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* [SPARK-7319][SQL] Improve the output from DataFrame.show()云峤2015-05-045-44/+112
| | | | | | | | | | | | | | | | | | | | Author: 云峤 <chensong.cs@alibaba-inc.com> Closes #5865 from kaka1992/df.show and squashes the following commits: c79204b [云峤] Update a1338f6 [云峤] Update python dataFrame show test and add empty df unit test. 734369c [云峤] Update python dataFrame show test and add empty df unit test. 84aec3e [云峤] Update python dataFrame show test and add empty df unit test. 159b3d5 [云峤] update 03ef434 [云峤] update 7394fd5 [云峤] update test show ced487a [云峤] update pep8 b6e690b [云峤] Merge remote-tracking branch 'upstream/master' into df.show 30ac311 [云峤] [SPARK-7294] ADD BETWEEN 7d62368 [云峤] [SPARK-7294] ADD BETWEEN baf839b [云峤] [SPARK-7294] ADD BETWEEN d11d5b9 [云峤] [SPARK-7294] ADD BETWEEN
* [SPARK-5956] [MLLIB] Pipeline components should be copyable.Xiangrui Meng2015-05-0456-805/+671
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR added `copy(extra: ParamMap): Params` to `Params`, which makes a copy of the current instance with a randomly generated uid and some extra param values. With this change, we only need to implement `fit` and `transform` without extra param values given the default implementation of `fit(dataset, extra)`: ~~~scala def fit(dataset: DataFrame, extra: ParamMap): Model = { copy(extra).fit(dataset) } ~~~ Inside `fit` and `transform`, since only the embedded values are used, I added `$` as an alias for `getOrDefault` to make the code easier to read. For example, in `LinearRegression.fit` we have: ~~~scala val effectiveRegParam = $(regParam) / yStd val effectiveL1RegParam = $(elasticNetParam) * effectiveRegParam val effectiveL2RegParam = (1.0 - $(elasticNetParam)) * effectiveRegParam ~~~ Meta-algorithm like `Pipeline` implements its own `copy(extra)`. So the fitted pipeline model stored all copied stages (no matter whether it is a transformer or a model). Other changes: * `Params$.inheritValues` is moved to `Params!.copyValues` and returns the target instance. * `fittingParamMap` was removed because the `parent` carries this information. * `validate` was renamed to `validateParams` to be more precise. TODOs: * [x] add tests for newly added methods * [ ] update documentation jkbradley dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #5820 from mengxr/SPARK-5956 and squashes the following commits: 7bef88d [Xiangrui Meng] address comments 05229c3 [Xiangrui Meng] assert -> assertEquals b2927b1 [Xiangrui Meng] organize imports f14456b [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956 93e7924 [Xiangrui Meng] add tests for hasParam & copy 463ecae [Xiangrui Meng] merge master 2b954c3 [Xiangrui Meng] update Binarizer 465dd12 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956 282a1a8 [Xiangrui Meng] fix test 819dd2d [Xiangrui Meng] merge master b642872 [Xiangrui Meng] example code runs 5a67779 [Xiangrui Meng] examples compile c76b4d1 [Xiangrui Meng] fix all unit tests 0f4fd64 [Xiangrui Meng] fix some tests 9286a22 [Xiangrui Meng] copyValues to trained models 53e0973 [Xiangrui Meng] move inheritValues to Params and rename it to copyValues 9ee004e [Xiangrui Meng] merge copy and copyWith; rename validate to validateParams d882afc [Xiangrui Meng] test compile f082a31 [Xiangrui Meng] make Params copyable and simply handling of extra params in all spark.ml components
* [MINOR] Fix python test typo?Andrew Or2015-05-041-1/+1
| | | | | | | | | | I suspect haven't been using anaconda in tests in a while. I wonder if this change actually does anything but this line as it stands looks strictly less correct. Author: Andrew Or <andrew@databricks.com> Closes #5883 from andrewor14/fix-run-tests-typo and squashes the following commits: a3ad720 [Andrew Or] Fix typo?
* [SPARK-5100] [SQL] add webui for thriftservertianyi2015-05-0410-22/+751
| | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR is a rebased version of #3946 , and mainly focused on creating an independent tab for the thrift server in spark web UI. Features: 1. Session related statistics ( username and IP are only supported in hive-0.13.1 ) 2. List all the SQL executing or executed on this server 3. Provide links to the job generated by SQL 4. Provide link to show all SQL executing or executed in a specified session Prototype snapshots: This is the main page for thrift server ![image](https://cloud.githubusercontent.com/assets/1411869/7361379/df7dcc64-ed89-11e4-9964-4df0b32f475e.png) Author: tianyi <tianyi.asiainfo@gmail.com> Closes #5730 from tianyi/SPARK-5100 and squashes the following commits: cfd14c7 [tianyi] style fix 0efe3d5 [tianyi] revert part of pom change c0f2fa0 [tianyi] extends HiveThriftJdbcTest to start/stop thriftserver for UI test aa20408 [tianyi] fix style problem c9df6f9 [tianyi] add testsuite for thriftserver ui and fix some style issue 9830199 [tianyi] add webui for thriftserver
* [SPARK-5563] [MLLIB] LDA with online variational inferenceYuhao Yang2015-05-044-74/+438
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-5563 The PR contains the implementation for [Online LDA] (https://www.cs.princeton.edu/~blei/papers/HoffmanBleiBach2010b.pdf) based on the research of Matt Hoffman and David M. Blei, which provides an efficient option for LDA users. Major advantages for the algorithm are the stream compatibility and economic time/memory consumption due to the corpus split. For more details, please refer to the jira. Online LDA can act as a fast option for LDA, and will be especially helpful for the users who needs a quick result or with large corpus. Correctness test. I have tested current PR with https://github.com/Blei-Lab/onlineldavb and the results are identical. I've uploaded the result and code to https://github.com/hhbyyh/LDACrossValidation. Author: Yuhao Yang <hhbyyh@gmail.com> Author: Joseph K. Bradley <joseph@databricks.com> Closes #4419 from hhbyyh/ldaonline and squashes the following commits: 1045eec [Yuhao Yang] Merge pull request #2 from jkbradley/hhbyyh-ldaonline2 cf376ff [Joseph K. Bradley] For private vars needed for testing, I made them private and added accessors. Java doesn’t understand package-private tags, so this minimizes the issues Java users might encounter. 6149ca6 [Yuhao Yang] fix for setOptimizer cf0007d [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline 54cf8da [Yuhao Yang] some style change 68c2318 [Yuhao Yang] add a java ut 4041723 [Yuhao Yang] add ut 138bfed [Yuhao Yang] Merge pull request #1 from jkbradley/hhbyyh-ldaonline-update 9e910d9 [Joseph K. Bradley] small fix 61d60df [Joseph K. Bradley] Minor cleanups: * Update *Concentration parameter documentation * EM Optimizer: createVertices() does not need to be a function * OnlineLDAOptimizer: typos in doc * Clean up the core code for online LDA (Scala style) a996a82 [Yuhao Yang] respond to comments b1178cf [Yuhao Yang] fit into the optimizer framework dbe3cff [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline 15be071 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline b29193b [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline d19ef55 [Yuhao Yang] change OnlineLDA to class 97b9e1a [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline e7bf3b0 [Yuhao Yang] move to seperate file f367cc9 [Yuhao Yang] change to optimization 8cb16a6 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline 62405cc [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline 02d0373 [Yuhao Yang] fix style in comment f6d47ca [Yuhao Yang] Merge branch 'ldaonline' of https://github.com/hhbyyh/spark into ldaonline d86cdec [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline a570c9a [Yuhao Yang] use sample to pick up batch 4a3f27e [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline e271eb1 [Yuhao Yang] remove non ascii 581c623 [Yuhao Yang] seperate API and adjust batch split 37af91a [Yuhao Yang] iMerge remote-tracking branch 'upstream/master' into ldaonline 20328d1 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline i aa365d1 [Yuhao Yang] merge upstream master 3a06526 [Yuhao Yang] merge with new example 0dd3947 [Yuhao Yang] kMerge remote-tracking branch 'upstream/master' into ldaonline 0d0f3ee [Yuhao Yang] replace random split with sliding fa408a8 [Yuhao Yang] ssMerge remote-tracking branch 'upstream/master' into ldaonline 45884ab [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline s f41c5ca [Yuhao Yang] style fix 26dca1b [Yuhao Yang] style fix and make class private 043e786 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline s Conflicts: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDA.scala d640d9c [Yuhao Yang] online lda initial checkin
* [SPARK-7241] Pearson correlation for DataFramesBurak Yavuz2015-05-036-26/+130
| | | | | | | | | | | | | | | | | submitting this PR from a phone, excuse the brevity. adds Pearson correlation to Dataframes, reusing the covariance calculation code cc mengxr rxin Author: Burak Yavuz <brkyvz@gmail.com> Closes #5858 from brkyvz/df-corr and squashes the following commits: 285b838 [Burak Yavuz] addressed comments v2.0 d10babb [Burak Yavuz] addressed comments v0.2 4b74b24 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into df-corr 4fe693b [Burak Yavuz] addressed comments v0.1 a682d06 [Burak Yavuz] ready for PR
* [SPARK-7329] [MLLIB] simplify ParamGridBuilder implXiangrui Meng2015-05-031-19/+9
| | | | | | | | | | | as suggested by justinuang on #5601. Author: Xiangrui Meng <meng@databricks.com> Closes #5873 from mengxr/SPARK-7329 and squashes the following commits: d08f9cf [Xiangrui Meng] simplify tests b7a7b9b [Xiangrui Meng] simplify grid build
* [SPARK-7302] [DOCS] SPARK building documentation still mentions building for ↵Sean Owen2015-05-034-22/+1
| | | | | | | | | | | | | | | | | | yarn 0.23 Remove references to Hadoop 0.23 CC tgravescs Is this what you had in mind? basically all refs to 0.23? We don't support YARN 0.23, but also don't support Hadoop 0.23 anymore AFAICT. There are no builds or releases for it. In fact, on a related note, refs to CDH3 (Hadoop 0.20.2) should be removed as this certainly isn't supported either. Author: Sean Owen <sowen@cloudera.com> Closes #5863 from srowen/SPARK-7302 and squashes the following commits: 42f5d1e [Sean Owen] Remove CDH3 (Hadoop 0.20.2) refs too dad02e3 [Sean Owen] Remove references to Hadoop 0.23
* [SPARK-6907] [SQL] Isolated client for HiveMetastoreMichael Armbrust2015-05-039-7/+1088
| | | | | | | | | | | | | | | | | | | | | | | | This PR adds initial support for loading multiple versions of Hive in a single JVM and provides a common interface for extracting metadata from the `HiveMetastoreClient` for a given version. This is accomplished by creating an isolated `ClassLoader` that operates according to the following rules: - __Shared Classes__: Java, Scala, logging, and Spark classes are delegated to `baseClassLoader` allowing the results of calls to the `ClientInterface` to be visible externally. - __Hive Classes__: new instances are loaded from `execJars`. These classes are not accessible externally due to their custom loading. - __Barrier Classes__: Classes such as `ClientWrapper` are defined in Spark but must link to a specific version of Hive. As a result, the bytecode is acquired from the Spark `ClassLoader` but a new copy is created for each instance of `IsolatedClientLoader`. This new instance is able to see a specific version of hive without using reflection where ever hive is consistent across versions. Since this is a unique instance, it is not visible externally other than as a generic `ClientInterface`, unless `isolationOn` is set to `false`. In addition to the unit tests, I have also tested this locally against mysql instances of the Hive Metastore. I've also successfully ported Spark SQL to run with this client, but due to the size of the changes, that will come in a follow-up PR. By default, Hive jars are currently downloaded from Maven automatically for a given version to ease packaging and testing. However, there is also support for specifying their location manually for deployments without internet. Author: Michael Armbrust <michael@databricks.com> Closes #5851 from marmbrus/isolatedClient and squashes the following commits: c72f6ac [Michael Armbrust] rxins comments 1e271fa [Michael Armbrust] [SPARK-6907][SQL] Isolated client for HiveMetastore
* [SPARK-7022] [PYSPARK] [ML] Add ML.Tuning.ParamGridBuilder to PySparkOmede Firouz2015-05-032-0/+95
| | | | | | | | | | | Author: Omede Firouz <ofirouz@palantir.com> Author: Omede <omedefirouz@gmail.com> Closes #5601 from oefirouz/paramgrid and squashes the following commits: c9e2481 [Omede Firouz] Make test a doctest 9a8ce22 [Omede] Fix linter issues 8b8a6d2 [Omede Firouz] [SPARK-7022][PySpark][ML] Add ML.Tuning.ParamGridBuilder to PySpark
* [SPARK-7031] [THRIFTSERVER] let thrift server take SPARK_DAEMON_MEMORY and ↵WangTaoTheTonic2015-05-031-1/+18
| | | | | | | | | | | | | | | | | | | SPARK_DAEMON_JAVA_OPTS We should let Thrift Server take these two parameters as it is a daemon. And it is better to read driver-related configs as an app submited by spark-submit. https://issues.apache.org/jira/browse/SPARK-7031 Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #5609 from WangTaoTheTonic/SPARK-7031 and squashes the following commits: 8d3fc16 [WangTaoTheTonic] indent 035069b [WangTaoTheTonic] better code style d3ddfb6 [WangTaoTheTonic] revert the unnecessary changes in suite 624e652 [WangTaoTheTonic] fix break tests 0565831 [WangTaoTheTonic] fix failed tests 4fb25ed [WangTaoTheTonic] let thrift server take SPARK_DAEMON_MEMORY and SPARK_DAEMON_JAVA_OPTS
* [SPARK-7255] [STREAMING] [DOCUMENTATION] Added documentation for ↵BenFradet2015-05-021-0/+10
| | | | | | | | | | | | | | | spark.streaming.kafka.maxRetries Added documentation for spark.streaming.kafka.maxRetries Author: BenFradet <benjamin.fradet@gmail.com> Closes #5808 from BenFradet/master and squashes the following commits: cc72e7a [BenFradet] updated doc for spark.streaming.kafka.maxRetries to explain the default value 18f823e [BenFradet] Added "consecutive" to the spark.streaming.kafka.maxRetries doc 597fdeb [BenFradet] Mention that spark.streaming.kafka.maxRetries only applies to the direct kafka api 0efad39 [BenFradet] Added documentation for spark.streaming.kafka.maxRetries
* [SPARK-5213] [SQL] Pluggable SQL Parser SupportCheng Hao2015-05-029-39/+196
| | | | | | | | | | | | | | | | | | | based on #4015, we should not delete `sqlParser` from sqlcontext, that leads to mima failed. Users implement dialect to give a fallback for `sqlParser` and we should construct `sqlParser` in sqlcontext according to the dialect `protected[sql] val sqlParser = new SparkSQLParser(getSQLDialect().parse(_))` Author: Cheng Hao <hao.cheng@intel.com> Author: scwf <wangfei1@huawei.com> Closes #5827 from scwf/sqlparser1 and squashes the following commits: 81b9737 [scwf] comment fix 0878bd1 [scwf] remove comments c19780b [scwf] fix mima tests c2895cf [scwf] Merge branch 'master' of https://github.com/apache/spark into sqlparser1 493775c [Cheng Hao] update the code as feedback 81a731f [Cheng Hao] remove the unecessary comment aab0b0b [Cheng Hao] polish the code a little bit 49b9d81 [Cheng Hao] shrink the comment for rebasing
* [MINOR] [HIVE] Fix QueryPartitionSuite.Marcelo Vanzin2015-05-021-3/+4
| | | | | | | | | | | | | | At least in the version of Hive I tested on, the test was deleting a temp directory generated by Hive instead of one containing partition data. So fix the filter to only consider partition directories when deciding what to delete. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5854 from vanzin/hive-test-fix and squashes the following commits: 7594ae9 [Marcelo Vanzin] Fix typo. 729fa80 [Marcelo Vanzin] [minor] [hive] Fix QueryPartitionSuite.
* [SPARK-6030] [CORE] Using simulated field layout method to compute class ↵Ye Xianjin2015-05-023-18/+100
| | | | | | | | | | | | | | | | | | | | shellSize SizeEstimator gives wrong result for Integer on 64bit JVM with UseCompressedOops on, this pr fixes that. For more details, please refer [SPARK-6030](https://issues.apache.org/jira/browse/SPARK-6030) sryza, I noticed there is a pr to expose SizeEstimator, maybe that should be waited by this pr get merged if we confirm this problem. And shivaram would you mind to review this pr since you contribute related code. Also cc to srowen and mateiz Author: Ye Xianjin <advancedxy@gmail.com> Closes #4783 from advancedxy/SPARK-6030 and squashes the following commits: c4dcb41 [Ye Xianjin] Add super.beforeEach in the beforeEach method to make the trait stackable.. Remove useless leading whitespace. 3f80640 [Ye Xianjin] The size of Integer class changes from 24 to 16 on a 64-bit JVM with -UseCompressedOops flag on after the fix. I don't how 100000 was originally calculated, It looks like 100000 is the magic number which makes sure spilling. Because of the size change, It fails because there is no spilling at all. Change the number to a slightly larger number fixes that. e849d2d [Ye Xianjin] Merge two shellSize assignments into one. Add some explanation to alignSizeUp method. 85a0b51 [Ye Xianjin] Fix typos and update wording in comments. Using alignSizeUp to compute alignSize. d27eb77 [Ye Xianjin] Add some detailed comments in the code. Add some test cases. It's very difficult to design test cases as the final object alignment will hide a lot of filed layout details if we just considering the whole size. 842aed1 [Ye Xianjin] primitiveSize(cls) can just return Int. Use a simplified class field layout method to calculate class instance size. Will add more documents and test cases. Add a new alignSizeUp function which uses bitwise operators to speedup. 62e8ab4 [Ye Xianjin] Don't alignSize for objects' shellSize, alignSize when added to state.size. Add some primitive wrapper objects size tests.
* [SPARK-7323] [SPARK CORE] Use insertAll instead of insert while merging ↵Mridul Muralidharan2015-05-021-4/+1
| | | | | | | | | | combiners in reducer Author: Mridul Muralidharan <mridulm@yahoo-inc.com> Closes #5862 from mridulm/optimize_aggregator and squashes the following commits: 61cf43a [Mridul Muralidharan] Use insertAll instead of insert - much more expensive to do it per tuple
* [SPARK-3444] Fix typo in Dataframes.py introduced in []Dean Chen2015-05-021-1/+1
| | | | | | | | Author: Dean Chen <deanchen5@gmail.com> Closes #5866 from deanchen/patch-1 and squashes the following commits: 0028bc4 [Dean Chen] Fix typo in Dataframes.py introduced in [SPARK-3444]
* [SPARK-7315] [STREAMING] [TEST] Fix flaky WALBackedBlockRDDSuiteTathagata Das2015-05-021-4/+8
| | | | | | | | | | | `FileUtils.getTempDirectoryPath()` path may or may not exist. We want to make sure that it does not exist. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #5853 from tdas/SPARK-7315 and squashes the following commits: 141afd5 [Tathagata Das] Removed use of FileUtils b08d4f1 [Tathagata Das] Fix flaky WALBackedBlockRDDSuite
* [SPARK-7120] [SPARK-7121] Closure cleaner nesting + documentation + testsAndrew Or2015-05-013-58/+831
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Note: ~600 lines of this is test code, and ~100 lines documentation. **[SPARK-7121]** ClosureCleaner does not handle nested closures properly. For instance, in SparkContext, I tried to do the following: ``` def scope[T](body: => T): T = body // no-op def myCoolMethod(path: String): RDD[String] = scope { parallelize(1 to 10).map { _ => path } } ``` and I got an exception complaining that SparkContext is not serializable. The issue here is that the inner closure is getting its path from the outer closure (the scope), but the outer closure references the SparkContext object itself to get the `parallelize` method. Note, however, that the inner closure doesn't actually need the SparkContext; it just needs a field from the outer closure. If we modify ClosureCleaner to clean the outer closure recursively using only the fields accessed by the inner closure, then we can serialize the inner closure. **[SPARK-7120]** Also, the other thing is that this file is one of the least understood, partly because it is very low level and is written a long time ago. This patch attempts to change that by adding the missing documentation. This is blocking my effort on a separate task #5729. Author: Andrew Or <andrew@databricks.com> Closes #5685 from andrewor14/closure-cleaner and squashes the following commits: cd46230 [Andrew Or] Revert a small change that affected streaming 0bbe77f [Andrew Or] Fix style ea874bc [Andrew Or] Fix tests 26c5072 [Andrew Or] Address comments 16fbcfd [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner 26c7aba [Andrew Or] Revert "In sc.runJob, actually clean the inner closure" 6f75784 [Andrew Or] Revert "Guard against NPE if CC is used outside of an application" e909a42 [Andrew Or] Guard against NPE if CC is used outside of an application 3998168 [Andrew Or] In sc.runJob, actually clean the inner closure 9187066 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner d889950 [Andrew Or] Revert "Bypass SerializationDebugger for now (SPARK-7180)" 9419efe [Andrew Or] Bypass SerializationDebugger for now (SPARK-7180) 6d4d3f1 [Andrew Or] Fix scala style? 4aab379 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner e45e904 [Andrew Or] More minor updates (wording, renaming etc.) 8b71cdb [Andrew Or] Update a few comments eb127e5 [Andrew Or] Use private method tester for a few things a3aa465 [Andrew Or] Add more tests for individual closure cleaner operations e672170 [Andrew Or] Guard against potential infinite cycles in method visitor 6d36f38 [Andrew Or] Fix closure cleaner visibility 2106f12 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner 263593d [Andrew Or] Finalize tests 06fd668 [Andrew Or] Make closure cleaning idempotent a4866e3 [Andrew Or] Add tests (still WIP) 438c68f [Andrew Or] Minor changes 2390a60 [Andrew Or] Feature flag this new behavior 86f7823 [Andrew Or] Implement transitive cleaning + add missing documentation
* [SPARK-7242] added python api for freqItems in DataFramesBurak Yavuz2015-05-013-3/+38
| | | | | | | | | | | | The python api for DataFrame's plus addressed your comments from previous PR. rxin Author: Burak Yavuz <brkyvz@gmail.com> Closes #5859 from brkyvz/df-freq-py2 and squashes the following commits: f9aa9ce [Burak Yavuz] addressed comments v0.1 4b25056 [Burak Yavuz] added python api for freqItems
* [SPARK-7317] [Shuffle] Expose shuffle handleMridul Muralidharan2015-05-011-1/+4
| | | | | | | | | | | | Details in JIRA, in a nut-shell, all machinary for custom RDD's to leverage spark shuffle directly (without exposing impl details of shuffle) exists - except for this small piece. Exposing this will allow for custom dependencies to get a handle to ShuffleHandle - which they can then leverage on reduce side. Author: Mridul Muralidharan <mridulm@yahoo-inc.com> Closes #5857 from mridulm/expose_shuffle_handle and squashes the following commits: d8b6bd4 [Mridul Muralidharan] Expose ShuffleHandle
* [SPARK-6229] Add SASL encryption to network library.Marcelo Vanzin2015-05-0127-106/+1070
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | There are two main parts of this change: - Extending the bootstrap mechanism in the network library to add a server-side bootstrap (which works a little bit differently than the client-side bootstrap), and to allow the bootstraps to modify the underlying channel. - Use SASL to encrypt data going through the RPC channel. The second item requires some non-optimal code to be able to work around the fact that the outbound path in netty is not thread-safe, and ordering is very important when encryption is in the picture. A lot of the changes outside the network/common library are just to adjust to the changed API for initializing the RPC server. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5377 from vanzin/SPARK-6229 and squashes the following commits: ff01966 [Marcelo Vanzin] Use fancy new size config style. be53f32 [Marcelo Vanzin] Merge branch 'master' into SPARK-6229 47d4aff [Marcelo Vanzin] Merge branch 'master' into SPARK-6229 7a2a805 [Marcelo Vanzin] Clean up some unneeded changes. 2f92237 [Marcelo Vanzin] Add comment. 67bb0c6 [Marcelo Vanzin] Revert "Avoid exposing ByteArrayWritableChannel outside of test code." 065f684 [Marcelo Vanzin] Add test to verify chunking. 3d1695d [Marcelo Vanzin] Minor cleanups. 73cff0e [Marcelo Vanzin] Skip bytes in decode path too. 318ad23 [Marcelo Vanzin] Avoid exposing ByteArrayWritableChannel outside of test code. 346f829 [Marcelo Vanzin] Avoid trip through channel selector by not reporting 0 bytes written. a4a5938 [Marcelo Vanzin] Review feedback. 4797519 [Marcelo Vanzin] Remove unused import. 9908ada [Marcelo Vanzin] Fix test, SASL backend disposal. 7fe1489 [Marcelo Vanzin] Add a test that makes sure encryption is actually enabled. adb6f9d [Marcelo Vanzin] Review feedback. cf2a605 [Marcelo Vanzin] Clean up some code. 8584323 [Marcelo Vanzin] Fix a comment. e98bc55 [Marcelo Vanzin] Add option to only allow encrypted connections to the server. dad42fc [Marcelo Vanzin] Make encryption thread-safe, less memory-intensive. b00999a [Marcelo Vanzin] Consolidate ByteArrayWritableChannel, fix SASL code to match master changes. b923cae [Marcelo Vanzin] Make SASL encryption handler thread-safe, handle FileRegion messages. 39539a7 [Marcelo Vanzin] Add config option to enable SASL encryption. 351a86f [Marcelo Vanzin] Add SASL encryption to network library. fbe6ccb [Marcelo Vanzin] Add TransportServerBootstrap, make SASL code use it.
* [SPARK-2691] [MESOS] Support for Mesos DockerInfoChris Heller2015-05-019-5/+280
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch adds partial support for running spark on mesos inside of a docker container. Only fine-grained mode is presently supported, and there is no checking done to ensure that the version of libmesos is recent enough to have a DockerInfo structure in the protobuf (other than pinning a mesos version in the pom.xml). Author: Chris Heller <hellertime@gmail.com> Closes #3074 from hellertime/SPARK-2691 and squashes the following commits: d504af6 [Chris Heller] Assist type inference f64885d [Chris Heller] Fix errant line length 17c41c0 [Chris Heller] Base Dockerfile on mesosphere/mesos image 8aebda4 [Chris Heller] Simplfy Docker image docs 1ae7f4f [Chris Heller] Style points 974bd56 [Chris Heller] Convert map to flatMap 5d8bdf7 [Chris Heller] Factor out the DockerInfo construction. 7b75a3d [Chris Heller] Align to styleguide 80108e7 [Chris Heller] Bend to the will of RAT ba77056 [Chris Heller] Explicit RAT exclude abda5e5 [Chris Heller] Wildcard .rat-excludes 2f2873c [Chris Heller] Exclude spark-mesos from RAT a589a5b [Chris Heller] Add example Dockerfile b6825ce [Chris Heller] Remove use of EasyMock eae1b86 [Chris Heller] Move properties under 'spark.mesos.' c184d00 [Chris Heller] Use map on Option to be consistent with non-coarse code fb9501a [Chris Heller] Bumped mesos version to current release fa11879 [Chris Heller] Add listenerBus to EasyMock 882151e [Chris Heller] Changes to scala style b22d42d [Chris Heller] Exclude template from RAT db536cf [Chris Heller] Remove unneeded mocks dea1bd5 [Chris Heller] Force default protocol 7dac042 [Chris Heller] Add test for DockerInfo 5456c0c [Chris Heller] Adjust syntax style 521c194 [Chris Heller] Adjust version info 6e38f70 [Chris Heller] Document Mesos Docker properties 29572ab [Chris Heller] Support all DockerInfo fields b8c0dea [Chris Heller] Support for mesos DockerInfo in coarse-mode. 482a9fd [Chris Heller] Support for mesos DockerInfo in fine-grained mode.
* [SPARK-6443] [SPARK SUBMIT] Could not submit app in standalone cluster mode ↵WangTaoTheTonic2015-05-018-95/+229
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | when HA is enabled **3/26 update:** * Akka-based: Use an array of `ActorSelection` to represent multiple master. Add an `activeMasterActor` for query status of driver. And will add lost masters( including the standby one) to `lostMasters`. When size of `lostMasters` equals or greater than # of all masters, we should give an error that all masters are not avalible. * Rest-based: When all masters are not available(throw an exception), we use akka gateway to submit apps. I have tested simply on standalone HA cluster(with two masters alive and one alive/one dead), it worked. There might remains some issues on style or message print, but we can check the solution then fix them together. /cc srowen andrewor14 Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #5116 from WangTaoTheTonic/SPARK-6443 and squashes the following commits: 2a28aab [WangTaoTheTonic] based the newest change https://github.com/apache/spark/pull/5144 76fd411 [WangTaoTheTonic] rebase f4f972b [WangTaoTheTonic] rebase...again a41de0b [WangTaoTheTonic] rebase 220cb3c [WangTaoTheTonic] move connect exception inside 35119a0 [WangTaoTheTonic] style and compile issues 9d636be [WangTaoTheTonic] per Andrew's comments 979760c [WangTaoTheTonic] rebase e4f4ece [WangTaoTheTonic] fix failed test 5d23958 [WangTaoTheTonic] refact some duplicated code, style and comments 7a881b3 [WangTaoTheTonic] when one of masters is gone, we still can submit 2b011c9 [WangTaoTheTonic] fix broken tests 60d97a4 [WangTaoTheTonic] rebase fa1fa80 [WangTaoTheTonic] submit app to HA cluster in standalone cluster mode
* [SPARK-7216] [MESOS] Add driver details page to Mesos cluster UI.Timothy Chen2015-05-016-11/+222
| | | | | | | | | | Add a details page that displays Mesos driver in the Mesos cluster UI Author: Timothy Chen <tnachen@gmail.com> Closes #5763 from tnachen/mesos_cluster_page and squashes the following commits: 55f36eb [Timothy Chen] Add driver details page to Mesos cluster UI.
* [SPARK-6954] [YARN] ExecutorAllocationManager can end up requesting a ↵Sandy Ryza2015-05-012-124/+148
| | | | | | | | | | | | | negative n... ...umber of executors Author: Sandy Ryza <sandy@cloudera.com> Closes #5704 from sryza/sandy-spark-6954 and squashes the following commits: b7890fb [Sandy Ryza] Avoid ramping up to an existing number of executors 6eb516a [Sandy Ryza] SPARK-6954. ExecutorAllocationManager can end up requesting a negative number of executors
* [SPARK-3444] Provide an easy way to change log levelHolden Karau2015-05-016-16/+61
| | | | | | | | | | | | | | | Add support for changing the log level at run time through the SparkContext. Based on an earlier PR, #2433 includes CR feedback from pwendel & davies Author: Holden Karau <holden@pigscanfly.ca> Closes #5791 from holdenk/SPARK-3444-provide-an-easy-way-to-change-log-level-r2 and squashes the following commits: 3bf3be9 [Holden Karau] fix exception 42ba873 [Holden Karau] fix exception 9117244 [Holden Karau] Only allow valid log levels, throw exception if invalid log level. 338d7bf [Holden Karau] rename setLoggingLevel to setLogLevel fac14a0 [Holden Karau] Fix style errors d9d03f3 [Holden Karau] Add support for changing the log level at run time through the SparkContext. Based on an earlier PR, #2433 includes CR feedback from @pwendel & @davies
* [SPARK-2808][Streaming][Kafka] update kafka to 0.8.2cody koeninger2015-05-016-27/+104
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | i don't think this should be merged until after 1.3.0 is final Author: cody koeninger <cody@koeninger.org> Author: Helena Edelson <helena.edelson@datastax.com> Closes #4537 from koeninger/wip-2808-kafka-0.8.2-upgrade and squashes the following commits: 803aa2c [cody koeninger] [SPARK-2808][Streaming][Kafka] code cleanup per TD e6dfaf6 [cody koeninger] [SPARK-2808][Streaming][Kafka] pointless whitespace change to trigger jenkins again 1770abc [cody koeninger] [SPARK-2808][Streaming][Kafka] make waitUntilLeaderOffset easier to call, call it from python tests as well d4267e9 [cody koeninger] [SPARK-2808][Streaming][Kafka] fix stderr redirect in python test script 30d991d [cody koeninger] [SPARK-2808][Streaming][Kafka] remove stderr prints since it breaks python 3 syntax 1d896e2 [cody koeninger] [SPARK-2808][Streaming][Kafka] add even even more logging to python test 4c4557f [cody koeninger] [SPARK-2808][Streaming][Kafka] add even more logging to python test 115aeee [cody koeninger] Merge branch 'master' into wip-2808-kafka-0.8.2-upgrade 2712649 [cody koeninger] [SPARK-2808][Streaming][Kafka] add more logging to python test, see why its timing out in jenkins 2b92d3f [cody koeninger] [SPARK-2808][Streaming][Kafka] wait for leader offsets in the java test as well 3824ce3 [cody koeninger] [SPARK-2808][Streaming][Kafka] naming / comments per tdas 61b3464 [cody koeninger] [SPARK-2808][Streaming][Kafka] delay for second send in boundary condition test af6f3ec [cody koeninger] [SPARK-2808][Streaming][Kafka] delay test until latest leader offset matches expected value 9edab4c [cody koeninger] [SPARK-2808][Streaming][Kafka] more shots in the dark on jenkins failing test c70ee43 [cody koeninger] [SPARK-2808][Streaming][Kafka] add more asserts to test, try to figure out why it fails on jenkins but not locally 1d10751 [cody koeninger] Merge branch 'master' into wip-2808-kafka-0.8.2-upgrade ed02d2c [cody koeninger] [SPARK-2808][Streaming][Kafka] move default argument for api version to overloaded method, for binary compat 407382e [cody koeninger] [SPARK-2808][Streaming][Kafka] update kafka to 0.8.2.1 77de6c2 [cody koeninger] Merge branch 'master' into wip-2808-kafka-0.8.2-upgrade 6953429 [cody koeninger] [SPARK-2808][Streaming][Kafka] update kafka to 0.8.2 2e67c66 [Helena Edelson] #SPARK-2808 Update to Kafka 0.8.2.0 GA from beta. d9dc2bc [Helena Edelson] Merge remote-tracking branch 'upstream/master' into wip-2808-kafka-0.8.2-upgrade e768164 [Helena Edelson] #2808 update kafka to version 0.8.2
* [SPARK-7112][Streaming][WIP] Add a InputInfoTracker to track all the input ↵jerryshao2015-05-0116-46/+247
| | | | | | | | | | | | | | | | | | streams Author: jerryshao <saisai.shao@intel.com> Author: Saisai Shao <saisai.shao@intel.com> Closes #5680 from jerryshao/SPARK-7111 and squashes the following commits: 339f854 [Saisai Shao] Add an end-to-end test 812bcaf [jerryshao] Continue address the comments abd0036 [jerryshao] Address the comments 727264e [jerryshao] Fix comment typo 6682bef [jerryshao] Fix compile issue 8325787 [jerryshao] Fix rebase issue 17fa251 [jerryshao] Refactor to build InputInfoTracker ee1b536 [jerryshao] Add DirectStreamTracker to track the direct streams
* [SPARK-7309] [CORE] [STREAMING] Shutdown the thread pools in ↵zsxwing2015-05-012-0/+2
| | | | | | | | | | | | ReceivedBlockHandler and DAGScheduler Shutdown the thread pools in ReceivedBlockHandler and DAGScheduler when stopping them. Author: zsxwing <zsxwing@gmail.com> Closes #5845 from zsxwing/SPARK-7309 and squashes the following commits: 6c004fd [zsxwing] Shutdown the thread pools in ReceivedBlockHandler and DAGScheduler
* [SPARK-6999] [SQL] Remove the infinite recursive method (useless)Cheng Hao2015-05-011-14/+0
| | | | | | | | | | | Remove the method, since it causes infinite recursive calls. And seems it's a dummy method, since we have the API: `def createDataFrame(rowRDD: JavaRDD[Row], schema: StructType): DataFrame` Author: Cheng Hao <hao.cheng@intel.com> Closes #5804 from chenghao-intel/spark_6999 and squashes the following commits: 63220a8 [Cheng Hao] remove the infinite recursive method (useless)
* [SPARK-7304] [BUILD] Include $@ in call to mvn consistently in ↵Rajendra Gokhale (rvgcentos)2015-05-011-1/+2
| | | | | | | | | | | | make-distribution.sh Adding the $ allows the caller of this script to supply additional arguments to the mvn command and is consistent with how mvn is being invoked elsewhere in the scripts Author: Rajendra Gokhale (rvgcentos) <rvg@cloudera.com> Closes #5846 from palamau/master and squashes the following commits: e5f2adb [Rajendra Gokhale (rvgcentos)] Add $@ in call to mvn consistently in make-distribution.sh
* [SPARK-7312][SQL] SPARK-6913 broke jdk6 buildYin Huai2015-05-011-2/+4
| | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-7312 Author: Yin Huai <yhuai@databricks.com> Closes #5847 from yhuai/jdbcJava6 and squashes the following commits: 68433a2 [Yin Huai] compile with Java 6
* Ignore flakey test in SparkSubmitUtilsSuitePatrick Wendell2015-05-011-1/+1
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* [SPARK-5342] [YARN] Allow long running Spark apps to run on secure YARN/HDFSHari Shreedharan2015-05-0116-109/+657
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Take 2. Does the same thing as #4688, but fixes Hadoop-1 build. Author: Hari Shreedharan <hshreedharan@apache.org> Closes #5823 from harishreedharan/kerberos-longrunning and squashes the following commits: 3c86bba [Hari Shreedharan] Import fixes. Import postfixOps explicitly. 4d04301 [Hari Shreedharan] Minor formatting fixes. b5e7a72 [Hari Shreedharan] Remove reflection, use a method in SparkHadoopUtil to update the token renewer. 7bff6e9 [Hari Shreedharan] Make sure all required classes are present in the jar. Fix import order. e851f70 [Hari Shreedharan] Move the ExecutorDelegationTokenRenewer to yarn module. Use reflection to use it. 36eb8a9 [Hari Shreedharan] Change the renewal interval config param. Fix a bunch of comments. 611923a [Hari Shreedharan] Make sure the namenodes are listed correctly for creating tokens. 09fe224 [Hari Shreedharan] Use token.renew to get token's renewal interval rather than using hdfs-site.xml 6963bbc [Hari Shreedharan] Schedule renewal in AM before starting user class. Else, a restarted AM cannot access HDFS if the user class tries to. 072659e [Hari Shreedharan] Fix build failure caused by thread factory getting moved to ThreadUtils. f041dd3 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning 42eead4 [Hari Shreedharan] Remove RPC part. Refactor and move methods around, use renewal interval rather than max lifetime to create new tokens. ebb36f5 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning bc083e3 [Hari Shreedharan] Overload RegisteredExecutor to send tokens. Minor doc updates. 7b19643 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning 8a4f268 [Hari Shreedharan] Added docs in the security guide. Changed some code to ensure that the renewer objects are created only if required. e800c8b [Hari Shreedharan] Restore original RegisteredExecutor message, and send new tokens via NewTokens message. 0e9507e [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning 7f1bc58 [Hari Shreedharan] Minor fixes, cleanup. bcd11f9 [Hari Shreedharan] Refactor AM and Executor token update code into separate classes, also send tokens via akka on executor startup. f74303c [Hari Shreedharan] Move the new logic into specialized classes. Add cleanup for old credentials files. 2f9975c [Hari Shreedharan] Ensure new tokens are written out immediately on AM restart. Also, pikc up the latest suffix from HDFS if the AM is restarted. 61b2b27 [Hari Shreedharan] Account for AM restarts by making sure lastSuffix is read from the files on HDFS. 62c45ce [Hari Shreedharan] Relogin from keytab periodically. fa233bd [Hari Shreedharan] Adding logging, fixing minor formatting and ordering issues. 42813b4 [Hari Shreedharan] Remove utils.sh, which was re-added due to merge with master. 0de27ee [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning 55522e3 [Hari Shreedharan] Fix failure caused by Preconditions ambiguity. 9ef5f1b [Hari Shreedharan] Added explanation of how the credentials refresh works, some other minor fixes. f4fd711 [Hari Shreedharan] Fix SparkConf usage. 2debcea [Hari Shreedharan] Change the file structure for credentials files. I will push a followup patch which adds a cleanup mechanism for old credentials files. The credentials files are small and few enough for it to cause issues on HDFS. af6d5f0 [Hari Shreedharan] Cleaning up files where changes weren't required. f0f54cb [Hari Shreedharan] Be more defensive when updating the credentials file. f6954da [Hari Shreedharan] Got rid of Akka communication to renew, instead the executors check a known file's modification time to read the credentials. 5c11c3e [Hari Shreedharan] Move tests to YarnSparkHadoopUtil to fix compile issues. b4cb917 [Hari Shreedharan] Send keytab to AM via DistributedCache rather than directly via HDFS 0985b4e [Hari Shreedharan] Write tokens to HDFS and read them back when required, rather than sending them over the wire. d79b2b9 [Hari Shreedharan] Make sure correct credentials are passed to FileSystem#addDelegationTokens() 8c6928a [Hari Shreedharan] Fix issue caused by direct creation of Actor object. fb27f46 [Hari Shreedharan] Make sure principal and keytab are set before CoarseGrainedSchedulerBackend is started. Also schedule re-logins in CoarseGrainedSchedulerBackend#start() 41efde0 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning d282d7a [Hari Shreedharan] Fix ClientSuite to set YARN mode, so that the correct class is used in tests. bcfc374 [Hari Shreedharan] Fix Hadoop-1 build by adding no-op methods in SparkHadoopUtil, with impl in YarnSparkHadoopUtil. f8fe694 [Hari Shreedharan] Handle None if keytab-login is not scheduled. 2b0d745 [Hari Shreedharan] [SPARK-5342][YARN] Allow long running Spark apps to run on secure YARN/HDFS. ccba5bc [Hari Shreedharan] WIP: More changes wrt kerberos 77914dd [Hari Shreedharan] WIP: Add kerberos principal and keytab to YARN client.
* [SPARK-7240][SQL] Single pass covariance calculation for dataframesBurak Yavuz2015-05-017-5/+157
| | | | | | | | | | | | | | | | | | | | | | Added the calculation of covariance between two columns to DataFrames. cc mengxr rxin Author: Burak Yavuz <brkyvz@gmail.com> Closes #5825 from brkyvz/df-cov and squashes the following commits: cb18046 [Burak Yavuz] changed to sample covariance f2e862b [Burak Yavuz] fixed failed test 51e39b8 [Burak Yavuz] moved implementation 0c6a759 [Burak Yavuz] addressed math comments 8456eca [Burak Yavuz] fix pyStyle3 aa2ad29 [Burak Yavuz] fix pyStyle2 4e97a50 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into df-cov e3b0b85 [Burak Yavuz] addressed comments v0.1 a7115f1 [Burak Yavuz] fix python style 7dc6dbc [Burak Yavuz] reorder imports 408cb77 [Burak Yavuz] initial commit
* [SPARK-7281] [YARN] Add option to set AM's lib path in client mode.Marcelo Vanzin2015-05-012-0/+11
| | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5813 from vanzin/SPARK-7281 and squashes the following commits: 1cb6f42 [Marcelo Vanzin] [SPARK-7281] [yarn] Add option to set AM's lib path in client mode.
* [SPARK-7213] [YARN] Check for read permissions before copying a Hadoop ↵Nishkam Ravi2015-05-011-3/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | config file Author: Nishkam Ravi <nravi@cloudera.com> Author: nishkamravi2 <nishkamravi@gmail.com> Author: nravi <nravi@c1704.halxg.cloudera.com> Closes #5760 from nishkamravi2/master_nravi and squashes the following commits: eaa13b5 [nishkamravi2] Update Client.scala 981afd2 [Nishkam Ravi] Check for read permission before initiating copy 1b81383 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 0f1abd0 [nishkamravi2] Update Utils.scala 474e3bf [nishkamravi2] Update DiskBlockManager.scala 97c383e [nishkamravi2] Update Utils.scala 8691e0c [Nishkam Ravi] Add a try/catch block around Utils.removeShutdownHook 2be1e76 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 1c13b79 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi bad4349 [nishkamravi2] Update Main.java 36a6f87 [Nishkam Ravi] Minor changes and bug fixes b7f4ae7 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 4a45d6a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 458af39 [Nishkam Ravi] Locate the jar using getLocation, obviates the need to pass assembly path as an argument d9658d6 [Nishkam Ravi] Changes for SPARK-6406 ccdc334 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 3faa7a4 [Nishkam Ravi] Launcher library changes (SPARK-6406) 345206a [Nishkam Ravi] spark-class merge Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi ac58975 [Nishkam Ravi] spark-class changes 06bfeb0 [nishkamravi2] Update spark-class 35af990 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 32c3ab3 [nishkamravi2] Update AbstractCommandBuilder.java 4bd4489 [nishkamravi2] Update AbstractCommandBuilder.java 746f35b [Nishkam Ravi] "hadoop" string in the assembly name should not be mandatory (everywhere else in spark we mandate spark-assembly*hadoop*.jar) bfe96e0 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi ee902fa [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi d453197 [nishkamravi2] Update NewHadoopRDD.scala 6f41a1d [nishkamravi2] Update NewHadoopRDD.scala 0ce2c32 [nishkamravi2] Update HadoopRDD.scala f7e33c2 [Nishkam Ravi] Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi ba1eb8b [Nishkam Ravi] Try-catch block around the two occurrences of removeShutDownHook. Deletion of semi-redundant occurrences of expensive operation inShutDown. 71d0e17 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 494d8c0 [nishkamravi2] Update DiskBlockManager.scala 3c5ddba [nishkamravi2] Update DiskBlockManager.scala f0d12de [Nishkam Ravi] Workaround for IllegalStateException caused by recent changes to BlockManager.stop 79ea8b4 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi b446edc [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 5c9a4cb [nishkamravi2] Update TaskSetManagerSuite.scala 535295a [nishkamravi2] Update TaskSetManager.scala 3e1b616 [Nishkam Ravi] Modify test for maxResultSize 9f6583e [Nishkam Ravi] Changes to maxResultSize code (improve error message and add condition to check if maxResultSize > 0) 5f8f9ed [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi 636a9ff [nishkamravi2] Update YarnAllocator.scala 8f76c8b [Nishkam Ravi] Doc change for yarn memory overhead 35daa64 [Nishkam Ravi] Slight change in the doc for yarn memory overhead 5ac2ec1 [Nishkam Ravi] Remove out dac1047 [Nishkam Ravi] Additional documentation for yarn memory overhead issue 42c2c3d [Nishkam Ravi] Additional changes for yarn memory overhead issue 362da5e [Nishkam Ravi] Additional changes for yarn memory overhead c726bd9 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi f00fa31 [Nishkam Ravi] Improving logging for AM memoryOverhead 1cf2d1e [nishkamravi2] Update YarnAllocator.scala ebcde10 [Nishkam Ravi] Modify default YARN memory_overhead-- from an additive constant to a multiplier (redone to resolve merge conflicts) 2e69f11 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi efd688a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark 2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark 3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark 5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456) 6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed) 5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456) 681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles
* Revert "[SPARK-7224] added mock repository generator for --packages tests"Patrick Wendell2015-05-015-403/+97
| | | | This reverts commit 7dacc08ab36188991a001df23880167433844767.
* Revert "[SPARK-7287] enabled fixed test"Patrick Wendell2015-05-011-1/+1
| | | | This reverts commit 7cf1eb79b1fa290aa1d867a8a1eaaea86d6b2239.
* [SPARK-7274] [SQL] Create Column expression for array/struct creation.Reynold Xin2015-05-015-29/+199
| | | | | | | | | | | | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #5802 from rxin/SPARK-7274 and squashes the following commits: 19aecaa [Reynold Xin] Fixed unicode tests. bfc1538 [Reynold Xin] Export all Python functions. 2517b8c [Reynold Xin] Code review. 23da335 [Reynold Xin] Fixed Python bug. 132002e [Reynold Xin] Fixed tests. 56fce26 [Reynold Xin] Added Python support. b0d591a [Reynold Xin] Fixed debug error. 86926a6 [Reynold Xin] Added test suite. 7dbb9ab [Reynold Xin] Ok one more. 470e2f5 [Reynold Xin] One more MLlib ... e2d14f0 [Reynold Xin] [SPARK-7274][SQL] Create Column expression for array/struct creation.
* [SPARK-7183] [NETWORK] Fix memory leak of TransportRequestHandler.streamIdsLiang-Chi Hsieh2015-05-013-24/+44
| | | | | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-7183 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #5743 from viirya/fix_requesthandler_memory_leak and squashes the following commits: cf2c086 [Liang-Chi Hsieh] For comments. 97e205c [Liang-Chi Hsieh] Remove unused import. d35f19a [Liang-Chi Hsieh] For comments. f9a0c37 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into fix_requesthandler_memory_leak 45908b7 [Liang-Chi Hsieh] for style. 17f020f [Liang-Chi Hsieh] Remove unused import. 37a4b6c [Liang-Chi Hsieh] Remove streamIds from TransportRequestHandler. 3b3f38a [Liang-Chi Hsieh] Fix memory leak of TransportRequestHandler.streamIds.
* [SPARK-6846] [WEBUI] [HOTFIX] return to GET for kill link in UI since YARN ↵Sean Owen2015-05-015-13/+23
| | | | | | | | | | | | AM won't proxy POST Partial undoing of SPARK-6846; YARN AM proxy won't forward POSTs, so go back to GET for kill links in Spark UI. Standalone UIs are not affected. Author: Sean Owen <sowen@cloudera.com> Closes #5837 from srowen/SPARK-6846.2 and squashes the following commits: c17c386 [Sean Owen] Partial undoing of SPARK-6846; YARN AM proxy won't forward POSTs, so go back to GET for kill links in Spark UI. Standalone UIs are not affected.
* [SPARK-5854] personalized page rankDan McClary2015-05-013-6/+159
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Here's a modification to PageRank which does personalized PageRank. The approach is basically similar to that outlined by Bahmani et al. from 2010 (http://arxiv.org/pdf/1006.2880.pdf). I'm sure this needs tuning up or other considerations, so let me know how I can improve this. Author: Dan McClary <dan.mcclary@gmail.com> Author: dwmclary <dan.mcclary@gmail.com> Closes #4774 from dwmclary/SPARK-5854-Personalized-PageRank and squashes the following commits: 8b907db [dwmclary] fixed scalastyle errors in PageRankSuite 2c20e5d [dwmclary] merged with upstream master d6cebac [dwmclary] updated as per style requests 7d00c23 [Dan McClary] fixed line overrun in personalizedVertexPageRank d711677 [Dan McClary] updated vertexProgram to restore binary compatibility for inner method bb8d507 [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank fba0edd [Dan McClary] fixed silly mistakes de51be2 [Dan McClary] cleaned up whitespace between comments and methods 0c30d0c [Dan McClary] updated to maintain binary compatibility aaf0b4b [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank 76773f6 [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank 44ada8e [Dan McClary] updated tolerance on chain PPR 1ffed95 [Dan McClary] updated tolerance on chain PPR b67ac69 [Dan McClary] updated tolerance on chain PPR a560942 [Dan McClary] rolled PPR into pregel code for PageRank 6dc2c29 [Dan McClary] initial implementation of personalized page rank
* changing persistence engine trait to an abstract classniranda2015-05-011-1/+1
| | | | | | | | Author: niranda <niranda.perera@gmail.com> Closes #5832 from nirandaperera/PersistanceEngine_abstract_class and squashes the following commits: 67b9d5a [niranda] changing persistence engine trait to an abstract class
* Limit help option regexChris Biow2015-05-011-1/+1
| | | | | | | | | | Added word-boundary delimiters so that embedded text such as "-h" within command line options and values doesn't trigger the usage script and exit. Author: Chris Biow <chris.biow@10gen.com> Closes #5816 from cbiow/patch-1 and squashes the following commits: 36b3726 [Chris Biow] Limit help option regex
* [SPARK-5891] [ML] Add Binarizer ML TransformerLiang-Chi Hsieh2015-05-012-0/+154
| | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-5891 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #5699 from viirya/add_binarizer and squashes the following commits: 1a0b9a4 [Liang-Chi Hsieh] For comments. bc397f2 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into add_binarizer cc4f03c [Liang-Chi Hsieh] Implement threshold param and use merged params map. 7564c63 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into add_binarizer 1682f8c [Liang-Chi Hsieh] Add Binarizer ML Transformer.
* [SPARK-3066] [MLLIB] Support recommendAll in matrix factorization modelDebasish Das2015-05-014-22/+138
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is based on #3098 from debasish83. 1. BLAS' GEMM is used to compute inner products. 2. Reverted changes to MovieLensALS. SPARK-4231 should be addressed in a separate PR. 3. ~~Fixed a bug in topByKey~~ Closes #3098 debasish83 coderxiang Author: Debasish Das <debasish.das@one.verizon.com> Author: Xiangrui Meng <meng@databricks.com> Closes #5829 from mengxr/SPARK-3066 and squashes the following commits: 22e6a87 [Xiangrui Meng] topByKey was correct. update its usage 389b381 [Xiangrui Meng] fix indentation 49953de [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3066 cb9799a [Xiangrui Meng] revert MovieLensALS f864f5e [Xiangrui Meng] update test and fix a bug in topByKey c5e0181 [Xiangrui Meng] use GEMM and topByKey 3a0c4eb [Debasish Das] updated with spark master 98fa424 [Debasish Das] updated with master ee99571 [Debasish Das] addressed initial review comments;merged with master;added tests for batch predict APIs in matrix factorization 3f97c49 [Debasish Das] fixed spark coding style for imports 7163a5c [Debasish Das] Added API for batch user and product recommendation; MAP calculation for product recommendation per user using randomized split d144f57 [Debasish Das] recommendAll API to MatrixFactorizationModel, uses topK finding using BoundedPriorityQueue similar to RDD.top f38a1b5 [Debasish Das] use sampleByKey for per user sampling 10cbb37 [Debasish Das] provide ratio for topN product validation; generate MAP and prec@k metric for movielens dataset 9fa063e [Debasish Das] import scala.math.round 4bbae0f [Debasish Das] comments fixed as per scalastyle cd3ab31 [Debasish Das] merged with AbstractParams serialization bug 9b3951f [Debasish Das] validate user/product on MovieLens dataset through user input and compute map measure along with rmse
* [SPARK-4705] Handle multiple app attempts event logs, history server.Marcelo Vanzin2015-05-0121-201/+546
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This change modifies the event logging listener to write the logs for different application attempts to different files. The attempt ID is set by the scheduler backend, so as long as the backend returns that ID to SparkContext, things should work. Currently, the YARN backend does that. The history server was also modified to model multiple attempts per application. Each attempt has its own UI and a separate row in the listing table, so that users can look at all the attempts separately. The UI "adapts" itself to avoid showing attempt-specific info when all the applications being shown have a single attempt. Author: Marcelo Vanzin <vanzin@cloudera.com> Author: twinkle sachdeva <twinkle@kite.ggn.in.guavus.com> Author: twinkle.sachdeva <twinkle.sachdeva@guavus.com> Author: twinkle sachdeva <twinkle.sachdeva@guavus.com> Closes #5432 from vanzin/SPARK-4705 and squashes the following commits: 7e289fa [Marcelo Vanzin] Review feedback. f66dcc5 [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 bc885b7 [Marcelo Vanzin] Review feedback. 76a3651 [Marcelo Vanzin] Fix log cleaner, add test. 7c381ec [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 1aa309d [Marcelo Vanzin] Improve sorting of app attempts. 2ad77e7 [Marcelo Vanzin] Missed a reference to the old property name. 9d59d92 [Marcelo Vanzin] Scalastyle... d5a9c37 [Marcelo Vanzin] Update JsonProtocol test, make property name consistent. ba34b69 [Marcelo Vanzin] Use Option[String] for attempt id. f1cb9b3 [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 c14ec19 [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 9092d39 [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 86de638 [Marcelo Vanzin] Merge branch 'master' into SPARK-4705 07446c6 [Marcelo Vanzin] Disable striping for app id / name when multiple attempts exist. 9092af5 [Marcelo Vanzin] Fix HistoryServer test. 3a14503 [Marcelo Vanzin] Argh scalastyle. 657ec18 [Marcelo Vanzin] Fix yarn history URL, app links. c3e0a82 [Marcelo Vanzin] Move app name to app info, more UI fixes. ce5ee5d [Marcelo Vanzin] Misc UI, test, style fixes. cbe8bba [Marcelo Vanzin] Attempt ID in listener event should be an option. 88b1de8 [Marcelo Vanzin] Add a test for apps with multiple attempts. 3245aa2 [Marcelo Vanzin] Make app attempts part of the history server model. 5fd5c6f [Marcelo Vanzin] Fix my broken rebase. 318525a [twinkle.sachdeva] SPARK-4705: 1) moved from directory structure to single file, as per the master branch. 2) Added the attempt id inside the SparkListenerApplicationStart, to make the info available independent of directory structure. 3) Changes in History Server to render the UI as per the snaphot II 6b2e521 [twinkle sachdeva] SPARK-4705 Incorporating the review comments regarding formatting, will do the rest of the changes after this 4c1fc26 [twinkle sachdeva] SPARK-4705 Incorporating the review comments regarding formatting, will do the rest of the changes after this 0eb7722 [twinkle sachdeva] SPARK-4705: Doing cherry-pick of fix into master
* [SPARK-3468] [WEBUI] Timeline-View featureKousuke Saruta2015-05-0115-32/+785
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I sometimes trouble-shoot and analyse the cause of long time spending job. At the time, I find the stages which spends long time or fails, then I find the tasks which spends long time or fails, next I analyse the proportion of each phase in a task. Another case, I find executors which spends long time for running a task and analyse the details of a task. In such situation, I think it's helpful to visualize timeline for each application, job, task and the details of proportion of activity for each task. I added 3 timeline features to existing Web UI. [Application Timeline View] This view shows following things. * When each executor was added/removed and the reason why it's removed. * When each job was started/finished. * Status of each job. ![screenshot from 2015-04-01 16 49 25](https://cloud.githubusercontent.com/assets/4736016/6936886/e35fd582-d891-11e4-980d-8de13f50e442.png) [Stage Timeline View] Similar to Application Timeline View, this view shows following things. * When each executor was added/removed and the reason why it's removed. * When each job was started/finished. * Status of each stage. ![screenshot from 2015-04-01 16 50 59](https://cloud.githubusercontent.com/assets/4736016/6936900/0dca6526-d892-11e4-84a8-efd9037af444.png) [Task Assignment Timeline View] This view shows following things. * When each task started/finished * How long each task spent and the proportion. * Status of each task. * Where each task ran on. ![screenshot from 2015-04-01 16 51 54](https://cloud.githubusercontent.com/assets/4736016/6936910/20fd5acc-d892-11e4-9018-80e463881fc2.png) All the view above is zoomable by mouse wheel action and scrollable by drag action. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2342 from sarutak/timeline-viewer-feature and squashes the following commits: 11fe67d [Kousuke Saruta] Fixed conflict 79ac03d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature a91abd3 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature ef34a5b [Kousuke Saruta] Implement tooltip using bootstrap b09d0c5 [Kousuke Saruta] Move `stroke` and `fill` attribute of rect elements to css d3c63c8 [Kousuke Saruta] Fixed a little bit bugs a36291b [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature 28714b6 [Kousuke Saruta] Fixed highlight issue 0dc4278 [Kousuke Saruta] Addressed most of Patrics's feedbacks 8110acf [Kousuke Saruta] Added scroll limit to Job timeline 974a64a [Kousuke Saruta] Removed unused function ee7a7f0 [Kousuke Saruta] Refactored 6a91872 [Kousuke Saruta] Temporary commit 6693f34 [Kousuke Saruta] Added link to job/stage box in the timeline in order to move to corresponding row when we click 8f88222 [Kousuke Saruta] Added job/stage description aeed4b1 [Kousuke Saruta] Removed stage timeline fc1696c [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature 999ccd4 [Kousuke Saruta] Improved scalability 0fc6a31 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature 19815ae [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature 68b7540 [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature 52b5f0b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature dec85db [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature fcdab7d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature dab7cc1 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature 09cce97 [Kousuke Saruta] Cleanuped 16f82cf [Kousuke Saruta] Cleanuped 9fb522e [Kousuke Saruta] Cleanuped d05f2c2 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature e85e9aa [Kousuke Saruta] Cleanup: Added TimelineViewUtils.scala a76e569 [Kousuke Saruta] Removed unused setting in timeline-view.css 5ce1b21 [Kousuke Saruta] Added vis.min.js, vis.min.css and vis.map to .rat-exclude 082f709 [Kousuke Saruta] Added Timeline-View feature for Applications, Jobs and Stages
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