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15225 commits

Author SHA1 Message Date
Wenchen Fan a2a9078028 [SPARK-14039][SQL][MINOR] make SubqueryHolder an inner class
## What changes were proposed in this pull request?

`SubqueryHolder` is only used when generate SQL string in `SQLBuilder`, it's more clear to make it an inner class in `SQLBuilder`.

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11861 from cloud-fan/gensql.
2016-03-21 10:04:49 -07:00
Dongjoon Hyun df61fbd978 [SPARK-13986][CORE][MLLIB] Remove DeveloperApi-annotations for non-publics
## What changes were proposed in this pull request?

Spark uses `DeveloperApi` annotation, but sometimes it seems to conflict with visibility. This PR tries to fix those conflict by removing annotations for non-publics. The following is the example.

**JobResult.scala**
```scala
DeveloperApi
sealed trait JobResult

DeveloperApi
case object JobSucceeded extends JobResult

-DeveloperApi
private[spark] case class JobFailed(exception: Exception) extends JobResult
```

## How was this patch tested?

Pass the existing Jenkins test.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11797 from dongjoon-hyun/SPARK-13986.
2016-03-21 14:57:52 +00:00
Wenchen Fan 17a3f00676 [SPARK-14000][SQL] case class with a tuple field can't work in Dataset
## What changes were proposed in this pull request?

When we validate an encoder, we may call `dataType` on unresolved expressions. This PR fix the validation so that we will resolve attributes first.

## How was this patch tested?

a new test in `DatasetSuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11816 from cloud-fan/encoder.
2016-03-21 22:22:15 +08:00
gatorsmile 2c5b18fb0f [SPARK-12789][SQL] Support Order By Ordinal in SQL
#### What changes were proposed in this pull request?
This PR is to support order by position in SQL, e.g.
```SQL
select c1, c2, c3 from tbl order by 1 desc, 3
```
should be equivalent to
```SQL
select c1, c2, c3 from tbl order by c1 desc, c3 asc
```

This is controlled by config option `spark.sql.orderByOrdinal`.
- When true, the ordinal numbers are treated as the position in the select list.
- When false, the ordinal number in order/sort By clause are ignored.

- Only convert integer literals (not foldable expressions). If found foldable expressions, ignore them
- This also works with select *.

**Question**: Do we still need sort by columns that contain zero reference? In this case, it will have no impact on the sorting results. IMO, we should not allow users do it. rxin cloud-fan marmbrus yhuai hvanhovell
-- Update: In these cases, they are ignored in this case.

**Note**: This PR is taken from https://github.com/apache/spark/pull/10731. When merging this PR, please give the credit to zhichao-li

Also cc all the people who are involved in the previous discussion: adrian-wang chenghao-intel tejasapatil

#### How was this patch tested?
Added a few test cases for both positive and negative test cases.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #11815 from gatorsmile/orderByPosition.
2016-03-21 18:08:41 +08:00
proflin c35c60fa91 [SPARK-14028][STREAMING][KINESIS][TESTS] Remove deprecated methods; fix two other warnings
## What changes were proposed in this pull request?

- Removed two methods that has been deprecated since 1.4
- Fixed two other compilation warnings

## How was this patch tested?

existing test suits

Author: proflin <proflin.me@gmail.com>

Closes #11850 from lw-lin/streaming-kinesis-deprecates-warnings.
2016-03-21 08:02:06 +00:00
Dongjoon Hyun 761c2d1b6e [MINOR][DOCS] Add proper periods and spaces for CLI help messages and config doc.
## What changes were proposed in this pull request?

This PR adds some proper periods and spaces to Spark CLI help messages and SQL/YARN conf docs for consistency.

## How was this patch tested?

Manual.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11848 from dongjoon-hyun/add_proper_period_and_space.
2016-03-21 08:00:09 +00:00
Dongjoon Hyun 20fd254101 [SPARK-14011][CORE][SQL] Enable LineLength Java checkstyle rule
## What changes were proposed in this pull request?

[Spark Coding Style Guide](https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide) has 100-character limit on lines, but it's disabled for Java since 11/09/15. This PR enables **LineLength** checkstyle again. To help that, this also introduces **RedundantImport** and **RedundantModifier**, too. The following is the diff on `checkstyle.xml`.

```xml
-        <!-- TODO: 11/09/15 disabled - the lengths are currently > 100 in many places -->
-        <!--
         <module name="LineLength">
             <property name="max" value="100"/>
             <property name="ignorePattern" value="^package.*|^import.*|a href|href|http://|https://|ftp://"/>
         </module>
-        -->
         <module name="NoLineWrap"/>
         <module name="EmptyBlock">
             <property name="option" value="TEXT"/>
 -167,5 +164,7
         </module>
         <module name="CommentsIndentation"/>
         <module name="UnusedImports"/>
+        <module name="RedundantImport"/>
+        <module name="RedundantModifier"/>
```

## How was this patch tested?

Currently, `lint-java` is disabled in Jenkins. It needs a manual test.
After passing the Jenkins tests, `dev/lint-java` should passes locally.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11831 from dongjoon-hyun/SPARK-14011.
2016-03-21 07:58:57 +00:00
hyukjinkwon e474088144 [SPARK-13764][SQL] Parse modes in JSON data source
## What changes were proposed in this pull request?

Currently, there is no way to control the behaviour when fails to parse corrupt records in JSON data source .

This PR adds the support for parse modes just like CSV data source. There are three modes below:

- `PERMISSIVE` :  When it fails to parse, this sets `null` to to field. This is a default mode when it has been this mode.
- `DROPMALFORMED`: When it fails to parse, this drops the whole record.
- `FAILFAST`: When it fails to parse, it just throws an exception.

This PR also make JSON data source share the `ParseModes` in CSV data source.

## How was this patch tested?

Unit tests were used and `./dev/run_tests` for code style tests.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #11756 from HyukjinKwon/SPARK-13764.
2016-03-21 15:42:35 +08:00
gatorsmile f58319a24f [SPARK-14019][SQL] Remove noop SortOrder in Sort
#### What changes were proposed in this pull request?

This PR is to add a new Optimizer rule for pruning Sort if its SortOrder is no-op. In the phase of **Optimizer**, if a specific `SortOrder` does not have any reference, it has no effect on the sorting results. If `Sort` is empty, remove the whole `Sort`.

For example, in the following SQL query
```SQL
SELECT * FROM t ORDER BY NULL + 5
```

Before the fix, the plan is like
```
== Analyzed Logical Plan ==
a: int, b: int
Sort [(cast(null as int) + 5) ASC], true
+- Project [a#92,b#93]
   +- SubqueryAlias t
      +- Project [_1#89 AS a#92,_2#90 AS b#93]
         +- LocalRelation [_1#89,_2#90], [[1,2],[1,2]]

== Optimized Logical Plan ==
Sort [null ASC], true
+- LocalRelation [a#92,b#93], [[1,2],[1,2]]

== Physical Plan ==
WholeStageCodegen
:  +- Sort [null ASC], true, 0
:     +- INPUT
+- Exchange rangepartitioning(null ASC, 5), None
   +- LocalTableScan [a#92,b#93], [[1,2],[1,2]]
```

After the fix, the plan is like
```
== Analyzed Logical Plan ==
a: int, b: int
Sort [(cast(null as int) + 5) ASC], true
+- Project [a#92,b#93]
   +- SubqueryAlias t
      +- Project [_1#89 AS a#92,_2#90 AS b#93]
         +- LocalRelation [_1#89,_2#90], [[1,2],[1,2]]

== Optimized Logical Plan ==
LocalRelation [a#92,b#93], [[1,2],[1,2]]

== Physical Plan ==
LocalTableScan [a#92,b#93], [[1,2],[1,2]]
```

cc rxin cloud-fan marmbrus Thanks!

#### How was this patch tested?
Added a test suite for covering this rule

Author: gatorsmile <gatorsmile@gmail.com>

Closes #11840 from gatorsmile/sortElimination.
2016-03-21 10:34:54 +08:00
Xusen Yin 454a00df2a [SPARK-13993][PYSPARK] Add pyspark Rformula/RforumlaModel save/load
## What changes were proposed in this pull request?

https://issues.apache.org/jira/browse/SPARK-13993

## How was this patch tested?

doctest

Author: Xusen Yin <yinxusen@gmail.com>

Closes #11807 from yinxusen/SPARK-13993.
2016-03-20 15:34:34 -07:00
sethah 811a524722 [SPARK-12182][ML] Distributed binning for trees in spark.ml
This PR changes the `findSplits` method in spark.ml to perform split calculations on the workers. This PR is meant to copy [PR-8246](https://github.com/apache/spark/pull/8246) which added the same feature for MLlib.

Author: sethah <seth.hendrickson16@gmail.com>

Closes #10231 from sethah/SPARK-12182.
2016-03-20 12:31:28 -07:00
Shixiong Zhu d630a203d6 [SPARK-10680][TESTS] Increase 'connectionTimeout' to make RequestTimeoutIntegrationSuite more stable
## What changes were proposed in this pull request?

Increase 'connectionTimeout' to make RequestTimeoutIntegrationSuite more stable

## How was this patch tested?

Existing unit tests

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #11833 from zsxwing/SPARK-10680.
2016-03-19 12:35:35 -07:00
Reynold Xin dcaa016610 [SPARK-13897][SQL] RelationalGroupedDataset and KeyValueGroupedDataset
## What changes were proposed in this pull request?
Previously, Dataset.groupBy returns a GroupedData, and Dataset.groupByKey returns a GroupedDataset. The naming is very similar, and unfortunately does not convey the real differences between the two.

Assume we are grouping by some keys (K). groupByKey is a key-value style group by, in which the schema of the returned dataset is a tuple of just two fields: key and value. groupBy, on the other hand, is a relational style group by, in which the schema of the returned dataset is flattened and contain |K| + |V| fields.

This pull request also removes the experimental tag from RelationalGroupedDataset. It has been with DataFrame since 1.3, and we have enough confidence now to stabilize it.

## How was this patch tested?
This is a rename to improve API understandability. Should be covered by all existing tests.

Author: Reynold Xin <rxin@databricks.com>

Closes #11841 from rxin/SPARK-13897.
2016-03-19 11:23:14 -07:00
Dongjoon Hyun 2082a49569 [MINOR][DOCS] Use spark-submit instead of sparkR to submit R script.
## What changes were proposed in this pull request?

Since `sparkR` is not used for submitting R Scripts from Spark 2.0, a user faces the following error message if he follows the instruction on `R/README.md`. This PR updates `R/README.md`.
```bash
$ ./bin/sparkR examples/src/main/r/dataframe.R
Running R applications through 'sparkR' is not supported as of Spark 2.0.
Use ./bin/spark-submit <R file>
```

## How was this patch tested?

Manual.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11842 from dongjoon-hyun/update_r_readme.
2016-03-19 13:23:34 +00:00
Reynold Xin 1970d911d9 [SPARK-14018][SQL] Use 64-bit num records in BenchmarkWholeStageCodegen
## What changes were proposed in this pull request?
500L << 20 is actually pretty close to 32-bit int limit. I was trying to increase this to 500L << 23 and got negative numbers instead.

## How was this patch tested?
I'm only modifying test code.

Author: Reynold Xin <rxin@databricks.com>

Closes #11839 from rxin/SPARK-14018.
2016-03-19 00:27:23 -07:00
Sameer Agarwal b39594472b [SPARK-14012][SQL] Extract VectorizedColumnReader from VectorizedParquetRecordReader
## What changes were proposed in this pull request?

This is a minor followup on https://github.com/apache/spark/pull/11799 that extracts out the `VectorizedColumnReader` from `VectorizedParquetRecordReader` into its own file.

## How was this patch tested?

N/A (refactoring only)

Author: Sameer Agarwal <sameer@databricks.com>

Closes #11834 from sameeragarwal/rename.
2016-03-18 22:33:43 -07:00
Dongjoon Hyun c11ea2e413 [MINOR][DOCS] Update build descriptions and commands
## What changes were proposed in this pull request?

This PR updates Scala and Hadoop versions in the build description and commands in `Building Spark` documents.

## How was this patch tested?

N/A

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11838 from dongjoon-hyun/fix_doc_building_spark.
2016-03-18 21:32:48 -07:00
Yuhao Yang f43a26ef92 [SPARK-13629][ML] Add binary toggle Param to CountVectorizer
## What changes were proposed in this pull request?

This is a continued work for https://github.com/apache/spark/pull/11536#issuecomment-198511013,
containing some comment update and style adjustment.
jkbradley

## How was this patch tested?

unit tests.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #11830 from hhbyyh/cvToggle.
2016-03-18 17:34:33 -07:00
Sameer Agarwal 54794113a6 [SPARK-13989] [SQL] Remove non-vectorized/unsafe-row parquet record reader
## What changes were proposed in this pull request?

This PR cleans up the new parquet record reader with the following changes:

1. Removes the non-vectorized parquet reader code from `UnsafeRowParquetRecordReader`.
2. Removes the non-vectorized column reader code from `ColumnReader`.
3. Renames `UnsafeRowParquetRecordReader` to `VectorizedParquetRecordReader` and `ColumnReader` to `VectorizedColumnReader`
4. Deprecate `PARQUET_UNSAFE_ROW_RECORD_READER_ENABLED`

## How was this patch tested?

Refactoring only; Existing tests should reveal any problems.

Author: Sameer Agarwal <sameer@databricks.com>

Closes #11799 from sameeragarwal/vectorized-parquet.
2016-03-18 14:04:42 -07:00
Yin Huai 238fb485be [SPARK-13972][SQL][FOLLOW-UP] When creating the query execution for a converted SQL query, we eagerly trigger analysis
## What changes were proposed in this pull request?
As part of testing generating SQL query from a analyzed SQL plan, we run the generated SQL for tests in HiveComparisonTest. This PR makes the generated SQL get eagerly analyzed. So, when a generated SQL has any analysis error, we can see the error message created by
```
                  case NonFatal(e) => fail(
                    s"""Failed to analyze the converted SQL string:
                        |
                        |# Original HiveQL query string:
                        |$queryString
                        |
                        |# Resolved query plan:
                        |${originalQuery.analyzed.treeString}
                        |
                        |# Converted SQL query string:
                        |$convertedSQL
                     """.stripMargin, e)
```

Right now, if we can parse a generated SQL but fail to analyze it, we will see error message generated by the following code (it only mentions that we cannot execute the original query, i.e. `queryString`).
```
            case e: Throwable =>
              val errorMessage =
                s"""
                  |Failed to execute query using catalyst:
                  |Error: ${e.getMessage}
                  |${stackTraceToString(e)}
                  |$queryString
                  |$query
                  |== HIVE - ${hive.size} row(s) ==
                  |${hive.mkString("\n")}
                """.stripMargin
```

## How was this patch tested?
Existing tests.

Author: Yin Huai <yhuai@databricks.com>

Closes #11825 from yhuai/SPARK-13972-follow-up.
2016-03-18 13:40:53 -07:00
Sital Kedia 2e0c5284fd [SPARK-13958] Executor OOM due to unbounded growth of pointer array in…
## What changes were proposed in this pull request?

This change fixes the executor OOM which was recently introduced in PR apache/spark#11095
(Please fill in changes proposed in this fix)

## How was this patch tested?
Tested by running a spark job on the cluster.
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

… Sorter

Author: Sital Kedia <skedia@fb.com>

Closes #11794 from sitalkedia/SPARK-13958.
2016-03-18 12:56:06 -07:00
jerryshao 3537782168 [SPARK-13885][YARN] Fix attempt id regression for Spark running on Yarn
## What changes were proposed in this pull request?

This regression is introduced in #9182, previously attempt id is simply as counter "1" or "2". With the change of #9182, it is changed to full name as "appattemtp-xxx-00001", this will affect all the parts which uses this attempt id, like event log file name, history server app url link. So here change it back to the counter to keep consistent with previous code.

Also revert back this patch #11518, this patch fix the url link of history log according to the new way of attempt id, since here we change back to the previous way, so this patch is not necessary, here to revert it.

Also clean "spark.yarn.app.id" and "spark.yarn.app.attemptId", since it is useless now.

## How was this patch tested?

Test it with unit test and manually test different scenario:

1. application running in yarn-client mode.
2. application running in yarn-cluster mode.
3. application running in yarn-cluster mode with multiple attempts.

Checked both the event log file name and url link.

CC vanzin tgravescs , please help to review, thanks a lot.

Author: jerryshao <sshao@hortonworks.com>

Closes #11721 from jerryshao/SPARK-13885.
2016-03-18 12:39:49 -07:00
Davies Liu 9c23c818ca [SPARK-13977] [SQL] Brings back Shuffled hash join
## What changes were proposed in this pull request?

ShuffledHashJoin (also outer join) is removed in 1.6, in favor of SortMergeJoin, which is more robust and also fast.

ShuffledHashJoin is still useful in this case: 1) one table is much smaller than the other one, then cost to build a hash table on smaller table is smaller than sorting the larger table 2) any partition of the small table could fit in memory.

This PR brings back ShuffledHashJoin, basically revert #9645, and fix the conflict. Also merging outer join and left-semi join into the same class. This PR does not implement full outer join, because it's not implemented efficiently (requiring build hash table on both side).

A simple benchmark (one table is 5x smaller than other one) show that ShuffledHashJoin could be 2X faster than SortMergeJoin.

## How was this patch tested?

Added new unit tests for ShuffledHashJoin.

Author: Davies Liu <davies@databricks.com>

Closes #11788 from davies/shuffle_join.
2016-03-18 10:32:53 -07:00
Cheng Lian 14c7236dc6 [SPARK-14004][SQL][MINOR] AttributeReference and Alias should only use the first qualifier to generate SQL strings
## What changes were proposed in this pull request?

Current implementations of `AttributeReference.sql` and `Alias.sql` joins all available qualifiers, which is logically wrong. But this implementation mistake doesn't cause any real SQL generation bugs though, since there is always at most one qualifier for any given `AttributeReference` or `Alias`.

This PR fixes this issue by only picking the first qualifiers.

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

Existing tests should be enough.

Author: Cheng Lian <lian@databricks.com>

Closes #11820 from liancheng/spark-14004-single-qualifier.
2016-03-19 00:22:17 +08:00
Wenchen Fan 0acb32a3f1 [SPARK-13972][SQ] hive tests should fail if SQL generation failed
## What changes were proposed in this pull request?

Now we should be able to convert all logical plans to SQL string, if they are parsed from hive query. This PR changes the error handling to throw exceptions instead of just log.

We will send new PRs for spotted bugs, and merge this one after all bugs are fixed.

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11782 from cloud-fan/test.
2016-03-18 23:16:14 +08:00
Zheng RuiFeng 53f32a22da [MINOR][DOC] Fix nits in JavaStreamingTestExample
## What changes were proposed in this pull request?

Fix some nits discussed in https://github.com/apache/spark/pull/11776#issuecomment-198207419
use !rdd.isEmpty instead of rdd.count > 0
use static instead of AtomicInteger
remove unneeded "throws Exception"

## How was this patch tested?

manual tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #11821 from zhengruifeng/je_fix.
2016-03-18 12:34:14 +00:00
Wenchen Fan 0f1015ffdd [SPARK-14001][SQL] support multi-children Union in SQLBuilder
## What changes were proposed in this pull request?

The fix is simple, use the existing `CombineUnions` rule to combine adjacent Unions before build SQL string.

## How was this patch tested?

The re-enabled test

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11818 from cloud-fan/bug-fix.
2016-03-18 19:42:33 +08:00
Yanbo Liang 7783b6f38f [MINOR][ML] When trainingSummary is None, it should throw RuntimeException.
## What changes were proposed in this pull request?
When trainingSummary is None, it should throw ```RuntimeException```.
cc mengxr
## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11784 from yanboliang/fix-summary.
2016-03-18 11:23:17 +00:00
Reynold Xin bb1fda01fe [SPARK-13826][SQL] Addendum: update documentation for Datasets
## What changes were proposed in this pull request?
This patch updates documentations for Datasets. I also updated some internal documentation for exchange/broadcast.

## How was this patch tested?
Just documentation/api stability update.

Author: Reynold Xin <rxin@databricks.com>

Closes #11814 from rxin/dataset-docs.
2016-03-18 00:57:23 -07:00
Liang-Chi Hsieh 750ed64cd9 [SPARK-13930] [SQL] Apply fast serialization on collect limit operator
## What changes were proposed in this pull request?

JIRA: https://issues.apache.org/jira/browse/SPARK-13930

Recently the fast serialization has been introduced to collecting DataFrame/Dataset (#11664). The same technology can be used on collect limit operator too.

## How was this patch tested?

Add a benchmark for collect limit to `BenchmarkWholeStageCodegen`.

Without this patch:

    model name      : Westmere E56xx/L56xx/X56xx (Nehalem-C)
    collect limit:                      Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
    -------------------------------------------------------------------------------------------
    collect limit 1 million                  3413 / 3768          0.3        3255.0       1.0X
    collect limit 2 millions                9728 / 10440          0.1        9277.3       0.4X

With this patch:

    model name      : Westmere E56xx/L56xx/X56xx (Nehalem-C)
    collect limit:                      Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
    -------------------------------------------------------------------------------------------
    collect limit 1 million                   833 / 1284          1.3         794.4       1.0X
    collect limit 2 millions                 3348 / 4005          0.3        3193.3       0.2X

Author: Liang-Chi Hsieh <simonh@tw.ibm.com>

Closes #11759 from viirya/execute-take.
2016-03-17 23:24:44 -07:00
Cheng Lian 10ef4f3e77 [SPARK-13826][SQL] Revises Dataset ScalaDoc
## What changes were proposed in this pull request?

This PR revises Dataset API ScalaDoc.  All public methods are divided into the following groups

* `groupname basic`: Basic Dataset functions
* `groupname action`: Actions
* `groupname untypedrel`: Untyped Language Integrated Relational Queries
* `groupname typedrel`: Typed Language Integrated Relational Queries
* `groupname func`: Functional Transformations
* `groupname rdd`: RDD Operations
* `groupname output`: Output Operations

`since` tag and sample code are also updated.  We may want to add more sample code for typed APIs.

## How was this patch tested?

Documentation change.  Checked by building unidoc locally.

Author: Cheng Lian <lian@databricks.com>

Closes #11769 from liancheng/spark-13826-ds-api-doc.
2016-03-17 21:31:11 -07:00
tedyu 90a1d8db70 [SPARK-12719][HOTFIX] Fix compilation against Scala 2.10
PR #11696 introduced a complex pattern match that broke Scala 2.10 match unreachability check and caused build failure.  This PR fixes this issue by expanding this pattern match into several simpler ones.

Note that tuning or turning off `-Dscalac.patmat.analysisBudget` doesn't work for this case.

Compilation against Scala 2.10

Author: tedyu <yuzhihong@gmail.com>

Closes #11798 from yy2016/master.
2016-03-18 12:11:32 +08:00
Josh Rosen 6c2d894a2f [SPARK-13921] Store serialized blocks as multiple chunks in MemoryStore
This patch modifies the BlockManager, MemoryStore, and several other storage components so that serialized cached blocks are stored as multiple small chunks rather than as a single contiguous ByteBuffer.

This change will help to improve the efficiency of memory allocation and the accuracy of memory accounting when serializing blocks. Our current serialization code uses a ByteBufferOutputStream, which doubles and re-allocates its backing byte array; this increases the peak memory requirements during serialization (since we need to hold extra memory while expanding the array). In addition, we currently don't account for the extra wasted space at the end of the ByteBuffer's backing array, so a 129 megabyte serialized block may actually consume 256 megabytes of memory. After switching to storing blocks in multiple chunks, we'll be able to efficiently trim the backing buffers so that no space is wasted.

This change is also a prerequisite to being able to cache blocks which are larger than 2GB (although full support for that depends on several other changes which have not bee implemented yet).

Author: Josh Rosen <joshrosen@databricks.com>

Closes #11748 from JoshRosen/chunked-block-serialization.
2016-03-17 20:00:56 -07:00
Wenchen Fan 6037ed0a1d [SPARK-13976][SQL] do not remove sub-queries added by user when generate SQL
## What changes were proposed in this pull request?

We haven't figured out the corrected logical to add sub-queries yet, so we should not clear all sub-queries before generate SQL. This PR changed the logic to only remove sub-queries above table relation.

an example for this bug, original SQL: `SELECT a FROM (SELECT a FROM tbl) t WHERE a = 1`
before this PR, we will generate:
```
SELECT attr_1 AS a FROM
  SELECT attr_1 FROM (
    SELECT a AS attr_1 FROM tbl
  ) AS sub_q0
  WHERE attr_1 = 1
```
We missed a sub-query and this SQL string is illegal.

After this PR, we will generate:
```
SELECT attr_1 AS a FROM (
  SELECT attr_1 FROM (
    SELECT a AS attr_1 FROM tbl
  ) AS sub_q0
  WHERE attr_1 = 1
) AS t
```

TODO: for long term, we should find a way to add sub-queries correctly, so that arbitrary logical plans can be converted to SQL string.

## How was this patch tested?

`LogicalPlanToSQLSuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11786 from cloud-fan/bug-fix.
2016-03-18 10:16:48 +08:00
Wenchen Fan 453455c479 [SPARK-13974][SQL] sub-query names do not need to be globally unique while generate SQL
## What changes were proposed in this pull request?

We only need to make sub-query names unique every time we generate a SQL string, but not all the time. This PR moves the `newSubqueryName` method to `class SQLBuilder` and remove `object SQLBuilder`.

also addressed 2 minor comments in https://github.com/apache/spark/pull/11696

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11783 from cloud-fan/tmp.
2016-03-18 09:30:36 +08:00
sethah 1614485fd9 [SPARK-10788][MLLIB][ML] Remove duplicate bins for decision trees
Decision trees in spark.ml (RandomForest.scala) communicate twice as much data as needed for unordered categorical features. Here's an example.

Say there are 3 categories A, B, C. We consider 3 splits:

* A vs. B, C
* A, B vs. C
* A, C vs. B

Currently, we collect statistics for each of the 6 subsets of categories (3 * 2 = 6). However, we could instead collect statistics for the 3 subsets on the left-hand side of the 3 possible splits: A and A,B and A,C. If we also have stats for the entire node, then we can compute the stats for the 3 subsets on the right-hand side of the splits. In pseudomath: stats(B,C) = stats(A,B,C) - stats(A).

This patch adds a parent stats array to the `DTStatsAggregator` so that the right child stats do not need to be stored. The right child stats are computed by subtracting left child stats from the parent stats for unordered categorical features.

Author: sethah <seth.hendrickson16@gmail.com>

Closes #9474 from sethah/SPARK-10788.
2016-03-17 16:44:41 -07:00
Joseph K. Bradley b39e80d39d [SPARK-13761][ML] Remove remaining uses of validateParams
## What changes were proposed in this pull request?

Cleanups from [https://github.com/apache/spark/pull/11620]: remove remaining uses of validateParams, and put functionality into transformSchema

## How was this patch tested?

Existing unit tests, modified to check using transformSchema instead of validateParams

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #11790 from jkbradley/SPARK-13761-cleanup.
2016-03-17 13:23:07 -07:00
Yin Huai 4c08e2c085 Revert "[SPARK-12719][HOTFIX] Fix compilation against Scala 2.10"
This reverts commit 3ee7996187.
2016-03-17 11:16:03 -07:00
Xusen Yin edf8b8775b [SPARK-11891] Model export/import for RFormula and RFormulaModel
https://issues.apache.org/jira/browse/SPARK-11891

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9884 from yinxusen/SPARK-11891.
2016-03-17 10:19:10 -07:00
Bryan Cutler 828213d4ca [SPARK-13937][PYSPARK][ML] Change JavaWrapper _java_obj from static to member variable
## What changes were proposed in this pull request?
In PySpark wrapper.py JavaWrapper change _java_obj from an unused static variable to a member variable that is consistent with usage in derived classes.

## How was this patch tested?
Ran python tests for ML and MLlib.

Author: Bryan Cutler <cutlerb@gmail.com>

Closes #11767 from BryanCutler/JavaWrapper-static-_java_obj-SPARK-13937.
2016-03-17 10:16:51 -07:00
tedyu 3ee7996187 [SPARK-12719][HOTFIX] Fix compilation against Scala 2.10
## What changes were proposed in this pull request?

Compilation against Scala 2.10 fails with:
```
[error] [warn] /home/jenkins/workspace/spark-master-compile-sbt-scala-2.10/sql/hive/src/main/scala/org/apache/spark/sql/hive/SQLBuilder.scala:483: Cannot check match for         unreachability.
[error] (The analysis required more space than allowed. Please try with scalac -Dscalac.patmat.analysisBudget=512 or -Dscalac.patmat.analysisBudget=off.)
[error] [warn]     private def addSubqueryIfNeeded(plan: LogicalPlan): LogicalPlan = plan match {
```

## How was this patch tested?

Compilation against Scala 2.10

Author: tedyu <yuzhihong@gmail.com>

Closes #11787 from yy2016/master.
2016-03-17 10:09:37 -07:00
Liang-Chi Hsieh 5f3bda6fe2 [SPARK-13838] [SQL] Clear variable code to prevent it to be re-evaluated in BoundAttribute
JIRA: https://issues.apache.org/jira/browse/SPARK-13838
## What changes were proposed in this pull request?

We should also clear the variable code in `BoundReference.genCode` to prevent it  to be evaluated twice, as we did in `evaluateVariables`.

## How was this patch tested?

Existing tests.

Author: Liang-Chi Hsieh <simonh@tw.ibm.com>

Closes #11674 from viirya/avoid-reevaluate.
2016-03-17 10:08:42 -07:00
Dilip Biswal 637a78f1d3 [SPARK-13427][SQL] Support USING clause in JOIN.
## What changes were proposed in this pull request?

Support queries that JOIN tables with USING clause.
SELECT * from table1 JOIN table2 USING <column_list>

USING clause can be used as a means to simplify the join condition
when :

1) Equijoin semantics is desired and
2) The column names in the equijoin have the same name.

We already have the support for Natural Join in Spark. This PR makes
use of the already existing infrastructure for natural join to
form the join condition and also the projection list.

## How was the this patch tested?

Have added unit tests in SQLQuerySuite, CatalystQlSuite, ResolveNaturalJoinSuite

Author: Dilip Biswal <dbiswal@us.ibm.com>

Closes #11297 from dilipbiswal/spark-13427.
2016-03-17 10:01:41 -07:00
Shixiong Zhu 65b75e66e8 [SPARK-13776][WEBUI] Limit the max number of acceptors and selectors for Jetty
## What changes were proposed in this pull request?

As each acceptor/selector in Jetty will use one thread, the number of threads should at least be the number of acceptors and selectors plus 1. Otherwise, the thread pool of Jetty server may be exhausted by acceptors/selectors and not be able to response any request.

To avoid wasting threads, the PR limits the max number of acceptors and selectors and also updates the max thread number if necessary.

## How was this patch tested?

Just make sure we don't break any existing tests

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #11615 from zsxwing/SPARK-13776.
2016-03-17 13:05:29 +00:00
Wenchen Fan 1974d1d34d [SPARK-12719][SQL] SQL generation support for Generate
## What changes were proposed in this pull request?

This PR adds SQL generation support for `Generate` operator. It always converts `Generate` operator into `LATERAL VIEW` format as there are many limitations to put UDTF in project list.

This PR is based on https://github.com/apache/spark/pull/11658, please see the last commit to review the real changes.

Thanks dilipbiswal for his initial work! Takes over https://github.com/apache/spark/pull/11596

## How was this patch tested?

new tests in `LogicalPlanToSQLSuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11696 from cloud-fan/generate.
2016-03-17 20:25:05 +08:00
Wenchen Fan 8ef3399aff [SPARK-13928] Move org.apache.spark.Logging into org.apache.spark.internal.Logging
## What changes were proposed in this pull request?

Logging was made private in Spark 2.0. If we move it, then users would be able to create a Logging trait themselves to avoid changing their own code.

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #11764 from cloud-fan/logger.
2016-03-17 19:23:38 +08:00
trueyao ea9ca6f04c [SPARK-13901][CORE] correct the logDebug information when jump to the next locality level
JIRA Issue:https://issues.apache.org/jira/browse/SPARK-13901
In getAllowedLocalityLevel method of TaskSetManager,we get wrong logDebug information when jump to the next locality level.So we should fix it.

Author: trueyao <501663994@qq.com>

Closes #11719 from trueyao/logDebug-localityWait.
2016-03-17 09:45:06 +00:00
Yuhao Yang 357d82d84d [SPARK-13629][ML] Add binary toggle Param to CountVectorizer
## What changes were proposed in this pull request?

It would be handy to add a binary toggle Param to CountVectorizer, as in the scikit-learn one: http://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.CountVectorizer.html
If set, then all non-zero counts will be set to 1.

## How was this patch tested?

unit tests

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #11536 from hhbyyh/cvToggle.
2016-03-17 11:21:11 +02:00
Zheng RuiFeng 204c9dec2c [MINOR][DOC] Add JavaStreamingTestExample
## What changes were proposed in this pull request?

Add the java example of StreamingTest

## How was this patch tested?

manual tests in CLI: bin/run-example mllib.JavaStreamingTestExample dataDir 5 100

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #11776 from zhengruifeng/streaming_je.
2016-03-17 11:09:02 +02:00
Davies Liu 30c18841e4 Revert "[SPARK-13840][SQL] Split Optimizer Rule ColumnPruning to ColumnPruning and EliminateOperator"
This reverts commit 99bd2f0e94.
2016-03-16 23:11:13 -07:00