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JIRA issues: - Main: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678) - Related: [SPARK-2874](https://issues.apache.org/jira/browse/SPARK-2874) Related PR: - #1715 This PR is both a fix for SPARK-2874 and a workaround for SPARK-2678. Fixing SPARK-2678 completely requires some API level changes that need further discussion, and we decided not to include it in Spark 1.1 release. As currently SPARK-2678 only affects Spark SQL scripts, this workaround is enough for Spark 1.1. Command line option handling logic in bash scripts looks somewhat dirty and duplicated, but it helps to provide a cleaner user interface as well as retain full downward compatibility for now. Author: Cheng Lian <lian.cs.zju@gmail.com> Closes #1801 from liancheng/spark-2874 and squashes the following commits: 8045d7a [Cheng Lian] Make sure test suites pass 8493a9e [Cheng Lian] Using eval to retain quoted arguments aed523f [Cheng Lian] Fixed typo in bin/spark-sql f12a0b1 [Cheng Lian] Worked arount SPARK-2678 daee105 [Cheng Lian] Fixed usage messages of all Spark SQL related scripts
As described in [SPARK-2627](https://issues.apache.org/jira/browse/SPARK-2627), we'd like Python code to automatically be checked for PEP 8 compliance by Jenkins. This pull request aims to do that. Notes: * We may need to install [`pep8`](https://pypi.python.org/pypi/pep8) on the build server. * I'm expecting tests to fail now that PEP 8 compliance is being checked as part of the build. I'm fine with cleaning up any remaining PEP 8 violations as part of this pull request. * I did not understand why the RAT and scalastyle reports are saved to text files. I did the same for the PEP 8 check, but only so that the console output style can match those for the RAT and scalastyle checks. The PEP 8 report is removed right after the check is complete. * Updates to the ["Contributing to Spark"](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) guide will be submitted elsewhere, as I don't believe that text is part of the Spark repo. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Author: nchammas <nicholas.chammas@gmail.com> Closes #1744 from nchammas/master and squashes the following commits: 274b238 [Nicholas Chammas] [SPARK-2627] [PySpark] minor indentation changes 983d963 [nchammas] Merge pull request #5 from apache/master 1db5314 [nchammas] Merge pull request #4 from apache/master 0e0245f [Nicholas Chammas] [SPARK-2627] undo erroneous whitespace fixes bf30942 [Nicholas Chammas] [SPARK-2627] PEP8: comment spacing 6db9a44 [nchammas] Merge pull request #3 from apache/master 7b4750e [Nicholas Chammas] merge upstream changes 91b7584 [Nicholas Chammas] [SPARK-2627] undo unnecessary line breaks 44e3e56 [Nicholas Chammas] [SPARK-2627] use tox.ini to exclude files b09fae2 [Nicholas Chammas] don't wrap comments unnecessarily bfb9f9f [Nicholas Chammas] [SPARK-2627] keep up with the PEP 8 fixes 9da347f [nchammas] Merge pull request #2 from apache/master aa5b4b5 [Nicholas Chammas] [SPARK-2627] follow Spark bash style for if blocks d0a83b9 [Nicholas Chammas] [SPARK-2627] check that pep8 downloaded fine dffb5dd [Nicholas Chammas] [SPARK-2627] download pep8 at runtime a1ce7ae [Nicholas Chammas] [SPARK-2627] space out test report sections 21da538 [Nicholas Chammas] [SPARK-2627] it's PEP 8, not PEP8 6f4900b [Nicholas Chammas] [SPARK-2627] more misc PEP 8 fixes fe57ed0 [Nicholas Chammas] removing merge conflict backups 9c01d4c [nchammas] Merge pull request #1 from apache/master 9a66cb0 [Nicholas Chammas] resolving merge conflicts a31ccc4 [Nicholas Chammas] [SPARK-2627] miscellaneous PEP 8 fixes beaa9ac [Nicholas Chammas] [SPARK-2627] fail check on non-zero status 723ed39 [Nicholas Chammas] always delete the report file 0541ebb [Nicholas Chammas] [SPARK-2627] call Python linter from run-tests 12440fa [Nicholas Chammas] [SPARK-2627] add Scala linter 61c07b9 [Nicholas Chammas] [SPARK-2627] add Python linter 75ad552 [Nicholas Chammas] make check output style consistent
I haven't tested this out on a cluster yet, but wanted to make sure the approach (passing ShuffleWriteMetrics down to DiskBlockObjectWriter) was ok Author: Sandy Ryza <sandy@cloudera.com> Closes #1481 from sryza/sandy-spark-2566 and squashes the following commits: 8090d88 [Sandy Ryza] Fix ExternalSorter b2a62ed [Sandy Ryza] Fix more test failures 8be6218 [Sandy Ryza] Fix test failures and mark a couple variables private c5e68e5 [Sandy Ryza] SPARK-2566. Update ShuffleWriteMetrics incrementally
This is part of SPARK-2828: 1. added a Java-friendly fit method to Word2Vec with tests 2. change DeveloperApi to Experimental for Normalizer & StandardScaler 3. change default feature dimension to 2^20 in HashingTF Author: Xiangrui Meng <meng@databricks.com> Closes #1807 from mengxr/feature-api-check and squashes the following commits: 773c1a9 [Xiangrui Meng] change default numFeatures to 2^20 in HashingTF change annotation from DeveloperApi to Experimental in Normalizer and StandardScaler 883e122 [Xiangrui Meng] add @experimental to Word2VecModel add a Java-friendly method to Word2Vec.fit with tests
This is failing my tests in #1777. @tdas Author: Andrew Or <andrewor14@gmail.com> Closes #1803 from andrewor14/fix-flaky-streaming-test and squashes the following commits: ea11a03 [Andrew Or] Catch all exceptions caused by BindExceptions 54a0ca0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into fix-flaky-streaming-test 664095c [Andrew Or] Tone down bind exception message af3ddc9 [Andrew Or] Handle port collisions in flume polling test
Fixes [SPARK-2882](https://issues.apache.org/jira/browse/SPARK-2882) Author: Gregory Owen <greowen@gmail.com> Closes #1818 from GregOwen/spark-2882 and squashes the following commits: 294446d [Gregory Owen] SPARK-2882: Spark build now checks local maven cache for dependencies
This patch modifies the ConnectionManager so that error messages are sent in reply when uncaught exceptions occur during message processing. This prevents message senders from hanging while waiting for an acknowledgment if the remote message processing failed. This is an updated version of sarutak's PR, #1490. The main change is to use Futures / Promises to signal errors. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Author: Josh Rosen <joshrosen@apache.org> Closes #1758 from JoshRosen/connection-manager-fixes and squashes the following commits: 68620cb [Josh Rosen] Fix test in BlockFetcherIteratorSuite: 83673de [Josh Rosen] Error ACKs should trigger IOExceptions, so catch only those exceptions in the test. b8bb4d4 [Josh Rosen] Fix manager.id vs managerServer.id typo that broke security tests. 659521f [Josh Rosen] Include previous exception when throwing new one a2f745c [Josh Rosen] Remove sendMessageReliablySync; callers can wait themselves. c01c450 [Josh Rosen] Return Try[Message] from sendMessageReliablySync. f1cd1bb [Josh Rosen] Clean up @sarutak's PR #1490 for [SPARK-2583]: ConnectionManager error reporting 7399c6b [Josh Rosen] Merge remote-tracking branch 'origin/pr/1490' into connection-manager-fixes ee91bb7 [Kousuke Saruta] Modified BufferMessage.scala to keep the spark code style 9dfd0d8 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 e7d9aa6 [Kousuke Saruta] rebase to master 326a17f [Kousuke Saruta] Add test cases to ConnectionManagerSuite.scala for SPARK-2583 2a18d6b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 22d7ebd [Kousuke Saruta] Add test cases to BlockManagerSuite for SPARK-2583 e579302 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 281589c [Kousuke Saruta] Add a test case to BlockFetcherIteratorSuite.scala for fetching block from remote from successfully 0654128 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 ffaa83d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 12d3de8 [Kousuke Saruta] Added BlockFetcherIteratorSuite.scala 4117b8f [Kousuke Saruta] Modified ConnectionManager to be alble to handle error during processing message 717c9c3 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 6635467 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2583 e2b8c4a [Kousuke Saruta] Modify to propagete error using ConnectionManager
Maven Central has just now enabled HTTPS access for everyone to Maven Central (http://central.sonatype.org/articles/2014/Aug/03/https-support-launching-now/) This is timely, as a reminder of how easily an attacker can slip malicious code into a build that's downloading artifacts over HTTP (http://blog.ontoillogical.com/blog/2014/07/28/how-to-take-over-any-java-developer/). In the meantime, it looks like the Spring repo also now supports HTTPS, so can be used this way too. I propose to use HTTPS to access these repos. Author: Sean Owen <srowen@gmail.com> Closes #1805 from srowen/SPARK-2879 and squashes the following commits: 7043a8e [Sean Owen] Use HTTPS for Maven Central libs and plugins; use id 'central' to override parent properly; use HTTPS for Spring repo
Added 6 static train methods to match Python API, but without default arguments (but with Python default args noted in docs). Added factory classes for Algo and Impurity, but made private[mllib]. CC: mengxr dorx Please let me know if there are other changes which would help with API consistency---thanks! Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1798 from jkbradley/dt-python-consistency and squashes the following commits: 6f7edf8 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-python-consistency a0d7dbe [Joseph K. Bradley] DecisionTree: In Java-friendly train* methods, changed to use JavaRDD instead of RDD. ee1d236 [Joseph K. Bradley] DecisionTree API updates: * Removed train() function in Python API (tree.py) ** Removed corresponding function in Scala/Java API (the ones taking basic types) 00f820e [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-python-consistency fe6dbfa [Joseph K. Bradley] removed unnecessary imports e358661 [Joseph K. Bradley] DecisionTree API change: * Added 6 static train methods to match Python API, but without default arguments (but with Python default args noted in docs). c699850 [Joseph K. Bradley] a few doc comments eaf84c0 [Joseph K. Bradley] Added DecisionTree static train() methods API to match Python, but without default parameters
… repos .. and use canonical repo1.maven.org Maven Central repo. (And make sure snapshots are disabled for plugins from Maven Central.) Author: Sean Owen <srowen@gmail.com> Closes #1828 from srowen/SPARK-2879.2 and squashes the following commits: 639f495 [Sean Owen] .. and use canonical repo1.maven.org Maven Central repo. (And make sure snapshots are disabled for plugins from Maven Central.)
Added some checks to Strategy to print out meaningful error messages when given invalid DecisionTree parameters. CC mengxr Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1821 from jkbradley/dt-robustness and squashes the following commits: 4dc449a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-robustness 7a61f7b [Joseph K. Bradley] Added some checks to Strategy to print out meaningful error messages when given invalid DecisionTree parameters
This is part of SPARK-2828: 1. separate IDF model from IDF algorithm (which generates a model) 2. separate StandardScaler model from StandardScaler CC: dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #1814 from mengxr/feature-api-update and squashes the following commits: 40d863b [Xiangrui Meng] move mean and variance to model 48a0fff [Xiangrui Meng] separate Model from StandardScaler algorithm 89f3486 [Xiangrui Meng] update IDF to separate Model from Algorithm
Author: Oleg Danilov <oleg.danilov@wandisco.com> Closes #1835 from dosoft/SPARK-2905 and squashes the following commits: 4df423c [Oleg Danilov] SPARK-2905 Fixed path sbin => bin
The reason for this bug was introduciton of OldDeps project. It had to be excluded to prevent unidocs from trying to put it on "docs compile" classpath. Author: Prashant Sharma <prashant.s@imaginea.com> Closes #1830 from ScrapCodes/doc-fix and squashes the following commits: e5d52e6 [Prashant Sharma] SPARK-2899 Doc generation is back to working in new SBT Build.
… no sorting/aggregation and # partitions is small As described in https://issues.apache.org/jira/browse/SPARK-2787, right now sort-based shuffle is more expensive than hash-based for map operations that do no partial aggregation or sorting, such as groupByKey. This is because it has to serialize each data item twice (once when spilling to intermediate files, and then again when merging these files object-by-object). This patch adds a code path to just write separate files directly if the # of output partitions is small, and concatenate them at the end to produce a sorted file. On the unit test side, I added some tests that force or don't force this bypass path to be used, and checked that our tests for other features (e.g. all the operations) cover both cases. Author: Matei Zaharia <matei@databricks.com> Closes #1799 from mateiz/SPARK-2787 and squashes the following commits: 88cf26a [Matei Zaharia] Fix rebase 10233af [Matei Zaharia] Review comments 398cb95 [Matei Zaharia] Fix looking up shuffle manager in conf ca3efd9 [Matei Zaharia] Add docs for shuffle manager properties, and allow short names for them d0ae3c5 [Matei Zaharia] Fix some comments 90d084f [Matei Zaharia] Add code path to bypass merge-sort in ExternalSorter, and tests 31e5d7c [Matei Zaharia] Move existing logic for writing partitioned files into ExternalSorter
Author: Sandy Ryza <sandy@cloudera.com> Closes #1507 from sryza/sandy-spark-2565 and squashes the following commits: 74dad41 [Sandy Ryza] SPARK-2565. Update ShuffleReadMetrics as blocks are fetched
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #1834 from sarutak/SPARK-2904 and squashes the following commits: 38e7d45 [Kousuke Saruta] Removed non-used variable in SparkSubmitArguments
Author: Erik Erlandson <eerlands@redhat.com> Closes #1841 from erikerlandson/spark-2911-pr and squashes the following commits: 4699e2f [Erik Erlandson] [SPARK-2911]: provide rdd.parent[T](j) to obtain jth parent RDD
JIRA: https://issues.apache.org/jira/browse/SPARK-2888 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1817 from yhuai/fixAddColumnMetadataToConf and squashes the following commits: fba728c [Yin Huai] Fix addColumnMetadataToConf.
…NullType to StringType JIRA: https://issues.apache.org/jira/browse/SPARK-2908 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1840 from yhuai/SPARK-2908 and squashes the following commits: 86e833e [Yin Huai] Update test. cb11759 [Yin Huai] nullTypeToStringType should check columns with the type of array of structs.
… creating the tableDesc JIRA: https://issues.apache.org/jira/browse/SPARK-2877 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1806 from yhuai/SPARK-2877 and squashes the following commits: 4142bcb [Yin Huai] Use Spark's classloader.
The command we will support is ``` ANALYZE TABLE tablename COMPUTE STATISTICS noscan ``` Other cases shown in https://cwiki.apache.org/confluence/display/Hive/StatsDev#StatsDev-ExistingTables will still be treated as Hive native commands. JIRA: https://issues.apache.org/jira/browse/SPARK-2919 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1848 from yhuai/sqlAnalyze and squashes the following commits: 0b79d36 [Yin Huai] Typo and format. c59d94b [Yin Huai] Support "ANALYZE TABLE tableName COMPUTE STATISTICS noscan".
…ld be filtered out by sqlContext.parquetFile Author: chutium <teng.qiu@gmail.com> Closes #1691 from chutium/SPARK-2700 and squashes the following commits: b76ae8c [chutium] [SPARK-2700] [SQL] fixed styling issue d75a8bd [chutium] [SPARK-2700] [SQL] Hidden files (such as .impala_insert_staging) should be filtered out by sqlContext.parquetFile
0.9 dependences (this version doesn't depend on scalalogging and I excluded commons-math3 from its transitive dependencies):
~~~
+-org.scalanlp:breeze_2.10:0.9 [S]
+-com.github.fommil.netlib:core:1.1.2
+-com.github.rwl:jtransforms:2.4.0
+-net.sf.opencsv:opencsv:2.3
+-net.sourceforge.f2j:arpack_combined_all:0.1
+-org.scalanlp:breeze-macros_2.10:0.3.1 [S]
| +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
|
+-org.slf4j:slf4j-api:1.7.5
+-org.spire-math:spire_2.10:0.7.4 [S]
+-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
|
+-org.spire-math:spire-macros_2.10:0.7.4 [S]
+-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
~~~
Closes #1749
CC: witgo avati
Author: Xiangrui Meng <meng@databricks.com>
Closes #1857 from mengxr/breeze-0.9 and squashes the following commits:
7fc16b6 [Xiangrui Meng] don't know why but exclude a private method for mima
dcc502e [Xiangrui Meng] update breeze to 0.9
…s specified in the spark option "spark.serializer" Author: GuoQiang Li <witgo@qq.com> Closes #1836 from witgo/SPARK-2897 and squashes the following commits: 23cdc5b [GuoQiang Li] review commit ada4fba [GuoQiang Li] TorrentBroadcast does not support broadcast compression fb91792 [GuoQiang Li] org.apache.spark.broadcast.TorrentBroadcast does use the serializer class specified in the spark option "spark.serializer"
…ster's The decision order of Worker's WebUI port is "--webui-port", SPARK_WORKER_WEBUI_POR, 8081(default), spark.worker.ui.port. But in Master, the order is "--webui-port", spark.master.ui.port, SPARK_MASTER_WEBUI_PORT and 8080(default). So we change the order in Worker's to keep it consistent with Master. Author: WangTao <barneystinson@aliyun.com> Closes #1838 from WangTaoTheTonic/reOrder and squashes the following commits: 460f4d4 [WangTao] Make decision order of Worker's WebUI consistent with Master's
Due to the way Yarn runs things through bash, normal quoting doesn't work as expected. This change applies the necessary voodoo to the user args to avoid issues with bash and special characters. The change also uncovered an issue with the event logger app name sanitizing code; it wasn't cleaning up all "bad" characters, so sometimes it would fail to create the log dirs. I just added some more bad character replacements. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #1724 from vanzin/SPARK-2718 and squashes the following commits: cc84b89 [Marcelo Vanzin] Review feedback. c1a257a [Marcelo Vanzin] Add test for backslashes. 55571d4 [Marcelo Vanzin] Unbreak yarn-client. 515613d [Marcelo Vanzin] [SPARK-2718] [yarn] Handle quotes and other characters in user args.
Small DecisionTree updates: * Changed main DecisionTree aggregate to treeAggregate. * Fixed bug in python example decision_tree_runner.py with missing argument (since categoricalFeaturesInfo is no longer an optional argument for trainClassifier). * Fixed same bug in python doc tests, and added tree.py to doc tests. CC: mengxr Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #2015 from jkbradley/dt-opt2 and squashes the following commits: b5114fa [Joseph K. Bradley] Fixed python tree.py doc test (extra newline) 8e4665d [Joseph K. Bradley] Added tree.py to python doc tests. Fixed bug from missing categoricalFeaturesInfo argument. b7b2922 [Joseph K. Bradley] Fixed bug in python example decision_tree_runner.py with missing argument. Changed main DecisionTree aggregate to treeAggregate. 85bbc1f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 66d076f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 a0ed0da [Joseph K. Bradley] Renamed DTMetadata to DecisionTreeMetadata. Small doc updates. 3726d20 [Joseph K. Bradley] Small code improvements based on code review. ac0b9f8 [Joseph K. Bradley] Small updates based on code review. Main change: Now using << instead of math.pow. db0d773 [Joseph K. Bradley] scala style fix 6a38f48 [Joseph K. Bradley] Added DTMetadata class for cleaner code 931a3a7 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 797f68a [Joseph K. Bradley] Fixed DecisionTreeSuite bug for training second level. Needed to update treePointToNodeIndex with groupShift. f40381c [Joseph K. Bradley] Merge branch 'dt-opt1' into dt-opt2 5f2dec2 [Joseph K. Bradley] Fixed scalastyle issue in TreePoint 6b5651e [Joseph K. Bradley] Updates based on code review. 1 major change: persisting to memory + disk, not just memory. 2d2aaaf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt1 26d10dd [Joseph K. Bradley] Removed tree/model/Filter.scala since no longer used. Removed debugging println calls in DecisionTree.scala. 356daba [Joseph K. Bradley] Merge branch 'dt-opt1' into dt-opt2 430d782 [Joseph K. Bradley] Added more debug info on binning error. Added some docs. d036089 [Joseph K. Bradley] Print timing info to logDebug. e66f1b1 [Joseph K. Bradley] TreePoint * Updated doc * Made some methods private 8464a6e [Joseph K. Bradley] Moved TimeTracker to tree/impl/ in its own file, and cleaned it up. Removed debugging println calls from DecisionTree. Made TreePoint extend Serialiable a87e08f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt1 c1565a5 [Joseph K. Bradley] Small DecisionTree updates: * Simplification: Updated calculateGainForSplit to take aggregates for a single (feature, split) pair. * Internal doc: findAggForOrderedFeatureClassification b914f3b [Joseph K. Bradley] DecisionTree optimization: eliminated filters + small changes b2ed1f3 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt 0f676e2 [Joseph K. Bradley] Optimizations + Bug fix for DecisionTree 3211f02 [Joseph K. Bradley] Optimizing DecisionTree * Added TreePoint representation to avoid calling findBin multiple times. * (not working yet, but debugging) f61e9d2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing bcf874a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing 511ec85 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing a95bc22 [Joseph K. Bradley] timing for DecisionTree internals
Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API) Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey Added sc.stop() to all examples. CorrelationSuite.scala * Added 1 test for RDDs with only 1 value RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message. Python SparseVector (pyspark/mllib/linalg.py) * Added toDense() function python/run-tests script * Added stat.py (doc test) CC: mengxr dorx Main changes were examples to show usage across APIs. Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1878 from jkbradley/mllib-stats-api-check and squashes the following commits: ea5c047 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check dafebe2 [Joseph K. Bradley] Bug fixes for examples SampledRDDs.scala and sampled_rdds.py: Check for division by 0 and for missing key in maps. 8d1e555 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 60c72d9 [Joseph K. Bradley] Fixed stat.py doc test to work for Python versions printing nan or NaN. b20d90a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 4e5d15e [Joseph K. Bradley] Changed pyspark/mllib/stat.py doc tests to use NaN instead of nan. 32173b7 [Joseph K. Bradley] Stats examples update. c8c20dc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check cf70b07 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 0b7cec3 [Joseph K. Bradley] Small updates based on code review. Renamed statistical_summary.py to correlations.py ab48f6e [Joseph K. Bradley] RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message. 65e4ebc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 8195c78 [Joseph K. Bradley] Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey 064985b [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check ee918e9 [Joseph K. Bradley] Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)
It is useful in streaming to allow users to carry extra data with the prediction, for monitoring the prediction error for example. freeman-lab Author: Xiangrui Meng <meng@databricks.com> Closes #2023 from mengxr/predict-on-values and squashes the following commits: cac47b8 [Xiangrui Meng] add classtag 2821b3b [Xiangrui Meng] use mapValues 0925efa [Xiangrui Meng] add predictOnValues to StreamingLR and fix predictOn
This fixes SPARK-3114, an issue where we inadvertently broke Python UDFs in Spark SQL. This PR modifiers the test runner script to always run the PySpark SQL tests, irrespective of whether SparkSQL itself has been modified. It also includes Davies' fix for the bug. Closes #2026. Author: Josh Rosen <joshrosen@apache.org> Author: Davies Liu <davies.liu@gmail.com> Closes #2027 from JoshRosen/pyspark-sql-fix and squashes the following commits: 9af2708 [Davies Liu] bugfix: disable compression of command 0d8d3a4 [Josh Rosen] Always run Python Spark SQL tests.
Author: Reynold Xin <rxin@apache.org> Closes #2028 from rxin/torrentBroadcast and squashes the following commits: 92c62a5 [Reynold Xin] Revert the MEMORY_AND_DISK_SER changes. 03a5221 [Reynold Xin] [SPARK-3116] Remove the excessive lockings in TorrentBroadcast
In some cases on hadoop 2.x the spark application master doesn't properly exit and hangs around for 10 minutes after its really done. We should make sure it exits properly and stops the driver. Author: Thomas Graves <tgraves@apache.org> Closes #2022 from tgravescs/SPARK-3072 and squashes the following commits: 665701d [Thomas Graves] Exit when reach max number failed executors
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2000 from sarutak/SPARK-3089 and squashes the following commits: 02dfdea [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3089 e759ce7 [Kousuke Saruta] Improved error message when closing SendingConnection
Refactored tests for streaming linear regression to use existing streaming test utilities. Summary of changes: - Made ``mllib`` depend on tests from ``streaming`` - Rewrote accuracy and convergence tests to use ``setupStreams`` and ``runStreams`` - Added new test for the accuracy of predictions generated by ``predictOnValue`` These tests should run faster, be easier to extend/maintain, and provide a reference for new tests. mengxr tdas Author: freeman <the.freeman.lab@gmail.com> Closes #2037 from freeman-lab/streamingLR-predict-tests and squashes the following commits: e851ca7 [freeman] Fixed long lines 50eb0bf [freeman] Refactored tests to use streaming test tools 32c43c2 [freeman] Added test for prediction
…ty group
- Uses the name tag to identify machines in a cluster.
- Allows overriding the security group name so it doesn't need to coincide with the cluster name.
- Outputs the request id's of up to 10 pending spot instance requests.
Author: Vida Ha <vida@databricks.com>
Closes #1899 from vidaha/vida/ec2-reuse-security-group and squashes the following commits:
c80d5c3 [Vida Ha] wrap retries in a try catch block
b2989d5 [Vida Ha] SPARK-2333: spark_ec2 script should allow option for existing security group
…batch sizes. If two RDDs have different batch size in serializers, then it will try to re-serialize the one with smaller batch size, then call RDD.zip() in Spark. Author: Davies Liu <davies.liu@gmail.com> Closes #1894 from davies/zip and squashes the following commits: c4652ea [Davies Liu] add more test cases 6d05fc8 [Davies Liu] Merge branch 'master' into zip 813b1e4 [Davies Liu] add more tests for failed cases a4aafda [Davies Liu] fix zip with serializers which have different batch sizes.
Though we don't use default argument for methods in RandomRDDs, it is still not easy for Java users to use because the output type is either `RDD[Double]` or `RDD[Vector]`. Java users should expect `JavaDoubleRDD` and `JavaRDD[Vector]`, respectively. We should create dedicated methods for Java users, and allow default arguments in Scala methods in RandomRDDs, to make life easier for both Java and Scala users. This PR also contains documentation for random data generation. brkyvz Author: Xiangrui Meng <meng@databricks.com> Closes #2041 from mengxr/stat-doc and squashes the following commits: fc5eedf [Xiangrui Meng] add missing comma ffde810 [Xiangrui Meng] address comments aef6d07 [Xiangrui Meng] add doc for random data generation b99d94b [Xiangrui Meng] add java-friendly methods to RandomRDDs
Previous pull request (#1907) was reverted. This brings it back. Still looking into the hang. Author: Reynold Xin <rxin@apache.org> Closes #1971 from rxin/netty1 and squashes the following commits: b0be96f [Reynold Xin] Added test to make sure outstandingRequests are cleaned after firing the events. 4c6d0ee [Reynold Xin] Pass callbacks cleanly. 603dce7 [Reynold Xin] Upgrade Netty to 4.0.23 to fix the DefaultFileRegion bug. 88be1d4 [Reynold Xin] Downgrade to 4.0.21 to work around a bug in writing DefaultFileRegion. 002626a [Reynold Xin] Remove netty-test-file.txt. db6e6e0 [Reynold Xin] Revert "Revert "[SPARK-2468] Netty based block server / client module""
Added a documentation section on StreamingLR to the ``MLlib - Linear Methods``, including a worked example. mengxr tdas Author: freeman <the.freeman.lab@gmail.com> Closes #2047 from freeman-lab/streaming-lr-docs and squashes the following commits: 568d250 [freeman] Tweaks to wording / formatting 05a1139 [freeman] Added documentation and example for StreamingLR
Refer to: http://stackoverflow.com/questions/510632/whats-the-difference-between-concurrenthashmap-and-collections-synchronizedmap Collections.synchronizedMap(map) creates a blocking Map which will degrade performance, albeit ensure consistency. So use ConcurrentHashMap(a more effective thread-safe hashmap) instead. also update HiveQuerySuite to fix test error when changed to ConcurrentHashMap. Author: wangfei <wangfei_hello@126.com> Author: scwf <wangfei1@huawei.com> Closes #1996 from scwf/sqlconf and squashes the following commits: 93bc0c5 [wangfei] revert change of HiveQuerySuite 0cc05dd [wangfei] add note for use synchronizedMap 3c224d3 [scwf] fix formate a7bcb98 [scwf] use ConcurrentHashMap in sql conf, intead synchronizedMap
or Jenkins will complain about no Apache header in checkpoint files. tdas rxin Author: Xiangrui Meng <meng@databricks.com> Closes #2046 from mengxr/tmp-checkpoint and squashes the following commits: 0d3ec73 [Xiangrui Meng] remove ssc.stop 9797843 [Xiangrui Meng] change checkpointDir to lazy val 89964ab [Xiangrui Meng] use temp folder for checkpoint
This is a re-implementation of TorrentBroadcast, with the following changes: 1. Removes most of the mutable, transient state from TorrentBroadcast (e.g. totalBytes, num of blocks fetched). 2. Removes TorrentInfo and TorrentBlock 3. Replaces the BlockManager.getSingle call in readObject with a getLocal, resuling in one less RPC call to the BlockManagerMasterActor to find the location of the block. 4. Removes the metadata block, resulting in one less block to fetch. 5. Removes an extra memory copy for deserialization (by using Java's SequenceInputStream). Basically for a regular broadcasted object with only one block, the number of RPC calls goes from 5+1 to 2+1). Old TorrentBroadcast for object of a single block: 1 RPC to ask for location of the broadcast variable 1 RPC to ask for location of the metadata block 1 RPC to fetch the metadata block 1 RPC to ask for location of the first data block 1 RPC to fetch the first data block 1 RPC to tell the driver we put the first data block in i.e. 5 + 1 New TorrentBroadcast for object of a single block: 1 RPC to ask for location of the first data block 1 RPC to get the first data block 1 RPC to tell the driver we put the first data block in i.e. 2 + 1 Author: Reynold Xin <rxin@apache.org> Closes #2030 from rxin/torrentBroadcast and squashes the following commits: 5bacb9d [Reynold Xin] Always add the object to driver's block manager. 0d8ed5b [Reynold Xin] Added getBytes to BlockManager and uses that in TorrentBroadcast. 2d6a5fb [Reynold Xin] Use putBytes/getRemoteBytes throughout. 3670f00 [Reynold Xin] Code review feedback. c1185cd [Reynold Xin] [SPARK-3119] Re-implementation of TorrentBroadcast.
This PR fixes two bugs related to `spark.local.dirs` and `SPARK_LOCAL_DIRS`, one where `Utils.getLocalDir()` might return an invalid directory (SPARK-2974) and another where the `SPARK_LOCAL_DIRS` override didn't affect the driver, which could cause problems when running tasks in local mode (SPARK-2975). This patch fixes both issues: the new `Utils.getOrCreateLocalRootDirs(conf: SparkConf)` utility method manages the creation of local directories and handles the precedence among the different configuration options, so we should see the same behavior whether we're running in local mode or on a worker. It's kind of a pain to mock out environment variables in tests (no easy way to mock System.getenv), so I added a `private[spark]` method to SparkConf for accessing environment variables (by default, it just delegates to System.getenv). By subclassing SparkConf and overriding this method, we can mock out SPARK_LOCAL_DIRS in tests. I also fixed a typo in PySpark where we used `SPARK_LOCAL_DIR` instead of `SPARK_LOCAL_DIRS` (I think this was technically innocuous, but it seemed worth fixing). Author: Josh Rosen <joshrosen@apache.org> Closes #2002 from JoshRosen/local-dirs and squashes the following commits: efad8c6 [Josh Rosen] Address review comments: 1dec709 [Josh Rosen] Minor updates to Javadocs. 7f36999 [Josh Rosen] Use env vars to detect if running in YARN container. 399ac25 [Josh Rosen] Update getLocalDir() documentation. bb3ad89 [Josh Rosen] Remove duplicated YARN getLocalDirs() code. 3e92d44 [Josh Rosen] Move local dirs override logic into Utils; fix bugs: b2c4736 [Josh Rosen] Add failing tests for SPARK-2974 and SPARK-2975. 007298b [Josh Rosen] Allow environment variables to be mocked in tests. 6d9259b [Josh Rosen] Fix typo in PySpark: SPARK_LOCAL_DIR should be SPARK_LOCAL_DIRS
This patch adds unit tests for Spark Sink. It also removes the private[flume] for Spark Sink, since the sink is instantiated from Flume configuration (looks like this is ignored by reflection which is used by Flume, but we should still remove it anyway). Author: Hari Shreedharan <hshreedharan@apache.org> Author: Hari Shreedharan <hshreedharan@cloudera.com> Closes #1958 from harishreedharan/spark-sink-test and squashes the following commits: e3110b9 [Hari Shreedharan] Add a sleep to allow sink to commit the transactions 120b81e [Hari Shreedharan] Fix complexity in threading model in test 4df5be6 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test c9190d1 [Hari Shreedharan] Indentation and spaces changes 7fedc5a [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test abc20cb [Hari Shreedharan] Minor test changes 7b9b649 [Hari Shreedharan] Merge branch 'master' into spark-sink-test f2c56c9 [Hari Shreedharan] Update SparkSinkSuite.scala a24aac8 [Hari Shreedharan] Remove unused var c86d615 [Hari Shreedharan] [SPARK-3054][STREAMING] Add unit tests for Spark Sink.
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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 apache#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.
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