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* [SPARK-3541][MLLIB] New ALS implementation with improved storageXiangrui Meng2015-01-221-0/+174
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR adds a new ALS implementation to `spark.ml` using the pipeline API, which should be able to scale to billions of ratings. Compared with the ALS under `spark.mllib`, the new implementation 1. uses the same algorithm, 2. uses float type for ratings, 3. uses primitive arrays to avoid GC, 4. sorts and compresses ratings on each block so that we can solve least squares subproblems one by one using only one normal equation instance. The following figure shows performance comparison on copies of the Amazon Reviews dataset using a 16-node (m3.2xlarge) EC2 cluster (the same setup as in http://databricks.com/blog/2014/07/23/scalable-collaborative-filtering-with-spark-mllib.html): ![als-wip](https://cloud.githubusercontent.com/assets/829644/5659447/4c4ff8e0-96c7-11e4-87a9-73c1c63d07f3.png) I keep the `spark.mllib`'s ALS untouched for easy comparison. If the new implementation works well, I'm going to match the features of the ALS under `spark.mllib` and then make it a wrapper of the new implementation, in a separate PR. TODO: - [X] Add unit tests for implicit preferences. Author: Xiangrui Meng <meng@databricks.com> Closes #3720 from mengxr/SPARK-3541 and squashes the following commits: 1b9e852 [Xiangrui Meng] fix compile 5129be9 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3541 dd0d0e8 [Xiangrui Meng] simplify test code c627de3 [Xiangrui Meng] add tests for implicit feedback b84f41c [Xiangrui Meng] address comments a76da7b [Xiangrui Meng] update ALS tests 2a8deb3 [Xiangrui Meng] add some ALS tests 857e876 [Xiangrui Meng] add tests for rating block and encoded block d3c1ac4 [Xiangrui Meng] rename some classes for better code readability add more doc and comments 213d163 [Xiangrui Meng] org imports 771baf3 [Xiangrui Meng] chol doc update ca9ad9d [Xiangrui Meng] add unit tests for chol b4fd17c [Xiangrui Meng] add unit tests for NormalEquation d0f99d3 [Xiangrui Meng] add tests for LocalIndexEncoder 80b8e61 [Xiangrui Meng] fix imports 4937fd4 [Xiangrui Meng] update ALS example 56c253c [Xiangrui Meng] rename product to item bce8692 [Xiangrui Meng] doc for parameters and project the output columns 3f2d81a [Xiangrui Meng] add doc 1efaecf [Xiangrui Meng] add example code 8ae86b5 [Xiangrui Meng] add a working copy of the new ALS implementation
* [SPARK-5233][Streaming] Fix error replaying of WAL introduced bugjerryshao2015-01-221-1/+1
| | | | | | | | | | | | | Because of lacking of `BlockAllocationEvent` in WAL recovery, the dangled event will mix into the new batch, which will lead to the wrong result. Details can be seen in [SPARK-5233](https://issues.apache.org/jira/browse/SPARK-5233). Author: jerryshao <saisai.shao@intel.com> Closes #4032 from jerryshao/SPARK-5233 and squashes the following commits: f0b0c0b [jerryshao] Further address the comments a237c75 [jerryshao] Address the comments e356258 [jerryshao] Fix bug in unit test 558bdc3 [jerryshao] Correctly replay the WAL log when recovering from failure
* SPARK-5019 [MLlib] - GaussianMixtureModel exposes instances of ↵Travis Galoppo2015-01-201-1/+1
| | | | | | | | | | | | | MultivariateGauss... This PR modifies GaussianMixtureModel to expose instances of MutlivariateGaussian rather than separate mean and covariance arrays. Author: Travis Galoppo <tjg2107@columbia.edu> Closes #4088 from tgaloppo/spark-5019 and squashes the following commits: 3ef6c7f [Travis Galoppo] In GaussianMixtureModel: Changed name of weight, gaussian to weights, gaussians. Other sources modified accordingly. 091e8da [Travis Galoppo] SPARK-5019 - GaussianMixtureModel exposes instances of MultivariateGaussian rather than mean/covariance matrices
* [SPARK-5193][SQL] Remove Spark SQL Java-specific API.Reynold Xin2015-01-164-40/+38
| | | | | | | | | | | | | | | | | | | | | | | | | After the following patches, the main (Scala) API is now usable for Java users directly. https://github.com/apache/spark/pull/4056 https://github.com/apache/spark/pull/4054 https://github.com/apache/spark/pull/4049 https://github.com/apache/spark/pull/4030 https://github.com/apache/spark/pull/3965 https://github.com/apache/spark/pull/3958 Author: Reynold Xin <rxin@databricks.com> Closes #4065 from rxin/sql-java-api and squashes the following commits: b1fd860 [Reynold Xin] Fix Mima 6d86578 [Reynold Xin] Ok one more attempt in fixing Python... e8f1455 [Reynold Xin] Fix Python again... 3e53f91 [Reynold Xin] Fixed Python. 83735da [Reynold Xin] Fix BigDecimal test. e9f1de3 [Reynold Xin] Use scala BigDecimal. 500d2c4 [Reynold Xin] Fix Decimal. ba3bfa2 [Reynold Xin] Updated javadoc for RowFactory. c4ae1c5 [Reynold Xin] [SPARK-5193][SQL] Remove Spark SQL Java-specific API.
* [SPARK-5234][ml]examples for ml don't have sparkContext.stopYuhao Yang2015-01-143-0/+6
| | | | | | | | | | | | JIRA issue: https://issues.apache.org/jira/browse/SPARK-5234 simply add the call. Author: Yuhao Yang <yuhao@yuhaodevbox.sh.intel.com> Closes #4044 from hhbyyh/addscStop and squashes the following commits: c1f75ac [Yuhao Yang] add SparkContext.stop to 3 ml examples
* SPARK-5172 [BUILD] spark-examples-***.jar shades a wrong Hadoop distributionSean Owen2015-01-121-23/+0
| | | | | | | | | | | | | | In addition to the `hadoop-2.x` profiles in the parent POM, there is actually another set of profiles in `examples` that has to be activated differently to get the right Hadoop 1 vs 2 flavor of HBase. This wasn't actually used in making Hadoop 2 distributions, hence the problem. To reduce complexity, I suggest merging them with the parent POM profiles, which is possible now. You'll see this changes appears to update the HBase version, but actually, the default 0.94 version was not being used. HBase is only used in examples, and the examples POM always chose one profile or the other that updated the version to 0.98.x anyway. Author: Sean Owen <sowen@cloudera.com> Closes #3992 from srowen/SPARK-5172 and squashes the following commits: 17830d9 [Sean Owen] Control hbase hadoop1/2 flavor in the parent POM with existing hadoop-2.x profiles
* [SPARK-4033][Examples]Input of the SparkPi too big causes the emption exceptionhuangzhaowei2015-01-111-2/+2
| | | | | | | | | | | | | | | If input of the SparkPi args is larger than the 25000, the integer 'n' inside the code will be overflow, and may be a negative number. And it causes the (0 until n) Seq as an empty seq, then doing the action 'reduce' will throw the UnsupportedOperationException("empty collection"). The max size of the input of sc.parallelize is Int.MaxValue - 1, not the Int.MaxValue. Author: huangzhaowei <carlmartinmax@gmail.com> Closes #2874 from SaintBacchus/SparkPi and squashes the following commits: 62d7cd7 [huangzhaowei] Add a commit to explain the modify 4cdc388 [huangzhaowei] Update SparkPi.scala 9a2fb7b [huangzhaowei] Input of the SparkPi is too big
* [SPARK-4048] Enhance and extend hadoop-provided profile.Marcelo Vanzin2015-01-081-162/+199
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This change does a few things to make the hadoop-provided profile more useful: - Create new profiles for other libraries / services that might be provided by the infrastructure - Simplify and fix the poms so that the profiles are only activated while building assemblies. - Fix tests so that they're able to run when the profiles are activated - Add a new env variable to be used by distributions that use these profiles to provide the runtime classpath for Spark jobs and daemons. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #2982 from vanzin/SPARK-4048 and squashes the following commits: 82eb688 [Marcelo Vanzin] Add a comment. eb228c0 [Marcelo Vanzin] Fix borked merge. 4e38f4e [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 9ef79a3 [Marcelo Vanzin] Alternative way to propagate test classpath to child processes. 371ebee [Marcelo Vanzin] Review feedback. 52f366d [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 83099fc [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 7377e7b [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 322f882 [Marcelo Vanzin] Fix merge fail. f24e9e7 [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 8b00b6a [Marcelo Vanzin] Merge branch 'master' into SPARK-4048 9640503 [Marcelo Vanzin] Cleanup child process log message. 115fde5 [Marcelo Vanzin] Simplify a comment (and make it consistent with another pom). e3ab2da [Marcelo Vanzin] Fix hive-thriftserver profile. 7820d58 [Marcelo Vanzin] Fix CliSuite with provided profiles. 1be73d4 [Marcelo Vanzin] Restore flume-provided profile. d1399ed [Marcelo Vanzin] Restore jetty dependency. 82a54b9 [Marcelo Vanzin] Remove unused profile. 5c54a25 [Marcelo Vanzin] Fix HiveThriftServer2Suite with *-provided profiles. 1fc4d0b [Marcelo Vanzin] Update dependencies for hive-thriftserver. f7b3bbe [Marcelo Vanzin] Add snappy to hadoop-provided list. 9e4e001 [Marcelo Vanzin] Remove duplicate hive profile. d928d62 [Marcelo Vanzin] Redirect child stderr to parent's log. 4d67469 [Marcelo Vanzin] Propagate SPARK_DIST_CLASSPATH on Yarn. 417d90e [Marcelo Vanzin] Introduce "SPARK_DIST_CLASSPATH". 2f95f0d [Marcelo Vanzin] Propagate classpath to child processes during testing. 1adf91c [Marcelo Vanzin] Re-enable maven-install-plugin for a few projects. 284dda6 [Marcelo Vanzin] Rework the "hadoop-provided" profile, add new ones.
* SPARK-4159 [CORE] Maven build doesn't run JUnit test suitesSean Owen2015-01-061-5/+0
| | | | | | | | | | | | | | | | | | This PR: - Reenables `surefire`, and copies config from `scalatest` (which is itself an old fork of `surefire`, so similar) - Tells `surefire` to test only Java tests - Enables `surefire` and `scalatest` for all children, and in turn eliminates some duplication. For me this causes the Scala and Java tests to be run once each, it seems, as desired. It doesn't affect the SBT build but works for Maven. I still need to verify that all of the Scala tests and Java tests are being run. Author: Sean Owen <sowen@cloudera.com> Closes #3651 from srowen/SPARK-4159 and squashes the following commits: 2e8a0af [Sean Owen] Remove specialized SPARK_HOME setting for REPL, YARN tests as it appears to be obsolete 12e4558 [Sean Owen] Append to unit-test.log instead of overwriting, so that both surefire and scalatest output is preserved. Also standardize/correct comments a bit. e6f8601 [Sean Owen] Reenable Java tests by reenabling surefire with config cloned from scalatest; centralize test config in the parent
* [SPARK-1010] Clean up uses of System.setProperty in unit testsJosh Rosen2014-12-301-4/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Several of our tests call System.setProperty (or test code which implicitly sets system properties) and don't always reset/clear the modified properties, which can create ordering dependencies between tests and cause hard-to-diagnose failures. This patch removes most uses of System.setProperty from our tests, since in most cases we can use SparkConf to set these configurations (there are a few exceptions, including the tests of SparkConf itself). For the cases where we continue to use System.setProperty, this patch introduces a `ResetSystemProperties` ScalaTest mixin class which snapshots the system properties before individual tests and to automatically restores them on test completion / failure. See the block comment at the top of the ResetSystemProperties class for more details. Author: Josh Rosen <joshrosen@databricks.com> Closes #3739 from JoshRosen/cleanup-system-properties-in-tests and squashes the following commits: 0236d66 [Josh Rosen] Replace setProperty uses in two example programs / tools 3888fe3 [Josh Rosen] Remove setProperty use in LocalJavaStreamingContext 4f4031d [Josh Rosen] Add note on why SparkSubmitSuite needs ResetSystemProperties 4742a5b [Josh Rosen] Clarify ResetSystemProperties trait inheritance ordering. 0eaf0b6 [Josh Rosen] Remove setProperty call in TaskResultGetterSuite. 7a3d224 [Josh Rosen] Fix trait ordering 3fdb554 [Josh Rosen] Remove setProperty call in TaskSchedulerImplSuite bee20df [Josh Rosen] Remove setProperty calls in SparkContextSchedulerCreationSuite 655587c [Josh Rosen] Remove setProperty calls in JobCancellationSuite 3f2f955 [Josh Rosen] Remove System.setProperty calls in DistributedSuite cfe9cce [Josh Rosen] Remove use of system properties in SparkContextSuite 8783ab0 [Josh Rosen] Remove TestUtils.setSystemProperty, since it is subsumed by the ResetSystemProperties trait. 633a84a [Josh Rosen] Remove use of system properties in FileServerSuite 25bfce2 [Josh Rosen] Use ResetSystemProperties in UtilsSuite 1d1aa5a [Josh Rosen] Use ResetSystemProperties in SizeEstimatorSuite dd9492b [Josh Rosen] Use ResetSystemProperties in AkkaUtilsSuite b0daff2 [Josh Rosen] Use ResetSystemProperties in BlockManagerSuite e9ded62 [Josh Rosen] Use ResetSystemProperties in TaskSchedulerImplSuite 5b3cb54 [Josh Rosen] Use ResetSystemProperties in SparkListenerSuite 0995c4b [Josh Rosen] Use ResetSystemProperties in SparkContextSchedulerCreationSuite c83ded8 [Josh Rosen] Use ResetSystemProperties in SparkConfSuite 51aa870 [Josh Rosen] Use withSystemProperty in ShuffleSuite 60a63a1 [Josh Rosen] Use ResetSystemProperties in JobCancellationSuite 14a92e4 [Josh Rosen] Use withSystemProperty in FileServerSuite 628f46c [Josh Rosen] Use ResetSystemProperties in DistributedSuite 9e3e0dd [Josh Rosen] Add ResetSystemProperties test fixture mixin; use it in SparkSubmitSuite. 4dcea38 [Josh Rosen] Move withSystemProperty to TestUtils class.
* SPARK-4156 [MLLIB] EM algorithm for GMMsTravis Galoppo2014-12-291-0/+67
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Implementation of Expectation-Maximization for Gaussian Mixture Models. This is my maiden contribution to Apache Spark, so I apologize now if I have done anything incorrectly; having said that, this work is my own, and I offer it to the project under the project's open source license. Author: Travis Galoppo <tjg2107@columbia.edu> Author: Travis Galoppo <travis@localhost.localdomain> Author: tgaloppo <tjg2107@columbia.edu> Author: FlytxtRnD <meethu.mathew@flytxt.com> Closes #3022 from tgaloppo/master and squashes the following commits: aaa8f25 [Travis Galoppo] MLUtils: changed privacy of EPSILON from [util] to [mllib] 709e4bf [Travis Galoppo] fixed usage line to include optional maxIterations parameter acf1fba [Travis Galoppo] Fixed parameter comment in GaussianMixtureModel Made maximum iterations an optional parameter to DenseGmmEM 9b2fc2a [Travis Galoppo] Style improvements Changed ExpectationSum to a private class b97fe00 [Travis Galoppo] Minor fixes and tweaks. 1de73f3 [Travis Galoppo] Removed redundant array from array creation 578c2d1 [Travis Galoppo] Removed unused import 227ad66 [Travis Galoppo] Moved prediction methods into model class. 308c8ad [Travis Galoppo] Numerous changes to improve code cff73e0 [Travis Galoppo] Replaced accumulators with RDD.aggregate 20ebca1 [Travis Galoppo] Removed unusued code 42b2142 [Travis Galoppo] Added functionality to allow setting of GMM starting point. Added two cluster test to testing suite. 8b633f3 [Travis Galoppo] Style issue 9be2534 [Travis Galoppo] Style issue d695034 [Travis Galoppo] Fixed style issues c3b8ce0 [Travis Galoppo] Merge branch 'master' of https://github.com/tgaloppo/spark Adds predict() method 2df336b [Travis Galoppo] Fixed style issue b99ecc4 [tgaloppo] Merge pull request #1 from FlytxtRnD/predictBranch f407b4c [FlytxtRnD] Added predict() to return the cluster labels and membership values 97044cf [Travis Galoppo] Fixed style issues dc9c742 [Travis Galoppo] Moved MultivariateGaussian utility class e7d413b [Travis Galoppo] Moved multivariate Gaussian utility class to mllib/stat/impl Improved comments 9770261 [Travis Galoppo] Corrected a variety of style and naming issues. 8aaa17d [Travis Galoppo] Added additional train() method to companion object for cluster count and tolerance parameters. 676e523 [Travis Galoppo] Fixed to no longer ignore delta value provided on command line e6ea805 [Travis Galoppo] Merged with master branch; update test suite with latest context changes. Improved cluster initialization strategy. 86fb382 [Travis Galoppo] Merge remote-tracking branch 'upstream/master' 719d8cc [Travis Galoppo] Added scala test suite with basic test c1a8e16 [Travis Galoppo] Made GaussianMixtureModel class serializable Modified sum function for better performance 5c96c57 [Travis Galoppo] Merge remote-tracking branch 'upstream/master' c15405c [Travis Galoppo] SPARK-4156
* [SPARK-4608][Streaming] Reorganize StreamingContext implicit to improve API ↵zsxwing2014-12-2512-12/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | convenience There is only one implicit function `toPairDStreamFunctions` in `StreamingContext`. This PR did similar reorganization like [SPARK-4397](https://issues.apache.org/jira/browse/SPARK-4397). Compiled the following codes with Spark Streaming 1.1.0 and ran it with this PR. Everything is fine. ```Scala import org.apache.spark._ import org.apache.spark.streaming._ import org.apache.spark.streaming.StreamingContext._ object StreamingApp { def main(args: Array[String]) { val conf = new SparkConf().setMaster("local[2]").setAppName("FileWordCount") val ssc = new StreamingContext(conf, Seconds(10)) val lines = ssc.textFileStream("/some/path") val words = lines.flatMap(_.split(" ")) val pairs = words.map(word => (word, 1)) val wordCounts = pairs.reduceByKey(_ + _) wordCounts.print() ssc.start() ssc.awaitTermination() } } ``` Author: zsxwing <zsxwing@gmail.com> Closes #3464 from zsxwing/SPARK-4608 and squashes the following commits: aa6d44a [zsxwing] Fix a copy-paste error f74c190 [zsxwing] Merge branch 'master' into SPARK-4608 e6f9cc9 [zsxwing] Update the docs 27833bb [zsxwing] Remove `import StreamingContext._` c15162c [zsxwing] Reorganize StreamingContext implicit to improve API convenience
* [SPARK-4932] Add help comments in AnalyticsTakeshi Yamamuro2014-12-231-0/+4
| | | | | | | | | | Trivial modifications for usability. Author: Takeshi Yamamuro <linguin.m.s@gmail.com> Closes #3775 from maropu/AddHelpCommentInAnalytics and squashes the following commits: fbea8f5 [Takeshi Yamamuro] Add help comments in Analytics
* [Minor] Improve some code in BroadcastTest for shortcarlmartin2014-12-221-4/+1
| | | | | | | | | | | | | | | | | Using val arr1 = (0 until num).toArray instead of val arr1 = new Array[Int](num) for (i <- 0 until arr1.length) { arr1(i) = i } for short. Author: carlmartin <carlmartinmax@gmail.com> Closes #3750 from SaintBacchus/BroadcastTest and squashes the following commits: 43adb70 [carlmartin] Improve some code in BroadcastTest for short
* [SPARK-4880] remove spark.locality.wait in AnalyticsErnest2014-12-181-1/+1
| | | | | | | | | | | spark.locality.wait set to 100000 in examples/graphx/Analytics.scala. Should be left to the user. Author: Ernest <earneyzxl@gmail.com> Closes #3730 from Earne/SPARK-4880 and squashes the following commits: d79ed04 [Ernest] remove spark.locality.wait in Analytics
* [SPARK-4774] [SQL] Makes HiveFromSpark more portableKostas Sakellis2014-12-081-2/+11
| | | | | | | | | | | | HiveFromSpark read the kv1.txt file from SPARK_HOME/examples/src/main/resources/kv1.txt which assumed you had a source tree checked out. Now we copy the kv1.txt file to a temporary file and delete it when the jvm shuts down. This allows us to run this example outside of a spark source tree. Author: Kostas Sakellis <kostas@cloudera.com> Closes #3628 from ksakellis/kostas-spark-4774 and squashes the following commits: 6770f83 [Kostas Sakellis] [SPARK-4774] [SQL] Makes HiveFromSpark more portable
* [FIX][DOC] Fix broken links in ml-guide.mdXiangrui Meng2014-12-042-2/+1
| | | | | | | | | | | | and some minor changes in ScalaDoc. Author: Xiangrui Meng <meng@databricks.com> Closes #3601 from mengxr/SPARK-4575-fix and squashes the following commits: c559768 [Xiangrui Meng] minor code update ce94da8 [Xiangrui Meng] Java Bean -> JavaBean 0b5c182 [Xiangrui Meng] fix links in ml-guide
* [SPARK-4575] [mllib] [docs] spark.ml pipelines doc + bug fixesJoseph K. Bradley2014-12-046-5/+457
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Documentation: * Added ml-guide.md, linked from mllib-guide.md * Updated mllib-guide.md with small section pointing to ml-guide.md Examples: * CrossValidatorExample * SimpleParamsExample * (I copied these + the SimpleTextClassificationPipeline example into the ml-guide.md) Bug fixes: * PipelineModel: did not use ParamMaps correctly * UnaryTransformer: issues with TypeTag serialization (Thanks to mengxr for that fix!) CC: mengxr shivaram etrain Documentation for Pipelines: I know the docs are not complete, but the goal is to have enough to let interested people get started using spark.ml and to add more docs once the package is more established/complete. Author: Joseph K. Bradley <joseph@databricks.com> Author: jkbradley <joseph.kurata.bradley@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #3588 from jkbradley/ml-package-docs and squashes the following commits: d393b5c [Joseph K. Bradley] fixed bug in Pipeline (typo from last commit). updated examples for CV and Params for spark.ml c38469c [Joseph K. Bradley] Updated ml-guide with CV examples 99f88c2 [Joseph K. Bradley] Fixed bug in PipelineModel.transform* with usage of params. Updated CrossValidatorExample to use more training examples so it is less likely to get a 0-size fold. ea34dc6 [jkbradley] Merge pull request #4 from mengxr/ml-package-docs 3b83ec0 [Xiangrui Meng] replace TypeTag with explicit datatype 41ad9b1 [Joseph K. Bradley] Added examples for spark.ml: SimpleParamsExample + Java version, CrossValidatorExample + Java version. CrossValidatorExample not working yet. Added programming guide for spark.ml, but need to add CrossValidatorExample to it once CrossValidatorExample works.
* [SPARK-4580] [SPARK-4610] [mllib] [docs] Documentation for tree ensembles + ↵Joseph K. Bradley2014-12-046-10/+241
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | DecisionTree API fix Major changes: * Added programming guide sections for tree ensembles * Added examples for tree ensembles * Updated DecisionTree programming guide with more info on parameters * **API change**: Standardized the tree parameter for the number of classes (for classification) Minor changes: * Updated decision tree documentation * Updated existing tree and tree ensemble examples * Use train/test split, and compute test error instead of training error. * Fixed decision_tree_runner.py to actually use the number of classes it computes from data. (small bug fix) Note: I know this is a lot of lines, but most is covered by: * Programming guide sections for gradient boosting and random forests. (The changes are probably best viewed by generating the docs locally.) * New examples (which were copied from the programming guide) * The "numClasses" renaming I have run all examples and relevant unit tests. CC: mengxr manishamde codedeft Author: Joseph K. Bradley <joseph@databricks.com> Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #3461 from jkbradley/ensemble-docs and squashes the following commits: 70a75f3 [Joseph K. Bradley] updated forest vs boosting comparison d1de753 [Joseph K. Bradley] Added note about toString and toDebugString for DecisionTree to migration guide 8e87f8f [Joseph K. Bradley] Combined GBT and RandomForest guides into one ensembles guide 6fab846 [Joseph K. Bradley] small fixes based on review b9f8576 [Joseph K. Bradley] updated decision tree doc 375204c [Joseph K. Bradley] fixed python style 2b60b6e [Joseph K. Bradley] merged Java RandomForest examples into 1 file. added header. Fixed small bug in same example in the programming guide. 706d332 [Joseph K. Bradley] updated python DT runner to print full model if it is small c76c823 [Joseph K. Bradley] added migration guide for mllib abe5ed7 [Joseph K. Bradley] added examples for random forest in Java and Python to examples folder 07fc11d [Joseph K. Bradley] Renamed numClassesForClassification to numClasses everywhere in trees and ensembles. This is a breaking API change, but it was necessary to correct an API inconsistency in Spark 1.1 (where Python DecisionTree used numClasses but Scala used numClassesForClassification). cdfdfbc [Joseph K. Bradley] added examples for GBT 6372a2b [Joseph K. Bradley] updated decision tree examples to use random split. tested all of them. ad3e695 [Joseph K. Bradley] added gbt and random forest to programming guide. still need to update their examples
* [SPARK-4710] [mllib] Eliminate MLlib compilation warningsJoseph K. Bradley2014-12-032-8/+10
| | | | | | | | | | | | | | Renamed StreamingKMeans to StreamingKMeansExample to avoid warning about name conflict with StreamingKMeans class. Added import to DecisionTreeRunner to eliminate warning. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #3568 from jkbradley/ml-compilation-warnings and squashes the following commits: 64d6bc4 [Joseph K. Bradley] Updated DecisionTreeRunner.scala and StreamingKMeans.scala to eliminate compilation warnings, including renaming StreamingKMeans to StreamingKMeansExample.
* [SQL] Minor fix for doc and commentwangfei2014-12-011-3/+4
| | | | | | | | Author: wangfei <wangfei1@huawei.com> Closes #3533 from scwf/sql-doc1 and squashes the following commits: 962910b [wangfei] doc and comment fix
* SPARK-4170 [CORE] Closure problems when running Scala app that "extends App"Sean Owen2014-11-271-34/+36
| | | | | | | | | | | Warn against subclassing scala.App, and remove one instance of this in examples Author: Sean Owen <sowen@cloudera.com> Closes #3497 from srowen/SPARK-4170 and squashes the following commits: 4a6131f [Sean Owen] Restore multiline string formatting a8ca895 [Sean Owen] Warn against subclassing scala.App, and remove one instance of this in examples
* [SPARK-4535][Streaming] Fix the error in commentsq002515982014-11-252-2/+2
| | | | | | | | | | | change `NetworkInputDStream` to `ReceiverInputDStream` change `ReceiverInputTracker` to `ReceiverTracker` Author: q00251598 <qiyadong@huawei.com> Closes #3400 from watermen/fix-comments and squashes the following commits: 75d795c [q00251598] change 'NetworkInputDStream' to 'ReceiverInputDStream' && change 'ReceiverInputTracker' to 'ReceiverTracker'
* [SQL] Fix path in HiveFromSparkscwf2014-11-241-1/+2
| | | | | | | | | | | | It require us to run ```HiveFromSpark``` in specified dir because ```HiveFromSpark``` use relative path, this leads to ```run-example``` error(http://apache-spark-developers-list.1001551.n3.nabble.com/src-main-resources-kv1-txt-not-found-in-example-of-HiveFromSpark-td9100.html). Author: scwf <wangfei1@huawei.com> Closes #3415 from scwf/HiveFromSpark and squashes the following commits: ed3d6c9 [scwf] revert no need change b00e20c [scwf] fix path usring spark_home dbd321b [scwf] fix path in hivefromspark
* [SPARK-4486][MLLIB] Improve GradientBoosting APIs and docXiangrui Meng2014-11-203-32/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | There are some inconsistencies in the gradient boosting APIs. The target is a general boosting meta-algorithm, but the implementation is attached to trees. This was partially due to the delay of SPARK-1856. But for the 1.2 release, we should make the APIs consistent. 1. WeightedEnsembleModel -> private[tree] TreeEnsembleModel and renamed members accordingly. 1. GradientBoosting -> GradientBoostedTrees 1. Add RandomForestModel and GradientBoostedTreesModel and hide CombiningStrategy 1. Slightly refactored TreeEnsembleModel (Vote takes weights into consideration.) 1. Remove `trainClassifier` and `trainRegressor` from `GradientBoostedTrees` because they are the same as `train` 1. Rename class `train` method to `run` because it hides the static methods with the same name in Java. Deprecated `DecisionTree.train` class method. 1. Simplify BoostingStrategy and make sure the input strategy is not modified. Users should put algo and numClasses in treeStrategy. We create ensembleStrategy inside boosting. 1. Fix a bug in GradientBoostedTreesSuite with AbsoluteError 1. doc updates manishamde jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #3374 from mengxr/SPARK-4486 and squashes the following commits: 7097251 [Xiangrui Meng] address joseph's comments 98dea09 [Xiangrui Meng] address manish's comments 4aae3b7 [Xiangrui Meng] add RandomForestModel and GradientBoostedTreesModel, hide CombiningStrategy ea4c467 [Xiangrui Meng] fix unit tests 751da4e [Xiangrui Meng] rename class method train -> run 19030a5 [Xiangrui Meng] update boosting public APIs
* SPARK-4455 Exclude dependency on hbase-annotations moduletedyu2014-11-191-0/+22
| | | | | | | | | | | | | pwendell Please take a look Author: tedyu <yuzhihong@gmail.com> Closes #3286 from tedyu/master and squashes the following commits: e61e610 [tedyu] SPARK-4455 Exclude dependency on hbase-annotations module 7e3a57a [tedyu] Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/spark 2f28b08 [tedyu] Exclude dependency on hbase-annotations module
* Bumping version to 1.3.0-SNAPSHOT.Marcelo Vanzin2014-11-181-1/+1
| | | | | | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #3277 from vanzin/version-1.3 and squashes the following commits: 7c3c396 [Marcelo Vanzin] Added temp repo to sbt build. 5f404ff [Marcelo Vanzin] Add another exclusion. 19457e7 [Marcelo Vanzin] Update old version to 1.2, add temporary 1.2 repo. 3c8d705 [Marcelo Vanzin] Workaround for MIMA checks. e940810 [Marcelo Vanzin] Bumping version to 1.3.0-SNAPSHOT.
* SPARK-2811 upgrade algebird to 0.8.1Adam Pingel2014-11-173-7/+7
| | | | | | | | | Author: Adam Pingel <adam@axle-lang.org> Closes #3282 from adampingel/master and squashes the following commits: 70c8d3c [Adam Pingel] relocate the algebird example back to example/src 7a9d8be [Adam Pingel] SPARK-2811 upgrade algebird to 0.8.1
* [SPARK-2321] Several progress API improvements / refactoringsJosh Rosen2014-11-141-3/+3
| | | | | | | | | | | | | | | | | | | | This PR refactors / extends the status API introduced in #2696. - Change StatusAPI from a mixin trait to a class. Before, the new status API methods were directly accessible through SparkContext, whereas now they're accessed through a `sc.statusAPI` field. As long as we were going to add these methods directly to SparkContext, the mixin trait seemed like a good idea, but this might be simpler to reason about and may avoid pitfalls that I've run into while attempting to refactor other parts of SparkContext to use mixins (see #3071, for example). - Change the name from SparkStatusAPI to SparkStatusTracker. - Make `getJobIdsForGroup(null)` return ids for jobs that aren't associated with any job group. - Add `getActiveStageIds()` and `getActiveJobIds()` methods that return the ids of whatever's currently active in this SparkContext. This should simplify davies's progress bar code. Author: Josh Rosen <joshrosen@databricks.com> Closes #3197 from JoshRosen/progress-api-improvements and squashes the following commits: 30b0afa [Josh Rosen] Rename SparkStatusAPI to SparkStatusTracker. d1b08d8 [Josh Rosen] Add missing newlines 2cc7353 [Josh Rosen] Add missing file. d5eab1f [Josh Rosen] Add getActive[Stage|Job]Ids() methods. a227984 [Josh Rosen] getJobIdsForGroup(null) should return jobs for default group c47e294 [Josh Rosen] Remove StatusAPI mixin trait.
* SPARK-4375. no longer require -Pscala-2.10Sandy Ryza2014-11-141-62/+3
| | | | | | | | | | | | It seems like the winds might have moved away from this approach, but wanted to post the PR anyway because I got it working and to show what it would look like. Author: Sandy Ryza <sandy@cloudera.com> Closes #3239 from sryza/sandy-spark-4375 and squashes the following commits: 0ffbe95 [Sandy Ryza] Enable -Dscala-2.11 in sbt cd42d94 [Sandy Ryza] Update doc f6644c3 [Sandy Ryza] SPARK-4375 take 2
* [SPARK-4372][MLLIB] Make LR and SVM's default parameters consistent in Scala ↵Xiangrui Meng2014-11-132-2/+2
| | | | | | | | | | | | | | | | | | and Python The current default regParam is 1.0 and regType is claimed to be none in Python (but actually it is l2), while regParam = 0.0 and regType is L2 in Scala. We should make the default values consistent. This PR sets the default regType to L2 and regParam to 0.01. Note that the default regParam value in LIBLINEAR (and hence scikit-learn) is 1.0. However, we use average loss instead of total loss in our formulation. Hence regParam=1.0 is definitely too heavy. In LinearRegression, we set regParam=0.0 and regType=None, because we have separate classes for Lasso and Ridge, both of which use regParam=0.01 as the default. davies atalwalkar Author: Xiangrui Meng <meng@databricks.com> Closes #3232 from mengxr/SPARK-4372 and squashes the following commits: 9979837 [Xiangrui Meng] update Ridge/Lasso to use default regParam 0.01 cast input arguments d3ba096 [Xiangrui Meng] change 'none' back to None 1909a6e [Xiangrui Meng] change default regParam to 0.01 and regType to L2 in LR and SVM
* [SPARK-3660][STREAMING] Initial RDD for updateStateByKey transformationSoumitra Kumar2014-11-121-2/+11
| | | | | | | | | | | | | | | | | | | | | | | | | SPARK-3660 : Initial RDD for updateStateByKey transformation I have added a sample StatefulNetworkWordCountWithInitial inspired by StatefulNetworkWordCount. Please let me know if any changes are required. Author: Soumitra Kumar <kumar.soumitra@gmail.com> Closes #2665 from soumitrak/master and squashes the following commits: ee8980b [Soumitra Kumar] Fixed copy/paste issue. 304f636 [Soumitra Kumar] Added simpler version of updateStateByKey API with initialRDD and test. 9781135 [Soumitra Kumar] Fixed test, and renamed variable. 3da51a2 [Soumitra Kumar] Adding updateStateByKey with initialRDD API to JavaPairDStream. 2f78f7e [Soumitra Kumar] Merge remote-tracking branch 'upstream/master' d4fdd18 [Soumitra Kumar] Renamed variable and moved method. d0ce2cd [Soumitra Kumar] Merge remote-tracking branch 'upstream/master' 31399a4 [Soumitra Kumar] Merge remote-tracking branch 'upstream/master' 4efa58b [Soumitra Kumar] [SPARK-3660][STREAMING] Initial RDD for updateStateByKey transformation 8f40ca0 [Soumitra Kumar] Merge remote-tracking branch 'upstream/master' dde4271 [Soumitra Kumar] Merge remote-tracking branch 'upstream/master' fdd7db3 [Soumitra Kumar] Adding support of initial value for state update. SPARK-3660 : Initial RDD for updateStateByKey transformation
* [SPARK-3530][MLLIB] pipeline and parameters with examplesXiangrui Meng2014-11-122-0/+179
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR adds package "org.apache.spark.ml" with pipeline and parameters, as discussed on the JIRA. This is a joint work of jkbradley etrain shivaram and many others who helped on the design, also with help from marmbrus and liancheng on the Spark SQL side. The design doc can be found at: https://docs.google.com/document/d/1rVwXRjWKfIb-7PI6b86ipytwbUH7irSNLF1_6dLmh8o/edit?usp=sharing **org.apache.spark.ml** This is a new package with new set of ML APIs that address practical machine learning pipelines. (Sorry for taking so long!) It will be an alpha component, so this is definitely not something set in stone. The new set of APIs, inspired by the MLI project from AMPLab and scikit-learn, takes leverage on Spark SQL's schema support and execution plan optimization. It introduces the following components that help build a practical pipeline: 1. Transformer, which transforms a dataset into another 2. Estimator, which fits models to data, where models are transformers 3. Evaluator, which evaluates model output and returns a scalar metric 4. Pipeline, a simple pipeline that consists of transformers and estimators Parameters could be supplied at fit/transform or embedded with components. 1. Param: a strong-typed parameter key with self-contained doc 2. ParamMap: a param -> value map 3. Params: trait for components with parameters For any component that implements `Params`, user can easily check the doc by calling `explainParams`: ~~~ > val lr = new LogisticRegression > lr.explainParams maxIter: max number of iterations (default: 100) regParam: regularization constant (default: 0.1) labelCol: label column name (default: label) featuresCol: features column name (default: features) ~~~ or user can check individual param: ~~~ > lr.maxIter maxIter: max number of iterations (default: 100) ~~~ **Please start with the example code in test suites and under `org.apache.spark.examples.ml`, where I put several examples:** 1. run a simple logistic regression job ~~~ val lr = new LogisticRegression() .setMaxIter(10) .setRegParam(1.0) val model = lr.fit(dataset) model.transform(dataset, model.threshold -> 0.8) // overwrite threshold .select('label, 'score, 'prediction).collect() .foreach(println) ~~~ 2. run logistic regression with cross-validation and grid search using areaUnderROC (default) as the metric ~~~ val lr = new LogisticRegression val lrParamMaps = new ParamGridBuilder() .addGrid(lr.regParam, Array(0.1, 100.0)) .addGrid(lr.maxIter, Array(0, 5)) .build() val eval = new BinaryClassificationEvaluator val cv = new CrossValidator() .setEstimator(lr) .setEstimatorParamMaps(lrParamMaps) .setEvaluator(eval) .setNumFolds(3) val bestModel = cv.fit(dataset) ~~~ 3. run a pipeline that consists of a standard scaler and a logistic regression component ~~~ val scaler = new StandardScaler() .setInputCol("features") .setOutputCol("scaledFeatures") val lr = new LogisticRegression() .setFeaturesCol(scaler.getOutputCol) val pipeline = new Pipeline() .setStages(Array(scaler, lr)) val model = pipeline.fit(dataset) val predictions = model.transform(dataset) .select('label, 'score, 'prediction) .collect() .foreach(println) ~~~ 4. a simple text classification pipeline, which recognizes "spark": ~~~ val training = sparkContext.parallelize(Seq( LabeledDocument(0L, "a b c d e spark", 1.0), LabeledDocument(1L, "b d", 0.0), LabeledDocument(2L, "spark f g h", 1.0), LabeledDocument(3L, "hadoop mapreduce", 0.0))) val tokenizer = new Tokenizer() .setInputCol("text") .setOutputCol("words") val hashingTF = new HashingTF() .setInputCol(tokenizer.getOutputCol) .setOutputCol("features") val lr = new LogisticRegression() .setMaxIter(10) val pipeline = new Pipeline() .setStages(Array(tokenizer, hashingTF, lr)) val model = pipeline.fit(training) val test = sparkContext.parallelize(Seq( Document(4L, "spark i j k"), Document(5L, "l m"), Document(6L, "mapreduce spark"), Document(7L, "apache hadoop"))) model.transform(test) .select('id, 'text, 'prediction, 'score) .collect() .foreach(println) ~~~ Java examples are very similar. I put example code that creates a simple text classification pipeline in Scala and Java, where a simple tokenizer is defined as a transformer outside `org.apache.spark.ml`. **What are missing now and will be added soon:** 1. ~~Runtime check of schemas. So before we touch the data, we will go through the schema and make sure column names and types match the input parameters.~~ 2. ~~Java examples.~~ 3. ~~Store training parameters in trained models.~~ 4. (later) Serialization and Python API. Author: Xiangrui Meng <meng@databricks.com> Closes #3099 from mengxr/SPARK-3530 and squashes the following commits: 2cc93fd [Xiangrui Meng] hide APIs as much as I can 34319ba [Xiangrui Meng] use local instead local[2] for unit tests 2524251 [Xiangrui Meng] rename PipelineStage.transform to transformSchema c9daab4 [Xiangrui Meng] remove mockito version 1397ab5 [Xiangrui Meng] use sqlContext from LocalSparkContext instead of TestSQLContext 6ffc389 [Xiangrui Meng] try to fix unit test a59d8b7 [Xiangrui Meng] doc updates 977fd9d [Xiangrui Meng] add scala ml package object 6d97fe6 [Xiangrui Meng] add AlphaComponent annotation 731f0e4 [Xiangrui Meng] update package doc 0435076 [Xiangrui Meng] remove ;this from setters fa21d9b [Xiangrui Meng] update extends indentation f1091b3 [Xiangrui Meng] typo 228a9f4 [Xiangrui Meng] do not persist before calling binary classification metrics f51cd27 [Xiangrui Meng] rename default to defaultValue b3be094 [Xiangrui Meng] refactor schema transform in lr 8791e8e [Xiangrui Meng] rename copyValues to inheritValues and make it do the right thing 51f1c06 [Xiangrui Meng] remove leftover code in Transformer 494b632 [Xiangrui Meng] compure score once ad678e9 [Xiangrui Meng] more doc for Transformer 4306ed4 [Xiangrui Meng] org imports in text pipeline 6e7c1c7 [Xiangrui Meng] update pipeline 4f9e34f [Xiangrui Meng] more doc for pipeline aa5dbd4 [Xiangrui Meng] fix typo 11be383 [Xiangrui Meng] fix unit tests 3df7952 [Xiangrui Meng] clean up 986593e [Xiangrui Meng] re-org java test suites 2b11211 [Xiangrui Meng] remove external data deps 9fd4933 [Xiangrui Meng] add unit test for pipeline 2a0df46 [Xiangrui Meng] update tests 2d52e4d [Xiangrui Meng] add @AlphaComponent to package-info 27582a4 [Xiangrui Meng] doc changes 73a000b [Xiangrui Meng] add schema transformation layer 6736e87 [Xiangrui Meng] more doc / remove HasMetricName trait 80a8b5e [Xiangrui Meng] rename SimpleTransformer to UnaryTransformer 62ca2bb [Xiangrui Meng] check param parent in set/get 1622349 [Xiangrui Meng] add getModel to PipelineModel a0e0054 [Xiangrui Meng] update StandardScaler to use SimpleTransformer d0faa04 [Xiangrui Meng] remove implicit mapping from ParamMap c7f6921 [Xiangrui Meng] move ParamGridBuilder test to ParamGridBuilderSuite e246f29 [Xiangrui Meng] re-org: 7772430 [Xiangrui Meng] remove modelParams add a simple text classification pipeline b95c408 [Xiangrui Meng] remove implicits add unit tests to params bab3e5b [Xiangrui Meng] update params fe0ee92 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3530 6e86d98 [Xiangrui Meng] some code clean-up 2d040b3 [Xiangrui Meng] implement setters inside each class, add Params.copyValues [ci skip] fd751fc [Xiangrui Meng] add java-friendly versions of fit and tranform 3f810cd [Xiangrui Meng] use multi-model training api in cv 5b8f413 [Xiangrui Meng] rename model to modelParams 9d2d35d [Xiangrui Meng] test varargs and chain model params f46e927 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3530 1ef26e0 [Xiangrui Meng] specialize methods/types for Java df293ed [Xiangrui Meng] switch to setter/getter 376db0a [Xiangrui Meng] pipeline and parameters
* Support cross building for Scala 2.11Prashant Sharma2014-11-115-54/+145
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Let's give this another go using a version of Hive that shades its JLine dependency. Author: Prashant Sharma <prashant.s@imaginea.com> Author: Patrick Wendell <pwendell@gmail.com> Closes #3159 from pwendell/scala-2.11-prashant and squashes the following commits: e93aa3e [Patrick Wendell] Restoring -Phive-thriftserver profile and cleaning up build script. f65d17d [Patrick Wendell] Fixing build issue due to merge conflict a8c41eb [Patrick Wendell] Reverting dev/run-tests back to master state. 7a6eb18 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into scala-2.11-prashant 583aa07 [Prashant Sharma] REVERT ME: removed hive thirftserver 3680e58 [Prashant Sharma] Revert "REVERT ME: Temporarily removing some Cli tests." 935fb47 [Prashant Sharma] Revert "Fixed by disabling a few tests temporarily." 925e90f [Prashant Sharma] Fixed by disabling a few tests temporarily. 2fffed3 [Prashant Sharma] Exclude groovy from sbt build, and also provide a way for such instances in future. 8bd4e40 [Prashant Sharma] Switched to gmaven plus, it fixes random failures observer with its predecessor gmaven. 5272ce5 [Prashant Sharma] SPARK_SCALA_VERSION related bugs. 2121071 [Patrick Wendell] Migrating version detection to PySpark b1ed44d [Patrick Wendell] REVERT ME: Temporarily removing some Cli tests. 1743a73 [Patrick Wendell] Removing decimal test that doesn't work with Scala 2.11 f5cad4e [Patrick Wendell] Add Scala 2.11 docs 210d7e1 [Patrick Wendell] Revert "Testing new Hive version with shaded jline" 48518ce [Patrick Wendell] Remove association of Hive and Thriftserver profiles. e9d0a06 [Patrick Wendell] Revert "Enable thritfserver for Scala 2.10 only" 67ec364 [Patrick Wendell] Guard building of thriftserver around Scala 2.10 check 8502c23 [Patrick Wendell] Enable thritfserver for Scala 2.10 only e22b104 [Patrick Wendell] Small fix in pom file ec402ab [Patrick Wendell] Various fixes 0be5a9d [Patrick Wendell] Testing new Hive version with shaded jline 4eaec65 [Prashant Sharma] Changed scripts to ignore target. 5167bea [Prashant Sharma] small correction a4fcac6 [Prashant Sharma] Run against scala 2.11 on jenkins. 80285f4 [Prashant Sharma] MAven equivalent of setting spark.executor.extraClasspath during tests. 034b369 [Prashant Sharma] Setting test jars on executor classpath during tests from sbt. d4874cb [Prashant Sharma] Fixed Python Runner suite. null check should be first case in scala 2.11. 6f50f13 [Prashant Sharma] Fixed build after rebasing with master. We should use ${scala.binary.version} instead of just 2.10 e56ca9d [Prashant Sharma] Print an error if build for 2.10 and 2.11 is spotted. 937c0b8 [Prashant Sharma] SCALA_VERSION -> SPARK_SCALA_VERSION cb059b0 [Prashant Sharma] Code review 0476e5e [Prashant Sharma] Scala 2.11 support with repl and all build changes.
* [SPARK-4047] - Generate runtime warnings for example implementation of PageRankVaradharajan Mukundan2014-11-109-8/+83
| | | | | | | | | | | | | Based on SPARK-2434, this PR generates runtime warnings for example implementations (Python, Scala) of PageRank. Author: Varadharajan Mukundan <srinathsmn@gmail.com> Closes #2894 from varadharajan/SPARK-4047 and squashes the following commits: 5f9406b [Varadharajan Mukundan] [SPARK-4047] - Point users to LogisticRegressionWithSGD and LogisticRegressionWithLBFGS instead of LogisticRegressionModel 252f595 [Varadharajan Mukundan] a. Generate runtime warnings for 05a018b [Varadharajan Mukundan] Fix PageRank implementation's package reference 5c2bf54 [Varadharajan Mukundan] [SPARK-4047] - Generate runtime warnings for example implementation of PageRank
* SPARK-1297 Upgrade HBase dependency to 0.98tedyu2014-11-101-27/+136
| | | | | | | | | | | pwendell rxin Please take a look Author: tedyu <yuzhihong@gmail.com> Closes #3115 from tedyu/master and squashes the following commits: 2b079c8 [tedyu] SPARK-1297 Upgrade HBase dependency to 0.98
* Update RecoverableNetworkWordCount.scalacomcmipi2014-11-101-2/+3
| | | | | | | | | | | Trying this example, I missed the moment when the checkpoint was iniciated Author: comcmipi <pitonak@fns.uniba.sk> Closes #2735 from comcmipi/patch-1 and squashes the following commits: b6d8001 [comcmipi] Update RecoverableNetworkWordCount.scala 96fe274 [comcmipi] Update RecoverableNetworkWordCount.scala
* SPARK-2548 [STREAMING] JavaRecoverableWordCount is missingSean Owen2014-11-103-17/+159
| | | | | | | | | | | | Here's my attempt to re-port `RecoverableNetworkWordCount` to Java, following the example of its Scala and Java siblings. I fixed a few minor doc/formatting issues along the way I believe. Author: Sean Owen <sowen@cloudera.com> Closes #2564 from srowen/SPARK-2548 and squashes the following commits: 0d0bf29 [Sean Owen] Update checkpoint call as in https://github.com/apache/spark/pull/2735 35f23e3 [Sean Owen] Remove old comment about running in standalone mode 179b3c2 [Sean Owen] Re-port RecoverableNetworkWordCount to Java example, and touch up doc / formatting in related examples
* Update JavaCustomReceiver.javaxiao3212014-11-071-1/+1
| | | | | | | | | | 数组下标越界 Author: xiao321 <1042460381@qq.com> Closes #3153 from xiao321/patch-1 and squashes the following commits: 0ed17b5 [xiao321] Update JavaCustomReceiver.java
* [SPARK-4254] [mllib] MovieLensALS bug fixJoseph K. Bradley2014-11-051-1/+3
| | | | | | | | | | | | Changed code so it does not try to serialize Params. CC: mengxr debasish83 srowen Author: Joseph K. Bradley <joseph@databricks.com> Closes #3116 from jkbradley/als-bugfix and squashes the following commits: e575bd8 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into als-bugfix 9401b16 [Joseph K. Bradley] changed implicitPrefs so it is not serialized to fix MovieLensALS example bug
* [SPARK-4197] [mllib] GradientBoosting API cleanup and examples in Scala, JavaJoseph K. Bradley2014-11-053-19/+317
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ### Summary * Made it easier to construct default Strategy and BoostingStrategy and to set parameters using simple types. * Added Scala and Java examples for GradientBoostedTrees * small cleanups and fixes ### Details GradientBoosting bug fixes (“bug” = bad default options) * Force boostingStrategy.weakLearnerParams.algo = Regression * Force boostingStrategy.weakLearnerParams.impurity = impurity.Variance * Only persist data if not yet persisted (since it causes an error if persisted twice) BoostingStrategy * numEstimators: renamed to numIterations * removed subsamplingRate (duplicated by Strategy) * removed categoricalFeaturesInfo since it belongs with the weak learner params (since boosting can be oblivious to feature type) * Changed algo to var (not val) and added BeanProperty, with overload taking String argument * Added assertValid() method * Updated defaultParams() method and eliminated defaultWeakLearnerParams() since that belongs in Strategy Strategy (for DecisionTree) * Changed algo to var (not val) and added BeanProperty, with overload taking String argument * Added setCategoricalFeaturesInfo method taking Java Map. * Cleaned up assertValid * Changed val’s to def’s since parameters can now be changed. CC: manishamde mengxr codedeft Author: Joseph K. Bradley <joseph@databricks.com> Closes #3094 from jkbradley/gbt-api and squashes the following commits: 7a27e22 [Joseph K. Bradley] scalastyle fix 52013d5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into gbt-api e9b8410 [Joseph K. Bradley] Summary of changes
* [SPARK-3573][MLLIB] Make MLlib's Vector compatible with SQL's SchemaRDDXiangrui Meng2014-11-032-0/+183
| | | | | | | | | | | | | | | Register MLlib's Vector as a SQL user-defined type (UDT) in both Scala and Python. With this PR, we can easily map a RDD[LabeledPoint] to a SchemaRDD, and then select columns or save to a Parquet file. Examples in Scala/Python are attached. The Scala code was copied from jkbradley. ~~This PR contains the changes from #3068 . I will rebase after #3068 is merged.~~ marmbrus jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #3070 from mengxr/SPARK-3573 and squashes the following commits: 3a0b6e5 [Xiangrui Meng] organize imports 236f0a0 [Xiangrui Meng] register vector as UDT and provide dataset examples
* [SPARK-3161][MLLIB] Adding a node Id caching mechanism for training deci...Sung Chung2014-11-011-2/+23
| | | | | | | | | | ...sion trees. jkbradley mengxr chouqin Please review this. Author: Sung Chung <schung@alpinenow.com> Closes #2868 from codedeft/SPARK-3161 and squashes the following commits: 5f5a156 [Sung Chung] [SPARK-3161][MLLIB] Adding a node Id caching mechanism for training decision trees.
* [SPARK-4142][GraphX] Default numEdgePartitionsJoseph E. Gonzalez2014-11-011-3/+3
| | | | | | | | | | Changing the default number of edge partitions to match spark parallelism. Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #3006 from jegonzal/default_partitions and squashes the following commits: a9a5c4f [Joseph E. Gonzalez] Changing the default number of edge partitions to match spark parallelism
* Streaming KMeans [MLLIB][SPARK-3254]freeman2014-10-311-0/+77
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This adds a Streaming KMeans algorithm to MLlib. It uses an update rule that generalizes the mini-batch KMeans update to incorporate a decay factor, which allows past data to be forgotten. The decay factor can be specified explicitly, or via a more intuitive "fractional decay" setting, in units of either data points or batches. The PR includes: - StreamingKMeans algorithm with decay factor settings - Usage example - Additions to documentation clustering page - Unit tests of basic behavior and decay behaviors tdas mengxr rezazadeh Author: freeman <the.freeman.lab@gmail.com> Author: Jeremy Freeman <the.freeman.lab@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #2942 from freeman-lab/streaming-kmeans and squashes the following commits: b2e5b4a [freeman] Fixes to docs / examples 078617c [Jeremy Freeman] Merge pull request #1 from mengxr/SPARK-3254 2e682c0 [Xiangrui Meng] take discount on previous weights; use BLAS; detect dying clusters 0411bf5 [freeman] Change decay parameterization 9f7aea9 [freeman] Style fixes 374a706 [freeman] Formatting ad9bdc2 [freeman] Use labeled points and predictOnValues in examples 77dbd3f [freeman] Make initialization check an assertion 9cfc301 [freeman] Make random seed an argument 44050a9 [freeman] Simpler constructor c7050d5 [freeman] Fix spacing 2899623 [freeman] Use pattern matching for clarity a4a316b [freeman] Use collect 1472ec5 [freeman] Doc formatting ea22ec8 [freeman] Fix imports 2086bdc [freeman] Log cluster center updates ea9877c [freeman] More documentation 9facbe3 [freeman] Bug fix 5db7074 [freeman] Example usage for StreamingKMeans f33684b [freeman] Add explanation and example to docs b5b5f8d [freeman] Add better documentation a0fd790 [freeman] Merge remote-tracking branch 'upstream/master' into streaming-kmeans 9fd9c15 [freeman] Merge remote-tracking branch 'upstream/master' into streaming-kmeans b93350f [freeman] Streaming KMeans with decay
* [MLLIB] SPARK-1547: Add Gradient Boosting to MLlibManish Amde2014-10-311-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Given the popular demand for gradient boosting and AdaBoost in MLlib, I am creating a WIP branch for early feedback on gradient boosting with AdaBoost to follow soon after this PR is accepted. This is based on work done along with hirakendu that was pending due to decision tree optimizations and random forests work. Ideally, boosting algorithms should work with any base learners. This will soon be possible once the MLlib API is finalized -- we want to ensure we use a consistent interface for the underlying base learners. In the meantime, this PR uses decision trees as base learners for the gradient boosting algorithm. The current PR allows "pluggable" loss functions and provides least squares error and least absolute error by default. Here is the task list: - [x] Gradient boosting support - [x] Pluggable loss functions - [x] Stochastic gradient boosting support – Re-use the BaggedPoint approach used for RandomForest. - [x] Binary classification support - [x] Support configurable checkpointing – This approach will avoid long lineage chains. - [x] Create classification and regression APIs - [x] Weighted Ensemble Model -- created a WeightedEnsembleModel class that can be used by ensemble algorithms such as random forests and boosting. - [x] Unit Tests Future work: + Multi-class classification is currently not supported by this PR since it requires discussion on the best way to support "deviance" as a loss function. + BaggedRDD caching -- Avoid repeating feature to bin mapping for each tree estimator after standard API work is completed. cc: jkbradley hirakendu mengxr etrain atalwalkar chouqin Author: Manish Amde <manish9ue@gmail.com> Author: manishamde <manish9ue@gmail.com> Closes #2607 from manishamde/gbt and squashes the following commits: 991c7b5 [Manish Amde] public api ff2a796 [Manish Amde] addressing comments b4c1318 [Manish Amde] removing spaces 8476b6b [Manish Amde] fixing line length 0183cb9 [Manish Amde] fixed naming and formatting issues 1c40c33 [Manish Amde] add newline, removed spaces e33ab61 [Manish Amde] minor comment eadbf09 [Manish Amde] parameter renaming 035a2ed [Manish Amde] jkbradley formatting suggestions 9f7359d [Manish Amde] simplified gbt logic and added more tests 49ba107 [Manish Amde] merged from master eff21fe [Manish Amde] Added gradient boosting tests 3fd0528 [Manish Amde] moved helper methods to new class a32a5ab [Manish Amde] added test for subsampling without replacement 781542a [Manish Amde] added support for fractional subsampling with replacement 3a18cc1 [Manish Amde] cleaned up api for conversion to bagged point and moved tests to it's own test suite 0e81906 [Manish Amde] improving caching unpersisting logic d971f73 [Manish Amde] moved RF code to use WeightedEnsembleModel class fee06d3 [Manish Amde] added weighted ensemble model 1b01943 [Manish Amde] add weights for base learners 9bc6e74 [Manish Amde] adding random seed as parameter d2c8323 [Manish Amde] Merge branch 'master' into gbt 2ae97b7 [Manish Amde] added documentation for the loss classes 9366b8f [Manish Amde] minor: using numTrees instead of trees.size 3b43896 [Manish Amde] added learning rate for prediction 9b2e35e [Manish Amde] Merge branch 'master' into gbt 6a11c02 [manishamde] fixing formatting 823691b [Manish Amde] fixing RF test 1f47941 [Manish Amde] changing access modifier 5b67102 [Manish Amde] shortened parameter list 5ab3796 [Manish Amde] minor reformatting 9155a9d [Manish Amde] consolidated boosting configuration and added public API 631baea [Manish Amde] Merge branch 'master' into gbt 2cb1258 [Manish Amde] public API support 3b8ffc0 [Manish Amde] added documentation 8e10c63 [Manish Amde] modified unpersist strategy f62bc48 [Manish Amde] added unpersist bdca43a [Manish Amde] added timing parameters 2fbc9c7 [Manish Amde] fixing binomial classification prediction 6dd4dd8 [Manish Amde] added support for log loss 9af0231 [Manish Amde] classification attempt 62cc000 [Manish Amde] basic checkpointing 4784091 [Manish Amde] formatting 78ed452 [Manish Amde] added newline and fixed if statement 3973dd1 [Manish Amde] minor indicating subsample is double during comparison aa8fae7 [Manish Amde] minor refactoring 1a8031c [Manish Amde] sampling with replacement f1c9ef7 [Manish Amde] Merge branch 'master' into gbt cdceeef [Manish Amde] added documentation 6251fd5 [Manish Amde] modified method name 5538521 [Manish Amde] disable checkpointing for now 0ae1c0a [Manish Amde] basic gradient boosting code from earlier branches
* [SPARK-3838][examples][mllib][python] Word2Vec example in pythonAnant2014-10-311-0/+50
| | | | | | | | | | | | | | | | | | | | This pull request refers to issue: https://issues.apache.org/jira/browse/SPARK-3838 Python example for word2vec mengxr Author: Anant <anant.asty@gmail.com> Closes #2952 from anantasty/SPARK-3838 and squashes the following commits: 87bd723 [Anant] remove stop line 4bd439e [Anant] Changes as per code review. Fized error in word2vec python example, simplified example in docs. 3d3c9ee [Anant] Added empty line after python imports 0c90c31 [Anant] Fixed erroneous code. I was still treating each line to be a single word instead of 16 words ee4f5f6 [Anant] Fixes from code review comments c637bcf [Anant] Added word2vec python example to docs 269f31f [Anant] added example in docs c015b14 [Anant] Added python example for word2vec
* SPARK-4022 [CORE] [MLLIB] Replace colt dependency (LGPL) with commons-mathSean Owen2014-10-273-96/+87
| | | | | | | | | | | | | | | This change replaces usages of colt with commons-math3 equivalents, and makes some minor necessary adjustments to related code and tests to match. Author: Sean Owen <sowen@cloudera.com> Closes #2928 from srowen/SPARK-4022 and squashes the following commits: 61a232f [Sean Owen] Fix failure due to different sampling in JavaAPISuite.sample() 16d66b8 [Sean Owen] Simplify seeding with call to reseedRandomGenerator a1a78e0 [Sean Owen] Use Well19937c 31c7641 [Sean Owen] Fix Python Poisson test by choosing a different seed; about 88% of seeds should work but 1 didn't, it seems 5c9c67f [Sean Owen] Additional test fixes from review d8f88e0 [Sean Owen] Replace colt with commons-math3. Some tests do not pass yet.
* Just fixing comment that shows usageanant asthana2014-10-261-1/+1
| | | | | | | | Author: anant asthana <anant.asty@gmail.com> Closes #2948 from anantasty/patch-1 and squashes the following commits: d8fea0b [anant asthana] Just fixing comment that shows usage
* [SPARK-2321] Stable pull-based progress / status APIJosh Rosen2014-10-251-0/+70
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This pull request is a first step towards the implementation of a stable, pull-based progress / status API for Spark (see [SPARK-2321](https://issues.apache.org/jira/browse/SPARK-2321)). For now, I'd like to discuss the basic implementation, API names, and overall interface design. Once we arrive at a good design, I'll go back and add additional methods to expose more information via these API. #### Design goals: - Pull-based API - Usable from Java / Scala / Python (eventually, likely with a wrapper) - Can be extended to expose more information without introducing binary incompatibilities. - Returns immutable objects. - Don't leak any implementation details, preserving our freedom to change the implementation. #### Implementation: - Add public methods (`getJobInfo`, `getStageInfo`) to SparkContext to allow status / progress information to be retrieved. - Add public interfaces (`SparkJobInfo`, `SparkStageInfo`) for our API return values. These interfaces consist entirely of Java-style getter methods. The interfaces are currently implemented in Java. I decided to explicitly separate the interface from its implementation (`SparkJobInfoImpl`, `SparkStageInfoImpl`) in order to prevent users from constructing these responses themselves. -Allow an existing JobProgressListener to be used when constructing a live SparkUI. This allows us to re-use this listeners in the implementation of this status API. There are a few reasons why this listener re-use makes sense: - The status API and web UI are guaranteed to show consistent information. - These listeners are already well-tested. - The same garbage-collection / information retention configurations can apply to both this API and the web UI. - Extend JobProgressListener to maintain `jobId -> Job` and `stageId -> Stage` mappings. The progress API methods are implemented in a separate trait that's mixed into SparkContext. This helps to avoid SparkContext.scala from becoming larger and more difficult to read. Author: Josh Rosen <joshrosen@databricks.com> Author: Josh Rosen <joshrosen@apache.org> Closes #2696 from JoshRosen/progress-reporting-api and squashes the following commits: e6aa78d [Josh Rosen] Add tests. b585c16 [Josh Rosen] Accept SparkListenerBus instead of more specific subclasses. c96402d [Josh Rosen] Address review comments. 2707f98 [Josh Rosen] Expose current stage attempt id c28ba76 [Josh Rosen] Update demo code: 646ff1d [Josh Rosen] Document spark.ui.retainedJobs. 7f47d6d [Josh Rosen] Clean up SparkUI constructors, per Andrew's feedback. b77b3d8 [Josh Rosen] Merge remote-tracking branch 'origin/master' into progress-reporting-api 787444c [Josh Rosen] Move status API methods into trait that can be mixed into SparkContext. f9a9a00 [Josh Rosen] More review comments: 3dc79af [Josh Rosen] Remove creation of unused listeners in SparkContext. 249ca16 [Josh Rosen] Address several review comments: da5648e [Josh Rosen] Add example of basic progress reporting in Java. 7319ffd [Josh Rosen] Add getJobIdsForGroup() and num*Tasks() methods. cc568e5 [Josh Rosen] Add note explaining that interfaces should not be implemented outside of Spark. 6e840d4 [Josh Rosen] Remove getter-style names and "consistent snapshot" semantics: 08cbec9 [Josh Rosen] Begin to sketch the interfaces for a stable, public status API. ac2d13a [Josh Rosen] Add jobId->stage, stageId->stage mappings in JobProgressListener 24de263 [Josh Rosen] Create UI listeners in SparkContext instead of in Tabs:
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