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* Evaluate all actions in signal handlers (don't short-circuit)SPARK-10001-hotfixJakob Odersky2016-04-271-3/+5
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* [SPARK-14940][SQL] Move ExternalCatalog to own fileAndrew Or2016-04-2712-188/+210
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? `interfaces.scala` was getting big. This just moves the biggest class in there to a new file for cleanliness. ## How was this patch tested? Just moving things around. Author: Andrew Or <andrew@databricks.com> Closes #12721 from andrewor14/move-external-catalog.
* [SPARK-14899][ML][PYSPARK] Remove spark.ml HashingTF hashingAlg optionYanbo Liang2016-04-275-91/+36
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Since [SPARK-10574](https://issues.apache.org/jira/browse/SPARK-10574) breaks behavior of ```HashingTF```, we should try to enforce good practice by removing the "native" hashAlgorithm option in spark.ml and pyspark.ml. We can leave spark.mllib and pyspark.mllib alone. ## How was this patch tested? Unit tests. cc jkbradley Author: Yanbo Liang <ybliang8@gmail.com> Closes #12702 from yanboliang/spark-14899.
* [SPARK-14954] [SQL] Add PARTITION BY and BUCKET BY clause for data source ↵Cheng Lian2016-04-273-3/+106
| | | | | | | | | | | | | | | | | | | | | CTAS syntax Currently, we can only create persisted partitioned and/or bucketed data source tables using the Dataset API but not using SQL DDL. This PR implements the following syntax to add partitioning and bucketing support to the SQL DDL: ``` CREATE TABLE <table-name> USING <provider> [OPTIONS (<key1> <value1>, <key2> <value2>, ...)] [PARTITIONED BY (col1, col2, ...)] [CLUSTERED BY (col1, col2, ...) [SORTED BY (col1, col2, ...)] INTO <n> BUCKETS] AS SELECT ... ``` Test cases are added in `MetastoreDataSourcesSuite` to check the newly added syntax. Author: Cheng Lian <lian@databricks.com> Author: Yin Huai <yhuai@databricks.com> Closes #12734 from liancheng/spark-14954.
* [SPARK-14867][BUILD] Remove `--force` option in `build/mvn`Dongjoon Hyun2016-04-272-22/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Currently, `build/mvn` provides a convenient option, `--force`, in order to use the recommended version of maven without changing PATH environment variable. However, there were two problems. - `dev/lint-java` does not use the newly installed maven. ```bash $ ./build/mvn --force clean $ ./dev/lint-java Using `mvn` from path: /usr/local/bin/mvn ``` - It's not easy to type `--force` option always. If '--force' option is used once, we had better prefer the installed maven recommended by Spark. This PR makes `build/mvn` check the existence of maven installed by `--force` option first. According to the comments, this PR aims to the followings: - Detect the maven version from `pom.xml`. - Install maven if there is no or old maven. - Remove `--force` option. ## How was this patch tested? Manual. ```bash $ ./build/mvn --force clean $ ./dev/lint-java Using `mvn` from path: /Users/dongjoon/spark/build/apache-maven-3.3.9/bin/mvn ... $ rm -rf ./build/apache-maven-3.3.9/ $ ./dev/lint-java Using `mvn` from path: /usr/local/bin/mvn ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12631 from dongjoon-hyun/SPARK-14867.
* [SPARK-14664][SQL] Implement DecimalAggregates optimization for Window queriesDongjoon Hyun2016-04-273-12/+161
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR aims to implement decimal aggregation optimization for window queries by improving existing `DecimalAggregates`. Historically, `DecimalAggregates` optimizer is designed to transform general `sum/avg(decimal)`, but it breaks recently added windows queries like the followings. The following queries work well without the current `DecimalAggregates` optimizer. **Sum** ```scala scala> sql("select sum(a) over () from (select explode(array(1.0,2.0)) a) t").head java.lang.RuntimeException: Unsupported window function: MakeDecimal((sum(UnscaledValue(a#31)),mode=Complete,isDistinct=false),12,1) scala> sql("select sum(a) over () from (select explode(array(1.0,2.0)) a) t").explain() == Physical Plan == WholeStageCodegen : +- Project [sum(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#23] : +- INPUT +- Window [MakeDecimal((sum(UnscaledValue(a#21)),mode=Complete,isDistinct=false),12,1) windowspecdefinition(ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING) AS sum(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#23] +- Exchange SinglePartition, None +- Generate explode([1.0,2.0]), false, false, [a#21] +- Scan OneRowRelation[] ``` **Average** ```scala scala> sql("select avg(a) over () from (select explode(array(1.0,2.0)) a) t").head java.lang.RuntimeException: Unsupported window function: cast(((avg(UnscaledValue(a#40)),mode=Complete,isDistinct=false) / 10.0) as decimal(6,5)) scala> sql("select avg(a) over () from (select explode(array(1.0,2.0)) a) t").explain() == Physical Plan == WholeStageCodegen : +- Project [avg(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#44] : +- INPUT +- Window [cast(((avg(UnscaledValue(a#42)),mode=Complete,isDistinct=false) / 10.0) as decimal(6,5)) windowspecdefinition(ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING) AS avg(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#44] +- Exchange SinglePartition, None +- Generate explode([1.0,2.0]), false, false, [a#42] +- Scan OneRowRelation[] ``` After this PR, those queries work fine and new optimized physical plans look like the followings. **Sum** ```scala scala> sql("select sum(a) over () from (select explode(array(1.0,2.0)) a) t").explain() == Physical Plan == WholeStageCodegen : +- Project [sum(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#35] : +- INPUT +- Window [MakeDecimal((sum(UnscaledValue(a#33)),mode=Complete,isDistinct=false) windowspecdefinition(ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING),12,1) AS sum(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#35] +- Exchange SinglePartition, None +- Generate explode([1.0,2.0]), false, false, [a#33] +- Scan OneRowRelation[] ``` **Average** ```scala scala> sql("select avg(a) over () from (select explode(array(1.0,2.0)) a) t").explain() == Physical Plan == WholeStageCodegen : +- Project [avg(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#47] : +- INPUT +- Window [cast(((avg(UnscaledValue(a#45)),mode=Complete,isDistinct=false) windowspecdefinition(ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING) / 10.0) as decimal(6,5)) AS avg(a) OVER ( ROWS BETWEEN UNBOUNDED PRECEDING AND UNBOUNDED FOLLOWING)#47] +- Exchange SinglePartition, None +- Generate explode([1.0,2.0]), false, false, [a#45] +- Scan OneRowRelation[] ``` In this PR, *SUM over window* pattern matching is based on the code of hvanhovell ; he should be credited for the work he did. ## How was this patch tested? Pass the Jenkins tests (with newly added testcases) Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12421 from dongjoon-hyun/SPARK-14664.
* [SPARK-14937][ML][DOCUMENT] spark.ml LogisticRegression sqlCtx in scala is ↵wm624@hotmail.com2016-04-273-7/+7
| | | | | | | | | | | | | | | | | inconsistent with java and python ## What changes were proposed in this pull request? In spark.ml document, the LogisticRegression scala example uses sqlCtx. It is inconsistent with java and python examples which use sqlContext. In addition, a user can't copy & paste to run the example in spark-shell as sqlCtx doesn't exist in spark-shell while sqlContext exists. Change the scala example referred by the spark.ml example. ## How was this patch tested? Compile the example scala file and it passes compilation. Author: wm624@hotmail.com <wm624@hotmail.com> Closes #12717 from wangmiao1981/doc.
* [SPARK-14930][SPARK-13693] Fix race condition in CheckpointWriter.stop()Josh Rosen2016-04-271-12/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | CheckpointWriter.stop() is prone to a race condition: if one thread calls `stop()` right as a checkpoint write task begins to execute, that write task may become blocked when trying to access `fs`, the shared Hadoop FileSystem, since both the `fs` getter and `stop` method synchronize on the same lock. Here's a thread-dump excerpt which illustrates the problem: ```java "pool-31-thread-1" #156 prio=5 os_prio=31 tid=0x00007fea02cd2000 nid=0x5c0b waiting for monitor entry [0x000000013bc4c000] java.lang.Thread.State: BLOCKED (on object monitor) at org.apache.spark.streaming.CheckpointWriter.org$apache$spark$streaming$CheckpointWriter$$fs(Checkpoint.scala:302) - waiting to lock <0x00000007bf53ee78> (a org.apache.spark.streaming.CheckpointWriter) at org.apache.spark.streaming.CheckpointWriter$CheckpointWriteHandler.run(Checkpoint.scala:224) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) "pool-1-thread-1-ScalaTest-running-MapWithStateSuite" #11 prio=5 os_prio=31 tid=0x00007fe9ff879800 nid=0x5703 waiting on condition [0x000000012e54c000] java.lang.Thread.State: TIMED_WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x00000007bf564568> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078) at java.util.concurrent.ThreadPoolExecutor.awaitTermination(ThreadPoolExecutor.java:1465) at org.apache.spark.streaming.CheckpointWriter.stop(Checkpoint.scala:291) - locked <0x00000007bf53ee78> (a org.apache.spark.streaming.CheckpointWriter) at org.apache.spark.streaming.scheduler.JobGenerator.stop(JobGenerator.scala:159) - locked <0x00000007bf53ea90> (a org.apache.spark.streaming.scheduler.JobGenerator) at org.apache.spark.streaming.scheduler.JobScheduler.stop(JobScheduler.scala:115) - locked <0x00000007bf53d3f0> (a org.apache.spark.streaming.scheduler.JobScheduler) at org.apache.spark.streaming.StreamingContext$$anonfun$stop$1.apply$mcV$sp(StreamingContext.scala:680) at org.apache.spark.util.Utils$.tryLogNonFatalError(Utils.scala:1219) at org.apache.spark.streaming.StreamingContext.stop(StreamingContext.scala:679) - locked <0x00000007bf516a70> (a org.apache.spark.streaming.StreamingContext) at org.apache.spark.streaming.StreamingContext.stop(StreamingContext.scala:644) - locked <0x00000007bf516a70> (a org.apache.spark.streaming.StreamingContext) [...] ``` We can fix this problem by having `stop` and `fs` be synchronized on different locks: the synchronization on `stop` only needs to guard against multiple threads calling `stop` at the same time, whereas the synchronization on `fs` is only necessary for cross-thread visibility. There's only ever a single active checkpoint writer thread at a time, so we don't need to guard against concurrent access to `fs`. Thus, `fs` can simply become a `volatile` var, similar to `lastCheckpointTime`. This change should fix [SPARK-13693](https://issues.apache.org/jira/browse/SPARK-13693), a flaky `MapWithStateSuite` test suite which has recently been failing several times per day. It also results in a huge test speedup: prior to this patch, `MapWithStateSuite` took about 80 seconds to run, whereas it now runs in less than 10 seconds. For the `streaming` project's tests as a whole, they now run in ~220 seconds vs. ~354 before. /cc zsxwing and tdas for review. Author: Josh Rosen <joshrosen@databricks.com> Closes #12712 from JoshRosen/fix-checkpoint-writer-race.
* [SPARK-14729][SCHEDULER] Refactored YARN scheduler creation code to use ↵Hemant Bhanawat2016-04-274-67/+58
| | | | | | | | | | | | | | newly added ExternalClusterManager ## What changes were proposed in this pull request? With the addition of ExternalClusterManager(ECM) interface in PR #11723, any cluster manager can now be integrated with Spark. It was suggested in ExternalClusterManager PR that one of the existing cluster managers should start using the new interface to ensure that the API is correct. Ideally, all the existing cluster managers should eventually use the ECM interface but as a first step yarn will now use the ECM interface. This PR refactors YARN code from SparkContext.createTaskScheduler function into YarnClusterManager that implements ECM interface. ## How was this patch tested? Since this is refactoring, no new tests has been added. Existing tests have been run. Basic manual testing with YARN was done too. Author: Hemant Bhanawat <hemant@snappydata.io> Closes #12641 from hbhanawat/yarnClusterMgr.
* [SPARK-9656][MLLIB][PYTHON] Add missing methods to PySpark's Distributed ↵Mike Dusenberry2016-04-273-4/+301
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Linear Algebra Classes This PR adds the remaining group of methods to PySpark's distributed linear algebra classes as follows: * `RowMatrix` <sup>**[1]**</sup> 1. `computeGramianMatrix` 2. `computeCovariance` 3. `computeColumnSummaryStatistics` 4. `columnSimilarities` 5. `tallSkinnyQR` <sup>**[2]**</sup> * `IndexedRowMatrix` <sup>**[3]**</sup> 1. `computeGramianMatrix` * `CoordinateMatrix` 1. `transpose` * `BlockMatrix` 1. `validate` 2. `cache` 3. `persist` 4. `transpose` **[1]**: Note: `multiply`, `computeSVD`, and `computePrincipalComponents` are already part of PR #7963 for SPARK-6227. **[2]**: Implementing `tallSkinnyQR` uncovered a bug with our PySpark `RowMatrix` constructor. As discussed on the dev list [here](http://apache-spark-developers-list.1001551.n3.nabble.com/K-Means-And-Class-Tags-td10038.html), there appears to be an issue with type erasure with RDDs coming from Java, and by extension from PySpark. Although we are attempting to construct a `RowMatrix` from an `RDD[Vector]` in [PythonMLlibAPI](https://github.com/apache/spark/blob/master/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala#L1115), the `Vector` type is erased, resulting in an `RDD[Object]`. Thus, when calling Scala's `tallSkinnyQR` from PySpark, we get a Java `ClassCastException` in which an `Object` cannot be cast to a Spark `Vector`. As noted in the aforementioned dev list thread, this issue was also encountered with `DecisionTrees`, and the fix involved an explicit `retag` of the RDD with a `Vector` type. Thus, this PR currently contains that fix applied to the `createRowMatrix` helper function in `PythonMLlibAPI`. `IndexedRowMatrix` and `CoordinateMatrix` do not appear to have this issue likely due to their related helper functions in `PythonMLlibAPI` creating the RDDs explicitly from DataFrames with pattern matching, thus preserving the types. However, this fix may be out of scope for this single PR, and it may be better suited in a separate JIRA/PR. Therefore, I have marked this PR as WIP and am open to discussion. **[3]**: Note: `multiply` and `computeSVD` are already part of PR #7963 for SPARK-6227. Author: Mike Dusenberry <mwdusenb@us.ibm.com> Closes #9441 from dusenberrymw/SPARK-9656_Add_Missing_Methods_to_PySpark_Distributed_Linear_Algebra.
* [SPARK-14874][SQL][STREAMING] Remove the obsolete Batch representationLiwei Lin2016-04-275-30/+4
| | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? The `Batch` class, which had been used to indicate progress in a stream, was abandoned by [[SPARK-13985][SQL] Deterministic batches with ids](https://github.com/apache/spark/commit/caea15214571d9b12dcf1553e5c1cc8b83a8ba5b) and then became useless. This patch: - removes the `Batch` class - ~~does some related renaming~~ (update: this has been reverted) - fixes some related comments ## How was this patch tested? N/A Author: Liwei Lin <lwlin7@gmail.com> Closes #12638 from lw-lin/remove-batch.
* [SPARK-14950][SQL] Fix BroadcastHashJoin's unique key Anti-JoinsHerman van Hovell2016-04-272-14/+67
| | | | | | | | | | | | | | ### What changes were proposed in this pull request? Anti-Joins using BroadcastHashJoin's unique key code path are broken; it currently returns Semi Join results . This PR fixes this bug. ### How was this patch tested? Added tests cases to `ExistenceJoinSuite`. cc davies gatorsmile Author: Herman van Hovell <hvanhovell@questtec.nl> Closes #12730 from hvanhovell/SPARK-14950.
* [SPARK-14949][SQL] Remove HiveConf dependency from InsertIntoHiveTableReynold Xin2016-04-271-16/+14
| | | | | | | | | | | | ## What changes were proposed in this pull request? This patch removes the use of HiveConf from InsertIntoHiveTable. I think this is the last major use of HiveConf and after this we can try to remove the execution HiveConf. ## How was this patch tested? Internal refactoring and should be covered by existing tests. Author: Reynold Xin <rxin@databricks.com> Closes #12728 from rxin/SPARK-14949.
* Unintentional white spaces in kryo classes configuration parametersVictor Chima2016-04-272-3/+4
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Pruned off white spaces present in the user provided comma separated list of classes for **spark.kryo.classesToRegister** and **spark.kryo.registrator**. ## How was this patch tested? Manual tests Author: Victor Chima <blazy2k9@gmail.com> Closes #12701 from blazy2k9/master.
* [MINOR][BUILD] Enable RAT checking on `LZ4BlockInputStream.java`.Dongjoon Hyun2016-04-272-3/+1
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Since `LZ4BlockInputStream.java` is not licensed to Apache Software Foundation (ASF), the Apache License header of that file is not monitored until now. This PR aims to enable RAT checking on `LZ4BlockInputStream.java` by excluding from `dev/.rat-excludes`. This will prevent accidental removal of Apache License header from that file. ## How was this patch tested? Pass the Jenkins tests (Specifically, RAT check stage). Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12677 from dongjoon-hyun/minor_rat_exclusion_file.
* [SPARK-14130][SQL] Throw exceptions for ALTER TABLE ADD/REPLACE/CHANGE ↵Yin Huai2016-04-27184-819/+194
| | | | | | | | | | | | | | COLUMN, ALTER TABLE SET FILEFORMAT, DFS, and transaction related commands ## What changes were proposed in this pull request? This PR will make Spark SQL not allow ALTER TABLE ADD/REPLACE/CHANGE COLUMN, ALTER TABLE SET FILEFORMAT, DFS, and transaction related commands. ## How was this patch tested? Existing tests. For those tests that I put in the blacklist, I am adding the useful parts back to SQLQuerySuite. Author: Yin Huai <yhuai@databricks.com> Closes #12714 from yhuai/banNativeCommand.
* [SPARK-14944][SPARK-14943][SQL] Remove HiveConf from HiveTableScanExec, ↵Reynold Xin2016-04-266-46/+37
| | | | | | | | | | | | | | HiveTableReader, and ScriptTransformation ## What changes were proposed in this pull request? This patch removes HiveConf from HiveTableScanExec and HiveTableReader and instead just uses our own configuration system. I'm splitting the large change of removing HiveConf into multiple independent pull requests because it is very difficult to debug test failures when they are all combined in one giant one. ## How was this patch tested? Should be covered by existing tests. Author: Reynold Xin <rxin@databricks.com> Closes #12727 from rxin/SPARK-14944.
* [SPARK-14911] [CORE] Fix a potential data race in TaskMemoryManagerLiwei Lin2016-04-261-1/+1
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? [[SPARK-13210][SQL] catch OOM when allocate memory and expand array](https://github.com/apache/spark/commit/37bc203c8dd5022cb11d53b697c28a737ee85bcc) introduced an `acquiredButNotUsed` field, but it might not be correctly synchronized: - the write `acquiredButNotUsed += acquired` is guarded by `this` lock (see [here](https://github.com/apache/spark/blame/master/core/src/main/java/org/apache/spark/memory/TaskMemoryManager.java#L271)); - the read `memoryManager.releaseExecutionMemory(acquiredButNotUsed, taskAttemptId, tungstenMemoryMode)` (see [here](https://github.com/apache/spark/blame/master/core/src/main/java/org/apache/spark/memory/TaskMemoryManager.java#L400)) might not be correctly synchronized, and thus might not see `acquiredButNotUsed`'s most recent value. This patch makes `acquiredButNotUsed` volatile to fix this. ## How was this patch tested? This should be covered by existing suits. Author: Liwei Lin <lwlin7@gmail.com> Closes #12681 from lw-lin/fix-acquiredButNotUsed.
* [SPARK-14913][SQL] Simplify configuration APIReynold Xin2016-04-2642-671/+368
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? We currently expose both Hadoop configuration and Spark SQL configuration in RuntimeConfig. I think we can remove the Hadoop configuration part, and simply generate Hadoop Configuration on the fly by passing all the SQL configurations into it. This way, there is a single interface (in Java/Scala/Python/SQL) for end-users. As part of this patch, I also removed some config options deprecated in Spark 1.x. ## How was this patch tested? Updated relevant tests. Author: Reynold Xin <rxin@databricks.com> Closes #12689 from rxin/SPARK-14913.
* [SPARK-13477][SQL] Expose new user-facing Catalog interfaceAndrew Or2016-04-2631-325/+1090
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? #12625 exposed a new user-facing conf interface in `SparkSession`. This patch adds a catalog interface. ## How was this patch tested? See `CatalogSuite`. Author: Andrew Or <andrew@databricks.com> Closes #12713 from andrewor14/user-facing-catalog.
* [SPARK-14445][SQL] Support native execution of SHOW COLUMNS and SHOW PARTITIONSDilip Biswal2016-04-2716-31/+401
| | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR adds Native execution of SHOW COLUMNS and SHOW PARTITION commands. Command Syntax: ``` SQL SHOW COLUMNS (FROM | IN) table_identifier [(FROM | IN) database] ``` ``` SQL SHOW PARTITIONS [db_name.]table_name [PARTITION(partition_spec)] ``` ## How was this patch tested? Added test cases in HiveCommandSuite to verify execution and DDLCommandSuite to verify plans. Author: Dilip Biswal <dbiswal@us.ibm.com> Closes #12222 from dilipbiswal/dkb_show_columns.
* [SPARK-14732][ML] spark.ml GaussianMixture should use MultivariateGaussian ↵Joseph K. Bradley2016-04-267-44/+353
| | | | | | | | | | | | | | | | | | | | | | | | | | in mllib-local ## What changes were proposed in this pull request? Before, spark.ml GaussianMixtureModel used the spark.mllib MultivariateGaussian in its public API. This was added after 1.6, so we can modify this API without breaking APIs. This PR copies MultivariateGaussian to mllib-local in spark.ml, with a few changes: * Renamed fields to match numpy, scipy: mu => mean, sigma => cov This PR then uses the spark.ml MultivariateGaussian in the spark.ml GaussianMixtureModel, which involves: * Modifying the constructor * Adding a computeProbabilities method Also: * Added EPSILON to mllib-local for use in MultivariateGaussian ## How was this patch tested? Existing unit tests Author: Joseph K. Bradley <joseph@databricks.com> Closes #12593 from jkbradley/sparkml-gmm-fix.
* [SPARK-13734][SPARKR] Added histogram functionOscar D. Lara Yejas2016-04-264-0/+170
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Added method histogram() to compute the histogram of a Column Usage: ``` ## Create a DataFrame from the Iris dataset irisDF <- createDataFrame(sqlContext, iris) ## Render a histogram for the Sepal_Length column histogram(irisDF, "Sepal_Length", nbins=12) ``` ![histogram](https://cloud.githubusercontent.com/assets/13985649/13588486/e1e751c6-e484-11e5-85db-2fc2115c4bb2.png) Note: Usage will change once SPARK-9325 is figured out so that histogram() only takes a Column as a parameter, as opposed to a DataFrame and a name ## How was this patch tested? All unit tests pass. I added specific unit cases for different scenarios. Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.usca.ibm.com> Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.attlocal.net> Closes #11569 from olarayej/SPARK-13734.
* [SPARK-14925][BUILD] Re-introduce 'unused' dependency so that published POMs ↵Josh Rosen2016-04-263-0/+31
| | | | | | | | | | are flattened Spark's published POMs are supposed to be flattened and not contain variable substitution (see SPARK-3812), but the dummy dependency that was required for this was accidentally removed. We should re-introduce this dependency in order to fix an issue where the un-flattened POMs cause the wrong dependencies to be included in Scala 2.10 published POMs. Author: Josh Rosen <joshrosen@databricks.com> Closes #12706 from JoshRosen/SPARK-14925-published-poms-should-be-flattened.
* [SPARK-14929] [SQL] Disable vectorized map for wide schemas & high-precision ↵Sameer Agarwal2016-04-264-31/+55
| | | | | | | | | | | | | | | | decimals ## What changes were proposed in this pull request? While the vectorized hash map in `TungstenAggregate` is currently supported for all primitive data types during partial aggregation, this patch only enables the hash map for a subset of cases that've been verified to show performance improvements on our benchmarks subject to an internal conf that sets an upper limit on the maximum length of the aggregate key/value schema. This list of supported use-cases should be expanded over time. ## How was this patch tested? This is no new change in functionality so existing tests should suffice. Performance tests were done on TPCDS benchmarks. Author: Sameer Agarwal <sameer@databricks.com> Closes #12710 from sameeragarwal/vectorized-enable.
* [SPARK-12301][ML] Made all tree and ensemble classes not finalJoseph K. Bradley2016-04-268-16/+16
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? There have been continuing requests (e.g., SPARK-7131) for allowing users to extend and modify MLlib models and algorithms. This PR makes tree and ensemble classes, Node types, and Split types in spark.ml no longer final. This matches most other spark.ml algorithms. Constructors for models are still private since we may need to refactor how stats are maintained in tree nodes. ## How was this patch tested? Existing unit tests Author: Joseph K. Bradley <joseph@databricks.com> Closes #12711 from jkbradley/final-trees.
* [SPARK-14514][DOC] Add python example for VectorSlicerZheng RuiFeng2016-04-262-0/+52
| | | | | | | | | | | | ## What changes were proposed in this pull request? Add the missing python example for VectorSlicer ## How was this patch tested? manual tests Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #12282 from zhengruifeng/vecslicer_pe.
* [SPARK-14907][MLLIB] Use repartition in GLMRegressionModel.saveDongjoon Hyun2016-04-261-4/+1
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR changes `GLMRegressionModel.save` function like the following code that is similar to other algorithms' parquet write. ``` - val dataRDD: DataFrame = sc.parallelize(Seq(data), 1).toDF() - // TODO: repartition with 1 partition after SPARK-5532 gets fixed - dataRDD.write.parquet(Loader.dataPath(path)) + sqlContext.createDataFrame(Seq(data)).repartition(1).write.parquet(Loader.dataPath(path)) ``` ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12676 from dongjoon-hyun/SPARK-14907.
* [SPARK-14853] [SQL] Support LeftSemi/LeftAnti in SortMergeJoinExecDavies Liu2016-04-2610-175/+194
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR update SortMergeJoinExec to support LeftSemi/LeftAnti, so it could support all the join types, same as other three join implementations: BroadcastHashJoinExec, ShuffledHashJoinExec,and BroadcastNestedLoopJoinExec. This PR also simplify the join selection in SparkStrategy. ## How was this patch tested? Added new tests. Author: Davies Liu <davies@databricks.com> Closes #12668 from davies/smj_semi.
* [SPARK-14903][SPARK-14071][ML][PYTHON] Revert : MLWritable.write propertyJoseph K. Bradley2016-04-262-8/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? SPARK-14071 changed MLWritable.write to be a property. This reverts that change since there was not a good way to make MLReadable.read appear to be a property. ## How was this patch tested? existing unit tests Author: Joseph K. Bradley <joseph@databricks.com> Closes #12671 from jkbradley/revert-MLWritable-write-py.
* [SPARK-11559][MLLIB] Make `runs` no effect in mllib.KMeansYanbo Liang2016-04-264-41/+16
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? We deprecated ```runs``` of mllib.KMeans in Spark 1.6 (SPARK-11358). In 2.0, we will make it no effect (with warning messages). We did not remove ```setRuns/getRuns``` for better binary compatibility. This PR change `runs` which are appeared at the public API. Usage inside of ```KMeans.runAlgorithm()``` will be resolved at #10806. ## How was this patch tested? Existing unit tests. cc jkbradley Author: Yanbo Liang <ybliang8@gmail.com> Closes #12608 from yanboliang/spark-11559.
* [MINOR] Follow-up to #12625Andrew Or2016-04-263-6/+6
| | | | | | | | | | ## What changes were proposed in this pull request? That patch mistakenly widened the visibility from `private[x]` to `protected[x]`. This patch reverts those changes. Author: Andrew Or <andrew@databricks.com> Closes #12686 from andrewor14/visibility.
* [SPARK-14912][SQL] Propagate data source options to Hadoop configurationReynold Xin2016-04-2612-57/+99
| | | | | | | | | | | | ## What changes were proposed in this pull request? We currently have no way for users to propagate options to the underlying library that rely in Hadoop configurations to work. For example, there are various options in parquet-mr that users might want to set, but the data source API does not expose a per-job way to set it. This patch propagates the user-specified options also into Hadoop Configuration. ## How was this patch tested? Used a mock data source implementation to test both the read path and the write path. Author: Reynold Xin <rxin@databricks.com> Closes #12688 from rxin/SPARK-14912.
* [SPARK-14313][ML][SPARKR] AFTSurvivalRegression model persistence in SparkRYanbo Liang2016-04-264-3/+91
| | | | | | | | | | | | ## What changes were proposed in this pull request? ```AFTSurvivalRegressionModel``` supports ```save/load``` in SparkR. ## How was this patch tested? Unit tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #12685 from yanboliang/spark-14313.
* [SPARK-14910][SQL] Native DDL Command Support for Describe Function in ↵gatorsmile2016-04-264-3/+79
| | | | | | | | | | | | | | | | | | | | | | | | Non-identifier Format #### What changes were proposed in this pull request? The existing `Describe Function` only support the function name in `identifier`. This is different from what Hive behaves. That is why many test cases `udf_abc` in `HiveCompatibilitySuite` are not using our native DDL support. For example, - udf_not.q - udf_bitwise_not.q This PR is to resolve the issues. Now, we can support the command of `Describe Function` whose function names are in the following format: - `qualifiedName` (e.g., `db.func1`) - `STRING` (e.g., `'func1'`) - `comparisonOperator` (e.g,. `<`) - `arithmeticOperator` (e.g., `+`) - `predicateOperator` (e.g., `or`) Note, before this PR, we only have a native command support when the function name is in the format of `qualifiedName`. #### How was this patch tested? Added test cases in `DDLSuite.scala`. Also manually verified all the related test cases in `HiveCompatibilitySuite` passed. Author: gatorsmile <gatorsmile@gmail.com> Closes #12679 from gatorsmile/descFunction.
* [MINOR][DOCS] Minor typo fixesJacek Laskowski2016-04-2610-15/+14
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Minor typo fixes (too minor to deserve separate a JIRA) ## How was this patch tested? local build Author: Jacek Laskowski <jacek@japila.pl> Closes #12469 from jaceklaskowski/minor-typo-fixes.
* [SPARK-14756][CORE] Use parseLong instead of valueOfAzeem Jiva2016-04-265-13/+13
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Use Long.parseLong which returns a primative. Use a series of appends() reduces the creation of an extra StringBuilder type ## How was this patch tested? Unit tests Author: Azeem Jiva <azeemj@gmail.com> Closes #12520 from javawithjiva/minor.
* [SPARK-14889][SPARK CORE] scala.MatchError: NONE (of class ↵Subhobrata Dey2016-04-262-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | scala.Enumeration) when spark.scheduler.mode=NONE ## What changes were proposed in this pull request? Handling exception for the below mentioned issue ``` ➜ spark git:(master) ✗ ./bin/spark-shell -c spark.scheduler.mode=NONE 16/04/25 09:15:00 ERROR SparkContext: Error initializing SparkContext. scala.MatchError: NONE (of class scala.Enumeration$Val) at org.apache.spark.scheduler.Pool.<init>(Pool.scala:53) at org.apache.spark.scheduler.TaskSchedulerImpl.initialize(TaskSchedulerImpl.scala:131) at org.apache.spark.SparkContext$.org$apache$spark$SparkContext$$createTaskScheduler(SparkContext.scala:2352) at org.apache.spark.SparkContext.<init>(SparkContext.scala:492) ``` The exception now looks like ``` java.lang.RuntimeException: The scheduler mode NONE is not supported by Spark. ``` ## How was this patch tested? manual tests Author: Subhobrata Dey <sbcd90@gmail.com> Closes #12666 from sbcd90/schedulerModeIssue.
* Fix dynamic allocation docs to address cached data.Michael Gummelt2016-04-261-2/+3
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Documentation changes ## How was this patch tested? No tests Author: Michael Gummelt <mgummelt@mesosphere.io> Closes #12664 from mgummelt/fix-dynamic-docs.
* [SPARK-13962][ML] spark.ml Evaluators should support other numeric types for ↵BenFradet2016-04-268-51/+88
| | | | | | | | | | | | | | | | label ## What changes were proposed in this pull request? Made BinaryClassificationEvaluator, MulticlassClassificationEvaluator and RegressionEvaluator accept all numeric types for label ## How was this patch tested? Unit tests Author: BenFradet <benjamin.fradet@gmail.com> Closes #12500 from BenFradet/SPARK-13962.
* [HOTFIX] Fix the problem for real this time.Reynold Xin2016-04-251-5/+5
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* [HOTFIX] Fix compilationReynold Xin2016-04-251-4/+4
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* [SPARK-14861][SQL] Replace internal usages of SQLContext with SparkSessionAndrew Or2016-04-25101-715/+785
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? In Spark 2.0, `SparkSession` is the new thing. Internally we should stop using `SQLContext` everywhere since that's supposed to be not the main user-facing API anymore. In this patch I took care to not break any public APIs. The one place that's suspect is `o.a.s.ml.source.libsvm.DefaultSource`, but according to mengxr it's not supposed to be public so it's OK to change the underlying `FileFormat` trait. **Reviewers**: This is a big patch that may be difficult to review but the changes are actually really straightforward. If you prefer I can break it up into a few smaller patches, but it will delay the progress of this issue a little. ## How was this patch tested? No change in functionality intended. Author: Andrew Or <andrew@databricks.com> Closes #12625 from andrewor14/spark-session-refactor.
* [SPARK-14904][SQL] Put removed HiveContext in compatibility moduleAndrew Or2016-04-253-0/+170
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This is for users who can't upgrade and need to continue to use HiveContext. ## How was this patch tested? Added some basic tests for sanity check. This is based on #12672 and closes #12672. Author: Andrew Or <andrew@databricks.com> Author: Reynold Xin <rxin@databricks.com> Closes #12682 from rxin/add-back-hive-context.
* [SPARK-14870][SQL][FOLLOW-UP] Move decimalDataWithNulls in ↵Sameer Agarwal2016-04-252-15/+9
| | | | | | | | | | | | | | | | DataFrameAggregateSuite ## What changes were proposed in this pull request? Minor followup to https://github.com/apache/spark/pull/12651 ## How was this patch tested? Test-only change Author: Sameer Agarwal <sameer@databricks.com> Closes #12674 from sameeragarwal/tpcds-fix-2.
* [SPARK-14902][SQL] Expose RuntimeConfig in SparkSessionAndrew Or2016-04-2538-81/+131
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? `RuntimeConfig` is the new user-facing API in 2.0 added in #11378. Until now, however, it's been dead code. This patch uses `RuntimeConfig` in `SessionState` and exposes that through the `SparkSession`. ## How was this patch tested? New test in `SQLContextSuite`. Author: Andrew Or <andrew@databricks.com> Closes #12669 from andrewor14/use-runtime-conf.
* [SPARK-14888][SQL] UnresolvedFunction should use FunctionIdentifierReynold Xin2016-04-2513-92/+117
| | | | | | | | | | | | ## What changes were proposed in this pull request? This patch changes UnresolvedFunction and UnresolvedGenerator to use a FunctionIdentifier rather than just a String for function name. Also changed SessionCatalog to accept FunctionIdentifier in lookupFunction. ## How was this patch tested? Updated related unit tests. Author: Reynold Xin <rxin@databricks.com> Closes #12659 from rxin/SPARK-14888.
* [SPARK-14828][SQL] Start SparkSession in REPL instead of SQLContextAndrew Or2016-04-256-50/+65
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? ``` Spark context available as 'sc' (master = local[*], app id = local-1461283768192). Spark session available as 'spark'. Welcome to ____ __ / __/__ ___ _____/ /__ _\ \/ _ \/ _ `/ __/ '_/ /___/ .__/\_,_/_/ /_/\_\ version 2.0.0-SNAPSHOT /_/ Using Scala version 2.11.8 (Java HotSpot(TM) 64-Bit Server VM, Java 1.7.0_51) Type in expressions to have them evaluated. Type :help for more information. scala> sql("SHOW TABLES").collect() 16/04/21 17:09:39 WARN ObjectStore: Version information not found in metastore. hive.metastore.schema.verification is not enabled so recording the schema version 1.2.0 16/04/21 17:09:39 WARN ObjectStore: Failed to get database default, returning NoSuchObjectException res0: Array[org.apache.spark.sql.Row] = Array([src,false]) scala> sql("SHOW TABLES").collect() res1: Array[org.apache.spark.sql.Row] = Array([src,false]) scala> spark.createDataFrame(Seq((1, 1), (2, 2), (3, 3))) res2: org.apache.spark.sql.DataFrame = [_1: int, _2: int] ``` Hive things are loaded lazily. ## How was this patch tested? Manual. Author: Andrew Or <andrew@databricks.com> Closes #12589 from andrewor14/spark-session-repl.
* [SPARK-14312][ML][SPARKR] NaiveBayes model persistence in SparkRYanbo Liang2016-04-256-5/+162
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? SparkR ```NaiveBayesModel``` supports ```save/load``` by the following API: ``` df <- createDataFrame(sqlContext, infert) model <- naiveBayes(education ~ ., df, laplace = 0) ml.save(model, path) model2 <- ml.load(path) ``` ## How was this patch tested? Add unit tests. cc mengxr Author: Yanbo Liang <ybliang8@gmail.com> Closes #12573 from yanboliang/spark-14312.
* [SPARK-13739][SQL] Push Predicate Through Windowgatorsmile2016-04-255-33/+294
| | | | | | | | | | | | | | | | | | | | #### What changes were proposed in this pull request? For performance, predicates can be pushed through Window if and only if the following conditions are satisfied: 1. All the expressions are part of window partitioning key. The expressions can be compound. 2. Deterministic #### How was this patch tested? TODO: - [X] DSL needs to be modified for window - [X] more tests will be added. Author: gatorsmile <gatorsmile@gmail.com> Author: xiaoli <lixiao1983@gmail.com> Author: Xiao Li <xiaoli@Xiaos-MacBook-Pro.local> Closes #11635 from gatorsmile/pushPredicateThroughWindow.
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