Commit graph

15961 commits

Author SHA1 Message Date
Yanbo Liang 19a6d192d5 [SPARK-15030][ML][SPARKR] Support formula in spark.kmeans in SparkR
## What changes were proposed in this pull request?
* ```RFormula``` supports empty response variable like ```~ x + y```.
* Support formula in ```spark.kmeans``` in SparkR.
* Fix some outdated docs for SparkR.

## How was this patch tested?
Unit tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12813 from yanboliang/spark-15030.
2016-04-30 08:37:56 -07:00
Herman van Hovell e5fb78baf9 [SPARK-14952][CORE][ML] Remove methods that were deprecated in 1.6.0
#### What changes were proposed in this pull request?

This PR removes three methods the were deprecated in 1.6.0:
- `PortableDataStream.close()`
- `LinearRegression.weights`
- `LogisticRegression.weights`

The rationale for doing this is that the impact is small and that Spark 2.0 is a major release.

#### How was this patch tested?
Compilation succeded.

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #12732 from hvanhovell/SPARK-14952.
2016-04-30 16:06:20 +01:00
Xiangrui Meng 0847fe4eb3 [SPARK-14653][ML] Remove json4s from mllib-local
## What changes were proposed in this pull request?

This PR moves Vector.toJson/fromJson to ml.linalg.VectorEncoder under mllib/ to keep mllib-local's dependency minimal. The json encoding is used by Params. So we still need this feature in SPARK-14615, where we will switch to ml.linalg in spark.ml APIs.

## How was this patch tested?

Copied existing unit tests over.

cc; dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #12802 from mengxr/SPARK-14653.
2016-04-30 06:30:39 -07:00
Junyang 1192fe4cd2 [SPARK-13289][MLLIB] Fix infinite distances between word vectors in Word2VecModel
## What changes were proposed in this pull request?

This PR fixes the bug that generates infinite distances between word vectors. For example,

Before this PR, we have
```
val synonyms = model.findSynonyms("who", 40)
```
will give the following results:
```
to Infinity
and Infinity
that Infinity
with Infinity
```
With this PR, the distance between words is a value between 0 and 1, as follows:
```
scala> model.findSynonyms("who", 10)
res0: Array[(String, Double)] = Array((Harvard-educated,0.5253688097000122), (ex-SAS,0.5213794708251953), (McMutrie,0.5187736749649048), (fellow,0.5166833400726318), (businessman,0.5145374536514282), (American-born,0.5127736330032349), (British-born,0.5062344074249268), (gray-bearded,0.5047978162765503), (American-educated,0.5035858750343323), (mentored,0.49849334359169006))

scala> model.findSynonyms("king", 10)
res1: Array[(String, Double)] = Array((queen,0.6787897944450378), (prince,0.6786158084869385), (monarch,0.659771203994751), (emperor,0.6490438580513), (goddess,0.643266499042511), (dynasty,0.635733425617218), (sultan,0.6166239380836487), (pharaoh,0.6150713562965393), (birthplace,0.6143025159835815), (empress,0.6109727025032043))

scala> model.findSynonyms("queen", 10)
res2: Array[(String, Double)] = Array((princess,0.7670737504959106), (godmother,0.6982434988021851), (raven-haired,0.6877717971801758), (swan,0.684934139251709), (hunky,0.6816608309745789), (Titania,0.6808111071586609), (heroine,0.6794036030769348), (king,0.6787897944450378), (diva,0.67848801612854), (lip-synching,0.6731793284416199))
```

### There are two places changed in this PR:
- Normalize the word vector to avoid overflow when calculating inner product between word vectors. This also simplifies the distance calculation, since the word vectors only need to be normalized once.
- Scale the learning rate by number of iteration, to be consistent with Google Word2Vec implementation

## How was this patch tested?

Use word2vec to train text corpus, and run model.findSynonyms() to get the distances between word vectors.

Author: Junyang <fly.shenjy@gmail.com>
Author: flyskyfly <fly.shenjy@gmail.com>

Closes #11812 from flyjy/TVec.
2016-04-30 10:16:35 +01:00
pshearer 0368ff30dd [SPARK-13973][PYSPARK] Make pyspark fail noisily if IPYTHON or IPYTHON_OPTS are set
## What changes were proposed in this pull request?

https://issues.apache.org/jira/browse/SPARK-13973

Following discussion with srowen the IPYTHON and IPYTHON_OPTS variables are removed. If they are set in the user's environment, pyspark will not execute and prints an error message. Failing noisily will force users to remove these options and learn the new configuration scheme, which is much more sustainable and less confusing.

## How was this patch tested?

Manual testing; set IPYTHON=1 and verified that the error message prints.

Author: pshearer <pshearer@massmutual.com>
Author: shearerp <shearerp@umich.edu>

Closes #12528 from shearerp/master.
2016-04-30 10:15:20 +01:00
Reynold Xin 8dc3987d09 [SPARK-15028][SQL] Remove HiveSessionState.setDefaultOverrideConfs
## What changes were proposed in this pull request?
This patch removes some code that are no longer relevant -- mainly HiveSessionState.setDefaultOverrideConfs.

## How was this patch tested?
N/A

Author: Reynold Xin <rxin@databricks.com>

Closes #12806 from rxin/SPARK-15028.
2016-04-30 01:32:00 -07:00
Xiangrui Meng b3ea579314 [SPARK-14831][.2][ML][R] rename ml.save/ml.load to write.ml/read.ml
## What changes were proposed in this pull request?

Continue the work of #12789 to rename ml.asve/ml.load to write.ml/read.ml, which are more consistent with read.df/write.df and other methods in SparkR.

I didn't rename `data` to `df` because we still use `predict` for prediction, which uses `newData` to match the signature in R.

## How was this patch tested?

Existing unit tests.

cc: yanboliang thunterdb

Author: Xiangrui Meng <meng@databricks.com>

Closes #12807 from mengxr/SPARK-14831.
2016-04-30 00:45:44 -07:00
Xiangrui Meng 7fbe1bb24d [SPARK-14412][.2][ML] rename *RDDStorageLevel to *StorageLevel in ml.ALS
## What changes were proposed in this pull request?

As discussed in #12660, this PR renames
* intermediateRDDStorageLevel -> intermediateStorageLevel
* finalRDDStorageLevel -> finalStorageLevel

The argument name in `ALS.train` will be addressed in SPARK-15027.

## How was this patch tested?

Existing unit tests.

Author: Xiangrui Meng <meng@databricks.com>

Closes #12803 from mengxr/SPARK-14412.
2016-04-30 00:41:28 -07:00
Sean Owen 5886b6217b [SPARK-14533][MLLIB] RowMatrix.computeCovariance inaccurate when values are very large (partial fix)
## What changes were proposed in this pull request?

Fix for part of SPARK-14533: trivial simplification and more accurate computation of column means. See also https://github.com/apache/spark/pull/12299 which contained a complete fix that was very slow. This PR does _not_ resolve SPARK-14533 entirely.

## How was this patch tested?

Existing tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #12779 from srowen/SPARK-14533.2.
2016-04-30 00:15:41 -07:00
Dongjoon Hyun f86f71763c [MINOR][EXAMPLE] Use SparkSession instead of SQLContext in RDDRelation.scala
## What changes were proposed in this pull request?

Now, `SQLContext` is used for backward-compatibility, we had better use `SparkSession` in Spark 2.0 examples.

## How was this patch tested?

It's just example change. After building, run `bin/run-example org.apache.spark.examples.sql.RDDRelation`.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12808 from dongjoon-hyun/rddrelation.
2016-04-30 00:15:04 -07:00
Xiangrui Meng 3d09ceeef9 [SPARK-14850][.2][ML] use UnsafeArrayData.fromPrimitiveArray in ml.VectorUDT/MatrixUDT
## What changes were proposed in this pull request?

This PR uses `UnsafeArrayData.fromPrimitiveArray` to implement `ml.VectorUDT/MatrixUDT` to avoid boxing/unboxing.

## How was this patch tested?

Exiting unit tests.

cc: cloud-fan

Author: Xiangrui Meng <meng@databricks.com>

Closes #12805 from mengxr/SPARK-14850.
2016-04-29 23:51:01 -07:00
Marcelo Vanzin 73c20bf325 [SPARK-14391][LAUNCHER] Fix launcher communication test, take 2.
There's actually a race here: the state of the handler was changed before
the connection was set, so the test code could be notified of the state
change, wake up, and still see the connection as null, triggering the assert.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #12785 from vanzin/SPARK-14391.
2016-04-29 23:13:50 -07:00
Timothy Hunter bc36fe6e89 [SPARK-14831][SPARKR] Make the SparkR MLlib API more consistent with Spark
## What changes were proposed in this pull request?

This PR splits the MLlib algorithms into two flavors:
 - the R flavor, which tries to mimic the existing R API for these algorithms (and works as an S4 specialization for Spark dataframes)
 - the Spark flavor, which follows the same API and naming conventions as the rest of the MLlib algorithms in the other languages

In practice, the former calls the latter.

## How was this patch tested?

The tests for the various algorithms were adapted to be run against both interfaces.

Author: Timothy Hunter <timhunter@databricks.com>

Closes #12789 from thunterdb/14831.
2016-04-29 23:13:03 -07:00
Wenchen Fan 43b149fb88 [SPARK-14850][ML] convert primitive array from/to unsafe array directly in VectorUDT/MatrixUDT
## What changes were proposed in this pull request?

This PR adds `fromPrimitiveArray` and `toPrimitiveArray` in `UnsafeArrayData`, so that we can do the conversion much faster in VectorUDT/MatrixUDT.

## How was this patch tested?

existing tests and new test suite `UnsafeArraySuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12640 from cloud-fan/ml.
2016-04-29 23:04:51 -07:00
hyukjinkwon 4bac703eb9 [SPARK-13667][SQL] Support for specifying custom date format for date and timestamp types at CSV datasource.
## What changes were proposed in this pull request?

This PR adds the support to specify custom date format for `DateType` and `TimestampType`.

For `TimestampType`, this uses the given format to infer schema and also to convert the values
For `DateType`, this uses the given format to convert the values.
If the `dateFormat` is not given, then it works with `DateTimeUtils.stringToTime()` for backwords compatibility.
When it's given, then it uses `SimpleDateFormat` for parsing data.

In addition, `IntegerType`, `DoubleType` and `LongType` have a higher priority than `TimestampType` in type inference. This means even if the given format is `yyyy` or `yyyy.MM`, it will be inferred as `IntegerType` or `DoubleType`. Since it is type inference, I think it is okay to give such precedences.

In addition, I renamed `csv.CSVInferSchema` to `csv.InferSchema` as JSON datasource has `json.InferSchema`. Although they have the same names, I did this because I thought the parent package name can still differentiate each.  Accordingly, the suite name was also changed from `CSVInferSchemaSuite` to `InferSchemaSuite`.

## How was this patch tested?

unit tests are used and `./dev/run_tests` for coding style tests.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #11550 from HyukjinKwon/SPARK-13667.
2016-04-29 22:52:21 -07:00
Yin Huai ac41fc648d [SPARK-14591][SQL] Remove DataTypeParser and add more keywords to the nonReserved list.
## What changes were proposed in this pull request?
CatalystSqlParser can parse data types. So, we do not need to have an individual DataTypeParser.

## How was this patch tested?
Existing tests

Author: Yin Huai <yhuai@databricks.com>

Closes #12796 from yhuai/removeDataTypeParser.
2016-04-29 22:49:12 -07:00
Reynold Xin 7945f9f6d4 [SPARK-14757] [SQL] Fix nullability bug in EqualNullSafe codegen
## What changes were proposed in this pull request?
This patch fixes a null handling bug in EqualNullSafe's code generation.

## How was this patch tested?
Updated unit test so they would fail without the fix.

Closes #12628.

Author: Reynold Xin <rxin@databricks.com>
Author: Arash Nabili <arash@levyx.com>

Closes #12799 from rxin/equalnullsafe.
2016-04-29 22:26:12 -07:00
Nick Pentreath 90fa2c6e7f [SPARK-14412][ML][PYSPARK] Add StorageLevel params to ALS
`mllib` `ALS` supports `setIntermediateRDDStorageLevel` and `setFinalRDDStorageLevel`. This PR adds these as Params in `ml` `ALS`. They are put in group **expertParam** since few users will need them.

## How was this patch tested?

New test cases in `ALSSuite` and `tests.py`.

cc yanboliang jkbradley sethah rishabhbhardwaj

Author: Nick Pentreath <nickp@za.ibm.com>

Closes #12660 from MLnick/SPARK-14412-als-storage-params.
2016-04-29 22:01:41 -07:00
hyukjinkwon d7755cfd07 [SPARK-14917][SQL] Enable some ORC compressions tests for writing
## What changes were proposed in this pull request?

https://issues.apache.org/jira/browse/SPARK-14917

As it is described in the JIRA, it seems Hive 1.2.1 which Spark uses now supports snappy and none.

So, this PR enables some tests for writing ORC files with compression codes, `SNAPPY` and `NONE`.

## How was this patch tested?

Unittests in `OrcQuerySuite` and `sbt scalastyle`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #12699 from HyukjinKwon/SPARK-14917.
2016-04-29 21:14:24 -07:00
Joseph K. Bradley 09da43d514 [SPARK-13786][ML][PYTHON] Removed save/load for python tuning
## What changes were proposed in this pull request?

Per discussion on [https://github.com/apache/spark/pull/12604], this removes ML persistence for Python tuning (TrainValidationSplit, CrossValidator, and their Models) since they do not handle nesting easily.  This support should be re-designed and added in the next release.

## How was this patch tested?

Removed unit test elements saving and loading the tuning algorithms, but kept tests to save and load their bestModel fields.

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

Closes #12782 from jkbradley/remove-python-tuning-saveload.
2016-04-29 20:51:24 -07:00
Andrew Or 66773eb8a5 [SPARK-15012][SQL] Simplify configuration API further
## What changes were proposed in this pull request?

1. Remove all the `spark.setConf` etc. Just expose `spark.conf`
2. Make `spark.conf` take in things set in the core `SparkConf` as well, otherwise users may get confused

This was done for both the Python and Scala APIs.

## How was this patch tested?
`SQLConfSuite`, python tests.

This one fixes the failed tests in #12787

Closes #12787

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

Closes #12798 from yhuai/conf-api.
2016-04-29 20:46:07 -07:00
Wenchen Fan b056e8cb0a [SPARK-15010][CORE] new accumulator shoule be tolerant of local RPC message delivery
## What changes were proposed in this pull request?

The RPC framework will not serialize and deserialize messages in local mode, we should not call `acc.value` when receive heartbeat message, because the serialization hook of new accumulator may not be triggered and the `atDriverSide` flag may not be set.

## How was this patch tested?

tested it locally via spark shell

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12795 from cloud-fan/bug.
2016-04-29 19:01:38 -07:00
Yin Huai b33d6b7288 [SPARK-15019][SQL] Propagate all Spark Confs to HiveConf created in HiveClientImpl
## What changes were proposed in this pull request?
This PR makes two changes:
1. We will propagate Spark Confs to HiveConf created in HiveClientImpl. So, users can also use spark conf to set warehouse location and metastore url.
2. In sql/hive, HiveClientImpl will be the only place where we create a new HiveConf.

## How was this patch tested?
Existing tests.

Author: Yin Huai <yhuai@databricks.com>

Closes #12791 from yhuai/onlyUseHiveConfInHiveClientImpl.
2016-04-29 17:07:15 -07:00
tedyu dcfaeadea7 [SPARK-15003] Use ConcurrentHashMap in place of HashMap for NewAccumulator.originals
## What changes were proposed in this pull request?

This PR proposes to use ConcurrentHashMap in place of HashMap for NewAccumulator.originals

This should result in better performance.

## How was this patch tested?

Existing unit test suite

cloud-fan

Author: tedyu <yuzhihong@gmail.com>

Closes #12776 from tedyu/master.
2016-04-30 07:54:53 +08:00
Herman van Hovell 83061be697 [SPARK-14858] [SQL] Enable subquery pushdown
The previous subquery PRs did not include support for pushing subqueries used in filters (`WHERE`/`HAVING`) down. This PR adds this support. For example :
```scala
range(0, 10).registerTempTable("a")
range(5, 15).registerTempTable("b")
range(7, 25).registerTempTable("c")
range(3, 12).registerTempTable("d")
val plan = sql("select * from a join b on a.id = b.id left join c on c.id = b.id where a.id in (select id from d)")
plan.explain(true)
```
Leads to the following Analyzed & Optimized plans:
```
== Parsed Logical Plan ==
...

== Analyzed Logical Plan ==
id: bigint, id: bigint, id: bigint
Project [id#0L,id#4L,id#8L]
+- Filter predicate-subquery#16 [(id#0L = id#12L)]
   :  +- SubqueryAlias predicate-subquery#16 [(id#0L = id#12L)]
   :     +- Project [id#12L]
   :        +- SubqueryAlias d
   :           +- Range 3, 12, 1, 8, [id#12L]
   +- Join LeftOuter, Some((id#8L = id#4L))
      :- Join Inner, Some((id#0L = id#4L))
      :  :- SubqueryAlias a
      :  :  +- Range 0, 10, 1, 8, [id#0L]
      :  +- SubqueryAlias b
      :     +- Range 5, 15, 1, 8, [id#4L]
      +- SubqueryAlias c
         +- Range 7, 25, 1, 8, [id#8L]

== Optimized Logical Plan ==
Join LeftOuter, Some((id#8L = id#4L))
:- Join Inner, Some((id#0L = id#4L))
:  :- Join LeftSemi, Some((id#0L = id#12L))
:  :  :- Range 0, 10, 1, 8, [id#0L]
:  :  +- Range 3, 12, 1, 8, [id#12L]
:  +- Range 5, 15, 1, 8, [id#4L]
+- Range 7, 25, 1, 8, [id#8L]

== Physical Plan ==
...
```
I have also taken the opportunity to move quite a bit of code around:
- Rewriting subqueris and pulling out correlated predicated from subqueries has been moved into the analyzer. The analyzer transforms `Exists` and `InSubQuery` into `PredicateSubquery` expressions. A PredicateSubquery exposes the 'join' expressions and the proper references. This makes things like type coercion, optimization and planning easier to do.
- I have added support for `Aggregate` plans in subqueries. Any correlated expressions will be added to the grouping expressions. I have removed support for `Union` plans, since pulling in an outer reference from beneath a Union has no value (a filtered value could easily be part of another Union child).
- Resolution of subqueries is now done using `OuterReference`s. These are used to wrap any outer reference; this makes the identification of these references easier, and also makes dealing with duplicate attributes in the outer and inner plans easier. The resolution of subqueries initially used a resolution loop which would alternate between calling the analyzer and trying to resolve the outer references. We now use a dedicated analyzer which uses a special rule for outer reference resolution.

These changes are a stepping stone for enabling correlated scalar subqueries, enabling all Hive tests & allowing us to use predicate subqueries anywhere.

Current tests and added test cases in FilterPushdownSuite.

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #12720 from hvanhovell/SPARK-14858.
2016-04-29 16:50:12 -07:00
Joseph K. Bradley 1eda2f10d9 [SPARK-14646][ML] Modified Kmeans to store cluster centers with one per row
## What changes were proposed in this pull request?

Modified Kmeans to store cluster centers with one per row

## How was this patch tested?

Existing tests

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

Closes #12792 from jkbradley/kmeans-save-fix.
2016-04-29 16:46:25 -07:00
Andrew Or d33e3d572e [SPARK-14988][PYTHON] SparkSession API follow-ups
## What changes were proposed in this pull request?

Addresses comments in #12765.

## How was this patch tested?

Python tests.

Author: Andrew Or <andrew@databricks.com>

Closes #12784 from andrewor14/python-followup.
2016-04-29 16:41:13 -07:00
Sun Rui 4ae9fe091c [SPARK-12919][SPARKR] Implement dapply() on DataFrame in SparkR.
## What changes were proposed in this pull request?

dapply() applies an R function on each partition of a DataFrame and returns a new DataFrame.

The function signature is:

	dapply(df, function(localDF) {}, schema = NULL)

R function input: local data.frame from the partition on local node
R function output: local data.frame

Schema specifies the Row format of the resulting DataFrame. It must match the R function's output.
If schema is not specified, each partition of the result DataFrame will be serialized in R into a single byte array. Such resulting DataFrame can be processed by successive calls to dapply().

## How was this patch tested?
SparkR unit tests.

Author: Sun Rui <rui.sun@intel.com>
Author: Sun Rui <sunrui2016@gmail.com>

Closes #12493 from sun-rui/SPARK-12919.
2016-04-29 16:41:07 -07:00
BenFradet d78fbcc3cc [SPARK-14570][ML] Log instrumentation in Random forests
## What changes were proposed in this pull request?

Added Instrumentation logging to DecisionTree{Classifier,Regressor} and RandomForest{Classifier,Regressor}

## How was this patch tested?

No tests involved since it's logging related.

Author: BenFradet <benjamin.fradet@gmail.com>

Closes #12536 from BenFradet/SPARK-14570.
2016-04-29 15:42:47 -07:00
Yin Huai af32f4aed6 [SPARK-15013][SQL] Remove hiveConf from HiveSessionState
## What changes were proposed in this pull request?
The hiveConf in HiveSessionState is not actually used anymore. Let's remove it.

## How was this patch tested?
Existing tests

Author: Yin Huai <yhuai@databricks.com>

Closes #12786 from yhuai/removeHiveConf.
2016-04-29 14:54:40 -07:00
Cheng Lian a04b1de5fa [SPARK-14981][SQL] Throws exception if DESC is specified for sorting columns
## What changes were proposed in this pull request?

Currently Spark SQL doesn't support sorting columns in descending order. However, the parser accepts the syntax and silently drops sorting directions. This PR fixes this by throwing an exception if `DESC` is specified as sorting direction of a sorting column.

## How was this patch tested?

A test case is added to test the invalid sorting order by checking exception message.

Author: Cheng Lian <lian@databricks.com>

Closes #12759 from liancheng/spark-14981.
2016-04-29 14:52:32 -07:00
Reynold Xin 8ebae466a3 [SPARK-15004][SQL] Remove zookeeper service discovery code in thrift-server
## What changes were proposed in this pull request?
We recently inlined Hive's thrift server code in SPARK-15004. This patch removes the code related to zookeeper service discovery, Tez, and Hive on Spark, since they are irrelevant.

## How was this patch tested?
N/A - removing dead code

Author: Reynold Xin <rxin@databricks.com>

Closes #12780 from rxin/SPARK-15004.
2016-04-29 13:32:08 -07:00
Yin Huai ac115f6628 [SPARK-15011][SQL][TEST] Ignore org.apache.spark.sql.hive.StatisticsSuite.analyze MetastoreRelation
This test always fail with sbt's hadoop 2.3 and 2.4 tests. Let'e disable it for now and investigate the problem.

Author: Yin Huai <yhuai@databricks.com>

Closes #12783 from yhuai/SPARK-15011-ignore.
2016-04-29 12:14:28 -07:00
Jeff Zhang 775772de36 [SPARK-11940][PYSPARK][ML] Python API for ml.clustering.LDA PR2
## What changes were proposed in this pull request?

pyspark.ml API for LDA
* LDA, LDAModel, LocalLDAModel, DistributedLDAModel
* includes persistence

This replaces [https://github.com/apache/spark/pull/10242]

## How was this patch tested?

* doc test for LDA, including Param setters
* unit test for persistence

Author: Joseph K. Bradley <joseph@databricks.com>
Author: Jeff Zhang <zjffdu@apache.org>

Closes #12723 from jkbradley/zjffdu-SPARK-11940.
2016-04-29 10:42:52 -07:00
Joseph K. Bradley f08dcdb8d3 [SPARK-14984][ML] Deprecated model field in LinearRegressionSummary
## What changes were proposed in this pull request?

Deprecated model field in LinearRegressionSummary

Removed unnecessary Since annotations

## How was this patch tested?

Existing tests

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

Closes #12763 from jkbradley/lr-summary-api.
2016-04-29 10:40:00 -07:00
Yanbo Liang 87ac84d437 [SPARK-14314][SPARK-14315][ML][SPARKR] Model persistence in SparkR (glm & kmeans)
SparkR ```glm``` and ```kmeans``` model persistence.

Unit tests.

Author: Yanbo Liang <ybliang8@gmail.com>
Author: Gayathri Murali <gayathri.m.softie@gmail.com>

Closes #12778 from yanboliang/spark-14311.
Closes #12680
Closes #12683
2016-04-29 09:43:04 -07:00
Andrew Or a7d0fedc94 [SPARK-14988][PYTHON] SparkSession catalog and conf API
## What changes were proposed in this pull request?

The `catalog` and `conf` APIs were exposed in `SparkSession` in #12713 and #12669. This patch adds those to the python API.

## How was this patch tested?

Python tests.

Author: Andrew Or <andrew@databricks.com>

Closes #12765 from andrewor14/python-spark-session-more.
2016-04-29 09:34:10 -07:00
Davies Liu 7feeb82cb7 [SPARK-14987][SQL] inline hive-service (cli) into sql/hive-thriftserver
## What changes were proposed in this pull request?

This PR copy the thrift-server from hive-service-1.2 (including  TCLIService.thrift and generated Java source code) into sql/hive-thriftserver, so we can do further cleanup and improvements.

## How was this patch tested?

Existing tests.

Author: Davies Liu <davies@databricks.com>

Closes #12764 from davies/thrift_server.
2016-04-29 09:32:42 -07:00
wm624@hotmail.com b6fa7e5934 [SPARK-14571][ML] Log instrumentation in ALS
## What changes were proposed in this pull request?

Add log instrumentation for parameters:
rank, numUserBlocks, numItemBlocks, implicitPrefs, alpha,
userCol, itemCol, ratingCol, predictionCol, maxIter,
regParam, nonnegative, checkpointInterval, seed

Add log instrumentation for numUserFeatures and numItemFeatures

## How was this patch tested?

Manual test: Set breakpoint in intellij and run def testALS(). Single step debugging and check the log method is called.

Author: wm624@hotmail.com <wm624@hotmail.com>

Closes #12560 from wangmiao1981/log.
2016-04-29 16:18:25 +02:00
dding3 6d5aeaae26 [SPARK-14969][MLLIB] Remove duplicate implementation of compute in LogisticGradient
## What changes were proposed in this pull request?

This PR removes duplicate implementation of compute in LogisticGradient class

## How was this patch tested?

unit tests

Author: dding3 <dingding@dingding-ubuntu.sh.intel.com>

Closes #12747 from dding3/master.
2016-04-29 10:19:51 +01:00
Jakob Odersky 7226e19067 [SPARK-14511][BUILD] Upgrade genjavadoc to latest upstream
## What changes were proposed in this pull request?
In the past, genjavadoc had issues with package private members which led the spark project to use a forked version. This issue has been fixed upstream (typesafehub/genjavadoc#70) and a release is available for scala versions 2.10, 2.11 **and 2.12**, hence a forked version for spark is no longer necessary.
This pull request updates the build configuration to use the newest upstream genjavadoc.

## How was this patch tested?
The build was run `sbt unidoc`. During the process javadoc emits some errors on the generated java stubs, however these errors were also present before the upgrade. Furthermore, the produced html is fine.

Author: Jakob Odersky <jakob@odersky.com>

Closes #12707 from jodersky/SPARK-14511-genjavadoc.
2016-04-29 10:10:20 +01:00
Reynold Xin 054f991c43 [SPARK-14994][SQL] Remove execution hive from HiveSessionState
## What changes were proposed in this pull request?
This patch removes executionHive from HiveSessionState and HiveSharedState.

## How was this patch tested?
Updated test cases.

Author: Reynold Xin <rxin@databricks.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #12770 from rxin/SPARK-14994.
2016-04-29 01:14:02 -07:00
Sameer Agarwal 2057cbcb0b [SPARK-14996][SQL] Add TPCDS Benchmark Queries for SparkSQL
## What changes were proposed in this pull request?

This PR adds support for easily running and benchmarking a set of common TPCDS queries locally in SparkSQL.

## How was this patch tested?

N/A

Author: Sameer Agarwal <sameer@databricks.com>

Closes #12771 from sameeragarwal/tpcds-2.
2016-04-29 00:52:42 -07:00
gatorsmile 222dcf7937 [SPARK-12660][SPARK-14967][SQL] Implement Except Distinct by Left Anti Join
#### What changes were proposed in this pull request?
Replaces a logical `Except` operator with a `Left-anti Join` operator. This way, we can take advantage of all the benefits of join implementations (e.g. managed memory, code generation, broadcast joins).
```SQL
  SELECT a1, a2 FROM Tab1 EXCEPT SELECT b1, b2 FROM Tab2
  ==>  SELECT DISTINCT a1, a2 FROM Tab1 LEFT ANTI JOIN Tab2 ON a1<=>b1 AND a2<=>b2
```
 Note:
 1. This rule is only applicable to EXCEPT DISTINCT. Do not use it for EXCEPT ALL.
 2. This rule has to be done after de-duplicating the attributes; otherwise, the enerated
    join conditions will be incorrect.

This PR also corrects the existing behavior in Spark. Before this PR, the behavior is like
```SQL
  test("except") {
    val df_left = Seq(1, 2, 2, 3, 3, 4).toDF("id")
    val df_right = Seq(1, 3).toDF("id")

    checkAnswer(
      df_left.except(df_right),
      Row(2) :: Row(2) :: Row(4) :: Nil
    )
  }
```
After this PR, the result is corrected. We strictly follow the SQL compliance of `Except Distinct`.

#### How was this patch tested?
Modified and added a few test cases to verify the optimization rule and the results of operators.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #12736 from gatorsmile/exceptByAntiJoin.
2016-04-29 15:30:36 +08:00
Reynold Xin e249e6f8b5 [HOTFIX] Disable flaky test StatisticsSuite.analyze MetastoreRelations 2016-04-29 00:23:59 -07:00
Sean Owen d1cf320105 [SPARK-14886][MLLIB] RankingMetrics.ndcgAt throw java.lang.ArrayIndexOutOfBoundsException
## What changes were proposed in this pull request?

Handle case where number of predictions is less than label set, k in nDCG computation

## How was this patch tested?

New unit test; existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #12756 from srowen/SPARK-14886.
2016-04-29 09:21:27 +02:00
Reynold Xin 24d07e45d4 [HOTFIX] Disable flaky LauncherServerSuite.testCommunication 2016-04-29 00:20:52 -07:00
Zheng RuiFeng 4f83e442b1 [MINOR][DOC] Minor typo fixes
## What changes were proposed in this pull request?
Minor typo fixes

## How was this patch tested?
local build

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #12755 from zhengruifeng/fix_doc_dataset.
2016-04-28 22:56:26 -07:00
Zheng RuiFeng cabd54d931 [SPARK-14829][MLLIB] Deprecate GLM APIs using SGD
## What changes were proposed in this pull request?
According to the [SPARK-14829](https://issues.apache.org/jira/browse/SPARK-14829), deprecate API of LogisticRegression and LinearRegression using SGD

## How was this patch tested?
manual tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #12596 from zhengruifeng/deprecate_sgd.
2016-04-28 22:44:14 -07:00
Timothy Hunter 769a909d13 [SPARK-7264][ML] Parallel lapply for sparkR
## What changes were proposed in this pull request?

This PR adds a new function in SparkR called `sparkLapply(list, function)`. This function implements a distributed version of `lapply` using Spark as a backend.

TODO:
 - [x] check documentation
 - [ ] check tests

Trivial example in SparkR:

```R
sparkLapply(1:5, function(x) { 2 * x })
```

Output:

```
[[1]]
[1] 2

[[2]]
[1] 4

[[3]]
[1] 6

[[4]]
[1] 8

[[5]]
[1] 10
```

Here is a slightly more complex example to perform distributed training of multiple models. Under the hood, Spark broadcasts the dataset.

```R
library("MASS")
data(menarche)
families <- c("gaussian", "poisson")
train <- function(family){glm(Menarche ~ Age  , family=family, data=menarche)}
results <- sparkLapply(families, train)
```

## How was this patch tested?

This PR was tested in SparkR. I am unfamiliar with R and SparkR, so any feedback on style, testing, etc. will be much appreciated.

cc falaki davies

Author: Timothy Hunter <timhunter@databricks.com>

Closes #12426 from thunterdb/7264.
2016-04-28 22:42:48 -07:00