SPARK-2058: Overriding SPARK_HOME/conf with SPARK_CONF_DIR

Update of PR #997.

With this PR, setting SPARK_CONF_DIR overrides SPARK_HOME/conf (not only spark-defaults.conf and spark-env).

Author: EugenCepoi <cepoi.eugen@gmail.com>

Closes #2481 from EugenCepoi/SPARK-2058 and squashes the following commits:

0bb32c2 [EugenCepoi] use orElse orNull and fixing trailing percent in compute-classpath.cmd
77f35d7 [EugenCepoi] SPARK-2058: Overriding SPARK_HOME/conf with SPARK_CONF_DIR
[SPARK-3696]Do not override the user-difined conf_dir

https://issues.apache.org/jira/browse/SPARK-3696

We see if SPARK_CONF_DIR is already defined before assignment.

Author: WangTaoTheTonic <barneystinson@aliyun.com>

Closes #2541 from WangTaoTheTonic/confdir and squashes the following commits:

c3f31e0 [WangTaoTheTonic] Do not override the user-difined conf_dir
[SPARK-2693][SQL] Supported for UDAF Hive Aggregates like PERCENTILE

Implemented UDAF Hive aggregates by adding wrapper to Spark Hive.

Author: ravipesala <ravindra.pesala@huawei.com>

Closes #2620 from ravipesala/SPARK-2693 and squashes the following commits:

a8df326 [ravipesala] Removed resolver from constructor arguments
caf25c6 [ravipesala] Fixed style issues
5786200 [ravipesala] Supported for UDAF Hive Aggregates like PERCENTILE
 [SPARK-2778] [yarn] Add workaround for race in MiniYARNCluster.

Sometimes the cluster's start() method returns before the configuration
having been updated, which is done by ClientRMService in, I assume, a
separate thread (otherwise there would be no race). That can cause tests
to fail if the old configuration data is read, since it will contain
the wrong RM address.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2605 from vanzin/SPARK-2778 and squashes the following commits:

8d02ce0 [Marcelo Vanzin] Minor cleanup.
5bebee7 [Marcelo Vanzin] [SPARK-2778] [yarn] Add workaround for race in MiniYARNCluster.
[SPARK-3007][SQL] Adds dynamic partitioning support

PR #2226 was reverted because it broke Jenkins builds for unknown reason. This debugging PR aims to fix the Jenkins build.

This PR also fixes two bugs:

1. Compression configurations in `InsertIntoHiveTable` are disabled by mistake

   The `FileSinkDesc` object passed to the writer container doesn't have compression related configurations. These configurations are not taken care of until `saveAsHiveFile` is called. This PR moves compression code forward, right after instantiation of the `FileSinkDesc` object.

1. `PreInsertionCasts` doesn't take table partitions into account

   In `castChildOutput`, `table.attributes` only contains non-partition columns, thus for partitioned table `childOutputDataTypes` never equals to `tableOutputDataTypes`. This results funny analyzed plan like this:

   ```
   == Analyzed Logical Plan ==
   InsertIntoTable Map(partcol1 -> None, partcol2 -> None), false
    MetastoreRelation default, dynamic_part_table, None
    Project [c_0#1164,c_1#1165,c_2#1166]
     Project [c_0#1164,c_1#1165,c_2#1166]
      Project [c_0#1164,c_1#1165,c_2#1166]
       ... (repeats 99 times) ...
        Project [c_0#1164,c_1#1165,c_2#1166]
         Project [c_0#1164,c_1#1165,c_2#1166]
          Project [1 AS c_0#1164,1 AS c_1#1165,1 AS c_2#1166]
           Filter (key#1170 = 150)
            MetastoreRelation default, src, None
   ```

   Awful though this logical plan looks, it's harmless because all projects will be eliminated by optimizer. Guess that's why this issue hasn't been caught before.

Author: Cheng Lian <lian.cs.zju@gmail.com>
Author: baishuo(白硕) <vc_java@hotmail.com>
Author: baishuo <vc_java@hotmail.com>

Closes #2616 from liancheng/dp-fix and squashes the following commits:

21935b6 [Cheng Lian] Adds back deleted trailing space
f471c4b [Cheng Lian] PreInsertionCasts should take table partitions into account
a132c80 [Cheng Lian] Fixes output compression
9c6eb2d [Cheng Lian] Adds tests to verify dynamic partitioning folder layout
0eed349 [Cheng Lian] Addresses @yhuai's comments
26632c3 [Cheng Lian] Adds more tests
9227181 [Cheng Lian] Minor refactoring
c47470e [Cheng Lian] Refactors InsertIntoHiveTable to a Command
6fb16d7 [Cheng Lian] Fixes typo in test name, regenerated golden answer files
d53daa5 [Cheng Lian] Refactors dynamic partitioning support
b821611 [baishuo] pass check style
997c990 [baishuo] use HiveConf.DEFAULTPARTITIONNAME to replace hive.exec.default.partition.name
761ecf2 [baishuo] modify according micheal's advice
207c6ac [baishuo] modify for some bad indentation
caea6fb [baishuo] modify code to pass scala style checks
b660e74 [baishuo] delete a empty else branch
cd822f0 [baishuo] do a little modify
8e7268c [baishuo] update file after test
3f91665 [baishuo(白硕)] Update Cast.scala
8ad173c [baishuo(白硕)] Update InsertIntoHiveTable.scala
051ba91 [baishuo(白硕)] Update Cast.scala
d452eb3 [baishuo(白硕)] Update HiveQuerySuite.scala
37c603b [baishuo(白硕)] Update InsertIntoHiveTable.scala
98cfb1f [baishuo(白硕)] Update HiveCompatibilitySuite.scala
6af73f4 [baishuo(白硕)] Update InsertIntoHiveTable.scala
adf02f1 [baishuo(白硕)] Update InsertIntoHiveTable.scala
1867e23 [baishuo(白硕)] Update SparkHadoopWriter.scala
6bb5880 [baishuo(白硕)] Update HiveQl.scala
[SPARK-3212][SQL] Use logical plan matching instead of temporary tables for table caching

_Also addresses: SPARK-1671, SPARK-1379 and SPARK-3641_

This PR introduces a new trait, `CacheManger`, which replaces the previous temporary table based caching system.  Instead of creating a temporary table that shadows an existing table with and equivalent cached representation, the cached manager maintains a separate list of logical plans and their cached data.  After optimization, this list is searched for any matching plan fragments.  When a matching plan fragment is found it is replaced with the cached data.

There are several advantages to this approach:
 - Calling .cache() on a SchemaRDD now works as you would expect, and uses the more efficient columnar representation.
 - Its now possible to provide a list of temporary tables, without having to decide if a given table is actually just a  cached persistent table. (To be done in a follow-up PR)
 - In some cases it is possible that cached data will be used, even if a cached table was not explicitly requested.  This is because we now look at the logical structure instead of the table name.
 - We now correctly invalidate when data is inserted into a hive table.

Author: Michael Armbrust <michael@databricks.com>

Closes #2501 from marmbrus/caching and squashes the following commits:

63fbc2c [Michael Armbrust] Merge remote-tracking branch 'origin/master' into caching.
0ea889e [Michael Armbrust] Address comments.
1e23287 [Michael Armbrust] Add support for cache invalidation for hive inserts.
65ed04a [Michael Armbrust] fix tests.
bdf9a3f [Michael Armbrust] Merge remote-tracking branch 'origin/master' into caching
b4b77f2 [Michael Armbrust] Address comments
6923c9d [Michael Armbrust] More comments / tests
80f26ac [Michael Armbrust] First draft of improved semantics for Spark SQL caching.
[SPARK-3535][Mesos] Fix resource handling.

Author: Brenden Matthews <brenden@diddyinc.com>

Closes #2401 from brndnmtthws/master and squashes the following commits:

4abaa5d [Brenden Matthews] [SPARK-3535][Mesos] Fix resource handling.
[SPARK-3775] Not suitable error message in spark-shell.cmd

Modified some sentence of error message in bin\*.cmd.

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

Closes #2640 from tsudukim/feature/SPARK-3775 and squashes the following commits:

3458afb [Masayoshi TSUZUKI] [SPARK-3775] Not suitable error message in spark-shell.cmd
[SPARK-3774] typo comment in bin/utils.sh

Modified the comment of bin/utils.sh.

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

Closes #2639 from tsudukim/feature/SPARK-3774 and squashes the following commits:

707b779 [Masayoshi TSUZUKI] [SPARK-3774] typo comment in bin/utils.sh
[SPARK-3606] [yarn] Correctly configure AmIpFilter for Yarn HA.

The existing code only considered one of the RMs when running in
Yarn HA mode, so it was possible to get errors if the active RM
was not registered in the filter.

The change makes use of a new API added to Yarn that returns all
proxy addresses, and falls back to the old behavior if the API
is not present. While there, I also made a change to look for the
scheme (http or https) being used by Yarn when building the proxy
URIs.

Since, in the case of multiple RMs, Yarn uses commas as a separator,
it was not possible anymore to use spark.filter.params to propagate
this information (which used commas to delimit different config params).
Instead, I added a new param (spark.filter.jsonParams) which expects
a JSON string containing a map with the config data. I chose not to
add it to the documentation at this point since I don't believe users
will use it directly.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2469 from vanzin/SPARK-3606 and squashes the following commits:

aeb458a [Marcelo Vanzin] Undelete needed import.
65e400d [Marcelo Vanzin] Remove unused import.
d121883 [Marcelo Vanzin] Use separate config for each param instead of json.
04bc156 [Marcelo Vanzin] Review feedback.
4d4d6b9 [Marcelo Vanzin] [SPARK-3606] [yarn] Correctly configure AmIpFilter for Yarn HA.
[SPARK-3763] The example of building with sbt should be "sbt assembly" instead of "sbt compile"

In building-spark.md, there are some examples for making assembled package with maven but the example for building with sbt is only about for compiling.

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

Closes #2627 from sarutak/SPARK-3763 and squashes the following commits:

fadb990 [Kousuke Saruta] Modified the example to build with sbt in building-spark.md
[SPARK-3377] [SPARK-3610] Metrics can be accidentally aggregated / History server log name should not be based on user input

This PR is another solution for #2250

I'm using codahale base MetricsSystem of Spark with JMX or Graphite, and I saw following 2 problems.

(1) When applications which have same spark.app.name run on cluster at the same time, some metrics names are mixed. For instance, if 2+ application is running on the cluster at the same time, each application emits the same named metric like "SparkPi.DAGScheduler.stage.failedStages" and Graphite cannot distinguish the metrics is for which application.

(2) When 2+ executors run on the same machine, JVM metrics of each executors are mixed. For instance, 2+ executors running on the same node can emit the same named metric "jvm.memory" and Graphite cannot distinguish the metrics is from which application.

And there is an similar issue. The directory for event logs is named using application name.
Application name is defined by user and the name can includes illegal character for path names.
Further more, the directory name consists of application name and System.currentTimeMillis even though each application has unique Application ID so if we run jobs which have same name, it's difficult to identify which directory is for which application.

Closes #2250
Closes #1067

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

Closes #2432 from sarutak/metrics-structure-improvement2 and squashes the following commits:

3288b2b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
39169e4 [Kousuke Saruta] Fixed style
6570494 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
817e4f0 [Kousuke Saruta] Simplified MetricsSystem#buildRegistryName
67fa5eb [Kousuke Saruta] Unified MetricsSystem#registerSources and registerSinks in start
10be654 [Kousuke Saruta] Fixed style.
990c078 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
f0c7fba [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
59cc2cd [Kousuke Saruta] Modified SparkContextSchedulerCreationSuite
f9b6fb3 [Kousuke Saruta] Modified style.
2cf8a0f [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
389090d [Kousuke Saruta] Replaced taskScheduler.applicationId() with getApplicationId in SparkContext#postApplicationStart
ff45c89 [Kousuke Saruta] Added some test cases to MetricsSystemSuite
69c46a6 [Kousuke Saruta] Added warning logging logic to MetricsSystem#buildRegistryName
5cca0d2 [Kousuke Saruta] Added Javadoc comment to SparkContext#getApplicationId
16a9f01 [Kousuke Saruta] Added data types to be returned to some methods
6434b06 [Kousuke Saruta] Reverted changes related to ApplicationId
0413b90 [Kousuke Saruta] Deleted ApplicationId.java and ApplicationIdSuite.java
a42300c [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
0fc1b09 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
42bea55 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
248935d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
f6af132 [Kousuke Saruta] Modified SchedulerBackend and TaskScheduler to return System.currentTimeMillis as an unique Application Id
1b8b53e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
97cb85c [Kousuke Saruta] Modified confliction of MimExcludes
2cdd009 [Kousuke Saruta] Modified defailt implementation of applicationId
9aadb0b [Kousuke Saruta] Modified NetworkReceiverSuite to ensure "executor.start()" is finished in test "network receiver life cycle"
3011efc [Kousuke Saruta] Added ApplicationIdSuite.scala
d009c55 [Kousuke Saruta] Modified ApplicationId#equals to compare appIds
dfc83fd [Kousuke Saruta] Modified ApplicationId to implement Serializable
9ff4851 [Kousuke Saruta] Modified MimaExcludes.scala to ignore createTaskScheduler method in SparkContext
4567ffc [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
6a91b14 [Kousuke Saruta] Modified SparkContextSchedulerCreationSuite, ExecutorRunnerTest and EventLoggingListenerSuite
0325caf [Kousuke Saruta] Added ApplicationId.scala
0a2fc14 [Kousuke Saruta] Modified style
eabda80 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
0f890e6 [Kousuke Saruta] Modified SparkDeploySchedulerBackend and Master to pass baseLogDir instead f eventLogDir
bcf25bf [Kousuke Saruta] Modified directory name for EventLogs
28d4d93 [Kousuke Saruta] Modified SparkContext and EventLoggingListener so that the directory for EventLogs is named same for Application ID
203634e [Kousuke Saruta] Modified comment in SchedulerBackend#applicationId and TaskScheduler#applicationId
424fea4 [Kousuke Saruta] Modified  the subclasses of TaskScheduler and SchedulerBackend so that they can return non-optional Unique Application ID
b311806 [Kousuke Saruta] Swapped last 2 arguments passed to CoarseGrainedExecutorBackend
8a2b6ec [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
086ee25 [Kousuke Saruta] Merge branch 'metrics-structure-improvement2' of github.com:sarutak/spark into metrics-structure-improvement2
e705386 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
36d2f7a [Kousuke Saruta] Added warning message for the situation we cannot get application id for the prefix for the name of metrics
eea6e19 [Kousuke Saruta] Modified CoarseGrainedMesosSchedulerBackend and MesosSchedulerBackend so that we can get Application ID
c229fbe [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
e719c39 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
4a93c7f [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2
4776f9e [Kousuke Saruta] Modified MetricsSystemSuite.scala
efcb6e1 [Kousuke Saruta] Modified to add application id to metrics name
2ec848a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
3ea7896 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
ead8966 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
08e627e [Kousuke Saruta] Revert "tmp"
7b67f5a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
45bd33d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
93e263a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
848819c [Kousuke Saruta] Merge branch 'metrics-structure-improvement' of github.com:sarutak/spark into metrics-structure-improvement
912a637 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
e4a4593 [Kousuke Saruta] tmp
3e098d8 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
4603a39 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
fa7175b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
15f88a3 [Kousuke Saruta] Modified MetricsSystem#buildRegistryName because conf.get does not return null when correspondin entry is absent
6f7dcd4 [Kousuke Saruta] Modified constructor of DAGSchedulerSource and BlockManagerSource because the instance of SparkContext is no longer used
6fc5560 [Kousuke Saruta] Modified sourceName of ExecutorSource, DAGSchedulerSource and BlockManagerSource
4e057c9 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement
85ffc02 [Kousuke Saruta] Revert "Modified sourceName of ExecutorSource, DAGSchedulerSource and BlockManagerSource"
868e326 [Kousuke Saruta] Modified MetricsSystem to set registry name with unique application-id and driver/executor-id
71609f5 [Kousuke Saruta] Modified sourceName of ExecutorSource, DAGSchedulerSource and BlockManagerSource
55debab [Kousuke Saruta] Modified SparkContext and Executor to set spark.executor.id to identifiers
4180993 [Kousuke Saruta] Modified SparkContext to retain spark.unique.app.name property in SparkConf
[SPARK-1860] More conservative app directory cleanup.

First contribution to the project, so apologize for any significant errors.

This PR addresses [SPARK-1860]. The application directories are now cleaned up in a more conservative manner.

Previously, app-* directories were cleaned up if the directory's timestamp was older than a given time. However, the timestamp on a directory does not reflect the modification times of the files in that directory. Therefore, app-* directories were wiped out even if the files inside them were created recently and possibly being used by Executor tasks.

The solution is to change the cleanup logic to inspect all files within the app-* directory and only eliminate the app-* directory if all files in the directory are stale.

Author: mcheah <mcheah@palantir.com>

Closes #2609 from mccheah/worker-better-app-dir-cleanup and squashes the following commits:

87b5d03 [mcheah] [SPARK-1860] Using more string interpolation. Better error logging.
802473e [mcheah] [SPARK-1860] Cleaning up the logs generated when cleaning directories.
e0a1f2e [mcheah] [SPARK-1860] Fixing broken unit test.
77a9de0 [mcheah] [SPARK-1860] More conservative app directory cleanup.
fix conflict