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https://issues.apache.org/jira/browse/FLINK-5506?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16279261#comment-16279261
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ASF GitHub Bot commented on FLINK-5506:
---------------------------------------
GitHub user greghogan opened a pull request:
https://github.com/apache/flink/pull/5126
[FLINK-5506] [gelly] Fix CommunityDetection NullPointerException
## What is the purpose of the change
This fixes a regression which can result in `NullPointerException` when
running the `CommunityDetection` algorithm. When a new highest valued label had
a negative summed value the lookup was performed on the old label value which
did not necessarily exist in the dictionary.
## Brief change log
- replaced `Double.MIN_VALUE` with the intended (and original)
`-Double.MAX_VALUE`
- added `Graph#mapVertices` and `Graph#mapEdges` variants accepting
`TypeHint` rather than `TypeInformation`; this seemed useful when using Java 8
lambdas which require explicit type definition with OpenJDK
- added additional tests for `CommunityDetection`
## Verifying this change
`CommunityDetectionTest#testWithSingletonEdgeGraph` is a user supplied
example which fails without the bug fix.
## Does this pull request potentially affect one of the following parts:
- Dependencies (does it add or upgrade a dependency): (yes / **no**)
- The public API, i.e., is any changed class annotated with
`@Public(Evolving)`: (yes / **no**)
- The serializers: (yes / **no** / don't know)
- The runtime per-record code paths (performance sensitive): (yes /
**no** / don't know)
- Anything that affects deployment or recovery: JobManager (and its
components), Checkpointing, Yarn/Mesos, ZooKeeper: (yes / **no** / don't know)
- The S3 file system connector: (yes / **no** / don't know)
## Documentation
- Does this pull request introduce a new feature? (yes / **no**)
- If yes, how is the feature documented? (**not applicable** / docs /
JavaDocs / not documented)
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/greghogan/flink
5506_communitydetection_nullpointerexception
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/flink/pull/5126.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #5126
----
commit 8d57371616a742ba29548192d5d8a4018cafd26b
Author: Greg Hogan <[email protected]>
Date: 2017-12-05T17:36:18Z
[hotfix] [gelly] Graph API mapVertices/mapEdges with TypeHint
commit 8c131b42cfa95df34333a9ca733c9337f75695ba
Author: Greg Hogan <[email protected]>
Date: 2017-12-05T17:38:50Z
[FLINK-5506] [gelly] Fix CommunityDetection NullPointerException
Double.MIN_VALUE != min(double)
----
> Java 8 - CommunityDetection.java:158 - java.lang.NullPointerException
> ---------------------------------------------------------------------
>
> Key: FLINK-5506
> URL: https://issues.apache.org/jira/browse/FLINK-5506
> Project: Flink
> Issue Type: Bug
> Components: Gelly
> Affects Versions: 1.1.4, 1.3.2, 1.4.1
> Reporter: Miguel E. Coimbra
> Assignee: Greg Hogan
> Labels: easyfix, newbie
> Original Estimate: 2h
> Remaining Estimate: 2h
>
> Reporting this here as per Vasia's advice.
> I am having the following problem while trying out the
> org.apache.flink.graph.library.CommunityDetection algorithm of the Gelly API
> (Java).
> Specs: JDK 1.8.0_102 x64
> Apache Flink: 1.1.4
> Suppose I have a very small (I tried an example with 38 vertices as well)
> dataset stored in a tab-separated file 3-vertex.tsv:
> {code}
> #id1 id2 score
> 0 1 0
> 0 2 0
> 0 3 0
> {code}
> This is just a central vertex with 3 neighbors (disconnected between
> themselves).
> I am loading the dataset and executing the algorithm with the following code:
> {code}
> // Load the data from the .tsv file.
> final DataSet<Tuple3<Long, Long, Double>> edgeTuples =
> env.readCsvFile(inputPath)
> .fieldDelimiter("\t") // node IDs are separated by spaces
> .ignoreComments("#") // comments start with "%"
> .types(Long.class, Long.class, Double.class);
> // Generate a graph and add reverse edges (undirected).
> final Graph<Long, Long, Double> graph = Graph.fromTupleDataSet(edgeTuples,
> new MapFunction<Long, Long>() {
> private static final long serialVersionUID = 8713516577419451509L;
> public Long map(Long value) {
> return value;
> }
> },
> env).getUndirected();
> // CommunityDetection parameters.
> final double hopAttenuationDelta = 0.5d;
> final int iterationCount = 10;
> // Prepare and trigger the execution.
> DataSet<Vertex<Long, Long>> vs = graph.run(new
> org.apache.flink.graph.library.CommunityDetection<Long>(iterationCount,
> hopAttenuationDelta)).getVertices();
> vs.print();
> {code}
> Running this code throws the following exception (check the bold line):
> {code}
> org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
> at
> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$8.apply$mcV$sp(JobManager.scala:805)
> at
> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$8.apply(JobManager.scala:751)
> at
> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$8.apply(JobManager.scala:751)
> at
> scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
> at
> scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
> at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41)
> at
> akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:401)
> at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
> at
> scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.pollAndExecAll(ForkJoinPool.java:1253)
> at
> scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1346)
> at
> scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
> at
> scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
> Caused by: java.lang.NullPointerException
> at
> org.apache.flink.graph.library.CommunityDetection$VertexLabelUpdater.updateVertex(CommunityDetection.java:158)
> at
> org.apache.flink.graph.spargel.ScatterGatherIteration$GatherUdfSimpleVV.coGroup(ScatterGatherIteration.java:389)
> at
> org.apache.flink.runtime.operators.CoGroupWithSolutionSetSecondDriver.run(CoGroupWithSolutionSetSecondDriver.java:218)
> at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:486)
> at
> org.apache.flink.runtime.iterative.task.AbstractIterativeTask.run(AbstractIterativeTask.java:146)
> at
> org.apache.flink.runtime.iterative.task.IterationTailTask.run(IterationTailTask.java:107)
> at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:351)
> at org.apache.flink.runtime.taskmanager.Task.run(Task.java:642)
> at java.lang.Thread.run(Thread.java:745)
> {code}
> After a further look, I set a breakpoint (Eclipse IDE debugging) at the line
> in bold:
> org.apache.flink.graph.library.CommunityDetection.java (source code accessed
> automatically by Maven)
> // find the highest score of maxScoreLabel
> double highestScore = labelsWithHighestScore.get(maxScoreLabel);
> - maxScoreLabel has the value 3.
> - labelsWithHighestScore was initialized as: Map<Long, Double>
> labelsWithHighestScore = new TreeMap<>();
> - labelsWithHighestScore is a TreeMap<Long, Double> and has the values:
> {0=0.0}
> null
> null
> [0=0.0]
> null
> 1
> It seems that the value 3 should have been added to that
> labelsWithHighestScore some time during execution, but because it wasn't, an
> exception is thrown.
> In the mailing list, Vasia speculates that the problem is that the
> implementation assumes that labelsWithHighestScores contains the vertex
> itself as initial label.
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