The "too many open files" error is due to running out of available FDs, usually due to a limit set in the OS.
The fix will depend on your specific OS, but under Linux it usually involves the "fs.file-max" syctl. On Fri, Jan 17, 2014 at 3:02 PM, Ryan Compton <[email protected]> wrote: > When I try .distinct() my jobs fail. Possibly related: > https://groups.google.com/forum/#!topic/shark-users/j2TO-GINuFo > > This works > > //get the node ids > val nodes = dupedKeyedEdgeList.map(x => x._1).cache() > //count the nodes > val numNodes = nodes.count() > logWarning("numNodes:\t"+numNodes) > > this fails > > //get the node ids > val nodes = dupedKeyedEdgeList.map(x => x._1).cache() > //count the nodes > val numNodes = nodes.distinct().count() > logWarning("numNodes:\t"+numNodes) > > with these stacktraces: > > 14/01/17 14:54:37 WARN scripts.ComputeNetworkStats: numEdges: 915189977 > 14/01/17 14:54:37 INFO rdd.MappedRDD: Removing RDD 1 from persistence list > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.io.IOException > java.io.IOException: Filesystem closed > at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:299) > at org.apache.hadoop.hdfs.DFSClient.access$1100(DFSClient.java:77) > at org.apache.hadoop.hdfs.DFSClient$DFSInputStream.read(DFSClient.java:2317) > at java.io.DataInputStream.read(DataInputStream.java:83) > at org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:205) > at org.apache.hadoop.util.LineReader.readLine(LineReader.java:169) > at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:160) > at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:38) > at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:103) > at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:83) > at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71) > at scala.collection.Iterator$$anon$19.hasNext(Iterator.scala:400) > at scala.collection.Iterator$$anon$19.hasNext(Iterator.scala:400) > at scala.collection.Iterator$$anon$19.hasNext(Iterator.scala:400) > at scala.collection.Iterator$$anon$19.hasNext(Iterator.scala:400) > at scala.collection.Iterator$$anon$19.hasNext(Iterator.scala:400) > at scala.collection.Iterator$class.foreach(Iterator.scala:772) > at scala.collection.Iterator$$anon$19.foreach(Iterator.scala:399) > at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48) > at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:102) > at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:74) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:224) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:70) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:224) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:36) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:1419 as TID 1396 on executor 6: node25 (PROCESS_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.lang.IllegalStateException > java.lang.IllegalStateException: Shutdown in progress > at java.lang.ApplicationShutdownHooks.add(ApplicationShutdownHooks.java:39) > at java.lang.Runtime.addShutdownHook(Runtime.java:192) > at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:1655) > at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:1627) > at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:254) > at org.apache.hadoop.fs.Path.getFileSystem(Path.java:183) > at org.apache.hadoop.mapred.LineRecordReader.<init>(LineRecordReader.java:92) > at > org.apache.hadoop.mapred.TextInputFormat.getRecordReader(TextInputFormat.java:54) > at org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:93) > at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:83) > at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:51) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.UnionPartition.iterator(UnionRDD.scala:29) > at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:69) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:70) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:224) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:70) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:224) > at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:29) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:36) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:237) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:226) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:1419 as TID 1403 on executor 6: node25 (PROCESS_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.io.FileNotFoundException > java.io.FileNotFoundException: > /tmp/spark-local-20140117145333-5d01/27/shuffle_0_54_1140 (Too many > open files) > at java.io.FileOutputStream.openAppend(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:192) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.open(DiskStore.scala:58) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.write(DiskStore.scala:107) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:152) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:149) > at scala.collection.Iterator$class.foreach(Iterator.scala:772) > at > scala.collection.JavaConversions$JMapWrapperLike$$anon$2.foreach(JavaConversions.scala:781) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:54 as TID 1407 on executor 6: node25 (NODE_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.io.FileNotFoundException > java.io.FileNotFoundException: > /tmp/spark-local-20140117145333-5d01/0b/shuffle_0_441_482 (Too many > open files) > at java.io.FileOutputStream.openAppend(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:192) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.open(DiskStore.scala:58) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.write(DiskStore.scala:107) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:152) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:149) > at scala.collection.Iterator$class.foreach(Iterator.scala:772) > at > scala.collection.JavaConversions$JMapWrapperLike$$anon$2.foreach(JavaConversions.scala:781) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:441 as TID 1415 on executor 6: node25 (PROCESS_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.io.FileNotFoundException > java.io.FileNotFoundException: > /tmp/spark-local-20140117145333-5d01/0b/shuffle_0_238_365 (Too many > open files) > at java.io.FileOutputStream.openAppend(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:192) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.open(DiskStore.scala:58) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.write(DiskStore.scala:107) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:152) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:149) > at scala.collection.Iterator$class.foreach(Iterator.scala:772) > at > scala.collection.JavaConversions$JMapWrapperLike$$anon$2.foreach(JavaConversions.scala:781) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:238 as TID 1423 on executor 6: node25 (NODE_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.io.FileNotFoundException > java.io.FileNotFoundException: > /tmp/spark-local-20140117145333-5d01/35/shuffle_0_37_144 (Too many > open files) > at java.io.FileOutputStream.openAppend(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:192) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.open(DiskStore.scala:58) > at > org.apache.spark.storage.DiskStore$DiskBlockObjectWriter.write(DiskStore.scala:107) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:152) > at > org.apache.spark.scheduler.ShuffleMapTask$$anonfun$run$1.apply(ShuffleMapTask.scala:149) > at scala.collection.Iterator$class.foreach(Iterator.scala:772) > at > scala.collection.JavaConversions$JMapWrapperLike$$anon$2.foreach(JavaConversions.scala:781) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:149) > at org.apache.spark.scheduler.ShuffleMapTask.run(ShuffleMapTask.scala:88) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:158) > at > java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) > at java.lang.Thread.run(Thread.java:662) > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Starting task > 2.0:37 as TID 1424 on executor 6: node25 (NODE_LOCAL) > -- > 14/01/17 14:56:07 INFO cluster.ClusterTaskSetManager: Loss was due to > java.lang.IllegalStateException: Shutdown in progress [duplicate 19] > 14/01/17 14:56:07 ERROR cluster.ClusterTaskSetManager: Task 2.0:1679 > failed more than 4 times; aborting job > 14/01/17 14:56:07 INFO cluster.ClusterScheduler: Remove TaskSet 2.0 from pool > -- > 14/01/17 14:56:07 INFO scheduler.DAGScheduler: Failed to run count at > ComputeNetworkStats.scala:59 > Exception in thread "main" org.apache.spark.SparkException: Job > failed: Task 2.0:1679 failed more than 4 times > at > org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:760) > at > org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:758) > at > scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60) > at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47) > at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:758) > at > org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:379) > at > org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$run(DAGScheduler.scala:441) > at org.apache.spark.scheduler.DAGScheduler$$anon$1.run(DAGScheduler.scala:149) > 14/01/17 14:56:07 INFO cluster.ClusterScheduler: Ignoring update from > TID 1418 because its task set is gone
