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15631 commits

Author SHA1 Message Date
Fokko Driesprong c80586d9e8 [SPARK-12869] Implemented an improved version of the toIndexedRowMatrix
Hi guys,

I've implemented an improved version of the `toIndexedRowMatrix` function on the `BlockMatrix`. I needed this for a project, but would like to share it with the rest of the community. In the case of dense matrices, it can increase performance up to 19 times:
https://github.com/Fokko/BlockMatrixToIndexedRowMatrix

If there are any questions or suggestions, please let me know. Keep up the good work! Cheers.

Author: Fokko Driesprong <f.driesprong@catawiki.nl>
Author: Fokko Driesprong <fokko@driesprongen.nl>

Closes #10839 from Fokko/master.
2016-04-14 17:32:20 -07:00
Yong Tang 01dd1f5c07 [SPARK-14565][ML] RandomForest should use parseInt and parseDouble for feature subset size instead of regexes
## What changes were proposed in this pull request?

This fix tries to change RandomForest's supported strategies from using regexes to using parseInt and
parseDouble, for the purpose of robustness and maintainability.

## How was this patch tested?

Existing tests passed.

Author: Yong Tang <yong.tang.github@outlook.com>

Closes #12360 from yongtang/SPARK-14565.
2016-04-14 17:23:16 -07:00
Dongjoon Hyun d7e124edfe [SPARK-14545][SQL] Improve LikeSimplification by adding a%b rule
## What changes were proposed in this pull request?

Current `LikeSimplification` handles the following four rules.
- 'a%' => expr.StartsWith("a")
- '%b' => expr.EndsWith("b")
- '%a%' => expr.Contains("a")
- 'a' => EqualTo("a")

This PR adds the following rule.
- 'a%b' => expr.Length() >= 2 && expr.StartsWith("a") && expr.EndsWith("b")

Here, 2 is statically calculated from "a".size + "b".size.

**Before**
```
scala> sql("select a from (select explode(array('abc','adc')) a) T where a like 'a%c'").explain()
== Physical Plan ==
WholeStageCodegen
:  +- Filter a#5 LIKE a%c
:     +- INPUT
+- Generate explode([abc,adc]), false, false, [a#5]
   +- Scan OneRowRelation[]
```

**After**
```
scala> sql("select a from (select explode(array('abc','adc')) a) T where a like 'a%c'").explain()
== Physical Plan ==
WholeStageCodegen
:  +- Filter ((length(a#5) >= 2) && (StartsWith(a#5, a) && EndsWith(a#5, c)))
:     +- INPUT
+- Generate explode([abc,adc]), false, false, [a#5]
   +- Scan OneRowRelation[]
```

## How was this patch tested?

Pass the Jenkins tests (including new testcase).

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12312 from dongjoon-hyun/SPARK-14545.
2016-04-14 13:34:29 -07:00
Yong Tang bc748b7b8f [SPARK-14238][ML][MLLIB][PYSPARK] Add binary toggle Param to PySpark HashingTF in ML & MLlib
## What changes were proposed in this pull request?

This fix tries to add binary toggle Param to PySpark HashingTF in ML & MLlib. If this toggle is set, then all non-zero counts will be set to 1.

Note: This fix (SPARK-14238) is extended from SPARK-13963 where Scala implementation was done.

## How was this patch tested?

This fix adds two tests to cover the code changes. One for HashingTF in PySpark's ML and one for HashingTF in PySpark's MLLib.

Author: Yong Tang <yong.tang.github@outlook.com>

Closes #12079 from yongtang/SPARK-14238.
2016-04-14 21:53:32 +02:00
Joseph K. Bradley bf65c87f70 [SPARK-14618][ML][DOC] Updated RegressionEvaluator.metricName param doc
## What changes were proposed in this pull request?

In Spark 1.4, we negated some metrics from RegressionEvaluator since CrossValidator always maximized metrics. This was fixed in 1.5, but the docs were not updated. This PR updates the docs.

## How was this patch tested?

no tests

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

Closes #12377 from jkbradley/regeval-doc.
2016-04-14 12:44:59 -07:00
Bryan Cutler c5172f8205 [SPARK-13967][PYSPARK][ML] Added binary Param to Python CountVectorizer
Added binary toggle param to CountVectorizer feature transformer in PySpark.

Created a unit test for using CountVectorizer with the binary toggle on.

Author: Bryan Cutler <cutlerb@gmail.com>

Closes #12308 from BryanCutler/binary-param-python-CountVectorizer-SPARK-13967.
2016-04-14 20:47:31 +02:00
Liang-Chi Hsieh 28efdd3fd7 [SPARK-14592][SQL] Native support for CREATE TABLE LIKE DDL command
## What changes were proposed in this pull request?
JIRA: https://issues.apache.org/jira/browse/SPARK-14592

This patch adds native support for DDL command `CREATE TABLE LIKE`.

The SQL syntax is like:

    CREATE TABLE table_name LIKE existing_table
    CREATE TABLE IF NOT EXISTS table_name LIKE existing_table

## How was this patch tested?
`HiveDDLCommandSuite`. `HiveQuerySuite` already tests `CREATE TABLE LIKE`.

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

This patch had conflicts when merged, resolved by
Committer: Andrew Or <andrew@databricks.com>

Closes #12362 from viirya/create-table-like.
2016-04-14 11:08:08 -07:00
gatorsmile c971aee40d [SPARK-14499][SQL][TEST] Drop Partition Does Not Delete Data of External Tables
#### What changes were proposed in this pull request?
This PR is to add a test to ensure drop partitions of an external table will not delete data.

cc yhuai andrewor14

#### How was this patch tested?
N/A

Author: gatorsmile <gatorsmile@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Andrew Or <andrew@databricks.com>

Closes #12350 from gatorsmile/testDropPartition.
2016-04-14 11:03:19 -07:00
Wenchen Fan 1d04c86fc5 [SPARK-14558][CORE] In ClosureCleaner, clean the outer pointer if it's a REPL line object
## What changes were proposed in this pull request?

When we clean a closure, if its outermost parent is not a closure, we won't clone and clean it as cloning user's objects is dangerous. However, if it's a REPL line object, which may carry a lot of unnecessary references(like hadoop conf, spark conf, etc.), we should clean it as it's not a user object.

This PR improves the check for user's objects to exclude REPL line object.

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12327 from cloud-fan/closure.
2016-04-14 10:58:06 -07:00
Reynold Xin a46f98d3f4 [SPARK-14617] Remove deprecated APIs in TaskMetrics
## What changes were proposed in this pull request?
This patch removes some of the deprecated APIs in TaskMetrics. This is part of my bigger effort to simplify accumulators and task metrics.

## How was this patch tested?
N/A - only removals

Author: Reynold Xin <rxin@databricks.com>

Closes #12375 from rxin/SPARK-14617.
2016-04-14 10:56:13 -07:00
Reynold Xin dac40b68dc [SPARK-14619] Track internal accumulators (metrics) by stage attempt
## What changes were proposed in this pull request?
When there are multiple attempts for a stage, we currently only reset internal accumulator values if all the tasks are resubmitted. It would make more sense to reset the accumulator values for each stage attempt. This will allow us to eventually get rid of the internal flag in the Accumulator class. This is part of my bigger effort to simplify accumulators and task metrics.

## How was this patch tested?
Covered by existing tests.

Author: Reynold Xin <rxin@databricks.com>

Closes #12378 from rxin/SPARK-14619.
2016-04-14 10:54:57 -07:00
Sean Owen 9fa43a33b9 [SPARK-14612][ML] Consolidate the version of dependencies in mllib and mllib-local into one place
## What changes were proposed in this pull request?

Move json4s, breeze dependency declaration into parent

## How was this patch tested?

Should be no functional change, but Jenkins tests will test that.

Author: Sean Owen <sowen@cloudera.com>

Closes #12390 from srowen/SPARK-14612.
2016-04-14 10:48:17 -07:00
Liwei Lin 3e27940a19 [SPARK-14630][BUILD][CORE][SQL][STREAMING] Code style: public abstract methods should have explicit return types
## What changes were proposed in this pull request?

Currently many public abstract methods (in abstract classes as well as traits) don't declare return types explicitly, such as in [o.a.s.streaming.dstream.InputDStream](https://github.com/apache/spark/blob/master/streaming/src/main/scala/org/apache/spark/streaming/dstream/InputDStream.scala#L110):
```scala
def start() // should be: def start(): Unit
def stop()  // should be: def stop(): Unit
```

These methods exist in core, sql, streaming; this PR fixes them.

## How was this patch tested?

N/A

## Which piece of scala style rule led to the changes?

the rule was added separately in https://github.com/apache/spark/pull/12396

Author: Liwei Lin <lwlin7@gmail.com>

Closes #12389 from lw-lin/public-abstract-methods.
2016-04-14 10:14:38 -07:00
Reynold Xin de2ad52855 [SPARK-14625] TaskUIData and ExecutorUIData shouldn't be case classes
## What changes were proposed in this pull request?
I was trying to understand the accumulator and metrics update source code and these two classes don't really need to be case classes. It would also be more consistent with other UI classes if they are not case classes. This is part of my bigger effort to simplify accumulators and task metrics.

## How was this patch tested?
This is a straightforward refactoring without behavior change.

Author: Reynold Xin <rxin@databricks.com>

Closes #12386 from rxin/SPARK-14625.
2016-04-14 10:12:29 -07:00
gatorsmile 0d22092cd9 [SPARK-14125][SQL] Native DDL Support: Alter View
#### What changes were proposed in this pull request?
This PR is to provide a native DDL support for the following three Alter View commands:

Based on the Hive DDL document:
https://cwiki.apache.org/confluence/display/Hive/LanguageManual+DDL
##### 1. ALTER VIEW RENAME
**Syntax:**
```SQL
ALTER VIEW view_name RENAME TO new_view_name
```
- to change the name of a view to a different name
- not allowed to rename a view's name by ALTER TABLE

##### 2. ALTER VIEW SET TBLPROPERTIES
**Syntax:**
```SQL
ALTER VIEW view_name SET TBLPROPERTIES ('comment' = new_comment);
```
- to add metadata to a view
- not allowed to set views' properties by ALTER TABLE
- ignore it if trying to set a view's existing property key when the value is the same
- overwrite the value if trying to set a view's existing key to a different value

##### 3. ALTER VIEW UNSET TBLPROPERTIES
**Syntax:**
```SQL
ALTER VIEW view_name UNSET TBLPROPERTIES [IF EXISTS] ('comment', 'key')
```
- to remove metadata from a view
- not allowed to unset views' properties by ALTER TABLE
- issue an exception if trying to unset a view's non-existent key

#### How was this patch tested?
Added test cases to verify if it works properly.

Author: gatorsmile <gatorsmile@gmail.com>
Author: xiaoli <lixiao1983@gmail.com>
Author: Xiao Li <xiaoli@Xiaos-MacBook-Pro.local>

Closes #12324 from gatorsmile/alterView.
2016-04-14 08:34:11 -07:00
Dhruve Ashar f83ba454a5 [SPARK-14572][DOC] Update config docs to allow -Xms in extraJavaOptions
## What changes were proposed in this pull request?
The configuration docs are updated to reflect the changes introduced with [SPARK-12384](https://issues.apache.org/jira/browse/SPARK-12384). This allows the user to specify initial heap memory settings through the extraJavaOptions for executor, driver and am.

## How was this patch tested?
The changes are tested in [SPARK-12384](https://issues.apache.org/jira/browse/SPARK-12384). This is just documenting the changes made.

Author: Dhruve Ashar <dhruveashar@gmail.com>

Closes #12333 from dhruve/doc/SPARK-14572.
2016-04-14 10:29:14 -05:00
gatorsmile 3cf3db17b3 [SPARK-14518][SQL] Support Comment in CREATE VIEW
#### What changes were proposed in this pull request?
**HQL Syntax**: [Create View](https://cwiki.apache.org/confluence/display/Hive/LanguageManual+DDL#LanguageManualDDL-Create/Drop/AlterView
)
```SQL
CREATE VIEW [IF NOT EXISTS] [db_name.]view_name [(column_name [COMMENT column_comment], ...) ]
  [COMMENT view_comment]
  [TBLPROPERTIES (property_name = property_value, ...)]
  AS SELECT ...;
```
Add a support for the `[COMMENT view_comment]` clause

#### How was this patch tested?
Modified the existing test cases to verify the correctness.

Author: gatorsmile <gatorsmile@gmail.com>
Author: xiaoli <lixiao1983@gmail.com>
Author: Xiao Li <xiaoli@Xiaos-MacBook-Pro.local>

Closes #12288 from gatorsmile/addCommentInCreateView.
2016-04-14 08:08:09 -07:00
hyukjinkwon 6fc3dc8839 [MINOR][SQL] Remove extra anonymous closure within functional transformations
## What changes were proposed in this pull request?

This PR removes extra anonymous closure within functional transformations.

For example,

```scala
.map(item => {
  ...
})
```

which can be just simply as below:

```scala
.map { item =>
  ...
}
```

## How was this patch tested?

Related unit tests and `sbt scalastyle`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #12382 from HyukjinKwon/minor-extra-closers.
2016-04-14 09:43:41 +01:00
Holden Karau 478af2f455 [SPARK-14573][PYSPARK][BUILD] Fix PyDoc Makefile & highlighting issues
## What changes were proposed in this pull request?

The PyDoc Makefile used "=" rather than "?=" for setting env variables so it overwrote the user values. This ignored the environment variables we set for linting allowing warnings through. This PR also fixes the warnings that had been introduced.

## How was this patch tested?

manual local export & make

Author: Holden Karau <holden@us.ibm.com>

Closes #12336 from holdenk/SPARK-14573-fix-pydoc-makefile.
2016-04-14 09:42:15 +01:00
hyukjinkwon b4819404a6 [SPARK-14596][SQL] Remove not used SqlNewHadoopRDD and some more unused imports
## What changes were proposed in this pull request?

Old `HadoopFsRelation` API includes `buildInternalScan()` which uses `SqlNewHadoopRDD` in `ParquetRelation`.
Because now the old API is removed, `SqlNewHadoopRDD` is not used anymore.

So, this PR removes `SqlNewHadoopRDD` and several unused imports.

This was discussed in https://github.com/apache/spark/pull/12326.

## How was this patch tested?

Several related existing unit tests and `sbt scalastyle`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #12354 from HyukjinKwon/SPARK-14596.
2016-04-14 15:43:44 +08:00
Davies Liu 62b7f306fb [SPARK-14607] [SPARK-14484] [SQL] fix case-insensitive predicates in FileSourceStrategy
## What changes were proposed in this pull request?

When prune the partitions or push down predicates, case-sensitivity is not respected. In order to make it work with case-insensitive, this PR update the AttributeReference inside predicate to use the name from schema.

## How was this patch tested?

Add regression tests for case-insensitive.

Author: Davies Liu <davies@databricks.com>

Closes #12371 from davies/case_insensi.
2016-04-13 17:17:19 -07:00
Bryan Cutler fc3cd2f509 [SPARK-14472][PYSPARK][ML] Cleanup ML JavaWrapper and related class hierarchy
Currently, JavaWrapper is only a wrapper class for pipeline classes that have Params and JavaCallable is a separate mixin that provides methods to make Java calls.  This change simplifies the class structure and to define the Java wrapper in a plain base class along with methods to make Java calls.  Also, renames Java wrapper classes to better reflect their purpose.

Ran existing Python ml tests and generated documentation to test this change.

Author: Bryan Cutler <cutlerb@gmail.com>

Closes #12304 from BryanCutler/pyspark-cleanup-JavaWrapper-SPARK-14472.
2016-04-13 14:08:57 -07:00
Yuhao Yang 781df49983 [SPARK-13089][ML] [Doc] spark.ml Naive Bayes user guide and examples
jira: https://issues.apache.org/jira/browse/SPARK-13089

Add section in ml-classification.md for NaiveBayes DataFrame-based API, plus example code (using include_example to clip code from examples/ folder files).

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #11015 from hhbyyh/naiveBayesDoc.
2016-04-13 13:58:35 -07:00
Zheng RuiFeng fcdd69260e [SPARK-14509][DOC] Add python CountVectorizerExample
## What changes were proposed in this pull request?
Add python CountVectorizerExample

## How was this patch tested?
manual tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #11917 from zhengruifeng/cv_pe.
2016-04-13 13:56:23 -07:00
Yanbo Liang a91aaf5a8c [SPARK-14375][ML] Unit test for spark.ml KMeansSummary
## What changes were proposed in this pull request?
* Modify ```KMeansSummary.clusterSizes``` method to make it robust to empty clusters.
* Add unit test for spark.ml ```KMeansSummary```.
* Add Since tag.

## How was this patch tested?
unit tests.

cc jkbradley

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12254 from yanboliang/spark-14375.
2016-04-13 13:23:10 -07:00
Yanbo Liang 0d17593b32 [SPARK-14461][ML] GLM training summaries should provide solver
## What changes were proposed in this pull request?
GLM training summaries should provide solver.

## How was this patch tested?
Unit tests.

cc jkbradley

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12253 from yanboliang/spark-14461.
2016-04-13 13:20:29 -07:00
Yanbo Liang b0adb9f543 [SPARK-10386][MLLIB] PrefixSpanModel supports save/load
```PrefixSpanModel``` supports ```save/load```. It's similar with #9267.

cc jkbradley

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10664 from yanboliang/spark-10386.
2016-04-13 13:18:02 -07:00
Davies Liu dbbe149070 [SPARK-14581] [SQL] push predicatese through more logical plans
## What changes were proposed in this pull request?

Right now, filter push down only works with Project, Aggregate, Generate and Join, they can't be pushed through many other plans.

This PR added support for Union, Intersect, Except and all unary plans.

## How was this patch tested?

Added tests.

Author: Davies Liu <davies@databricks.com>

Closes #12342 from davies/filter_hint.
2016-04-13 13:01:13 -07:00
Yanbo Liang f9d578eaa1 [SPARK-13783][ML] Model export/import for spark.ml: GBTs
## What changes were proposed in this pull request?
* Added save/load for ```GBTClassifier/GBTClassificationModel/GBTRegressor/GBTRegressionModel```.
* Meanwhile, I modified ```EnsembleModelReadWrite.saveImpl/loadImpl``` to support save/load ```treeWeights```.

## How was this patch tested?
Adds standard unit tests for GBT save/load.

cc jkbradley GayathriMurali

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12230 from yanboliang/spark-13783.
2016-04-13 11:31:10 -07:00
Andrew Or 7d2ed8cc03 [SPARK-14388][SQL] Implement CREATE TABLE
## What changes were proposed in this pull request?

This patch implements the `CREATE TABLE` command using the `SessionCatalog`. Previously we handled only `CTAS` and `CREATE TABLE ... USING`. This requires us to refactor `CatalogTable` to accept various fields (e.g. bucket and skew columns) and pass them to Hive.

WIP: Note that I haven't verified whether this actually works yet! But I believe it does.

## How was this patch tested?

Tests will come in a future commit.

Author: Andrew Or <andrew@databricks.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #12271 from andrewor14/create-table-ddl.
2016-04-13 11:08:34 -07:00
Timothy Hunter 1018a1c1eb [SPARK-14568][ML] Instrumentation framework for logistic regression
## What changes were proposed in this pull request?

This adds extra logging information about a `LogisticRegression` estimator when being fit on a dataset. With this PR, you see the following extra lines when running the example in the documentation:

```
16/04/13 07:19:00 INFO Instrumentation: Instrumentation(LogisticRegression-logreg_55dd3c09f164-1230977381-1): training: numPartitions=1 storageLevel=StorageLevel(disk=true, memory=true, offheap=false, deserialized=true, replication=1)
16/04/13 07:19:00 INFO Instrumentation: Instrumentation(LogisticRegression-logreg_55dd3c09f164-1230977381-1): {"regParam":0.3,"elasticNetParam":0.8,"maxIter":10}
...
16/04/12 11:48:07 INFO Instrumentation: Instrumentation(LogisticRegression-logreg_a89eb23cb386-358781145):numClasses=2
16/04/12 11:48:07 INFO Instrumentation: Instrumentation(LogisticRegression-logreg_a89eb23cb386-358781145):numFeatures=692
...
16/04/13 07:19:01 INFO Instrumentation: Instrumentation(LogisticRegression-logreg_55dd3c09f164-1230977381-1): training finished
```

## How was this patch tested?

This PR was manually tested.

Author: Timothy Hunter <timhunter@databricks.com>

Closes #12331 from thunterdb/1604-instrumentation.
2016-04-13 11:06:42 -07:00
Xiangrui Meng 323e7390a5 Revert "[SPARK-14154][MLLIB] Simplify the implementation for Kolmogorov–Smirnov test"
This reverts commit d2a819a636.
2016-04-13 09:17:46 -07:00
Charles Allen dd11e401e4 [SPARK-14537][CORE] Make TaskSchedulerImpl waiting fail if context is shut down
This patch makes the postStartHook throw an IllegalStateException if the SparkContext is shutdown while it is waiting for the backend to be ready

Author: Charles Allen <charles@allen-net.com>

Closes #12301 from drcrallen/SPARK-14537.
2016-04-13 16:02:49 +01:00
Liwei Lin 23f93f559c [SPARK-13992][CORE][PYSPARK][FOLLOWUP] Update OFF_HEAP semantics for Java api and Python api
## What changes were proposed in this pull request?

- updated `OFF_HEAP` semantics for `StorageLevels.java`
- updated `OFF_HEAP` semantics for `storagelevel.py`

## How was this patch tested?

no need to test

Author: Liwei Lin <lwlin7@gmail.com>

Closes #12126 from lw-lin/storagelevel.py.
2016-04-12 23:06:55 -07:00
Wenchen Fan a5f8c9b15b [SPARK-14554][SQL][FOLLOW-UP] use checkDataset to check the result
## What changes were proposed in this pull request?

address this comment: https://github.com/apache/spark/pull/12322#discussion_r59417359

## How was this patch tested?

N/A

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12346 from cloud-fan/tmp.
2016-04-13 11:41:09 +08:00
hyukjinkwon 587cd554af [MINOR][SQL] Remove some unused imports in datasources.
## What changes were proposed in this pull request?

It looks several recent commits for datasources (maybe while removing old `HadoopFsRelation` interface) missed removing some unused imports.

This PR removes some unused imports in datasources.

## How was this patch tested?

`sbt scalastyle` and some unit tests for them.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #12326 from HyukjinKwon/minor-imports.
2016-04-13 10:20:03 +08:00
Shixiong Zhu 768b3d623c [SPARK-14579][SQL] Fix a race condition in StreamExecution.processAllAvailable
## What changes were proposed in this pull request?

There is a race condition in `StreamExecution.processAllAvailable`. Here is an execution order to reproduce it.

| Time        |Thread 1           | MicroBatchThread  |
|:-------------:|:-------------:|:-----:|
| 1 | |  `dataAvailable in constructNextBatch` returns false  |
| 2 | addData(newData)      |   |
| 3 | `noNewData = false` in  processAllAvailable |  |
| 4 | | noNewData = true |
| 5 | `noNewData` is true so just return | |

The root cause is that `checking dataAvailable and change noNewData to true` is not atomic. This PR puts these two actions into `synchronized` to make sure they are atomic.

In addition, this PR also has the following changes:

- Make `committedOffsets` and `availableOffsets` volatile to make sure they can be seen in other threads.
- Copy the reference of `availableOffsets` to a local variable so that `sourceStatuses` can use a snapshot of `availableOffsets`.

## How was this patch tested?

Existing unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #12339 from zsxwing/race-condition.
2016-04-12 17:31:47 -07:00
Davies Liu 372baf0479 [SPARK-14578] [SQL] Fix codegen for CreateExternalRow with nested wide schema
## What changes were proposed in this pull request?

The wide schema, the expression of fields will be splitted into multiple functions, but the variable for loopVar can't be accessed in splitted functions, this PR change them as class member.

## How was this patch tested?

Added regression test.

Author: Davies Liu <davies@databricks.com>

Closes #12338 from davies/nested_row.
2016-04-12 17:26:37 -07:00
Sital Kedia d187e7dea9 [SPARK-14363] Fix executor OOM due to memory leak in the Sorter
## What changes were proposed in this pull request?

Fix memory leak in the Sorter. When the UnsafeExternalSorter spills the data to disk, it does not free up the underlying pointer array. As a result, we see a lot of executor OOM and also memory under utilization.
This is a regression partially introduced in PR https://github.com/apache/spark/pull/9241

## How was this patch tested?

Tested by running a job and observed around 30% speedup after this change.

Author: Sital Kedia <skedia@fb.com>

Closes #12285 from sitalkedia/executor_oom.
2016-04-12 16:10:07 -07:00
Reynold Xin c439d88e99 [SPARK-14547] Avoid DNS resolution for reusing connections
## What changes were proposed in this pull request?
This patch changes the connection creation logic in the network client module to avoid DNS resolution when reusing connections.

## How was this patch tested?
Testing in production. This is too difficult to test in isolation (for high fidelity unit tests, we'd need to change the DNS resolution behavior in the JVM).

Author: Reynold Xin <rxin@databricks.com>

Closes #12315 from rxin/SPARK-14547.
2016-04-12 15:28:08 -07:00
Davies Liu 1ef5f8cfa6 [SPARK-14544] [SQL] improve performance of SQL UI tab
## What changes were proposed in this pull request?

This PR improve the performance of SQL UI by:

1) remove the details column in all executions page (the first page in SQL tab). We can check the details by enter the execution page.
2) break-all is super slow in Chrome recently, so switch to break-word.
3) Using "display: none" to hide a block.
4) using one js closure for  for all the executions, not one for each.
5) remove the height limitation of details, don't need to scroll it in the tiny window.

## How was this patch tested?

Exists tests.

![ui](https://cloud.githubusercontent.com/assets/40902/14445712/68d7b258-0004-11e6-9b48-5d329b05d165.png)

Author: Davies Liu <davies@databricks.com>

Closes #12311 from davies/ui_perf.
2016-04-12 15:03:00 -07:00
Terence Yim 3e53de4bdd [SPARK-14513][CORE] Fix threads left behind after stopping SparkContext
## What changes were proposed in this pull request?

Shutting down `QueuedThreadPool` used by Jetty `Server` to avoid threads leakage after SparkContext is stopped.

Note: If this fix is going to apply to the `branch-1.6`, one more patch on the `NettyRpcEnv` class is needed so that the `NettyRpcEnv._fileServer.shutdown` is called in the `NettyRpcEnv.cleanup` method. This is due to the removal of `_fileServer` field in the `NettyRpcEnv` class in the master branch. Please advice if a second PR is necessary for bring this fix back to `branch-1.6`

## How was this patch tested?

Ran the ./dev/run-tests locally

Author: Terence Yim <terence@cask.co>

Closes #12318 from chtyim/fixes/SPARK-14513-thread-leak.
2016-04-12 13:46:39 -07:00
bomeng bcd2076274 [SPARK-14414][SQL] improve the error message class hierarchy
## What changes were proposed in this pull request?

Before we are using `AnalysisException`, `ParseException`, `NoSuchFunctionException` etc when a parsing error encounters. I am trying to make it consistent and also **minimum** code impact to the current implementation by changing the class hierarchy.
1. `NoSuchItemException` is removed, since it is an abstract class and it just simply takes a message string.
2. `NoSuchDatabaseException`, `NoSuchTableException`, `NoSuchPartitionException` and `NoSuchFunctionException` now extends `AnalysisException`, as well as `ParseException`, they are all under `AnalysisException` umbrella, but you can also determine how to use them in a granular way.

## How was this patch tested?
The existing test cases should cover this patch.

Author: bomeng <bmeng@us.ibm.com>

Closes #12314 from bomeng/SPARK-14414.
2016-04-12 13:43:39 -07:00
Davies Liu 85e68b4bea [SPARK-14562] [SQL] improve constraints propagation in Union
## What changes were proposed in this pull request?

Currently, Union only takes intersect of the constraints from it's children, all others are dropped, we should try to merge them together.

This PR try to merge the constraints that have the same reference but came from different children, for example: `a > 10` and `a < 100` could be merged as `a > 10 || a < 100`.

## How was this patch tested?

Added more cases in existing test.

Author: Davies Liu <davies@databricks.com>

Closes #12328 from davies/union_const.
2016-04-12 12:29:54 -07:00
Liwei Lin 852bbc6c00 [SPARK-14556][SQL] Code clean-ups for package o.a.s.sql.execution.streaming.state
## What changes were proposed in this pull request?

- `StateStoreConf.**max**DeltasForSnapshot` was renamed to `StateStoreConf.**min**DeltasForSnapshot`
- some state switch checks were added
- improved consistency between method names and string literals
- other comments & typo fix

## How was this patch tested?

N/A

Author: Liwei Lin <lwlin7@gmail.com>

Closes #12323 from lw-lin/streaming-state-clean-up.
2016-04-12 11:50:51 -07:00
Yanbo Liang 111a62474a [SPARK-14147][ML][SPARKR] SparkR predict should not output feature column
## What changes were proposed in this pull request?
SparkR does not support type of vector which is the default type of feature column in ML. R predict also does not output intermediate feature column. So SparkR ```predict``` should not output feature column. In this PR, I only fix this issue for ```naiveBayes``` and ```survreg```. ```kmeans``` has the right code route already and  ```glm``` will be fixed at SparkRWrapper refactor(#12294).

## How was this patch tested?
No new tests.

cc mengxr shivaram

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11958 from yanboliang/spark-14147.
2016-04-12 11:34:40 -07:00
Xiangrui Meng 1995c2e648 [SPARK-14563][ML] use a random table name instead of __THIS__ in SQLTransformer
## What changes were proposed in this pull request?

Use a random table name instead of `__THIS__` in SQLTransformer, and add a test for `transformSchema`. The problems of using `__THIS__` are:

* It doesn't work under HiveContext (in Spark 1.6)
* Race conditions

## How was this patch tested?

* Manual test with HiveContext.
* Added a unit test for `transformSchema` to improve coverage.

cc: yhuai

Author: Xiangrui Meng <meng@databricks.com>

Closes #12330 from mengxr/SPARK-14563.
2016-04-12 11:30:09 -07:00
Kai Jiang 7f024c4744 [SPARK-13597][PYSPARK][ML] Python API for GeneralizedLinearRegression
## What changes were proposed in this pull request?

Python API for GeneralizedLinearRegression
JIRA: https://issues.apache.org/jira/browse/SPARK-13597

## How was this patch tested?

The patch is tested with Python doctest.

Author: Kai Jiang <jiangkai@gmail.com>

Closes #11468 from vectorijk/spark-13597.
2016-04-12 11:29:12 -07:00
Yanbo Liang 101663f1ae [SPARK-13322][ML] AFTSurvivalRegression supports feature standardization
## What changes were proposed in this pull request?
AFTSurvivalRegression should support feature standardization, it will improve the convergence rate.
Test the convergence rate on the [Ovarian](https://stat.ethz.ch/R-manual/R-devel/library/survival/html/ovarian.html) data which is standard data comes with Survival library in R,
* without standardization(before this PR) -> 74 iterations.
* with standardization(after this PR) -> 38 iterations.

But after this fix, with or without ```standardization``` will converge to the same solution. It means that ```standardization = false``` will run the same code route as ```standardization = true```. Because if the features are not standardized at all, it will result convergency issue when the features have very different scales. This behavior is the same as ML [```LinearRegression``` and ```LogisticRegression```](https://issues.apache.org/jira/browse/SPARK-8522). See more discussion about this topic at #11247.
cc mengxr
## How was this patch tested?
unit test.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11365 from yanboliang/spark-13322.
2016-04-12 11:27:16 -07:00
Yanbo Liang 75e05a5a96 [SPARK-12566][SPARK-14324][ML] GLM model family, link function support in SparkR:::glm
* SparkR glm supports families and link functions which match R's signature for family.
* SparkR glm API refactor. The comparative standard of the new API is R glm, so I only expose the arguments that R glm supports: ```formula, family, data, epsilon and maxit```.
* This PR is focus on glm() and predict(), summary statistics will be done in a separate PR after this get in.
* This PR depends on #12287 which make GLMs support link prediction at Scala side. After that merged, I will add more tests for predict() to this PR.

Unit tests.

cc mengxr jkbradley hhbyyh

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12294 from yanboliang/spark-12566.
2016-04-12 10:51:09 -07:00