This PR adds the URLs to the driver logs to `SparkListenerApplicationStarted` event, which is later used by the `ExecutorsListener` to populate the URLs to the driver logs in its own state. This info is then used when the UI is rendered to display links to the logs.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #6166 from harishreedharan/am-log-link and squashes the following commits:

943fc4f [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into am-log-link
9e5c04b [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into am-log-link
b3f9b9d [Hari Shreedharan] Updated comment based on feedback.
0840a95 [Hari Shreedharan] Move the result and sc.stop back to original location, minor import changes.
537a2f7 [Hari Shreedharan] Add test to ensure the log urls are populated and valid.
4033725 [Hari Shreedharan] Adding comments explaining how node reports are used to get the log urls.
6c5c285 [Hari Shreedharan] Import order.
346f4ea [Hari Shreedharan] Review feedback fixes.
629c1dc [Hari Shreedharan] Cleanup.
99fb1a3 [Hari Shreedharan] Send the log urls in App start event, to ensure that other listeners are not affected.
c0de336 [Hari Shreedharan] Ensure new unit test cleans up after itself.
50cdae3 [Hari Shreedharan] Added unit test, made the approach generic.
402e8e4 [Hari Shreedharan] Use `NodeReport` to get the URL for the logs. Also, make the environment variables generic so other cluster managers can use them as well.
1cf338f [Hari Shreedharan] [SPARK-7657][YARN] Add driver link in application UI, in cluster mode.

According to yhuai we spent 6-7 seconds cleaning closures in a partitioning job that takes 12 seconds. Since we provide these closures in Spark we know for sure they are serializable, so we can bypass the cleaning.

Author: Andrew Or <andrew@databricks.com>

Closes #6256 from andrewor14/sql-partition-speed-up and squashes the following commits:

a82b451 [Andrew Or] Fix style
10f7e3e [Andrew Or] Avoid getting call sites and cleaning closures
17e2943 [Andrew Or] Merge branch 'master' of github.com:apache/spark into sql-partition-speed-up
523f042 [Andrew Or] Skip unnecessary Utils.getCallSites too
f7fe143 [Andrew Or] Avoid unnecessary closure cleaning

Document current limitation of rdd.fold.

This does not resolve SPARK-6416 but just documents the issue.
CC JoshRosen

Author: Sean Owen <sowen@cloudera.com>

Closes #6231 from srowen/SPARK-6416 and squashes the following commits:

9fef39f [Sean Owen] Add comment to other languages; reword to highlight the difference from non-distributed collections and to not suggest it is a bug that is to be fixed
da40d84 [Sean Owen] Document current limitation of rdd.fold.

Two main changes:

Add two functions in ExternalBlockManager, which are putValues and getValues
because the implementation may not rely on the putBytes and getBytes

improve Tachyon integration.
Currently, when putting data into Tachyon, Spark first serialize all data in one partition into a ByteBuffer, and then write into Tachyon, this will uses much memory and increase GC overhead

when get data from Tachyon, getValues depends on getBytes, which also read all data into On heap byte arry, and result in much memory usage.
This PR changes the approach of the two functions, make them read / write data by stream to reduce memory usage.

In our testing,  when data size is huge, this patch reduces about 30% GC time and 70% full GC time, and total execution time reduces about 10%

Author: Mingfei <mingfei.shi@intel.com>

Closes #5908 from shimingfei/Tachyon-integration-rebase and squashes the following commits:

033bc57 [Mingfei] modify accroding to comments
747c69a [Mingfei] modify according to comments - format changes
ce52c67 [Mingfei] put close() in a finally block
d2c60bb [Mingfei] modify according to comments, some code style change
4c11591 [Mingfei] modify according to comments split putIntoExternalBlockStore into two functions add default implementation for getValues and putValues
cc0a32e [Mingfei] Make getValues read data from Tachyon by stream Make putValues write data to Tachyon by stream
017593d [Mingfei] add getValues and putValues in ExternalBlockManager's Interface

…rther extension to non-json outputs too.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #6273 from harishreedharan/json-to-api and squashes the following commits:

e14b73b [Hari Shreedharan] Rename `getJsonServlet` to `getServletHandler` i
42f8acb [Hari Shreedharan] Import order fixes.
2ef852f [Hari Shreedharan] [SPARK-7750][WebUI] Rename endpoints from `json` to `api` to allow further extension to non-json outputs too.

This patch re-adds a test which was removed in 9ebb44f8 due to a Java 6 compatibility issue.  We now use Guava's `Iterators.emptyIterator()` in place of `Collections.emptyIterator()`, which isn't present in all Java 6 versions.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6298 from JoshRosen/SPARK-7719-fix-java-6-test-code and squashes the following commits:

5c9bd85 [Josh Rosen] Re-add UnsafeShuffleWriterSuite.emptyIterator() test which was removed due to Java 6 issue

Currently, the background checkpointing thread fails silently if the checkpoint is not serializable. It is hard to debug and therefore its best to fail fast at `start()` when checkpointing is enabled and the checkpoint is not serializable.

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

Closes #6292 from tdas/SPARK-7767 and squashes the following commits:

51304e6 [Tathagata Das] Addressed comments.
c35237b [Tathagata Das] Added test for checkpoint serialization in StreamingContext.start()

SPARK-7741 is the equivalent of SPARK-7237 in streaming. This is an alternative to #6268.

Author: Andrew Or <andrew@databricks.com>

Closes #6269 from andrewor14/clean-moar and squashes the following commits:

c51c9ab [Andrew Or] Add periods (trivial)
6c686ac [Andrew Or] Merge branch 'master' of github.com:apache/spark into clean-moar
79a435b [Andrew Or] Fix tests
d18c9f9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into clean-moar
65ef07b [Andrew Or] Fix tests?
4b487a3 [Andrew Or] Add tests for closures passed to DStream operations
328139b [Andrew Or] Do not forget foreachRDD
5431f61 [Andrew Or] Clean streaming closures
72b7b73 [Andrew Or] Clean core closures

cc rxin, please take a quick look, I'm working on tests.

Author: Davies Liu <davies@databricks.com>

Closes #6238 from davies/readwrite and squashes the following commits:

c7200eb [Davies Liu] update tests
9cbf01b [Davies Liu] Merge branch 'master' of github.com:apache/spark into readwrite
f0c5a04 [Davies Liu] use sqlContext.read.load
5f68bc8 [Davies Liu] update tests
6437e9a [Davies Liu] Merge branch 'master' of github.com:apache/spark into readwrite
bcc6668 [Davies Liu] add reader amd writer API in Python

These were blocking RC1 so I fixed them manually.

This PR is based on #6081, thanks adrian-wang.

Closes #6081

Author: Daoyuan Wang <daoyuan.wang@intel.com>
Author: Davies Liu <davies@databricks.com>

Closes #6230 from davies/range and squashes the following commits:

d3ce5fe [Davies Liu] add tests
789eda5 [Davies Liu] add range() in Python
4590208 [Davies Liu] Merge commit 'refs/pull/6081/head' of github.com:apache/spark into range
cbf5200 [Daoyuan Wang] let's add python support in a separate PR
f45e3b2 [Daoyuan Wang] remove redundant toLong
617da76 [Daoyuan Wang] fix safe marge for corner cases
867c417 [Daoyuan Wang] fix
13dbe84 [Daoyuan Wang] update
bd998ba [Daoyuan Wang] update comments
d3a0c1b [Daoyuan Wang] add range api()

Author: Davies Liu <davies@databricks.com>

Closes #6172 from davies/revert_4147 and squashes the following commits:

3bfbbde [Davies Liu] Revert #4147

This is similar to #5999, but for streaming. Roughly 200 lines are tests.

One thing to note here is that we already do some kind of scoping thing for call sites, so this patch adds the new RDD operation scoping logic in the same place. Also, this patch adds a `try finally` block to set the relevant variables in a safer way.

tdas zsxwing

------------------------
**Before**
<img src="https://cloud.githubusercontent.com/assets/2133137/7625996/d88211b8-f9b4-11e4-90b9-e11baa52d6d7.png" width="450px"/>

--------------------------
**After**
<img src="https://cloud.githubusercontent.com/assets/2133137/7625997/e0878f8c-f9b4-11e4-8df3-7dd611b13c87.png" width="650px"/>

Author: Andrew Or <andrew@databricks.com>

Closes #6034 from andrewor14/dag-viz-streaming and squashes the following commits:

932a64a [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
e685df9 [Andrew Or] Rename createRDDWith
84d0656 [Andrew Or] Review feedback
697c086 [Andrew Or] Fix tests
53b9936 [Andrew Or] Set scopes for foreachRDD properly
1881802 [Andrew Or] Refactor DStream scope names again
af4ba8d [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
fd07d22 [Andrew Or] Make MQTT lower case
f6de871 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
0ca1801 [Andrew Or] Remove a few unnecessary withScopes on aliases
fa4e5fb [Andrew Or] Pass in input stream name rather than defining it from within
1af0b0e [Andrew Or] Fix style
074c00b [Andrew Or] Review comments
d25a324 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
e4a93ac [Andrew Or] Fix tests?
25416dc [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
9113183 [Andrew Or] Add tests for DStream scopes
b3806ab [Andrew Or] Fix test
bb80bbb [Andrew Or] Fix MIMA?
5c30360 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
5703939 [Andrew Or] Rename operations that create InputDStreams
7c4513d [Andrew Or] Group RDDs by DStream operations and batches
bf0ab6e [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
05c2676 [Andrew Or] Wrap many more methods in withScope
c121047 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-streaming
65ef3e9 [Andrew Or] Fix NPE
a0d3263 [Andrew Or] Scope streaming operations instead of RDD operations

This PR revert #5404, change to pass the version of python in driver into JVM, check it in worker before deserializing closure, then it can works with different major version of Python.

Author: Davies Liu <davies@databricks.com>

Closes #6203 from davies/py_version and squashes the following commits:

b8fb76e [Davies Liu] fix test
6ce5096 [Davies Liu] use string for version
47c6278 [Davies Liu] check python version of worker with driver

This patch fixes two things:

**SPARK-7627.** Cached RDDs no longer light up on the job page. This is a simple fix.
**SPARK-7472.** Display skipped stages differently from normal stages.

The latter is a major UX issue. Because we link the job viz to the stage viz even for skipped stages, the user may inadvertently click into the stage page of a skipped stage, which is empty.

-------------------
<img src="https://cloud.githubusercontent.com/assets/2133137/7675241/de1a3da6-fcea-11e4-8101-88055cef78c5.png" width="300px" />

Author: Andrew Or <andrew@databricks.com>

Closes #6171 from andrewor14/dag-viz-skipped and squashes the following commits:

f261797 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
0eda358 [Andrew Or] Tweak skipped stage border color
c604150 [Andrew Or] Tweak grayscale colors
7010676 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
762b541 [Andrew Or] Use special prefix for stage clusters to avoid collisions
51c95b9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
b928cd4 [Andrew Or] Fix potential leak + write tests for it
7c4c364 [Andrew Or] Show skipped stages differently
7cc34ce [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
c121fa2 [Andrew Or] Fix cache color

Learnt a lesson from SPARK-7655: Spark should avoid to use `scala.concurrent.ExecutionContext.Implicits.global` because the user may submit blocking actions to `scala.concurrent.ExecutionContext.Implicits.global` and exhaust all threads in it. This could crash Spark. So Spark should always use its own thread pools for safety.

This PR removes all usages of `scala.concurrent.ExecutionContext.Implicits.global` and uses proper thread pools to replace them.

Author: zsxwing <zsxwing@gmail.com>

Closes #6223 from zsxwing/SPARK-7693 and squashes the following commits:

a33ff06 [zsxwing] Decrease the max thread number from 1024 to 128
cf4b3fc [zsxwing] Remove "import scala.concurrent.ExecutionContext.Implicits.global"

This patch wraps `SnappyOutputStream` to ensure that `close()` is idempotent and to guard against write-after-`close()` bugs. This is a workaround for https://github.com/xerial/snappy-java/issues/107, a bug where a non-idempotent `close()` method can lead to stream corruption. We can remove this workaround if we upgrade to a snappy-java version that contains my fix for this bug, but in the meantime this patch offers a backportable Spark fix.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6176 from JoshRosen/SPARK-7660-wrap-snappy and squashes the following commits:

8b77aae [Josh Rosen] Wrap SnappyOutputStream to fix SPARK-7660

We should not call `DirectTaskResult.value` when holding the `TaskSchedulerImpl` lock. It may cost dozens of seconds to deserialize a large object.

Author: zsxwing <zsxwing@gmail.com>

Closes #6195 from zsxwing/SPARK-7655 and squashes the following commits:

21f502e [zsxwing] Add more comments
e25fa88 [zsxwing] Add comments
15010b5 [zsxwing] Deserialize value should not hold the TaskSchedulerImpl lock

[SPARK-7655][Core][SQL] Remove 'scala.concurrent.ExecutionContext.Implicits.global' in 'ask' and 'BroadcastHashJoin'

Because both `AkkaRpcEndpointRef.ask` and `BroadcastHashJoin` uses `scala.concurrent.ExecutionContext.Implicits.global`. However, because the tasks in `BroadcastHashJoin` are usually long-running tasks, which will occupy all threads in `global`. Then `ask` cannot get a chance to process the replies.

For `ask`, actually the tasks are very simple, so we can use `MoreExecutors.sameThreadExecutor()`. For `BroadcastHashJoin`, it's better to use `ThreadUtils.newDaemonCachedThreadPool`.

Author: zsxwing <zsxwing@gmail.com>

Closes #6200 from zsxwing/SPARK-7655-2 and squashes the following commits:

cfdc605 [zsxwing] Remove redundant imort and minor doc fix
cf83153 [zsxwing] Add "sameThread" and "newDaemonCachedThreadPool with maxThreadNumber" to ThreadUtils
08ad0ee [zsxwing] Remove 'scala.concurrent.ExecutionContext.Implicits.global' in 'ask' and 'BroadcastHashJoin'

[SPARK-7672] [CORE] Use int conversion in translating kryoserializer.buffer.mb to kryoserializer.buffer

In translating spark.kryoserializer.buffer.mb to spark.kryoserializer.buffer, use of toDouble will lead to "Fractional values not supported" error even when spark.kryoserializer.buffer.mb is an integer.
ilganeli, andrewor14

Author: Nishkam Ravi <nravi@cloudera.com>
Author: nishkamravi2 <nishkamravi@gmail.com>
Author: nravi <nravi@c1704.halxg.cloudera.com>

Closes #6198 from nishkamravi2/master_nravi and squashes the following commits:

171a53c [nishkamravi2] Update SparkConfSuite.scala
5261bf6 [Nishkam Ravi] Add a test for deprecated config spark.kryoserializer.buffer.mb
5190f79 [Nishkam Ravi] In translating from deprecated spark.kryoserializer.buffer.mb to spark.kryoserializer.buffer use int conversion since fractions are not permissible
059ce82 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
eaa13b5 [nishkamravi2] Update Client.scala
981afd2 [Nishkam Ravi] Check for read permission before initiating copy
1b81383 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
0f1abd0 [nishkamravi2] Update Utils.scala
474e3bf [nishkamravi2] Update DiskBlockManager.scala
97c383e [nishkamravi2] Update Utils.scala
8691e0c [Nishkam Ravi] Add a try/catch block around Utils.removeShutdownHook
2be1e76 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
1c13b79 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
bad4349 [nishkamravi2] Update Main.java
36a6f87 [Nishkam Ravi] Minor changes and bug fixes
b7f4ae7 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
4a45d6a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
458af39 [Nishkam Ravi] Locate the jar using getLocation, obviates the need to pass assembly path as an argument
d9658d6 [Nishkam Ravi] Changes for SPARK-6406
ccdc334 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
3faa7a4 [Nishkam Ravi] Launcher library changes (SPARK-6406)
345206a [Nishkam Ravi] spark-class merge Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ac58975 [Nishkam Ravi] spark-class changes
06bfeb0 [nishkamravi2] Update spark-class
35af990 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
32c3ab3 [nishkamravi2] Update AbstractCommandBuilder.java
4bd4489 [nishkamravi2] Update AbstractCommandBuilder.java
746f35b [Nishkam Ravi] "hadoop" string in the assembly name should not be mandatory (everywhere else in spark we mandate spark-assembly*hadoop*.jar)
bfe96e0 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
ee902fa [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
d453197 [nishkamravi2] Update NewHadoopRDD.scala
6f41a1d [nishkamravi2] Update NewHadoopRDD.scala
0ce2c32 [nishkamravi2] Update HadoopRDD.scala
f7e33c2 [Nishkam Ravi] Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ba1eb8b [Nishkam Ravi] Try-catch block around the two occurrences of removeShutDownHook. Deletion of semi-redundant occurrences of expensive operation inShutDown.
71d0e17 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
494d8c0 [nishkamravi2] Update DiskBlockManager.scala
3c5ddba [nishkamravi2] Update DiskBlockManager.scala
f0d12de [Nishkam Ravi] Workaround for IllegalStateException caused by recent changes to BlockManager.stop
79ea8b4 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
b446edc [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
5c9a4cb [nishkamravi2] Update TaskSetManagerSuite.scala
535295a [nishkamravi2] Update TaskSetManager.scala
3e1b616 [Nishkam Ravi] Modify test for maxResultSize
9f6583e [Nishkam Ravi] Changes to maxResultSize code (improve error message and add condition to check if maxResultSize > 0)
5f8f9ed [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
636a9ff [nishkamravi2] Update YarnAllocator.scala
8f76c8b [Nishkam Ravi] Doc change for yarn memory overhead
35daa64 [Nishkam Ravi] Slight change in the doc for yarn memory overhead
5ac2ec1 [Nishkam Ravi] Remove out
dac1047 [Nishkam Ravi] Additional documentation for yarn memory overhead issue
42c2c3d [Nishkam Ravi] Additional changes for yarn memory overhead issue
362da5e [Nishkam Ravi] Additional changes for yarn memory overhead
c726bd9 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
f00fa31 [Nishkam Ravi] Improving logging for AM memoryOverhead
1cf2d1e [nishkamravi2] Update YarnAllocator.scala
ebcde10 [Nishkam Ravi] Modify default YARN memory_overhead-- from an additive constant to a multiplier (redone to resolve merge conflicts)
2e69f11 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
efd688a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark
2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark
3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark
5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark
eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark
df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456)
6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed)
5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456)
681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles

This fixes a bug where an executor that exits can cause the driver's OutputCommitCoordinator to stop. To fix this, we use an `isDriver` flag and check it in `stop()`.

See https://issues.apache.org/jira/browse/SPARK-7563 for more details.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6197 from JoshRosen/SPARK-7563 and squashes the following commits:

04b2cc5 [Josh Rosen] [SPARK-7563] OutputCommitCoordinator.stop() should only be executed on the driver

cc pwendell sarutak

This commit cleans up some unnecessary code, eliminates the feature where when you mouse-over a box in the timeline, the corresponding task is highlighted in the table (because that feature is only useful in the rare case when you have a very small number of tasks, in which case it's easy to figure out the mapping anyway), and fixes a bug where nothing shows up if you try to visualize a stage with only 1 task.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #6202 from kayousterhout/SPARK-7676 and squashes the following commits:

dfd29d4 [Kay Ousterhout] [SPARK-7676] Bug fix and cleanup of stage timeline view

This PR builds on #2342 by adding a timeline view for the Stage page,
showing how tasks spend their time.

With this timeline, we can understand following things of a Stage.

* When/where each task ran
* Total duration of each task
* Proportion of the time each task spends

Also, this timeline view can scrollable and zoomable.

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

Closes #5843 from sarutak/stage-page-timeline and squashes the following commits:

4ba9604 [Kousuke Saruta] Fixed the order of legends
16bb552 [Kousuke Saruta] Removed border of legend area
2e5d605 [Kousuke Saruta] Modified warning message
16cb2e6 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into stage-page-timeline
7ae328f [Kousuke Saruta] Modified code style
d5f794a [Kousuke Saruta] Fixed performance issues more
64e6642 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into stage-page-timeline
e4a3354 [Kousuke Saruta] minor code style change
878e3b8 [Kousuke Saruta] Fixed a bug that tooltip remains
b9d8f1b [Kousuke Saruta] Fixed performance issue
ac8842b [Kousuke Saruta] Fixed layout
2319739 [Kousuke Saruta] Modified appearances more
81903ab [Kousuke Saruta] Modified appearances
a79dcc3 [Kousuke Saruta] Modified appearance
55a390c [Kousuke Saruta] Ignored scalastyle for a line-comment
29eae3e [Kousuke Saruta] limited to longest 1000 tasks
2a9e376 [Kousuke Saruta] Minor cleanup
385b6d2 [Kousuke Saruta] Added link feature
ba1ac3e [Kousuke Saruta] Fixed style
2ae8520 [Kousuke Saruta] Updated bootstrap-tooltip.js from 2.2.2 to 2.3.2
af430f1 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into stage-page-timeline
e694b8e [Kousuke Saruta] Added timeline view to StagePage
8f6610c [Kousuke Saruta] Fixed conflict
b587cf2 [Kousuke Saruta] initial commit
11fe67d [Kousuke Saruta] Fixed conflict
79ac03d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
a91abd3 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature
ef34a5b [Kousuke Saruta] Implement tooltip using bootstrap
b09d0c5 [Kousuke Saruta] Move `stroke` and `fill` attribute of rect elements to css
d3c63c8 [Kousuke Saruta] Fixed a little bit bugs
a36291b [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature
28714b6 [Kousuke Saruta] Fixed highlight issue
0dc4278 [Kousuke Saruta] Addressed most of Patrics's feedbacks
8110acf [Kousuke Saruta] Added scroll limit to Job timeline
974a64a [Kousuke Saruta] Removed unused function
ee7a7f0 [Kousuke Saruta] Refactored
6a91872 [Kousuke Saruta] Temporary commit
6693f34 [Kousuke Saruta] Added link to job/stage box in the timeline in order to move to corresponding row when we click
8f88222 [Kousuke Saruta] Added job/stage description
aeed4b1 [Kousuke Saruta] Removed stage timeline
fc1696c [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature
999ccd4 [Kousuke Saruta] Improved scalability
0fc6a31 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
19815ae [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
68b7540 [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature
52b5f0b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
dec85db [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
fcdab7d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
dab7cc1 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
09cce97 [Kousuke Saruta] Cleanuped
16f82cf [Kousuke Saruta] Cleanuped
9fb522e [Kousuke Saruta] Cleanuped
d05f2c2 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
e85e9aa [Kousuke Saruta] Cleanup: Added TimelineViewUtils.scala
a76e569 [Kousuke Saruta] Removed unused setting in timeline-view.css
5ce1b21 [Kousuke Saruta] Added vis.min.js, vis.min.css and vis.map to .rat-exclude
082f709 [Kousuke Saruta] Added Timeline-View feature for Applications, Jobs and Stages

Added a simple checking for SparkContext.
Also added two rational checking against null at AM object.

Author: ehnalis <zoltan.zvara@gmail.com>

Closes #6083 from ehnalis/cluster and squashes the following commits:

926bd96 [ehnalis] Moved check to SparkContext.
7c89b6e [ehnalis] Remove false line.
ea2a5fe [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
4924e01 [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
39e4fa3 [ehnalis] SPARK-7504 [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
9f287c5 [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode

In JobPage, we can jump a StagePage when we click corresponding box of DAG viz but the link path is incorrect.

When we click a box like as follows ...
![screenshot_from_2015-05-15 19 24 25](https://cloud.githubusercontent.com/assets/4736016/7651528/5f7ef824-fb3c-11e4-9518-8c9ade2dff7a.png)

We jump to index page.
![screenshot_from_2015-05-15 19 24 45](https://cloud.githubusercontent.com/assets/4736016/7651534/6d666274-fb3c-11e4-971c-c3f2dc2b1da2.png)

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

Closes #6184 from sarutak/fix-link-path-of-dag-viz and squashes the following commits:

faba3ba [Kousuke Saruta] Fix a incorrect link

Fix more places in which some test variables could be collected early by aggressive JVM optimization.
Added a couple of comments to note where existing references are sufficient in the same test pattern.

Author: Tim Ellison <t.p.ellison@gmail.com>

Closes #6187 from tellison/DefeatEarlyGC and squashes the following commits:

27329d9 [Tim Ellison] [CORE] Protect additional test vars from early GC

<h3>Description</h3>
Detect REPL mode once per JVM lifespan.
Previous behavior was to check presence of interpreter mode every time a job was submitted. In the case of execution of multiple short-living jobs this was causing massive mutual blocks between submission threads.

For more details please refer to https://issues.apache.org/jira/browse/SPARK-7233.

<h3>Notes</h3>
* I inverted the return value in case of catching an exception from `true` to `false`. It seems more logical to assume that if the REPL class is not found, we aren't in the interpreter mode.
* I'd personally would call `classForName` with just a Spark classloader (`org.apache.spark.util.Utils#getSparkClassLoader`) but `org.apache.spark.util.Utils#getContextOrSparkClassLoader` is said to be preferable.
* I struggled to come up with a concise, readable and clear unit test. Suggestions are welcome if you feel necessary.

Author: Oleksii Kostyliev <etander@gmail.com>
Author: Oleksii Kostyliev <okostyliev@thunderhead.com>

Closes #5835 from preeze/SPARK-7233 and squashes the following commits:

69bb9e4 [Oleksii Kostyliev] SPARK-7527: fixed explanatory comment to meet style-checker requirements
26dcc24 [Oleksii Kostyliev] SPARK-7527: fixed explanatory comment to meet style-checker requirements
c6f9685 [Oleksii Kostyliev] Merge remote-tracking branch 'remotes/upstream/master' into SPARK-7233
b78a983 [Oleksii Kostyliev] SPARK-7527: revert the fix and let it be addressed separately at a later stage
b64d441 [Oleksii Kostyliev] SPARK-7233: inline inInterpreter parameter into instantiateClass
86e2606 [Oleksii Kostyliev] SPARK-7233, SPARK-7527: Handle interpreter mode properly.
c7ee69c [Oleksii Kostyliev] Merge remote-tracking branch 'upstream/master' into SPARK-7233
d6c07fc [Oleksii Kostyliev] SPARK-7233: properly handle the inverted meaning of isInInterpreter
c319039 [Oleksii Kostyliev] SPARK-7233: move inInterpreter to Utils and make it lazy

cc tdas

Author: zsxwing <zsxwing@gmail.com>

Closes #6160 from zsxwing/SPARK-7650 and squashes the following commits:

fe6ae15 [zsxwing] Fix the import order
a4ffd99 [zsxwing] Merge branch 'master' into SPARK-7650
dc402b6 [zsxwing] Move streaming css and js files to the streaming project

It doesn't look to me Heartbeat is sent to Worker from anyone.

Author: Kan Zhang <kzhang@apache.org>

Closes #6163 from kanzhang/deadwood and squashes the following commits:

56be118 [Kan Zhang] [core] Remove unreachable Heartbeat message from Worker

I also updated the summary of the Streaming page.

![screen shot 2015-05-14 at 11 52 59 am](https://cloud.githubusercontent.com/assets/1000778/7640103/13cdf68e-fa36-11e4-84ec-e2a3954f4319.png)
![screen shot 2015-05-14 at 12 39 33 pm](https://cloud.githubusercontent.com/assets/1000778/7640151/4cc066ac-fa36-11e4-8494-2821d6a6f17c.png)

Author: zsxwing <zsxwing@gmail.com>

Closes #6154 from zsxwing/SPARK-7645 and squashes the following commits:

5db6ca1 [zsxwing] Add UIUtils.formatBatchTime
e4802df [zsxwing] Show milliseconds in the UI if the batch interval < 1 second

Use window.localStorage to store the status rather than the url so that the url won't be changed.

cc tdas

Author: zsxwing <zsxwing@gmail.com>

Closes #6158 from zsxwing/SPARK-7649 and squashes the following commits:

3c56fef [zsxwing] Use window.localStorage to store the status rather than the url

`dataDistribution` and `partitions` are `Option[Seq[_]]`. andrewor14 squito

Author: Xiangrui Meng <meng@databricks.com>

Closes #6157 from mengxr/SPARK-7643 and squashes the following commits:

99fe8a4 [Xiangrui Meng] use the correct size in RDDPage for storage info and partitions

In Spark Standalone setup, when some workers are DEAD, they will stay in master worker list for a while.
master.workers metrics for master is only showing the total number of workers, we need to monitor how many real ALIVE workers are there to ensure the cluster is healthy.

Author: Rex Xiong <pengx@microsoft.com>

Closes #6117 from twilightgod/add-aliveWorker-metrics and squashes the following commits:

6be69a5 [Rex Xiong] Fix comment for aliveWorkers metrics
a882f39 [Rex Xiong] Fix style for aliveWorkers metrics
38ce955 [Rex Xiong] Add aliveWorkers metrics in Master

zsxwing

Author: Andrew Or <andrew@databricks.com>

Closes #6138 from andrewor14/dag-viz-clean-properly and squashes the following commits:

19d4e98 [Andrew Or] Add synchronize
02542d6 [Andrew Or] Rename overloaded variable
d11bee1 [Andrew Or] Don't wait until all stages have started before rendering

This patch introduces a new shuffle manager that enhances the existing sort-based shuffle with a new cache-friendly sort algorithm that operates directly on binary data. The goals of this patch are to lower memory usage and Java object overheads during shuffle and to speed up sorting. It also lays groundwork for follow-up patches that will enable end-to-end processing of serialized records.

The new shuffle manager, `UnsafeShuffleManager`, can be enabled by setting `spark.shuffle.manager=tungsten-sort` in SparkConf.

The new shuffle manager uses directly-managed memory to implement several performance optimizations for certain types of shuffles. In cases where the new performance optimizations cannot be applied, the new shuffle manager delegates to SortShuffleManager to handle those shuffles.

UnsafeShuffleManager's optimizations will apply when _all_ of the following conditions hold:

 - The shuffle dependency specifies no aggregation or output ordering.
 - The shuffle serializer supports relocation of serialized values (this is currently supported
   by KryoSerializer and Spark SQL's custom serializers).
 - The shuffle produces fewer than 16777216 output partitions.
 - No individual record is larger than 128 MB when serialized.

In addition, extra spill-merging optimizations are automatically applied when the shuffle compression codec supports concatenation of serialized streams. This is currently supported by Spark's LZF serializer.

At a high-level, UnsafeShuffleManager's design is similar to Spark's existing SortShuffleManager.  In sort-based shuffle, incoming records are sorted according to their target partition ids, then written to a single map output file. Reducers fetch contiguous regions of this file in order to read their portion of the map output. In cases where the map output data is too large to fit in memory, sorted subsets of the output can are spilled to disk and those on-disk files are merged to produce the final output file.

UnsafeShuffleManager optimizes this process in several ways:

 - Its sort operates on serialized binary data rather than Java objects, which reduces memory consumption and GC overheads. This optimization requires the record serializer to have certain properties to allow serialized records to be re-ordered without requiring deserialization.  See SPARK-4550, where this optimization was first proposed and implemented, for more details.

 - It uses a specialized cache-efficient sorter (UnsafeShuffleExternalSorter) that sorts arrays of compressed record pointers and partition ids. By using only 8 bytes of space per record in the sorting array, this fits more of the array into cache.

 - The spill merging procedure operates on blocks of serialized records that belong to the same partition and does not need to deserialize records during the merge.

 - When the spill compression codec supports concatenation of compressed data, the spill merge simply concatenates the serialized and compressed spill partitions to produce the final output partition.  This allows efficient data copying methods, like NIO's `transferTo`, to be used and avoids the need to allocate decompression or copying buffers during the merge.

The shuffle read path is unchanged.

This patch is similar to [SPARK-4550](http://issues.apache.org/jira/browse/SPARK-4550) / #4450 but uses a slightly different implementation. The `unsafe`-based implementation featured in this patch lays the groundwork for followup patches that will enable sorting to operate on serialized data pages that will be prepared by Spark SQL's new `unsafe` operators (such as the new aggregation operator introduced in #5725).

### Future work

There are several tasks that build upon this patch, which will be left to future work:

- [SPARK-7271](https://issues.apache.org/jira/browse/SPARK-7271) Redesign / extend the shuffle interfaces to accept binary data as input. The goal here is to let us bypass serialization steps in cases where the sort input is produced by an operator that operates directly on binary data.
- Extension / redesign of the `Serializer` API. We can add new methods which allow serializers to determine the size requirements for serializing objects and for serializing objects directly to a specified memory address (similar to how `UnsafeRowConverter` works in Spark SQL).

<!-- Reviewable:start -->
[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/5868)
<!-- Reviewable:end -->

Author: Josh Rosen <joshrosen@databricks.com>

Closes #5868 from JoshRosen/unsafe-sort and squashes the following commits:

ef0a86e [Josh Rosen] Fix scalastyle errors
7610f2f [Josh Rosen] Add tests for proper cleanup of shuffle data.
d494ffe [Josh Rosen] Fix deserialization of JavaSerializer instances.
52a9981 [Josh Rosen] Fix some bugs in the address packing code.
51812a7 [Josh Rosen] Change shuffle manager sort name to tungsten-sort
4023fa4 [Josh Rosen] Add @Private annotation to some Java classes.
de40b9d [Josh Rosen] More comments to try to explain metrics code
df07699 [Josh Rosen] Attempt to clarify confusing metrics update code
5e189c6 [Josh Rosen] Track time spend closing / flushing files; split TimeTrackingOutputStream into separate file.
d5779c6 [Josh Rosen] Merge remote-tracking branch 'origin/master' into unsafe-sort
c2ce78e [Josh Rosen] Fix a missed usage of MAX_PARTITION_ID
e3b8855 [Josh Rosen] Cleanup in UnsafeShuffleWriter
4a2c785 [Josh Rosen] rename 'sort buffer' to 'pointer array'
6276168 [Josh Rosen] Remove ability to disable spilling in UnsafeShuffleExternalSorter.
57312c9 [Josh Rosen] Clarify fileBufferSize units
2d4e4f4 [Josh Rosen] Address some minor comments in UnsafeShuffleExternalSorter.
fdcac08 [Josh Rosen] Guard against overflow when expanding sort buffer.
85da63f [Josh Rosen] Cleanup in UnsafeShuffleSorterIterator.
0ad34da [Josh Rosen] Fix off-by-one in nextInt() call
56781a1 [Josh Rosen] Rename UnsafeShuffleSorter to UnsafeShuffleInMemorySorter
e995d1a [Josh Rosen] Introduce MAX_SHUFFLE_OUTPUT_PARTITIONS.
e58a6b4 [Josh Rosen] Add more tests for PackedRecordPointer encoding.
4f0b770 [Josh Rosen] Attempt to implement proper shuffle write metrics.
d4e6d89 [Josh Rosen] Update to bit shifting constants
69d5899 [Josh Rosen] Remove some unnecessary override vals
8531286 [Josh Rosen] Add tests that automatically trigger spills.
7c953f9 [Josh Rosen] Add test that covers UnsafeShuffleSortDataFormat.swap().
e1855e5 [Josh Rosen] Fix a handful of misc. IntelliJ inspections
39434f9 [Josh Rosen] Avoid integer multiplication overflow in getMemoryUsage (thanks FindBugs!)
1e3ad52 [Josh Rosen] Delete unused ByteBufferOutputStream class.
ea4f85f [Josh Rosen] Roll back an unnecessary change in Spillable.
ae538dc [Josh Rosen] Document UnsafeShuffleManager.
ec6d626 [Josh Rosen] Add notes on maximum # of supported shuffle partitions.
0d4d199 [Josh Rosen] Bump up shuffle.memoryFraction to make tests pass.
b3b1924 [Josh Rosen] Properly implement close() and flush() in DummySerializerInstance.
1ef56c7 [Josh Rosen] Revise compression codec support in merger; test cross product of configurations.
b57c17f [Josh Rosen] Disable some overly-verbose logs that rendered DEBUG useless.
f780fb1 [Josh Rosen] Add test demonstrating which compression codecs support concatenation.
4a01c45 [Josh Rosen] Remove unnecessary log message
27b18b0 [Josh Rosen] That for inserting records AT the max record size.
fcd9a3c [Josh Rosen] Add notes + tests for maximum record / page sizes.
9d1ee7c [Josh Rosen] Fix MiMa excludes for ShuffleWriter change
fd4bb9e [Josh Rosen] Use own ByteBufferOutputStream rather than Kryo's
67d25ba [Josh Rosen] Update Exchange operator's copying logic to account for new shuffle manager
8f5061a [Josh Rosen] Strengthen assertion to check partitioning
01afc74 [Josh Rosen] Actually read data in UnsafeShuffleWriterSuite
1929a74 [Josh Rosen] Update to reflect upstream ShuffleBlockManager -> ShuffleBlockResolver rename.
e8718dd [Josh Rosen] Merge remote-tracking branch 'origin/master' into unsafe-sort
9b7ebed [Josh Rosen] More defensive programming RE: cleaning up spill files and memory after errors
7cd013b [Josh Rosen] Begin refactoring to enable proper tests for spilling.
722849b [Josh Rosen] Add workaround for transferTo() bug in merging code; refactor tests.
9883e30 [Josh Rosen] Merge remote-tracking branch 'origin/master' into unsafe-sort
b95e642 [Josh Rosen] Refactor and document logic that decides when to spill.
1ce1300 [Josh Rosen] More minor cleanup
5e8cf75 [Josh Rosen] More minor cleanup
e67f1ea [Josh Rosen] Remove upper type bound in ShuffleWriter interface.
cfe0ec4 [Josh Rosen] Address a number of minor review comments:
8a6fe52 [Josh Rosen] Rename UnsafeShuffleSpillWriter to UnsafeShuffleExternalSorter
11feeb6 [Josh Rosen] Update TODOs related to shuffle write metrics.
b674412 [Josh Rosen] Merge remote-tracking branch 'origin/master' into unsafe-sort
aaea17b [Josh Rosen] Add comments to UnsafeShuffleSpillWriter.
4f70141 [Josh Rosen] Fix merging; now passes UnsafeShuffleSuite tests.
133c8c9 [Josh Rosen] WIP towards testing UnsafeShuffleWriter.
f480fb2 [Josh Rosen] WIP in mega-refactoring towards shuffle-specific sort.
57f1ec0 [Josh Rosen] WIP towards packed record pointers for use in optimized shuffle sort.
69232fd [Josh Rosen] Enable compressible address encoding for off-heap mode.
7ee918e [Josh Rosen] Re-order imports in tests
3aeaff7 [Josh Rosen] More refactoring and cleanup; begin cleaning iterator interfaces
3490512 [Josh Rosen] Misc. cleanup
f156a8f [Josh Rosen] Hacky metrics integration; refactor some interfaces.
2776aca [Josh Rosen] First passing test for ExternalSorter.
5e100b2 [Josh Rosen] Super-messy WIP on external sort
595923a [Josh Rosen] Remove some unused variables.
8958584 [Josh Rosen] Fix bug in calculating free space in current page.
f17fa8f [Josh Rosen] Add missing newline
c2fca17 [Josh Rosen] Small refactoring of SerializerPropertiesSuite to enable test re-use:
b8a09fe [Josh Rosen] Back out accidental log4j.properties change
bfc12d3 [Josh Rosen] Add tests for serializer relocation property.
240864c [Josh Rosen] Remove PrefixComputer and require prefix to be specified as part of insert()
1433b42 [Josh Rosen] Store record length as int instead of long.
026b497 [Josh Rosen] Re-use a buffer in UnsafeShuffleWriter
0748458 [Josh Rosen] Port UnsafeShuffleWriter to Java.
87e721b [Josh Rosen] Renaming and comments
d3cc310 [Josh Rosen] Flag that SparkSqlSerializer2 supports relocation
e2d96ca [Josh Rosen] Expand serializer API and use new function to help control when new UnsafeShuffle path is used.
e267cee [Josh Rosen] Fix compilation of UnsafeSorterSuite
9c6cf58 [Josh Rosen] Refactor to use DiskBlockObjectWriter.
253f13e [Josh Rosen] More cleanup
8e3ec20 [Josh Rosen] Begin code cleanup.
4d2f5e1 [Josh Rosen] WIP
3db12de [Josh Rosen] Minor simplification and sanity checks in UnsafeSorter
767d3ca [Josh Rosen] Fix invalid range in UnsafeSorter.
e900152 [Josh Rosen] Add test for empty iterator in UnsafeSorter
57a4ea0 [Josh Rosen] Make initialSize configurable in UnsafeSorter
abf7bfe [Josh Rosen] Add basic test case.
81d52c5 [Josh Rosen] WIP on UnsafeSorter

Old stages are removed without much feedback to the user. This happens very often in streaming. See screenshots below for more detail. zsxwing

**Before**

<img src="https://cloud.githubusercontent.com/assets/2133137/7621031/643cc1e0-f978-11e4-8f42-09decaac44a7.png" width="500px"/>

-------------------------
**After**
<img src="https://cloud.githubusercontent.com/assets/2133137/7621037/6e37348c-f978-11e4-84a5-e44e154f9b13.png" width="400px"/>

Author: Andrew Or <andrew@databricks.com>

Closes #6132 from andrewor14/dag-viz-remove-gracefully and squashes the following commits:

43175cd [Andrew Or] Handle removed jobs and stages gracefully

This is pretty useful for MLlib.

<img src="https://cloud.githubusercontent.com/assets/2133137/7599650/c7d03dd8-f8b8-11e4-8c0a-0a89e786c90f.png" width="400px"/>

Author: Andrew Or <andrew@databricks.com>

Closes #6100 from andrewor14/dag-viz-hover and squashes the following commits:

fefe2af [Andrew Or] Link tooltips for nodes that belong to the same RDD
90c6a7e [Andrew Or] Assign classes to clusters and nodes, not IDs

Subsequent fix following #5966. I tried this out locally.

Author: Andrew Or <andrew@databricks.com>

Closes #6129 from andrewor14/211-compilation and squashes the following commits:

713868f [Andrew Or] Fix compilation issue for scala 2.11

This is necessary for streaming and long-running Spark applications. zsxwing tdas

Author: Andrew Or <andrew@databricks.com>

Closes #6125 from andrewor14/viz-listener-leak and squashes the following commits:

8660949 [Andrew Or] Fix thing + add tests
33c0843 [Andrew Or] Clean up old job state