I think I've shuffled this data before (I often join on it), and I know I was using distinct() in 0.7.3 for the same computation.
What do people usually have in /proc/sys/fs/file-max? I'm real surprised that 13M isn't enough. On Sat, Jan 18, 2014 at 11:47 PM, Mark Hamstra <[email protected]> wrote: > 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 > >
