analyzer
6e60c20 [Kousuke Saruta] Fixed conflicts
cb5b7e9 [Kousuke Saruta] Added test case for SPARK-4487
282d529 [Kousuke Saruta] Fixed attributes reference resolution error
b6123e6 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into concat-feature
317b7fb [Kousuke Saruta] WIP
[SPARK-4145] Web UI job pages

This PR adds two new pages to the Spark Web UI:

- A jobs overview page, which shows details on running / completed / failed jobs.
- A job details page, which displays information on an individual job's stages.

The jobs overview page is now the default UI homepage; the old homepage is still accessible at `/stages`.

### Screenshots

#### New UI homepage

![image](https://cloud.githubusercontent.com/assets/50748/5119035/fd0a69e6-701f-11e4-89cb-db7e9705714f.png)

#### Job details page

(This is effectively a per-job version of the stages page that can be extended later with other things, such as DAG visualizations)

![image](https://cloud.githubusercontent.com/assets/50748/5134910/50b340d4-70c7-11e4-88e1-6b73237ea7c8.png)

### Key changes in this PR

- Rename `JobProgressPage` to `AllStagesPage`
- Expose `StageInfo` objects in the ``SparkListenerJobStart` event; add backwards-compatibility tests to JsonProtocol.
- Add additional data structures to `JobProgressListener` to map from stages to jobs.
- Add several fields to `JobUIData`.

I also added ~150 lines of Selenium tests as I uncovered UI issues while developing this patch.

### Limitations

If a job contains stages that aren't run, then its overall job progress bar may be an underestimate of the total job progress; in other words, a completed job may appear to have a progress bar that's not at 100%.

If stages or tasks fail, then the progress bar will not go backwards to reflect the true amount of remaining work.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3009 from JoshRosen/job-page and squashes the following commits:

eb05e90 [Josh Rosen] Disable kill button in completed stages tables.
f00c851 [Josh Rosen] Fix JsonProtocol compatibility
b89c258 [Josh Rosen] More JSON protocol backwards-compatibility fixes.
ff804cd [Josh Rosen] Don't write "Stage Ids" field in JobStartEvent JSON.
6f17f3f [Josh Rosen] Only store StageInfos in SparkListenerJobStart event.
2bbf41a [Josh Rosen] Update job progress bar to reflect skipped tasks/stages.
61c265a [Josh Rosen] Add “skipped stages” table; only display non-empty tables.
1f45d44 [Josh Rosen] Incorporate a bunch of minor review feedback.
0b77e3e [Josh Rosen] More bug fixes for phantom stages.
034aa8d [Josh Rosen] Use `.max()` to find result stage for job.
eebdc2c [Josh Rosen] Don’t display pending stages for completed jobs.
67080ba [Josh Rosen] Ensure that "phantom stages" don't cause memory leaks.
7d10b97 [Josh Rosen] Merge remote-tracking branch 'apache/master' into job-page
d69c775 [Josh Rosen] Fix table sorting on all jobs page.
5eb39dc [Josh Rosen] Add pending stages table to job page.
f2a15da [Josh Rosen] Add status field to job details page.
171b53c [Josh Rosen] Move `startTime` to the start of SparkContext.
e2f2c43 [Josh Rosen] Fix sorting of stages in job details page.
8955f4c [Josh Rosen] Display information for pending stages on jobs page.
8ab6c28 [Josh Rosen] Compute numTasks from job start stage infos.
5884f91 [Josh Rosen] Add StageInfos to SparkListenerJobStart event.
79793cd [Josh Rosen] Track indices of completed stage to avoid overcounting when failures occur.
d62ea7b [Josh Rosen] Add failing Selenium test for stage overcounting issue.
1145c60 [Josh Rosen] Display text instead of progress bar for stages.
3d0a007 [Josh Rosen] Merge remote-tracking branch 'origin/master' into job-page
8a2351b [Josh Rosen] Add help tooltip to Spark Jobs page.
b7bf30e [Josh Rosen] Add stages progress bar; fix bug where active stages show as completed.
4846ce4 [Josh Rosen] Hide "(Job Group") if no jobs were submitted in job groups.
4d58e55 [Josh Rosen] Change label to "Tasks (for all stages)"
85e9c85 [Josh Rosen] Extract startTime into separate variable.
1cf4987 [Josh Rosen] Fix broken kill links; add Selenium test to avoid future regressions.
56701fa [Josh Rosen] Move last stage name / description logic out of markup.
a475ea1 [Josh Rosen] Add progress bars to jobs page.
45343b8 [Josh Rosen] More comments
4b206fb [Josh Rosen] Merge remote-tracking branch 'origin/master' into job-page
bfce2b9 [Josh Rosen] Address review comments, except for progress bar.
4487dcb [Josh Rosen] [SPARK-4145] Web UI job pages
2568a6c [Josh Rosen] Rename JobProgressPage to AllStagesPage:
[SPARK-4518][SPARK-4519][Streaming] Refactored file stream to prevent files from being processed multiple times

Because of a corner case, a file already selected for batch t can get considered again for batch t+2. This refactoring fixes it by remembering all the files selected in the last 1 minute, so that this corner case does not arise. Also uses spark context's hadoop configuration to access the file system API for listing directories.

pwendell Please take look. I still have not run long-running integration tests, so I cannot say for sure whether this has indeed solved the issue. You could do a first pass on this in the meantime.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #3419 from tdas/filestream-fix2 and squashes the following commits:

c19dd8a [Tathagata Das] Addressed PR comments.
513b608 [Tathagata Das] Updated docs.
d364faf [Tathagata Das] Added the current time condition back
5526222 [Tathagata Das] Removed unnecessary imports.
38bb736 [Tathagata Das] Fix long line.
203bbc7 [Tathagata Das] Un-ignore tests.
eaef4e1 [Tathagata Das] Fixed SPARK-4519
9dbd40a [Tathagata Das] Refactored FileInputDStream to remember last few batches.
[SPARK-4562] [MLlib] speedup vector

This PR change the underline array of DenseVector to numpy.ndarray to avoid the conversion, because most of the users will using numpy.array.

It also improve the serialization of DenseVector.

Before this change:

trial	| trainingTime | 	testTime
-------|--------|--------
0	| 5.126 | 	1.786
1	|2.698	|1.693

After the change:

trial	| trainingTime |	testTime
-------|--------|--------
0	|4.692	|0.554
1	|2.307	|0.525

This could partially fix the performance regression during test.

Author: Davies Liu <davies@databricks.com>

Closes #3420 from davies/ser2 and squashes the following commits:

0e1e6f3 [Davies Liu] fix tests
426f5db [Davies Liu] impove toArray()
44707ec [Davies Liu] add name for ISO-8859-1
fa7d791 [Davies Liu] address comments
1cfb137 [Davies Liu] handle zero sparse vector
2548ee2 [Davies Liu] fix tests
9e6389d [Davies Liu] bugfix
470f702 [Davies Liu] speed up DenseMatrix
f0d3c40 [Davies Liu] speedup SparseVector
ef6ce70 [Davies Liu] speed up dense vector
[SPARK-4578] fix asDict() with nested Row()

The Row object is created on the fly once the field is accessed, so we should access them by getattr() in asDict(0

Author: Davies Liu <davies@databricks.com>

Closes #3434 from davies/fix_asDict and squashes the following commits:

b20f1e7 [Davies Liu] fix asDict() with nested Row()
[SPARK-4548] []SPARK-4517] improve performance of python broadcast

Re-implement the Python broadcast using file:

1) serialize the python object using cPickle, write into disks.
2) Create a wrapper in JVM (for the dumped file), it read data from during serialization
3) Using TorrentBroadcast or HttpBroadcast to transfer the data (compressed) into executors
4) During deserialization, writing the data into disk.
5) Passing the path into Python worker, read data from disk and unpickle it into python object, until the first access.

It fixes the performance regression introduced in #2659, has similar performance as 1.1, but support object larger than 2G, also improve the memory efficiency (only one compressed copy in driver and executor).

Testing with a 500M broadcast and 4 tasks (excluding the benefit from reused worker in 1.2):

         name |   1.1   | 1.2 with this patch |  improvement
---------|--------|---------|--------
      python-broadcast-w-bytes  |	25.20  |	9.33   |	170.13% |
        python-broadcast-w-set	  |     4.13	   |    4.50  |	-8.35%  |

Testing with 100 tasks (16 CPUs):

         name |   1.1   | 1.2 with this patch |  improvement
---------|--------|---------|--------
     python-broadcast-w-bytes	| 38.16	| 8.40	 | 353.98%
        python-broadcast-w-set	| 23.29	| 9.59 |	142.80%

Author: Davies Liu <davies@databricks.com>

Closes #3417 from davies/pybroadcast and squashes the following commits:

50a58e0 [Davies Liu] address comments
b98de1d [Davies Liu] disable gc while unpickle
e5ee6b9 [Davies Liu] support large string
09303b8 [Davies Liu] read all data into memory
dde02dd [Davies Liu] improve performance of python broadcast
[SPARK-4266] [Web-UI] Reduce stage page load time.

The commit changes the java script used to show/hide additional
metrics in order to reduce page load time. SPARK-4016 significantly
increased page load time for the stage page when stages had a lot
(thousands or tens of thousands) of tasks, due to the additional
Javascript to hide some metrics by default and stripe the tables.
This commit reduces page load time in two ways:

(1) Now, all of the metrics that are hidden by default are
hidden by setting "display: none;" using CSS for the page,
rather than hiding them using javascript after the page loads.
Without this change, for stages with thousands of tasks, there
was a few second delay after page load, where first the additional
metrics were shown, and then after a delay were hidden once the
relevant JS finished running.

(2) CSS is used to stripe all of the tables except for the summary
table. The summary table needs javascript to do the striping because
some rows are hidden, but the javascript striping is slower, which
again resulted in a delay when it was used for the task table (where
for a few seconds after page load, all of the rows in the task table
would be white, while the browser finished running the JS to stripe
the table).

cc pwendell

This change is intended to be backported to 1.2 to avoid a regression in
UI performance when users run large jobs.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #3328 from kayousterhout/SPARK-4266 and squashes the following commits:

f964091 [Kay Ousterhout] [SPARK-4266] [Web-UI] Reduce stage page load time.
[SPARK-4525] Mesos should decline unused offers

Functionally, this is just a small change on top of #3393 (by jongyoul). The issue being addressed is discussed in the comments there. I have not yet added a test for the bug there. I will add one shortly.

I've also done some minor renaming/clean-up of variables in this class and tests.

Author: Patrick Wendell <pwendell@gmail.com>
Author: Jongyoul Lee <jongyoul@gmail.com>

Closes #3436 from pwendell/mesos-issue and squashes the following commits:

58c35b5 [Patrick Wendell] Adding unit test for this situation
c4f0697 [Patrick Wendell] Additional clean-up and fixes on top of existing fix
f20f1b3 [Jongyoul Lee] [SPARK-4525] MesosSchedulerBackend.resourceOffers cannot decline unused offers from acceptedOffers - Added code for declining unused offers among acceptedOffers - Edited testCase for checking declining unused offers
Revert "[SPARK-4525] Mesos should decline unused offers"

This reverts commit b043c27424d05e3200e7ba99a1a65656b57fa2f0.

I accidentally committed this using my own authorship credential. However,
I should have given authoriship to the original author: Jongyoul Lee.
[SPARK-4525] Mesos should decline unused offers

Functionally, this is just a small change on top of #3393 (by jongyoul). The issue being addressed is discussed in the comments there. I have not yet added a test for the bug there. I will add one shortly.

I've also done some minor renaming/clean-up of variables in this class and tests.

Author: Patrick Wendell <pwendell@gmail.com>
Author: Jongyoul Lee <jongyoul@gmail.com>

Closes #3436 from pwendell/mesos-issue and squashes the following commits:

58c35b5 [Patrick Wendell] Adding unit test for this situation
c4f0697 [Patrick Wendell] Additional clean-up and fixes on top of existing fix
f20f1b3 [Jongyoul Lee] [SPARK-4525] MesosSchedulerBackend.resourceOffers cannot decline unused offers from acceptedOffers - Added code for declining unused offers among acceptedOffers - Edited testCase for checking declining unused offers
[SPARK-4582][MLLIB] get raw vectors for further processing in Word2Vec

This is #3309 for the master branch.

e.g. clustering

Author: tkaessmann <tobias.kaessmanns24.com>

Closes #3309 from tkaessmann/branch-1.2 and squashes the following commits:

e3a3142 [tkaessmann] changes the comment for getVectors
58d3d83 [tkaessmann] removes sign from comment
a5be213 [tkaessmann] fixes getVectors to fit code guidelines
3782fa9 [tkaessmann] get raw vectors for further processing

Author: tkaessmann <tobias.kaessmann@s24.com>

Closes #3437 from mengxr/SPARK-4582 and squashes the following commits:

6c666b4 [tkaessmann] get raw vectors for further processing in Word2Vec
[SQL] Compute timeTaken correctly

```timeTaken``` should not count the time of printing result.

Author: w00228970 <wangfei1@huawei.com>

Closes #3423 from scwf/time-taken-bug and squashes the following commits:

da7e102 [w00228970] compute time taken correctly