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* [SPARK-2849] Handle driver configs separately in client modeAndrew Or2014-08-2010-56/+250
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | In client deploy mode, the driver is launched from within `SparkSubmit`'s JVM. This means by the time we parse Spark configs from `spark-defaults.conf`, it is already too late to control certain properties of the driver's JVM. We currently ignore these configs in client mode altogether. ``` spark.driver.memory spark.driver.extraJavaOptions spark.driver.extraClassPath spark.driver.extraLibraryPath ``` This PR handles these properties before launching the driver JVM. It achieves this by spawning a separate JVM that runs a new class called `SparkSubmitDriverBootstrapper`, which spawns `SparkSubmit` as a sub-process with the appropriate classpath, library paths, java opts and memory. Author: Andrew Or <andrewor14@gmail.com> Closes #1845 from andrewor14/handle-configs-bash and squashes the following commits: bed4bdf [Andrew Or] Change a few comments / messages (minor) 24dba60 [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash 08fd788 [Andrew Or] Warn against external usages of SparkSubmitDriverBootstrapper ff34728 [Andrew Or] Minor comments 51aeb01 [Andrew Or] Filter out JVM memory in Scala rather than Bash (minor) 9a778f6 [Andrew Or] Fix PySpark: actually kill driver on termination d0f20db [Andrew Or] Don't pass empty library paths, classpath, java opts etc. a78cb26 [Andrew Or] Revert a few changes in utils.sh (minor) 9ba37e2 [Andrew Or] Don't barf when the properties file does not exist 8867a09 [Andrew Or] A few more naming things (minor) 19464ad [Andrew Or] SPARK_SUBMIT_JAVA_OPTS -> SPARK_SUBMIT_OPTS d6488f9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash 1ea6bbe [Andrew Or] SparkClassLauncher -> SparkSubmitDriverBootstrapper a91ea19 [Andrew Or] Fix precedence of library paths, classpath, java opts and memory 158f813 [Andrew Or] Remove "client mode" boolean argument c84f5c8 [Andrew Or] Remove debug print statement (minor) b71f52b [Andrew Or] Revert a few more changes (minor) 7d94a8d [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash 3a8235d [Andrew Or] Only parse the properties file if special configs exist c37e08d [Andrew Or] Revert a few more changes a396eda [Andrew Or] Nullify my own hard work to simplify bash 0effa1e [Andrew Or] Add code in Scala that handles special configs c886568 [Andrew Or] Fix lines too long + a few comments / style (minor) 7a4190a [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash 7396be2 [Andrew Or] Explicitly comment that multi-line properties are not supported fa11ef8 [Andrew Or] Parse the properties file only if the special configs exist 371cac4 [Andrew Or] Add function prefix (minor) be99eb3 [Andrew Or] Fix tests to not include multi-line configs bd0d468 [Andrew Or] Simplify parsing config file by ignoring multi-line arguments 56ac247 [Andrew Or] Use eval and set to simplify splitting 8d4614c [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash aeb79c7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into handle-configs-bash 2732ac0 [Andrew Or] Integrate BASH tests into dev/run-tests + log error properly 8d26a5c [Andrew Or] Add tests for bash/utils.sh 4ae24c3 [Andrew Or] Fix bug: escape properly in quote_java_property b3c4cd5 [Andrew Or] Fix bug: count the number of quotes instead of detecting presence c2273fc [Andrew Or] Fix typo (minor) e793e5f [Andrew Or] Handle multi-line arguments 5d8f8c4 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-driver-extra c7b9926 [Andrew Or] Minor changes to spark-defaults.conf.template a992ae2 [Andrew Or] Escape spark.*.extraJavaOptions correctly aabfc7e [Andrew Or] escape -> split (minor) 45a1eb9 [Andrew Or] Fix bug: escape escaped backslashes and quotes properly... 1cdc6b1 [Andrew Or] Fix bug: escape escaped double quotes properly c854859 [Andrew Or] Add small comment c13a2cb [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-driver-extra 8e552b7 [Andrew Or] Include an example of spark.*.extraJavaOptions de765c9 [Andrew Or] Print spark-class command properly a4df3c4 [Andrew Or] Move parsing and escaping logic to utils.sh dec2343 [Andrew Or] Only export variables if they exist fa2136e [Andrew Or] Escape Java options + parse java properties files properly ef12f74 [Andrew Or] Minor formatting 4ec22a1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-driver-extra e5cfb46 [Andrew Or] Collapse duplicate code + fix potential whitespace issues 4edcaa8 [Andrew Or] Redirect stdout to stderr for python 130f295 [Andrew Or] Handle spark.driver.memory too 98dd8e3 [Andrew Or] Add warning if properties file does not exist 8843562 [Andrew Or] Fix compilation issues... 75ee6b4 [Andrew Or] Remove accidentally added file 63ed2e9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-driver-extra 0025474 [Andrew Or] Revert SparkSubmit handling of --driver-* options for only cluster mode a2ab1b0 [Andrew Or] Parse spark.driver.extra* in bash 250cb95 [Andrew Or] Do not ignore spark.driver.extra* for client mode
* [SPARK-3149] Connection establishment information is not enough.Kousuke Saruta2014-08-201-1/+1
| | | | | | | | Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2060 from sarutak/SPARK-3149 and squashes the following commits: 1cc89af [Kousuke Saruta] Modified log message of accepting connection
* [SPARK-3062] [SPARK-2970] [SQL] spark-sql script ends with IOException when ↵Kousuke Saruta2014-08-201-1/+14
| | | | | | | | | | | | | | | | | | EventLogging is enabled #1891 was to avoid IOException when EventLogging is enabled. The solution used ShutdownHookManager but it was defined only Hadoop 2.x. Hadoop 1.x don't have ShutdownHookManager so #1891 doesn't compile on Hadoop 1.x Now, I had a compromised solution for both Hadoop 1.x and 2.x. Only for FileLogger, an unique FileSystem object is created. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #1970 from sarutak/SPARK-2970 and squashes the following commits: 240c91e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2970 0e7b45d [Kousuke Saruta] Revert "[SPARK-2970] [SQL] spark-sql script ends with IOException when EventLogging is enabled" e1262ec [Kousuke Saruta] Modified Filelogger to use unique FileSystem instance
* [SPARK-3126][SPARK-3127][SQL] Fixed HiveThriftServer2SuiteCheng Lian2014-08-203-16/+6
| | | | | | | | | | | | | | | | This PR fixes two issues: 1. Fixes wrongly quoted command line option in `HiveThriftServer2Suite` that makes test cases hang until timeout. 1. Asks `dev/run-test` to run Spark SQL tests when `bin/spark-sql` and/or `sbin/start-thriftserver.sh` are modified. Author: Cheng Lian <lian.cs.zju@gmail.com> Closes #2036 from liancheng/fix-thriftserver-test and squashes the following commits: f38c4eb [Cheng Lian] Fixed the same quotation issue in CliSuite 26b82a0 [Cheng Lian] Run SQL tests when dff contains bin/spark-sql and/or sbin/start-thriftserver.sh a87f83d [Cheng Lian] Extended timeout e5aa31a [Cheng Lian] Fixed metastore JDBC URI quotation
* BUILD: Bump Hadoop versions in the release build.Patrick Wendell2014-08-202-9/+40
| | | | Also, minor modifications to the MapR profile.
* SPARK-3092 [SQL]: Always include the thriftserver when -Phive is enabled.Patrick Wendell2014-08-208-27/+12
| | | | | | | | | | | | | Currently we have a separate profile called hive-thriftserver. I originally suggested this in case users did not want to bundle the thriftserver, but it's ultimately lead to a lot of confusion. Since the thriftserver is only a few classes, I don't see a really good reason to isolate it from the rest of Hive. So let's go ahead and just include it in the same profile to simplify things. This has been suggested in the past by liancheng. Author: Patrick Wendell <pwendell@gmail.com> Closes #2006 from pwendell/hiveserver and squashes the following commits: 742ea40 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into hiveserver 034ad47 [Patrick Wendell] SPARK-3092: Always include the thriftserver when -Phive is enabled.
* [SPARK-3054][STREAMING] Add unit tests for Spark Sink.Hari Shreedharan2014-08-204-2/+212
| | | | | | | | | | | | | | | | | | | | | | | | This patch adds unit tests for Spark Sink. It also removes the private[flume] for Spark Sink, since the sink is instantiated from Flume configuration (looks like this is ignored by reflection which is used by Flume, but we should still remove it anyway). Author: Hari Shreedharan <hshreedharan@apache.org> Author: Hari Shreedharan <hshreedharan@cloudera.com> Closes #1958 from harishreedharan/spark-sink-test and squashes the following commits: e3110b9 [Hari Shreedharan] Add a sleep to allow sink to commit the transactions 120b81e [Hari Shreedharan] Fix complexity in threading model in test 4df5be6 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test c9190d1 [Hari Shreedharan] Indentation and spaces changes 7fedc5a [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test abc20cb [Hari Shreedharan] Minor test changes 7b9b649 [Hari Shreedharan] Merge branch 'master' into spark-sink-test f2c56c9 [Hari Shreedharan] Update SparkSinkSuite.scala a24aac8 [Hari Shreedharan] Remove unused var c86d615 [Hari Shreedharan] [SPARK-3054][STREAMING] Add unit tests for Spark Sink.
* [SPARK-3141] [PySpark] fix sortByKey() with take()Davies Liu2014-08-191-10/+8
| | | | | | | | | | | | Fix sortByKey() with take() The function `f` used in mapPartitions should always return an iterator. Author: Davies Liu <davies.liu@gmail.com> Closes #2045 from davies/fix_sortbykey and squashes the following commits: 1160f59 [Davies Liu] fix sortByKey() with take()
* [DOCS] Fixed wrong linksKen Takagiwa2014-08-191-2/+2
| | | | | | | | Author: Ken Takagiwa <ugw.gi.world@gmail.com> Closes #2042 from giwa/patch-1 and squashes the following commits: 216fe0e [Ken Takagiwa] Fixed wrong links
* [SPARK-2974] [SPARK-2975] Fix two bugs related to spark.local.dirsJosh Rosen2014-08-1914-118/+145
| | | | | | | | | | | | | | | | | | | | | | | | This PR fixes two bugs related to `spark.local.dirs` and `SPARK_LOCAL_DIRS`, one where `Utils.getLocalDir()` might return an invalid directory (SPARK-2974) and another where the `SPARK_LOCAL_DIRS` override didn't affect the driver, which could cause problems when running tasks in local mode (SPARK-2975). This patch fixes both issues: the new `Utils.getOrCreateLocalRootDirs(conf: SparkConf)` utility method manages the creation of local directories and handles the precedence among the different configuration options, so we should see the same behavior whether we're running in local mode or on a worker. It's kind of a pain to mock out environment variables in tests (no easy way to mock System.getenv), so I added a `private[spark]` method to SparkConf for accessing environment variables (by default, it just delegates to System.getenv). By subclassing SparkConf and overriding this method, we can mock out SPARK_LOCAL_DIRS in tests. I also fixed a typo in PySpark where we used `SPARK_LOCAL_DIR` instead of `SPARK_LOCAL_DIRS` (I think this was technically innocuous, but it seemed worth fixing). Author: Josh Rosen <joshrosen@apache.org> Closes #2002 from JoshRosen/local-dirs and squashes the following commits: efad8c6 [Josh Rosen] Address review comments: 1dec709 [Josh Rosen] Minor updates to Javadocs. 7f36999 [Josh Rosen] Use env vars to detect if running in YARN container. 399ac25 [Josh Rosen] Update getLocalDir() documentation. bb3ad89 [Josh Rosen] Remove duplicated YARN getLocalDirs() code. 3e92d44 [Josh Rosen] Move local dirs override logic into Utils; fix bugs: b2c4736 [Josh Rosen] Add failing tests for SPARK-2974 and SPARK-2975. 007298b [Josh Rosen] Allow environment variables to be mocked in tests. 6d9259b [Josh Rosen] Fix typo in PySpark: SPARK_LOCAL_DIR should be SPARK_LOCAL_DIRS
* [SPARK-3142][MLLIB] output shuffle data directly in Word2VecXiangrui Meng2014-08-191-11/+12
| | | | | | | | | | Sorry I didn't realize this in #2043. Ishiihara Author: Xiangrui Meng <meng@databricks.com> Closes #2049 from mengxr/more-w2v and squashes the following commits: 050b1c5 [Xiangrui Meng] output shuffle data directly
* [SPARK-3119] Re-implementation of TorrentBroadcast.Reynold Xin2014-08-193-240/+181
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is a re-implementation of TorrentBroadcast, with the following changes: 1. Removes most of the mutable, transient state from TorrentBroadcast (e.g. totalBytes, num of blocks fetched). 2. Removes TorrentInfo and TorrentBlock 3. Replaces the BlockManager.getSingle call in readObject with a getLocal, resuling in one less RPC call to the BlockManagerMasterActor to find the location of the block. 4. Removes the metadata block, resulting in one less block to fetch. 5. Removes an extra memory copy for deserialization (by using Java's SequenceInputStream). Basically for a regular broadcasted object with only one block, the number of RPC calls goes from 5+1 to 2+1). Old TorrentBroadcast for object of a single block: 1 RPC to ask for location of the broadcast variable 1 RPC to ask for location of the metadata block 1 RPC to fetch the metadata block 1 RPC to ask for location of the first data block 1 RPC to fetch the first data block 1 RPC to tell the driver we put the first data block in i.e. 5 + 1 New TorrentBroadcast for object of a single block: 1 RPC to ask for location of the first data block 1 RPC to get the first data block 1 RPC to tell the driver we put the first data block in i.e. 2 + 1 Author: Reynold Xin <rxin@apache.org> Closes #2030 from rxin/torrentBroadcast and squashes the following commits: 5bacb9d [Reynold Xin] Always add the object to driver's block manager. 0d8ed5b [Reynold Xin] Added getBytes to BlockManager and uses that in TorrentBroadcast. 2d6a5fb [Reynold Xin] Use putBytes/getRemoteBytes throughout. 3670f00 [Reynold Xin] Code review feedback. c1185cd [Reynold Xin] [SPARK-3119] Re-implementation of TorrentBroadcast.
* [HOTFIX][Streaming][MLlib] use temp folder for checkpointXiangrui Meng2014-08-192-12/+11
| | | | | | | | | | | | or Jenkins will complain about no Apache header in checkpoint files. tdas rxin Author: Xiangrui Meng <meng@databricks.com> Closes #2046 from mengxr/tmp-checkpoint and squashes the following commits: 0d3ec73 [Xiangrui Meng] remove ssc.stop 9797843 [Xiangrui Meng] change checkpointDir to lazy val 89964ab [Xiangrui Meng] use temp folder for checkpoint
* [SPARK-3130][MLLIB] detect negative values in naive BayesXiangrui Meng2014-08-193-6/+53
| | | | | | | | | | | because NB treats feature values as term frequencies. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #2038 from mengxr/nb-neg and squashes the following commits: 52c37c3 [Xiangrui Meng] address comments 65f892d [Xiangrui Meng] detect negative values in nb
* [SQL] add note of use synchronizedMap in SQLConfwangfei2014-08-191-0/+1
| | | | | | | | | | | | | | | | | | Refer to: http://stackoverflow.com/questions/510632/whats-the-difference-between-concurrenthashmap-and-collections-synchronizedmap Collections.synchronizedMap(map) creates a blocking Map which will degrade performance, albeit ensure consistency. So use ConcurrentHashMap(a more effective thread-safe hashmap) instead. also update HiveQuerySuite to fix test error when changed to ConcurrentHashMap. Author: wangfei <wangfei_hello@126.com> Author: scwf <wangfei1@huawei.com> Closes #1996 from scwf/sqlconf and squashes the following commits: 93bc0c5 [wangfei] revert change of HiveQuerySuite 0cc05dd [wangfei] add note for use synchronizedMap 3c224d31 [scwf] fix formate a7bcb98 [scwf] use ConcurrentHashMap in sql conf, intead synchronizedMap
* [SPARK-3112][MLLIB] Add documentation and example for StreamingLRfreeman2014-08-191-0/+75
| | | | | | | | | | | | | Added a documentation section on StreamingLR to the ``MLlib - Linear Methods``, including a worked example. mengxr tdas Author: freeman <the.freeman.lab@gmail.com> Closes #2047 from freeman-lab/streaming-lr-docs and squashes the following commits: 568d250 [freeman] Tweaks to wording / formatting 05a1139 [freeman] Added documentation and example for StreamingLR
* [MLLIB] minor update to word2vecXiangrui Meng2014-08-191-10/+8
| | | | | | | | | | | very minor update Ishiihara Author: Xiangrui Meng <meng@databricks.com> Closes #2043 from mengxr/minor-w2v and squashes the following commits: be649fd [Xiangrui Meng] remove map because we only need append eccefcc [Xiangrui Meng] minor updates to word2vec
* [SPARK-2468] Netty based block server / client moduleReynold Xin2014-08-1929-664/+1484
| | | | | | | | | | | | | | | Previous pull request (#1907) was reverted. This brings it back. Still looking into the hang. Author: Reynold Xin <rxin@apache.org> Closes #1971 from rxin/netty1 and squashes the following commits: b0be96f [Reynold Xin] Added test to make sure outstandingRequests are cleaned after firing the events. 4c6d0ee [Reynold Xin] Pass callbacks cleanly. 603dce7 [Reynold Xin] Upgrade Netty to 4.0.23 to fix the DefaultFileRegion bug. 88be1d4 [Reynold Xin] Downgrade to 4.0.21 to work around a bug in writing DefaultFileRegion. 002626a [Reynold Xin] Remove netty-test-file.txt. db6e6e0 [Reynold Xin] Revert "Revert "[SPARK-2468] Netty based block server / client module""
* [SPARK-3136][MLLIB] Create Java-friendly methods in RandomRDDsXiangrui Meng2014-08-196-306/+418
| | | | | | | | | | | | | Though we don't use default argument for methods in RandomRDDs, it is still not easy for Java users to use because the output type is either `RDD[Double]` or `RDD[Vector]`. Java users should expect `JavaDoubleRDD` and `JavaRDD[Vector]`, respectively. We should create dedicated methods for Java users, and allow default arguments in Scala methods in RandomRDDs, to make life easier for both Java and Scala users. This PR also contains documentation for random data generation. brkyvz Author: Xiangrui Meng <meng@databricks.com> Closes #2041 from mengxr/stat-doc and squashes the following commits: fc5eedf [Xiangrui Meng] add missing comma ffde810 [Xiangrui Meng] address comments aef6d07 [Xiangrui Meng] add doc for random data generation b99d94b [Xiangrui Meng] add java-friendly methods to RandomRDDs
* [SPARK-2790] [PySpark] fix zip with serializers which have different batch ↵Davies Liu2014-08-193-1/+54
| | | | | | | | | | | | | | | sizes. If two RDDs have different batch size in serializers, then it will try to re-serialize the one with smaller batch size, then call RDD.zip() in Spark. Author: Davies Liu <davies.liu@gmail.com> Closes #1894 from davies/zip and squashes the following commits: c4652ea [Davies Liu] add more test cases 6d05fc8 [Davies Liu] Merge branch 'master' into zip 813b1e4 [Davies Liu] add more tests for failed cases a4aafda [Davies Liu] fix zip with serializers which have different batch sizes.
* Move a bracket in validateSettings of SparkConfhzw199004162014-08-191-1/+1
| | | | | | | | | | Move a bracket in validateSettings of SparkConf Author: hzw19900416 <carlmartinmax@gmail.com> Closes #2012 from hzw19900416/codereading and squashes the following commits: e717fb6 [hzw19900416] Move a bracket in validateSettings of SparkConf
* SPARK-2333 - spark_ec2 script should allow option for existing security groupVida Ha2014-08-192-28/+57
| | | | | | | | | | | | | - Uses the name tag to identify machines in a cluster. - Allows overriding the security group name so it doesn't need to coincide with the cluster name. - Outputs the request id's of up to 10 pending spot instance requests. Author: Vida Ha <vida@databricks.com> Closes #1899 from vidaha/vida/ec2-reuse-security-group and squashes the following commits: c80d5c3 [Vida Ha] wrap retries in a try catch block b2989d5 [Vida Ha] SPARK-2333: spark_ec2 script should allow option for existing security group
* [SPARK-3128][MLLIB] Use streaming test suite for StreamingLRfreeman2014-08-193-55/+77
| | | | | | | | | | | | | | | | | | | Refactored tests for streaming linear regression to use existing streaming test utilities. Summary of changes: - Made ``mllib`` depend on tests from ``streaming`` - Rewrote accuracy and convergence tests to use ``setupStreams`` and ``runStreams`` - Added new test for the accuracy of predictions generated by ``predictOnValue`` These tests should run faster, be easier to extend/maintain, and provide a reference for new tests. mengxr tdas Author: freeman <the.freeman.lab@gmail.com> Closes #2037 from freeman-lab/streamingLR-predict-tests and squashes the following commits: e851ca7 [freeman] Fixed long lines 50eb0bf [freeman] Refactored tests to use streaming test tools 32c43c2 [freeman] Added test for prediction
* [SPARK-3089] Fix meaningless error message in ConnectionManagerKousuke Saruta2014-08-191-1/+1
| | | | | | | | | Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2000 from sarutak/SPARK-3089 and squashes the following commits: 02dfdea [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3089 e759ce7 [Kousuke Saruta] Improved error message when closing SendingConnection
* [SPARK-3072] YARN - Exit when reach max number failed executorsThomas Graves2014-08-194-19/+40
| | | | | | | | | | In some cases on hadoop 2.x the spark application master doesn't properly exit and hangs around for 10 minutes after its really done. We should make sure it exits properly and stops the driver. Author: Thomas Graves <tgraves@apache.org> Closes #2022 from tgravescs/SPARK-3072 and squashes the following commits: 665701d [Thomas Graves] Exit when reach max number failed executors
* Fix typo in decision tree docsMatt Forbes2014-08-181-2/+2
| | | | | | | | | | Candidate splits were inconsistent with the example. Author: Matt Forbes <matt@tellapart.com> Closes #1837 from emef/tree-doc and squashes the following commits: 3be14a1 [Matt Forbes] Fix typo in decision tree docs
* [SPARK-3116] Remove the excessive lockings in TorrentBroadcastReynold Xin2014-08-181-39/+27
| | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #2028 from rxin/torrentBroadcast and squashes the following commits: 92c62a5 [Reynold Xin] Revert the MEMORY_AND_DISK_SER changes. 03a5221 [Reynold Xin] [SPARK-3116] Remove the excessive lockings in TorrentBroadcast
* [SPARK-3114] [PySpark] Fix Python UDFs in Spark SQL.Josh Rosen2014-08-184-9/+16
| | | | | | | | | | | | | | | | This fixes SPARK-3114, an issue where we inadvertently broke Python UDFs in Spark SQL. This PR modifiers the test runner script to always run the PySpark SQL tests, irrespective of whether SparkSQL itself has been modified. It also includes Davies' fix for the bug. Closes #2026. Author: Josh Rosen <joshrosen@apache.org> Author: Davies Liu <davies.liu@gmail.com> Closes #2027 from JoshRosen/pyspark-sql-fix and squashes the following commits: 9af2708 [Davies Liu] bugfix: disable compression of command 0d8d3a4 [Josh Rosen] Always run Python Spark SQL tests.
* [SPARK-3108][MLLIB] add predictOnValues to StreamingLR and fix predictOnXiangrui Meng2014-08-182-8/+27
| | | | | | | | | | | | It is useful in streaming to allow users to carry extra data with the prediction, for monitoring the prediction error for example. freeman-lab Author: Xiangrui Meng <meng@databricks.com> Closes #2023 from mengxr/predict-on-values and squashes the following commits: cac47b8 [Xiangrui Meng] add classtag 2821b3b [Xiangrui Meng] use mapValues 0925efa [Xiangrui Meng] add predictOnValues to StreamingLR and fix predictOn
* [SPARK-2850] [SPARK-2626] [mllib] MLlib stats examples + small fixesJoseph K. Bradley2014-08-1829-20/+664
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API) Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey Added sc.stop() to all examples. CorrelationSuite.scala * Added 1 test for RDDs with only 1 value RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message. Python SparseVector (pyspark/mllib/linalg.py) * Added toDense() function python/run-tests script * Added stat.py (doc test) CC: mengxr dorx Main changes were examples to show usage across APIs. Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1878 from jkbradley/mllib-stats-api-check and squashes the following commits: ea5c047 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check dafebe2 [Joseph K. Bradley] Bug fixes for examples SampledRDDs.scala and sampled_rdds.py: Check for division by 0 and for missing key in maps. 8d1e555 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 60c72d9 [Joseph K. Bradley] Fixed stat.py doc test to work for Python versions printing nan or NaN. b20d90a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 4e5d15e [Joseph K. Bradley] Changed pyspark/mllib/stat.py doc tests to use NaN instead of nan. 32173b7 [Joseph K. Bradley] Stats examples update. c8c20dc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check cf70b07 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 0b7cec3 [Joseph K. Bradley] Small updates based on code review. Renamed statistical_summary.py to correlations.py ab48f6e [Joseph K. Bradley] RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message. 65e4ebc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check 8195c78 [Joseph K. Bradley] Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey 064985b [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check ee918e9 [Joseph K. Bradley] Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)
* [mllib] DecisionTree: treeAggregate + Python example bug fixJoseph K. Bradley2014-08-184-8/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Small DecisionTree updates: * Changed main DecisionTree aggregate to treeAggregate. * Fixed bug in python example decision_tree_runner.py with missing argument (since categoricalFeaturesInfo is no longer an optional argument for trainClassifier). * Fixed same bug in python doc tests, and added tree.py to doc tests. CC: mengxr Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #2015 from jkbradley/dt-opt2 and squashes the following commits: b5114fa [Joseph K. Bradley] Fixed python tree.py doc test (extra newline) 8e4665d [Joseph K. Bradley] Added tree.py to python doc tests. Fixed bug from missing categoricalFeaturesInfo argument. b7b2922 [Joseph K. Bradley] Fixed bug in python example decision_tree_runner.py with missing argument. Changed main DecisionTree aggregate to treeAggregate. 85bbc1f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 66d076f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 a0ed0da [Joseph K. Bradley] Renamed DTMetadata to DecisionTreeMetadata. Small doc updates. 3726d20 [Joseph K. Bradley] Small code improvements based on code review. ac0b9f8 [Joseph K. Bradley] Small updates based on code review. Main change: Now using << instead of math.pow. db0d773 [Joseph K. Bradley] scala style fix 6a38f48 [Joseph K. Bradley] Added DTMetadata class for cleaner code 931a3a7 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt2 797f68a [Joseph K. Bradley] Fixed DecisionTreeSuite bug for training second level. Needed to update treePointToNodeIndex with groupShift. f40381c [Joseph K. Bradley] Merge branch 'dt-opt1' into dt-opt2 5f2dec2 [Joseph K. Bradley] Fixed scalastyle issue in TreePoint 6b5651e [Joseph K. Bradley] Updates based on code review. 1 major change: persisting to memory + disk, not just memory. 2d2aaaf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt1 26d10dd [Joseph K. Bradley] Removed tree/model/Filter.scala since no longer used. Removed debugging println calls in DecisionTree.scala. 356daba [Joseph K. Bradley] Merge branch 'dt-opt1' into dt-opt2 430d782 [Joseph K. Bradley] Added more debug info on binning error. Added some docs. d036089 [Joseph K. Bradley] Print timing info to logDebug. e66f1b1 [Joseph K. Bradley] TreePoint * Updated doc * Made some methods private 8464a6e [Joseph K. Bradley] Moved TimeTracker to tree/impl/ in its own file, and cleaned it up. Removed debugging println calls from DecisionTree. Made TreePoint extend Serialiable a87e08f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt1 c1565a5 [Joseph K. Bradley] Small DecisionTree updates: * Simplification: Updated calculateGainForSplit to take aggregates for a single (feature, split) pair. * Internal doc: findAggForOrderedFeatureClassification b914f3b [Joseph K. Bradley] DecisionTree optimization: eliminated filters + small changes b2ed1f3 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt 0f676e2 [Joseph K. Bradley] Optimizations + Bug fix for DecisionTree 3211f02 [Joseph K. Bradley] Optimizing DecisionTree * Added TreePoint representation to avoid calling findBin multiple times. * (not working yet, but debugging) f61e9d2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing bcf874a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing 511ec85 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing a95bc22 [Joseph K. Bradley] timing for DecisionTree internals
* [SPARK-2718] [yarn] Handle quotes and other characters in user args.Marcelo Vanzin2014-08-186-10/+101
| | | | | | | | | | | | | | | | | | | | Due to the way Yarn runs things through bash, normal quoting doesn't work as expected. This change applies the necessary voodoo to the user args to avoid issues with bash and special characters. The change also uncovered an issue with the event logger app name sanitizing code; it wasn't cleaning up all "bad" characters, so sometimes it would fail to create the log dirs. I just added some more bad character replacements. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #1724 from vanzin/SPARK-2718 and squashes the following commits: cc84b89 [Marcelo Vanzin] Review feedback. c1a257a [Marcelo Vanzin] Add test for backslashes. 55571d4 [Marcelo Vanzin] Unbreak yarn-client. 515613d [Marcelo Vanzin] [SPARK-2718] [yarn] Handle quotes and other characters in user args.
* [SPARK-3103] [PySpark] fix saveAsTextFile() with utf-8Davies Liu2014-08-182-1/+12
| | | | | | | | | | bugfix: It will raise an exception when it try to encode non-ASCII strings into unicode. It should only encode unicode as "utf-8". Author: Davies Liu <davies.liu@gmail.com> Closes #2018 from davies/fix_utf8 and squashes the following commits: 4db7967 [Davies Liu] fix saveAsTextFile() with utf-8
* Removed .travis.yml file since we are not using Travis.Reynold Xin2014-08-181-32/+0
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* [SPARK-2169] Don't copy appName / basePath everywhere.Marcelo Vanzin2014-08-1819-71/+51
| | | | | | | | | | | | | Instead of keeping copies in all pages, just reference the values kept in the base SparkUI instance (by making them available via getters). Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #1252 from vanzin/SPARK-2169 and squashes the following commits: 4412fc6 [Marcelo Vanzin] Simplify UIUtils.headerSparkPage signature. 4e5d35a [Marcelo Vanzin] [SPARK-2169] Don't copy appName / basePath everywhere.
* [SPARK-2406][SQL] Initial support for using ParquetTableScan to read ↵Michael Armbrust2014-08-188-23/+427
| | | | | | | | | | | | | | | | | | | | | | | | HiveMetaStore tables. This PR adds an experimental flag `spark.sql.hive.convertMetastoreParquet` that when true causes the planner to detects tables that use Hive's Parquet SerDe and instead plans them using Spark SQL's native `ParquetTableScan`. Author: Michael Armbrust <michael@databricks.com> Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1819 from marmbrus/parquetMetastore and squashes the following commits: 1620079 [Michael Armbrust] Revert "remove hive parquet bundle" cc30430 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into parquetMetastore 4f3d54f [Michael Armbrust] fix style 41ebc5f [Michael Armbrust] remove hive parquet bundle a43e0da [Michael Armbrust] Merge remote-tracking branch 'origin/master' into parquetMetastore 4c4dc19 [Michael Armbrust] Fix bug with tree splicing. ebb267e [Michael Armbrust] include parquet hive to tests pass (Remove this later). c0d9b72 [Michael Armbrust] Avoid creating a HadoopRDD per partition. Add dirty hacks to retrieve partition values from the InputSplit. 8cdc93c [Michael Armbrust] Merge pull request #8 from yhuai/parquetMetastore a0baec7 [Yin Huai] Partitioning columns can be resolved. 1161338 [Michael Armbrust] Add a test to make sure conversion is actually happening 212d5cd [Michael Armbrust] Initial support for using ParquetTableScan to read HiveMetaStore tables.
* [SPARK-3091] [SQL] Add support for caching metadata on Parquet filesMatei Zaharia2014-08-182-13/+72
| | | | | | | | | | | | | | | | | For larger Parquet files, reading the file footers (which is done in parallel on up to 5 threads) and HDFS block locations (which is serial) can take multiple seconds. We can add an option to cache this data within FilteringParquetInputFormat. Unfortunately ParquetInputFormat only caches footers within each instance of ParquetInputFormat, not across them. Note: this PR leaves this turned off by default for 1.1, but I believe it's safe to turn it on after. The keys in the hash maps are FileStatus objects that include a modification time, so this will work fine if files are modified. The location cache could become invalid if files have moved within HDFS, but that's rare so I just made it invalidate entries every 15 minutes. Author: Matei Zaharia <matei@databricks.com> Closes #2005 from mateiz/parquet-cache and squashes the following commits: dae8efe [Matei Zaharia] Bug fix c71e9ed [Matei Zaharia] Handle empty statuses directly 22072b0 [Matei Zaharia] Use Guava caches and add a config option for caching metadata 8fb56ce [Matei Zaharia] Cache file block locations too 453bd21 [Matei Zaharia] Bug fix 4094df6 [Matei Zaharia] First attempt at caching Parquet footers
* SPARK-3025 [SQL]: Allow JDBC clients to set a fair scheduler poolPatrick Wendell2014-08-183-7/+28
| | | | | | | | | | | This definitely needs review as I am not familiar with this part of Spark. I tested this locally and it did seem to work. Author: Patrick Wendell <pwendell@gmail.com> Closes #1937 from pwendell/scheduler and squashes the following commits: b858e33 [Patrick Wendell] SPARK-3025: Allow JDBC clients to set a fair scheduler pool
* [SPARK-3085] [SQL] Use compact data structures in SQL joinsMatei Zaharia2014-08-181-34/+33
| | | | | | | | | | | | | | | This reuses the CompactBuffer from Spark Core to save memory and pointer dereferences. I also tried AppendOnlyMap instead of java.util.HashMap but unfortunately that slows things down because it seems to do more equals() calls and the equals on GenericRow, and especially JoinedRow, is pretty expensive. Author: Matei Zaharia <matei@databricks.com> Closes #1993 from mateiz/spark-3085 and squashes the following commits: 188221e [Matei Zaharia] Remove unneeded import 5f903ee [Matei Zaharia] [SPARK-3085] [SQL] Use compact data structures in SQL joins
* [SPARK-3084] [SQL] Collect broadcasted tables in parallel in joinsMatei Zaharia2014-08-181-1/+1
| | | | | | | | | | | | | | | BroadcastHashJoin has a broadcastFuture variable that tries to collect the broadcasted table in a separate thread, but this doesn't help because it's a lazy val that only gets initialized when you attempt to build the RDD. Thus queries that broadcast multiple tables would collect and broadcast them sequentially. I changed this to a val to let it start collecting right when the operator is created. Author: Matei Zaharia <matei@databricks.com> Closes #1990 from mateiz/spark-3084 and squashes the following commits: f468766 [Matei Zaharia] [SPARK-3084] Collect broadcasted tables in parallel in joins
* SPARK-3096: Include parquet hive serde by default in buildPatrick Wendell2014-08-181-0/+5
| | | | | | | | | | A small change - we should just add this dependency. It doesn't have any recursive deps and it's needed for reading have parquet tables. Author: Patrick Wendell <pwendell@gmail.com> Closes #2009 from pwendell/parquet and squashes the following commits: e411f9f [Patrick Wendell] SPARk-309: Include parquet hive serde by default in build
* [SPARK-2862] histogram method fails on some choices of bucketCountChandan Kumar2014-08-182-4/+34
| | | | | | | | | | Author: Chandan Kumar <chandan.kumar@imaginea.com> Closes #1787 from nrchandan/spark-2862 and squashes the following commits: a76bbf6 [Chandan Kumar] [SPARK-2862] Fix for a broken test case and add new test cases 4211eea [Chandan Kumar] [SPARK-2862] Add Scala bug id 13854f1 [Chandan Kumar] [SPARK-2862] Use shorthand range notation to avoid Scala bug
* SPARK-3093 : masterLock in Worker is no longer needCrazyJvm2014-08-181-27/+14
| | | | | | | | | | | there's no need to use masterLock in Worker now since all communications are within Akka actor Author: CrazyJvm <crazyjvm@gmail.com> Closes #2008 from CrazyJvm/no-need-master-lock and squashes the following commits: dd39e20 [CrazyJvm] fix format 58e7fa5 [CrazyJvm] there's no need to use masterLock now since all communications are within Akka actor
* [MLlib] Remove transform(dataset: RDD[String]) from Word2Vec public APILiquan Pei2014-08-181-9/+0
| | | | | | | | | | | mengxr Remove transform(dataset: RDD[String]) from public API. Author: Liquan Pei <liquanpei@gmail.com> Closes #2010 from Ishiihara/Word2Vec-api and squashes the following commits: 17b1031 [Liquan Pei] remove transform(dataset: RDD[String]) from public API
* [SPARK-2842][MLlib]Word2Vec documentationLiquan Pei2014-08-171-1/+62
| | | | | | | | | | | | | mengxr Documentation for Word2Vec Author: Liquan Pei <liquanpei@gmail.com> Closes #2003 from Ishiihara/Word2Vec-doc and squashes the following commits: 4ff11d4 [Liquan Pei] minor fix 8d7458f [Liquan Pei] code reformat 6df0dcb [Liquan Pei] add Word2Vec documentation
* [SPARK-3097][MLlib] Word2Vec performance improvementLiquan Pei2014-08-171-15/+35
| | | | | | | | | | | | | | | | mengxr Please review the code. Adding weights in reduceByKey soon. Only output model entry for words appeared in the partition before merging and use reduceByKey to combine model. In general, this implementation is 30s or so faster than implementation using big array. Author: Liquan Pei <liquanpei@gmail.com> Closes #1932 from Ishiihara/Word2Vec-improve2 and squashes the following commits: d5377a9 [Liquan Pei] use syn0Global and syn1Global to represent model cad2011 [Liquan Pei] bug fix for synModify array out of bound 083aa66 [Liquan Pei] update synGlobal in place and reduce synOut size 9075e1c [Liquan Pei] combine syn0Global and syn1Global to synGlobal aa2ab36 [Liquan Pei] use reduceByKey to combine models
* SPARK-2900. aggregate inputBytes per stageSandy Ryza2014-08-172-1/+14
| | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #1826 from sryza/sandy-spark-2900 and squashes the following commits: 43f9091 [Sandy Ryza] SPARK-2900
* SPARK-2884: Create binary builds in parallel with release script.Patrick Wendell2014-08-171-4/+5
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* [SPARK-3087][MLLIB] fix col indexing bug in chi-square and add a check for ↵Xiangrui Meng2014-08-173-17/+59
| | | | | | | | | | | | number of distinct values There is a bug determining the column index. dorx Author: Xiangrui Meng <meng@databricks.com> Closes #1997 from mengxr/chisq-index and squashes the following commits: 8fc2ab2 [Xiangrui Meng] fix col indexing bug and add a check for number of distinct values
* [HOTFIX][STREAMING] Allow the JVM/Netty to decide which port to bind to in ↵Hari Shreedharan2014-08-172-29/+34
| | | | | | | | | | | | | | | | | | Flume Polling Tests. Author: Hari Shreedharan <harishreedharan@gmail.com> Closes #1820 from harishreedharan/use-free-ports and squashes the following commits: b939067 [Hari Shreedharan] Remove unused import. 67856a8 [Hari Shreedharan] Remove findFreePort. 0ea51d1 [Hari Shreedharan] Make some changes to getPort to use map on the serverOpt. 1fb0283 [Hari Shreedharan] Merge branch 'master' of https://github.com/apache/spark into use-free-ports b351651 [Hari Shreedharan] Allow Netty to choose port, and query it to decide the port to bind to. Leaving findFreePort as is, if other tests want to use it at some point. e6c9620 [Hari Shreedharan] Making sure the second sink uses the correct port. 11c340d [Hari Shreedharan] Add info about race condition to scaladoc. e89d135 [Hari Shreedharan] Adding Scaladoc. 6013bb0 [Hari Shreedharan] [STREAMING] Find free ports to use before attempting to create Flume Sink in Flume Polling Suite
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