Update #11
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As [reported][1] on the mailing list, GraphX throws
```
java.lang.ClassCastException: java.lang.Long cannot be cast to scala.Tuple2
at org.apache.spark.graphx.impl.RoutingTableMessageSerializer$$anon$1$$anon$2.writeObject(Serializers.scala:39)
at org.apache.spark.storage.DiskBlockObjectWriter.write(BlockObjectWriter.scala:195)
at org.apache.spark.util.collection.ExternalSorter.spillToMergeableFile(ExternalSorter.scala:329)
```
when sort-based shuffle attempts to spill to disk. This is because GraphX defines custom serializers for shuffling pair RDDs that assume Spark will always serialize the entire pair object rather than breaking it up into its components. However, the spill code path in sort-based shuffle [violates this assumption][2].
GraphX uses the custom serializers to compress vertex ID keys using variable-length integer encoding. However, since the serializer can no longer rely on the key and value being serialized and deserialized together, performing such encoding would either require writing a tag byte (costly) or maintaining state in the serializer and assuming that serialization calls will alternate between key and value (fragile).
Instead, this PR simply removes the custom serializers. This causes a **10% slowdown** (494 s to 543 s) and **16% increase in per-iteration communication** (2176 MB to 2518 MB) for PageRank (averages across 3 trials, 10 iterations per trial, uk-2007-05 graph, 16 r3.2xlarge nodes).
[1]: http://apache-spark-user-list.1001560.n3.nabble.com/java-lang-ClassCastException-java-lang-Long-cannot-be-cast-to-scala-Tuple2-td13926.html#a14501
[2]: https://github.com/apache/spark/blob/f9d6220c792b779be385f3022d146911a22c2130/core/src/main/scala/org/apache/spark/util/collection/ExternalSorter.scala#L329
Author: Ankur Dave <ankurdave@gmail.com>
Closes #2503 from ankurdave/SPARK-3649 and squashes the following commits:
a49c2ad [Ankur Dave] [SPARK-3649] Remove GraphX custom serializers
In running-on-yarn.md, a link to YARN overview is here. But the URL is to YARN alpha's. It should be stable's. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #3196 from sarutak/SPARK-4330 and squashes the following commits: 30baa21 [Kousuke Saruta] Fixed running-on-yarn.md to point proper URL for YARN
This PR check all of the existing Python MLlib API to make sure that numpy.array is supported as Vector (also RDD of numpy.array). It also improve some docstring and doctest. cc mateiz mengxr Author: Davies Liu <davies@databricks.com> Closes #3189 from davies/numpy and squashes the following commits: d5057c4 [Davies Liu] fix tests 6987611 [Davies Liu] support numpy.array for all MLlib API
Netty's DefaultFileRegion requires a FileDescriptor in its constructor, which means we need to have a opened file handle. In super large workloads, this could lead to too many open files due to the way these file descriptors are cleaned. This pull request creates a new LazyFileRegion that initializes the FileDescriptor when we are sending data for the first time. Author: Reynold Xin <rxin@databricks.com> Author: Reynold Xin <rxin@apache.org> Closes #3172 from rxin/lazyFD and squashes the following commits: 0bdcdc6 [Reynold Xin] Added reference to Netty's DefaultFileRegion d4564ae [Reynold Xin] Added SparkConf to the ctor argument of IndexShuffleBlockManager. 6ed369e [Reynold Xin] Code review feedback. 04cddc8 [Reynold Xin] [SPARK-4307] Initialize FileDescriptor lazily in FileRegion.
Handle exception in SparkSinkSuite, please refer to [SPARK-4295] Author: maji2014 <maji3@asiainfo.com> Closes #3177 from maji2014/spark-4295 and squashes the following commits: 312620a [maji2014] change a new statement for spark-4295 24c3d21 [maji2014] add log4j.properties for SparkSinkSuite and spark-4295 c807bf6 [maji2014] Fix exception in SparkSinkSuite
…ka 0.8 Update the KafkaReceiver's behavior when auto.offset.reset is set. In Kafka 0.8, `auto.offset.reset` is a hint for out-range offset to seek to the beginning or end of the partition. While in the previous code `auto.offset.reset` is a enforcement to seek to the beginning or end immediately, this is different from Kafka 0.8 defined behavior. Also deleting extesting ZK metadata in Receiver when multiple consumers are launched will introduce issue as mentioned in [SPARK-2383](https://issues.apache.org/jira/browse/SPARK-2383). So Here we change to offer user to API to explicitly reset offset before create Kafka stream, while in the meantime keep the same behavior as Kafka 0.8 for parameter `auto.offset.reset`. @tdas, would you please review this PR? Thanks a lot. Author: jerryshao <saisai.shao@intel.com> Closes #1420 from jerryshao/kafka-fix and squashes the following commits: d6ae94d [jerryshao] Address the comment to remove the resetOffset() function de3a4c8 [jerryshao] Fix compile error 4a1c3f9 [jerryshao] Doc changes b2c1430 [jerryshao] Move offset reset to a helper function to let user explicitly delete ZK metadata by calling this API fac8fd6 [jerryshao] Changes to align with Kafka 0.8
…luggable Author: Prashant Sharma <prashant.s@imaginea.com> Closes #771 from ScrapCodes/deploy-failover-pluggable and squashes the following commits: 29ba440 [Prashant Sharma] fixed a compilation error fef35ec [Prashant Sharma] Code review 57ee6f0 [Prashant Sharma] SPARK-1830 Deploy failover, Make Persistence engine and LeaderAgent Pluggable.
… module SPARK-3797 introduced the `network/yarn` module, but its YARN code depends on YARN APIs not present in older versions covered by the `yarn-alpha` profile. As a result builds like `mvn -Pyarn-alpha -Phadoop-0.23 -Dhadoop.version=0.23.7 -DskipTests clean package` fail. The solution is just to not build `network/yarn` with profile `yarn-alpha`. Author: Sean Owen <sowen@cloudera.com> Closes #3167 from srowen/SPARK-4305 and squashes the following commits: 88938cb [Sean Owen] Don't build network/yarn in yarn-alpha profile as it won't compile
… be volatile In YarnClientSchedulerBackend, a variable "stopping" is used as a flag and it's accessed by some threads so it should be volatile. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #3143 from sarutak/stopping-flag-volatile and squashes the following commits: 58fdcc9 [Kousuke Saruta] Marked stoppig flag as volatile
Author: Timothy Chen <tnachen@gmail.com> Closes #1487 from tnachen/resource_offer_refactor and squashes the following commits: 4ea5dec [Timothy Chen] Rebase from master and address comments 9ccab09 [Timothy Chen] Address review comments e6494dc [Timothy Chen] Refactor class loading 8207428 [Timothy Chen] Refactor mesos scheduler resourceOffers and add unit test
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.
Before: [info] GradientBoostingSuite: [info] - Regression with continuous features: SquaredError (22 seconds, 115 milliseconds) [info] - Regression with continuous features: Absolute Error (19 seconds, 330 milliseconds) [info] - Binary classification with continuous features: Log Loss (19 seconds, 17 milliseconds) After: [info] - Regression with continuous features: SquaredError (7 seconds, 69 milliseconds) [info] - Regression with continuous features: Absolute Error (4 seconds, 617 milliseconds) [info] - Binary classification with continuous features: Log Loss (4 seconds, 658 milliseconds) cc: mengxr, jkbradley Author: Manish Amde <manish9ue@gmail.com> Closes #3214 from manishamde/gbt_test_speedup and squashes the following commits: 8994552 [Manish Amde] reducing gbt test run times
aggregateMessages enables neighborhood computation similarly to mapReduceTriplets, but it introduces two API improvements: 1. Messages are sent using an imperative interface based on EdgeContext rather than by returning an iterator of messages. 2. Rather than attempting bytecode inspection, the required triplet fields must be explicitly specified by the user by passing a TripletFields object. This fixes SPARK-3936. Additionally, this PR includes the following optimizations for aggregateMessages and EdgePartition: 1. EdgePartition now stores local vertex ids instead of global ids. This avoids hash lookups when looking up vertex attributes and aggregating messages. 2. Internal iterators in aggregateMessages are inlined into a while loop. In total, these optimizations were tested to provide a 37% speedup on PageRank (uk-2007-05 graph, 10 iterations, 16 r3.2xlarge machines, sped up from 513 s to 322 s). Subsumes #2815. Also fixes SPARK-4173. Author: Ankur Dave <ankurdave@gmail.com> Closes #3100 from ankurdave/aggregateMessages and squashes the following commits: f5b65d0 [Ankur Dave] Address @rxin comments on #3054 and #3100 1e80aca [Ankur Dave] Add aggregateMessages, which supersedes mapReduceTriplets 194a2df [Ankur Dave] Test triplet iterator in EdgePartition serialization test e0f8ecc [Ankur Dave] Take activeSet in ExistingEdgePartitionBuilder c85076d [Ankur Dave] Readability improvements b567be2 [Ankur Dave] iter.foreach -> while loop 4a566dc [Ankur Dave] Optimizations for mapReduceTriplets and EdgePartition
See inline comment about the bug. I also did some code clean-up. dbtsai I moved `update` to a private method of `MultivariateOnlineSummarizer`. I don't think it will cause performance regression, but it would be great if you have some time to test. Author: Xiangrui Meng <meng@databricks.com> Closes #3220 from mengxr/SPARK-4355 and squashes the following commits: 5ef601f [Xiangrui Meng] fix OnlineSummarizer.merge when other.mean is zero and some code clean-up
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
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
Before: ``` Exception in thread "main" java.lang.Exception: Could not load user defined classes inside of executors at org.apache.spark.deploy.JarCreationTest$.main(SparkSubmitSuite.scala:471) at org.apache.spark.deploy.JarCreationTest.main(SparkSubmitSuite.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ``` After: ``` Exception in thread "main" java.lang.Exception: Could not load user class from jar: java.lang.UnsupportedClassVersionError: SparkSubmitClassA : Unsupported major.minor version 51.0 java.lang.ClassLoader.defineClass1(Native Method) java.lang.ClassLoader.defineClass(ClassLoader.java:643) ... at org.apache.spark.deploy.JarCreationTest$.main(SparkSubmitSuite.scala:472) at org.apache.spark.deploy.JarCreationTest.main(SparkSubmitSuite.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ``` Author: Andrew Or <andrew@databricks.com> Closes #3212 from andrewor14/submit-suite-message and squashes the following commits: 7779248 [Andrew Or] Format exception 8fe6719 [Andrew Or] Better exception message from failed test
This is another addendum to #3082, which added the Yarn shuffle service to run inside the NM. This PR makes the feature much more usable by packaging enough dependencies into the jar to run the service inside an NM. After these changes, the user can run `./make-distribution.sh` and find a `spark-network-yarn*.jar` in their `lib` directory. The equivalent change is done in SBT by making the `network-yarn` module an assembly project. Author: Andrew Or <andrew@databricks.com> Closes #3147 from andrewor14/yarn-shuffle-build and squashes the following commits: bda58d0 [Andrew Or] Fix line too long 81e9705 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-build fb7f398 [Andrew Or] Rename jar to spark-{VERSION}-yarn-shuffle.jar 65db822 [Andrew Or] Actually mark slf4j as provided abcefd1 [Andrew Or] Do the same for SBT c653028 [Andrew Or] Package network-yarn and its dependencies
1. Add EdgeActiveness enum to represent activeness criteria more cleanly than using booleans. 2. Comments and whitespace. Author: Ankur Dave <ankurdave@gmail.com> Closes #3231 from ankurdave/aggregateMessages-followup and squashes the following commits: 3d485c3 [Ankur Dave] Internal cleanup for aggregateMessages
This discourages users from calling the VertexRDD and EdgeRDD constructor and makes it easier for future changes to ensure backward compatibility. Author: Ankur Dave <ankurdave@gmail.com> Closes #2530 from ankurdave/SPARK-3666 and squashes the following commits: d681f45 [Ankur Dave] Define getPartitions and compute in abstract class for MIMA 1472390 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into SPARK-3666 24201d4 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into SPARK-3666 cbe15f2 [Ankur Dave] Remove specialized annotation from VertexRDD and EdgeRDD 931b587 [Ankur Dave] Use abstract class instead of trait for binary compatibility 9ba4ec4 [Ankur Dave] Mark (Vertex|Edge)RDDImpl constructors package-private 620e603 [Ankur Dave] Extract VertexRDD interface and move implementation to VertexRDDImpl 55b6398 [Ankur Dave] Extract EdgeRDD interface and move implementation to EdgeRDDImpl
The wholeFile() can not read compressed files, it should be, just like textFile(). Author: Davies Liu <davies@databricks.com> Closes #3005 from davies/whole and squashes the following commits: a43fcfb [Davies Liu] remove semicolon c83571a [Davies Liu] remove = if return type is Unit 83c844f [Davies Liu] Merge branch 'master' of github.com:apache/spark into whole 22e8b3e [Davies Liu] support compressed file in wholeTextFile
This involves a few main changes: - Log all output message to the log file. Previously the log file was not useful because it did not indicate progress. - Remove hive-site.xml in sbt_hive_app to avoid interference - Add the appropriate repositories for new dependencies
We want to make sure there is at most one spark context inside the same jvm. JoshRosen Author: Xiangrui Meng <meng@databricks.com> Closes #3235 from mengxr/SPARK-4373 and squashes the following commits: 6574b69 [Xiangrui Meng] rename LocalSparkContext to MLlibTestSparkContext 913d48d [Xiangrui Meng] make sure there is at most one spark context inside the same jvm
Author: Aaron Davidson <aaron@databricks.com> Closes #3155 from aarondav/conf and squashes the following commits: 7045e77 [Aaron Davidson] Add mesos comment 4770f6e [Aaron Davidson] [SPARK-4370] [Core] Limit number of Netty cores based on executor size
…s where there ar... ...e 0 positive or 0 negative examples. Author: Andrew Bullen <andrew.bullen@workday.com> Closes #3118 from abull/master and squashes the following commits: c2bf2b1 [Andrew Bullen] [SPARK-4256] Update Code formatting for BinaryClassificationMetricsSpec 36b0533 [Andrew Bullen] [SYMAN-4256] Extract BinaryClassificationMetricsSuite assertions into private method 4d2f79a [Andrew Bullen] [SPARK-4256] Refactor classification metrics tests - extract comparison functions in test f411e70 [Andrew Bullen] [SPARK-4256] Define precision as 1.0 when there are no positive examples; update code formatting per pull request comments d9a09ef [Andrew Bullen] Make Binary Evaluation Metrics functions defined in cases where there are 0 positive or 0 negative examples.
This PR rename random.py to rand.py to avoid the side affects of conflict with random module, but still keep the same interface as before.
```
>>> from pyspark.mllib.random import RandomRDDs
```
```
$ pydoc pyspark.mllib.random
Help on module random in pyspark.mllib:
NAME
random - Python package for random data generation.
FILE
/Users/davies/work/spark/python/pyspark/mllib/rand.py
CLASSES
__builtin__.object
pyspark.mllib.random.RandomRDDs
class RandomRDDs(__builtin__.object)
| Generator methods for creating RDDs comprised of i.i.d samples from
| some distribution.
|
| Static methods defined here:
|
| normalRDD(sc, size, numPartitions=None, seed=None)
```
cc mengxr
reference link: http://xion.org.pl/2012/05/06/hacking-python-imports/
Author: Davies Liu <davies@databricks.com>
Closes #3216 from davies/random and squashes the following commits:
7ac4e8b [Davies Liu] rename random.py to rand.py
…ThriftServer2 This PR disables HiveThriftServer2 asynchronous execution by setting `runInBackground` argument in `ExecuteStatementOperation` to `false`, and reverting `SparkExecuteStatementOperation.run` in Hive 13 shim to Hive 12 version. This change makes Simba ODBC driver v1.0.0.1000 work. <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/3506) <!-- Reviewable:end --> Author: Cheng Lian <lian@databricks.com> Closes #3506 from liancheng/disable-async-exec and squashes the following commits: 593804d [Cheng Lian] Disables asynchronous execution in Hive 0.13.1 HiveThriftServer2
when building spark by sbt, the function “runAlternateBoot" in sbt/sbt-launch-lib.bash is not used. And this function is not used by spark code. So I think this function is not necessary. And the option of "sbt.boot.properties" can be configured in the command line when building spark, eg: sbt/sbt assembly -Dsbt.boot.properties=$bootpropsfile. The file from https://github.com/sbt/sbt-launcher-package is changed. And the function “runAlternateBoot" is deleted in upstream project. I think spark project should delete this function in file sbt/sbt-launch-lib.bash. Thanks. Author: KaiXinXiaoLei <huleilei1@huawei.com> Closes #3224 from KaiXinXiaoLei/deleteFunction and squashes the following commits: e8eac49 [KaiXinXiaoLei] Delete blank lines. efe36d4 [KaiXinXiaoLei] Delete unnecessary function
…rror. Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #3058 from ueshin/issues/SPARK-4193 and squashes the following commits: e096bb1 [Takuya UESHIN] Add a plugin declaration to pluginManagement. 6762ec2 [Takuya UESHIN] Fix usage of -Xdoclint javadoc option. fdb280a [Takuya UESHIN] Fix Javadoc errors. 4745f3c [Takuya UESHIN] Merge branch 'master' into issues/SPARK-4193 923e2f0 [Takuya UESHIN] Use doclint option `-missing` instead of `none`. 30d6718 [Takuya UESHIN] Fix Javadoc errors. b548017 [Takuya UESHIN] Disable doclint in Java 8 to prevent from build error.
The security manager adds a lot of overhead to the runtime of the app, and causes a severe performance regression. Even stubbing out all unneeded methods (all except checkExit()) does not help. So, instead, penalize users who do an explicit System.exit() by leaving them in "undefined behavior" territory: if they do that, the Yarn backend won't be able to report the final app status to the RM. The result is that the final status of the application might not match the user's expectations. One side-effect of the change is that users who do an explicit System.exit() will lose the AM retry functionality. Since there is no way to know if the exit was because of success or failure, the AM right now errs on the side of it being a successful exit. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #3484 from vanzin/SPARK-4584 and squashes the following commits: 21f2502 [Marcelo Vanzin] Do not retry apps that use System.exit(). 4198b3b [Marcelo Vanzin] [SPARK-4584] [yarn] Remove security manager from Yarn AM.
This looks like a one-liner, so I took a shot at it. There can be no fixed default availability zone since the names are different per region. But the default behavior can be documented:
```
if opts.zone == "":
opts.zone = random.choice(conn.get_all_zones()).name
```
Author: Sean Owen <sowen@cloudera.com>
Closes #3454 from srowen/SPARK-1450 and squashes the following commits:
9193cf3 [Sean Owen] Document that --zone defaults to a single random zone
…empDir() `File.exists()` and `File.mkdirs()` only throw `SecurityException` instead of `IOException`. Then, when an exception is thrown, `dir` should be reset too. Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #3449 from viirya/fix_createtempdir and squashes the following commits: 36cacbd [Liang-Chi Hsieh] Use proper exception and reset variable.
This PR re-introduces [0e648bc](0e648bc) from PR #2339, which somehow never made it into the codebase. Additionally, it removes a now-unnecessary linear backoff on the SSH checks since we are blocking on EC2 status checks before testing SSH. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Closes #3195 from nchammas/remove-ec2-ssh-backoff and squashes the following commits: efb29e1 [Nicholas Chammas] Revert "Remove linear backoff." ef3ca99 [Nicholas Chammas] reuse conn adb4eaa [Nicholas Chammas] Remove linear backoff. 55caa24 [Nicholas Chammas] Check EC2 status checks before SSH.
…for debugging In -launch-lib.bash, -Xdebug option is used for debugging. We should use -agentlib option for Java 6+. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2904 from sarutak/SPARK-4057 and squashes the following commits: 39b5320 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-4057 26b4af8 [Kousuke Saruta] Improved java option for debugging
Added a ClassTag parameter to CompactBuffer. So CompactBuffer[T] can create primitive arrays for primitive types. It will reduce the memory usage for primitive types significantly and only pay minor performance lost.
Here is my test code:
```Scala
// Call org.apache.spark.util.SizeEstimator.estimate
def estimateSize(obj: AnyRef): Long = {
val c = Class.forName("org.apache.spark.util.SizeEstimator$")
val f = c.getField("MODULE$")
val o = f.get(c)
val m = c.getMethod("estimate", classOf[Object])
m.setAccessible(true)
m.invoke(o, obj).asInstanceOf[Long]
}
sc.parallelize(1 to 10000).groupBy(_ => 1).foreach {
case (k, v) =>
println(v.getClass() + " size: " + estimateSize(v))
}
```
Using the previous CompactBuffer outputed
```
class org.apache.spark.util.collection.CompactBuffer size: 313358
```
Using the new CompactBuffer outputed
```
class org.apache.spark.util.collection.CompactBuffer size: 65712
```
In this case, the new `CompactBuffer` only used 20% memory of the previous one. It's really helpful for `groupByKey` when using a primitive value.
Author: zsxwing <zsxwing@gmail.com>
Closes #3378 from zsxwing/SPARK-4505 and squashes the following commits:
4abdbba [zsxwing] Add a ClassTag parameter to reduce the memory usage of CompactBuffer[T] when T is a primitive type
This will fix SPARK-4507. For pull requests that reference multiple JIRAs in their titles, it would be helpful if the PR merge script offered to close all of them. Author: Takayuki Hasegawa <takayuki.hasegawa0311@gmail.com> Closes #3428 from hase1031/SPARK-4507 and squashes the following commits: bf6d64b [Takayuki Hasegawa] SPARK-4507: try to resolve issue when no JIRAs in title 401224c [Takayuki Hasegawa] SPARK-4507: moved codes as before ce89021 [Takayuki Hasegawa] SPARK-4507: PR merge script should support closing multiple JIRA tickets
…ilding for Scala 2.11'. To build with Scala 2.11, we have to execute `change-version-to-2.11.sh` before Maven execute, otherwise inter-module dependencies are broken. Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #3361 from ueshin/docs/building-spark_2.11 and squashes the following commits: 1d29126 [Takuya UESHIN] Add instruction to use change-version-to-2.11.sh in 'Building for Scala 2.11'.
This PR adds the Spark version number to the UI footer; this is how it looks:  Author: Sean Owen <sowen@cloudera.com> Closes #3410 from srowen/SPARK-2143 and squashes the following commits: e9b3a7a [Sean Owen] Add Spark version to footer
…cluster mode If using spark-sql in yarn-cluster mode, print an error infomation just as the spark shell in yarn-cluster mode. Author: carlmartin <carlmartinmax@gmail.com> Author: huangzhaowei <carlmartinmax@gmail.com> Closes #3479 from SaintBacchus/sparkSqlShell and squashes the following commits: 35829a9 [carlmartin] improve the description of comment e6c1eb7 [carlmartin] add a comment in bin/spark-sql to remind user who wants to change the class f1c5c8d [carlmartin] Merge branch 'master' into sparkSqlShell 8e112c5 [huangzhaowei] singular form ec957bc [carlmartin] Add the some error infomation if using spark-sql in yarn-cluster mode 7bcecc2 [carlmartin] Merge branch 'master' of https://github.com/apache/spark into codereview 4fad75a [carlmartin] Add the Error infomation using spark-sql in yarn-cluster mode
<!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/3498) <!-- Reviewable:end --> Author: Cheng Lian <lian@databricks.com> Closes #3498 from liancheng/fix-sql-doc-typo and squashes the following commits: 865ecd7 [Cheng Lian] Fixes formatting typo in SQL programming guide
Author: Prabeesh K <prabsmails@gmail.com> Closes #3495 from prabeesh/master and squashes the following commits: ab03d50 [Prabeesh K] Update pom.xml 8c6437e [Prabeesh K] Revert e10b40a [Prabeesh K] version update dbac9eb [Prabeesh K] Revert ec0b1c3 [Prabeesh K] [SPARK-4632] version update a835505 [Prabeesh K] [SPARK-4632] version update 831391b [Prabeesh K] [SPARK-4632] version update
In .gitignore, there is an entry for spark-*-bin.tar.gz but considering make-distribution.sh, the name pattern should be spark-*-bin-*.tgz. This change is really small so I don't open issue in JIRA. If it's needed, please let me know. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #3529 from sarutak/fix-wrong-tgz-pattern and squashes the following commits: de3c70a [Kousuke Saruta] Fixed wrong file name pattern in .gitignore
Simply, add data/ to distributions. This adds about 291KB (compressed) to the tarball, FYI. Author: Sean Owen <sowen@cloudera.com> Closes #3480 from srowen/SPARK-2192 and squashes the following commits: 47688f1 [Sean Owen] Add data/ to distributions
If `spark.akka.frameSize` > 2047, it will overflow and become negative. Should have some assertion in `maxFrameSizeBytes` to warn people. Author: zsxwing <zsxwing@gmail.com> Closes #3527 from zsxwing/SPARK-4664 and squashes the following commits: 0089c7a [zsxwing] Throw an exception when spark.akka.frameSize > 2047
Author: zsxwing <zsxwing@gmail.com> Closes #3521 from zsxwing/SPARK-4661 and squashes the following commits: 03cbe3f [zsxwing] Minor code and docs cleanup
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…if sql has null
val jsc = new org.apache.spark.api.java.JavaSparkContext(sc)
val jhc = new org.apache.spark.sql.hive.api.java.JavaHiveContext(jsc)
val nrdd = jhc.hql("select null from spark_test.for_test")
println(nrdd.schema)
Then the error is thrown as follows:
scala.MatchError: NullType (of class org.apache.spark.sql.catalyst.types.NullType$)
at org.apache.spark.sql.types.util.DataTypeConversions$.asJavaDataType(DataTypeConversions.scala:43)
Author: YanTangZhai <hakeemzhai@tencent.com>
Author: yantangzhai <tyz0303@163.com>
Author: Michael Armbrust <michael@databricks.com>
Closes apache#3538 from YanTangZhai/MatchNullType and squashes the following commits:
e052dff [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
4b4bb34 [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
896c7b7 [yantangzhai] fix NullType MatchError in JavaSchemaRDD when sql has null
6e643f8 [YanTangZhai] Merge pull request #11 from apache/master
e249846 [YanTangZhai] Merge pull request #10 from apache/master
d26d982 [YanTangZhai] Merge pull request #9 from apache/master
76d4027 [YanTangZhai] Merge pull request #8 from apache/master
03b62b0 [YanTangZhai] Merge pull request #7 from apache/master
8a00106 [YanTangZhai] Merge pull request #6 from apache/master
cbcba66 [YanTangZhai] Merge pull request #3 from apache/master
cdef539 [YanTangZhai] Merge pull request #1 from apache/master
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…ins an empty AttributeSet() references The sql "select * from spark_test::for_test where abs(20141202) is not null" has predicates=List(IS NOT NULL HiveSimpleUdf#org.apache.hadoop.hive.ql.udf.UDFAbs(20141202)) and partitionKeyIds=AttributeSet(). PruningPredicates is List(IS NOT NULL HiveSimpleUdf#org.apache.hadoop.hive.ql.udf.UDFAbs(20141202)). Then the exception "java.lang.IllegalArgumentException: requirement failed: Partition pruning predicates only supported for partitioned tables." is thrown. The sql "select * from spark_test::for_test_partitioned_table where abs(20141202) is not null and type_id=11 and platform = 3" with partitioned key insert_date has predicates=List(IS NOT NULL HiveSimpleUdf#org.apache.hadoop.hive.ql.udf.UDFAbs(20141202), (type_id#12 = 11), (platform#8 = 3)) and partitionKeyIds=AttributeSet(insert_date#24). PruningPredicates is List(IS NOT NULL HiveSimpleUdf#org.apache.hadoop.hive.ql.udf.UDFAbs(20141202)). Author: YanTangZhai <hakeemzhai@tencent.com> Author: yantangzhai <tyz0303@163.com> Closes apache#3556 from YanTangZhai/SPARK-4693 and squashes the following commits: 620ebe3 [yantangzhai] [SPARK-4693] [SQL] PruningPredicates may be wrong if predicates contains an empty AttributeSet() references 37cfdf5 [yantangzhai] [SPARK-4693] [SQL] PruningPredicates may be wrong if predicates contains an empty AttributeSet() references 70a3544 [yantangzhai] [SPARK-4693] [SQL] PruningPredicates may be wrong if predicates contains an empty AttributeSet() references efa9b03 [YanTangZhai] Update HiveQuerySuite.scala 72accf1 [YanTangZhai] Update HiveQuerySuite.scala e572b9a [YanTangZhai] Update HiveStrategies.scala 6e643f8 [YanTangZhai] Merge pull request #11 from apache/master e249846 [YanTangZhai] Merge pull request #10 from apache/master d26d982 [YanTangZhai] Merge pull request #9 from apache/master 76d4027 [YanTangZhai] Merge pull request #8 from apache/master 03b62b0 [YanTangZhai] Merge pull request #7 from apache/master 8a00106 [YanTangZhai] Merge pull request #6 from apache/master cbcba66 [YanTangZhai] Merge pull request #3 from apache/master cdef539 [YanTangZhai] Merge pull request #1 from apache/master
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…askTracker to reduce the chance of the communicating problem Using AkkaUtils.askWithReply in MapOutputTracker.askTracker to reduce the chance of the communicating problem Author: YanTangZhai <hakeemzhai@tencent.com> Author: yantangzhai <tyz0303@163.com> Closes apache#3785 from YanTangZhai/SPARK-4946 and squashes the following commits: 9ca6541 [yantangzhai] [SPARK-4946] [CORE] Using AkkaUtils.askWithReply in MapOutputTracker.askTracker to reduce the chance of the communicating problem e4c2c0a [YanTangZhai] Merge pull request #15 from apache/master 718afeb [YanTangZhai] Merge pull request #12 from apache/master 6e643f8 [YanTangZhai] Merge pull request #11 from apache/master e249846 [YanTangZhai] Merge pull request #10 from apache/master d26d982 [YanTangZhai] Merge pull request #9 from apache/master 76d4027 [YanTangZhai] Merge pull request #8 from apache/master 03b62b0 [YanTangZhai] Merge pull request #7 from apache/master 8a00106 [YanTangZhai] Merge pull request #6 from apache/master cbcba66 [YanTangZhai] Merge pull request #3 from apache/master cdef539 [YanTangZhai] Merge pull request #1 from apache/master
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Support ! boolean logic operator like NOT in sql as follows select * from for_test where !(col1 > col2) Author: YanTangZhai <hakeemzhai@tencent.com> Author: Michael Armbrust <michael@databricks.com> Closes apache#3555 from YanTangZhai/SPARK-4692 and squashes the following commits: 1a9f605 [YanTangZhai] Update HiveQuerySuite.scala 7c03c68 [YanTangZhai] Merge pull request #23 from apache/master 992046e [YanTangZhai] Update HiveQuerySuite.scala ea618f4 [YanTangZhai] Update HiveQuerySuite.scala 192411d [YanTangZhai] Merge pull request #17 from YanTangZhai/master e4c2c0a [YanTangZhai] Merge pull request #15 from apache/master 1e1ebb4 [YanTangZhai] Update HiveQuerySuite.scala efc4210 [YanTangZhai] Update HiveQuerySuite.scala bd2c444 [YanTangZhai] Update HiveQuerySuite.scala 1893956 [YanTangZhai] Merge pull request #14 from marmbrus/pr/3555 59e4de9 [Michael Armbrust] make hive test 718afeb [YanTangZhai] Merge pull request #12 from apache/master 950b21e [YanTangZhai] Update HiveQuerySuite.scala 74175b4 [YanTangZhai] Update HiveQuerySuite.scala 92242c7 [YanTangZhai] Update HiveQl.scala 6e643f8 [YanTangZhai] Merge pull request #11 from apache/master e249846 [YanTangZhai] Merge pull request #10 from apache/master d26d982 [YanTangZhai] Merge pull request #9 from apache/master 76d4027 [YanTangZhai] Merge pull request #8 from apache/master 03b62b0 [YanTangZhai] Merge pull request #7 from apache/master 8a00106 [YanTangZhai] Merge pull request #6 from apache/master cbcba66 [YanTangZhai] Merge pull request #3 from apache/master cdef539 [YanTangZhai] Merge pull request #1 from apache/master
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