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* [SPARK-1592][streaming] Automatically remove streaming input blocksTathagata Das2014-04-247-25/+135
| | | | | | | | | | | | | | | The raw input data is stored as blocks in BlockManagers. Earlier they were cleared by cleaner ttl. Now since streaming does not require cleaner TTL to be set, the block would not get cleared. This increases up the Spark's memory usage, which is not even accounted and shown in the Spark storage UI. It may cause the data blocks to spill over to disk, which eventually slows down the receiving of data (persisting to memory become bottlenecked by writing to disk). The solution in this PR is to automatically remove those blocks. The mechanism to keep track of which BlockRDDs (which has presents the raw data blocks as a RDD) can be safely cleared already exists. Just use it to explicitly remove blocks from BlockRDDs. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #512 from tdas/block-rdd-unpersist and squashes the following commits: d25e610 [Tathagata Das] Merge remote-tracking branch 'apache/master' into block-rdd-unpersist 5f46d69 [Tathagata Das] Merge remote-tracking branch 'apache/master' into block-rdd-unpersist 2c320cd [Tathagata Das] Updated configuration with spark.streaming.unpersist setting. 2d4b2fd [Tathagata Das] Automatically removed input blocks
* SPARK-1438 RDD.sample() make seed param optionalArun Ramakrishnan2014-04-2413-41/+88
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | copying form previous pull request https://github.com/apache/spark/pull/462 Its probably better to let the underlying language implementation take care of the default . This was easier to do with python as the default value for seed in random and numpy random is None. In Scala/Java side it might mean propagating an Option or null(oh no!) down the chain until where the Random is constructed. But, looks like the convention in some other methods was to use System.nanoTime. So, followed that convention. Conflict with overloaded method in sql.SchemaRDD.sample which also defines default params. sample(fraction, withReplacement=false, seed=math.random) Scala does not allow more than one overloaded to have default params. I believe the author intended to override the RDD.sample method and not overload it. So, changed it. If backward compatible is important, 3 new method can be introduced (without default params) like this sample(fraction) sample(fraction, withReplacement) sample(fraction, withReplacement, seed) Added some tests for the scala RDD takeSample method. Author: Arun Ramakrishnan <smartnut007@gmail.com> This patch had conflicts when merged, resolved by Committer: Matei Zaharia <matei@databricks.com> Closes #477 from smartnut007/master and squashes the following commits: 07bb06e [Arun Ramakrishnan] SPARK-1438 fixing more space formatting issues b9ebfe2 [Arun Ramakrishnan] SPARK-1438 removing redundant import of random in python rddsampler 8d05b1a [Arun Ramakrishnan] SPARK-1438 RDD . Replace System.nanoTime with a Random generated number. python: use a separate instance of Random instead of seeding language api global Random instance. 69619c6 [Arun Ramakrishnan] SPARK-1438 fix spacing issue 0c247db [Arun Ramakrishnan] SPARK-1438 RDD language apis to support optional seed in RDD methods sample/takeSample
* SPARK-1104: kill Process in workerThread of ExecutorRunnerCodingCat2014-04-241-17/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | As reported in https://spark-project.atlassian.net/browse/SPARK-1104 By @pwendell: "Sometimes due to large shuffles executors will take a long time shutting down. In particular this can happen if large numbers of shuffle files are around (this will be alleviated by SPARK-1103, but nonetheless...). The symptom is you have DEAD workers sitting around in the UI and the existing workers keep trying to re-register but can't because they've been assumed dead." In this patch, I add lines in the handler of InterruptedException in workerThread of executorRunner, so that the process.destroy() and process.waitFor() can only block the workerThread instead of blocking the worker Actor... --------- analysis: process.destroy() is a blocking method, i.e. it only returns when all shutdownHook threads return...so calling it in Worker thread will make Worker block for a long while.... about what will happen on the shutdown hooks when the JVM process is killed: http://www.tutorialspoint.com/java/lang/runtime_addshutdownhook.htm Author: CodingCat <zhunansjtu@gmail.com> Closes #35 from CodingCat/SPARK-1104 and squashes the following commits: 85767da [CodingCat] add null checking and remove unnecessary killProce 3107aeb [CodingCat] address Aaron's comments eb615ba [CodingCat] kill the process when the error happens 0accf2f [CodingCat] set process to null after killed it 1d511c8 [CodingCat] kill Process in workerThread
* Fix Scala StyleSandeep2014-04-2420-83/+109
| | | | | | | | | | | | | | Any comments are welcome Author: Sandeep <sandeep@techaddict.me> Closes #531 from techaddict/stylefix-1 and squashes the following commits: 7492730 [Sandeep] Pass 4 98b2428 [Sandeep] fix rxin suggestions b5e2e6f [Sandeep] Pass 3 05932d7 [Sandeep] fix if else styling 2 08690e5 [Sandeep] fix if else styling
* SPARK-1494 Don't initialize classes loaded by MIMA excludes, attempt 2Michael Armbrust2014-04-241-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | [WIP] Looks like scala reflection was invoking the static initializer: ``` ... at org.apache.spark.sql.test.TestSQLContext$.<init>(TestSQLContext.scala:25) at org.apache.spark.sql.test.TestSQLContext$.<clinit>(TestSQLContext.scala) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:270) at scala.reflect.runtime.JavaMirrors$JavaMirror.javaClass(JavaMirrors.scala:500) at scala.reflect.runtime.JavaMirrors$JavaMirror.tryJavaClass(JavaMirrors.scala:505) at scala.reflect.runtime.SymbolLoaders$PackageScope.lookupEntry(SymbolLoaders.scala:109) ... ``` Need to make sure that this doesn't change the exclusion semantics before merging. Author: Michael Armbrust <michael@databricks.com> Closes #526 from marmbrus/mima and squashes the following commits: 8168dea [Michael Armbrust] Spurious change afba262 [Michael Armbrust] Prevent Scala reflection from running static class initializer.
* Spark 1490 Add kerberos support to the HistoryServerThomas Graves2014-04-243-0/+44
| | | | | | | | | | | | | Here I've added the ability for the History server to login from a kerberos keytab file so that the history server can be run as a super user and stay up for along period of time while reading the history files from HDFS. Author: Thomas Graves <tgraves@apache.org> Closes #513 from tgravescs/SPARK-1490 and squashes the following commits: e204a99 [Thomas Graves] remove extra logging 5418daa [Thomas Graves] fix typo in config 0076b99 [Thomas Graves] Update docs 4d76545 [Thomas Graves] SPARK-1490 Add kerberos support to the HistoryServer
* SPARK-1611: Fix incorrect initialization order in AppendOnlyMapzsxwing2014-04-241-2/+2
| | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-1611 Author: zsxwing <zsxwing@gmail.com> Closes #534 from zsxwing/SPARK-1611 and squashes the following commits: 96af089 [zsxwing] SPARK-1611: Fix incorrect initialization order in AppendOnlyMap
* SPARK-1488. Squash more language feature warnings in new commits by ↵Sean Owen2014-04-246-0/+7
| | | | | | | | | | | | | importing implicitConversion A recent commit reintroduced some of the same warnings that SPARK-1488 resolved. These are just a few more of the same changes to remove these warnings. Author: Sean Owen <sowen@cloudera.com> Closes #528 from srowen/SPARK-1488.2 and squashes the following commits: 62d592c [Sean Owen] More feature warnings in tests 4e2e94b [Sean Owen] Squash more language feature warnings in new commits by importing implicitConversion
* Small changes to release scriptPatrick Wendell2014-04-242-3/+2
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* [SPARK-1610] [SQL] Fix Cast to use exact type value when cast from ↵Takuya UESHIN2014-04-242-5/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | BooleanType to NumericTy... ...pe. `Cast` from `BooleanType` to `NumericType` are all using `Int` value. But it causes `ClassCastException` when the casted value is used by the following evaluation like the code below: ``` scala scala> import org.apache.spark.sql.catalyst._ import org.apache.spark.sql.catalyst._ scala> import types._ import types._ scala> import expressions._ import expressions._ scala> Add(Cast(Literal(true), ShortType), Literal(1.toShort)).eval() java.lang.ClassCastException: java.lang.Integer cannot be cast to java.lang.Short at scala.runtime.BoxesRunTime.unboxToShort(BoxesRunTime.java:102) at scala.math.Numeric$ShortIsIntegral$.plus(Numeric.scala:72) at org.apache.spark.sql.catalyst.expressions.Add$$anonfun$eval$2.apply(arithmetic.scala:58) at org.apache.spark.sql.catalyst.expressions.Add$$anonfun$eval$2.apply(arithmetic.scala:58) at org.apache.spark.sql.catalyst.expressions.Expression.n2(Expression.scala:114) at org.apache.spark.sql.catalyst.expressions.Add.eval(arithmetic.scala:58) at .<init>(<console>:17) at .<clinit>(<console>) at .<init>(<console>:7) at .<clinit>(<console>) at $print(<console>) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:483) at scala.tools.nsc.interpreter.IMain$ReadEvalPrint.call(IMain.scala:734) at scala.tools.nsc.interpreter.IMain$Request.loadAndRun(IMain.scala:983) at scala.tools.nsc.interpreter.IMain.loadAndRunReq$1(IMain.scala:573) at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:604) at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:568) at scala.tools.nsc.interpreter.ILoop.reallyInterpret$1(ILoop.scala:760) at scala.tools.nsc.interpreter.ILoop.interpretStartingWith(ILoop.scala:805) at scala.tools.nsc.interpreter.ILoop.command(ILoop.scala:717) at scala.tools.nsc.interpreter.ILoop.processLine$1(ILoop.scala:581) at scala.tools.nsc.interpreter.ILoop.innerLoop$1(ILoop.scala:588) at scala.tools.nsc.interpreter.ILoop.loop(ILoop.scala:591) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply$mcZ$sp(ILoop.scala:882) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:837) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:837) at scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135) at scala.tools.nsc.interpreter.ILoop.process(ILoop.scala:837) at scala.tools.nsc.MainGenericRunner.runTarget$1(MainGenericRunner.scala:83) at scala.tools.nsc.MainGenericRunner.process(MainGenericRunner.scala:96) at scala.tools.nsc.MainGenericRunner$.main(MainGenericRunner.scala:105) at scala.tools.nsc.MainGenericRunner.main(MainGenericRunner.scala) ``` Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #533 from ueshin/issues/SPARK-1610 and squashes the following commits: 70f36e8 [Takuya UESHIN] Fix Cast to use exact type value when cast from BooleanType to NumericType.
* SPARK-1601 & SPARK-1602: two bug fixes related to cancellationReynold Xin2014-04-245-15/+86
| | | | | | | | | | | | | | | | | | This should go into 1.0 since it would return wrong data when the bug happens (which is pretty likely if cancellation is used). Test case attached. 1. Do not put partially executed partitions into cache (in task killing). 2. Iterator returned by CacheManager#getOrCompute was not an InterruptibleIterator, and was thus leading to uninterruptible jobs. Thanks @aarondav and @ahirreddy for reporting and helping debug. Author: Reynold Xin <rxin@apache.org> Closes #521 from rxin/kill and squashes the following commits: 401033f [Reynold Xin] Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/spark into kill 7a7bdd2 [Reynold Xin] Add a new line in the end of JobCancellationSuite.scala. 35cd9f7 [Reynold Xin] Fixed a bug that partially executed partitions can be put into cache (in task killing).
* SPARK-1587 Fix thread leakMridul Muralidharan2014-04-237-21/+42
| | | | | | | | | | | mvn test fails (intermittently) due to thread leak - since scalatest runs all tests in same vm. Author: Mridul Muralidharan <mridulm80@apache.org> Closes #504 from mridulm/resource_leak_fixes and squashes the following commits: a5d10d0 [Mridul Muralidharan] Prevent thread leaks while running tests : cleanup all threads when SparkContext.stop is invoked. Causes tests to fail 7b5e19c [Mridul Muralidharan] Prevent NPE while running tests
* [Fix #79] Replace Breakable For Loops By While LoopsSandeep2014-04-231-29/+31
| | | | | | | | | | Author: Sandeep <sandeep@techaddict.me> Closes #503 from techaddict/fix-79 and squashes the following commits: e3f6746 [Sandeep] Style changes 07a4f6b [Sandeep] for loop to While loop 0a6d8e9 [Sandeep] Breakable for loop to While loop
* SPARK-1589: Fix the incorrect comparezsxwing2014-04-231-1/+5
| | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-1589 Author: zsxwing <zsxwing@gmail.com> Closes #508 from zsxwing/SPARK-1589 and squashes the following commits: 570c67a [zsxwing] SPARK-1589: Fix the incorrect compare
* Mark all fields of EdgePartition, Graph, and GraphOps transientAnkur Dave2014-04-233-12/+12
| | | | | | | | | | | | These classes are only serializable to work around closure capture, so their fields should all be marked `@transient` to avoid wasteful serialization. This PR supersedes apache/spark#519 and fixes the same bug. Author: Ankur Dave <ankurdave@gmail.com> Closes #520 from ankurdave/graphx-transient and squashes the following commits: 6431760 [Ankur Dave] Mark all fields of EdgePartition, Graph, and GraphOps `@transient`
* Update Java api for setJobGroup with interruptOnCancelAaron Davidson2014-04-232-2/+49
| | | | | | | | | | | Also adds a unit test. Author: Aaron Davidson <aaron@databricks.com> Closes #522 from aarondav/cancel2 and squashes the following commits: 565c253 [Aaron Davidson] Update Java api for setJobGroup with interruptOnCancel 65b33d8 [Aaron Davidson] Add unit test for Thread interruption on cancellation
* [Hot Fix #469] Fix flaky test in SparkListenerSuiteAndrew Or2014-04-231-2/+3
| | | | | | | | | | The two modified tests may fail if the race condition does not bid in our favor... Author: Andrew Or <andrewor14@gmail.com> Closes #516 from andrewor14/stage-info-test-fix and squashes the following commits: b4b6100 [Andrew Or] Add/replace missing waitUntilEmpty() calls to listener bus
* [SPARK-1540] Add an optional Ordering parameter to PairRDDFunctions.Matei Zaharia2014-04-238-49/+124
| | | | | | | | | | | | | | | | | | | | In https://issues.apache.org/jira/browse/SPARK-1540 we'd like to look at Spark's API to see if we can take advantage of Comparable keys in more places, which will make external spilling more efficient. This PR is a first step towards that that shows how to pass an Ordering when available and still continue functioning otherwise. It does this using a new implicit parameter with a default value of null. The API is currently only in Scala -- in Java we'd have to add new versions of mapToPair and such that take a Comparator, or a new method to add a "type hint" to an RDD. We can address those later though. Unfortunately requiring all keys to be Comparable would not work without requiring RDDs in general to contain only Comparable types. The reason is that methods such as distinct() and intersection() do a shuffle, but should be usable on RDDs of any type. So ordering will have to remain an optimization for the types that can be ordered. I think this isn't a horrible outcome though because one of the nice things about Spark's API is that it works on objects of *any* type, without requiring you to specify a schema or implement Writable or stuff like that. Author: Matei Zaharia <matei@databricks.com> This patch had conflicts when merged, resolved by Committer: Reynold Xin <rxin@apache.org> Closes #487 from mateiz/ordered-keys and squashes the following commits: bd565f6 [Matei Zaharia] Pass an Ordering to only one version of groupBy because the Scala language spec doesn't allow having an optional parameter on all of them (this was only compiling in Scala 2.10 due to a bug). 4629965 [Matei Zaharia] Add tests for other versions of groupBy 3beae85 [Matei Zaharia] Added a test for implicit orderings 80b7a3b [Matei Zaharia] Add an optional Ordering parameter to PairRDDFunctions.
* SPARK-1582 Invoke Thread.interrupt() when cancelling jobsAaron Davidson2014-04-2315-30/+57
| | | | | | | | | | | | | | | Sometimes executor threads are blocked waiting for IO or monitors, and the current implementation of job cancellation may never recover these threads. By simply invoking Thread.interrupt() during cancellation, we can often safely unblock the threads and use them for subsequent work. Note that this feature must remain optional for now because of a bug in HDFS where Thread.interrupt() may cause nodes to be marked as permanently dead (as the InterruptedException is reinterpreted as an IOException during communication with some node). Author: Aaron Davidson <aaron@databricks.com> Closes #498 from aarondav/cancel and squashes the following commits: e52b829 [Aaron Davidson] Don't use job.properties when null 82f78bb [Aaron Davidson] Update DAGSchedulerSuite b67f472 [Aaron Davidson] Add comment on why interruptOnCancel is in setJobGroup 4cb9fd6 [Aaron Davidson] SPARK-1582 Invoke Thread.interrupt() when cancelling jobs
* Honor default fs name when initializing event logger.Marcelo Vanzin2014-04-233-33/+41
| | | | | | | | | | | | | | This is related to SPARK-1459 / PR #375. Without this fix, FileLogger.createLogDir() may try to create the log dir on HDFS, while createWriter() will try to open the log file on the local file system, leading to interesting errors and confusion. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #450 from vanzin/event-file-2 and squashes the following commits: 592cdb3 [Marcelo Vanzin] Honor default fs name when initializing event logger.
* SPARK-1572 Don't kill Executor if PythonRDD fails while computing parentAaron Davidson2014-04-231-11/+21
| | | | | | | | | | | | | | | | | Previously, the behavior was that if the parent RDD threw any exception other than IOException or FileNotFoundException (which is quite possible for Hadoop input sources), the entire Executor would crash, because the default thread a uncaught exception handler calls System.exit(). This patch avoids two related issues: 1. Always catch exceptions in this reader thread. 2. Don't mask readerException when Python throws an EOFError after worker.shutdownOutput() is called. Author: Aaron Davidson <aaron@databricks.com> Closes #486 from aarondav/pyspark and squashes the following commits: fbb11e9 [Aaron Davidson] Make sure FileNotFoundExceptions are handled same as before b9acb3e [Aaron Davidson] SPARK-1572 Don't kill Executor if PythonRDD fails while computing parent
* SPARK-1583: Fix a bug that using java.util.HashMap by mistakezsxwing2014-04-231-1/+1
| | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-1583 Does anyone know why using `java.util.HashMap` rather than `mutable.HashMap`? Some methods of `java.util.HashMap` are not generics and compiler can not help us find similar problems. Author: zsxwing <zsxwing@gmail.com> Closes #500 from zsxwing/SPARK-1583 and squashes the following commits: 7bfd74d [zsxwing] SPARK-1583: Fix a bug that using java.util.HashMap by mistake
* SPARK-1119 and other build improvementsPatrick Wendell2014-04-237-41/+70
| | | | | | | | | | | | 1. Makes assembly and examples jar naming consistent in maven/sbt. 2. Updates make-distribution.sh to use Maven and fixes some bugs. 3. Updates the create-release script to call make-distribution script. Author: Patrick Wendell <pwendell@gmail.com> Closes #502 from pwendell/make-distribution and squashes the following commits: 1a97f0d [Patrick Wendell] SPARK-1119 and other build improvements
* [SQL] SPARK-1571 Mistake in java example codeMichael Armbrust2014-04-222-8/+8
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #496 from marmbrus/javaBeanBug and squashes the following commits: 644fedd [Michael Armbrust] Bean methods must be public.
* SPARK-1494 Don't initialize classes loaded by MIMA excludes.Michael Armbrust2014-04-221-4/+3
| | | | | | | | | | | [WIP] Just seeing how Jenkins likes this... Author: Michael Armbrust <michael@databricks.com> Closes #494 from marmbrus/mima and squashes the following commits: 6eec616 [Michael Armbrust] Force hive tests to run. acaf682 [Michael Armbrust] Don't initialize loaded classes.
* SPARK-1562 Fix visibility / annotation of Spark SQL APIsMichael Armbrust2014-04-2232-59/+143
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #489 from marmbrus/sqlDocFixes and squashes the following commits: acee4f3 [Michael Armbrust] Fix visibility / annotation of Spark SQL APIs
* [FIX: SPARK-1376] use --arg instead of --args in SparkSubmit to avoid ↵Xiangrui Meng2014-04-222-2/+2
| | | | | | | | | | | | | | | | | | | warning messages Even if users use `--arg`, `SparkSubmit` still uses `--args` for child args internally, which triggers a warning message that may confuse users: ~~~ --args is deprecated. Use --arg instead. ~~~ @sryza Does it look good to you? Author: Xiangrui Meng <meng@databricks.com> Closes #485 from mengxr/submit-arg and squashes the following commits: 5e1b9fe [Xiangrui Meng] update test cebbeb7 [Xiangrui Meng] use --arg instead of --args in SparkSubmit to avoid warning messages
* [streaming][SPARK-1578] Removed requirement for TTL in StreamingContext.Tathagata Das2014-04-224-49/+14
| | | | | | | | | | Since shuffles and RDDs that are out of context are automatically cleaned by Spark core (using ContextCleaner) there is no need for setting the cleaner TTL while creating a StreamingContext. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #491 from tdas/ttl-fix and squashes the following commits: cf01dc7 [Tathagata Das] Removed requirement for TTL in StreamingContext.
* [Spark-1538] Fix SparkUI incorrectly hiding persisted RDDsAndrew Or2014-04-2215-81/+318
| | | | | | | | | | | | | | | | | | | | | | | **Bug**: After the following command `sc.parallelize(1 to 1000).persist.map(_ + 1).count()` is run, the the persisted RDD is missing from the storage tab of the SparkUI. **Cause**: The command creates two RDDs in one stage, a `ParallelCollectionRDD` and a `MappedRDD`. However, the existing StageInfo only keeps the RDDInfo of the last RDD associated with the stage (`MappedRDD`), and so all RDD information regarding the first RDD (`ParallelCollectionRDD`) is discarded. In this case, we persist the first RDD, but the StorageTab doesn't know about this RDD because it is not encoded in the StageInfo. **Fix**: Record information of all RDDs in StageInfo, instead of just the last RDD (i.e. `stage.rdd`). Since stage boundaries are marked by shuffle dependencies, the solution is to traverse the last RDD's dependency tree, visiting only ancestor RDDs related through a sequence of narrow dependencies. --- This PR also moves RDDInfo to its own file, includes a few style fixes, and adds a unit test for constructing StageInfos. Author: Andrew Or <andrewor14@gmail.com> Closes #469 from andrewor14/storage-ui-fix and squashes the following commits: 07fc7f0 [Andrew Or] Add back comment that was accidentally removed (minor) 5d799fe [Andrew Or] Add comment to justify testing of getNarrowAncestors with cycles 9d0e2b8 [Andrew Or] Hide details of getNarrowAncestors from outsiders d2bac8a [Andrew Or] Deal with cycles in RDD dependency graph + add extensive tests 2acb177 [Andrew Or] Move getNarrowAncestors to RDD.scala bfe83f0 [Andrew Or] Backtrace RDD dependency tree to find all RDDs that belong to a Stage
* Assorted clean-up for Spark-on-YARN.Patrick Wendell2014-04-224-10/+18
| | | | | | | | | | | | In particular when the HADOOP_CONF_DIR is not not specified. Author: Patrick Wendell <pwendell@gmail.com> Closes #488 from pwendell/hadoop-cleanup and squashes the following commits: fe95f13 [Patrick Wendell] Changes based on Andrew's feeback 18d09c1 [Patrick Wendell] Review comments from Andrew 17929cc [Patrick Wendell] Assorted clean-up for Spark-on-YARN.
* [SPARK-1570] Fix classloading in JavaSQLContext.applySchemaKan Zhang2014-04-221-2/+4
| | | | | | | | | | I think I hit a class loading issue when running JavaSparkSQL example using spark-submit in local mode. Author: Kan Zhang <kzhang@apache.org> Closes #484 from kanzhang/SPARK-1570 and squashes the following commits: feaaeba [Kan Zhang] [SPARK-1570] Fix classloading in JavaSQLContext.applySchema
* Fix compilation on Hadoop 2.4.x.Marcelo Vanzin2014-04-221-1/+2
| | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #483 from vanzin/yarn-2.4 and squashes the following commits: 0fc57d8 [Marcelo Vanzin] Fix compilation on Hadoop 2.4.x.
* [Fix #204] Eliminate delay between binding and log checkingAndrew Or2014-04-222-4/+20
| | | | | | | | | | | | | | | **Bug**: In the existing history server, there is a `spark.history.updateInterval` seconds delay before application logs show up on the UI. **Cause**: This is because the following events happen in this order: (1) The background thread that checks for logs starts, but realizes the server has not yet bound and so waits for N seconds, (2) server binds, (3) N seconds later the background thread finds that the server has finally bound to a port, and so finally checks for application logs. **Fix**: This PR forces the log checking thread to start immediately after binding. It also documents two relevant environment variables that are currently missing. Author: Andrew Or <andrewor14@gmail.com> Closes #441 from andrewor14/history-server-fix and squashes the following commits: b2eb46e [Andrew Or] Document SPARK_PUBLIC_DNS and SPARK_HISTORY_OPTS for the history server e8d1fbc [Andrew Or] Eliminate delay between binding and checking for logs
* [SPARK-1506][MLLIB] Documentation improvements for MLlib 1.0Xiangrui Meng2014-04-2212-769/+1543
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Preview: http://54.82.240.23:4000/mllib-guide.html Table of contents: * Basics * Data types * Summary statistics * Classification and regression * linear support vector machine (SVM) * logistic regression * linear linear squares, Lasso, and ridge regression * decision tree * naive Bayes * Collaborative Filtering * alternating least squares (ALS) * Clustering * k-means * Dimensionality reduction * singular value decomposition (SVD) * principal component analysis (PCA) * Optimization * stochastic gradient descent * limited-memory BFGS (L-BFGS) Author: Xiangrui Meng <meng@databricks.com> Closes #422 from mengxr/mllib-doc and squashes the following commits: 944e3a9 [Xiangrui Meng] merge master f9fda28 [Xiangrui Meng] minor 9474065 [Xiangrui Meng] add alpha to ALS examples 928e630 [Xiangrui Meng] initialization_mode -> initializationMode 5bbff49 [Xiangrui Meng] add imports to labeled point examples c17440d [Xiangrui Meng] fix python nb example 28f40dc [Xiangrui Meng] remove localhost:4000 369a4d3 [Xiangrui Meng] Merge branch 'master' into mllib-doc 7dc95cc [Xiangrui Meng] update linear methods 053ad8a [Xiangrui Meng] add links to go back to the main page abbbf7e [Xiangrui Meng] update ALS argument names 648283e [Xiangrui Meng] level down statistics 14e2287 [Xiangrui Meng] add sample libsvm data and use it in guide 8cd2441 [Xiangrui Meng] minor updates 186ab07 [Xiangrui Meng] update section names 6568d65 [Xiangrui Meng] update toc, level up lr and svm 162ee12 [Xiangrui Meng] rename section names 5c1e1b1 [Xiangrui Meng] minor 8aeaba1 [Xiangrui Meng] wrap long lines 6ce6a6f [Xiangrui Meng] add summary statistics to toc 5760045 [Xiangrui Meng] claim beta cc604bf [Xiangrui Meng] remove classification and regression 92747b3 [Xiangrui Meng] make section titles consistent e605dd6 [Xiangrui Meng] add LIBSVM loader f639674 [Xiangrui Meng] add python section to migration guide c82ffb4 [Xiangrui Meng] clean optimization 31660eb [Xiangrui Meng] update linear algebra and stat 0a40837 [Xiangrui Meng] first pass over linear methods 1fc8271 [Xiangrui Meng] update toc 906ed0a [Xiangrui Meng] add a python example to naive bayes 5f0a700 [Xiangrui Meng] update collaborative filtering 656d416 [Xiangrui Meng] update mllib-clustering 86e143a [Xiangrui Meng] remove data types section from main page 8d1a128 [Xiangrui Meng] move part of linear algebra to data types and add Java/Python examples d1b5cbf [Xiangrui Meng] merge master 72e4804 [Xiangrui Meng] one pass over tree guide 64f8995 [Xiangrui Meng] move decision tree guide to a separate file 9fca001 [Xiangrui Meng] add first version of linear algebra guide 53c9552 [Xiangrui Meng] update dependencies f316ec2 [Xiangrui Meng] add migration guide f399f6c [Xiangrui Meng] move linear-algebra to dimensionality-reduction 182460f [Xiangrui Meng] add guide for naive Bayes 137fd1d [Xiangrui Meng] re-organize toc a61e434 [Xiangrui Meng] update mllib's toc
* [SPARK-1281] Improve partitioning in ALSTor Myklebust2014-04-222-23/+54
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ALS was using HashPartitioner and explicit uses of `%` together. Further, the naked use of `%` meant that, if the number of partitions corresponded with the stride of arithmetic progressions appearing in user and product ids, users and products could be mapped into buckets in an unfair or unwise way. This pull request: 1) Makes the Partitioner an instance variable of ALS. 2) Replaces the direct uses of `%` with calls to a Partitioner. 3) Defines an anonymous Partitioner that scrambles the bits of the object's hashCode before reducing to the number of present buckets. This pull request does not make the partitioner user-configurable. I'm not all that happy about the way I did (1). It introduces an icky lifetime issue and dances around it by nulling something. However, I don't know a better way to make the partitioner visible everywhere it needs to be visible. Author: Tor Myklebust <tmyklebu@gmail.com> Closes #407 from tmyklebu/master and squashes the following commits: dcf583a [Tor Myklebust] Remove the partitioner member variable; instead, thread that needle everywhere it needs to go. 23d6f91 [Tor Myklebust] Stop making the partitioner configurable. 495784f [Tor Myklebust] Merge branch 'master' of https://github.com/apache/spark 674933a [Tor Myklebust] Fix style. 40edc23 [Tor Myklebust] Fix missing space. f841345 [Tor Myklebust] Fix daft bug creating 'pairs', also for -> foreach. 5ec9e6c [Tor Myklebust] Clean a couple of things up using 'map'. 36a0f43 [Tor Myklebust] Make the partitioner private. d872b09 [Tor Myklebust] Add negative id ALS test. df27697 [Tor Myklebust] Support custom partitioners. Currently we use the same partitioner for users and products. c90b6d8 [Tor Myklebust] Scramble user and product ids before bucketing. c774d7d [Tor Myklebust] Make the partitioner a member variable and use it instead of modding directly.
* fix bugs of dot in pythonXusen Yin2014-04-222-5/+5
| | | | | | | | | | | | | | If there are no `transpose()` in `self.theta`, a *ValueError: matrices are not aligned* is occurring. The former test case just ignore this situation. Author: Xusen Yin <yinxusen@gmail.com> Closes #463 from yinxusen/python-naive-bayes and squashes the following commits: fcbe3bc [Xusen Yin] fix bugs of dot in python
* [SPARK-1560]: Updated Pyrolite Dependency to be Java 6 compatibleAhir Reddy2014-04-222-2/+2
| | | | | | | | | | | Changed the Pyrolite dependency to a build which targets Java 6. Author: Ahir Reddy <ahirreddy@gmail.com> Closes #479 from ahirreddy/java6-pyrolite and squashes the following commits: 8ea25d3 [Ahir Reddy] Updated maven build to use java 6 compatible pyrolite dabc703 [Ahir Reddy] Updated Pyrolite dependency to be Java 6 compatible
* [HOTFIX] SPARK-1399: remove outdated commentsCodingCat2014-04-221-1/+0
| | | | | | | | | | | | as the original PR was merged before this mistake is found....fix here, Sorry about that @pwendell, @andrewor14, I will be more careful next time Author: CodingCat <zhunansjtu@gmail.com> Closes #474 from CodingCat/hotfix_1399 and squashes the following commits: f3a8ba9 [CodingCat] move outdated comments
* SPARK-1496: Have jarOfClass return Option[String]Patrick Wendell2014-04-2238-42/+42
| | | | | | | | | | A simple change, mostly had to change a bunch of example code. Author: Patrick Wendell <pwendell@gmail.com> Closes #438 from pwendell/jar-of-class and squashes the following commits: aa010ff [Patrick Wendell] SPARK-1496: Have jarOfClass return Option[String]
* [SPARK-1459] Use local path (and not complete URL) when opening local lo...Marcelo Vanzin2014-04-211-1/+1
| | | | | | | | | | ...g file. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #375 from vanzin/event-file and squashes the following commits: f673029 [Marcelo Vanzin] [SPARK-1459] Use local path (and not complete URL) when opening local log file.
* [Fix #274] Document + fix annotation usagesAndrew Or2014-04-2111-19/+29
| | | | | | | | | | | | | | | ... so that we don't follow an unspoken set of forbidden rules for adding **@AlphaComponent**, **@DeveloperApi**, and **@Experimental** annotations in the code. In addition, this PR (1) removes unnecessary `:: * ::` tags, (2) adds missing `:: * ::` tags, and (3) removes annotations for internal APIs. Author: Andrew Or <andrewor14@gmail.com> Closes #470 from andrewor14/annotations-fix and squashes the following commits: 92a7f42 [Andrew Or] Document + fix annotation usages
* [SPARK-1439, SPARK-1440] Generate unified Scaladoc across projects and JavadocsMatei Zaharia2014-04-2125-284/+296
| | | | | | | | | | | | | | | | | | | | | | I used the sbt-unidoc plugin (https://github.com/sbt/sbt-unidoc) to create a unified Scaladoc of our public packages, and generate Javadocs as well. One limitation is that I haven't found an easy way to exclude packages in the Javadoc; there is a SBT task that identifies Java sources to run javadoc on, but it's been very difficult to modify it from outside to change what is set in the unidoc package. Some SBT-savvy people should help with this. The Javadoc site also lacks package-level descriptions and things like that, so we may want to look into that. We may decide not to post these right now if it's too limited compared to the Scala one. Example of the built doc site: http://people.csail.mit.edu/matei/spark-unified-docs/ Author: Matei Zaharia <matei@databricks.com> This patch had conflicts when merged, resolved by Committer: Patrick Wendell <pwendell@gmail.com> Closes #457 from mateiz/better-docs and squashes the following commits: a63d4a3 [Matei Zaharia] Skip Java/Scala API docs for Python package 5ea1f43 [Matei Zaharia] Fix links to Java classes in Java guide, fix some JS for scrolling to anchors on page load f05abc0 [Matei Zaharia] Don't include java.lang package names 995e992 [Matei Zaharia] Skip internal packages and class names with $ in JavaDoc a14a93c [Matei Zaharia] typo 76ce64d [Matei Zaharia] Add groups to Javadoc index page, and a first package-info.java ed6f994 [Matei Zaharia] Generate JavaDoc as well, add titles, update doc site to use unified docs acb993d [Matei Zaharia] Add Unidoc plugin for the projects we want Unidoced
* [SPARK-1332] Improve Spark Streaming's Network Receiver and InputDStream API ↵Tathagata Das2014-04-2155-731/+1836
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | [WIP] The current Network Receiver API makes it slightly complicated to right a new receiver as one needs to create an instance of BlockGenerator as shown in SocketReceiver https://github.com/apache/spark/blob/master/streaming/src/main/scala/org/apache/spark/streaming/dstream/SocketInputDStream.scala#L51 Exposing the BlockGenerator interface has made it harder to improve the receiving process. The API of NetworkReceiver (which was not a very stable API anyways) needs to be change if we are to ensure future stability. Additionally, the functions like streamingContext.socketStream that create input streams, return DStream objects. That makes it hard to expose functionality (say, rate limits) unique to input dstreams. They should return InputDStream or NetworkInputDStream. This is still not yet implemented. This PR is blocked on the graceful shutdown PR #247 Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #300 from tdas/network-receiver-api and squashes the following commits: ea27b38 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into network-receiver-api 3a4777c [Tathagata Das] Renamed NetworkInputDStream to ReceiverInputDStream, and ActorReceiver related stuff. 838dd39 [Tathagata Das] Added more events to the StreamingListener to report errors and stopped receivers. a75c7a6 [Tathagata Das] Address some PR comments and fixed other issues. 91bfa72 [Tathagata Das] Fixed bugs. 8533094 [Tathagata Das] Scala style fixes. 028bde6 [Tathagata Das] Further refactored receiver to allow restarting of a receiver. 43f5290 [Tathagata Das] Made functions that create input streams return InputDStream and NetworkInputDStream, for both Scala and Java. 2c94579 [Tathagata Das] Fixed graceful shutdown by removing interrupts on receiving thread. 9e37a0b [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into network-receiver-api 3223e95 [Tathagata Das] Refactored the code that runs the NetworkReceiver into further classes and traits to make them more testable. a36cc48 [Tathagata Das] Refactored the NetworkReceiver API for future stability.
* Dev script: include RC name in git tagPatrick Wendell2014-04-211-1/+1
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* SPARK-1399: show stage failure reason in UICodingCat2014-04-213-39/+61
| | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1399 refactor StageTable a bit to support additional column for failed stage Author: CodingCat <zhunansjtu@gmail.com> Author: Nan Zhu <CodingCat@users.noreply.github.com> Closes #421 from CodingCat/SPARK-1399 and squashes the following commits: 2caba36 [CodingCat] remove dummy tag 77cf305 [CodingCat] create dummy element to wrap columns 3989ce2 [CodingCat] address Aaron's comments 18fc09f [Nan Zhu] fix compile error 00ea30a [Nan Zhu] address Kay's comments 16ac83d [CodingCat] set a default value of failureReason 35df3df [CodingCat] address andrew's comments 06d21a4 [CodingCat] address andrew's comments 25a6db6 [CodingCat] style fix dc8856d [CodingCat] show stage failure reason in UI
* SPARK-1539: RDDPage.scala contains RddPage classXiangrui Meng2014-04-212-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | SPARK-1386 changed RDDPage to RddPage but didn't change the filename. I tried sbt/sbt publish-local. Inside the spark-core jar, the unit name is RDDPage.class and hence I got the following error: ~~~ [error] (run-main) java.lang.NoClassDefFoundError: org/apache/spark/ui/storage/RddPage java.lang.NoClassDefFoundError: org/apache/spark/ui/storage/RddPage at org.apache.spark.ui.SparkUI.initialize(SparkUI.scala:59) at org.apache.spark.ui.SparkUI.<init>(SparkUI.scala:52) at org.apache.spark.ui.SparkUI.<init>(SparkUI.scala:42) at org.apache.spark.SparkContext.<init>(SparkContext.scala:215) at MovieLensALS$.main(MovieLensALS.scala:38) at MovieLensALS.main(MovieLensALS.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) Caused by: java.lang.ClassNotFoundException: org.apache.spark.ui.storage.RddPage at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) at org.apache.spark.ui.SparkUI.initialize(SparkUI.scala:59) at org.apache.spark.ui.SparkUI.<init>(SparkUI.scala:52) at org.apache.spark.ui.SparkUI.<init>(SparkUI.scala:42) at org.apache.spark.SparkContext.<init>(SparkContext.scala:215) at MovieLensALS$.main(MovieLensALS.scala:38) at MovieLensALS.main(MovieLensALS.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) ~~~ This can be fixed after renaming RddPage to RDDPage, or renaming RDDPage.scala to RddPage.scala. I chose the former since the name `RDD` is common in Spark code. Author: Xiangrui Meng <meng@databricks.com> Closes #454 from mengxr/rddpage-fix and squashes the following commits: f75e544 [Xiangrui Meng] rename RddPage to RDDPage
* [Hot Fix] Ignore org.apache.spark.ui.UISuite testsAndrew Or2014-04-211-3/+3
| | | | | | | | | | | | #446 faced a connection refused exception from these tests, causing them to timeout and fail after a long time. For now, let's disable these tests. (We recently disabled the corresponding test in streaming in 7863ecca35be9af1eca0dfe5fd8806c5dd710fd6. These tests are very similar). Author: Andrew Or <andrewor14@gmail.com> Closes #466 from andrewor14/ignore-ui-tests and squashes the following commits: 6f5a362 [Andrew Or] Ignore org.apache.spark.ui.UISuite tests
* Clean up and simplify Spark configurationPatrick Wendell2014-04-2144-401/+886
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Over time as we've added more deployment modes, this have gotten a bit unwieldy with user-facing configuration options in Spark. Going forward we'll advise all users to run `spark-submit` to launch applications. This is a WIP patch but it makes the following improvements: 1. Improved `spark-env.sh.template` which was missing a lot of things users now set in that file. 2. Removes the shipping of SPARK_CLASSPATH, SPARK_JAVA_OPTS, and SPARK_LIBRARY_PATH to the executors on the cluster. This was an ugly hack. Instead it introduces config variables spark.executor.extraJavaOpts, spark.executor.extraLibraryPath, and spark.executor.extraClassPath. 3. Adds ability to set these same variables for the driver using `spark-submit`. 4. Allows you to load system properties from a `spark-defaults.conf` file when running `spark-submit`. This will allow setting both SparkConf options and other system properties utilized by `spark-submit`. 5. Made `SPARK_LOCAL_IP` an environment variable rather than a SparkConf property. This is more consistent with it being set on each node. Author: Patrick Wendell <pwendell@gmail.com> Closes #299 from pwendell/config-cleanup and squashes the following commits: 127f301 [Patrick Wendell] Improvements to testing a006464 [Patrick Wendell] Moving properties file template. b4b496c [Patrick Wendell] spark-defaults.properties -> spark-defaults.conf 0086939 [Patrick Wendell] Minor style fixes af09e3e [Patrick Wendell] Mention config file in docs and clean-up docs b16e6a2 [Patrick Wendell] Cleanup of spark-submit script and Scala quick start guide af0adf7 [Patrick Wendell] Automatically add user jar a56b125 [Patrick Wendell] Responses to Tom's review d50c388 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into config-cleanup a762901 [Patrick Wendell] Fixing test failures ffa00fe [Patrick Wendell] Review feedback fda0301 [Patrick Wendell] Note 308f1f6 [Patrick Wendell] Properly escape quotes and other clean-up for YARN e83cd8f [Patrick Wendell] Changes to allow re-use of test applications be42f35 [Patrick Wendell] Handle case where SPARK_HOME is not set c2a2909 [Patrick Wendell] Test compile fixes 4ee6f9d [Patrick Wendell] Making YARN doc changes consistent afc9ed8 [Patrick Wendell] Cleaning up line limits and two compile errors. b08893b [Patrick Wendell] Additional improvements. ace4ead [Patrick Wendell] Responses to review feedback. b72d183 [Patrick Wendell] Review feedback for spark env file 46555c1 [Patrick Wendell] Review feedback and import clean-ups 437aed1 [Patrick Wendell] Small fix 761ebcd [Patrick Wendell] Library path and classpath for drivers 7cc70e4 [Patrick Wendell] Clean up terminology inside of spark-env script 5b0ba8e [Patrick Wendell] Don't ship executor envs 84cc5e5 [Patrick Wendell] Small clean-up 1f75238 [Patrick Wendell] SPARK_JAVA_OPTS --> SPARK_MASTER_OPTS for master settings 4982331 [Patrick Wendell] Remove SPARK_LIBRARY_PATH 6eaf7d0 [Patrick Wendell] executorJavaOpts 0faa3b6 [Patrick Wendell] Stash of adding config options in submit script and YARN ac2d65e [Patrick Wendell] Change spark.local.dir -> SPARK_LOCAL_DIRS
* REPL cleanup.Michael Armbrust2014-04-191-22/+33
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #451 from marmbrus/replCleanup and squashes the following commits: 088526a [Michael Armbrust] REPL cleanup.
* [SPARK-1535] ALS: Avoid the garbage-creating ctor of DoubleMatrixTor Myklebust2014-04-191-2/+11
| | | | | | | | | | | `new DoubleMatrix(double[])` creates a garbage `double[]` of the same length as its argument and immediately throws it away. This pull request avoids that constructor in the ALS code. Author: Tor Myklebust <tmyklebu@gmail.com> Closes #442 from tmyklebu/foo2 and squashes the following commits: 2784fc5 [Tor Myklebust] Mention that this is probably fixed as of jblas 1.2.4; repunctuate. a09904f [Tor Myklebust] Helper function for wrapping Array[Double]'s with DoubleMatrix's.
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