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* [SPARK-7451] [YARN] Preemption of executors is counted as failure causing ↵Ashwin Shankar2015-05-081-1/+3
| | | | | | | | | | | | | | Spark job to fail Added a check to handle container exit status for the preemption scenario, log an INFO message in such cases and move on. andrewor14 Author: Ashwin Shankar <ashankar@netflix.com> Closes #5993 from ashwinshankar77/SPARK-7451 and squashes the following commits: 90900cf [Ashwin Shankar] Fix log info message cf8b6cf [Ashwin Shankar] Stop counting preemption of executors as failure
* [SPARK-6869] [PYSPARK] Add pyspark archives path to PYTHONPATHLianhui Wang2015-05-081-6/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Based on https://github.com/apache/spark/pull/5478 that provide a PYSPARK_ARCHIVES_PATH env. within this PR, we just should export PYSPARK_ARCHIVES_PATH=/user/spark/pyspark.zip,/user/spark/python/lib/py4j-0.8.2.1-src.zip in conf/spark-env.sh when we don't install PySpark on each node of Yarn. i run python application successfully on yarn-client and yarn-cluster with this PR. andrewor14 sryza Sephiroth-Lin Can you take a look at this?thanks. Author: Lianhui Wang <lianhuiwang09@gmail.com> Closes #5580 from lianhuiwang/SPARK-6869 and squashes the following commits: 66ffa43 [Lianhui Wang] Update Client.scala c2ad0f9 [Lianhui Wang] Update Client.scala 1c8f664 [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869 008850a [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869 f0b4ed8 [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869 150907b [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869 20402cd [Lianhui Wang] use ZipEntry 9d87c3f [Lianhui Wang] update scala style e7bd971 [Lianhui Wang] address vanzin's comments 4b8a3ed [Lianhui Wang] use pyArchivesEnvOpt e6b573b [Lianhui Wang] address vanzin's comments f11f84a [Lianhui Wang] zip pyspark archives 5192cca [Lianhui Wang] update import path 3b1e4c8 [Lianhui Wang] address tgravescs's comments 9396346 [Lianhui Wang] put zip to make-distribution.sh 0d2baf7 [Lianhui Wang] update import paths e0179be [Lianhui Wang] add zip pyspark archives in build or sparksubmit 31e8e06 [Lianhui Wang] update code style 9f31dac [Lianhui Wang] update code and add comments f72987c [Lianhui Wang] add archives path to PYTHONPATH
* [SPARK-6653] [YARN] New config to specify port for sparkYarnAM actor systemshekhar.bansal2015-05-051-1/+2
| | | | | | | | | | | | Author: shekhar.bansal <shekhar.bansal@guavus.com> Closes #5719 from zuxqoj/master and squashes the following commits: 5574ff7 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system 5117258 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system 9de5330 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system 456a592 [shekhar.bansal] [SPARK-6653][yarn] New configuration property to specify port for sparkYarnAM actor system 803e93e [shekhar.bansal] [SPARK-6653][yarn] New configuration property to specify port for sparkYarnAM actor system
* [SPARK-5342] [YARN] Allow long running Spark apps to run on secure YARN/HDFSHari Shreedharan2015-05-019-105/+540
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-7281] [YARN] Add option to set AM's lib path in client mode.Marcelo Vanzin2015-05-011-0/+4
| | | | | | | | 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
* [SPARK-4705] Handle multiple app attempts event logs, history server.Marcelo Vanzin2015-05-012-4/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Revert "[SPARK-5342] [YARN] Allow long running Spark apps to run on secure ↵Patrick Wendell2015-04-308-422/+106
| | | | | | YARN/HDFS" This reverts commit 6c65da6bb7d1213e6a4a9f7fd1597d029d87d07c.
* [SPARK-5342] [YARN] Allow long running Spark apps to run on secure YARN/HDFSHari Shreedharan2015-04-308-106/+422
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Current Spark apps running on Secure YARN/HDFS would not be able to write data to HDFS after 7 days, since delegation tokens cannot be renewed beyond that. This means Spark Streaming apps will not be able to run on Secure YARN. This commit adds basic functionality to fix this issue. In this patch: - new parameters are added - principal and keytab, which can be used to login to a KDC - the client logs in, and then get tokens to start the AM - the keytab is copied to the staging directory - the AM waits for 60% of the time till expiry of the tokens and then logs in using the keytab - each time after 60% of the time, new tokens are created and sent to the executors Currently, to avoid complicating the architecture, we set the keytab and principal in the SparkHadoopUtil singleton, and schedule a login. Once the login is completed, a callback is scheduled. This is being posted for feedback, so I can gather feedback on the general implementation. There are currently a bunch of things to do: - [x] logging - [x] testing - I plan to manually test this soon. If you have ideas of how to add unit tests, comment. - [x] add code to ensure that if these params are set in non-YARN cluster mode, we complain - [x] documentation - [x] Have the executors request for credentials from the AM, so that retries are possible. Author: Hari Shreedharan <hshreedharan@apache.org> Closes #4688 from harishreedharan/kerberos-longrunning and squashes the following commits: 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-6918] [YARN] Secure HBase support.Dean Chen2015-04-291-1/+37
| | | | | | | | | | | | | | Obtain HBase security token with Kerberos credentials locally to be sent to executors. Tested on eBay's secure HBase cluster. Similar to obtainTokenForNamenodes and fails gracefully if HBase classes are not included in path. Requires hbase-site.xml to be in the classpath(typically via conf dir) for the zookeeper configuration. Should that go in the docs somewhere? Did not see an HBase section. Author: Dean Chen <deanchen5@gmail.com> Closes #5586 from deanchen/master and squashes the following commits: 0c190ef [Dean Chen] [SPARK-6918][YARN] Secure HBase support.
* [SPARK-7162] [YARN] Launcher error in yarn-clientGuoQiang Li2015-04-271-1/+1
| | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-7162 Author: GuoQiang Li <witgo@qq.com> Closes #5716 from witgo/SPARK-7162 and squashes the following commits: b64564c [GuoQiang Li] Launcher error in yarn-client
* [SPARK-3090] [CORE] Stop SparkContext if user forgets to.Marcelo Vanzin2015-04-271-8/+2
| | | | | | | | | | | | | Set up a shutdown hook to try to stop the Spark context in case the user forgets to do it. The main effect is that any open logs files are flushed and closed, which is particularly interesting for event logs. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5696 from vanzin/SPARK-3090 and squashes the following commits: 3b554b5 [Marcelo Vanzin] [SPARK-3090] [core] Stop SparkContext if user forgets to.
* [SPARK-6014] [core] Revamp Spark shutdown hooks, fix shutdown races.Marcelo Vanzin2015-04-211-36/+27
| | | | | | | | | | | | | | | | | | | | This change adds some new utility code to handle shutdown hooks in Spark. The main goal is to take advantage of Hadoop 2.x's API for shutdown hooks, which allows Spark to register a hook that will run before the one that cleans up HDFS clients, and thus avoids some races that would cause exceptions to show up and other issues such as failure to properly close event logs. Unfortunately, Hadoop 1.x does not have such APIs, so in that case correctness is still left to chance. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5560 from vanzin/SPARK-6014 and squashes the following commits: edfafb1 [Marcelo Vanzin] Better scaladoc. fcaeedd [Marcelo Vanzin] Merge branch 'master' into SPARK-6014 e7039dc [Marcelo Vanzin] [SPARK-6014] [core] Revamp Spark shutdown hooks, fix shutdown races.
* [SPARK-6975][Yarn] Fix argument validation errorjerryshao2015-04-171-2/+6
| | | | | | | | | | | `numExecutors` checking is failed when dynamic allocation is enabled with default configuration. Details can be seen is [SPARK-6975](https://issues.apache.org/jira/browse/SPARK-6975). sryza, please help me to review this, not sure is this the correct way, I think previous you change this part :) Author: jerryshao <saisai.shao@intel.com> Closes #5551 from jerryshao/SPARK-6975 and squashes the following commits: 4335da1 [jerryshao] Change according to the comments 77bdcbd [jerryshao] Fix argument validation error
* [SPARK-5933] [core] Move config deprecation warnings to SparkConf.Marcelo Vanzin2015-04-171-8/+1
| | | | | | | | | | | | | | | I didn't find many deprecated configs after a grep-based search, but the ones I could find were moved to the centralized location in SparkConf. While there, I deprecated a couple more HS configs that mentioned time units. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5562 from vanzin/SPARK-5933 and squashes the following commits: dcb617e7 [Marcelo Vanzin] [SPARK-5933] [core] Move config deprecation warnings to SparkConf.
* [SPARK-2669] [yarn] Distribute client configuration to AM.Marcelo Vanzin2015-04-174-35/+127
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Currently, when Spark launches the Yarn AM, the process will use the local Hadoop configuration on the node where the AM launches, if one is present. A more correct approach is to use the same configuration used to launch the Spark job, since the user may have made modifications (such as adding app-specific configs). The approach taken here is to use the distributed cache to make all files in the Hadoop configuration directory available to the AM. This is a little overkill since only the AM needs them (the executors use the broadcast Hadoop configuration from the driver), but is the easier approach. Even though only a few files in that directory may end up being used, all of them are uploaded. This allows supporting use cases such as when auxiliary configuration files are used for SSL configuration, or when uploading a Hive configuration directory. Not all of these may be reflected in a o.a.h.conf.Configuration object, but may be needed when a driver in cluster mode instantiates, for example, a HiveConf object instead. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #4142 from vanzin/SPARK-2669 and squashes the following commits: f5434b9 [Marcelo Vanzin] Merge branch 'master' into SPARK-2669 013f0fb [Marcelo Vanzin] Review feedback. f693152 [Marcelo Vanzin] Le sigh. ed45b7d [Marcelo Vanzin] Zip all config files and upload them as an archive. 5927b6b [Marcelo Vanzin] Merge branch 'master' into SPARK-2669 cbb9fb3 [Marcelo Vanzin] Remove stale test. e3e58d0 [Marcelo Vanzin] Merge branch 'master' into SPARK-2669 e3d0613 [Marcelo Vanzin] Review feedback. 34bdbd8 [Marcelo Vanzin] Fix test. 022a688 [Marcelo Vanzin] Merge branch 'master' into SPARK-2669 a77ddd5 [Marcelo Vanzin] Merge branch 'master' into SPARK-2669 79221c7 [Marcelo Vanzin] [SPARK-2669] [yarn] Distribute client configuration to AM.
* [SPARK-6046] [core] Reorganize deprecated config support in SparkConf.Marcelo Vanzin2015-04-171-2/+1
| | | | | | | | | | | | | | | | | | | | | This change tries to follow the chosen way for handling deprecated configs in SparkConf: all values (old and new) are kept in the conf object, and newer names take precedence over older ones when retrieving the value. Warnings are logged when config options are set, which generally happens on the driver node (where the logs are most visible). Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5514 from vanzin/SPARK-6046 and squashes the following commits: 9371529 [Marcelo Vanzin] Avoid math. 6cf3f11 [Marcelo Vanzin] Review feedback. 2445d48 [Marcelo Vanzin] Fix (and cleanup) update interval initialization. b6824be [Marcelo Vanzin] Clean up the other deprecated config use also. ab20351 [Marcelo Vanzin] Update FsHistoryProvider to only retrieve new config key. 2c93209 [Marcelo Vanzin] [SPARK-6046] [core] Reorganize deprecated config support in SparkConf.
* [SPARK-6769][YARN][TEST] Usage of the ListenerBus in YarnClusterSuite is wrongKousuke Saruta2015-04-141-7/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | In YarnClusterSuite, a test case uses `SaveExecutorInfo` to handle ExecutorAddedEvent as follows. ``` private class SaveExecutorInfo extends SparkListener { val addedExecutorInfos = mutable.Map[String, ExecutorInfo]() override def onExecutorAdded(executor: SparkListenerExecutorAdded) { addedExecutorInfos(executor.executorId) = executor.executorInfo } } ... listener = new SaveExecutorInfo val sc = new SparkContext(new SparkConf() .setAppName("yarn \"test app\" 'with quotes' and \\back\\slashes and $dollarSigns")) sc.addSparkListener(listener) val status = new File(args(0)) var result = "failure" try { val data = sc.parallelize(1 to 4, 4).collect().toSet assert(sc.listenerBus.waitUntilEmpty(WAIT_TIMEOUT_MILLIS)) data should be (Set(1, 2, 3, 4)) result = "success" } finally { sc.stop() Files.write(result, status, UTF_8) } ``` But, the usage is wrong because Executors will spawn during initializing SparkContext and SparkContext#addSparkListener should be invoked after the initialization, thus after Executors spawn, so SaveExecutorInfo cannot handle ExecutorAddedEvent. Following code refers the result of the handling ExecutorAddedEvent. Because of the reason above, we cannot reach the assertion. ``` // verify log urls are present listener.addedExecutorInfos.values.foreach { info => assert(info.logUrlMap.nonEmpty) } ``` Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #5417 from sarutak/SPARK-6769 and squashes the following commits: 8adc8ba [Kousuke Saruta] Fixed compile error e258530 [Kousuke Saruta] Fixed style 591cf3e [Kousuke Saruta] Fixed style 48ec89a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-6769 860c965 [Kousuke Saruta] Simplified code 207d325 [Kousuke Saruta] Added findListenersByClass method to ListenerBus 2408c84 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-6769 2d7e409 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-6769 3874adf [Kousuke Saruta] Fixed the usage of listener bus in LogUrlsStandaloneSuite 153a91b [Kousuke Saruta] Fixed the usage of listener bus in YarnClusterSuite
* [SPARK-6700] [yarn] Re-enable flaky test.Marcelo Vanzin2015-04-141-1/+1
| | | | | | | | | | Test runs have been successful on jenkins. So let's re-enable the test and look out for any failures, and fix things appropriately. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5459 from vanzin/SPARK-6700 and squashes the following commits: 2ead85b [Marcelo Vanzin] WIP: re-enable flaky test to catch failure in jenkins.
* [SPARK-5931][CORE] Use consistent naming for time propertiesIlya Ganelin2015-04-131-4/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I've added new utility methods to do the conversion from times specified as e.g. 120s, 240ms, 360us to convert to a consistent internal representation. I've updated usage of these constants throughout the code to be consistent. I believe I've captured all usages of time-based properties throughout the code. I've also updated variable names in a number of places to reflect their units for clarity and updated documentation where appropriate. Author: Ilya Ganelin <ilya.ganelin@capitalone.com> Author: Ilya Ganelin <ilganeli@gmail.com> Closes #5236 from ilganeli/SPARK-5931 and squashes the following commits: 4526c81 [Ilya Ganelin] Update configuration.md de3bff9 [Ilya Ganelin] Fixing style errors f5fafcd [Ilya Ganelin] Doc updates 951ca2d [Ilya Ganelin] Made the most recent round of changes bc04e05 [Ilya Ganelin] Minor fixes and doc updates 25d3f52 [Ilya Ganelin] Minor nit fixes 642a06d [Ilya Ganelin] Fixed logic for invalid suffixes and addid matching test 8927e66 [Ilya Ganelin] Fixed handling of -1 69fedcc [Ilya Ganelin] Added test for zero dc7bd08 [Ilya Ganelin] Fixed error in exception handling 7d19cdd [Ilya Ganelin] Added fix for possible NPE 6f651a8 [Ilya Ganelin] Now using regexes to simplify code in parseTimeString. Introduces getTimeAsSec and getTimeAsMs methods in SparkConf. Updated documentation cbd2ca6 [Ilya Ganelin] Formatting error 1a1122c [Ilya Ganelin] Formatting fixes and added m for use as minute formatter 4e48679 [Ilya Ganelin] Fixed priority order and mixed up conversions in a couple spots d4efd26 [Ilya Ganelin] Added time conversion for yarn.scheduler.heartbeat.interval-ms cbf41db [Ilya Ganelin] Got rid of thrown exceptions 1465390 [Ilya Ganelin] Nit 28187bf [Ilya Ganelin] Convert straight to seconds ff40bfe [Ilya Ganelin] Updated tests to fix small bugs 19c31af [Ilya Ganelin] Added cleaner computation of time conversions in tests 6387772 [Ilya Ganelin] Updated suffix handling to handle overlap of units more gracefully 5193d5f [Ilya Ganelin] Resolved merge conflicts 76cfa27 [Ilya Ganelin] [SPARK-5931] Minor nit fixes' bf779b0 [Ilya Ganelin] Special handling of overlapping usffixes for java dd0a680 [Ilya Ganelin] Updated scala code to call into java b2fc965 [Ilya Ganelin] replaced get or default since it's not present in this version of java 39164f9 [Ilya Ganelin] [SPARK-5931] Updated Java conversion to be similar to scala conversion. Updated conversions to clean up code a little using TimeUnit.convert. Added Unit tests 3b126e1 [Ilya Ganelin] Fixed conversion to US from seconds 1858197 [Ilya Ganelin] Fixed bug where all time was being converted to us instead of the appropriate units bac9edf [Ilya Ganelin] More whitespace 8613631 [Ilya Ganelin] Whitespace 1c0c07c [Ilya Ganelin] Updated Java code to add day, minutes, and hours 647b5ac [Ilya Ganelin] Udpated time conversion to use map iterator instead of if fall through 70ac213 [Ilya Ganelin] Fixed remaining usages to be consistent. Updated Java-side time conversion 68f4e93 [Ilya Ganelin] Updated more files to clean up usage of default time strings 3a12dd8 [Ilya Ganelin] Updated host revceiver 5232a36 [Ilya Ganelin] [SPARK-5931] Changed default behavior of time string conversion. 499bdf0 [Ilya Ganelin] Merge branch 'SPARK-5931' of github.com:ilganeli/spark into SPARK-5931 9e2547c [Ilya Ganelin] Reverting doc changes 8f741e1 [Ilya Ganelin] Update JavaUtils.java 34f87c2 [Ilya Ganelin] Update Utils.scala 9a29d8d [Ilya Ganelin] Fixed misuse of time in streaming context test 42477aa [Ilya Ganelin] Updated configuration doc with note on specifying time properties cde9bff [Ilya Ganelin] Updated spark.streaming.blockInterval c6a0095 [Ilya Ganelin] Updated spark.core.connection.auth.wait.timeout 5181597 [Ilya Ganelin] Updated spark.dynamicAllocation.schedulerBacklogTimeout 2fcc91c [Ilya Ganelin] Updated spark.dynamicAllocation.executorIdleTimeout 6d1518e [Ilya Ganelin] Upated spark.speculation.interval 3f1cfc8 [Ilya Ganelin] Updated spark.scheduler.revive.interval 3352d34 [Ilya Ganelin] Updated spark.scheduler.maxRegisteredResourcesWaitingTime 272c215 [Ilya Ganelin] Updated spark.locality.wait 7320c87 [Ilya Ganelin] updated spark.akka.heartbeat.interval 064ebd6 [Ilya Ganelin] Updated usage of spark.cleaner.ttl 21ef3dd [Ilya Ganelin] updated spark.shuffle.sasl.timeout c9f5cad [Ilya Ganelin] Updated spark.shuffle.io.retryWait 4933fda [Ilya Ganelin] Updated usage of spark.storage.blockManagerSlaveTimeout 7db6d2a [Ilya Ganelin] Updated usage of spark.akka.timeout 404f8c3 [Ilya Ganelin] Updated usage of spark.core.connection.ack.wait.timeout 59bf9e1 [Ilya Ganelin] [SPARK-5931] Updated Utils and JavaUtils classes to add helper methods to handle time strings. Updated time strings in a few places to properly parse time
* [SPARK-6662][YARN] Allow variable substitution in ↵Cheolsoo Park2015-04-131-0/+1
| | | | | | | | | | | | | | | | | | | | spark.yarn.historyServer.address In Spark on YARN, explicit hostname and port number need to be set for "spark.yarn.historyServer.address" in SparkConf to make the HISTORY link. If the history server address is known and static, this is usually not a problem. But in cloud, that is usually not true. Particularly in EMR, the history server always runs on the same node as with RM. So I could simply set it to ${yarn.resourcemanager.hostname}:18080 if variable substitution is allowed. In fact, Hadoop configuration already implements variable substitution, so if this property is read via YarnConf, this can be easily achievable. Author: Cheolsoo Park <cheolsoop@netflix.com> Closes #5321 from piaozhexiu/SPARK-6662 and squashes the following commits: e37de75 [Cheolsoo Park] Preserve the space between the Hadoop and Spark imports 79757c6 [Cheolsoo Park] Incorporate review comments 10e2917 [Cheolsoo Park] Add helper function that substitutes hadoop vars to SparkHadoopUtil 589b52c [Cheolsoo Park] Revert "Allow variable substitution for spark.yarn. properties" ff9c35d [Cheolsoo Park] Allow variable substitution for spark.yarn. properties
* [SPARK-6765] Enable scalastyle on test code.Reynold Xin2015-04-133-9/+18
| | | | | | | | | | | | | | | | | | | Turn scalastyle on for all test code. Most of the violations have been resolved in my previous pull requests: Core: https://github.com/apache/spark/pull/5484 SQL: https://github.com/apache/spark/pull/5412 MLlib: https://github.com/apache/spark/pull/5411 GraphX: https://github.com/apache/spark/pull/5410 Streaming: https://github.com/apache/spark/pull/5409 Author: Reynold Xin <rxin@databricks.com> Closes #5486 from rxin/test-style-enable and squashes the following commits: 01683de [Reynold Xin] Fixed new code. a4ab46e [Reynold Xin] Fixed tests. 20adbc8 [Reynold Xin] Missed one violation. 5e36521 [Reynold Xin] [SPARK-6765] Enable scalastyle on test code.
* [SPARK-6207] [YARN] [SQL] Adds delegation tokens for metastore to conf.Doug Balog2015-04-131-0/+63
| | | | | | | | | | | | | | | | | | | | | | | Adds hive2-metastore delegation token to conf when running in secure mode. Without this change, running on YARN in cluster mode fails with a GSS exception. This is a rough patch that adds a dependency to spark/yarn on hive-exec. I'm looking for suggestions on how to make this patch better. This contribution is my original work and that I licenses the work to the Apache Spark project under the project's open source licenses. Author: Doug Balog <doug.balogtarget.com> Author: Doug Balog <doug.balog@target.com> Closes #5031 from dougb/SPARK-6207 and squashes the following commits: 3e9ac16 [Doug Balog] [SPARK-6207] Fixes minor code spacing issues. e260765 [Doug Balog] [SPARK-6207] Second pass at adding Hive delegation token to conf. - Use reflection instead of adding dependency on hive. - Tested on Hive 0.13 and Hadoop 2.4.1 1ab1729 [Doug Balog] Merge branch 'master' of git://github.com/apache/spark into SPARK-6207 bf356d2 [Doug Balog] [SPARK-6207] [YARN] [SQL] Adds delegation tokens for metastore to conf. Adds hive2-metastore delagations token to conf when running in securemode. Without this change, runing on YARN in cluster mode fails with a GSS exception.
* [SPARK-6870][Yarn] Catch InterruptedException when yarn application state ↵linweizhong2015-04-131-4/+7
| | | | | | | | | | | | | | | monitor thread been interrupted On PR #5305 we interrupt the monitor thread but forget to catch the InterruptedException, then in the log will print the stack info, so we need to catch it. Author: linweizhong <linweizhong@huawei.com> Closes #5479 from Sephiroth-Lin/SPARK-6870 and squashes the following commits: f775f93 [linweizhong] Update, don't need to call Thread.currentThread() on monitor thread 0e2ef1f [linweizhong] Update 0d8958a [linweizhong] Update 3513fdb [linweizhong] Catch InterruptedException
* [SPARK-6868][YARN] Fix broken container log link on executor page when ↵Dean Chen2015-04-131-2/+11
| | | | | | | | | | | | | | | | HTTPS_ONLY. Correct http schema in YARN container log link in Spark UI when container logs when YARN is configured to be HTTPS_ONLY. Uses the same logic as the YARN jobtracker webapp. Entry point is [JobBlock](https://github.com/apache/hadoop/blob/e1109fb65608a668cd53dc324dadc6f63a74eeb9/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-app/src/main/java/org/apache/hadoop/mapreduce/v2/app/webapp/JobBlock.java#L108) and logic is in [MRWebAppUtil](https://github.com/apache/hadoop/blob/e1109fb65608a668cd53dc324dadc6f63a74eeb9/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-common/src/main/java/org/apache/hadoop/mapreduce/v2/util/MRWebAppUtil.java#L75). I chose to migrate the logic over instead of importing MRWebAppUtil(but can update the PR to do so) since the class is designated as private and the logic was straightforward. Author: Dean Chen <deanchen5@gmail.com> Closes #5477 from deanchen/container-url and squashes the following commits: 91d3090 [Dean Chen] Correct http schema in YARN container log link in Spark UI when container logs when YARN is configured to be HTTPS_ONLY.
* [SPARK-6758]block the right jetty package in logWangTaoTheTonic2015-04-091-1/+1
| | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-6758 I am not sure if it is ok to block them in test resources too (as we shade jetty in assembly?). Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #5406 from WangTaoTheTonic/SPARK-6758 and squashes the following commits: e09605b [WangTaoTheTonic] block the right jetty package
* [SPARK-5654] Integrate SparkRShivaram Venkataraman2015-04-084-2/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This pull requests integrates SparkR, an R frontend for Spark. The SparkR package contains both RDD and DataFrame APIs in R and is integrated with Spark's submission scripts to work on different cluster managers. Some integration points that would be great to get feedback on: 1. Build procedure: SparkR requires R to be installed on the machine to be built. Right now we have a new Maven profile `-PsparkR` that can be used to enable SparkR builds 2. YARN cluster mode: The R package that is built needs to be present on the driver and all the worker nodes during execution. The R package location is currently set using SPARK_HOME, but this might not work on YARN cluster mode. The SparkR package represents the work of many contributors and attached below is a list of people along with areas they worked on edwardt (edwart) - Documentation improvements Felix Cheung (felixcheung) - Documentation improvements Hossein Falaki (falaki) - Documentation improvements Chris Freeman (cafreeman) - DataFrame API, Programming Guide Todd Gao (7c00) - R worker Internals Ryan Hafen (hafen) - SparkR Internals Qian Huang (hqzizania) - RDD API Hao Lin (hlin09) - RDD API, Closure cleaner Evert Lammerts (evertlammerts) - DataFrame API Davies Liu (davies) - DataFrame API, R worker internals, Merging with Spark Yi Lu (lythesia) - RDD API, Worker internals Matt Massie (massie) - Jenkins build Harihar Nahak (hnahak87) - SparkR examples Oscar Olmedo (oscaroboto) - Spark configuration Antonio Piccolboni (piccolbo) - SparkR examples, Namespace bug fixes Dan Putler (dputler) - Dataframe API, SparkR Install Guide Ashutosh Raina (ashutoshraina) - Build improvements Josh Rosen (joshrosen) - Travis CI build Sun Rui (sun-rui)- RDD API, JVM Backend, Shuffle improvements Shivaram Venkataraman (shivaram) - RDD API, JVM Backend, Worker Internals Zongheng Yang (concretevitamin) - RDD API, Pipelined RDDs, Examples and EC2 guide Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Author: Shivaram Venkataraman <shivaram.venkataraman@gmail.com> Author: Zongheng Yang <zongheng.y@gmail.com> Author: cafreeman <cfreeman@alteryx.com> Author: Shivaram Venkataraman <shivaram@eecs.berkeley.edu> Author: Davies Liu <davies@databricks.com> Author: Davies Liu <davies.liu@gmail.com> Author: hlin09 <hlin09pu@gmail.com> Author: Sun Rui <rui.sun@intel.com> Author: lythesia <iranaikimi@gmail.com> Author: oscaroboto <oscarjr@gmail.com> Author: Antonio Piccolboni <antonio@piccolboni.info> Author: root <edward> Author: edwardt <edwardt.tril@gmail.com> Author: hqzizania <qian.huang@intel.com> Author: dputler <dan.putler@gmail.com> Author: Todd Gao <todd.gao.2013@gmail.com> Author: Chris Freeman <cfreeman@alteryx.com> Author: Felix Cheung <fcheung@AVVOMAC-119.local> Author: Hossein <hossein@databricks.com> Author: Evert Lammerts <evert@apache.org> Author: Felix Cheung <fcheung@avvomac-119.t-mobile.com> Author: felixcheung <felixcheung_m@hotmail.com> Author: Ryan Hafen <rhafen@gmail.com> Author: Ashutosh Raina <ashutoshraina@users.noreply.github.com> Author: Oscar Olmedo <oscarjr@gmail.com> Author: Josh Rosen <rosenville@gmail.com> Author: Yi Lu <iranaikimi@gmail.com> Author: Harihar Nahak <hnahak87@users.noreply.github.com> Closes #5096 from shivaram/R and squashes the following commits: da64742 [Davies Liu] fix Date serialization 59266d1 [Davies Liu] check exclusive of primary-py-file and primary-r-file 55808e4 [Davies Liu] fix tests 5581c75 [Davies Liu] update author of SparkR f731b48 [Shivaram Venkataraman] Only run SparkR tests if R is installed 64eda24 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R d7c3f22 [Shivaram Venkataraman] Address code review comments Changes include 1. Adding SparkR docs to API docs generated 2. Style fixes in SparkR scala files 3. Clean up of shell scripts and explanation of install-dev.sh 377151f [Shivaram Venkataraman] Merge remote-tracking branch 'apache/master' into R eb5da53 [Shivaram Venkataraman] Merge pull request #3 from davies/R2 a18ff5c [Davies Liu] Update sparkR.R 5133f3a [Shivaram Venkataraman] Merge pull request #7 from hqzizania/R3 940b631 [hqzizania] [SPARKR-92] Phase 2: implement sum(rdd) 0e788c0 [Shivaram Venkataraman] Merge pull request #5 from hlin09/doc-fix 3487461 [hlin09] Add tests log in .gitignore. 1d1802e [Shivaram Venkataraman] Merge pull request #4 from felixcheung/r-require 11981b7 [felixcheung] Update R to fail early if SparkR package is missing c300e08 [Davies Liu] remove duplicated file b045701 [Davies Liu] Merge branch 'remote_r' into R 19c9368 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into remote_r f8fa8af [Davies Liu] mute logging when start/stop context e7104b6 [Davies Liu] remove ::: in SparkR a1777eb [Davies Liu] move rules into R/.gitignore e88b649 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R 6e20e71 [Davies Liu] address comments b433817 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R a1cedad [Shivaram Venkataraman] Merge pull request #228 from felixcheung/doc e089151 [Davies Liu] Merge pull request #225 from sun-rui/SPARKR-154_2 463e28c [Davies Liu] Merge pull request #2 from shivaram/doc-fixes bc2d6d8 [Shivaram Venkataraman] Remove arg from sparkR.stop and update docs d425363 [Shivaram Venkataraman] Some doc fixes for column, generics, group 1f1a7e0 [Shivaram Venkataraman] Some fixes to DataFrame, RDD, SQLContext docs 104ad4e [Shivaram Venkataraman] Check the right env in exists cf5cd99 [Shivaram Venkataraman] Remove unused numCols argument 85a50ec [Shivaram Venkataraman] Merge pull request #226 from RevolutionAnalytics/master 3eacfc0 [Davies Liu] fix flaky test 733380d [Davies Liu] update R examples (remove master from args) b21a0da [Davies Liu] Merge pull request #1 from shivaram/log4j-tests a1493d7 [Shivaram Venkataraman] Address comments e1f83ab [Shivaram Venkataraman] Send Spark INFO logs to a file in SparkR tests 58276f5 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R 52cc92d [Shivaram Venkataraman] Add license to create-docs.sh 6ff5ea2 [Shivaram Venkataraman] Add instructions to generate docs 1f478c5 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R 02b4833 [Shivaram Venkataraman] Add a script to generate R docs (Rd, html) Also fix some issues with our documentation d6d3729 [Davies Liu] enable spark and pyspark tests 0e5a83f [Davies Liu] fix code style afd8a77 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R d87a181 [Davies Liu] fix flaky tests 7100fb9 [Shivaram Venkataraman] Fix libPaths in README bdf3a14 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R 05e7375 [Davies Liu] sort generics b44e371 [Shivaram Venkataraman] Include RStudio instructions in README 855537f [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R 9fb6af3 [Davies Liu] mark R classes/objects are private 423ea3c [Shivaram Venkataraman] Ignore unknown jobj in cleanup 974e4ea [Davies Liu] fix flaky test 410ec18 [Davies Liu] fix zipRDD() tests d8b24fc [Davies Liu] disable spark and python tests temporary ce3ca62 [Davies Liu] fix license check 7da0049 [Davies Liu] fix build 2892e29 [Davies Liu] support R in YARN cluster ebd4d07 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R 38cbf59 [Davies Liu] fix test of zipRDD() 756ece0 [Shivaram Venkataraman] Update README remove outdated TODO d436f26 [Davies Liu] add missing files 40d193a [Shivaram Venkataraman] Merge pull request #224 from sun-rui/SPARKR-224-new 1a16cd6 [Davies Liu] rm PROJECT_HOME 56670ef [Davies Liu] rm man page ba4b80b [Davies Liu] Merge branch 'remote_r' into R f04080c [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into remote_r 028cbfb [Davies Liu] fix exit code of sparkr unit test 42d8b4c [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R ef26015 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R a1870e8 [Shivaram Venkataraman] Merge pull request #214 from sun-rui/SPARKR-156_3 cb6e5e3 [Shivaram Venkataraman] Add scripts to start SparkR on windows 8030847 [Shivaram Venkataraman] Set windows file separators, install dirs 05afef0 [Shivaram Venkataraman] Only stop backend JVM if R launched it 95d2de3 [Davies Liu] fix spark-submit with R scripot baefd9e [Shivaram Venkataraman] Make bin/sparkR use spark-submit As a part of this move the R initialization functions into first.R and first-submit.R d6f2bdd [Shivaram Venkataraman] Fix run-tests path ea90fab [Davies Liu] fix spark-submit with R path and sparkR -h 0e2412c [Davies Liu] fix bin/sparkR 9f6aa1f [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R 479e3fe [Davies Liu] change println() to logging 52ca6e5 [Shivaram Venkataraman] Add missing comma 716b16f [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R 2d235d4 [Shivaram Venkataraman] Build SparkR with Maven profile aae881b [Davies Liu] fix rat ff776aa [Shivaram Venkataraman] Fix style e4f1937 [Shivaram Venkataraman] Remove DFC example f7b6936 [Davies Liu] remove Spark prefix for class 043959e [Davies Liu] cleanup ba53b09 [Davies Liu] support R in spark-submit f403b4a [Davies Liu] rm .travis.yml c4a5bdf [Davies Liu] run sparkr tests in Spark e8fc7ca [Davies Liu] fix .gitignore 35e5755 [Davies Liu] reduce size of example data 50bff63 [Davies Liu] add LICENSE header for R sources facb6e0 [Davies Liu] add .gitignore for .o, .so, .Rd 18e5eed [Davies Liu] update docs 0a0e632 [Davies Liu] move sparkR into bin/ a76472f [Davies Liu] fix path of assembly jar df3eeea [Davies Liu] move R/examples into examples/src/main/r 3415cc7 [Davies Liu] move Scala source into core/ and sql/ 180fc9c [Davies Liu] move scala 014d253 [Davies Liu] delete man pages 49a8133 [Davies Liu] Merge branch 'remote_r' into R 44994c2 [Davies Liu] Moved files to R/ 2fc553f [Shivaram Venkataraman] Merge pull request #222 from davies/column2 b043876 [Davies Liu] fix test 5e610cb [Davies Liu] add more API for Column 6f95d49 [Shivaram Venkataraman] Merge pull request #221 from shivaram/sparkr-stop-start 3214c6d [Shivaram Venkataraman] Merge pull request #217 from hlin09/cleanClosureFix f5d3355 [Shivaram Venkataraman] Merge pull request #218 from davies/merge 70f620c [Davies Liu] address comments 4b1628d [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into merge 3139325 [Shivaram Venkataraman] Merge pull request #212 from davies/toDF 6122e0e [Davies Liu] handle NULL bc2ff38 [Davies Liu] handle NULL 7f5e70c [Davies Liu] Update SerDe.scala 46454e4 [Davies Liu] address comments dd52cbc [Shivaram Venkataraman] Merge pull request #220 from shivaram/sparkr-utils-include 662938a [Shivaram Venkataraman] Include utils before SparkR for `head` to work Before this change calling `head` on a DataFrame would not work from the sparkR script as utils would be loaded after SparkR and placed ahead in the search list. This change requires utils to be loaded before SparkR 1bc2998 [Shivaram Venkataraman] Merge pull request #179 from evertlammerts/sparkr-sql 7695d36 [Evert Lammerts] added tests 8190127 [Evert Lammerts] fixed parquetFile signature d8c8fcc [Shivaram Venkataraman] Merge pull request #219 from shivaram/sparkr-build-final 963c7ee [Davies Liu] Merge branch 'master' into merge 8bff523 [Shivaram Venkataraman] Remove staging repo now that 1.3 is released e52258f [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into toDF 05b9126 [Shivaram Venkataraman] Merge pull request #215 from davies/agg 8e1497d [Davies Liu] Update DataFrame.R 72adb14 [Davies Liu] Update SQLContext.R 66cc92a [Davies Liu] address commets 55c38bc [Shivaram Venkataraman] Merge pull request #216 from davies/select2 3e0555d [Shivaram Venkataraman] Merge pull request #193 from davies/daemon 0467474 [Davies Liu] add more selecter for DataFrame 9a6be74 [Davies Liu] include grouping columns in agg() e87bb98 [Davies Liu] improve comment and logging a6dc435 [Davies Liu] remove dependency of jsonlite 26a3621 [Davies Liu] support date.frame and Date/Time 4e4908a [Davies Liu] createDataFrame from rdd 5757b95 [Shivaram Venkataraman] Merge pull request #196 from davies/die 90f2692 [Shivaram Venkataraman] Merge pull request #211 from hlin09/generics 8583968 [Davies Liu] readFully() 46cea3d [Davies Liu] retry 01aa5ee [Davies Liu] add config for using daemon, refactor ff948db [hlin09] Remove missingOrInteger. ecdfda1 [hlin09] Remove duplication. 411b751 [Davies Liu] make RStudio happy 8f8813f [Davies Liu] switch back to use parallel 6bccbbf [hlin09] Move roxygen doc back to implementation. ffd6e8e [Shivaram Venkataraman] Merge pull request #210 from hlin09/hlin09 471c794 [hlin09] Move getJRDD and broadcast's value to 00-generic.R. 89b886d [hlin09] Move setGeneric() to 00-generics.R. 97dde1a [hlin09] Add a test for access operators. 09ff163 [Shivaram Venkataraman] Merge pull request #204 from cafreeman/sparkr-sql 15a713f [cafreeman] Fix example for `dropTempTable` dc1291b [hlin09] Add checks for namespace access operators in cleanClosure. b4c0b2e [Davies Liu] use fork package 3db5649 [cafreeman] Merge branch 'sparkr-sql' of https://github.com/amplab-extras/SparkR-pkg into sparkr-sql 789be97 [Shivaram Venkataraman] Merge pull request #207 from shivaram/err-remove e60578a [cafreeman] update tests to guarantee row order 5eec6fc [Shivaram Venkataraman] Merge pull request #206 from sun-rui/SPARKR-156_2 3f7aed6 [Sun Rui] Fix minor typos in the function description. a8cebf0 [Shivaram Venkataraman] Remove print statement in SparkRBackendHandler This print statement is noisy for SQL methods which have multiple APIs (like loadDF). We already have a better error message when no valid methods are found 5e3a576 [Sun Rui] Fix indentation. f3d99a6 [Sun Rui] [SPARKR-156] phase 2: implement zipWithIndex() of the RDD class. a582810 [cafreeman] Merge branch 'dfMethods' into sparkr-sql 7a5d6fd [cafreeman] `withColumn` and `withColumnRenamed` c5fa3b9 [cafreeman] New `select` method bcb0bf5 [Shivaram Venkataraman] Merge pull request #180 from davies/group 9dd6a5a [Davies Liu] Update SparkRBackendHandler.scala e6fb8d8 [Davies Liu] improve logging 428a99a [Davies Liu] remove test, catch exception fef99de [cafreeman] `intersect`, `subtract`, `unionAll` befbd32 [cafreeman] `insertInto` 9d01bcd [cafreeman] `dropTempTable` d8c1c09 [Davies Liu] add test to start and stop context multiple times 18c6004 [Shivaram Venkataraman] Merge pull request #201 from sun-rui/SPARKR-156_1 dfb399a [Davies Liu] address comments f06ccec [Sun Rui] Use mapply() instead of for statement. 3c7674f [Davies Liu] Merge branch 'die' of github.com:davies/SparkR-pkg into die ac8a852 [Davies Liu] close monitor connection in sparkR.stop() 4d0fb56 [Shivaram Venkataraman] Merge pull request #203 from shivaram/sparkr-hive-fix 62b0760 [Shivaram Venkataraman] Fix test hive context package name 47a613f [Shivaram Venkataraman] Fix HiveContext package name fb3b139 [Davies Liu] fix tests d0d4626 [Shivaram Venkataraman] Merge pull request #199 from davies/load 8b7fb67 [Davies Liu] fix HiveContext bb46832 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load e9e2a03 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into group b875b4f [Davies Liu] fix style de2abfa [Shivaram Venkataraman] Merge pull request #202 from cafreeman/sparkr-sql 3675fcf [cafreeman] Update `explain` and fixed doc for `toJSON` 5fd9575 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load 6fac596 [Davies Liu] support Column expression in agg() f10a24e [Davies Liu] address comments ff8b005 [cafreeman] 'saveAsParquetFile` a5c2887 [cafreeman] fix test 3fab0f8 [cafreeman] `showDF` 779c102 [cafreeman] `isLocal` 68b11cf [cafreeman] `toJSON` 0ac4abc [cafreeman] 'explain` 20242c4 [cafreeman] clean up docs 6a1fe64 [Shivaram Venkataraman] Merge pull request #198 from cafreeman/sparkr-sql 198c130 [Shivaram Venkataraman] Merge pull request #200 from shivaram/sparkr-sql-build 870acd4 [Shivaram Venkataraman] Use rc2 explicitly 8b9a963 [cafreeman] Merge branch 'sparkr-sql' of https://github.com/amplab-extras/SparkR-pkg into sparkr-sql bc90115 [cafreeman] Fixed docs 3865f39 [Sun Rui] [SPARKR-156] phase 1: implement zipWithUniqueId() of the RDD class. a37fd80 [Davies Liu] Update sparkR.R d18f9d3 [Shivaram Venkataraman] Remove SparkR snapshot build We now have 1.3.0 RC2 on Apache Staging 8de958d [Davies Liu] Update SparkRBackend.scala 4e0becc [Shivaram Venkataraman] Merge pull request #194 from davies/api 197a79b [Davies Liu] add HiveContext (commented) 32aa01d [Shivaram Venkataraman] Merge pull request #191 from felixcheung/doc 5073e07 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load 7918634 [cafreeman] Fix test acea146 [cafreeman] remove extra line 74269f3 [cafreeman] Merge branch 'dfMethods' into sparkr-sql cd7ac8a [Shivaram Venkataraman] Merge pull request #197 from cafreeman/sparkr-sql 494a4dd [cafreeman] update export e14c328 [cafreeman] `selectExpr` 32b37d1 [cafreeman] Fixed indent in `join` test. 2e7b190 [Felix Cheung] small update on yarn deploy mode. 8ff29d6 [Davies Liu] fix tests 12a6db2 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into api 294ca4a [cafreeman] `join`, `sort`, and `filter` 4fa6343 [cafreeman] Refactor `join` generic for use with `DataFrame` 3f22c8d [Shivaram Venkataraman] Merge pull request #195 from cafreeman/sparkr-sql 2b6f980 [Davies Liu] shutdown the JVM after R process die e8639c3 [cafreeman] New 1.3 repo and updates to `column.R` ed9a89f [Davies Liu] address comments 03bcf20 [Davies Liu] Merge branch 'group' of github.com:davies/SparkR-pkg into group 39c253d [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into group 98cc97a [Davies Liu] fix test and docs e2d144a [Felix Cheung] Fixed small typos 3beadcf [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into api 06cbc2d [Davies Liu] launch R worker by a daemon 8a676b1 [Shivaram Venkataraman] Merge pull request #188 from davies/column 524c122 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into column f798402 [Davies Liu] Update column.R 1d0f2ae [Davies Liu] Update DataFrame.R 03402eb [Felix Cheung] Updates as per feedback on sparkR-submit 76cf2e0 [Shivaram Venkataraman] Merge pull request #192 from cafreeman/sparkr-sql 1955a09 [cafreeman] return object instead of a list of one object f585929 [cafreeman] Fix brackets e998356 [cafreeman] define generic for 'first' in RDD API 71d66a1 [Davies Liu] fix first(0 8ec21af [Davies Liu] fix signature acae527 [Davies Liu] refactor d7b17a4 [Davies Liu] fix approxCountDistinct 7dfe27d [Davies Liu] fix cyclic namespace dependency 8caf5bb [Davies Liu] use S4 methods 5c0bb24 [Felix Cheung] Doc updates: build and running on YARN 773baf0 [Zongheng Yang] Merge pull request #178 from davies/random 862f07c [Shivaram Venkataraman] Merge pull request #190 from shivaram/SPARKR-79 b457833 [Shivaram Venkataraman] Merge pull request #189 from shivaram/stdErrFix f7caeb8 [Davies Liu] Update SparkRBackend.scala 8c4deae [Shivaram Venkataraman] Remove unused function 6e51c7f [Shivaram Venkataraman] Fix stderr redirection on executors 7afa4c9 [Shivaram Venkataraman] Merge pull request #186 from hlin09/funcDep3 4d36ab1 [hlin09] Add tests for broadcast variables. 3f57e56 [hlin09] Fix comments. 7b72487 [hlin09] Fix comments. ae05bf1 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into column abb4bb9 [Davies Liu] add Column and expression eb8ac11 [Shivaram Venkataraman] Set Spark version 1.3.0 in Windows build 5c72e73 [Davies Liu] wait atmost 100 seconds e425437 [Shivaram Venkataraman] Merge pull request #177 from lythesia/master a00f502 [lythesia] fix indents 0346e5f [Davies Liu] address comment 6134649 [Shivaram Venkataraman] Merge pull request #187 from cafreeman/sparkr-sql ad0935e [lythesia] minor fixes b0e7f73 [cafreeman] Update `sampleDF` test 7b0d070 [lythesia] keep partitions check 889c265 [cafreeman] numToInt utility function 27dd3a0 [lythesia] modify tests for repartition cad0f0c [cafreeman] Fix docs and indents 2808dcf [cafreeman] Three more DataFrame methods 5ef66fb [Davies Liu] send back the port via temporary file 3b46429 [Davies Liu] Merge branch 'master' of github.com:amplab-extras/SparkR-pkg into random 798f453 [cafreeman] Merge branch 'sparkr-sql' into dev 9aa4acf [Shivaram Venkataraman] Merge pull request #184 from davies/socket 020bce8 [Shivaram Venkataraman] Merge pull request #183 from cafreeman/sparkr-sql 222e06b [cafreeman] Lazy evaluation and formatting changes e776324 [Davies Liu] fix import 211cc15 [cafreeman] Merge branch 'sparkr-sql' into dev 3351afd [hlin09] Replaces getDependencies with cleanClosure, to serialize UDFs to workers. e7c56d6 [lythesia] fix random partition key 50c74b1 [Davies Liu] address comments 083c89f [cafreeman] Remove commented lines an unused import dfa119b [hlin09] Improve the coverage of processClosure. a41c9b9 [cafreeman] Merge branch 'wrapper' into sparkr-sql 1cd714f [cafreeman] Wrapper function docs. db0cd9e [cafreeman] Clean up for wrapper functions 818c19f [cafreeman] Update schema-related functions a57884e [cafreeman] Remove unused import d72e830 [cafreeman] Add wrapper for `StructField` and `StructType` 2ea2ecf [lythesia] use generic arg 09b9512 [hlin09] add docs f4f077c [hlin09] Add recursive cleanClosure for function access. f84ad27 [hlin09] Merge remote-tracking branch 'upstream/master' into funcDep2 5300766 [Shivaram Venkataraman] Merge pull request #185 from hlin09/hlin09 07aa7c0 [hlin09] Unifies the implementation of lapply with lapplyParitionsWithIndex. f4dbb0b [Davies Liu] use socket in worker 8282c59 [Davies Liu] Update DataFrame.R ba495a8 [Davies Liu] Update NAMESPACE 36dffb3 [cafreeman] Add 'head` and `first` 534a95f [cafreeman] Schema-related methods 64f488d [cafreeman] Cache and Persist Methods 30d71fd [cafreeman] Standardize method arguments for DataFrame methods 785898b [Shivaram Venkataraman] Merge pull request #182 from cafreeman/sparkr-sql 2619003 [Shivaram Venkataraman] Merge pull request #181 from cafreeman/master a9bbe0b [cafreeman] Update existing SparkSQL functions 8c241a3 [cafreeman] Merge with master, include changes to method args 68d6de4 [cafreeman] Fix typos 8d2ec6e [Davies Liu] add sum/max/min/avg/mean 774e687 [Davies Liu] add missing API in SQLContext 1e72b4b [Davies Liu] missing API in SQLContext 3294949 [Chris Freeman] Restore `rdd` argument to `getJRDD` 3a58ebc [Davies Liu] rm unrelated file 8bd93b5 [Davies Liu] fix signature c652b4c [cafreeman] Update method signatures to use generic arg 48c8827 [Davies Liu] update NAMESPACE 84e2d8c [Davies Liu] groupBy and agg() 7c3ddbd [Davies Liu] create jmode in JVM 9465426 [Davies Liu] load and save 982f342 [lythesia] fix numeric issue 7651d84 [lythesia] fix coalesce 4e712e1 [Davies Liu] use random port in backend 041d22b [Shivaram Venkataraman] Merge pull request #172 from cafreeman/sparkr-sql 0d07770 [cafreeman] Added `limit` and updated `take` 301d8e5 [cafreeman] Remove extraneous map functions 0387db2 [cafreeman] Remove colNames 04c4b65 [lythesia] add repartition/coalesce 231deab [cafreeman] Change reserialize to serializeToBytes acf7e1a [cafreeman] Rework the Scala to R DataFrame Conversion 481ae37 [cafreeman] Updated stale comments and standardized arg names 21d4a97 [hlin09] Adds cleanClosure to capture the function closures. d24ffb4 [hlin09] Merge remote-tracking branch 'upstream/master' into funcDep2 8be02de [hlin09] Revert "loop 1-12 test pass." fddb9cc [hlin09] Revert "add docs" f8ef0ab [hlin09] Revert "More docs" 8e4b3da [hlin09] Revert "More docs" 57e005b [hlin09] Revert "fix tests." c10148e [Shivaram Venkataraman] Merge pull request #174 from shivaram/sparkr-runner 910e3be [Shivaram Venkataraman] Add a timeout for initialization Also move sparkRBackend.stop into a finally block bf52b17 [Shivaram Venkataraman] Merge remote-tracking branch 'amplab-sparkr/master' into sparkr-runner 08102b0 [Shivaram Venkataraman] Merge pull request #176 from lythesia/master 9c77b20 [Chris Freeman] Merge pull request #2 from shivaram/sparkr-sql 179ab38 [lythesia] add try counts and increase time interval 71a73b2 [Shivaram Venkataraman] Use a getter for serialization mode This change encapsulates the semantics of serialization mode for RDDs inside a getter function. For PipelinedRDDs if a backing JavaRDD is available we use that else we fall back to a default serialization mode 06bf250 [Shivaram Venkataraman] Merge pull request #173 from shivaram/windows-space-fix 88bf97f [Shivaram Venkataraman] Create SparkContext for R shell launch f9268d9 [Shivaram Venkataraman] Fix code review comments e6ad12d [Shivaram Venkataraman] Update comment describing sparkR-submit 17eda4c [Shivaram Venkataraman] Merge pull request #175 from falaki/docfix ba2b72b [Hossein] Spark 1.1.0 is default 4cd7d3f [lythesia] retry backend connection 749e2d0 [Hossein] Updated README bc04cf4 [Shivaram Venkataraman] Use SPARKR_BACKEND_PORT in sparkR.R as default Change SparkRRunner to use EXISTING_SPARKR_BACKEND_PORT to differentiate between the two 22a19ac [Shivaram Venkataraman] Use a semaphore to wait for backend to initalize Also pick a random port to avoid collisions 7f1f0f8 [cafreeman] Move comments to fit 100 char line length 8b84e4e [cafreeman] Make if statements more explicit ce5d5ab [cafreeman] New tests for Union and Object File b063320 [cafreeman] Changed 'serialized' to 'serializedMode' 0981dff [Zongheng Yang] Merge pull request #168 from sun-rui/SPARKR-153_2 86fc639 [Shivaram Venkataraman] Move sparkR-submit into pkg/inst fd8f8a9 [Shivaram Venkataraman] Merge branch 'hqzizania-master' a33dbea [Shivaram Venkataraman] Merge branch 'master' of https://github.com/hqzizania/SparkR-pkg into hqzizania-master 384e6e2 [Shivaram Venkataraman] Merge pull request #171 from hlin09/hlin09 1f5a6ac [hlin09] fixed comments 7f7596a [cafreeman] Additional handling for "row" serialization 8c3b8c5 [cafreeman] Add test for UnionRDD on "row" serialization b1141f8 [cafreeman] Fixed formatting issues. 5db30bf [cafreeman] Changed serialized from bool to string 2f0c0b8 [cafreeman] Add check for serialized type d243dfb [cafreeman] Clean up code 5ff63a2 [cafreeman] Change test from boolean to string 77fec1a [cafreeman] Updated .Rd files 9224989 [cafreeman] Various updates for DataFrame to RRDD 26af62b [cafreeman] DataFrame to RRDD e004481 [cafreeman] Update UnionRDD test 5292be7 [hlin09] Adds support of pipeRDD(). e2a7560 [Shivaram Venkataraman] Merge pull request #170 from cafreeman/sparkr-sql 5d537f4 [cafreeman] Add pairRDD to Description b6fa88e [cafreeman] Updating to current master 0cda231 [Sun Rui] [SPARKR-153] phase 2: implement aggregateByKey() and foldByKey(). 95ee6b4 [Shivaram Venkataraman] Merge remote-tracking branch 'amplab-sparkr/master' into sparkr-runner 67fbc60 [Shivaram Venkataraman] Add support for SparkR shell to use spark-submit This ensures that SparkConf options are read in both in batch and interactive modes 2271030 [Shivaram Venkataraman] Merge pull request #167 from sun-rui/removePartionByInRDD 7fcb46a [Sun Rui] Remove partitionBy() in RDD. 52f94c4 [Shivaram Venkataraman] Merge pull request #160 from lythesia/master 59e2d54 [lythesia] merge with upstream 5836650 [Zongheng Yang] Merge pull request #163 from sun-rui/SPARKR-153_1 141723e [Sun Rui] fix comments. f73a07e [Shivaram Venkataraman] Merge pull request #165 from shivaram/sparkr-sql-build 10ffc6d [Shivaram Venkataraman] Set Spark version to 1.3 using staging dependency Also fix the maven build c91ede2 [Shivaram Venkataraman] Merge pull request #164 from hlin09/hlin09 9d335a9 [hlin09] Makes git to ignore Eclipse meta files. 94066bf [Sun Rui] [SPARKR-153] phase 1: implement fold() and aggregate(). 9c391c7 [hqzizania] Merge remote-tracking branch 'upstream/master' 5f29551 [hqzizania] modified: pkg/R/RDD.R modified: pkg/R/context.R d968664 [lythesia] fix comment 7972858 [Shivaram Venkataraman] Merge pull request #159 from sun-rui/SPARKR-150_2 7690878 [lythesia] separate out pair RDD functions f4573c1 [Sun Rui] Use reduce() instead of sortBy().take() to get the ordered elements. 63e62ed [Sun Rui] [SPARKR-150] phase 2: implement takeOrdered() and top(). 050390b [Shivaram Venkataraman] Fix bugs in inferring R file 8398f2e [Shivaram Venkataraman] Add sparkR-submit helper script Also adjust R file path for YARN cluster mode bd6705b [Zongheng Yang] Merge pull request #154 from sun-rui/SPARKR-150 c7964c9 [Sun Rui] Merge with upstream master. 7feac38 [Sun Rui] Use default arguments for sortBy() and sortKeyBy(). de2bfb3 [Sun Rui] Fix minor comments and add more test cases. 0c6e071 [Zongheng Yang] Merge pull request #157 from lythesia/master f5038c0 [lythesia] pull out anonymous functions in groupByKey ba6f044 [lythesia] fixes for reduceByKeyLocally 343b6ab [Oscar Olmedo] Export sparkR.stop Closes #156 from oscaroboto/master 25639cf [Shivaram Venkataraman] Replace tabs with spaces bb25920 [Shivaram Venkataraman] Merge branch 'dputler-master' fd836db [hlin09] fix tests. 24a7f13 [hlin09] More docs a465165 [hlin09] More docs 6ad4fc3 [hlin09] add docs b082a35 [lythesia] add reduceByKeyLocally 7ca6512 [Shivaram Venkataraman] First cut of SparkRRunner 193f5fe [hlin09] loop 1-12 test pass. 345f1b8 [dputler] [SPARKR-195] Implemented project style guidelines for if-else statements 8043559 [Sun Rui] Add a TODO to use binary search in the range partitioner. 91b2fd6 [Sun Rui] Add more test cases. e8ebbe4 [Shivaram Venkataraman] Merge pull request #152 from cafreeman/sparkr-sql 0c53d6c [dputler] Data frames now coerced to lists, and messages issued for a data frame or matrix on how they are parallelized 6d57ec0 [cafreeman] Remove json test file since we're using a temp ac1ef09 [cafreeman] Update registerTempTable test d9da451 [Sun Rui] [SPARKR-150] phase 1: implement sortBy() and sortByKey(). 08ff30b [Shivaram Venkataraman] Merge pull request #153 from hqzizania/master 9767e8e [hqzizania] modified: pkg/man/collect-methods.Rd 5d69f0a [hqzizania] modified: pkg/R/RDD.R 4914091 [hqzizania] modified: pkg/inst/tests/test_rdd.R 742a68b [cafreeman] Update test_sparkRSQL.R a95823e [hqzizania] modified: pkg/R/RDD.R 2d04526 [cafreeman] Formatting fae9bdd [cafreeman] Renamed to SQLUtils.scala 39888ea [Chris Freeman] Update test_sparkSQL.R fce2453 [cafreeman] Updated documentation for SQLContext 13fbf12 [cafreeman] Regenerated .Rd files 51ecf41 [cafreeman] Updated Scala object 30d7337 [cafreeman] Added SparkSQL test 74b3ed6 [cafreeman] Incorporate code feedback 554bda0 [Zongheng Yang] Merge pull request #147 from shivaram/sparkr-ec2-fixes a5f4f8f [cafreeman] Squashed commit of the following: f34bb88 [Shivaram Venkataraman] Remove profiling information from this PR c662f29 [Zongheng Yang] Merge pull request #146 from shivaram/spark-1.2-build 21e9b74 [Zongheng Yang] Merge pull request #145 from lythesia/master 76f6b9e [Shivaram Venkataraman] Merge pull request #149 from hqzizania/master 1c2dbec [lythesia] minor fix for refactoring join code 5b380d3 [hqzizania] modified: pkg/man/combineByKey.Rd modified: pkg/man/groupByKey.Rd modified: pkg/man/partitionBy.Rd modified: pkg/man/reduceByKey.Rd 98794fe [hqzizania] modified: pkg/R/RDD.R b66534d [Zongheng Yang] Merge pull request #144 from shivaram/fix-rd-files 60da1df [Shivaram Venkataraman] Initialize timing variables 179aa75 [Shivaram Venkataraman] Bunch of fixes for longer running jobs 1. Increase the timeout for socket connection to wait for long jobs 2. Add some profiling information in worker.R 3. Put temp file writes before stdin writes in RRDD.scala 06d99f0 [Shivaram Venkataraman] Fix URI to have right number of slashes add97f5 [Shivaram Venkataraman] Use URL encode to create valid URIs for jars 4eec962 [lythesia] refactor join functions 73430c6 [Shivaram Venkataraman] Make SparkR work on paths with spaces on Windows aaf8f47 [Shivaram Venkataraman] Exclude hadoop client from Spark dependency 227ee42 [Zongheng Yang] Merge pull request #141 from shivaram/SPARKR-140 ac5ceb1 [Shivaram Venkataraman] Fix code review comments 32394de [Shivaram Venkataraman] Regenerate Rd files for SparkR This fixes a number of issues in SparkR man pages. The main changes are 1. Don't export or generate docs for PipelineRDD 2. Fix variable names for Filter, count to match base methods 3. Document missing arguments for sparkR.init, print.jobj etc. e157bf6 [Shivaram Venkataraman] Use prev_serialized to track if JRDD is serialized This changes introduces a new variable in PipelineRDD environment to track if the prev_jrdd is serialized or not. 7428a7e [Zongheng Yang] Merge pull request #143 from shivaram/SPARKR-181 7dd1797 [Shivaram Venkataraman] Address code review comments 8f81c45 [Shivaram Venkataraman] Remove roxygen export for PipelinedRDD 0cb90f1 [Zongheng Yang] Merge pull request #142 from shivaram/SPARKR-169 d1c6e6c [Shivaram Venkataraman] Buffer stderr from R and return it on Exception This change buffers the last 100 lines from R process and passes these lines back to the driver if we have an exception. This will help users debug why their tasks failed on the cluster d6c1393 [Shivaram Venkataraman] Suppress warnings from normalizePath a382835 [Shivaram Venkataraman] Fix serialization tracking in pipelined RDDs When creating a pipeline RDD, we need to check if the JavaRDD belonging to the parent is serialized. da39529 [Zongheng Yang] Merge pull request #140 from sun-rui/SPARKR-183 2814caa [Sun Rui] Merge with upstream master. cd2a5b3 [Sun Rui] Add reference to Nagle's algorithm and clean code. 52356b6 [Shivaram Venkataraman] Merge pull request #139 from shivaram/fix-backend-exit 97e5a1f [Sun Rui] [SPARKR-183] Fix the issue that parallelize collect tests are slow. a9f8e8e [Shivaram Venkataraman] Merge pull request #138 from concretevitamin/fix-collect-test 125ae43 [Shivaram Venkataraman] Fix SparkR backend to exit in more cases This change has two fixes 1. When the workspace is saved (from R or RStudio) the backend connection seems to be closed before the finalizer is run. In such cases we reopen the connection and stop the backend 2. With RStudio when R is restarted, there are port-conflicts which appear due to a race condition between the JVM and rsession restart. This change adds a 1 sec sleep to avoid this race. 12c102a [Zongheng Yang] Simplify a unit test. 9c0637a [Zongheng Yang] Merge pull request #137 from shivaram/fix-docs 0df0e18 [Shivaram Venkataraman] Fix documentation for includePackage 7549f88 [Zongheng Yang] Merge pull request #136 from shivaram/man-updates 7edbe46 [Shivaram Venkataraman] Add missing man pages 9cb9567 [Shivaram Venkataraman] Merge pull request #131 from shivaram/rJavaExpt 1fa722e [Shivaram Venkataraman] Rename to SerDe now 2fcb051 [Shivaram Venkataraman] Rename to SerDeJVMR d112cf0 [Shivaram Venkataraman] Style fixes 9fd01cc [Shivaram Venkataraman] Remove unnecessary braces 0881931 [Shivaram Venkataraman] Some more style fixes f00b531 [Shivaram Venkataraman] Address code review comments. Big changes include style fixes throughout for named arguments c09ba05 [Shivaram Venkataraman] Change jobj id to be just an integer Add a new print.jobj that gets the class name and prints it Also add a utility function isInstanceOf be05b16 [Shivaram Venkataraman] Check if context, connection exist before stopping d596a23 [Shivaram Venkataraman] Address code review comments 396e7ac [Shivaram Venkataraman] Changes to make new backend work on Windows This change uses file.path to construct the Java binary path in a OS agnostic way and uses system2 to handle quoting binary paths correctly. Tests pass on Mac OSX and a Windows EC2 instance. e7a4e03 [Shivaram Venkataraman] Remove unused file BACKEND.md 62f380b [Shivaram Venkataraman] Update worker.R to use new deserialization call 8b9c4e6 [Shivaram Venkataraman] Change RDD name, setName to use new backend 6dcd5c5 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into rJavaExpt 0873397 [Shivaram Venkataraman] Refactor java object tracking into a new singleton. Also add comments describing each class 95db964 [Shivaram Venkataraman] Add comments, cleanup new R code bcd4258 [Zongheng Yang] Merge pull request #130 from lythesia/master 74dbc5e [Sun Rui] Match method using parameter types. 7ad4a4d [Sun Rui] Use 1 char to represent types on the backend->client direction. bace887 [Sun Rui] Use an integer count for the backend java object ID because Uniqueness isn't guaranteed by System.identityHashCode(). b38d04f [Sun Rui] Use 1 char to represent types on the client -> backend direction. f88bc68 [lythesia] Merge branch 'master' of github.com:lythesia/SparkR-pkg 71d41f5 [lythesia] add test case for fullOuterJoin eb4f423 [lythesia] --amend cffecc5 [lythesia] add test case for fullOuterJoin a547dd2 [Shivaram Venkataraman] Move classTag, rddRef into newJObject call This avoids them getting eagerly garbage collected 1255391 [Shivaram Venkataraman] Add a finalizer for jobj objects This enables Java objects to be garbage collected on the backend when they are no longer referenced in R. Also rename newJava to newJObject to be more consistent with callJMethod 70fa409 [Sun Rui] Add YARN Conf Dir to the class path when launching the backend. a1108ca [lythesia] add fullOuterJoin in RDD.R 2152727 [Shivaram Venkataraman] Remove empty file cd08bee [Shivaram Venkataraman] Update all functions to use new backend All unit tests pass. 9de49b7 [Shivaram Venkataraman] Add high level calls for methods, constructors Also update BACKEND.md 5a97ea4 [Shivaram Venkataraman] Add jobj S3 class that holds backend refs e071d3e [Shivaram Venkataraman] Change SparkRBackend to use general method calls This change uses a custom protocl + JNI to invoke any method on a given object type. Also update serializers, deserializers to make code more concise 49f0404 [Shivaram Venkataraman] Merge pull request #129 from lythesia/master 7f8cd82 [lythesia] update man 4715ed2 [Yi Lu] Update RDD.R 5a53801 [lythesia] fix name,setName 4f3870b [lythesia] add name,setName in RDD.R 1c25700 [Shivaram Venkataraman] Merge pull request #128 from sun-rui/SPARKR-165 c8507d8 [Sun Rui] [SPARKR-165] IS_SCALAR is not present in R before 3.1 2cff2bd [Sun Rui] Add function to invoke Java method. 7a31da1 [Shivaram Venkataraman] Merge branch 'dputler-master'. Closes #119 0ceba82 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/dputler/SparkR-pkg into dputler-master 735f70c [Shivaram Venkataraman] Merge pull request #125 from 7c00/rawcon fccfe6c [Shivaram Venkataraman] Merge pull request #127 from sun-rui/SPARKR-164 387bd57 [Sun Rui] [SPARKR-164] Temporary files used by SparkR accumulat as time goes on. 5f2268f [Shivaram Venkataraman] Add support to stop backend 5f745c0 [Shivaram Venkataraman] Update notes in backend 22015c1 [Shivaram Venkataraman] Add first cut of SparkR Backend 52821da [Todd Gao] switch the order of packages and function deps d7b0007 [Todd Gao] remove memCompress cb6873e [Shivaram Venkataraman] Merge pull request #126 from sun-rui/SPARKR-147 c5962eb [Todd Gao] further optimize using rawConnection f04c6e0 [Sun Rui] [SPARKR-147] Support multiple directories as input to textFile. b7de604 [Todd Gao] optimize execFunctionDeps loading in worker.R 4d4fc30 [Shivaram Venkataraman] Merge pull request #122 from cafreeman/master b508877 [cafreeman] Update SparkR_IDE_Setup.sh 21ed9d7 [cafreeman] Update build.sbt f73ec16 [cafreeman] Delete SparkR_IDE_Setup_Guide.md d63b026 [cafreeman] Delete SparkR_Quick_Start_Guide.md 6e6cb62 [cafreeman] Update SparkR_IDE_Setup.sh bc6042b [cafreeman] Update build.sbt a8197d5 [cafreeman] Merge remote-tracking branch 'upstream/master' d671564 [Zongheng Yang] Merge pull request #123 from shivaram/jcheck-void 76b8d00 [Zongheng Yang] Merge pull request #124 from shivaram/master b690d58 [Shivaram Venkataraman] Specify how to change Spark versions in README 0fb003d [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into jcheck-void 1c227b4 [Shivaram Venkataraman] Also add a check in context.R 96812b6 [Shivaram Venkataraman] Check for exceptions after void method calls f5c216d [cafreeman] Merge remote-tracking branch 'upstream/master' 90c8933 [Zongheng Yang] Merge pull request #121 from shivaram/fix-sort-order bd0e3b4 [Shivaram Venkataraman] Fix saveAsTextFile test case 2e55f67 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into fix-sort-order f10c607 [Shivaram Venkataraman] Merge pull request #118 from sun-rui/saveAsTextFile 6c9bfc0 [Sun Rui] Merge remote-tracking branch 'SparkR_upstream/master' into saveAsTextFile 6faedbe [cafreeman] Update SparkR_IDE_Setup_Guide.md 57008bc [cafreeman] Update SparkR_IDE_Setup.sh bb1c17d [cafreeman] Update SparkR_IDE_Setup.sh 538bfdb [cafreeman] Update SparkR_Quick_Start_Guide.md 31322c6 [cafreeman] Update SparkR_IDE_Setup.sh ca3f593 [Sun Rui] Refactor RRDD code. df58d95 [cafreeman] Update SparkR_Quick_Start_Guide.md b488c88 [cafreeman] Rename Spark_IDE_Setup.sh to SparkR_IDE_Setup.sh b2545a4 [cafreeman] Added IDE Setup Guide 0ffb5de [cafreeman] Merge branch 'master' of https://github.com/cafreeman/SparkR-pkg bd8fbfb [cafreeman] Merge remote-tracking branch 'upstream/master' 98efa5b [cafreeman] Added Quick Start Guide 3cf88f2 [Shivaram Venkataraman] Sort lists before comparing in unit tests Since Spark doesn't guarantee that shuffle results will always be in the same order, we need to sort the results before comparing for deterministic behavior d621dbc [Shivaram Venkataraman] Merge pull request #120 from sun-rui/objectFile c4a44d7 [Sun Rui] Add @seealso in comments and extract some common code into a function. 724e3a4 [cafreeman] Update Spark_IDE_Setup.sh 8153e5a [Sun Rui] [SPARKR-146] Support read/save object files in SparkR. 17f9909 [cafreeman] Update Spark_IDE_Setup.sh a9eb080 [cafreeman] IDE Shell Script 64d800c [dputler] Merge remote branch 'upstream/master' 1fbdb2e [dputler] Added the ability for the user to specify a text file location throught the use of tilde expansion or just the file name if it is in the working directory. d83c017 [Shivaram Venkataraman] Merge pull request #113 from sun-rui/stringHashCodeInC a7d9cdb [Sun Rui] Fix build on Windows. 7d81b05 [Shivaram Venkataraman] Merge pull request #114 from hlin09/hlin09 47c4bb7 [hlin09] fix reviews a457f7f [Shivaram Venkataraman] Merge pull request #116 from dputler/master 0fa48d1 [Shivaram Venkataraman] Merge pull request #117 from sun-rui/keyBy 85cfeb4 [Sun Rui] [SPARKR-144] Implement saveAsTextFile() in the RDD class. 09083d9 [Sun Rui] Add keyBy() to the RDD class. caad5d7 [dputler] Adding the script to install software on the Cloudera Quick Start VM. dca3d05 [hlin09] Minor fix. ece5f7d [hlin09] Merge remote-tracking branch 'upstream/master' into hlin09 a40874b [hlin09] Use extendible accumulators aggregate the cogroup values. d0347ce [Zongheng Yang] Merge pull request #112 from sun-rui/outer_join 492f76e [Sun Rui] Refine code and add description. ba01358 [Shivaram Venkataraman] Merge pull request #115 from sun-rui/SPARKR-130 5c8e46e [Sun Rui] Fix per the review comments. 7190a2c [Sun Rui] Update comment to add a reference to storage levels. 1da705e [hlin09] Fix the review comments. c4b77be [Sun Rui] [SPARKR-130] Add persist(storageLevel) API to RDD. b424a1a [hlin09] Add function cogroup(). 9770312 [Shivaram Venkataraman] Merge pull request #111 from hlin09/hlin09 cead7df [hlin09] fix review comments. 54f712e [Sun Rui] Implement string hash code in C. 425f0c6 [Sun Rui] Add leftOuterJoin() and rightOuterJoin() to the RDD class. 39509c7 [hlin09] add Rd file for foreach and foreachPartition. 63d6ac7 [hlin09] Adds function foreach() and foreachPartition(). 9c954df [Zongheng Yang] Merge pull request #105 from sun-rui/join c71228d [Sun Rui] Pre-allocate list with fixed length. Add test case for join() using string key. bc3e9f6 [Shivaram Venkataraman] Merge pull request #108 from concretevitamin/take-optimize c06fc90 [Zongheng Yang] Fix: only optimize for unserialized dataset case. d399aeb [Zongheng Yang] Apply size-capping on logical representation instead of physical. e4217dd [Zongheng Yang] Merge pull request #107 from shivaram/master 7952180 [Shivaram Venkataraman] Copy, use getLocalDirs from Spark Utils.scala 08e24c3 [Zongheng Yang] Merge pull request #109 from hlin09/hlin09 97d4e02 [Zongheng Yang] Min() upper-bound size with actual size. bb779bf [hlin09] Rename the filter function to filterRDD to follow the API consistency. Filter() is also kept. ce1661f [Zongheng Yang] Fix slow take(): deserialize only up to necessary # of elements. 4dca9b1 [Shivaram Venkataraman] Merge pull request #106 from hlin09/hlin09 1220d92 [hlin09] Adds function numPartitions(). 2326a65 [Shivaram Venkataraman] Use SPARK_LOCAL_DIRS to create tmp files e119757 [hlin09] Minor fix. 9c24c8b [hlin09] Adds function countByKey(). 48fce67 [hlin09] Adds countByValue(). 6679eef [Sun Rui] Update documentation for join(). 70586b4 [Sun Rui] Add join() to the RDD class. e6fb999 [Zongheng Yang] Merge pull request #103 from shivaram/rlibdir-fix a21f146 [Shivaram Venkataraman] Merge pull request #102 from hlin09/hlin09 32eb619 [Shivaram Venkataraman] Merge pull request #104 from sun-rui/add_keys_values d8692e9 [Sun Rui] Add keys() and values() for the RDD class. 18b9be1 [Shivaram Venkataraman] Allow users to set where SparkR is installed This also adds a warning if somebody tries to call sparkR.init multiple times. a17f135 [hlin09] Adds tests for flatMap and flatMapValues. 4bcf59b [hlin09] Adds function flatMapValues. 4a193ef [Zongheng Yang] Merge pull request #101 from ashutoshraina/master 60d22f2 [Ashutosh Raina] changed sbt version 5400793 [Zongheng Yang] Merge pull request #98 from shivaram/windows-fixes-build 36d61a7 [Shivaram Venkataraman] Merge pull request #97 from hlin09/hlin09 f7d7d89 [hlin09] Remove redundant code in test. 6bbe823 [hlin09] minor style fix. 9b47f3a [Shivaram Venkataraman] Merge pull request #100 from hnahak87/patch-1 7f6e4ea [Harihar Nahak] Update logistic_regression.R a605047 [Shivaram Venkataraman] Merge pull request #99 from hlin09/makefile 323151d [hlin09] Fix yar flag in Makefile to remove build error in Maven. 8911897 [hlin09] Make reserialize() private function in package. 79aee73 [Shivaram Venkataraman] Add notes on how to build SparkR on windows 49a99e7 [Shivaram Venkataraman] Clean up some commented code ddc271b [Shivaram Venkataraman] Only append file:/// to non empty jar paths a53952e [Shivaram Venkataraman] Add windows build scripts 325b179 [hlin09] Merge remote-tracking branch 'upstream/master' into hlin09 daf5040 [hlin09] Add reserialize() before union if two RDDs are not both serialized. 536afb1 [hlin09] Add new function of union(). 7044677 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into windows-fixes d22a02d [Zongheng Yang] Merge pull request #94 from shivaram/windows-fixes-stdin 51924f7 [Shivaram Venkataraman] Merge pull request #90 from oscaroboto/master eb97d85 [Shivaram Venkataraman] Merge pull request #96 from sun-rui/add_clarification_readme 5a128f4 [Sun Rui] Add clarification on setting Spark master when launching the SparkR shell. 187526a [oscaroboto] Update sparkR.R 32c567b [Shivaram Venkataraman] Merge pull request #95 from concretevitamin/master 4cd2d5e [Zongheng Yang] Notes about spark-ec2. 1c28e3b [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into windows-fixes 8e8a029 [Zongheng Yang] Merge pull request #92 from shivaram/sparkr-yarn 721043b [Zongheng Yang] Update README.md with YARN instructions. 1681f58 [Shivaram Venkataraman] Use temporary files for input instead of stdin This fixes a bug for Windows where stdin would get truncated b084314 [oscaroboto] removed ... from example 44c93d4 [oscaroboto] Added example to SparkR.R be82dcc [Shivaram Venkataraman] Merge pull request #93 from hlin09/hlin09 868554d [oscaroboto] Update sparkR.R 488ac47 [hlin09] Add generated Rd file of previous added functions, distinct() and mapValues(). b2740ad [hlin09] Add test for filter all elements. Add filter() as alias. 08d3631 [hlin09] Minor style fixes. 2c0e34f [hlin09] Adds function Filter(), which extracts the elements that satisfy a predicate. 5951d3b [Shivaram Venkataraman] Remove SBT plugin 4e70ced [oscaroboto] changed ExecutorEnv to sparkExecutorEnvMap, to make it consistent with sparkEnvirMap 903d18a [oscaroboto] changed executorEnv to sparkExecutorEnvMap, will do the same in R f97346e [oscaroboto] executorEnv to lower-case e 88a524e [oscaroboto] Added LD_LIBRARY_PATH to the ExecutorEnv. This is need so that the nodes can find libjvm.so, or if the master has a different LD_LIBRARY_PATH then the nodes. Make sure to export LD_LIBRARY_PATH that includes the path to libjvm.so in the nodes. 1d208ae [oscaroboto] added the YARN_CONF_DIR to the classpath 8a9b75c [oscaroboto] forgot to change hm and ee inside the for loops 579db58 [Shivaram Venkataraman] Merge pull request #91 from sun-rui/add_max_min 4381efa [Sun Rui] use reduce() to implemement max() and min(). a5459c5 [Shivaram Venkataraman] Consolidate yarn flags 86b04eb [Shivaram Venkataraman] Don't use quotes around yarn bf0797f [Shivaram Venkataraman] Add dependency on spark yarn module af5fe77 [Shivaram Venkataraman] Fix SBT build, add dependency tree plugin 4917607 [Sun Rui] Add maximum() and minimum() API to RDD. 51bbbe4 [Shivaram Venkataraman] Changes to make SparkR work with YARN 9d5e3ab [oscaroboto] a few stylistic changes. Also change vars to sparkEnvirMap and eevars to ExecutorEnv, to match sparkR.R 578f545 [oscaroboto] a few stylistic changes 39eea2f [oscaroboto] Modification to dynamically create a sparkContext with YARN. Added .setExecutorEnv to the sparkConf in createSparkContext within the RRDD object. This modification was made together with sparkR.R 17ec42e [oscaroboto] A modification to dynamically create a sparkContext with YARN. sparkR.R modified to pass custom Jar file names and EnvironmentEnv to the sparkConf. RRDD.scala was also modified to accept the new inputs to creatSparkContext. 624ac9d [Shivaram Venkataraman] Merge pull request #87 from sun-rui/SPARKR-125 4f213db [Shivaram Venkataraman] Merge pull request #89 from sun-rui/SPARKR-108 eb833c5 [Shivaram Venkataraman] Merge pull request #88 from hlin09/hlin09 07bf971 [Sun Rui] [SPARKR-108] Implement map-side reduction for reduceByKey(). 4accba1 [hlin09] Fixes style and adds an optional param 'numPartition' in distinct(). 80d303a [hlin09] typo fixed. e37a9b5 [hlin09] Adds function distinct() and mapValues(). 08dac06 [Sun Rui] [SPARKR-125] Get the iterator of the parent RDD before launching a R worker process in compute() of RRDD/PairwiseRRDD c4ba53c [Shivaram Venkataraman] Merge pull request #85 from edwardt/master 72a9d27 [root] reorder to keep relative ordering the same f3fcb10 [root] fix up build.sbt also to match pom.xml 5ecbe3e [root] Make spark verison configurable in build script per ISSUE122 a44e63d [Shivaram Venkataraman] Merge pull request #84 from sun-rui/SPARKR-94 fbb5663 [Sun Rui] Add {} to one-line functions and add a test case for lookup where no match is found. 95beb4e [Shivaram Venkataraman] Merge pull request #82 from edwardt/master 36776c5 [edwardt] missed one 0.9.0 revert b26deec [Sun Rui] [SPARKR-94] Add a method to get an element of a pair RDD object by key. 1ba256e [edwardt] Keep 0.9.0 and says uses 1.1.0 by default 5380c43 [root] missed one version 21f74da [root] upgrade to spark version 1.1.0 to match lastest merge list ddfcde9 [root] merge 67d067a [Shivaram Venkataraman] Merge pull request #81 from sun-rui/SparkR-117 993868f [Sun Rui] [SPARKR-117] Update Spark dependency to 1.1.0 d20661a [Zongheng Yang] Merge pull request #80 from sun-rui/master 0b2da9f [Sun Rui] Update Rd file and add a test case for mapPartitions. 5879648 [Sun Rui] Add mapPartitions() method to RDD for API consistency. c033461 [Shivaram Venkataraman] Merge pull request #79 from sun-rui/fix-kmeans f62b77e [Sun Rui] Adjust coding style. b40911d [Sun Rui] Fix syntax error in examples/kmeans.R. 5304451 [Shivaram Venkataraman] Merge pull request #78 from sun-rui/master 70ffbfb [Sun Rui] Fix a bug that modifications to build.sbt won't trigger rebuilding. a25696c [Shivaram Venkataraman] Merge pull request #76 from edwardt/addjira b8bbd93 [edwardt] Update README.md 615d930 [edwardt] Update README.md e522e69 [edwardt] Update README.md 03e6ced [edwardt] Update README.md 3007015 [root] don't check in gedit buffer file' c35c9a6 [root] Add where to enter bugs ad feeback 469eae3 [edwardt] Update README.md 61b4a43 [edwardt] Update Makefile (style uniformity) ce3337d [edwardt] Update README.md 7ff68fc [root] Merge branch 'master' of https://github.com/edwardt/SparkR-pkg 16353f5 [root] add links to devtools and install_github 513b9e5 [Shivaram Venkataraman] Merge pull request #72 from edwardt/master 31608a4 [edwardt] Update Makefile (style uniformity) 4ffe146 [root] Makefile: factor out SPARKR_VERSION to reduce potential copy&paste error; cp & rm called with -f in build/clean phase; .gitignore includes checkpoints and unit test log generated by run-tests.sh 715275f [Zongheng Yang] Merge pull request #68 from shivaram/master 90e2083 [Shivaram Venkataraman] Add return type to hasNext 8eb983d [Shivaram Venkataraman] Fix up comment 2206164 [Shivaram Venkataraman] Delete temporary files after they are read This change deletes temporary files used for communication between Rscript and the JVM once they have been completely read. 5881da7 [Zongheng Yang] Merge pull request #67 from shivaram/improve-shuffle 81251e2 [Shivaram Venkataraman] Address code review comments a5f573f [Shivaram Venkataraman] Use a better list append in shuffles This is helpful in scenarios where we have a large number of values in a bucket 388e64d [Shivaram Venkataraman] Merge pull request #55 from RevolutionAnalytics/master e1f95b6 [Zongheng Yang] Merge pull request #65 from concretevitamin/parallelize-fix fc1a71a [Zongheng Yang] Fix that collect(parallelize(sc,1:72,15)) drops elements. b8204c5 [Zongheng Yang] Minor: update a URL in README. 86f30c3 [Antonio Piccolboni] better fix for amplab-extras/SparkR-pkg#53 b3c318d [Antonio Piccolboni] delayed loading to have all namespaces available. f323e97 [Antonio Piccolboni] tentative fix for amplab-extras/SparkR-pkg#53 6f82269 [Zongheng Yang] Merge pull request #48 from shivaram/master 8f433e5 [Shivaram Venkataraman] Move up Hadoop in pom.xml and add back protobufs As Hadoop 1.0.4 doesn't use protobufs, we can't exclude protobufs from Spark always. This change tries to order the dependencies so that the shader first picks up Hadoop's protobufs over Mesos. bfe7e26 [Shivaram Venkataraman] Merge pull request #36 from RevolutionAnalytics/vectorize-examples 059ae41 [Antonio Piccolboni] and more formatting 9dbd531 [Antonio Piccolboni] more formatting per committer request 948738a [Antonio Piccolboni] converted tabs to spaces per project request 49f5f5a [Shivaram Venkataraman] Merge pull request #35 from shivaram/master 3eb5ad3 [Shivaram Venkataraman] on_failure -> after_failure in travis.yml 139bdee [Shivaram Venkataraman] Cache sbt, maven, ivy dependencies 4ebced2 [Shivaram Venkataraman] Merge pull request #34 from shivaram/master 8437061 [Shivaram Venkataraman] Exclude protobuf from Spark dependency in Maven This avoids pulling in multiple versions of protobuf from Mesos and Hadoop. 91aa527 [Antonio Piccolboni] vectorized version, 36s 10 slices 10^6 per slice. The older version takes 30 sec on 1/10th of data. f137a57 [Antonio Piccolboni] for rstudio users 1f7ffb0 [Antonio Piccolboni] implemented using matrices and vectorized calls wherever possible 46b23df [Antonio Piccolboni] replace require with library b15d7db [Antonio Piccolboni] faster parsing 8b7aeb3 [Antonio Piccolboni] 22x speed improvement, 3X mem impovement c5bce07 [Zongheng Yang] Merge pull request #30 from shivaram/string-tests 21fa2d8 [Shivaram Venkataraman] Fix bug where serialized was not changed for RRRD Reason: When an RRDD is created in getJRDD we have converted any possibly unserialized RDD to a serialized RDD. 9d1ea20 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg into string-tests 7b9348c [Shivaram Venkataraman] Add tests for partition with string keys Add two tests one with a string array and one from a textFile to test both codepaths aacd726 [Shivaram Venkataraman] Update README with maven proxy instructions 803e62c [Shivaram Venkataraman] Merge pull request #28 from concretevitamin/master 7c093e6 [Zongheng Yang] Use inherits() to test an object's class. 061c591 [Shivaram Venkataraman] Merge pull request #26 from hafen/master 90f9fda [Ryan Hafen] Fix isRdd() to properly check for class 5b10cc7 [Zongheng Yang] Merge pull request #24 from shivaram/master 7014f83 [Shivaram Venkataraman] Remove unused transformers in maven's pom.xml b00cea5 [Shivaram Venkataraman] Add support for a Maven build 11ec9b2 [Shivaram Venkataraman] Merge pull request #12 from concretevitamin/pipelined 6b18a90 [Zongheng Yang] Merge branch 'master' into pipelined 57127b8 [Zongheng Yang] Merge pull request #23 from shivaram/master 1ac3940 [Zongheng Yang] Review feedback. a06fb34 [Zongheng Yang] Remove outdated comment. 0a1fc13 [Shivaram Venkataraman] Fixes for using SparkR with Hadoop2. 1. Exclude ASM, Netty from Hadoop similar to Spark. 2. Concat services files to ensure HDFS filesystems work. 3. Update README with an example 9a1db44 [Zongheng Yang] Merge pull request #22 from shivaram/master e462448 [Shivaram Venkataraman] Use `$` for calling `put` instead of .jrcall ed4559a [Shivaram Venkataraman] Add support for passing Spark environment vars This change creates a new `createSparkContext` method in RRDD as we can't pass Map<String, String> through rJava. Also use SPARK_MEM in local mode to increase heap size and update the README with some examples. 10228fb [Shivaram Venkataraman] Merge pull request #20 from concretevitamin/digit-ex 1398d9f [Zongheng Yang] Add linear_solver_mnist to examples/. d484c2a [Zongheng Yang] Add tests for actions on PipelinedRDD. d9cb95c [Zongheng Yang] Add setCheckpointDir() to context.R; comment fix. f8bc8a9 [Zongheng Yang] Minor edits per Shivaram's comments. 8cd67f7 [Shivaram Venkataraman] Merge pull request #15 from shivaram/master d4468a9 [Shivaram Venkataraman] Remove trailing comma e2714b8 [Shivaram Venkataraman] Remove Apache Staging repo and update README 334eace [Zongheng Yang] Add a multi-transformation test to benchmark on pipelining. 5650ad7 [Zongheng Yang] Put serialized field inside env for both RDD and PipelinedRDD. 0b9e8bb [Zongheng Yang] First cut at PipelinedRDD. a4c431e [Zongheng Yang] Add `isCheckpointed` field and checkpoint(). dac0795 [Zongheng Yang] Minor inline comment style fix. bfb8e26 [Zongheng Yang] Add isCached field (inside an env) and unpersist(). 295bff6 [Zongheng Yang] Merge pull request #11 from shivaram/master 4cb209c [Shivaram Venkataraman] Search rLibDir in worker before libPaths This ensures we pick up the SparkR intended and not an older version installed on the same machine ef198ff [Zongheng Yang] Merge pull request #10 from shivaram/unit-tests e0557a8 [Shivaram Venkataraman] Update travis to install plyr 8b18bc1 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg into unit-tests 4a9ca31 [Shivaram Venkataraman] Use smaller broadcast and plyr instead of Matrix Matrix package takes around 2s to load and slows down unit tests. 21c6a61 [Zongheng Yang] Merge pull request #8 from shivaram/master 08c2947 [Shivaram Venkataraman] Move dev install directory to front of libPaths bda42ee [Shivaram Venkataraman] Merge pull request #7 from JoshRosen/travis cc5f5c0 [Josh Rosen] Add Travis CI integration (using craigcitro/r-travis) b6c864b [Shivaram Venkataraman] Merge pull request #6 from concretevitamin/env-style-fix 4fcef22 [Zongheng Yang] Use one style ($) for accessing names in environments. 8a948c6 [Shivaram Venkataraman] Merge pull request #4 from shivaram/master 24978eb [Shivaram Venkataraman] Update README to use install_github 8899db4 [Shivaram Venkataraman] Update TODO.md 91792de [Shivaram Venkataraman] Update Spark requirements f34f4bf [Shivaram Venkataraman] Check tests for failures and output error msg cd750d3 [Shivaram Venkataraman] Update run-tests to use new path 1877b7c [Shivaram Venkataraman] Unset R_TESTS to make tests work with R CMD check Also silence Akka remoting logs and update Makefile to build on log4j changes e60e18a [Shivaram Venkataraman] Update README to remove Spark installation notes 4450189 [Shivaram Venkataraman] Add Spark 0.9 dependency from Apache Staging Also clean up assembly jar from inst on make clean 5eb2131 [Shivaram Venkataraman] Update repo path in README ec8210e [Shivaram Venkataraman] Remove broadcastId hack as it is public in Spark 9f0e080 [Shivaram Venkataraman] Merge branch 'install-github' 5c88fbd [Shivaram Venkataraman] Add helper script to run tests 77450a1 [Shivaram Venkataraman] Remove dependency on Spark Logging 6cb00d1 [Shivaram Venkataraman] Update README and add helper script install-dev.sh 28346ca [Shivaram Venkataraman] Only normalize if SPARK_HOME is not empty 0fd6571 [Shivaram Venkataraman] Normalize SPARK_HOME before passing it ff96d5c [Shivaram Venkataraman] Pass in SPARK_HOME and jar file path 34c4dce [Shivaram Venkataraman] Move src into pkg and update Makefile This enables the package to be installed using install_github using devtools and automates the build procedure. b25afed [Shivaram Venkataraman] Change package name to edu.berkeley.cs.amplab c691464 [Shivaram Venkataraman] Add Apache 2.0 License file 27a4a4b [Shivaram Venkataraman] Add notes on how to compile roxygen2 docs ca63844 [Shivaram Venkataraman] Add broadcast documentation Also generate documentation for sample, takeSample etc. e4dd976 [Shivaram Venkataraman] Update TODO.md e42d435 [Shivaram Venkataraman] Add support for broadcast variables 6b638e7 [Shivaram Venkataraman] Add the assembly jar to SparkContext bf24e32 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg 43c05ce [Zongheng Yang] Fix a flaky/incorrect test for sampleRDD(). c6a9dfc [Zongheng Yang] Initial port of the kmeans example. 6885581 [Zongheng Yang] Implement element-level sampleRDD() and takeSample() with tests. d3a4987 [Zongheng Yang] Add a test for lapplyPartitionsWithIndex on pairwise RDD. c7899c1 [Zongheng Yang] Add lapplyPartitionsWithIndex, with a test and an alias function. a9a7436 [Shivaram Venkataraman] Add DFC example from Tselil, Benjamin and Jonah fbc5a95 [Zongheng Yang] Implement take() and takeSample(). c4a3409 [Shivaram Venkataraman] Use RDD instead of RRDD dfad3f5 [Zongheng Yang] Add test_utils.R: a unit test for convertJListToRList(). a45227d [Zongheng Yang] Update .gitignore. 238fe6e [Zongheng Yang] Add a unit test for textFile(). a88898b [Zongheng Yang] Rename test_rrd to test_rrdd 10c8baa [Shivaram Venkataraman] Make SparkR work as a standalone package. Changes include: 1. Adding a new `sbt` project that builds RRDD.scala 2. Change the onLoad functions to load the assembly jar for SparkR 3. Set rLibDir in RRDD.scala and worker.R to load things correctly 78adcd8 [Shivaram Venkataraman] Add a gitignore ca6108f [Shivaram Venkataraman] Merge branch 'SparkR-scalacode' of ../SparkR 999bd61 [Shivaram Venkataraman] Update collectPartition in R and use ClassTag c58f63e [Shivaram Venkataraman] Update collectPartition in R and use ClassTag 48265fd [Shivaram Venkataraman] Use new version of collectPartitions in take d4fe086 [Shivaram Venkataraman] Move collectPartitions to JavaRDDLike Also remove numPartitions in JavaRDD and update R code bfecd7b [Shivaram Venkataraman] Scala 2.10 changes 1. Update sparkR script 2. Use classTag instead of classManifest 092a4b3 [Shivaram Venkataraman] Add combineByKey, update TODO ac0d81d [Shivaram Venkataraman] Add more documentation d1dc3fa [Shivaram Venkataraman] Add more documentation c515e3a [Shivaram Venkataraman] Update TODO db56a34 [Shivaram Venkataraman] Add a test case for include package 41cea51 [Shivaram Venkataraman] Ensure all parent environments are serialized. Also add a test case with an inline function a978e84 [Shivaram Venkataraman] Add support to include packages in the worker 12bf8ce [Shivaram Venkataraman] Add support to include packages in the worker fb7e72c [Shivaram Venkataraman] Cleanup TODO 16ac314 [Shivaram Venkataraman] Add documentation for functions in context, sparkR 85b1d25 [Shivaram Venkataraman] Set license to Apache 88f1101 [Shivaram Venkataraman] Add unit test running instructions c40768e [Shivaram Venkataraman] Update TODO 0c7efbf [Shivaram Venkataraman] Refactor RRDD.scala and add comments to functions 5880d42 [Shivaram Venkataraman] Refactor RRDD.scala and add comments to functions 2dee36c [Shivaram Venkataraman] Remove empty test file a82219b [Shivaram Venkataraman] Update TODOs 5db00dc [Shivaram Venkataraman] Add reduceByKey, groupByKey and refactor shuffle Other changes include 1. Adding unit tests for basic RDD functions and shuffle 2. Add a word count example 3. Change the dependency serialization to handle double loading of SparkR package 4. Allow partitionBy to operate on any RDDs to create pair-wise RDD. f196479 [Shivaram Venkataraman] Add reduceByKey, groupByKey and refactor shuffle Other changes include 1. Adding unit tests for basic RDD functions and shuffle 2. Add a word count example 3. Change the dependency serialization to handle double loading of SparkR package 4. Allow partitionBy to operate on any RDDs to create pair-wise RDD. 987e36f [Shivaram Venkataraman] Add perf todo 0b03265 [Shivaram Venkataraman] Update TODO with testing, docs todo 685aaad [Zongheng Yang] First cut at refactoring worker.R. Remove pairwiseWorker.R. 95b9ddc [Zongheng Yang] First cut at refactoring worker.R. Remove pairwiseWorker.R. 4f00895 [Zongheng Yang] Remove the unnecessary `pairwise' flag in RRDD class. Reasons: 75d36d9 [Zongheng Yang] Working versions: partitionBy() and collectPartition() for RRDD. e3fbd9d [Zongheng Yang] Working versions: partitionBy() and collectPartition() for RRDD. 67a4335 [Zongheng Yang] Add unit test for parallelize() and collect() pairwise data. 100ae65 [Zongheng Yang] Properly parallelize() and collect() pairwise data. cd0a5e2 [Zongheng Yang] Properly parallelize() and collect() pairwise data. aea16c3 [Zongheng Yang] WIP: second cut at partitionBy. Running into R/Scala communication issues. 45eb943 [Zongheng Yang] WIP: second cut at partitionBy. Running into R/Scala communication issues. 11c893b [Zongheng Yang] WIP: need to figure out the logic of (whether or not) shipping a hash func 82c201a [Zongheng Yang] WIP: need to figure out the logic of (whether or not) shipping a hash func b3bfad2 [Zongheng Yang] Update TODO: take() done. 0e45293 [Zongheng Yang] Add ability to parallelize key-val collections in R. f60406a [Zongheng Yang] Add ability to parallelize key-val collections in R. 7d7fe3b [Zongheng Yang] Re-implement take(): take a partition at a time and append. a054e55 [Zongheng Yang] Fix take() tests(): mode difference. 9de0935 [Zongheng Yang] Implement take() for RRDD. 1e4427e [Zongheng Yang] Implement take() for RRDD. ec3cd67 [Shivaram Venkataraman] Use temp file in Spark to pipe output 417aaed [Shivaram Venkataraman] Use temp file in Spark to pipe output bb0a3c3 [Shivaram Venkataraman] Add conf directory to classpath 9594d8a [Shivaram Venkataraman] Clean up LR example 3b26b58 [Shivaram Venkataraman] Add a list of things to do. cabce68 [Shivaram Venkataraman] Fix warnings from package check fde3f9c [Shivaram Venkataraman] Flatten by default and disable recursive unlist ab2e061 [Shivaram Venkataraman] Create LIB_DIR before installing SparkR package 555220a [Shivaram Venkataraman] Add readme and update Makefile 1319cda [Shivaram Venkataraman] Make standalone programs run with sparkR ae19fa8 [Shivaram Venkataraman] Add support for cache and use `tempfile` 4e89ca4 [Shivaram Venkataraman] Add support for apply, reduce, count Also serialize closures using `save` and add two examples 25a0bea [Shivaram Venkataraman] Add support for apply, reduce, count Also serialize closures using `save` and add two examples f50223f [Zongheng Yang] Make parallelize() and collect() use lists. Add a few more tests for them. fc7693f [Zongheng Yang] Refactor and enhance the previously added unit test a little bit. 6de9b81 [Zongheng Yang] Add a simple unit test for parallelize(). 8b95155 [Zongheng Yang] Add testthat skeleton infrastructure ef305bf [Zongheng Yang] parallelize() followed by collect() now work for vectors/lists of strings and numerics (should work for other primitives as well). dc16af4 [Zongheng Yang] Comment: toArray() allocates memory for a copy f50121e [Zongheng Yang] Make parallelize() return JavaRDD[Array[Byte]]. Add RRDD.scala with a helper function in the singleton object. 46eb063 [Zongheng Yang] Make parallelize() return JavaRDD[Array[Byte]]. Add RRDD.scala with a helper function in the singleton object. 6b4938a [Zongheng Yang] parallelize(): a raw can be parallelized by JavaSparkContext and get back JavaRDD 978aa0f [Zongheng Yang] Add parallelize() skeleton: only return serialized slices now 84c1fd2 [Zongheng Yang] Use .jsimplify() to get around generic List's get() type erasure problem f16b891 [Zongheng Yang] Convert a few reflectionc alls to .jcall 1284c13 [Zongheng Yang] WIP on collect(): JavaListToRList() failed with errors. 4c2e516 [Zongheng Yang] Add simple prototype of S4 class RRDD. Make TextFile() returns an RRDD. 82aa17a [Zongheng Yang] Add textFile() 83ce63f [Zongheng Yang] Create a JavaSparkContext and save it in .sparkEnv using sparkR.init() 01cdf0e [Zongheng Yang] Add Makefile for SparkR fc9cae2 [Shivaram Venkataraman] Add skeleton R package
* [SPARK-4346][SPARK-3596][YARN] Commonize the monitor logicunknown2015-04-082-24/+18
| | | | | | | | | | | | | | | | | | | | 1. YarnClientSchedulerBack.asyncMonitorApplication use Client.monitorApplication so that commonize the monitor logic 2. Support changing the yarn client monitor interval, see #5292 3. More details see discussion on https://github.com/apache/spark/pull/3143 Author: unknown <l00251599@HGHY1L002515991.china.huawei.com> Author: Sephiroth-Lin <linwzhong@gmail.com> Closes #5305 from Sephiroth-Lin/SPARK-4346_3596 and squashes the following commits: 47c0014 [unknown] Edit conflicts 52b29fe [unknown] Interrupt thread when we call stop() d4298a1 [unknown] Unused, don't push aaacb42 [Sephiroth-Lin] don't wrap the entire block in the try ee2b2fd [Sephiroth-Lin] update 6483a2a [unknown] Catch exception 6b47ff7 [unknown] Update code 568f46f [unknown] YarnClientSchedulerBack.asyncMonitorApplication should be common with Client.monitorApplication
* [SPARK-3591][YARN]fire and forget for YARN cluster modeWangTaoTheTonic2015-04-071-33/+50
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-3591 The output after this patch: >doggie153:/opt/oss/spark-1.3.0-bin-hadoop2.4/bin # ./spark-submit --class org.apache.spark.examples.SparkPi --master yarn-cluster ../lib/spark-examples*.jar 15/03/31 21:15:25 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 15/03/31 21:15:25 INFO RMProxy: Connecting to ResourceManager at doggie153/10.177.112.153:8032 15/03/31 21:15:25 INFO Client: Requesting a new application from cluster with 4 NodeManagers 15/03/31 21:15:25 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (8192 MB per container) 15/03/31 21:15:25 INFO Client: Will allocate AM container, with 896 MB memory including 384 MB overhead 15/03/31 21:15:25 INFO Client: Setting up container launch context for our AM 15/03/31 21:15:25 INFO Client: Preparing resources for our AM container 15/03/31 21:15:26 INFO Client: Uploading resource file:/opt/oss/spark-1.3.0-bin-hadoop2.4/lib/spark-assembly-1.4.0-SNAPSHOT-hadoop2.4.1.jar -> hdfs://doggie153:9000/user/root/.sparkStaging/application_1427257505534_0016/spark-assembly-1.4.0-SNAPSHOT-hadoop2.4.1.jar 15/03/31 21:15:27 INFO Client: Uploading resource file:/opt/oss/spark-1.3.0-bin-hadoop2.4/lib/spark-examples-1.3.0-hadoop2.4.0.jar -> hdfs://doggie153:9000/user/root/.sparkStaging/application_1427257505534_0016/spark-examples-1.3.0-hadoop2.4.0.jar 15/03/31 21:15:28 INFO Client: Setting up the launch environment for our AM container 15/03/31 21:15:28 INFO SecurityManager: Changing view acls to: root 15/03/31 21:15:28 INFO SecurityManager: Changing modify acls to: root 15/03/31 21:15:28 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(root); users with modify permissions: Set(root) 15/03/31 21:15:28 INFO Client: Submitting application 16 to ResourceManager 15/03/31 21:15:28 INFO YarnClientImpl: Submitted application application_1427257505534_0016 15/03/31 21:15:28 INFO Client: ... waiting before polling ResourceManager for application state 15/03/31 21:15:33 INFO Client: ... polling ResourceManager for application state 15/03/31 21:15:33 INFO Client: Application report for application_1427257505534_0016 (state: RUNNING) 15/03/31 21:15:33 INFO Client: client token: N/A diagnostics: N/A ApplicationMaster host: doggie157 ApplicationMaster RPC port: 0 queue: default start time: 1427807728307 final status: UNDEFINED tracking URL: http://doggie153:8088/proxy/application_1427257505534_0016/ user: root /cc andrewor14 Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #5297 from WangTaoTheTonic/SPARK-3591 and squashes the following commits: c76d232 [WangTaoTheTonic] wrap lines 16c90a8 [WangTaoTheTonic] move up lines to avoid duplicate fea390d [WangTaoTheTonic] log failed/killed report, style and comment be1cc2e [WangTaoTheTonic] reword f0bc54f [WangTaoTheTonic] minor: expose appid in excepiton messages ba9b22b [WangTaoTheTonic] wrong config name e1a4013 [WangTaoTheTonic] revert to the old version and do some robust 19706c0 [WangTaoTheTonic] add a config to control whether to forget 0cbdce8 [WangTaoTheTonic] fire and forget for YARN cluster mode
* [SPARK-6602][Core] Replace direct use of Akka with Spark RPC interface - part 1zsxwing2015-04-042-49/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR replaced the following `Actor`s to `RpcEndpoint`: 1. HeartbeatReceiver 1. ExecutorActor 1. BlockManagerMasterActor 1. BlockManagerSlaveActor 1. CoarseGrainedExecutorBackend and subclasses 1. CoarseGrainedSchedulerBackend.DriverActor This is the first PR. I will split the work of SPARK-6602 to several PRs for code review. Author: zsxwing <zsxwing@gmail.com> Closes #5268 from zsxwing/rpc-rewrite and squashes the following commits: 287e9f8 [zsxwing] Fix the code style 26c56b7 [zsxwing] Merge branch 'master' into rpc-rewrite 9cc825a [zsxwing] Rmove setupThreadSafeEndpoint and add ThreadSafeRpcEndpoint 30a9036 [zsxwing] Make self return null after stopping RpcEndpointRef; fix docs and error messages 705245d [zsxwing] Fix some bugs after rebasing the changes on the master 003cf80 [zsxwing] Update CoarseGrainedExecutorBackend and CoarseGrainedSchedulerBackend to use RpcEndpoint 7d0e6dc [zsxwing] Update BlockManagerSlaveActor to use RpcEndpoint f5d6543 [zsxwing] Update BlockManagerMaster to use RpcEndpoint 30e3f9f [zsxwing] Update ExecutorActor to use RpcEndpoint 478b443 [zsxwing] Update HeartbeatReceiver to use RpcEndpoint
* [SPARK-6700] disable flaky testDavies Liu2015-04-031-1/+2
| | | | | | | | Author: Davies Liu <davies@databricks.com> Closes #5356 from davies/flaky and squashes the following commits: 08955f4 [Davies Liu] disable flaky test
* [SPARK-6428] Turn on explicit type checking for public methods.Reynold Xin2015-04-032-32/+36
| | | | | | | | | | | | | | This builds on my earlier pull requests and turns on the explicit type checking in scalastyle. Author: Reynold Xin <rxin@databricks.com> Closes #5342 from rxin/SPARK-6428 and squashes the following commits: 7b531ab [Reynold Xin] import ordering 2d9a8a5 [Reynold Xin] jl e668b1c [Reynold Xin] override 9b9e119 [Reynold Xin] Parenthesis. 82e0cf5 [Reynold Xin] [SPARK-6428] Turn on explicit type checking for public methods.
* [SPARK-6371] [build] Update version to 1.4.0-SNAPSHOT.Marcelo Vanzin2015-03-201-1/+1
| | | | | | | | | | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5056 from vanzin/SPARK-6371 and squashes the following commits: 63220df [Marcelo Vanzin] Merge branch 'master' into SPARK-6371 6506f75 [Marcelo Vanzin] Use more fine-grained exclusion. 178ba71 [Marcelo Vanzin] Oops. 75b2375 [Marcelo Vanzin] Exclude VertexRDD in MiMA. a45a62c [Marcelo Vanzin] Work around MIMA warning. 1d8a670 [Marcelo Vanzin] Re-group jetty exclusion. 0e8e909 [Marcelo Vanzin] Ignore ml, don't ignore graphx. cef4603 [Marcelo Vanzin] Indentation. 296cf82 [Marcelo Vanzin] [SPARK-6371] [build] Update version to 1.4.0-SNAPSHOT.
* SPARK-6338 [CORE] Use standard temp dir mechanisms in tests to avoid ↵Sean Owen2015-03-201-1/+1
| | | | | | | | | | | | | | | orphaned temp files Use `Utils.createTempDir()` to replace other temp file mechanisms used in some tests, to further ensure they are cleaned up, and simplify Author: Sean Owen <sowen@cloudera.com> Closes #5029 from srowen/SPARK-6338 and squashes the following commits: 27b740a [Sean Owen] Fix hive-thriftserver tests that don't expect an existing dir 4a212fa [Sean Owen] Standardize a bit more temp dir management 9004081 [Sean Owen] Revert some added recursive-delete calls 57609e4 [Sean Owen] Use Utils.createTempDir() to replace other temp file mechanisms used in some tests, to further ensure they are cleaned up, and simplify
* [SPARK-6325] [core,yarn] Do not change target executor count when killing ↵Marcelo Vanzin2015-03-183-6/+30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | executors. The dynamic execution code has two ways to reduce the number of executors: one where it reduces the total number of executors it wants, by asking for an absolute number of executors that is lower than the previous one. The second is by explicitly killing idle executors. YarnAllocator was mixing those up and lowering the target number of executors when a kill was issued. Instead, trust the frontend knows what it's doing, and kill executors without messing with other accounting. That means that if the frontend kills an executor without lowering the target, it will get a new executor shortly. The one situation where both actions (lower the target and kill executor) need to happen together is when user code explicitly calls `SparkContext.killExecutors`. In that case, issue two calls to the backend to achieve the goal. I also did some minor cleanup in related code: - avoid sending a request for executors when target is unchanged, to avoid log spam in the AM - avoid printing misleading log messages in the AM when there are no requests to cancel - fix a slow memory leak plus misleading error message on the driver caused by failing to completely unregister the executor. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5018 from vanzin/SPARK-6325 and squashes the following commits: 2e782a3 [Marcelo Vanzin] Avoid redundant logging on the AM side. a3567cd [Marcelo Vanzin] Add parentheses. a363926 [Marcelo Vanzin] Update logic. a158101 [Marcelo Vanzin] [SPARK-6325] [core,yarn] Disallow reducing executor count past running count.
* SPARK-6389 YARN app diagnostics report doesn't report NPEsSteve Loughran2015-03-181-3/+3
| | | | | | | | | | | | | Trivial patch to implicitly call `Exception.toString()` over `Exception.getMessage()` —this defaults to including the exception class & any non-null message; some subclasses include more. No test. Author: Steve Loughran <stevel@hortonworks.com> Closes #5070 from steveloughran/stevel/patches/SPARK-6389-NPE-reporting and squashes the following commits: 8239d85 [Steve Loughran] SPARK-6389 cull use of getMessage over toString in the container launcher 6fbaf6a [Steve Loughran] SPARK-6389 YARN app diagnostics report doesn't report NPEs
* SPARK-6182 [BUILD] spark-parent pom needs to be published for both 2.10 and 2.11Sean Owen2015-03-051-1/+1
| | | | | | | | | | Option 1 of 2: Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11 Author: Sean Owen <sowen@cloudera.com> Closes #4912 from srowen/SPARK-6182.1 and squashes the following commits: eff60de [Sean Owen] Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11
* SPARK-6085 Increase default value for memory overheadtedyu2015-03-041-2/+2
| | | | | | | | | Author: tedyu <yuzhihong@gmail.com> Closes #4836 from tedyu/master and squashes the following commits: d65b495 [tedyu] SPARK-6085 Increase default value for memory overhead 1fdd4df [tedyu] SPARK-6085 Increase default value for memory overhead
* [SPARK-6048] SparkConf should not translate deprecated configs on setAndrew Or2015-03-021-1/+2
| | | | | | | | | | | | | | | | | There are multiple issues with translating on set outlined in the JIRA. This PR reverts the translation logic added to `SparkConf`. In the future, after the 1.3.0 release we will figure out a way to reorganize the internal structure more elegantly. For now, let's preserve the existing semantics of `SparkConf` since it's a public interface. Unfortunately this means duplicating some code for now, but this is all internal and we can always clean it up later. Author: Andrew Or <andrew@databricks.com> Closes #4799 from andrewor14/conf-set-translate and squashes the following commits: 11c525b [Andrew Or] Move warning to driver 10e77b5 [Andrew Or] Add documentation for deprecation precedence a369cb1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into conf-set-translate c26a9e3 [Andrew Or] Revert all translate logic in SparkConf fef6c9c [Andrew Or] Restore deprecation logic for spark.executor.userClassPathFirst 94b4dfa [Andrew Or] Translate on get, not set
* [SPARK-6050] [yarn] Relax matching of vcore count in received containers.Marcelo Vanzin2015-03-021-2/+8
| | | | | | | | | | | | | | | Some YARN configurations return a vcore count for allocated containers that does not match the requested resource. That means Spark would always ignore those containers. So relax the the matching of the vcore count to allow the Spark jobs to run. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #4818 from vanzin/SPARK-6050 and squashes the following commits: 991c803 [Marcelo Vanzin] Remove config option, standardize on legacy behavior (no vcore matching). 8c9c346 [Marcelo Vanzin] Restrict lax matching to vcores only. 3359692 [Marcelo Vanzin] [SPARK-6050] [yarn] Add config option to do lax resource matching.
* [SPARK-6059][Yarn] Add volatile to ApplicationMaster's reporterThread and ↵zsxwing2015-02-271-2/+2
| | | | | | | | | | | | allocator `ApplicationMaster.reporterThread` and `ApplicationMaster.allocator` are accessed in multiple threads, so they should be marked as `volatile`. Author: zsxwing <zsxwing@gmail.com> Closes #4814 from zsxwing/SPARK-6059 and squashes the following commits: 17d9386 [zsxwing] Add volatile to ApplicationMaster's reporterThread and allocator
* [SPARK-6058][Yarn] Log the user class exception in ApplicationMasterzsxwing2015-02-271-2/+1
| | | | | | | | | | Because ApplicationMaster doesn't set SparkUncaughtExceptionHandler, the exception in the user class won't be logged. This PR added a `logError` for it. Author: zsxwing <zsxwing@gmail.com> Closes #4813 from zsxwing/SPARK-6058 and squashes the following commits: 806c932 [zsxwing] Log the user class exception
* [SPARK-5951][YARN] Remove unreachable driver memory properties in yarn ↵mohit.goyal2015-02-261-6/+0
| | | | | | | | | | | | client mode Remove unreachable driver memory properties in yarn client mode Author: mohit.goyal <mohit.goyal@guavus.com> Closes #4730 from zuxqoj/master and squashes the following commits: 977dc96 [mohit.goyal] remove not rechable deprecated variables in yarn client mode
* [SPARK-6018] [YARN] NoSuchMethodError in Spark app is swallowed by YARN AMCheolsoo Park2015-02-261-3/+3
| | | | | | | | | | Author: Cheolsoo Park <cheolsoop@netflix.com> Closes #4773 from piaozhexiu/SPARK-6018 and squashes the following commits: 2a919d5 [Cheolsoo Park] Rename e with cause to avoid duplicate names 1e71d2d [Cheolsoo Park] Replace placeholder with throwable eb5750d [Cheolsoo Park] NoSuchMethodError in Spark app is swallowed by YARN AM
* [SPARK-5937][YARN] Fix ClientSuite to set YARN mode, so that the correct ↵Hari Shreedharan2015-02-211-3/+10
| | | | | | | | | | | | | | | class is used in t... ...ests. Without this SparkHadoopUtil is used by the Client instead of YarnSparkHadoopUtil. Author: Hari Shreedharan <hshreedharan@apache.org> Closes #4711 from harishreedharan/SPARK-5937 and squashes the following commits: d154de6 [Hari Shreedharan] Use System.clearProperty() instead of setting the value of SPARK_YARN_MODE to empty string. f729f70 [Hari Shreedharan] Fix ClientSuite to set YARN mode, so that the correct class is used in tests.
* [SPARK-5759][Yarn]ExecutorRunnable should catch YarnException while NMClient ↵lianhuiwang2015-02-121-2/+8
| | | | | | | | | | | | | | | start contain... some time since some reasons, it lead to some exception while NMClient start some containers.example:we do not config spark_shuffle on some machines, so it will throw a exception: java.lang.Error: org.apache.hadoop.yarn.exceptions.InvalidAuxServiceException: The auxService:spark_shuffle does not exist. because YarnAllocator use ThreadPoolExecutor to start Container, so we can not find which container or hostname throw exception. I think we should catch YarnException in ExecutorRunnable when start container. if there are some exceptions, we can know the container id or hostname of failed container. Author: lianhuiwang <lianhuiwang09@gmail.com> Closes #4554 from lianhuiwang/SPARK-5759 and squashes the following commits: caf5a99 [lianhuiwang] use SparkException to warp exception c02140f [lianhuiwang] ExecutorRunnable should catch YarnException while NMClient start container
* [SPARK-2996] Implement userClassPathFirst for driver, yarn.Marcelo Vanzin2015-02-096-168/+301
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Yarn's config option `spark.yarn.user.classpath.first` does not work the same way as `spark.files.userClassPathFirst`; Yarn's version is a lot more dangerous, in that it modifies the system classpath, instead of restricting the changes to the user's class loader. So this change implements the behavior of the latter for Yarn, and deprecates the more dangerous choice. To be able to achieve feature-parity, I also implemented the option for drivers (the existing option only applies to executors). So now there are two options, each controlling whether to apply userClassPathFirst to the driver or executors. The old option was deprecated, and aliased to the new one (`spark.executor.userClassPathFirst`). The existing "child-first" class loader also had to be fixed. It didn't handle resources, and it was also doing some things that ended up causing JVM errors depending on how things were being called. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #3233 from vanzin/SPARK-2996 and squashes the following commits: 9cf9cf1 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 a1499e2 [Marcelo Vanzin] Remove SPARK_HOME propagation. fa7df88 [Marcelo Vanzin] Remove 'test.resource' file, create it dynamically. a8c69f1 [Marcelo Vanzin] Review feedback. cabf962 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 a1b8d7e [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 3f768e3 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 2ce3c7a [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 0e6d6be [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 70d4044 [Marcelo Vanzin] Fix pyspark/yarn-cluster test. 0fe7777 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 0e6ef19 [Marcelo Vanzin] Move class loaders around and make names more meaninful. fe970a7 [Marcelo Vanzin] Review feedback. 25d4fed [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 3cb6498 [Marcelo Vanzin] Call the right loadClass() method on the parent. fbb8ab5 [Marcelo Vanzin] Add locking in loadClass() to avoid deadlocks. 2e6c4b7 [Marcelo Vanzin] Mention new setting in documentation. b6497f9 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 a10f379 [Marcelo Vanzin] Some feedback. 3730151 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 f513871 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 44010b6 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 7b57cba [Marcelo Vanzin] Remove now outdated message. 5304d64 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 35949c8 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 54e1a98 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996 d1273b2 [Marcelo Vanzin] Add test file to rat exclude. fa1aafa [Marcelo Vanzin] Remove write check on user jars. 89d8072 [Marcelo Vanzin] Cleanups. a963ea3 [Marcelo Vanzin] Implement spark.driver.userClassPathFirst for standalone cluster mode. 50afa5f [Marcelo Vanzin] Fix Yarn executor command line. 7d14397 [Marcelo Vanzin] Register user jars in executor up front. 7f8603c [Marcelo Vanzin] Fix yarn-cluster mode without userClassPathFirst. 20373f5 [Marcelo Vanzin] Fix ClientBaseSuite. 55c88fa [Marcelo Vanzin] Run all Yarn integration tests via spark-submit. 0b64d92 [Marcelo Vanzin] Add deprecation warning to yarn option. 4a84d87 [Marcelo Vanzin] Fix the child-first class loader. d0394b8 [Marcelo Vanzin] Add "deprecated configs" to SparkConf. 46d8cf2 [Marcelo Vanzin] Update doc with new option, change name to "userClassPathFirst". a314f2d [Marcelo Vanzin] Enable driver class path isolation in SparkSubmit. 91f7e54 [Marcelo Vanzin] [yarn] Enable executor class path isolation. a853e74 [Marcelo Vanzin] Re-work CoarseGrainedExecutorBackend command line arguments. 89522ef [Marcelo Vanzin] Add class path isolation support for Yarn cluster mode.
* SPARK-4267 [YARN] Failing to launch jobs on Spark on YARN with Hadoop 2.5.0 ↵Sean Owen2015-02-093-14/+18
| | | | | | | | | | | | | | or later Before passing to YARN, escape arguments in "extraJavaOptions" args, in order to correctly handle cases like -Dfoo="one two three". Also standardize how these args are handled and ensure that individual args are treated as stand-alone args, not one string. vanzin andrewor14 Author: Sean Owen <sowen@cloudera.com> Closes #4452 from srowen/SPARK-4267.2 and squashes the following commits: c8297d2 [Sean Owen] Before passing to YARN, escape arguments in "extraJavaOptions" args, in order to correctly handle cases like -Dfoo="one two three". Also standardize how these args are handled and ensure that individual args are treated as stand-alone args, not one string.
* SPARK-5613: Catch the ApplicationNotFoundException exception to avoid thread ↵Kashish Jain2015-02-061-2/+9
| | | | | | | | | | | | | from getting killed on yarn restart. [SPARK-5613] Added a catch block to catch the ApplicationNotFoundException. Without this catch block the thread gets killed on occurrence of this exception. This Exception occurs when yarn restarts and tries to find an application id for a spark job which got interrupted due to yarn getting stopped. See the stacktrace in the bug for more details. Author: Kashish Jain <kashish.jain@guavus.com> Closes #4392 from kasjain/branch-1.2 and squashes the following commits: 4831000 [Kashish Jain] SPARK-5613: Catch the ApplicationNotFoundException exception to avoid thread from getting killed on yarn restart.
* SPARK-2450 Adds executor log links to Web UIKostas Sakellis2015-02-062-5/+38
| | | | | | | | | | | | | | | | | | | | | | | | Adds links to stderr/stdout in the executor tab of the webUI for: 1) Standalone 2) Yarn client 3) Yarn cluster This tries to add the log url support in a general way so as to make it easy to add support for all the cluster managers. This is done by using environment variables to pass to the executor the log urls. The SPARK_LOG_URL_ prefix is used and so additional logs besides stderr/stdout can also be added. To propagate this information to the UI we use the onExecutorAdded spark listener event. Although this commit doesn't add log urls when running on a mesos cluster, it should be possible to add using the same mechanism. Author: Kostas Sakellis <kostas@cloudera.com> Author: Josh Rosen <joshrosen@databricks.com> Closes #3486 from ksakellis/kostas-spark-2450 and squashes the following commits: d190936 [Josh Rosen] Fix a few minor style / formatting nits. Reset listener after each test Don't null listener out at end of main(). 8673fe1 [Kostas Sakellis] CR feedback. Hide the log column if there are no logs available 5bf6952 [Kostas Sakellis] [SPARK-2450] [CORE] Adds exeuctor log links to Web UI
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