coGroup exception or something else in Gelly job

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coGroup exception or something else in Gelly job

Kaepke, Marc
Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc

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Re: coGroup exception or something else in Gelly job

Greg Hogan
Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc


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Re: coGroup exception or something else in Gelly job

Kaepke, Marc
It seems Flink used a different exception graph outside of my IDE (intellij)

The job anatomy is:
load data from csv and build an initial graph => reduce that graph (remove loops and combine multi edges) => extend the modified graph by a new vertex value => run a gather-scatter iteration

I have to extend the vertex value, because each vertex need its incident edges inside the iteration. My CustomVertexValue is able to hold all incident edges. Vertex<Double, CustomVertexValue> vertex

Flink is try to optimize the execution graph, but that’s the issue. 
Maybe Flink provides an influence by the programmer?


Best and thanks
Marc


Am 10.06.2017 um 00:49 schrieb Greg Hogan <[hidden email]>:

Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc



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Re: coGroup exception or something else in Gelly job

Greg Hogan
I don't think it is possible for anyone to debug your exception without the source code. Storing the adjacency list within the Vertex value is not scalable. Can you share a basic description of the algorithm you are working to implement?

On Mon, Jun 12, 2017 at 5:47 AM, Kaepke, Marc <[hidden email]> wrote:
It seems Flink used a different exception graph outside of my IDE (intellij)

The job anatomy is:
load data from csv and build an initial graph => reduce that graph (remove loops and combine multi edges) => extend the modified graph by a new vertex value => run a gather-scatter iteration

I have to extend the vertex value, because each vertex need its incident edges inside the iteration. My CustomVertexValue is able to hold all incident edges. Vertex<Double, CustomVertexValue> vertex

Flink is try to optimize the execution graph, but that’s the issue. 
Maybe Flink provides an influence by the programmer?


Best and thanks
Marc


Am 10.06.2017 um 00:49 schrieb Greg Hogan <[hidden email]>:

Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc




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Re: coGroup exception or something else in Gelly job

Kaepke, Marc
I’m working on an implementation of SemiClustering [1]. 
I used two graph models (Pregel aka. vertexcentric iteration and gather scatter).

Short description of the algorithm
  • input is a weighted, undirected graph
  • output are greedy clusters

  • Each vertex V maintains a list containing at most Cmax semi-clusters, sorted by score. 
  • In superstep 0 V enters itself in that list as a semi-cluster of size 1 and score 1, and publishes itself to all of its neighbors. 
  • In subsequent supersteps:
    • Vertex V iterates over the semi-clusters c1,...,ck sent to it on the previous superstep. If a semi-cluster c does not already contain V , and Vc < Mmax, then V is added to c to form c′.
    • The semi-clusters c1,…,ck,c′1,…,c′k are sorted by their scores, and the best ones are sent to V ’s neighbors.
    • Vertex V updates its list of semi-clusters with the semi-clusters from c1,…,ck, c′1,…,c′k that contain V.
  • The algorithm terminates either when the semi-clusters stop changing or (to improve performance) when the number of supersteps reaches a user-specified limit. At that point the list of best semi-cluster candidates for each vertex may be aggregated into a global list of best semi-clusters. 

It’s a simple algorithm, except the access to the edges of each vertex. If I iterate every time across all edges to find the incident ones I gain a horrible landau (time complexity).


Best
Marc




Am 12.06.2017 um 18:28 schrieb Greg Hogan <[hidden email]>:

I don't think it is possible for anyone to debug your exception without the source code. Storing the adjacency list within the Vertex value is not scalable. Can you share a basic description of the algorithm you are working to implement?

On Mon, Jun 12, 2017 at 5:47 AM, Kaepke, Marc <[hidden email]> wrote:
It seems Flink used a different exception graph outside of my IDE (intellij)

The job anatomy is:
load data from csv and build an initial graph => reduce that graph (remove loops and combine multi edges) => extend the modified graph by a new vertex value => run a gather-scatter iteration

I have to extend the vertex value, because each vertex need its incident edges inside the iteration. My CustomVertexValue is able to hold all incident edges. Vertex<Double, CustomVertexValue> vertex

Flink is try to optimize the execution graph, but that’s the issue. 
Maybe Flink provides an influence by the programmer?


Best and thanks
Marc


Am 10.06.2017 um 00:49 schrieb Greg Hogan <[hidden email]>:

Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc





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Re: coGroup exception or something else in Gelly job

Kaepke, Marc
Hi Greg,

I wanna ask if there was any news about the implementation or opportunities?

Thanks and best regards,
Marc

Am 12.06.2017 um 19:28 schrieb Kaepke, Marc <[hidden email]>:

I’m working on an implementation of SemiClustering [1]. 
I used two graph models (Pregel aka. vertexcentric iteration and gather scatter).

Short description of the algorithm
  • input is a weighted, undirected graph
  • output are greedy clusters

  • Each vertex V maintains a list containing at most Cmax semi-clusters, sorted by score. 
  • In superstep 0 V enters itself in that list as a semi-cluster of size 1 and score 1, and publishes itself to all of its neighbors. 
  • In subsequent supersteps:
    • Vertex V iterates over the semi-clusters c1,...,ck sent to it on the previous superstep. If a semi-cluster c does not already contain V , and Vc < Mmax, then V is added to c to form c′.
    • The semi-clusters c1,…,ck,c′1,…,c′k are sorted by their scores, and the best ones are sent to V ’s neighbors.
    • Vertex V updates its list of semi-clusters with the semi-clusters from c1,…,ck, c′1,…,c′k that contain V.
  • The algorithm terminates either when the semi-clusters stop changing or (to improve performance) when the number of supersteps reaches a user-specified limit. At that point the list of best semi-cluster candidates for each vertex may be aggregated into a global list of best semi-clusters. 

It’s a simple algorithm, except the access to the edges of each vertex. If I iterate every time across all edges to find the incident ones I gain a horrible landau (time complexity).


Best
Marc




Am 12.06.2017 um 18:28 schrieb Greg Hogan <[hidden email]>:

I don't think it is possible for anyone to debug your exception without the source code. Storing the adjacency list within the Vertex value is not scalable. Can you share a basic description of the algorithm you are working to implement?

On Mon, Jun 12, 2017 at 5:47 AM, Kaepke, Marc <[hidden email]> wrote:
It seems Flink used a different exception graph outside of my IDE (intellij)

The job anatomy is:
load data from csv and build an initial graph => reduce that graph (remove loops and combine multi edges) => extend the modified graph by a new vertex value => run a gather-scatter iteration

I have to extend the vertex value, because each vertex need its incident edges inside the iteration. My CustomVertexValue is able to hold all incident edges. Vertex<Double, CustomVertexValue> vertex

Flink is try to optimize the execution graph, but that’s the issue. 
Maybe Flink provides an influence by the programmer?


Best and thanks
Marc


Am 10.06.2017 um 00:49 schrieb Greg Hogan <[hidden email]>:

Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc






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Re: coGroup exception or something else in Gelly job

Kaepke, Marc
Hi Greg

if you have an idea, I'm still interested. In case you didn't, please give me a feedback too.

Best,
Marc


Sent from my iPhone

On 15. Jun 2017, at 15:19, Kaepke, Marc <[hidden email]> wrote:

Hi Greg,

I wanna ask if there was any news about the implementation or opportunities?

Thanks and best regards,
Marc

Am 12.06.2017 um 19:28 schrieb Kaepke, Marc <[hidden email]>:

I’m working on an implementation of SemiClustering [1]. 
I used two graph models (Pregel aka. vertexcentric iteration and gather scatter).

Short description of the algorithm
  • input is a weighted, undirected graph
  • output are greedy clusters

  • Each vertex V maintains a list containing at most Cmax semi-clusters, sorted by score. 
  • In superstep 0 V enters itself in that list as a semi-cluster of size 1 and score 1, and publishes itself to all of its neighbors. 
  • In subsequent supersteps:
    • Vertex V iterates over the semi-clusters c1,...,ck sent to it on the previous superstep. If a semi-cluster c does not already contain V , and Vc < Mmax, then V is added to c to form c′.
    • The semi-clusters c1,…,ck,c′1,…,c′k are sorted by their scores, and the best ones are sent to V ’s neighbors.
    • Vertex V updates its list of semi-clusters with the semi-clusters from c1,…,ck, c′1,…,c′k that contain V.
  • The algorithm terminates either when the semi-clusters stop changing or (to improve performance) when the number of supersteps reaches a user-specified limit. At that point the list of best semi-cluster candidates for each vertex may be aggregated into a global list of best semi-clusters. 

It’s a simple algorithm, except the access to the edges of each vertex. If I iterate every time across all edges to find the incident ones I gain a horrible landau (time complexity).


Best
Marc




Am 12.06.2017 um 18:28 schrieb Greg Hogan <[hidden email]>:

I don't think it is possible for anyone to debug your exception without the source code. Storing the adjacency list within the Vertex value is not scalable. Can you share a basic description of the algorithm you are working to implement?

On Mon, Jun 12, 2017 at 5:47 AM, Kaepke, Marc <[hidden email]> wrote:
It seems Flink used a different exception graph outside of my IDE (intellij)

The job anatomy is:
load data from csv and build an initial graph => reduce that graph (remove loops and combine multi edges) => extend the modified graph by a new vertex value => run a gather-scatter iteration

I have to extend the vertex value, because each vertex need its incident edges inside the iteration. My CustomVertexValue is able to hold all incident edges. Vertex<Double, CustomVertexValue> vertex

Flink is try to optimize the execution graph, but that’s the issue. 
Maybe Flink provides an influence by the programmer?


Best and thanks
Marc


Am 10.06.2017 um 00:49 schrieb Greg Hogan <[hidden email]>:

Have you looked at org.apache.flink.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)?


On Jun 9, 2017, at 4:53 PM, Kaepke, Marc <[hidden email]> wrote:

Hi everyone,

I don’t have any exceptions if I execute my Gelly job in my IDE (local) directly.
The next step is an execution with a real kubernetes cluster (1 JobManager and 3 TaskManager on dedicated machines). The word count example is running without exceptions. My Gelly job throws following exception and I don’t know why.

org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:478)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:105)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:442)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:429)
at org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:62)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:926)
at org.apache.flink.api.java.DataSet.collect(DataSet.java:410)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:84)
at org.apache.flink.gelly.Algorithm.SemiClusteringPregel.run(SemiClusteringPregel.java:34)
at org.apache.flink.graph.Graph.run(Graph.java:1850)
at org.apache.flink.gelly.job.GellyMain.main(GellyMain.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:528)
at org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:419)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:381)
at org.apache.flink.client.CliFrontend.executeProgram(CliFrontend.java:838)
at org.apache.flink.client.CliFrontend.run(CliFrontend.java:259)
at org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1086)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1133)
at org.apache.flink.client.CliFrontend$2.call(CliFrontend.java:1130)
at org.apache.flink.runtime.security.HadoopSecurityContext$1.run(HadoopSecurityContext.java:43)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.flink.runtime.security.HadoopSecurityContext.runSecured(HadoopSecurityContext.java:40)
at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1129)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply$mcV$sp(JobManager.scala:933)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$6.apply(JobManager.scala:876)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
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.gelly.GraphExtension.CustomVertexValue.createInitSemiCluster(CustomVertexValue.java:51)
at org.apache.flink.gelly.PreModification.IncidentEdgesCollector.iterateEdges(IncidentEdgesCollector.java:37)
at org.apache.flink.graph.Graph$ApplyCoGroupFunctionOnAllEdges.coGroup(Graph.java:1252)
at org.apache.flink.runtime.operators.CoGroupDriver.run(CoGroupDriver.java:159)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
at java.lang.Thread.run(Thread.java:748)

I guess the trigger is the coGroup function, but I’m not sure and need your help.


Best,

Marc






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