[SPARK-874] adding a --wait flag

This PR adds a --wait flag to the `./sbin/stop-all.sh` script.

Author: jbencook <jbenjamincook@gmail.com>

Closes #3567 from jbencook/master and squashes the following commits:

d05c5bb [jbencook] [SPARK-874] adding a --wait flag
 [SPARK-4691][shuffle] Restructure a few lines in shuffle code

In HashShuffleReader.scala and HashShuffleWriter.scala, no need to judge "dep.aggregator.isEmpty" again as this is judged by "dep.aggregator.isDefined"

In SortShuffleWriter.scala, "dep.aggregator.isEmpty"  is better than "!dep.aggregator.isDefined" ?

Author: maji2014 <maji3@asiainfo.com>

Closes #3553 from maji2014/spark-4691 and squashes the following commits:

bf7b14d [maji2014] change a elegant way for SortShuffleWriter.scala
10d0cf0 [maji2014] change a elegant way
d8f52dc [maji2014] code optimization for judgement
[SPARK-4765] Make GC time always shown in UI.

This commit removes the GC time for each task from the set of
optional, additional metrics, and instead always shows it for
each task.

cc pwendell

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #3622 from kayousterhout/gc_time and squashes the following commits:

15ac242 [Kay Ousterhout] Make TaskDetailsClassNames private[spark]
e71d893 [Kay Ousterhout] [SPARK-4765] Make GC time always shown in UI.
[SPARK-4714] BlockManager.dropFromMemory() should check whether block has been removed after synchronizing on BlockInfo instance.

After synchronizing on the `info` lock in the `removeBlock`/`dropOldBlocks`/`dropFromMemory` methods in BlockManager, the block that `info` represented may have already removed.

The three methods have the same logic to get the `info` lock:
```
   info = blockInfo.get(id)
   if (info != null) {
     info.synchronized {
       // do something
     }
   }
```

So, there is chance that when a thread enters the `info.synchronized` block, `info` has already been removed from the `blockInfo` map by some other thread who entered `info.synchronized` first.

The `removeBlock` and `dropOldBlocks` methods are idempotent, so it's safe for them to run on blocks that have already been removed.
But in `dropFromMemory` it may be problematic since it may drop block data which already removed into the diskstore, and this calls data store operations that are not designed to handle missing blocks.

This patch fixes this issue by adding a check to `dropFromMemory` to test whether blocks have been removed by a racing thread.

Author: hushan[胡珊] <hushan@xiaomi.com>

Closes #3574 from suyanNone/refine-block-concurrency and squashes the following commits:

edb989d [hushan[胡珊]] Refine code style and comments position
55fa4ba [hushan[胡珊]] refine code
e57e270 [hushan[胡珊]] add check info is already remove or not while having gotten info.syn
SPARK-4567. Make SparkJobInfo and SparkStageInfo serializable

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3426 from sryza/sandy-spark-4567 and squashes the following commits:

cb4b8d2 [Sandy Ryza] SPARK-4567. Make SparkJobInfo and SparkStageInfo serializable
SPARK-4805 [CORE] BlockTransferMessage.toByteArray() trips assertion

Allocate enough room for type byte as well as message, to avoid tripping assertion about capacity of the buffer

Author: Sean Owen <sowen@cloudera.com>

Closes #3650 from srowen/SPARK-4805 and squashes the following commits:

9e1d502 [Sean Owen] Allocate enough room for type byte as well as message, to avoid tripping assertion about capacity of the buffer
[SPARK-4740] Create multiple concurrent connections between two peer nodes in Netty.

It's been reported that when the number of disks is large and the number of nodes is small, Netty network throughput is low compared with NIO. We suspect the problem is that only a small number of disks are utilized to serve shuffle files at any given point, due to connection reuse. This patch adds a new config parameter to specify the number of concurrent connections between two peer nodes, default to 2.

Author: Reynold Xin <rxin@databricks.com>

Closes #3625 from rxin/SPARK-4740 and squashes the following commits:

ad4241a [Reynold Xin] Updated javadoc.
f33c72b [Reynold Xin] Code review feedback.
0fefabb [Reynold Xin] Use double check in synchronization.
41dfcb2 [Reynold Xin] Added test case.
9076b4a [Reynold Xin] Fixed two NPEs.
3e1306c [Reynold Xin] Minor style fix.
4f21673 [Reynold Xin] [SPARK-4740] Create multiple concurrent connections between two peer nodes in Netty.
Config updates for the new shuffle transport.

Author: Reynold Xin <rxin@databricks.com>

Closes #3657 from rxin/conf-update and squashes the following commits:

7370eab [Reynold Xin] Config updates for the new shuffle transport.
[Minor] Use <sup> tag for help icon in web UI page header

This small commit makes the `(?)` web UI help link into a superscript, which should address feedback that the current design makes it look like an error occurred or like information is missing.

Before:

![image](https://cloud.githubusercontent.com/assets/50748/5370611/a3ed0034-7fd9-11e4-870f-05bd9faad5b9.png)

After:

![image](https://cloud.githubusercontent.com/assets/50748/5370602/6c5ca8d6-7fd9-11e4-8d1a-568d71290aa7.png)

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3659 from JoshRosen/webui-help-sup and squashes the following commits:

bd72899 [Josh Rosen] Use <sup> tag for help icon in web UI page header.
[SPARK-4772] Clear local copies of accumulators as soon as we're done with them

Accumulators keep thread-local copies of themselves.  These copies were only cleared at the beginning of a task.  This meant that (a) the memory they used was tied up until the next task ran on that thread, and (b) if a thread died, the memory it had used for accumulators was locked up forever on that worker.

This PR clears the thread-local copies of accumulators at the end of each task, in the tasks finally block, to make sure they are cleaned up between tasks.  It also stores them in a ThreadLocal object, so that if, for some reason, the thread dies, any memory they are using at the time should be freed up.

Author: Nathan Kronenfeld <nkronenfeld@oculusinfo.com>

Closes #3570 from nkronenfeld/Accumulator-Improvements and squashes the following commits:

a581f3f [Nathan Kronenfeld] Change Accumulators to private[spark] instead of adding mima exclude to get around false positive in mima tests
b6c2180 [Nathan Kronenfeld] Include MiMa exclude as per build error instructions - this version incompatibility should be irrelevent, as it will only surface if a master is talking to a worker running a different version of spark.
537baad [Nathan Kronenfeld] Fuller refactoring as intended, incorporating JR's suggestions for ThreadLocal localAccums, and keeping clear(), but also calling it in tasks' finally block, rather than just at the beginning of the task.
39a82f2 [Nathan Kronenfeld] Clear local copies of accumulators as soon as we're done with them
[SPARK-4161]Spark shell class path is not correctly set if "spark.driver.extraClassPath" is set in defaults.conf

Author: GuoQiang Li <witgo@qq.com>

Closes #3050 from witgo/SPARK-4161 and squashes the following commits:

abb6fa4 [GuoQiang Li] move usejavacp opt to spark-shell
89e39e7 [GuoQiang Li] review commit
c2a6f04 [GuoQiang Li] Spark shell class path is not correctly set if "spark.driver.extraClassPath" is set in defaults.conf
[SPARK-4329][WebUI] HistoryPage pagenation

Current HistoryPage have links only to previous page or next page.
I suggest to add index to access history pages easily.

I implemented like following pics.

If there are many pages, current page +/- N pages, head page and last page are indexed.

![2014-11-10 16 13 25](https://cloud.githubusercontent.com/assets/4736016/4986246/9c7bbac4-6937-11e4-8695-8634d039d5b6.png)
![2014-11-10 16 03 21](https://cloud.githubusercontent.com/assets/4736016/4986210/3951bb74-6937-11e4-8b4e-9f90d266d736.png)
![2014-11-10 16 03 39](https://cloud.githubusercontent.com/assets/4736016/4986211/3b196ad8-6937-11e4-9f81-74bc0a6dad5b.png)
![2014-11-10 16 03 49](https://cloud.githubusercontent.com/assets/4736016/4986213/40686138-6937-11e4-86c0-41100f0404f6.png)
![2014-11-10 16 04 04](https://cloud.githubusercontent.com/assets/4736016/4986215/4326c9b4-6937-11e4-87ac-0f30c86ec6e3.png)

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

Closes #3194 from sarutak/history-page-indexing and squashes the following commits:

15d3d2d [Kousuke Saruta] Simplified code
c93932e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into history-page-indexing
1c2f605 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into history-page-indexing
76b05e3 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into history-page-indexing
b2240f8 [Kousuke Saruta] Fixed style
ec7922e [Kousuke Saruta] Simplified code
755a004 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into history-page-indexing
cfa242b [Kousuke Saruta] Added index to HistoryPage
[SPARK-4771][Docs] Document standalone cluster supervise mode

tdas looks like streaming already refers to the supervise mode. The link from there is broken though.

Author: Andrew Or <andrew@databricks.com>

Closes #3627 from andrewor14/document-supervise and squashes the following commits:

9ca0908 [Andrew Or] Wording changes
2b55ed2 [Andrew Or] Document standalone cluster supervise mode
[SPARK-4215] Allow requesting / killing executors only in YARN mode

Currently this doesn't do anything in other modes, so we might as well just disable it rather than having the user mistakenly rely on it.

Author: Andrew Or <andrew@databricks.com>

Closes #3615 from andrewor14/dynamic-allocation-yarn-only and squashes the following commits:

ce6487a [Andrew Or] Allow requesting / killing executors only in YARN mode
[SPARK-4793] [Deploy] ensure .jar at end of line

sometimes I switch between different version and do not want to rebuild spark, so I rename assembly.jar into .jar.bak, but still caught by `compute-classpath.sh`

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #3641 from adrian-wang/jar and squashes the following commits:

45cbfd0 [Daoyuan Wang] ensure .jar at end of line
[SPARK-4569] Rename 'externalSorting' in Aggregator

Hi all - I've renamed the unhelpfully named variable and added a comment clarifying what's actually happening.

Author: Ilya Ganelin <ilya.ganelin@capitalone.com>

Closes #3666 from ilganeli/SPARK-4569B and squashes the following commits:

1810394 [Ilya Ganelin] [SPARK-4569] Rename 'externalSorting' in Aggregator
e2d2092 [Ilya Ganelin] [SPARK-4569] Rename 'externalSorting' in Aggregator
d7cefec [Ilya Ganelin] [SPARK-4569] Rename 'externalSorting' in Aggregator
5b3f39c [Ilya Ganelin] [SPARK-4569] Rename  in Aggregator
[SPARK-4759] Fix driver hanging from coalescing partitions

The driver hangs sometimes when we coalesce RDD partitions. See JIRA for more details and reproduction.

This is because our use of empty string as default preferred location in `CoalescedRDDPartition` causes the `TaskSetManager` to schedule the corresponding task on host `""` (empty string). The intended semantics here, however, is that the partition does not have a preferred location, and the TSM should schedule the corresponding task accordingly.

Author: Andrew Or <andrew@databricks.com>

Closes #3633 from andrewor14/coalesce-preferred-loc and squashes the following commits:

e520d6b [Andrew Or] Oops
3ebf8bd [Andrew Or] A few comments
f370a4e [Andrew Or] Fix tests
2f7dfb6 [Andrew Or] Avoid using empty string as default preferred location
MAINTENANCE: Automated closing of pull requests.

This commit exists to close the following pull requests on Github:

Closes #2883 (close requested by 'pwendell')
Closes #3364 (close requested by 'pwendell')
Closes #4458 (close requested by 'pwendell')
Closes #1574 (close requested by 'andrewor14')
Closes #2546 (close requested by 'andrewor14')
Closes #2516 (close requested by 'andrewor14')
Closes #154 (close requested by 'andrewor14')
SPARK-3526 Add section about data locality to the tuning guide

cc kayousterhout

I have a few outstanding questions from compiling this documentation:
- What's the difference between NO_PREF and ANY?  I understand the implications of the ordering but don't know what an example of each would be
- Why is NO_PREF ahead of RACK_LOCAL?  I would think it'd be better to schedule rack-local tasks ahead of no preference if you could only do one or the other.  Is the idea to wait longer and hope for the rack-local tasks to turn into node-local or better?
- Will there be a datacenter-local locality level in the future?  Apache Cassandra for example has this level

Author: Andrew Ash <andrew@andrewash.com>

Closes #2519 from ash211/SPARK-3526 and squashes the following commits:

44cff28 [Andrew Ash] Link to spark.locality parameters rather than copying the list
6d5d966 [Andrew Ash] Stay focused on Spark, no astronaut architecture mumbo-jumbo
20e0e31 [Andrew Ash] SPARK-3526 Add section about data locality to the tuning guide
[CORE]codeStyle: uniform ConcurrentHashMap define in StorageLevel.scala with other places

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #2793 from liyezhang556520/uniformHashMap and squashes the following commits:

5884735 [Zhang, Liye] [CORE]codeStyle: uniform ConcurrentHashMap define in StorageLevel.scala