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* [FIX] make coalesce test deterministic in RDDSuiteXiangrui Meng2014-04-111-28/+33
| | | | | | | | | | Make coalesce test deterministic by setting pre-defined seeds. (Saw random failures in other PRs.) Author: Xiangrui Meng <meng@databricks.com> Closes #387 from mengxr/fix-random and squashes the following commits: 59bc16f [Xiangrui Meng] make coalesce test deterministic in RDDSuite
* HOTFIX: Ignore python metastore files in RAT checks.Patrick Wendell2014-04-111-1/+3
| | | | | | | | | | This was causing some errors with pull request tests. Author: Patrick Wendell <pwendell@gmail.com> Closes #393 from pwendell/hotfix and squashes the following commits: 6201dd3 [Patrick Wendell] HOTFIX: Ignore python metastore files in RAT checks.
* [SPARK-1225, 1241] [MLLIB] Add AreaUnderCurve and BinaryClassificationMetricsXiangrui Meng2014-04-119-0/+671
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR implements a generic version of `AreaUnderCurve` using the `RDD.sliding` implementation from https://github.com/apache/spark/pull/136 . It also contains refactoring of https://github.com/apache/spark/pull/160 for binary classification evaluation. Author: Xiangrui Meng <meng@databricks.com> Closes #364 from mengxr/auc and squashes the following commits: a05941d [Xiangrui Meng] replace TP/FP/TN/FN by their full names 3f42e98 [Xiangrui Meng] add (0, 0), (1, 1) to roc, and (0, 1) to pr fb4b6d2 [Xiangrui Meng] rename Evaluator to Metrics and add more metrics b1b7dab [Xiangrui Meng] fix code styles 9dc3518 [Xiangrui Meng] add tests for BinaryClassificationEvaluator ca31da5 [Xiangrui Meng] remove PredictionAndResponse 3d71525 [Xiangrui Meng] move binary evalution classes to evaluation.binary 8f78958 [Xiangrui Meng] add PredictionAndResponse dda82d5 [Xiangrui Meng] add confusion matrix aa7e278 [Xiangrui Meng] add initial version of binary classification evaluator 221ebce [Xiangrui Meng] add a new test to sliding a920865 [Xiangrui Meng] Merge branch 'sliding' into auc a9b250a [Xiangrui Meng] move sliding to mllib cab9a52 [Xiangrui Meng] use last for the last element db6cb30 [Xiangrui Meng] remove unnecessary toSeq 9916202 [Xiangrui Meng] change RDD.sliding return type to RDD[Seq[T]] 284d991 [Xiangrui Meng] change SlidedRDD to SlidingRDD c1c6c22 [Xiangrui Meng] add AreaUnderCurve 65461b2 [Xiangrui Meng] Merge branch 'sliding' into auc 5ee6001 [Xiangrui Meng] add TODO d2a600d [Xiangrui Meng] add sliding to rdd
* Some clean up in build/docsPatrick Wendell2014-04-111-2/+0
| | | | | | | | | | | (a) Deleted an outdated line from the docs (b) Removed a work around that is no longer necessary given the mesos version bump. Author: Patrick Wendell <pwendell@gmail.com> Closes #382 from pwendell/maven-clean and squashes the following commits: f0447fa [Patrick Wendell] Minor doc clean-up
* SPARK-1417: Spark on Yarn - spark UI link from resourcemanager is brokenThomas Graves2014-04-114-3/+43
| | | | | | | | | | | | | | Author: Thomas Graves <tgraves@apache.org> Closes #344 from tgravescs/SPARK-1417 and squashes the following commits: c450b5f [Thomas Graves] fix test e1c1d7e [Thomas Graves] add missing $ to appUIAddress e982ddb [Thomas Graves] use appUIHostPort in appUIAddress 0803ec2 [Thomas Graves] Review comment updates - remove extra newline, simplify assert in test 658a8ec [Thomas Graves] Add a appUIHostPort routine 0614208 [Thomas Graves] Fix test 2a6b1b7 [Thomas Graves] SPARK-1417: Spark on Yarn - spark UI link from resourcemanager is broken
* SPARK-1202: Improvements to task killing in the UI.Patrick Wendell2014-04-106-22/+38
| | | | | | | | | | | | 1. Adds a separate endpoint for the killing logic that is outside of a page. 2. Narrows the scope of the killingEnabled tracking. 3. Some style improvements. Author: Patrick Wendell <pwendell@gmail.com> Closes #386 from pwendell/kill-link and squashes the following commits: 8efe02b [Patrick Wendell] Improvements to task killing in the UI.
* Add Spark v0.9.1 to ec2 launch script and use it as the defaultHarvey Feng2014-04-101-2/+2
| | | | | | | | | | Mainly ported from branch-0.9. Author: Harvey Feng <hyfeng224@gmail.com> Closes #385 from harveyfeng/0.9.1-ec2 and squashes the following commits: 769ac2f [Harvey Feng] Add Spark v0.9.1 to ec2 launch script and use it as the default
* Set spark.executor.uri from environment variable (needed by Mesos)Ivan Wick2014-04-101-0/+3
| | | | | | | | | | | | | The Mesos backend uses this property when setting up a slave process. It is similarly set in the Scala repl (org.apache.spark.repl.SparkILoop), but I couldn't find any analogous for pyspark. Author: Ivan Wick <ivanwick+github@gmail.com> This patch had conflicts when merged, resolved by Committer: Matei Zaharia <matei@databricks.com> Closes #311 from ivanwick/master and squashes the following commits: da0c3e4 [Ivan Wick] Set spark.executor.uri from environment variable (needed by Mesos)
* SPARK-1202 - Add a "cancel" button in the UI for stagesSundeep Narravula2014-04-1010-12/+87
| | | | | | | | | | | | Author: Sundeep Narravula <sundeepn@superduel.local> Author: Sundeep Narravula <sundeepn@dhcpx-204-110.corp.yahoo.com> Closes #246 from sundeepn/uikilljob and squashes the following commits: 5fdd0e2 [Sundeep Narravula] Fix test string f6fdff1 [Sundeep Narravula] Format fix; reduced line size to less than 100 chars d1daeb9 [Sundeep Narravula] Incorporating review comments. 8d97923 [Sundeep Narravula] Ability to kill jobs thru the UI. This behavior can be turned on be settings the following variable: spark.ui.killEnabled=true (default=false) Adding DAGScheduler event StageCancelled and corresponding handlers. Added cancellation reason to handlers.
* [SQL] Improve column pruning in the optimizer.Michael Armbrust2014-04-102-2/+51
| | | | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #378 from marmbrus/columnPruning and squashes the following commits: 779da56 [Michael Armbrust] More consistent naming. 1a4e9ea [Michael Armbrust] More comments. 2f4e7b9 [Michael Armbrust] Improve column pruning in the optimizer.
* Remove Unnecessary Whitespace'sSandeep2014-04-1082-467/+467
| | | | | | | | | | stack these together in a commit else they show up chunk by chunk in different commits. Author: Sandeep <sandeep@techaddict.me> Closes #380 from techaddict/white_space and squashes the following commits: b58f294 [Sandeep] Remove Unnecessary Whitespace's
* Update tuning.mdAndrew Ash2014-04-101-2/+3
| | | | | | | | | | http://stackoverflow.com/questions/9699071/what-is-the-javas-internal-represention-for-string-modified-utf-8-utf-16 Author: Andrew Ash <andrew@andrewash.com> Closes #384 from ash211/patch-2 and squashes the following commits: da1b0be [Andrew Ash] Update tuning.md
* Revert "SPARK-1433: Upgrade Mesos dependency to 0.17.0"Patrick Wendell2014-04-105-10/+8
| | | | This reverts commit 12c077d5aa0b76a808a55db625c9677a52bd43f9.
* SPARK-1428: MLlib should convert non-float64 NumPy arrays to float64 instead ↵Sandeep2014-04-101-4/+14
| | | | | | | | | | of complaining Author: Sandeep <sandeep@techaddict.me> Closes #356 from techaddict/1428 and squashes the following commits: 3bdf5f6 [Sandeep] SPARK-1428: MLlib should convert non-float64 NumPy arrays to float64 instead of complaining
* [SPARK-1276] Add a HistoryServer to render persisted UIAndrew Or2014-04-1038-201/+1075
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The new feature of event logging, introduced in #42, allows the user to persist the details of his/her Spark application to storage, and later replay these events to reconstruct an after-the-fact SparkUI. Currently, however, a persisted UI can only be rendered through the standalone Master. This greatly limits the use case of this new feature as many people also run Spark on Yarn / Mesos. This PR introduces a new entity called the HistoryServer, which, given a log directory, keeps track of all completed applications independently of a Spark Master. Unlike Master, the HistoryServer needs not be running while the application is still running. It is relatively light-weight in that it only maintains static information of applications and performs no scheduling. To quickly test it out, generate event logs with ```spark.eventLog.enabled=true``` and run ```sbin/start-history-server.sh <log-dir-path>```. Your HistoryServer awaits on port 18080. Comments and feedback are most welcome. --- A few other changes introduced in this PR include refactoring the WebUI interface, which is beginning to have a lot of duplicate code now that we have added more functionality to it. Two new SparkListenerEvents have been introduced (SparkListenerApplicationStart/End) to keep track of application name and start/finish times. This PR also clarifies the semantics of the ReplayListenerBus introduced in #42. A potential TODO in the future (not part of this PR) is to render live applications in addition to just completed applications. This is useful when applications fail, a condition that our current HistoryServer does not handle unless the user manually signals application completion (by creating the APPLICATION_COMPLETION file). Handling live applications becomes significantly more challenging, however, because it is now necessary to render the same SparkUI multiple times. To avoid reading the entire log every time, which is inefficient, we must handle reading the log from where we previously left off, but this becomes fairly complicated because we must deal with the arbitrary behavior of each input stream. Author: Andrew Or <andrewor14@gmail.com> Closes #204 from andrewor14/master and squashes the following commits: 7b7234c [Andrew Or] Finished -> Completed b158d98 [Andrew Or] Address Patrick's comments 69d1b41 [Andrew Or] Do not block on posting SparkListenerApplicationEnd 19d5dd0 [Andrew Or] Merge github.com:apache/spark f7f5bf0 [Andrew Or] Make history server's web UI port a Spark configuration 2dfb494 [Andrew Or] Decouple checking for application completion from replaying d02dbaa [Andrew Or] Expose Spark version and include it in event logs 2282300 [Andrew Or] Add documentation for the HistoryServer 567474a [Andrew Or] Merge github.com:apache/spark 6edf052 [Andrew Or] Merge github.com:apache/spark 19e1fb4 [Andrew Or] Address Thomas' comments 248cb3d [Andrew Or] Limit number of live applications + add configurability a3598de [Andrew Or] Do not close file system with ReplayBus + fix bind address bc46fc8 [Andrew Or] Merge github.com:apache/spark e2f4ff9 [Andrew Or] Merge github.com:apache/spark 050419e [Andrew Or] Merge github.com:apache/spark 81b568b [Andrew Or] Fix strange error messages... 0670743 [Andrew Or] Decouple page rendering from loading files from disk 1b2f391 [Andrew Or] Minor changes a9eae7e [Andrew Or] Merge branch 'master' of github.com:apache/spark d5154da [Andrew Or] Styling and comments 5dbfbb4 [Andrew Or] Merge branch 'master' of github.com:apache/spark 60bc6d5 [Andrew Or] First complete implementation of HistoryServer (only for finished apps) 7584418 [Andrew Or] Report application start/end times to HistoryServer 8aac163 [Andrew Or] Add basic application table c086bd5 [Andrew Or] Add HistoryServer and scripts ++ Refactor WebUI interface
* Fix SPARK-1413: Parquet messes up stdout and stdin when used in Spark REPLwitgo2014-04-102-28/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | Author: witgo <witgo@qq.com> Closes #325 from witgo/SPARK-1413 and squashes the following commits: e57cd8e [witgo] use scala reflection to access and call the SLF4JBridgeHandler methods 45c8f40 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 5e35d87 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 0d5f819 [witgo] review commit 45e5b70 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 fa69dcf [witgo] Merge branch 'master' into SPARK-1413 3c98dc4 [witgo] Merge branch 'master' into SPARK-1413 38160cb [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 ba09bcd [witgo] remove set the parquet log level a63d574 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 5231ecd [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 3feb635 [witgo] parquet logger use parent handler fa00d5d [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 8bb6ffd [witgo] enableLogForwarding note fix edd9630 [witgo] move to f447f50 [witgo] merging master 5ad52bd [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1413 76670c1 [witgo] review commit 70f3c64 [witgo] Fix SPARK-1413
* Revert "SPARK-729: Closures not always serialized at capture time"Patrick Wendell2014-04-108-218/+14
| | | | This reverts commit 8ca3b2bc90a63b23a03f339e390174cd7a672b40.
* SPARK-1446: Spark examples should not do a System.exitSandeep2014-04-1035-67/+60
| | | | | | | | | | | Spark examples should exit nice using SparkContext.stop() method, rather than System.exit System.exit can cause issues like in SPARK-1407 Author: Sandeep <sandeep@techaddict.me> Closes #370 from techaddict/1446 and squashes the following commits: e9234cf [Sandeep] SPARK-1446: Spark examples should not do a System.exit Spark examples should exit nice using SparkContext.stop() method, rather than System.exit System.exit can cause issues like in SPARK-1407
* SPARK-729: Closures not always serialized at capture timeWilliam Benton2014-04-098-14/+218
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | [SPARK-729](https://spark-project.atlassian.net/browse/SPARK-729) concerns when free variables in closure arguments to transformations are captured. Currently, it is possible for closures to get the environment in which they are serialized (not the environment in which they are created). There are a few possible approaches to solving this problem and this PR will discuss some of them. The approach I took has the advantage of being simple, obviously correct, and minimally-invasive, but it preserves something that has been bothering me about Spark's closure handling, so I'd like to discuss an alternative and get some feedback on whether or not it is worth pursuing. ## What I did The basic approach I took depends on the work I did for #143, and so this PR is based atop that. Specifically: #143 modifies `ClosureCleaner.clean` to preemptively determine whether or not closures are serializable immediately upon closure cleaning (rather than waiting for an job involving that closure to be scheduled). Thus non-serializable closure exceptions will be triggered by the line defining the closure rather than triggered where the closure is used. Since the easiest way to determine whether or not a closure is serializable is to attempt to serialize it, the code in #143 is creating a serialized closure as part of `ClosureCleaner.clean`. `clean` currently modifies its argument, but the method in `SparkContext` that wraps it to return a value (a reference to the modified-in-place argument). This branch modifies `ClosureCleaner.clean` so that it returns a value: if it is cleaning a serializable closure, it returns the result of deserializing its serialized argument; therefore it is returning a closure with an environment captured at cleaning time. `SparkContext.clean` then returns the result of `ClosureCleaner.clean`, rather than a reference to its modified-in-place argument. I've added tests for this behavior (777a1bc). The pull request as it stands, given the changes in #143, is nearly trivial. There is some overhead from deserializing the closure, but it is minimal and the benefit of obvious operational correctness (vs. a more sophisticated but harder-to-validate transformation in `ClosureCleaner`) seems pretty important. I think this is a fine way to solve this problem, but it's not perfect. ## What we might want to do The thing that has been bothering me about Spark's handling of closures is that it seems like we should be able to statically ensure that cleaning and serialization happen exactly once for a given closure. If we serialize a closure in order to determine whether or not it is serializable, we should be able to hang on to the generated byte buffer and use it instead of re-serializing the closure later. By replacing closures with instances of a sum type that encodes whether or not a closure has been cleaned or serialized, we could handle clean, to-be-cleaned, and serialized closures separately with case matches. Here's a somewhat-concrete sketch (taken from my git stash) of what this might look like: ```scala package org.apache.spark.util import java.nio.ByteBuffer import scala.reflect.ClassManifest sealed abstract class ClosureBox[T] { def func: T } final case class RawClosure[T](func: T) extends ClosureBox[T] {} final case class CleanedClosure[T](func: T) extends ClosureBox[T] {} final case class SerializedClosure[T](func: T, bytebuf: ByteBuffer) extends ClosureBox[T] {} object ClosureBoxImplicits { implicit def closureBoxFromFunc[T <: AnyRef](fun: T) = new RawClosure[T](fun) } ``` With these types declared, we'd be able to change `ClosureCleaner.clean` to take a `ClosureBox[T=>U]` (possibly generated by implicit conversion) and return a `ClosureBox[T=>U]` (either a `CleanedClosure[T=>U]` or a `SerializedClosure[T=>U]`, depending on whether or not serializability-checking was enabled) instead of a `T=>U`. A case match could thus short-circuit cleaning or serializing closures that had already been cleaned or serialized (both in `ClosureCleaner` and in the closure serializer). Cleaned-and-serialized closures would be represented by a boxed tuple of the original closure and a serialized copy (complete with an environment quiesced at transformation time). Additional implicit conversions could convert from `ClosureBox` instances to the underlying function type where appropriate. Tracking this sort of state in the type system seems like the right thing to do to me. ### Why we might not want to do that _It's pretty invasive._ Every function type used by every `RDD` subclass would have to change to reflect that they expected a `ClosureBox[T=>U]` instead of a `T=>U`. This obscures what's going on and is not a little ugly. Although I really like the idea of using the type system to enforce the clean-or-serialize once discipline, it might not be worth adding another layer of types (even if we could hide some of the extra boilerplate with judicious application of implicit conversions). _It statically guarantees a property whose absence is unlikely to cause any serious problems as it stands._ It appears that all closures are currently dynamically cleaned once and it's not obvious that repeated closure-cleaning is likely to be a problem in the future. Furthermore, serializing closures is relatively cheap, so doing it once to check for serialization and once again to actually ship them across the wire doesn't seem like a big deal. Taken together, these seem like a high price to pay for statically guaranteeing that closures are operated upon only once. ## Other possibilities I felt like the serialize-and-deserialize approach was best due to its obvious simplicity. But it would be possible to do a more sophisticated transformation within `ClosureCleaner.clean`. It might also be possible for `clean` to modify its argument in a way so that whether or not a given closure had been cleaned would be apparent upon inspection; this would buy us some of the operational benefits of the `ClosureBox` approach but not the static cleanliness. I'm interested in any feedback or discussion on whether or not the problems with the type-based approach indeed outweigh the advantage, as well as of approaches to this issue and to closure handling in general. Author: William Benton <willb@redhat.com> Closes #189 from willb/spark-729 and squashes the following commits: f4cafa0 [William Benton] Stylistic changes and cleanups b3d9c86 [William Benton] Fixed style issues in tests 9b56ce0 [William Benton] Added array-element capture test 97e9d91 [William Benton] Split closure-serializability failure tests 12ef6e3 [William Benton] Skip proactive closure capture for runJob 8ee3ee7 [William Benton] Predictable closure environment capture 12c63a7 [William Benton] Added tests for variable capture in closures d6e8dd6 [William Benton] Don't check serializability of DStream transforms. 4ecf841 [William Benton] Make proactive serializability checking optional. d8df3db [William Benton] Adds proactive closure-serializablilty checking 21b4b06 [William Benton] Test cases for SPARK-897. d5947b3 [William Benton] Ensure assertions in Graph.apply are asserted.
* [SPARK-1357 (fix)] remove empty line after :: DeveloperApi/Experimental ::Xiangrui Meng2014-04-0933-71/+21
| | | | | | | | | | Remove empty line after :: DeveloperApi/Experimental :: in comments to make the original doc show up in the preview of the generated html docs. Thanks @andrewor14 ! Author: Xiangrui Meng <meng@databricks.com> Closes #373 from mengxr/api and squashes the following commits: 9c35bdc [Xiangrui Meng] remove the empty line after :: DeveloperApi/Experimental ::
* SPARK-1407 drain event queue before stopping event loggerKan Zhang2014-04-094-16/+67
| | | | | | | | | Author: Kan Zhang <kzhang@apache.org> Closes #366 from kanzhang/SPARK-1407 and squashes the following commits: cd0629f [Kan Zhang] code refactoring and adding test b073ee6 [Kan Zhang] SPARK-1407 drain event queue before stopping event logger
* [SPARK-1357] [MLLIB] Annotate developer and experimental APIsXiangrui Meng2014-04-0942-122/+355
| | | | | | | | | | | | | | | | | | | | | Annotate developer and experimental APIs in MLlib. Author: Xiangrui Meng <meng@databricks.com> Closes #298 from mengxr/api and squashes the following commits: 13390e8 [Xiangrui Meng] Merge branch 'master' into api dc4cbb3 [Xiangrui Meng] mark distribute matrices experimental 6b9f8e2 [Xiangrui Meng] add Experimental annotation 8773d0d [Xiangrui Meng] add DeveloperApi annotation da31733 [Xiangrui Meng] update developer and experimental tags 555e0fe [Xiangrui Meng] Merge branch 'master' into api ef1a717 [Xiangrui Meng] mark some constructors private add default parameters to JavaDoc 00ffbcc [Xiangrui Meng] update tree API annotation 0b674fa [Xiangrui Meng] mark decision tree APIs 86b9e34 [Xiangrui Meng] one pass over APIs of GLMs, NaiveBayes, and ALS f21d862 [Xiangrui Meng] Merge branch 'master' into api 2b133d6 [Xiangrui Meng] intial annotation of developer and experimental apis
* SPARK-1093: Annotate developer and experimental API'sPatrick Wendell2014-04-0984-130/+614
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch marks some existing classes as private[spark] and adds two types of API annotations: - `EXPERIMENTAL API` = experimental user-facing module - `DEVELOPER API - UNSTABLE` = developer-facing API that might change There is some discussion of the different mechanisms for doing this here: https://issues.apache.org/jira/browse/SPARK-1081 I was pretty aggressive with marking things private. Keep in mind that if we want to open something up in the future we can, but we can never reduce visibility. A few notes here: - In the past we've been inconsistent with the visiblity of the X-RDD classes. This patch marks them private whenever there is an existing function in RDD that can directly creat them (e.g. CoalescedRDD and rdd.coalesce()). One trade-off here is users can't subclass them. - Noted that compression and serialization formats don't have to be wire compatible across versions. - Compression codecs and serialization formats are semi-private as users typically don't instantiate them directly. - Metrics sources are made private - user only interacts with them through Spark's reflection Author: Patrick Wendell <pwendell@gmail.com> Author: Andrew Or <andrewor14@gmail.com> Closes #274 from pwendell/private-apis and squashes the following commits: 44179e4 [Patrick Wendell] Merge remote-tracking branch 'apache-github/master' into private-apis 042c803 [Patrick Wendell] spark.annotations -> spark.annotation bfe7b52 [Patrick Wendell] Adding experimental for approximate counts 8d0c873 [Patrick Wendell] Warning in SparkEnv 99b223a [Patrick Wendell] Cleaning up annotations e849f64 [Patrick Wendell] Merge pull request #2 from andrewor14/annotations 982a473 [Andrew Or] Generalize jQuery matching for non Spark-core API docs a01c076 [Patrick Wendell] Merge pull request #1 from andrewor14/annotations c1bcb41 [Andrew Or] DeveloperAPI -> DeveloperApi 0d48908 [Andrew Or] Comments and new lines (minor) f3954e0 [Andrew Or] Add identifier tags in comments to work around scaladocs bug 99192ef [Andrew Or] Dynamically add badges based on annotations 824011b [Andrew Or] Add support for injecting arbitrary JavaScript to API docs 037755c [Patrick Wendell] Some changes after working with andrew or f7d124f [Patrick Wendell] Small fixes c318b24 [Patrick Wendell] Use CSS styles e4c76b9 [Patrick Wendell] Logging f390b13 [Patrick Wendell] Better visibility for workaround constructors d6b0afd [Patrick Wendell] Small chang to existing constructor 403ba52 [Patrick Wendell] Style fix 870a7ba [Patrick Wendell] Work around for SI-8479 7fb13b2 [Patrick Wendell] Changes to UnionRDD and EmptyRDD 4a9e90c [Patrick Wendell] EXPERIMENTAL API --> EXPERIMENTAL c581dce [Patrick Wendell] Changes after building against Shark. 8452309 [Patrick Wendell] Style fixes 1ed27d2 [Patrick Wendell] Formatting and coloring of badges cd7a465 [Patrick Wendell] Code review feedback 2f706f1 [Patrick Wendell] Don't use floats 542a736 [Patrick Wendell] Small fixes cf23ec6 [Patrick Wendell] Marking GraphX as alpha d86818e [Patrick Wendell] Another naming change 5a76ed6 [Patrick Wendell] More visiblity clean-up 42c1f09 [Patrick Wendell] Using better labels 9d48cbf [Patrick Wendell] Initial pass
* [SPARK-1390] Refactoring of matrices backed by RDDsXiangrui Meng2014-04-0822-1102/+1280
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is to refactor interfaces for matrices backed by RDDs. It would be better if we have a clear separation of local matrices and those backed by RDDs. Right now, we have 1. `org.apache.spark.mllib.linalg.SparseMatrix`, which is a wrapper over an RDD of matrix entries, i.e., coordinate list format. 2. `org.apache.spark.mllib.linalg.TallSkinnyDenseMatrix`, which is a wrapper over RDD[Array[Double]], i.e. row-oriented format. We will see naming collision when we introduce local `SparseMatrix`, and the name `TallSkinnyDenseMatrix` is not exact if we switch to `RDD[Vector]` from `RDD[Array[Double]]`. It would be better to have "RDD" in the class name to suggest that operations may trigger jobs. The proposed names are (all under `org.apache.spark.mllib.linalg.rdd`): 1. `RDDMatrix`: trait for matrices backed by one or more RDDs 2. `CoordinateRDDMatrix`: wrapper of `RDD[(Long, Long, Double)]` 3. `RowRDDMatrix`: wrapper of `RDD[Vector]` whose rows do not have special ordering 4. `IndexedRowRDDMatrix`: wrapper of `RDD[(Long, Vector)]` whose rows are associated with indices The current code also introduces local matrices. Author: Xiangrui Meng <meng@databricks.com> Closes #296 from mengxr/mat and squashes the following commits: 24d8294 [Xiangrui Meng] fix for groupBy returning Iterable bfc2b26 [Xiangrui Meng] merge master 8e4f1f5 [Xiangrui Meng] Merge branch 'master' into mat 0135193 [Xiangrui Meng] address Reza's comments 03cd7e1 [Xiangrui Meng] add pca/gram to IndexedRowMatrix add toBreeze to DistributedMatrix for test simplify tests b177ff1 [Xiangrui Meng] address Matei's comments be119fe [Xiangrui Meng] rename m/n to numRows/numCols for local matrix add tests for matrices b881506 [Xiangrui Meng] rename SparkPCA/SVD to TallSkinnyPCA/SVD e7d0d4a [Xiangrui Meng] move IndexedRDDMatrixRow to IndexedRowRDDMatrix 0d1491c [Xiangrui Meng] fix test errors a85262a [Xiangrui Meng] rename RDDMatrixRow to IndexedRDDMatrixRow b8b6ac3 [Xiangrui Meng] Remove old code 4cf679c [Xiangrui Meng] port pca to RowRDDMatrix, and add multiply and covariance 7836e2f [Xiangrui Meng] initial refactoring of matrices backed by RDDs
* Spark-939: allow user jars to take precedence over spark jarsHolden Karau2014-04-0810-21/+287
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I still need to do a small bit of re-factoring [mostly the one Java file I'll switch it back to a Scala file and use it in both the close loaders], but comments on other things I should do would be great. Author: Holden Karau <holden@pigscanfly.ca> Closes #217 from holdenk/spark-939-allow-user-jars-to-take-precedence-over-spark-jars and squashes the following commits: cf0cac9 [Holden Karau] Fix the executorclassloader 1955232 [Holden Karau] Fix long line in TestUtils 8f89965 [Holden Karau] Fix tests for new class name 7546549 [Holden Karau] CR feedback, merge some of the testutils methods down, rename the classloader 644719f [Holden Karau] User the class generator for the repl class loader tests too f0b7114 [Holden Karau] Fix the core/src/test/scala/org/apache/spark/executor/ExecutorURLClassLoaderSuite.scala tests 204b199 [Holden Karau] Fix the generated classes 9f68f10 [Holden Karau] Start rewriting the ExecutorURLClassLoaderSuite to not use the hard coded classes 858aba2 [Holden Karau] Remove a bunch of test junk 261aaee [Holden Karau] simplify executorurlclassloader a bit 7a7bf5f [Holden Karau] CR feedback d4ae848 [Holden Karau] rewrite component into scala aa95083 [Holden Karau] CR feedback 7752594 [Holden Karau] re-add https comment a0ef85a [Holden Karau] Fix style issues 125ea7f [Holden Karau] Easier to just remove those files, we don't need them bb8d179 [Holden Karau] Fix issues with the repl class loader 241b03d [Holden Karau] fix my rat excludes a343350 [Holden Karau] Update rat-excludes and remove a useless file d90d217 [Holden Karau] Fix fall back with custom class loader and add a test for it 4919bf9 [Holden Karau] Fix parent calling class loader issue 8a67302 [Holden Karau] Test are good 9e2d236 [Holden Karau] It works comrade 691ee00 [Holden Karau] It works ish dc4fe44 [Holden Karau] Does not depend on being in my home directory 47046ff [Holden Karau] Remove bad import' 22d83cb [Holden Karau] Add a test suite for the executor url class loader suite 7ef4628 [Holden Karau] Clean up 792d961 [Holden Karau] Almost works 16aecd1 [Holden Karau] Doesn't quite work 8d2241e [Holden Karau] Adda FakeClass for testing ClassLoader precedence options 648b559 [Holden Karau] Both class loaders compile. Now for testing e1d9f71 [Holden Karau] One loader workers.
* [SPARK-1434] [MLLIB] change labelParser from anonymous function to traitXiangrui Meng2014-04-084-25/+97
| | | | | | | | | | | | | | | | This is a patch to address @mateiz 's comment in https://github.com/apache/spark/pull/245 MLUtils#loadLibSVMData uses an anonymous function for the label parser. Java users won't like it. So I make a trait for LabelParser and provide two implementations: binary and multiclass. Author: Xiangrui Meng <meng@databricks.com> Closes #345 from mengxr/label-parser and squashes the following commits: ac44409 [Xiangrui Meng] use singleton objects for label parsers 3b1a7c6 [Xiangrui Meng] add tests for label parsers c2e571c [Xiangrui Meng] rename LabelParser.apply to LabelParser.parse use extends for singleton 11c94e0 [Xiangrui Meng] add return types 7f8eb36 [Xiangrui Meng] change labelParser from annoymous function to trait
* Spark 1271: Co-Group and Group-By should pass Iterable[X]Holden Karau2014-04-0824-153/+252
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #242 from holdenk/spark-1320-cogroupandgroupshouldpassiterator and squashes the following commits: f289536 [Holden Karau] Fix bad merge, should have been Iterable rather than Iterator 77048f8 [Holden Karau] Fix merge up to master d3fe909 [Holden Karau] use toSeq instead 7a092a3 [Holden Karau] switch resultitr to resultiterable eb06216 [Holden Karau] maybe I should have had a coffee first. use correct import for guava iterables c5075aa [Holden Karau] If guava 14 had iterables 2d06e10 [Holden Karau] Fix Java 8 cogroup tests for the new API 11e730c [Holden Karau] Fix streaming tests 66b583d [Holden Karau] Fix the core test suite to compile 4ed579b [Holden Karau] Refactor from iterator to iterable d052c07 [Holden Karau] Python tests now pass with iterator pandas 3bcd81d [Holden Karau] Revert "Try and make pickling list iterators work" cd1e81c [Holden Karau] Try and make pickling list iterators work c60233a [Holden Karau] Start investigating moving to iterators for python API like the Java/Scala one. tl;dr: We will have to write our own iterator since the default one doesn't pickle well 88a5cef [Holden Karau] Fix cogroup test in JavaAPISuite for streaming a5ee714 [Holden Karau] oops, was checking wrong iterator e687f21 [Holden Karau] Fix groupbykey test in JavaAPISuite of streaming ec8cc3e [Holden Karau] Fix test issues\! 4b0eeb9 [Holden Karau] Switch cast in PairDStreamFunctions fa395c9 [Holden Karau] Revert "Add a join based on the problem in SVD" ec99e32 [Holden Karau] Revert "Revert this but for now put things in list pandas" b692868 [Holden Karau] Revert 7e533f7 [Holden Karau] Fix the bug 8a5153a [Holden Karau] Revert me, but we have some stuff to debug b4e86a9 [Holden Karau] Add a join based on the problem in SVD c4510e2 [Holden Karau] Revert this but for now put things in list pandas b4e0b1d [Holden Karau] Fix style issues 71e8b9f [Holden Karau] I really need to stop calling size on iterators, it is the path of sadness. b1ae51a [Holden Karau] Fix some of the types in the streaming JavaAPI suite. Probably still needs more work 37888ec [Holden Karau] core/tests now pass 249abde [Holden Karau] org.apache.spark.rdd.PairRDDFunctionsSuite passes 6698186 [Holden Karau] Revert "I think this might be a bad rabbit hole. Started work to make CoGroupedRDD use iterator and then went crazy" fe992fe [Holden Karau] hmmm try and fix up basic operation suite 172705c [Holden Karau] Fix Java API suite caafa63 [Holden Karau] I think this might be a bad rabbit hole. Started work to make CoGroupedRDD use iterator and then went crazy 88b3329 [Holden Karau] Fix groupbykey to actually give back an iterator 4991af6 [Holden Karau] Fix some tests be50246 [Holden Karau] Calling size on an iterator is not so good if we want to use it after 687ffbc [Holden Karau] This is the it compiles point of replacing Seq with Iterator and JList with JIterator in the groupby and cogroup signatures
* SPARK-1433: Upgrade Mesos dependency to 0.17.0Sandeep2014-04-085-8/+10
| | | | | | | | | | | Mesos 0.13.0 was released 6 months ago. Upgrade Mesos dependency to 0.17.0 Author: Sandeep <sandeep@techaddict.me> Closes #355 from techaddict/mesos_update and squashes the following commits: f1abeee [Sandeep] SPARK-1433: Upgrade Mesos dependency to 0.17.0 Mesos 0.13.0 was released 6 months ago. Upgrade Mesos dependency to 0.17.0
* [SPARK-1397] Notify SparkListeners when stages fail or are cancelled.Kay Ousterhout2014-04-0811-78/+151
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | [I wanted to post this for folks to comment but it depends on (and thus includes the changes in) a currently outstanding PR, #305. You can look at just the second commit: https://github.com/kayousterhout/spark-1/commit/93f08baf731b9eaf5c9792a5373560526e2bccac to see just the changes relevant to this PR] Previously, when stages fail or get cancelled, the SparkListener is only notified indirectly through the SparkListenerJobEnd, where we sometimes pass in a single stage that failed. This worked before job cancellation, because jobs would only fail due to a single stage failure. However, with job cancellation, multiple running stages can fail when a job gets cancelled. Right now, this is not handled correctly, which results in stages that get stuck in the “Running Stages” window in the UI even though they’re dead. This PR changes the SparkListenerStageCompleted event to a SparkListenerStageEnded event, and uses this event to tell SparkListeners when stages fail in addition to when they complete successfully. This change is NOT publicly backward compatible for two reasons. First, it changes the SparkListener interface. We could alternately add a new event, SparkListenerStageFailed, and keep the existing SparkListenerStageCompleted. However, this is less consistent with the listener events for tasks / jobs ending, and will result in some code duplication for listeners (because failed and completed stages are handled in similar ways). Note that I haven’t finished updating the JSON code to correctly handle the new event because I’m waiting for feedback on whether this is a good or bad idea (hence the “WIP”). It is also not backwards compatible because it changes the publicly visible JobWaiter.jobFailed() method to no longer include a stage that caused the failure. I think this change should definitely stay, because with cancellation (as described above), a failure isn’t necessarily caused by a single stage. Author: Kay Ousterhout <kayousterhout@gmail.com> Closes #309 from kayousterhout/stage_cancellation and squashes the following commits: 5533ecd [Kay Ousterhout] Fixes in response to Mark's review 320c7c7 [Kay Ousterhout] Notify SparkListeners when stages fail or are cancelled.
* SPARK-1445: compute-classpath should not print error if lib_managed not foundAaron Davidson2014-04-081-1/+1
| | | | | | | | | | This was added to the check for the assembly jar, forgot it for the datanucleus jars. Author: Aaron Davidson <aaron@databricks.com> Closes #361 from aarondav/cc and squashes the following commits: 8facc16 [Aaron Davidson] SPARK-1445: compute-classpath should not print error if lib_managed not found
* SPARK-1348 binding Master, Worker, and App Web UI to all interfacesKan Zhang2014-04-083-3/+3
| | | | | | | | | Author: Kan Zhang <kzhang@apache.org> Closes #318 from kanzhang/SPARK-1348 and squashes the following commits: e625a5f [Kan Zhang] reverting the changes to startJettyServer() 7a8084e [Kan Zhang] SPARK-1348 binding Master, Worker, and App Web UI to all interfaces
* Remove extra semicolon in import statement and unused import in ↵Henry Saputra2014-04-081-2/+1
| | | | | | | | | | | | ApplicationMaster Small nit cleanup to remove extra semicolon and unused import in Yarn's stable ApplicationMaster (it bothers me every time I saw it) Author: Henry Saputra <hsaputra@apache.org> Closes #358 from hsaputra/nitcleanup_removesemicolon_import_applicationmaster and squashes the following commits: bffb685 [Henry Saputra] Remove extra semicolon in import statement and unused import in ApplicationMaster.scala
* [SPARK-1396] Properly cleanup DAGScheduler on job cancellation.Kay Ousterhout2014-04-082-21/+115
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Previously, when jobs were cancelled, not all of the state in the DAGScheduler was cleaned up, leading to a slow memory leak in the DAGScheduler. As we expose easier ways to cancel jobs, it's more important to fix these issues. This commit also fixes a second and less serious problem, which is that previously, when a stage failed, not all of the appropriate stages were cancelled. See the "failure of stage used by two jobs" test for an example of this. This just meant that extra work was done, and is not a correctness problem. This commit adds 3 tests. “run shuffle with map stage failure” is a new test to more thoroughly test this functionality, and passes on both the old and new versions of the code. “trivial job cancellation” fails on the old code because all state wasn’t cleaned up correctly when jobs were cancelled (we didn’t remove the job from resultStageToJob). “failure of stage used by two jobs” fails on the old code because taskScheduler.cancelTasks wasn’t called for one of the stages (see test comments). This should be checked in before #246, which makes it easier to cancel stages / jobs. Author: Kay Ousterhout <kayousterhout@gmail.com> Closes #305 from kayousterhout/incremental_abort_fix and squashes the following commits: f33d844 [Kay Ousterhout] Mark review comments 9217080 [Kay Ousterhout] Properly cleanup DAGScheduler on job cancellation.
* [SPARK-1331] Added graceful shutdown to Spark StreamingTathagata Das2014-04-0815-215/+552
| | | | | | | | | | | | | | | | | | | | | Current version of StreamingContext.stop() directly kills all the data receivers (NetworkReceiver) without waiting for the data already received to be persisted and processed. This PR provides the fix. Now, when the StreamingContext.stop() is called, the following sequence of steps will happen. 1. The driver will send a stop signal to all the active receivers. 2. Each receiver, when it gets a stop signal from the driver, first stop receiving more data, then waits for the thread that persists data blocks to BlockManager to finish persisting all receive data, and finally quits. 3. After all the receivers have stopped, the driver will wait for the Job Generator and Job Scheduler to finish processing all the received data. It also fixes the semantics of StreamingContext.start and stop. It will throw appropriate errors and warnings if stop() is called before start(), stop() is called twice, etc. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #247 from tdas/graceful-shutdown and squashes the following commits: 61c0016 [Tathagata Das] Updated MIMA binary check excludes. ae1d39b [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into graceful-shutdown 6b59cfc [Tathagata Das] Minor changes based on Andrew's comment on PR. d0b8d65 [Tathagata Das] Reduced time taken by graceful shutdown unit test. f55bc67 [Tathagata Das] Fix scalastyle c69b3a7 [Tathagata Das] Updates based on Patrick's comments. c43b8ae [Tathagata Das] Added graceful shutdown to Spark Streaming.
* [SPARK-1103] Automatic garbage collection of RDD, shuffle and broadcast dataTathagata Das2014-04-0740-469/+2571
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR allows Spark to automatically cleanup metadata and data related to persisted RDDs, shuffles and broadcast variables when the corresponding RDDs, shuffles and broadcast variables fall out of scope from the driver program. This is still a work in progress as broadcast cleanup has not been implemented. **Implementation Details** A new class `ContextCleaner` is responsible cleaning all the state. It is instantiated as part of a `SparkContext`. RDD and ShuffleDependency classes have overridden `finalize()` function that gets called whenever their instances go out of scope. The `finalize()` function enqueues the object’s identifier (i.e. RDD ID, shuffle ID, etc.) with the `ContextCleaner`, which is a very short and cheap operation and should not significantly affect the garbage collection mechanism. The `ContextCleaner`, on a different thread, performs the cleanup, whose details are given below. *RDD cleanup:* `ContextCleaner` calls `RDD.unpersist()` is used to cleanup persisted RDDs. Regarding metadata, the DAGScheduler automatically cleans up all metadata related to a RDD after all jobs have completed. Only the `SparkContext.persistentRDDs` keeps strong references to persisted RDDs. The `TimeStampedHashMap` used for that has been replaced by `TimeStampedWeakValueHashMap` that keeps only weak references to the RDDs, allowing them to be garbage collected. *Shuffle cleanup:* New BlockManager message `RemoveShuffle(<shuffle ID>)` asks the `BlockManagerMaster` and currently active `BlockManager`s to delete all the disk blocks related to the shuffle ID. `ContextCleaner` cleans up shuffle data using this message and also cleans up the metadata in the `MapOutputTracker` of the driver. The `MapOutputTracker` at the workers, that caches the shuffle metadata, maintains a `BoundedHashMap` to limit the shuffle information it caches. Refetching the shuffle information from the driver is not too costly. *Broadcast cleanup:* To be done. [This PR](https://github.com/apache/incubator-spark/pull/543/) adds mechanism for explicit cleanup of broadcast variables. `Broadcast.finalize()` will enqueue its own ID with ContextCleaner and the PRs mechanism will be used to unpersist the Broadcast data. *Other cleanup:* `ShuffleMapTask` and `ResultTask` caches tasks and used TTL based cleanup (using `TimeStampedHashMap`), so nothing got cleaned up if TTL was not set. Instead, they now use `BoundedHashMap` to keep a limited number of map output information. Cost of repopulating the cache if necessary is very small. **Current state of implementation** Implemented RDD and shuffle cleanup. Things left to be done are. - Cleaning up for broadcast variable still to be done. - Automatic cleaning up keys with empty weak refs as values in `TimeStampedWeakValueHashMap` Author: Tathagata Das <tathagata.das1565@gmail.com> Author: Andrew Or <andrewor14@gmail.com> Author: Roman Pastukhov <ignatich@mail.ru> Closes #126 from tdas/state-cleanup and squashes the following commits: 61b8d6e [Tathagata Das] Fixed issue with Tachyon + new BlockManager methods. f489fdc [Tathagata Das] Merge remote-tracking branch 'apache/master' into state-cleanup d25a86e [Tathagata Das] Fixed stupid typo. cff023c [Tathagata Das] Fixed issues based on Andrew's comments. 4d05314 [Tathagata Das] Scala style fix. 2b95b5e [Tathagata Das] Added more documentation on Broadcast implementations, specially which blocks are told about to the driver. Also, fixed Broadcast API to hide destroy functionality. 41c9ece [Tathagata Das] Added more unit tests for BlockManager, DiskBlockManager, and ContextCleaner. 6222697 [Tathagata Das] Fixed bug and adding unit test for removeBroadcast in BlockManagerSuite. 104a89a [Tathagata Das] Fixed failing BroadcastSuite unit tests by introducing blocking for removeShuffle and removeBroadcast in BlockManager* a430f06 [Tathagata Das] Fixed compilation errors. b27f8e8 [Tathagata Das] Merge pull request #3 from andrewor14/cleanup cd72d19 [Andrew Or] Make automatic cleanup configurable (not documented) ada45f0 [Andrew Or] Merge branch 'state-cleanup' of github.com:tdas/spark into cleanup a2cc8bc [Tathagata Das] Merge remote-tracking branch 'apache/master' into state-cleanup c5b1d98 [Andrew Or] Address Patrick's comments a6460d4 [Andrew Or] Merge github.com:apache/spark into cleanup 762a4d8 [Tathagata Das] Merge pull request #1 from andrewor14/cleanup f0aabb1 [Andrew Or] Correct semantics for TimeStampedWeakValueHashMap + add tests 5016375 [Andrew Or] Address TD's comments 7ed72fb [Andrew Or] Fix style test fail + remove verbose test message regarding broadcast 634a097 [Andrew Or] Merge branch 'state-cleanup' of github.com:tdas/spark into cleanup 7edbc98 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into state-cleanup 8557c12 [Andrew Or] Merge github.com:apache/spark into cleanup e442246 [Andrew Or] Merge github.com:apache/spark into cleanup 88904a3 [Andrew Or] Make TimeStampedWeakValueHashMap a wrapper of TimeStampedHashMap fbfeec8 [Andrew Or] Add functionality to query executors for their local BlockStatuses 34f436f [Andrew Or] Generalize BroadcastBlockId to remove BroadcastHelperBlockId 0d17060 [Andrew Or] Import, comments, and style fixes (minor) c92e4d9 [Andrew Or] Merge github.com:apache/spark into cleanup f201a8d [Andrew Or] Test broadcast cleanup in ContextCleanerSuite + remove BoundedHashMap e95479c [Andrew Or] Add tests for unpersisting broadcast 544ac86 [Andrew Or] Clean up broadcast blocks through BlockManager* d0edef3 [Andrew Or] Add framework for broadcast cleanup ba52e00 [Andrew Or] Refactor broadcast classes c7ccef1 [Andrew Or] Merge branch 'bc-unpersist-merge' of github.com:ignatich/incubator-spark into cleanup 6c9dcf6 [Tathagata Das] Added missing Apache license d2f8b97 [Tathagata Das] Removed duplicate unpersistRDD. a007307 [Tathagata Das] Merge remote-tracking branch 'apache/master' into state-cleanup 620eca3 [Tathagata Das] Changes based on PR comments. f2881fd [Tathagata Das] Changed ContextCleaner to use ReferenceQueue instead of finalizer e1fba5f [Tathagata Das] Style fix 892b952 [Tathagata Das] Removed use of BoundedHashMap, and made BlockManagerSlaveActor cleanup shuffle metadata in MapOutputTrackerWorker. a7260d3 [Tathagata Das] Added try-catch in context cleaner and null value cleaning in TimeStampedWeakValueHashMap. e61daa0 [Tathagata Das] Modifications based on the comments on PR 126. ae9da88 [Tathagata Das] Removed unncessary TimeStampedHashMap from DAGScheduler, added try-catches in finalize() methods, and replaced ArrayBlockingQueue to LinkedBlockingQueue to avoid blocking in Java's finalizing thread. cb0a5a6 [Tathagata Das] Fixed docs and styles. a24fefc [Tathagata Das] Merge remote-tracking branch 'apache/master' into state-cleanup 8512612 [Tathagata Das] Changed TimeStampedHashMap to use WrappedJavaHashMap. e427a9e [Tathagata Das] Added ContextCleaner to automatically clean RDDs and shuffles when they fall out of scope. Also replaced TimeStampedHashMap to BoundedHashMaps and TimeStampedWeakValueHashMap for the necessary hashmap behavior. 80dd977 [Roman Pastukhov] Fix for Broadcast unpersist patch. 1e752f1 [Roman Pastukhov] Added unpersist method to Broadcast.
* [SPARK-1402] Added 3 more compression schemesCheng Lian2014-04-0711-179/+586
| | | | | | | | | | | | | | | | | | | | | | | JIRA issue: [SPARK-1402](https://issues.apache.org/jira/browse/SPARK-1402) This PR provides 3 more compression schemes for Spark SQL in-memory columnar storage: * `BooleanBitSet` * `IntDelta` * `LongDelta` Now there are 6 compression schemes in total, including the no-op `PassThrough` scheme. Also fixed a bug in PR #286: not all compression schemes are added as available schemes when accessing an in-memory column, and when a column is compressed with an unrecognised scheme, `ColumnAccessor` throws exception. Author: Cheng Lian <lian.cs.zju@gmail.com> Closes #330 from liancheng/moreCompressionSchemes and squashes the following commits: 1d037b8 [Cheng Lian] Fixed SPARK-1436: in-memory column byte buffer must be able to be accessed multiple times d7c0e8f [Cheng Lian] Added test suite for IntegralDelta (IntDelta & LongDelta) 3c1ad7a [Cheng Lian] Added test suite for BooleanBitSet, refactored other test suites 44fe4b2 [Cheng Lian] Refactored CompressionScheme, added 3 more compression schemes.
* Change timestamp cast semantics. When cast to numeric types, return the unix ↵Reynold Xin2014-04-073-12/+40
| | | | | | | | | | | | | time in seconds (instead of millis). @marmbrus @chenghao-intel Author: Reynold Xin <rxin@apache.org> Closes #352 from rxin/timestamp-cast and squashes the following commits: 18aacd3 [Reynold Xin] Fixed precision for double. 2adb235 [Reynold Xin] Change timestamp cast semantics. When cast to numeric types, return the unix time in seconds (instead of millis).
* Added eval for Rand (without any support for user-defined seed).Reynold Xin2014-04-071-3/+10
| | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #349 from rxin/rand and squashes the following commits: fd11322 [Reynold Xin] Added eval for Rand (without any support for user-defined seed).
* Removed the default eval implementation from Expression, and added a bunch ↵Reynold Xin2014-04-078-45/+89
| | | | | | | | | | | | of override's in classes I touched. It is more robust to not provide a default implementation for Expression's. Author: Reynold Xin <rxin@apache.org> Closes #350 from rxin/eval-default and squashes the following commits: 0a83b8f [Reynold Xin] Removed the default eval implementation from Expression, and added a bunch of override's in classes I touched.
* [sql] Rename execution/aggregates.scala Aggregate.scala, and added a bunch ↵Reynold Xin2014-04-071-9/+9
| | | | | | | | | | of private[this] to variables. Author: Reynold Xin <rxin@apache.org> Closes #348 from rxin/aggregate and squashes the following commits: f4bc36f [Reynold Xin] Rename execution/aggregates.scala Aggregate.scala, and added a bunch of private[this] to variables.
* SPARK-1099: Introduce local[*] mode to infer number of coresAaron Davidson2014-04-077-12/+25
| | | | | | | | | | | This is the default mode for running spark-shell and pyspark, intended to allow users running spark for the first time to see the performance benefits of using multiple cores, while not breaking backwards compatibility for users who use "local" mode and expect exactly 1 core. Author: Aaron Davidson <aaron@databricks.com> Closes #182 from aarondav/110 and squashes the following commits: a88294c [Aaron Davidson] Rebased changes for new spark-shell a9f393e [Aaron Davidson] SPARK-1099: Introduce local[*] mode to infer number of cores
* HOTFIX: Disable actor input stream test.Patrick Wendell2014-04-071-2/+2
| | | | | | | | | | This test makes incorrect assumptions about the behavior of Thread.sleep(). Author: Patrick Wendell <pwendell@gmail.com> Closes #347 from pwendell/stream-tests and squashes the following commits: 10e09e0 [Patrick Wendell] HOTFIX: Disable actor input stream.
* SPARK-1252. On YARN, use container-log4j.properties for executorsSandy Ryza2014-04-077-5/+53
| | | | | | | | | | | | | | | | | container-log4j.properties is a file that YARN provides so that containers can have log4j.properties distinct from that of the NodeManagers. Logs now go to syslog, and stderr and stdout just have the process's standard err and standard out. I tested this on pseudo-distributed clusters for both yarn (Hadoop 2.2) and yarn-alpha (Hadoop 0.23.7)/ Author: Sandy Ryza <sandy@cloudera.com> Closes #148 from sryza/sandy-spark-1252 and squashes the following commits: c0043b8 [Sandy Ryza] Put log4j.properties file under common 55823da [Sandy Ryza] Add license headers to new files 10934b8 [Sandy Ryza] Add log4j-spark-container.properties and support SPARK_LOG4J_CONF e74450b [Sandy Ryza] SPARK-1252. On YARN, use container-log4j.properties for executors
* [sql] Rename Expression.apply to eval for better readability.Reynold Xin2014-04-0724-159/+156
| | | | | | | | | | | | | | Also used this opportunity to add a bunch of override's and made some members private. Author: Reynold Xin <rxin@apache.org> Closes #340 from rxin/eval and squashes the following commits: a7c7ca7 [Reynold Xin] Fixed conflicts in merge. 9069de6 [Reynold Xin] Merge branch 'master' into eval 3ccc313 [Reynold Xin] Merge branch 'master' into eval 1a47e10 [Reynold Xin] Renamed apply to eval for generators and added a bunch of override's. ea061de [Reynold Xin] Rename Expression.apply to eval for better readability.
* SPARK-1432: Make sure that all metadata fields are properly cleanedDavis Shepherd2014-04-071-2/+3
| | | | | | | | | | While working on spark-1337 with @pwendell, we noticed that not all of the metadata maps in JobProgessListener were being properly cleaned. This could lead to a (hypothetical) memory leak issue should a job run long enough. This patch aims to address the issue. Author: Davis Shepherd <davis@conviva.com> Closes #338 from dgshep/master and squashes the following commits: a77b65c [Davis Shepherd] In the contex of SPARK-1337: Make sure that all metadata fields are properly cleaned
* [SQL] SPARK-1427 Fix toString for SchemaRDD NativeCommands.Michael Armbrust2014-04-074-2/+13
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #343 from marmbrus/toStringFix and squashes the following commits: 37198fe [Michael Armbrust] Fix toString for SchemaRDD NativeCommands.
* [SQL] SPARK-1371 Hash Aggregation ImprovementsMichael Armbrust2014-04-078-160/+157
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Given: ```scala case class Data(a: Int, b: Int) val rdd = sparkContext .parallelize(1 to 200) .flatMap(_ => (1 to 50000).map(i => Data(i % 100, i))) rdd.registerAsTable("data") cacheTable("data") ``` Before: ``` SELECT COUNT(*) FROM data:[10000000] 16795.567ms SELECT a, SUM(b) FROM data GROUP BY a 7536.436ms SELECT SUM(b) FROM data 10954.1ms ``` After: ``` SELECT COUNT(*) FROM data:[10000000] 1372.175ms SELECT a, SUM(b) FROM data GROUP BY a 2070.446ms SELECT SUM(b) FROM data 958.969ms ``` Author: Michael Armbrust <michael@databricks.com> Closes #295 from marmbrus/hashAgg and squashes the following commits: ec63575 [Michael Armbrust] Add comment. d0495a9 [Michael Armbrust] Use scaladoc instead. b4a6887 [Michael Armbrust] Address review comments. a2d90ba [Michael Armbrust] Capture child output statically to avoid issues with generators and serialization. 7c13112 [Michael Armbrust] Rewrite Aggregate operator to stream input and use projections. Remove unused local RDD functions implicits. 5096f99 [Michael Armbrust] Make HiveUDAF fields transient since object inspectors are not serializable. 6a4b671 [Michael Armbrust] Add option to avoid binding operators expressions automatically. 92cca08 [Michael Armbrust] Always include serialization debug info when running tests. 1279df2 [Michael Armbrust] Increase default number of partitions.
* SPARK-1431: Allow merging conflicting pull requestsPatrick Wendell2014-04-061-4/+22
| | | | | | | | | | | Sometimes if there is a small conflict it's nice to be able to just manually fix it up rather than have another RTT with the contributor. Author: Patrick Wendell <pwendell@gmail.com> Closes #342 from pwendell/merge-conflicts and squashes the following commits: cdce61a [Patrick Wendell] SPARK-1431: Allow merging conflicting pull requests
* SPARK-1154: Clean up app folders in worker nodesEvan Chan2014-04-065-4/+83
| | | | | | | | | | | | | | | | | | | | | | | | | | | This is a fix for [SPARK-1154](https://issues.apache.org/jira/browse/SPARK-1154). The issue is that worker nodes fill up with a huge number of app-* folders after some time. This change adds a periodic cleanup task which asynchronously deletes app directories older than a configurable TTL. Two new configuration parameters have been introduced: spark.worker.cleanup_interval spark.worker.app_data_ttl This change does not include moving the downloads of application jars to a location outside of the work directory. We will address that if we have time, but that potentially involves caching so it will come either as part of this PR or a separate PR. Author: Evan Chan <ev@ooyala.com> Author: Kelvin Chu <kelvinkwchu@yahoo.com> Closes #288 from velvia/SPARK-1154-cleanup-app-folders and squashes the following commits: 0689995 [Evan Chan] CR from @aarondav - move config, clarify for standalone mode 9f10d96 [Evan Chan] CR from @pwendell - rename configs and add cleanup.enabled f2f6027 [Evan Chan] CR from @andrewor14 553d8c2 [Kelvin Chu] change the variable name to currentTimeMillis since it actually tracks in seconds 8dc9cb5 [Kelvin Chu] Fixed a bug in Utils.findOldFiles() after merge. cb52f2b [Kelvin Chu] Change the name of findOldestFiles() to findOldFiles() 72f7d2d [Kelvin Chu] Fix a bug of Utils.findOldestFiles(). file.lastModified is returned in milliseconds. ad99955 [Kelvin Chu] Add unit test for Utils.findOldestFiles() dc1a311 [Evan Chan] Don't recompute current time with every new file e3c408e [Evan Chan] Document the two new settings b92752b [Evan Chan] SPARK-1154: Add a periodic task to clean up app directories
* SPARK-1314: Use SPARK_HIVE to determine if we include Hive in packagingAaron Davidson2014-04-068-32/+83
| | | | | | | | | | | | | | | | | | | | | | | | Previously, we based our decision regarding including datanucleus jars based on the existence of a spark-hive-assembly jar, which was incidentally built whenever "sbt assembly" is run. This means that a typical and previously supported pathway would start using hive jars. This patch has the following features/bug fixes: - Use of SPARK_HIVE (default false) to determine if we should include Hive in the assembly jar. - Analagous feature in Maven with -Phive (previously, there was no support for adding Hive to any of our jars produced by Maven) - assemble-deps fixed since we no longer use a different ASSEMBLY_DIR - avoid adding log message in compute-classpath.sh to the classpath :) Still TODO before mergeable: - We need to download the datanucleus jars outside of sbt. Perhaps we can have spark-class download them if SPARK_HIVE is set similar to how sbt downloads itself. - Spark SQL documentation updates. Author: Aaron Davidson <aaron@databricks.com> Closes #237 from aarondav/master and squashes the following commits: 5dc4329 [Aaron Davidson] Typo fixes dd4f298 [Aaron Davidson] Doc update dd1a365 [Aaron Davidson] Eliminate need for SPARK_HIVE at runtime by d/ling datanucleus from Maven a9269b5 [Aaron Davidson] [WIP] Use SPARK_HIVE to determine if we include Hive in packaging
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