[SPARK-3701][MLLIB] update python linalg api and small fixes

1. doc updates
2. simple checks on vector dimensions
3. use column major for matrices

davies jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #2548 from mengxr/mllib-py-clean and squashes the following commits:

6dce2df [Xiangrui Meng] address comments
116b5db [Xiangrui Meng] use np.dot instead of array.dot
75f2fcc [Xiangrui Meng] fix python style
fefce00 [Xiangrui Meng] better check of vector size with more tests
067ef71 [Xiangrui Meng] majored -> major
ef853f9 [Xiangrui Meng] update python linalg api and small fixes
[SPARK-3478] [PySpark] Profile the Python tasks

This patch add profiling support for PySpark, it will show the profiling results
before the driver exits, here is one example:

```
============================================================
Profile of RDD<id=3>
============================================================
         5146507 function calls (5146487 primitive calls) in 71.094 seconds

   Ordered by: internal time, cumulative time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
  5144576   68.331    0.000   68.331    0.000 statcounter.py:44(merge)
       20    2.735    0.137   71.071    3.554 statcounter.py:33(__init__)
       20    0.017    0.001    0.017    0.001 {cPickle.dumps}
     1024    0.003    0.000    0.003    0.000 t.py:16(<lambda>)
       20    0.001    0.000    0.001    0.000 {reduce}
       21    0.001    0.000    0.001    0.000 {cPickle.loads}
       20    0.001    0.000    0.001    0.000 copy_reg.py:95(_slotnames)
       41    0.001    0.000    0.001    0.000 serializers.py:461(read_int)
       40    0.001    0.000    0.002    0.000 serializers.py:179(_batched)
       62    0.000    0.000    0.000    0.000 {method 'read' of 'file' objects}
       20    0.000    0.000   71.072    3.554 rdd.py:863(<lambda>)
       20    0.000    0.000    0.001    0.000 serializers.py:198(load_stream)
    40/20    0.000    0.000   71.072    3.554 rdd.py:2093(pipeline_func)
       41    0.000    0.000    0.002    0.000 serializers.py:130(load_stream)
       40    0.000    0.000   71.072    1.777 rdd.py:304(func)
       20    0.000    0.000   71.094    3.555 worker.py:82(process)
```

Also, use can show profile result manually by `sc.show_profiles()` or dump it into disk
by `sc.dump_profiles(path)`, such as

```python
>>> sc._conf.set("spark.python.profile", "true")
>>> rdd = sc.parallelize(range(100)).map(str)
>>> rdd.count()
100
>>> sc.show_profiles()
============================================================
Profile of RDD<id=1>
============================================================
         284 function calls (276 primitive calls) in 0.001 seconds

   Ordered by: internal time, cumulative time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        4    0.000    0.000    0.000    0.000 serializers.py:198(load_stream)
        4    0.000    0.000    0.000    0.000 {reduce}
     12/4    0.000    0.000    0.001    0.000 rdd.py:2092(pipeline_func)
        4    0.000    0.000    0.000    0.000 {cPickle.loads}
        4    0.000    0.000    0.000    0.000 {cPickle.dumps}
      104    0.000    0.000    0.000    0.000 rdd.py:852(<genexpr>)
        8    0.000    0.000    0.000    0.000 serializers.py:461(read_int)
       12    0.000    0.000    0.000    0.000 rdd.py:303(func)
```
The profiling is disabled by default, can be enabled by "spark.python.profile=true".

Also, users can dump the results into disks automatically for future analysis, by "spark.python.profile.dump=path_to_dump"

This is bugfix of #2351 cc JoshRosen

Author: Davies Liu <davies.liu@gmail.com>

Closes #2556 from davies/profiler and squashes the following commits:

e68df5a [Davies Liu] Merge branch 'master' of github.com:apache/spark into profiler
858e74c [Davies Liu] compatitable with python 2.6
7ef2aa0 [Davies Liu] bugfix, add tests for show_profiles and dump_profiles()
2b0daf2 [Davies Liu] fix docs
7a56c24 [Davies Liu] bugfix
cba9463 [Davies Liu] move show_profiles and dump_profiles to SparkContext
fb9565b [Davies Liu] Merge branch 'master' of github.com:apache/spark into profiler
116d52a [Davies Liu] Merge branch 'master' of github.com:apache/spark into profiler
09d02c3 [Davies Liu] Merge branch 'master' into profiler
c23865c [Davies Liu] Merge branch 'master' into profiler
15d6f18 [Davies Liu] add docs for two configs
dadee1a [Davies Liu] add docs string and clear profiles after show or dump
4f8309d [Davies Liu] address comment, add tests
0a5b6eb [Davies Liu] fix Python UDF
4b20494 [Davies Liu] add profile for python
[SPARK-3747] TaskResultGetter could incorrectly abort a stage if it cannot get result for a specific task

Author: Reynold Xin <rxin@apache.org>

Closes #2599 from rxin/SPARK-3747 and squashes the following commits:

a74c04d [Reynold Xin] Added a line of comment explaining NonFatal
0e8d44c [Reynold Xin] [SPARK-3747] TaskResultGetter could incorrectly abort a stage if it cannot get result for a specific task
[SPARK-3751] [mllib] DecisionTree: example update + print options

DecisionTreeRunner functionality additions:
* Allow user to pass in a test dataset
* Do not print full model if the model is too large.

As part of this, modify DecisionTreeModel and RandomForestModel to allow printing less info.  Proposed updates:
* toString: prints model summary
* toDebugString: prints full model (named after RDD.toDebugString)

Similar update to Python API:
* __repr__() now prints a model summary
* toDebugString() now prints the full model

CC: mengxr  chouqin manishamde codedeft  Small update (whomever can take a look).  Thanks!

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #2604 from jkbradley/dtrunner-update and squashes the following commits:

b2b3c60 [Joseph K. Bradley] re-added python sql doc test, temporarily removed before
07b1fae [Joseph K. Bradley] repr() now prints a model summary toDebugString() now prints the full model
1d0d93d [Joseph K. Bradley] Updated DT and RF to print less when toString is called. Added toDebugString for verbose printing.
22eac8c [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
e007a95 [Joseph K. Bradley] Updated DecisionTreeRunner to accept a test dataset.
[SPARK-3748] Log thread name in unit test logs

Thread names are useful for correlating failures.

Author: Reynold Xin <rxin@apache.org>

Closes #2600 from rxin/log4j and squashes the following commits:

83ffe88 [Reynold Xin] [SPARK-3748] Log thread name in unit test logs
[SPARK-3757] mvn clean doesn't delete some files

Added directory to be deleted into maven-clean-plugin in pom.xml.

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

Closes #2613 from tsudukim/feature/SPARK-3757 and squashes the following commits:

8804bfc [Masayoshi TSUZUKI] Modified indent.
67c7171 [Masayoshi TSUZUKI] [SPARK-3757] mvn clean doesn't delete some files
[SPARK-3749] [PySpark] fix bugs in broadcast large closure of RDD

1. broadcast is triggle unexpected
2. fd is leaked in JVM (also leak in parallelize())
3. broadcast is not unpersisted in JVM after RDD is not be used any more.

cc JoshRosen , sorry for these stupid bugs.

Author: Davies Liu <davies.liu@gmail.com>

Closes #2603 from davies/fix_broadcast and squashes the following commits:

080a743 [Davies Liu] fix bugs in broadcast large closure of RDD
SPARK-2626 [DOCS] Stop SparkContext in all examples

Call SparkContext.stop() in all examples (and touch up minor nearby code style issues while at it)

Author: Sean Owen <sowen@cloudera.com>

Closes #2575 from srowen/SPARK-2626 and squashes the following commits:

5b2baae [Sean Owen] Call SparkContext.stop() in all examples (and touch up minor nearby code style issues while at it)
[SPARK-3755][Core] Do not bind port 1 - 1024 to server in spark

Non-root user use port 1- 1024 to start jetty server will get the exception " java.net.SocketException: Permission denied", so not use these ports

Author: scwf <wangfei1@huawei.com>

Closes #2610 from scwf/1-1024 and squashes the following commits:

cb8cc76 [scwf] do not use port 1 - 1024
[SPARK-3756] [Core]check exception is caused by an address-port collision properly

Jetty server use MultiException to handle exceptions when start server
refer https://github.com/eclipse/jetty.project/blob/jetty-8.1.14.v20131031/jetty-server/src/main/java/org/eclipse/jetty/server/Server.java

So in ```isBindCollision``` add the logical to cover MultiException

Author: scwf <wangfei1@huawei.com>

Closes #2611 from scwf/fix-isBindCollision and squashes the following commits:

984cb12 [scwf] optimize the fix
3a6c849 [scwf] fix bug in isBindCollision
[SQL] Kill dangerous trailing space in query string

MD5 of query strings in `createQueryTest` calls are used to generate golden files, leaving trailing spaces there can be really dangerous. Got bitten by this while working on #2616: my "smart" IDE automatically removed a trailing space and makes Jenkins fail.

(Really should add "no trailing space" to our coding style guidelines!)

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2619 from liancheng/kill-trailing-space and squashes the following commits:

034f119 [Cheng Lian] Kill dangerous trailing space in query string
Typo error in KafkaWordCount example

topicpMap to topicMap

Author: Gaspar Munoz <munozs.88@gmail.com>

Closes #2614 from gasparms/patch-1 and squashes the following commits:

00aab2c [Gaspar Munoz] Typo error in KafkaWordCount example
Python SQL Example Code

SQL example code for Python, as shown on [SQL Programming Guide](https://spark.apache.org/docs/1.0.2/sql-programming-guide.html)

Author: jyotiska <jyotiska123@gmail.com>

Closes #2521 from jyotiska/sql_example and squashes the following commits:

1471dcb [jyotiska] added imports for sql
b25e436 [jyotiska] pep 8 compliance
43fd10a [jyotiska] lines broken to maintain 80 char limit
b4fdf4e [jyotiska] removed blank lines
83d5ab7 [jyotiska] added inferschema and applyschema to the demo
306667e [jyotiska] replaced blank line with end line
c90502a [jyotiska] fixed new line
4939a70 [jyotiska] added new line at end for python style
0b46148 [jyotiska] fixed appname for python sql example
8f67b5b [jyotiska] added python sql example
[SPARK-3746][SQL] Lock hive client when creating tables

Author: Michael Armbrust <michael@databricks.com>

Closes #2598 from marmbrus/hiveClientLock and squashes the following commits:

ca89fe8 [Michael Armbrust] Lock hive client when creating tables
[SPARK-3658][SQL] Start thrift server as a daemon

https://issues.apache.org/jira/browse/SPARK-3658

And keep the `CLASS_NOT_FOUND_EXIT_STATUS` and exit message in `SparkSubmit.scala`.

Author: WangTaoTheTonic <barneystinson@aliyun.com>
Author: WangTao <barneystinson@aliyun.com>

Closes #2509 from WangTaoTheTonic/thriftserver and squashes the following commits:

5dcaab2 [WangTaoTheTonic] issue about coupling
8ad9f95 [WangTaoTheTonic] generalization
598e21e [WangTao] take thrift server as a daemon
[SPARK-3708][SQL] Backticks aren't handled correctly is aliases

The below query gives error
sql("SELECT k FROM (SELECT \`key\` AS \`k\` FROM src) a")
It gives error because the aliases are not cleaned so it could not be resolved in further processing.

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

Closes #2594 from ravipesala/SPARK-3708 and squashes the following commits:

d55db54 [ravipesala] Fixed SPARK-3708 (Backticks aren't handled correctly is aliases)
[SPARK-3705][SQL] Add case for VoidObjectInspector to cover NullType

add case for VoidObjectInspector in ```inspectorToDataType```

Author: scwf <wangfei1@huawei.com>

Closes #2552 from scwf/inspectorToDataType and squashes the following commits:

453d892 [scwf] add case for VoidObjectInspector
[SPARK-3593][SQL] Add support for sorting BinaryType

BinaryType is derived from NativeType and added Ordering support.

Author: Venkata Ramana G <ramana.gollamudihuawei.com>

Author: Venkata Ramana Gollamudi <ramana.gollamudi@huawei.com>

Closes #2617 from gvramana/binarytype_sort and squashes the following commits:

1cf26f3 [Venkata Ramana Gollamudi] Supported Sorting of BinaryType
[SQL] Made Command.sideEffectResult protected

Considering `Command.executeCollect()` simply delegates to `Command.sideEffectResult`, we no longer need to leave the latter `protected[sql]`.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2431 from liancheng/narrow-scope and squashes the following commits:

1bfc16a [Cheng Lian] Made Command.sideEffectResult protected
Revert "[SPARK-3755][Core] Do not bind port 1 - 1024 to server in spark"

This reverts commit 6390aae4eacbabfb1c53fb828b824f6a6518beff.