Mojmir Vinkler created SPARK-5250: ------------------------------------- Summary: EOFException in when reading gzipped files from S3 with wholeTextFiles Key: SPARK-5250 URL: https://issues.apache.org/jira/browse/SPARK-5250 Project: Spark Issue Type: Bug Components: PySpark Affects Versions: 1.2.0 Reporter: Mojmir Vinkler
I get an `EOFException` error when reading *some* gzipped files using `sc.wholeTextFiles`. It happens to just a few files, I thought that the file is corrupted, but I was able to read it without problems using `sc.textFile` (and pandas). Traceback for command `sc.wholeTextFiles('s3n://s3bucket/2525322021051.csv.gz').collect()` {code} --------------------------------------------------------------------------- Py4JJavaError Traceback (most recent call last) <ipython-input-104-943aab11de03> in <module>() ----> 1 sc.wholeTextFiles('s3n://s3bucket/2525322021051.csv.gz').collect() /home/ubuntu/databricks/spark/python/pyspark/rdd.py in collect(self) 674 """ 675 with SCCallSiteSync(self.context) as css: --> 676 bytesInJava = self._jrdd.collect().iterator() 677 return list(self._collect_iterator_through_file(bytesInJava)) 678 /home/ubuntu/databricks/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/java_gateway.py in __call__(self, *args) 536 answer = self.gateway_client.send_command(command) 537 return_value = get_return_value(answer, self.gateway_client, --> 538 self.target_id, self.name) 539 540 for temp_arg in temp_args: /home/ubuntu/databricks/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name) 298 raise Py4JJavaError( 299 'An error occurred while calling {0}{1}{2}.\n'. --> 300 format(target_id, '.', name), value) 301 else: 302 raise Py4JError( Py4JJavaError: An error occurred while calling o1576.collect. : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 41.0 failed 4 times, most recent failure: Lost task 0.3 in stage 41.0 (TID 4720, ip-10-0-241-126.ec2.internal): java.io.EOFException: Unexpected end of input stream at org.apache.hadoop.io.compress.DecompressorStream.decompress(DecompressorStream.java:137) at org.apache.hadoop.io.compress.DecompressorStream.read(DecompressorStream.java:77) at java.io.InputStream.read(InputStream.java:101) at com.google.common.io.ByteStreams.copy(ByteStreams.java:207) at com.google.common.io.ByteStreams.toByteArray(ByteStreams.java:252) at org.apache.spark.input.WholeTextFileRecordReader.nextKeyValue(WholeTextFileRecordReader.scala:73) at org.apache.hadoop.mapreduce.lib.input.CombineFileRecordReader.nextKeyValue(CombineFileRecordReader.java:69) at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:145) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at scala.collection.Iterator$class.foreach(Iterator.scala:727) at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273) at org.apache.spark.InterruptibleIterator.to(InterruptibleIterator.scala:28) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265) at org.apache.spark.InterruptibleIterator.toBuffer(InterruptibleIterator.scala:28) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252) at org.apache.spark.InterruptibleIterator.toArray(InterruptibleIterator.scala:28) at org.apache.spark.rdd.RDD$$anonfun$16.apply(RDD.scala:780) at org.apache.spark.rdd.RDD$$anonfun$16.apply(RDD.scala:780) at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1314) at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1314) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61) at org.apache.spark.scheduler.Task.run(Task.scala:56) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1214) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1203) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1202) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1202) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696) at scala.Option.foreach(Option.scala:236) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:696) at org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1420) at akka.actor.Actor$class.aroundReceive(Actor.scala:465) at org.apache.spark.scheduler.DAGSchedulerEventProcessActor.aroundReceive(DAGScheduler.scala:1375) at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516) at akka.actor.ActorCell.invoke(ActorCell.scala:487) at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238) at akka.dispatch.Mailbox.run(Mailbox.scala:220) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393) at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) {code} -- This message was sent by Atlassian JIRA (v6.3.4#6332) 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