distinct() needs to do a shuffle -- which is resulting in the need to materialize the map outputs as files. count() doesn't.
On Sat, Jan 18, 2014 at 10:33 PM, Ryan Compton <[email protected]>wrote: > I'm able to open ~13M files. I expect the output of > .distinct().count() to be under 100M, why do I need so many files > open? > > rfcompton@node19 ~> cat /etc/redhat-release > CentOS release 5.7 (Final) > rfcompton@node19 ~> cat /proc/sys/fs/file-max > 13069279 > > On Sat, Jan 18, 2014 at 9:12 AM, Jey Kottalam <[email protected]> wrote: > > 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 >
