[SPARK-2652] [PySpark] donot use KyroSerializer as default serializer

KyroSerializer can not serialize customized class without registered explicitly, use it as default serializer in PySpark will introduce some regression in MLlib.

cc mengxr

Author: Davies Liu <davies@databricks.com>

Closes #2916 from davies/revert and squashes the following commits:

43eb6d3 [Davies Liu] donot use KyroSerializer as default serializer

(cherry picked from commit 809c785bcc33e684a68ea14240a466def864199a)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[SPARK-4076] Parameter expansion in spark-config is wrong

In sbin/spark-config.sh, parameter expansion is used to extract source root as follows.

    this="${BASH_SOURCE-$0}"

I think, the parameter expansion should be ":" instead of "".
If we use "-" and BASH_SOURCE="", (empty character is set, not unset),
"" (empty character) is set to $this.

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

Closes #2930 from sarutak/SPARK-4076 and squashes the following commits:

32a0370 [Kousuke Saruta] Fixed wrong parameter expansion

(cherry picked from commit 30ea2868e7afbec20bfc83818249b6d2d7dc6aec)
Signed-off-by: Andrew Or <andrew@databricks.com>

Conflicts:
	sbin/spark-config.sh
[SPARK-4075] [Deploy] Jar url validation is not enough for Jar file

In deploy.ClientArguments.isValidJarUrl, the url is checked as follows.

    def isValidJarUrl(s: String): Boolean = s.matches("(.+):(.+)jar")

So, it allows like 'hdfs:file.jar' (no authority).

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

Closes #2925 from sarutak/uri-syntax-check-improvement and squashes the following commits:

cf06173 [Kousuke Saruta] Improved URI syntax checking

(cherry picked from commit 098f83c7ccd7dad9f9228596da69fe5f55711a52)
Signed-off-by: Andrew Or <andrew@databricks.com>
[SPARK-4006] In long running contexts, we encountered the situation of d...

...ouble registe...

...r without a remove in between. The cause for that is unknown, and assumed a temp network issue.

However, since the second register is with a BlockManagerId on a different port, blockManagerInfo.contains() returns false, while blockManagerIdByExecutor returns Some. This inconsistency is caught in a conditional statement that does System.exit(1), which is a huge robustness issue for us.

The fix - simply remove the old id from both maps during register when this happens. We are mimicking the behavior of expireDeadHosts(), by doing local cleanup of the maps before trying to add new ones.

Also - added some logging for register and unregister.

This is just like https://github.com/apache/spark/pull/2886 except it's on branch-1.1

Author: Tal Sliwowicz <tal.s@taboola.com>

Closes #2915 from tsliwowicz/branch-1.1-block-mgr-removal and squashes the following commits:

d122236 [Tal Sliwowicz] [SPARK-4006] In long running contexts, we encountered the situation of double registe...
[SPARK-4080] Only throw IOException from [write|read][Object|External]

If classes implementing Serializable or Externalizable interfaces throw
exceptions other than IOException or ClassNotFoundException from their
(de)serialization methods, then this results in an unhelpful
"IOException: unexpected exception type" rather than the actual exception that
produced the (de)serialization error.

This patch fixes this by adding a utility method that re-wraps any uncaught
exceptions in IOException (unless they are already instances of IOException).

Author: Josh Rosen <joshrosen@databricks.com>

Closes #2932 from JoshRosen/SPARK-4080 and squashes the following commits:

cd3a9be [Josh Rosen] [SPARK-4080] Only throw IOException from [write|read][Object|External].

(cherry picked from commit 6c98c29ae0033556fd4424f41d1de005c509e511)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>

Conflicts:
	core/src/main/scala/org/apache/spark/broadcast/TorrentBroadcast.scala
	core/src/main/scala/org/apache/spark/scheduler/MapStatus.scala
	streaming/src/main/scala/org/apache/spark/streaming/api/python/PythonDStream.scala
[SPARK-4056] Upgrade snappy-java to 1.1.1.5

This upgrades snappy-java to 1.1.1.5, which improves error messages when attempting to deserialize empty inputs using SnappyInputStream (see https://github.com/xerial/snappy-java/issues/89).

Author: Josh Rosen <rosenville@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>

Closes #2911 from JoshRosen/upgrade-snappy-java and squashes the following commits:

adec96c [Josh Rosen] Use snappy-java 1.1.1.5
cc953d6 [Josh Rosen] [SPARK-4056] Upgrade snappy-java to 1.1.1.4

(cherry picked from commit 898b22ab1fe90e8a3935b19566465046f2256fa6)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>

Conflicts:
	pom.xml
Revert "[SPARK-4056] Upgrade snappy-java to 1.1.1.5"

This reverts commit b7541ae89c3db71979f11f2f0b2cb737cb5d1fb3.
Fix build breakage introduced by 6c10c2770c718287f9cc2af4109b701fa1057b70
[MLlib] SPARK-3987: add test case on objective value for NNLS

Also update step parameter to pass the proposed test

Author: coderxiang <shuoxiangpub@gmail.com>

Closes #2965 from coderxiang/nnls-test and squashes the following commits:

24b06f9 [coderxiang] add test case on objective value for NNLS; update step parameter to pass the test

(cherry picked from commit 7e3a1ada86e6adf1ddd4d8a321824daf5f3b2c75)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[SPARK-4110] Wrong comments about default settings in spark-daemon.sh

In spark-daemon.sh, thare are following comments.

    #   SPARK_CONF_DIR  Alternate conf dir. Default is ${SPARK_PREFIX}/conf.
    #   SPARK_LOG_DIR   Where log files are stored.  PWD by default.

But, I think the default value for SPARK_CONF_DIR is `${SPARK_HOME}/conf` and for SPARK_LOG_DIR is `${SPARK_HOME}/logs`.

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

Closes #2972 from sarutak/SPARK-4110 and squashes the following commits:

5a171a2 [Kousuke Saruta] Fixed wrong comments

(cherry picked from commit 44d8b45a38c8d934628373a3b21084432516ee00)
Signed-off-by: Andrew Or <andrew@databricks.com>
[SPARK-4107] Fix incorrect handling of read() and skip() return values (branch-1.1 backport)

`read()` may return fewer bytes than requested; when this occurred, the old code would silently return less data than requested, which might cause stream corruption errors.  `skip()` faces similar issues, too.

This patch fixes several cases where we mis-handle these methods' return values.

This is a backport of #2969 to `branch-1.1`.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #2974 from JoshRosen/spark-4107-branch-1.1-backport and squashes the following commits:

d82c05b [Josh Rosen] [SPARK-4107] Fix incorrect handling of read() and skip() return values
[SPARK-4065] Add check for IPython on Windows

This issue employs logic similar to the bash launcher (pyspark) to check
if IPTYHON=1, and if so launch ipython with options in IPYTHON_OPTS.
This fix assumes that ipython is available in the system Path, and can
be invoked with a plain "ipython" command.

Author: Michael Griffiths <msjgriffiths@gmail.com>

Closes #2910 from msjgriffiths/pyspark-windows and squashes the following commits:

ef34678 [Michael Griffiths] Change build message to comply with [SPARK-3775]
361e3d8 [Michael Griffiths] [SPARK-4065] Add check for IPython on Windows
9ce72d1 [Michael Griffiths] [SPARK-4065] Add check for IPython on Windows

(cherry picked from commit 2f254dacf4b7ab9c59c7cef59fd364ca682162ae)
Signed-off-by: Andrew Or <andrew@databricks.com>
[SPARK-4097] Fix the race condition of 'thread'

There is a chance that `thread` is null when calling `thread.interrupt()`.

```Scala
  override def cancel(): Unit = this.synchronized {
    _cancelled = true
    if (thread != null) {
      thread.interrupt()
    }
  }
```
Should put `thread = null` into a `synchronized` block to fix the race condition.

Author: zsxwing <zsxwing@gmail.com>

Closes #2957 from zsxwing/SPARK-4097 and squashes the following commits:

edf0aee [zsxwing] Add comments to explain the lock
c5cfeca [zsxwing] Fix the race condition of 'thread'

(cherry picked from commit e7fd80413d531e23b6c4def0ee32e52a39da36fa)
Signed-off-by: Reynold Xin <rxin@databricks.com>
[SPARK-4115][GraphX] Add overrided count for edge counting of EdgeRDD.

Accumulate sizes of all the EdgePartitions just like the VertexRDD.

Author: luluorta <luluorta@gmail.com>

Closes #2975 from luluorta/graph-edge-count and squashes the following commits:

86ef0e5 [luluorta] Add overrided count for edge counting of EdgeRDD.

(cherry picked from commit ee29ef3800438501e0ff207feb00a28973fc0769)
Signed-off-by: Reynold Xin <rxin@databricks.com>
[branch-1.1][SPARK-4148][PySpark] fix seed distribution and add some tests for rdd.sample

Port #3010 to branch-1.1.

Author: Xiangrui Meng <meng@databricks.com>

Closes #3104 from mengxr/SPARK-4148-1.1 and squashes the following commits:

684c002 [Xiangrui Meng] apply SPARK-4148 to branch-1.1
SPARK-3223 runAsSparkUser cannot change HDFS write permission properly i...

...n mesos cluster mode

- change master newer

Author: Jongyoul Lee <jongyoul@gmail.com>

Closes #3034 from jongyoul/SPARK-3223 and squashes the following commits:

42b2ed3 [Jongyoul Lee] SPARK-3223 runAsSparkUser cannot change HDFS write permission properly in mesos cluster mode - change master newer

(cherry picked from commit f7ac8c2b1de96151231617846b7468d23379c74a)
Signed-off-by: Andrew Or <andrew@databricks.com>
[SPARK-4158] Fix for missing resources.

Mesos offers may not contain all resources, and Spark needs to check to
ensure they are present and sufficient.  Spark may throw an erroneous
exception when resources aren't present.

Author: Brenden Matthews <brenden@diddyinc.com>

Closes #3024 from brndnmtthws/fix-mesos-resource-misuse and squashes the following commits:

e5f9580 [Brenden Matthews] [SPARK-4158] Fix for missing resources.

(cherry picked from commit cb0eae3b78d7f6f56c0b9521ee48564a4967d3de)
Signed-off-by: Andrew Or <andrew@databricks.com>
[SPARK-4249][GraphX]fix a problem of EdgePartitionBuilder in Graphx

at first srcIds is not initialized and are all 0. so we use edgeArray(0).srcId to currSrcId

Author: lianhuiwang <lianhuiwang09@gmail.com>

Closes #3138 from lianhuiwang/SPARK-4249 and squashes the following commits:

3f4e503 [lianhuiwang] fix a problem of EdgePartitionBuilder in Graphx

(cherry picked from commit d15c6e9dc2860bbe56e31ddf71218ccc6d5c841d)
Signed-off-by: Ankur Dave <ankurdave@gmail.com>
Update JavaCustomReceiver.java

数组下标越界

Author: xiao321 <1042460381@qq.com>

Closes #3153 from xiao321/patch-1 and squashes the following commits:

0ed17b5 [xiao321] Update JavaCustomReceiver.java

(cherry picked from commit 7c9ec529a3483fab48f728481dd1d3663369e50a)
Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>
[SPARK-4304] [PySpark] Fix sort on empty RDD

This PR fix sortBy()/sortByKey() on empty RDD.

This should be back ported into 1.1/1.2

Author: Davies Liu <davies@databricks.com>

Closes #3162 from davies/fix_sort and squashes the following commits:

84f64b7 [Davies Liu] add tests
52995b5 [Davies Liu] fix sortByKey() on empty RDD

(cherry picked from commit 7779109796c90d789464ab0be35917f963bbe867)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>

Conflicts:
	python/pyspark/tests.py