[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()
SPARK-3082. yarn.Client.logClusterResourceDetails throws NPE if requeste...

...d queue doesn't exist

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1984 from sryza/sandy-spark-3082 and squashes the following commits:

fe08c37 [Sandy Ryza] Remove log message entirely
85253ad [Sandy Ryza] SPARK-3082. yarn.Client.logClusterResourceDetails throws NPE if requested queue doesn't exist
[SPARK-3277] Fix external spilling with LZ4 assertion error

**Summary of the changes**

The bulk of this PR is comprised of tests and documentation; the actual fix is really just adding 1 line of code (see `BlockObjectWriter.scala`). We currently do not run the `External*` test suites with different compression codecs, and this would have caught the bug reported in [SPARK-3277](https://issues.apache.org/jira/browse/SPARK-3277). This PR extends the existing code to test spilling using all compression codecs known to Spark, including `LZ4`.

**The bug itself**

In `DiskBlockObjectWriter`, we only report the shuffle bytes written before we close the streams. With `LZ4`, all the bytes written reported by our metrics were 0 because `flush()` was not taking effect for some reason. In general, compression codecs may write additional bytes to the file after we call `close()`, and so we must also capture those bytes in our shuffle write metrics.

Thanks mridulm and pwendell for help with debugging.

Author: Andrew Or <andrewor14@gmail.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #2187 from andrewor14/fix-lz4-spilling and squashes the following commits:

1b54bdc [Andrew Or] Speed up tests by not compressing everything
1c4624e [Andrew Or] Merge branch 'master' of github.com:apache/spark into fix-lz4-spilling
6b2e7d1 [Andrew Or] Fix compilation error
92e251b [Patrick Wendell] Better documentation for BlockObjectWriter.
a1ad536 [Andrew Or] Fix tests
089593f [Andrew Or] Actually fix SPARK-3277 (tests still fail)
4bbcf68 [Andrew Or] Update tests to actually test all compression codecs
b264a84 [Andrew Or] ExternalAppendOnlyMapSuite code style fixes (minor)
1bfa743 [Andrew Or] Add more information to assert for better debugging
[Spark QA] Link to console output on test time out

When tests time out we should link to the Jenkins console output for easy review. We already do this for when tests start or complete normally.

Here's [a recent example](https://github.com/apache/spark/pull/2109#issuecomment-53374032) of where this would be helpful.

Author: nchammas <nicholas.chammas@gmail.com>

Closes #2140 from nchammas/patch-1 and squashes the following commits:

3b26c8d [nchammas] [Spark QA] Link to console output on test time out
[SPARK-1912] Lazily initialize buffers for local shuffle blocks.

This is a simplified fix for SPARK-1912.

Author: Reynold Xin <rxin@apache.org>

Closes #2179 from rxin/SPARK-1912 and squashes the following commits:

b2f0e9e [Reynold Xin] Fix unit tests.
a8eddfe [Reynold Xin] [SPARK-1912] Lazily initialize buffers for local shuffle blocks.
[SPARK-3279] Remove useless field variable in ApplicationMaster

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

Closes #2177 from sarutak/SPARK-3279 and squashes the following commits:

2955edc [Kousuke Saruta] Removed useless field variable from ApplicationMaster
Merge branch 'master' into pypy