Update DecisionTreeRunner.scala

Author: strat0sphere <stratos.dimopoulos@gmail.com>

Closes #1676 from strat0sphere/patch-1 and squashes the following commits:

044d2fa [strat0sphere] Update DecisionTreeRunner.scala
SPARK-2045 Sort-based shuffle

This adds a new ShuffleManager based on sorting, as described in https://issues.apache.org/jira/browse/SPARK-2045. The bulk of the code is in an ExternalSorter class that is similar to ExternalAppendOnlyMap, but sorts key-value pairs by partition ID and can be used to create a single sorted file with a map task's output. (Longer-term I think this can take on the remaining functionality in ExternalAppendOnlyMap and replace it so we don't have code duplication.)

The main TODOs still left are:
- [x] enabling ExternalSorter to merge across spilled files
  - [x] with an Ordering
  - [x] without an Ordering, using the keys' hash codes
- [x] adding more tests (e.g. a version of our shuffle suite that runs on this)
- [x] rebasing on top of the size-tracking refactoring in #1165 when that is merged
- [x] disabling spilling if spark.shuffle.spill is set to false

Despite this though, this seems to work pretty well (running successfully in cases where the hash shuffle would OOM, such as 1000 reduce tasks on executors with only 1G memory), and it seems to be comparable in speed or faster than hash-based shuffle (it will create much fewer files for the OS to keep track of). So I'm posting it to get some early feedback.

After these TODOs are done, I'd also like to enable ExternalSorter to sort data within each partition by a key as well, which will allow us to use it to implement external spilling in reduce tasks in `sortByKey`.

Author: Matei Zaharia <matei@databricks.com>

Closes #1499 from mateiz/sort-based-shuffle and squashes the following commits:

bd841f9 [Matei Zaharia] Various review comments
d1c137fd [Matei Zaharia] Various review comments
a611159 [Matei Zaharia] Compile fixes due to rebase
62c56c8 [Matei Zaharia] Fix ShuffledRDD sometimes not returning Tuple2s.
f617432 [Matei Zaharia] Fix a failing test (seems to be due to change in SizeTracker logic)
9464d5f [Matei Zaharia] Simplify code and fix conflicts after latest rebase
0174149 [Matei Zaharia] Add cleanup behavior and cleanup tests for sort-based shuffle
eb4ee0d [Matei Zaharia] Remove customizable element type in ShuffledRDD
fa2e8db [Matei Zaharia] Allow nextBatchStream to be called after we're done looking at all streams
a34b352 [Matei Zaharia] Fix tracking of indices within a partition in SpillReader, and add test
03e1006 [Matei Zaharia] Add a SortShuffleSuite that runs ShuffleSuite with sort-based shuffle
3c7ff1f [Matei Zaharia] Obey the spark.shuffle.spill setting in ExternalSorter
ad65fbd [Matei Zaharia] Rebase on top of Aaron's Sorter change, and use Sorter in our buffer
44d2a93 [Matei Zaharia] Use estimateSize instead of atGrowThreshold to test collection sizes
5686f71 [Matei Zaharia] Optimize merging phase for in-memory only data:
5461cbb [Matei Zaharia] Review comments and more tests (e.g. tests with 1 element per partition)
e9ad356 [Matei Zaharia] Update ContextCleanerSuite to make sure shuffle cleanup tests use hash shuffle (since they were written for it)
c72362a [Matei Zaharia] Added bug fix and test for when iterators are empty
de1fb40 [Matei Zaharia] Make trait SizeTrackingCollection private[spark]
4988d16 [Matei Zaharia] tweak
c1b7572 [Matei Zaharia] Small optimization
ba7db7f [Matei Zaharia] Handle null keys in hash-based comparator, and add tests for collisions
ef4e397 [Matei Zaharia] Support for partial aggregation even without an Ordering
4b7a5ce [Matei Zaharia] More tests, and ability to sort data if a total ordering is given
e1f84be [Matei Zaharia] Fix disk block manager test
5a40a1c [Matei Zaharia] More tests
614f1b4 [Matei Zaharia] Add spill metrics to map tasks
cc52caf [Matei Zaharia] Add more error handling and tests for error cases
bbf359d [Matei Zaharia] More work
3a56341 [Matei Zaharia] More partial work towards sort-based shuffle
7a0895d [Matei Zaharia] Some more partial work towards sort-based shuffle
b615476 [Matei Zaharia] Scaffolding for sort-based shuffle
[SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDs

Author: Reynold Xin <rxin@apache.org>

Closes #1675 from rxin/unionrdd and squashes the following commits:

941d316 [Reynold Xin] Clear RDDs for checkpointing.
c9f05f2 [Reynold Xin] [SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDs
Required AM memory is "amMem", not "args.amMemory"

"ERROR yarn.Client: Required AM memory (1024) is above the max threshold (1048) of this cluster" appears if this code is not changed. obviously, 1024 is less than 1048, so change this

Author: derek ma <maji3@asiainfo-linkage.com>

Closes #1494 from maji2014/master and squashes the following commits:

b0f6640 [derek ma] Required AM memory is "amMem", not "args.amMemory"
[SPARK-2340] Resolve event logging and History Server paths properly

We resolve relative paths to the local `file:/` system for `--jars` and `--files` in spark submit (#853). We should do the same for the history server.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1280 from andrewor14/hist-serv-fix and squashes the following commits:

13ff406 [Andrew Or] Merge branch 'master' of github.com:apache/spark into hist-serv-fix
b393e17 [Andrew Or] Strip trailing "/" from logging directory
622a471 [Andrew Or] Fix test in EventLoggingListenerSuite
0e20f71 [Andrew Or] Shift responsibility of resolving paths up one level
b037c0c [Andrew Or] Use resolved paths for everything in history server
c7e36ee [Andrew Or] Resolve paths for event logging too
40e3933 [Andrew Or] Resolve history server file paths
[SPARK-2737] Add retag() method for changing RDDs' ClassTags.

The Java API's use of fake ClassTags doesn't seem to cause any problems for Java users, but it can lead to issues when passing JavaRDDs' underlying RDDs to Scala code (e.g. in the MLlib Java API wrapper code). If we call collect() on a Scala RDD with an incorrect ClassTag, this causes ClassCastExceptions when we try to allocate an array of the wrong type (for example, see SPARK-2197).

There are a few possible fixes here. An API-breaking fix would be to completely remove the fake ClassTags and require Java API users to pass java.lang.Class instances to all parallelize() calls and add returnClass fields to all Function implementations. This would be extremely verbose.

Instead, this patch adds internal APIs to "repair" a Scala RDD with an incorrect ClassTag by wrapping it and overriding its ClassTag. This should be okay for cases where the Scala code that calls collect() knows what type of array should be allocated, which is the case in the MLlib wrappers.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1639 from JoshRosen/SPARK-2737 and squashes the following commits:

572b4c8 [Josh Rosen] Replace newRDD[T] with mapPartitions().
469d941 [Josh Rosen] Preserve partitioner in retag().
af78816 [Josh Rosen] Allow retag() to get classTag implicitly.
d1d54e6 [Josh Rosen] [SPARK-2737] Add retag() method for changing RDDs' ClassTags.
[SPARK-2497] Included checks for module symbols too.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #1463 from ScrapCodes/SPARK-2497/mima-exclude-all and squashes the following commits:

72077b1 [Prashant Sharma] Check separately for module symbols.
cd96192 [Prashant Sharma] SPARK-2497 Produce "member excludes" irrespective of the fact that class itself is excluded or not.
automatically set master according to `spark.master` in `spark-defaults....

automatically set master according to `spark.master` in `spark-defaults.conf`

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1644 from CrazyJvm/standalone-guide and squashes the following commits:

bb12b95 [CrazyJvm] automatically set master according to `spark.master` in `spark-defaults.conf`
[SPARK-2762] SparkILoop leaks memory in multi-repl configurations

This pull request is a small refactor so that a partial function (hence a closure) is not created. Instead, a regular function is used. The behavior of the code is not changed.

Author: Timothy Hunter <timhunter@databricks.com>

Closes #1674 from thunterdb/closure_issue and squashes the following commits:

e1e664d [Timothy Hunter] simplify closure
[SPARK-2743][SQL] Resolve original attributes in ParquetTableScan

Author: Michael Armbrust <michael@databricks.com>

Closes #1647 from marmbrus/parquetCase and squashes the following commits:

a1799b7 [Michael Armbrust] move comment
2a2a68b [Michael Armbrust] Merge remote-tracking branch 'apache/master' into parquetCase
bb35d5b [Michael Armbrust] Fix test case that produced an invalid plan.
e6870bf [Michael Armbrust] Better error message.
539a2e1 [Michael Armbrust] Resolve original attributes in ParquetTableScan
[SPARK-2397][SQL] Deprecate LocalHiveContext

LocalHiveContext is redundant with HiveContext.  The only difference is it creates `./metastore` instead of `./metastore_db`.

Author: Michael Armbrust <michael@databricks.com>

Closes #1641 from marmbrus/localHiveContext and squashes the following commits:

e5ec497 [Michael Armbrust] Add deprecation version
626e056 [Michael Armbrust] Don't remove from imports yet
905cc5f [Michael Armbrust] Merge remote-tracking branch 'apache/master' into localHiveContext
1c2727e [Michael Armbrust] Deprecate LocalHiveContext
SPARK-2028: Expose mapPartitionsWithInputSplit in HadoopRDD

This allows users to gain access to the InputSplit which backs each partition.

An alternative solution would have been to have a .withInputSplit() method which returns a new RDD[(InputSplit, (K, V))], but this is confusing because you could not cache this RDD or shuffle it, as InputSplit is not inherently serializable.

Author: Aaron Davidson <aaron@databricks.com>

Closes #973 from aarondav/hadoop and squashes the following commits:

9c9112b [Aaron Davidson] Add JavaAPISuite test
9942cd7 [Aaron Davidson] Add Java API
1284a3a [Aaron Davidson] SPARK-2028: Expose mapPartitionsWithInputSplit in HadoopRDD
SPARK-2664. Deal with `--conf` options in spark-submit that relate to fl...

...ags

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1665 from sryza/sandy-spark-2664 and squashes the following commits:

0518c63 [Sandy Ryza] SPARK-2664. Deal with `--conf` options in spark-submit that relate to flags
SPARK-2749 [BUILD] Part 2. Fix a follow-on scalastyle error

The test compile error is fixed, but the build still fails because of one scalastyle error.

https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/lastFailedBuild/hadoop.version=1.0.4,label=centos/console

Author: Sean Owen <srowen@gmail.com>

Closes #1690 from srowen/SPARK-2749 and squashes the following commits:

1c9e7a6 [Sean Owen] Also: fix scalastyle error by wrapping a long line
SPARK-2646. log4j initialization not quite compatible with log4j 2.x

The logging code that handles log4j initialization leads to an stack overflow error when used with log4j 2.x, which has just been released. This occurs even a downstream project has correctly adjusted SLF4J bindings, and that is the right thing to do for log4j 2.x, since it is effectively a separate project from 1.x.

Here is the relevant bit of Logging.scala:

```
  private def initializeLogging() {
    // If Log4j is being used, but is not initialized, load a default properties file
    val binder = StaticLoggerBinder.getSingleton
    val usingLog4j = binder.getLoggerFactoryClassStr.endsWith("Log4jLoggerFactory")
    val log4jInitialized = LogManager.getRootLogger.getAllAppenders.hasMoreElements
    if (!log4jInitialized && usingLog4j) {
      val defaultLogProps = "org/apache/spark/log4j-defaults.properties"
      Option(Utils.getSparkClassLoader.getResource(defaultLogProps)) match {
        case Some(url) =>
          PropertyConfigurator.configure(url)
          log.info(s"Using Spark's default log4j profile: $defaultLogProps")
        case None =>
          System.err.println(s"Spark was unable to load $defaultLogProps")
      }
    }
    Logging.initialized = true

    // Force a call into slf4j to initialize it. Avoids this happening from mutliple threads
    // and triggering this: http://mailman.qos.ch/pipermail/slf4j-dev/2010-April/002956.html
    log
  }
```

The first minor issue is that there is a call to a logger inside this method, which is initializing logging. In this situation, it ends up causing the initialization to be called recursively until the stack overflow. It would be slightly tidier to log this only after Logging.initialized = true. Or not at all. But it's not the root problem, or else, it would not work at all now.

The calls to log4j classes here always reference log4j 1.2 no matter what. For example, there is not getAllAppenders in log4j 2.x. That's fine. Really, "usingLog4j" means "using log4j 1.2" and "log4jInitialized" means "log4j 1.2 is initialized".

usingLog4j should be false for log4j 2.x, because the initialization only matters for log4j 1.2. But, it's true, and that's the real issue. And log4jInitialized is always false, since calls to the log4j 1.2 API are stubs and no-ops in this setup, where the caller has swapped in log4j 2.x. Hence the loop.

This is fixed, I believe, if "usingLog4j" can be false for log4j 2.x. The SLF4J static binding class has the same name for both versions, unfortunately, which causes the issue. However they're in different packages. For example, if the test included "... and begins with org.slf4j", it should work, as the SLF4J binding for log4j 2.x is provided by log4j 2.x at the moment, and is in package org.apache.logging.slf4j.

Of course, I assume that SLF4J will eventually offer its own binding. I hope to goodness they at least name the binding class differently, or else this will again not work. But then some other check can probably be made.

Author: Sean Owen <srowen@gmail.com>

Closes #1547 from srowen/SPARK-2646 and squashes the following commits:

92a9898 [Sean Owen] System.out -> System.err
94be4c7 [Sean Owen] Add back log message as System.out, with informational comment
a7f8876 [Sean Owen] Updates from review
6f3c1d3 [Sean Owen] Remove log statement in logging initialization, and distinguish log4j 1.2 from 2.0, to avoid stack overflow in initialization
[SPARK-2511][MLLIB] add HashingTF and IDF

This is roughly the TF-IDF implementation used in the Databricks Cloud Demo: http://databricks.com/cloud/ .

Both `HashingTF` and `IDF` are implemented as transformers, similar to scikit-learn.

Author: Xiangrui Meng <meng@databricks.com>

Closes #1671 from mengxr/tfidf and squashes the following commits:

7d65888 [Xiangrui Meng] use JavaConverters._
5fe9ec4 [Xiangrui Meng] fix unit test
6e214ec [Xiangrui Meng] add apache header
cfd9aed [Xiangrui Meng] add Java-friendly methods move classes to mllib.feature
3814440 [Xiangrui Meng] add HashingTF and IDF
[SPARK-2523] [SQL] Hadoop table scan bug fixing (fix failing Jenkins maven test)

This PR tries to resolve the broken Jenkins maven test issue introduced by #1439. Now, we create a single query test to run both the setup work and the test query.

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1669 from yhuai/SPARK-2523-fixTest and squashes the following commits:

358af1a [Yin Huai] Make partition_based_table_scan_with_different_serde run atomically.
Improvements to merge_spark_pr.py

This commit fixes a couple of issues in the merge_spark_pr.py developer script:

- Allow recovery from failed cherry-picks.
- Fix detection of pull requests that have already been merged.

Both of these fixes are useful when backporting changes.

Author: Josh Rosen <joshrosen@apache.org>

Closes #1668 from JoshRosen/pr-script-improvements and squashes the following commits:

ff4f33a [Josh Rosen] Default SPARK_HOME to cwd(); detect missing JIRA credentials.
ed5bc57 [Josh Rosen] Improvements for backporting using merge_spark_pr:
Docs: monitoring, streaming programming guide

Fix several awkward wordings and grammatical issues in the following
documents:

*   docs/monitoring.md

*   docs/streaming-programming-guide.md

Author: kballou <kballou@devnulllabs.io>

Closes #1662 from kennyballou/grammar_fixes and squashes the following commits:

e1b8ad6 [kballou] Docs: monitoring, streaming programming guide
SPARK-2740: allow user to specify ascending and numPartitions for sortBy...

It should be more convenient if user can specify ascending and numPartitions when calling sortByKey.

Author: Rui Li <rui.li@intel.com>

Closes #1645 from lirui-intel/spark-2740 and squashes the following commits:

fb5d52e [Rui Li] SPARK-2740: allow user to specify ascending and numPartitions for sortByKey