[graphX] GraphOps: random pick vertex bug

When `numVertices > 50`, probability is set to 0. This would cause infinite loop.

Author: yingjieMiao <yingjie@42go.com>

Closes #2553 from yingjieMiao/graphx and squashes the following commits:

6adf3c8 [yingjieMiao] [graphX] GraphOps: random pick vertex bug
Fixed the condition in StronglyConnectedComponents Issue: SPARK-3635

Author: oded <oded@HP-DV6.c4internal.c4-security.com>

Closes #2486 from odedz/master and squashes the following commits:

dd7890a [oded] Fixed the condition in StronglyConnectedComponents Issue: SPARK-3635
Minor cleanup of code.

Author: Reynold Xin <rxin@apache.org>

Closes #2581 from rxin/minor-cleanup and squashes the following commits:

736a91b [Reynold Xin] Minor cleanup of code.
[SPARK-3613] Record only average block size in MapStatus for large stages

This changes the way we send MapStatus from executors back to driver for large stages (>2000 tasks). For large stages, we no longer send one byte per block. Instead, we just send the average block size.

This makes large jobs (tens of thousands of tasks) much more reliable since the driver no longer sends huge amount of data.

Author: Reynold Xin <rxin@apache.org>

Closes #2470 from rxin/mapstatus and squashes the following commits:

822ff54 [Reynold Xin] Code review feedback.
3b86f56 [Reynold Xin] Added MimaExclude.
f89d182 [Reynold Xin] Fixed a bug in MapStatus
6a0401c [Reynold Xin] [SPARK-3613] Record only average block size in MapStatus for large stages.
[SPARK-3709] Executors don't always report broadcast block removal properly back to the driver

The problem was that the 2nd argument in RemoveBroadcast is not tellMaster! It is "removeFromDriver". Basically when removeFromDriver is not true, we don't report broadcast block removal back to the driver, and then other executors mistakenly think that the executor would still have the block, and try to fetch from it.

cc @tdas

Author: Reynold Xin <rxin@apache.org>

Closes #2588 from rxin/debug and squashes the following commits:

6dab2e3 [Reynold Xin] Don't log random messages.
f430686 [Reynold Xin] Always report broadcast removal back to master.
2a13f70 [Reynold Xin] iii
[SPARK-3734] DriverRunner should not read SPARK_HOME from submitter's environment

When using spark-submit in `cluster` mode to submit a job to a Spark Standalone
cluster, if the JAVA_HOME environment variable was set on the submitting
machine then DriverRunner would attempt to use the submitter's JAVA_HOME to
launch the driver process (instead of the worker's JAVA_HOME), causing the
driver to fail unless the submitter and worker had the same Java location.

This commit fixes this by reading JAVA_HOME from sys.env instead of
command.environment.

Author: Josh Rosen <joshrosen@apache.org>

Closes #2586 from JoshRosen/SPARK-3734 and squashes the following commits:

e9513d9 [Josh Rosen] [SPARK-3734] DriverRunner should not read SPARK_HOME from submitter's environment.
Revert "[SPARK-3007][SQL]Add Dynamic Partition support to Spark Sql hive"

This reverts commit 0bbe7faeffa17577ae8a33dfcd8c4c783db5c909.
HOTFIX: Ignore flaky tests in YARN
[SPARK-3356] [DOCS] Document when RDD elements' ordering within partitions is nondeterministic

As suggested by mateiz , and because it came up on the mailing list again last week, this attempts to document that ordering of elements is not guaranteed across RDD evaluations in groupBy, zip, and partition-wise RDD methods. Suggestions welcome about the wording, or other methods that need a note.

Author: Sean Owen <sowen@cloudera.com>

Closes #2508 from srowen/SPARK-3356 and squashes the following commits:

b7c96fd [Sean Owen] Undo change to programming guide
ad4aeec [Sean Owen] Don't mention ordering in partition-wise methods, reword description of ordering for zip methods per review, and add similar note to programming guide, which mentions groupByKey (but not zip methods)
fce943b [Sean Owen] Note that ordering of elements is not guaranteed across RDD evaluations in groupBy, zip, and partition-wise RDD methods
SPARK-3745 - fix check-license to properly download and check jar

for details, see: https://issues.apache.org/jira/browse/SPARK-3745

Author: shane knapp <incomplete@gmail.com>

Closes #2596 from shaneknapp/SPARK-3745 and squashes the following commits:

c95eea9 [shane knapp] SPARK-3745 - fix check-license to properly download and check jar
[Build] Post commit hash with timeout messages

[By request](https://github.com/apache/spark/pull/2588#issuecomment-57266871), and because it also makes sense.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2597 from nchammas/timeout-commit-hash and squashes the following commits:

3d90714 [Nicholas Chammas] Revert "testing: making timeout 1 minute"
2353c95 [Nicholas Chammas] testing: making timeout 1 minute
e3a477e [Nicholas Chammas] post commit hash with timeout
SPARK-3744 [STREAMING] FlumeStreamSuite will fail during port contention

Since it looked quite easy, I took the liberty of making a quick PR that just uses `Utils.startServiceOnPort` to fix this. It works locally for me.

Author: Sean Owen <sowen@cloudera.com>

Closes #2601 from srowen/SPARK-3744 and squashes the following commits:

ddc9319 [Sean Owen] Avoid port contention in tests by retrying several ports for Flume stream
Remove compiler warning from TaskContext change.

Author: Reynold Xin <rxin@apache.org>

Closes #2602 from rxin/warning and squashes the following commits:

130186b [Reynold Xin] Remove compiler warning from TaskContext change.
[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