Spark-3213 Fixes issue with spark-ec2 not detecting slaves created with "Launch More like this"

... copy the spark_cluster_tag from a spot instance requests over to the instances.

Author: Vida Ha <vida@databricks.com>

Closes #2163 from vidaha/vida/spark-3213 and squashes the following commits:

5070a70 [Vida Ha] Spark-3214 Fix issue with spark-ec2 not detecting slaves created with 'Launch More Like This' and using Spot Requests
[SPARK-3243] Don't use stale spark-driver.* system properties

If we set both `spark.driver.extraClassPath` and `--driver-class-path`, then the latter correctly overrides the former. However, the value of the system property `spark.driver.extraClassPath` still uses the former, which is actually not added to the class path. This may cause some confusion...

Of course, this also affects other options (i.e. java options, library path, memory...).

Author: Andrew Or <andrewor14@gmail.com>

Closes #2154 from andrewor14/driver-submit-configs-fix and squashes the following commits:

17ec6fc [Andrew Or] Fix tests
0140836 [Andrew Or] Don't forget spark.driver.memory
e39d20f [Andrew Or] Also set spark.driver.extra* configs in client mode
[SPARK-3252][SQL] Add missing condition for test

According to the text message, both relations should be tested. So add the missing condition.

Author: viirya <viirya@gmail.com>

Closes #2159 from viirya/fix_test and squashes the following commits:

b1c0f52 [viirya] add missing condition.
[SQL] [SPARK-3236] Reading Parquet tables from Metastore mangles location

Currently we do `relation.hiveQlTable.getDataLocation.getPath`, which returns the path-part of the URI (e.g., "s3n://my-bucket/my-path" => "/my-path"). We should do `relation.hiveQlTable.getDataLocation.toString` instead, as a URI's toString returns a faithful representation of the full URI, which can later be passed into a Hadoop Path.

Author: Aaron Davidson <aaron@databricks.com>

Closes #2150 from aarondav/parquet-location and squashes the following commits:

459f72c [Aaron Davidson] [SQL] [SPARK-3236] Reading Parquet tables from Metastore mangles location
[SPARK-3065][SQL] Add locale setting to fix results do not match for udf_unix_timestamp format "yyyy MMM dd h:mm:ss a" run with not "America/Los_Angeles" TimeZone in HiveCompatibilitySuite

When run the udf_unix_timestamp of org.apache.spark.sql.hive.execution.HiveCompatibilitySuite testcase
with not "America/Los_Angeles" TimeZone throws error. [https://issues.apache.org/jira/browse/SPARK-3065]
add locale setting on beforeAll and afterAll method to fix the bug of HiveCompatibilitySuite testcase

Author: luogankun <luogankun@gmail.com>

Closes #1968 from luogankun/SPARK-3065 and squashes the following commits:

c167832 [luogankun] [SPARK-3065][SQL] Add Locale setting to HiveCompatibilitySuite
0a25e3a [luogankun] [SPARK-3065][SQL] Add Locale setting to HiveCompatibilitySuite
[SPARK-3235][SQL] Ensure in-memory tables don't always broadcast.

Author: Michael Armbrust <michael@databricks.com>

Closes #2147 from marmbrus/inMemDefaultSize and squashes the following commits:

5390360 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into inMemDefaultSize
14204d3 [Michael Armbrust] Set the context before creating SparkLogicalPlans.
8da4414 [Michael Armbrust] Make sure we throw errors when leaf nodes fail to provide statistcs
18ce029 [Michael Armbrust] Ensure in-memory tables don't always broadcast.
HOTFIX: Don't build with YARN support for Mapr3
Add line continuation for script to work w/ py2.7.5

Error was -

$ SPARK_HOME=$PWD/dist ./dev/create-release/generate-changelist.py
  File "./dev/create-release/generate-changelist.py", line 128
    if day < SPARK_REPO_CHANGE_DATE1 or
                                      ^
SyntaxError: invalid syntax

Author: Matthew Farrellee <matt@redhat.com>

Closes #2139 from mattf/master-fix-generate-changelist.py-0 and squashes the following commits:

6b3a900 [Matthew Farrellee] Add line continuation for script to work w/ py2.7.5
[SPARK-3271] delete unused methods in Utils

delete no used method in Utils

Author: scwf <wangfei1@huawei.com>

Closes #2160 from scwf/delete-no-use-method and squashes the following commits:

d8f6b0d [scwf] delete no use method in Utils
SPARK-3265 Allow using custom ipython executable with pyspark

Although you can make pyspark use ipython with `IPYTHON=1`, and also change the python executable with `PYSPARK_PYTHON=...`, you can't use both at the same time because it hardcodes the default ipython script.

This makes it use the `PYSPARK_PYTHON` variable if present and fall back to default python, similarly to how the default python executable is handled.

So you can use a custom ipython like so:
`PYSPARK_PYTHON=./anaconda/bin/ipython IPYTHON_OPTS="notebook" pyspark`

Author: Rob O'Dwyer <odwyerrob@gmail.com>

Closes #2167 from robbles/patch-1 and squashes the following commits:

d98e8a9 [Rob O'Dwyer] Allow using custom ipython executable with pyspark
[HOTFIX] Wait for EOF only for the PySpark shell

In `SparkSubmitDriverBootstrapper`, we wait for the parent process to send us an `EOF` before finishing the application. This is applicable for the PySpark shell because we terminate the application the same way. However if we run a python application, for instance, the JVM actually never exits unless it receives a manual EOF from the user. This is causing a few tests to timeout.

We only need to do this for the PySpark shell because Spark submit runs as a python subprocess only in this case. Thus, the normal Spark shell doesn't need to go through this case even though it is also a REPL.

Thanks davies for reporting this.

Author: Andrew Or <andrewor14@gmail.com>

Closes #2170 from andrewor14/bootstrap-hotfix and squashes the following commits:

42963f5 [Andrew Or] Do not wait for EOF unless this is the pyspark shell
[HOTFIX][SQL] Remove cleaning of UDFs

It is not safe to run the closure cleaner on slaves.  #2153 introduced this which broke all UDF execution on slaves.  Will re-add cleaning of UDF closures in a follow-up PR.

Author: Michael Armbrust <michael@databricks.com>

Closes #2174 from marmbrus/fixUdfs and squashes the following commits:

55406de [Michael Armbrust] [HOTFIX] Remove cleaning of UDFs
[SQL] Fixed 2 comment typos in SQLConf

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

Closes #2172 from liancheng/sqlconf-typo and squashes the following commits:

115cc71 [Cheng Lian] Fixed 2 comment typos in SQLConf
[SPARK-3230][SQL] Fix udfs that return structs

We need to convert the case classes into Rows.

Author: Michael Armbrust <michael@databricks.com>

Closes #2133 from marmbrus/structUdfs and squashes the following commits:

189722f [Michael Armbrust] Merge remote-tracking branch 'origin/master' into structUdfs
8e29b1c [Michael Armbrust] Use existing function
d8d0b76 [Michael Armbrust] Fix udfs that return structs
[SPARK-3150] Fix NullPointerException in in Spark recovery: Add initializing default values in DriverInfo.init()

The issue happens when Spark is run standalone on a cluster.
When master and driver fall simultaneously on one node in a cluster, master tries to recover its state and restart spark driver.
While restarting driver, it falls with NPE exception (stacktrace is below).
After falling, it restarts and tries to recover its state and restart Spark driver again. It happens over and over in an infinite cycle.
Namely, Spark tries to read DriverInfo state from zookeeper, but after reading it happens to be null in DriverInfo.worker.

https://issues.apache.org/jira/browse/SPARK-3150

Author: Tatiana Borisova <tanyatik@yandex.ru>

Closes #2062 from tanyatik/spark-3150 and squashes the following commits:

9936043 [Tatiana Borisova] Add initializing default values in DriverInfo.init()
[SPARK-2608][Core] Fixed command line option passing issue over Mesos via SPARK_EXECUTOR_OPTS

This is another try after #2145 to fix [SPARK-2608](https://issues.apache.org/jira/browse/SPARK-2608).

The basic idea is to pass `extraJavaOpts` and `extraLibraryPath` together via environment variable `SPARK_EXECUTOR_OPTS`. This variable is recognized by `spark-class` and not used anywhere else. In this way, we still launch Mesos executors with `spark-class`/`spark-executor`, but avoids the executor side Spark home issue.

Quoted string with spaces is not allowed in either `extraJavaOpts` or `extraLibraryPath` when using Spark over Mesos. The reason is that Mesos passes the whole command line as a single string argument to `sh -c` to start the executor, and this makes shell string escaping non-trivial to handle. This should be fixed in a later release.

Classes in package `org.apache.spark.deploy` shouldn't be used as they assume Spark is deployed in standalone mode, and give wrong executor side Spark home directory. Please refer to comments in #2145 for more details.

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

Closes #2161 from liancheng/mesos-fix-with-env-var and squashes the following commits:

ba59190 [Cheng Lian] Added fine grained Mesos executor support
1174076 [Cheng Lian] Draft fix for CoarseMesosSchedulerBackend

(cherry picked from commit 935bffe3bf6c91a42288bff8c1ec69fecb41a769)
Signed-off-by: Reynold Xin <rxin@apache.org>
[SPARK-3264] Allow users to set executor Spark home in Mesos

The executors and the driver may not share the same Spark home. There is currently one way to set the executor side Spark home in Mesos, through setting `spark.home`. However, this is neither documented nor intuitive. This PR adds a more specific config `spark.mesos.executor.home` and exposes this to the user.

liancheng tnachen

Author: Andrew Or <andrewor14@gmail.com>

Closes #2166 from andrewor14/mesos-spark-home and squashes the following commits:

b87965e [Andrew Or] Merge branch 'master' of github.com:apache/spark into mesos-spark-home
f6abb2e [Andrew Or] Document spark.mesos.executor.home
ca7846d [Andrew Or] Add more specific configuration for executor Spark home in Mesos
[SPARK-3281] Remove Netty specific code in BlockManager / shuffle

Netty functionality will be added back in subsequent PRs by using the BlockTransferService interface.

Author: Reynold Xin <rxin@apache.org>

Closes #2181 from rxin/SPARK-3281 and squashes the following commits:

5494b0e [Reynold Xin] Fix extra port.
ff6d1e1 [Reynold Xin] [SPARK-3281] Remove Netty specific code in BlockManager.
[SPARK-3285] [examples] Using values.sum is easier to understand than using values.foldLeft(0)(_ + _)

def sum[B >: A](implicit num: Numeric[B]): B = foldLeft(num.zero)(num.plus)
Using values.sum is easier to understand than using values.foldLeft(0)(_ + _), so we'd better use values.sum instead of values.foldLeft(0)(_ + _)

Author: Yadong Qi <qiyadong2010@gmail.com>

Closes #2182 from watermen/bug-fix3 and squashes the following commits:

17be9fb [Yadong Qi] Update CheckpointSuite.scala
714bda5 [Yadong Qi] Update BasicOperationsSuite.scala
57e704c [Yadong Qi] Update StatefulNetworkWordCount.scala
[SPARK-3190] Avoid overflow in VertexRDD.count()

VertexRDDs with more than 4 billion elements are counted incorrectly due to integer overflow when summing partition sizes. This PR fixes the issue by converting partition sizes to Longs before summing them.

The following code previously returned -10000000. After applying this PR, it returns the correct answer of 5000000000 (5 billion).

```scala
val pairs = sc.parallelize(0L until 500L).map(_ * 10000000)
  .flatMap(start => start until (start + 10000000)).map(x => (x, x))
VertexRDD(pairs).count()
```

Author: Ankur Dave <ankurdave@gmail.com>

Closes #2106 from ankurdave/SPARK-3190 and squashes the following commits:

641f468 [Ankur Dave] Avoid overflow in VertexRDD.count()