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From José Luis Larroque <larroques...@gmail.com>
Subject Re: OutOfMemory error while reading byes from edges in yarn
Date Tue, 08 Sep 2015 03:47:25 GMT
This was a memory configuration issue, after i fix it, the real problem was
another (i will send a different email with it)

Thanks!
Jose

2015-08-20 11:38 GMT-03:00 José Luis Larroque <larroquester@gmail.com>:

> I'm doing a BFS algorithm in yarn, and i make a custom value for the data
> on my vertex (Vertex Data). But, after i did this, something went wrong for
> the process of reading edges.
>
> I trace the error to the following lines of code:
>
>  - In ByteArrayEdges, the variable **serializedEdgesBytesUsed** get the
> value 1987015248 and gives OutOfMemory error when a new array is allocated
> (java limit is 64K as far as i know)
>
>         @Override
>         public void readFields(DataInput in) throws IOException {
>         serializedEdgesBytesUsed = in.readInt();
>         if (serializedEdgesBytesUsed > 0) {
>           // Only create a new buffer if the old one isn't big enough
>           if (serializedEdges == null ||
>               serializedEdgesBytesUsed > serializedEdges.length) {
>             serializedEdges = new byte[serializedEdgesBytesUsed];
>           }
>           in.readFully(serializedEdges, 0, serializedEdgesBytesUsed);
>         }
>         edgeCount = in.readInt();
>       }
>
> I'm not sure why this started happening, but previous to use custom vertex
> data, this problem doesn´t exist.
>
> The full log is here (i'm testing directly from eclipse, because in a
> pseudo distributed cluster was far more difficult):
>
>     2015-08-20 01:52:21,103 INFO  [LocalJobRunner Map Task Executor #0]
> utils.ProgressableUtils (ProgressableUtils.java:waitFor(315)) - waitFor:
> Future result not ready yet java.util.concurrent.FutureTask@b2dd686
>     2015-08-20 01:52:21,103 INFO  [LocalJobRunner Map Task Executor #0]
> utils.ProgressableUtils (ProgressableUtils.java:waitFor(197)) - waitFor:
> Waiting for
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     2015-08-20 01:53:12,527 ERROR [LocalJobRunner Map Task Executor #0]
> graph.GraphMapper (GraphMapper.java:run(101)) - Caught an unrecoverable
> exception waitFor: ExecutionException occurred while waiting for
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     java.lang.IllegalStateException: waitFor: ExecutionException occurred
> while waiting for
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     at
> org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:193)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:151)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:136)
>     at
> org.apache.giraph.utils.ProgressableUtils.getFutureResult(ProgressableUtils.java:99)
>     at
> org.apache.giraph.utils.ProgressableUtils.getResultsWithNCallables(ProgressableUtils.java:233)
>     at
> org.apache.giraph.worker.BspServiceWorker.loadInputSplits(BspServiceWorker.java:316)
>     at
> org.apache.giraph.worker.BspServiceWorker.loadVertices(BspServiceWorker.java:409)
>     at
> org.apache.giraph.worker.BspServiceWorker.setup(BspServiceWorker.java:629)
>     at
> org.apache.giraph.graph.GraphTaskManager.execute(GraphTaskManager.java:284)
>     at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:93)
>     at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:764)
>     at org.apache.hadoop.mapred.MapTask.run(MapTask.java:340)
>     at
> org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
>     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>     at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>     at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>     at java.lang.Thread.run(Thread.java:745)
>     Caused by: java.util.concurrent.ExecutionException:
> java.lang.OutOfMemoryError: Java heap space
>     at java.util.concurrent.FutureTask.report(FutureTask.java:122)
>     at java.util.concurrent.FutureTask.get(FutureTask.java:202)
>     at
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable.waitFor(ProgressableUtils.java:312)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:185)
>     ... 17 more
>     Caused by: java.lang.OutOfMemoryError: Java heap space
>     at
> org.apache.giraph.edge.ByteArrayEdges.readFields(ByteArrayEdges.java:193)
>     at
> org.apache.giraph.utils.WritableUtils.reinitializeVertexFromDataInput(WritableUtils.java:541)
>     at org.apache.giraph.utils.VertexIterator.next(VertexIterator.java:98)
>     at
> org.apache.giraph.partition.BasicPartition.addPartitionVertices(BasicPartition.java:99)
>     at
> org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:115)
>     at
> org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:466)
>     at
> org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.flush(NettyWorkerClientRequestProcessor.java:412)
>     at
> org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:241)
>     at
> org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60)
>     at
> org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51)
>     ... 4 more
>     2015-08-20 01:53:12,532 ERROR [LocalJobRunner Map Task Executor #0]
> worker.BspServiceWorker (BspServiceWorker.java:unregisterHealth(777)) -
> unregisterHealth: Got failure, unregistering health on
> /_hadoopBsp/job_local1113753160_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir/localhost_0
> on superstep -1
>     2015-08-20 01:53:12,558 INFO  [Thread-13] mapred.LocalJobRunner
> (LocalJobRunner.java:runTasks(456)) - map task executor complete.
>     2015-08-20 01:53:12,562 WARN  [Thread-13] mapred.LocalJobRunner
> (LocalJobRunner.java:run(560)) - job_local1113753160_0001
>     java.lang.Exception: java.lang.IllegalStateException: run: Caught an
> unrecoverable exception waitFor: ExecutionException occurred while waiting
> for org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     at
> org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:462)
>     at
> org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:522)
>     Caused by: java.lang.IllegalStateException: run: Caught an
> unrecoverable exception waitFor: ExecutionException occurred while waiting
> for org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:104)
>     at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:764)
>     at org.apache.hadoop.mapred.MapTask.run(MapTask.java:340)
>     at
> org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
>     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>     at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>     at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>     at java.lang.Thread.run(Thread.java:745)
>     Caused by: java.lang.IllegalStateException: waitFor:
> ExecutionException occurred while waiting for
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable@6e5efd25
>     at
> org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:193)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:151)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:136)
>     at
> org.apache.giraph.utils.ProgressableUtils.getFutureResult(ProgressableUtils.java:99)
>     at
> org.apache.giraph.utils.ProgressableUtils.getResultsWithNCallables(ProgressableUtils.java:233)
>     at
> org.apache.giraph.worker.BspServiceWorker.loadInputSplits(BspServiceWorker.java:316)
>     at
> org.apache.giraph.worker.BspServiceWorker.loadVertices(BspServiceWorker.java:409)
>     at
> org.apache.giraph.worker.BspServiceWorker.setup(BspServiceWorker.java:629)
>     at
> org.apache.giraph.graph.GraphTaskManager.execute(GraphTaskManager.java:284)
>     at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:93)
>     ... 8 more
>     Caused by: java.util.concurrent.ExecutionException:
> java.lang.OutOfMemoryError: Java heap space
>     at java.util.concurrent.FutureTask.report(FutureTask.java:122)
>     at java.util.concurrent.FutureTask.get(FutureTask.java:202)
>     at
> org.apache.giraph.utils.ProgressableUtils$FutureWaitable.waitFor(ProgressableUtils.java:312)
>     at
> org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:185)
>     ... 17 more
>     Caused by: java.lang.OutOfMemoryError: Java heap space
>     at
> org.apache.giraph.edge.ByteArrayEdges.readFields(ByteArrayEdges.java:193)
>     at
> org.apache.giraph.utils.WritableUtils.reinitializeVertexFromDataInput(WritableUtils.java:541)
>     at org.apache.giraph.utils.VertexIterator.next(VertexIterator.java:98)
>     at
> org.apache.giraph.partition.BasicPartition.addPartitionVertices(BasicPartition.java:99)
>     at
> org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:115)
>     at
> org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:466)
>     at
> org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.flush(NettyWorkerClientRequestProcessor.java:412)
>     at
> org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:241)
>     at
> org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60)
>     at
> org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51)
>     ... 4 more
>
> The line from terminal used for executing this is:
>
>     $HADOOP_HOME/bin/yarn jar
> $GIRAPH_HOME/gaph-examples/target/giraph-examples-1.1.0-for-hadoop-2.4.0-jar-with-dependencies.jar
> algoritmos.masivos.BusquedaDeCaminosNavegacionalesWikiquotesMasivo
> lectura_de_grafo.BusquedaDeCaminosNavegacionalesWikiquote -vif
> pruebas.IdTextWithValueDoubleInputFormat -vip
> /user/hduser/input/wiki-graph-chiquito.txt -vof
> pruebas.IdTextWithValueTextOutputFormat -op
> /user/hduser/output/caminosNavegacionales -w 2 -yh 250
>
> Maybe i should use a EdgeInputFormat?
>
> Thanks for reading.
> Jose.
>

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