SPARK-3428. TaskMetrics for running tasks is missing GC time metrics

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3684 from sryza/sandy-spark-3428 and squashes the following commits:

cb827fe [Sandy Ryza] SPARK-3428. TaskMetrics for running tasks is missing GC time metrics
[SPARK-4901] [SQL] Hot fix for ByteWritables.copyBytes

HiveInspectors.scala failed in compiling with Hadoop 1, as the BytesWritable.copyBytes is not available in Hadoop 1.

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

Closes #3742 from chenghao-intel/settable_oi_hotfix and squashes the following commits:

bb04d1f [Cheng Hao] hot fix for ByteWritables.copyBytes
[Build] Remove spark-staging-1038

Author: scwf <wangfei1@huawei.com>

Closes #3743 from scwf/abc and squashes the following commits:

7d98bc8 [scwf] removing spark-staging-1038
Small refactoring to pass SparkEnv into Executor rather than creating SparkEnv in Executor.

This consolidates some code path and makes constructor arguments simpler for a few classes.

Author: Reynold Xin <rxin@databricks.com>

Closes #3738 from rxin/sparkEnvDepRefactor and squashes the following commits:

82e02cc [Reynold Xin] Fixed couple bugs.
217062a [Reynold Xin] Code review feedback.
bd00af7 [Reynold Xin] Small refactoring to pass SparkEnv into Executor rather than creating SparkEnv in Executor.
[SPARK-4889] update history server example cmds

Author: Ryan Williams <ryan.blake.williams@gmail.com>

Closes #3736 from ryan-williams/hist and squashes the following commits:

421d8ff [Ryan Williams] add another random typo fix
76d6a4c [Ryan Williams] remove hdfs example
a2d0f82 [Ryan Williams] code review feedback
9ca7629 [Ryan Williams] [SPARK-4889] update history server example cmds
[SPARK-4896] don’t redundantly overwrite executor JAR deps

Author: Ryan Williams <ryan.blake.williams@gmail.com>

Closes #2848 from ryan-williams/fetch-file and squashes the following commits:

c14daff [Ryan Williams] Fix copy that was changed to a move inadvertently
8e39c16 [Ryan Williams] code review feedback
788ed41 [Ryan Williams] don’t redundantly overwrite executor JAR deps
[SPARK-4890] Upgrade Boto to 2.34.0; automatically download Boto from PyPi instead of packaging it

This patch upgrades `spark-ec2`'s Boto version to 2.34.0, since this is blocking several features.  Newer versions of Boto don't work properly when they're loaded from a zipfile since they try to read a JSON file from a path relative to the Boto library sources.

Therefore, this patch also changes spark-ec2 to automatically download Boto from PyPi if it's not present in `SPARK_EC2_DIR/lib`, similar to what we do in the `sbt/sbt` script. This shouldn't ben an issue for users since they already need to have an internet connection to launch an EC2 cluster.  By performing the downloading in spark_ec2.py instead of the Bash script, this should also work for Windows users.

I've tested this with Python 2.6, too.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3737 from JoshRosen/update-boto and squashes the following commits:

0aa43cc [Josh Rosen] Remove unused setup_standalone_cluster() method.
f02935d [Josh Rosen] Enable Python deprecation warnings and fix one Boto warning:
587ae89 [Josh Rosen] [SPARK-4890] Upgrade Boto to 2.34.0; automatically download Boto from PyPi instead of packaging it
[SPARK-2261] Make event logger use a single file.

Currently the event logger uses a directory and several files to
describe an app's event log, all but one of which are empty. This
is not very HDFS-friendly, since creating lots of nodes in HDFS
(especially when they don't contain any data) is frowned upon due
to the node metadata being kept in the NameNode's memory.

Instead, add a header section to the event log file that contains metadata
needed to read the events. This metadata includes things like the Spark
version (for future code that may need it for backwards compatibility) and
the compression codec used for the event data.

With the new approach, aside from reducing the load on the NN, there's
also a lot less remote calls needed when reading the log directory.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #1222 from vanzin/hist-server-single-log and squashes the following commits:

cc8f5de [Marcelo Vanzin] Store header in plain text.
c7e6123 [Marcelo Vanzin] Update comment.
59c561c [Marcelo Vanzin] Review feedback.
216c5a3 [Marcelo Vanzin] Review comments.
dce28e9 [Marcelo Vanzin] Fix log overwrite test.
f91c13e [Marcelo Vanzin] Handle "spark.eventLog.overwrite", and add unit test.
346f0b4 [Marcelo Vanzin] Review feedback.
ed0023e [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
3f4500f [Marcelo Vanzin] Unit test for SPARK-3697.
45c7a1f [Marcelo Vanzin] Version of SPARK-3697 for this branch.
b3ee30b [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
a6d5c50 [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
16fd491 [Marcelo Vanzin] Use unique log directory for each codec.
0ef3f70 [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
d93c44a [Marcelo Vanzin] Add a newline to make the header more readable.
9e928ba [Marcelo Vanzin] Add types.
bd6ba8c [Marcelo Vanzin] Review feedback.
a624a89 [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
04364dc [Marcelo Vanzin] Merge branch 'master' into hist-server-single-log
bb7c2d3 [Marcelo Vanzin] Fix scalastyle warning.
16661a3 [Marcelo Vanzin] Simplify some internal code.
cc6bce4 [Marcelo Vanzin] Some review feedback.
a722184 [Marcelo Vanzin] Do not encode metadata in log file name.
3700586 [Marcelo Vanzin] Restore log flushing.
f677930 [Marcelo Vanzin] Fix botched rebase.
ae571fa [Marcelo Vanzin] Fix end-to-end event logger test.
9db0efd [Marcelo Vanzin] Show prettier name in UI.
8f42274 [Marcelo Vanzin] Make history server parse old-style log directories.
6251dd7 [Marcelo Vanzin] Make event logger use a single file.
change signature of example to match released code

the signature of registerKryoClasses is actually of Array[Class[_]]  not Seq

Author: Eran Medan <ehrann.mehdan@gmail.com>

Closes #3747 from eranation/patch-1 and squashes the following commits:

ee9885d [Eran Medan] change signature of example to match released code
[SPARK-3060] spark-shell.cmd doesn't accept application options in Windows OS

Added equivalent module as utils.sh and modified spark-shell2.cmd to use it to parse options.

Now we can use application options.
  ex) `bin\spark-shell.cmd --master spark://master:7077 -i path\to\script.txt`

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3350 from tsudukim/feature/SPARK-3060 and squashes the following commits:

4551e56 [Masayoshi TSUZUKI] Modified too long line which defines the submission options to pass findstr command.
3a11361 [Masayoshi TSUZUKI] [SPARK-3060] spark-shell.cmd doesn't accept application options in Windows OS
SPARK-2641: Passing num executors to spark arguments from properties file

Since we can set spark executor memory and executor cores using property file, we must also be allowed to set the executor instances.

Author: Kanwaljit Singh <kanwaljit.singh@guavus.com>

Closes #1657 from kjsingh/branch-1.0 and squashes the following commits:

d8a5a12 [Kanwaljit Singh] SPARK-2641: Fixing how spark arguments are loaded from properties file for num executors

Conflicts:
	core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala
[SPARK-4831] Do not include SPARK_CLASSPATH if empty

My guess for fixing https://issues.apache.org/jira/browse/SPARK-4831.

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

Closes #3678 from darabos/patch-1 and squashes the following commits:

36e1243 [Daniel Darabos] Do not include SPARK_CLASSPATH if empty.
[SPARK-4140] Document dynamic allocation

Once the external shuffle service is also documented, the dynamic allocation section will link to it. Let me know if the whole dynamic allocation should be moved to its separate page; I personally think the organization might be cleaner that way.

This patch builds on top of oza's work in #3689.

aarondav pwendell

Author: Andrew Or <andrew@databricks.com>
Author: Tsuyoshi Ozawa <ozawa.tsuyoshi@gmail.com>

Closes #3731 from andrewor14/document-dynamic-allocation and squashes the following commits:

1281447 [Andrew Or] Address a few comments
b9843f2 [Andrew Or] Document the configs as well
246fb44 [Andrew Or] Merge branch 'SPARK-4839' of github.com:oza/spark into document-dynamic-allocation
8c64004 [Andrew Or] Add documentation for dynamic allocation (without configs)
6827b56 [Tsuyoshi Ozawa] Fixing a documentation of spark.dynamicAllocation.enabled.
53cff58 [Tsuyoshi Ozawa] Adding a documentation about dynamic resource allocation.
[Minor] Build Failed: value defaultProperties not found

Mvn Build Failed: value defaultProperties not found .Maybe related to this pr:
https://github.com/apache/spark/commit/1d648123a77bbcd9b7a34cc0d66c14fa85edfecd
andrewor14 can you look at this problem?

Author: huangzhaowei <carlmartinmax@gmail.com>

Closes #3749 from SaintBacchus/Mvn-Build-Fail and squashes the following commits:

8e2917c [huangzhaowei] Build Failed: value defaultProperties not found
SPARK-4910 [CORE] build failed (use of FileStatus.isFile in Hadoop 1.x)

Fix small Hadoop 1 compile error from SPARK-2261. In Hadoop 1.x, all we have is FileStatus.isDir, so these "is file" assertions are changed to "is not a dir". This is how similar checks are done so far in the code base.

Author: Sean Owen <sowen@cloudera.com>

Closes #3754 from srowen/SPARK-4910 and squashes the following commits:

52c5e4e [Sean Owen] Fix small Hadoop 1 compile error from SPARK-2261
[SPARK-2075][Core] Make the compiler generate same bytes code for Hadoop 1.+ and Hadoop 2.+

`NullWritable` is a `Comparable` rather than `Comparable[NullWritable]` in Hadoop 1.+, so the compiler cannot find an implicit Ordering for it. It will generate different anonymous classes for `saveAsTextFile` in Hadoop 1.+ and Hadoop 2.+. Therefore, here we provide an Ordering for NullWritable so that the compiler will generate same codes.

I used the following commands to confirm the generated byte codes are some.
```
mvn -Dhadoop.version=1.2.1 -DskipTests clean package -pl core -am
javap -private -c -classpath core/target/scala-2.10/classes org.apache.spark.rdd.RDD > ~/hadoop1.txt

mvn -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0 -DskipTests clean package -pl core -am
javap -private -c -classpath core/target/scala-2.10/classes org.apache.spark.rdd.RDD > ~/hadoop2.txt

diff ~/hadoop1.txt ~/hadoop2.txt
```

However, the compiler will generate different codes for the classes which call methods of `JobContext/TaskAttemptContext`. `JobContext/TaskAttemptContext` is a class in Hadoop 1.+, and calling its method will use `invokevirtual`, while it's an interface in Hadoop 2.+, and will use `invokeinterface`.

To fix it, we can use reflection to call `JobContext/TaskAttemptContext.getConfiguration`.

Author: zsxwing <zsxwing@gmail.com>

Closes #3740 from zsxwing/SPARK-2075 and squashes the following commits:

39d9df2 [zsxwing] Fix the code style
e4ad8b5 [zsxwing] Use null for the implicit Ordering
734bac9 [zsxwing] Explicitly set the implicit parameters
ca03559 [zsxwing] Use reflection to access JobContext/TaskAttemptContext.getConfiguration
fa40db0 [zsxwing] Add an Ordering for NullWritable to make the compiler generate same byte codes for RDD
[SPARK-4918][Core] Reuse Text in saveAsTextFile

Reuse Text in saveAsTextFile to reduce GC.

/cc rxin

Author: zsxwing <zsxwing@gmail.com>

Closes #3762 from zsxwing/SPARK-4918 and squashes the following commits:

59f03eb [zsxwing] Reuse Text in saveAsTextFile
[SPARK-4915][YARN] Fix classname to be specified for external shuffle service.

Author: Tsuyoshi Ozawa <ozawa.tsuyoshi@lab.ntt.co.jp>

Closes #3757 from oza/SPARK-4915 and squashes the following commits:

3b0d6d6 [Tsuyoshi Ozawa] Fix classname to be specified for external shuffle service.
[SPARK-4870] Add spark version to driver log

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

Closes #3717 from liyezhang556520/version2Log and squashes the following commits:

ccd30d7 [Zhang, Liye] delete log in sparkConf
330f70c [Zhang, Liye] move the log from SaprkConf to SparkContext
96dc115 [Zhang, Liye] remove curly brace
e833330 [Zhang, Liye] add spark version to driver log
[SPARK-4883][Shuffle] Add a name to the directoryCleaner thread

Author: zsxwing <zsxwing@gmail.com>

Closes #3734 from zsxwing/SPARK-4883 and squashes the following commits:

e6f2b61 [zsxwing] Fix the name
cc74727 [zsxwing] Add a name to the directoryCleaner thread