It seems like the problem is related to —executor-cores. Is there possibly some sort of race condition when using multiple cores per executor?
On Nov 22, 2015, at 12:38 PM, Jeremy Davis <jda...@marketshare.com<mailto:jda...@marketshare.com>> wrote: Hello, I’m at a loss trying to diagnose why my spark job is failing. (works fine on small data) It is failing during the repartition, or on the subsequent steps.. which then seem to fail and fall back to repartitioning.. I’ve tried adjusting every parameter I can find, but have had no success. Input is only 23GB of LZO )probably 8x compression), and I’ve verified all files are valid (not corrupted). I’ve tried more and less of : memory, partitions, executors, cores... I’ve set maxFailures up to 300. Setting 4GB heap usually makes it through repartitioning, but fails on subsequent steps (Sometimes being killed from running past memory limits). Larger Heaps usually don’t even make it through the first repartition due to all kinds of weird errors that look like read errors... I’m at a loss on how to debug this thing. Is there a tutorial somewhere? —————— Spark 1.4.1 Java 7 Cluster has 3TB of memory, and 400 cores. Here are a collection of exceptions java.io.FileNotFoundException: /var/storage/sdd3/nm-local/usercache/jeremy/appcache/application_1447722466442_1649/blockmgr-9ed5583f-cac1-4701-9f70-810c215b954f/13/shuffle_0_5_0.data (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(FileOutputStream.java:221) at org.apache.spark.storage.DiskBlockObjectWriter.open(BlockObjectWriter.scala:128) at org.apache.spark.storage.DiskBlockObjectWriter.write(BlockObjectWriter.scala:215) at org.apache.spark.util.collection.ChainedBuffer.read(ChainedBuffer.scala:56) at org.apache.spark.util.collection.PartitionedSerializedPairBuffer$$anon$2.writeNext(PartitionedSerializedPairBuffer.scala:137) at org.apache.spark.util.collection.ExternalSorter.writePartitionedFile(ExternalSorter.scala:757) at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41) at org.apache.spark.scheduler.Task.run(Task.scala:70) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) java.lang.InternalError: lzo1x_decompress_safe returned: -6 at com.hadoop.compression.lzo.LzoDecompressor.decompressBytesDirect(Native Method) at com.hadoop.compression.lzo.LzoDecompressor.decompress(LzoDecompressor.java:315) at com.hadoop.compression.lzo.LzopDecompressor.decompress(LzopDecompressor.java:122) at com.hadoop.compression.lzo.LzopInputStream.decompress(LzopInputStream.java:247) at org.apache.hadoop.io.compress.DecompressorStream.read(DecompressorStream.java:85) at java.io.InputStream.read(InputStream.java:101) at org.apache.hadoop.util.LineReader.fillBuffer(LineReader.java:180) at org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:216) at org.apache.hadoop.util.LineReader.readLine(LineReader.java:174) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:209) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:47) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:248) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:216) at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:216) at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41) at org.apache.spark.scheduler.Task.run(Task.scala:70) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) java.io.IOException: Filesystem closed at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:707) at org.apache.hadoop.hdfs.DFSInputStream.readWithStrategy(DFSInputStream.java:776) at org.apache.hadoop.hdfs.DFSInputStream.read(DFSInputStream.java:837) at java.io.DataInputStream.read(DataInputStream.java:149) at com.hadoop.compression.lzo.LzopInputStream.readFully(LzopInputStream.java:73) at com.hadoop.compression.lzo.LzopInputStream.readInt(LzopInputStream.java:88) at com.hadoop.compression.lzo.LzopInputStream.decompress(LzopInputStream.java:238) at org.apache.hadoop.io.compress.DecompressorStream.read(DecompressorStream.java:85) at java.io.InputStream.read(InputStream.java:101) at org.apache.hadoop.util.LineReader.fillBuffer(LineReader.java:180) at org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:216) at org.apache.hadoop.util.LineReader.readLine(LineReader.java:174) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:209) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:47) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:248) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:216) at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:216) at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41) at org.apache.spark.scheduler.Task.run(Task.scala:70) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) java.io.IOException: Compressed length 1630678372 exceeds max block size 67108864 (probably corrupt file) at com.hadoop.compression.lzo.LzopInputStream.getCompressedData(LzopInputStream.java:286) at com.hadoop.compression.lzo.LzopInputStream.decompress(LzopInputStream.java:256) at org.apache.hadoop.io.compress.DecompressorStream.read(DecompressorStream.java:85) at java.io.InputStream.read(InputStream.java:101) at org.apache.hadoop.util.LineReader.fillBuffer(LineReader.java:180) at org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:216) at org.apache.hadoop.util.LineReader.readLine(LineReader.java:174) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:209) at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:47) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:248) at org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:216) at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:216) at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41) at org.apache.spark.scheduler.Task.run(Task.scala:70) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) 15/11/22 19:27:37 WARN scheduler.TaskSetManager: Lost task 30.0 in stage 11.7 (TID 2010, 204-01-02.sc1.verticloud.com<http://204-01-02.sc1.verticloud.com/>): FetchFailed(BlockManagerId(102, 204-17-04.sc1.verticloud.com<http://204-17-04.sc1.verticloud.com/>, 45305), shuffleId=0, mapId=190, reduceId=49, message= org.apache.spark.shuffle.FetchFailedException: java.io.FileNotFoundException: /var/storage/sdc3/nm-local/usercache/jeremy/appcache/application_1447722466442_1650/blockmgr-91439edc-75e5-4058-8eac-c8abb510d4bf/3c/shuffle_0_190_0.index (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:146) at org.apache.spark.shuffle.IndexShuffleBlockResolver.getBlockData(IndexShuffleBlockResolver.scala:98) at org.apache.spark.storage.BlockManager.getBlockData(BlockManager.scala:300) at org.apache.spark.network.netty.NettyBlockRpcServer$$anonfun$2.apply(NettyBlockRpcServer.scala:57) at org.apache.spark.network.netty.NettyBlockRpcServer$$anonfun$2.apply(NettyBlockRpcServer.scala:57) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108) at org.apache.spark.network.netty.NettyBlockRpcServer.receive(NettyBlockRpcServer.scala:57) at org.apache.spark.network.server.TransportRequestHandler.processRpcRequest(TransportRequestHandler.java:114) at org.apache.spark.network.server.TransportRequestHandler.handle(TransportRequestHandler.java:87) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:101) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:51) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:254) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:163) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:787) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:130) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116) at java.lang.Thread.run(Thread.java:744) at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$.org$apache$spark$shuffle$hash$BlockStoreShuffleFetcher$$unpackBlock$1(BlockStoreShuffleFetcher.scala:67) at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$$anonfun$3.apply(BlockStoreShuffleFetcher.scala:84) at org.apache.spark.shuffle.hash.BlockStoreShuffleFetcher$$anonfun$3.apply(BlockStoreShuffleFetcher.scala:84) at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371) at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:388) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:276) at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171) at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78) at org.apache.spark.rdd.RDD.iterator(RDD.scala:242) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277) at org.apache.spark.rdd.RDD.iterator(RDD.scala:244) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277) at org.apache.spark.rdd.RDD.iterator(RDD.scala:244) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41) at org.apache.spark.scheduler.Task.run(Task.scala:70) at org.apache.spark.executor.Executor$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:744) Caused by: java.lang.RuntimeException: java.io.FileNotFoundException: /var/storage/sdc3/nm-local/usercache/jeremy/appcache/application_1447722466442_1650/blockmgr-91439edc-75e5-4058-8eac-c8abb510d4bf/3c/shuffle_0_190_0.index (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:146) at org.apache.spark.shuffle.IndexShuffleBlockResolver.getBlockData(IndexShuffleBlockResolver.scala:98) at org.apache.spark.storage.BlockManager.getBlockData(BlockManager.scala:300) at org.apache.spark.network.netty.NettyBlockRpcServer$$anonfun$2.apply(NettyBlockRpcServer.scala:57) at org.apache.spark.network.netty.NettyBlockRpcServer$$anonfun$2.apply(NettyBlockRpcServer.scala:57) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108) at org.apache.spark.network.netty.NettyBlockRpcServer.receive(NettyBlockRpcServer.scala:57) at org.apache.spark.network.server.TransportRequestHandler.processRpcRequest(TransportRequestHandler.java:114) at org.apache.spark.network.server.TransportRequestHandler.handle(TransportRequestHandler.java:87) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:101) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:51) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:254) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:163) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:787) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:130) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116) at java.lang.Thread.run(Thread.java:744) at org.apache.spark.network.client.TransportResponseHandler.handle(TransportResponseHandler.java:162) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:103) at org.apache.spark.network.server.TransportChannelHandler.channelRead0(TransportChannelHandler.java:51) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:254) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:163) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:787) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:130) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116) ... 1 more ) 15/11/22 19:27:17 INFO yarn.YarnAllocator: Container marked as failed: container_1447722466442_1650_01_000136. Exit status: 143. Diagnostics: Container [pid=10278,containerID=container_1447722466442_1650_01_000136] is running beyond physical memory limits. Current usage: 4.6 GB of 4.5 GB physical memory used; 4.9 GB of 22.5 GB virtual memory used. Killing container. Container killed on request. Exit code is 143 Container exited with a non-zero exit code 143 ExecutorLostFailure (executor 14 lost)
