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* [SPARK-13214][DOCS] update dynamicAllocation documentationBill Chambers2016-02-051-2/+2
| | | | | | Author: Bill Chambers <bill@databricks.com> Closes #11094 from anabranch/dynamic-docs.
* [SPARK-12939][SQL] migrate encoder resolution logic to AnalyzerWenchen Fan2016-02-0512-104/+230
| | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-12939 Now we will catch `ObjectOperator` in `Analyzer` and resolve the `fromRowExpression/deserializer` inside it. Also update the `MapGroups` and `CoGroup` to pass in `dataAttributes`, so that we can correctly resolve value deserializer(the `child.output` contains both groupking key and values, which may mess things up if they have same-name attribtues). End-to-end tests are added. follow-ups: * remove encoders from typed aggregate expression. * completely remove resolve/bind in `ExpressionEncoder` Author: Wenchen Fan <wenchen@databricks.com> Closes #10852 from cloud-fan/bug.
* [SPARK-13166][SQL] Rename DataStreamReaderWriterSuite to ↵Shixiong Zhu2016-02-051-1/+1
| | | | | | | | | | DataFrameReaderWriterSuite A follow up PR for #11062 because it didn't rename the test suite. Author: Shixiong Zhu <shixiong@databricks.com> Closes #11096 from zsxwing/rename.
* [SPARK-13187][SQL] Add boolean/long/double options in DataFrameReader/WriterReynold Xin2016-02-043-0/+67
| | | | | | | | | | | | | | | | | | | This patch adds option function for boolean, long, and double types. This makes it slightly easier for Spark users to specify options without turning them into strings. Using the JSON data source as an example. Before this patch: ```scala sqlContext.read.option("primitivesAsString", "true").json("/path/to/json") ``` After this patch: Before this patch: ```scala sqlContext.read.option("primitivesAsString", true).json("/path/to/json") ``` Author: Reynold Xin <rxin@databricks.com> Closes #11072 from rxin/SPARK-13187.
* [SPARK-13208][CORE] Replace use of Pairs with Tuple2sJakob Odersky2016-02-044-7/+7
| | | | | | | | Another trivial deprecation fix for Scala 2.11 Author: Jakob Odersky <jakob@odersky.com> Closes #11089 from jodersky/SPARK-13208.
* [SPARK-12850][SQL] Support Bucket Pruning (Predicate Pushdown for Bucketed ↵gatorsmile2016-02-043-10/+245
| | | | | | | | | | | | | | | | | | | | Tables) JIRA: https://issues.apache.org/jira/browse/SPARK-12850 This PR is to support bucket pruning when the predicates are `EqualTo`, `EqualNullSafe`, `IsNull`, `In`, and `InSet`. Like HIVE, in this PR, the bucket pruning works when the bucketing key has one and only one column. So far, I do not find a way to verify how many buckets are actually scanned. However, I did verify it when doing the debug. Could you provide a suggestion how to do it properly? Thank you! cloud-fan yhuai rxin marmbrus BTW, we can add more cases to support complex predicate including `Or` and `And`. Please let me know if I should do it in this PR. Maybe we also need to add test cases to verify if bucket pruning works well for each data type. Author: gatorsmile <gatorsmile@gmail.com> Closes #10942 from gatorsmile/pruningBuckets.
* [SPARK-13052] waitingApps metric doesn't show the number of apps currently ↵Raafat Akkad2016-02-042-2/+2
| | | | | | | | in the WAITING state Author: Raafat Akkad <raafat.akkad@gmail.com> Closes #10959 from RaafatAkkad/master.
* [HOTFIX] Fix style violation caused by c756bdaAndrew Or2016-02-041-2/+3
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* [SPARK-13195][STREAMING] Fix NoSuchElementException when a state is not set ↵Shixiong Zhu2016-02-042-1/+7
| | | | | | | | | | but timeoutThreshold is defined Check the state Existence before calling get. Author: Shixiong Zhu <shixiong@databricks.com> Closes #11081 from zsxwing/SPARK-13195.
* [SPARK-13079][SQL] InMemoryCatalog follow-upsAndrew Or2016-02-042-5/+22
| | | | | | | | This patch incorporates review feedback from #11069, which is already merged. Author: Andrew Or <andrew@databricks.com> Closes #11080 from andrewor14/catalog-follow-ups.
* [SPARK-12330][MESOS][HOTFIX] Rename timeout configAndrew Or2016-02-041-2/+2
| | | | | | The config already describes time and accepts a general format that is not restricted to ms. This commit renames the internal config to use a format that's consistent in Spark.
* [SPARK-13168][SQL] Collapse adjacent repartition operatorsJosh Rosen2016-02-046-10/+33
| | | | | | | | Spark SQL should collapse adjacent `Repartition` operators and only keep the last one. Author: Josh Rosen <joshrosen@databricks.com> Closes #11064 from JoshRosen/collapse-repartition.
* MAINTENANCE: Automated closing of pull requests.Andrew Or2016-02-040-0/+0
| | | | | | | | | | | | | | | | | This commit exists to close the following pull requests on Github: Closes #7971 (requested by yhuai) Closes #8539 (requested by srowen) Closes #8746 (requested by yhuai) Closes #9288 (requested by andrewor14) Closes #9321 (requested by andrewor14) Closes #9935 (requested by JoshRosen) Closes #10442 (requested by andrewor14) Closes #10585 (requested by srowen) Closes #10785 (requested by srowen) Closes #10832 (requested by andrewor14) Closes #10941 (requested by marmbrus) Closes #11024 (requested by andrewor14)
* [SPARK-13053][TEST] Unignore tests in InternalAccumulatorSuiteAndrew Or2016-02-042-78/+102
| | | | | | | | | | These were ignored because they are incorrectly written; they don't actually trigger stage retries, which is what the tests are testing. These tests are now rewritten to induce stage retries through fetch failures. Note: there were 2 tests before and now there's only 1. What happened? It turns out that the case where we only resubmit a subset of of the original missing partitions is very difficult to simulate in tests without potentially introducing flakiness. This is because the `DAGScheduler` removes all map outputs associated with a given executor when this happens, and we will need multiple executors to trigger this case, and sometimes the scheduler still removes map outputs from all executors. Author: Andrew Or <andrew@databricks.com> Closes #10969 from andrewor14/unignore-accum-test.
* [SPARK-13162] Standalone mode does not respect initial executorsAndrew Or2016-02-045-6/+34
| | | | | | | | Currently the Master would always set an application's initial executor limit to infinity. If the user specified `spark.dynamicAllocation.initialExecutors`, the config would not take effect. This is similar to #11047 but for standalone mode. Author: Andrew Or <andrew@databricks.com> Closes #11054 from andrewor14/standalone-da-initial.
* [SPARK-13164][CORE] Replace deprecated synchronized buffer in coreHolden Karau2016-02-044-39/+40
| | | | | | | | Building with scala 2.11 results in the warning trait SynchronizedBuffer in package mutable is deprecated: Synchronization via traits is deprecated as it is inherently unreliable. Consider java.util.concurrent.ConcurrentLinkedQueue as an alternative. Investigation shows we are already using ConcurrentLinkedQueue in other locations so switch our uses of SynchronizedBuffer to ConcurrentLinkedQueue. Author: Holden Karau <holden@us.ibm.com> Closes #11059 from holdenk/SPARK-13164-replace-deprecated-synchronized-buffer-in-core.
* [SPARK-12330][MESOS] Fix mesos coarse mode cleanupCharles Allen2016-02-042-2/+45
| | | | | | | | | | | | | | In the current implementation the mesos coarse scheduler does not wait for the mesos tasks to complete before ending the driver. This causes a race where the task has to finish cleaning up before the mesos driver terminates it with a SIGINT (and SIGKILL after 3 seconds if the SIGINT doesn't work). This PR causes the mesos coarse scheduler to wait for the mesos tasks to finish (with a timeout defined by `spark.mesos.coarse.shutdown.ms`) This PR also fixes a regression caused by [SPARK-10987] whereby submitting a shutdown causes a race between the local shutdown procedure and the notification of the scheduler driver disconnection. If the scheduler driver disconnection wins the race, the coarse executor incorrectly exits with status 1 (instead of the proper status 0) With this patch the mesos coarse scheduler terminates properly, the executors clean up, and the tasks are reported as `FINISHED` in the Mesos console (as opposed to `KILLED` in < 1.6 or `FAILED` in 1.6 and later) Author: Charles Allen <charles@allen-net.com> Closes #10319 from drcrallen/SPARK-12330.
* [SPARK-12828][SQL] Natural join follow-upReynold Xin2016-02-033-12/+17
| | | | | | | | This is a small addendum to #10762 to make the code more robust again future changes. Author: Reynold Xin <rxin@databricks.com> Closes #11070 from rxin/SPARK-12828-natural-join.
* [SPARK-13113] [CORE] Remove unnecessary bit operation when decoding page numberLiang-Chi Hsieh2016-02-031-1/+1
| | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-13113 As we shift bits right, looks like the bitwise AND operation is unnecessary. Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #11002 from viirya/improve-decodepagenumber.
* [ML][DOC] fix wrong api link in ml onevsrestYuhao Yang2016-02-031-1/+1
| | | | | | | | minor fix for api link in ml onevsrest Author: Yuhao Yang <hhbyyh@gmail.com> Closes #11068 from hhbyyh/onevsrestDoc.
* [SPARK-12828][SQL] add natural join supportDaoyuan Wang2016-02-0311-11/+198
| | | | | | | | | Jira: https://issues.apache.org/jira/browse/SPARK-12828 Author: Daoyuan Wang <daoyuan.wang@intel.com> Closes #10762 from adrian-wang/naturaljoin.
* [SPARK-13079][SQL] Extend and implement InMemoryCatalogAndrew Or2016-02-033-47/+328
| | | | | | | | | | | | This is a step towards consolidating `SQLContext` and `HiveContext`. This patch extends the existing Catalog API added in #10982 to include methods for handling table partitions. In particular, a partition is identified by `PartitionSpec`, which is just a `Map[String, String]`. The Catalog is still not used by anything yet, but its API is now more or less complete and an implementation is fully tested. About 200 lines are test code. Author: Andrew Or <andrew@databricks.com> Closes #11069 from andrewor14/catalog.
* [SPARK-13152][CORE] Fix task metrics deprecation warningHolden Karau2016-02-036-10/+15
| | | | | | | | | | | | Make an internal non-deprecated version of incBytesRead and incRecordsRead so we don't have unecessary deprecation warnings in our build. Right now incBytesRead and incRecordsRead are marked as deprecated and for internal use only. We should make private[spark] versions which are not deprecated and switch to those internally so as to not clutter up the warning messages when building. cc andrewor14 who did the initial deprecation Author: Holden Karau <holden@us.ibm.com> Closes #11056 from holdenk/SPARK-13152-fix-task-metrics-deprecation-warnings.
* [SPARK-13131] [SQL] Use best and average time in benchmarkDavies Liu2016-02-032-103/+89
| | | | | | | | | | | | | | | | | | | | | Best time is stabler than average time, also added a column for nano seconds per row (which could be used to estimate contributions of each components in a query). Having best time and average time together for more information (we can see kind of variance). rate, time per row and relative are all calculated using best time. The result looks like this: ``` Intel(R) Core(TM) i7-4558U CPU 2.80GHz rang/filter/sum: Best/Avg Time(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------- rang/filter/sum codegen=false 14332 / 16646 36.0 27.8 1.0X rang/filter/sum codegen=true 845 / 940 620.0 1.6 17.0X ``` Author: Davies Liu <davies@databricks.com> Closes #11018 from davies/gen_bench.
* [SPARK-13166][SQL] Remove DataStreamReader/WriterReynold Xin2016-02-038-315/+86
| | | | | | | | | | | | | | They seem redundant and we can simply use DataFrameReader/Writer. The new usage looks like: ```scala val df = sqlContext.read.stream("...") val handle = df.write.stream("...") handle.stop() ``` Author: Reynold Xin <rxin@databricks.com> Closes #11062 from rxin/SPARK-13166.
* [SPARK-3611][WEB UI] Show number of cores for each executor in application ↵Alex Bozarth2016-02-034-2/+12
| | | | | | | | | | web UI Added a Cores column in the Executors UI Author: Alex Bozarth <ajbozart@us.ibm.com> Closes #11039 from ajbozarth/spark3611.
* [SPARK-13157] [SQL] Support any kind of input for SQL commands.Herman van Hovell2016-02-034-6/+46
| | | | | | | | | | | | The ```SparkSqlLexer``` currently swallows characters which have not been defined in the grammar. This causes problems with SQL commands, such as: ```add jar file:///tmp/ab/TestUDTF.jar```. In this example the `````` is swallowed. This PR adds an extra Lexer rule to handle such input, and makes a tiny modification to the ```ASTNode```. cc davies liancheng Author: Herman van Hovell <hvanhovell@questtec.nl> Closes #11052 from hvanhovell/SPARK-13157.
* [SPARK-12798] [SQL] generated BroadcastHashJoinDavies Liu2016-02-037-20/+169
| | | | | | | | A row from stream side could match multiple rows on build side, the loop for these matched rows should not be interrupted when emitting a row, so we buffer the output rows in a linked list, check the termination condition on producer loop (for example, Range or Aggregate). Author: Davies Liu <davies@databricks.com> Closes #10989 from davies/gen_join.
* [SPARK-12739][STREAMING] Details of batch in Streaming tab uses two Duration ↵Mario Briggs2016-02-032-4/+5
| | | | | | | | | | | columns I have clearly prefix the two 'Duration' columns in 'Details of Batch' Streaming tab as 'Output Op Duration' and 'Job Duration' Author: Mario Briggs <mario.briggs@in.ibm.com> Author: mariobriggs <mariobriggs@in.ibm.com> Closes #11022 from mariobriggs/spark-12739.
* [SPARK-12957][SQL] Initial support for constraint propagation in SparkSQLSameer Agarwal2016-02-024-7/+302
| | | | | | | | | | | | | | | Based on the semantics of a query, we can derive a number of data constraints on output of each (logical or physical) operator. For instance, if a filter defines `‘a > 10`, we know that the output data of this filter satisfies 2 constraints: 1. `‘a > 10` 2. `isNotNull(‘a)` This PR proposes a possible way of keeping track of these constraints and propagating them in the logical plan, which can then help us build more advanced optimizations (such as pruning redundant filters, optimizing joins, among others). We define constraints as a set of (implicitly conjunctive) expressions. For e.g., if a filter operator has constraints = `Set(‘a > 10, ‘b < 100)`, it’s implied that the outputs satisfy both individual constraints (i.e., `‘a > 10` AND `‘b < 100`). Design Document: https://docs.google.com/a/databricks.com/document/d/1WQRgDurUBV9Y6CWOBS75PQIqJwT-6WftVa18xzm7nCo/edit?usp=sharing Author: Sameer Agarwal <sameer@databricks.com> Closes #10844 from sameeragarwal/constraints.
* [SPARK-13147] [SQL] improve readability of generated codeDavies Liu2016-02-027-39/+63
| | | | | | | | | | | 1. try to avoid the suffix (unique id) 2. remove the comment if there is no code generated. 3. re-arrange the order of functions 4. trop the new line for inlined blocks. Author: Davies Liu <davies@databricks.com> Closes #11032 from davies/better_suffix.
* [SPARK-7997][CORE] Add rpcEnv.awaitTermination() back to SparkEnvShixiong Zhu2016-02-022-2/+3
| | | | | | | | | | | | `rpcEnv.awaitTermination()` was not added in #10854 because some Streaming Python tests hung forever. This patch fixed the hung issue and added rpcEnv.awaitTermination() back to SparkEnv. Previously, Streaming Kafka Python tests shutdowns the zookeeper server before stopping StreamingContext. Then when stopping StreamingContext, KafkaReceiver may be hung due to https://issues.apache.org/jira/browse/KAFKA-601, hence, some thread of RpcEnv's Dispatcher cannot exit and rpcEnv.awaitTermination is hung.The patch just changed the shutdown order to fix it. Author: Shixiong Zhu <shixiong@databricks.com> Closes #11031 from zsxwing/awaitTermination.
* [SPARK-12732][ML] bug fix in linear regression trainImran Younus2016-02-022-25/+146
| | | | | | | | Fixed the bug in linear regression train for the case when the target variable is constant. The two cases for `fitIntercept=true` or `fitIntercept=false` should be treated differently. Author: Imran Younus <iyounus@us.ibm.com> Closes #10702 from iyounus/SPARK-12732_bug_fix_in_linear_regression_train.
* [SPARK-12951] [SQL] support spilling in generated aggregateDavies Liu2016-02-021-30/+142
| | | | | | | | | | | | This PR add spilling support for generated TungstenAggregate. If spilling happened, it's not that bad to do the iterator based sort-merge-aggregate (not generated). The changes will be covered by TungstenAggregationQueryWithControlledFallbackSuite Author: Davies Liu <davies@databricks.com> Closes #10998 from davies/gen_spilling.
* [SPARK-13122] Fix race condition in MemoryStore.unrollSafely()Adam Budde2016-02-021-5/+9
| | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-13122 A race condition can occur in MemoryStore's unrollSafely() method if two threads that return the same value for currentTaskAttemptId() execute this method concurrently. This change makes the operation of reading the initial amount of unroll memory used, performing the unroll, and updating the associated memory maps atomic in order to avoid this race condition. Initial proposed fix wraps all of unrollSafely() in a memoryManager.synchronized { } block. A cleaner approach might be introduce a mechanism that synchronizes based on task attempt ID. An alternative option might be to track unroll/pending unroll memory based on block ID rather than task attempt ID. Author: Adam Budde <budde@amazon.com> Closes #11012 from budde/master.
* [SPARK-12992] [SQL] Update parquet reader to support more types when ↵Nong Li2016-02-026-21/+424
| | | | | | | | | | | | | | | | | decoding to ColumnarBatch. This patch implements support for more types when doing the vectorized decode. There are a few more types remaining but they should be very straightforward after this. This code has a few copy and paste pieces but they are difficult to eliminate due to performance considerations. Specifically, this patch adds support for: - String, Long, Byte types - Dictionary encoding for those types. Author: Nong Li <nong@databricks.com> Closes #10908 from nongli/spark-12992.
* [SPARK-13020][SQL][TEST] fix random generator for map typeWenchen Fan2016-02-032-4/+25
| | | | | | | | | | when we generate map, we first randomly pick a length, then create a seq of key value pair with the expected length, and finally call `toMap`. However, `toMap` will remove all duplicated keys, which makes the actual map size much less than we expected. This PR fixes this problem by put keys in a set first, to guarantee we have enough keys to build a map with expected length. Author: Wenchen Fan <wenchen@databricks.com> Closes #10930 from cloud-fan/random-generator.
* [SPARK-13150] [SQL] disable two flaky testsDavies Liu2016-02-021-2/+4
| | | | | | Author: Davies Liu <davies@databricks.com> Closes #11037 from davies/disable_flaky.
* [DOCS] Update StructType.scalaKevin (Sangwoo) Kim2016-02-021-0/+1
| | | | | | | | | | | | The example will throw error like <console>:20: error: not found: value StructType Need to add this line: import org.apache.spark.sql.types._ Author: Kevin (Sangwoo) Kim <sangwookim.me@gmail.com> Closes #10141 from swkimme/patch-1.
* [SPARK-13121][STREAMING] java mapWithState mishandles scala OptionGabriele Nizzoli2016-02-021-1/+1
| | | | | | | | Already merged into 1.6 branch, this PR is to commit to master the same change Author: Gabriele Nizzoli <mail@nizzoli.net> Closes #11028 from gabrielenizzoli/patch-1.
* [SPARK-12913] [SQL] Improve performance of stat functionsDavies Liu2016-02-0214-755/+331
| | | | | | | | As benchmarked and discussed here: https://github.com/apache/spark/pull/10786/files#r50038294, benefits from codegen, the declarative aggregate function could be much faster than imperative one. Author: Davies Liu <davies@databricks.com> Closes #10960 from davies/stddev.
* [SPARK-13138][SQL] Add "logical" package prefix for ddl.scalaReynold Xin2016-02-021-6/+7
| | | | | | | | ddl.scala is defined in the execution package, and yet its reference of "UnaryNode" and "Command" are logical. This was fairly confusing when I was trying to understand the ddl code. Author: Reynold Xin <rxin@databricks.com> Closes #11021 from rxin/SPARK-13138.
* [SPARK-12711][ML] ML StopWordsRemover does not protect itself from column ↵Grzegorz Chilkiewicz2016-02-023-8/+19
| | | | | | | | | | | | name duplication Fixes problem and verifies fix by test suite. Also - adds optional parameter: nullable (Boolean) to: SchemaUtils.appendColumn and deduplicates SchemaUtils.appendColumn functions. Author: Grzegorz Chilkiewicz <grzegorz.chilkiewicz@codilime.com> Closes #10741 from grzegorz-chilkiewicz/master.
* [SPARK-13056][SQL] map column would throw NPE if value is nullDaoyuan Wang2016-02-022-6/+19
| | | | | | | | | | | | | | | Jira: https://issues.apache.org/jira/browse/SPARK-13056 Create a map like { "a": "somestring", "b": null} Query like SELECT col["b"] FROM t1; NPE would be thrown. Author: Daoyuan Wang <daoyuan.wang@intel.com> Closes #10964 from adrian-wang/npewriter.
* [SPARK-12631][PYSPARK][DOC] PySpark clustering parameter desc to consistent ↵Bryan Cutler2016-02-026-103/+228
| | | | | | | | | | format Part of task for [SPARK-11219](https://issues.apache.org/jira/browse/SPARK-11219) to make PySpark MLlib parameter description formatting consistent. This is for the clustering module. Author: Bryan Cutler <cutlerb@gmail.com> Closes #10610 from BryanCutler/param-desc-consistent-cluster-SPARK-12631.
* [SPARK-13114][SQL] Add a test for tokens more than the fields in schemahyukjinkwon2016-02-022-0/+18
| | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-13114 This PR adds a test for tokens more than the fields in schema. Author: hyukjinkwon <gurwls223@gmail.com> Closes #11020 from HyukjinKwon/SPARK-13114.
* [SPARK-13094][SQL] Add encoders for seq/array of primitivesMichael Armbrust2016-02-023-2/+91
| | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #11014 from marmbrus/seqEncoders.
* [SPARK-10820][SQL] Support for the continuous execution of structured queriesMichael Armbrust2016-02-0224-32/+1828
| | | | | | | | | | | | | | | | | | | | | | | | | | This is a follow up to 9aadcffabd226557174f3ff566927f873c71672e that extends Spark SQL to allow users to _repeatedly_ optimize and execute structured queries. A `ContinuousQuery` can be expressed using SQL, DataFrames or Datasets. The purpose of this PR is only to add some initial infrastructure which will be extended in subsequent PRs. ## User-facing API - `sqlContext.streamFrom` and `df.streamTo` return builder objects that are analogous to the `read/write` interfaces already available to executing queries in a batch-oriented fashion. - `ContinuousQuery` provides an interface for interacting with a query that is currently executing in the background. ## Internal Interfaces - `StreamExecution` - executes streaming queries in micro-batches The following are currently internal, but public APIs will be provided in a future release. - `Source` - an interface for providers of continually arriving data. A source must have a notion of an `Offset` that monotonically tracks what data has arrived. For fault tolerance, a source must be able to replay data given a start offset. - `Sink` - an interface that accepts the results of a continuously executing query. Also responsible for tracking the offset that should be resumed from in the case of a failure. ## Testing - `MemoryStream` and `MemorySink` - simple implementations of source and sink that keep all data in memory and have methods for simulating durability failures - `StreamTest` - a framework for performing actions and checking invariants on a continuous query Author: Michael Armbrust <michael@databricks.com> Author: Tathagata Das <tathagata.das1565@gmail.com> Author: Josh Rosen <rosenville@gmail.com> Closes #11006 from marmbrus/structured-streaming.
* [SPARK-13087][SQL] Fix group by function for sort based aggregationMichael Armbrust2016-02-022-3/+10
| | | | | | | | It is not valid to call `toAttribute` on a `NamedExpression` unless we know for sure that the child produced that `NamedExpression`. The current code worked fine when the grouping expressions were simple, but when they were a derived value this blew up at execution time. Author: Michael Armbrust <michael@databricks.com> Closes #11013 from marmbrus/groupByFunction-master.
* Closes #10662. Closes #10661Reynold Xin2016-02-010-0/+0
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