Exception in task 0.0 in stage 13.0 (TID 13) java.lang.OutOfMemoryError: Java heap space

Question

We are experimenting problems when we use "mahout spark-rowsimilarity” operation. We have an input matrix with 100k rows and 100 items and process throws an exception about “Exception in task 0.0 in stage 13.0 (TID 13) java.lang.OutOfMemoryError: Java heap space” and we try to increase JAVA HEAP MEMORY, MAHOUT HEAP MEMORY and spark.driver.memory.

Environment versions: Mahout: 0.11.1 Spark: 1.6.0.

Mahout command line:

/opt/mahout/bin/mahout spark-rowsimilarity -i 50k_rows__50items.dat -o test_output.tmp --maxObservations 500 --maxSimilaritiesPerRow 100 --omitStrength --master local --sparkExecutorMem 8g

This process is running on a machine with following specifications:

Mem RAM: 8gb 
CPU with 8 cores

.profile file:

export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
export HADOOP_HOME=/opt/hadoop-2.6.0
export SPARK_HOME=/opt/spark
export MAHOUT_HOME=/opt/mahout
export MAHOUT_HEAPSIZE=8192

Throws exception:

16/01/22 11:45:06 ERROR Executor: Exception in task 0.0 in stage 13.0 (TID 13)
java.lang.OutOfMemoryError: Java heap space
        at org.apache.mahout.math.DenseMatrix.<init>(DenseMatrix.java:66)
        at org.apache.mahout.sparkbindings.drm.package$$anonfun$blockify$1.apply(package.scala:70)
        at org.apache.mahout.sparkbindings.drm.package$$anonfun$blockify$1.apply(package.scala:59)
        at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
        at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
        at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
        at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
        at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
        at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
        at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
        at org.apache.spark.scheduler.Task.run(Task.scala:89)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
16/01/22 11:45:06 WARN NettyRpcEndpointRef: Error sending message [message = Heartbeat(driver,[Lscala.Tuple2;@12498227,BlockManagerId(driver, localhost, 42107))] in 1 attempts
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [120 seconds]. This timeout is controlled by spark.rpc.askTimeout
        at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:48)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:63)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:33)
        at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
        at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:101)
        at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:77)
        at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:448)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply$mcV$sp(Executor.scala:468)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:468)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:468)
        at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1741)
        at org.apache.spark.executor.Executor$$anon$1.run(Executor.scala:468)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
16/01/22 11:45:06 WARN NettyRpcEndpointRef: Error sending message [message = Heartbeat(driver,[Lscala.Tuple2;@12498227,BlockManagerId(driver, localhost, 42107))] in 1 attempts
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [120 seconds]. This timeout is controlled by spark.rpc.askTimeout
        at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:48)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:63)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:33)
        at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
        at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:101)
        at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:77)
        at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:448)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply$mcV$sp(Executor.scala:468)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:468)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:468)
        at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1741)
        at org.apache.spark.executor.Executor$$anon$1.run(Executor.scala:468)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [120 seconds]
        at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:219)
        at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
        at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107)
        at scala.concurrent.BlockContext$DefaultBlockContext$.blockOn(BlockContext.scala:53)
        at scala.concurrent.Await$.result(package.scala:107)
        at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
        ...

Can you please advise?

Thanks for advance. Cheers.

Answer 1

I had a similar issue and solved it by reverting this commit:

https://github.com/apache/mahout/pull/10/commits/162c5ca36e00af91a9599075332c577d9b1a13c4