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* [MINOR] [DOCS] Fix the link to test building info on the wikiSean Owen2015-05-121-1/+1
| | | | | | | | Author: Sean Owen <sowen@cloudera.com> Closes #6063 from srowen/FixRunningTestsLink and squashes the following commits: db62018 [Sean Owen] Fix the link to test building info on the wiki
* Update Documentation: leftsemi instead of semijoinLCY Vincent2015-05-111-1/+1
| | | | | | | | | | | should sync up with here? https://github.com/apache/spark/blob/119f45d61d7b48d376cca05e1b4f0c7fcf65bfa8/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/plans/joinTypes.scala#L26 Author: LCY Vincent <lauchunyin@gmail.com> Closes #5944 from vincentlaucy/master and squashes the following commits: fc0e454 [LCY Vincent] Update DataFrame.scala
* [STREAMING] [MINOR] Close files correctly when iterator is finished in ↵jerryshao2015-05-111-2/+3
| | | | | | | | | | | | streaming WAL recovery Currently there's no chance to close the file correctly after the iteration is finished, change to `CompletionIterator` to avoid resource leakage. Author: jerryshao <saisai.shao@intel.com> Closes #6050 from jerryshao/close-file-correctly and squashes the following commits: 52dfaf5 [jerryshao] Close files correctly when iterator is finished
* [SPARK-7516] [Minor] [DOC] Replace depreciated inferSchema() with ↵gchen2015-05-111-1/+1
| | | | | | | | | | | | | | | | | createDataFrame() JIRA: https://issues.apache.org/jira/browse/SPARK-7516 In sql-programming-guide, deprecated python data frame api inferSchema() should be replaced by createDataFrame(): schemaPeople = sqlContext.inferSchema(people) -> schemaPeople = sqlContext.createDataFrame(people) Author: gchen <chenguancheng@gmail.com> Closes #6041 from gchen/python-docs and squashes the following commits: c27eb7c [gchen] replace inferSchema() with createDataFrame()
* [SPARK-7515] [DOC] Update documentation for PySpark on YARN with cluster modeKousuke Saruta2015-05-111-1/+1
| | | | | | | | | | | | Now PySpark on YARN with cluster mode is supported so let's update doc. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #6040 from sarutak/update-doc-for-pyspark-on-yarn and squashes the following commits: ad9f88c [Kousuke Saruta] Brushed up sentences 469fd2e [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into update-doc-for-pyspark-on-yarn fcfdb92 [Kousuke Saruta] Updated doc for PySpark on YARN with cluster mode
* [SPARK-7508] JettyUtils-generated servlets to log & report all errorsSteve Loughran2015-05-111-0/+6
| | | | | | | | | | | | | | | | | | | | | | | Patch for SPARK-7508 This logs warn then generates a response which include the message body and stack trace as text/plain, no-cache. The exit code is 500. In practise (in some tests in SPARK-1537 to be precise), jetty is getting in between this servlet and the web response the user sees —the body of the response is lost for any error response (500, even 404 and bad request). The standard Jetty handlers must be getting in the way. This patch doesn't address that, it ensures that 1. if the jetty handlers were put to one side the users would see the errors 2. at least the exceptions appear in the server-side logs. This is better to users saying "I saw a 500 error" and you not having anything in the logs to see what went wrong. Author: Steve Loughran <stevel@hortonworks.com> Closes #6033 from steveloughran/stevel/feature/SPARK-7508-JettyUtils and squashes the following commits: 584836f [Steve Loughran] SPARK-7508 drop trailing semicolon ad6f185 [Steve Loughran] SPARK-7508: jetty handles exception reporting itself; spark just sets this up and logs exceptions before being relayed 258d9f9 [Steve Loughran] SPARK-7508 fix typo manually-edited before patch pushed 69c8263 [Steve Loughran] SPARK-7508 JettyUtils-generated servlets to log & report all errors
* [SPARK-6470] [YARN] Add support for YARN node labels.Sandy Ryza2015-05-112-1/+39
| | | | | | | | | | | This is difficult to write a test for because it relies on the latest version of YARN, but I verified manually that the patch does pass along the label expression on this version and containers are successfully launched. Author: Sandy Ryza <sandy@cloudera.com> Closes #5242 from sryza/sandy-spark-6470 and squashes the following commits: 6af87b9 [Sandy Ryza] Change info to warning 6e22d99 [Sandy Ryza] [YARN] SPARK-6470. Add support for YARN node labels.
* [SPARK-7462] By default retain group by columns in aggregateReynold Xin2015-05-1110-172/+218
| | | | | | | | | | | | | | | | | Updated Java, Scala, Python, and R. Author: Reynold Xin <rxin@databricks.com> Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #5996 from rxin/groupby-retain and squashes the following commits: aac7119 [Reynold Xin] Merge branch 'groupby-retain' of github.com:rxin/spark into groupby-retain f6858f6 [Reynold Xin] Merge branch 'master' into groupby-retain 5f923c0 [Reynold Xin] Merge pull request #15 from shivaram/sparkr-groupby-retrain c1de670 [Shivaram Venkataraman] Revert workaround in SparkR to retain grouped cols Based on reverting code added in commit https://github.com/amplab-extras/spark/commit/9a6be746efc9fafad88122fa2267862ef87aa0e1 b8b87e1 [Reynold Xin] Fixed DataFrameJoinSuite. d910141 [Reynold Xin] Updated rest of the files 1e6e666 [Reynold Xin] [SPARK-7462] By default retain group by columns in aggregate
* [SPARK-7361] [STREAMING] Throw unambiguous exception when attempting to ↵Tathagata Das2015-05-112-8/+58
| | | | | | | | | | | | | | | start multiple StreamingContexts in the same JVM Currently attempt to start a streamingContext while another one is started throws a confusing exception that the action name JobScheduler is already registered. Instead its best to throw a proper exception as it is not supported. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #5907 from tdas/SPARK-7361 and squashes the following commits: fb81c4a [Tathagata Das] Fix typo a9cd5bb [Tathagata Das] Added startSite to StreamingContext 5fdfc0d [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into SPARK-7361 5870e2b [Tathagata Das] Added check for multiple streaming contexts
* [SPARK-7522] [EXAMPLES] Removed angle brackets from dataFormat optionBryan Cutler2015-05-115-5/+5
| | | | | | | | | | As is, to specify this option on command line, you have to escape the angle brackets. Author: Bryan Cutler <bjcutler@us.ibm.com> Closes #6049 from BryanCutler/dataFormat-option-7522 and squashes the following commits: b34afb4 [Bryan Cutler] [SPARK-7522] Removed angle brackets from dataFormat option
* [SPARK-6092] [MLLIB] Add RankingMetrics in PySpark/MLlibYanbo Liang2015-05-112-2/+86
| | | | | | | | | Author: Yanbo Liang <ybliang8@gmail.com> Closes #6044 from yanboliang/spark-6092 and squashes the following commits: 726a9b1 [Yanbo Liang] add newRankingMetrics 33f649c [Yanbo Liang] Add RankingMetrics in PySpark/MLlib
* [SPARK-7326] [STREAMING] Performing window() on a WindowedDStream doesn't ↵Wesley Miao2015-05-113-8/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | work all the time tdas https://issues.apache.org/jira/browse/SPARK-7326 The problem most likely resides in DStream.slice() implementation, as shown below. def slice(fromTime: Time, toTime: Time): Seq[RDD[T]] = { if (!isInitialized) { throw new SparkException(this + " has not been initialized") } if (!(fromTime - zeroTime).isMultipleOf(slideDuration)) { logWarning("fromTime (" + fromTime + ") is not a multiple of slideDuration (" + slideDuration + ")") } if (!(toTime - zeroTime).isMultipleOf(slideDuration)) { logWarning("toTime (" + fromTime + ") is not a multiple of slideDuration (" + slideDuration + ")") } val alignedToTime = toTime.floor(slideDuration, zeroTime) val alignedFromTime = fromTime.floor(slideDuration, zeroTime) logInfo("Slicing from " + fromTime + " to " + toTime + " (aligned to " + alignedFromTime + " and " + alignedToTime + ")") alignedFromTime.to(alignedToTime, slideDuration).flatMap(time => { if (time >= zeroTime) getOrCompute(time) else None }) } Here after performing floor() on both fromTime and toTime, the result (alignedFromTime - zeroTime) and (alignedToTime - zeroTime) may no longer be multiple of the slidingDuration, thus making isTimeValid() check failed for all the remaining computation. The fix is to add a new floor() function in Time.scala to respect the zeroTime while performing the floor : def floor(that: Duration, zeroTime: Time): Time = { val t = that.milliseconds new Time(((this.millis - zeroTime.milliseconds) / t) * t + zeroTime.milliseconds) } And then change the DStream.slice to call this new floor function by passing in its zeroTime. val alignedToTime = toTime.floor(slideDuration, zeroTime) val alignedFromTime = fromTime.floor(slideDuration, zeroTime) This way the alignedToTime and alignedFromTime are *really* aligned in respect to zeroTime whose value is not really a 0. Author: Wesley Miao <wesley.miao@gmail.com> Author: Wesley <wesley.miao@autodesk.com> Closes #5871 from wesleymiao/spark-7326 and squashes the following commits: 82a4d8c [Wesley Miao] [SPARK-7326] [STREAMING] Performing window() on a WindowedDStream dosen't work all the time 48b4dc0 [Wesley] [SPARK-7326] [STREAMING] Performing window() on a WindowedDStream doesn't work all the time 6ade399 [Wesley] [SPARK-7326] [STREAMING] Performing window() on a WindowedDStream doesn't work all the time 2611745 [Wesley Miao] [SPARK-7326] [STREAMING] Performing window() on a WindowedDStream doesn't work all the time
* [SPARK-7519] [SQL] fix minor bugs in thrift server UItianyi2015-05-112-6/+8
| | | | | | | | | | | | | | Bugs description: 1. There are extra commas on the top of session list. 2. The format of time in "Start at:" part is not the same as others. 3. The total number of online sessions is wrong. Author: tianyi <tianyi.asiainfo@gmail.com> Closes #6048 from tianyi/SPARK-7519 and squashes the following commits: ed366b7 [tianyi] fix bug
* [SPARK-7512] [SPARKR] Fix RDD's show method to use getJRDDShivaram Venkataraman2015-05-101-2/+2
| | | | | | | | | | | | | | | Since the RDD object might be a Pipelined RDD we should use `getJRDD` to get the right handle to the Java object. Fixes the bug reported at http://stackoverflow.com/questions/30057702/sparkr-filterrdd-and-flatmap-not-working cc concretevitamin Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6035 from shivaram/sparkr-show-bug and squashes the following commits: d70145c [Shivaram Venkataraman] Fix RDD's show method to use getJRDD Fixes the bug reported at http://stackoverflow.com/questions/30057702/sparkr-filterrdd-and-flatmap-not-working
* [SPARK-7427] [PYSPARK] Make sharedParams match in Scala, PythonGlenn Weidner2015-05-104-22/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | Modified 2 files: python/pyspark/ml/param/_shared_params_code_gen.py python/pyspark/ml/param/shared.py Generated shared.py on Linux using Python 2.6.6 on Redhat Enterprise Linux Server 6.6. python _shared_params_code_gen.py > shared.py Only changed maxIter, regParam, rawPredictionCol based on strings from SharedParamsCodeGen.scala. Note warning was displayed when committing shared.py: warning: LF will be replaced by CRLF in python/pyspark/ml/param/shared.py. Author: Glenn Weidner <gweidner@us.ibm.com> Closes #6023 from gweidner/br-7427 and squashes the following commits: db72e32 [Glenn Weidner] [SPARK-7427] [PySpark] Make sharedParams match in Scala, Python 825e4a9 [Glenn Weidner] [SPARK-7427] [PySpark] Make sharedParams match in Scala, Python e6a865e [Glenn Weidner] [SPARK-7427] [PySpark] Make sharedParams match in Scala, Python 1eee702 [Glenn Weidner] Merge remote-tracking branch 'upstream/master' 1ac10e5 [Glenn Weidner] Merge remote-tracking branch 'upstream/master' cafd104 [Glenn Weidner] Merge remote-tracking branch 'upstream/master' 9bea1eb [Glenn Weidner] Merge remote-tracking branch 'upstream/master' 4a35c20 [Glenn Weidner] Merge remote-tracking branch 'upstream/master' 9790cbe [Glenn Weidner] Merge remote-tracking branch 'upstream/master' d9c30f4 [Glenn Weidner] [SPARK-7275] [SQL] [WIP] Make LogicalRelation public
* [SPARK-5521] PCA wrapper for easy transform vectorsKirill A. Korinskiy2015-05-104-2/+213
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I implement a simple PCA wrapper for easy transform of vectors by PCA for example LabeledPoint or another complicated structure. Example of usage: ``` import org.apache.spark.mllib.regression.LinearRegressionWithSGD import org.apache.spark.mllib.regression.LabeledPoint import org.apache.spark.mllib.linalg.Vectors import org.apache.spark.mllib.feature.PCA val data = sc.textFile("data/mllib/ridge-data/lpsa.data").map { line => val parts = line.split(',') LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(' ').map(_.toDouble))) }.cache() val splits = data.randomSplit(Array(0.6, 0.4), seed = 11L) val training = splits(0).cache() val test = splits(1) val pca = PCA.create(training.first().features.size/2, data.map(_.features)) val training_pca = training.map(p => p.copy(features = pca.transform(p.features))) val test_pca = test.map(p => p.copy(features = pca.transform(p.features))) val numIterations = 100 val model = LinearRegressionWithSGD.train(training, numIterations) val model_pca = LinearRegressionWithSGD.train(training_pca, numIterations) val valuesAndPreds = test.map { point => val score = model.predict(point.features) (score, point.label) } val valuesAndPreds_pca = test_pca.map { point => val score = model_pca.predict(point.features) (score, point.label) } val MSE = valuesAndPreds.map{case(v, p) => math.pow((v - p), 2)}.mean() val MSE_pca = valuesAndPreds_pca.map{case(v, p) => math.pow((v - p), 2)}.mean() println("Mean Squared Error = " + MSE) println("PCA Mean Squared Error = " + MSE_pca) ``` Author: Kirill A. Korinskiy <catap@catap.ru> Author: Joseph K. Bradley <joseph@databricks.com> Closes #4304 from catap/pca and squashes the following commits: 501bcd9 [Joseph K. Bradley] Small updates: removed k from Java-friendly PCA fit(). In PCASuite, converted results to set for comparison. Added an error message for bad k in PCA. 9dcc02b [Kirill A. Korinskiy] [SPARK-5521] fix scala style 1892a06 [Kirill A. Korinskiy] [SPARK-5521] PCA wrapper for easy transform vectors
* [SPARK-7431] [ML] [PYTHON] Made CrossValidatorModel call parent init in PySparkJoseph K. Bradley2015-05-103-3/+4
| | | | | | | | | | | | | Fixes bug with PySpark cvModel not having UID Also made small PySpark fixes: Evaluator should inherit from Params. MockModel should inherit from Model. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #5968 from jkbradley/pyspark-cv-uid and squashes the following commits: 57f13cd [Joseph K. Bradley] Made CrossValidatorModel call parent init in PySpark
* [MINOR] [SQL] Fixes variable name typoCheng Lian2015-05-108-9/+9
| | | | | | | | | | | | <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/6038) <!-- Reviewable:end --> Author: Cheng Lian <lian@databricks.com> Closes #6038 from liancheng/fix-typo and squashes the following commits: 572c2a4 [Cheng Lian] Fixes variable name typo
* [SPARK-7345][SQL] Spark cannot detect renamed columns using JDBC connectorOleg Sidorkin2015-05-102-1/+17
| | | | | | | | | | | | | | | | | | | | | | | | | Issue appears when one tries to create DataFrame using sqlContext.load("jdbc"...) statement when "dbtable" contains query with renamed columns. If original column is used in SQL query once the resulting DataFrame will contain non-renamed column. If original column is used in SQL query several times with different aliases, sqlContext.load will fail. Original implementation of JDBCRDD.resolveTable uses getColumnName to detect column names in RDD schema. Suggested implementation uses getColumnLabel to handle column renames in SQL statement which is aware of SQL "AS" statement. Readings: http://stackoverflow.com/questions/4271152/getcolumnlabel-vs-getcolumnname http://stackoverflow.com/questions/12259829/jdbc-getcolumnname-getcolumnlabel-db2 Official documentation unfortunately a bit misleading in definition of "suggested title" purpose however clearly defines behavior of AS keyword in SQL statement. http://docs.oracle.com/javase/7/docs/api/java/sql/ResultSetMetaData.html getColumnLabel - Gets the designated column's suggested title for use in printouts and displays. The suggested title is usually specified by the SQL AS clause. If a SQL AS is not specified, the value returned from getColumnLabel will be the same as the value returned by the getColumnName method. Author: Oleg Sidorkin <oleg.sidorkin@gmail.com> Closes #6032 from osidorkin/master and squashes the following commits: 10fc44b [Oleg Sidorkin] [SPARK-7345][SQL] Regression test for JDBCSuite (resolved scala style test error) 2aaf6f7 [Oleg Sidorkin] [SPARK-7345][SQL] Regression test for JDBCSuite (renamed fields in JDBC query) b7d5b22 [Oleg Sidorkin] [SPARK-7345][SQL] Regression test for JDBCSuite 09559a0 [Oleg Sidorkin] [SPARK-7345][SQL] Spark cannot detect renamed columns using JDBC connector
* [SPARK-6091] [MLLIB] Add MulticlassMetrics in PySpark/MLlibYanbo Liang2015-05-102-0/+137
| | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-6091 Author: Yanbo Liang <ybliang8@gmail.com> Closes #6011 from yanboliang/spark-6091 and squashes the following commits: bb3e4ba [Yanbo Liang] trigger jenkins 53c045d [Yanbo Liang] keep compatibility for python 2.6 972d5ac [Yanbo Liang] Add MulticlassMetrics in PySpark/MLlib
* [SPARK-7475] [MLLIB] adjust ldaExample for online LDAYuhao Yang2015-05-091-6/+25
| | | | | | | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-7475 Add a new argument to specify the algorithm applied to LDA, to exhibit the basic usage of LDAOptimizer. cc jkbradley Author: Yuhao Yang <hhbyyh@gmail.com> Closes #6000 from hhbyyh/ldaExample and squashes the following commits: 0a7e2bc [Yuhao Yang] fix according to comments 5810b0f [Yuhao Yang] adjust ldaExample for online LDA
* [BUILD] Reference fasterxml.jackson.version in sql/core/pom.xmltedyu2015-05-091-1/+1
| | | | | | | | | | Author: tedyu <yuzhihong@gmail.com> Closes #6031 from tedyu/master and squashes the following commits: 5c2580c [tedyu] Reference fasterxml.jackson.version in sql/core/pom.xml ff2a44f [tedyu] Merge branch 'master' of github.com:apache/spark 28c8394 [tedyu] Upgrade version of jackson-databind in sql/core/pom.xml
* Upgrade version of jackson-databind in sql/core/pom.xmltedyu2015-05-091-1/+1
| | | | | | | | | | | | | | Currently version of jackson-databind in sql/core/pom.xml is 2.3.0 This is older than the version specified in root pom.xml This PR upgrades the version in sql/core/pom.xml so that they're consistent. Author: tedyu <yuzhihong@gmail.com> Closes #6028 from tedyu/master and squashes the following commits: 28c8394 [tedyu] Upgrade version of jackson-databind in sql/core/pom.xml
* [STREAMING] [DOCS] Fix wrong url about API docs of StreamingListenerdobashim2015-05-091-1/+1
| | | | | | | | | | A little fix about wrong url of the API document. (org.apache.spark.streaming.scheduler.StreamingListener) Author: dobashim <dobashim@oss.nttdata.co.jp> Closes #6024 from dobashim/master and squashes the following commits: ac9a955 [dobashim] [STREAMING][DOCS] Fix wrong url about API docs of StreamingListener
* [SPARK-7403] [WEBUI] Link URL in objects on Timeline View is wrong in case ↵Kousuke Saruta2015-05-093-20/+30
| | | | | | | | | | | | | | | | | | | | | | | | of running on YARN When we use Spark on YARN and have AllJobPage via ResourceManager's proxy, the link URL in objects which represent each job on timeline view is wrong. In timeline-view.js, the link is generated as follows. ``` window.location.href = "job/?id=" + getJobId(this); ``` This assumes the URL displayed on the web browser ends with "jobs/" but when we access AllJobPage via the proxy, the url displayed does not end with "jobs/" The proxy doesn't return status code 301 or 302 so the url displayed still indicates the base url, not "/jobs" even though displaying AllJobPages. ![2015-05-07 3 34 37](https://cloud.githubusercontent.com/assets/4736016/7501079/a8507ad6-f46c-11e4-9bed-62abea170f4c.png) Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #5947 from sarutak/fix-link-in-timeline and squashes the following commits: aaf40e1 [Kousuke Saruta] Added Copyright for vis.js 01bee7b [Kousuke Saruta] Fixed timeline-view.js in order to get correct href
* [SPARK-7438] [SPARK CORE] Fixed validation of relativeSD in countApproxDistinctVinod K C2015-05-094-6/+6
| | | | | | | | | | | | Author: Vinod K C <vinod.kc@huawei.com> Closes #5974 from vinodkc/fix_countApproxDistinct_Validation and squashes the following commits: 3a3d59c [Vinod K C] Reverted removal of validation relativeSD<0.000017 799976e [Vinod K C] Removed testcase to assert IAE when relativeSD>3.7 8ddbfae [Vinod K C] Remove blank line b1b00a3 [Vinod K C] Removed relativeSD validation from python API,RDD.scala will do validation 122d378 [Vinod K C] Fixed validation of relativeSD in countApproxDistinct
* [SPARK-7498] [ML] removed varargs annotation from Params.setDefaultsJoseph K. Bradley2015-05-082-2/+2
| | | | | | | | | | | In SPARK-7429 and PR https://github.com/apache/spark/pull/5960, I added the varargs annotation to Params.setDefault which takes a variable number of ParamPairs. It worked locally and on Jenkins for me. However, mengxr reported issues compiling on his machine. So I'm reverting the change introduced in https://github.com/apache/spark/pull/5960 by removing varargs. Author: Joseph K. Bradley <joseph@databricks.com> Closes #6021 from jkbradley/revert-varargs and squashes the following commits: 098ed39 [Joseph K. Bradley] removed varargs annotation from Params.setDefaults taking multiple ParamPairs
* [SPARK-7262] [ML] Binary LogisticRegression with L1/L2 (elastic net) using ↵DB Tsai2015-05-085-40/+821
| | | | | | | | | | | | | | | | | | | | | | OWLQN in new ML package 1) Handle scaling and addBias internally. 2) L1/L2 elasticnet using OWLQN optimizer. Author: DB Tsai <dbt@netflix.com> Closes #5967 from dbtsai/lor and squashes the following commits: fa029bb [DB Tsai] made the bound smaller 0806002 [DB Tsai] better initial intercept and more test 5c31824 [DB Tsai] fix import c387e25 [DB Tsai] Merge branch 'master' into lor c84e931 [DB Tsai] Made MultiClassSummarizer private f98e711 [DB Tsai] address feedback a784321 [DB Tsai] fix style 8ec65d2 [DB Tsai] remove new line f3f8c88 [DB Tsai] add more tests and they match R which is good. fix a bug 34705bc [DB Tsai] first commit
* [SPARK-7375] [SQL] Avoid row copying in exchange when ↵Josh Rosen2015-05-081-56/+100
| | | | | | | | | | | | | | | | | | | | | | sort.serializeMapOutputs takes effect This patch refactors the SQL `Exchange` operator's logic for determining whether map outputs need to be copied before being shuffled. As part of this change, we'll now avoid unnecessary copies in cases where sort-based shuffle operates on serialized map outputs (as in #4450 / SPARK-4550). This patch also includes a change to copy the input to RangePartitioner partition bounds calculation, which is necessary because this calculation buffers mutable Java objects. <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/5948) <!-- Reviewable:end --> Author: Josh Rosen <joshrosen@databricks.com> Closes #5948 from JoshRosen/SPARK-7375 and squashes the following commits: f305ff3 [Josh Rosen] Reduce scope of some variables in Exchange 899e1d7 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-7375 6a6bfce [Josh Rosen] Fix issue related to RangePartitioning: ad006a4 [Josh Rosen] [SPARK-7375] Avoid defensive copying in exchange operator when sort.serializeMapOutputs takes effect.
* [SPARK-7231] [SPARKR] Changes to make SparkR DataFrame dplyr friendly.Shivaram Venkataraman2015-05-088-29/+249
| | | | | | | | | | | | | | | | | | | | | | Changes include 1. Rename sortDF to arrange 2. Add new aliases `group_by` and `sample_frac`, `summarize` 3. Add more user friendly column addition (mutate), rename 4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr Using these changes we can pretty much run the examples as described in http://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html with the same syntax The only thing missing in SparkR is auto resolving column names when used in an expression i.e. making something like `select(flights, delay)` works in dply but we right now need `select(flights, flights$delay)` or `select(flights, "delay")`. But this is a complicated change and I'll file a new issue for it cc sun-rui rxin Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6005 from shivaram/sparkr-df-api and squashes the following commits: 5e0716a [Shivaram Venkataraman] Fix some roxygen bugs 1254953 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/apache/spark into sparkr-df-api 0521149 [Shivaram Venkataraman] Changes to make SparkR DataFrame dplyr friendly. Changes include 1. Rename sortDF to arrange 2. Add new aliases `group_by` and `sample_frac`, `summarize` 3. Add more user friendly column addition (mutate), rename 4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr
* [SPARK-7451] [YARN] Preemption of executors is counted as failure causing ↵Ashwin Shankar2015-05-081-1/+3
| | | | | | | | | | | | | | Spark job to fail Added a check to handle container exit status for the preemption scenario, log an INFO message in such cases and move on. andrewor14 Author: Ashwin Shankar <ashankar@netflix.com> Closes #5993 from ashwinshankar77/SPARK-7451 and squashes the following commits: 90900cf [Ashwin Shankar] Fix log info message cf8b6cf [Ashwin Shankar] Stop counting preemption of executors as failure
* [SPARK-7488] [ML] Feature Parity in PySpark for ml.recommendationBurak Yavuz2015-05-084-4/+318
| | | | | | | | | | | | | | Adds Python Api for `ALS` under `ml.recommendation` in PySpark. Also adds seed as a settable parameter in the Scala Implementation of ALS. Author: Burak Yavuz <brkyvz@gmail.com> Closes #6015 from brkyvz/ml-rec and squashes the following commits: be6e931 [Burak Yavuz] addressed comments eaed879 [Burak Yavuz] readd numFeatures 0bd66b1 [Burak Yavuz] fixed seed 7f6d964 [Burak Yavuz] merged master 52e2bda [Burak Yavuz] added ALS
* [SPARK-7237] Clean function in several RDD methodstedyu2015-05-082-10/+41
| | | | | | | | | | | | | | | | | | | Author: tedyu <yuzhihong@gmail.com> Closes #5959 from ted-yu/master and squashes the following commits: f83d445 [tedyu] Move cleaning outside of mapPartitionsWithIndex 56d7c92 [tedyu] Consolidate import of Random f6014c0 [tedyu] Remove cleaning in RDD#filterWith 36feb6c [tedyu] Try to get correct syntax 55d01eb [tedyu] Try to get correct syntax c2786df [tedyu] Correct syntax d92bfcf [tedyu] Correct syntax in test 164d3e4 [tedyu] Correct variable name 8b50d93 [tedyu] Address Andrew's review comments 0c8d47e [tedyu] Add test for mapWith() 6846e40 [tedyu] Add test for flatMapWith() 6c124a9 [tedyu] Clean function in several RDD methods
* [SPARK-7469] [SQL] DAG visualization: show SQL query operatorsAndrew Or2015-05-0828-50/+71
| | | | | | | | | | | | | | | | | | | | | | | | The DAG visualization currently displays only low-level Spark primitives (e.g. `map`, `reduceByKey`, `filter` etc.). For SQL, these aren't particularly useful. Instead, we should display higher level physical operators (e.g. `Filter`, `Exchange`, `ShuffleHashJoin`). cc marmbrus ----------------- **Before** <img src="https://issues.apache.org/jira/secure/attachment/12731586/before.png" width="600px"/> ----------------- **After** (Pay attention to the words) <img src="https://issues.apache.org/jira/secure/attachment/12731587/after.png" width="600px"/> ----------------- Author: Andrew Or <andrew@databricks.com> Closes #5999 from andrewor14/dag-viz-sql and squashes the following commits: 0db23a4 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-sql 1e211db [Andrew Or] Update comment 0d49fd6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-sql ffd237a [Andrew Or] Fix style 202dac1 [Andrew Or] Make ignoreParent false by default e61b1ab [Andrew Or] Visualize SQL operators, not low-level Spark primitives 569034a [Andrew Or] Add a flag to ignore parent settings and scopes
* [SPARK-6955] Perform port retries at NettyBlockTransferService levelAaron Davidson2015-05-084-39/+102
| | | | | | | | | | | | | Currently we're doing port retries in the TransportServer level, but this is not specified by the TransportContext API and it has other further-reaching impacts like causing undesirable behavior for the Yarn and Standalone shuffle services. Author: Aaron Davidson <aaron@databricks.com> Closes #5575 from aarondav/port-bind and squashes the following commits: 3c2d6ed [Aaron Davidson] Oops, never do it. a5d9432 [Aaron Davidson] Remove shouldHostShuffleServiceIfEnabled e901eb2 [Aaron Davidson] fix local-cluster mode for ExternalShuffleServiceSuite 59e5e38 [Aaron Davidson] [SPARK-6955] Perform port retries at NettyBlockTransferService level
* updated ec2 instance typesBrendan Collins2015-05-081-23/+47
| | | | | | | | | | | | | | | I needed to run some d2 instances, so I updated the spark_ec2.py accordingly Author: Brendan Collins <bcollins@blueraster.com> Closes #6014 from brendancol/ec2-instance-types-update and squashes the following commits: d7b4191 [Brendan Collins] Merge branch 'ec2-instance-types-update' of github.com:brendancol/spark into ec2-instance-types-update 6366c45 [Brendan Collins] added back cc1.4xlarge fc2931f [Brendan Collins] updated ec2 instance types 80c2aa6 [Brendan Collins] vertically aligned whitespace 85c6236 [Brendan Collins] vertically aligned whitespace 1657c26 [Brendan Collins] updated ec2 instance types
* [SPARK-5913] [MLLIB] Python API for ChiSqSelectorYanbo Liang2015-05-082-2/+67
| | | | | | | | | | | Add a Python API for mllib.feature.ChiSqSelector https://issues.apache.org/jira/browse/SPARK-5913 Author: Yanbo Liang <ybliang8@gmail.com> Closes #5939 from yanboliang/spark-5913 and squashes the following commits: cdaac99 [Yanbo Liang] Python API for ChiSqSelector
* [SPARK-4699] [SQL] Make caseSensitive configurable in spark sql analyzerJacky Li2015-05-0815-70/+127
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | based on #3558 Author: Jacky Li <jacky.likun@huawei.com> Author: wangfei <wangfei1@huawei.com> Author: scwf <wangfei1@huawei.com> Closes #5806 from scwf/case and squashes the following commits: cd51712 [wangfei] fix compile d4b724f [wangfei] address michael's comment af512c7 [wangfei] fix conflicts 4ef1be7 [wangfei] fix conflicts 269cf21 [scwf] fix conflicts b73df6c [scwf] style issue 9e11752 [scwf] improve SimpleCatalystConf b35529e [scwf] minor style a3f7659 [scwf] remove unsed imports 2a56515 [scwf] fix conflicts 6db4bf5 [scwf] also fix for HiveContext 7fc4a98 [scwf] fix test case d5a9933 [wangfei] fix style eee75ba [wangfei] fix EmptyConf 6ef31cf [wangfei] revert pom changes 5d7c456 [wangfei] set CASE_SENSITIVE false in TestHive 966e719 [wangfei] set CASE_SENSITIVE false in hivecontext fd30e25 [wangfei] added override 69b3b70 [wangfei] fix AnalysisSuite 5472b08 [wangfei] fix compile issue 56034ca [wangfei] fix conflicts and improve for catalystconf 664d1e9 [Jacky Li] Merge branch 'master' of https://github.com/apache/spark into case 12eca9a [Jacky Li] solve conflict with master 39e369c [Jacky Li] fix confilct after DataFrame PR dee56e9 [Jacky Li] fix test case failure 05b09a3 [Jacky Li] fix conflict base on the latest master branch 73c16b1 [Jacky Li] fix bug in sql/hive 9bf4cc7 [Jacky Li] fix bug in catalyst 005c56d [Jacky Li] make SQLContext caseSensitivity configurable 6332e0f [Jacky Li] fix bug fcbf0d9 [Jacky Li] fix scalastyle check e7bca31 [Jacky Li] make caseSensitive configuration in Analyzer and Catalog 91b1b96 [Jacky Li] make caseSensitive configurable in Analyzer f57f15c [Jacky Li] add testcase 578d167 [Jacky Li] make caseSensitive configurable
* [SPARK-7390] [SQL] Only merge other CovarianceCounter when its count is ↵Liang-Chi Hsieh2015-05-081-10/+12
| | | | | | | | | | | | | | greater than zero JIRA: https://issues.apache.org/jira/browse/SPARK-7390 Also fix a minor typo. Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #5931 from viirya/fix_covariancecounter and squashes the following commits: 352eda6 [Liang-Chi Hsieh] Only merge other CovarianceCounter when its count is greater than zero.
* [SPARK-7378] [CORE] Handle deep links to unloaded apps.Marcelo Vanzin2015-05-081-19/+29
| | | | | | | | | | | | | | | | | | | | | The code was treating deep links as if they were attempt IDs, so for example if you tried to load "/history/app1/jobs" directly, that would fail because the code would treat "jobs" as an attempt id. This change modifies the code to try both cases - first without an attempt id, then with it, so that deep links are handled correctly. This assumes that the links in the Spark UI do not clash with the attempt id namespace, though, which is the case for YARN at least, which is the only backend that currently publishes attempt IDs. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5922 from vanzin/SPARK-7378 and squashes the following commits: 96f648b [Marcelo Vanzin] Fix comparison. ed3bcd4 [Marcelo Vanzin] Merge branch 'master' into SPARK-7378 23483e4 [Marcelo Vanzin] Fat fingers. b728f08 [Marcelo Vanzin] [SPARK-7378] [core] Handle deep links to unloaded apps.
* [MINOR] [CORE] Allow History Server to read kerberos opts from config file.Marcelo Vanzin2015-05-081-1/+1
| | | | | | | | | | Order of initialization code was wrong. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5998 from vanzin/hs-conf-fix and squashes the following commits: 00b6b6b [Marcelo Vanzin] [minor] [core] Allow History Server to read kerberos opts from config file.
* [SPARK-7466] DAG visualization: fix orphan nodesAndrew Or2015-05-081-1/+1
| | | | | | | | | | | | | | | Simple fix. We were comparing an option with `null`. Before: <img src="https://issues.apache.org/jira/secure/attachment/12731383/before.png" width="250px"/> After: <img src="https://issues.apache.org/jira/secure/attachment/12731384/after.png" width="250px"/> Author: Andrew Or <andrew@databricks.com> Closes #6002 from andrewor14/dag-viz-orphan-nodes and squashes the following commits: a1468dc [Andrew Or] Fix null check
* [MINOR] Defeat early garbage collection of test suite variableTim Ellison2015-05-081-0/+1
| | | | | | | | | | | | The JVM is free to collect references to variables that no longer participate in a computation. This simple patch adds an operation to the variable 'rdd' to ensure it is not collected early in the test suite's explicit calls to GC. ref: http://bugs.java.com/view_bug.do?bug_id=6721588 Author: Tim Ellison <t.p.ellison@gmail.com> Closes #6010 from tellison/master and squashes the following commits: 77d1c8f [Tim Ellison] Defeat early garbage collection of test suite variable by aggressive JVMs
* [SPARK-7489] [SPARK SHELL] Spark shell crashes when compiled with scala 2.11vinodkc2015-05-081-1/+1
| | | | | | | | | | | | Spark shell crashes when compiled with scala 2.11 and SPARK_PREPEND_CLASSES=true There is a similar Resolved JIRA issue -SPARK-7470 and a PR https://github.com/apache/spark/pull/5997 , which handled same issue only in scala 2.10 Author: vinodkc <vinod.kc.in@gmail.com> Closes #6013 from vinodkc/fix_sqlcontext_exception_scala_2.11 and squashes the following commits: 119061c [vinodkc] Spark shell crashes when compiled with scala 2.11
* [WEBUI] Remove debug feature for vis.jsKousuke Saruta2015-05-083-3/+0
| | | | | | | | | | | | | | | `vis.min.js` refers `vis.map` and this even refers `vis.js` which is used for debug `vis.js` but this debug feature is not needed for Spark itself. This issue is really minor so I don't file this in JIRA. /CC andrewor14 Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #5994 from sarutak/remove-debug-feature-for-vis and squashes the following commits: 8be038f [Kousuke Saruta] Remove vis.map entry from .rat-exclude 7404945 [Kousuke Saruta] Removed debug feature for vis.js
* [MINOR] Ignore python/lib/pyspark.zipzsxwing2015-05-081-0/+1
| | | | | | | | | | Add `python/lib/pyspark.zip` to `.gitignore`. After merging #5580, `python/lib/pyspark.zip` will be generated when building Spark. Author: zsxwing <zsxwing@gmail.com> Closes #6017 from zsxwing/gitignore and squashes the following commits: 39b10c4 [zsxwing] Ignore python/lib/pyspark.zip
* [SPARK-7490] [CORE] [Minor] MapOutputTracker.deserializeMapStatuses: close ↵Evan Jones2015-05-081-1/+5
| | | | | | | | | | | | | | | | | input streams GZIPInputStream allocates native memory that is not freed until close() or when the finalizer runs. It is best to close() these streams explicitly. stephenh made the same change for serializeMapStatuses in commit b0d884f0. This is the same change for deserialize. (I ran the unit test suite! it seems to have passed. I did not make a JIRA since this seems "trivial", and the guidelines suggest it is not required for trivial changes) Author: Evan Jones <ejones@twitter.com> Closes #5982 from evanj/master and squashes the following commits: 0d76e85 [Evan Jones] [CORE] MapOutputTracker.deserializeMapStatuses: close input streams
* [SPARK-6627] Finished rename to ShuffleBlockResolverKay Ousterhout2015-05-0816-95/+94
| | | | | | | | | | | | | | | | | | The previous cleanup-commit for SPARK-6627 renamed ShuffleBlockManager to ShuffleBlockResolver, but didn't rename the associated subclasses and variables; this commit does that. I'm unsure whether it's ok to rename ExternalShuffleBlockManager, since that's technically a public class? cc pwendell Author: Kay Ousterhout <kayousterhout@gmail.com> Closes #5764 from kayousterhout/SPARK-6627 and squashes the following commits: 43add1e [Kay Ousterhout] Spacing fix 96080bf [Kay Ousterhout] Test fixes d8a5d36 [Kay Ousterhout] [SPARK-6627] Finished rename to ShuffleBlockResolver
* [SPARK-7133] [SQL] Implement struct, array, and map field accessorWenchen Fan2015-05-0816-191/+327
| | | | | | | | | | | | | | | | | | | | | | It's the first step: generalize UnresolvedGetField to support all map, struct, and array TODO: add `apply` in Scala and `__getitem__` in Python, and unify the `getItem` and `getField` methods to one single API(or should we keep them for compatibility?). Author: Wenchen Fan <cloud0fan@outlook.com> Closes #5744 from cloud-fan/generalize and squashes the following commits: 715c589 [Wenchen Fan] address comments 7ea5b31 [Wenchen Fan] fix python test 4f0833a [Wenchen Fan] add python test f515d69 [Wenchen Fan] add apply method and test cases 8df6199 [Wenchen Fan] fix python test 239730c [Wenchen Fan] fix test compile 2a70526 [Wenchen Fan] use _bin_op in dataframe.py 6bf72bc [Wenchen Fan] address comments 3f880c3 [Wenchen Fan] add java doc ab35ab5 [Wenchen Fan] fix python test b5961a9 [Wenchen Fan] fix style c9d85f5 [Wenchen Fan] generalize UnresolvedGetField to support all map, struct, and array
* [SPARK-7298] Harmonize style of new visualizationsMatei Zaharia2015-05-0812-151/+255
| | | | | | | | | | | | | | | | | | | | - Colors on the timeline now match the rest of the UI - The expandable buttons to show timeline view, DAG, etc are now more visible - Timeline text is smaller - DAG visualization text and colors are more consistent throughout - Fix some JavaScript style issues - Various small fixes throughout (e.g. inconsistent capitalization, some confusing names, HTML escaping, etc) Author: Matei Zaharia <matei@databricks.com> Closes #5942 from mateiz/ui and squashes the following commits: def38d0 [Matei Zaharia] Add some tooltips 4c5a364 [Matei Zaharia] Reduce stage and rank separation slightly 43dcbe3 [Matei Zaharia] Some updates to DAG fac734a [Matei Zaharia] tweaks 6a6705d [Matei Zaharia] More fixes 67629f5 [Matei Zaharia] Various small tweaks
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