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* [SPARK-18692][BUILD][DOCS] Test Java 8 unidoc build on Jenkinshyukjinkwon2017-04-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR proposes to run Spark unidoc to test Javadoc 8 build as Javadoc 8 is easily re-breakable. There are several problems with it: - It introduces little extra bit of time to run the tests. In my case, it took 1.5 mins more (`Elapsed :[94.8746569157]`). How it was tested is described in "How was this patch tested?". - > One problem that I noticed was that Unidoc appeared to be processing test sources: if we can find a way to exclude those from being processed in the first place then that might significantly speed things up. (see joshrosen's [comment](https://issues.apache.org/jira/browse/SPARK-18692?focusedCommentId=15947627&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-15947627)) To complete this automated build, It also suggests to fix existing Javadoc breaks / ones introduced by test codes as described above. There fixes are similar instances that previously fixed. Please refer https://github.com/apache/spark/pull/15999 and https://github.com/apache/spark/pull/16013 Note that this only fixes **errors** not **warnings**. Please see my observation https://github.com/apache/spark/pull/17389#issuecomment-288438704 for spurious errors by warnings. ## How was this patch tested? Manually via `jekyll build` for building tests. Also, tested via running `./dev/run-tests`. This was tested via manually adding `time.time()` as below: ```diff profiles_and_goals = build_profiles + sbt_goals print("[info] Building Spark unidoc (w/Hive 1.2.1) using SBT with these arguments: ", " ".join(profiles_and_goals)) + import time + st = time.time() exec_sbt(profiles_and_goals) + print("Elapsed :[%s]" % str(time.time() - st)) ``` produces ``` ... ======================================================================== Building Unidoc API Documentation ======================================================================== ... [info] Main Java API documentation successful. ... Elapsed :[94.8746569157] ... Author: hyukjinkwon <gurwls223@gmail.com> Closes #17477 from HyukjinKwon/SPARK-18692.
* [SPARK-18847][GRAPHX] PageRank gives incorrect results for graphs with sinksAndrew Ray2017-03-171-46/+112
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Graphs with sinks (vertices with no outgoing edges) don't have the expected rank sum of n (or 1 for personalized). We fix this by normalizing to the expected sum at the end of each implementation. Additionally this fixes the dynamic version of personal pagerank which gave incorrect answers that were not detected by existing unit tests. ## How was this patch tested? Revamped existing and additional unit tests with reference values (and reproduction code) from igraph and NetworkX. Note that for comparison on personal pagerank we use the arpack algorithm in igraph as prpack (the current default) redistributes rank to all vertices uniformly instead of just to the personalization source. We could take the alternate convention (redistribute rank to all vertices uniformly) but that would involve more extensive changes to the algorithms (the dynamic version would no longer be able to use Pregel). Author: Andrew Ray <ray.andrew@gmail.com> Closes #16483 from aray/pagerank-sink2.
* [SPARK-14804][SPARK][GRAPHX] Fix checkpointing of VertexRDD/EdgeRDDTathagata Das2017-01-252-0/+53
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? EdgeRDD/VertexRDD overrides checkpoint() and isCheckpointed() to forward these to the internal partitionRDD. So when checkpoint() is called on them, its the partitionRDD that actually gets checkpointed. However since isCheckpointed() also overridden to call partitionRDD.isCheckpointed, EdgeRDD/VertexRDD.isCheckpointed returns true even though this RDD is actually not checkpointed. This would have been fine except the RDD's internal logic for computing the RDD depends on isCheckpointed(). So for VertexRDD/EdgeRDD, since isCheckpointed is true, when computing Spark tries to read checkpoint data of VertexRDD/EdgeRDD even though they are not actually checkpointed. Through a crazy sequence of call forwarding, it reads checkpoint data of partitionsRDD and tries to cast it to types in Vertex/EdgeRDD. This leads to ClassCastException. The minimal fix that does not change any public behavior is to modify RDD internal to not use public override-able API for internal logic. ## How was this patch tested? New unit tests. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #15396 from tdas/SPARK-14804.
* [SPARK-18845][GRAPHX] PageRank has incorrect initialization value that leads ↵Andrew Ray2016-12-151-4/+30
| | | | | | | | | | | | | | | | | | | | | | | to slow convergence ## What changes were proposed in this pull request? Change the initial value in all PageRank implementations to be `1.0` instead of `resetProb` (default `0.15`) and use `outerJoinVertices` instead of `joinVertices` so that source vertices get updated in each iteration. This seems to have been introduced a long time ago in https://github.com/apache/spark/commit/15a564598fe63003652b1e24527c432080b5976c#diff-b2bf3f97dcd2f19d61c921836159cda9L90 With the exception of graphs with sinks (which currently give incorrect results see SPARK-18847) this gives faster convergence as the sum of ranks is already correct (sum of ranks should be number of vertices). Convergence comparision benchmark for small graph: http://imgur.com/a/HkkZf Code for benchmark: https://gist.github.com/aray/a7de1f3801a810f8b1fa00c271a1fefd ## How was this patch tested? (corrected) existing unit tests and additional test that verifies against result of igraph and NetworkX on a loop with a source. Author: Andrew Ray <ray.andrew@gmail.com> Closes #16271 from aray/pagerank-initial-value.
* [SPARK-11496][GRAPHX] Parallel implementation of personalized pagerankYves Raimond2016-09-101-0/+24
| | | | | | | | | | | | | | (Updated version of [PR-9457](https://github.com/apache/spark/pull/9457), rebased on latest Spark master, and using mllib-local). This implements a parallel version of personalized pagerank, which runs all propagations for a list of source vertices in parallel. I ran a few benchmarks on the full [DBpedia](http://dbpedia.org/) graph. When running personalized pagerank for only one source node, the existing implementation is twice as fast as the parallel one (because of the SparseVector overhead). However for 10 source nodes, the parallel implementation is four times as fast. When increasing the number of source nodes, this difference becomes even greater. ![image](https://cloud.githubusercontent.com/assets/2491/10927702/dd82e4fa-8256-11e5-89a8-4799b407f502.png) Author: Yves Raimond <yraimond@netflix.com> Closes #14998 from moustaki/parallel-ppr.
* [SPARK-16694][CORE] Use for/foreach rather than map for Unit expressions ↵Sean Owen2016-07-301-1/+1
| | | | | | | | | | | | | | | | whose side effects are required ## What changes were proposed in this pull request? Use foreach/for instead of map where operation requires execution of body, not actually defining a transformation ## How was this patch tested? Jenkins Author: Sean Owen <sowen@cloudera.com> Closes #14332 from srowen/SPARK-16694.
* [SPARK-14219][GRAPHX] Fix `pickRandomVertex` not to fall into infinite loops ↵Dongjoon Hyun2016-03-281-0/+9
| | | | | | | | | | | | | | | | | | | | for graphs with one vertex ## What changes were proposed in this pull request? Currently, `GraphOps.pickRandomVertex()` falls into infinite loops for graphs having only one vertex. This PR fixes it by modifying the following termination-checking condition. ```scala - if (selectedVertices.count > 1) { + if (selectedVertices.count > 0) { ``` ## How was this patch tested? Pass the Jenkins tests (including new test case). Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12018 from dongjoon-hyun/SPARK-14219.
* [MINOR][DOCS] Fix more typos in comments/strings.Dongjoon Hyun2016-03-141-1/+1
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR fixes 135 typos over 107 files: * 121 typos in comments * 11 typos in testcase name * 3 typos in log messages ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11689 from dongjoon-hyun/fix_more_typos.
* [SPARK-13823][CORE][STREAMING][SQL] Always specify Charset in String <-> ↵Sean Owen2016-03-131-1/+2
| | | | | | | | | | | | | | | | | | | | byte[] conversions (and remaining Coverity items) ## What changes were proposed in this pull request? - Fixes calls to `new String(byte[])` or `String.getBytes()` that rely on platform default encoding, to use UTF-8 - Same for `InputStreamReader` and `OutputStreamWriter` constructors - Standardizes on UTF-8 everywhere - Standardizes specifying the encoding with `StandardCharsets.UTF-8`, not the Guava constant or "UTF-8" (which means handling `UnuspportedEncodingException`) - (also addresses the other remaining Coverity scan issues, which are pretty trivial; these are separated into commit https://github.com/srowen/spark/commit/1deecd8d9ca986d8adb1a42d315890ce5349d29c ) ## How was this patch tested? Jenkins tests Author: Sean Owen <sowen@cloudera.com> Closes #11657 from srowen/SPARK-13823.
* [MINOR] Fix typos in comments and testcase name of codeDongjoon Hyun2016-03-031-1/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR fixes typos in comments and testcase name of code. ## How was this patch tested? manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11481 from dongjoon-hyun/minor_fix_typos_in_code.
* [SPARK-13583][CORE][STREAMING] Remove unused imports and add checkstyle ruleDongjoon Hyun2016-03-036-16/+4
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? After SPARK-6990, `dev/lint-java` keeps Java code healthy and helps PR review by saving much time. This issue aims remove unused imports from Java/Scala code and add `UnusedImports` checkstyle rule to help developers. ## How was this patch tested? ``` ./dev/lint-java ./build/sbt compile ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11438 from dongjoon-hyun/SPARK-13583.
* [SPARK-13423][WIP][CORE][SQL][STREAMING] Static analysis fixes for 2.xSean Owen2016-03-031-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Make some cross-cutting code improvements according to static analysis. These are individually up for discussion since they exist in separate commits that can be reverted. The changes are broadly: - Inner class should be static - Mismatched hashCode/equals - Overflow in compareTo - Unchecked warnings - Misuse of assert, vs junit.assert - get(a) + getOrElse(b) -> getOrElse(a,b) - Array/String .size -> .length (occasionally, -> .isEmpty / .nonEmpty) to avoid implicit conversions - Dead code - tailrec - exists(_ == ) -> contains find + nonEmpty -> exists filter + size -> count - reduce(_+_) -> sum map + flatten -> map The most controversial may be .size -> .length simply because of its size. It is intended to avoid implicits that might be expensive in some places. ## How was the this patch tested? Existing Jenkins unit tests. Author: Sean Owen <sowen@cloudera.com> Closes #11292 from srowen/SPARK-13423.
* [SPARK-3650][GRAPHX] Triangle Count handles reverse edges incorrectlyRobin East2016-02-212-3/+19
| | | | | | | | | | | | | | | | | jegonzal ankurdave please could you review ## What changes were proposed in this pull request? Reworking of jegonzal PR #2495 to address the issue identified in SPARK-3650. Code amended to use the convertToCanonicalEdges method. ## How was the this patch tested? Patch was tested using the unit tests created in PR #2495 Author: Robin East <robin.east@xense.co.uk> Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #11290 from insidedctm/spark-3650.
* [SPARK-12995][GRAPHX] Remove deprecate APIs from PregelTakeshi YAMAMURO2016-02-151-46/+6
| | | | | | Author: Takeshi YAMAMURO <linguin.m.s@gmail.com> Closes #10918 from maropu/RemoveDeprecateInPregel.
* [SPARK-12655][GRAPHX] GraphX does not unpersist RDDsJason Lee2016-01-151-0/+16
| | | | | | | | | | Some VertexRDD and EdgeRDD are created during the intermediate step of g.connectedComponents() but unnecessarily left cached after the method is done. The fix is to unpersist these RDDs once they are no longer in use. A test case is added to confirm the fix for the reported bug. Author: Jason Lee <cjlee@us.ibm.com> Closes #10713 from jasoncl/SPARK-12655.
* [SPARK-3873][TESTS] Import ordering fixes.Marcelo Vanzin2016-01-052-4/+2
| | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #10582 from vanzin/SPARK-3873-tests.
* [SPARK-5882][GRAPHX] Add a test for GraphLoader.edgeListFileTakeshi YAMAMURO2015-12-211-0/+47
| | | | | | Author: Takeshi YAMAMURO <linguin.m.s@gmail.com> Closes #4674 from maropu/AddGraphLoaderSuite.
* [SPARK-12112][BUILD] Upgrade to SBT 0.13.9Josh Rosen2015-12-051-1/+1
| | | | | | | | | | We should upgrade to SBT 0.13.9, since this is a requirement in order to use SBT's new Maven-style resolution features (which will be done in a separate patch, because it's blocked by some binary compatibility issues in the POM reader plugin). I also upgraded Scalastyle to version 0.8.0, which was necessary in order to fix a Scala 2.10.5 compatibility issue (see https://github.com/scalastyle/scalastyle/issues/156). The newer Scalastyle is slightly stricter about whitespace surrounding tokens, so I fixed the new style violations. Author: Josh Rosen <joshrosen@databricks.com> Closes #10112 from JoshRosen/upgrade-to-sbt-0.13.9.
* [SPARK-11432][GRAPHX] Personalized PageRank shouldn't use uniform initializationYves Raimond2015-11-021-4/+9
| | | | | | | | Changes the personalized pagerank initialization to be non-uniform. Author: Yves Raimond <yraimond@netflix.com> Closes #9386 from moustaki/personalized-pagerank-init.
* [SPARK-7977] [BUILD] Disallowing printlnJonathan Alter2015-07-101-0/+2
| | | | | | | | | | | | | | | | | | | | | | | Author: Jonathan Alter <jonalter@users.noreply.github.com> Closes #7093 from jonalter/SPARK-7977 and squashes the following commits: ccd44cc [Jonathan Alter] Changed println to log in ThreadingSuite 7fcac3e [Jonathan Alter] Reverting to println in ThreadingSuite 10724b6 [Jonathan Alter] Changing some printlns to logs in tests eeec1e7 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 0b1dcb4 [Jonathan Alter] More println cleanup aedaf80 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 925fd98 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 0c16fa3 [Jonathan Alter] Replacing some printlns with logs 45c7e05 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 5c8e283 [Jonathan Alter] Allowing println in audit-release examples 5b50da1 [Jonathan Alter] Allowing printlns in example files ca4b477 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 83ab635 [Jonathan Alter] Fixing new printlns 54b131f [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977 1cd8a81 [Jonathan Alter] Removing some unnecessary comments and printlns b837c3a [Jonathan Alter] Disallowing println
* [SPARK-3850] Trim trailing spaces for examples/streaming/yarn.Reynold Xin2015-05-311-5/+5
| | | | | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #6530 from rxin/trim-whitespace-1 and squashes the following commits: 7b7b3a0 [Reynold Xin] Reset again. dc14597 [Reynold Xin] Reset scalastyle. cd556c4 [Reynold Xin] YARN, Kinesis, Flume. 4223fe1 [Reynold Xin] [SPARK-3850] Trim trailing spaces for examples/streaming.
* [SPARK-7558] Demarcate tests in unit-tests.logAndrew Or2015-05-2917-57/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Right now `unit-tests.log` are not of much value because we can't tell where the test boundaries are easily. This patch adds log statements before and after each test to outline the test boundaries, e.g.: ``` ===== TEST OUTPUT FOR o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ===== 15/05/27 12:36:39.596 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO SparkContext: Starting job: count at KryoSerializerSuite.scala:230 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Got job 3 (count at KryoSerializerSuite.scala:230) with 4 output partitions (allowLocal=false) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Final stage: ResultStage 3(count at KryoSerializerSuite.scala:230) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Parents of final stage: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Missing parents: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Submitting ResultStage 3 (ParallelCollectionRDD[5] at parallelize at KryoSerializerSuite.scala:230), which has no missing parents ... 15/05/27 12:36:39.624 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO DAGScheduler: Job 3 finished: count at KryoSerializerSuite.scala:230, took 0.028563 s 15/05/27 12:36:39.625 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO KryoSerializerSuite: ***** FINISHED o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ***** ... ``` Author: Andrew Or <andrew@databricks.com> Closes #6441 from andrewor14/demarcate-tests and squashes the following commits: 879b060 [Andrew Or] Fix compile after rebase d622af7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 017c8ba [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 7790b6c [Andrew Or] Fix tests after logical merge conflict c7460c0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests c43ffc4 [Andrew Or] Fix tests? 8882581 [Andrew Or] Fix tests ee22cda [Andrew Or] Fix log message fa9450e [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 12d1e1b [Andrew Or] Various whitespace changes (minor) 69cbb24 [Andrew Or] Make all test suites extend SparkFunSuite instead of FunSuite bbce12e [Andrew Or] Fix manual things that cannot be covered through automation da0b12f [Andrew Or] Add core tests as dependencies in all modules f7d29ce [Andrew Or] Introduce base abstract class for all test suites
* [SPARK-7927] whitespace fixes for GraphX.Reynold Xin2015-05-285-20/+23
| | | | | | | | | | | So we can enable a whitespace enforcement rule in the style checker to save code review time. Author: Reynold Xin <rxin@databricks.com> Closes #6474 from rxin/whitespace-graphx and squashes the following commits: 4d3cd26 [Reynold Xin] Fixed tests. 869dde4 [Reynold Xin] [SPARK-7927] whitespace fixes for GraphX.
* [SPARK-5854] personalized page rankDan McClary2015-05-011-0/+47
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Here's a modification to PageRank which does personalized PageRank. The approach is basically similar to that outlined by Bahmani et al. from 2010 (http://arxiv.org/pdf/1006.2880.pdf). I'm sure this needs tuning up or other considerations, so let me know how I can improve this. Author: Dan McClary <dan.mcclary@gmail.com> Author: dwmclary <dan.mcclary@gmail.com> Closes #4774 from dwmclary/SPARK-5854-Personalized-PageRank and squashes the following commits: 8b907db [dwmclary] fixed scalastyle errors in PageRankSuite 2c20e5d [dwmclary] merged with upstream master d6cebac [dwmclary] updated as per style requests 7d00c23 [Dan McClary] fixed line overrun in personalizedVertexPageRank d711677 [Dan McClary] updated vertexProgram to restore binary compatibility for inner method bb8d507 [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank fba0edd [Dan McClary] fixed silly mistakes de51be2 [Dan McClary] cleaned up whitespace between comments and methods 0c30d0c [Dan McClary] updated to maintain binary compatibility aaf0b4b [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank 76773f6 [Dan McClary] Merge branch 'master' of https://github.com/apache/spark into SPARK-5854-Personalized-PageRank 44ada8e [Dan McClary] updated tolerance on chain PPR 1ffed95 [Dan McClary] updated tolerance on chain PPR b67ac69 [Dan McClary] updated tolerance on chain PPR a560942 [Dan McClary] rolled PPR into pregel code for PageRank 6dc2c29 [Dan McClary] initial implementation of personalized page rank
* [SPARK-6765] Fix test code style for graphx.Reynold Xin2015-04-086-85/+88
| | | | | | | | | | So we can turn style checker on for test code. Author: Reynold Xin <rxin@databricks.com> Closes #5410 from rxin/test-style-graphx and squashes the following commits: 89e253a [Reynold Xin] [SPARK-6765] Fix test code style for graphx.
* [SPARK-6510][GraphX]: Add Graph#minus method to act as Set#differenceBrennon York2015-03-261-2/+31
| | | | | | | | | | | | | | | | | | | | | Adds a `Graph#minus` method which will return only unique `VertexId`'s from the calling `VertexRDD`. To demonstrate a basic example with pseudocode: ``` Set((0L,0),(1L,1)).minus(Set((1L,1),(2L,2))) > Set((0L,0)) ``` Author: Brennon York <brennon.york@capitalone.com> Closes #5175 from brennonyork/SPARK-6510 and squashes the following commits: 248d5c8 [Brennon York] added minus(VertexRDD[VD]) method to avoid createUsingIndex and updated the mask operations to simplify with andNot call 3fb7cce [Brennon York] updated graphx doc to reflect the addition of minus method 6575d92 [Brennon York] updated mima exclude aaa030b [Brennon York] completed graph#minus functionality 7227c0f [Brennon York] beginning work on minus functionality
* SPARK-6338 [CORE] Use standard temp dir mechanisms in tests to avoid ↵Sean Owen2015-03-201-4/+2
| | | | | | | | | | | | | | | orphaned temp files Use `Utils.createTempDir()` to replace other temp file mechanisms used in some tests, to further ensure they are cleaned up, and simplify Author: Sean Owen <sowen@cloudera.com> Closes #5029 from srowen/SPARK-6338 and squashes the following commits: 27b740a [Sean Owen] Fix hive-thriftserver tests that don't expect an existing dir 4a212fa [Sean Owen] Standardize a bit more temp dir management 9004081 [Sean Owen] Revert some added recursive-delete calls 57609e4 [Sean Owen] Use Utils.createTempDir() to replace other temp file mechanisms used in some tests, to further ensure they are cleaned up, and simplify
* [SPARK-5922][GraphX]: Add diff(other: RDD[VertexId, VD]) in VertexRDDBrennon York2015-03-161-0/+13
| | | | | | | | | | | | | | | | | | | Changed method invocation of 'diff' to match that of 'innerJoin' and 'leftJoin' from VertexRDD[VD] to RDD[(VertexId, VD)]. This change maintains backwards compatibility and better unifies the VertexRDD methods to match each other. Author: Brennon York <brennon.york@capitalone.com> Closes #4733 from brennonyork/SPARK-5922 and squashes the following commits: e800f08 [Brennon York] fixed merge conflicts b9274af [Brennon York] fixed merge conflicts f86375c [Brennon York] fixed minor include line 398ddb4 [Brennon York] fixed merge conflicts aac1810 [Brennon York] updated to aggregateUsingIndex and added test to ensure that method works properly 2af0b88 [Brennon York] removed deprecation line 753c963 [Brennon York] fixed merge conflicts and set preference to use the diff(other: VertexRDD[VD]) method 2c678c6 [Brennon York] added mima exclude to exclude new public diff method from VertexRDD 93186f3 [Brennon York] added back the original diff method to sustain binary compatibility f18356e [Brennon York] changed method invocation of 'diff' to match that of 'innerJoin' and 'leftJoin' from VertexRDD[VD] to RDD[(VertexId, VD)]
* [SPARK-5790][GraphX]: VertexRDD's won't zip properly for `diff` capability ↵Brennon York2015-03-141-1/+37
| | | | | | | | | | | | (added tests) Added tests that maropu [created](https://github.com/maropu/spark/blob/1f64794b2ce33e64f340e383d4e8a60639a7eb4b/graphx/src/test/scala/org/apache/spark/graphx/VertexRDDSuite.scala) for vertices with differing partition counts. Wanted to make sure his work got captured /merged as its not in the master branch and I don't believe there's a PR out already for it. Author: Brennon York <brennon.york@capitalone.com> Closes #5023 from brennonyork/SPARK-5790 and squashes the following commits: 83bbd29 [Brennon York] added maropu's tests for vertices with differing partition counts
* [SPARK-5814][MLLIB][GRAPHX] Remove JBLAS from runtimeXiangrui Meng2015-03-121-3/+3
| | | | | | | | | | | | | | | | | The issue is discussed in https://issues.apache.org/jira/browse/SPARK-5669. Replacing all JBLAS usage by netlib-java gives us a simpler dependency tree and less license issues to worry about. I didn't touch the test scope in this PR. The user guide is not modified to avoid merge conflicts with branch-1.3. srowen ankurdave pwendell Author: Xiangrui Meng <meng@databricks.com> Closes #4699 from mengxr/SPARK-5814 and squashes the following commits: 48635c6 [Xiangrui Meng] move netlib-java version to parent pom ca21c74 [Xiangrui Meng] remove jblas from ml-guide 5f7767a [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5814 c5c4183 [Xiangrui Meng] merge master 0f20cad [Xiangrui Meng] add mima excludes e53e9f4 [Xiangrui Meng] remove jblas from mllib runtime ceaa14d [Xiangrui Meng] replace jblas by netlib-java in graphx fa7c2ca [Xiangrui Meng] move jblas to test scope
* SPARK-5815 [MLLIB] Deprecate SVDPlusPlus APIs that expose DoubleMatrix from ↵Sean Owen2015-02-151-1/+1
| | | | | | | | | | | | | | | JBLAS Deprecate SVDPlusPlus.run and introduce SVDPlusPlus.runSVDPlusPlus with return type that doesn't include DoubleMatrix CC mengxr Author: Sean Owen <sowen@cloudera.com> Closes #4614 from srowen/SPARK-5815 and squashes the following commits: 288cb05 [Sean Owen] Clarify deprecation plans in scaladoc 497458e [Sean Owen] Deprecate SVDPlusPlus.run and introduce SVDPlusPlus.runSVDPlusPlus with return type that doesn't include DoubleMatrix
* [SPARK-4795][Core] Redesign the "primitive type => Writable" implicit APIs ↵zsxwing2015-02-031-1/+1
| | | | | | | | | | | | | | | | | | to make them be activated automatically Try to redesign the "primitive type => Writable" implicit APIs to make them be activated automatically and without breaking binary compatibility. However, this PR will breaking the source compatibility if people use `xxxToXxxWritable` occasionally. See the unit test in `graphx`. Author: zsxwing <zsxwing@gmail.com> Closes #3642 from zsxwing/SPARK-4795 and squashes the following commits: 914b2d6 [zsxwing] Add implicit back to the Writables methods 0b9017f [zsxwing] Add some docs a0e8509 [zsxwing] Merge branch 'master' into SPARK-4795 39343de [zsxwing] Fix the unit test 64853af [zsxwing] Reorganize the rest 'implicit' methods in SparkContext
* [SPARK-5534] [graphx] Graph getStorageLevel fixJoseph K. Bradley2015-02-023-4/+67
| | | | | | | | | | | | | | | | | | | This fixes getStorageLevel for EdgeRDDImpl and VertexRDDImpl (and therefore for Graph). See code example on JIRA which failed before but works with this patch: [https://issues.apache.org/jira/browse/SPARK-5534] (The added unit tests also failed before but work with this fix.) Note: I used partitionsRDD, assuming that getStorageLevel will only be called on the driver. CC: mengxr (related to LDA PR), rxin ankurdave Thanks in advance! Author: Joseph K. Bradley <joseph@databricks.com> Closes #4317 from jkbradley/graphx-storagelevel and squashes the following commits: 1c21e49 [Joseph K. Bradley] made graph getStorageLevel test more robust 18d64ca [Joseph K. Bradley] Added tests for getStorageLevel in VertexRDDSuite, EdgeRDDSuite, GraphSuite 17b488b [Joseph K. Bradley] overrode getStorageLevel in Vertex/EdgeRDDImpl to use partitionsRDD
* [SPARK-5461] [graphx] Add isCheckpointed, getCheckpointedFiles methods to GraphJoseph K. Bradley2015-02-021-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | Added the 2 methods to Graph and GraphImpl. Both make calls to the underlying vertex and edge RDDs. This is needed for another PR (for LDA): [https://github.com/apache/spark/pull/4047] Notes: * getCheckpointedFiles is plural and returns a Seq[String] instead of an Option[String]. * I attempted to test to make sure the methods returned the correct values after checkpointing. It did not work; I guess that checkpointing does not occur quickly enough? I noticed that there are not checkpointing tests for RDDs; is it just hard to test well? CC: rxin CC: mengxr (since related to LDA) Author: Joseph K. Bradley <joseph@databricks.com> Closes #4253 from jkbradley/graphx-checkpoint and squashes the following commits: b680148 [Joseph K. Bradley] added class tag to firstParent call in VertexRDDImpl.isCheckpointed, though not needed to compile 250810e [Joseph K. Bradley] In EdgeRDDImple, VertexRDDImpl, added transient back to partitionsRDD, and made isCheckpointed check firstParent instead of partitionsRDD 695b7a3 [Joseph K. Bradley] changed partitionsRDD in EdgeRDDImpl, VertexRDDImpl to be non-transient cc00767 [Joseph K. Bradley] added overrides for isCheckpointed, getCheckpointFile in EdgeRDDImpl, VertexRDDImpl. The corresponding Graph methods now work. 188665f [Joseph K. Bradley] improved documentation 235738c [Joseph K. Bradley] Added isCheckpointed and getCheckpointFiles to Graph, GraphImpl
* [SPARK-5351][GraphX] Do not use Partitioner.defaultPartitioner as a ↵Takeshi Yamamuro2015-01-231-0/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | partitioner of EdgeRDDImp... If the value of 'spark.default.parallelism' does not match the number of partitoins in EdgePartition(EdgeRDDImpl), the following error occurs in ReplicatedVertexView.scala:72; object GraphTest extends Logging { def run[VD: ClassTag, ED: ClassTag](graph: Graph[VD, ED]): VertexRDD[Int] = { graph.aggregateMessages( ctx => { ctx.sendToSrc(1) ctx.sendToDst(2) }, _ + _) } } val g = GraphLoader.edgeListFile(sc, "graph.txt") val rdd = GraphTest.run(g) java.lang.IllegalArgumentException: Can't zip RDDs with unequal numbers of partitions at org.apache.spark.rdd.ZippedPartitionsBaseRDD.getPartitions(ZippedPartitionsRDD.scala:57) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:206) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:204) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.rdd.RDD.partitions(RDD.scala:204) at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:32) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:206) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:204) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.rdd.RDD.partitions(RDD.scala:204) at org.apache.spark.ShuffleDependency.<init>(Dependency.scala:82) at org.apache.spark.rdd.ShuffledRDD.getDependencies(ShuffledRDD.scala:80) at org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:193) at org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:191) ... Author: Takeshi Yamamuro <linguin.m.s@gmail.com> Closes #4136 from maropu/EdgePartitionBugFix and squashes the following commits: 0cd8942 [Ankur Dave] Use more concise getOrElse aad4a2c [Ankur Dave] Add unit test for non-default number of edge partitions 0a2f32b [Takeshi Yamamuro] Do not use Partitioner.defaultPartitioner as a partitioner of EdgeRDDImpl
* [SPARK-5064][GraphX] Add numEdges upperbound validation for R-MAT graph ↵Kenji Kikushima2015-01-211-0/+10
| | | | | | | | | | | | | | generator to prevent infinite loop I looked into GraphGenerators#chooseCell, and found that chooseCell can't generate more edges than pow(2, (2 * (log2(numVertices)-1))) to make a Power-law graph. (Ex. numVertices:4 upperbound:4, numVertices:8 upperbound:16, numVertices:16 upperbound:64) If we request more edges over the upperbound, rmatGraph fall into infinite loop. So, how about adding an argument validation? Author: Kenji Kikushima <kikushima.kenji@lab.ntt.co.jp> Closes #3950 from kj-ki/SPARK-5064 and squashes the following commits: 4ee18c7 [Ankur Dave] Reword error message and add unit test d760bc7 [Kenji Kikushima] Add numEdges upperbound validation for R-MAT graph generator to prevent infinite loop.
* [SPARK-4917] Add a function to convert into a graph with canonical edges in ↵Takeshi Yamamuro2015-01-081-0/+15
| | | | | | | | | | | | | | GraphOps Convert bi-directional edges into uni-directional ones instead of 'canonicalOrientation' in GraphLoader.edgeListFile. This function is useful when a graph is loaded as it is and then is transformed into one with canonical edges. It rewrites the vertex ids of edges so that srcIds are bigger than dstIds, and merges the duplicated edges. Author: Takeshi Yamamuro <linguin.m.s@gmail.com> Closes #3760 from maropu/ConvertToCanonicalEdgesSpike and squashes the following commits: 7f8b580 [Takeshi Yamamuro] Add a function to convert into a graph with canonical edges in GraphOps
* [SPARK-3623][GraphX] GraphX should support the checkpoint operationGuoQiang Li2014-12-061-0/+21
| | | | | | | | | | Author: GuoQiang Li <witgo@qq.com> Closes #2631 from witgo/SPARK-3623 and squashes the following commits: a70c500 [GuoQiang Li] Remove java related 4d1e249 [GuoQiang Li] Add comments e682724 [GuoQiang Li] Graph should support the checkpoint operation
* Removing confusing TripletFieldsJoseph E. Gonzalez2014-11-261-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | After additional discussion with rxin, I think having all the possible `TripletField` options is confusing. This pull request reduces the triplet fields to: ```java /** * None of the triplet fields are exposed. */ public static final TripletFields None = new TripletFields(false, false, false); /** * Expose only the edge field and not the source or destination field. */ public static final TripletFields EdgeOnly = new TripletFields(false, false, true); /** * Expose the source and edge fields but not the destination field. (Same as Src) */ public static final TripletFields Src = new TripletFields(true, false, true); /** * Expose the destination and edge fields but not the source field. (Same as Dst) */ public static final TripletFields Dst = new TripletFields(false, true, true); /** * Expose all the fields (source, edge, and destination). */ public static final TripletFields All = new TripletFields(true, true, true); ``` Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #3472 from jegonzal/SimplifyTripletFields and squashes the following commits: 91796b5 [Joseph E. Gonzalez] removing confusing triplet fields
* [SPARK-3936] Add aggregateMessages, which supersedes mapReduceTripletsAnkur Dave2014-11-113-68/+29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | aggregateMessages enables neighborhood computation similarly to mapReduceTriplets, but it introduces two API improvements: 1. Messages are sent using an imperative interface based on EdgeContext rather than by returning an iterator of messages. 2. Rather than attempting bytecode inspection, the required triplet fields must be explicitly specified by the user by passing a TripletFields object. This fixes SPARK-3936. Additionally, this PR includes the following optimizations for aggregateMessages and EdgePartition: 1. EdgePartition now stores local vertex ids instead of global ids. This avoids hash lookups when looking up vertex attributes and aggregating messages. 2. Internal iterators in aggregateMessages are inlined into a while loop. In total, these optimizations were tested to provide a 37% speedup on PageRank (uk-2007-05 graph, 10 iterations, 16 r3.2xlarge machines, sped up from 513 s to 322 s). Subsumes apache/spark#2815. Also fixes SPARK-4173. Author: Ankur Dave <ankurdave@gmail.com> Closes #3100 from ankurdave/aggregateMessages and squashes the following commits: f5b65d0 [Ankur Dave] Address @rxin comments on apache/spark#3054 and apache/spark#3100 1e80aca [Ankur Dave] Add aggregateMessages, which supersedes mapReduceTriplets 194a2df [Ankur Dave] Test triplet iterator in EdgePartition serialization test e0f8ecc [Ankur Dave] Take activeSet in ExistingEdgePartitionBuilder c85076d [Ankur Dave] Readability improvements b567be2 [Ankur Dave] iter.foreach -> while loop 4a566dc [Ankur Dave] Optimizations for mapReduceTriplets and EdgePartition
* [SPARK-3649] Remove GraphX custom serializersAnkur Dave2014-11-101-122/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | As [reported][1] on the mailing list, GraphX throws ``` java.lang.ClassCastException: java.lang.Long cannot be cast to scala.Tuple2 at org.apache.spark.graphx.impl.RoutingTableMessageSerializer$$anon$1$$anon$2.writeObject(Serializers.scala:39) at org.apache.spark.storage.DiskBlockObjectWriter.write(BlockObjectWriter.scala:195) at org.apache.spark.util.collection.ExternalSorter.spillToMergeableFile(ExternalSorter.scala:329) ``` when sort-based shuffle attempts to spill to disk. This is because GraphX defines custom serializers for shuffling pair RDDs that assume Spark will always serialize the entire pair object rather than breaking it up into its components. However, the spill code path in sort-based shuffle [violates this assumption][2]. GraphX uses the custom serializers to compress vertex ID keys using variable-length integer encoding. However, since the serializer can no longer rely on the key and value being serialized and deserialized together, performing such encoding would either require writing a tag byte (costly) or maintaining state in the serializer and assuming that serialization calls will alternate between key and value (fragile). Instead, this PR simply removes the custom serializers. This causes a **10% slowdown** (494 s to 543 s) and **16% increase in per-iteration communication** (2176 MB to 2518 MB) for PageRank (averages across 3 trials, 10 iterations per trial, uk-2007-05 graph, 16 r3.2xlarge nodes). [1]: http://apache-spark-user-list.1001560.n3.nabble.com/java-lang-ClassCastException-java-lang-Long-cannot-be-cast-to-scala-Tuple2-td13926.html#a14501 [2]: https://github.com/apache/spark/blob/f9d6220c792b779be385f3022d146911a22c2130/core/src/main/scala/org/apache/spark/util/collection/ExternalSorter.scala#L329 Author: Ankur Dave <ankurdave@gmail.com> Closes #2503 from ankurdave/SPARK-3649 and squashes the following commits: a49c2ad [Ankur Dave] [SPARK-3649] Remove GraphX custom serializers
* SPARK-1813. Add a utility to SparkConf that makes using Kryo really easySandy Ryza2014-10-213-11/+7
| | | | | | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #789 from sryza/sandy-spark-1813 and squashes the following commits: 48b05e9 [Sandy Ryza] Simplify b824932 [Sandy Ryza] Allow both spark.kryo.classesToRegister and spark.kryo.registrator at the same time 6a15bb7 [Sandy Ryza] Small fix a2278c0 [Sandy Ryza] Respond to review comments 6ef592e [Sandy Ryza] SPARK-1813. Add a utility to SparkConf that makes using Kryo really easy
* [SPARK-3578] Fix upper bound in GraphGenerators.sampleLogNormalAnkur Dave2014-09-221-2/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | GraphGenerators.sampleLogNormal is supposed to return an integer strictly less than maxVal. However, it violates this guarantee. It generates its return value as follows: ```scala var X: Double = maxVal while (X >= maxVal) { val Z = rand.nextGaussian() X = math.exp(mu + sigma*Z) } math.round(X.toFloat) ``` When X is sampled to be close to (but less than) maxVal, then it will pass the while loop condition, but the rounded result will be equal to maxVal, which will violate the guarantee. For example, if maxVal is 5 and X is 4.9, then X < maxVal, but `math.round(X.toFloat)` is 5. This PR instead rounds X before checking the loop condition, guaranteeing that the condition will hold for the return value. Author: Ankur Dave <ankurdave@gmail.com> Closes #2439 from ankurdave/SPARK-3578 and squashes the following commits: f6655e5 [Ankur Dave] Go back to math.floor 5900c22 [Ankur Dave] Round X in loop condition 6fd5fb1 [Ankur Dave] Run sampleLogNormal bounds check 1000 times 1638598 [Ankur Dave] Round down in sampleLogNormal to guarantee upper bound
* [SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFuncLarry Xiao2014-09-181-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | VertexRDD.apply had a bug where it ignored the merge function for duplicate vertices and instead used whichever vertex attribute occurred first. This commit fixes the bug by passing the merge function through to ShippableVertexPartition.apply, which merges any duplicates using the merge function and then fills in missing vertices using the specified default vertex attribute. This commit also adds a unit test for VertexRDD.apply. Author: Larry Xiao <xiaodi@sjtu.edu.cn> Author: Blie Arkansol <xiaodi@sjtu.edu.cn> Author: Ankur Dave <ankurdave@gmail.com> Closes #1903 from larryxiao/2062 and squashes the following commits: 625aa9d [Blie Arkansol] Merge pull request #1 from ankurdave/SPARK-2062 476770b [Ankur Dave] ShippableVertexPartition.initFrom: Don't run mergeFunc on default values 614059f [Larry Xiao] doc update: note about the default null value vertices construction dfdb3c9 [Larry Xiao] minor fix 1c70366 [Larry Xiao] scalastyle check: wrap line, parameter list indent 4 spaces e4ca697 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc 6a35ea8 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc 4fbc29c [Blie Arkansol] undo unnecessary change efae765 [Larry Xiao] fix mistakes: should be able to call with or without mergeFunc b2422f9 [Larry Xiao] Merge branch '2062' of github.com:larryxiao/spark into 2062 52dc7f7 [Larry Xiao] pass mergeFunc to VertexPartitionBase, where merge is handled 581e9ee [Larry Xiao] TODO: VertexRDDSuite 20d80a3 [Larry Xiao] [SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFunc
* [HOTFIX] [SPARK-3400] Revert 9b225ac "fix GraphX EdgeRDD zipPartitions"Ankur Dave2014-09-031-16/+0
| | | | | | | | | | | 9b225ac3072de522b40b46aba6df1f1c231f13ef has been causing GraphX tests to fail nondeterministically, which is blocking development for others. Author: Ankur Dave <ankurdave@gmail.com> Closes #2271 from ankurdave/SPARK-3400 and squashes the following commits: 10c2a97 [Ankur Dave] [HOTFIX] [SPARK-3400] Revert 9b225ac "fix GraphX EdgeRDD zipPartitions"
* [SPARK-3263][GraphX] Fix changes made to GraphGenerator.logNormalGraph in PR ↵RJ Nowling2014-09-031-0/+110
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | #720 PR #720 made multiple changes to GraphGenerator.logNormalGraph including: * Replacing the call to functions for generating random vertices and edges with in-line implementations with different equations. Based on reading the Pregel paper, I believe the in-line functions are incorrect. * Hard-coding of RNG seeds so that method now generates the same graph for a given number of vertices, edges, mu, and sigma -- user is not able to override seed or specify that seed should be randomly generated. * Backwards-incompatible change to logNormalGraph signature with introduction of new required parameter. * Failed to update scala docs and programming guide for API changes * Added a Synthetic Benchmark in the examples. This PR: * Removes the in-line calls and calls original vertex / edge generation functions again * Adds an optional seed parameter for deterministic behavior (when desired) * Keeps the number of partitions parameter that was added. * Keeps compatibility with the synthetic benchmark example * Maintains backwards-compatible API Author: RJ Nowling <rnowling@gmail.com> Author: Ankur Dave <ankurdave@gmail.com> Closes #2168 from rnowling/graphgenrand and squashes the following commits: f1cd79f [Ankur Dave] Style fixes e11918e [RJ Nowling] Fix bad comparisons in unit tests 785ac70 [RJ Nowling] Fix style error c70868d [RJ Nowling] Fix logNormalGraph scala doc for seed 41fd1f8 [RJ Nowling] Fix logNormalGraph scala doc for seed 799f002 [RJ Nowling] Added test for different seeds for sampleLogNormal 43949ad [RJ Nowling] Added test for different seeds for generateRandomEdges 2faf75f [RJ Nowling] Added unit test for logNormalGraph 82f22397 [RJ Nowling] Add unit test for sampleLogNormal b99cba9 [RJ Nowling] Make sampleLogNormal private to Spark (vs private) for unit testing 6803da1 [RJ Nowling] Add GraphGeneratorsSuite with test for generateRandomEdges 1c8fc44 [RJ Nowling] Connected components part of SynthBenchmark was failing to call count on RDD before printing dfbb6dd [RJ Nowling] Fix parameter name in SynthBenchmark docs b5eeb80 [RJ Nowling] Add optional seed parameter to SynthBenchmark and set default to randomly generate a seed 1ff8d30 [RJ Nowling] Fix bug in generateRandomEdges where numVertices instead of numEdges was used to control number of edges to generate 98bb73c [RJ Nowling] Add documentation for logNormalGraph parameters d40141a [RJ Nowling] Fix style error 684804d [RJ Nowling] revert PR #720 which introduce errors in logNormalGraph and messed up seeding of RNGs. Add user-defined optional seed for deterministic behavior c183136 [RJ Nowling] Fix to deterministic GraphGenerators.logNormalGraph that allows generating graphs randomly using optional seed. 015010c [RJ Nowling] Fixed GraphGenerator logNormalGraph API to make backward-incompatible change in commit 894ecde04
* [SPARK-2823][GraphX]fix GraphX EdgeRDD zipPartitionsluluorta2014-09-021-0/+16
| | | | | | | | | | | If the users set “spark.default.parallelism” and the value is different with the EdgeRDD partition number, GraphX jobs will throw: java.lang.IllegalArgumentException: Can't zip RDDs with unequal numbers of partitions Author: luluorta <luluorta@gmail.com> Closes #1763 from luluorta/fix-graph-zip and squashes the following commits: 8338961 [luluorta] fix GraphX EdgeRDD zipPartitions
* Remove GraphX MessageToPartition for compatibility with sort-based shuffleAnkur Dave2014-07-221-73/+0
| | | | | | | | | | | MessageToPartition was used in `Graph#partitionBy`. Unlike a Tuple2, it marked the key as transient to avoid sending it over the network. However, it was incompatible with sort-based shuffle (SPARK-2045) and represented only a minor optimization: for partitionBy, it improved performance by 6.3% (30.4 s to 28.5 s) and reduced communication by 5.6% (114.2 MB to 107.8 MB). Author: Ankur Dave <ankurdave@gmail.com> Closes #1537 from ankurdave/remove-MessageToPartition and squashes the following commits: f9d0054 [Ankur Dave] Remove MessageToPartition ab71364 [Ankur Dave] Remove unused VertexBroadcastMsg
* [SPARK-2455] Mark (Shippable)VertexPartition serializableAnkur Dave2014-07-122-11/+33
| | | | | | | | | | | | | VertexPartition and ShippableVertexPartition are contained in RDDs but are not marked Serializable, leading to NotSerializableExceptions when using Java serialization. The fix is simply to mark them as Serializable. This PR does that and adds a test for serializing them using Java and Kryo serialization. Author: Ankur Dave <ankurdave@gmail.com> Closes #1376 from ankurdave/SPARK-2455 and squashes the following commits: ed4a51b [Ankur Dave] Make (Shippable)VertexPartition serializable 1fd42c5 [Ankur Dave] Add failing tests for Java serialization
* [SPARK-1552] Fix type comparison bug in {map,outerJoin}VerticesAnkur Dave2014-06-051-0/+25
| | | | | | | | | | | | | | | | | | | | | In GraphImpl, mapVertices and outerJoinVertices use a more efficient implementation when the map function conserves vertex attribute types. This is implemented by comparing the ClassTags of the old and new vertex attribute types. However, ClassTags store erased types, so the comparison will return a false positive for types with different type parameters, such as Option[Int] and Option[Double]. This PR resolves the problem by requesting that the compiler generate evidence of equality between the old and new vertex attribute types, and providing a default value for the evidence parameter if the two types are not equal. The methods can then check the value of the evidence parameter to see whether the types are equal. It also adds a test called "mapVertices changing type with same erased type" that failed before the PR and succeeds now. Callers of mapVertices and outerJoinVertices can no longer use a wildcard for a graph's VD type. To avoid "Error occurred in an application involving default arguments," they must bind VD to a type parameter, as this PR does for ShortestPaths and LabelPropagation. Author: Ankur Dave <ankurdave@gmail.com> Closes #967 from ankurdave/SPARK-1552 and squashes the following commits: 68a4fff [Ankur Dave] Undo conserve naming 7388705 [Ankur Dave] Remove unnecessary ClassTag for VD parameters a704e5f [Ankur Dave] Use type equality constraint with default argument 29a5ab7 [Ankur Dave] Add failing test f458c83 [Ankur Dave] Revert "[SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices" 16d6af8 [Ankur Dave] [SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices
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