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From José Luis Larroque <larroques...@gmail.com>
Subject OutOfMemory error while reading byes from edges in yarn
Date Thu, 20 Aug 2015 14:38:23 GMT
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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