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* BUILD: Add more content to make-distribution.sh.Patrick Wendell2014-05-121-0/+13
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* SPARK-1815. SparkContext should not be marked DeveloperApiSandy Ryza2014-05-121-2/+0
| | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #753 from sryza/sandy-spark-1815 and squashes the following commits: 957a8ac [Sandy Ryza] SPARK-1815. SparkContext should not be marked DeveloperApi
* [SPARK-1753 / 1773 / 1814] Update outdated docs for spark-submit, YARN, ↵Andrew Or2014-05-1213-125/+184
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | standalone etc. YARN - SparkPi was updated to not take in master as an argument; we should update the docs to reflect that. - The default YARN build guide should be in maven, not sbt. - This PR also adds a paragraph on steps to debug a YARN application. Standalone - Emphasize spark-submit more. Right now it's one small paragraph preceding the legacy way of launching through `org.apache.spark.deploy.Client`. - The way we set configurations / environment variables according to the old docs is outdated. This needs to reflect changes introduced by the Spark configuration changes we made. In general, this PR also adds a little more documentation on the new spark-shell, spark-submit, spark-defaults.conf etc here and there. Author: Andrew Or <andrewor14@gmail.com> Closes #701 from andrewor14/yarn-docs and squashes the following commits: e2c2312 [Andrew Or] Merge in changes in #752 (SPARK-1814) 25cfe7b [Andrew Or] Merge in the warning from SPARK-1753 a8c39c5 [Andrew Or] Minor changes 336bbd9 [Andrew Or] Tabs -> spaces 4d9d8f7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs 041017a [Andrew Or] Abstract Spark submit documentation to cluster-overview.html 3cc0649 [Andrew Or] Detail how to set configurations + remove legacy instructions 5b7140a [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs 85a51fc [Andrew Or] Update run-example, spark-shell, configuration etc. c10e8c7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs 381fe32 [Andrew Or] Update docs for standalone mode 757c184 [Andrew Or] Add a note about the requirements for the debugging trick f8ca990 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs 924f04c [Andrew Or] Revert addition of --deploy-mode d5fe17b [Andrew Or] Update the YARN docs
* [SPARK-1780] Non-existent SPARK_DAEMON_OPTS is lurking aroundAndrew Or2014-05-122-2/+2
| | | | | | | | | | What they really mean is SPARK_DAEMON_***JAVA***_OPTS Author: Andrew Or <andrewor14@gmail.com> Closes #751 from andrewor14/spark-daemon-opts and squashes the following commits: 70c41f9 [Andrew Or] SPARK_DAEMON_OPTS -> SPARK_DAEMON_JAVA_OPTS
* SPARK-1757 Failing test for saving null primitives with .saveAsParquetFile()Andrew Ash2014-05-122-3/+47
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1757 The first test succeeds, but the second test fails with exception: ``` [info] - save and load case class RDD with Nones as parquet *** FAILED *** (14 milliseconds) [info] java.lang.RuntimeException: Unsupported datatype StructType(List()) [info] at scala.sys.package$.error(package.scala:27) [info] at org.apache.spark.sql.parquet.ParquetTypesConverter$.fromDataType(ParquetRelation.scala:201) [info] at org.apache.spark.sql.parquet.ParquetTypesConverter$$anonfun$1.apply(ParquetRelation.scala:235) [info] at org.apache.spark.sql.parquet.ParquetTypesConverter$$anonfun$1.apply(ParquetRelation.scala:235) [info] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) [info] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) [info] at scala.collection.immutable.List.foreach(List.scala:318) [info] at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) [info] at scala.collection.AbstractTraversable.map(Traversable.scala:105) [info] at org.apache.spark.sql.parquet.ParquetTypesConverter$.convertFromAttributes(ParquetRelation.scala:234) [info] at org.apache.spark.sql.parquet.ParquetTypesConverter$.writeMetaData(ParquetRelation.scala:267) [info] at org.apache.spark.sql.parquet.ParquetRelation$.createEmpty(ParquetRelation.scala:143) [info] at org.apache.spark.sql.parquet.ParquetRelation$.create(ParquetRelation.scala:122) [info] at org.apache.spark.sql.execution.SparkStrategies$ParquetOperations$.apply(SparkStrategies.scala:139) [info] at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58) [info] at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58) [info] at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371) [info] at org.apache.spark.sql.catalyst.planning.QueryPlanner.apply(QueryPlanner.scala:59) [info] at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan$lzycompute(SQLContext.scala:264) [info] at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan(SQLContext.scala:264) [info] at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan$lzycompute(SQLContext.scala:265) [info] at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan(SQLContext.scala:265) [info] at org.apache.spark.sql.SQLContext$QueryExecution.toRdd$lzycompute(SQLContext.scala:268) [info] at org.apache.spark.sql.SQLContext$QueryExecution.toRdd(SQLContext.scala:268) [info] at org.apache.spark.sql.SchemaRDDLike$class.saveAsParquetFile(SchemaRDDLike.scala:66) [info] at org.apache.spark.sql.SchemaRDD.saveAsParquetFile(SchemaRDD.scala:98) ``` Author: Andrew Ash <andrew@andrewash.com> Author: Michael Armbrust <michael@databricks.com> Closes #690 from ash211/rdd-parquet-save and squashes the following commits: 747a0b9 [Andrew Ash] Merge pull request #1 from marmbrus/pr/690 54bd00e [Michael Armbrust] Need to put Option first since Option <: Seq. 8f3f281 [Andrew Ash] SPARK-1757 Add failing test for saving SparkSQL Schemas with Option[?] fields as parquet
* Modify a typo in monitoring.mdKousuke Saruta2014-05-121-1/+1
| | | | | | | | | | | As I mentioned in SPARK-1765, there is a word 'JXM' in monitoring.md. I think it's typo for 'JMX'. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #698 from sarutak/SPARK-1765 and squashes the following commits: bae9843 [Kousuke Saruta] modified a typoe in monitoring.md
* L-BFGS DocumentationDB Tsai2014-05-121-4/+116
| | | | | | | | | | | | | | Documentation for L-BFGS, and an example of training binary L2 logistic regression using L-BFGS. Author: DB Tsai <dbtsai@alpinenow.com> Closes #702 from dbtsai/dbtsai-lbfgs-doc and squashes the following commits: 0712215 [DB Tsai] Update 38fdfa1 [DB Tsai] Removed extra empty line 5745b64 [DB Tsai] Update again e9e418e [DB Tsai] Update 7381521 [DB Tsai] L-BFGS Documentation
* Typo: resond -> respondAndrew Ash2014-05-121-1/+1
| | | | | | | | Author: Andrew Ash <andrew@andrewash.com> Closes #743 from ash211/patch-4 and squashes the following commits: c959f3b [Andrew Ash] Typo: resond -> respond
* [SQL] Make Hive Metastore conversion functions publicly visible.Michael Armbrust2014-05-121-1/+7
| | | | | | | | | | I need this to be public for the implementation of SharkServer2. However, I think this functionality is generally useful and should be pretty stable. Author: Michael Armbrust <michael@databricks.com> Closes #750 from marmbrus/metastoreTypes and squashes the following commits: f51b62e [Michael Armbrust] Make Hive Metastore conversion functions publicly visible.
* Adding hadoop-2.2 profile to the buildPatrick Wendell2014-05-121-2/+2
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* [SPARK-1736] Spark submit for WindowsAndrew Or2014-05-122-3/+58
| | | | | | | | | | | | | Tested on Windows 7. Author: Andrew Or <andrewor14@gmail.com> Closes #745 from andrewor14/windows-submit and squashes the following commits: c0b58fb [Andrew Or] Allow spaces in parameters 162e54d [Andrew Or] Merge branch 'master' of github.com:apache/spark into windows-submit 91597ce [Andrew Or] Make spark-shell.cmd use spark-submit.cmd af6fd29 [Andrew Or] Add spark submit for Windows
* SPARK-1802. (Addendium) Audit dependency graph when Spark is built with -PyarnSean Owen2014-05-121-0/+20
| | | | | | | | | | | | | | Following on a few more items from SPARK-1802 -- The first commit touches up a few similar problems remaining with the YARN profile. I think this is worth cherry-picking. The second commit is more of the same for hadoop-client, although the fix is a little more complex. It may or may not be worth bothering with. Author: Sean Owen <sowen@cloudera.com> Closes #746 from srowen/SPARK-1802.2 and squashes the following commits: 52aeb41 [Sean Owen] Add more commons-logging, servlet excludes to avoid conflicts in assembly when building for YARN
* SPARK-1623: Use File objects instead of String's in HTTPBroadcastPatrick Wendell2014-05-121-4/+4
| | | | | | | | | | | | | | This seems strictly better, and I think it's justified only the grounds of clean-up. It might also fix issues with path conversions, but I haven't yet isolated any instance of that happening. /cc @srowen @tdas Author: Patrick Wendell <pwendell@gmail.com> Closes #749 from pwendell/broadcast-cleanup and squashes the following commits: d6d54f2 [Patrick Wendell] SPARK-1623: Use File objects instead of string's in HTTPBroadcast
* Rename testExecutorEnvs --> executorEnvs.Patrick Wendell2014-05-124-9/+8
| | | | | | | | | | | This was changed, but in fact, it's used for things other than tests. So I've changed it back. Author: Patrick Wendell <pwendell@gmail.com> Closes #747 from pwendell/executor-env and squashes the following commits: 36a60a5 [Patrick Wendell] Rename testExecutorEnvs --> executorEnvs.
* SPARK-1802. Audit dependency graph when Spark is built with -PhiveSean Owen2014-05-122-0/+37
| | | | | | | | | | | | | | | | This initial commit resolves the conflicts in the Hive profiles as noted in https://issues.apache.org/jira/browse/SPARK-1802 . Most of the fix was to note that Hive drags in Avro, and so if the hive module depends on Spark's version of the `avro-*` dependencies, it will pull in our exclusions as needed too. But I found we need to copy some exclusions between the two Avro dependencies to get this right. And then had to squash some commons-logging intrusions. This turned up another annoying find, that `hive-exec` is basically an "assembly" artifact that _also_ packages all of its transitive dependencies. This means the final assembly shows lots of collisions between itself and its dependencies, and even other project dependencies. I have a TODO to examine whether that is going to be a deal-breaker or not. In the meantime I'm going to tack on a second commit to this PR that will also fix some similar, last collisions in the YARN profile. Author: Sean Owen <sowen@cloudera.com> Closes #744 from srowen/SPARK-1802 and squashes the following commits: a856604 [Sean Owen] Resolve JAR version conflicts specific to Hive profile
* SPARK-1798. Tests should clean up temp filesSean Owen2014-05-1235-114/+193
| | | | | | | | | | | | | | | | | | | | Three issues related to temp files that tests generate – these should be touched up for hygiene but are not urgent. Modules have a log4j.properties which directs the unit-test.log output file to a directory like `[module]/target/unit-test.log`. But this ends up creating `[module]/[module]/target/unit-test.log` instead of former. The `work/` directory is not deleted by "mvn clean", in the parent and in modules. Neither is the `checkpoint/` directory created under the various external modules. Many tests create a temp directory, which is not usually deleted. This can be largely resolved by calling `deleteOnExit()` at creation and trying to call `Utils.deleteRecursively` consistently to clean up, sometimes in an `@After` method. _If anyone seconds the motion, I can create a more significant change that introduces a new test trait along the lines of `LocalSparkContext`, which provides management of temp directories for subclasses to take advantage of._ Author: Sean Owen <sowen@cloudera.com> Closes #732 from srowen/SPARK-1798 and squashes the following commits: 5af578e [Sean Owen] Try to consistently delete test temp dirs and files, and set deleteOnExit() for each b21b356 [Sean Owen] Remove work/ and checkpoint/ dirs with mvn clean bdd0f41 [Sean Owen] Remove duplicate module dir in log4j.properties output path for tests
* BUILD: Include Hive with default packages when creating a releasePatrick Wendell2014-05-121-3/+3
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* SPARK-1786: Reopening PR 724Ankur Dave2014-05-1212-26/+49
| | | | | | | | | | | | | | | Addressing issue in MimaBuild.scala. Author: Ankur Dave <ankurdave@gmail.com> Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #742 from jegonzal/edge_partition_serialization and squashes the following commits: 8ba6e0d [Ankur Dave] Add concatenation operators to MimaBuild.scala cb2ed3a [Joseph E. Gonzalez] addressing missing exclusion in MimaBuild.scala 5d27824 [Ankur Dave] Disable reference tracking to fix serialization test c0a9ae5 [Ankur Dave] Add failing test for EdgePartition Kryo serialization a4a3faa [Joseph E. Gonzalez] Making EdgePartition serializable.
* SPARK-1806: Upgrade Mesos dependency to 0.18.1Bernardo Gomez Palacio2014-05-125-5/+14
| | | | | | | | | | | | | | | | | | | | Enabled Mesos (0.18.1) dependency with shaded protobuf Why is this needed? Avoids any protobuf version collision between Mesos and any other dependency in Spark e.g. Hadoop HDFS 2.2+ or 1.0.4. Ticket: https://issues.apache.org/jira/browse/SPARK-1806 * Should close https://issues.apache.org/jira/browse/SPARK-1433 Author berngp Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com> Closes #741 from berngp/feature/SPARK-1806 and squashes the following commits: 5d70646 [Bernardo Gomez Palacio] SPARK-1806: Upgrade Mesos dependency to 0.18.1
* SPARK-1772 Stop catching Throwable, let Executors dieAaron Davidson2014-05-1219-140/+127
| | | | | | | | | | | | | | | | | The main issue this patch fixes is [SPARK-1772](https://issues.apache.org/jira/browse/SPARK-1772), in which Executors may not die when fatal exceptions (e.g., OOM) are thrown. This patch causes Executors to delegate to the ExecutorUncaughtExceptionHandler when a fatal exception is thrown. This patch also continues the fight in the neverending war against `case t: Throwable =>`, by only catching Exceptions in many places, and adding a wrapper for Threads and Runnables to make sure any uncaught exceptions are at least printed to the logs. It also turns out that it is unlikely that the IndestructibleActorSystem actually works, given testing ([here](https://gist.github.com/aarondav/ca1f0cdcd50727f89c0d)). The uncaughtExceptionHandler is not called from the places that we expected it would be. [SPARK-1620](https://issues.apache.org/jira/browse/SPARK-1620) deals with part of this issue, but refactoring our Actor Systems to ensure that exceptions are dealt with properly is a much bigger change, outside the scope of this PR. Author: Aaron Davidson <aaron@databricks.com> Closes #715 from aarondav/throwable and squashes the following commits: f9b9bfe [Aaron Davidson] Remove other redundant 'throw e' e937a0a [Aaron Davidson] Address Prashant and Matei's comments 1867867 [Aaron Davidson] [RFC] SPARK-1772 Stop catching Throwable, let Executors die
* Revert "SPARK-1786: Edge Partition Serialization"Patrick Wendell2014-05-1211-44/+23
| | | | This reverts commit a6b02fb7486356493474c7f42bb714c9cce215ca.
* SPARK-1786: Edge Partition SerializationAnkur Dave2014-05-1111-23/+44
| | | | | | | | | | | | | This appears to address the issue with edge partition serialization. The solution appears to be just registering the `PrimitiveKeyOpenHashMap`. However I noticed that we appear to have forked that code in GraphX but retained the same name (which is confusing). I also renamed our local copy to `GraphXPrimitiveKeyOpenHashMap`. We should consider dropping that and using the one in Spark if possible. Author: Ankur Dave <ankurdave@gmail.com> Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #724 from jegonzal/edge_partition_serialization and squashes the following commits: b0a525a [Ankur Dave] Disable reference tracking to fix serialization test bb7f548 [Ankur Dave] Add failing test for EdgePartition Kryo serialization 67dac22 [Joseph E. Gonzalez] Making EdgePartition serializable.
* Fix error in 2d Graph PartitionerJoseph E. Gonzalez2014-05-111-2/+2
| | | | | | | | | | Their was a minor bug in which negative partition ids could be generated when constructing a 2D partitioning of a graph. This could lead to an inefficient 2D partition for large vertex id values. Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #709 from jegonzal/fix_2d_partitioning and squashes the following commits: 937c562 [Joseph E. Gonzalez] fixing bug in 2d partitioning algorithm where negative partition ids could be generated.
* SPARK-1652: Set driver memory correctly in spark-submit.Patrick Wendell2014-05-111-2/+4
| | | | | | | | | | | | | | | The previous check didn't account for the fact that the default deploy mode is "client" unless otherwise specified. Also, this sets the more narrowly defined SPARK_DRIVER_MEMORY instead of setting SPARK_MEM. Author: Patrick Wendell <pwendell@gmail.com> Closes #730 from pwendell/spark-submit and squashes the following commits: 430b98f [Patrick Wendell] Feedback from Aaron e788edf [Patrick Wendell] Changes based on Aaron's feedback f508146 [Patrick Wendell] SPARK-1652: Set driver memory correctly in spark-submit.
* SPARK-1770: Load balance elements when repartitioning.Patrick Wendell2014-05-112-2/+46
| | | | | | | | | | | | | | | | | | | This patch adds better balancing when performing a repartition of an RDD. Previously the elements in the RDD were hash partitioned, meaning if the RDD was skewed certain partitions would end up being very large. This commit adds load balancing of elements across the repartitioned RDD splits. The load balancing is not perfect: a given output partition can have up to N more elements than the average if there are N input partitions. However, some randomization is used to minimize the probabiliy that this happens. Author: Patrick Wendell <pwendell@gmail.com> Closes #727 from pwendell/load-balance and squashes the following commits: f9da752 [Patrick Wendell] Response to Matei's feedback acfa46a [Patrick Wendell] SPARK-1770: Load balance elements when repartitioning.
* remove outdated runtime Information scala homewitgo2014-05-111-2/+1
| | | | | | | | | Author: witgo <witgo@qq.com> Closes #728 from witgo/scala_home and squashes the following commits: cdfd8be [witgo] Merge branch 'master' of https://github.com/apache/spark into scala_home fac094a [witgo] remove outdated runtime Information scala home
* Enabled incremental build that comes with sbt 0.13.2Prashant Sharma2014-05-101-1/+1
| | | | | | | | | | More info at. https://github.com/sbt/sbt/issues/1010 Author: Prashant Sharma <prashant.s@imaginea.com> Closes #525 from ScrapCodes/sbt-inc-opt and squashes the following commits: ba8fa42 [Prashant Sharma] Enabled incremental build that comes with sbt 0.13.2
* [SPARK-1774] Respect SparkSubmit --jars on YARN (client)Andrew Or2014-05-104-53/+102
| | | | | | | | | | | | | | | | | | | | SparkSubmit ignores `--jars` for YARN client. This is a bug. This PR also automatically adds the application jar to `spark.jar`. Previously, when running as yarn-client, you must specify the jar additionally through `--files` (because `--jars` didn't work). Now you don't have to explicitly specify it through either. Tested on a YARN cluster. Author: Andrew Or <andrewor14@gmail.com> Closes #710 from andrewor14/yarn-jars and squashes the following commits: 35d1928 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-jars c27bf6c [Andrew Or] For yarn-cluster and python, do not add primaryResource to spark.jar c92c5bf [Andrew Or] Minor cleanups 269f9f3 [Andrew Or] Fix format 013d840 [Andrew Or] Fix tests 1407474 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-jars 3bb75e8 [Andrew Or] Allow SparkSubmit --jars to take effect in yarn-client mode
* SPARK-1789. Multiple versions of Netty dependencies cause FlumeStreamSuite ↵Sean Owen2014-05-108-70/+24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | failure TL;DR is there is a bit of JAR hell trouble with Netty, that can be mostly resolved and will resolve a test failure. I hit the error described at http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-startup-time-out-td1753.html while running FlumeStreamingSuite, and have for a short while (is it just me?) velvia notes: "I have found a workaround. If you add akka 2.2.4 to your dependencies, then everything works, probably because akka 2.2.4 brings in newer version of Jetty." There are at least 3 versions of Netty in play in the build: - the new Flume 1.4.0 dependency brings in io.netty:netty:3.4.0.Final, and that is the immediate problem - the custom version of akka 2.2.3 depends on io.netty:netty:3.6.6. - but, Spark Core directly uses io.netty:netty-all:4.0.17.Final The POMs try to exclude other versions of netty, but are excluding org.jboss.netty:netty, when in fact older versions of io.netty:netty (not netty-all) are also an issue. The org.jboss.netty:netty excludes are largely unnecessary. I replaced many of them with io.netty:netty exclusions until everything agreed on io.netty:netty-all:4.0.17.Final. But this didn't work, since Akka 2.2.3 doesn't work with Netty 4.x. Down-grading to 3.6.6.Final across the board made some Spark code not compile. If the build *keeps* io.netty:netty:3.6.6.Final as well, everything seems to work. Part of the reason seems to be that Netty 3.x used the old `org.jboss.netty` packages. This is less than ideal, but is no worse than the current situation. So this PR resolves the issue and improves the JAR hell, even if it leaves the existing theoretical Netty 3-vs-4 conflict: - Remove org.jboss.netty excludes where possible, for clarity; they're not needed except with Hadoop artifacts - Add io.netty:netty excludes where needed -- except, let akka keep its io.netty:netty - Change a bit of test code that actually depended on Netty 3.x, to use 4.x equivalent - Update SBT build accordingly A better change would be to update Akka far enough such that it agrees on Netty 4.x, but I don't know if that's feasible. Author: Sean Owen <sowen@cloudera.com> Closes #723 from srowen/SPARK-1789 and squashes the following commits: 43661b7 [Sean Owen] Update and add Netty excludes to prevent some JAR conflicts that cause test issues
* Unify GraphImpl RDDs + other graph load optimizationsAnkur Dave2014-05-1028-851/+1353
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR makes the following changes, primarily in e4fbd329aef85fe2c38b0167255d2a712893d683: 1. *Unify RDDs to avoid zipPartitions.* A graph used to be four RDDs: vertices, edges, routing table, and triplet view. This commit merges them down to two: vertices (with routing table), and edges (with replicated vertices). 2. *Avoid duplicate shuffle in graph building.* We used to do two shuffles when building a graph: one to extract routing information from the edges and move it to the vertices, and another to find nonexistent vertices referred to by edges. With this commit, the latter is done as a side effect of the former. 3. *Avoid no-op shuffle when joins are fully eliminated.* This is a side effect of unifying the edges and the triplet view. 4. *Join elimination for mapTriplets.* 5. *Ship only the needed vertex attributes when upgrading the triplet view.* If the triplet view already contains source attributes, and we now need both attributes, only ship destination attributes rather than re-shipping both. This is done in `ReplicatedVertexView#upgrade`. Author: Ankur Dave <ankurdave@gmail.com> Closes #497 from ankurdave/unify-rdds and squashes the following commits: 332ab43 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds 4933e2e [Ankur Dave] Exclude RoutingTable from binary compatibility check 5ba8789 [Ankur Dave] Add GraphX upgrade guide from Spark 0.9.1 13ac845 [Ankur Dave] Merge remote-tracking branch 'apache-spark/master' into unify-rdds a04765c [Ankur Dave] Remove unnecessary toOps call 57202e8 [Ankur Dave] Replace case with pair parameter 75af062 [Ankur Dave] Add explicit return types 04d3ae5 [Ankur Dave] Convert implicit parameter to context bound c88b269 [Ankur Dave] Revert upgradeIterator to if-in-a-loop 0d3584c [Ankur Dave] EdgePartition.size should be val 2a928b2 [Ankur Dave] Set locality wait 10b3596 [Ankur Dave] Clean up public API ae36110 [Ankur Dave] Fix style errors e4fbd32 [Ankur Dave] Unify GraphImpl RDDs + other graph load optimizations d6d60e2 [Ankur Dave] In GraphLoader, coalesce to minEdgePartitions 62c7b78 [Ankur Dave] In Analytics, take PageRank numIter d64e8d4 [Ankur Dave] Log current Pregel iteration
* [SPARK-1690] Tolerating empty elements when saving Python RDD to text filesKan Zhang2014-05-102-2/+11
| | | | | | | | | | | Tolerate empty strings in PythonRDD Author: Kan Zhang <kzhang@apache.org> Closes #644 from kanzhang/SPARK-1690 and squashes the following commits: c62ad33 [Kan Zhang] Adding Python doctest 473ec4b [Kan Zhang] [SPARK-1690] Tolerating empty elements when saving Python RDD to text files
* Add Python includes to path before depickling broadcast valuesBouke van der Bijl2014-05-102-12/+12
| | | | | | | | | | | | This fixes https://issues.apache.org/jira/browse/SPARK-1731 by adding the Python includes to the PYTHONPATH before depickling the broadcast values @airhorns Author: Bouke van der Bijl <boukevanderbijl@gmail.com> Closes #656 from bouk/python-includes-before-broadcast and squashes the following commits: 7b0dfe4 [Bouke van der Bijl] Add Python includes to path before depickling broadcast values
* fix broken in link in python docsAndy Konwinski2014-05-101-1/+1
| | | | | | | | Author: Andy Konwinski <andykonwinski@gmail.com> Closes #650 from andyk/python-docs-link-fix and squashes the following commits: a1f9d51 [Andy Konwinski] fix broken in link in python docs
* SPARK-1708. Add a ClassTag on Serializer and things that depend on itMatei Zaharia2014-05-1022-72/+103
| | | | | | | | | | | | | | | | | This pull request contains a rebased patch from @heathermiller (https://github.com/heathermiller/spark/pull/1) to add ClassTags on Serializer and types that depend on it (Broadcast and AccumulableCollection). Putting these in the public API signatures now will allow us to use Scala Pickling for serialization down the line without breaking binary compatibility. One question remaining is whether we also want them on Accumulator -- Accumulator is passed as part of a bigger Task or TaskResult object via the closure serializer so it doesn't seem super useful to add the ClassTag there. Broadcast and AccumulableCollection in contrast were being serialized directly. CC @rxin, @pwendell, @heathermiller Author: Matei Zaharia <matei@databricks.com> Closes #700 from mateiz/spark-1708 and squashes the following commits: 1a3d8b0 [Matei Zaharia] Use fake ClassTag in Java 3b449ed [Matei Zaharia] test fix 2209a27 [Matei Zaharia] Code style fixes 9d48830 [Matei Zaharia] Add a ClassTag on Serializer and things that depend on it
* [SPARK-1778] [SQL] Add 'limit' transformation to SchemaRDD.Takuya UESHIN2014-05-102-0/+15
| | | | | | | | | | Add `limit` transformation to `SchemaRDD`. Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #711 from ueshin/issues/SPARK-1778 and squashes the following commits: 33169df [Takuya UESHIN] Add 'limit' transformation to SchemaRDD.
* [SQL] Upgrade parquet library.Michael Armbrust2014-05-102-2/+2
| | | | | | | | | | | | I think we are hitting this issue in some perf tests: https://github.com/Parquet/parquet-mr/commit/6aed5288fd4a1398063a5a219b2ae4a9f71b02cf Credit to @aarondav ! Author: Michael Armbrust <michael@databricks.com> Closes #684 from marmbrus/upgradeParquet and squashes the following commits: e10a619 [Michael Armbrust] Upgrade parquet library.
* [SPARK-1644] The org.datanucleus:* should not be packaged into ↵witgo2014-05-102-5/+7
| | | | | | | | | | | | | spark-assembly-*.jar Author: witgo <witgo@qq.com> Closes #688 from witgo/SPARK-1644 and squashes the following commits: 56ad6ac [witgo] review commit 87c03e4 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1644 6ffa7e4 [witgo] review commit a597414 [witgo] The org.datanucleus:* should not be packaged into spark-assembly-*.jar
* SPARK-1686: keep schedule() calling in the main threadCodingCat2014-05-091-3/+12
| | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1686 moved from original JIRA (by @markhamstra): In deploy.master.Master, the completeRecovery method is the last thing to be called when a standalone Master is recovering from failure. It is responsible for resetting some state, relaunching drivers, and eventually resuming its scheduling duties. There are currently four places in Master.scala where completeRecovery is called. Three of them are from within the actor's receive method, and aren't problems. The last starts from within receive when the ElectedLeader message is received, but the actual completeRecovery() call is made from the Akka scheduler. That means that it will execute on a different scheduler thread, and Master itself will end up running (i.e., schedule() ) from that Akka scheduler thread. In this PR, I added a new master message TriggerSchedule to trigger the "local" call of schedule() in the scheduler thread Author: CodingCat <zhunansjtu@gmail.com> Closes #639 from CodingCat/SPARK-1686 and squashes the following commits: 81bb4ca [CodingCat] rename variable 69e0a2a [CodingCat] style fix 36a2ac0 [CodingCat] address Aaron's comments ec9b7bb [CodingCat] address the comments 02b37ca [CodingCat] keep schedule() calling in the main thread
* SPARK-1770: Revert accidental(?) fixAaron Davidson2014-05-091-2/+2
| | | | | | | | | | | | | Looks like this change was accidentally committed here: https://github.com/apache/spark/commit/06b15baab25951d124bbe6b64906f4139e037deb but the change does not show up in the PR itself (#704). Other than not intending to go in with that PR, this also broke the test JavaAPISuite.repartition. Author: Aaron Davidson <aaron@databricks.com> Closes #716 from aarondav/shufflerand and squashes the following commits: b1cf70b [Aaron Davidson] SPARK-1770: Revert accidental(?) fix
* [SPARK-1760]: fix building spark with maven documentationwitgo2014-05-091-1/+1
| | | | | | | | Author: witgo <witgo@qq.com> Closes #712 from witgo/building-with-maven and squashes the following commits: 215523b [witgo] fix building spark with maven documentation
* Converted bang to ask to avoid scary warning when a block is removedTathagata Das2014-05-081-1/+1
| | | | | | | | | | | | | | | | | | Removing a block through the blockmanager gave a scary warning messages in the driver. ``` 2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true 2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true 2014-05-08 20:16:19,172 WARN BlockManagerMasterActor: Got unknown message: true ``` This is because the [BlockManagerSlaveActor](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/storage/BlockManagerSlaveActor.scala#L44) would send back an acknowledgement ("true"). But the BlockManagerMasterActor would have sent the RemoveBlock message as a send, not as ask(), so would reject the receiver "true" as a unknown message. @pwendell Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #708 from tdas/bm-fix and squashes the following commits: ed4ef15 [Tathagata Das] Converted bang to ask to avoid scary warning when a block is removed.
* MINOR: Removing dead code.Patrick Wendell2014-05-081-1/+0
| | | | Meant to do this when patching up the last merge.
* SPARK-1775: Unneeded lock in ShuffleMapTask.deserializeInfoSandeep2014-05-081-9/+7
| | | | | | | | | | This was used in the past to have a cache of deserialized ShuffleMapTasks, but that's been removed, so there's no need for a lock. It slows down Spark when task descriptions are large, e.g. due to large lineage graphs or local variables. Author: Sandeep <sandeep@techaddict.me> Closes #707 from techaddict/SPARK-1775 and squashes the following commits: 18d8ebf [Sandeep] SPARK-1775: Unneeded lock in ShuffleMapTask.deserializeInfo This was used in the past to have a cache of deserialized ShuffleMapTasks, but that's been removed, so there's no need for a lock. It slows down Spark when task descriptions are large, e.g. due to large lineage graphs or local variables.
* SPARK-1565 (Addendum): Replace `run-example` with `spark-submit`.Patrick Wendell2014-05-087-65/+37
| | | | | | | | | | | | | Gives a nicely formatted message to the user when `run-example` is run to tell them to use `spark-submit`. Author: Patrick Wendell <pwendell@gmail.com> Closes #704 from pwendell/examples and squashes the following commits: 1996ee8 [Patrick Wendell] Feedback form Andrew 3eb7803 [Patrick Wendell] Suggestions from TD 2474668 [Patrick Wendell] SPARK-1565 (Addendum): Replace `run-example` with `spark-submit`.
* [SPARK-1631] Correctly set the Yarn app name when launching the AM.Marcelo Vanzin2014-05-081-3/+3
| | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #539 from vanzin/yarn-app-name and squashes the following commits: 7d1ca4f [Marcelo Vanzin] [SPARK-1631] Correctly set the Yarn app name when launching the AM.
* [SPARK-1755] Respect SparkSubmit --name on YARNAndrew Or2014-05-082-8/+11
| | | | | | | | | | | | | | | | | | | | Right now, SparkSubmit ignores the `--name` flag for both yarn-client and yarn-cluster. This is a bug. In client mode, SparkSubmit treats `--name` as a [cluster config](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala#L170) and does not propagate this to SparkContext. In cluster mode, SparkSubmit passes this flag to `org.apache.spark.deploy.yarn.Client`, which only uses it for the [YARN ResourceManager](https://github.com/apache/spark/blob/master/yarn/stable/src/main/scala/org/apache/spark/deploy/yarn/Client.scala#L80), but does not propagate this to SparkContext. This PR ensures that `spark.app.name` is always set if SparkSubmit receives the `--name` flag, which is what the usage promises. This makes it possible for applications to start a SparkContext with an empty conf `val sc = new SparkContext(new SparkConf)`, and inherit the app name from SparkSubmit. Tested both modes on a YARN cluster. Author: Andrew Or <andrewor14@gmail.com> Closes #699 from andrewor14/yarn-app-name and squashes the following commits: 98f6a79 [Andrew Or] Fix tests dea932f [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-app-name c86d9ca [Andrew Or] Respect SparkSubmit --name on YARN
* Include the sbin/spark-config.sh in spark-executorBouke van der Bijl2014-05-081-0/+3
| | | | | | | | | | | | | This is needed because broadcast values are broken on pyspark on Mesos, it tries to import pyspark but can't, as the PYTHONPATH is not set due to changes in ff5be9a4 https://issues.apache.org/jira/browse/SPARK-1725 Author: Bouke van der Bijl <boukevanderbijl@gmail.com> Closes #651 from bouk/include-spark-config-in-mesos-executor and squashes the following commits: b2f1295 [Bouke van der Bijl] Inline PYTHONPATH in spark-executor eedbbcc [Bouke van der Bijl] Include the sbin/spark-config.sh in spark-executor
* Bug fix of sparse vector conversionFunes2014-05-082-1/+14
| | | | | | | | | | | | | | | Fixed a small bug caused by the inconsistency of index/data array size and vector length. Author: Funes <tianshaocun@gmail.com> Author: funes <tianshaocun@gmail.com> Closes #661 from funes/bugfix and squashes the following commits: edb2b9d [funes] remove unused import 75dced3 [Funes] update test case d129a66 [Funes] Add test for sparse breeze by vector builder 64e7198 [Funes] Copy data only when necessary b85806c [Funes] Bug fix of sparse vector conversion
* [SPARK-1157][MLlib] Bug fix: lossHistory should exclude rejection steps, and ↵DB Tsai2014-05-082-48/+30
| | | | | | | | | | | | | | remove miniBatch Getting the lossHistory from Breeze's API which already excludes the rejection steps in line search. Also, remove the miniBatch in LBFGS since those quasi-Newton methods approximate the inverse of Hessian. It doesn't make sense if the gradients are computed from a varying objective. Author: DB Tsai <dbtsai@alpinenow.com> Closes #582 from dbtsai/dbtsai-lbfgs-bug and squashes the following commits: 9cc6cf9 [DB Tsai] Removed the miniBatch in LBFGS. 1ba6a33 [DB Tsai] Formatting the code. d72c679 [DB Tsai] Using Breeze's states to get the loss.
* MLlib documentation fixDB Tsai2014-05-082-5/+5
| | | | | | | | | | Fixed the documentation for that `loadLibSVMData` is changed to `loadLibSVMFile`. Author: DB Tsai <dbtsai@alpinenow.com> Closes #703 from dbtsai/dbtsai-docfix and squashes the following commits: 71dd508 [DB Tsai] loadLibSVMData is changed to loadLibSVMFile
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