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* [SPARK-18490][SQL] duplication nodename extrainfo for ShuffleExchangeroot2016-11-171-3/+1
| | | | | | | | | | | | | ## What changes were proposed in this pull request? In ShuffleExchange, the nodename's extraInfo are the same when exchangeCoordinator.isEstimated is true or false. Merge the two situation in the PR. Author: root <root@iZbp1gsnrlfzjxh82cz80vZ.(none)> Closes #15920 from windpiger/DupNodeNameShuffleExchange.
* [SPARK-18480][DOCS] Fix wrong links for ML guide docsZheng RuiFeng2016-11-178-22/+19
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? 1, There are two `[Graph.partitionBy]` in `graphx-programming-guide.md`, the first one had no effert. 2, `DataFrame`, `Transformer`, `Pipeline` and `Parameter` in `ml-pipeline.md` were linked to `ml-guide.html` by mistake. 3, `PythonMLLibAPI` in `mllib-linear-methods.md` was not accessable, because class `PythonMLLibAPI` is private. 4, Other link updates. ## How was this patch tested? manual tests Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15912 from zhengruifeng/md_fix.
* [SPARK-17462][MLLIB]use VersionUtils to parse Spark version stringsVinceShieh2016-11-172-8/+4
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Several places in MLlib use custom regexes or other approaches to parse Spark versions. Those should be fixed to use the VersionUtils. This PR replaces custom regexes with VersionUtils to get Spark version numbers. ## How was this patch tested? Existing tests. Signed-off-by: VinceShieh vincent.xieintel.com Author: VinceShieh <vincent.xie@intel.com> Closes #15055 from VinceShieh/SPARK-17462.
* [SPARK-18365][DOCS] Improve Sample Method Documentationanabranch2016-11-176-5/+30
| | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? I found the documentation for the sample method to be confusing, this adds more clarification across all languages. - [x] Scala - [x] Python - [x] R - [x] RDD Scala - [ ] RDD Python with SEED - [X] RDD Java - [x] RDD Java with SEED - [x] RDD Python ## How was this patch tested? NA Please review https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark before opening a pull request. Author: anabranch <wac.chambers@gmail.com> Author: Bill Chambers <bill@databricks.com> Closes #15815 from anabranch/SPARK-18365.
* [YARN][DOC] Remove non-Yarn specific configurations from running-on-yarn.mdWeiqing Yang2016-11-171-36/+0
| | | | | | | | | | | | | ## What changes were proposed in this pull request? Remove `spark.driver.memory`, `spark.executor.memory`, `spark.driver.cores`, and `spark.executor.cores` from `running-on-yarn.md` as they are not Yarn-specific, and they are also defined in`configuration.md`. ## How was this patch tested? Build passed & Manually check. Author: Weiqing Yang <yangweiqing001@gmail.com> Closes #15869 from weiqingy/yarnDoc.
* [SPARK-18464][SQL] support old table which doesn't store schema in metastoreWenchen Fan2016-11-174-2/+37
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Before Spark 2.1, users can create an external data source table without schema, and we will infer the table schema at runtime. In Spark 2.1, we decided to infer the schema when the table was created, so that we don't need to infer it again and again at runtime. This is a good improvement, but we should still respect and support old tables which doesn't store table schema in metastore. ## How was this patch tested? regression test. Author: Wenchen Fan <wenchen@databricks.com> Closes #15900 from cloud-fan/hive-catalog.
* [SPARK-18442][SQL] Fix nullability of WrapOption.Takuya UESHIN2016-11-171-1/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? The nullability of `WrapOption` should be `false`. ## How was this patch tested? Existing tests. Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #15887 from ueshin/issues/SPARK-18442.
* [YARN][DOC] Increasing NodeManager's heap size with External Shuffle ServiceArtur Sukhenko2016-11-161-0/+2
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Suggest users to increase `NodeManager's` heap size if `External Shuffle Service` is enabled as `NM` can spend a lot of time doing GC resulting in shuffle operations being a bottleneck due to `Shuffle Read blocked time` bumped up. Also because of GC `NodeManager` can use an enormous amount of CPU and cluster performance will suffer. I have seen NodeManager using 5-13G RAM and up to 2700% CPU with `spark_shuffle` service on. ## How was this patch tested? #### Added step 5: ![shuffle_service](https://cloud.githubusercontent.com/assets/15244468/20355499/2fec0fde-ac2a-11e6-8f8b-1c80daf71be1.png) Author: Artur Sukhenko <artur.sukhenko@gmail.com> Closes #15906 from Devian-ua/nmHeapSize.
* [SPARK-18186] Migrate HiveUDAFFunction to TypedImperativeAggregate for ↵Cheng Lian2016-11-162-50/+301
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | partial aggregation support ## What changes were proposed in this pull request? While being evaluated in Spark SQL, Hive UDAFs don't support partial aggregation. This PR migrates `HiveUDAFFunction`s to `TypedImperativeAggregate`, which already provides partial aggregation support for aggregate functions that may use arbitrary Java objects as aggregation states. The following snippet shows the effect of this PR: ```scala import org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax sql(s"CREATE FUNCTION hive_max AS '${classOf[GenericUDAFMax].getName}'") spark.range(100).createOrReplaceTempView("t") // A query using both Spark SQL native `max` and Hive `max` sql(s"SELECT max(id), hive_max(id) FROM t").explain() ``` Before this PR: ``` == Physical Plan == SortAggregate(key=[], functions=[max(id#1L), default.hive_max(default.hive_max, HiveFunctionWrapper(org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax,org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax7475f57e), id#1L, false, 0, 0)]) +- Exchange SinglePartition +- *Range (0, 100, step=1, splits=Some(1)) ``` After this PR: ``` == Physical Plan == SortAggregate(key=[], functions=[max(id#1L), default.hive_max(default.hive_max, HiveFunctionWrapper(org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax,org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax5e18a6a7), id#1L, false, 0, 0)]) +- Exchange SinglePartition +- SortAggregate(key=[], functions=[partial_max(id#1L), partial_default.hive_max(default.hive_max, HiveFunctionWrapper(org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax,org.apache.hadoop.hive.ql.udf.generic.GenericUDAFMax5e18a6a7), id#1L, false, 0, 0)]) +- *Range (0, 100, step=1, splits=Some(1)) ``` The tricky part of the PR is mostly about updating and passing around aggregation states of `HiveUDAFFunction`s since the aggregation state of a Hive UDAF may appear in three different forms. Let's take a look at the testing `MockUDAF` added in this PR as an example. This UDAF computes the count of non-null values together with the count of nulls of a given column. Its aggregation state may appear as the following forms at different time: 1. A `MockUDAFBuffer`, which is a concrete subclass of `GenericUDAFEvaluator.AggregationBuffer` The form used by Hive UDAF API. This form is required by the following scenarios: - Calling `GenericUDAFEvaluator.iterate()` to update an existing aggregation state with new input values. - Calling `GenericUDAFEvaluator.terminate()` to get the final aggregated value from an existing aggregation state. - Calling `GenericUDAFEvaluator.merge()` to merge other aggregation states into an existing aggregation state. The existing aggregation state to be updated must be in this form. Conversions: - To form 2: `GenericUDAFEvaluator.terminatePartial()` - To form 3: Convert to form 2 first, and then to 3. 2. An `Object[]` array containing two `java.lang.Long` values. The form used to interact with Hive's `ObjectInspector`s. This form is required by the following scenarios: - Calling `GenericUDAFEvaluator.terminatePartial()` to convert an existing aggregation state in form 1 to form 2. - Calling `GenericUDAFEvaluator.merge()` to merge other aggregation states into an existing aggregation state. The input aggregation state must be in this form. Conversions: - To form 1: No direct method. Have to create an empty `AggregationBuffer` and merge it into the empty buffer. - To form 3: `unwrapperFor()`/`unwrap()` method of `HiveInspectors` 3. The byte array that holds data of an `UnsafeRow` with two `LongType` fields. The form used by Spark SQL to shuffle partial aggregation results. This form is required because `TypedImperativeAggregate` always asks its subclasses to serialize their aggregation states into a byte array. Conversions: - To form 1: Convert to form 2 first, and then to 1. - To form 2: `wrapperFor()`/`wrap()` method of `HiveInspectors` Here're some micro-benchmark results produced by the most recent master and this PR branch. Master: ``` Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14 on Mac OS X 10.10.5 Intel(R) Core(TM) i7-4960HQ CPU 2.60GHz hive udaf vs spark af: Best/Avg Time(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------ w/o groupBy 339 / 372 3.1 323.2 1.0X w/ groupBy 503 / 529 2.1 479.7 0.7X ``` This PR: ``` Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14 on Mac OS X 10.10.5 Intel(R) Core(TM) i7-4960HQ CPU 2.60GHz hive udaf vs spark af: Best/Avg Time(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------ w/o groupBy 116 / 126 9.0 110.8 1.0X w/ groupBy 151 / 159 6.9 144.0 0.8X ``` Benchmark code snippet: ```scala test("Hive UDAF benchmark") { val N = 1 << 20 sparkSession.sql(s"CREATE TEMPORARY FUNCTION hive_max AS '${classOf[GenericUDAFMax].getName}'") val benchmark = new Benchmark( name = "hive udaf vs spark af", valuesPerIteration = N, minNumIters = 5, warmupTime = 5.seconds, minTime = 5.seconds, outputPerIteration = true ) benchmark.addCase("w/o groupBy") { _ => sparkSession.range(N).agg("id" -> "hive_max").collect() } benchmark.addCase("w/ groupBy") { _ => sparkSession.range(N).groupBy($"id" % 10).agg("id" -> "hive_max").collect() } benchmark.run() sparkSession.sql(s"DROP TEMPORARY FUNCTION IF EXISTS hive_max") } ``` ## How was this patch tested? New test suite `HiveUDAFSuite` is added. Author: Cheng Lian <lian@databricks.com> Closes #15703 from liancheng/partial-agg-hive-udaf.
* [SPARK-1267][SPARK-18129] Allow PySpark to be pip installedHolden Karau2016-11-1631-24/+660
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR aims to provide a pip installable PySpark package. This does a bunch of work to copy the jars over and package them with the Python code (to prevent challenges from trying to use different versions of the Python code with different versions of the JAR). It does not currently publish to PyPI but that is the natural follow up (SPARK-18129). Done: - pip installable on conda [manual tested] - setup.py installed on a non-pip managed system (RHEL) with YARN [manual tested] - Automated testing of this (virtualenv) - packaging and signing with release-build* Possible follow up work: - release-build update to publish to PyPI (SPARK-18128) - figure out who owns the pyspark package name on prod PyPI (is it someone with in the project or should we ask PyPI or should we choose a different name to publish with like ApachePySpark?) - Windows support and or testing ( SPARK-18136 ) - investigate details of wheel caching and see if we can avoid cleaning the wheel cache during our test - consider how we want to number our dev/snapshot versions Explicitly out of scope: - Using pip installed PySpark to start a standalone cluster - Using pip installed PySpark for non-Python Spark programs *I've done some work to test release-build locally but as a non-committer I've just done local testing. ## How was this patch tested? Automated testing with virtualenv, manual testing with conda, a system wide install, and YARN integration. release-build changes tested locally as a non-committer (no testing of upload artifacts to Apache staging websites) Author: Holden Karau <holden@us.ibm.com> Author: Juliet Hougland <juliet@cloudera.com> Author: Juliet Hougland <not@myemail.com> Closes #15659 from holdenk/SPARK-1267-pip-install-pyspark.
* [SPARK-18461][DOCS][STRUCTUREDSTREAMING] Added more information about ↵Tathagata Das2016-11-161-3/+179
| | | | | | | | | | | | monitoring streaming queries ## What changes were proposed in this pull request? <img width="941" alt="screen shot 2016-11-15 at 6 27 32 pm" src="https://cloud.githubusercontent.com/assets/663212/20332521/4190b858-ab61-11e6-93a6-4bdc05105ed9.png"> <img width="940" alt="screen shot 2016-11-15 at 6 27 45 pm" src="https://cloud.githubusercontent.com/assets/663212/20332525/44a0d01e-ab61-11e6-8668-47f925490d4f.png"> Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #15897 from tdas/SPARK-18461.
* [SPARK-18459][SPARK-18460][STRUCTUREDSTREAMING] Rename triggerId to batchId ↵Tathagata Das2016-11-166-17/+35
| | | | | | | | | | | | | | | | | and add triggerDetails to json in StreamingQueryStatus ## What changes were proposed in this pull request? SPARK-18459: triggerId seems like a number that should be increasing with each trigger, whether or not there is data in it. However, actually, triggerId increases only where there is a batch of data in a trigger. So its better to rename it to batchId. SPARK-18460: triggerDetails was missing from json representation. Fixed it. ## How was this patch tested? Updated existing unit tests. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #15895 from tdas/SPARK-18459.
* [SPARK-18415][SQL] Weird Plan Output when CTE used in RunnableCommandgatorsmile2016-11-162-1/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ### What changes were proposed in this pull request? Currently, when CTE is used in RunnableCommand, the Analyzer does not replace the logical node `With`. The child plan of RunnableCommand is not resolved. Thus, the output of the `With` plan node looks very confusing. For example, ``` sql( """ |CREATE VIEW cte_view AS |WITH w AS (SELECT 1 AS n), cte1 (select 2), cte2 as (select 3) |SELECT n FROM w """.stripMargin).explain() ``` The output is like ``` ExecutedCommand +- CreateViewCommand `cte_view`, WITH w AS (SELECT 1 AS n), cte1 (select 2), cte2 as (select 3) SELECT n FROM w, false, false, PersistedView +- 'With [(w,SubqueryAlias w +- Project [1 AS n#16] +- OneRowRelation$ ), (cte1,'SubqueryAlias cte1 +- 'Project [unresolvedalias(2, None)] +- OneRowRelation$ ), (cte2,'SubqueryAlias cte2 +- 'Project [unresolvedalias(3, None)] +- OneRowRelation$ )] +- 'Project ['n] +- 'UnresolvedRelation `w` ``` After the fix, the output is as shown below. ``` ExecutedCommand +- CreateViewCommand `cte_view`, WITH w AS (SELECT 1 AS n), cte1 (select 2), cte2 as (select 3) SELECT n FROM w, false, false, PersistedView +- CTE [w, cte1, cte2] : :- SubqueryAlias w : : +- Project [1 AS n#16] : : +- OneRowRelation$ : :- 'SubqueryAlias cte1 : : +- 'Project [unresolvedalias(2, None)] : : +- OneRowRelation$ : +- 'SubqueryAlias cte2 : +- 'Project [unresolvedalias(3, None)] : +- OneRowRelation$ +- 'Project ['n] +- 'UnresolvedRelation `w` ``` BTW, this PR also fixes the output of the view type. ### How was this patch tested? Manual Author: gatorsmile <gatorsmile@gmail.com> Closes #15854 from gatorsmile/cteName.
* [SPARK-18420][BUILD] Fix the errors caused by lint check in JavaXianyang Liu2016-11-169-9/+25
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Small fix, fix the errors caused by lint check in Java - Clear unused objects and `UnusedImports`. - Add comments around the method `finalize` of `NioBufferedFileInputStream`to turn off checkstyle. - Cut the line which is longer than 100 characters into two lines. ## How was this patch tested? Travis CI. ``` $ build/mvn -T 4 -q -DskipTests -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install $ dev/lint-java ``` Before: ``` Checkstyle checks failed at following occurrences: [ERROR] src/main/java/org/apache/spark/network/util/TransportConf.java:[21,8] (imports) UnusedImports: Unused import - org.apache.commons.crypto.cipher.CryptoCipherFactory. [ERROR] src/test/java/org/apache/spark/network/sasl/SparkSaslSuite.java:[516,5] (modifier) RedundantModifier: Redundant 'public' modifier. [ERROR] src/main/java/org/apache/spark/io/NioBufferedFileInputStream.java:[133] (coding) NoFinalizer: Avoid using finalizer method. [ERROR] src/main/java/org/apache/spark/sql/catalyst/expressions/UnsafeMapData.java:[71] (sizes) LineLength: Line is longer than 100 characters (found 113). [ERROR] src/main/java/org/apache/spark/sql/catalyst/expressions/UnsafeArrayData.java:[112] (sizes) LineLength: Line is longer than 100 characters (found 110). [ERROR] src/test/java/org/apache/spark/sql/catalyst/expressions/HiveHasherSuite.java:[31,17] (modifier) ModifierOrder: 'static' modifier out of order with the JLS suggestions. [ERROR]src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java:[64] (sizes) LineLength: Line is longer than 100 characters (found 103). [ERROR] src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java:[22,8] (imports) UnusedImports: Unused import - org.apache.spark.ml.linalg.Vectors. [ERROR] src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java:[51] (regexp) RegexpSingleline: No trailing whitespace allowed. ``` After: ``` $ build/mvn -T 4 -q -DskipTests -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install $ dev/lint-java Using `mvn` from path: /home/travis/build/ConeyLiu/spark/build/apache-maven-3.3.9/bin/mvn Checkstyle checks passed. ``` Author: Xianyang Liu <xyliu0530@icloud.com> Closes #15865 from ConeyLiu/master.
* [SPARK-18446][ML][DOCS] Add links to API docs for ML algosZheng RuiFeng2016-11-163-0/+81
| | | | | | | | | | | ## What changes were proposed in this pull request? Add links to API docs for ML algos ## How was this patch tested? Manual checking for the API links Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15890 from zhengruifeng/algo_link.
* [SPARK-18434][ML] Add missing ParamValidations for ML algosZheng RuiFeng2016-11-166-10/+22
| | | | | | | | | | | ## What changes were proposed in this pull request? Add missing ParamValidations for ML algos ## How was this patch tested? existing tests Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15881 from zhengruifeng/arg_checking.
* [MINOR][DOC] Fix typos in the 'configuration', 'monitoring' and ↵Weiqing Yang2016-11-163-5/+5
| | | | | | | | | | | | | | | 'sql-programming-guide' documentation ## What changes were proposed in this pull request? Fix typos in the 'configuration', 'monitoring' and 'sql-programming-guide' documentation. ## How was this patch tested? Manually. Author: Weiqing Yang <yangweiqing001@gmail.com> Closes #15886 from weiqingy/fixTypo.
* [SPARK-18410][STREAMING] Add structured kafka exampleuncleGen2016-11-163-0/+271
| | | | | | | | | | | | ## What changes were proposed in this pull request? This PR provides structured kafka wordcount examples ## How was this patch tested? Author: uncleGen <hustyugm@gmail.com> Closes #15849 from uncleGen/SPARK-18410.
* [SPARK-18400][STREAMING] NPE when resharding Kinesis StreamSean Owen2016-11-161-19/+23
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Avoid NPE in KinesisRecordProcessor when shutdown happens without successful init ## How was this patch tested? Existing tests Author: Sean Owen <sowen@cloudera.com> Closes #15882 from srowen/SPARK-18400.
* [DOC][MINOR] Kafka doc: breakup into linesLiwei Lin2016-11-161-0/+1
| | | | | | | | | | | | | | ## Before ![before](https://cloud.githubusercontent.com/assets/15843379/20340231/99b039fe-ac1b-11e6-9ba9-b44582427459.png) ## After ![after](https://cloud.githubusercontent.com/assets/15843379/20340236/9d5796e2-ac1b-11e6-92bb-6da40ba1a383.png) Author: Liwei Lin <lwlin7@gmail.com> Closes #15903 from lw-lin/kafka-doc-lines.
* [SPARK-18433][SQL] Improve DataSource option keys to be more case-insensitiveDongjoon Hyun2016-11-1618-49/+133
| | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR aims to improve DataSource option keys to be more case-insensitive DataSource partially use CaseInsensitiveMap in code-path. For example, the following fails to find url. ```scala val df = spark.createDataFrame(sparkContext.parallelize(arr2x2), schema2) df.write.format("jdbc") .option("UrL", url1) .option("dbtable", "TEST.SAVETEST") .options(properties.asScala) .save() ``` This PR makes DataSource options to use CaseInsensitiveMap internally and also makes DataSource to use CaseInsensitiveMap generally except `InMemoryFileIndex` and `InsertIntoHadoopFsRelationCommand`. We can not pass them CaseInsensitiveMap because they creates new case-sensitive HadoopConfs by calling newHadoopConfWithOptions(options) inside. ## How was this patch tested? Pass the Jenkins test with newly added test cases. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #15884 from dongjoon-hyun/SPARK-18433.
* [SPARK-18438][SPARKR][ML] spark.mlp should support RFormula.Yanbo Liang2016-11-164-60/+96
| | | | | | | | | | | | | ## What changes were proposed in this pull request? ```spark.mlp``` should support ```RFormula``` like other ML algorithm wrappers. BTW, I did some cleanup and improvement for ```spark.mlp```. ## How was this patch tested? Unit tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #15883 from yanboliang/spark-18438.
* [SPARK-18377][SQL] warehouse path should be a static confWenchen Fan2016-11-157-209/+142
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? it's weird that every session can set its own warehouse path at runtime, we should forbid it and make it a static conf. ## How was this patch tested? existing tests. Author: Wenchen Fan <wenchen@databricks.com> Closes #15825 from cloud-fan/warehouse.
* [SPARK-18300][SQL] Fix scala 2.10 build for FoldablePropagationHerman van Hovell2016-11-151-6/+27
| | | | | | | | | | | | ## What changes were proposed in this pull request? Commit https://github.com/apache/spark/commit/f14ae4900ad0ed66ba36108b7792d56cd6767a69 broke the scala 2.10 build. This PR fixes this by simplifying the used pattern match. ## How was this patch tested? Tested building manually. Ran `build/sbt -Dscala-2.10 -Pscala-2.10 package`. Author: Herman van Hovell <hvanhovell@databricks.com> Closes #15891 from hvanhovell/SPARK-18300-scala-2.10.
* [SPARK-17732][SQL] ALTER TABLE DROP PARTITION should support comparatorsDongjoon Hyun2016-11-157-24/+185
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR aims to support `comparators`, e.g. '<', '<=', '>', '>=', again in Apache Spark 2.0 for backward compatibility. **Spark 1.6** ``` scala scala> sql("CREATE TABLE sales(id INT) PARTITIONED BY (country STRING, quarter STRING)") res0: org.apache.spark.sql.DataFrame = [result: string] scala> sql("ALTER TABLE sales DROP PARTITION (country < 'KR')") res1: org.apache.spark.sql.DataFrame = [result: string] ``` **Spark 2.0** ``` scala scala> sql("CREATE TABLE sales(id INT) PARTITIONED BY (country STRING, quarter STRING)") res0: org.apache.spark.sql.DataFrame = [] scala> sql("ALTER TABLE sales DROP PARTITION (country < 'KR')") org.apache.spark.sql.catalyst.parser.ParseException: mismatched input '<' expecting {')', ','}(line 1, pos 42) ``` After this PR, it's supported. ## How was this patch tested? Pass the Jenkins test with a newly added testcase. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #15704 from dongjoon-hyun/SPARK-17732-2.
* [SPARK-18423][STREAMING] ReceiverTracker should close checkpoint dir when ↵hyukjinkwon2016-11-151-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | stopped even if it was not started ## What changes were proposed in this pull request? Several tests are being failed on Windows due to the failure of removing the checkpoint dir between each tests. This is caused by not closed file in `ReceiverTracker`. When it is not started, it does not close it even if `stop()` is called. ``` Test org.apache.spark.streaming.JavaAPISuite.testCheckpointMasterRecovery started Test org.apache.spark.streaming.JavaAPISuite.testCheckpointMasterRecovery failed: java.io.IOException: Failed to delete: C:\projects\spark\target\tmp\1478983663710-0, took 3.828 sec at org.apache.spark.util.Utils$.deleteRecursively(Utils.scala:1010) at org.apache.spark.util.Utils.deleteRecursively(Utils.scala) at org.apache.spark.streaming.JavaAPISuite.testCheckpointMasterRecovery(JavaAPISuite.java:1809) ... ``` ``` - mapWithState - basic operations with simple API (7 seconds, 640 milliseconds) Exception encountered when attempting to run a suite with class name: org.apache.spark.streaming.MapWithStateSuite *** ABORTED *** (12 seconds, 688 milliseconds) java.io.IOException: Failed to delete: C:\projects\spark\streaming\checkpoint\spark-b8486e2b-6468-4e6f-bb24-88277d2c033c ... ``` ## How was this patch tested? Tests in `JavaAPISuite` and `MapWithStateSuite`. Manually tested via AppVeyor: **Before** - `org.apache.spark.streaming.JavaAPISuite` Build: https://ci.appveyor.com/project/spark-test/spark/build/71-MapWithStateSuite-1 Diff: https://github.com/apache/spark/compare/master...spark-test:188c828e682ec45b75d15c3dfc782bcdc8ce024c - `org.apache.spark.streaming.MapWithStateSuite` Build: https://ci.appveyor.com/project/spark-test/spark/build/72-MapWithStateSuite-1 Diff: https://github.com/apache/spark/compare/master...spark-test:8f6945d0ccde022a23d3848f6b7fe6da1e7c902e **After** - `org.apache.spark.streaming.JavaAPISuite` Build started: [Streaming] `org.apache.spark.streaming.JavaAPISuite` [![PR-15867](https://ci.appveyor.com/api/projects/status/github/spark-test/spark?branch=3D74F2D5-B0D5-4E1D-874C-685AE694FD37&svg=true)](https://ci.appveyor.com/project/spark-test/spark/branch/3D74F2D5-B0D5-4E1D-874C-685AE694FD37) Diff: https://github.com/apache/spark/compare/master...spark-test:3D74F2D5-B0D5-4E1D-874C-685AE694FD37 - `org.apache.spark.streaming.MapWithStateSuite` Build started: [Streaming] `org.apache.spark.streaming.MapWithStateSuite` [![PR-15867](https://ci.appveyor.com/api/projects/status/github/spark-test/spark?branch=C8E88B64-49F0-4157-9AFA-FC3ACC442351&svg=true)](https://ci.appveyor.com/project/spark-test/spark/branch/C8E88B64-49F0-4157-9AFA-FC3ACC442351) Diff: https://github.com/apache/spark/compare/master...spark-test:C8E88B64-49F0-4157-9AFA-FC3ACC442351 Author: hyukjinkwon <gurwls223@gmail.com> Closes #15867 from HyukjinKwon/SPARK-18423.
* [SPARK-18440][STRUCTURED STREAMING] Pass correct query execution to ↵Tathagata Das2016-11-154-12/+79
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | FileFormatWriter ## What changes were proposed in this pull request? SPARK-18012 refactored the file write path in FileStreamSink using FileFormatWriter which always uses the default non-streaming QueryExecution to perform the writes. This is wrong for FileStreamSink, because the streaming QueryExecution (i.e. IncrementalExecution) should be used for correctly incrementalizing aggregation. The addition of watermarks in SPARK-18124, file stream sink should logically supports aggregation + watermark + append mode. But actually it fails with ``` 16:23:07.389 ERROR org.apache.spark.sql.execution.streaming.StreamExecution: Query query-0 terminated with error java.lang.AssertionError: assertion failed: No plan for EventTimeWatermark timestamp#7: timestamp, interval 10 seconds +- LocalRelation [timestamp#7] at scala.Predef$.assert(Predef.scala:170) at org.apache.spark.sql.catalyst.planning.QueryPlanner.plan(QueryPlanner.scala:92) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2$$anonfun$apply$2.apply(QueryPlanner.scala:77) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2$$anonfun$apply$2.apply(QueryPlanner.scala:74) at scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:157) at scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:157) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157) at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1336) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2.apply(QueryPlanner.scala:74) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2.apply(QueryPlanner.scala:66) at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434) at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440) at org.apache.spark.sql.catalyst.planning.QueryPlanner.plan(QueryPlanner.scala:92) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2$$anonfun$apply$2.apply(QueryPlanner.scala:77) at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$2$$anonfun$apply$2.apply(QueryPlanner.scala:74) ``` This PR fixes it by passing the correct query execution. ## How was this patch tested? New unit test Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #15885 from tdas/SPARK-18440.
* [SPARK-18417][YARN] Define 'spark.yarn.am.port' in yarn config objectWeiqing Yang2016-11-152-1/+6
| | | | | | | | | | | | ## What changes were proposed in this pull request? This PR is to define 'spark.yarn.am.port' in yarn config.scala just like other Yarn configurations. That makes code easier to maintain. ## How was this patch tested? Build passed & tested some Yarn unit tests. Author: Weiqing Yang <yangweiqing001@gmail.com> Closes #15858 from weiqingy/yarn.
* [SPARK-18337] Complete mode memory sinks should be able to recover from ↵Burak Yavuz2016-11-152-2/+69
| | | | | | | | | | | | | | | | checkpoints ## What changes were proposed in this pull request? It would be nice if memory sinks can also recover from checkpoints. For correctness reasons, the only time we should support it is in `Complete` OutputMode. We can support this in CompleteMode, because the output of the StateStore is already persisted in the checkpoint directory. ## How was this patch tested? Unit test Author: Burak Yavuz <brkyvz@gmail.com> Closes #15801 from brkyvz/mem-stream.
* [SPARK-13027][STREAMING] Added batch time as a parameter to updateStateByKeyAaditya Ramesh2016-11-154-20/+126
| | | | | | | | Added RDD batch time as an input parameter to the update function in updateStateByKey. Author: Aaditya Ramesh <aramesh@conviva.com> Closes #11122 from aramesh117/SPARK-13027.
* [SPARK-18379][SQL] Make the parallelism of parallelPartitionDiscovery ↵genmao.ygm2016-11-152-1/+14
| | | | | | | | | | | | | | | | | configurable. ## What changes were proposed in this pull request? The largest parallelism in PartitioningAwareFileIndex #listLeafFilesInParallel() is 10000 in hard code. We may need to make this number configurable. And in PR, I reduce it to 100. ## How was this patch tested? Existing ut. Author: genmao.ygm <genmao.ygm@genmaoygmdeMacBook-Air.local> Author: dylon <hustyugm@gmail.com> Closes #15829 from uncleGen/SPARK-18379.
* [SPARK-18300][SQL] Do not apply foldable propagation with expand as a child.Herman van Hovell2016-11-154-31/+67
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? The `FoldablePropagation` optimizer rule, pulls foldable values out from under an `Expand`. This breaks the `Expand` in two ways: - It rewrites the output attributes of the `Expand`. We explicitly define output attributes for `Expand`, these are (unfortunately) considered as part of the expressions of the `Expand` and can be rewritten. - Expand can actually change the column (it will typically re-use the attributes or the underlying plan). This means that we cannot safely propagate the expressions from under an `Expand`. This PR fixes this and (hopefully) other issues by explicitly whitelisting allowed operators. ## How was this patch tested? Added tests to `FoldablePropagationSuite` and to `SQLQueryTestSuite`. Author: Herman van Hovell <hvanhovell@databricks.com> Closes #15857 from hvanhovell/SPARK-18300.
* [SPARK-18427][DOC] Update docs of mllib.KMeansZheng RuiFeng2016-11-152-6/+3
| | | | | | | | | | | | ## What changes were proposed in this pull request? 1,Remove `runs` from docs of mllib.KMeans 2,Add notes for `k` according to comments in sources ## How was this patch tested? existing tests Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15873 from zhengruifeng/update_doc_mllib_kmeans.
* [SPARK-18232][MESOS] Support CNIMichael Gummelt2016-11-147-101/+131
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Adds support for CNI-isolated containers ## How was this patch tested? I launched SparkPi both with and without `spark.mesos.network.name`, and verified the job completed successfully. Author: Michael Gummelt <mgummelt@mesosphere.io> Closes #15740 from mgummelt/spark-342-cni.
* [SPARK-18430][SQL] Fixed Exception Messages when Hitting an Invocation ↵gatorsmile2016-11-143-1/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Exception of Function Lookup ### What changes were proposed in this pull request? When the exception is an invocation exception during function lookup, we return a useless/confusing error message: For example, ```Scala df.selectExpr("concat_ws()") ``` Below is the error message we got: ``` null; line 1 pos 0 org.apache.spark.sql.AnalysisException: null; line 1 pos 0 ``` To get the meaningful error message, we need to get the cause. The fix is exactly the same as what we did in https://github.com/apache/spark/pull/12136. After the fix, the message we got is the exception issued in the constuctor of function implementation: ``` requirement failed: concat_ws requires at least one argument.; line 1 pos 0 org.apache.spark.sql.AnalysisException: requirement failed: concat_ws requires at least one argument.; line 1 pos 0 ``` ### How was this patch tested? Added test cases. Author: gatorsmile <gatorsmile@gmail.com> Closes #15878 from gatorsmile/functionNotFound.
* [SPARK-18428][DOC] Update docs for GraphXZheng RuiFeng2016-11-141-33/+35
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? 1, Add link of `VertexRDD` and `EdgeRDD` 2, Notify in `Vertex and Edge RDDs` that not all methods are listed 3, `VertexID` -> `VertexId` ## How was this patch tested? No tests, only docs is modified Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15875 from zhengruifeng/update_graphop_doc.
* [SPARK-18124] Observed delay based Event Time WatermarksMichael Armbrust2016-11-1422-111/+597
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR adds a new method `withWatermark` to the `Dataset` API, which can be used specify an _event time watermark_. An event time watermark allows the streaming engine to reason about the point in time after which we no longer expect to see late data. This PR also has augmented `StreamExecution` to use this watermark for several purposes: - To know when a given time window aggregation is finalized and thus results can be emitted when using output modes that do not allow updates (e.g. `Append` mode). - To minimize the amount of state that we need to keep for on-going aggregations, by evicting state for groups that are no longer expected to change. Although, we do still maintain all state if the query requires (i.e. if the event time is not present in the `groupBy` or when running in `Complete` mode). An example that emits windowed counts of records, waiting up to 5 minutes for late data to arrive. ```scala df.withWatermark("eventTime", "5 minutes") .groupBy(window($"eventTime", "1 minute") as 'window) .count() .writeStream .format("console") .mode("append") // In append mode, we only output finalized aggregations. .start() ``` ### Calculating the watermark. The current event time is computed by looking at the `MAX(eventTime)` seen this epoch across all of the partitions in the query minus some user defined _delayThreshold_. An additional constraint is that the watermark must increase monotonically. Note that since we must coordinate this value across partitions occasionally, the actual watermark used is only guaranteed to be at least `delay` behind the actual event time. In some cases we may still process records that arrive more than delay late. This mechanism was chosen for the initial implementation over processing time for two reasons: - it is robust to downtime that could affect processing delay - it does not require syncing of time or timezones between the producer and the processing engine. ### Other notable implementation details - A new trigger metric `eventTimeWatermark` outputs the current value of the watermark. - We mark the event time column in the `Attribute` metadata using the key `spark.watermarkDelay`. This allows downstream operations to know which column holds the event time. Operations like `window` propagate this metadata. - `explain()` marks the watermark with a suffix of `-T${delayMs}` to ease debugging of how this information is propagated. - Currently, we don't filter out late records, but instead rely on the state store to avoid emitting records that are both added and filtered in the same epoch. ### Remaining in this PR - [ ] The test for recovery is currently failing as we don't record the watermark used in the offset log. We will need to do so to ensure determinism, but this is deferred until #15626 is merged. ### Other follow-ups There are some natural additional features that we should consider for future work: - Ability to write records that arrive too late to some external store in case any out-of-band remediation is required. - `Update` mode so you can get partial results before a group is evicted. - Other mechanisms for calculating the watermark. In particular a watermark based on quantiles would be more robust to outliers. Author: Michael Armbrust <michael@databricks.com> Closes #15702 from marmbrus/watermarks.
* [SPARK-17348][SQL] Incorrect results from subquery transformationNattavut Sutyanyong2016-11-143-9/+137
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Return an Analysis exception when there is a correlated non-equality predicate in a subquery and the correlated column from the outer reference is not from the immediate parent operator of the subquery. This PR prevents incorrect results from subquery transformation in such case. Test cases, both positive and negative tests, are added. ## How was this patch tested? sql/test, catalyst/test, hive/test, and scenarios that will produce incorrect results without this PR and product correct results when subquery transformation does happen. Author: Nattavut Sutyanyong <nsy.can@gmail.com> Closes #15763 from nsyca/spark-17348.
* [SPARK-11496][GRAPHX][FOLLOWUP] Add param checking for ↵Zheng RuiFeng2016-11-141-0/+7
| | | | | | | | | | | | | | runParallelPersonalizedPageRank ## What changes were proposed in this pull request? add the param checking to keep in line with other algos ## How was this patch tested? existing tests Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #15876 from zhengruifeng/param_check_runParallelPersonalizedPageRank.
* [SPARK-17510][STREAMING][KAFKA] config max rate on a per-partition basiscody koeninger2016-11-145-18/+131
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Allow configuration of max rate on a per-topicpartition basis. ## How was this patch tested? Unit tests. The reporter (Jeff Nadler) said he could test on his workload, so let's wait on that report. Author: cody koeninger <cody@koeninger.org> Closes #15132 from koeninger/SPARK-17510.
* [SPARK-18416][STRUCTURED STREAMING] Fixed temp file leak in state storeTathagata Das2016-11-142-5/+68
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? StateStore.get() causes temporary files to be created immediately, even if the store is not used to make updates for new version. The temp file is not closed as store.commit() is not called in those cases, thus keeping the output stream to temp file open forever. This PR fixes it by opening the temp file only when there are updates being made. ## How was this patch tested? New unit test Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #15859 from tdas/SPARK-18416.
* [SPARK-18432][DOC] Changed HDFS default block size from 64MB to 128MBNoritaka Sekiyama2016-11-142-5/+5
| | | | | | | | | Changed HDFS default block size from 64MB to 128MB. https://issues.apache.org/jira/browse/SPARK-18432 Author: Noritaka Sekiyama <moomindani@gmail.com> Closes #15879 from moomindani/SPARK-18432.
* [SPARK-18396][HISTORYSERVER] Duration" column makes search result confused, ↵WangTaoTheTonic2016-11-141-0/+3
| | | | | | | | | | | | | | | | | | | | | | | maybe we should make it unsearchable ## What changes were proposed in this pull request? When we search data in History Server, it will check if any columns contains the search string. Duration is represented as long value in table, so if we search simple string like "003", "111", the duration containing "003", ‘111“ will be showed, which make not much sense to users. We cannot simply transfer the long value to meaning format like "1 h", "3.2 min" because they are also used for sorting. Better way to handle it is ban "Duration" columns from searching. ## How was this patch tested manually tests. Before("local-1478225166651" pass the filter because its duration in long value, which is "257244245" contains search string "244"): ![before](https://cloud.githubusercontent.com/assets/5276001/20203166/f851ffc6-a7ff-11e6-8fe6-91a90ca92b23.jpg) After: ![after](https://cloud.githubusercontent.com/assets/5276001/20178646/2129fbb0-a78d-11e6-9edb-39f885ce3ed0.jpg) Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #15838 from WangTaoTheTonic/duration.
* [SPARK-18166][MLLIB] Fix Poisson GLM bug due to wrong requirement of ↵actuaryzhang2016-11-142-2/+47
| | | | | | | | | | | | | | | response values ## What changes were proposed in this pull request? The current implementation of Poisson GLM seems to allow only positive values. This is incorrect since the support of Poisson includes the origin. The bug is easily fixed by changing the test of the Poisson variable from 'require(y **>** 0.0' to 'require(y **>=** 0.0'. mengxr srowen Author: actuaryzhang <actuaryzhang10@gmail.com> Author: actuaryzhang <actuaryzhang@uber.com> Closes #15683 from actuaryzhang/master.
* [SPARK-18382][WEBUI] "run at null:-1" in UI when no file/line info in call ↵Sean Owen2016-11-141-2/+6
| | | | | | | | | | | | | | | | site info ## What changes were proposed in this pull request? Avoid reporting null/-1 file / line number in call sites if encountering StackTraceElement without this info ## How was this patch tested? Existing tests Author: Sean Owen <sowen@cloudera.com> Closes #15862 from srowen/SPARK-18382.
* [SPARK-18412][SPARKR][ML] Fix exception for some SparkR ML algorithms ↵Yanbo Liang2016-11-136-41/+68
| | | | | | | | | | | | | | | | | | | | training on libsvm data ## What changes were proposed in this pull request? * Fix the following exceptions which throws when ```spark.randomForest```(classification), ```spark.gbt```(classification), ```spark.naiveBayes``` and ```spark.glm```(binomial family) were fitted on libsvm data. ``` java.lang.IllegalArgumentException: requirement failed: If label column already exists, forceIndexLabel can not be set with true. ``` See [SPARK-18412](https://issues.apache.org/jira/browse/SPARK-18412) for more detail about how to reproduce this bug. * Refactor out ```getFeaturesAndLabels``` to RWrapperUtils, since lots of ML algorithm wrappers use this function. * Drop some unwanted columns when making prediction. ## How was this patch tested? Add unit test. Author: Yanbo Liang <ybliang8@gmail.com> Closes #15851 from yanboliang/spark-18412.
* [SPARK-18426][STRUCTURED STREAMING] Python Documentation Fix for Structured ↵Denny Lee2016-11-131-1/+1
| | | | | | | | | | | | | | | | | | | | | Streaming Programming Guide ## What changes were proposed in this pull request? Update the python section of the Structured Streaming Guide from .builder() to .builder ## How was this patch tested? Validated documentation and successfully running the test example. Please review https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark before opening a pull request. 'Builder' object is not callable object hence changed .builder() to .builder Author: Denny Lee <dennylee@gallifrey.local> Closes #15872 from dennyglee/master.
* [SPARK-18418] Fix flags for make_binary_release for hadoop profileHolden Karau2016-11-121-4/+4
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fix the flags used to specify the hadoop version ## How was this patch tested? Manually tested as part of https://github.com/apache/spark/pull/15659 by having the build succeed. cc joshrosen Author: Holden Karau <holden@us.ibm.com> Closes #15860 from holdenk/minor-fix-release-build-script.
* [SPARK-14077][ML][FOLLOW-UP] Minor refactor and cleanup for NaiveBayesYanbo Liang2016-11-122-39/+39
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? * Refactor out ```trainWithLabelCheck``` and make ```mllib.NaiveBayes``` call into it. * Avoid capturing the outer object for ```modelType```. * Move ```requireNonnegativeValues``` and ```requireZeroOneBernoulliValues``` to companion object. ## How was this patch tested? Existing tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #15826 from yanboliang/spark-14077-2.
* [SPARK-18375][SPARK-18383][BUILD][CORE] Upgrade netty to 4.0.42.FinalGuoqiang Li2016-11-127-6/+10
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? One of the important changes for 4.0.42.Final is "Support any FileRegion implementation when using epoll transport netty/netty#5825". In 4.0.42.Final, `MessageWithHeader` can work properly when `spark.[shuffle|rpc].io.mode` is set to epoll ## How was this patch tested? Existing tests Author: Guoqiang Li <witgo@qq.com> Closes #15830 from witgo/SPARK-18375_netty-4.0.42.
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