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* [MLLIB] SPARK-5912 Programming guide for feature selectionAlexander Ulanov2015-02-231-0/+54
| | | | | | | | | | | | | | Added description of ChiSqSelector and few words about feature selection in general. I could add a code example, however it would not look reasonable in the absence of feature discretizer or a dataset in the `data` folder that has redundant features. Author: Alexander Ulanov <nashb@yandex.ru> Closes #4709 from avulanov/SPARK-5912 and squashes the following commits: 19a8a4e [Alexander Ulanov] Addressing reviewers comments @jkbradley 58d9e4d [Alexander Ulanov] Addressing reviewers comments @jkbradley eb6b9fe [Alexander Ulanov] Typo 2921a1d [Alexander Ulanov] ChiSqSelector example of use c845350 [Alexander Ulanov] ChiSqSelector docs
* [SPARK-5939][MLLib] make FPGrowth example app take parametersJacky Li2015-02-233-27/+81
| | | | | | | | | | | | | Add parameter parsing in FPGrowth example app in Scala and Java And a sample data file is added in data/mllib folder Author: Jacky Li <jacky.likun@huawei.com> Closes #4714 from jackylk/parameter and squashes the following commits: 8c478b3 [Jacky Li] fix according to comments 3bb74f6 [Jacky Li] make FPGrowth exampl app take parameters f0e4d10 [Jacky Li] make FPGrowth exampl app take parameters
* [SPARK-5724] fix the misconfiguration in AkkaUtilsCodingCat2015-02-232-27/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-5724 In AkkaUtil, we set several failure detector related the parameters as following ``` al akkaConf = ConfigFactory.parseMap(conf.getAkkaConf.toMap[String, String]) .withFallback(akkaSslConfig).withFallback(ConfigFactory.parseString( s""" |akka.daemonic = on |akka.loggers = [""akka.event.slf4j.Slf4jLogger""] |akka.stdout-loglevel = "ERROR" |akka.jvm-exit-on-fatal-error = off |akka.remote.require-cookie = "$requireCookie" |akka.remote.secure-cookie = "$secureCookie" |akka.remote.transport-failure-detector.heartbeat-interval = $akkaHeartBeatInterval s |akka.remote.transport-failure-detector.acceptable-heartbeat-pause = $akkaHeartBeatPauses s |akka.remote.transport-failure-detector.threshold = $akkaFailureDetector |akka.actor.provider = "akka.remote.RemoteActorRefProvider" |akka.remote.netty.tcp.transport-class = "akka.remote.transport.netty.NettyTransport" |akka.remote.netty.tcp.hostname = "$host" |akka.remote.netty.tcp.port = $port |akka.remote.netty.tcp.tcp-nodelay = on |akka.remote.netty.tcp.connection-timeout = $akkaTimeout s |akka.remote.netty.tcp.maximum-frame-size = ${akkaFrameSize}B |akka.remote.netty.tcp.execution-pool-size = $akkaThreads |akka.actor.default-dispatcher.throughput = $akkaBatchSize |akka.log-config-on-start = $logAkkaConfig |akka.remote.log-remote-lifecycle-events = $lifecycleEvents |akka.log-dead-letters = $lifecycleEvents |akka.log-dead-letters-during-shutdown = $lifecycleEvents """.stripMargin)) ``` Actually, we do not have any parameter naming "akka.remote.transport-failure-detector.threshold" see: http://doc.akka.io/docs/akka/2.3.4/general/configuration.html what we have is "akka.remote.watch-failure-detector.threshold" Author: CodingCat <zhunansjtu@gmail.com> Closes #4512 from CodingCat/SPARK-5724 and squashes the following commits: bafe56e [CodingCat] fix the grammar in configuration doc 338296e [CodingCat] remove failure-detector related info 8bfcfd4 [CodingCat] fix the misconfiguration in AkkaUtils
* [SPARK-5943][Streaming] Update the test to use new API to reduce the warningSaisai Shao2015-02-233-7/+7
| | | | | | | | Author: Saisai Shao <saisai.shao@intel.com> Closes #4722 from jerryshao/SPARK-5943 and squashes the following commits: 1b01233 [Saisai Shao] Update the test to use new API to reduce the warning
* [EXAMPLES] fix typo.Makoto Fukuhara2015-02-231-1/+1
| | | | | | | | Author: Makoto Fukuhara <fukuo33@gmail.com> Closes #4724 from fukuo33/fix-typo and squashes the following commits: 8c806b9 [Makoto Fukuhara] fix typo.
* [SPARK-3885] Provide mechanism to remove accumulators once they are no ↵Ilya Ganelin2015-02-227-17/+107
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | longer used Instead of storing a strong reference to accumulators, I've replaced this with a weak reference and updated any code that uses these accumulators to check whether the reference resolves before using the accumulator. A weak reference will be cleared when there is no longer an existing copy of the variable versus using a soft reference in which case accumulators would only be cleared when the GC explicitly ran out of memory. Author: Ilya Ganelin <ilya.ganelin@capitalone.com> Closes #4021 from ilganeli/SPARK-3885 and squashes the following commits: 4ba9575 [Ilya Ganelin] Fixed error in test suite 8510943 [Ilya Ganelin] Extra code bb76ef0 [Ilya Ganelin] File deleted somehow 283a333 [Ilya Ganelin] Added cleanup method for accumulators to remove stale references within Accumulators.original to accumulators that are now out of scope 345fd4f [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885 7485a82 [Ilya Ganelin] Fixed build error c8e0f2b [Ilya Ganelin] Added working test for accumulator garbage collection 94ce754 [Ilya Ganelin] Still not being properly garbage collected 8722b63 [Ilya Ganelin] Fixing gc test 7414a9c [Ilya Ganelin] Added test for accumulator garbage collection 18d62ec [Ilya Ganelin] Updated to throw Exception when accessing a GCd accumulator 9a81928 [Ilya Ganelin] Reverting permissions changes 28f705c [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885 b820ab4b [Ilya Ganelin] reset d78f4bf [Ilya Ganelin] Removed obsolete comment 0746e61 [Ilya Ganelin] Updated DAGSchedulerSUite to fix bug 3350852 [Ilya Ganelin] Updated DAGScheduler and Suite to correctly use new implementation of WeakRef Accumulator storage c49066a [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885 cbb9023 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885 a77d11b [Ilya Ganelin] Updated Accumulators class to store weak references instead of strong references to allow garbage collection of old accumulators
* [SPARK-911] allow efficient queries for a range if RDD is partitioned wi...Aaron Josephs2015-02-222-0/+51
| | | | | | | | | | ...th RangePartitioner Author: Aaron Josephs <ajoseph4@binghamton.edu> Closes #1381 from aaronjosephs/PLAT-911 and squashes the following commits: e30ade5 [Aaron Josephs] [SPARK-911] allow efficient queries for a range if RDD is partitioned with RangePartitioner
* [DataFrame] [Typo] Fix the typoCheng Hao2015-02-221-1/+1
| | | | | | | | Author: Cheng Hao <hao.cheng@intel.com> Closes #4717 from chenghao-intel/typo1 and squashes the following commits: 858d7b0 [Cheng Hao] update the typo
* [DOCS] Fix typo in API for custom InputFormats based on the “new” ↵Alexander2015-02-221-2/+2
| | | | | | | | | | | | MapReduce API This looks like a simple typo ```SparkContext.newHadoopRDD``` instead of ```SparkContext.newAPIHadoopRDD``` as in actual http://spark.apache.org/docs/1.2.1/api/scala/index.html#org.apache.spark.SparkContext Author: Alexander <abezzubov@nflabs.com> Closes #4718 from bzz/hadoop-InputFormats-doc-fix and squashes the following commits: 680a4c4 [Alexander] Fix typo in docs on custom Hadoop InputFormats
* MAINTENANCE: Automated closing of pull requests.Patrick Wendell2015-02-210-0/+0
| | | | | | | | | | | | | | | This commit exists to close the following pull requests on Github: Closes #3490 (close requested by 'andrewor14') Closes #4646 (close requested by 'srowen') Closes #3591 (close requested by 'andrewor14') Closes #3656 (close requested by 'andrewor14') Closes #4553 (close requested by 'JoshRosen') Closes #4202 (close requested by 'srowen') Closes #4497 (close requested by 'marmbrus') Closes #4150 (close requested by 'andrewor14') Closes #2409 (close requested by 'andrewor14') Closes #4221 (close requested by 'srowen')
* [SPARK-5860][CORE] JdbcRDD: overflow on large range with high number of ↵Evan Yu2015-02-212-18/+50
| | | | | | | | | | | | | | | partitions Fix a overflow bug in JdbcRDD when calculating partitions for large BIGINT ids Author: Evan Yu <ehotou@gmail.com> Closes #4701 from hotou/SPARK-5860 and squashes the following commits: 9e038d1 [Evan Yu] [SPARK-5860][CORE] Prevent overflowing at the length level 7883ad9 [Evan Yu] [SPARK-5860][CORE] Prevent overflowing at the length level c88755a [Evan Yu] [SPARK-5860][CORE] switch to BigInt instead of BigDecimal 4e9ff4f [Evan Yu] [SPARK-5860][CORE] JdbcRDD overflow on large range with high number of partitions
* [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-5841 [CORE] [HOTFIX 2] Memory leak in DiskBlockManagerNishkam Ravi2015-02-212-2/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Continue to see IllegalStateException in YARN cluster mode. Adding a simple workaround for now. Author: Nishkam Ravi <nravi@cloudera.com> Author: nishkamravi2 <nishkamravi@gmail.com> Author: nravi <nravi@c1704.halxg.cloudera.com> Closes #4690 from nishkamravi2/master_nravi and squashes the following commits: 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
* [MLlib] fix typoJacky Li2015-02-211-1/+1
| | | | | | | | | | fix typo: it should be "default:" instead of "default;" Author: Jacky Li <jackylk@users.noreply.github.com> Closes #4713 from jackylk/patch-10 and squashes the following commits: 15daf2e [Jacky Li] [MLlib] fix typo
* [SPARK-5898] [SPARK-5896] [SQL] [PySpark] create DataFrame from pandas and ↵Davies Liu2015-02-203-20/+20
| | | | | | | | | | | | | | | tuple/list Fix createDataFrame() from pandas DataFrame (not tested by jenkins, depends on SPARK-5693). It also support to create DataFrame from plain tuple/list without column names, `_1`, `_2` will be used as column names. Author: Davies Liu <davies@databricks.com> Closes #4679 from davies/pandas and squashes the following commits: c0cbe0b [Davies Liu] fix tests 8466d1d [Davies Liu] fix create DataFrame from pandas
* [SPARK-5867] [SPARK-5892] [doc] [ml] [mllib] Doc cleanups for 1.3 releaseJoseph K. Bradley2015-02-2030-290/+1940
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | For SPARK-5867: * The spark.ml programming guide needs to be updated to use the new SQL DataFrame API instead of the old SchemaRDD API. * It should also include Python examples now. For SPARK-5892: * Fix Python docs * Various other cleanups BTW, I accidentally merged this with master. If you want to compile it on your own, use this branch which is based on spark/branch-1.3 and cherry-picks the commits from this PR: [https://github.com/jkbradley/spark/tree/doc-review-1.3-check] CC: mengxr (ML), davies (Python docs) Author: Joseph K. Bradley <joseph@databricks.com> Closes #4675 from jkbradley/doc-review-1.3 and squashes the following commits: f191bb0 [Joseph K. Bradley] small cleanups e786efa [Joseph K. Bradley] small doc corrections 6b1ab4a [Joseph K. Bradley] fixed python lint test 946affa [Joseph K. Bradley] Added sample data for ml.MovieLensALS example. Changed spark.ml Java examples to use DataFrames API instead of sql() da81558 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into doc-review-1.3 629dbf5 [Joseph K. Bradley] Updated based on code review: * made new page for old migration guides * small fixes * moved inherit_doc in python b9df7c4 [Joseph K. Bradley] Small cleanups: toDF to toDF(), adding s for string interpolation 34b067f [Joseph K. Bradley] small doc correction da16aef [Joseph K. Bradley] Fixed python mllib docs 8cce91c [Joseph K. Bradley] GMM: removed old imports, added some doc 695f3f6 [Joseph K. Bradley] partly done trying to fix inherit_doc for class hierarchies in python docs a72c018 [Joseph K. Bradley] made ChiSqTestResult appear in python docs b05a80d [Joseph K. Bradley] organize imports. doc cleanups e572827 [Joseph K. Bradley] updated programming guide for ml and mllib
* SPARK-5744 [CORE] Take 2. RDD.isEmpty / take fails for (empty) RDD of NothingSean Owen2015-02-205-1/+24
| | | | | | | | | | | | | | | Follow-on to https://github.com/apache/spark/pull/4591 Document isEmpty / take / parallelize and their interaction with (an empty) RDD[Nothing] and RDD[Null]. Also, fix a marginally related minor issue with histogram() and EmptyRDD. CC rxin since you reviewed the last one although I imagine this is an uncontroversial resolution. Author: Sean Owen <sowen@cloudera.com> Closes #4698 from srowen/SPARK-5744.2 and squashes the following commits: 9b2a811 [Sean Owen] 2 extra javadoc fixes d1b9fba [Sean Owen] Document isEmpty / take / parallelize and their interaction with (an empty) RDD[Nothing] and RDD[Null]. Also, fix a marginally related minor issue with histogram() and EmptyRDD.
* [SPARK-5909][SQL] Add a clearCache command to Spark SQL's cache managerYin Huai2015-02-206-4/+53
| | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-5909 Author: Yin Huai <yhuai@databricks.com> Closes #4694 from yhuai/clearCache and squashes the following commits: 397ecc4 [Yin Huai] Address comments. a2702fc [Yin Huai] Update parser. 3a54506 [Yin Huai] add isEmpty to CacheManager. 6d14460 [Yin Huai] Python clearCache. f7b8dbd [Yin Huai] Add clear cache command.
* [SPARK-4808] Removing minimum number of elements read before spill checkmcheah2015-02-191-5/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | In the general case, Spillable's heuristic of checking for memory stress on every 32nd item after 1000 items are read is good enough. In general, we do not want to be enacting the spilling checks until later on in the job; checking for disk-spilling too early can produce unacceptable performance impact in trivial cases. However, there are non-trivial cases, particularly if each serialized object is large, where checking for the necessity to spill too late would allow the memory to overflow. Consider if every item is 1.5 MB in size, and the heap size is 1000 MB. Then clearly if we only try to spill the in-memory contents to disk after 1000 items are read, we would have already accumulated 1500 MB of RAM and overflowed the heap. Patch #3656 attempted to circumvent this by checking the need to spill on every single item read, but that would cause unacceptable performance in the general case. However, the convoluted cases above should not be forced to be refactored to shrink the data items. Therefore it makes sense that the memory spilling thresholds be configurable. Author: mcheah <mcheah@palantir.com> Closes #4420 from mingyukim/memory-spill-configurable and squashes the following commits: 6e2509f [mcheah] [SPARK-4808] Removing minimum number of elements read before spill check
* [SPARK-5900][MLLIB] make PIC and FPGrowth Java-friendlyXiangrui Meng2015-02-1911-74/+93
| | | | | | | | | | | | | | | | | | | In the previous version, PIC stores clustering assignments as an `RDD[(Long, Int)]`. This is mapped to `RDD<Tuple2<Object, Object>>` in Java and hence Java users have to cast types manually. We should either create a new method called `javaAssignments` that returns `JavaRDD[(java.lang.Long, java.lang.Int)]` or wrap the result pair in a class. I chose the latter approach in this PR. Now assignments are stored as an `RDD[Assignment]`, where `Assignment` is a class with `id` and `cluster`. Similarly, in FPGrowth, the frequent itemsets are stored as an `RDD[(Array[Item], Long)]`, which is mapped to `RDD<Tuple2<Object, Object>>`. Though we provide a "Java-friendly" method `javaFreqItemsets` that returns `JavaRDD[(Array[Item], java.lang.Long)]`. It doesn't really work because `Array[Item]` is mapped to `Object` in Java. So in this PR I created a class `FreqItemset` to wrap the results. It has `items` and `freq`, as well as a `javaItems` method that returns `List<Item>` in Java. I'm not certain that the names I chose are proper: `Assignment`/`id`/`cluster` and `FreqItemset`/`items`/`freq`. Please let me know if there are better suggestions. CC: jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #4695 from mengxr/SPARK-5900 and squashes the following commits: 865b5ca [Xiangrui Meng] make Assignment serializable cffa96e [Xiangrui Meng] fix test 9c0e590 [Xiangrui Meng] remove unused Tuple2 1b9db3d [Xiangrui Meng] make PIC and FPGrowth Java-friendly
* SPARK-5570: No docs stating that `new SparkConf().set("spark.driver.memory", ↵Ilya Ganelin2015-02-191-1/+22
| | | | | | | | | | | | | | | | | | | | ...) will not work I've updated documentation to reflect true behavior of this setting in client vs. cluster mode. Author: Ilya Ganelin <ilya.ganelin@capitalone.com> Closes #4665 from ilganeli/SPARK-5570 and squashes the following commits: 5d1c8dd [Ilya Ganelin] Added example configuration code a51700a [Ilya Ganelin] Getting rid of extra spaces 85f7a08 [Ilya Ganelin] Reworded note 5889d43 [Ilya Ganelin] Formatting adjustment f149ba1 [Ilya Ganelin] Minor updates 1fec7a5 [Ilya Ganelin] Updated to add clarification for other driver properties db47595 [Ilya Ganelin] Slight formatting update c899564 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5570 17b751d [Ilya Ganelin] Updated documentation for driver-memory to reflect its true behavior in client vs cluster mode
* SPARK-4682 [CORE] Consolidate various 'Clock' classesSean Owen2015-02-1937-337/+301
| | | | | | | | | | | | | | | Another one from JoshRosen 's wish list. The first commit is much smaller and removes 2 of the 4 Clock classes. The second is much larger, necessary for consolidating the streaming one. I put together implementations in the way that seemed simplest. Almost all the change is standardizing class and method names. Author: Sean Owen <sowen@cloudera.com> Closes #4514 from srowen/SPARK-4682 and squashes the following commits: 5ed3a03 [Sean Owen] Javadoc Clock classes; make ManualClock private[spark] 169dd13 [Sean Owen] Add support for legacy org.apache.spark.streaming clock class names 277785a [Sean Owen] Reduce the net change in this patch by reversing some unnecessary syntax changes along the way b5e53df [Sean Owen] FakeClock -> ManualClock; getTime() -> getTimeMillis() 160863a [Sean Owen] Consolidate Streaming Clock class into common util Clock 7c956b2 [Sean Owen] Consolidate Clocks except for Streaming Clock
* [Spark-5889] Remove pid file after stopping service.Zhan Zhang2015-02-191-1/+1
| | | | | | | | | | | | | | Currently the pid file is not deleted, and potentially may cause some problem after service is stopped. The fix remove the pid file after service stopped. Author: Zhan Zhang <zhazhan@gmail.com> Closes #4676 from zhzhan/spark-5889 and squashes the following commits: eb01be1 [Zhan Zhang] solve review comments b4c009e [Zhan Zhang] solve review comments 018110a [Zhan Zhang] spark-5889: remove pid file after stopping service 088d2a2 [Zhan Zhang] squash all commits c1f1fa5 [Zhan Zhang] test
* [SPARK-5902] [ml] Made PipelineStage.transformSchema public instead of ↵Joseph K. Bradley2015-02-195-12/+20
| | | | | | | | | | | | | | | | private to ml For users to implement their own PipelineStages, we need to make PipelineStage.transformSchema be public instead of private to ml. This would be nice to include in Spark 1.3 CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #4682 from jkbradley/SPARK-5902 and squashes the following commits: 6f02357 [Joseph K. Bradley] Made transformSchema public 0e6d0a0 [Joseph K. Bradley] made implementations of transformSchema protected as well fdaf26a [Joseph K. Bradley] Made PipelineStage.transformSchema protected instead of private[ml]
* [SPARK-5904][SQL] DataFrame API fixes.Reynold Xin2015-02-199-1024/+427
| | | | | | | | | | | | | 1. Column is no longer a DataFrame to simplify class hierarchy. 2. Don't use varargs on abstract methods (see Scala compiler bug SI-9013). Author: Reynold Xin <rxin@databricks.com> Closes #4686 from rxin/SPARK-5904 and squashes the following commits: fd9b199 [Reynold Xin] Fixed Python tests. df25cef [Reynold Xin] Non final. 5221530 [Reynold Xin] [SPARK-5904][SQL] DataFrame API fixes.
* [SPARK-5825] [Spark Submit] Remove the double checking instance name when ↵Cheng Hao2015-02-191-1/+1
| | | | | | | | | | | | | stopping the service `spark-daemon.sh` will confirm the process id by fuzzy matching the class name while stopping the service, however, it will fail if the java process arguments is very long (greater than 4096 characters). This PR looses the check for the service process. Author: Cheng Hao <hao.cheng@intel.com> Closes #4611 from chenghao-intel/stopping_service and squashes the following commits: a0051f6 [Cheng Hao] loosen the process checking while stopping a service
* [SPARK-5423][Core] Cleanup resources in DiskMapIterator.finalize to ensure ↵zsxwing2015-02-191-9/+43
| | | | | | | | | | | | deleting the temp file This PR adds a `finalize` method in DiskMapIterator to clean up the resources even if some exception happens during processing data. Author: zsxwing <zsxwing@gmail.com> Closes #4219 from zsxwing/SPARK-5423 and squashes the following commits: d4b2ca6 [zsxwing] Cleanup resources in DiskMapIterator.finalize to ensure deleting the temp file
* [SPARK-5816] Add huge compatibility warning in DriverWrapperAndrew Or2015-02-191-0/+7
| | | | | | | | | | | | The stability of the new submission gateway assumes that the arguments in `DriverWrapper` are consistent across multiple Spark versions. However, this is not at all clear from the code itself. In fact, this was broken in 20a6013106b56a1a1cc3e8cda092330ffbe77cc3, which is fortunately OK because both that commit and the original commit that added this gateway are part of the same release. To prevent this from happening again we should at the very least add a huge warning where appropriate. Author: Andrew Or <andrew@databricks.com> Closes #4687 from andrewor14/driver-wrapper-warning and squashes the following commits: 7989b56 [Andrew Or] Add huge compatibility warning
* SPARK-5548: Fix for AkkaUtilsSuite failure - attempt 2Jacek Lewandowski2015-02-191-2/+7
| | | | | | | | | Author: Jacek Lewandowski <lewandowski.jacek@gmail.com> Closes #4653 from jacek-lewandowski/SPARK-5548-2-master and squashes the following commits: 0e199b6 [Jacek Lewandowski] SPARK-5548: applied reviewer's comments 843eafb [Jacek Lewandowski] SPARK-5548: Fix for AkkaUtilsSuite failure - attempt 2
* [SPARK-5846] Correctly set job description and pool for SQL jobsKay Ousterhout2015-02-192-8/+8
| | | | | | | | | | marmbrus am I missing something obvious here? I verified that this fixes the problem for me (on 1.2.1) on EC2, but I'm confused about how others wouldn't have noticed this? Author: Kay Ousterhout <kayousterhout@gmail.com> Closes #4630 from kayousterhout/SPARK-5846_1.3 and squashes the following commits: 2022ad4 [Kay Ousterhout] [SPARK-5846] Correctly set job description and pool for SQL jobs
* [SPARK-5879][MLLIB] update PIC user guide and add a Java exampleXiangrui Meng2015-02-184-13/+149
| | | | | | | | | | | | Updated PIC user guide to reflect API changes and added a simple Java example. The API is still not very Java-friendly. I created SPARK-5990 for this issue. Author: Xiangrui Meng <meng@databricks.com> Closes #4680 from mengxr/SPARK-5897 and squashes the following commits: 847d216 [Xiangrui Meng] apache header 87719a2 [Xiangrui Meng] remove PIC image 2dd921f [Xiangrui Meng] update PIC user guide and add a Java example
* [SPARK-5722] [SQL] [PySpark] infer int as LongTypeDavies Liu2015-02-185-11/+35
| | | | | | | | | | | | The `int` is 64-bit on 64-bit machine (very common now), we should infer it as LongType for it in Spark SQL. Also, LongType in SQL will come back as `int`. Author: Davies Liu <davies@databricks.com> Closes #4666 from davies/long and squashes the following commits: 6bc6cc4 [Davies Liu] infer int as LongType
* [SPARK-5840][SQL] HiveContext cannot be serialized due to tuple extractionReynold Xin2015-02-183-16/+84
| | | | | | | | | | | Also added test cases for checking the serializability of HiveContext and SQLContext. Author: Reynold Xin <rxin@databricks.com> Closes #4628 from rxin/SPARK-5840 and squashes the following commits: ecb3bcd [Reynold Xin] test cases and reviews. 55eb822 [Reynold Xin] [SPARK-5840][SQL] HiveContext cannot be serialized due to tuple extraction.
* [SPARK-5507] Added documentation for BlockMatrixBurak Yavuz2015-02-181-0/+75
| | | | | | | | | | Docs for BlockMatrix. mengxr Author: Burak Yavuz <brkyvz@gmail.com> Closes #4664 from brkyvz/SPARK-5507PR and squashes the following commits: 4db30b0 [Burak Yavuz] [SPARK-5507] Added documentation for BlockMatrix
* [SPARK-5519][MLLIB] add user guide with example code for fp-growthXiangrui Meng2015-02-184-0/+216
| | | | | | | | | | The API is still not very Java-friendly because `Array[Item]` in `freqItemsets` is recognized as `Object` in Java. We might want to define a case class to wrap the return pair to make it Java friendly. Author: Xiangrui Meng <meng@databricks.com> Closes #4661 from mengxr/SPARK-5519 and squashes the following commits: 58ccc25 [Xiangrui Meng] add user guide with example code for fp-growth
* SPARK-5669 [BUILD] [HOTFIX] Spark assembly includes incompatibly licensed ↵Sean Owen2015-02-181-3/+3
| | | | | | | | | | | | | libgfortran, libgcc code via JBLAS Correct exclusion path for JBLAS native libs. (More explanation coming soon on the mailing list re: 1.3.0 RC1) Author: Sean Owen <sowen@cloudera.com> Closes #4673 from srowen/SPARK-5669.2 and squashes the following commits: e29693c [Sean Owen] Correct exclusion path for JBLAS native libs
* [SPARK-4949]shutdownCallback in SparkDeploySchedulerBackend should be ↵Kousuke Saruta2015-02-181-19/+16
| | | | | | | | | | | | | | | | | | enclosed by synchronized block. A variable `shutdownCallback` in SparkDeploySchedulerBackend can be accessed from multiple threads so it should be enclosed by synchronized block. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #3781 from sarutak/SPARK-4949 and squashes the following commits: c146c93 [Kousuke Saruta] Removed "setShutdownCallback" method c7265dc [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-4949 42ca528 [Kousuke Saruta] Changed the declaration of the variable "shutdownCallback" as a volatile reference instead of AtomicReference 552df7c [Kousuke Saruta] Changed the declaration of the variable "shutdownCallback" as a volatile reference instead of AtomicReference f556819 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-4949 1b60fd1 [Kousuke Saruta] Improved the locking logics 5942765 [Kousuke Saruta] Enclosed shutdownCallback in SparkDeploySchedulerBackend by synchronized block
* SPARK-4610 addendum: [Minor] [MLlib] Minor doc fix in GBT classification exampleMechCoder2015-02-181-1/+1
| | | | | | | | | | numClassesForClassification has been renamed to numClasses. Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #4672 from MechCoder/minor-doc and squashes the following commits: d2ddb7f [MechCoder] Minor doc fix in GBT classification example
* [SPARK-5878] fix DataFrame.repartition() in PythonDavies Liu2015-02-181-1/+7
| | | | | | | | | | | Also add tests for distinct() Author: Davies Liu <davies@databricks.com> Closes #4667 from davies/repartition and squashes the following commits: 79059fd [Davies Liu] add test cb4915e [Davies Liu] fix repartition
* Avoid deprecation warnings in JDBCSuite.Tor Myklebust2015-02-181-13/+20
| | | | | | | | | | This pull request replaces calls to deprecated methods from `java.util.Date` with near-equivalents in `java.util.Calendar`. Author: Tor Myklebust <tmyklebu@gmail.com> Closes #4668 from tmyklebu/master and squashes the following commits: 66215b1 [Tor Myklebust] Use GregorianCalendar instead of Timestamp get methods.
* [Minor] [SQL] Cleans up DataFrame variable names and toDF() callsCheng Lian2015-02-1737-259/+250
| | | | | | | | | | | | | | Although we've migrated to the DataFrame API, lots of code still uses `rdd` or `srdd` as local variable names. This PR tries to address these naming inconsistencies and some other minor DataFrame related style issues. <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/4670) <!-- Reviewable:end --> Author: Cheng Lian <lian@databricks.com> Closes #4670 from liancheng/df-cleanup and squashes the following commits: 3e14448 [Cheng Lian] Cleans up DataFrame variable names and toDF() calls
* [SPARK-5731][Streaming][Test] Fix incorrect test in DirectKafkaStreamSuiteTathagata Das2015-02-171-12/+16
| | | | | | | | | | | | | | | The test was incorrect. Instead of counting the number of records, it counted the number of partitions of RDD generated by DStream. Which is not its intention. I will be testing this patch multiple times to understand its flakiness. PS: This was caused by my refactoring in https://github.com/apache/spark/pull/4384/ koeninger check it out. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #4597 from tdas/kafka-flaky-test and squashes the following commits: d236235 [Tathagata Das] Unignored last test. e9a1820 [Tathagata Das] fix test
* [SPARK-5723][SQL]Change the default file format to Parquet for CTAS statements.Yin Huai2015-02-175-25/+158
| | | | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-5723 Author: Yin Huai <yhuai@databricks.com> This patch had conflicts when merged, resolved by Committer: Michael Armbrust <michael@databricks.com> Closes #4639 from yhuai/defaultCTASFileFormat and squashes the following commits: a568137 [Yin Huai] Merge remote-tracking branch 'upstream/master' into defaultCTASFileFormat ad2b07d [Yin Huai] Update tests and error messages. 8af5b2a [Yin Huai] Update conf key and unit test. 5a67903 [Yin Huai] Use data source write path for Hive's CTAS statements when no storage format/handler is specified.
* [SPARK-5875][SQL]logical.Project should not be resolved if it contains ↵Yin Huai2015-02-173-2/+53
| | | | | | | | | | | | aggregates or generators https://issues.apache.org/jira/browse/SPARK-5875 has a case to reproduce the bug and explain the root cause. Author: Yin Huai <yhuai@databricks.com> Closes #4663 from yhuai/projectResolved and squashes the following commits: 472f7b6 [Yin Huai] If a logical.Project has any AggregateExpression or Generator, it's resolved field should be false.
* [SPARK-4454] Revert getOrElse() cleanup in DAGScheduler.getCacheLocs()Josh Rosen2015-02-171-3/+5
| | | | This method is performance-sensitive and this change wasn't necessary.
* [SPARK-4454] Properly synchronize accesses to DAGScheduler cacheLocs mapJosh Rosen2015-02-171-10/+24
| | | | | | | | | | | | | | | | This patch addresses a race condition in DAGScheduler by properly synchronizing accesses to its `cacheLocs` map. This map is accessed by the `getCacheLocs` and `clearCacheLocs()` methods, which can be called by separate threads, since DAGScheduler's `getPreferredLocs()` method is called by SparkContext and indirectly calls `getCacheLocs()`. If this map is cleared by the DAGScheduler event processing thread while a user thread is submitting a job and computing preferred locations, then this can cause the user thread to throw "NoSuchElementException: key not found" errors. Most accesses to DAGScheduler's internal state do not need synchronization because that state is only accessed from the event processing loop's thread. An alternative approach to fixing this bug would be to refactor this code so that SparkContext sends the DAGScheduler a message in order to get the list of preferred locations. However, this would involve more extensive changes to this code and would be significantly harder to backport to maintenance branches since some of the related code has undergone significant refactoring (e.g. the introduction of EventLoop). Since `cacheLocs` is the only state that's accessed in this way, adding simple synchronization seems like a better short-term fix. See #3345 for additional context. Author: Josh Rosen <joshrosen@databricks.com> Closes #4660 from JoshRosen/SPARK-4454 and squashes the following commits: 12d64ba [Josh Rosen] Properly synchronize accesses to DAGScheduler cacheLocs map.
* [SPARK-5811] Added documentation for maven coordinates and added Spark ↵Burak Yavuz2015-02-175-27/+131
| | | | | | | | | | | | | | | | | | | | | | | Packages support Documentation for maven coordinates + Spark Package support. Added pyspark tests for `--packages` Author: Burak Yavuz <brkyvz@gmail.com> Author: Davies Liu <davies@databricks.com> Closes #4662 from brkyvz/SPARK-5811 and squashes the following commits: 56ccccd [Burak Yavuz] fixed broken test 64cb8ee [Burak Yavuz] passed pep8 on local c07b81e [Burak Yavuz] fixed pep8 a8bd6b7 [Burak Yavuz] submit PR 4ef4046 [Burak Yavuz] ready for PR 8fb02e5 [Burak Yavuz] merged master 25c9b9f [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into python-jar 560d13b [Burak Yavuz] before PR 17d3f76 [Davies Liu] support .jar as python package a3eb717 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into SPARK-5811 c60156d [Burak Yavuz] [SPARK-5811] Added documentation for maven coordinates
* [SPARK-5785] [PySpark] narrow dependency for cogroup/join in PySparkDavies Liu2015-02-177-25/+101
| | | | | | | | | | | | | | | | | | Currently, PySpark does not support narrow dependency during cogroup/join when the two RDDs have the partitioner, another unnecessary shuffle stage will come in. The Python implementation of cogroup/join is different than Scala one, it depends on union() and partitionBy(). This patch will try to use PartitionerAwareUnionRDD() in union(), when all the RDDs have the same partitioner. It also fix `reservePartitioner` in all the map() or mapPartitions(), then partitionBy() can skip the unnecessary shuffle stage. Author: Davies Liu <davies@databricks.com> Closes #4629 from davies/narrow and squashes the following commits: dffe34e [Davies Liu] improve test, check number of stages for join/cogroup 1ed3ba2 [Davies Liu] Merge branch 'master' of github.com:apache/spark into narrow 4d29932 [Davies Liu] address comment cc28d97 [Davies Liu] add unit tests 940245e [Davies Liu] address comments ff5a0a6 [Davies Liu] skip the partitionBy() on Python side eb26c62 [Davies Liu] narrow dependency in PySpark
* [SPARK-5852][SQL]Fail to convert a newly created empty metastore parquet ↵Yin Huai2015-02-173-6/+164
| | | | | | | | | | | | | | | | | | | | | | | table to a data source parquet table. The problem is that after we create an empty hive metastore parquet table (e.g. `CREATE TABLE test (a int) STORED AS PARQUET`), Hive will create an empty dir for us, which cause our data source `ParquetRelation2` fail to get the schema of the table. See JIRA for the case to reproduce the bug and the exception. This PR is based on #4562 from chenghao-intel. JIRA: https://issues.apache.org/jira/browse/SPARK-5852 Author: Yin Huai <yhuai@databricks.com> Author: Cheng Hao <hao.cheng@intel.com> Closes #4655 from yhuai/CTASParquet and squashes the following commits: b8b3450 [Yin Huai] Update tests. 2ac94f7 [Yin Huai] Update tests. 3db3d20 [Yin Huai] Minor update. d7e2308 [Yin Huai] Revert changes in HiveMetastoreCatalog.scala. 36978d1 [Cheng Hao] Update the code as feedback a04930b [Cheng Hao] fix bug of scan an empty parquet based table 442ffe0 [Cheng Hao] passdown the schema for Parquet File in HiveContext
* [SPARK-5872] [SQL] create a sqlCtx in pyspark shellDavies Liu2015-02-172-3/+22
| | | | | | | | | | | | The sqlCtx will be HiveContext if hive is built in assembly jar, or SQLContext if not. It also skip the Hive tests in pyspark.sql.tests if no hive is available. Author: Davies Liu <davies@databricks.com> Closes #4659 from davies/sqlctx and squashes the following commits: 0e6629a [Davies Liu] sqlCtx in pyspark
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