[SPARK-3623][GraphX] GraphX should support the checkpoint operation

Author: GuoQiang Li <witgo@qq.com>

Closes #2631 from witgo/SPARK-3623 and squashes the following commits:

a70c500 [GuoQiang Li] Remove java related
4d1e249 [GuoQiang Li] Add comments
e682724 [GuoQiang Li] Graph should support the checkpoint operation
[SPARK-4646] Replace Scala.util.Sorting.quickSort with Sorter(TimSort) in Spark

This patch just replaces a native quick sorter with Sorter(TimSort) in Spark.
It could get performance gains by ~8% in my quick experiments.

Author: Takeshi Yamamuro <linguin.m.s@gmail.com>

Closes #3507 from maropu/TimSortInEdgePartitionBuilderSpike and squashes the following commits:

8d4e5d2 [Takeshi Yamamuro] Remove a wildcard import
3527e00 [Takeshi Yamamuro] Replace Scala.util.Sorting.quickSort with Sorter(TimSort) in Spark
[SPARK-4620] Add unpersist in Graph and GraphImpl

Add an IF to uncache both vertices and edges of Graph/GraphImpl.
This IF is useful when iterative graph operations build a new graph in each iteration, and the vertices and edges of previous iterations are no longer needed for following iterations.

Author: Takeshi Yamamuro <linguin.m.s@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Ankur Dave <ankurdave@gmail.com>

Closes #3476 from maropu/UnpersistInGraphSpike and squashes the following commits:

77a006a [Takeshi Yamamuro] Add unpersist in Graph and GraphImpl
[SPARK-4764] Ensure that files are fetched atomically

tempFile is created in the same directory than targetFile, so that the
move from tempFile to targetFile is always atomic

Author: Christophe Préaud <christophe.preaud@kelkoo.com>

Closes #2855 from preaudc/master and squashes the following commits:

9ba89ca [Christophe Préaud] Ensure that files are fetched atomically
54419ae [Christophe Préaud] Merge remote-tracking branch 'upstream/master'
c6a5590 [Christophe Préaud] Revert commit 8ea871f8130b2490f1bad7374a819bf56f0ccbbd
7456a33 [Christophe Préaud] Merge remote-tracking branch 'upstream/master'
8ea871f [Christophe Préaud] Ensure that files are fetched atomically
[SPARK-4774] [SQL] Makes HiveFromSpark more portable

HiveFromSpark read the kv1.txt file from SPARK_HOME/examples/src/main/resources/kv1.txt which assumed
you had a source tree checked out. Now we copy the kv1.txt file to a temporary file and delete it when
the jvm shuts down. This allows us to run this example outside of a spark source tree.

Author: Kostas Sakellis <kostas@cloudera.com>

Closes #3628 from ksakellis/kostas-spark-4774 and squashes the following commits:

6770f83 [Kostas Sakellis] [SPARK-4774] [SQL] Makes HiveFromSpark more portable
[SPARK-4750] Dynamic allocation - synchronize kills

Simple omission on my part.

Author: Andrew Or <andrew@databricks.com>

Closes #3612 from andrewor14/dynamic-allocation-synchronization and squashes the following commits:

1f03b60 [Andrew Or] Synchronize kills
SPARK-3926 [CORE] Reopened: result of JavaRDD collectAsMap() is not serializable

My original 'fix' didn't fix at all. Now, there's a unit test to check whether it works. Of the two options to really fix it -- copy the `Map` to a `java.util.HashMap`, or copy and modify Scala's implementation in `Wrappers.MapWrapper`, I went with the latter.

Author: Sean Owen <sowen@cloudera.com>

Closes #3587 from srowen/SPARK-3926 and squashes the following commits:

8586bb9 [Sean Owen] Remove unneeded no-arg constructor, and add additional note about copied code in LICENSE
7bb0e66 [Sean Owen] Make SerializableMapWrapper actually serialize, and add unit test
SPARK-4770. [DOC] [YARN] spark.scheduler.minRegisteredResourcesRatio doc...

...umented default is incorrect for YARN

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3624 from sryza/sandy-spark-4770 and squashes the following commits:

bd81a3a [Sandy Ryza] SPARK-4770. [DOC] [YARN] spark.scheduler.minRegisteredResourcesRatio documented default is incorrect for YARN
[SQL] remove unnecessary import in spark-sql

Author: Jacky Li <jacky.likun@huawei.com>

Closes #3630 from jackylk/remove and squashes the following commits:

150e7e0 [Jacky Li] remove unnecessary import
[SPARK-4769] [SQL] CTAS does not work when reading from temporary tables

This is the code refactor and follow ups for #2570

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

Closes #3336 from chenghao-intel/createtbl and squashes the following commits:

3563142 [Cheng Hao] remove the unused variable
e215187 [Cheng Hao] eliminate the compiling warning
4f97f14 [Cheng Hao] fix bug in unittest
5d58812 [Cheng Hao] revert the API changes
b85b620 [Cheng Hao] fix the regression of temp tabl not found in CTAS
[SPARK-3154][STREAMING] Replace ConcurrentHashMap with mutable.HashMap and remove @volatile from 'stopped'

Since `sequenceNumberToProcessor` and `stopped` are both protected by the lock `sequenceNumberToProcessor`, `ConcurrentHashMap` and `volatile` is unnecessary. So this PR updated them accordingly.

Author: zsxwing <zsxwing@gmail.com>

Closes #3634 from zsxwing/SPARK-3154 and squashes the following commits:

0d087ac [zsxwing] Replace ConcurrentHashMap with mutable.HashMap and remove @volatile from 'stopped'
[SPARK-4785][SQL] Initilize Hive UDFs on the driver and serialize them with a wrapper

Different from Hive 0.12.0, in Hive 0.13.1 UDF/UDAF/UDTF (aka Hive function) objects should only be initialized once on the driver side and then serialized to executors. However, not all function objects are serializable (e.g. GenericUDF doesn't implement Serializable). Hive 0.13.1 solves this issue with Kryo or XML serializer. Several utility ser/de methods are provided in class o.a.h.h.q.e.Utilities for this purpose. In this PR we chose Kryo for efficiency. The Kryo serializer used here is created in Hive. Spark Kryo serializer wasn't used because there's no available SparkConf instance.

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

Closes #3640 from chenghao-intel/udf_serde and squashes the following commits:

8e13756 [Cheng Hao] Update the comment
74466a3 [Cheng Hao] refactor as feedbacks
396c0e1 [Cheng Hao] avoid Simple UDF to be serialized
e9c3212 [Cheng Hao] update the comment
19cbd46 [Cheng Hao] support udf instance ser/de after initialization
SPARK-4338. [YARN] Ditch yarn-alpha.

Sorry if this is a little premature with 1.2 still not out the door, but it will make other work like SPARK-4136 and SPARK-2089 a lot easier.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3215 from sryza/sandy-spark-4338 and squashes the following commits:

1c5ac08 [Sandy Ryza] Update building Spark docs and remove unnecessary newline
9c1421c [Sandy Ryza] SPARK-4338. Ditch yarn-alpha.
[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.